Tom Gilson

“Is Religion Adaptive? It’s Complicated” — Scientific American

Here’s an interesting discussion at Scientific American: “Is Religion Adaptive? It’s Complicated.”

Schloss’s point is the one that gets most people thinking. “That’s all fine and dandy about the scientific research, but what does it all tell us about the existence of God?” What if, as I suggested in my answer to this year’s “Annual Question” at Edge. The data suggest that God is actually just a psychological blemish etched onto the core cognitive substrate of your brain? Would you still believe if you knew God were a byproduct of your evolved mental architecture?

What if, indeed? That’s easy. If (and it’s a very big if) the data showed God was just a psychological blemish on my brain, then I could no longer believe.

That the question could even be asked is telling. “Could you believe in God if you knew he didn’t exist?” The question only makes sense if belief means something divorced from what we know to be true about the world. It’s another illustration of the commonly observed fact-value dichotomy: facts are about objective knowledge, while values (which include what we decide to believe) are private matters with no necessary connection to external realities, or so it is thought. For whatever reason, far too many Christians, even, have bought into this relativistic dichotomy.

Christianity, properly understood in its evangelical historical form, makes objective concrete statements about reality, and if they are wrong, then Christianity is wrong. Our belief is that God actually created the world, called Abraham, formed the nation of Israel, brought them out of Egypt through a parted Red Sea, spoke through the prophets, was incarnated in Christ who lived, died, and rose again in real history. If I ever came to know that these things were false, how could I “believe” they were true? As J.I. Packer wrote as long ago as 1972,

Nor is this all. Scepticism about both divine revelation and Christian origins has bred a wider scepticism which abandons all idea of a unity of truth, and with it any hope of unified human knowledge; so that it is now commonly assumed that my religious apprehensions have nothing to do with my scientific view of things external to myself, since God is not ‘out there’ in the world, but only ‘down here’ in the psyche. The uncertainty and confusion about God which marks our day is worse than anything since Gnostic theosophy tried to swallow Christianity in the second century.

(Knowing God, Foreword)

Amen to that. It hasn’t become noticeably better in 37 years since then.

As to the question posed in the article’s title, the answer is of course religion is adaptive. Any dummy knows it could never have evolved if it weren’t! Either it’s adaptive in that sense, or (and they apparently spent precious little time considering this) people are religious because there’s a reality beyond nature that we know we need to tap into. I’ll buy that latter option, myself.

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177 thoughts on ““Is Religion Adaptive? It’s Complicated” — Scientific American

  1. Schloss’ point doesn’t only come across as wildly oversimplified, but downright confused.

    Particularly, it seems to fail to distinguish between feelings and intellect – say a sensation that God is present, like Rupert Sheldrake’s ‘the sense of being stared at’ writ large – and a rational conclusion that God either exists, is very likely, is possible, etc. To make the claim that to prove a sensation of God is the result of workings in the brain would hardly go far in demonstrating the sense itself is false – much less a ‘blemish’, as Schloss wants to call it. It could well be indicative of a properly-operating human physiology. So Schloss is putting the cart before the horse even in the limited scope of biology – when it comes to whether God (among other things) actually exists, the line of inquiry is hardly of any use at all.

    As for his Edge entry, it’s filled with so much question-begging, razor-fumbling, and worse that it’s hard to take seriously. Except to say ‘Plantinga would love this testimony for his EAAN’.

  2. Here’s a question: would you still accept that science tells you about the world if you knew that it was a facility that relied on an evolved brain?

    Science does exactly that, and yet few scientists think that science is somehow at risk for relying thus. The question is not whether religion is something that involves an evolved facet of a brain, but whether or not any particular religious belief refers to the truth.

    That, of course, is something neither science nor religion can show to be either the case or not.

    Regards from an agnostic.

  3. Let’s make sure we put this in context. Under what conditions would the very slow, gradual emergence of true rationality bestow a survival advantage?

  4. j:
         Excellent spot-on question, dude. WHAT does it MEAN to reason, i.e., what IS the capacity to reason, and why is it somehow different (or not?) from the material/physical properties of things?

    John S. Wilkins:
         Your statement, “… is something neither science nor religion can show to be either the case or not” is, frankly, empty. Which one of those (science or faith) are you using as a basis for the assertion? (That is intentional baiting, by the way… let’s see if you get it.) Moreover, why are you being so epistemologically limiting? What happened to the philosophy of nature (as opposed to the more paltry philosophy of science)? That’s the problem in most of these discussions: the artificial war between science and faith has claimed two casualties (science and faith) and one missing in action (philosophy of nature). Who needs that kind of foolishness, anyway? Why is it that so often faith is set against reason, or vise versa? Why is science automatically granted carte blanche epistemological superiority/priviledge over other forms of knowledge? Certainly it can’t look to itself (or its tools or methodologies or analyses) to justify such an assumption, for that would be circular.

  5. @Holopupenko

    Um, I’m afraid you missed JSW’s point…

    At least I think you did — perhaps I missed yours!

  6. Make the appearance of rationality slow and gradual, if you like.

    And define rationality the way you want to (beg the question as much or as little as you feel comfortable).

    Since the EAAN is about epistemology, I suggest starting from a definition of rationality like, say, “the ability of an individual to effectively infer models of the future from information gathered in the past using rules that preserve consistency.” Don’t like this definition? Use your own. Just tell me whether you think your version of rationality has survival advantages in any natural environment.

  7. Doctor Logic,

    The question is not specific enough, which is why I tried to focus it earlier. Obviously rationality has survival advantage. Humans would not be a very successful species if we were not able to communicate, plan, build, adapt mentally to new environments, think, etc.

    And here’s something else that would provide additional survival advantage: wings attached to our bodies so we could fly everywhere we go. No one would ever have to get in another automobile accident.

    You see, it’s one thing to posit that some feature provides a survival advantage. It’s another thing to propose a way to acquire that feature through an extremely slow and gradual process. Wings will never happen to humans through evolution. And I very highly doubt that some proto-human one day unexpectedly was born with “the ability of an individual to effectively infer models of the future from information gathered in the past using rules that preserve consistency.” (I can just see him walking up to his parents and saying, “Hey ma, hey pa! I can think! It’s really cool—you should try it!”)

    So if we’re going to suppose that evolution tossed rationality up out of some non-rational beginning, we really have to think of what that might have looked like at the first, the very beginning; and we have to explain how rationality took the right road, the road toward being able to discern what is true rather than just what works.

    Daniel Dennett has done some work related to this in Consciousness Explained, though as in his more recent Breaking the Spell, he’s long on supposition and short on evidence.

  8. Tom, there are two issues: whether the very beginnings of rationality evolutionarily are conceptually possible, and whether there is evidence that it happened. This theory has a two-step process: it must first (logically) be conceptually possible, and then we may or may not find evidence for that possibility. But lack of evidence says nothing about whether it’s conceptually possible.

    Your critique of Dennett’s efforts in this theory seem to conflate the two. “Long on supposition” means that he’s working out the conceptual possibilities, which is a good thing for making the first hurdle. Lack of evidence only speaks to the second hurdle.

  9. That’s a good point, Paul, and I agree with you. I don’t have Dennett’s book nearby, it was a library book I had for a while. The whole book was interesting… but I really don’t know how likely his scenario was.

  10. “the ability of an individual to effectively infer models of the future from information gathered in the past using rules that preserve consistency.”

    your use of “individual” causes problems for me: isnt the individual the *vehicle* by dawkins standard? so if its an ability of the individual, youve already tried to rule out the possibility that the genes are doing it, but instead that the “longer-leash” is doing it, no?

    cant “rationality” be a communicative adaption evolved specifically to deal with the ever-changing sociolinguistic world (Pinker & Bloom 1990, Carruthers 2002, Andrews 2003, Atran 2003) and effectively predict its future based on info, and thus providing a genetic survival advantage?

  11. Tom Gilson,

    Have you picked up The Last Superstition by Edward Feser yet? He makes some interesting arguments specific to Dennett, and on philosophy of mind questions in general (in particular about rationality, etc.) that I think you’d find interesting.

  12. Also, one thing about the EAAN: So many people tend to take it as an argument against evolution, or a challenge to explain the development of human rationality in evolutionary terms. Whenever I look over the argument and papers relating to it, though, that seems far from the case. Plantinga is willing to accept an evolutionary development of rational thought. The question is whether giving such an account is going to retain its naturalism, in particular a materialist naturalism.

    Again, this is a point Feser develops in his book (and supposedly moreso in his philosophy of mind book). I won’t develop the arguments contained therein here, but on this subject it amounts to ‘evolutionary explanations tend to be suffused with teleology that people are unjustly asked to ignore, and materialist explanations of mind – when they do work – do so because they’re subconsciously borrowing from a non-mechanistic understanding of physical nature.’

  13. Tom, I’ll keep a lookout for Dennett’s book, it sounds interesting, depending, as always, on how well the author can demonstrate his thesis.

  14. j,

    your use of “individual” causes problems for me: isnt the individual the *vehicle* by dawkins standard? so if its an ability of the individual, youve already tried to rule out the possibility that the genes are doing it, but instead that the “longer-leash” is doing it, no?

    Understood. My point is that rationality facilitates the ability of individuals or small groups to adapt new features to suit a changing environment within a generation. Genetic evolution typically cannot do that because, over short timescales, natural selection would simply be killing-off those not already suited to the environment.

  15. Tom, you’re basically saying that we don’t yet have a verified theory about how humans gained rationality. I’m not so sure of that, but I don’t see that this is an argument against naturalism.

    I think there are obvious ways that rationality can appear gradually. We humans are not very rational. We’re just a little bit rational, and we amplify that through education, culture, symbolic manipulation, etc. Most of what we do is automatic behavior. The little rationality we have creates a feedback loop that alters our automatic responses, but it’s clear that we’re not rational all the time.

    Evolutionary psychology has a lot to say in this area too.

  16. If you, a physicist, are looking to evolutionary psychology to support your views, then you are really scraping the bottom, Doctor Logic. There is no branch of science so utterly evidence-free as that, except possibly the multiverse theory. Both exist for one reason only: to provide naturalistic explanations (with or without evidence), on the assumption that those are the only kinds of explanations that are permitted.

    More in a moment… I just got a phone call that will take a while.

  17. Last point:

    Tom, you’re basically saying that we don’t yet have a verified theory about how humans gained rationality. I’m not so sure of that, but I don’t see that this is an argument against naturalism.

    Then why do naturalists say it’s an argument against ID that we don’t have a verified theory of how a designer gave humans rationality?

    The only evidence we have that evolution is responsible for human rationality is that evolutionists can’t think of any other source for it; and a good many of them don’t want to encourage anyone else to try to think of another source for it either. It’s rationality/evolution of the gaps, promissory science, guess-and-hope hypothesizing; especially hoping (desperately hoping) to come up with an answer whereby those who don’t want God will find a way, as they have in inventing their invisible friend, the multiverse, to avoid encountering him.

  18. Tom,

    All right, I’ll throw in here:

    You wrote:

    And here’s something else that would provide additional survival advantage: wings attached to our bodies so we could fly everywhere we go. No one would ever have to get in another automobile accident.

    This is a surprising thing to say (along with the paragraph below it) for someone who says he reads the best of the biological / naturalist writings. I think it’s surprising because I have come across many times, starting with Dawkins, the claim that every adaptation bears a cost. (The case usually cited are fish who have evolved eyes that no longer work; it’s more efficient, in the total darkness in which these fish have flourished, to no longer bear the cost of maintaining a working organ that offers no benefit.) While not up there with the “how come we don’t see any fish spontaneously evolving into a dog” comments I’d say this approach from personal incredulity either tends to mis-state what is expected from the evolutionary process or has a poor record for withstanding focused research when the problem appears real (eyes, bacterial flagellum, etc.). Long way to say that it’s a (famous) strawman to claim that evolution is supposed to be a never failing advancement toward a single uber-species that can fly, shoot lasers out of its eyes, is impervious to gunfire, etc.

    I agree that the origin of consciousness is hard to explain, and I think it counts among the big three (life, eukaryotes, consciousness) of biological origin questions. But if the question is about explaining how it could theoretically arise gradually I think the possibilities are obvious, consistent with natural selection.

    I haven’t read Dennet’s two books you mention (I’m halfway through his “Darwin’s Dangerous Idea”), but it makes sense to me that rationality (as defined by Dr. Logic above) could proceed from the kind of genetic “sharing” seen in phenotypes, where models for this (2 of these, recoil from pain) are used by phenotypes of that (eyes, burning & cutting & intense pressure & intense noise & intense light). I’m sure that everyone has better examples.

    I wonder, though, what kind of evidence you would accept for the origin and evolution of rationality. I think your previous positions along this line are that evolution is not experimentally verifiable, and that behavioral psychology is not falsifiable, so I have to ask what you would consider as persuasive evidence on this topic.

  19. Long way to say that it’s a (famous) strawman to claim that evolution is supposed to be a never failing advancement toward a single uber-species that can fly, shoot lasers out of its eyes, is impervious to gunfire, etc.

    Lasers!

  20. Hi Tony,
    I believe you are misrepresenting Tom and not reading carefully what he wrote.
    He did not make the strawman argument that you imply, he did not represent evolution as an unfailing process toward a flying uberspecies and he is not arguing from personal incredulity.
    He said that positing the survival advantages of rationality does nothing to explain its origin or its development.
    Just as, to posit the survival advantage of humans with wings would do nothing to make one expect we would gain wings. He is in no way arguing that since we don’t have wings evolution must not be what the experts say it is, or that since it has failed to provide wings evolution must be falsified. He is drawing an altogether different comparison which you have missed in your response to him.
    In fact, he is demonstrating his knowledge of the theory, that it does not expect wings merely because there would be a survival advantage, and using this fact to demonstrate that just-so stories about the survival advantage of rationality do not make rationality a prediction of evolution – much less does “survival advantage”, in and of itself, constitute an evolutionary explanation.

    Have I represented you properly, Tom?

  21. Thank you for that response, Charlie. That’s a good representation.

    @Tony Hoffman:

    I wonder, though, what kind of evidence you would accept for the origin and evolution of rationality. I think your previous positions along this line are that evolution is not experimentally verifiable, and that behavioral psychology is not falsifiable, so I have to ask what you would consider as persuasive evidence on this topic.

    Let me note in passing that this would be a marvelous opportunity to point the same question back at those of you who doubt Intelligent Design. What kind of evidence would you accept?

    But I won’t use that as an excuse not to respond to the question. First, I’m not sure where you picked up that I consider behavioral psychology not to be falsifiable. We haven’t really talked about behavioral psychology except very briefly, long ago. I’m speaking of the psychology put forth by Watson, Skinner and others. Behaviorism as an overarching model, an über-explanation of psychology has been thoroughly rejected by psychologists (falsified, in effect), though some of its methods are still considered extremely useful in a cognitive/behavioral context.

    I’m not at all sure what could suffice as evidence for the evolution of rationality. It’s not the kind of thing that could have left us an historical record, in artifacts, fossils, or documents. Distinguishing an evolving rationality from one that was endowed by an intelligent designer would be extremely difficult, probably even impossible.

    If one were looking at behavior only, or rationality only, or consciousness only, especially from an empirical perspective, one could only say “we don’t know where it came from.” That remains true unless and until some thoroughly surprising (unimaginable, really) breakthrough in paleontology or archaeology comes through with a different answer.

    Clearly those who insist on rationality coming from one source or another are saying so because of other philosophical or theological commitments. I believe the philosophical arguments in favor of designed, rather than evolved, rationality are powerful; and that on that philosophical basis there is good evidence that rationality did not result from blind processes of chance events inventing rationality.

    Never forget that evolution’s inventions are all produced by chance. Evolutionists get annoyed when people say evolution is nothing but chance or randomness; natural selection, they say, is anything but random. But natural selection is not what invents, it is what conserves. It has no good ideas, no new ideas at all to throw into biology, it can only (metaphorically of course) recognize ideas thrown up into the world randomly and say, “there’s a good one, let’s keep it.” Every biological and behavioral novelty in natural history has been purely by chance, if evolution is true. That alone makes the evolution of rationality seem dubious, but there are many reasons more than that, which we’ve discussed in the past.

  22. Tom,

    Then why do naturalists say it’s an argument against ID that we don’t have a verified theory of how a designer gave humans rationality?

    ID doesn’t have a theory, period. There’s not even anything to verify. If they had a verifiable theory, they’d have an experimental program, but they don’t.

    The only evidence we have that evolution is responsible for human rationality is that evolutionists can’t think of any other source for it; and a good many of them don’t want to encourage anyone else to try to think of another source for it either.

    No, that’s not right either. There’s overwhelming evidence that we humans evolved. That’s what the science says. Just knowing this fact implies quite strongly that all of our systems, including rationality, evolved also.

    No one would suggest that, given the fact that rabbits evolved from fish (if you go far enough back), we ought to search for an alternative to evolution to explain the rabbit digestive system. So why should cognition be any different?

    As for your criticism of EvoPsych, I don’t think EP is as much of a pariah as you suggest. Besides, don’t you think it would be hypocritical to tell me to stick to the established science when you deny the tenets of evolutionary biology?

    It’s rationality/evolution of the gaps, promissory science, guess-and-hope hypothesizing; especially hoping (desperately hoping) to come up with an answer whereby those who don’t want God will find a way, as they have in inventing their invisible friend, the multiverse, to avoid encountering him.

    You’re writing as if you don’t know what gaps thinking really means.

    Science is all too happy to admit gaps. There will likely always be gaps in our scientific knowledge.

    The fallacy of gaps thinking is to adhere to one’s own, less-probable theory as evidence mounts for a competitor, and to rely on gaps in the competing theory as air bubbles to keep one’s own theory alive.

    I’ll bring up the same old example. Suppose we find a suspect’s DNA and fingerprints at the scene of the crime, and find the victim’s stuff at the suspect’s house. The prosecution is in good shape if it prosecutes the suspect, right? The defense is weak. Their theory is that their client was framed. Obviously, given only this information, the defense’s theory is much less probable.

    Now it would not be gaps thinking for the prosecution to maintain the guilt of the suspect without knowing, say, what the suspect had for lunch on the day of the crime. The evidence places strong probabilistic constraints on the suspect, even if certain unknowns (like lunch menus) remain.

    In contrast, it would be gaps thinking for the defense to claim that their client is innocent because the prosecution failed to determine what their client had for lunch on the day the crime was committed.

    Evolutionary biology tells us that we evolved from smaller less intellectual primates, and that the skills and abilities of our ancestors increased over time (mastering fire, abstraction, etc). This places strong constraints on where our rationality came from, and points the finger squarely at evolution. Just because evolutionary biology does not yet have all the details of how this happened, does not mean that scientists are using gaps thinking when they assume rationality evolved. They have the suspects fingerprints and DNA.

    In contrast, it is your thinking that exemplifies gaps thinking. You’re not saying rationality could not possibly have evolved. (You’re not saying the suspect could not have committed the crime.) You’re saying that we haven’t discovered the details of how rationality evolved, and so you want to suggest some sort of conspiracy theory instead that frames evolution for our origins. You are trying to overthrow the prosecution’s case based on gaps in the case, not based on alibis.

  23. @Doctor Logic

    So why should cognition be any different?

    Might you detect a teeny-tiny bit of recursive irony in this question?

    BTW: your forensic examples really do not represent the positions of your opponents. If you can’t understand someone else’s position, don’t bother making one up that is more convenient for you.

  24. @Tom Gilson:

    Never forget that evolution’s inventions are all produced by chance. Evolutionists get annoyed when people say evolution is nothing but chance or randomness; natural selection, they say, is anything but random.

    Hmm. Surely you know that evolution tries things that worked in the past, so it’s not blind guessing. But even when it blind guesses, it does the same thing we humans do. We try things at random. The only difference is that we humans simulate the outcome of the trial instead of having to actually perform the trial.

    Let’s suppose I’m trying to decide the best route to carry some bulky objects from site A to site B. There are different strategies I can use.

    Simulation Strategy. If there are 5 routes, I will simulate taking each route, preferring routes with fewer stairways, easier accessibility, shorter distances, etc. I pick the route that has the best outcome in the simulation.

    Competition Strategy. But another possibility is to send 5 people, one person along each route, and see which one arrives first. Then I can say that this winner’s route is the best route to take.

    Obviously, it will generally take less time and result in fewer lost goods (and people), if I use the simulation strategy.

    But would you call the competition strategy random? Sure, it may be random which route is taken by which person, but the competition is a valid and very powerful search algorithm.

    So why would you say that the presence of randomness in the algorithm means it is dubious that the algorithm could create rationality? If rationality is what is rewarded in the search (because it’s a survival advantage), then there’s nothing dubious about it.

  25. doctor logic:

    ID doesn’t have a theory, period. There’s not even anything to verify. If they had a verifiable theory, they’d have an experimental program, but they don’t.>ID doesn’t have a theory, period. There’s not even anything to verify. If they had a verifiable theory, they’d have an experimental program, but they don’t.

    I’m not sure where I first read this, but it’s applicable here, with respect to the evolution of rationality and the selection just quoted:

    “Pot. Kettle. Black.”

    No, that’s not right either. There’s overwhelming evidence that we humans evolved. That’s what the science says. Just knowing this fact implies quite strongly that all of our systems, including rationality, evolved also.

    What if the lack of a credible pathway for evolution of rationality counts against the “overwhelming evidence” for evolution?

    Besides, don’t you think it would be hypocritical to tell me to stick to the established science when you deny the tenets of evolutionary biology?

    I don’t think Evo Psych is an established science. It has no falsifiable theories, it has no way of generating evidence, it amounts to coming up with stories of what might have been.

    The fallacy of gaps thinking is to adhere to one’s own, less-probable theory as evidence mounts for a competitor, and to rely on gaps in the competing theory as air bubbles to keep one’s own theory alive.

    Altenberg 16. Punk Eek. Self-organization. Worries about the tree of life. Questions about the role of DNA. Pot. Kettle. Black.

    Surely you know that evolution tries things that worked in the past, so it’s not blind guessing.

    That’s just a tad anthropomorphic, don’t you think? “Hmmm… let’s see, I’ve got this on the toolbench, and this on the shelf, and, oh yes, here’s one that worked before, looks like it might be useful here—so I’ll give it a whirl!”

    No, even if evolution “tried” something that worked in the past, it would just be blind guessing when it was “tried” again in a new system. The nearby presence of the something, whatever it is, would be a matter of serendipity. Its “experimental” (anthropomorphizing again) insertion in a new location could not happen by any intentional means, and generally would be a matter of pure chance.

    But even when it blind guesses, it does the same thing we humans do. We try things at random. The only difference is that we humans simulate the outcome of the trial instead of having to actually perform the trial.

    I can’t believe you would think that, and I’m not even going to dignify it with a counter-argument. Not if you think this explains all of human rationality!

  26. @Doctor Logic

    Surely you know that evolution tries things that worked in the past, so it’s not blind guessing.

    Only a proponent of ID would claim that rationality was a precursor to the evolution of rationality. What did you really mean to say?

  27. Good point, Doug (and Tom). DL can’t use rational behavior to explain how rationality came into existence. Well, I guess he can but then he’d be an IDist.

  28. @Doctor Logic:

    Evolutionary biology tells us that we evolved from smaller less intellectual primates, and that the skills and abilities of our ancestors increased over time (mastering fire, abstraction, etc). This places strong constraints on where our rationality came from, and points the finger squarely at evolution.

    This is a remarkably clear example of the point I made earlier:

    Both exist for one reason only: to provide naturalistic explanations (with or without evidence), on the assumption that those are the only kinds of explanations that are permitted.

    The question on the table is whether rationality arose by mindless forces. Let’s assume for the sake of argument that you are correct in this:

    Evolutionary biology tells us that we evolved from smaller less intellectual primates, and that the skills and abilities of our ancestors increased over time (mastering fire, abstraction, etc).

    You go on to say that this places “strong constraints on where our rationality came from.” But why would this be true? Where do the constraints come from? If we evolved from smaller, less intellectual primates, and if our ancestors’ abilities increased over time, does that entail that there was no guiding process, no teleology, no rational being to oversee the project? Not at all!

    But if the word “naturalistic” is assumed it does, as in,

    *Naturalistic* Evolutionary biology tells us that we evolved from smaller less intellectual primates, and that the skills and abilities of our ancestors increased over time (mastering fire, abstraction, etc). This places strong *naturalistic* constraints on where our rationality came from, and points the finger squarely at *naturalistic* evolution.

    If you could prove evolution is strictly naturalistic, then you could say that. There are those of us who say evolution itself is not yet proven. I know you disagree with that. Let’s grant arguendo that you’re right in that. Do you propose also to tell us science has proved that evolution happened by strictly natural means? What was the laboratory or field test that demonstrated that?

  29. Tom,

    You wrote:

    First, I’m not sure where you picked up that I consider behavioral psychology not to be falsifiable.

    Sorry, my mistake – when I typed “behavioral psychology” I meant to type “evolutionary psychology.” Previously you had said that evolutionary psychology was not falsifable.

    If one were looking at behavior only, or rationality only, or consciousness only, especially from an empirical perspective, one could only say “we don’t know where it came from.”

    I think it’s pretty much agreed that a great deal (an overwhelming amount) of animal behavior is inherited. So I think those of us who subscribe to the Theory of Evolution would disagree, and say that we we can say where it came from.

    I believe the philosophical arguments in favor of designed, rather than evolved, rationality are powerful; and that on that philosophical basis there is good evidence that rationality did not result from blind processes of chance events inventing rationality.

    I don’t know about your first statement, but the second one (after the semicolon) seems a bit bold. I have to ask, what is that evidence?

  30. sorry but still asking:

    small groups ——> rationality ——> win

    or

    rationality ——-> small groups —–> win

    (no small importance that dr l stresses the *inter-subjectivity* of science in uniting [toward shared value-goals] (my rewording of course, and hand-waving concerning just-so, “possessing better mechanisms” stories about this group over that group), point is: rationality unites, coincidence?)

  31. Tom,

    I just wanted to respond to this.

    Let me note in passing that this would be a marvelous opportunity to point the same question back at those of you who doubt Intelligent Design. What kind of evidence would you accept?

    Regarding Intelligent Design, I think that gap identification alone is not so persuasive – we don’t yet know according to this theory, so we must, by default, accept that the only explanation is unknowable. That’s how I read Intelligent Design, and I’m sure you’ll disagree with my definition, but that’s the problem – what is the definition of Intelligent Design? What is it explaining and predicting? If it did explain and predict something, and it ran an experiment (not even a laboratory one, I’d go for something that risks falsification), then that would go a long way with me.

    So, something along the lines of a scientific experiment would be acceptable to me.

  32. @Tom Gilson:

    What if the lack of a credible pathway for evolution of rationality counts against the “overwhelming evidence” for evolution?

    But this isn’t an alibi. It’s the argumentum ad ignorantiam.

    Altenberg 16. Punk Eek. Self-organization. Worries about the tree of life. Questions about the role of DNA. Pot. Kettle. Black.

    Surely, you must realize that none of these things in any way contradicts evolutionary biology or the fundamental thesis of evolution. Given the constraints of evolution, it has always made sense to assume an initial theory featuring the simplest possible mechanism that implemented that mechanism. Finding that the actual mechanism is not the simplest doesn’t invalidate the theory in any way.

    It’s like finding our crime suspect rode a unicycle to the crime scene, or took a circuitous route. So what? That wouldn’t sway the jury.

    I can’t believe you would think that, and I’m not even going to dignify it with a counter-argument. Not if you think this explains all of human rationality!

    “Explains all of human rationality”? I was explaining creativity, not rationality.

    How did airplanes get created? Well, people took experiences they had building cars and bicycles and sails, experiences they had with birds and feathers, and experiences with umbrellas and capes, etc. They brainstormed. Brainstorming means allowing oneself to combine ideas with minimum criticism in order to create new permutations. Of course, each of these permutations wasn’t totally new. Each permutation had ideas and concepts that worked in previous contexts, or worked by analogy.

    Rational thinking comes in after the brainstorming. Rational thinking takes knowledge and predicts the outcomes of implementing the various permutations, eliminating those that are inconsistent with the facts. If man had not dreamed and brainstormed and played with bicycles and feathers, he would never have invented airplanes. Man did not derive flight by using deduction. He created many random variations and LATER applied deduction to filter out the ideas that would not work. As well as some empirical testing, of course.

    However, we don’t go around saying that the 747 was built “purely by chance.” Chance had a lot to do with it, but so did constraining factors that filtered out the bad ideas (often before they were implemented and tested).

    Do you find this an alien and radical viewpoint? Have you heard of the term “brainstorm”?

    If we evolved from smaller, less intellectual primates, and if our ancestors’ abilities increased over time, does that entail that there was no guiding process, no teleology, no rational being to oversee the project? Not at all!

    It is not impossible that there is design somewhere, but it is extremely improbable, all things being equal.

    We’ve been over this before. There are many orders of magnitude more ways of designing the world without the constraints of evolution than there are ways of designing the world with those constraints.

    You have all sorts of things you want to do today, like shower, eat breakfast, drive to work, etc. Now, could you do all this an also limit yourself to using only the muscles in your left arm? Yeah, you could do that. It would take you a really long time to do everything, and you would need to heavily modify your car and your house to facilitate the constraint that you would only use one arm to do everything instead of legs, torso, neck, etc. The choice to disable everything but that one limb is arbitrary. There are many more ways to do what you want in the day when you don’t have this constraint. This is why seeing someone use only one limb is a strong indicator that they are unable to use their other limbs.

    We see a world built using common descent and made of common systems. That’s a massive and totally unnecessary constraint for a designer. So if you can’t say why the designer used evolution and then predict something from that fine-tuning, your design theory is suppressed by the ratio of possibilities imposed by the constraint.

  33. @Doctor Logic

    I was explaining creativity

    You insist on a very high threshold for the word “explain” when it is something that your opponent is attempting, but demonstrate a remarkably low threshold for the word “explain” when it is something that you are doing.

    I wonder if you are capable of any evolutionary explanation without teleological language…! And yet you seem entirely unperturbed in your denial of any teleology.

    That’s a massive and totally unnecessary constraint for a designer.

    Do you have any actual experience in design? Anyone who designs software systems knows that reuse and modularity are by no means totally unnecessary.

  34. @j:

    I don’t know what you are saying. Are you saying that humans (and their ancestors) formed small groups because they were rational? Are you saying that rationality helped humans form larger groups through trade and reciprocal relationships?

    BTW, even when I respond on my mobile, I still use proper case and punctuation.

  35. The origin of rationality from non-rationality is no less of a jump than the origin of life from non-life, or the origin of matter from non-matter.

    Folks talk about the Big Bang, but the Big Bang is not the cause of the creation of the universe — it is the effect. Folks talk about abiogenesis. But there isn’t even a scientifically coherent theory of abiogenesis yet. Folks can talk about the origins of rationality, but they don’t even have the feeblest grasp of what the origin of rationality from non-rationality would entail!

    Interestingly enough, the ancient creation myth calls out these three events. In Genesis 1, there are two different verbs for God’s actions. One, translated “made” could be used to describe “making a salad” — raw materials are re-arranged (this is, incidentally, by no means in conflict with evolution). The other, translated “created”, is a “magical poofing into existence”. That second verb is only used three times:

    – the heavens and the earth (i.e. the Big Bang)
    – life (i.e., abiogenesis)
    – humanity (i.e., rationality)

    Even Richard Dawkins publicly admits that these were “extraordinarily improbable” events. Call it a coincidence if you like… 😉

  36. Are you saying that humans (and their ancestors) formed small groups because they were rational? Are you saying that rationality helped humans form larger groups through trade and reciprocal relationships?

    a survival advantage would be given to genes that had “rationality” because they were then able to form better groups (leading to the “longer-leash”). think of it like language (some evidence for adaption of language, as well as genetic evidence as well):

    small groups ——> language use ——> win

    or

    language gene —–> small groups ——> win

    BTW, even when I respond on my mobile, I still use proper case and punctuation.

    i done cant understand your hip talk, yo. (dont lecture an english grad on his use of english: he will demolish you there. and lets leave ya’lls folklinguistics outta it.)

  37. @Doug Peters:

    Yeah, we’ll never understand the magic that made the Earth. Or that makes the Sun go around the Earth. Or that makes the stars. Or that makes our hearts beat. Or the magic of conception and giving birth. Nor will we ever understand lighting bolts from the heavens. Or aurora borealis. Or the flight of birds. Or the dark magic of disease.

    Don’t you get it? You’re not presenting an argument, here. You’re making an argument from ignorance. You’re saying that because we don’t know how X, X must be false. The same argument could be made for most of our scientific discoveries.

    Quoting the Bible and pretending there are coincidences in it is just numerology and superstition.

    But beyond this, you don’t have an explanation for these things either. Just saying “God did it” is no better an explanation than saying “some as-yet-undiscovered theory did it.”

  38. If anyone would like to seriously claim that rationality came into existence via a series of small adjustments, I have one question…
    Folks can speculate (with more or less credibility) about biological precursors to eyes, placentas, lungs, wings, and feathers. But what is a biological precursor to rationality? Are we even capable of imagining such a thing (NB: there is a difference between imagining that something of sort X exists, and imagining that thing) We don’t even understand the biological “platform” for rationality! Do we have any real evidence that a biological precursor to rationality has ever existed? Well, no, we don’t. (and yes, I am aware that absence of evidence does not make a case, I’m just reminding folk that real science likes evidence, thank you very much).

  39. j.:

    dont lecture an english grad on his use of english: he will demolish you there. and lets leave ya’lls folklinguistics outta it.

    … contrasted with Doctor Logic …

    BTW, even when I respond on my mobile, I still use proper case and punctuation.

    Thank you for taking the time to do that, Doctor Logic. It’s not about some imposed standard of correctness, it’s about readability. The care you display in doing that is care for your readers. Failing to do that (as I have already said to j.) is really to express a lack of interest in the reader; for without proper capitalization, punctuation and grammar (which an English major ought to know), it’s considerably harder to read.

    j., I would find it much easier to be involved in what you offer if you would do us the courtesy of not making it unnecessarily difficult to read. I’m not trying to chase you off for that, by any means. I already told you it wasn’t one of the comment guidelines. Others seem to be willing to engage with you in these discussions, and you have interesting things to say. It’s just that I’ve got a limited amount of time to study what others write here, and it takes additional time and effort to sort out your very non-standard English.

    Only you know your motivations for writing this way, but I would ask you one more time to consider who it really serves: yourself, possibly? It’s certainly not helping your readers. That’s just a question, which I put forward with all tentativeness; only you can judge whether it hits the mark.

    That’s all I’ll have to say about it. Thanks.

  40. @Doctor Logic

    Just saying “God did it” is no better an explanation than saying “some as-yet-undiscovered theory did it.”

    Exactly so. The good doctor’s logic has brought him to the perfectly logical conclusion that his position is no better than an ancient myth.

    But something is missing: if the object of the exercise is to decide on the origins of the universe or of life, then we are at an impasse. However, if the object of the exercise is to discuss the origins of language, or rationality, or love, or art, then the actions of the True Word, the True Wisdom, the True Love, and the True Beauty in those origins are thoroughly more logical than a promissory materialism (which cannot even begin to describe those “phenomena” in materialistic terms!)

  41. I can only offer a vague hint of where the answer to the beginning of rationality is, but surely it must be in the animal kingdom. One might (and perhaps someone already has, but I haven’t read that much) produced a list of animals in order of their use of rationality, perhaps even correlated with size of the brain or frontal lobe. Just as there are precursors to the eye (mere light-sensitive cells), there should be an organism that makes some basic, simple rational decision (as opposed to a mere autonomic reflex). I haven’t read anyone who has done this, but it doesn’t seem conceptually difficult to do, it would just take the work to do it.

    Also, the place where rationality is going to start is not, I think, at homo sapiens. Even though I can’t quote you chapter and verse, I strongly suspect it will be elsewhere in the animal kingdom, at least with the other primates, if not elsewhere, where some basic rationality (more basic or simple or limited than what people can do) is found.

  42. @Paul

    You answer is a good one. Everything that you have said is sound. However… it highlights the fact that the definition of the word “rationality” is lacking. Certainly, there are actions that crows and orangutans perform that have signs of rationality. But to define rationality so broadly is certainly to sell the type of rationality peculiar to homo sapiens very short indeed.

    For example, the conversation that we are having has no analog in the animal kingdom. The conversation is about an abstract idea. The conversation involves speculation, deduction, inference, association, and sympathy at a level unknown in any other species. You could legitimately claim that the difference was one of quantity rather than quality (many have), but you could have no grounds to dismiss the counter-claim that the difference was qualitative.

  43. J.,

    This will probably seem like “piling on” but I’ve stopped addressing your comments because I find them inscrutable as well. I honestly don’t know what you are trying to say most of the time.

    There is a term in a popular book called “What Sticks” that I read a year or so ago. The term is “the curse of knowledge.” It uses the example of a psychological study where one person is given a list of well known tunes (Jingle Bells, Mary Had a Little Lamb, etc.), and that person was asked to drum the cadence of the melody to another person, who had to guess what the tune was.

    The interesting part of the study was that the tappers guessed that a high percentage of listeners would be able to guess the tune they tapped, whereas in reality a much smaller percentage were able to do so. The writers of the book used this to illustrate a popular problem they called the curse of knowledge, showing that when we understand something (what we are thinking, what we have been trained to know, etc.) we tend to forget that our listeners (readers, whatever) don’t have the same initial understanding.

    dont lecture an english grad on his use of english: he will demolish you there.

    This reminds me of Inigo Montaya promising the man in the black mask that he will reach the top alive by giving his “word as a Spaniard. “No good,” replies the man in the black mask, “I know too many Spaniards.”

    Doug,

    By speculating on how we can imagine the precursors of rationality are you accepting Dr. Logic’s definition? Because I think that pointing out the difficulties with finding the origins of rationality isn’t going to be possible until we agree of what we’re exploring the origins.

    In other words, I think you could make an argument that a predatory animal behaves rationally when it stalks its prey. But I think that we also might be talking about rationality that appears to be exclusive to humans.

    Also, you wrote:

    Dr. Logic: Just saying “God did it” is no better an explanation than saying “some as-yet-undiscovered theory did it.”

    You: Exactly so. The good doctor’s logic has brought him to the perfectly logical conclusion that his position is no better than an ancient myth.

    I disagree with your second statement. When we say “God did it.” or “an ancient myth is the answer” we have closed the case. Irreducible complexity says, “there’s no natural explanation for this so we should stop trying to explain it using natural explanations.” Some undiscovered theory says, “we don’t know, so let’s keep trying to figure it out.” As far as I’m concerned, that’s a lot better than an ancient myth.

  44. Hi Tony,

    Irreducible complexity says, “there’s no natural explanation for this so we should stop trying to explain it using natural explanations.”

    No it doesn’t.
    You are misrepresenting the concept and its proponents.

  45. @Tony Hoffman

    Some undiscovered theory says, “we don’t know, so let’s keep trying to figure it out.”

    As a researcher and scientist, I have never been disinclined to explore, study, or “figure things out.” However, as every good researcher (or chess player, or…) knows, the real question isn’t so much whether or not we explore an avenue. The real question is which avenue is worth exploring!

    Feel free to explore the origins of rationality or life if you like. Please publish whatever you find. Just don’t be surprised if other folks are doing more productive research elsewhere. 🙂

  46. Charlie,

    Feel free to educate me. As your comment stands now, though, it’s just an empty assertion.

    There’s a trend I can’t help but notice; a lot of people are quick to correct definitions of ID and IR, but no seems capable of providing the definition from which they are basing their correction.

    I stand by my (albeit loose) statement.

  47. Could someone provide for me an example of Evolutionary Psychology “explaining” something with more than a “just-so” story?

  48. Doug,

    I’d be happy to try and find an example but I’m not sure what you mean by a ‘”just-so” story.’

  49. @Tony Hoffman

    Rudyard Kipling’s just-so stories are the prototype for all manner of Evolutionary Psychological speculation.

    A “just-so story” is characterized by:
    – no opportunity for verification
    – no real evidence
    – no questions asked by true believers

    🙂

  50. Just-so stories:

    Evolutionary psychology explains polygamy in that it gives men a reproductive advantage, spreading their gametes around. Evolutionary psychology explains monogamy in that it gives men a re-generative advantage (their kids not only get born but grow up healthy to have more kids). Evolutionary psychology explains that we don’t eat Grandma because we need her to take care of the kids. But supposing we did eat our ancestors (yuck!), evo psych could easily explain that, too (too messy for me to go into details here, thank you). Evo psych explains why we eat vegetables and why we don’t like to eat vegetables. It tells us why all women prefer men with beards, except for the ones who don’t. And on and on.

    The name “just-so story” comes from Rudyard Kipling’s (“Do you like Kipling?” “I don’t know, I’ve never kippled.”) set of stories by the same name. They are stories you’re expected to believe because someone said so, with no reference to evidence or other support. But Wikipedia can give you a better answer than I can.

  51. Tony,

    A definition of ID? You haven’t been looking very hard.

    Intelligent Design is defined as research into the proposal that certain features of the natural world are best explained as the product of intelligence rather than by blind natural processes.

    Irreducible complexity does not say,

    There’s no natural explanation for this so we should stop trying to explain it using natural explanations.

    Where IC is found, it indicates that an ultimate natural explanation without intelligent guidance is unlikely or impossible. It does not say to stop researching (oh where oh where oh where, other than prejudice, did anybody ever come up with that ridiculous tenet?). It does not say to quit asking questions.

    It does not say to stop trying to understand the IC system. It does not even say to stop trying to understand the IC system’s precursors in natural history. Just because a system is IC does not mean it can’t have parts, after all (drive a car lately?) and parts may have been precursors in natural history.

    If you ever find an actual recommendation from an ID proponent that says, “Well, we’ve got it all figured out now that we know it’s irreducibly complex, so let’s just drop our research altogether,” then you can make the claim you’re making. In the meantime you ought to see it for what it is: an empty, evidence-free theory of the sort no self-respecting scientist ought to entertain for one second.

  52. @Tom Gilson:

    Where IC is found, it indicates that an ultimate natural explanation without intelligent guidance is unlikely or impossible.

    This statement of yours is false. Evolution with cooption/exaptation can construct IC structures. This has been debunked numerous times, and when the debate gets into details, it’s always acknowledged that IC status does not mean a system cannot evolve, nor even that the evolution of the IC structure is improbable. I’m not sure that Behe even accepts what you wrote above.

    As for EP, here is a good article that discusses the issues:
    http://www.human-nature.com/nibbs/02/palmer.html

  53. if reason is really “being reasonable” (ie following grice’s communication maxims) could we not then just say that it is language that has evolved up the animal kingdom, and so in species which possess better language skills (ie better rationality skills) we see larger groups able to be bound together (ie species being more rational)?

    (oh thnaks yall for the nice comemnts on my legiblity, sorry to have innconvnienced everyone)(inb4 banhammer)

  54. Doug, I think you’re trying to hang too much on what is special about rationality as practiced by humans. Not that we don’t (obviously) practice rationality different than all other animals, but that *in and of itself* does not make it different in kind.

    Furthermore, and this is the crucial point, I think, the original issue was to find the beginnings of rationality – period. I offered a starting point, one to which you agreed. It would be moving the goalposts to a finer level of detail (much like evolution deniers want more and more intermediary fossils) to then require the beginnings of more specialized aspects of rationality, as practiced by humans. Or, perhaps we can now *change* the original question to “what are the beginnings of *human* rationality?” But changing the question to this removes the more metaphysical implications, doesn’t it? If physicalism through evolution can produce *any* sort of rationality in animals, then it could produce even the more abstract forms seen in humans.

  55. @Doctor Logic

    Thanks for the link! Excellent review. My request still stands, though 🙂

    @Paul

    I’m sorry: while “origins” can mean “a starting point”, in the context of the current discussion I thought that we were discussing the “big origins” question of “not just the starting point, but the path from there to here.”

  56. I agree, Doug, that is a good review. The definition it gives is quite helpful, really:

    EP, Palmer and Palmer tell us, is “the study of the adaptive significance of behavior” (xiii).

    There’s much of value to be learned from studying adaptive behavior, I’m sure. If you come at it from an evolutionary perspective, you’re likely to conclude that adaptiveness supports evolution. For my part, I think that evidence of design is poor evidence against a designer. Adaptive behavior is an artifact that points to no unambiguous source. The evolutionary aspect of EP is a borrowed paradigm, not one that could have ever been derived or even confirmed through the behavioral sciences.

  57. Doug:

    I’m sorry: while “origins” can mean “a starting point”, in the context of the current discussion I thought that we were discussing the “big origins” question of “not just the starting point, but the path from there to here.”

    Doug, I don’t get it. Considering the animal kingdom’s rationality gives us both the starting point as well as much of the path, that is, the path from the starting point to some place before full human rationality. If your complaint is that we don’t have the details filled in between animal rationality and human rationality, then you’re just looking at the gaps. There’s no problem at the fundamentals, unless you re-define the fundamentals as something above the fundamental level, but, then, that would be problematic, eh?

  58. Hi Tony,

    Charlie,

    Feel free to educate me.

    My pleasure.

    As your comment stands now, though, it’s just an empty assertion.

    No, it’s not. It’s a factual recounting of the truth – which you would know already if you pursued this issue or if you’d cared to search before attempting to call my assumed bluff.

    There’s a trend I can’t help but notice; a lot of people are quick to correct definitions of ID and IR, but no seems capable of providing the definition from which they are basing their correction.

    I don’t know where you’ve been tracking these trends but I think you could help but notice it if you stuck to facts instead of rhetoric.

    I stand by my (albeit loose) statement.

    Then you stand by a misrepresentation and compound it by defending it without testing your presumptions.

    First, since irreducible complexity is recognized even by evolutionary biologists who think it can be explained (as DL witnesses above – I know you prefer to learn from DL) by naturalistic evolutionary processes (exaptation/cooption) it is obvious that “irreducible complexity” does not say “there’s no natural explanation for this so we should stop trying to explain it using natural explanations”. Some people think there is a perfectly natural explanation for irreducible complexity.
    For instance: http://www.ncbi.nlm.nih.gov/sites/entrez

    Second, since the term has entered the debate via Mike Behe let’s see what he says about it:
    ” Irreducible complexity is just a fancy phrase I use to mean a single system which is composed of several interacting parts, and where the removal of any one of the parts causes the system to cease functioning.”
    He then describes the irreducible complexity of the mousetrap (you’ll not prove anything regarding this discussion or your misrepresentation by bringing up claims that the mousetrap is not IC – since we are discussing what IC says, or rather, what it means and what its proponents say of it). The mousetrap, of course, does not defy natural explanation.
    Behe continues:

    An irreducibly complex system cannot be produced directly by numerous, successive, slight modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

    That, of course, is the implication of a system being irreducible complex – again, no reference to its defiance of naturalistic explanations.
    Notice that the challenge, for which DL pretends there is indisputable proof, of exaptation was anticipated by Behe and, that he allows here that there can be a naturalistic explanation for irreducibly complex biological systems:

    An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.

    Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can’t be produced directly, one can’t definitively rule out the possibility of an indirect, circuitous route. However, as the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin’s criterion of failure has been met skyrockets toward the maximum that science allows.

    So, not only does IC not say that there is no natural explanation (there just might be – although IDists do not think this the inference to the best explanation) but neither the concept nor its proponents say anybody ought to quit searching for one. You’ll also notice that the debate does not have to drag on and on in order to find out that IC does not assert unevolvability – this is the position from the onset.
    Tom covered this above.

    As with Luther, you really ought to read the people and ideas you mean to enlist for your arguments.

  59. Oops.
    I thought I had edited my second reference to DL.
    Upon reflection I didn’t want to use that language, which refers to a previous conversation and not the remarks above, but accidentally have left it in.
    My apologies, DL.

  60. Doug (and Tom),

    Thanks for explaining the “just-so story” thing.

    As I understand behavioral psychology it basically says that much of our behavior is inherited and adaptive.

    At the end of Steven Pinker’s book “The Blank Slate”, Pinker lists pages and pages of human universals compiled by Donald E. Brown. These are traits that are found in every human culture. They include things like “childhood fear of strangers, reciprocity, sexual jealousy, etc.”

    So a very basic experiment would be to work from Donald E. Brown’s list and find the most completely isolated culture in the world and see how many human universal items in that list they exhibited. If behavioral psychology is complete bunk, then they should show few if any shared items on that list (children have no fear of strangers, there is no sense of reciprocity and accounting, there is no such thing as sexual jealous), and I think that evolutionary psychology itself would be falsified.

    Throughout history utopic societies have attempted to form their own community (Oneida, Kibbutz, etc.). To the extent that they attempt to regulate against the human universals (communal love, no reciprocity, etc.), they fail. This is evidence that we share heritable behaviors, and it is not a “just so story” to say that any society that tries to repeat these utopic societies will fail.

    But I think the most obvious direction for evolutionary psychology to go is to compare our brains with chimpanzees and to see how, from a genetic and brain development standpoint, our structures and abilities differ. If a human brain was damaged in the place where we believe language is located (both from our knowledge of humans and the differences with chimpanzees), and that person retained the ability to use language, then evolutionary psychology is not a just-so-story. Similarly, if a chimpanzee could be trained to use language, despite the genetic and brain development differences that we have found to be essential to language, then evolutionary psychology is not a just-so-story. If chimpanzees and other primates retained their similarities to humans (social behaviors, etc.) despite damage to the shared structures found to control these abilities, then evolutionary psychology is not a just-so-story.

    At is most basic I think that evolutionary psychology shows that for similar and different behaviors among groups with common ancestry, there are similar and different structures that are heritable. So although I agree that there is probably some idiotic “research” going on out there, at its heart I don’t think Evo Psych is the failed enterprise you make it out to be.

  61. @Tony Hoffman

    Did I make Evolutionary Psychology out to be a failed enterprise…? 🙂 I simply asked

    Could someone provide for me an example of Evolutionary Psychology “explaining” something with more than a “just-so” story?

    For it not to be a failed enterprise, it needs to be genuinely able to explain something. And my threshold for “explanation” won’t be as stringent as DL’s, I promise… but I won’t be fooled by wild speculation, either.

    Back in pre-enlightenment times, folks could and did publish all kinds of twaddle. As long as said twaddle was couched in the reassuring platitudes of accepted “Christian” thinking, it could at least see publication. Recently, I’ve been amazed at the twaddle that I’ve seen published — stuff that only sees print because it purports to “explain our behavior” using “evolutionary principles” when, in fact, the mechanism of “explanation” is wild speculation couched in evolutionary jargon. I’m quite willing to discard the conclusion that this is the currency of Evolutionary Psychology … as long as I have a single example of it actually explaining something.

  62. Incidentally, for your entertainment pleasure, my five-year-old review of The Blank Slate for Amazon:
    ———————————————
    Pinker attempts to do four things in “The Blank Slate”:
    1. demolish “the blank slate” concept
    2. demolish “the noble savage” concept
    3. demolish “the ghost in the machine” concept
    4. use statistics according to Disraeli.

    Strawman-baiting notwithstanding, Pinker makes a good show toward his first two goals. He only deserves partial credit, however, as those ideas have far outlasted their intrinsic value and deserve the burial he gleefully supplies.

    Unfortunately for Pinker, the same cannot be said of “the ghost in the machine”. That it should be conflated with the previous two over-ripe ideas is odd. While the “ghost” has appeared in many dubious incarnations, some of which Pinker uses as foils, “the ghost in the machine” can be reduced to the idea that “there is something about human nature that is beyond our ability to understand (AKA ‘science’)”. Put in those terms, the concept resists sophisticated attempts at dismissal, let alone the light-weight ones Pinker employs. A clause like “we have every reason to believe that” (consciousness [derives from] neural networks in the brain – p.240) really means “we cannot conceive other than that” or “our faith affirms that”. Apparently, what should be obvious is not: science is unable to define its own limits.

    Pinker also gets the proverbial raspberry for playing fast-and-loose with statistics in the final chapters. At least he is honest enough to mitigate his stance with some necessary caveats. He admits that prizing apart genetics and environment can be a tricky business. He admits that the adopting demographic has huge correlation within it. He mentions the crucial differences between “determines/affects” and “variance/outcome” but appears to have trouble interpreting these differences on occasion. He mentions the necessity of systematic influence. He could have mentioned the sample set size problem for twins-reared-apart studies, studies that have shown as much as 25% environmental influence, linearity and independence assumptions, free will as a source of measurement noise, etc. I suppose that the glosses were made in an attempt to make the whole more accessible to the masses, but the end result is that conclusions derive more from the assumptions than from the evidence itself.

    Finally, Pinker also indulges in the just-so-story-making that true believers have gobbled up throughout history. Passive? Aggressive? Got them both covered. Ethical? Violent? No problem. We can “explain” them both with ease. If a theory can explain any two conflicting phenomena without so much as a flinch, it is non-falsifiable and hence non-scientific.

    Bottom line: I learned precious little about human nature from this book. Plenty about the foibles of academia, the politics of science, and the inertia of dogma — but I was already familiar with all those topics. Recognizing this weakness in his book, Pinker defers, in closing, to the real experts on human nature: poets and novelists. Wanna learn about human nature? Read Tolstoy, Austen, Dickens, Hardy, Dostoevsky…

  63. @Tony Hoffman:

    If behavioral psychology is complete bunk, then they should show few if any shared items on that list (children have no fear of strangers, there is no sense of reciprocity and accounting, there is no such thing as sexual jealous), and I think that evolutionary psychology itself would be falsified.

    I don’t think anybody doubts that human nature, whatever it is, includes universal characteristics that are adaptive. Studying this, and learning just how our behaviors are adaptive, is valuable and should be encouraged. I don’t have any problem with that kind of science.

    The difficulty EP faces is in proving how adaptive behaviors arose, or that they came about just because of evolution, or even just by natural processes broadly considered. “Adaptive” is pretty much synonymous with “it works.” If EP shows that behavior works, that’s fine. If they go on to say, “therefore it came about by evolution,” that’s a serious non sequitur, for things that work are quite typically the result of intelligent design.

  64. @Doctor Logic

    Don’t you get it? You’re not presenting an argument, here.

    Don’t you get it? I was never even pretending to be making an argument, there. I was, in fact, just stating some facts — that just happen to look nice when juxtaposed…

    Fact 1: Science does not and cannot explain “matter from non-matter”

    Fact 2: Science does not [and cannot]* explain “life from non-life”

    Fact 3: Science does not [and cannot]* explain “rationality from non-rationality”

    Fact 4: The Bible happens to call out these three events explicitly as the work of God.

    *I grant that these “cannot” clauses are claims rather than facts… but I like the symmetry, so sue me.

    Quoting the Bible and [observing that] there are coincidences in it is just numerology and superstition.

    Simply false. Observing that there are coincidences between the Bible and modern science has nothing whatsoever to do with numerology or superstition. It has to do with understanding the meanings of words. Your momentary lapse into complete illogic is not logical, DL — care to explain it?

  65. Charlie,

    This from the second paragraph of Wikipedia on irreducible complexity:

    Biochemistry professor Michael Behe, the originator of the argument of irreducible complexity, defines an irreducibly complex system as one “composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning”.[4] These examples are said to demonstrate that modern biological forms could not have evolved naturally.

    I imagine that you are “shocked, shocked” to find the last sentence in the Wikipedia entry above. How did anyone ever get that idea?

    Tom,

    I think I agree with your last comment, except for this:

    If EP shows that behavior works, that’s fine. If they go on to say, “therefore it came about by evolution,” that’s a serious non sequitur, for things that work are quite typically the result of intelligent design.

    I don’t think it’s the purpose of evolutionary psychology to prove evolution; I think it’s simply assumes evolution and sees where that leads to explaining and predicting behavior. I understand your point that you think it fails on that level as well, but I think the quote above is like saying that the study of physics shows how objects move in space, “therefore it came about by math.” I don’t think that’s a necessary inference of physics; it’s an axiom from which physics has been productive.

    And your very last clause in particular I can’t agree with – eyes, bacterial flagellum, my hope for laser shooting eyes, etc.

    Doug,

    I guess I don’t understand what you mean by explaining something. Can you give me an example of a (preferably biological) theory that does explain something for you? If not biological, then whatever else you think is a field of study that explains something in a way that’s not a “just so story.”

  66. Hi Tony,
    I am not shocked by anything cited from wikipedia. I am shocked that a trained scholar such as yourself would resort to using it when discussing a matter of any cultural controversy.
    So is that your argument? The interpretation of an editor at wikipedia? Then you’ve added to your misrepresentation shoddy scholarship.
    What may or may not be said about the examples of irreducible complexity neither follows from the definition provided in that second paragraph nor refutes the fact that opponents of ID, publishing in peer-reviewed articles, have claimed that irreducible complexity does evolve naturally. Indeed, even your own wiki makes this case:

    Mainstream critics, however, argue that irreducible complexity, as defined by Behe, can be generated by known evolutionary mechanisms.

    This falsifies your claim immediately as to what irreducible complexity itself says and your statement is proven a misrepresentation.
    Next, even your wiki does not say that either irreducible complexity or its ID proponents have said anything about anyone searching for natural explanations of biological complexity.

    Since your wiki cite does nothing to argue against the case I’ve already made, citing directly from Behe himself, one has to wonder why you would even bother with it.
    Since you have not even dented it I will just quote from my previous comment to sum:

    First, since irreducible complexity is recognized even by evolutionary biologists who think it can be explained (as DL witnesses above – I know you prefer to learn from DL) by naturalistic evolutionary processes (exaptation/cooption) it is obvious that “irreducible complexity” does not say “there’s no natural explanation for this so we should stop trying to explain it using natural explanations”. Some people think there is a perfectly natural explanation for irreducible complexity.
    For instance: http://www.ncbi.nlm.nih.gov/sites/entrez

    So, not only does IC not say that there is no natural explanation (there just might be – although IDists do not think this the inference to the best explanation) but neither the concept nor its proponents say anybody ought to quit searching for one. You’ll also notice that the debate does not have to drag on and on in order to find out that IC does not assert unevolvability – this is the position from the onset.
    Tom covered this above.

    As with Luther, you really ought to read the people and ideas you mean to enlist for your arguments.

  67. Charlie,

    You wrote:

    So, not only does IC not say that there is no natural explanation (there just might be – although IDists do not think this the inference to the best explanation) but neither the concept nor its proponents say anybody ought to quit searching for one.

    That would be more believable if not for facts like this (from a transcript of the Dover trial):

    “…on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not ‘good enough.’”

    So, as you can see, Behe’s determination that the immune system is irreducibly complex led him to still leave no stone unturned in searching out alternative natural solutions. And you seriously wonder how I ever came to fear that IC could be bad for biological research?

    As with Luther, you really ought to read the people and ideas you mean to enlist for your arguments.

    I’ll just leave that there; I think it’s a nice ender too.

  68. Still quoting wiki, Tony? Your attempt to defend your misrepresentation is only digging you in deeper and deeper, confirming your allegiance to bias over scholarship.
    1) First, Behe never said “not good enough”.
    2) The literature dump had nothing to do with Behe’s claim and that’s exactly what he did say.
    3) Whereas Behe in 1996 made an empirical case regarding the state of the literature on the evolution of the immune system, I don’t recall in either of his books or his many articles his ever saying that science would never find an evolutionary explanation for the immune system. Do correct me if I’m wrong, but given the direct quote from his book (which you’ve not read) above I don’t expect that the claim will stand up to any contextual evaluation.
    4) This is not my first rodeo and if you think I’ll be bluffed by wiki cites of “facts” such as Judge Jones’ findings you are mistaken.
    5) On Luther, thanks, glad to see we can stand by my previous admonition about your scholarship and your continuing misrepresentation and defence of same. These obvious errors could easily be avoided by attaining to the principle of gracious reading rather than grasping at any rhetoric that fits your preconceptions.

  69. Oh, and since you liked it so much, and I do as well ….

    As with Luther, you really ought to read the people and ideas you mean to enlist for your arguments.

  70. Charlie,

    I’ll keep this up for awhile longer. If you want to some time you could surprise me and consider that I might not be only full of prejudice and determined to hide from all facts. You did it once before, and although I know that IC is a sensitive topic for you, maybe what I’m about to say you haven’t heard so I’ll keep on trying.

    You: Whereas Behe in 1996 made an empirical case regarding the state of the literature on the evolution of the immune system, I don’t recall in either of his books or his many articles his ever saying that science would never find an evolutionary explanation for the immune system.

    Except there’s this from the infamous page 139 of Darwin’s Black Box:

    Behe: “As scientists we yearn to understand how this magnificent mechanism [the V(D)J mechanism] came to be, but the complexity of the system dooms all Darwinian explanations to frustration.”

    Any direct quotes aside, I would go on further to say that the notion of Irreducible Complexity is something of a modern scientific oddity. By that I mean that I can’t think of another scientific field where its equivalent would be accepted. Can you imagine supporting these concepts:

    Untreatable Cancericity: Identifying those kinds of cancer from which no treatment will ever halt or reverse the disease.
    Unfathomable Anthropology: Those ancient tools and artifacts from which we will never be able to explain their original purpose.
    Unexplainable Aeronautics: Those objects whose dynamics can never be explained.

    I believe the reason the examples above have no charm is because none of them are tied to a theistic conclusion. For instance, if I change the first one to say: “Identifying those kinds of cancer from which no treatment will ever halt or reverse the disease and for which prayer is the only remaining resort” then it somehow seems, I would imagine, not so offensive.

    And that is, at heart, all that IC boils down to. It is a sophisticated, seductive, historically proven way of drawing our eye to our own ignorance and, I think, mistakenly sanctifying it with the stamp of God and the unknowable.

    Lastly, I can imagine you saying (among other things) that Behe is only speaking of discovering a limit to evolutionary theory, not methodological naturalism. If that were the case then I think virtually all of my objections would disappear. But it seems clear to me that the proponents of IC are looking for a double play – (peremptorily) underdetermining evolutionary theory and using that ploy to switch fields from the practice of methodological naturalism to philosophical conclusion.

  71. Hi Tony,

    If you want to some time you could surprise me and consider that I might not be only full of prejudice and determined to hide from all facts. You did it once before, and although I know that IC is a sensitive topic for you, maybe what I’m about to say you haven’t heard so I’ll keep on trying.

    I draw my conclusions on a case by case basis and highlight, for the thread-policing gander that you’ve become, that you are thriving on goose-sauce. Yes, this definitely highlights your prejudice.
    I’m not sure what you mean about my doing something once before, but I presume you mean that I treated you as a respectful dialogue partner. Yes, I did indeed.
    I don’t know why you think that IC is a sensitive topic for me, or what that is even supposed to mean or how it is supposed to be relevant. My point has been that you misrepresented it and that you continue, into this comment, to dig yourself into a greater hole by claiming otherwise. As to whether or not I ever heard your snippet from DBB, continue on.

    You quote me and Behe:

    You: Whereas Behe in 1996 made an empirical case regarding the state of the literature on the evolution of the immune system, I don’t recall in either of his books or his many articles his ever saying that science would never find an evolutionary explanation for the immune system.

    Behe: “As scientists we yearn to understand how this magnificent mechanism [the V(D)J mechanism] came to be, but the complexity of the system dooms all Darwinian explanations to frustration.”

    Except what? If this is meant to contradict my argument then you are merely misrepresenting Behe yet again. You cite page 139 and all you would have to do is look six inches to the left at page 138 to see that Behe is merely concluding what I already said:

    We can look high and low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.

    In this chapter I have looked at three features of the immune system … and demonstrated that each individually poses massive challenges to a putative step-by-step evolution. But showing that the parts can’t be built step-by-step only tells part for the story, because the parts interact with each other.

    Of course your misrepresentation continues and now has to coil about itself the equivocation of “step by step, Darwinian explanation” with “natural explanation” and claiming that because such a Darwinian explanation is doomed to frustration that Behe has said that one ought to quit looking for an explanation. This, in addition to failing to support your claim, exposes your preconception as you present “Darwinian” as coterminous with “natural”.

    Your list of unsolvable problems only highlights even more your bias and misrepresentation. Again, Behe never said that no explanation will be forthcoming. Indeed, it is only your bias and a priori allegiance to the paradigm that presumes that no Darwinian explanation = no natural explanation = no explanation whatsoever. That is not to say that if you don’t like his explanation you ought not continue the search for that which has eluded the reigning paradigm.

    And that is, at heart, all that IC boils down to. It is a sophisticated, seductive, historically proven way of drawing our eye to our own ignorance and, I think, mistakenly sanctifying it with the stamp of God and the unknowable.

    Not at all. IC directly answers Darwin’s challenge:

    If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case.

    While coming short of proving the universal negative Behe is making his case against step by step, gradualistic, evolution by insensible modifications culled by natural selection. Like it or lump it, he is answering the scientific challenge to the theory upon ground-rules set by Darwin himself.
    Don’t buy it? Fine. Just don’t misrepresent it.

    Lastly, I can imagine you saying (among other things) that Behe is only speaking of discovering a limit to evolutionary theory, not methodological naturalism. If that were the case then I think virtually all of my objections would disappear. But it seems clear to me that the proponents of IC are looking for a double play – (peremptorily) underdetermining evolutionary theory and using that ploy to switch fields from the practice of methodological naturalism to philosophical conclusion.

    Whatever secret motivations you suspect, even if they exist, it doesn’t justify your misrepresentation of the concept and of what Behe says.
    If your position is so strong, if your arguments valid, then make them without distortion and support them with real scholarship and not wiki cites and out-of-context quotes.
    Your motive-suspecting ends do not justify your means.

  72. Charlie,

    You wrote:

    I draw my conclusions on a case by case basis and highlight, for the thread-policing gander that you’ve become, that you are thriving on goose-sauce.

    This is a richly ironic sentence; first you claim to draw your conclusions on a case-by-case basis at the same time you reference a comment I made on an earlier post some weeks ago. You are many things, Charlie, but as your constant references to old battles over old comments from long ago attests, you are anything but case by case.

    I don’t know why you think that IC is a sensitive topic for me, or what that is even supposed to mean or how it is supposed to be relevant.

    You seemed eager for me to learn something from you. I thought it would make you happy if I adopted some of your style. 😉

    But enough of that. My quoting of you and Behe together was to counter your explicit claim that Behe never said that science would never find an evolutionary explanation for the immune system. His quote does contradict your statement. (But maybe you meant to say “natural” instead of evolutionary, and if that was your intention I would then agree; I’ve done that kind of thing typing hastily before, and that would make sense to me.)

    Indeed, it is only your bias and a priori allegiance to the paradigm that presumes that no Darwinian explanation = no natural explanation = no explanation whatsoever.

    Or perhaps you are biased by having contended with only those who have only come to their conclusions this way and have (incorrectly) surmised that I must have done the same?

    Here’s a Behe excerpt I find illuminating ( the whole editorial is here http://www.discovery.org/a/60 ):

    A few scientists have suggested non-Darwinian theories to account for the cell, but I don’t find them persuasive. Instead, I think that the complex systems were designed — purposely arranged by an intelligent agent.

    Whenever we see interactive systems (such as a mousetrap) in the everyday world, we assume that they are the products of intelligent activity. We should extend the reasoning to cellular systems. We know of no other mechanism, including Darwin’s, which produces such complexity. Only intelligence does.

    Of course, I could be proved wrong. If someone demonstrated that, say, a type of bacteria without a flagellum could gradually produce such a system, or produce any new, comparably complex structure, my idea would be neatly disproved. But I don’t expect that to happen.

    Intelligent design may mean that the ultimate explanation for life is beyond scientific explanation. That assessment is premature. But even if it is true, I would not be troubled. I don’t want the best scientific explanation for the origins of life; I want the correct explanation.

    There is something for everybody in this quote. I think it’s a good example of Behe speaking honestly about what IC means to him. What I still find horrifying is that he concedes that adoption of ID (brought about by IC) would mean that “the ultimate explanation for life is beyond scientific explanation.” Of course he doesn’t think we’re there yet, and of course he doesn’t promote stopping scientific research now (and he has no power to effect that in any event), but he is openly promoting a theory whose acceptance could mean that “the ultimate explanation for life is beyond scientific explanation.” And that’s something that I think enlightened Christians who say they value understanding nature but still support Behe haven’t come fully to grips with yet.

    “The ultimate explanation for life is beyond scientific explanation,” and my original (albeit loose) quote that started this discussion, that IC means that “there’s no natural explanation for this [natural structures] so we should stop trying to explain it using natural explanations.” don’t seem so incompatible to me still.

    Charlie, I admire your passion. And these arguments (about the implications of things like IC) go on in seemingly endless cycles precisely because of that – if they were overwhelmingly weighted to one side there’d be no life to these discussions. My hope is that you can come around to viewing those of us on both sides of the debate who have shown some signs of respect and honest engagement as honorable opponents, and not enemies.

  73. @Tony Hoffman:

    I think you’re doing a great job here, Tony.

    Charlie is misrepresenting the facts. He says:

    We can look high and low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.

    Of course what Charlie means is that the scientific literature doesn’t have a COMPLETE answer. Well this isn’t a good enough complaint in the face of all the evidence for evolution. It’s like complaining we don’t know what the suspect had for lunch on the day of the crime.

    If ID had proof that evolution was impossible, they would have a case. But we all know they have no such proof. The argument for IC was initially that evolution could not create an IC structure. That turned out to be false. In fact, IC arguments don’t even tell us that co-optation is unlikely. Indeed, we know that co-optation does happen. So we’re back at square one. Evolution has amassed evidence and verified predictions, and design is suppressed because there are far more ways of designing life than evolving it.

    Behe says in that quote that there’s no evidence of a mechanism (apart from design) that produces useful complexity. Either Behe is incredibly ignorant, or he’s being dishonest. Genetic algorithms produce useful complexity, so the algorithm does work.

  74. Hi Tony,

    This is a richly ironic sentence; first you claim to draw your conclusions on a case-by-case basis at the same time you reference a comment I made on an earlier post some weeks ago. You are many things, Charlie, but as your constant references to old battles over old comments from long ago attests, you are anything but case by case.

    It’s not ironic – it supposes a false dilemma. Your bias is evidenced case by case and highlighted case by case.
    Just because it is a pattern doesn’t mean I don’t conclude on each case.

    You seemed eager for me to learn something from you. I thought it would make you happy if I adopted some of your style

    Neither does this vague ad hominem mean anything.

    But enough of that. My quoting of you and Behe together was to counter your explicit claim that Behe never said that science would never find an evolutionary explanation for the immune system.

    Which he didn’t.

    His quote does contradict your statement.

    But it doesn’t.

    (But maybe you meant to say “natural” instead of evolutionary, and if that was your intention I would then agree; I’ve done that kind of thing typing hastily before, and that would make sense to me.)

    That’s a generous out you’ve left me, but unnecessary. In context, as you note, the reference is most relevant to your claim about natural explanations and IC but, of course, Behe’s quote didn’t say anything, as I stated, about there not being an evolutionary explanation in the future. You continue to conflate “Darwinian” with “evolutionary” – Behe does not do this (you continue to misrepresent him)- as you note below.

    Or perhaps you are biased by having contended with only those who have only come to their conclusions this way and have (incorrectly) surmised that I must have done the same?

    Not at all. You continued it above. Behe said that Darwinian explanations are doomed and you think he said that science will never find anevolutionary explanation. This point was plainly made in my previous comment.

    What I still find horrifying is that he concedes that adoption of ID (brought about by IC) would mean that “the ultimate explanation for life is beyond scientific explanation.”

    Horrifying? Oh my word. Not all explanations are scientific, not all knowledge is scientific and sometimes some problems just may lie outside of the realm of science. Like, for instance, “what caused the Big Bang”. Sometimes science itself leads you to these end points.
    Oh, and he didn’t say it “would”, he said it “may” – you’ve misrepresented him again.

    Of course he doesn’t think we’re there yet, and of course he doesn’t promote stopping scientific research now (and he has no power to effect that in any event), but he is openly promoting a theory whose acceptance could mean that “the ultimate explanation for life is beyond scientific explanation.” And that’s something that I think enlightened Christians who say they value understanding nature but still support Behe haven’t come fully to grips with yet.

    Glad to see you’ve admitted the errors of your ways and the misrepresentation in your first pronouncement on IC. The Big Bang, as an example, is also openly promoted and it tells us the same thing about the universe, and panspermia admits the same thing about life – sometimes those are the breaks when you investigate nature. Then again, it’s a slam-dunk that science does not have any ultimate answers.

    “The ultimate explanation for life is beyond scientific explanation,” and my original (albeit loose) quote that started this discussion, that IC means that “there’s no natural explanation for this [natural structures] so we should stop trying to explain it using natural explanations.” don’t seem so incompatible to me still.

    These are light years apart, first and foremost, because only the most scientistic would ever claim that science can answer the ultimate questions. But perhaps that’s an equivocation.
    Second, as demonstrated, Behe says there “may” not be and, as you admit, says nothing about how the search should proceed. In fact, when Behe concluded the BF was IC his cohort, Scott Minnich took up the search and demonstrated empirically that Behe’s conclusion was correct. And Seelke went into the lab and searched the empirical implications of that conclusion.
    Third, because not only does IC not say anything about the ultimate questions, neither does it even rule out evolution, or even naturalistic explanations, as Behe and his opponents admit.

    My hope is that you can come around to viewing those of us on both sides of the debate who have shown some signs of respect and honest engagement as honorable opponents, and not enemies.

    Like I said, case-by-case, Goose. I see your signs of respect as intermittent at best and sadly punctuated by a great deal of disrespect.
    I hope to see you come around, however, and this last comment seems a beginning.

    Charlie, I admire your passion. And these arguments (about the implications of things like IC) go on in seemingly endless cycles precisely because of that – if they were overwhelmingly weighted to one side there’d be no life to these discussions.

    Thanks.
    There are all kinds of reasons that arguments are difficult to settle but what I have primarily promoted here is at least a proper representation of what it is we are arguing about in the face of many uninformed statements.

  75. Hi DL,

    Of course what Charlie means is that the scientific literature doesn’t have a COMPLETE answer. Well this isn’t a good enough complaint in the face of all the evidence for evolution. It’s like complaining we don’t know what the suspect had for lunch on the day of the crime.

    Actually, what Behe means here (you are misrepresenting both him and me) is exactly what he says. He is not arguing against all the so-called evidence for “evolution” (which Behe isn’t arguing against – another misrepresentation) or your goofy analogy. He is presenting an empirical case regarding the state of scientific knowledge in light of the case he is making. The fact, properly represented, is just as stated, that there are no answers as to the origin. Behe explains this point in his book and his many web articles on the subject.

    If ID had proof that evolution was impossible, they would have a case.

    This is science, DL, not math. I thought you knew the difference.

    The argument for IC was initially that evolution could not create an IC structure. That turned out to be false.

    No it wasn’t. Read the book and become informed so that you can end your misrepresentations – if you care about honesty.
    I already helped you out with this misrepresentation:

    Back to your famous dichotomies again, I see.
    Behe’s case is not one of two possibilities. Where’d you get that? – from Orr? At least you’re actually thinking about engaging the idea now – the book’s only eleven years old, afterall.
    Behe’s case is that IC cannot, logically, result from direct NDE processes: that being gradualistic, step by step changes through selectable intermediates. That’s the logical part (I’ve already explained this, of course). It’s in his book as well.
    At the same time, probability argues against the claim that the IC was accomplished in multiple simultaneous mutations.
    In addition, the indirect circuitous route (exaptation) is not ruled out logically. It is merely highly unlikely and, as Behe has said from the start, there are no examples in the literature. This is the empirical case. You think it is defeated by the conjecture about exaptation, but it is not. This absence exists not only for demonstrable cases, but even for speculative ones. Now I see you’ve dropped a link to a talkorigins explanation of the flagellum. I’ll have a look. I bet it

    doesn’t answer Behe on the “detailed and testable” criteria, does it?

    —-

    . In fact, IC arguments don’t even tell us that co-optation is unlikely.

    IC says nothing about cooption’s likelihood. Empirical study and logic tell us about its being unlikely – as even Behe’s opponents agreed.

    Indeed, we know that co-optation does happen.

    You said this before (IIR, you claimed it was “empirically observed”). As I asked last time around:

    I am unaware of this. To what are you referring? Something other than the TTSS, I presume? And has this located co-option been able to explain IC?

    —-

    Behe says in that quote that there’s no evidence of a mechanism (apart from design) that produces useful complexity. Either Behe is incredibly ignorant, or he’s being dishonest. Genetic algorithms produce useful complexity, so the algorithm does work.

    “Useful” complexity? What’s that?
    And I see you’re back on about GAs. Were you going to assert again that a directed, goal seeking mechanism with the to-be-outputted-information front-loaded is analogous to how evolution works? Welcome to ID.

  76. Charlie,

    And I see you’re back on about GAs. Were you going to assert again that a directed, goal seeking mechanism with the to-be-outputted-information front-loaded is analogous to how evolution works? Welcome to ID.

    You’re deliberately inhibiting your own thinking.

    First of all, GA’s create IC structures. So the idea that NDE can’t create them is pure nonsense.

    Second, you are sneaking teleology in by conflating goal-seeking with fitness-seeking. There’s no difference except that in the former case a mind had envisioned what constitutes “fitness” at the start. In GA’s, the developer doesn’t know how to implement the solution. The developer is sometimes incapable of designing a solution. And yet the GA creates an IC solution that meets the goal because the goal is equivalent to a fitness. This is NOT front-loading. It would be front-loading if the developer knew what the GA was going to make ahead of time.

    In NDE, fitness is the one known fitness that is compatible with the lack of a mind: survival. Think about it. In a GA, survival and population are determined by a fitness function that represents some desirable human goal, like RF signal amplification. But if the fitness function represents the terrain and the environmental forces of the planet, then it will breed life that is fittest for living on that terrain and in those environmental conditions.

  77. Morning DL,
    You are wrong all over teh place, starting with my deliberate inhibitions.

    First of all, GA’s create IC structures. So the idea that NDE can’t create them is pure nonsense.

    This statement is nonsense. GAs are not NDE.
    GAs cannot create IC in a direct route without artificially selecting the unselectable. GAs, of course, do artificially select the unselectable, in a number of ways. The first is the obvious, search parameters are fine-tuned in real time by the human participant toward a selected goal. Second, random survival is allowed when unselectable qualities are are outnumbering selectable qualities in order to maintain useful population sizes. This is not NDE – which is a selection process. Third, when the NDE “goal”, survival and fecundity is the “goal”, GAs, as logic would dictate, wash out “useful” adaptations and move toward simplicty, not complexity. The parameters and fitness functions ahve to be fine-tuned during the process to keep this from happening or such information written in in the beginning – more features NDE doesn’t, supposedly, benefit from.
    Fourth, the GA programmer doesn’t know what the solution will be but it is not survival and fecundity, it is an actual target, and when he is not approaching that target he can change the process.

    In NDE, fitness is the one known fitness that is compatible with the lack of a mind: survival. Think about it.

    I have.

    . Think about it. In a GA, survival and population are determined by a fitness function that represents some desirable human goal, like RF signal amplification.

    Exactly. And that is goal-directed. “Survival” does not tend toward a target, as this teleology does. Survival might be lots of offspring and it might be few, it might be bigger and it might be smaller, it might have more and it might have less – NDE does not know and neither do its proponents. There is no function which adds B to A and then C to B and so on. As Gould tells us, it stumbles to and fro with no destination in mind – this will not build complexity toward a target (teleology) … but a GA can because GAs do not represent NDE.
    When GAs are getting closer to a target and you institute “survival” you do so not with survival in mind but with the target in mind.
    However, if you subtly equivocate ont e selection process and tweak this conversation to make this goal-seeking analogous to the survival in NDE you lose the direct route to IC at the other turn – selectability. Either the GA product is not IC, by definition, or it was created with artificial selections when it was not approaching its target (was not able to survive) or it did so via a circuitous route along which it was performing other tasks than that which is finally selected for (exaptation/cooption). If the final is the case then it provides no challenge to IC and we return again to its probability in the real world and do an empirical search for this happening or being plausibly outlines as per Behe in the literature.

  78. No editing feature this morning. Sorry about all the typos.

    DL, I know the sentence about equivocation on “survival” as it pertains to “fitness” and the GA’s “goal” will require deeper thinking from you. Please apply it before responding that I’ve missed the point. I haven’t.
    As with the inherent circularity in the term itself, this GA claim about complexity only demonstrates the tautology of the “survival of the fittest”. Real thinking reveals that this is not a strawman, and that it cannot be escaped by changing terms, but that the tautology is at the base of the claim. And your GA claim demonstrates it empirically.

    Think about it this way. I’ll make it simple, and please do not say that this means I”ve missed the point until you’ve thought it over – this will make the point and it willbe expandable.
    Say that the “goal” of the GA is “increased complexity), as it can be and sometimes is.
    So does this mean NDE can increase complexity? Of course not, we’ll all agree, because increased complexity was written into the program and it is not here where the GA is analogous to NDE anyway.
    Since “increased complexity” was the goal it is merely analogous in NDE to survival. So what was demonstrated by increasing the complexity? Survival. The tautology is proven yet again, that which survives survives.

    So we expand this.
    Now make the goal signal amplification.
    Increasing toward signal amplification may increase complexity, and it may not. If it does, it does so because increased complexity was necessary for signal amplification (If it is not necessary [ie, is not already a built in criterion] then any gain in complexity will be washed out by the simpler, easier and more numerous competitors).
    But here, again, as you say, signal aplification is a stand-in for survival.
    Unless you can show that increased complexity is a necessary element for survival, and, empirically, it neither is nor can it be shown to be then the analogy breaks right where you want to enlist it for your conclusion. So when you show that complexity increases toward the solution (disregarding the impossibility of doing so without that complexity hidden in the process already) you only demonstrate that when complexity is necessary and it is selected for it increases. You have stood this complexity in for “survival” in the analogy of the GA and have demonstrated again only that that which survives survives.
    If RF amplification is the goal, and it is achieved, all it shows is that survival happens, since RF amplification only stands for survival. The tautology is invoked once again.

  79. Charlie,

    So is your claim that we don’t know that complexity provides a survival advantage? And that, therefore, having survival as fitness measure is not enough to produce complexity?

  80. Hi DL,
    My claim is as above.
    If complexity is written into a program as its goal (its fitness function), or is a necessity of achieving its goal then “developing complexity” is analogous in NDE only to “survived” (the only fitness function of evolution).
    We don’t have to demonstrate that survivors survive, we already know that.

    As for its relevance to NDE beyond that, yes, it is true that survival is not a function of complexity. If it were we would have the uberspecies flying around shooting laser beams out of their eyes as lampooned above. Instead we have admonition after admonition that complexity is neither a goal, a necessity nor an unavoidable consequence of NDE. Rather, when we do “observe evolution” we see exactly the opposite – NDE is good at breaking things and decreasing complexity.
    This is where applying your standards of prediction to explanation would come in handy, since complexity is not a prediction of NDE (anymore than any other already-observed state is).

  81. Well, Charlie, you’re right that complexity is not an advantage in and of itself. Complexity does not equal survival advantage. It is orthogonal to survival advantage. However, the number of possible survival solutions goes up with complexity, so complexity provides access to survival advantage.

    Instead we have admonition after admonition that complexity is neither a goal, a necessity nor an unavoidable consequence of NDE.

    You’ve gone too far. Complexity is not a goal, but complexity affords opportunity. If a single-celled species can gain a survival advantage with some additional complexity, then there’s no reason that NDE can’t create that additional complexity.

    Suppose there is only one single-celled species on this planet, and it lives in the oceans, feeding off inorganic compounds. Even if there were just this one species, there would be thousands of ecological niches accessible by adding complexity. Warm water, cold water, fast current, still water, consuming different compounds with different toxicities, switching to organic compounds, etc. All of these are niches because if an individual mutates (into a new species) to survive in warmer water or to survive higher toxicity, then it will no longer be in competition for resources with the rest of the life forms. These extra abilities require more complexity. Mutations create and destroy complexity, but not all less-complex and not all more-complex species are better adapted. So a species could fork into a regressed, less-complex species if that provides some advantages in a new niche.

    I’ll say this again, because you’ve disputed it before: not every mutation creates a competitor for the prior species. If a mutation enables a species to survive in cooler climates, that doesn’t put more pressure on the original species, and may not significantly reduce the population of the original species. It just opens the door for the new species in new territory.

    Complexity is a prediction of NDE because NDE finds solutions to survival problems, and there are more solutions with more complexity. That doesn’t mean there won’t be simple solutions too. Just because amphibians evolved from simpler fish doesn’t mean sharks will go extinct (unless frogs start competing with those sharks).

    Again, go back to GA’s. GA’s are not written to create complexity. They are written with the ability to increase (or decrease) complexity. Complexity is orthogonal to fitness, providing nothing more than an opportunity to be fitter. And yet GA’s create complexity when that is not the explicit goal. So the idea that GA’s only decrease complexity or that they are explicitly programmed to create complexity is just wrong. They merely have the ability to create complexity, and they do so because it provides advantages in new niches.

  82. Hi DL,

    
Well, Charlie, you’re right that complexity is not an advantage in and of itself. Complexity does not equal survival advantage.

    Thankyou. It is refreshing when we can start off with some agreement.

    It is orthogonal to survival advantage. However, the number of possible survival solutions goes up with complexity, so complexity provides access to survival advantage.

    This is question-begging. You do not know that survival solutions increase with complexity and exactly the opposite is at least as obvious.
    The very fact that complexity will bear greater energy and reproductive costs advantages simplicity over complexity in survival advantage.

    
Instead we have admonition after admonition that complexity is neither a goal, a necessity nor an unavoidable consequence of NDE.



    You’ve gone too far. Complexity is not a goal, but complexity affords opportunity.

    Question begged again. It is just as intuitive to say that simplicity affords opportunity. Without empirical science and predictions here, as opposed to specialized case by case story telling, you have no basis for this claim.

    If a single-celled species can gain a survival advantage with some additional complexity, then there’s no reason that NDE can’t create that additional complexity.

    This is the entire question and you can’t just take it all on your side with one scoop. First, the question is if additional complexity equates to survival advantage. There is no general theory explaining or predicting such is the case and to claim so is to make an unjustified ad hoc allowance – i.e. a “just so story.
    Second, the very question on the table is whether or not there is a reason NDE can or can’t, or should be expected to “create” the required complexity.

    
Suppose there is only one single-celled species on this planet, and it lives in the oceans, feeding off inorganic compounds. Even if there were just this one species, there would be thousands of ecological niches accessible by adding complexity. Warm water, cold water, fast current, still water, consuming different compounds with different toxicities, switching to organic compounds, etc.

    None of these conditions requires complexity. When fish “evolve” antifreeze blood they do so by simplifying. When viruses “evolve” protection against vaccines they do so by simplifying. Complexity is not required in adaptation.

    All of these are niches because if an individual mutates (into a new species) to survive in warmer water or to survive higher toxicity, then it will no longer be in competition for resources with the rest of the life forms.

    Again, this necessary mutation has nothing to say about complexity, much less increasing complexity, much less IC.

    These extra abilities require more complexity.

    No, they do not. They can just as easily, moreso in fact, require simplicity.

    Mutations create and destroy complexity, but not all less-complex and not all more-complex species are better adapted. So a species could fork into a regressed, less-complex species if that provides some advantages in a new niche.

    This is the observed case and it is question-begigng to say that mutations create increased complexity which adds survival value. You are entitled to speculate thus, and, given a commitment to NDE I would expect no less. But this does not make increasing complexity a prediction of NDE and it does not make increasing complexity a necessity in any way for survival and it does not justify extrapolating from GA to NDE.

    
I’ll say this again, because you’ve disputed it before: not every mutation creates a competitor for the prior species. If a mutation enables a species to survive in cooler climates, that doesn’t put more pressure on the original species, and may not significantly reduce the population of the original species. It just opens the door for the new species in new territory.

    Since this issue made you storm away from the blog previously I’m torn over whether or not to address it … but I do continue to dispute this. I did not present this as a logical necessity but as the more probable event, given the claims of NDE. A mutation in a population will either flourish or be washed out. In either case the theory demands competition and extinction. Extinction is every bit as necessary to Darwinian theory as innovation – the whole point is replacement.
    Again, this does not meant he theory is false, but when you look for the most likely, non-question-begging consequences of the theory, non-life is by far the more probable outcome. But here you don’t want to deal in probabilities.

    
Complexity is a prediction of NDE because NDE finds solutions to survival problems,

    Question-begging.

    and there are more solutions with more complexity.

    Quesiton-begging.

    That doesn’t mean there won’t be simple solutions too.

    . True enough. In fact, simple solutions would be the prediction.

    
Again, go back to GA’s. GA’s are not written to create complexity.

    Some are. I wonder if you can point to any GA that was designed to actually perform a function, which did not utilize human selection, which did not artificially select for the unselectable and still maintin your opsition that GAs create IC. I highly doubt it.
    I would wager that any GA for which IC is a claim was designed with complexity generation in mind, i.e., complexity itself was the fitness function.

  83. Charlie,
    Is ‘complexity’ a concept that evolutionary science can point to as an explanation one way or the other? I’m wondering if this doesn’t compare to the concept of ‘design’ as an explanation?

  84. Charlie,

    Boiling it down, there are two issues. The central one is raised here:

    I would wager that any GA for which IC is a claim was designed with complexity generation in mind, i.e., complexity itself was the fitness function.

    So if we have a fitness function that is not measuring complexity, just output (e.g., best solution to some problem like amplification, noise rejection, etc.), and it generates complexity, will you be convinced that GA’s create complexity and don’t need to be front-loaded?

    Second issue:

    A mutation in a population will either flourish or be washed out. In either case the theory demands competition and extinction. Extinction is every bit as necessary to Darwinian theory as innovation – the whole point is replacement.

    Not all mutations open up totally new niches, but some do. If a mutant form is able to expand into new territory without displacing the prior form, this does not contradict NDE in any way. Of course, after a certain period of time, the population of the new species will grow to the point that it competes with itself. Any second mutant that improves on the first mutant’s abilities will displace the first mutant but not the original. I don’t see why you would have a problem with this.

  85. Charlie:
         Superb unpacking and exposing DL’s errors and fallacies.

    SteveK:
         Your question to Charlie is insightful.

         Of course things were “designed,” but one does not and cannot “detect” design scientifically the same way one detects a neutrino. William Dembski is fundamentally incorrect to reduce the detection of design to the level of the detection of neutrinos. Why? (One need only ask Demski: what is it that’s “seeing” design in the data collected scientifically? And, by extension, what is that “sees” injustice when candy is taken from a baby in the data collected scientifically?) These “things” are two ontologically very different entities! We don’t need to descend to Dembski’s envy of science in employing it to detect something which is not detectable by its very NATURE in the first place. Of course, Dembski tries to rectify the situation by mathematicizing not just the external (accidental) aspects of biological entities but the natures of those entities themselves: “whatness” is not reducible to mathematics, but patterns in DNA can certainly be described mathematically (see digression below).

         Now, what about “complexity”? The word “RED” is mathematically more complex than the word “red”, similarly to the way a mountain is more complex mathematically than a human being. But there is NO tool or methodology at the disposal of the MESs to extract “meaning” from either of the two cases of “red” just provided, when in fact the two words have the SAME meaning even while both words are mathematically more complex. “Meaning” is what “whatness” (form) of a word, while the pigments of ink of a printed word are the “out of what” (material) a printed word is organized. The organization of that word had to come from the outside of that word—imposed upon it by a nous (an intelligent agent). The MESs cannot distinguish what “whatness” (quiddity, essence, intelligent aspect) is, and it certainly cannot distinguish between a mountain and a human being except using its own epistemological tools. There is NO ontological distinctions in the MESs to speak of: differences “seen” by the MESs are based only on accidents (“measureable properties” in MES-talk): “catness” is not merely the mathematical sum of all properties common to cats.

         [Digression: The organization of inFORMation “contained” in DNA had to come from the outside of the DNA, but the physical mechanisms that brought it about might very well have been Darwinian: it’s the NATURE of the entities that leads to descent with modification. That kind of knowledge IS accessible by the MES, and we should not retreat from them nor interfere in their work. The real question is not who created “single-celled organisms,” but (1) what is it about natures that “causes” things to behave the way they do—say, to evolve?, and (2) who or what created “natures”? Put a bit provocatively: Does a bird fly because it has wings (scientific perspective) or does it fly because by its nature it is a “flying creature” (perspective of natural philosophy)? The answer is both: truth cannot contradict truth. And, stepping back for a wider perspective: faith cannot contradict reason, and visa versa. Only those who desire them to be contradictory and independent a priori will find every false reason under the sun in the vain attempt to instigate a wholly artificial war between faith and reason.]

         Anyway, continuing on with the analogy: A human being is ontologically on a different level than a mountain even though the latter is roughly one million times larger (and hence more mathematically complex) than a human being. “Humanness” or “personhood” are NOT accessible to the MESs. But, so what? Does it follow they don’t exist or are reducible to the merely material? Of course not. The very act of reductionism is a non-material act—that’s the huge irony hanging over the heads of reductionists and scientismists. How can the MESs distinguish between a human person and a mountain? Only through operational (MES) definitions. (Here’s a wonderful Chesterton quote: “It is typical of the mechanistic moderns that, even when they try to imagine a live thing, they can only think of a mechanical metaphor from a dead thing.” (from Saint Thomas Aquinas: “The Dumb Ox” by G.K. Chesterton))

         Those who claim either exclusive or privileged epistemological status to the MESs can only do so (to avoid circular arguments) by appealing to something beyond the MESs… but then they can’t be exclusive or privileged, can they? Here’s a simple example of concepts the MESs take for granted and cannot themselves “see” (measure, predict, describe, etc.): one can imagine (as opposed to conceive!) an apple falling because the twig holding it failed. One can also imagine (as opposed to conceive!) an apple falling, but not knowing why and hence spurring investigation. But can one image causality per se in one’s looking for a concrete cause for the latter apple’s fall? Of course not, for causality is a concept certainly not limited to physically efficient causes, and certainly not even limited to efficient causes.

  86. Hi DL,

    So if we have a fitness function that is not measuring complexity, just output (e.g., best solution to some problem like amplification, noise rejection, etc.), and it generates complexity, will you be convinced that GA’s create complexity and don’t need to be front-loaded?

    Before speculating too broadly let’s deal with your claim first. You say that GAs falsify Behe’s claim and demonstrate him to be incredibly ignorant or dishonest. So let’s see that demonstrated. As I said in your quote, and the part not quoted:

    I wonder if you can point to any GA that was designed to actually perform a function, which did not utilize human selection, which did not artificially select for the unselectable and still maintain your position that GAs create IC. I highly doubt it.
    I would wager that any GA for which IC is a claim was designed with complexity generation in mind, i.e., complexity itself was the fitness function.

    (repaired typos)
    As well as backing up your position we have here the added benefit that with IC we know what we mean operationally when we say “complex” so this will eliminate the need for new definitions and nebulous meanings. Is there such an animal as demonstrates what you said about Behe, which does not rely upon interventions, front-loading, inputted information, free lunches or other informational resources not available to NDE?

    On your second issue, I don’t know that it is much worth our efforts to discuss too fully as it was an aside (spawned by your analogy) and not really relevant. I will pursue it for a while, just to see where it goes, however.
    First, I didn’t claim a violation of NDE. I said that I stand by what I said would be the most probable outcome of an evolutionary scenario. In addition to that you can follow the history of the discussion of the fossil record to see that what I am saying is true. It was pointed to as evidence that evolution was taking place that older forms were disappearing in the fossil record to be replaced by newer forms. Slowly but surely what was obviously the case had to be admitted, however. That is that there was no evidence of the older forms transitioning into newer forms during their extinction. Rather, they disappeared suddenly with no lead up to anything new over an average of a million year span and whatever new appeared came out of nowhere and had not gradually replaced the old, as the theory had predicted.
    So, as Gould said, evolution was said to always be happening somewhere else – in isolated populations – filling your niches and extinguishing their predecessors. In this scenario populations split off, mutations occurred, the old was replaced by the new, and the new stepped out to reveal itself fully-formed to the fossil record (as it would then persist for its million years) without evidence that it did what it was supposed to have done – replace the former. Since the former persisted it must have out-competed it only in that niche in which it had evolved.
    As Gould also said, we can’t keep claiming, against the data, that evolution always happened someplace else, at another time, where nobody can see the evidence. The fact that this solution ever was invoked demonstrates my point – and Darwin’s – that extinction is a necessary player and the selective force in speciation.

    While we are discussing “suppose there was”s let’s look some at empirical evidence.
    By far the most common, by number, bulk, longevity, etc., organisms on the planet are those of the “simple” variety – the single-celled bacteria and archaea. Everywhere there is an environment we find them: in clouds, in the upper atmosphere, in ice, in geysers, at the bottom of the ocean, in the earth’s bedrock, in the gut, on the skin, salt water, fresh water, no water, etc. We find them eating virtually everything there is to eat and making their own energy when need be. For billions of years they were all we had, thriving and keeping on keeping on. Whatever would have possessed these highly successful, relatively “simple” (no life is simple) to have become more “complex”, to evolve more bells and whistles and to piggy-back into multicellularity? In what niche do they already not prosper? Into what niche did the multi-celled organisms ever expand at their expense and out-compete them?
    What general theory would predict that the prokaryotes and then eukaryotes would have to rise in complexity to better survive when they didn’t for billions of years before the explosion, have not since, and yet still dominate the planet? Why didn’t evolution just stand pat as I say is the more probable case given its claims? The fact that their survival and fecundity were just fine for billions of years and continue to be show there is no evidence that a rise in complexity was necessary, and no prediction that it ought to have occurred. Again, the only way to say evolution predicts this rise in complexity is to see that complexity has been generated and to find a way to accommodate it within the theory. Against your previous admonitions on explanation, there is no preferential prediction entailed generally toward complexity.

  87. Hi Holopupenko,
    Thanks for that encouragement and for that perspective on complexity and design. I’ll have to give it another read in the morning.

    Steve,
    I just got stuck in my own head describing the circularity of the problem for NDE and have become high-centered.
    I’ll try to add something in the morning.

    DL,
    I forgot to mention this time around the most probable outcome of naturalism, both logically and by empirical observation. That is the simplicity that is sterility, non-life.
    As far as we know this is the only planet ever to give rise to life. Compared to all the ways naturalism can give rise to not-life the probabilities against naturalism doing it on this planet must be billions and billions (cue Sagan) to one.

    All,
    Sorry for all the typos.

  88. Charlie,

    You wrote:

    …Behe’s quote didn’t say anything, as I stated, about there not being an evolutionary explanation in the future.

    Then I am missing something. Do you think that Behe is making an important distinction between Darwinian and evolutionary? Keep in mind I was comparing your representation of Behe’s position (above) with Behe’s statement about Darwinian explanations for the immune system being doomed. To my reading your representation (above) and his statement still contradict each other.

    Oh, and he didn’t say it “would”, he said it “may” – you’ve misrepresented him again.

    Small thing here, but I was taught that “would” in the context I used it is the proper form of the (somewhat archaic) English subjunctive. As in “should this happen, that would occur.” A declarative statement that would have misrepresented Behe’s would have used “will.” So my sentence wasn’t a misrepresentation, it accurately represented a sense of continengcy – that something would occur should other things transpire.

    Then again, it’s a slam-dunk that science does not have any ultimate answers.

    Well, with the (very little) that I understand of the implications of the Big Bang there’s no scientific explanation for the ultimate answer because at some point – the instant just before creation – there’s nothing upon which to direct an empirical question.

    The difference with Behe’s IC is that it chooses natural structures and proposes that their (best / proper) explanation may only be metaphysical. That seems fundamentally different than the point at which the other modern empirical sciences fields terminate their inquiry. Like I tried saying before, I can’t think of it’s equivalent for any other field in the modern empirical sciences.

    I have to re-read and catch up on where the discussion is now going. I do have one request for you all – I didn’t know all the acronyms (although I think I’ve found all their antecedents here, it took some back-checking, and some, like NDE were hard for me to narrow down) so if you could parenthetically define them occasionally NDE (Neo Darwinian Evolution[?]) that would help make this more readable for me.

  89. Hi Tony,

    Then I am missing something.

    True that.

    Do you think that Behe is making an important distinction between Darwinian and evolutionary?

    Of course he is. You know neither IC, by your previous statements, nor Behe by this question. Like I said, if you’re going to cite somebody or some ideas negatively in support of your position it would be best if you’ve read them.

    Keep in mind I was comparing your representation of Behe’s position (above) with Behe’s statement about Darwinian explanations for the immune system being doomed. To my reading your representation (above) and his statement still contradict each other.

    You are not reading well, then. I have pointed out repeatedly that for Behe, or anyone, to critique Darwinian processes is not to critique “evolution”, per se. You only maintain this reading of contradiction by conflating the two – but I’ve said that.
    FYI, before he started thinking about ID Behe was a mainstream, publishing evolutionary, Darwinian biologist.
    He believes that the universe is its estimated 15-18 billion years old. He believes that all of life likely has , in Darwin’s words, one or a few common ancestors, and he believes that man shares a common ancestor with modern apes. He thinks our genome provides good evidence of this and, much to the (constant and repeated) shock of his constant interlocutor, Ken Miller, and the shock several times of atheists (and even theistic evolutionists) on this board, he shares Miller’s view of the fossil record and the evolutionary history of man.
    He believes that life unfolded by evolutionary means and that this could well have been entirely naturalistic as due to secondary causes.
    Contrary to your reading of IC, Behe doesn’t think that IC argues against any of this or that ID itself necessitates against this. He believes in the cosmic fine-tuning of the universe and thinks that the design of life (traceable now, in his opinion all the way to level of the divide between orders and familes or families and genera if not even deeper) could have been instantiated by just such a finetuning of laws and events right from the moment of the Big Bang.
    As you can see, there is no rationale for stopping the search for secondary causes or temporal events in any of his scientific work.

    And he has said all of this from the beginning. Nobody had to worm it out of him through long debate, no matter what his critics say when they suddenly revel in his recent “admissions”.

    So my sentence wasn’t a misrepresentation, it accurately represented a sense of continengcy – that something would occur should other things transpire.

    Not tracking you here. Using your “should this, then that” your claim was “should ID be adopted then “the ultimate explanation for life is beyond scientific explanation.”” Are you taking pains here to say that even if ID is adopted then, by your reading and use of the word “would” that Behe’s statement leaves open the possibility of scientific explanation for the ultimate explanation of life? Are you agreeing, and for some reason restating by your sentence, that Behe said “may”?

    But I concede that just because one charges “misrepresentation” willy-nilly it doesn’t mean that the misrepresentation actually occurred. As you point out, there is nuance to language and interpretation.

    Maybe I would be better off just stating facts as I see them or providing clarifications rather than charging that you misrepresented every time I think I see it. It might even be more respectful. What do you think?

    Well, with the (very little) that I understand of the implications of the Big Bang there’s no scientific explanation for the ultimate answer because at some point – the instant just before creation – there’s nothing upon which to direct an empirical question.

    That’s right. A scientific theory based upon observation and hypothesis testing has led us to a point beyond which there is no further scientific explanation and no scientific ultimate answer. Not actually so horrifying, is it?

    The difference with Behe’s IC is that it chooses natural structures and proposes that their (best / proper) explanation may only be metaphysical. That seems fundamentally different than the point at which the other modern empirical sciences fields terminate their inquiry.

    The distinction provides little difference. The Big Bang theory chooses a natural structure and leads us to the realization that the best/proper/final explanation may only be beyond physics (metaphysics) as well.
    I see no fundamental difference and I already took pains to debunk your comparison to other fields.

  90. This is far from the first time I have shared this here. I bet it will be far from the last time as well.:

    Perhaps the single most stunning thing about Darwin’s Black Box, Michael Behe’s “Biochemical Challenge to Evolution,” is the amount of territory that its author concedes to Darwinism. As tempted as they might be to pick up this book in their own defense, “scientific creationists” should think twice about enlisting an ally who has concluded that the Earth is several billion years old, that evolutionary biology has had “much success in accounting for the patterns of life we see around us (1),” that evolution accounts for the appearance of new organisms including antibiotic-resistant bacteria, and who is convinced that all organisms share a “common ancestor.” In plain language, this means that Michael Behe and I share an evolutionary view of the natural history of the Earth and the meaning of the fossil record; namely, that present-day organisms have been produced by a process of descent with modification from their ancient ancestors. Behe is clear, firm, and consistent on this point. For example, when Michael and I engaged in debate at the 1995 meeting of the American Scientific Affiliation, I argued that the 100% match of DNA sequences in the pseudogene region of beta-globin was proof that humans and gorillas shared a recent common ancestor. To my surprise, Behe said that he shared that view, and had no problem with the notion of common ancestry. Creationists who believe that Behe is on their side should proceed with caution – he states very clearly that evolution can produce new species, and that human beings are one of those species.

    Ken Miller’s review of Darwin’s Black Box
    http://www.millerandlevine.com/km/evol/behe-review/index.html

  91. Charlie:

         Good for Behe! The problem, however, is his climbing on the Dembski bandwagon and believing design is as detectable as starlight or neutrinos. These are two ontologically very classes of things, and hence must be studied differently. The irony is ceding to the MESs what they can’t deal with in the first place. And, typically, when the MESs can’t study something that would have a profound impact on a secularist worldview, they hand-wave it away as “irrelevant” or “nonexistent.” Funny kind of intellectual dishonesty, that.

         Anyway, you guys may be interested in the following classically-scientistic article (book review) by evolutionary scientist Jerry A. Coyne (http://www.tnr.com/story_print.html?id=1e3851a3-bdf7-438a-ac2a-a5e381a70472) “Seeing is Believing”. Note that Coyne, a scientist, feels he is capable of correctly passing judgment on non-MES things, and hence he intentionally (based on his worldview) instigates the artificial war between faith and reason. Why is a solid philosopher of nature not permitted to say something? Why is not a theologian permitted to say something? Why? Because it’s not “scientific.” Oooh! Everyone bow, remove their hats, and shiver in the presence of scientism, please. Almost every week one sees this type of foolishness make its way into the press.

  92. Hi Holopupenko,
    I do not hold to all of Behe’s views on either science or design. It is only fair, however, that he be properly represented when critiqued.
    Since everyone from St. Paul, to Aquinas, to Luther to Behe (sorry for listing him in that category of geniuses) seems to agree that reason and observation of God’s handiwork play some part in being able to ascertain not only His actions but many of His attributes I am unsure as to where the line of demarcation must rightly fall. As Paul told us, and the above agree, by our senses we can gain enough knowledge of God that we are left without excuse for our disbelief.

    Thanks for the remarks on Coyne and scientism. I have just enough time to go peruse it.

    Cheers and prayers.

  93. Charlie,

    Okay, so you demand that the generated complexity is IC.

    As a side question though, are you also saying that GA’s will not generate non-IC complexity either? Or are you just raising the bar for this test?

    Also, you say:

    Is there such an animal as demonstrates what you said about Behe, which does not rely upon interventions, front-loading, inputted information, free lunches or other informational resources not available to NDE?

    Let’s not put in excessive conditions. This is a test of NDE, not OOL. The GA designer is allowed to create a mechanism of evolution, an environment and base components suitable for evolutionary algorithm to work on. This setup doesn’t count as front-loading or intervention. Intervention would be stopping the GA halfway and moving genes around because we we know those moves would lead to solutions. The question is, if the environment is suitable and the components are sufficiently general for creating fit solutions, does the GA create new, complex, IC-complex, unforeseen solutions?

    If it does, that has implications. It means that evolution in general can create complexity, IC complexity, and information without input from a designer.

    Sound fair?

    It is a completely separate question whether the environment and components on Earth are suitable fodder for evolution. Theistic evolutionists would say that a designer setup the Earth and the physics in the same way a GA designer sets up the software system. Yet even theistic evolution isn’t front-loading.

    It was pointed to as evidence that evolution was taking place that older forms were disappearing in the fossil record to be replaced by newer forms. Slowly but surely what was obviously the case had to be admitted, however. That is that there was no evidence of the older forms transitioning into newer forms during their extinction. Rather, they disappeared suddenly with no lead up to anything new over an average of a million year span and whatever new appeared came out of nowhere and had not gradually replaced the old, as the theory had predicted.
    So, as Gould said, evolution was said to always be happening somewhere else – in isolated populations – filling your niches and extinguishing their predecessors.

    As Gould also said, we can’t keep claiming, against the data, that evolution always happened someplace else, at another time, where nobody can see the evidence.

    Your use of “against the data” in the last lines there… what do you mean? You explain that punctuated equilibrium seems to be how evolution is working in natural history based on the evidence/data. Some mutants take over new niches and then take over the whole ball game if the ancestor species collapses. Fair enough. Is your last line here just reiterating what you said in the earlier paragraph? Because none of this contradicts NDE.

    To say that Darwin’s simple assumptions about the underlying mechanisms of evolution were wrong is a trivially true statement. The fossil record shows points on a tree, shows common descent, with a small number of scattered data points spread over millions of years. The simplest assumption is that species gradually move from one point on the tree to another. It turns out that this simplest solution isn’t quite correct. Some processes may be slow, but some are fast, caused by environmental changes, mass extinctions, land bridges, etc. This doesn’t contradict the NDE thesis. It only contradicts the simplest model consistent with the thesis.

    Whatever would have possessed these highly successful, relatively “simple” (no life is simple) to have become more “complex”, to evolve more bells and whistles and to piggy-back into multicellularity? In what niche do they already not prosper? Into what niche did the multi-celled organisms ever expand at their expense and out-compete them?

    Well, simpler life forms are limited. They have very limited control over their mobility. They cannot structurally resist attack from predators. They have limited awareness of their surroundings and limited ability to leverage that awareness. They cannot see a food source and move towards it.

    They also have more difficulty creating symbiotic relationships. In a typical multicellular organism, there are cells that physically protect the organism, cells that are used for propulsion, cells that are used for reproduction, cells that are used for digestion, and cells that are used for sensation. Single-celled life that can evolve this specialization have huge advantages. Each kind of cell makes a trade-off. A cell that is optimized for digestion will be more efficient than a cell that needs to provide for defense, mobility, and reproduction. And each cell benefits from the specialization by passing on its genes, even if it is not directly reproducing.

    Why should you hire someone to build your house, landscape your lawn, check your health, do your taxes? In theory, you could do all of this yourself. However, it would be inefficient to do so as a society. The society is stronger for the specialization.

  94. Hi DL,

    Okay, so you demand that the generated complexity is IC.
    As a side question though, are you also saying that GA’s will not generate non-IC complexity either? Or are you just raising the bar for this test?

    Raised bar? Mine is the same bar it’s always been , ever since before Behe wrote DBB. He never moved his goalposts and I never raised any bar.
    You said that Behe is either incredibly ignorant or dishonest because GAs have produced “useful complexity”.
    I don’t recall Behe saying evolution can’t produce “useful complexity”, and asked you to demonstrate that he ignorantly or dishonestly said this or what it meant but you never did. What he has said is that Darwinian processes can’t directly produce IC.
    If he is incredibly ignorant or dishonest then it must be with regard to this claim.

    With regard to that, you then specifically said:

    First of all, GA’s create IC structures. So the idea that NDE can’t create them is pure nonsense.

    So how is it that I am the one who wants to make this about IC and that I am raising the bar?

    I disputed this claim:

    GAs cannot create IC in a direct route without artificially selecting the unselectable.

    Then you decided to try to lower the bar.
    DL:

    1. So is your claim that we don’t know that complexity provides a survival advantage? And that, therefore, having survival as fitness measure is not enough to produce complexity?
    ….
    So if we have a fitness function that is not measuring complexity, just output (e.g., best solution to some problem like amplification, noise rejection, etc.), and it generates complexity, will you be convinced that GA’s create complexity and don’t need to be front-loaded?

    But no sale:
    Moi:

    Before speculating too broadly let’s deal with your claim first. You say that GAs falsify Behe’s claim and demonstrate him to be incredibly ignorant or dishonest. So let’s see that demonstrated. As I said in your quote, and the part not quoted:
    I wonder if you can point to any GA that was designed to actually perform a function, which did not utilize human selection, which did not artificially select for the unselectable and still maintain your position that GAs create IC. I highly doubt it.
I would wager that any GA for which IC is a claim was designed with complexity generation in mind, i.e., complexity itself was the fitness function.

    Is there such an animal as demonstrates what you said about Behe, which does not rely upon interventions, front-loading, inputted information, free lunches or other informational resources not available to NDE?

    Let’s not put in excessive conditions. This is a test of NDE, not OOL.

    I didn’t say a word about OOL and you placed the conditions by calling Behe either ignorant or dishonest as demonstrated by GAs.

    The GA designer is allowed to create a mechanism of evolution, an environment and base components suitable for evolutionary algorithm to work on. This setup doesn’t count as front-loading or intervention.

    That’s an interesting assertion. We’ll have to decide whether or not it is front-loaded or whether or not the programmer somehow found a free lunch once you demonstrate the IC of the product.

    Intervention would be stopping the GA halfway and moving genes around because we we know those moves would lead to solutions.

    This bar must now be on springs. Intervention would also occur if the programmer saw nothing useful was happening or knew it wouldn’t and allowed unselectable intermediates to survive. Intervention need have nothing to do with his clairvoyance.

    The question is, if the environment is suitable and the components are sufficiently general for creating fit solutions, does the GA create new, complex, IC-complex, unforeseen solutions?

    Yes, the question is, did the GA directly create IC only through a series of small, gradual, selectable steps in a manner consistent with NDE or was there intervention, exaptation/cooption, non-Darwinain processes, without front-loading the rise in complexity and artificially ensuring it.

    If it does, that has implications. It means that evolution in general can create complexity, IC complexity, and information without input from a designer.
    Sound fair?

    What sounds fair is your demonstrating what you said exists with the implications for Behe (he is ignorant or dishonest) and Darwinism (not “evolution”) as you claimed.

    To say that Darwin’s simple assumptions about the underlying mechanisms of evolution were wrong is a trivially true statement.

    This isn’t about showing Darwin’s assumptions to be wrong but the most probable result of the philosophical theory that is NDE. The idea that competition, replacement and extinction are necessary for NS to operate did not end with Darwin. In theory, extinction of the parent species is the exact result, the side-effect of speciation.
    The fact that evolution’s theoretical predictions (extinctions as well as gradualism as well as randomness, etc.) do not accord well with real life and that the theory must be constantly tweaked to make it match the previously ignored facts is nothing new. Extinctions have generally been moved around to the front now, where catastrophic extinctions (anathema to Darwin and his like-minded popularizers) allow for speciation by opening up niches, but extinction is still the player.

    This doesn’t contradict the NDE thesis. It only contradicts the simplest model consistent with the thesis.

    You aren’t listening. I didn’t say NDE was false or that it was contradicted – I said what was the most probable result of NDE.

    Well, simpler life forms are limited.

    So is complexity – it is costly.
    Cost must be outweighed by reward, but since the simple organisms have not been outperformed or replaced it is not evident that such a reward exists.

    They have very limited control over their mobility. They cannot structurally resist attack from predators. They have limited awareness of their surroundings and limited ability to leverage that awareness. They cannot see a food source and move towards it.

    You have assumed a lot of evolved complexity before justifying the necessity of complexity. When we return to the “simple” first replicators, metabolizing organic or even inorganic material there are no predators, for instance, and there are no multicellular organism with whom to enter into symbiosis. As you so often do you are presuming exactly what it is you are supposed to be arguing for.

    1. Why should you hire someone to build your house, landscape your lawn, check your health, do your taxes? In theory, you could do all of this yourself. However, it would be inefficient to do so as a society. The society is stronger for the specialization.

    You are leaping forward here as well. This is the IC argument written on the ecosystem – a very compelling argument in my opinion.
    As with the impossibility of a direct-route IC formation, this “society” to which you allude is not the probable result of Darwinian evolution from a single first life. In a population of “simple” organisms, which have never disappeared and never been at a survival or reproductive disadvantage (the fit have survived, after all), there is no general prediction for this increased complexity and specialization vs. being a jack-of-all-trades, is the more costly, and unrewardable condition. A single specialized cell, increasing in complexity, is experiencing a greater cost and detriment in some other area. And this cost is not paid back by some other single-celled organism which has specialized to provide it a need because evolution has yet to act upon the second putative specialist. Darwinists will again shrug this off and chalk up its possibility as a result of gradualism, incrementalism, etc. But, as with IC, you are skipping over unselectable steps.
    As before, given the truth of the theory, and given reality as it exists today these truths can be packaged into the theory. But they are not the predictions of the theory and they are not the most likely results.
    Again, the most likely result is simplicity, not complexity, it is death, not life; especially since extinction is far more likely the smaller the population size and we are talking here about an original population of one or very few.

  95. I just wanted to say, Charlie…

    I have strong sympathy for ID, but generally don’t regard it as science. And I have no problem with evolution either. However, you are making some very powerful points here. It certainly keeps me looking at evolution in different ways, and finding even more skepticism as far as atheistic extrapolations of it tend to go.

    My own perspective would be, if evolution is able to account for all of what you list (complexity rather than simplicity, death rather than life, etc) then the options are either to see profound teleology at work within the system, or be told to accept ‘it was just blind luck’ on the level of the inane.

  96. Thanks for the rescue Tom. Sorry for the duplicate.
    ===
    Hi Joseph,
    Thank you very much for speaking up.
    I agree with your choices at the end. I’m not saying that belief in “evolution” can’t be fine-tuned (as it has) to fit observation or that one can’t harmonize reality to the theory (to disputable degrees of success) with story telling and special pleading but that’s not what DL is supposed to be about.
    He is supposed to be about probabilities and explanations accepted only when they preferentially predict the observed outcome – I think it much more obvious that the prediction of materialism/naturalism is sterility. As you say, this argues much more strongly for profound teleology (even the generation and selectivity of “complexity” in DL’s discussion itself implies teleology).
    Thanks again.

  97. Charlie,

    You said that Behe is either incredibly ignorant or dishonest because GAs have produced “useful complexity”.
    I don’t recall Behe saying evolution can’t produce “useful complexity”, and asked you to demonstrate that he ignorantly or dishonestly said this or what it meant but you never did. What he has said is that Darwinian processes can’t directly produce IC.
    If he is incredibly ignorant or dishonest then it must be with regard to this claim.

    I stand by my claim. Behe is either ignorant or dishonest. Co-option explains IC in Darwinian evolution. Behe’s claim has been debunked. Biologists answered Behe’s challenge long ago, but Behe keeps pretending they haven’t. This is why the judge in the Dover case didn’t just rule against ID, he wrote a scathing judgment against dishonest ID buffoonery in general.

    The only way I can reconcile your statements with the facts is if you claim (incorrectly) that co-option isn’t Darwinian. That’s a straw man argument, and irrelevant to the questions at hand. NDE stands for NEO Darwinian Evolution. Evolution is a search algorithm that finds complex solutions that survive. Before Darwin came along, people did not think solutions could be found except by design. They were wrong. The theory can be seen to work from a purely logical standpoint, proven by GA’s, and proven as the explanation for speciation on Earth by common descent.

    In theory, extinction of the parent species is the exact result, the side-effect of speciation.

    Sorry, but you are mistaken.

    The fact that evolution’s theoretical predictions (extinctions as well as gradualism as well as randomness, etc.) do not accord well with real life and that the theory must be constantly tweaked to make it match the previously ignored facts is nothing new. Extinctions have generally been moved around to the front now, where catastrophic extinctions (anathema to Darwin and his like-minded popularizers) allow for speciation by opening up niches, but extinction is still the player.

    This is a ridiculous straw man version of NDE, and, again, irrelevant to the issue at hand. Who cares if we allow for extinctions and sudden population explosions caused by changes in environment? That doesn’t contradict the central thesis which is common descent, mutation, natural selection. What you describe is a refinement of earlier more simplistic theories of evolution.

    Where’s the contradiction with NDE?

    Cost must be outweighed by reward, but since the simple organisms have not been outperformed or replaced it is not evident that such a reward exists.

    So why do complex life forms exist, Charlie? Why aren’t they wiped out by bacteria? Destroying another species is not the “reward”. Survival is the “reward”.

    You have assumed a lot of evolved complexity before justifying the necessity of complexity. When we return to the “simple” first replicators, metabolizing organic or even inorganic material there are no predators, for instance, and there are no multicellular organism with whom to enter into symbiosis.

    Surely, you know that there are single-celled predators.
    http://en.wikipedia.org/wiki/Bacteria#Interactions_with_other_organisms

    There are also theories about the origins of multicellular life:
    http://en.wikipedia.org/wiki/Multicellular_animal#Hypotheses_for_origin

    If your complaint is that we are, as yet, unable to say which theory is correct, then you’re just making an argument from ignorance.

    In a population of “simple” organisms, which have never disappeared and never been at a survival or reproductive disadvantage (the fit have survived, after all), there is no general prediction for this increased complexity and specialization vs. being a jack-of-all-trades, is the more costly, and unrewardable condition.

    You misunderstand biology. Members within every species compete against other members for resources. The genes of individuals are not identical just because they are members of the same species. To say they have never been at a survival disadvantage or reproductive disadvantage is to miss the forest for the trees. It’s like saying that human survival and reproduction has never rewarded humans for doing anything different. Members of a species where the population is relatively stable are in a battle for survival against other members of their own species.

    Many evolution deniers are also free marketeers. So it’s weird that they don’t see the parallels.

    Why shouldn’t I open a pizza parlour? Everyone else is doing that, so why not me? Pizza parlours are commonplace and not likely to disappear. If I open a pizza parlour just like the one down the street, we will be the same species, and everything will be great.

    Well, the obvious answer is that the environment only supports a limited number of pizza parlours. If I compete in that niche, my personal odds of success are low even if the odds of someone in the neighborhood being successful are very high. Instead, I would do better to develop a niche in which there is little competition. If I start the only 1-hour photo business in town, or start the only personal auction web site business in the world, then I personally have better odds of business survival. And my auction or 1-hour photo business is not going to make pizza parlours go out of business. (This reminds me of Ghostbusters II where Lewis Tulley says to the prosecution attorney “Hey! Gimme a break! We’re both lawyers!”) Just because pizza parlours are the same species doesn’t mean they’re cooperative. Moreover, the measure of success of my 1-hour photo business is not the number of other businesses it bankrupts. My “reward” is not the failure of the pizza parlours (which won’t happen anyway). It’s not even a direct “reward” if I put other 1-hour photomarts out of business unless i get their business. My “reward” is my own economic survival.

    So your understanding of evolutionary biology is all askew. You assume that new mutants must render their ancestors extinct. That’s just not true. Pizza parlours that accept credit cards might render extinct many pizza parlours that accept only cash, but that’s not the only path evolution takes, and this was obvious from the very beginning. I’m sure even Darwin could see this.

    Again, the most likely result is simplicity, not complexity, it is death, not life; especially since extinction is far more likely the smaller the population size and we are talking here about an original population of one or very few.

    I don’t see your argument for this, just your statement without support. Why is simplicity more probable? Why is death more probable?

    The facts about life on Earth show that the opposite is true. Are you saying the designer is, to this day, artificially keeping all life going on this planet? If not, why are we still alive? Why are sponges and algae still alive? Why are plankton still alive?

  98. Charlie,

    You wrote:

    I have pointed out repeatedly that for Behe, or anyone, to critique Darwinian processes is not to critique “evolution”, per se.

    What I have read of Behe he seems to use the terms evolutionary and Darwinian interchangeably – there’s an example here ( http://www.discovery.org/a/8 ) and an even better, but longer, one here ( http://www.discovery.org/a/443 ) and there seem to be many others. Do you have some passage where he distinguishes between the two? It sounds as if you contend that Behe is imagining three camps – Darwinian, Evolutionary, and Designed. But it seems that he is dividing into two camps, (Darwinian-inspired) Evolution, and Intelligent Design. (E.g, here is a title slide of Behe’s – “Modeling the evolution of protein binding sites: probing the dividing line between natural selection and intelligent design,” and in Behe’s “Answering Scientific Criticisms of Intelligent Design,” Behe wrote: “… I proposed that, rather than Darwinian evolution, a more compelling explanation for the irreduciblely complex molecular machines discovered in the cell is that they were designed…”)

    So while I agree that Behe concedes a great deal of ground to modern Evolutionary understanding, I fail to see him as distinguishing between Darwinism and Evolution – he seems to conflate them in everything I’ve read so far.

    Maybe I would be better off just stating facts as I see them or providing clarifications rather than charging that you misrepresented every time I think I see it. It might even be more respectful. What do you think?

    I appreciate this question and the sentiment behind it. For my part, I will try to use less confrontational language and not sound so snotty.

    The Big Bang theory chooses a natural structure and leads us to the realization that the best/proper/final explanation may only be beyond physics (metaphysics) as well.
    I see no fundamental difference and I already took pains to debunk your comparison to other fields.

    I’m not sure about this. I want to think about it a little more. Mostly, I just don’t know enough about the Big Bang to understand what its (proper) implications are.

  99. Hi DL,

    I stand by my claim.

    Standing by your claim is useless if you aren’t gong to back it up.

    Behe is either ignorant or dishonest. Co-option explains IC in Darwinian evolution.

    So you’ve said. Are you going to ever show it?

    Behe’s claim has been debunked. Biologists answered Behe’s challenge long ago, but Behe keeps pretending they haven’t. This is why the judge in the Dover case didn’t just rule against ID, he wrote a scathing judgment against dishonest ID buffoonery in general.

    Actually, Jones didn’t write much of anything – Matzke and crew did – and Jones is no authority anyway. At any rate, you are standing by your error. Behe’s claim is nowhere near debunked, he himself, not his critics, introduced cooption and he dealt with it. Your assertion is empty and you’ve not supported your claim.

    The only way I can reconcile your statements with the facts is if you claim (incorrectly) that co-option isn’t Darwinian. That’s a straw man argument, and irrelevant to the questions at hand.

    Cooption might be Darwinian. Answer the empirical challenge Behe posits and the probability challenge other biologists raise and show that it debunks his claim.
    You’ve claimed it exists, that we’ve found it, that it explains IC, etc.. Now show that you are not bluffing.

    They were wrong. The theory can be seen to work from a purely logical standpoint, proven by GA’s, and proven as the explanation for speciation on Earth by common descent.

    When are you going to show that GAs create IC such that they debunk Behe’s claim? Where is the science behind this logic? Why do you keep enlisting logic against an empirical claim – you aren’t a rationalist now, are you?

    This is a ridiculous straw man version of NDE, and, again, irrelevant to the issue at hand. Who cares if we allow for extinctions and sudden population explosions caused by changes in environment? That doesn’t contradict the central thesis which is common descent, mutation, natural selection. What you describe is a refinement of earlier more simplistic theories of evolution.
    Where’s the contradiction with NDE?

    Yeah, I know DL, everything’s a strawman when you disagree with it.
    Have you noticed any of the times that I’ve said my probability case does not provide a contradiction to NDE? Not yet? Read again then.

    So why do complex life forms exist, Charlie? Why aren’t they wiped out by bacteria? Destroying another species is not the “reward”. Survival is the “reward”.

    Very good question, DL. Why indeed? Of course NDE did it, right? Of course complexity is a survival benefit – the complex have survived, right?
    You are so used to fitting facts to the theory that you can’t even think outside it for a second. Yes, there is complexity. But if complexity is such an advantage, and NDE is true (as it just must be, in your view) then why have the simple survived and continue to thrive and outperform the complex?

    Surely, you know that there are single-celled predators.

    Surely you noticed we were talking about first life. Predators don’t exist without prey. Again you show what is wrong with the theory. If the organisms depleted their food source then they would have died off. If some became predators (that’s not a single mutation, by the way) and ate the first, as a way of utilizing other sources they would have eaten the prior organisms, chased them into extinction (easy to do when the were running out food already), and then died off themselves. To weave contrary scenarios is to tell just-so stories to support the theory – not to evidence it or provide its predictions.

    If your complaint is that we are, as yet, unable to say which theory is correct, then you’re just making an argument from ignorance.

    Of course I am. When it’s not strawmen it’s ignorance.
    On the other hand, maybe I made a pretty nice argument about the implications of the theory and how it doesn’t predict complexity – or even life.

    You misunderstand biology.

    Do tell me.

    Members within every species compete against other members for resources. The genes of individuals are not identical just because they are members of the same species. To say they have never been at a survival disadvantage or reproductive disadvantage is to miss the forest for the trees.

    This has nothing to do with the statement you are responding to. When you go to educate me on the theory tell me something new and something relevant.
    Instead, off to more analogies which have nothing to do with the point.
    And somehow, on the basis of your pizza parlor, my understanding is asserted to be askew. A little actual evidence would suffice over and above your assertions.

    You assume that new mutants must render their ancestors extinct. That’s just not true.

    I don’t assume this but demonstrate why this is the case when accounting for speciation, and how it is relevant to the point I made.
    The mutation, according to NS, must be beneficial or be lost. Of course this is not the observed case so, as always, theories have had to be tacked on (neutral drift theories, for instance) but this is the logical result of the theory – and is exactly why such conditions as “founder effects” are added (a poor theory, empirically, by the way).

    I don’t see your argument for this, just your statement without support. Why is simplicity more probable? Why is death more probable?

    Suddenly bare assertions aren’t enough?
    Then I’ll remind you of my argument. Simplicity is more probable because it’s easier to create, easier to duplicate and easier to maintain. It is, afterall, the absolute necessary starting point, right? Complexity is so improbable that your theory can only imagine starting with the simple. By your own theory if we are to have life at all we are to be guaranteed the simple – complexity is a luxury.
    Simplicity, in theory, is less costly and by empirical observation is by far the most abundant; in fact, eukaryotes would die off without the simpler prokaryotes. The life form that can exist on its own is by far the more probable of the two.

    Why is death more probable? All life dies, right? This is the end result of all life, 100% of the time. But not all non-life was alive. Not all non-life will become life. For the most part, non-life reigns. And non-life is by far the easier to maintain and has the fewer requirements. Non-life can exist anywhere but life, not so much. All conditions are conducive to non-life but few to life. It requires no apparati, no energy source, no conversion mechanisms, no organelles, no reproduction. It fears no catastrophes and must never adapt – there are no contingencies and one need not replay the tape of non-life. Death thrives.

    The facts about life on Earth show that the opposite is true

    They certainly do not.

    Are you saying the designer is, to this day, artificially keeping all life going on this planet? If not, why are we still alive? Why are sponges and algae still alive? Why are plankton still alive?

    Very good questions, indeed. Yes, the Creator upholds all of Creation at all times. He has created an environment in which life can exist – against the improbabilities under naturalism/materialism – and maintains it.
    Again, your only tool is a hammer so every problem is a nail. Metaphysical materialism must be true, so it must be able to account for the improbable – life – the miraculous – the creation of life – and the providential – the fine tuned universe. You don’t question the observations because you dare not question the theory.
    Your theory fails so badly within the realm of probability that it must invent infinite universes to overcome the odds and refer to OOL as near-miraculous, one time lucky events or, more realistically, shuffle if off into another corner if the universe where our ignorance can claim it evolved via Darwinian processes, from simple to complex, before somehow seeding our planet.

  100. —–
    Hi Tony,
    Should I follow your links? Does Behe use the terms interchangeably or does he define them, tell you how he is using them and then let one stand in for the other for simplicity sake? Does he say anything to detract from what I’ve already told you – that he believes that man evolved from ape-like ancestors, that all of life shares common ancestry and that common descent is true? Can you think of anything that this means other than that evolution occurred and is not synonymous exclusively with Darwinism?
    Have you read anything that can refute Miller’s assessment of Behe:

    In plain language, this means that Michael Behe and I share an evolutionary view of the natural history of the Earth and the meaning of the fossil record; namely, that present-day organisms have been produced by a process of descent with modification from their ancient ancestors. Behe is clear, firm, and consistent on this point.

    To my surprise, Behe said that he shared that view, and had no problem with the notion of common ancestry. Creationists who believe that Behe is on their side should proceed with caution – he states very clearly that evolution can produce new species, and that human beings are one of those species.

    ——-

    So while I agree that Behe concedes a great deal of ground to modern Evolutionary understanding, I fail to see him as distinguishing between Darwinism and Evolution – he seems to conflate them in everything I’ve read so far.

    I can’t imagine that you are reading well (evidenced by your three camps, two camps observation) or taking context into consideration and when I can navigate from this page I might show you why with your own sources.
    For now, as for what he is talking about when he challenges “evolution”, you can read his books or I can take a quick glance for you. The first line of DBB is “This book is about an idea – Darwinian evolution – that is being pushed to its limits by discoveries in biochemistry”. As he says to close that first chapter – “Yet for the Darwinian theory of evolution to be true, it has to account for the molecular structure of life. It is the purpose of this book to show that it does not.”
    So IC, a challenge presented in his book, is a challenge to the very subject of the book, the Darwinian theory of evolution – quite a mouthful if all he really means is “evolution”.

    “An irreducibly complex system, if there is such a thing, would be a powerful challenge to Darwinian evolution.”
    If you were to read this book you would see that he qualifies evolution as “Darwinian”, Darwinism” or “Darwin’s theory of evolution” dozens if not hundreds of times as he chooses to critique it.
    Then, in his next book, The Edge Of Evolution he also tells you just what he means right in the title of chapter one – The Elements Of Darwinism.

    Life on earth developed over billions of years by utter chance, filtered through natural selection. So says Darwinism ….
    Darwin’s theory has to be sifted carefully, because it isn’t just as ingle concept ….
    The three most important ideas to keep straight from the start are random mutation, natural selection, and common descent.
    Common descent is what most people think of when they hear the word “evolution”.

    Yet in a very strong sense the explanation of common descent is also trivial.

    In contrast , Darwin’s hypothesized mechanism of evolution -… is decidely more ambitious.

    …the question Is Darwinism true? has several possible answers. One possibility, of course, is that those separate ideas – common descent, natural selection, and random mutation – could all be completely true , and sufficient to explain evolution. Or they could all be correct in the sense that RM and NS happen, but they might be inconsequential, unable to account for most of evolution.

    Because they are separate ideas , evidence for each facet of Darwin’s theory has to be evaluated independently.

    In brief, the evidence for common descent seems compelling.

    Second, there’s also great evidence that RM paired with NS can modify life in important ways.

    As a theory-of-everything, Darwinism is usually presented as a take-it-or leave proposition. Either accept the whole theory or decide that evolution is all hype and throw out the baby with the bathwater. Both are mistakes. page 4

    I’m going to give you the benefit of the doubt now, presume that you recognize that Behe does not conflate “evolution” with “Darwinism ” or “Darwinian explanations” and admit that when he critiques Darwin’s theory or Darwinian explanations he is not critiquing evolution.
    If this benefit is misplaced I can continue again later.

    I appreciate this question and the sentiment behind it. For my part, I will try to use less confrontational language and not sound so snotty.

    Thank you. I think we can both do so – but, perhaps unfortunately, I was being ironic throughout the entire “misrepresentation” affair. I guess the point was being lost.

  101. Hi again, Tony,
    I read your links – both articles I’ve been over several times before – and realize that the benefit I offered you above likely is misplaced afterall, given your reading of these articles.

    You offer them here:

    Charlie: I have pointed out repeatedly that for Behe, or anyone, to critique Darwinian processes is not to critique “evolution”, per se.

    Tony:
    What I have read of Behe he seems to use the terms evolutionary and Darwinian interchangeably

    The “longer”, “better”, cite you give is especially telling. Not once does Behe mention evolution without explicitly clarifying that his critique is of the proposed Darwinian explanations, and not of evolution, per se.
    Where he is quoted using the word “evolution” without the qualifier, from his book DBB, he clarifies it in the discussion of this paper and alerts the reader that if one read his book and knew the context the clarification would be unnecessary.

    Here are the references from the paper in question:

    I fully expect such research would heighten awareness of the difficulties of Darwinian evolution.

    the origins of many intricate cellular systems have not yet been explained in Darwinian terms.

    most also admitted to a lack of Darwinian explanations.

    “There are no detailed Darwinian accounts for the evolution [notice that Darwinian accounts and evolution are not the same thing]

    In the context of my book it is easy to realize that I meant there has been little work on the details of the evolution of irreducibly complex biochemical systems by Darwinian means.[evolution and Darwinian means are not the same thing]

    “molecular evolution,” but that, overwhelmingly, it was either limited to comparing sequences or did not propose sufficiently detailed routes to justify a Darwinian conclusion.

    Li’s book also contains chapters on the mechanisms (such as gene duplication, domain shuffling, and concerted evolution of multigene families) that are thought to be involved in evolution at the molecular level. Again, however, no specific system is justified in Darwinian terms.

    As I explained in Darwin’s Black Box, sequence studies by themselves can’t answer the question of what the mechanism of evolution is.

    Once again I reiterate, sequence comparisons by themselves cannot tell us how a complex system might have arisen by Darwinian means.

    Instead of listing further examples let me just say that I have not seen a paper using Ussery’s search criteria that addresses the Darwinian evolution of intracellular vesicular transport in a detailed manner, as I had originally asserted in my book.

    Yes, there are a lot of papers published on “molecular evolution,” as I had clearly acknowledged in Darwin’s Black Box. But very few of them concern Darwinian details of irreducibly complex systems, which is exactly the point I was making.

    Clearly that is inadequate to show refining of petroleum developed step by step. Analogously, someone who is seriously interested in showing that a metabolic pathway could evolve by Darwinian means has to deal with the enzymic machinery and its regulation.

    In pointing out that not much research has been done on the Darwinian evolution of irreducibly complex biochemical systems I should emphasize that I do not prefer it that way. I would sincerely welcome more research (especially experimental research, such as done by Barry Hall–see my discussion of Hall’s work in the essay on the “acid test” at this web site) into the supposed Darwinian origins of the complex systems I described in my book. I fully expect that, as in the field of origin-of-life studies, the more we know, the more difficult the problem will be recognized to be.

    This doesn’t even come close, not by miles, to rebutting my claim “that for Behe, or anyone, to critique Darwinian processes is not to critique “evolution”, per se.”
    It only makes the point over and over and over again.

    Behe also refutes your other claim about throwing up your hands and ending the search for naturalistic solutions – he says keep going and he is confident that this will only strengthen his case.

  102. Interesting to read those quotes, Charlie. I haven’t read the books. Sounds like Behe thinks the True Evolutionary Theory(tm) lies somewhere between Darwin’s original theory and today’s theory — or is it something else?

  103. Charlie,

    Quotes from the Dover ruling:

    “Professor Behe’s concept of irreducible complexity depends on ignoring ways in which evolution is known to occur. Although Professor Behe is adamant in his definition of irreducible complexity when he says a precursor “missing a part is by definition nonfunctional,” what he obviously means is that it will not function in the same way the system functions when all the parts are present. For example in the case of the bacterial flagellum, removal of a part may prevent it from acting as a rotary motor. However, Professor Behe excludes, by definition, the possibility that a precursor to the bacterial flagellum functioned not as a rotary motor, but in some other way, for example as a secretory system.”

    And, wouldn’t you know it, it looks like we’ve actually seen IC systems evolve:
    http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html#how2eatpcp

    Behe has no argument for why co-option is improbable, so he has no argument against NDE. And yet he persists. In the face of the evidence and many papers explaining the situation. He is making an argument from ignorance. What does Behe want today? He wants scientists to show the exact series of co-option steps that occurred during the formation of an IC system. But that is again an argument from ignorance. I refer back to the trial analogy. Behe does not have an alibi for evolution. He just lacks total knowledge of it.

    You are so used to fitting facts to the theory that you can’t even think outside it for a second. Yes, there is complexity. But if complexity is such an advantage, and NDE is true (as it just must be, in your view) then why have the simple survived and continue to thrive and outperform the complex?

    In what way do they outperform the complex? In population? Mutation rate? Biomass? So what? Why would you expect complexity to lead to higher populations than bacteria under NDE? Or to survive in harsher conditions? Or to mutate faster? Show your work.

    You brush off the pizza parlour analogy as if it has nothing to teach you and then you commit the same illogical thinking all over again. Pizza parlours are outperforming internet auction web sites ! (In terms of sheer numbers, numbers of brands, numbers of customers, etc). Internet auction sites haven’t caused the extinction of pizza parlours! Oh no! There must be something wrong!

    If the organisms depleted their food source then they would have died off. If some became predators (that’s not a single mutation, by the way) and ate the first, as a way of utilizing other sources they would have eaten the prior organisms, chased them into extinction (easy to do when the were running out food already), and then died off themselves.

    Why are there antelopes? The lions should have eaten them all, right? Why not? Let me guess… God intervenes to prevent the lions from catching too many antelopes? Or could it be that the more antelopes that are killed, the smaller the food source for the lions, so the smaller the population of lions, so the larger the next generation population of antelopes?

    Now suppose a new mutant species B eats species A. Obviously, there needs to be enough species A around to eat for the mutant B to survive. So why will the mutation only work when species A is on the decline due to lack of food? It won’t!! The mutation can come along at any time there is species A. Again, mutants kill off their ancestors when they compete in the same niche. There’s no reason to suppose that the first predators were the same species as their prey. There would have been many thousands of species of single-celled organisms, specializing in different food sources in different environments. The first predator was probably a species that co-opted its ability to eat a niche food source into an ability to eat another living species. You write as if the single-celled life turned to cannibalism when its food sources started to dry up. But that’s like arguing that 1-hour photo marts or hot dog stands only started when all the pizza parlours started to go out of business.

    And I see that your statement about simplicity being more probable or death being more probable is being taken in some alternate context. I thought you were saying that simplicity is a more likely outcome of NDE or that death was a more likely outcome of NDE. If you’re stating the trivial fact that NDE requires single-celled life as a starting point, or that things die, then few could fail to agree.

    But that is utterly irrelevant to the discussion, Charlie.

    The pertinent question is this. Given the Earth’s roughly stable environment, given simple single-celled species, what is the likelihood of total extinction, and the likelihood of creating more complex species (whether single-celled or multi-celled)? That’s what NDE is about. It’s not about OOL. And you have said nothing substantial in relation to this question. All you’ve said is that you don’t believe life would exist or be complex under NDE.

    Yes, the Creator upholds all of Creation at all times. He has created an environment in which life can exist – against the improbabilities under naturalism/materialism – and maintains it.

    How, specifically? What experiment will reveal God’s hand? What exactly is God doing? Yours is not a scientific notion. It’s an aesthetic notion. It’s the way you want the world to be.

  104. Hi DL,
    You quote from Dover:

    “Professor Behe’s concept of irreducible complexity depends on ignoring ways in which evolution is known to occur. Although Professor Behe is adamant in his definition of irreducible complexity when he says a precursor “missing a part is by definition nonfunctional,” what he obviously means is that it will not function in the same way the system functions when all the parts are present. For example in the case of the bacterial flagellum, removal of a part may prevent it from acting as a rotary motor.

    Yes, Behe obviously means that. Of course it can’t be produced directly if it does not work the same way. Imagine your RF GA going through selectable intermediate steps which have nothing to do with signal amplification.
    Moreover from Dover:

    However, Professor Behe excludes, by definition, the possibility that a precursor to the bacterial flagellum functioned not as a rotary motor, but in some other way, for example as a secretory system.”

    No, Behe does not exclude this by definition. He covers it directly in DBB. Why do you insist on using faulty second-hand information year after year when the primary sources are available? Why do you keep using material that does not represent Behe?

    And, wouldn’t you know it, it looks like we’ve actually seen IC systems evolve:
http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html#how2eatpcp

    Yeah, I bet they have. I’ll check that link next.

    Behe has no argument for why co-option is improbable, so he has no argument against NDE. And yet he persists.

    Don’t ask Behe, ask the literature. He doesn’t have to prove logically why the circuitous route to complexity is improbable when he can point to the evidence that demonstrates that nobody has ever discovered it to develop complexity and nobody has a scientific, testable, hypothesis to explain a single IC feature this way.

    In the face of the evidence and many papers explaining the situation.

    Bluff. Never happened.

    He is making an argument from ignorance.

    What does Behe want today? He wants scientists to show the exact series of co-option steps that occurred during the formation of an IC system.

    You get it first DL. I’ve typed and erased this dozens of not hundreds if times on the internet.

    You are a liar.
    Behe never asks for the exact steps, he never asks for an historical accounting, he never did in DBB and he still doesn’t. He has asked for the same thing throughout and he has never deviated.
    You know this.
    You are lying.

    You are so used to fitting facts to the theory that you can’t even think outside it for a second. Yes, there is complexity. But if complexity is such an advantage, and NDE is true (as it just must be, in your view) then why have the simple survived and continue to thrive and outperform the complex?

    In what way do they outperform the complex? In population? Mutation rate? Biomass? So what?

    So what? That’s Natural Selection. Are you ignorant of your own theory as you arrogate to teach me about it?

    Why would you expect complexity to lead to higher populations than bacteria under NDE? Or to survive in harsher conditions? Or to mutate faster? Show your work.

    Because complexity evolved from simplicity and at some point HAD to outperform it, in some situation, in some environment. Where does it do this, you know, empirically?

    You brush off the pizza parlour analogy as if it has nothing to teach you and then you commit the same illogical thinking all over again. Pizza parlours are outperforming internet auction web sites ! (In terms of sheer numbers, numbers of brands, numbers of customers, etc). Internet auction sites haven’t caused the extinction of pizza parlours! Oh no! There must be something wrong!

    Nice exclamation marks. Once again, I encourage you to tone down your emotive responses as that generally only tends to compound on you.
    Internet auction marts and pizza parlors do not evolve from one another through a series of selectable steps culled by NS. Here’s another for you talk.origins fans – the analogy doesn’t work because pizza parlors and auction sites are not self-replicaing.

    If the organisms depleted their food source then they would have died off. If some became predators (that’s not a single mutation, by the way) and ate the first, as a way of utilizing other sources they would have eaten the prior organisms, chased them into extinction (easy to do when the were running out food already), and then died off themselves.

    Why are there antelopes? The lions should have eaten them all, right?

    That’s right DL. You can’t merely observe nature and pretend that NDE predicts every aspect of it. Yo have to face the logic.
    There is no speciation without extinction. whether it be mass, global or pseudo. The theory requires it – prior to its post hoc fixes.

    Why not? Let me guess… God intervenes to prevent the lions from catching too many antelopes? Or could it be that the more antelopes that are killed, the smaller the food source for the lions, so the smaller the population of lions, so the larger the next generation population of antelopes?

    Keep going, you’re almost there. You did it once with sharks, now you can do it with lions. Smaller population of antelopes … smaller …. smaller ….. gone.
    Oops, less lions … less … less …. gone.
    NDE predicts sterility. Just because it didn’t happen doesn’t mean NDE doesn’t predict it. It just means NDE does not accord well with the facts and has to be doctored with empirically-weak solutions. Natural Selection just does not do the trick. Of course, you need to ignore the extinction problem so you can keep Natural Selection (another empirical failure on its own) so you can keep your complexity ratchet.
    But you don’t get any of it. Natural Selection is bust, Dawkins’ escape for the failure of randomness and chance – his “oh, but evolution is anything but random” mantra – is bust, and so is your case for complexity, because you are left with nothing but randomness and drift. And lots of patches.

    Now suppose a new mutant species B eats species A. Obviously, there needs to be enough species A around to eat for the mutant B to survive. So why will the mutation only work when species A is on the decline due to lack of food? It won’t!!

    Two exclamation marks. You must really be right.
    Mutant B must out-compete species A. If there is plenty of food for all, if it is not declining and requires no search then mutation B is not selectable.

    The mutation can come along at any time there is species A. Again, mutants kill off their ancestors when they compete in the same niche.

    Ah, nice. So here we at least have the admission that speciation requires the killing off and extinction of the parent species. This is my whole point in a nutshell. This is what NDE requires and this is what it predicts. To postulate niches and separate populations to account for the fact that this is not what the record shows is special pleading – it is not a prediction of the theory.

    There’s no reason to suppose that the first predators were the same species as their prey.

    Then you’ve waited a longtime down the line, presumed a lot of speciation and a lot of “evolution”(as I said, predation isn’t going to be a single mutation away) before introducing your predator. So forget the predator, since I guess it was a red herring. I was going to write more here, but you admit above that death and extinciton (called pseudo extinctions in your vernacular) are a necessity and the prediction of the theory. You’ve merely decided it can wait until there is enough pre-evolution to absorb it.

    There would have been many thousands of species of single-celled organisms, specializing in different food sources in different environments.

    There would have been? Really? Is that a prediction of the theory or a way to account for its failed prediction? The latter, I think, as I showed above.
    Why did these thousands of species mutate to specialize to these different food sources when the original food source was so readily available and when their ancestors were doing so well? What was this mysterious new food source, how did they evolve to metabolize it?

    The first predator was probably a species that co-opted its ability to eat a niche food source into an ability to eat another living species.

    Of course, cooption. Why didn’t I think of that? Easy as pie, that, since we see it all around and can empirically show where it’s been found. You were going to do that, right?
    Ah yes, I forgot the link you provided without argument.

    And I see that your statement about simplicity being more probable or death being more probable is being taken in some alternate context. I thought you were saying that simplicity is a more likely outcome of NDE or that death was a more likely outcome of NDE. If you’re stating the trivial fact that NDE requires single-celled life as a starting point, or that things die, then few could fail to agree.

    I am saying that the more likely outcome of NDE is death and sterility. You are feeding in factors that the theory is not allowed if you want to talk about its predictions. To start with, you have only randomness – forget Dawkins’ disingenuous salve – only nature, and only material with which to work. Only nature, only randomness and only material tend toward death. All over the place they favour death, destruction, and entropy. You have to have something to account for the reversal of entropy that is life (right, right, closed systems, increase here, decrease there – that’s no answer).
    So NDE is the solution.
    Oops, no it’s not.
    It presumes, by philosophical necessity, massive fecundity and success of first life against the empirical fragility of life (99% extinction, isn’t it?). But against this it presumes progress – it has to, because it starts by necessity (to avoid miracles) at such extreme simplicity (still too complex for chance, but whatever).
    And whence the progress? By defeat and competition of the less fit. This is a necessity of the theory as you’ve admitted above. That’s the only way Natural Selection, progressive evolution (and progress is undeniable if you start with the most imaginably simple, as you must) can work. Extinction is necessary to avoid what I told you was the real implication of the theory (which led to the final sterility of my case), the single species – if it only leads to variation within species then it does not lead to speciation and fails the entire purpose of the theory – to explain discrete divisions of life. It is necessary to explain away the fact that there is not a seamless chain of being rather than the discrete divisions of life we actually see. In order to explain some of observable reality (seams) NS and NDE have to posit the extinctions (of, for instance, the transitions) which, it turns out, must have occurred in a manner which violates another observable reality (they are not slow and gradual). In fact NS doesn’t do the trick either theoretically or empirically. Only a very small proportion of observed genetic change can be postulated to have anything to do with selection, founder effects don’t happen, sexual selection is impotent and NS selects little in nature. It’s all randomness. But randomness fails the mathematical test and with it you lose your ratchet.
    But why is slow and steady and necessary extinction no longer part of the package? Because it does not fit the data (it never did, but it is not a dat-derived theory). So the theory, had to ignore the extinction problem and keep plugging along for the simple reason that, philosophically, it is the only thing one can consider.

    But that is utterly irrelevant to the discussion, Charlie.

    It sure is. But you were really keen on resurrecting it. I presume you did so because last time around it proved to you that I am so incredibly ignorant, have nothing on the ball and am unworthy of your consideration. I guess that was supposed to be a nice distraction and expose of my fleshy underbelly.

    The pertinent question is this. Given the Earth’s roughly stable environment, given simple single-celled species, what is the likelihood of total extinction, and the likelihood of creating more complex species (whether single-celled or multi-celled)?
    That’s what NDE is about. It’s not about OOL. And you have said nothing substantial in relation to this question. All you’ve said is that you don’t believe life would exist or be complex under NDE.

    No, I have not only said this. I have argued why. Life is not likely. It is fragile. Nature would rather it not than it be.
    Given your stable earth and single-celled creatures you have to presume fecundity. Enough so that it expands all over the place so that it can be replaced in niches rather than in general. In those niches you admit that replacement by extermination is required for speciation.
    So this incredibly robust first life, so robust that you’ve got it expanding all over the place (giving the original population plenty of room to exist when being replaced in nooks and crannies) and slipping into niche after niche, is also very easily replaced (or else its very few and rare mutant kin would not survive to speciate).
    At the same time it must be replicating well enough to avoid extinction and spawn all of its descendants, but you must also presume it is replicating poorly enough that its descendants are mutating. You always have to presume one lucky balance after another. The only reason you can do this is you are starting with givens – the main one being the incredible complexity of life as we know it and the incredible improbability of this happening by chance – and then working backwards to fit the facts to the theory.

    Yes, the Creator upholds all of Creation at all times. He has created an environment in which life can exist – against the improbabilities under naturalism/materialism – and maintains it.

    How, specifically? What experiment will reveal God’s hand? What exactly is God doing? Yours is not a scientific notion. It’s an aesthetic notion. It’s the way you want the world to be.

    Another news alert- not, DL. God isn’t a scientific notion. When will you stop pretending that pointing this out is feathering your cap somehow?
    You asked a theological question and I answered it and suddenly, much to your glee, the answer is not scientifically testable. So what? All of the time – so what?

  105. Really, DL?

    1) The first enzyme, while inefficient, is already metabolizing PCP.
    2) The second enzyme, coded by pcpD, immediately downstream of the first PCP hydroxylase, can be knocked out and the system continues to function, albeit less efficiently, and at lower concentrations.
    3) This is exactly NOT irreducible complexity. Not every step is essential. In fact, this is exactly the Darwinian solution Behe (and Darwin) says can be built by step-by-step additions increasing functionality by a series of gradual intermediates.

    re:
    http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html#how2eatpcp

    I thought you’d at least come up with something jargon-filled enough that I’d have to scratch my head a second.
    Even from your own information-poor link you could have deduced that this was not IC:

    Evolution to the rescue! A few soil bacteria have already worked out a way to break it down and even eat it. And conveniently for us, they do it in an irreducibly complex way.

    S. chlorophenolica uses three enzymes in succession to break it dow.

    the first one replaces one chlorine with OH. The resulting compound is toxic, but not quite as bad as PCP itself. [selectable direct step toward goal].
    …First of all, bacteria of this type could already metabolize some milder chlorophenols which occur naturally in small amounts. In fact the first … enzymes were used for this.
    [in fact, though inefficient with regards to PCP, the first enzyme, PCP hydroxylase, is already operating toward this end goal in vitro].

    The second enzyme is able to act on this compound to replace two chlorines, one after the other, with hydrogen atoms. The resulting compound, while still bad, is much easier to deal with. [selectable step toward goal].
    The second enzyme[is] effective all the time instead of just when it is needed in its normal metabolic role.


    third enzyme is able to break the ring open. At this point, what is left of PCP is well on its way to being food for the bacterium.[selectable step toward goal]

    I sure hate literature bluffs that waste my time.
    Here’s what I wrote at first, and confirmed by looking at the original paper:
    First, if we have to take the time, and have access to all the materials, I can all but guarantee that every product along the way here provides a selectable advantage, even in the absence of the other two steps. Your link gives completely insufficient details to conclude as you and your talkdots have.

    The following points were not needed upon establishing those I made at the beginning of this comment.

  106. Charlie,

    I was honestly confused about Behe’s terms. I do think that his definition of Evolution to mean “common descent’ and not the process (either strictly Darwinian or NDE) of change over successive generations is confusing, and that his promotion of ID complicates his criticism of the explanatory power of Darwinian processes.

    I still think that this sentence by you,…

    “that for Behe, or anyone, to critique Darwinian processes is not to critique “evolution”, per se.”

    …is splitting hairs. Evolution, in the popular science press and on a more specialized site like this one (http://www.biology-online.org/dictionary/Evolution) is commonly understood to mean the process, not the fact of common descent. And I still don’t understand what the naturalistic alternative to evolution would be (if not Darwinian) that Behe is supposedly considering. In other words, you make it sound as if Behe is looking to fine tune Darwinian theory (similar to the criticism of a Gould), but in fact he appears happy to throw it out with the bath water.

    I’ve been busy and have to catch up a bit more and re-read. There are some other things that popped out that I wanted to ask about, though.

    There is no speciation without extinction.

    I don’t think that this is necessarily true. I believe it’s considered possible that great geographic distances could result in a continuum of change from one extreme to the other where the two groups at the furthest extremes could be deemed separate species and yet share species-hood with cousins in the middle. I might be wrong about this but I believe that’s a considered a possible phenomenon.

    Mutant B must out-compete species A. If there is plenty of food for all, if it is not declining and requires no search then mutation B is not selectable.

    Doesn’t the Lenski experiment (http://www.newscientist.com/article/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html) show how a mutation can create a selective advantage (the ability to consume a second nutritient available in the culture) that does not perforce result in the ancestral line’s extermination?

  107. Hi Tony,

    I still think that this sentence by you,…

    “that for Behe, or anyone, to critique Darwinian processes is not to critique “evolution”, per se.”is splitting hairs.

    I disagree.

    Evolution, in the popular science press and on a more specialized site like this one (http://www.biology-online.org/dictionary/Evolution) is commonly understood to mean the process, not the fact of common descent.

    Evolution is not its mechanism.

    And I still don’t understand what the naturalistic alternative to evolution would be (if not Darwinian) that Behe is supposedly considering. In other words, you make it sound as if Behe is looking to fine tune Darwinian theory (similar to the criticism of a Gould), but in fact he appears happy to throw it out with the bath water.

    Still, you need to read Behe. He is not throwing out the evolution baby just because he makes a case against the Darwinian mechanism. And he is not throwing the Darwinian mechanism out either – he is just telling you what it doesn’t account for. He is not providing a replacement for the failed mechanism but he does offer some possibilities, including frontloading and a finely tuned environment.
    By the way, here is what I said:

    So, not only does IC not say that there is no natural explanation (there just might be – although IDists do not think this the inference to the best explanation) but neither the concept nor its proponents say anybody ought to quit searching for one.

    ====

    I believe it’s considered possible that great geographic distances could result in a continuum of change from one extreme to the other where the two groups at the furthest extremes could be deemed separate species and yet share species-hood with cousins in the middle.

    I think it is considered possible and I’ll have to read up on ring species to see if they are actually examples of speciation (a little bit of a fuzzy term, I’ll admit). I will also suggest that they do not evidence the speciation required to evolve the rising complexity of life, which is at issue. Continued after next …

    Doesn’t the Lenski experiment (http://www.newscientist.com/article/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html) show how a mutation can create a selective advantage (the ability to consume a second nutritient available in the culture) that does not perforce result in the ancestral line’s extermination?

    1) Please tell me what Lenski found out and how you interpret it to answer my point as I am a little strapped for time also and have chased down enough links for this thread.
    2) A lot of things can be induced in the laboratory that have no real world relevance.
    3) A lot of things have real-world relevance which do not accord with the theory’s predictions.
    4) The extinctions posited by the theory do not happen overnight but accompany the speciation – in fact, go hand in hand with it.
    5) Tomorrow when I have time I will discuss Lenski’s work with you and what Behe has to say about it in Edge Of Evolution.

  108. Charlie,

    1) Please tell me what Lenski found out and how you interpret it to answer my point as I am a little strapped for time also and have chased down enough links for this thread.

    Previously, you had written: “Mutant B must out-compete species A.” I took this to mean that a selectable mutation must lead to the ancestral species extinction. In the Lenski experiment, bacteria mutated to be able to consume a second nutrient, citrate. The article I cited states that “The citrate-using mutants increased in population size and diversity.” It does not report, “The citrate-using mutants drove the non-mutants into extinction.” I don’t know this, but my reading of the experiment implies a stasis where both non-mutants and mutants reached a stable proportion.

    2) A lot of things can be induced in the laboratory that have no real world relevance.

    Okay. But isn’t a criticism of evolutionary theory that it’s short on experimental evidence? And doesn’t the Lenski experiment dispel what many doubters of evolutionary theory voice, that mutations are seldom (never) beneficial, that they don’t’ “add information,” and that no one’s ever seen a this turn into a that?

    3) A lot of things have real-world relevance which do not accord with the theory’s predictions.

    I have no doubt that NDE has some things not quite right. But there’s a difference between fine tuning a theory which fails to predict accurately and throwing it out altogether. (I think that Behe is still susceptible to being accused of “panicking” at the gaps in natural explanatory mechanisms, similar to Kelvin surmising that the world couldn’t be more than 30 million years old because the sun couldn’t (chemically) fuel itself for any longer than that.) But, of course, Behe’s biggest problem isn’t from the likes of me – it’s that the vast majority of Behe’s peers do not share his doubts about Darwinian mechanisms, and the failure to posit an explanation that better describes the mechanisms and makes better predictions.

    4) The extinctions posited by the theory do not happen overnight but accompany the speciation – in fact, go hand in hand with it.

    I think the theory predicts that extinctions may occur, not that they must occur. But I do agree with you that the notion of species and also speciation is fuzzy — I think that it’s a shorthand concept that’s useful for discussing the concepts but risks being misleading.

    5) Tomorrow when I have time I will discuss Lenski’s work with you and what Behe has to say about it in Edge Of Evolution.

    I am very curious about what Behe has to say about the experiment. I should also be more familiar with Lenski’s experiment than I am as well, so I’ll try to do some more research on that topic.

  109. Hi Tony,

    Previously, you had written: “Mutant B must out-compete species A.” I took this to mean that a selectable mutation must lead to the ancestral species extinction. In the Lenski experiment, bacteria mutated to be able to consume a second nutrient, citrate. The article I cited states that “The citrate-using mutants increased in population size and diversity.” It does not report, “The citrate-using mutants drove the non-mutants into extinction.” I don’t know this, but my reading of the experiment implies a stasis where both non-mutants and mutants reached a stable proportion.

    This reference is too light on details to tell us much about the fitness of the two populations and this experiment demonstrates a short-term change and has not played out to fruition yet. I’m not saying that a parent population must go extinct the moment a new adaptation shows up, but am talking about speciation and evolution. The citrate mutant is not a new species but the same critter with a new feature (of course “species” is notoriously difficult to define, especially as pertains to bacteria) and we don’t know its future in this population.
    You have not mentioned Lenski’s methodology. I know he has created a sucrose shortage in cycles to prompt the mutation and that he is drawing populations off from the parent population, which may (I’m not up on his methods right now) create isolation and protection for the new mutant which would, in fact, lead to the destruction of the parent lineage in competition.

    And doesn’t the Lenski experiment dispel what many doubters of evolutionary theory voice, that mutations are seldom (never) beneficial, that they don’t’ “add information,” and that no one’s ever seen a this turn into a that?

    Whatever this experiment shows Lenski is to be commended for actually trying to find out what happens to populations as they evolve, what kind of time is necessary, the numbers of resources required, etc.
    I don’t think that showing that a trait has revealed itself answers my point about what speciation requires of a Darwinian explanation or the predictions of the theory itself. We have not seen the speciation here or what would be the long term effects of its existence vis the parent population.

    But, of course, Behe’s biggest problem isn’t from the likes of me – it’s that the vast majority of Behe’s peers do not share his doubts about Darwinian mechanisms, and the failure to posit an explanation that better describes the mechanisms and makes better predictions.

    As a fan of fallacies I’m sure you realize the problems with argumentum ad populum. I think you also underestimate the problems for Natural Selection vs. neutral drift/random survival, and random mutation vs. constrained or directed ones. With the surge in interest in evo-devo, epigenetics, lateral transfer, stucturalism, etc. I think Behe’s peers do, in fact, share his doubts about the mechanisms. The ability Natural Selection and Random Variation are very much in doubt and under challenge. They are under challenge for the very reason you cite when you discuss Lenski – they do not accord well with reality.

    I think the theory predicts that extinctions may occur, not that they must occur. But I do agree with you that the notion of species and also speciation is fuzzy — I think that it’s a shorthand concept that’s useful for discussing the concepts but risks being misleading.

    We do agree on “speciation” and you are right that it works as a general shorthand but fails us as we go too deep. The fact that NDE no longer insists on extinction is where it admits the failure of the theory. Extinctions have been long neglected for the fact that they do not match what is necessary in order to have speciation. As Darwin tried to give progressive, complexity-generating evolution plausibility he had to deny the obvious fact that of catastrophic extinctions in favour of gradualism and uniformitarianism. This was because in order to perform the miraculous rise in complexity, the forming of eyes, etc., he needed tiny increments over a long period of time. But this would lead to a continuum of species, like your ring-species, but this is not the rule in nature. Nature has discrete categories. You need extinctions to account for the gaps between them, you need ancestors to have disappeared. At the same time on order to have orderly progress as opposed to capricious survival (no selection value) he had to deny catastrophic extincitons. This leaves on slow and gradual – the constant culling of traits the least bit deleterious and the constant preservation of traits the least bit advantageous. There is not option but for the former to be out-competed and replaced by the future.
    I am not saying that this matches observation or experiment. But this is the prediction, and it is the prediction that has to be explained away and accounted for with story-telling.
    ====
    Re: Behe and Lenski.
    Behe is a fan. He thinks it is great that people are testing the theory and he is satisfied with Lenski’s results.
    As per my discussion above about not seeing real Natural Selectiona t work, re: extinctions, Behe states that the bacteria in Lenski’s lab

    “were coddled. They had a stable environment, daily food, and no predators. …. Even in a controlled lab culture where bacteria are warm and well fed, the bug that reproduces the fasted or outcompetes others will dominate the population. LIke gravity, Darwinian evolution never stops.
    But what does it yield?

    By now over thirty thousand generations of E. coli, roughly the equivalent of a million years in the history of humans, have been born and died in Lenski’s lab.

    A host of incoherent changes have slightly altered preexisting systems. Nothing fundamentally new has been produced. No new protein-protein interactions, no new molecular machines. … some very large evolutionary changes have been conferred by breaking things. Several populations of bacteria lost heir ability to repair DNA.
    … Breaking some genes and turning others off, however, won;t make much of anything. After a while, beneficial changes from the experiment petered out.
    … that’s all Darwinism can do”

    He discusses the citrate change elsewhere, but I have to run and will get back to you on that later.

  110. Charlie,

    You are a liar.

    Sticks ‘n’ stones, luv.

    But since the complexity of the cilium is irreducible, then it can not have functional precursors. Since the irreducibly complex cilium can not have functional precursors it can not be produced by natural selection, which requires a continuum of function to work. Natural selection is powerless when there is no function to select. We can go further and say that, if the cilium can not be produced by natural selection, then the cilium was designed. – Michael Behe

    Enjoy. He’s making a false statement in sentence one. It’s false because it fails to consider co-option. He thinks one-dimensionally, just like you. Or maybe he’s just oversimplifying to make his argument?

    Because complexity evolved from simplicity and at some point HAD to outperform it, in some situation, in some environment. Where does it do this, you know, empirically?

    Aha! “In some situation, in some environment.”

    So if a mutant B of species A develops immunity to a toxin at the cost of efficiency in environments where the toxin is not present, then species B outperforms species A in toxic water whereas species A outperforms species B in clean water. And yet species B does not kill off species A. Getting this yet?

    Internet auction marts and pizza parlors do not evolve from one another through a series of selectable steps culled by NS.

    I really think it’s a stretch that you fail to understand the point of the analogy, Charlie. In fact, I think you do understand the point, and that’s why you’re so upset.

    Again, suppose species A mutates into species B where B cannot compete against A in A’s niche, but B can survive in an empty niche where A cannot. This is a normal evolutionary scenario. NS prevents B from having significant population in A’s environment, and prevents A from having a foothold in B’s environment. And yet NS does not cause B to replace A, or B to be exterminated by A.

    Here’s another for you talk.origins fans – the analogy doesn’t work because pizza parlors and auction sites are not self-replicaing.

    Isn’t it amazing that every pizza parlour independently invented the concept of pizza? That they just happened upon the same recipe by chance? Amazing.

    That’s right DL. You can’t merely observe nature and pretend that NDE predicts every aspect of it. You have to face the logic. There is no speciation without extinction. whether it be mass, global or pseudo. The theory requires it – prior to its post hoc fixes.

    You cannot explain ALL speciation in Earth’s history without extinction, but you can explain a lot. So your statement is false. Unless you would care to explain why species A and B in my example above can’t work?

    Actually, further down, you said:

    Mutant B must out-compete species A. If there is plenty of food for all, if it is not declining and requires no search then mutation B is not selectable.

    NS selects A in A’s niche, and B in B’s niche. Problem?

    Keep going, you’re almost there. You did it once with sharks, now you can do it with lions. Smaller population of antelopes … smaller …. smaller ….. gone.
    Oops, less lions … less … less …. gone.

    So why does this not happen, Charlie? You have not answered the question. Why do you think it doesn’t happen? Why doesn’t the lion population boom until all the prey are wiped out?

    Is God stepping in? Or could it be that simple natural assumptions about predators and prey are enough to account for the relationships:
    http://www.tiem.utk.edu/~mbeals/predator-prey.html

    So here we at least have the admission that speciation requires the killing off and extinction of the parent species. This is my whole point in a nutshell. This is what NDE requires and this is what it predicts. To postulate niches and separate populations to account for the fact that this is not what the record shows is special pleading – it is not a prediction of the theory.

    Yawn. False.

    Why did these thousands of species mutate to specialize to these different food sources when the original food source was so readily available and when their ancestors were doing so well?

    What does the well-being of their ancestor population have to do with it? In NDE theory, it has nothing to do with it, Charlie.

    If the mutation gives the mutant access to a new food source, then the mutant population will boom even if the ancestor population is also booming.

    Given your stable earth and single-celled creatures you have to presume fecundity. Enough so that it expands all over the place so that it can be replaced in niches rather than in general. In those niches you admit that replacement by extermination is required for speciation.

    I’m assuming the fecundity of single-celled life? Where would I get that idea? Oh, yes. The observed facts.

    So this incredibly robust first life, so robust that you’ve got it expanding all over the place (giving the original population plenty of room to exist when being replaced in nooks and crannies) and slipping into niche after niche, is also very easily replaced (or else its very few and rare mutant kin would not survive to speciate).

    I’ve read this several times and it still makes no sense. Under NDE, if a mutant eats a new food source, why is the original species going to be displaced? You still haven’t answered this simple question.

    If a mutant of the mutant eats the new food source more efficiently, then it will likely replace the original mutant, and STILL leave the original ancestor species alone.

    1) The first enzyme, while inefficient, is already metabolizing PCP.
    2) The second enzyme, coded by pcpD, immediately downstream of the first PCP hydroxylase, can be knocked out and the system continues to function, albeit less efficiently, and at lower concentrations.
    3) This is exactly NOT irreducible complexity. Not every step is essential. In fact, this is exactly the Darwinian solution Behe (and Darwin) says can be built by step-by-step additions increasing functionality by a series of gradual intermediates.

    Go back and read it again. If you remove ANY of the enzymes, the bacterium will die. It doesn’t matter that the first enzyme metabolizes PCP because it metabolizes PCP into a TOXIN. The second enzyme cannot metabolize PCP. It can only metabolize the result of the first enzyme, and it can only do that some of the time. When the second enzyme stops (which it does in the ancestor), the bacterium dies. So the bacterium cannot survive in a PCP environment with the original enzymes. There’s no survival advantage to bacterium from enzymes 1 and 3 in a PCP environment because the bacterium will die.

    Being able to metabolize milder chlorophenols is not the same thing as being able to metabolize PCP. But it illustrates the point. Metabolizing the (non-PCP) milder chlorophenols is a different function that was co-opted by the PCP-eating system. The original enzymes have no selectable function in a PCP environment. They do, however, have a function in another environment where there’s no PCP.

    IC has nothing important to say about NDE unless you first ignore co-option and assume every component is present for some “final function” like eating PCP or clotting blood or propelling bacteria.

  111. DL,
    I don’t consider myself to be very knowledgeable when it comes to this topic, but it sounds like you are asking Charlie to consider your argument possible as a means to validate the theory, whereas Charlie is asking you to empirically demonstrate that it happened as a means to validate the theory.

    Regarding extinction….doesn’t every node/split in the tree of life eventually represent an extinction event as well as a common ancestor?

  112. Hi DL,
    Why did you quote Behe on the cilium when the charge against your honesty was regarding this claim:

    What does Behe want today? He wants scientists to show the exact series of co-option steps that occurred during the formation of an IC system.

    ?
    This is false and your red herring about the cilium says nothing about this false claim.

    As per your quote on the cilium and function, even “Jones” got that part right:

    Although Professor Behe is adamant in his definition of irreducible complexity when he says a precursor “missing a part is by definition nonfunctional,” what he obviously means is that it will not function in the same way the system functions when all the parts are present.

    Behe: Yes, it’s obvious that’s what I meant because that’s exactly what I wrote in Darwin’s Black Box: “An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism)…” (DBB, p. 39)If it doesn’t work the same way when a part is missing, then it can’t be produced directly, which is just what I wrote. Nonetheless, I do agree that, for example, a computer missing a critical part can still “function” as, say, a door stop. That hardly constitutes a concession on my part

    ===

    So why does this not happen, Charlie? You have not answered the question. Why do you think it doesn’t happen? Why doesn’t the lion population boom until all the prey are wiped out?

    Because the theory does not describe reality and requires ad hoc fixes.

    I’m assuming the fecundity of single-celled life? Where would I get that idea? Oh, yes. The observed facts.

    You have no observed facts with regard to the first replicators or first single-cells.
    I am going to take a break here from your pizza parlour lesson on biology and take a different route:
    Since you like thought experiments let’s put your theory to the test.
    Say you have a barren planet and you would like to have complex creatures, molecular machines and intelligence capable of contemplating the universe.
    Do you PREDICT that you will most PROBABLY achieve this end by placing one replicator on the planet, or one single cell? Would the most probable outcome be complex life? Is that really your prediction?
    ===
    As for PCP metabolizing bacteria, you are wrong. Knocking out neither the third nor the second enzymes will necessarily result in cell death. The first step is selectable because it reduces the toxicity of PCP. The second step acts as a catalyst to improve the further degradation but the cell does not die but continues to grow and remove PCP in lower concentration (100 uM as opposed to 300 uM) without it. And the reduction product of step 1, TCBQ, is subsequently further reduced to the even less toxic TBHQ without the help of any enzymes (the purpose of step 2), in the chain or not – again, this is the very first step, without steps 2 or 3 and demonstrates the selectability of step 1 and thus the reducibility of the sequence. At the same time, neither does the cell require the PCP as its carbon source as it already has sources, including tetrachlorophenol in the wild, the metabolizing of which is not knocked out when pcpD is knocked out, and the sodium glutamate medium upon which it was cultured in vitro. With only the first enzyme the bacteria can reduce the toxicity of PCP and can continue other metabolic activity not reliant upon PCP as a food source. With the second enzyme the toxicity is reduced even further and more quickly, so step 2 is selectable without step 3. IC – not.

  113. Man, you guys are prolific! Do you know this thread prints out to over 90 pages (and that’s at a reduced print size percentage).

    I stepped out of this discussion a week or so ago, and now I’ve read it to catch up. Charlie, I have a question for you: when you say that lions eating antelopes should cause antelopes’ extinction, are you bearing in mind that there ought to be an equilibrium point, where a reduced number of antelopes would cause a corresponding reduction in the lion population, and a corresponding reduction in antelope kills, and that this would happen before the antelopes were all gone? I didn’t see you address this.

    Otherwise I think you’re doing yeoman’s work in representing what Behe has said, in the face of repeated misunderstandings. The word “liar” was rather strong; I might have asked DL instead whether he was misrepresenting Behe intentionally or otherwise. But then, I think you had already done something like that.

    Doctor Logic, whenever you call Behe dishonest for not accounting for co-option, I think of multiple articles he has posted on the Internet where he has addressed that issue. When you say he’s not dealing with it at all, or ignoring it, that’s tantamount to saying he’s a blithering idiot, a blind, ignorant, stupid fool. Can you really imagine that he has failed to notice this aspect of the debate? Can you really imagine that he wouldn’t have developed a response? Do you imagine that if he developed a response, that it must be completely blitheringly obviously inane? Have you actually read any of his responses, or only what shows up on TalkReason or Panda’s Thumb?

    For the umpteenth time I make my non-strategic suggestion (non-strategic in that it gives advice that might be useful to those who disagree with my position): the more you oppose some distorted caricature of ID, the more you’re fighting the wrong battle. You’re defending some other beach in France while the troops are landing at Normandy. And you’ve got real control of the one you’re defending, yes, sir! Come to the real beach, though, and see if your counter-attack works there.

    But if you choose to stay on your own beach, and if you continue to underestimate Behe in particular, that’s fine. Eventually it will become clear that while you were winning one battle, Behe et al. were winning another one—the one that counts.

  114. Hi Tom,
    Thank you for that gracious rejoinder.
    Yes, I certainly thought about the wisdom of the remark; before I typed it as well as the many times over the months when I’ve erased it. But mostly soon after I typed it.
    You are right, of course, that I could have chosen greater diplomacy.
    I’m not sure here of the should, however, and accept that I may have made the wrong call.

    As for the lions, I am trying to be clear that I am not discussing what the real world presents but what the theory presents. As you can see from DL’s mathematical link models and fixes have to be created to try to account for what we see v. what should be.
    I see only two ways that a declining antelope population would result in a declining lion population in reference only to the theory of NS and progressive evolution ( the kind that could somehow predict complexity from simplicity).
    This immediately rules out the truth – that the lion population is limited not by how many antelopes there are but by how many they can take – and that NS is a preserving cull eliminating the slow and weak, not ratcheting up speed and strength.

    One would be that the remaining lions were somehow denied access to the declining antelopes. If this were the case then we are not discussing the theory of NS any longer, but allowing for where it is not functioning. To test this we can take it to the extremes. Imagine one antelope on a plain with ten prides of lions. Will the lions decline? Certainly – because there is not enough food and they will kill the antelope. The same holds as you multiply the antelopes. If the lions are so successful that they are diminishing the antelope population there will be no lions gong hungry until there are no antelopes left to eat. The very fact of the decline of the antelope population should not hamper the ability of the lions to eat those that remain. If they can eat a large population they can surely eat a small one. To say otherwise is like saying that a room of hungry people will eat three apple pies but not the fourth because it is the last one.

    The other option has already been dismissed as a strawman – the arms race. If NS made an uber predator out of the lion, as it should, the lion would exterminate all antelopes. If it went the other way, as it also is just as likely, and made an uber escaper out of the antelope then the lions ought to have starved. If it struck an equilibrium the two ought to have become locked in am arms race with both of their respective skill-sets spiraling ever higher. Here you should likely predict the ecosystem gives way to one uber predator and one uber prey and the others ought to disappear to leave only these two in constant warfare. For some reason the theory that made man out of mud somehow recognizes all kinds of developmental limits when it has to deal with observable reality and not deep history speculation. Of course, neither do lions keep becoming better hunters, nor do antelopes become faster and more vigilant nor do chimps become smarter and more artistic.

    Evolution doesn’t work that way, we are reminded repeatedly. Well, there must be some way it works other than to merely restate what nature has already demonstrated.

    I think here again of seeding another planet. Would a person put a pride of lions and a herd of antelopes on a plain on an otherwise empty planet (presuming yummy grasses for the antelope) if his plan were a flourishing ecosystem, or even the success of the lions?
    Not probably.

  115. Hi Tony,
    As to your suggestion that Behe’s peers don’t doubt the Darwinian mechanism, I submit one of your own – vociferous critic of ID, Larry Moran:
    http://sandwalk.blogspot.com/2008/12/testing-natural-selection-part-1.html

    Please don’t point out to me that he believes in naturalistic evolution and mutation, I know that. This is why I’ve selected him. From the standpoint of our discussion he represents a large population (larger than indicated here, even) of Behe’s peers who question the efficacy of Natural Selection. On this point he is a mild critic. As well, Tom just recently posted on this.
    So that leaves random mutation as the driving force behind evolution. This debunks the Dawkinsian retreat from math – “evolution is anything but random” – as though it weren’t already obviously false, and deprives you of the complexity ratchet which DL is throwing out anyway with his argument against extinction and selection.
    So chance it is. Chance or design.

    My guess? Design.
    http://www.uncommondescent.com/intelligent-design/self-assembling-nanomachine-a-film-about-flagellar-biosynthesis/

  116. Charlie,

    I read the article you linked to as a side discussing the importance of natural selection (as opposed to genetic drift) in accounting for changes in the genome.

    Here are some quotes from the article:

    What Orr says is simply not true. There are many biologists who seriously doubt that natural selection drives the evolution most physical traits, even though such pluralists readily agree that most adaptions are due to natural selection. Random genetic drift is a plausible way to explain many physical traits.

    ….

    As I indicated above, since the vast majority of animal and plant genomes is non-essential, it stands to reason that the vast majority of alleles will be neutral. Thus at the molecular level, at least, random genetic drift must be the dominant mechanism of evolution.

    I read the whole entry as an internecine battle over the relative importance of natural mechanisms (natural selection or genetic drift) in effecting phenotypic and molecular changes. If anything, I read it as an embarrassment of riches to what natural mechanisms an evolutionary biologist should attribute evolution.

    But I should have written more clearly earlier, especially in light of this discussion – I should have said that the majority of Behe’s peers do not share his doubts about natural mechanisms (I think of genetic drift and other natural modifications as being Darwinian, but I’m sure lots of people would disagree with my classification) being able to create complex and even irreducibly complex structures.

    I understand that even my amended statement is susceptible to being viewed as ad populum (and it isn’t meant to be imply that Behe’s position is de facto hopeless), but at some point Behe will have to explain how it is that Darwin’s big idea – that the very complex can come from the very simple – is not yet viewed as a failed paradigm by the vast majority of his fellow biologists. I.e., finding discord on the proper weighting of natural evolutionary mechanisms – whether they be strictly Darwinian or based on Darwinian principles – is still a far cry from finding adherents to Behe’s proposed end of methodological naturalism in biology.

    As a further aside, I have to say that I have a soft spot for contrarians, and I do think that Behe often writes well and can be pretty funny. So although I still do find the implications of his proposal to still be (yes) horrifyingly defeatist, there’s still a small part of me that roots for him and admires the way that he has tweaked a number of people from their complacency. (Starting with me).

  117. Hi Tony,

    I should have said that the majority of Behe’s peers do not share his doubts about natural mechanisms (I think of genetic drift and other natural modifications as being Darwinian, but I’m sure lots of people would disagree with my classification) being able to create complex and even irreducibly complex structures.

    All you’ve said is they aren’t IDists. This is pretty trivial and only highlights what I’ve been talking about. The idea is a failure and has so many patches only because of what you mention here – a commitment to “natural mechanisms”. And, like you implied, these are all rolled into one as though they confirm the theory.

    Behe will have to explain how it is that Darwin’s big idea – that the very complex can come from the very simple – is not yet viewed as a failed paradigm by the vast majority of his fellow biologists.

    Once again, if you were to read Behe you would find out that he does explain this – unfortunately there are many factors involved and some it requires psycho-analysis. But you’ve given us a pretty good example of one of the reasons – every hypothetical explanatory patch, no matter how contradictory to the next, is seen as supporting, rather than defeating the theory.
    Why do they not view the failure yet? Why did they ignore Mendel for 50 years? Why have the brushed over the extinction problem?

    Darwinism was disproved out-of-the-box but it didn’t matter:

    But, in a singular demonstration of the limits of even great minds, he didn’t notice that domestication evidence massively contradicted his theory. It disproved his key premise that continuous selection of a single trait would evolve a population of better adapted organisms. Domestication shows on the contrary that selection for a single trait results in changes in numerous traits – changes that are usually maladaptive.

    Domestication also provided abundant documentation of events that Darwin stoutly declared cannot happen: single generation “leaps”, such as the two-headed calf and other “sports of nature”, that disprove his “gradualist” theory of organic change.

    http://www.onlineopinion.com.au/view.asp?article=4193

    Short of a conspiracy, the explanation is most likely somewhat along the lines described below:

    Maciej Giertych.

    In my studies I went on to a B.A. and M.A. in forestry, a Ph.D. in plant physiology and finally a D.Sc. in genetics. For a long time I was not bothered by geology, Evolution or any suspicious thoughts. I had my own field of research in population genetics of forest trees, with no immediate relevance to the controversy over Evolution.

    Gradually, as my children got to the stage of learning biology in school and discussing their problems with Dad, I realized that the evidence for Evolution had shifted from paleontology and embryology to population genetics. But population genetics is my subject! I knew it was used to explain how Evolution progressed, but I was not aware it is used to prove it. Without my noticing it, my special field had become the supplier of the most pertinent evidence supporting the theory.

    If Evolution were proved in some field I was not familiar with, I understood the need to accommodate my field to this fact, to suggest explanations how it occurred in terms of genetics. But to claim that these attempted explanations are the primary evidence for the theory was quite unacceptable to me. I started reading the current literature on the topic of Evolution. Until then I was not aware how shaky the evidence for Evolution was, how much of what was “evidence” had to be discarded, how little new evidence had been accumulated over the years, and how very much ideas dominate facts. These ideas have become dogma, yet they have no footing in natural sciences. They stem from materialistic philosophies.

    ….

    No. Genetics has no proofs for Evolution. It has trouble explaining it. The closer one looks at the evidence for Evolution, the less one finds of substance. In fact, the theory keeps on postulating evidence and failing to find it, and moves on to other postulates (fossil missing links, natural selection of improved forms, positive mutations, molecular phylogenetic sequences, etc.). This is not science.

    This certainly explains why current IDists like Behe and Kenyon accepted Darwinian explanations for so long, and even published and, in Kenyons case, wrote textbooks supporting the paradigm.

    Here’s a little something I wrote on this topic previously (links removed):

    ‘Evolution’ is: slow, stately, gradual, minute variation by minute variation, incremental, accumulating, inexorable, unguided, blind, natural, unpredictable, random, chance.
    These insensible variations mount to lead from the exceedingly simple to the extraordinarily complex.

    Doubters have said all along that this makes no sense. That this cannot account for the kinds of complexity and design we see. That the evidence does not lead to such a conclusion.
    They were told they were wrong.

    The fossil evidence, biogeography, molecular analyses, population genetics, etc., all tell us evolution happened and happens.
    At first traits blended, then they were thought to be inherited as distinct, and, of course, mutable, proteins. Then DNA was discovered, necessitating a code. Ah, but the code is simple, one gene=one protein, and when the gene changes, the protein changes, and the organism changes. Then it was found that the code is not simple, it is one-in-a-million, the DNA is transcribed into RNA, and then to proteins, wait, no, it is transcribed into mRNA which is matched to tRNA which is translated to the amino acids. And all of this requires coordinating enzymes, and machines to accomplish the unzipping, the reading, the error correcting and the folding. And each mRNA can be disassembled and retranslated to produce several, maybe hundreds, of different proteins.
    And the cell itself functions in inheritance, and the proteins can reverse transcribe, etc. etc.

    So we have dissenters. Those who understand the central dogma is a failure, those who understand that the fossil record is as even the creationists had claimed, a disconfirmation of the theory, those who understand that the molecular evidence may, in general, reflect taxonomy, but that is not evolution, those who understand that natural selection is not a force, and does not create novelty, that ‘ToE’ provides no such mechanism.
    You have people like Stephen Gould, Lynne Margulis, Will “Natural Selection is the result of these causes, not a cause that is by itself. It is not a mechanism” Provine, and Allen “The “modern synthesis” is dead – long live the evolving synthesis! ” MacNeill who know that ToE and neo-Darwinism do not cut it.

    So we have the punctuated equilibrium, endosymbiosis, evo-devo, etc.
    But these are not solutions.
    These are admissions that evolution did not and cannot occur as propounded.
    Not as described in the beginning of this post. And that, of course, is what the dissenters have been saying all along.
    They can keep adding vague fixes which tell us nothing but that they were wrong, but that does not get around the fact that the evidence is not for the hypothesis, and that, in fact, it is a grand failure.

    Ask those like Dobzhansky and Nilsson, who actually tried to demonstrate it but instead falsified it.

    As [evolutionary biologist] Allen MacNeill says, in defence of evolution on Uncommon Descent (links above)”

    So, the history of the concept of macroevolution is not entirely compatitible with the neo-darwinian “modern synthesis” – this is supposed to be some sort of surprise, or to undermine the idea that macroevolution has not occurred? You folks need to pay a little more attention to what has actually been going on in evolutionary biology over the last half century, and less time tilting at “modern synthesis” windmills that have long since fallen into disrepair within our discipline.

    The theory is in disrepair. But he doesn’t realize that there is nothing to glue his evo-devo patches on. Nothing but his philosophy, which will cling tenaciously to any excuse it is offered.
    Kind of reminds one of the warm-little pond, spontaneous generation, hot-dilute soup, moist clay, volcanic plumes, deep-sea vents, subterranean laboratories, Martian meteorites, directed panspermia saga, doesn’t it? Any port in a storm.

    So that gives some of the explanation as to why Behe’s peers do not accept ID – they are committed to the paradigm, they do not properly question the paradigm and presume it is proven in other fields (in which they are laymen and accept authority), everything is force-fit into the paradigm, some publishers won’t countenance anything that disputes the paradigm (they say they are publishing “biology” or “genetics” but admit they are publishing only paradigm-supporting information), etc.

    whether they be strictly Darwinian or based on Darwinian principles – is still a far cry from finding adherents to Behe’s proposed end of methodological naturalism in biology.

    You still haven’t looked hard enough. If you actually seek out rather than try to rationalize the disagreements you will find Behe’s peers are very much is discord over Darwinian mechanisms. I was going to ask that instead of taking the time to respond to my comment above that instead you dedicate an identical number of minutes to Googling for doubters of Natural Selection or Random Mutation I think this would be much more fruitful.
    To call the processes “Darwinian” is merely to bow before the paradigm and commit the errors discussed above. You are just accepting that everything that can be seen as a scientific explanation ought to be rolled under the “Darwinian” umbrella so that the theorists can maintain their position that they are right and always have been. The evidence for the last 150 years has all been against the grand theory even though its proponents keep claiming mountains of evidence have proven it.

    Abiogenesis does not happen, has never been seen to happen, is not an empirical observation, and defies all explanation. Sorry, but claiming “abiogenesis has nothing to do with “evolution” will not wash. The theory is a metaphysical necessity and, as Darwin mentioned of it in a different context, if it fails at all it fails completely. As a grand narrative doing what its only real purpose is – exclude God – it fails at OOL so there is no reason to keep supposing (against the evidence) that it holds after OOL. On a less ambitious note the failure of OOL explanations takes away the raw material that Darwin needs. You have no idea if the theory can be allowed a first life, a first replication and a first competitive population.
    There is no explanation of the simplicity or complexity of this first life and no knowledge then how evolution was to proceed from its inception. With no starting point how can there be a theory of what proceeded from that starting point or how it did?

    Extinctions do not happen in a Darwinian fashion. His entire case against catastrophism was a failure from the beginning and was demanded by his theory. He had to ignore the true evidence of extinctions in order to support the theory.

    There is no Tree Of Life – as researchers admit now, it was a useful fiction which can be abandoned now that the biological community is solidly onboard.

    The fossil record does not and never did support gradualistic evolution and uniformitarianism. It was waved away at the time and explanations that try to account for it are not Darwinian.

    Darwinian adaptations do not explain Margulis’ endosymbiosis (even though she avers, after stating that she is firmly not a neo-Darwinist, that she remains a Darwinist (philosophical position)). They do not explain the necessary complexity at the beginning of life, the evidence that first life would have been more complex and getting simpler, that eukaryotes may have preceded their more simple kin, the prokaryotes, etc. Indeed, people like Doolittle, studying this side of the issue, dispute the Margulis patch which is getting wide acceptance after many years of abuse as the community realizes it can take her idea and stitch it onto the original.

    When tested in fruit flies and bacteria over years upon years Darwinian processes dry up and do not generate the kind of progress required by the theory. Extrapolated, the changes observed could never account for the diversity of life in the time span allowed – or many times that.

    The math has never worked, and this has been demonstrated since at least Wistar in the 60s and has been ignored by biologists the whole time – just as they ignored the obvious empirical and mathematical case of Mendel’s for 50 years.

    It fails every test and yet persists. Why? Because, like you demonstrated above, the proponents need it and can bundle every explanation into the package and claim them as evidence, no matter how contradictory.


    Those were kind words about Behe. Imagine what it must be like to be him.

  118. Sorry, I forgot this on your first quote there.

    I should have said that the majority of Behe’s peers do not share his doubts about natural mechanisms (I think of genetic drift and other natural modifications as being Darwinian, but I’m sure lots of people would disagree with my classification) being able to create complex and even irreducibly complex structures.

    If we are going to discuss IC and the authority of science it will do no good to references the opinions of Behe’s peers. His case is not one of stating one opinion against another but of logic and observation – science. Hanging your hat either on the previous errors of what Behe is saying or on the authority of his opponents does not make the case against IC. If you want to trust their opinions show where they’ve refuted him. DL has claimed, I think for your benefit, that this has happened – but he cannot support that.
    Show that, against the solid logic, Darwinian processes actually can directly form an IC mechanism. As this fails, show that they actually have done so via the indirect route – exaptation. Don’t just say that they can in theory – as we’ve seen, in Darwinian theory anything and its exact opposite can happen – but show that they have. As Behe, and his opponents have said, this is neither observed nor is it the least bit probable as the complexity of the system in question grows. Even if DL’s case panned out, how does our scanty knowledge of the components in a three step process , utilizing enzymes which already exist and already perform virtually identical functions, do anything toward explaining what you saw in that video on the BF, for instance?
    If they actually have the case against Behe why do they constantly misrepresent him to make it? When you have the facts why don’t you just put them on the table and let them speak?

  119. Charlie,

    So why does this not happen, Charlie? You have not answered the question. Why do you think it doesn’t happen? Why doesn’t the lion population boom until all the prey are wiped out?

    Because the theory does not describe reality and requires ad hoc fixes.

    That’s not answering the question. This isn’t a question about NDE. I’m asking you why you think the lions don’t wipe out their prey, and, in turn, themselves.

    I want to know why you think that what is happening with the lions and their prey is not predicted by NDE. Are the fittest not surviving?

    One would be that the remaining lions were somehow denied access to the declining antelopes. If this were the case then we are not discussing the theory of NS any longer, but allowing for where it is not functioning. To test this we can take it to the extremes. Imagine one antelope on a plain with ten prides of lions. Will the lions decline? Certainly – after they kill the antelope. The same holds as you multiply the antelopes. If the lions are so successful that they are diminishing the antelope population there will be no lions gong hungry until there are no antelopes left to eat. To say otherwise is like saying that a room of hungry people will quit eating pie as there gets to be less and less of it.

    If you think about why the lions don’t kill all their prey, you’ll have your answer.

    When lions chase prey, they don’t get their pick of prey. They are opportunists, and can often only catch the younger and weaker prey, not the best and fastest prey. The best lions generally cannot catch (or can’t make a living catching) the strongest prey.

    Furthermore, the more antelope, the easier they are to catch. The lions can spend less time hunting, and end up with more food. Lions have to work for their food, and they’ll be working much much harder as the number of prey declines. It’s not like a piece of pie in a dining room where the feeders need exert no effort.

    The prey are scattered across a vast area. Some of these areas are not easy to migrate between. If a very lethal breed of lions did emerge, they would probably kill off their food source before they could replicate their clan to other regions.

    And this is exactly what NDE is about. It’s not a “fix” to NDE, but a discovery about the mechanics of NDE.

    Behe: Yes, it’s obvious that’s what I meant because that’s exactly what I wrote in Darwin’s Black Box: “An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism)…” (DBB, p. 39)If it doesn’t work the same way when a part is missing, then it can’t be produced directly, which is just what I wrote. Nonetheless, I do agree that, for example, a computer missing a critical part can still “function” as, say, a door stop. That hardly constitutes a concession on my part

    Behe says that “direct” means no co-option. He shows that certain structures can’t be reached “directly”. So what is Behe’s complaint against evolutionary biology, Charlie?

    Say you have a barren planet and you would like to have complex creatures, molecular machines and intelligence capable of contemplating the universe.

    Why would I want to do this when I can contemplate the universe for myself? Whatever.

    Do you PREDICT that you will most PROBABLY achieve this end by placing one replicator on the planet, or one single cell? Would the most probable outcome be complex life? Is that really your prediction?

    No. I will most probably achieve this by building the target life forms directly without evolving them. Evolution tries survival solutions at random. Solutions that work are replicated, and feed into the next generation. This will result in a proliferation of more complex survival solutions, but not necessarily intelligence. So evolution would be a stupid way to go about creating intelligent life unless I had no idea how to design it myself.

    But suppose that I did want to evolve life on this planet. Not because I wanted the final product (that would be silly), but because I just want to evolve stuff for kicks. Then my answer is yes.

    If there is plenty of food on the barren planet, and the climate is hospitable, then a single-celled life form will most likely replicate in huge numbers. Because the planet is covered in niches for mutated life, there will soon (within a few years) be many thousands of species of single-celled life across its surface. The mutants will be more complex that the initial life form that was deposited because that complexity provides access to the new niches.

    I do not know the odds of evolving multicellular life and intelligent life as a function of time. Presumably it is something like once per 2 billion years and once per 4 billion years respectively. So if my goal was either of these two, I would have a lot of waiting time during which I could contemplate the universe for myself.

    You say that the PCP metabolizing mechanism isn’t IC. I’d like to know where you’re getting these claims from. From what I hear, even Behe thinks the mechanism is IC, but he thinks that metabolic cascades can evolve IC, but not some other IC things cannot.

  120. Hi DL,

    Behe says that “direct” means no co-option. He shows that certain structures can’t be reached “directly”. So what is Behe’s complaint against evolutionary biology, Charlie?

    You tell me. I know you haven’t read him but you must know why you are so exorcised by his works that you must continually misrepresent him.

    You say that the PCP metabolizing mechanism isn’t IC. I’d like to know where you’re getting these claims from. From what I hear, even Behe thinks the mechanism is IC, but he thinks that metabolic cascades can evolve IC, but not some other IC things cannot.

    Unlike you, I’m not “getting” my claims. Unlike you I don’t need some talkDOT to tell me what I think. I read the relevant paper, cited the results and demonstrated, without repeating someone else’s claim, why the mechanism is not IC.
    I don’t know what Behe said, but I see you acknowledge that he has addressed this and does not see it as a challenge to his case. I don’t presume you’ve actually read his response, as opposed to somebody’s castigation of it, but if you find it perhaps you could share it with me.

    This isn’t a question about NDE. I’m asking you why you think the lions don’t wipe out their prey, and, in turn, themselves.

    I can tell you why but it has nothing to do with the predictions I made about NDE. Although I’ve already givent he answer to Tom I am not trying to explain reality – I am commenting on a theory which can’t explain reality.

    When lions chase prey, they don’t get their pick of prey. They are opportunists, and can often only catch the younger and weaker prey, not the best and fastest prey. The best lions generally cannot catch (or can’t make a living catching) the strongest prey.

    Exactly (when you appeal to reality and not to the theory). Natural selection is not an improvement mechanism at all. I already covered this in my response to Tom.

    Furthermore, the more antelope, the easier they are to catch.

    This is not true. This is like saying its easier to outrun one man than five. If lions can catch and eat the best antelope then they can catch and eat all the best antelopes. As I said to Tom, if you are merely removing access then you are eliminating the role of NS. But this is a question about NS, so introducing more and more and different species and requirements is exactly the jury-rigging I am talking about. You’ve chosen lions and antelopes because there are supposedly millions of years of evolution as a buffer here. Place lions and antelopes back where it is only lions and antelopes in competition and the result is sterility.

    t’s not like a piece of pie in a dining room where the feeders need exert no effort.

    The prey are scattered across a vast area. Some of these areas are not easy to migrate between.

    As I was saying.

    If a very lethal breed of lions did emerge, they would probably kill off their food source before they could replicate their clan to other regions.

    And if a very fast antelope evolved the lions would die off. You are still jury-rigging. You make the tacit admission here of my case but you won’t face its implications. Of course the very lethal lion would kill off its food source and then die off. That’s my point. You are merely insulating your case by making these ones disposable. But as you state here, the prediction of the ratchet is extinction – first of the prey, then the predator => sterility.
    You just hide the result in one niche or another. But if your complexity ratchet is working this is happening in all niches – especially in the first and only niche – and sterility is more likely the result than biodiversity.

    Why would I want to do this when I can contemplate the universe for myself? Whatever.

    Right, whatever whatever. You are a talent.

    Do you PREDICT that you will most PROBABLY achieve this end by placing one replicator on the planet, or one single cell? Would the most probable outcome be complex life? Is that really your prediction?

    No. I will most probably achieve this by building the target life forms directly without evolving them.

    Thank you – case made.

    Evolution tries survival solutions at random. Solutions that work are replicated, and feed into the next generation. This will result in a proliferation of more complex survival solutions,

    Question-begging.

    but not necessarily intelligence. So evolution would be a stupid way to go about creating intelligent life unless I had no idea how to design it myself.

    I agree.

    If there is plenty of food on the barren planet, and the climate is hospitable, then a single-celled life form will most likely replicate in huge numbers.

    I give you the presumptions of the environment as part of the of the thought experiment, but you are also presuming fecundity of first life. There is no reason to do this. You are stacking the deck at the first.

    ecause the planet is covered in niches for mutated life, there will soon (within a few years) be many thousands of species of single-celled life across its surface.

    Now you are also presuming mutations. But mutations are mostly deleterious. You are already making special pleas for your case. You’ve got life so fecund it covers the planet and fills niches but yet it suffers mutations enough that it becomes thousands of species. The mechanism that creates these presumed species is more likely to kill than create, so you are battling the probabilities already. Not to mention that you are begging the question as well by allowing yourself the very thing we are debating – speciation.
    At the same time that your fecund first life is covering the planet you are presuming it is evolving evolvability. But, since mutations are most likely deleterious, and you will now have to admit that and say that in the general, pre-niche population, they were eliminated, but awaitedthe other niches, you will argue against the theory in another way. If mutation is most likely deleterious, as it is, and the mutants are being removed fromt he general population, then NS, complexity ratchet that it is, would eliminate the mechanism for mutations.
    Mutations are not selectable until life has spread, so there is no reason for mutations at all.
    Now, as you determine to claim that mutations are just a fact of life you will 1) beg the question and 2) remove biology from the realm of science. If you want to claim that “mistakes are going to happen” then you have to admit that mistakes of chemistry will just happen, and mistakes of physics will just happen – sometimes masses just won’t attract, accidentally, usually electrons will repel, but sometimes they will mistakenly attract. As you can see, “mistakes just happen” will just be more question-begging in a probability case.

    The mutants will be more complex that the initial life form that was deposited because that complexity provides access to the new niches.

    No it doesn’t, simplicity does. See how we can both beg the question. Again you are merely presuming what you are supposed to be demonstrating. As Steve alluded to earlier, you are making complexity in and of itself a selectable feature, as though “complexity” is preadaptive and is evolved itself.
    Empirical study demonstrates that you are wrong – complexity is not the more adaptive as it is the simplest life forms that inhabit the most niches, are the most adaptive, and provide the bulk of our biomass. You are claiming facts against the data.

    So if my goal was either of these two, I would have a lot of waiting time during which I could contemplate the universe for myself.

    If this was your goal, as you said earlier, this is not the way to achieve it. You have made no case for the probability of complexity short of presuming first, against facts, what you are supposed to be showing.
    No, I conclude that even you can see that NDE does not preferentially predict complexity. Rather, it most assuredly preferentially predicts sterility, if not at least simplicity.
    Interestingly, this is the thesis behind the books like Rare Earth which argue that even if there is life out there it is very likely to be very simple – the odds are simply against your claim.

  121. Tom,

    Doctor Logic, whenever you call Behe dishonest for not accounting for co-option, I think of multiple articles he has posted on the Internet where he has addressed that issue. When you say he’s not dealing with it at all, or ignoring it, that’s tantamount to saying he’s a blithering idiot, a blind, ignorant, stupid fool. Can you really imagine that he has failed to notice this aspect of the debate? Can you really imagine that he wouldn’t have developed a response? Do you imagine that if he developed a response, that it must be completely blitheringly obviously inane? Have you actually read any of his responses, or only what shows up on TalkReason or Panda’s Thumb?

    I’m puzzled here. Why is Behe assumed to be a pretty competent chap while the thousands of other evolutionary biologists who say Behe is plainly wrong are not competent?

    I think it’s likely that Behe does know about co-option.

    Here’s the basic idea. Behe comes up with the idea of IC. He argues that if some system has function F, and F is composed of many parts, and taking away any single part prevents the system from performing F, then numerous simultaneous mutations would be needed for the system to have evolved its function. That’s pretty clever. And if NDE relied on such a mechanism to create systems with function F, Behe would have a good argument against NDE.

    But it is well known that NDE does not work this way because evolution doesn’t “aim” for targets like function F. NDE rewards (which is not 100% of the time, e.g., drift) any function that has some survival advantage in some context. There are millions of F’s that evolution rewards simultaneously. Just as in human society, many of the inventions we use were not the result of multiple direct innovations aimed at the final function. Many (if not most) of our inventions make do with components that were invented for another purpose. So the idea that co-option is improbable is unjustified.

    Now, let’s review. Since ID makes no positive predictions because it refuses to say anything about the designer or the design process, it has to rely on proving the impossibility (or extreme improbability) of evolution. Behe doesn’t do that, but he is still claiming that evolutionary biologists answer his complaint. So what is his complaint?

    Apparently, his complaint is not that, for certain very complex systems, we cannot detail the exact steps that led to its formation. In other words, for Behe, it’s not enough to show that there is SOME co-option in the process, but we have to say exactlyt what happened. In other words, he’s making an argument from ignorance. He’s saying that certain molecular systems as yet have no detailed evolutionary explanation. NOT that there can be no explanation, NOR that NDE cannot explain them.

    So IC is NOT a challenge to NDE, but Behe and the DI keep parroting this nonsense despite having it debunked by the scientific community numerous times. This is not the behavior of a scientist, but the behavior of a showman.

    I don’t see you guys explaining Behe any differently. You just point out surprises evolutionary biology as if they were contradictions, but they’re not. It’s like learning that the orbits of the planets are elliptical (and not circular), and claiming this contradicts Christianity because Christians thought the orbits would be circular (reflecting God’s perfection). If there were good evidence that God invented the solar system, the fact of elliptical orbits wouldn’t cause us to throw out the invention theory.

    Likewise, NDE says there are successive modifications and natural selection. The naive (and false) assumption is that everything evolves at a constant speed, and co-option is non-obvious implication of the theory. But it is an implication of the theory nonetheless, and most certainly a possible variation of the theory that doesn’t contradict the premises of NDE.

  122. DL, it doesn’t seem to me that you addressed Tom’s points in his last post.

    Tom, I did a quick google on Behe and co-opt (and “coopt”) and didn’t find anything. Can you post the link to the articles online where Behe addressed co-option?

    Is that even-handed enough for everyone?

  123. Hi DL,

    I’m puzzled here. Why is Behe assumed to be a pretty competent chap while the thousands of other evolutionary biologists who say Behe is plainly wrong are not competent?

    It’s like when you debunked Tony’s claim about rationality – you can be wrong and still be competent.

    I think it’s likely that Behe does know about co-option.

    Since he’s discussed it for over a decade I’d guess it’s quite likely you are right.

    Here’s the basic idea. Behe comes up with the idea of IC. He argues that if some system has function F, and F is composed of many parts, and taking away any single part prevents the system from performing F, then numerous simultaneous mutations would be needed for the system to have evolved its function. That’s pretty clever.

    Yes, it’s the all-at-once argument – a very strong one.

    But it is well known that NDE does not work this way because evolution doesn’t “aim” for targets like function F. NDE rewards (which is not 100% of the time, e.g., drift) any function that has some survival advantage in some context.

    1) Strawman. NDE mechanisms don’t need to have a target to require selectability. These are independent.
    2) re: targets. When you knock out one crucial element in an IC machine RM and NS can replace it fairly readily. Two, very, very rarely. Three – not at all.

    This is a question Seelke investigate and answered. When he applied for funds he was told [paraphrase alert] “we don’t have to investigate whether or not “evolution” can create complexity; look around – there is complexity and evolution is our only player, so we already know it can do this.”
    Again, this is why other biologists need be neither dishonest nor incompetent to disagree – they merely need to be focused on their own questions while assuming someone else has solved the problem.

    So the idea that co-option is improbable is unjustified.

    Non-sequitur. It seems very improbable even to Behe’s opponents.

    Apparently, his complaint is not that, for certain very complex systems, we cannot detail the exact steps that led to its formation.

    False again. Behe says nothing about demonstrating the steps that the led to its formation. He says “show me in a rigourous, scientific, testable way the Darwinian steps that might have or could have. Do this for the BF, or anything of similar irreducible complexity and you will have defeated my entire IC case.”
    Nobody can or has, and your claims to the contrary are false.

    He’s saying that certain molecular systems as yet have no detailed evolutionary explanation. NOT that there can be no explanation, NOR that NDE cannot explain them.

    AND he’s presenting both and empirical and probability argument against such explanations. Like his arguments or don’t – but tell the truth about them.

    So IC is NOT a challenge to NDE, but Behe and the DI keep parroting this nonsense despite having it debunked by the scientific community numerous times. This is not the behavior of a scientist, but the behavior of a showman.

    “Dishonest” “showman” “parroting” “debunked” “nonsense”

  124. Especially for Tony …
    Since we are summing up, here are some of the claims made by ID opponents on this thread:
    Tony Hoffman:

    Irreducible complexity says, “there’s no natural explanation for this so we should stop trying to explain it using natural explanations.”

    False – contradicted by Tony’s own statements on Behe.

    There’s a trend I can’t help but notice; a lot of people are quick to correct definitions of ID and IR, but no seems capable of providing the definition from which they are basing their correction.

    False. The definitions are readily available and are sufficient to demonstrate the errors.

    Quoting Wiki:

    “He was presented with fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not ‘good enough.’”

    False. This was a literature bluff and Behe never said “not good enough” – nor anything to the effect.

    DL:
    [to Tom]

    This statement of yours is false. Evolution with cooption/exaptation can construct IC structures. This has been debunked numerous times, and when the debate gets into details, it’s always acknowledged that IC status does not mean a system cannot evolve, nor even that the evolution of the IC structure is improbable.

    False. This has nothing to do with the end result of debate – Behe’s case was presented in 1996 and stands without further acknowledgment.

    The argument for IC was initially that evolution could not create an IC structure.

    False. See above.

    First of all, GA’s create IC structures. So the idea that NDE can’t create them is pure nonsense.

    False. Challenge to provide evidence ignored.

    DL then tried to claim this was my demand rather that his own claim:

    “Okay, so you demand that the generated complexity is IC.
… are you just raising the bar for this test?”

    As above, the claim was DL’s.

    Behe is either ignorant or dishonest. Co-option explains IC in Darwinian evolution. Behe’s claim has been debunked. Biologists answered Behe’s challenge long ago, but Behe keeps pretending they haven’t.

    False. Behe raised the issue himself and has been neither answered nor debunked.

    This is why the judge in the Dover case didn’t just rule against ID, he wrote a scathing judgment against dishonest ID buffoonery in general.

    This quote speaks for itself.

    Quoting Dover:

    “However, Professor Behe excludes, by definition, the possibility that a precursor to the bacterial flagellum functioned not as a rotary motor, but in some other way, for example as a secretory system.”

    False.

    What does Behe want today? He wants scientists to show the exact series of co-option steps that occurred during the formation of an IC system.

    False.

    Go back and read it again. If you remove ANY of the enzymes, the bacterium will die.

    False

    There’s no survival advantage to bacterium from enzymes 1 and 3 in a PCP environment because the bacterium will die.

    False.

    ====
    Tony, leaving aside your own errors, this is the debater with whom you’ve chosen to share the smoking lounge.

  125. Anyone,
    I was reading one of Behe’s articles here and got to asking myself, do Darwinists think designs or IC structures even exist in nature – be it from humans or nature itself? If all that is required to discredit the concept of IC is that something be used for some other function (any function) prior to the IC structure, then I can see why they say IC doesn’t exist in nature because everything that exists has some prior function.

    But, if IC doesn’t exist in nature then human design doesn’t exist because it is technically no different than an outcome that a random process of trial-and-error could generate.

    Is this what Darwinists think – that human designs could, over long periods of time, be produced via a random co-opt process?

    If the answer to that is “No”, then what is the difference between human co-opt techniques to build structures (design) and random co-opt techniques to build BF motors?

  126. Charlie,

    I’m puzzled here. Why is Behe assumed to be a pretty competent chap while the thousands of other evolutionary biologists who say Behe is plainly wrong are not competent?

    It’s like when you debunked Tony’s claim about rationality – you can be wrong and still be competent.

    It’s not that Behe’s critics just disagree. They think Behe is ignorant of the evidence, ignoring his critics, and misunderstanding the science altogether.

    But it is well known that NDE does not work this way because evolution doesn’t “aim” for targets like function F. NDE rewards (which is not 100% of the time, e.g., drift) any function that has some survival advantage in some context.

    1) Strawman. NDE mechanisms don’t need to have a target to require selectability. These are independent.
    2) re: targets. When you knock out one crucial element in an IC machine RM and NS can replace it fairly readily. Two, very, very rarely. Three – not at all.

    (1) Huh? Sounds like you’re agreeing with me that there is some huge array of F1, F2, …Fn that NDE will reward, not just F. Or are you saying there are no neutral mutations?

    (2) Why is this relevant? If the components of the IC mechanism existed because it was beneficial in other contexts, you’re not going to get evolution to backtrack simply by mutating the final IC mechanism in the final context.

    Behe says nothing about demonstrating the steps that the led to its formation. He says “show me in a rigourous, scientific, testable way the Darwinian steps that might have or could have. Do this for the BF, or anything of similar irreducible complexity and you will have defeated my entire IC case.”
    Nobody can or has, and your claims to the contrary are false.

    You are admitting that Behe has no disproof of NDE, and that he is demanding NDE explain some particular details. This is an argument from ignorance.

    Behe’s Edge of Evolution has been reviewed in Science, Nature, on blogs and elsewhere. The scientific journals are unanimous: Behe is wrong, incompetent and ignoring refutations of his earlier works.

    Here are a couple of detailed reviews from Pharyngula and Science.

    In Sean B. Carrol’s Science review he says:

    This lack of quantitative thinking underlies a second, fatal blunder resulting from the mistaken assumptions Behe makes about protein interactions… But Behe bases his arguments on unfounded requirements for protein interactions. He insists, based on consideration of just one type of protein structure (the combining sites of antibodies), that five or six positions must change at once in order to make a good fit between proteins–and, therefore, good fits are impossible to evolve. An immense body of experimental data directly refutes this claim.

    Is it possible that Behe does not know this body of data? Or does he just choose to ignore it? Behe has quite a record of declaring what is impossible and of disregarding the scientific literature, and he has clearly not learned any lessons from some earlier gaffes. He has again gone “public” with assertions without the benefit (or wisdom) of first testing their strength before qualified experts.

    For instance, Behe once wrote, “if random evolution is true, there must have been a large number of transitional forms between the Mesonychid [a whale ancestor] and the ancient whale. Where are they?” (12). He assumed such forms would not or could not be found, but three transitional species were identified by paleontologists within a year of that statement.

    Scientists agree that Behe as obviously wrong, and Behe just goes on pretending his (incompetent) questions remain unanswered.

    Here’s another review of Edge of Evolution that explains some more of the shortfalls and contradictions in Behe’s book.

    A giant conspiracy theory in which 99+% of all the biologists in the world are conspiring against a few brilliant ID Galileo’s?

  127. Charlie,

    You wrote a longer entry that included this:

    If you actually seek out rather than try to rationalize the disagreements you will find Behe’s peers are very much is discord over Darwinian mechanisms. I was going to ask that instead of taking the time to respond to my comment above that instead you dedicate an identical number of minutes to Googling for doubters of Natural Selection or Random Mutation I think this would be much more fruitful.
    To call the processes “Darwinian” is merely to bow before the paradigm and commit the errors discussed above. You are just accepting that everything that can be seen as a scientific explanation ought to be rolled under the “Darwinian” umbrella so that the theorists can maintain their position that they are right and always have been. The evidence for the last 150 years has all been against the grand theory even though its proponents keep claiming mountains of evidence have proven it.

    And this

    When tested in fruit flies and bacteria over years upon years Darwinian processes dry up and do not generate the kind of progress required by the theory. Extrapolated, the changes observed could never account for the diversity of life in the time span allowed – or many times that.

    Both of which I think are typical of the longer comment. Many of the statements here are just false. The whole entry seems to assume that there either is a vast conspiracy afoot or that the biological sciences are populated with narrow-minded folk only interested in protecting a paradigm they are too obtuse to recognize as manifestly failed. That’s too much of a stretch for me.

    If we are going to discuss IC and the authority of science it will do no good to references the opinions of Behe’s peers. His case is not one of stating one opinion against another but of logic and observation – science. Hanging your hat either on the previous errors of what Behe is saying or on the authority of his opponents does not make the case against IC. If you want to trust their opinions show where they’ve refuted him. DL has claimed, I think for your benefit, that this has happened – but he cannot support that.

    I believe DL has provided links that do refute your assessment of how Behe’s work on IC is regarded by his peers. (I remember that Behe’s website says on the home page or thereabouts that his own department has pretty much disowned him over what he’s doing. He may have taken that down, but I doubt it.) But there is something odd about Behe taking his argument to the people, so to speak. I do have to bring up as well that I’ve heard it said many times that Dawkins embarrasses himself by portraying (sophisticated) philosophical arguments for God as silly. If that is true, isn’t Behe guilty of doing the same with (I think) far more technical biological issues?

    I think a lot of your recent posts present an isolated and mistaken view of NDE. You write things like:

    But mutations are mostly deleterious.

    But the website you pointed me to earlier that you contend doubts Darwinian mechanisms says:

    In animals and plants, for example, most of the DNA does not seem to be essential so that the overwhelming majority of mutations are neutral and a smaller number—those that interfere with an essential function—are deleterious.

    Regarding some of your conclusions, I originally wrote:

    Me: Irreducible complexity says, “there’s no natural explanation for this so we should stop trying to explain it using natural explanations.”

    You: False – contradicted by Tony’s own statements on Behe.

    Well, I haven’t gotten into this yet, but the acceptance of IC would be normative. We don’t say that Chemistry has nothing to say about the future prospects of the practice of Alchemy. It does. Behe’s (somewhat contradictory) statements don’t free IC from its methodological conclusions. So I still don’t agree with your assessment above.

    There’s too much other stuff in here to go over right now. But that’s where I am after reading through all this the one time.

  128. Hi Tony,
    Thanks for the continued tone of your posts.

    Charlie: When tested in fruit flies and bacteria over years upon years Darwinian processes dry up and do not generate the kind of progress required by the theory. Extrapolated, the changes observed could never account for the diversity of life in the time span allowed – or many times that.

    Tony:
    …Both of which I think are typical of the longer comment. Many of the statements here are just false.

    You’ll have to show me in what way. Lenski’s own experiments show that useful adaptations in bacteria come to an end. No amount of mutating, irradiating, poisoning or stressing has ever demonstrated the kind of evolution necessary to generate the kind of progress required.

    Regarding fruit-flies and bacteria:
    “My attempts to demonstrate evolution by an experiment carried on for more than 40 years have completely failed. At least I should hardly be accused of having started from any preconceived anti-evolutionary standpoint.”—*H. Nilsson, Synthetic Speciation (1953), p. 31.

    The clear-cut mutants of Drosophila, with which so much of the classical research in genetics were done, are almost without exception inferior to wild-type flies in viability, fertility, longevity.”—*Theodosius Dobzhansky, Heredity and the Nature of Man (1964), p. 126.
    .

    “A review of known facts about their ability to survive has led to no other conclusion than that they [the mutated offspring] are always constitutionally weaker than their parent form or species, and in a population with free competition they are eliminated . . Therefore they are never found in nature (e.g. not a single one of the several hundred [types] of Drosophila mutation), and therefore, they are able to appear only in the favorable environment of the experimental field or laboratory.”—*H. Nilsson, Synthetische Artbildng (1957), p. 1186.

    “Most mutants which arise in any organism are more or less disadvantageous to their possessors. The classical mutants obtained in Drosophila usually show deterioration, breakdown, or disappearance of some organs. Mutants are known which diminish the quantity or destroy the pigment in the eyes, and in the body reduce the wings, eyes, bristles, legs. Many mutants are, in fact lethal to their possessors. Mutants which equal the normal fly in vigor are a minority, and mutants that would make a major improvement of the normal organization in the normal environments are unknown.”—*Theodosius Dobzhansky, Evolution, Genetics, and Man (1955), p. 105.

    “It is a striking, but not much mentioned fact that, though geneticists have been breeding fruit flies for sixty years or more in labs all round the world—flies which produce a new generation every eleven days—they have never yet seen the emergence of a new species or even a new enzyme.”—*Gordon R. Taylor, The Great Evolution Mystery (1983), p. 48.

    http://www.pathlights.com/ce_encyclopedia/Encyclopedia/10mut10.htm

    “Mutants which equal the normal fly in vigor are a
    minority, and mutants that would make a major
    improvement of the normal organization in the normal
    environments are unknown.” —*Theodosius Dobzhansky ,
    Evolution, Genetics, and Man (1955), p. 105.

    “Mutation never produced anything new. They [mutant
    fruit flies ] had malformed wings, legs and bodies and
    other distortions, but they always remained fruit
    flies ” (Theodosius Dobzhansky in Heredity and the
    Nature of Man. New York: Harcourt, Brace and World,
    1964. p. 126.).
    Google search Dobzhansky+fruit+flies+failed+admitted

    “Mutation is a destructive, not a creative, force.
    Some mutations occur naturally, and those are probably
    the result of cosmic radiation” ( Dobzhansky 1960,
    39).
    “It can hardly be questioned that
    most visible mutations are deleterious” (Mayr 1963,
    174).

    You’ll recall that the comment I made, from which you extracted my remark on deleterious mutations, was a post on adaptations, speciation and natural selection. In order for these to have any effect or to be in action the mutations in question must have a phenotypic result. They can’t be invisible if the ratchet is to work. And when they are not invisible, they are mostly deleterious.
    ===
    The website I pointed you to to show you that there is shared doubt in biology about the efficacy of Darwinian mechanisms also quotes Behe opponent and evolutionary biologist, A. Orr saying:

    Orr begins his article by describing natural selection. He explains that there are several kinds of mutations …
    Most important, we know something about the effects of mutations on fitness. The overwhelming majority of mutations are harmful—that is, they reduce fitness; only a tiny minority are beneficial, increasing fitness.

    Orr goes on to say ….
    Most mutations are bad for the same reason that most typos in computer code are bad: in finely tuned systems, random tweaks are far more likely to disrupt function than to improve it.

    You quote one biologist against me (but not effectively) and ignore the one who supports my point while calling my view mistaken. That’s not cricket.
    ====

    I do have to bring up as well that I’ve heard it said many times that Dawkins embarrasses himself by portraying (sophisticated) philosophical arguments for God as silly. If that is true, isn’t Behe guilty of doing the same with (I think) far more technical biological issues?

    Again, you’ll have to show how. I’ve shown that Behe is not refuted, merely disagreed with. Just because his own department disagrees with him doesn’t mean he was refuted – no more than Gonzales’ drumming out disproves his case. I have argued his case and demonstrated throughout this thread why it is not refuted.

  129. Hi DL,

    It’s not that Behe’s critics just disagree. They think Behe is ignorant of the evidence, ignoring his critics, and misunderstanding the science altogether.

    And their error does not make them incompetent – just in error.

    (1) Huh? Sounds like you’re agreeing with me that there is some huge array of F1, F2, …Fn that NDE will reward, not just F. Or are you saying there are no neutral mutations?

    Huh?
    How is neutrality rewarded? What does this have to do with fitness requiring no target?

    (2) Why is this relevant? If the components of the IC mechanism existed because it was beneficial in other contexts, you’re not going to get evolution to backtrack simply by mutating the final IC mechanism in the final context.

    Yeah, you are. When you knock out one gene, in the final context, mutation will replace it quite rapidly. It seems to target it quite nicely.

    You are admitting that Behe has no disproof of NDE,

    What’s wrong with you? How many times are you going to look out your window and state the sky is blue? Let me repeat – this is science, not math – we are not talking about proofs.

    and that he is demanding NDE explain some particular details.

    You are leaving out an important qualifier and obscuring the truth with your claim about an “explanation” here to make like you didn’t misrepresent Behe previously. Yes, he wants details. He wants a testable model – you know, science – to support the claims. He is not, let me repeat again, not demanding an historical explanation of what did happen, merely a detailed, testable model outlining possible steps, likelihood and selectability to account for the claims the theory makes. There are no such models.

    This is an argument from ignorance.

    No it’s not.

    Behe’s Edge of Evolution has been reviewed in Science, Nature, on blogs and elsewhere. The scientific journals are unanimous: Behe is wrong, incompetent and ignoring refutations of his earlier works.

    There are no refutations and your continued inability to present them while blustering that they exist is telling.
    Carroll’s bluster is not evidence and instead of citing opinion why don’t you cite some facts? Like the ones that back up your claims?

    Hey, if you say “incompetent” enough times you might hurt my feelings and I might go away and let you bluff to your heart’s content. What are the probabilities of that?

  130. http://creationontheweb.com/images/pdfs/tj/j21_3/j21_3_111-117.pdf
    re: Darwin’s mechanisms/Natural Selection:

    Natural selection—irrelevant!
    The most surprising result of the ENCODE project,
    according to its authors, is that 95% of the functional
    transcripts (genic and UTR transcripts with at least one
    known function) show no sign of selection pressure (i.e.
    they are not noticeably conserved and are mutating at the
    average rate). Why were they surprised? Because man
    is supposed to have evolved from ape-like ancestors via
    mutation and natural selection. But if 95% of the human
    functional information shows no sign of natural selection
    then it means that natural selection has not been a significant
    contributor to our ancestry.15
    While this result surprised the neo-Darwinists, it is
    perfectly in line with current research in human genetics.


    re: Darwin’s mechanisms/Random variation:

    In his ground-breaking exposé of current knowledge, Genetic
    Entropy & The Mystery of the Genome,16 geneticist Dr John
    Sanford of Cornell University showed that deleterious
    mutations are accumulating at an alarming rate in the human
    population and that both natural selection and even the worst
    possible nightmare scenario of eugenics is powerless to stop
    it. This is because the vast majority are deleterious single
    nucleotide mutations that have a miniscule effect on fitness
    so natural selection cannot detect them amongst the ‘noise’
    and thus is unable to delete them.

    re: Darwin’s mechanisms/random variation and the appearance of \new\ traits:
    This astonishing discovery that
    the so-called ‘junk’ regions are far more
    functionally active than the gene regions
    suggests that probably none of the human
    genome is inactive junk. Junk is, by
    definition, useless (or at least, presently
    unused). But UTRs are being actively
    used right now. That means they are not fossils of bygone
    evolutionary ages—they are being used right now because
    they are needed right now! If other animals have similar
    DNA sequences then it means they have similar needs
    that we do. This is sound logic based upon observable
    biology—as opposed to the fanciful mutational suppositions
    of neo-Darwinism.7

    7. Mutations have been intensively researched in medical laboratories
    over many years now and almost all of them are deleterious. The only
    exceptions appear to be those that disable an existing mechanism such
    that some specialized result is beneficial in some specialized conditions.

  131. Charlie,

    You quote one biologist against me (but not effectively) and ignore the one who supports my point while calling my view mistaken. That’s not cricket.

    I thought you were saying that most mutations are deleterious, and to point out that it’s more complicated than that I thought it would be fastest to quote from the site you referred me to earlier.

    But maybe you are saying that most mutations that result in phenotypic changes are deleterious, and if that is the case I would say that most biologist appear to agree, but that Orr’s correction on his website (“In animals and plants, for example, most of the DNA does not seem to be essential so that the overwhelming majority of mutations are neutral and a smaller number—those that interfere with an essential function—are deleterious.”) is important.

    That’s because as you later say:

    If mutation is most likely deleterious, as it is, and the mutants are being removed from the general population, then NS, complexity ratchet that it is, would eliminate the mechanism for mutations.

    But if, as Orr points out, mutations are happening overwhelmingly in a manner that NS cannot see them, then the mutational mechanism would not be eliminated by NS because NS rarely has the opportunity to do so. Furthermore, even though it is true that when mutations occur that have a phenotypic effect they are overwhelmingly deleterious (and hence eliminated through NS), some are indeed beneficial, and the mutation (and presumably the susceptibility to mutation) are selected. Orr’s clarification isn’t insignificant – it explains how the mechanisms would work according to Darwinian principles in a way that your (uncorrected, per Orr) definition has led you to conclude is impossible.

    I have to say that a lot of the criticism I am reading of NDE (Behe, some of the sources you cite, etc.) reads to me like a fringe group of engineers claiming that a Boeing 747 cannot fly because of all its imperfections. (What is it about the 747 that seems to make everyone use it in biological similes? I don’t know, but I can’t stop myself either.) Admittedly, the 747 is not perfect, can be improved, and sometimes fails outright. But it can fly, and that’s a brute fact.

  132. Hi Tony,
    Your comment is good and I agree with your logic except you ignore at least one more problem. I was talking about first life, the initial populations on Earth as discussed with DL, and as RM/NS is supposed to be getting up and running. In this situation, as described in a fair amount of detail in the comment from which you are quoting, there will be no invisible mutations. The argument for neutral mutations depends upon there being non-coding DNA in which mutations can occur with no effect to the phenotype. Non-coding DNA, however, does not exist in the initial population because it, itself, is accumulated through genetic mutation. In other words, there is no place for them to hide. The argument to DL stands. He’s got first life reproducing so quickly and efficiently that it covers the planet, but so inefficiently that it has mutated into thousands of species. This requires mutations evident in the phenotype. But this rapid rate of expressed mutations would more likely have wiped out his first life than create all these new species – especially with no place for these mostly deleterious mutations to hide.

    On the other hand, I couldn’t find a reference to this fact before so I didn’t want to make the case even though I have read it and think it true, but even in non-coding DNA the mutations are just as deleterious as they are in the coding regions.
    thttp://www.pnas.org/content/100/23/13402.full.pdf
    pstream and

    Our estimate
    of the genomic deleterious point mutation rate for noncoding DNA
    (0.22 per diploid per generation) is similar to that for coding DNA.

    Mammalian populations therefore experience a substantial ge-
    netic load associated with selection against deleterious mutations
    in noncoding DNA. Deleterious mutations in noncoding DNA have
    predominantly quantitative effects and could be an important
    source of the burden of complex genetic disease variation in
    human populations.

    ===

    But maybe you are saying that most mutations that result in phenotypic changes are deleterious, and if that is the case I would say that most biologist appear to agree

    True enough. I was saying that – as per the discussion of natural selection. But, as above, you can see that I am saying it for mutations overall as well.

    Here’s another small correction.

    But maybe you are saying that most mutations that result in phenotypic changes are deleterious, and if that is the case I would say that most biologist appear to agree, but that Orr’s correction on his website (“In animals and plants, for example, most of the DNA does not seem to be essential so that the overwhelming majority of mutations are neutral and a smaller number—those that interfere with an essential function—are deleterious.”) is important.

    It was not Orr’s website but Larry Moran’s and Orr does not correct himself, but is disputed by Moran. Does Orr correct himself on his own website? I don’t think you are saying that, are you?

    But if, as Orr points out, mutations are happening overwhelmingly in a manner that NS cannot see them, then the mutational mechanism would not be eliminated by NS because NS rarely has the opportunity to do so.

    Orr wasn’t the one pointing this out. But you are right, NS is not eliminating the deleterious mutations, visible or invisible, because NS isn’t really in operation for 95% of mutations and traits – and so does not provide DL’s necessary complexity-ratchet.
    So what happens in actuality is genomes degrade and populations go extinct rather than improving and increasing in “complexity”.

    Orr’s clarification isn’t insignificant – it explains how the mechanisms would work according to Darwinian principles in a way that your (uncorrected, per Orr) definition has led you to conclude is impossible.

    No, Orr is not correcting my point. No, I did not conclude impossibility. Over and over again I make the case one of probability against the realistic predictions of the theory – not against possibility.

  133. Hi Tony,
    After finding the necessary terms “silent mutations”, “nearly neutral theory”, and “slightly deleterious” and spending a couple of hours going over papers on these I confidently aver and restate, without qualification to phenotype or anything else, that most mutations are deleterious. In humans, 80%, with 19% apparently neutral. Of that 80%, less than 20% are “slightly deleterious”.
    In other tests, with other presumptions the deleterious mutations in bacteria, for instance are about 67%.
    The neutral theory has been amended to the “nearly neutral” theory and most relevant research shows that there really is very little that can be said to be truly (provisionally, at this time) neutral.
    The neutral theory was, again, a fix on the failure of the NDE when selection was seen to be ineffective and the number of non-beneficial accumulated mutations had to be accounted for. The realization has been hampered and still seems slow because of the obvious presumption and prediction of the theory that NS daily scrutinizes evolution and eliminates every variation which is the least bit deleterious.

  134. Tony,
    I came back to see if my links have been rescued from the filter and glanced back up and saw this:

    But it can fly, and that’s a brute fact.

    Are you serious about this criticism and observation? Behe’s complaint seems to you to be analogous to actually observing a flying 747 and claiming that it can’t fly?
    That’s the whole point of all of this – you guys are saying it flies but when are we going to see it in the air? This is like the preposterous claim that “evolution” is more and better verified than gravity. Well, we can see gravity at work every single second of every single day and we can test it at the drop of a hat – literally. NDE is a theory explaining a body of data – it is not an observation like seeing a plane fly. And it is a theory which Behe is challenging with IC and his newer arguments. He does not even ask you to point to the flying plane, he’s just saying show me a model that scientifically demonstrates that it could. You are missing the entire point if your caricature is meant to accurately represent the way the criticisms appear to you.
    But you made similar statements about trends, definitions and your reading of ID early on in this thread so I suggest you might want to rethink your perceptions on this.

  135. Charlie,

    In my last post I wrote that Orr was the author of the comments and blog when I meant to credit Moran. I think you figured this out halfway through, but I apologize for jumbling their names.

    Previously you wrote:

    No, I did not conclude impossibility [regarding my statement that Darwinian principles could explain all biological structures]. Over and over again I make the case one of probability against the realistic predictions of the theory – not against possibility.

    I understood your argument to be that Darwinism was impossible as an explanation when you wrote this:

    Darwinism was disproved out-of-the-box but it didn’t matter: [You then quoted an opinion piece for two paragraphs, which I’m not including here for space considerations.]

    and this:

    NDE predicts sterility. Just because it didn’t happen doesn’t mean NDE doesn’t predict it. It just means NDE does not accord well with the facts and has to be doctored with empirically-weak solutions. Natural Selection just does not do the trick. Of course, you need to ignore the extinction problem so you can keep Natural Selection (another empirical failure on its own) so you can keep your complexity ratchet.
    But you don’t get any of it. Natural Selection is bust, Dawkins’ escape for the failure of randomness and chance – his “oh, but evolution is anything but random” mantra – is bust, and so is your case for complexity, because you are left with nothing but randomness and drift. And lots of patches.

    Also, isn’t supporting Behe’s contention that IC represents an explanatory boundary for NDE basically saying that Darwinian mechanisms could not have produced certain biological structures – that it’s impossible for Darwinian mechanisms to have created something like the bacterial flagellum? How is that Behe’s position, that Darwinian principles cannot explain the existence of IC structures, can be true and that it remains possible that Darwinian principles can explain all biological structures?

    NDE is a theory explaining a body of data – it is not an observation like seeing a plane fly. And it is a theory which Behe is challenging with IC and his newer arguments. He does not even ask you to point to the flying plane, he’s just saying show me a model that scientifically demonstrates that it could.

    I think that Lenski’s experiment demonstrates experimentally that complex evolutionary adaptations occur through random mutation (clarified as contingent mutations as opposed to cumulative ones) and natural selection. The history of biology over the last 150 years is basically one of finding confirming evidence for Darwin’s original theory. It appears to me that Behe sees the 747 flying but is claiming something like it couldn’t have taken off from any known runway.

    Lastly, I’m not sure about your links to the percentage of mutations that are deemed deleterious. It appears that the quote I referred to from Moran (incorrectly attributed to Orr) contradicts your assessment (although Orr’s original remarks accord with your final conclusion). This appears to be a fine point of biology that I imagine would be clarified with greater technical precision – which organisms we’re talking about, genomic mutations, junk mutations, etc. I find it hard to believe that all these trained biologists would be blithely going on with their research and not have done a fundamental mathematical assessment that the frequency of random mutations makes life impossible.

  136. Hi Tony,

    Also, isn’t supporting Behe’s contention that IC represents an explanatory boundary for NDE basically saying that Darwinian mechanisms could not have produced certain biological structures – that it’s impossible for Darwinian mechanisms to have created something like the bacterial flagellum?

    No. This has been explained many times.

    How is that Behe’s position, that Darwinian principles cannot explain the existence of IC structures, can be true and that it remains possible that Darwinian principles can explain all biological structures?

    It’s a probability argument – not an impossibility argument.
    You quoted me above, but I have also said:

    If the final is the case then it provides no challenge to IC and we return again to its probability in the real world and do an empirical search for this happening or being plausibly outlines as per Behe in the literature.

    Cooption might be Darwinian. Answer the empirical challenge Behe posits and the probability challenge other biologists raise and show that it debunks his claim.
    You’ve claimed it exists, that we’ve found it, that it explains IC, etc.. Now show that you are not bluffing.

    Yeah, I know DL, everything’s a strawman when you disagree with it.
    Have you noticed any of the times that I’ve said my probability case does not provide a contradiction to NDE? Not yet? Read again then.

    If this was your goal, as you said earlier, this is not the way to achieve it. You have made no case for the probability of complexity short of presuming first, against facts, what you are supposed to be showing.
    No, I conclude that even you can see that NDE does not preferentially predict complexity. Rather, it most assuredly preferentially predicts sterility, if not at least simplicity.
    Interestingly, this is the thesis behind the books like Rare Earth which argue that even if there is life out there it is very likely to be very simple – the odds are simply against your claim.

    AND he’s presenting both and empirical and probability argument against such explanations. Like his arguments or don’t – but tell the truth about them.

    ====

    I think that Lenski’s experiment demonstrates experimentally that complex evolutionary adaptations occur through random mutation (clarified as contingent mutations as opposed to cumulative ones) and natural selection.

    Why do you think this? What complexity evolved in Lenski’s experiments? How do you square the limits he found and the drying up of interesting adaptations with the Darwinian claim that this process accounts for all of the rise in incredible complexity form “simple” first life to the diversity of the biosphere today?

    The history of biology over the last 150 years is basically one of finding confirming evidence for Darwin’s original theory.

    That’s the interesting authoritative assertion but it is exactly what I am arguing against and what you ought to be demonstrating rather than declaring. You challenged me on Dobzhansky’s fruitflies and Lenski’s bacteria, but you have no answer to the empirical findings. You claim again
    that Darwinian mechanisms are being confirmed and ignore the very source you’ve been citing that says that Darwin’s theory of Natural Selection is not supported by observation, the existence of biologists like MacNeill and Provine, the existence of theories like “Neutral Theory” and then “Near Neutral Theory”, the existence of Punk Eek, the fact that 95% of our genes do not show evidence of selective pressure, the fact that our genome is 97% percent functional rather than 97% junk, the continuing attack on NS, the failure of population genetics to support the theory, etc.
    You avoid all these by effectually claiming that whatever evolutionary biologists come up with, no matter how speculative (emergence, self-organization, evo-devo, for example) as any kind of explanation is really just Darwinism anyway. This demonstrates your commitment not to the scientific theory, or the mechanism involved, but to the metaphysical aspect. As long as it is metaphysically “natural” it’s good enough for you and it qualifies as confirmation.

    I find it hard to believe that all these trained biologists would be blithely going on with their research and not have done a fundamental mathematical assessment that the frequency of random mutations makes life impossible.

    Join the club – that’s why paradigm shifts take so long. When you’ve only got a hammer everything looks like a nail.
    They’ve been ignoring and sweeping the math under the carpet since Mendel, Haldane, Hoyle and Wistar.
    You’ve stated many times that I am wrong, mistaken, ignorant, etc. You have yet to show one instance.

    Lastly, I’m not sure about your links to the percentage of mutations that are deemed deleterious.

    You ought to have a better argument against it than that those who wouldn’t want it to be the case don’t investigate and show that it is the case. Especially since this is new evidence against the neutral theory – now dubbed the “near neutral theory” (because the “neutral”part is false) – which is only about 40 years old and has only relatively recently come into its own ascendancy. Every generation of biologists raised on one theory must be supplanted by the next coming along to promote the next version.

    It appears that the quote I referred to from Moran (incorrectly attributed to Orr) contradicts your assessment (although Orr’s original remarks accord with your final conclusion).

    Sure it does. He knows that Natural Selection is not driving evolution (Darwinism is falsified) so he appeals t neutrality. But he even tells you what he means by “neutrality” – those mutations occurring in unexpressed regions of the genome. The links I’ve provided show experimental evidence that even these mutations are not neutral. They cause the genome to bear a negative load and, because Natural Selection cannot see them, cause even a greater chance of extinction and genomic failure – they argue even more strongly against the complexity ratchet and for my sterility case.
    It is a matter of must-need theory to say that these “silent” mutations will spring forth with complexity solutions and this theoretical desire is, as always, belied by the empirical evidence.
    What’s more, ENCODE now shows us that almost all (so far) DNA is, in fact, transcribed. The fact that it doesn’t all result in protein production has hidden the fact that any change to DNA is an expressed change. And as all the sources say, when a mutation lands in an area of DNA which is expressed it is overwhelmingly more likely to be negative than positive.

    Every new fact argues against Darwinism, not for it. All you have on your side are “latest claims” cases which have yet to be thoroughly vetted and debunked – like DL’s “IC evolved” claim. Since there’s no shortage of these it does take time to get around to them. For instance, the fact that even “silent” mutations are deleterious has been lurking under the surface for about twenty years and nobody seems that keen on putting that information on your lunchtime news program with the discovery of the Hobbit.

    For this reason I can’t be expected to answer every literature bluff that comes my way, and if a real biologist steps in here with specialized knowledge and head-spinning jargon I will have to bow to his superior knowledge. This will not make Darwinism true, however. But looking at the real information instead of press releases and talk.DOT rhetoric has given me confidence that even the bluffs I can’t solve myself are just that. If they weren’t I wouldn’t be able, as a complete laymen, to debunk so many claims with nothing more than Google and a slight OCD.

  137. Since you merely restated the contention that since Darwin we have seen a basic series of confirmations of his theory I will repost what I said before and defended against your (only?) rebuttal – that I don’t know what I’m talking about.

    To call the processes “Darwinian” is merely to bow before the paradigm and commit the errors discussed above. You are just accepting that everything that can be seen as a scientific explanation ought to be rolled under the “Darwinian” umbrella so that the theorists can maintain their position that they are right and always have been. The evidence for the last 150 years has all been against the grand theory even though its proponents keep claiming mountains of evidence have proven it.

    Abiogenesis does not happen, has never been seen to happen, is not an empirical observation, and defies all explanation. Sorry, but claiming “abiogenesis has nothing to do with “evolution” will not wash. The theory is a metaphysical necessity and, as Darwin mentioned of it in a different context, if it fails at all it fails completely. As a grand narrative doing what its only real purpose is – exclude God – it fails at OOL so there is no reason to keep supposing (against the evidence) that it holds after OOL. On a less ambitious note the failure of OOL explanations takes away the raw material that Darwin needs. You have no idea if the theory can be allowed a first life, a first replication and a first competitive population.
    There is no explanation of the simplicity or complexity of this first life and no knowledge then how evolution was to proceed from its inception. With no starting point how can there be a theory of what proceeded from that starting point or how it did?

    Extinctions do not happen in a Darwinian fashion. His entire case against catastrophism was a failure from the beginning and was demanded by his theory. He had to ignore the true evidence of extinctions in order to support the theory.

    There is no Tree Of Life – as researchers admit now, it was a useful fiction which can be abandoned now that the biological community is solidly onboard.

    The fossil record does not and never did support gradualistic evolution and uniformitarianism. It was waved away at the time and explanations that try to account for it are not Darwinian.

    Darwinian adaptations do not explain Margulis’ endosymbiosis (even though she avers, after stating that she is firmly not a neo-Darwinist, that she remains a Darwinist (philosophical position)). They do not explain the necessary complexity at the beginning of life, the evidence that first life would have been more complex and getting simpler, that eukaryotes may have preceded their more simple kin, the prokaryotes, etc. Indeed, people like Doolittle, studying this side of the issue, dispute the Margulis patch which is getting wide acceptance after many years of abuse as the community realizes it can take her idea and stitch it onto the original.

    When tested in fruit flies and bacteria over years upon years Darwinian processes dry up and do not generate the kind of progress required by the theory. Extrapolated, the changes observed could never account for the diversity of life in the time span allowed – or many times that.

    The math has never worked, and this has been demonstrated since at least Wistar in the 60s and has been ignored by biologists the whole time – just as they ignored the obvious empirical and mathematical case of Mendel’s for 50 years.

    It fails every test and yet persists. Why? Because, like you demonstrated above, the proponents need it and can bundle every explanation into the package and claim them as evidence, no matter how contradictory.

  138. Charlie,

    Thanks for your prompt reply. I apologize that my own have been more sporadic.

    Regarding possibility and probability I was using the term impossibility as a shorthand for “so improbable that it need not seriously be considered.” If you substitute the longer version in place of the previous ones where I used “impossible / possible” do you think that makes a significant difference? And at this point I have to say that I may need a few sentence summary of what it is that you think Behe is arguing for (as opposed to what I say I think he is arguing for), especially in light of your recent statement that “Darwinism is falsified.”

    You wrote:

    What complexity evolved in Lenski’s experiments? How do you square the limits he found and the drying up of interesting adaptations with the Darwinian claim that this process accounts for all of the rise in incredible complexity form “simple” first life to the diversity of the biosphere today?

    I read the entire Lenski paper this morning prior to my last post. (Although some commenters say it’s technical I didn’t find it to be so unreadable – some of the graphs were inscrutable to me and some of the technology used I am not familiar with but most of the concepts I think are pretty accessible.) So, I don’t know what you mean by the limits that he found, nor the drying up of interesting adaptations. (As I read the paper, Lenski set out to see if E. coli could mutate the ability to consume Citrate in an oxic environment, an inability that is a defining characteristic of the bacteria. The experiment was basically a test of this potential mutation – the experiment was highly limited (in terms of available nutrients), and the environment offered a control / experiment response to this adaptation; Lenski wasn’t looking to see what mutations in general could arise – he was very specifically creating an experimental environment where Selection was geared to reward a mutation to process Citrate in an oxic environment.)

    So, regarding your question, the complexity that evolved was the ability to process Citrate in an oxic environment. I don’t believe that any other E. coli that we know of have this ability. Lenski has shown that, under the right circumstances, E. coli can mutate to process Citrate. (Incidentally, the mutation is not a single one – the ability relies on a prior mutation that enables the second mutation to have its phenotypic effect.) This is, under any definition I can think of, an instance of evolved complexity.

    Some of your comment speculates on my prior commitments and lack of curiosity, etc. I don’t agree with these assessments, but I do think that this is always a fair caution:

    Join the club – that’s why paradigm shifts take so long. When you’ve only got a hammer everything looks like a nail.

    And of course, I hope that you consider your own beliefs to exactly the same extent that you wish I consider mine. (Despite what I gather you perceive of my tone and sometimes my motives, I do respect you and your opinions, and don’t think that you are wrong for holding them. I do not, and I find the difference between us fascinating.)

    Since you brought up Mendel, one interesting aside – I was talking to cancer researcher this weekend at a party, and I was asking him about amino acid mutations (because of this discussion), and he remarked during the discussion that Mendel was basically right but that it was widely considered that he had faked some of his results. I don’t mean to impugn Mendel (whose work I can’t help but admire) with such an unverified remark, but this was the first I had heard of any such criticism.

    But he even tells you what he means by “neutrality” – those mutations occurring in unexpressed regions of the genome. The links I’ve provided show experimental evidence that even these mutations are not neutral.

    Here I think you are missing a crux to Darwinism revealed wonderfully through Lenski’s paper. Lenski’s experiment does demonstrate that a prior, unrecognized mutation enabled a second mutation to effect the phenotypic result of citrate processing in an oxic environment. So, despite your attestation above, sometime seemingly neutral (or, I imagine, only somewhat deleterious) mutations can ultimately have jackpot effects from a second mutation.

    Lastly, I don’t, despite your characterization, think that you’re “ignorant” or “don’t know what [you’re] talking about.” I do agree that most of our disagreements come from prior philosophical assumptions, but that shouldn’t stop us from testing those assumptions.

    If you don’t respond soon, I’ll try and gather what I think are good, confirming evidences for Darwin’s theory. I would bet that you’ve heard before what I’ll pull together, but I am interested to know why you find them unpersuasive.

  139. Hi Tony,
    Thanks again for your comments.

    Regarding possibility and probability I was using the term impossibility as a shorthand for “so improbable that it need not seriously be considered.” If you substitute the longer version in place of the previous ones where I used “impossible / possible” do you think that makes a significant difference?

    It does indeed. As you’ve noted from DL the issue is of huge inportance as he continually tries to scarecrow the topic by saying “Behe hasn’t proven that it is impossible for NDE to achieve such and such results…”.
    But that is not the point and that is not science. As you will no doubt point to when you go to show the evidence you find compelling for NDE, there is no knock-down proof available. You will point to a “mountain” of evidence, a “cumulative” body that demonstrates the great probability that your case is true. You will, with Darwin, infer that the explanation you accept is the most consistent with the evidence. But you will not have proof. And you will not supply evidence that it is impossible for you to be wrong. When you guys keep putting the opposite claim in the mouths of your opponents, or in DL’s case, refuse to even accept that there is an argument if there is not “proof” of “impossibility” you are stacking the deck in your own favour and setting the bar so high that it can not even be approached by such a speculative, historical science as origins.
    Even with me guarding against such creep notice the burden you carry is very much lower. All you have to do is argue plausibility of mechanisms, the mere possibility that NDE can do what is claimed for it makes it fact for your side. Never mind that you could show that NDE can do everything its proponents claim and you could never show that it did. Nonetheless, nobody puts that burden on you. My side must show not that you can’t prove history worked like you claim, but that it is very unlikely that it did, that the processes in question do not evidence the ability. And then, “whammo”, I must also prove that it is impossible, or defend a charge that that is my claim. Universal negatives are notoriously hard to prove. I’ll stick to the inference to the best explanation.

    With regard to Lenski and citrate, the bacteria in question already have the ability to metabolize citrate in the wild. They are also known to do so under oxic conditions, as he was testing for, in other experiments. This was not a novel finding nor is it something the E. coli does not already have the ability to do. The genes are already present and prepared to do this function and a minor tweak is all that is needed. The problem is most likely that they have been broken – resulting in an inability to get the citrate into the cell. This happens a lot and is basically what random mutation/natural selection is good at -breaking things.
    So the E.coli in the lab had to get an enzyme that would take care of this transport under oxic. They did not have to evolve a new function, an ability to metabolize a foreign substance, make a new machine, increase complexity, etc. It only had to repair a defect. Selke showed, as I’ve argued previously, that this is not so difficulty when one mutation is required. It is much more difficult when two are, and not likely to ever happen when three are required. This experiment backs up his findings – two mutations were needed to (likely) restore a lost function. As the rarity of Lenski’s result shows, and as he surmises himself by the rarity, this “evolution” was likely a two-step problem requiring an earlier mutation. This exactly backs up Behe’s EoE argument and Ralph Seelke’s findings. When two mutations are needed, and are not independently selectable (near neutral or “slightly” deleterious) you have to rely upon chance to generate them. And chance takes much time and great resources. In this case to do something very simple, which the bacteria is already known to do, and for which it already has in place all or most of of the necessary mechanisms (odd that, if RM and NS were actually at work here, since “Evolution” can’t see into the future and predict a need – teleology being streng verboten).
    By the very fact that all the other mechanisms for the transport and metabolism were already in place we see that the complexity is not generated in this experiment but was pre-existing. Lenski is showing that to evolve something very simple it takes multiple mutations. Lenski himself is showing that achieving complexity is not something NS and RM are likely to do.
    Behe and Snoke made this point in 2004, discussing the time and populations required to produce one, two or a few mutations without guidance. They were chastised because, of course, there are lots of bacteria and they have had lots of time. But, of course, the same principle applies to all other organisms, all of which are supposedly evolving from bacteria, and these organisms have neither the time nor the population resources that bacteria have had – and yet the complexity generated is necessary orders of magnitude greater than a few mutations.

    ===
    So, what does Behe argue for?
    In 1996 he used the Irreducible Complexity argument to demonstrate two things: 1) there are biological machines which require each of their parts in order to function. He used this argument to show that they can not be built piece by piece through selectable stages toward the end function. The stages on the way to completion do not function in the end manner and so cannot be selected.
    2) He described with reference to common sense and the literature the difficulty posed to exaptation. The more complex a machine the less likely that it has a functional precursor performing some other (dispensable job) and the less likely the ability to move from that precursor to the end product. How, in fact, are you going to do this without reverting to step-by-step Darwinian mechanisms again?

    In his paper with Snoke, and then inEdge Of Evolution he constructed the empirical case against chance mutations arriving at complex end products. He found that RM could, by chance, and with a lot of time and resources, hit upon two necessary simultaneous mutations, or, equivalently, get them sequentially (if the first is near neutral and not extremely deleterious). This kind of mutational event is rare, but does occur where resources are great (Lenski demonstrates). He then uses the rarity to calculate the odds of this happening. Then, by studying other acquired traits he extrapolates from the rarity to determine that either multiple mutations or mutations of equal difficulty to multiple mutations are necessary for even simple advances (Lenski concurs).
    He then discusses how great complexity (as in the IC machine she discussed previously) would require many more than one or two or even three (which is getting out of reach of probabilities) mutations. He points out that the kind of complexity that life exhibits is out of reach of the observed mechanisms. Again, he can’t prove it is impossible, he can only show its extreme improbability, giving what we know and not arguing from ignorance.
    This now loops back in the cumulative case to buttress his design inference in the case of IC. He has been shutting the door to the supposed rebuttal that it is reasonable to expect the multiple mutations necessary to occur simultaneously and he uses the empirical evidence to show that we can’t expect them to occur and be preserved sequentially either.
    He does not have to argue from deleterious mutations or mutational rates because he is arguing from observed data – in the field and in experiments like Lenki’s.

  140. Citing Lenski’s 2002 paper (via Behe):

    Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has declined substantially over this period … Instead, the pronounced deceleration in its rate of fitness improvement indicates that the population early on incorporated most of those mutations that provided the greatest gains, and subsequently relied on beneficial mutations that were fewer in number, smaller in effect, or both”

    de Visser and Lenski 2002. Long-term experimental evolution in Eschirichia coli.

    Behe sums up in EoE:

    A host of incoherent changes have slightly altered preexisting systems. Nothing fundamentally new has been produced. No new protein-protein interactions, no new molecular machines. As with thalassemia in humans, some large evolutionary advantages have been conferred by breaking things.
    … Breaking some genes and turning others off, however, won’t make much of anything. After a while, beneficial changes from the experiment petered out. The fact that malaria, with a billion fold more chances, gave a pattern very similar to the more modest studies on E. coli strongly suggests that that’s all Darwinism can do.

    page 142

  141. re: Mendel. Yes, I heard his numbers were too perfectly in keeping with the math of the theory to have been experimentally derived. Wherever I read this first had attributed the likely fudging to an assistant. I don’t recall why.

  142. re:

    And of course, I hope that you consider your own beliefs to exactly the same extent that you wish I consider mine.

    Of course I do. Being the “creationist”, “science denier”, “IDiot”, “whack-job” in these conversations my motivations and beliefs are front and centre every time the subject arises. I have to consider them each and every time. I think it only fair that both feet wear the shoes (I know you are a fan of such fairness) and that parties on both sides of the debate, and not just one, understand that we all (professional biologists nonetheleast) view the same evidence through different filters and come to our own conclusions.
    What I am hoping to point out is that hand-waving statements like “Behe is a liar” and “Behe has been refuted by so-and-so” have a lot more to do with looking through these filters than they do the objective reality. Appeals to authority do not accomplish much when the filter is not taken into account and when I can so easily demonstrate that the filter has distorted the presentation not only of the layman but of the professionals distilling it.

    On the other hand, I have said before and am quite sure that I do not yield the single use hammer that you atheists must, by necessity. In every discussion I have far more options open to me than you all have. Because God is a God of reason and order I have no fear of secondary causation. When it is in play, or when it is evidenced I am perfectly at home recognizing it. When the “natural” is all that is evidenced then I have no reason to deny it. When matter in motion seems to be the only formal or efficient cause then that’s all I need to conclude. I never have to deny any evidence of such. Indeed, I don’t even need ID or special creation. Mike Behe, Dean Kenyon, Michael Denton, David Berlinski, etc., didn’t either. It just so happens I can take the results and implications of any scientific endeavour and my world-view is not damaged in the least.
    Atheism, on the other hand, requires the hammer. Materialism is your world view – science, by definition, must have access to everything that exists for you, even though it is at a rudimentary stage right now. Not one ounce of non-natural causation can be recognized, no divine foot is allowed in the door, not an inkling of non-material causation can be admitted. As Lewis said, one can not guard his atheism too carefully.

  143. Tony,
    It occurs to me now that we have been reading the same Lenski paper so I should point out that the drying up of evolutionary change, the existence of citrate-metabolizing aerobic bacteria, the findings of citrate metabolizing in vitro, and the extreme rarity of this single, simple two-mutation process are all pointed out in the original.
    http://www.pnas.org/content/105/23/7899.full

    Also, it is worth noting that every possible single point mutation has been explored many times over in these e. coli lines and this two-step process was stumbled upon only once, was the most significant finding of his twenty year study, and relied upon a mechanism with which the bacteria was already “not indifferent to”.

  144. Charlie,

    Regarding probability, possibility, and the burden of proof I understand that we’re ultimately talking about probabilities. And I don’t think anyone is asking you (or Behe) to prove the impossible, but to justify methods and conclusions. This is especially difficult to sort out in a discussion like this because I don’t have the professional expertise to evaluate the appropriateness of Behe’s methods, and Behe has either chosen to not or is not able to submit his conclusions to those who do have the professional expertise. We either have to accept a) a conspiracy among 99% of Behe’s peers, b) the gross incompetence of 99% of Behe’s peers, or c) Behe is in fact using method and making claims that peer-reviewed trade journals fairly reject.

    With regard to Lenski and citrate, the bacteria in question already have the ability to metabolize citrate in the wild. They are also known to do so under oxic conditions, as he was testing for, in other experiments. This was not a novel finding nor is it something the E. coli does not already have the ability to do. The genes are already present and prepared to do this function and a minor tweak is all that is needed.

    The bacteria in question have the ability to metabolize citrate in the Petri dish (not just the wild) – what they definitely did not have was the ability to transport it across the membrane in an oxic environment. That was what the experiment was geared to observe – whether or not the bacteria would, through random mutation and natural selection, evolve a transport mechanism that they did not possess. (But you go on and say as much later, I just think that you imply otherwise in the paragraph I just quoted.)

    In your second sentence above, do you mean that the E. coli that Lenski was experimenting upon had been observed to transport and metabolize citrate in other experiments? If so, do you have this reference?

    Lastly, you characterize the mutation as a “minor tweak,” but Behe characterizes it as “an improbable series of mutations.” [ Lenski’s Amazon page, http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O%5D. Because the ability to generate the enyme that enable transport of Citrate through the cell membrane relied upon two mutations, I think I agree with Behe that it does not represent a minor tweak.

    Where the basic criticism comes down on Behe, and that he seems to ignore in his response to Lenski’s experiment, is that the E. coli in question do not appear to have developed the two mutations required simultaneously. Behe’s argument against NS and RM are based on simultaneous mutations for multiple point mutations, but Lenski’s experiment seems to indicate that simultaneity of mutations is not, in fact, a necessity. I haven’t seen Behe address this criticism of his mathematical analysis, but I can’t imagine he would leave it unanswered – do you know if he has answered it, and if so, do you have a reference?

    Regarding your comment about the drying up of evolutionary change I don’t know if this is meant as a further criticism of NDE. Stable environments are supposed to, I believe, lead to a lessening of evolutionary changes as NS effects changes that leave those organisms better adapted to that stable environment.

    The last two paragraphs that begin this way…

    On the other hand, I have said before and am quite sure that I do not yield the single use hammer that you atheists must, by necessity. In every discussion I have far more options open to me than you all have. Because God is a God of reason and order I have no fear of secondary causation.

    … reads to me as gratuitous. I always wonder why some folks can’t allow that skeptics could have come to their philosophical conclusions honestly. I think it would more productive (and charitable) for me to allow that you have not come to your theistic conclusions because you’re stupid, and for you to allow that I have not come to mine because I have pre-committed myself to guarding something like philosophical materialism.

  145. Hi Tony,
    Excuse this if it is terse, I just lost my entire response.

    We either have to accept a) a conspiracy among 99% of Behe’s peers, b) the gross incompetence of 99% of Behe’s peers, or c) Behe is in fact using method and making claims that peer-reviewed trade journals fairly reject.

    This is not an exhaustive list of options at all. I’ve already explained previously why there need be no conspiracy or incompetence, but that doesn’t mean the rejection is fair.
    Here’s what happens when Behe approaches journals – he is told, basically, “we are committed to the paradigm, better luck elsewhere”.
    Indeed, check out this response:

    As you no doubt know, our journal has supported and demonstrated a strong evolutionary position from the very beginning, and believes that evolutionary explanations of all structures and phenomena of life are possible and inevitable. Hence a position such as yours, which opposes this view on other than scientific grounds, cannot be appropriate for our pages.

    The journal already knows what kinds of answers it will countenance and, from a philosophical position, that all of nature can be thus explained.
    http://www.arn.org/docs/behe/mb_correspondencewithsciencejournals.htm

    As Behe answered Coyne on his blog with regard to burden of proof:

    So even though “we may forever be unable to envisage” how unintelligent processes could produce some “dauntingly complex” system, Coyne is not willing to concede that maybe, just maybe, unintelligent processes did not produce them. Rather, ID proponents apparently are assigned the burden of proving that no one could even imagine a pathway. Good luck. What are the chances that a manuscript on intelligent design submitted to a science journal would be published if a fellow with his views, quite common in the science community, were a reviewer?

    http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2?_encoding=UTF8&cursor=1179182203.215&cursorType=after

    And Behe certainly has been critiqued, soundly, by professional biologists – far more so than had he merely published a paper. As you ahve seen from above responses, Behe is well aware, as am I, of these critiques. As my answers have shown, they don’t even address his real claims (evidenced by you, DL, talk.DOTs, Judge Jones, etc.) let alone refute him.

    The bacteria in question have the ability to metabolize citrate in the Petri dish (not just the wild) – what they definitely did not have was the ability to transport it across the membrane in an oxic environment. …
    (But you go on and say as much later, I just think that you imply otherwise in the paragraph I just quoted.)

    Wouldn’t it be more charitable and productive not to act as though I am contradicting myself so obviously?

    In your second sentence above, do you mean that the E. coli that Lenski was experimenting upon had been observed to transport and metabolize citrate in other experiments? If so, do you have this reference?

    Yes, that’s what I am saying. We have the same reference – it is Lenksi. The ability to transport citrate in aerobic as well as anaerobic conditions shows up in vitro and in vivo.

    Lastly, you characterize the mutation as a “minor tweak,” but Behe characterizes it as “an improbable series of mutations.” [ Lenski’s Amazon page, http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O. Because the ability to generate the enyme that enable transport of Citrate through the cell membrane relied upon two mutations, I think I agree with Behe that it does not represent a minor tweak.

    Behe, Lenski, you and I all agree it is a rare occurance. That does not make it one of complexity. The likely solution here was either the over-expression of an existing enzyme which already transports citrate, or the adjustment of an enzyme which moves other similar nutrients across the membrane such that it can move citrate. In any case the ability to move citrate already exists and the mechanisms to metabolize it already exist. No new features, no new machines, nothing complex is required.

    Where the basic criticism comes down on Behe, and that he seems to ignore in his response to Lenski’s experiment, is that the E. coli in question do not appear to have developed the two mutations required simultaneously.

    What makes you think he is ignoring sequential mutations (he addresses them directly) and how would further consideration be relevant?

    Behe’s argument against NS and RM are based on simultaneous mutations for multiple point mutations, but Lenski’s experiment seems to indicate that simultaneity of mutations is not, in fact, a necessity.

    Behe’s critique is not based upon simultaneous mutations and he addresses cumulative mutations in both his books.
    Whether or not he ignores cumulative mutations:

    But I certainly do not say that multipleamino acid replacements “can’t happen”. A centerpiece of The Edge of Evolution is that it can and did happen. I stress in Chapter 3 that in the case of malarial resistance to chloroquine, multiple necessary mutations did happen in the membrane protein PfCRT. I also of course emphasize that it took a huge population size, one that would not be available to larger organisms. But Carroll seems uninterested in making distinctions.

    Carroll cites several instances where multiple changes do accumulate gradually in proteins. (So do I. I discuss gradual evolution of antifreeze resistance, resistance to some insecticides by “tiny, incremental steps — amino acid by amino acid — leading from one biological level to another”, hemoglobin C-Harlem, and other examples, in order to make the critically important distinction between beneficial intermediate mutations and detrimental intermediate ones.) But, as Carroll might say, it is a non sequitur to leap to the conclusion that all biological features therefore can gradually accumulate. Incredibly, he ignores the book’s centerpiece example of chloroquine resistance, where beneficial changes do not accumulate gradually.

    From his blog -link above.

    He is drawing his conclusions based upon empirical data regarding the actual appearance of mutations and drawing his inferences from that. He infers exactly as Lenski did and has no dispute with him – the very rarity of this feature indicates it likely required two mutations to confer the advantage. This does not depend upon simultaneity.
    About Behe’s discussions of multiple mutations:

    And for the life of me, I don’t see why that proposition — that two mutations might be needed for some adaptations, and that that would be a big evolutionary impediment — is being treated by Coyne and other Darwinists with such horror. It certainly has been discussed in the evolutionary literature in the past. In my book I quote Allan Orr remarking, “Given realistically low mutation rates, double mutants will be so rare that adaptation is essentially constrained to surveying — and substituting — one-mutational step neighbors. Thus if a double-mutant sequence is favorable but all single amino acid mutants are deleterious, adaptation will generally not proceed.” All I have done is to point to an example of the situation he envisioned, to quantify it, and to argue that it’s likely to be a fairly general phenomenon. Why the shock?

    From his blog.

    but Lenski’s experiment seems to indicate that simultaneity of mutations is not, in fact, a necessity. I haven’t seen Behe address this criticism of his mathematical analysis, but I can’t imagine he would leave it unanswered – do you know if he has answered it, and if so, do you have a reference?

    Are you saying Lenski has provided a criticism of Behe’s mathematical analysis? Where is that? Since Behe agrees with and accepts Lenki’s math and his findings I don’t see why Behe would be bothered.

    I think your link above is to this Behe response, but I will supply it as well. You will see most of your previous questions answered here:

    I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. So random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell.

    In his new paper Lenski reports that, after 30,000 generations, one of his lines of cells has developed the ability to utilize citrate as a food source in the presence of oxygen. (E. coli in the wild can’t do that.) Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it’s not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a “citrate permease” which can transport citrate from outside the cell through the cell’s membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1)

    Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.)

    It took trillions of cells and 30,000 generations to develop it, and only one of a dozen lines of cells did so. What’s more, Lenski carefully went back to cells from the same line he had frozen away after evolving for fewer generations and showed that, for the most part, only cells that had evolved at least 20,000 generations could give rise to the citrate-using mutation. From this he deduced that a previous, lucky mutation had arisen in the one line, a mutation which was needed before a second mutation could give rise to the new ability.

    I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.

    As Lenski and co-workers observe: (1)

    Such a low rate suggests that the final mutation to Cit+ is not a point mutation but instead involves some rarer class of mutation or perhaps multiple mutations. The possibility of multiple mutations is especially relevant, given our evidence that the emergence of Cit+ colonies on MC plates involved events both during the growth of cultures before plating and during prolonged incubation on the plates.

    In The Edge of Evolution I had argued that the extreme rarity of the development of chloroquine resistance in malaria was likely the result of the need for several mutations to occur before the trait appeared. Even though the evolutionary literature contains discussions of multiple mutations (5), Darwinian reviewers drew back in horror, acted as if I had blasphemed, and argued desperately that a series of single beneficial mutations certainly could do the trick. Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.

    If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did.

    http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O

    Stable environments are supposed to, I believe, lead to a lessening of evolutionary changes as NS effects changes that leave those organisms better adapted to that stable environment.

    Another black eye for the theoretical fixes. Evolutionary change does not accompany environmental change in the fossil record and “near neutral theory” is an admission of the fact that it is not environmental factors, but random accumulation, that builds up the genome.

    … reads to me as gratuitous. I always wonder why some folks can’t allow that skeptics could have come to their philosophical conclusions honestly. I think it would more productive (and charitable) for me to allow that you have not come to your theistic conclusions because you’re stupid, and for you to allow that I have not come to mine because I have pre-committed myself to guarding something like philosophical materialism.

    You are trying much harder of late, and I appreciate and respect that, but you are still too eager to take offence. There was nothing gratuitous, or ungracious about my comment and I said nothing about how you’ve come to your philosophical conclusions or your theistic conclusions. I merely pointed out that my view can accommodate every class of explanation and yours can’t. Whether we are discussing the information in the DNA, the complexity of the cell, OOL, the implications of the Big Bang, the grounding of morality, the consciousness problem, the Cambrian explosion, the argument from reason, the efficacy of NDE, etc., you can only admit naturalistic/materialistic answers. In most of these cases there are not even plausible ones, which, if they exist, are taken as evidence that naturalism is adequate, but the problem is merely shuffled off to some future discovery. And yet, like Jerry Coyne and the journal in Behe’s correspondence above, the naturalist/materialist must just presume that one day such an answer will present itself – because the option just is no option.
    This point ought to be obvious and completely uncontroversial.
    Evidence the fact that you likely now agree with the assessment above and are thinking of responding that this commitment on your part is preferable to 1) non-scientific answers or 2) God of the gaps arguments.

  146. Charlie,

    It reads to me like you are saying that scientific journals rejects Behe’s methods because they are prejudicially committed to their paradigm. Were that true I would classify it as gross incompetence – Kuhn’s The Structure of Scientific Revolutions is one of the best read and widely discussed books of the last 50 years. Uniform failure to recognize a real challenge to a scientific paradigm across every scientific journal on the subject would be gross incompetence, fair and simple.

    The ability to transport citrate in aerobic as well as anaerobic conditions shows up in vitro and in vivo.

    It sounds like you are saying that Lenski’s bacteria already had the ability to transport bacteria (through the cell membrane) prior to their mutations. That would mean that Lenski conducted a very tedious, 20 year non-experiment. I can’t believe, though, that you are refuting that Lenski’s bacteria could not transport Citrate through the membrane prior to the mutations that were observed, so, just to clarify, what you must mean is that the membrane transportation was (only) one mechanism in a more complex process that was prepared to function when this mechanism was activated. (Correct me if I’m wrong.)

    In any case the ability to move citrate already exists and the mechanisms to metabolize it already exist. No new features, no new machines, nothing complex is required.

    Why is the ability to transport Citrate through the cell membrane not a new feature of Lenski’s bacteria, which could previously not do so? Why doesn’t this (and the other parts used in the process) represent a new, Oxic-condition-Citrate-consumption machine?

    What makes you think he [Behe] is ignoring sequential mutations (he addresses them directly) and how would further consideration be relevant?

    Behe seems intent on coming up with the most improbable mathematical models for complex mutations – that mutations that require two point mutations, among other things, are most probably going to come about through simultaneous mutation (because natural selection will be at best indifferent to one of the two mutations until both exist simultaneously). Lenski’s experiment shows that one of the two required mutations has sufficient strength in natural selection to propagate in sufficient numbers until the later mutation occurs. It seems reasonable to me that Behe would need to reassess his models and wonder if his premise that contingent mutations are as improbable as his chance-based projections predicts.

    Behe continues to assert that the centerpiece example in EoE (the development of chloroquine resistance in malaria) does not accumulate gradually.

    Behe: Incredibly, he [Carroll] ignores the book’s centerpiece example of chloroquine resistance, where beneficial changes do not accumulate gradually.

    But biologists don’t agree with Behe’s statement above, nor his math for calculating the likelihood of chloroquine resistant bacteria, nor his use of his this calculation to establish the probability of mutations in other species.

    First, as we discussed earlier, the number of “resistance events” seen by researchers is almost certain to underestimate the chance that the DNA will mutate to produce resistance. Second, CQR arises from a sequence of mutations, each conferring a greater benefit than the last, with the change at position 220 one of at least three possibilities for the last step. Third, there’s no reason to assume a priori that CQR is the model for all mutations. Why should the probability of seeing the last step in this particular chain of genetic changes have anything to do with the probability of other mutations, many of which don’t even involve the pointwise substitution of one amino acid for another? This is a good time to recall Mark Chu-Carroll’s observation that Behe completely ignores gene duplication, frameshifting and all other types of genetic change besides point mutation.

    Behe assumes, or rather declares by fiat that chloroquine resistance arises by two point mutations, and he takes a bogus measurement of how likely that process is to occur and applies it to the entire history of evolution. As Nick Matzke notes, it’s his “central measuring stick throughout the book”.

    Frankly, this still dazzles me. Behe ignores the facts which are known about a subject, takes a guesstimate of one number, interprets it as something else, plugs that into a bad model which covers only a fraction of the ways that mutations can happen, and then trumpets the “discovery” that evolution is impossible. (And he gets paid for it, too.) The mixture of gall and negligence, the sheer brazen quality of this ignorance, is a wonder to behold.
    http://www.sunclipse.org/?p=133

    So the point I was trying to make earlier is that Lenski provides another instance of a contingent mutation that demonstrates how a two point beneficial mutation does occur that does not rely on the simultaneous mutation math that is the centerpiece of Behe’s criticism of NDE. Highly improbable for a given organism? Of course. As improbable as Behe contends, and so improbable as to be implausible, I don’t think so.

    Sorry still so sporadic with my replies. I have to say that I am still very much enjoying the conversation, and that I appreciate your providing so much information in your responses (even though I don’t agree with your conclusions).

  147. Hi Tony,

    Uniform failure to recognize a real challenge to a scientific paradigm across every scientific journal on the subject would be gross incompetence, fair and simple.

    I don’t agree that we have to go this far. But I am asserting that the failure is there. It seems to me that by declaring it gross incompetence, and then denying the gross incompetence could exist, you can dismiss the failure. Without a label I can show you only the facts; Behe has presented his challenge and the journals refuse to publish it. They publish rebuttals of the challenge, but not Behe’s answers to the rebuttals. Call it what you will.

    I can’t believe, though, that you are refuting that Lenski’s bacteria could not transport Citrate through the membrane prior to the mutations that were observed, so, just to clarify, what you must mean is that the membrane transportation was (only) one mechanism in a more complex process that was prepared to function when this mechanism was activated. (Correct me if I’m wrong.)

    .1) Correct, Lenski’s bacteria could not (in sufficient numbers, at least) transport citrate across the membrane prior to the mutation/s in question. 2) They were not indifferent to citrate. They were already to move it across the membrane in anaerobic conditions and they were already able to metabolize it. 3) The same bacteria have demonstrated this ability in previous experiments and in the wild. 4) They are not building an unknown mechanism. They are not starting from scratch. They are not developing complexity. Most likely they are exhibiting a very rarely expressed function which is a repair of a lost function.

    Why is the ability to transport Citrate through the cell membrane not a new feature of Lenski’s bacteria, which could previously not do so? Why doesn’t this (and the other parts used in the process) represent a new, Oxic-condition-Citrate-consumption machine?

    There are no other parts. There are only parts which previously existed. They may only be more numerous than before. They may only be moving citrate instead of another nutrient. Why would you consider this more complex than the previous state? Why would you consider this an answer to Behe’s complexity question, and why, in the face of its extreme rarity, would you consider it an answer to his mathematical case?

    Behe seems intent on coming up with the most improbable mathematical models for complex mutations – that mutations that require two point mutations, among other things, are most probably going to come about through simultaneous mutation (because natural selection will be at best indifferent to one of the two mutations until both exist simultaneously).

    He’s not intent on this. He’s telling you what the odds are when this is the case. He is describing why this would most likely and most often be the case and he is describing why this is a challenge to evolution. Everyone agrees with him, from Lenski to Orr. The very fact that Lenski concludes that this rare event is rare because it likely required two mutations demonstrates Behe’s case.

    Lenski’s experiment shows that one of the two required mutations has sufficient strength in natural selection to propagate in sufficient numbers until the later mutation occurs.

    And when it does so it does so very rarely. And, as Behe said in EoE, this is about the limit – two random mutations.

    But biologists don’t agree with Behe’s statement above, nor his math for calculating the likelihood of chloroquine resistant bacteria, nor his use of his this calculation to establish the probability of mutations in other species.

    1) Your cite is a knockdown of Behe’s diatribe, gall, negligence and ignorance (more critique to follow) so I wouldn’t consider it much of an unbiased source. 2) Behe didn’t calculate the likelihood of chloroquine resistance – he calculated the actual frequency.
    From your cite:

    Second, CQR arises from a sequence of mutations, each conferring a greater benefit than the last, with the change at position 220 one of at least three possibilities for the last step.

    So much the worse for their case and for yours. Your source claims here that each mutation is individually beneficial. Right away this no longer touches Behe’s case (which is to describe the challenge when mutations are not individually beneficial) and proves only too much. If each mutation is beneficial, and resistance is rare (which it is) then RM/NS is even less potent than Behe is suggesting. Here it has everything going for it and still presents solutions only rarely.

    This is a good time to recall Mark Chu-Carroll’s observation that Behe completely ignores gene duplication, frameshifting and all other types of genetic change besides point mutation.

    None of his critics allows Behe an ounce of latitude that they allow any other researcher. Nobody has to present a knockdown case-closed investigation – they are all allowed to present one more bit of evidence, one more bit of knowledge to consider. Behe has done that. He is showing how rare it is for RM/NS to come across two-step solutions. He is not ignoring (how the critiques love that charge) duplication, frame-shift, etc.. He has no ability to limit what malaria is going to do in the wild in response to the vaccine. Malaria had access to every possible type of genetic change suggested and theorized by biologists. It can frameshift, point mutate, substitute to its heart content. In the end, none of these helped increase its resistance.
    EoE page 62:

    Someone might object that, since there are thousands of other proteins in an organism, much other DNA, and many kinds of mutations than just amino acid changes, aren’t the odds of finding some beneficial complex of mutations much better than the odds of finding just teh specific complex we isolated?
    No. Many , many other mutations in addition to the ones we discussed have popped up by chance in the vast worldwide malarial pool over the course of a few years. In fact mutations in all the amino acid positions of all the proteins of malaria – taken both one and two at a time – can be expected to occur by chance during the same stretch of time. And other mutations besides just changes in amino acids would also occur (such as insertions, deletions, inversions, gene duplications, mobile DNA transpositions, changes in regulatory regions, and others, perhaps even including whole genome duplication – some of these mutations are discussed in teh next chapter).

    of all the possible mutations in all the different proteins of malaria, only a miniscule number have the ability to help at all against chloroquine, and only one, PfCRT, is really effective. Natural selection gets to choose from a staggering number of variations, yet at best only a handful help. So a CCC isn’t just the odds of a particular protein getting the right mutations; it’s the probability of an effective cluster of mutations arising in an entire organism.

    He actually responded to this charge on his blog as well:

    Miller asserts that I have ruled out cumulative selection and required Plasmodium falciparum to achieve a predetermined result. I’m flattered that he thinks I have such powers. However, the malaria parasite does not take orders from me or anyone else. I had no ability to rule out or require anything. The parasite was free in the wild to come up with any solution that might help it, by any mutational pathway that was available. I simply reported the results of what the parasite achieved. In 1020 chances, it would be expected to have undergone huge numbers of all types of mutations — substitutions, deletions, insertions, gene duplications, and more. And in that astronomical number of opportunities, at best a handful of mutations were useful to it.

    As per this charge and another in your source:

    Certainly, there may be several routes, maybe permutations of pathways, too. But whether or not there are several routes, the bottom line is that resistance arises only once for every 1020 parasites.

    http://www.amazon.com/gp/blog/post/PLNK1WNX2AI5EMGXN
    So Behe looks at how difficult it is to solve a problem in the wild, rates that problem and its solution. Then he doubles the problem and asks whether we can expect 1) that there are many such problems in the history of life and 2) that RM/NS can reasonably solve many of them. This is an empirical case, not a theoretical one. Behe is demonstrating, and adding to the pile of knowledge, what we can expect from RM/NS. Just like Seelke didn’t disprove evolution when he showed how likely a single gene repair is versus a double or triple, and neither did Minnich when he showed that the BF was, indeed, IC. They have added to the knowledge, and in each case, undermined assumptions that are being made by those who claim that RM/NS can account for all the features of life – and that it inevitably will.
    In addition, to further improve his overall case, the beneficial mutation that provides drug resistance, is, yet again, one which damages the cell in general and does not increase its complexity – it breaks a function, it doesn’t add one.

    Further to your source:
    The author claims to have dug down in the research to find that chloroquine resistance has developed in South America and Southeast Asia independently. Either he never actually read Behe’s book (a common malady among his critics) or he’s trying to paint Behe in a negative light (equally common) because Behe announces this very fact in EoE. He even tells us that, given the number of cells and infected people, chloroquine resistance is waiting to be found in one person, somewhere in the world, at any given time. It has the population numbers to get around the odds.

    Further , your source cites research in 1997 by Su et al. But Behe discussed the 2004 paper already and said:

    Because concurrent mutations in two different genes occur at reduced frequency, this would help explain the rarity with which resistance has evolved. (Nair,S., Williams,J.T., Brockman,A., Paiphun,L., Mayxay,M., Newton,P.N., Guthmann,J.P., Smithuis,F.M., Hien,T.T., White,N.J., Nosten,F., and Anderson,T.J. 2003. A selective sweep driven by pyrimethamine treatment in southeast asian malaria parasites. Mol. Biol. Evol. 20:1526-1536)
    (By the way, Hayton and Su 2004 also remark that, “Based on the mutant pfcrt haplotypes known so far, it is likely that simultaneous multipoint changes in pfcrt are necessary to confer [chloroquine resistance]”.)

    Given this and the above, Behe seems to be the far more thorough than his critics, and far more thorough than they would have you know.

  148. Charlie,

    Thanks for the (as always) prompt reply.

    It seems to me that by declaring it [Behe’s inability to get published in the scientific journals] gross incompetence, and then denying the gross incompetence could exist, you can dismiss the failure. Without a label I can show you only the facts; Behe has presented his challenge and the journals refuse to publish it. They publish rebuttals of the challenge, but not Behe’s answers to the rebuttals. Call it what you will.

    All right. But I would say that a Bayesian analysis would indicate that there’s a very low probability that Behe’s inability to be published is due to the lack of professionalism (unfairness, incompetence, etc.) by all professional journals in his field.

    Why would you consider this [the new ability to move Citrate through the membrane in an oxic environment] more complex than the previous state?

    I suppose it depends on your definition of “more complex.” I would say that adding a mechanism that enables an additional function makes a machine more complex.

    He [Behe]’s not intent on this [formulating the most improbable math for beneficial mutations]. He’s telling you what the odds are when this is the case. He is describing why this would most likely and most often be the case and he is describing why this is a challenge to evolution. Everyone agrees with him, from Lenski to Orr. The very fact that Lenski concludes that this rare event is rare because it likely required two mutations demonstrates Behe’s case.

    Behe has proposed a criticism of NDE and explained his rationale. It appears to my laymen’s understanding that he makes some fundamental assumptions which are highly questionable. (More below.)

    Your cite is a knockdown of Behe’s diatribe, gall, negligence and ignorance (more critique to follow) so I wouldn’t consider it much of an unbiased source.

    I don’t know that I would concede that all harsh criticism indicates bias. There is a great deal of substantive criticism on that cite, so while I wish that all sides would refrain from pillory I’ve been learning to see if there’s anything real to back up the scorn; in this case I think there is substance as well.

    Behe didn’t calculate the likelihood of chloroquine resistance – he calculated the actual frequency.

    I think this needs to be clarified. Behe estimated the actual frequency based on this footnote:

    Footnote from “Antimalarial drug resistance” (2004): Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years (14). This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 10[to the power of]20 parasite multiplications.

    But achieving recognition as having developed resistance (among a viable mutatant, propogating group of resistant bacteria) is qualitatively different than a bacteria undergoing the necessary mutations. It appears that Behe is basing his math for the likelihood of a mutation in malaria generating chloroquine resistance on recognized instances of the event, and does not take into account the probability of such mutations occurring but not, for whatever reason, achieving recognition. In other words, it sounds to me like Behe is citing the work of someone who watched the sky all night and then took that tally to proclaim that so many meteorites fall on earth each day because that’s how many the watcher saw; there are additional and more sophisticated tools that we should also use to supplement our estimates, is all I’m saying.

    Your source claims here that each mutation [of malaria toward chloroquine resistance] is individually beneficial. Right away this no longer touches Behe’s case (which is to describe the challenge when mutations are not individually beneficial) and proves only too much.

    It’s getting late for me, so I wonder if I’m misreading all this. But it does appear to me that Behe is basing his criticism largely on his understanding of chloroquine resistance in malaria. A quote from Behe you provided above says:

    Behe: Incredibly, he [Carroll] ignores the book’s centerpiece example of chloroquine resistance, where beneficial changes do not accumulate gradually.

    So it appears to me that the criticism does touch Behe’s case, not least of all because it contradicts what Behe is asserting about what he calls the centerpiece of his argument.

    I apologize I could only get through half your post, and I’d still like to catch up on some of your earlier comments as well, but this is all I could find time to address tonight.

  149. Tony Hoffman says:
    February 22, 2009 at 9:31 pm
    Charlie,

    Thanks for the (as always) prompt reply.

    My pleasure. Thanks for the continued exchange.

    All right. But I would say that a Bayesian analysis would indicate that there’s a very low probability that Behe’s inability to be published is due to the lack of professionalism (unfairness, incompetence, etc.) by all professional journals in his field.

    I haven’t crunched the subjective numbers of a Bayesian analysis but I would agree. I’ve given you many plausible reasons which fall short of conspiracy or lack of professionalism, but I also include links to their own words, by way of explanation. You can also check the uproar that accompanied the publishing of his very mild 2004 paper, as well as the ever-popular Sternberg affair, for more data on why he is unpublishable. Not to equate ID and creationism, but you could also Google the likes of Steve Austin and Robert Gentry and see what happens when the implications of a published scientist’s work become known and are seen as contradicting the paradigm. The short answer is, previously good science by good scientists is no longer fit for publishing. You can dismiss these results by saying this means the journals are unprofessional and you don’t believe they can be, but you can’t deny the fact that Behe is a published scientist who can not publish on this opinion.
    The fact is, Behe has done his work, he knows science and has been published dozens of times, and now he can’t publish his opinions. Others can publish reviews and opinions and speculations, but only if they mesh with the journal’s pre-existing commitments.

    I suppose it depends on your definition of “more complex.” I would say that adding a mechanism that enables an additional function makes a machine more complex.

    In a way I’d agree. But you are right, it does depend upon one’s definition of complexity. It certainly does nothing to answer Behe’s IC argument. It only corresponds to his EoE argument by confirming what he termed the edge. It has added no parts to a mechanism, is has made no new machine, it has added no structure (I’ll substitute this for “feature”). Is the new phenotype more complex than the previous? I don’t know. It is far less competitive on the original substrate, so it has, once again, lost general fitness as compared to the original. Given the possible explanations for this phenotype we have either 1) just more of the same enzyme, or 2) an enzyme in replacement of another and 3) just another example of a rare but not unheard of phenotype within the population – a phenotype that disappears presumably because it is less, not more, fit. It is certainly not doing anything which can be compared to developing the kind of complexity required to generate the molecular machinery so common to life.

    Footnote from “Antimalarial drug resistance” (2004): Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years (14). This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 10[to the power of]20 parasite multiplications.

    Accurate – to a degree. The number is not Behe’s estimate but Whites.

    But achieving recognition as having developed resistance (among a viable mutatant, propogating group of resistant bacteria) is qualitatively different than a bacteria undergoing the necessary mutations.

    Accurate.

    It appears that Behe is basing his math for the likelihood of a mutation in malaria generating chloroquine resistance on recognized instances of the event, and does not take into account the probability of such mutations occurring but not, for whatever reason, achieving recognition. In other words, it sounds to me like Behe is citing the work of someone who watched the sky all night and then took that tally to proclaim that so many meteorites fall on earth each day because that’s how many the watcher saw; there are additional and more sophisticated tools that we should also use to supplement our estimates, is all I’m saying.

    1) Yes, there is always the possibility that science is missing data when it draws its conclusions, but you can only work with the data it provides, not speculated data. 2) It’s not Behe’s number. 3) But why would we expect that resistance is being achieved but being unrecognized? We know who is being treated by vaccinations, we know what populations are involved, and we know when the vaccine becomes ineffective. It’s not like there are lost tribes using the vaccine beyond the scrutiny of our data-gatherers. And when the resistance shows up, as it does rarely, we even have the ability to track its origin and determine if it has done so uniquely or spread from a previously resistant population. We can even compare it to resistance to vaccines which require a single mutation, calculate the recognition factor against fairly accepted mutation rates and find that they correlate quite well. So even though he is not trying to calculate a mutation rate we can conclude that the appearance/recognition of resistance is fairly representative of its actual instances.

    me:Your source claims here that each mutation [of malaria toward chloroquine resistance] is individually beneficial. Right away this no longer touches Behe’s case (which is to describe the challenge when mutations are not individually beneficial) and proves only too much.
    you: But it does appear to me that Behe is basing his criticism largely on his understanding of chloroquine resistance in malaria. A quote from Behe you provided above says:
    from me: Behe: Incredibly, he [Carroll] ignores the book’s centerpiece example of chloroquine resistance, where beneficial changes do not accumulate gradually.
    you: So it appears to me that the criticism does touch Behe’s case, not least of all because it contradicts what Behe is asserting about what he calls the centerpiece of his argument.

    First, as you noted, Behe disputes the notion that the steps are beneficial – mentioning that the claim is speculative. Second, Behe discusses the case upon the assumption that the CCR is not built up cumulatively on individually beneficially mutations. If they are beneficial, then so much the worse for RM/NS and so much the better for Behe. It doesn’t touch his claim in the sense that it is no critique of it; worst case scenario, it’s a false claim; best, it only reinforces Behe’s thesis.
    Behe has demonstrated himself that the PfCRT mutation took several steps – and that it is very rare for these steps to occur. If his opponents want to add to the rarity the additional fact that those steps were beneficial, which would make their accumulation easier, then good on Behe. Whatever degree of benefit any putatively cumulative mutations might have added is unimportant – the fact remains that resistance appears in every 10^20 parasites. And that empirical fact is a demonstration of what RM/NS actually do in the real world – not just in theory. The number is a statistical one and is not dependent upon the mutations arising simultaneously – whether Behe thinks that best explains the data or not.

    Later.

  150. Hi Charlie,

    The fact is, Behe has done his work, he knows science and has been published dozens of times, and now he can’t publish his opinions. Others can publish reviews and opinions and speculations, but only if they mesh with the journal’s pre-existing commitments.

    Well, nobody should be automatically published in a scientific journal based only on prior achievements. And Behe can publish reviews and opinions and speculations as well, but the issue is one of peer-reviewed publication in his field. I just don’t find it that outrageous that a scientific journal would guard methodological naturalism as a premise of its studies. If I think of an analogy it would be like the Norton Anthology of English Literature refusing to publish poems written in languages other than English. The rules of acceptance seem appropriate to me.

    Is the new phenotype more complex than the previous? I don’t know. It is far less competitive on the original substrate, so it has, once again, lost general fitness as compared to the original.

    While, the Petri dish of glucose only or glucose and Citrate is a laboratory condition so I wouldn’t qualify that environment as representing one of general fitness testing. And Lenski’s paper doesn’t conclude what you have – he writes that the mutated strain “… has acquired a key innovation that substantially changed its ecological niche.”

    Regarding my questioning of Behe’s use of White’s estimate of malarial mutation for chloroquine resistance, you wrote:

    1) Yes, there is always the possibility that science is missing data when it draws its conclusions, but you can only work with the data it provides, not speculated data. 2) It’s not Behe’s number. 3) But why would we expect that resistance is being achieved but being unrecognized?

    But science has lots of data about malarial mutations – it appears that Behe is being selective about which data he uses. And White’s number is clearly not about the frequency of mutations occurring, but the probability of full-blown resistance developing in a viable strain (as a result of mutations and the other complex circumstances needed for the resistant malaria multiplying sufficiently – the second paragraph from White I quote below explains why resistance being achieved would not necessarily lead to that mutation being recognized). I could also throw in that Behe has determined that chloroquine resistance occurs as a result of two mutations, but that my reading of both White’s papers and Su et al.’s considers that the resistance probably involves two genes, not that only two genes are involved. (Here’s a typical statement from Su et al’s paper: “While the linkage and protein localization data provide strong evidence for a central role of cg2 in chloroquine resistance, additional determinants are likely to have a complementary or permissive role in the resistance mechanism.” And in White’s paper here’s another similar conclusion regarding resistance: “At least one other as-yet unidentified gene is thought to be involved.”)

    White, in his paper (from the point that Behe quotes it), writes;

    This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 10[to the power of]20 parasite multiplications. The single point mutations in the gene encoding cytochrome b (cytB), which confer atovaquone resistance, or in the gene encoding dihydrofolate reductase (dhfr), which confer pyrimethamine resistance, have a per-parasite probability of arising de novo of approximately 1 in 10[to the power of]12 parasite multiplications (5). To put this in context, an adult with approximately 2% parasitemia has 10[to the power of]12 parasites in his or her body. But in the laboratory, much higher mutation rates thane 1 in every 10[to the power of]12 are recorded (12).

    Mutations may be associated with fitness disadvantages (i.e., in the absence of the drug they are less fit and multiply less well than their drug-sensitive counterparts). Another factor that may explain the discrepancy between in vitro and much lower apparent in vivo rates of spontaneous mutation is host immunity. Even a previously nonimmune individual develops a specific immune response to a malaria infection. This response is systematically evaded by the parasite population through programmed antigenic variation of the main red cell surface–expressed epitopes. In falciparum malaria, P. falciparum erythrocyte membrane protein 1 (PfEMP1), which is encoded by the var multigene family, changes in 2–3% of parasites each asexual cycle (15). The untreated infection is characterized by successive waves of parasites, each comprising largely one antigenically distinct surface phenotype. It is likely that this specific immune response directed against the immunodominant surface antigens will reduce the probability of the usually single mutant parasite ever multiplying sufficiently to transmit as for P. falciparum; there is only a 2–3% chance that the genetic event causing resistance would arise in the antigenically variant subpopulation that will expand to reach transmissible densities. (http://www.jci.org/articles/view/21682/version/1)

    I think the paragraph above shows why you and Behe are mistaken when you write:

    So even though he [Behe] is not trying to calculate a mutation rate we can conclude that the appearance/recognition of resistance is fairly representative of its actual instances.

  151. Hi Tony,

    Well, nobody should be automatically published in a scientific journal based only on prior achievements.

    That’s absolutely true but then I didn’t say he should be.

    And Behe can publish reviews and opinions and speculations as well, but the issue is one of peer-reviewed publication in his field.

    I’m glad we are agreed that that is the issue here. But when Behe wishes to publish opinions and reviews he is told that the journals are committed to advancingt he current theory.

    I just don’t find it that outrageous that a scientific journal would guard methodological naturalism as a premise of its studies. If I think of an analogy it would be like the Norton Anthology of English Literature refusing to publish poems written in languages other than English. The rules of acceptance seem appropriate to me.

    So you acknowledge the rules are what keep Behe out and you justify this rather than call the enforcement of these rules “gross incompetence” or widespread unprofessionalism. So then I think we are agreed on this point?
    Behe’s work is not getting in front of his peers because his peers, as editors, reviewers and funders, have predetermined the ground rules and, based upon the existing paradigm, have effectively banned discussion of his points.
    Notice, too, that in his exchanges with editors as linked previously it was not Behe talking about metaphysics or religion, but his reviewers/rejectors.
    So, all in all, the “his peers don;t agree” is pretty much a moot point – they have a vested interest in not agreeing and they have a commitment to a system that won’t allow them to consider, let alone agree with his position. And now we agree that this is not gross incompetence but that you even agree with the policy. So to answer your question, this is how it is possible that Behe has a legitimate challenge to RM/NS but has not convinced his peers.

    While, the Petri dish of glucose only or glucose and Citrate is a laboratory condition so I wouldn’t qualify that environment as representing one of general fitness testing. And Lenski’s paper doesn’t conclude what you have – he writes that the mutated strain “… has acquired a key innovation that substantially changed its ecological niche.”

    1) On the germane point, and back to fitness, this acquisition as not made a new machine, created a new binding site, added any parts, etc. It has not increased the complexity.
    2) Granted, the niche has changed.
    3) The bacteria, like so-called super bugs, are less efficient than their predecessors. This is why the mutant, which is not unique and is observed in the wild, does not flourish in the wild. We have the same phenomenon occurring CQR.

    I am glad to see, however, that you acknowledge that laboratory petri dish/test tube experiments are not nature and do not model NS or what RM/NS actually can do in the wild.

    I could also throw in that Behe has determined that chloroquine resistance occurs as a result of two mutations, but that my reading of both White’s papers and Su et al.’s considers that the resistance probably involves two genes, not that only two genes are involved. (Here’s a typical statement from Su et al’s paper: “While the linkage and protein localization data provide strong evidence for a central role of cg2 in chloroquine resistance, additional determinants are likely to have a complementary or permissive role in the resistance mechanism.” And in White’s paper here’s another similar conclusion regarding resistance: “At least one other as-yet unidentified gene is thought to be involved.”)

    This “throw-in” is an unusual statement and even if White is right how would it be relevant to Behe ? Two mutations on one gene or on two genes require the same theoretical resources – and CQR develops at an observable frequency regardless of what combination of mutations is required.
    As Behe investigates, however, it’s not even two genes, but two points on a single gene, the pfCRT, which are in question. While there are various other mutations often associated they are not necessary to confer the resistance – the high correlation of the two named, 76T and 220, to resistance sets them up as the two necessary (with a possible sub of 75 for 76, and a complex available to replace 220) and the others being associated but not necessary -and certainly not sufficient – for the trait.

    In this study 76T is absolutely necessary, but not sufficient, to confer resistance.
    A second gene other than pfCRT, such as pfMDR 1 (a usual suspect), is not required in mutations.
    http://jeb.biologists.org/cgi/content/full/206/21/3745

    This paper also highlights another relevant fact referenced in the Lenski discussion – fitness. When chloroquine is not longer used as a treatment CQR disappears, as it is not more fit than its predecessor. Likewise, the disappearance, non-prevalence of the Cit + bacteria in the wild, although not unknown, demonstrates that the ability to transport citrate in oxic conditions does not confer increased general fitness. It decreases it. Even the much rarer and so-called beneficial mutations are, on the whole, detrimental.

    pfMDR, as implicated by Su in your references, is found here not to be a factor:
    http://cat.inist.fr/?aModele=afficheN&cpsidt=20183069

    As White says in the paper you cite, and as Behe confirms, by studying the regions surrounding the affected gene one can tell whether the mutation has arisen many times, or if the many cases of resistance can be tracked to one event. And, as has been demonstrated repeatedly, CQR has arisen very few times and has spread rapidly around the world from those few spontaneous episodes. And it has done so not because a variety of different mutations to different genes will confer it but on the basis of a few necessary mutations.
    http://www.jci.org/articles/view/21682/version/1

    Behe said on nhis blog:

    Therefore, we need to get our ideas about what should or shouldn’t evolve not from evolutionary theory, but from evolutionary data. And what we see in our best set of data from malaria is that no such protein sites evolved by Darwinian means in an astronomical number of opportunities. Furthermore, mutations in only one protein, pfcrt, were really able to do much in the face of chloroquine, showing that the number of proteins that it may be helpful to evolve in any given situation might be extremely small: one, maybe none. Ditto for pyrimethamine resistance.

    If only one protein could evolve to help malaria avoid chloroquine poisoning, why should we think that a cell will luckily have a dozen or score of proteins that happen to be able to evolve to make a molecular machine?

    http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2?%5Fencoding=UTF8&cursor=1195239241.598&cursorType=before

    Back to SU, he concurs, as pointed out earlier, that:

    (By the way, Hayton and Su 2004 also remark that, “Based on the mutant pfcrt haplotypes known so far, it is likely that simultaneous multipoint changes in pfcrt are necessary to confer [chloroquine resistance]”.)

    http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2?%5Fencoding=UTF8&cursor=1193328991.375&cursorType=before

    And from your referenced paper by White:

    A single genetic event may be all that is required, or multiple unlinked events may be necessary (epistasis). As the probability of multigenic resistance arising is the product of the individual component probabilities, this is a significantly rarer event. P. falciparum parasites from Southeast Asia have been shown to have an increased propensity to develop drug resistance (12).

    White shows above that unlinked mutations are significantly rarer than single ones. This is Behe’s point, and an uncontroversial one at that, in a nutshell.

  152. Re: your argument against in vivo mutations rates. You are right, of course, that pure mutation rates in vitro are much higher in the cases discussed. But first, as I said, this is not Behe’s point – he is discussing not mutation rate but development of the trait. You make a subtle admission here, relevant to the Lenski discussion, that in vitro is not necessarily representative of what is occurring in nature, in the wild, where all of our evolution has to have taken place and that, rare as it is in the lab, it is many times more rare in vivo. Also, in one of the papers above and I’m sorry I forget which one, the researchers point out that the very act of studying the virus can affect its mutation rate, what with sampling, freezing, selecting, etc. – as Behe says, we have the data from the field to tell us what RM/NS is actually capable of in real life. You mention the complicated and confounding factors which will affect the appearance of the trait, but that is also one more point for my side. Yes, life is complicated, not just for plasmodium falciparum but for all organisms thought to have evolved from the simplest imaginable self-replicator to today’s panoply of complexity. And that tricky route to success includes the fact that most mutations are deleterious, even beneficial ones do not confer increased complexity by any appreciable measure, and even beneficial mutations are more likely to be lost than to be fixed in a population. As further noted by Behe, even though p. falciparum can solve, rarely, this two-fold problem it has had ten thousand years (200 times the opportunities) to solve sickle cell but the RM/NS trench warfare, complexity ratchet has failed to do so. This at a reproduction rate and population sizes that positively dwarf all resources available to al mammals ever. For instance, there are more malaria cells in the body of one sick person at any given time than there have been individual hominids on the line from chimp to man.
    On the other hand, and in defence of my hasty proposition, regardless of all the confounding factors, as White says in his paper, at any given time the majority of the parasites in the world are to be found in ill people. And this is the “lab” number used to calculate how often resistance arises. These ill people have the lessened ability to fight off any of the parasites, arguing against one of the cited options by White, that the mutant might be showing up but that the host might be destroying it – the host’s ability to destroy it is greatly compromised. These are also the people who are being treated with the drugs in question and, therefore, the ones in whom the resistance is most likely to occur.

    You say that both Behe and I made an error, but I point you back to Behe:

    Miller makes the same mistake here that I addressed earlier when replying to Jerry Coyne’s response. The number of one in 1020 is not a probability calculation. Rather, it is statistical data. It is perhaps not too surprising that both Miller and Coyne make that mistake, because in general Darwinists are not used to constraining their speculations with quantitative data. The fundamental message of The Edge of Evolution, however, is that such data are now available. Instead of imagining what the power of random mutation and selection might do, we can look at examples of what it has done. And when we do look at the best, clearest examples, the results are, to say the least, quite modest. Time and again we see that random mutations are incoherent and much more likely to degrade a genome than to add to it — and these are the positively-selected, “beneficial” random mutations.
     
    Miller asserts that I have ruled out cumulative selection and required Plasmodium falciparum to achieve a predetermined result. I’m flattered that he thinks I have such powers. However, the malaria parasite does not take orders from me or anyone else. I had no ability to rule out or require anything. The parasite was free in the wild to come up with any solution that might help it, by any mutational pathway that was available. I simply reported the results of what the parasite achieved. In 1020 chances, it would be expected to have undergone huge numbers of all types of mutations — substitutions, deletions, insertions, gene duplications, and more. And in that astronomical number of opportunities, at best a handful of mutations were useful to it.


    It matters much less than he implies. Certainly, there may be several routes, maybe permutations of pathways, too. But whether or not there are several routes, the bottom line is that resistance arises only once for every 1020 parasites.


    Here is where Professor Coyne and other Darwinist reviewers really miss the boat and overlook the considerable power of the malaria results. The number I cite, one parasite in every 1020 for de novo chloroquine resistance, is not a probability calculation. Rather, it is a statistic, a result, a data point. (Furthermore, it is not my number, but that of the eminent malariologist Nicholas White.) I do not assume that “adaptation cannot occur one mutation at a time”; I assume nothing at all. I am simply looking at the results. The malaria parasite was free to do whatever it could in nature; to evolve resistance, or outcompete its fellow parasites, by whatever evolutionary pathway was available in the wild. Neither I nor anyone else were manipulating the results. What we see when we look at chloroquine-resistant malaria is pristine data — it is the best that random mutation plus selection was able to accomplish in the wild in 1020 tries.
     
    Let me elaborate that last point. The fact that de novo chloroquine resistance is observed to be an event of frequency 1 in 1020 means that mutational events of greater frequency are of little help, because events of greater frequency would have been expected to occur many times in the same time interval. For example, if a single point mutation such as K76T alone in PfCRT in the wild were sufficient to confer chloroquine resistance, then resistance would occur de novo in virtually every person treated with chloroquine, as it does in almost every person treated with atovaquone. In 1020 parasites that single mutation would have been expected to have occurred about 1010 times or more. What’s more, every other possible single point mutation, at every position of the parasite’s genome, would also be expected to have occurred roughly the same number of times. And enormous numbers of other types of mutations — deletions, insertions, gene duplications, and more — in every gene of the parasite, would also have occurred. The result: a very few mutations helped the parasite a bit; the overwhelming number of mutations did not help at all.

    My argument does not depend on exactly which changes are needed in the protein. Rather, the important point is that multiple changes appear to be required for resistance in the wild.
     
    And for the life of me, I don’t see why that proposition — that two mutations might be needed for some adaptations, and that that would be a big evolutionary impediment — is being treated by Coyne and other Darwinists with such horror. It certainly has been discussed in the evolutionary literature in the past. In my book I quote Allan Orr remarking, “Given realistically low mutation rates, double mutants will be so rare that adaptation is essentially constrained to surveying — and substituting — one-mutational step neighbors. Thus if a double-mutant sequence is favorable but all single amino acid mutants are deleterious, adaptation will generally not proceed.” All I have done is to point to an example of the situation he envisioned, to quantify it, and to argue that it’s likely to be a fairly general phenomenon. Why the shock?

    http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2?%5Fencoding=UTF8&cursor=1186184895.697&cursorType=before
    Again, he is not talking about a mutation rate, but the rate of appearance of the trait dependent upon mutation. I was probably too hasty relying upon memory to say that the appearance rate and mutation rate are likely fairly close. What I was recalling was that the occurance of resistance to a drug arising from one mutation, such as atovaquone, when multiplied by itself gets us in the neighborhood of the occurance of resistance to chloroquine, demonstrating another reason to suspect the necessity of two instead of one mutation in the latter case. Both would appear then to be treated equally by NS acting on RM and the correlation would indicate the necessity of two mutations for something as simple as damaging a membrane pump. Again, this rare mutation does nothing to increase complexity, although it confers a limited, and disappearing survival advantage, and, as usual, degrades the genome and decreases general fitness. Not the stuff of Darwinian lore.

    Parting this out I may have lost parts of my response. We’ll probably know as we go.

  153. Charlie,

    So you acknowledge the rules are what keep Behe out and you justify this rather than call the enforcement of these rules “gross incompetence” or widespread unprofessionalism. So then I think we are agreed on this point?

    Yes, I agree with what you wrote above.

    Behe’s work is not getting in front of his peers because his peers, as editors, reviewers and funders, have predetermined the ground rules and, based upon the existing paradigm, have effectively banned discussion of his points.

    I don’t know that I would say that his peers have so much predetermined the ground rules as they’ve agreed to follow them. I think Behe’s musings are appropriate to a philosophy of science journal.

    Notice, too, that in his exchanges with editors as linked previously it was not Behe talking about metaphysics or religion, but his reviewers/rejectors.

    This seems disingenuous. It is Behe’s work that raises the issue of defining a limit to methodological naturalism in biology. The issue is philosophical, or metaphysical. But Behe is a biologist, and so are his peers. It would be like Behe offering a paper that defines the limit to what biological research can achieve without government funding and pointing out which political party is most likely to fund research; the issue might be relevant to his field, but that doesn’t mean the correct place to publish the article is in a biological journal.

    So, all in all, the “his peers don’t agree” is pretty much a moot point – they have a vested interest in not agreeing and they have a commitment to a system that won’t allow them to consider, let alone agree with his position. And now we agree that this is not gross incompetence but that you even agree with the policy. So to answer your question, this is how it is possible that Behe has a legitimate challenge to RM/NS but has not convinced his peers.

    After some reflection I am starting to think that likening a philosophical challenge to the methodological naturalism employed by the empirical sciences is not the same thing as a challenge to a scientific paradigm; I’m not even sure that we should consider Behe’s challenge to Darwinism as representing a potential paradigm switch. I don’t think it rises to that.

    But I do still believe that if the biological challenges Behe poses falsified Darwinism then failure by his peers to recognize it would be gross incompetence. That remains possible but implausible for me. And I have to say the more I read about the biological criticism to Behe’s argument the less inclined I am to consider gross incompetence by Behe’s peers.

    1) On the germane point, and back to fitness, this acquisition as not made a new machine, created a new binding site, added any parts, etc. It has not increased the complexity.

    If the experimental environment remained constant, with both glucose and Citrate available, the mutated E. coli are more fit – they exist far greater percentages of the population, and Lenski predicts the mutated strain’s greater numbers will give it a mutational advantage over the Cit- strains. If the glucose were diminished or eliminated, the only bacteria to survive would be the mutated ones. In the altered environment that is the lab, the Cit+ strain is more fit. And that’s really all that matters in that experiment.

    Your argument about fitness reads to me like this: blind cave fish are less fit than the fish from which they evolved because if they returned to the environment from which their ancestors evolved their blindness would seriously hinder their survival. But the blind fish are better adapted to their lightless environment, and makes them more fit (fitness is defined by environmental parameters). The Cit+ bacteria are better adapted to their (Petri dish) environment.

    The bacteria, like so-called super bugs, are less efficient than their predecessors.

    This statement is only true if you the mutated bacteria to the wild. If you leave them in the environment to which they adapted then this is not true. The experiment was not to accelerate evolution or make a super bug; it was to see if a mutation would occur and result in a viable strain that was better adapted to its environment. The experiment proved that this can happen in the lab. (Most of us feel it has already been proven in the wild, so it’s not really that great an achievement I’ll admit, except that it does put to rest the “no one’s ever seen something evolve in a lab” argument.)

    I am glad to see, however, that you acknowledge that laboratory petri dish/test tube experiments are not nature and do not model NS or what RM/NS actually can do in the wild.

    Yes on the laboratory being not nature. I apologize if I gave you the impression that I agree that experiments do not model NS or what RM/NS actually can do in the wild. They are different; that does not mean they are dissimilar.

    This “throw-in” [my stating that the paper’s Behe referenced do not declare that chloroquine resistance is based on only two mutations] is an unusual statement and even if White is right how would it be relevant to Behe ?

    It’s relevant to Behe because he has made a two point mutation the centerpiece of his book. If the mutation relies on a third currently unrecognized mutation in another gene, or also requires a combination of other mutations or other genetic sequences involved in other function as well, then Behe’s argument about the data falls apart. How can Behe conclude that, like the contingent mutation that enabled later generations of Lenski’s bacteria to evolve their Citrate transport ability, there is not a third unrecognized mutation or combination of genetic factors that are required? In other words, how can Behe know that chloroquine resistance only requires two point mutations, and not also more mutations or other genetic combinations? How can he definitively (or even probabilistically) surmise that chloroquine resistance in malaria requires only a two point mutation? (Maybe I missed this in my first read of the literature?)

    Behe: Therefore, we need to get our ideas about what should or shouldn’t evolve not from evolutionary theory, but from evolutionary data. And what we see in our best set of data from malaria is that no such protein sites evolved by Darwinian means in an astronomical number of opportunities.

    I’ll repeat part of the second paragraph from White I quoted earlier:

    The untreated infection is characterized by successive waves of parasites, each comprising largely one antigenically distinct surface phenotype. It is likely that this specific immune response directed against the immunodominant surface antigens will reduce the probability of the usually single mutant parasite ever multiplying sufficiently to transmit as for P. falciparum; there is only a 2–3% chance that the genetic event causing resistance would arise in the antigenically variant subpopulation that will expand to reach transmissible densities.

    I think that the above describes an evolved behavior in malaria that forfeits some opportunity for beneficial mutations to take place for the advantage of defeating the immune response of its host. Doesn’t this seem like something that might incline one to wonder if malaria might evolve atypically, and even if there is something like a broadly typical evolution? At the very least it should make you wonder if Behe’s use of bacterial evolution should have much to tell us about the evolution of other organisms – that the data he is so quick to flog Miller and Coyne with (Behe: “It is perhaps not too surprising that both Miller and Coyne make that mistake, because in general Darwinists are not used to constraining their speculations with quantitative data.”) might be more misleading than illuminating.

    White shows above that unlinked mutations are significantly rarer than single ones. This is Behe’s point, and an uncontroversial one at that, in a nutshell.

    I didn’t mean to give the impression that I thought that a beneficial mutation that relied on two point mutations would be as common as one that relied on one. But I don’t think you’re nutshell restatement is really Behe’s point — if it was I don’t think we’d be having this discussion. Beh’s (latest) point seems to be that because of malaria’s known evolutionary changes Darwinism cannot therefore explain the diversity and complexity of biological structures – that malaria’s evolutionary response to sporadic human drug treatment represents an experiment so thorough that it disproves NDE. I have to say that the more I read about of other biologists’ work in this field the consensus seems to be they don’t really even know where to begin, and I think I’m starting to see why.

    On another note, I just wanted to get back and respond to this statement of yours (I didn’t have time before, and I didn’t want to risk getting sidetracked from the interesting Behe discussion):

    I merely pointed out that my view can accommodate every class of explanation and yours can’t. Whether we are discussing the information in the DNA, the complexity of the cell, OOL, the implications of the Big Bang, the grounding of morality, the consciousness problem, the Cambrian explosion, the argument from reason, the efficacy of NDE, etc., you can only admit naturalistic/materialistic answers. In most of these cases there are not even plausible ones, which, if they exist, are taken as evidence that naturalism is adequate, but the problem is merely shuffled off to some future discovery. And yet, like Jerry Coyne and the journal in Behe’s correspondence above, the naturalist/materialist must just presume that one day such an answer will present itself – because the option just is no option.
    This point ought to be obvious and completely uncontroversial.
    Evidence the fact that you likely now agree with the assessment above and are thinking of responding that this commitment on your part is preferable to 1) non-scientific answers or 2) God of the gaps arguments.

    I don’t think that your point is obvious nor uncontroversial. It is a good example of the kind of thing that I imagine you feel is merely factual and cannot be construed as an insult, but an insult is how it is taken. Your statement is normative and accusatory – it basically says that it is better to accept supernaturalism and that those who do not are close-minded.

    But I think you anticipated my response, as the second part of your statement indicates. I can only say that I believe in a statement like yours the burden of proof remains yours – you owe it to yourself, at least, to demonstrate what your addition to Occam’s razor gives you in terms of practical, explanatory knowledge. (I’ll concede that it might make you feel better. But I don’t think you “know” anything more based on your philosophical assumption than I do with mine.)

  154. Hi Tony,
    Thanks for getting back to me so soon.

    Me:So you acknowledge the rules are what keep Behe out and you justify this rather than call the enforcement of these rules “gross incompetence” or widespread unprofessionalism. So then I think we are agreed on this point? 

You: Yes, I agree with what you wrote above.

    Thanks.

    I think Behe’s musings are appropriate to a philosophy of science journal.

    Then why are musings and speculations about the efficacy of naturalism not relegated to such philosophical journals? Why are reviews and opinions which merely say what it is possible for us to imagine nature doing by itself publishable and the responses are not? This isn ot a matter of metaphysical and philosophical ideas being out-of-bounds, but a matter of blocking the inappropriate ones.

    Me:Notice, too, that in his exchanges with editors as linked previously it was not Behe talking about metaphysics or religion, but his reviewers/rejectors. 
You:This seems disingenuous.

    Does it?

    It is Behe’s work that raises the issue of defining a limit to methodological naturalism in biology. The issue is philosophical, or metaphysical.

    No more than the claim that there is no limit – but the journal editor specifically told Behe that was the position of his journal. And the ultimate implications, or Behe’s motivations shouldn’t affect whether or not he can describe the irreducibility of the BF in a journal – his opponents certainly can. Or whether or not he ought to be shut out for discussing the the limitations of RM/NS – again, his opponents can do this. Even if his work has nothing to say about ID, philosophy, or anything metaphysical it is rejected on metaphysical grounds. The door is closed to his observations because they come from somebody who does not support the paradigm and because they might be used in his hands to challenge the paradigm. (Motivations shouldn’t have affected Gentry’s ability to publish on po-halos, but once the young earth implications of his thinking became apparent they did. They shouldn’t cost astronomers telescope time as well or professors their jobs but they do.)
    The door is closed not because of the scientific merits of his proposals so what strikes me as disingenuous is to make “peer review” or “peer acceptance” any kind of a litmus test when the peers have closed the door to his ideas – justifiably, according to you.
    If there are such rules, and of course there are, for publishing and making your case, then so be it. Defend those rules all you want, but the critique that he is not published or convincing to his peers on this issue then says nothing meaningful about the truth of his position.

    Me: So, all in all, the “his peers don’t agree” is pretty much a moot point – they have a vested interest in not agreeing and they have a commitment to a system that won’t allow them to consider, let alone agree with his position. And now we agree that this is not gross incompetence but that you even agree with the policy. So to answer your question, this is how it is possible that Behe has a legitimate challenge to RM/NS but has not convinced his peers. 

You: After some reflection I am starting to think that likening a philosophical challenge to the methodological naturalism employed by the empirical sciences is not the same thing as a challenge to a scientific paradigm; I’m not even sure that we should consider Behe’s challenge to Darwinism as representing a potential paradigm switch. I don’t think it rises to that.

    All the less reason for the reactions from editors and “science defenders” pressuring journals who deign to give him a venue.

    But I do still believe that if the biological challenges Behe poses falsified Darwinism then failure by his peers to recognize it would be gross incompetence.

    When and how will they consider it?

    That remains possible but implausible for me. And I have to say the more I read about the biological criticism to Behe’s argument the less inclined I am to consider gross incompetence by Behe’s peers.

    Still not asking you to. But it is interesting, is it not, that all of these supposedly scientific critiques exist on the biological grounds of what you term a metaphysical or philosophical challenge?

    Me:1) On the germane point, and back to fitness, this acquisition has not made a new machine, created a new binding site, added any parts, etc. It has not increased the complexity. 

You: If the experimental environment remained constant, with both glucose and Citrate available, the mutated E. coli are more fit – they exist far greater percentages of the population, and Lenski predicts the mutated strain’s greater numbers will give it a mutational advantage over the Cit- strains. If the glucose were diminished or eliminated, the only bacteria to survive would be the mutated ones. In the altered environment that is the lab, the Cit+ strain is more fit. And that’s really all that matters in that experiment.

    Not really. There are far greater implications and whether or not bacteria can re-access a dormant or damaged trait, or whether or not they can damage genes and systems which give some benefit in some locale also matter. The kind of evolution you are seeing here is insignificant compared to the claims – not just in degree but in kind. We are not seeing the kind of rising fitness,(for instance, its not a constant environment, but a constantly manipulated one), the kind of rising adaptability or the increase in fitness that is necessary. Yes, we are seeing niche-filling, but, once again, not novelty. This is like saying if I shoot all the brunettes in a village I am evolving blondes. It is trivial in nature to say that every species occupies its own niche, it is far more ambitious to say that every niche will be filled or that in filling niches (or, in actuality, by creating them) RM/NS is going to evolve men from mud.

    Your argument about fitness reads to me like this: blind cave fish are less fit than the fish from which they evolved because if they returned to the environment from which their ancestors evolved their blindness would seriously hinder their survival. But the blind fish are better adapted to their lightless environment, and makes them more fit (fitness is defined by environmental parameters). The Cit+ bacteria are better adapted to their (Petri dish) environment.

    This is a good analogy, thanks. Yes, blind cave fish are broken and are less fit. They lose a trait which does not affect their fitness in dark caves – and they can even restore that trait when blindness becomes a detriment. But this says nothing whatsoever about how fish came to have eyes – or any other complex feature – in the first place. And it says nothing about increasing complexity. All it does is reinforce what creationists were saying about NS long before Darwin – it is a cull, not a creative force. And, as we see from experiments, neither is RM much of a creative force, although this is where all the creativity of Darwinian evolution must reside – Dawkins’ “survival is guided by survival” notwithstanding.

    Me: The bacteria, like so-called super bugs, are less efficient than their predecessors. 
You: This statement is only true if you the mutated bacteria to the wild. If you leave them in the environment to which they adapted then this is not true. The experiment was not to accelerate evolution or make a super bug; it was to see if a mutation would occur and result in a viable strain that was better adapted to its environment. The experiment proved that this can happen in the lab. (Most of us feel it has already been proven in the wild, so it’s not really that great an achievement I’ll admit, except that it does put to rest the “no one’s ever seen something evolve in a lab” argument.)

    Me: It might end that argument for anybody ignorant enough to make it. What we haven’t seen here is an increase in complexity or anything that would warrant any interpolation of the ability of RM/NS to create the kind of complexity necessary to account for all of life – as it is claimed to have done.

    Me:
This “throw-in” [my stating that the paper’s Behe referenced do not declare that chloroquine resistance is based on only two mutations] is an unusual statement and even if White is right how would it be relevant to Behe ? 

You: It’s relevant to Behe because he has made a two point mutation the centerpiece of his book. If the mutation relies on a third currently unrecognized mutation in another gene, or also requires a combination of other mutations or other genetic sequences involved in other function as well, then Behe’s argument about the data falls apart. How can Behe conclude that, like the contingent mutation that enabled later generations of Lenski’s bacteria to evolve their Citrate transport ability, there is not a third unrecognized mutation or combination of genetic factors that are required? In other words, how can Behe know that chloroquine resistance only requires two point mutations, and not also more mutations or other genetic combinations?

    1) This is an appeal to ignorance. Why should Behe not make a case based upon what we do know and without speculating about unknown factors?
    2) As per ” made a two point mutation the centerpiece of his book …how can Behe know that chloroquine resistance only requires two point mutations” : He doesn’t. He several times mentions that it might be more, but the data actually suggests that two are enough. And that mutations to the other gene are not required. There are two mutations that show up almost 100% of the time and the others observed mutations are not necessary. This is also consistent with the rarity of the mutation. It is consistent with the data extrapolated from the appearance of atovaquone or pyrimethamine resistance which rely upon one mutation. He also compares the rarity of the double-mutant required for additional pyrimethamine resistance and finds them to be similar, pointing again two necessary mutations.
    Back to White, he is not saying that multiple genes are required for the conferral of CQR.

    Chloroquine resistance in P. falciparum may be multigenic and is initially conferred by mutations in a gene encoding a transporter (PfCRT) (13).

    Resistance arises immediately with the mutations to the PfCRT.
    He then mentions PfMDR, which has been shown above to be unnecessary, which he acknowledges himself:

    In the presence of PfCRT mutations, mutations in a second transporter (PfMDR1) modulate the level of resistance in vitro, but the role of PfMDR1 mutations in determining the therapeutic response following chloroquine treatment remains unclear (13).

    Then he mentions that a third is thought to be involved, not necessary to confer resistance.

    At least one other as-yet unidentified gene is thought to be involved. Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years (14).

    ===

    How can he definitively (or even probabilistically) surmise that chloroquine resistance in malaria requires only a two point mutation? (Maybe I missed this in my first read of the literature?)

    Because there are two mutations which show up in virtually every clinical case and in which any joining mutations are superfluous to the conferral of resistance. He goes by the data and the hard work of the biologists studying the genome.
    He is certainly not alone in surmising that two mutations are required. In fact , in arguing that Behe is too short some will say that the mutations add up cumulatively (ie: two are not required) while now you have him too tall and say that maybe this trait is hard to produce because it requires more than two mutations. If this is the case, for this simple pump-damaging trait, how much more the difficulty in producing real complexity? How many mutations must be required for the vast majority of beneficial protein adaptations?

    Doesn’t this seem like something that might incline one to wonder if malaria might evolve atypically, and even if there is something like a broadly typical evolution?

    Very good point, the second one here. On the first, why should we consider that the resistance to this trait evolving is atypical? Why should not all evolution be this difficult? All life is complex. Nearly all mutations are deleterious, even the “beneficial” ones come with a disadvantage and are very hard to fix in a population. All changes affect a cascade of events and interact with a myriad of limiting factors. This is what Behe is talking about. Why should we think that it is so difficult for E coli. to do something as simple as transport citrate aerobically when it can already do so anaerobically and already has all the metabolizing machinery in place, or that it is so difficult for p. falciparum to damage a pump, but somehow whales and bats evolved from a common ancestor with a fraction of the generational resources? Why should we take mere possibility claims and unrealistic mutation rates as being evidence for the theory in the face of real evidence?

    Is there something like a broadly typical evolution? Ought there not better be, if there is to be a theory claimed as fact?

    At the very least it should make you wonder if Behe’s use of bacterial evolution should have much to tell us about the evolution of other organisms – that the data he is so quick to flog Miller and Coyne with (Behe: “It is perhaps not too surprising that both Miller and Coyne make that mistake, because in general Darwinists are not used to constraining their speculations with quantitative data.”) might be more misleading than illuminating.

    True enough. Have you questioned the use of bacterial evolution to “prove” the efficacy of RM/NS? How often have you heard “antibiotic resistance” or “drug resistance” proves evolution? Have you questioned your use above with regard to Cit+? According to your statement and standard hasn’t Lenski only shown that in this particular experiment Cit+ arose without his actually saying anything about broadly typical evolution?
    Of course, it is accepted as evidence for the theory because all that is needed to maintain the paradigm is in-principle possibility.

    I didn’t mean to give the impression that I thought that a beneficial mutation that relied on two point mutations would be as common as one that relied on one. But I don’t think you’re nutshell restatement is really Behe’s point — if it was I don’t think we’d be having this discussion.

    Somehow I think we would. You’ve had a myriad of complaints against Beh, many of which are demonstrably false.

    Beh’s (latest) point seems to be that because of malaria’s known evolutionary changes Darwinism cannot therefore explain the diversity and complexity of biological structures – that malaria’s evolutionary response to sporadic human drug treatment represents an experiment so thorough that it disproves NDE.

    This is a very poor reading of his case. He goes through not only this case, to demonstrate the rarity of finding even a simple solution, but discusses the thousands of years of failed attempts to solve sickle cell in the purported arms race, as well as the mutations available to HiV in response to drug cocktails, as well as the fact that most mutations are deleterious and most beneficial ones are lost, as well as discussing the complex pathways required even if mutations accumulate beneficially, etc. The book is quite interesting and the case does not rely upon one example – even if it is the “centre piece”.

    I have to say that the more I read about of other biologists’ work in this field the consensus seems to be they don’t really even know where to begin, and I think I’m starting to see why.

    Here I agree quite closely with your last statement. I agree that the issue is so complex that it is difficult to know where to begin. But it is likewise difficult for all of life and for all explanations regarding these supposed mechanisms of evolution. And yet we are told time and again that it is a fact, and we find that only one side is allowed to present its data.
    When drug resistance is enlisted repeatedly as the great demonstration of what Darwinian evolution can do then it is perfectly permissible for one to use the available data and say “it doesn’t appear to be doing very much”. But you want, by appeal to our ignorance, for Behe to sit on the sidelines and keep quiet while others can crow triumphantly – but with equal ignorance – that we ‘ve seen enough to extrapolate to the ability to carry us from the simplest self-replicator to the complexity of the human brain.

    You:On another note, I just wanted to get back and respond to this statement of yours (I didn’t have time before, and I didn’t want to risk getting sidetracked from the interesting Behe discussion):
Me:I merely pointed out that my view can accommodate every class of explanation and yours can’t. Whether we are discussing the information in the DNA, the complexity of the cell, OOL, the implications of the Big Bang, the grounding of morality, the consciousness problem, the Cambrian explosion, the argument from reason, the efficacy of NDE, etc., you can only admit naturalistic/materialistic answers. In most of these cases there are not even plausible ones, which, if they exist, are taken as evidence that naturalism is adequate, but the problem is merely shuffled off to some future discovery. And yet, like Jerry Coyne and the journal in Behe’s correspondence above, the naturalist/materialist must just presume that one day such an answer will present itself – because the option just is no option.
This point ought to be obvious and completely uncontroversial.
Evidence the fact that you likely now agree with the assessment above and are thinking of responding that this commitment on your part is preferable to 1) non-scientific answers or 2) God of the gaps arguments.
    

You:I don’t think that your point is obvious nor uncontroversial.

    You don’t? So you believe that these problems above may never have naturalistic explanations? Your world view accommodates the fact that this might not just be a measure of our current ignorance but an actual in-principle limitation of naturalism/materialism to encompass all of reality?

    It is a good example of the kind of thing that I imagine you feel is merely factual and cannot be construed as an insult, but an insult is how it is taken. Your statement is normative and accusatory – it basically says that it is better to accept supernaturalism and that those who do not are close-minded.

    No it doesn’t. If philosophical naturalism/materialism is true then it is better not to accept the supernatural. I’ ve really admired your recent posts and your reliance upon evidence and your desire to get into the research but I do wish you’d find a way to read without your raw nerves exposed. Did you notice the insulting accusation you just made? You accused me of being accusatory. I’ll bet it is normative that one ought not be accusatory.

    But I think you anticipated my response, as the second part of your statement indicates. I can only say that I believe in a statement like yours the burden of proof remains yours – you owe it to yourself, at least, to demonstrate what your addition to Occam’s razor gives you in terms of practical, explanatory knowledge. (I’ll concede that it might make you feel better. But I don’t think you “know” anything more based on your philosophical assumption than I do with mine.)

    Isn’t this insulting? How dare you say my epistemology depends upon my emotional well-being? See how that works? Not very helpful.
    If we are going to discuss our differences of opinion you really have to allow me the right to make points even if you might find them insulting. I’m not going to be held hostage to your emotional responses, even though eliciting them or hurting your feelings is something I will and do try to avoid.

    Anyway, on to the substance.
    There is no violation of Ockham’s razor nor any addition and it is telling that you would think there is. The principle warns against multiplying entities beyond necessity. Since we haven’t a clue, scientifically speaking, what entities are required to explain any of the cases described above your criticism that I have multiplied anything, or that your view has even approached the necessity of explanation, is groundless.
    This is the similar to what you suggested above with Behe. You take a state of ignorance, say we can’t know for sure, and then somehow end up with your incomplete or insufficient explanation being the valid one while the challenge is out-of-bounds. If we don’t know enough for Behe to challenge the paradigm we don;t know enough to offer these instances as evidence. To claim that the “supernatural” is a superfluously-multiplied entity is to claim to know how what entities are actually involved; that is, to claim to know that philosophical naturalism/materialism is true. Not only can you not know this, not only can you not derive this from the science, but to make such a claim is to do exactly as I said above that your worldview demands. You cannot allow any hint that naturalism/materialism will not provide the answer, or that any other answer is valid, because if you do you lose the entire edifice. You say I am insulting you by suggesting this but you verify that this is the case by presuming, without evidence, that to implicate non-natural/material explanations is to go beyond what is necessary. You can only know what is necessary if you already know what exists, since we do not have answers or promises of answers to these questions within your paradigm.

    Here’s an example I’ve used before. If you ask me why the car turned left I can accommodate every level of material explanation. The car turned because the wheels turned. What caused them to turn? The position of the tie rod changed. This changed because the rack gear moved, because the steering column rotated, because the steering wheel was turned, because the hands on the wheel turned it, because muscles in the arm were flexed, etc. etc.
    Every level of secondary causation is sufficient to some degree but incomplete and insufficient in the end. I do not have to deny any step there and every detail given adds to the knowledge. And if the car turned without the will or cause of an agent I can accept this as well without any damage to my belief in agents. But, as an analogy, you can never admit the final cause – because the agent wanted to go left – and all you are able to accommodate is the string of secondary causes. And you must act like these are sufficient. And in cases where there is no chain of secondary causes (OOL, for instance) you have no explanation whatsoever.

    Finally, there is nothing more practical or explanatory than acknowledging our Creator, Lord and Savior and living according to the reality that is His will.

    Wish me luck posting this…

  155. Charlie,

    Sorry, I’ve been buried at work and busy at home. I have enjoyed this discussion, and I don’t want my late commenting pass as a lack of interest in continuing it.

    I’ll respond as soon as I can get some free time to go over your last.

  156. Thanks Tony,
    I’ve got a ton of things to attend to here in real-life as well, and as you can see, I’ve got enough on my plate at this blog anyway.
    Take your time and we’ll see where we’re at later on.

    Charlie

  157. Hi Charlie,

    To respond to the last part of your comment first, I’ll say that I have enjoyed this discussion more than any we’ve had on other posts, and I think that’s partly because you’ve met me halfway on figuring out how to express our viewpoints without (seeming to) assail the other.

    I pulled out your statement that began “I merely pointed out that my viewpoint can accommodate…” and replied in the kind to which I perceived it. I did honestly wonder if you considered that someone like me would read its message as insulting, and considered that you simply might not have. Anyway, I talk about all that a little bit more at the end of the post.

    But back to the discussion.

    Why are reviews and opinions which merely say what it is possible for us to imagine nature doing by itself publishable and the responses are not?

    I don’t think the scientific journals are in the business of questioning the philosophical assumptions necessary for methodological naturalism. They are keepers of the paradigm, more or less, and they are edited and published to record the progress of what Kuhn called “normal science.”

    As for biological journals publishing musings about the efficacy of naturalism I don’t know of any examples of that – but I just don’t read the biological journals as entire publications –what little I read is along the lines of the Lenski paper we’re discussing. Do you have typical examples of these metaphysical and philosophical ideas being published in biological journals? (Maybe you mean stuff like Gould’s more philosophical essays, one or two of which I’ve read, but I don’t know offhand where they were originally published – as I said, maybe there is space set aside for these kinds of articles and I just don’t know about the practice.)

    Even if his work has nothing to say about ID, philosophy, or anything metaphysical it is rejected on metaphysical grounds.

    Not sure about this one. I think that Behe has been published before, so presumably he has written biological work that has nothing to do with ID, philosophy, or anything metaphysical. The previous rejection letter you cited read:

    As you no doubt know, our journal has supported and demonstrated a strong evolutionary position from the very beginning, and believes that evolutionary explanations of all structures and phenomena of life are possible and inevitable. Hence a position such as yours, which opposes this view on other than scientific grounds, cannot be appropriate for our pages.

    The first sentence says to me, “our premise is methodological naturalism, and our theory is NDE. We’re going to see how far these take us.” And the second part seems to say that Behe’s criticism doesn’t represent a real scientific case, and I have to agree that the more I read of criticism of Behe’s books and arguments the more inclined I am to agree.

    Of course, lurking in the background of Behe’s criticism there has to be some awareness that pronouncements of scientific implausibility have a history of being demolished. From Werner von Braun’s warning about impossibility, to Lord Kelvin determining that heavier than air flying machines are impossible, Milham pronouncing atomic power to have zero likelihood, etc., there are lots of cases of seemingly-informed skepticism being wrong.

    Me: But I do still believe that if the biological challenges Behe poses falsified Darwinism then failure by his peers to recognize it would be gross incompetence.
    You: When and how will they consider it?

    I think that’s an outstanding question. I think Behe would be better considered if he or someone else came up with a competing theory as opposed to arguments of implausibility – a new theory that (better) explained and (better) predicted. Without that, though, he can be discounted as just another crank or kook. In other words, criticism of a prevailing and ultimately winning paradigms is quite common – I think of Priestly developing more and more elaborate constructs that denied the existence of oxygen (instead of phlogiston). What Priestly failed to do was develop an experiment that proved that phlogiston (and not oxygen) existed. Without that positive experiment, his criticism of (the theory of) oxygen had no real persuasive power other than the force of his reputation.

    But it is interesting, is it not, that all of these supposedly scientific critiques exist on the biological grounds of what you term a metaphysical or philosophical challenge?

    I don’t think I understand this question.

    There are far greater implications and whether or not bacteria can re-access a dormant or damaged trait, or whether or not they can damage genes and systems which give some benefit in some locale also matter. The kind of evolution you are seeing here is insignificant compared to the claims – not just in degree but in kind. We are not seeing the kind of rising fitness, (for instance, its not a constant environment, but a constantly manipulated one), the kind of rising adaptability or the increase in fitness that is necessary. Yes, we are seeing niche-filling, but, once again, not novelty. This is like saying if I shoot all the brunettes in a village I am evolving blondes. It is trivial in nature to say that every species occupies its own niche, it is far more ambitious to say that every niche will be filled or that in filling niches (or, in actuality, by creating them) RM/NS is going to evolve men from mud.

    The above reads like a kind of glass-half empty reading of evolutionary theory to me. I disagree with practically all of your interpretations above, but I guess that’s to be expected from the opposite sides with which we approach this issue.

    But this [my analogy about blind fish and fitness being tied to environment] says nothing whatsoever about how fish came to have eyes – or any other complex feature – in the first place.

    Well, I was trying to make an argument about fitness, not about complexity. And your statement that “blind cave fish are broken and are less fit” seems to be based on a premise that greater complexity equals more fit, and I don’t think that this is necessarily true.

    Regarding the eye and complexity I believe the evolutionary origins of eyes are pretty well-explained. I thought I remembered Dawkins talking about it in the Blind Watchmaker, for one. I’ll bet that you’ve read them as well, and find them as unpersuasive as I found them persuasive, though, so I’ll leave it at that.

    Regarding my complaint that Behe is basing his argument that NDE fails at a roughly defined edge with his argument on chloroquine resistance arising from a two point mutation (when he cannot know this), you wrote:

    Why should Behe not make a case based upon what we do know and without speculating about unknown factors?

    I think that Behe is basically making a deductive argument – if this premise and this premise are true, then we can conclude this. An argument like this fails if its premises are false. Behe appears to be playing a game where he uses the kind of probabilistic data employed in inductive arguments to make a deductive one. In other words, I don’t think that Behe’s premises are things that we “know” well enough to employ them deductively.

    In Behe’s case, he is taking at least these things are “known” well enough to be used as premises: 1) that the reported instances of chloroquine resistance in malaria are definitive for the frequency of this event occurring; 2) that chloroquine resistance in malaria is the result of only two point mutations; 3) that chloroquine resistance in bacteria is the model by which all beneficial two point mutations occur; and 4) that two point mutations in malaria resulting in chloroquine resistance have broad implications for how NDE must occur. If chloroquine resistance in malaria is the centerpiece of his book’s argument, then it appears that the centerpiece relies on lots of sketchy knowns.

    I think you’re missing my point with the section that begins with…

    Back to White, he is not saying that multiple genes are required for the conferral of CQR.

    White is saying, quite clearly, that “Chloroquine resistance in P. falciparum may be multigenic…” and “At least one other as-yet unidentified gene is thought to be involved.” How you can surmise from this that “…any joining mutations are superfluous to the conferral of resistance” is beyond me. My point is that White (nor any other biologist I’ve read so far on this topic) is ready to make the leap that Behe takes – that chloroquine resistance is the result of only two point mutations. It may definitely require two point mutations, but declaring that those two point mutations alone are all that is required is a leap – what one critic called a determination by fiat.

    Why should we take mere possibility claims and unrealistic mutation rates as being evidence for the theory in the face of real evidence?

    I would say that because evolutionary theory continues to predict, explain, and be productive, and because nothing even remotely more explanatory has been offered, we should continue to work within its framework (why not?). I would ask, why should we accept deductive arguments based on weak premises as an argument that a productive theory is fatally flawed?

    Is there something like a broadly typical evolution? Ought there not better be, if there is to be a theory claimed as fact?

    I think we talked about this a long time ago, regarding the difference between scientific facts, laws, and theories. I don’t think that proponents of NDE claim that it is a fact; it’s a theory that tries to explain scientific facts (among which is evolution).

    Regarding the question of whether or not there should be a broadly typical evolution I don’t think this is a requirement, as the scientific facts are what they are. To the extent there are similarities they should be explained in the theory. Clearly, there are enough scientific facts to buttress the explanatory power of RM, NS, and common descent, although I would say there’s a great deal of room for refining these principles.

    Have you questioned the use of bacterial evolution to “prove” the efficacy of RM/NS? How often have you heard “antibiotic resistance” or “drug resistance” proves evolution?

    This question seems a little backward to me. I would say that NDE explains the structures and behavior of biological organisms, and that observations of bacterial evolution support this claim. I think I would say that “proves” belongs in the same class as “impossible” when discussing scientific conclusions – it’s a convenient shorthand but shouldn’t be used when it can be confused with its literal and technical definitions.

    You’ve had a myriad of complaints against Behe, many of which are demonstrably false.

    Yes on myriad, but I don’t know that so many have been false. I’m not pleading for a perfect record here, but I wouldn’t classify a large portion of my complaints as false either.

    The book is quite interesting and the case does not rely upon one example – even if it is the “centre piece”.

    This could be true, and I apologize for not having read the book, and appreciate your taking the time to share your knowledge. (Although at this point it might have been a more efficient use of my time to have read the darn thing.)

    And yet we are told time and again that it [evolution] is a fact, and we find that only one side is allowed to present its data.

    Well, and sorry for repeating myself, I think evolution (even taking Behe’s definition of common descent) is a fact, but the theory is not a fact, it’s a theory. As for presenting data, Behe appears to be borrowing data, not presenting any – what he’s been prevented from doing is publishing his philosophical conclusions (based on this borrowed data) in biological journals, for reasons I find appropriate.

    When drug resistance is enlisted repeatedly as the great demonstration of what Darwinian evolution can do then it is perfectly permissible for one to use the available data and say “it doesn’t appear to be doing very much”.

    I don’t believe that “therefore, Darwininan evolution is proved” is a conclusion you’ll find in many articles published in the biological journals. The biological papers we cite in these comments make no such claims, for one. I agree that they are working within that framework, but that is to be expected from the format. Behe’s conclusions (NDE is doomed as an explanatory theory) are much bigger than, say, Lenski’s (E. coli can achieve a contingent mutation that enables them to process Citrate through the membrane in oxic conditions), and as I tried to say above Behe’s argument is based on shaky premises, but more importantly the journals themselves are not the format for such an argument should it exist, and lastly criticism of a theory’s purported limitations does not, perforce, supplant the theory; it’s one thing to notice that planetary movement doesn’t match up with a geocentric system, but it’s another altogether to put forward a system that better explains the data that we have.

    I think that the point you’re driving at here – that where and how are those like Behe going to cause the underdetermination of NDE? – is a really good one, and I do think there should be (and probably is) a proper method for doing so. What I’m trying to say is that Behe’s argument does appear like a square peg in the round holes of the biological journals, and that I don’t know what the proper steps are for Behe’s argument. I’d guess that an experiment that operated on induction and resulted in positive knowledge would be the best starting point from within the journal system.

    The principle warns against multiplying entities beyond necessity. Since we haven’t a clue, scientifically speaking, what entities are required to explain any of the cases described above your criticism that I have multiplied anything, or that your view has even approached the necessity of explanation, is groundless.

    I think that this and the last part of your comment that follows it is overreaching (you really want to say that we don’t have a clue about the origins of biological structures and behaviors?), and I don’t think you’ve addressed my question. This, for instance, is a non-answer: “Finally, there is nothing more practical or explanatory than acknowledging our Creator, Lord and Savior and living according to the reality that is His will.”

    To claim that the “supernatural” is a superfluously-multiplied entity is to claim to know how what entities are actually involved; that is, to claim to know that philosophical naturalism/materialism is true.

    I don’t think I agree with your understanding of Occam’s razor. As I understand it, one doesn’t need to know all the entities that could be involved to invoke Occam’s razor; one only needs to recognize entities that are superfluous.

    There are at least two problems with supernatural explanations regarding Occam’s Razor: one is that the supernatural adds no prediction or explanation to the theory, and the other is that there is no way to perceive it (perception of the supernatural redefines it to the natural – I’ve never understood how a supernatural definition can avoid the paradox of a) being perceived and b) remaining supernatural). Defining everything “we don’t know” as “supernatural” adds nothing to a theory that is not superfluous, and I think it falls on the wrong side of Occam’s razor.

    You cannot allow any hint that naturalism/materialism will not provide the answer, or that any other answer is valid, because if you do you lose the entire edifice.

    Statements like this imply that I hold some kind of slavish devotion to a worldview that I deem more important than opening mind to every kind of evidence. It’s gratuitous because it paints your opponents in these discussions as intellectually dishonest, and I don’t believe that you can’t imagine another way for me to come to my views. I’m not saying you can’t or shouldn’t make these kinds of accusations, but likewise I will take the time to classify them for what I believe they are.

    Also, I haven’t fully addressed this repeated charge, but I do read over and over again in conversations like these that theism presents a superior, more open worldview than one like mine, which is agnostic, skeptical, and relies mostly on a minimum of philosophical assumptions and methodological naturalism. It has never been demonstrated to me that my worldview somehow limits me from knowing anything that theists truly know, nor do I believe it’s true that I am dedicated to my worldview as a prior commitment to the evidence. Since you brought it up, however, I’ll suggest that the same could be true of you. In fact, I believe that my belief in a theistic god could be initiated by any number of events, whereas I believe your theism would be unshaken by virtually any evidence. In fact, the small percentage of atheists and agnostics throughout history and worldwide compared to theists could be construed as evidence that atheists are more open to worldview changes than their counterparts.

  158. Hi Tony,
    Thanks for your lengthy and thought-out reply.

    I want to move the last up here to the first. I think your discussion of Ockham’s Razor illuminates the rest of your response and so I’ll use it to set the stage.
    I have written a long reply here but am going back to edit out much that is extraneous. Before I’m done I hope to have left out most of my responses to your beliefs and opinions. I doubt I will have because that is the bulk of what I see here – we seem to have fallen to where all we are going to do is repeat our own viewpoints. I’ll see how much remains ….

    Me, on Ockham:
    The principle warns against multiplying entities beyond necessity. Since we haven’t a clue, scientifically speaking, what entities are required to explain any of the cases described above your criticism that I have multiplied anything, or that your view has even approached the necessity of explanation, is groundless.
    Tony:
    I think that this and the last part of your comment that follows it is overreaching (you really want to say that we don’t have a clue about the origins of biological structures and behaviors?),

    Before I begin I will use this to highlight why I might be about done here.
    I know I told you to take your time but the fact that there is so much delay between your responses is destroying any ability here to have a conversation. You seem to be forgetting context and what I’ve said previously. This will become obvious later as well. The double problem here is that when you respond in a negative manner then I am first, likely to respond likewise, second, likely to have forgotten the context and accept in part, your characterization of my words, third, likely to have lost at least part of my train of thought and fourth, forced then to find the context, reacquaint myself with it, and, in some cases below, go find papers again and do my own research again.
    This process is time-consuming enough without this extra feature, so, just so you know, I may not continue much longer in this vein. Or at least I won’t be giving responses any priority.

    As to the quote above I said “the cases above”. That pertained to:
    “Whether we are discussing the information in the DNA, the complexity of the cell, OOL, the implications of the Big Bang, the grounding of morality, the consciousness problem, the Cambrian explosion, the argument from reason, the efficacy of NDE, etc., you can only admit naturalistic/materialistic answers. ”

    and I don’t think you’ve addressed my question. This, for instance, is a non-answer: “Finally, there is nothing more practical or explanatory than acknowledging our Creator, Lord and Savior and living according to the reality that is His will.”

    This is not a non-answer – this is the ultimate answer.
    It is the answer to the question you ought to be asking. I answered the question you were actually asking well before I made this most important remark. That was on why my viewpoint is not a violation of Ockham’s Razor. That answer continues below as you found it unacceptable.

    Me:To claim that the “supernatural” is a superfluously-multiplied entity is to claim to know how what entities are actually involved; that is, to claim to know that philosophical naturalism/materialism is true.
    You: I don’t think I agree with your understanding of Occam’s razor. As I understand it, one doesn’t need to know all the entities that could be involved to invoke Occam’s razor; one only needs to recognize entities that are superfluous.

    I’ll reply with the rest of my previous point.
    “You say I am insulting you by suggesting this but you verify that this is the case by presuming, without evidence, that to implicate non-natural/material explanations is to go beyond what is necessary. You can only know what is necessary if you already know what exists, since we do not have answers or promises of answers to these questions within your paradigm.”
    How can you possibly know which entities are superfluous, as answers to questions, when you don’t know which entities are required to answer those questions ? You haven’t a clue, as I said before, for instance, what entities are required to account for the above observations – so you have no rational basis for saying that God is superfluous to the question, so Ockham has nothing to say about invoking Divine causation.

    There are at least two problems with supernatural explanations regarding Occam’s Razor: one is that the supernatural adds no prediction or explanation to the theory,

    I’m certainly not interested in going around on the “all knowledge is scientifically predictive” carousel again.
    This argument is scientism, ignores the practicality of knowing the Truth, and is irrelevant to my world-view and the question of parsimony.
    Interestingly to me, as your language looks to be straight off the Wiki page on Ockham I will point you back to that page. The principle is a metaphysical claim, not a scientific one (it is not justified by your world view, it is not proven or explained by science). It provides no principle by which we can gauge truth or ontological reality but merely adds a heuristic to scientific endeavours.
    Not all questions are scientistic.

    and the other is that there is no way to perceive it (perception of the supernatural redefines it to the natural – I’ve never understood how a supernatural definition can avoid the paradox of a) being perceived and b) remaining supernatural). Defining everything “we don’t know” as “supernatural” adds nothing to a theory that is not superfluous, and I think it falls on the wrong side of Occam’s razor.

    You are mistaken in your dismissive definition, your scientism and the superfluity of the explanation. There are dozens of philosophical lines of inquiry for which God is the best answer – including the teleological and ontological arguments, as well as the arguments from reason, abstract objects, morality, etc.. But we are not about to re-explore these here either.
    This thread is quickly becoming too full of all kinds of assertions about theism (now we’re supposed to debate the utility of the term “supernatural”?) and I’m not going to spend much more time tracking them down. They have been answered and argued throughout this blog and they have nothing to do with your claim about Ockham’s razor.
    My world view is in no way a violation of it and there is nothing science has to say about the question.

    Me: You cannot allow any hint that naturalism/materialism will not provide the answer, or that any other answer is valid, because if you do you lose the entire edifice.
    You: Statements like this imply that I hold some kind of slavish devotion to a worldview that I deem more important than opening mind to every kind of evidence.

    No it doesn’t. It implies that you have a worldview that can only look at the problem in one way and, therefore, the problems/answers all must conform to one class of answer. Your inference about slavish devotions is your own.

    It’s gratuitous because it paints your opponents in these discussions as intellectually dishonest, and I don’t believe that you can’t imagine another way for me to come to my views.

    You can read everything as an insult and argue to justify your emotional indignation if you want but the game is uninteresting to me and I won’t be blackmailed by your perceptions. You have given ample evidence in this last comment alone to demonstrate that my observation is not gratuitous but is accurate and instructive.

    For instance, you accept Dawkins’ account of the evolution of the eye even though it contains no science (no model, no tests, no falsifiability, etc.) but you hold Behe to an incredibly greater standard. You also accept the philosophical position of the journals that rejected Behe , commend their position, and can’t even see that it is a philosophical position. Whether you are dishonest or not is not the question when we have the empirical facts about how your view colours your perceptions.

    I’m not saying you can’t or shouldn’t make these kinds of accusations, but likewise I will take the time to classify them for what I believe they are.

    As you will. Can you go back and classify for me what it means when you call me disingenuous, and my arguments gratuitous, and when you imply of my world view that I’ve chosen it for comfort?

    It has never been demonstrated to me that my worldview somehow limits me from knowing anything that theists truly know, nor do I believe it’s true that I am dedicated to my worldview as a prior commitment to the evidence.

    This is one I should probably edit out, but I’ve demonstrated your limitations several time on this blog, in this thread and in this very comment (on Ockham and to come).
    And of course, you are begging the question on “truly know” and you will justify this question-begging with further appeals to your scientism.

    Since you brought it up, however, I’ll suggest that the same could be true of you.

    You already said the same of me – when I was talking about evolutionary biologists. That’s why we’re on this. I said evolutionary biologists see every problem as a nail and you said that I am likewise limited. I showed you that theism allows me to see problems as both nails and screws, because I am not limited to a hammer; but neither must I deny the existence of nails and the utility of hammers.
    Then you decided that my defence of my claim was personally insulting to you, and here we are again/still, arguing over whether or not you should be offended.

    In fact, the small percentage of atheists and agnostics throughout history and worldwide compared to theists could be construed as evidence that atheists are more open to worldview changes than their counterparts.

    That’s an interesting point but without argument I can’t see any way that it follows from your premise. But I’ll agree that atheists are open to just about anything – as long as it’s not God; such as multiverses (talk about violating the famed razor), something coming from nothing, morality from amorality, reason from non-reason, a naturally and miraculously intelligible universe, unintelligent abiogenesis, alien life-seeders, an infinite regress of causes, etc. And, on evidence, the evidence is that Christianity allows people to better see what is presented to them (while atheists miss patterns that actually exist) and are less likely to believe (as there is no evidence) in such things as astrology and UFOs.

    But back to the discussion.
    Me: Why are reviews and opinions which merely say what it is possible for us to imagine nature doing by itself publishable and the responses are not?
    You: I don’t think the scientific journals are in the business of questioning the philosophical assumptions necessary for methodological naturalism.

    This questioning is not required in order to contemplate Behe’s case or publish him (nor in the cases of Gentry, Austin or countless creation scientists, either) and Darwinian evolution is not the sum of all science nor the only post holding “methodological naturalism” in place.

    They are keepers of the paradigm, more or less, and they are edited and published to record the progress of what Kuhn called “normal science.”

    Good. So we are still agreed. You happen to think this is fine, but you also happen to present Behe’s lack of publishing, his inability to get past the gatekeepers – in what you continually admit is a field from which he is disqualified – as saying something about the veracity of his case when it isn’t.
    But we are just repeating ourselves here.

    As for biological journals publishing musings about the efficacy of naturalism I don’t know of any examples of that – but I just don’t read the biological journals as entire publications –what little I read is along the lines of the Lenski paper we’re discussing.

    They are full of such musings. The one that first caught my attention was on the 1-in-a-million genetic code. Our code is by far the best imaginable, and its error resistance and correction puts it above all other possible codes. The investigators on this article could not leave their discussion at that empirical description. Almost as though they were required to pay their due there was a tacked-on discussion at the end about how natural, unguided evolution could have produced such a code. This was entirely unnecessary to the paper and had only to do with buttressing the philosophical position that naturalism somehow took care of this. You will see this superfluous tack-on in paper after paer when you read more of them, and if you do so with an eye toward it.
    I next noted the same thing in a review article (borrowed data, no new data) on the Big Bang where, for no reason at all, biological evolution was invoked, asserted to be naturalistic and true, in some irrelevant comparison to the Big Bang. If you can stomach it, and not return here to argue about how you don’t like the website, I’d recommend you read creationsafari to see how often “evolution did it” is tacked onto journal articles where it is completely unnecessary and unjustified byt the content.

    You: The previous rejection letter you cited read:
    As you no doubt know, our journal has supported and demonstrated a strong evolutionary position from the very beginning, and believes that evolutionary explanations of all structures and phenomena of life are possible and inevitable. Hence a position such as yours, which opposes this view on other than scientific grounds, cannot be appropriate for our pages.
    The first sentence says to me, “our premise is methodological naturalism, and our theory is NDE. We’re going to see how far these take us.” And the second part seems to say that Behe’s criticism doesn’t represent a real scientific case, and I have to agree that the more I read of criticism of Behe’s books and arguments the more inclined I am to agree.

    You are skipping their philosophical commitment to naturalism. They told Behe that naturalistic solutions are inevitable and that to oppose this inevitability is inappropriate. As seen above on Ockham, you can only know that naturalistic answers are inevitable if you already happen to know that “nature” is all that is acting. This is a philosophical position.
    This has nothing to do with a given methodology (which you present here as the ‘game’ of science’) but a belief that every biological problem has a naturalistic solution. This is adherence to a philosophy, not a methodology. This is making a claim that they already know what class of causes exists – and that they are naturalistic. This is the same eror you brought to the Ockham discussion.

    Of course, lurking in the background of Behe’s criticism there has to be some awareness that pronouncements of scientific implausibility have a history of being demolished. …
    there are lots of cases of seemingly-informed skepticism being wrong.

    All scientific findings have a history of being demolished. Most of what is published today is wrong, and publishers know it. It has nothing to do with the worry that the idea might be overturned one day – they all will be – that’s the history of science.
    It has only to do with the fact that they already think Behe is wrong philosophically.

    I think that’s an outstanding question. I think Behe would be better considered if he or someone else came up with a competing theory as opposed to arguments of implausibility – a new theory that (better) explained and (better) predicted.

    Maybe so. But in order to demonstrate that one position is wrong there is no requirement that you have to offer another. If science is a search for the truth and not merely a game governed by rules of admissibility then this criterion is counter-productive.

    Without that, though, he can be discounted as just another crank or kook.

    Why can he be?
    Are you making an obvious statement of fact – that it is possible to dismiss Behe as a kook- as has been done? Or are you justifying that dismissal?

    Me: But it is interesting, is it not, that all of these supposedly scientific critiques exist on the biological grounds of what you term a metaphysical or philosophical challenge?
    You: I don’t think I understand this question.

    I’ll elaborate. You say that Behe is providing a merely philosophical /metaphysical challenge and not a scientific one (you repeat in this comment above that Behe is presenting no real scientific case). But then you point to scientific answers to his challenge. If his challenge is not scientific then there would be no scientific answers to it. If his questions can be answered on the biological bases why can his challenges on these not be presented?
    You guys can’t have it both ways. “ID is unfalsifiable, and here’s how I’ve falsified it” or “ID is purely metaphysical, and here’s a scientific argument against it”.
    Typing that I just realized that your claim is another result of your scientistic world view – you think Behe is making a metaphysical claim, but you think naturalistic science has defeated it. This is a category error.
    And what Behe is doing is making a scientific claim with metaphysical implications. He is being dismissed because of the implication – not the claim.

    Me: But this [my analogy about blind fish and fitness being tied to environment] says nothing whatsoever about how fish came to have eyes – or any other complex feature – in the first place.
    You:Well, I was trying to make an argument about fitness, not about complexity. And your statement that “blind cave fish are broken and are less fit” seems to be based on a premise that greater complexity equals more fit, and I don’t think that this is necessarily true.

    You are correct – it isn’t. But if it isn’t then you lose the complexity ratchet that I’ve been discussing since DL re- introduced this side-topic for whatever reasons he had. If complexity is not necessarily more fit, then selecting for fitness will not necessarily select for complexity. In fact, in the bulk of the examples we have (arguably, all of them) all we have is fitness equating to less complexity or, at best, no gain in complexity. But mud to man evolution requires ever-increasing complexity. Everyone knows this even as they try to deny it. Darwin would throw the caveat around once in a while that we must not think of evolution as linear or moving toward greater complexity, but then he would fall back on the necessity of increasing complexity repeatedly because the ratchet needs it.
    You’ve got too little time, too few resources, and too little variation to account for the grand claims of the theory in the first place. When you add to the mix the fact that complexity is not necessarily fitter you take away the just-so stories as well.
    When you add to this the fact that most “increases” in fitness are losses of genetic information, as in your analogy, or breaking of parts, you further damage the grand claims.

    Regarding the eye and complexity I believe the evolutionary origins of eyes are pretty well-explained.

    The eye is entirely beside the point of whether or not mutations which, conditionally, have some positive effect on survival, are actually increasing the complexity, improving the species, or adding any knowledge about the origination of new parts, machines, etc. … but now I am curious. You have questioned me above on practical explanations and now you offer this. I would love to see what scientific ( detailed, testable, falsifiable, all-natural) explanation has persuaded you.

    On the other hand, if your example is Dawkins, as follows, I believe your belief is mistaken.

    I thought I remembered Dawkins talking about it in the Blind Watchmaker, for one. I’ll bet that you’ve read them as well, and find them as unpersuasive as I found them persuasive, though, so I’ll leave it at that.

    You ought not leave it at that. You should look into it. There is nothing whatsoever explanatory or persuasive about Dawkins’ explanation. There is no modeling and he … was wrong …. about there being a computer “simulation”.
    There is no science behind his metaphysically=motivated claims.
    http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1061

    Me: Why should Behe not make a case based upon what we do know and without speculating about unknown factors?
    You: I think that Behe is basically making a deductive argument – if this premise and this premise are true, then we can conclude this.

    No, he’s making an empirical argument. Here are the known facts, here are the observations, here’s what we can observe happening.

    I am always suspicious when new terms are introduced late in a discussion to eliminate concepts, in-principle, which we’ve been already been discussing without those terms.

    In Behe’s case, he is taking at least these things are “known” well enough to be used as premises: 1) that the reported instances of chloroquine resistance in malaria are definitive for the frequency of this event occurring;

    This is true – depending upon what you mean by “occuring”. As has been elaborated repeatedly, he is not talking about a mutation rate. He is talking about the frequency of the event actually coming to form a population. This is what evolution has to do – it can’t just come up with traits and then lose them to the vagaries of history. Of course, not only are most mutations deleterious, but the researchers admit that even the beneficial ones are most likely to be lost – another shot against the theory.

    2) that chloroquine resistance in malaria is the result of only two point mutations;

    This is what the evidence tells us. But he draws his inerence further than that. He is showing that what evolution has actually accomplished here, slight damage to a pump, is very minimal. One, two or ten mutations, this is a very simple little bit of tinkering – and it is very rare. He then dissusses this as a CCC, he doubles its rarity, a double CCC, and then says, “is it not likely that things twice as difficult as breaking a pump were required in the evolution of mud to man?” He answers in the affirmative.

    3) that chloroquine resistance in bacteria is the model by which all beneficial two point mutations occur; and

    He is not making it the model. Anybody can select another model and show how evolution works better. It just so happens, again, that this is the data we have, this is where we see the most generations, the greatest number of mutations, and a very observable arms race all of the necessary ingredients for evolution. This is also where we hear the claims “drug resistance and insecticide resistance” provide great evidence for evolution. He shows they don’t – or at least, that that great evidence actually goes to demonstrating the limitations to evolution.

    4) that two point mutations in malaria resulting in chloroquine resistance have broad implications for how NDE must occur. If chloroquine resistance in malaria is the centerpiece of his book’s argument, then it appears that the centerpiece relies on lots of sketchy knowns.

    It says nothing about how NDE must occur. It dismantles one of the strongest claimed evidences of how NDE does occur. It also, as a matter of fact, argues against the best and truest method of achieving sequences change – random point mutations.
    I don’t think your sketch is very accurate.

    You: I think you’re missing my point with the section that begins with…
    Me: Back to White, he is not saying that multiple genes are required for the conferral of CQR.
    You: White is saying, quite clearly, that “Chloroquine resistance in P. falciparum may be multigenic…”

    True. But you must read him further than that.

    and “At least one other as-yet unidentified gene is thought to be involved.” How you can surmise from this that “…any joining mutations are superfluous to the conferral of resistance” is beyond me.

    It is? It’s impossible for you to imagine how I might surmise?
    You must read him further.
    In fact, I already showed you why it is superfluous to the conferral of resistance” and I used White’s own words and the same source you used (didn’t I do this in the very comment to which you are responding?)”

    White:Chloroquine resistance in P. falciparum may be multigenic and is initially conferred by mutations in a gene encoding a transporter (PfCRT) (13).
    Me: Resistance arises immediately with the mutations to the PfCRT [independently and without requirement of any other mutations to any other genes].
He then mentions PfMDR, which has been shown above to be unnecessary, which he acknowledges himself:
    White:In the presence of PfCRT mutations, mutations in a second transporter (PfMDR1) modulate the level of resistance in vitro, but the role of PfMDR1 mutations in determining the therapeutic response following chloroquine treatment remains unclear (13).

    http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2?%5Fencoding=UTF8&cursor=1193328991.375&cursorType=before

    As I said above, this lag between comments is not really working. You seem to be forgetting what I’ve already presented.

    It may definitely require two point mutations, but declaring that those two point mutations alone are all that is required is a leap – what one critic called a determination by fiat.

    That critic is wrong. Behe is using the best evidence including, as I showed previously, the mathematical correlation.
    I already pointed out that:

    What I was recalling was that the occurance of resistance to a drug arising from one mutation, such as atovaquone, when multiplied by itself gets us in the neighborhood of the occurance of resistance to chloroquine, demonstrating another reason to suspect the necessity of two instead of one mutation in the latter case. Both would appear then to be treated equally by NS acting on RM and the correlation would indicate the necessity of two mutations for something as simple as damaging a membrane pump.

    He gives us further information on page 59 when he demonstrates that CQR arises about 100 million times less frequently than resistance to atovaquone. Atovaquone requires one mutation and there are roughly 100 million nucleotides in the malaria genome. Therefore, it takes, after finding the one mutation, as in atovaquone resistance, another 100 million tries to find a second.

    Me: Why should we take mere possibility claims and unrealistic mutation rates as being evidence for the theory in the face of real evidence?
    You: I would say that because evolutionary theory continues to predict, explain, and be productive, and because nothing even remotely more explanatory has been offered, we should continue to work within its framework (why not?).

    You didn’t answer the question. The question wasn’t why we ought not work within the framework, but why non-evidence ought to be taken as evidence.
    Why not? Because the evidence is against the theory. But the ability to present that evidence is suppressed – and you approve, as above.

    I would ask, why should we accept deductive arguments based on weak premises as an argument that a productive theory is fatally flawed?

    This side-alley about deductive/ inductive is going to need more fleshing out if you want it to bear any weight. The better question is why don’t you accept the empirical evidence about the weaknesses of the theory and weigh them against the claims made for the theory? Drug -resistance, the go-to evidence of NDE tells us more about its limitations than its ability to produce complexity.

    Me: Is there something like a broadly typical evolution? Ought there not better be, if there is to be a theory claimed as fact?
    You: …Regarding the question of whether or not there should be a broadly typical evolution I don’t think this is a requirement, as the scientific facts are what they are. To the extent there are similarities they should be explained in the theory. Clearly, there are enough scientific facts to buttress the explanatory power of RM, NS, and common descent, although I would say there’s a great deal of room for refining these principles.

    1) You say that the theory (the paradigm) is not a fact, but we see the keeper’s of the paradigm protecting it as though it were. And to your approval.
    2) Behe ‘s work, the math, and the widespread and building rejection of NS as a potentiating factor all argue against your position.
    If the broad theory can’t explain the particulars, if you need a new fix and a different explanation for every observation – which you do (note analogous/homologous features, neutral/near neutral [now dead] and adaptationist theory, convergence/divergence, molecular clock heterogeneity, punk eek, endosymbiosis, lateral transfer, founder effect, allopatry, etc.) – then you don’t really have a scientific theory. All you have is a metaphysical position based upon sheer possibility – “nature can do it, therefore, nature did it”.

    Me: Have you questioned the use of bacterial evolution to “prove” the efficacy of RM/NS? How often have you heard “antibiotic resistance” or “drug resistance” proves evolution?
    You: This question seems a little backward to me. I would say that NDE explains the structures and behavior of biological organisms, and that observations of bacterial evolution support this claim. I think I would say that “proves” belongs in the same class as “impossible” when discussing scientific conclusions – it’s a convenient shorthand but shouldn’t be used when it can be confused with its literal and technical definitions.

    Let me re-ask then. How many times have you heard that the fact that bacteria can become drug-resistant or that insects can become insecticide-resistant provides strong evidence – perhaps the strongest evidence – for the efficacy of RM? Shouldn’t we explore what this really means and the significance of such evidences? When we see that this strongest evidence points to evolution doing very little don’t you think that is significant and ought to be discussed?

    On this point, I already told you previously about population geneticist
    Maciej Giertych, and how biologists in different fields just presume somebody else has the evidence and how those “strongest evidences” are really not.

    Gradually, as my children got to the stage of learning biology in school and discussing their problems with Dad, I realized that the evidence for Evolution had shifted from paleontology and embryology to population genetics. But population genetics is my subject! I knew it was used to explain how Evolution progressed, but I was not aware it is used to prove it. Without my noticing it, my special field had become the supplier of the most pertinent evidence supporting the theory.

    If Evolution were proved in some field I was not familiar with, I understood the need to accommodate my field to this fact, to suggest explanations how it occurred in terms of genetics. But to claim that these attempted explanations are the primary evidence for the theory was quite unacceptable to me. I started reading the current literature on the topic of Evolution. Until then I was not aware how shaky the evidence for Evolution was, how much of what was “evidence” had to be discarded, how little new evidence had been accumulated over the years, and how very much ideas dominate facts. These ideas have become dogma, yet they have no footing in natural sciences. They stem from materialistic philosophies.

    —-

    Me: And yet we are told time and again that it [evolution] is a fact, and we find that only one side is allowed to present its data.
    You: Well, and sorry for repeating myself, I think evolution (even taking Behe’s definition of common descent) is a fact, but the theory is not a fact, it’s a theory. As for presenting data, Behe appears to be borrowing data, not presenting any –

    Even if he borrowed it he still presented it. And he deliberated upon it and drew new data from the data he “borrowed”. Everybody does this, this is science, and these slights against every legitimate aspect of his work and throughout this comment are not doing your case any good.

    what he’s been prevented from doing is publishing his philosophical conclusions (based on this borrowed data) in biological journals, for reasons I find appropriate.

    But he’s also prevented from presenting his non-philosophical conclusions when paradigm supporters are allowed to. And he is prevented upon philosophical grounds. But we are repeating ourselves. If you look at the correspondences I linked you will see that Behe was not making a philosophical point, but his reviewers were. You’ve already commended this as well, because they ‘know’ that lurking behind his scientific case he has an IDist’s agenda.
    If you look into what happened when he published in 2004, with zero philosophical content, you’ll see the paradigm-supporters don’t care whether he makes a philosophical case or not.

    Me: When drug resistance is enlisted repeatedly as the great demonstration of what Darwinian evolution can do then it is perfectly permissible for one to use the available data and say “it doesn’t appear to be doing very much”.
    You: I don’t believe that “therefore, Darwininan evolution is proved” is a conclusion you’ll find in many articles published in the biological journals. The biological papers we cite in these comments make no such claims, for one. I agree that they are working within that framework, but that is to be expected from the format. Behe’s conclusions (NDE is doomed as an explanatory theory) are much bigger than, say, Lenski’s (E. coli can achieve a contingent mutation that enables them to process Citrate through the membrane in oxic conditions), and as I tried to say above Behe’s argument is based on shaky premises,

    You did say this above, but you were mistaken – as I tried to say above.

    but more importantly the journals themselves are not the format for such an argument should it exist,

    Only because they have a philosophical bias against his empirical case.
    We saw it when Seelke proposed a test to knock out two bases in a gene and see if RM can replace them and re-create its complexity. When he was turned down the reviewers told him we already know that RM/NS can produce complexity (just look around) – this is based upon philosophical naturalism, and that there is no point in doing the experiment because we already know RM/NS can do this so what is proven by finding an instance where it fails? Again, the acting entity is already known to do everything credited to it, so why investigate?

    and lastly criticism of a theory’s purported limitations does not, perforce, supplant the theory;

    Science is a process of adding pieces to the puzzle. Behe’s pieces are not being added, the gate-keepers only allow certain pieces, and the people who could assess Behe’s case and perhaps look at their own evidence in different ways neither are encouraged by his rejection to do so, nor are fairly presented with his case.

    I think that the point you’re driving at here – that where and how are those like Behe going to cause the underdetermination of NDE? – is a really good one, and I do think there should be (and probably is) a proper method for doing so. What I’m trying to say is that Behe’s argument does appear like a square peg in the round holes of the biological journals, and that I don’t know what the proper steps are for Behe’s argument. I’d guess that an experiment that operated on induction and resulted in positive knowledge would be the best starting point from within the journal system.

    Like Seelke’s demonstration that RM has, as Behe has inferred from real-world observation (induction), a great deal of difficulty coming up with two necessary mutations? Seelke has shown through his work with bacteria the same thing that Lenksi did – that two mutations are very hard to come by. But Lenski is allowed to say so, while Behe and Seelke are not.
    He has shown the same thing I presented early in this thread – that when “evolution” is properly tested it does very little. RM mostly breaks things and does very little to aid an organism or to add to the upward complexity required by the theory. Dobzhansky and Nilsson, as seen previously, showed this experimentally, as has Lenski now, as has Seelke, and as have others.

  159. Hi Charlie,

    I agree that the discussion as it’s been progressing recently risks losing its focus re Behe et al.

    The double problem here is that when you respond in a negative manner then I am first, likely to respond likewise, second, likely to have forgotten the context and accept in part, your characterization of my words, third, likely to have lost at least part of my train of thought and fourth, forced then to find the context, reacquaint myself with it, and, in some cases below, go find papers again and do my own research again.

    Agreed. I hesitate to set off a cycle of negative comments here as well, mostly because I’ve enjoyed most of our discussion.

    As to the quote above I said “the cases above”. That pertained to:
    “Whether we are discussing the information in the DNA, the complexity of the cell, OOL, the implications of the Big Bang, the grounding of morality, the consciousness problem, the Cambrian explosion, the argument from reason, the efficacy of NDE, etc., you can only admit naturalistic/materialistic answers. ”

    I sincerely misunderstood your language then. I mistook your term “cases” to mean smaller questions, not the broad questions you must have intended.

    Regarding Occam’s razor, you wrote:

    Interestingly to me, as your language looks to be straight off the Wiki page on Ockham I will point you back to that page.

    I don’t remember if I have ever read the Wiki page for Occam’s razor – if I have, I can say for certain that it hasn’t been during this discussion. I promise you I did not quote nor paraphrase from there (and have never intentionally plagiarized.) and I will reveal my sources if you are ever curious.

    You can only know what is necessary if you already know what exists, since we do not have answers or promises of answers to these questions within your paradigm.

    and

    You haven’t a clue, as I said before, for instance, what entities are required to account for the above observations – so you have no rational basis for saying that God is superfluous to the question, so Ockham has nothing to say about invoking Divine causation.

    I do have to ask where you’ve gotten this notion of Occam’s razor from. Again, as I understand Occam’s razor (and I don’t think this is a strange reading), we know what to remove because it’s been inserted into the theory. A theory, under Occam’s razor, should accommodate any input that enhances the theory’s ability to do what theories do, and remove those that do not – call that scientism if you want, but Occam’s Razor and science are about as inextricably linked as two principles can be.

    My question to you is, what use is a theory that accepts inputs and/or gives outputs that we can’t perceive? It’s like saying, “Every theory works because of what’s on the page plus invisible input that also makes everything work and that is counted in secret totals additionally at the end.” Even if it’s true, the information is useless because we can’t perceive it or affect it any way. Occam’s razor is clear on this point. It’s not about metaphysics and philosophy, it’s about studying the theory in front of you, recognizing everything that’s in it, and removing those that aren’t necessary.

    But if we can’t agree on what Occam’s razor means then we have probably reached the point in this discussion where further dialogue on this topic won’t be productive. If you concur in that assessment, then I’d rather end this discussion with our having shared more productive dialogue than usual, and hope to build on that sometime in the future.

  160. Hi Tony,

    Me, in the previous comment:
    As to the quote above I said “the cases above”. That pertained to:
    “Whether we are discussing the information in the DNA, the complexity of the cell, OOL, the implications of the Big Bang, the grounding of morality, the consciousness problem, the Cambrian explosion, the argument from reason, the efficacy of NDE, etc., you can only admit naturalistic/materialistic answers. ”

    You:
    I sincerely misunderstood your language then. I mistook your term “cases” to mean smaller questions, not the broad questions you must have intended.

    Again, I think this is caused by the time gaps.

    Just for clarification, here’s the exchange, in sequence, where each comment followed and quoted the one previous:

    I merely pointed out that my view can accommodate every class of explanation and yours can’t. Whether we are discussing the information in the DNA, the complexity of the cell, OOL, the implications of the Big Bang, the grounding of morality, the consciousness problem, the Cambrian explosion, the argument from reason, the efficacy of NDE, etc., you can only admit naturalistic/materialistic answers. In most of these cases there are not even plausible ones, which, if they exist, are taken as evidence that naturalism is adequate, but the problem is merely shuffled off to some future discovery. And yet, like Jerry Coyne and the journal in Behe’s correspondence above, the naturalist/materialist must just presume that one day such an answer will present itself – because the option just is no option.
    This point ought to be obvious and completely uncontroversial.
    Evidence the fact that you likely now agree with the assessment above and are thinking of responding that this commitment on your part is preferable to 1) non-scientific answers or 2) God of the gaps arguments.

    You:

    I can only say that I believe in a statement like yours the burden of proof remains yours – you owe it to yourself, at least, to demonstrate what your addition to Occam’s razor gives you in terms of practical, explanatory knowledge.

    Me:
    There is no violation of Ockham’s razor nor any addition and it is telling that you would think there is. The principle warns against multiplying entities beyond necessity. Since we haven’t a clue, scientifically speaking, what entities are required to explain any of the cases described above your criticism that I have multiplied anything, or that your view has even approached the necessity of explanation, is groundless.

    ===

    I do have to ask where you’ve gotten this notion of Occam’s razor from.

    From its formulation – do not multiply entities beyond encessity. When you have no idea what is necessary you have no idea what is superfluous.

    Again, as I understand Occam’s razor (and I don’t think this is a strange reading), we know what to remove because it’s been inserted into the theory

    As I have gone back to include the exchange above I see that what follows is redundant. I’ll leave it in anyway.
    God has been inserted into no theory. God is the logical result of asking meaningful philosophical questions and from observing our environment.
    On the questions above, there is no theory – especially no scientific theory – and certainly no self-contained and satisfactory theory.
    Why is there something rather than nothing? What preceded or caused the Big Bang (you’ve even said the question is scientifically meaningless,(I think?) so neither science nor Ockham has a word to say about this)? Whence life … consciousness …. reason… morality … etc.? Philosophically, naturalism can’t even touch many of these questions. So much so that, as in the case of consciousness, they are called the “hard problems” of their disciplines, are written off by some naturalists as epiphenomena or illusions, and demonstrated to be of a different category than naturalism can even address. There certainly are no detailed, empirical, testable and falsifiable theories to explain these – therefore, again, neither science nor Ockham has anything to say about the necessary entities involved.

    A theory, under Occam’s razor, should accommodate any input that enhances the theory’s ability to do what theories do, and remove those that do not – call that scientism if you want, but Occam’s Razor and science are about as inextricably linked as two principles can be.

    Your worldview is limited to what science, rudimentary and fragmented as it is, can tell you – mine is not. My worldview includes things not amenable to the methods of science. So Ockham’s Razor, a philosophical, heuristic tool to be applied, because of aesthetic considerations, to the scientific pursuits, has nothing to say about the entities necessary to account for this view.

    Occam’s razor is clear on this point. It’s not about metaphysics and philosophy, it’s about studying the theory in front of you, recognizing everything that’s in it, and removing those that aren’t necessary.

    And, as I’ve stated over and over again, you have no idea what is necessary. Even with NDE there is no satisfactory theory. There is, at best, a metaphysical hypothesis with a constellation of competing and contradictory theories, none of which is complete, satisfactory , or uncontested. Ockham doesn’t know what to cut out when Ockham doesn’t know what to leave in.

    But if we can’t agree on what Occam’s razor means then we have probably reached the point in this discussion where further dialogue on this topic won’t be productive. If you concur in that assessment, then I’d rather end this discussion with our having shared more productive dialogue than usual, and hope to build on that sometime in the future.

    I think this is a wise assessment.

  161. Oh wait ….

    I don’t remember if I have ever read the Wiki page for Occam’s razor – if I have, I can say for certain that it hasn’t been during this discussion. I promise you I did not quote nor paraphrase from there (and have never intentionally plagiarized.) and I will reveal my sources if you are ever curious.

    That’s too bad. As I said, I’d refer you back to it:

    Ockham himself was a theist. He considered some Christian sources to be valid sources of factual data, equal to both logic and sense perception. He wrote, “No plurality should be assumed unless it can be proved (a) by reason, or (b) by experience, or (c) by some infallible authority”; referring in the last clause “to the Bible, the Saints and certain pronouncements of the Church” (Hoffmann 1997).

    Walter of Chatton was a contemporary of William of Ockham (1287–1347) who took exception to Occam’s razor and Ockham’s use of it. In response he devised his own anti-razor: “If three things are not enough to verify an affirmative proposition about things, a fourth must be added, and so on“. Although there have been a number of philosophers who have formulated similar anti-razors since Chatton’s time, no one anti-razor has perpetuated in as much notoriety as Occam’s razor.
    Anti-razors have also been created by Gottfried Wilhelm Leibniz (1646–1716), Immanuel Kant (1724–1804), and Karl Menger. Leibniz’s version took the form of a principle of plenitude, as Arthur Lovejoy has called it, the idea being that God created the most varied and populous of possible worlds. Kant felt a need to moderate the effects of Occam’s Razor and thus created his own counter-razor: “The variety of beings should not rashly be diminished.”[33] Einstein supposedly remarked, “Everything should be made as simple as possible, but not simpler.”[34]
    Karl Menger found mathematicians to be too parsimonious with regard to variables so he formulated his Law Against Miserliness which took one of two forms: “Entities must not be reduced to the point of inadequacy” and “It is vain to do with fewer what requires more”

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