Update inserted at 5:45 pm, August 1:
There is a group I call “the loyal opposition” who have frequently disagreed with me and other Christians writing here. Of that group, my logs indicate that David Ellis, Ordinary Seeker, Tom Clark, Jacob, Tony Hoffman, and doctor(logic) have visited this blog since I posted this entry. All of them except possibly doctor(logic) visited this entry or the main page which includes it.
It’s fascinating what they have found to criticize here—and what they have not found to criticize. The only complaint that was raised was an irrelevant one, having to do with how accurate it is to say the majority of ID proponents are theists. Jacob had an additional note to add to the discussion, but I don’t think it really amounted to a disagreement. (Bobxxx’s rant was too crazy too count.)
No other dispute has been offered. Considering the post is about “why Intelligent Design is essential to mainstream biology,” I find that very interesting.
There is no such thing as purely objective scientific research. It is always conditioned by culture, and thus it is always going to have biases. Its best defense against culturally-conditioned bias is a combination of good philosophical work, honesty in research and reporting (a moral dimension), and cross-cultural challenges to test the reigning cultural biases. These challenges may come through work done by others with different philosophical starting points, and they also come by the passage of time, for cultures change over time.
Evolutionary science is strongly associated with agnosticism or atheism. More than eighty percent of evolutionary biologists hold those positions. Wherever there exists a monolithic mindset of that sort, there is the danger that it will lead to badly skewed interpretations of reality. This is a simple and widely agreed fact of human nature.
Biologists often complain that ID is strongly influenced by theism, for the majority of ID proponents are theists. This must be acknowledged: ID researchers are typically biased toward theism, and universally biased against philosophical naturalism.
To be biased is not necessarily to be wrong. Either there is a theistic God or there isn’t; either philosophical naturalism is true or it isn’t. One side or the other has a more nearly correct view of reality. Each side naturally thinks its own is the one. Good philosophical work can (idealistically) help determine which is which; more realistically, it can at least contribute to understanding how to correct for biases. Even with that work being done, though, each side is still likely to emphasize interpretations and findings that support its own preferred view of reality.
Culturally aware mainstream biologists therefore ought to be encouraging work on intelligent design, just because it might prove to be a corrective to their monolithically shared view of reality.
Let me re-state that in plainer English, and the difficulty with it will become clear. Mainstream biologists ought to recognize that they have biases, and because of those biases they might be wrong. They ought to welcome work by people with opposing views of reality, because there is a chance they will be successfully corrected in case they are wrong. The difficulty with acknowledging one has biases is that it means admitting one might be wrong.
I have directed this advice specifically toward mainstream biologists, not because I think ID proponents have no biases, but because I don’t know of a single ID proponent who says evolutionary science should be discouraged from moving forward. ID is not standing in the way of this cultural correction process. Mainstream biology is. The dominant culture is always the one that needs the most reminding that it is not necessarily right. This too is a widely recognized fact of human nature.
This applies to the question of origins more than to any other science, because in most other sciences, direct contact with experimental results provides strong corrective power. This is not so for historical sciences. Archaeologists may interpret a certain pattern of artifacts as having religious or sexual significance, but if their view is mistaken because of cultural conditioning, the dead will not rise and tell them their prejudices have led them astray. The science of origins is the ultimate in historical sciences. Correction to biases will not come by watching the universe, or life, or the various species appearing anew all over again. It will come through good philosophical work, a commitment to honesty in research and reporting, and cross-cultural challenges.
Such challenges also come through the progress of time, as I’ve already said. It is very difficult to give up our usual ways of looking at things, but time has a way of helping make that happen, in cultures if not always in individuals. Discovering truth is partly a matter of patience as the work proceeds, and partly a matter of holding somewhat loosely to our scientific conclusions, especially those that cannot be tested by experiment. If the goal is to reach truth more quickly, the best way to speed the process is to encourage respectful confrontations between research programs with differing cultural starting points. If biology includes a search for what is really true about origins, biologists ought to be encouraging work on intelligent design.
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Possibly related posts (automatically generated):
“the majority of ID proponents are theists.”
That’s extremely dishonest. ALL ID proponents are theists. ID = supernatural magic, so believing in ID requires a belief in the supernatural. There are exactly zero atheists who believe in supernatural nonsense.
Your “Why Intelligent Design Is Essential to Mainstream Biology” is just plain nuts. You are saying “Why MAGIC Is Essential to Mainstream Biology”. There is no branch of science that requires magic, which is an idea for Harry Potter, not scientists.
bobxxx,
Not all ID proponents are theists. To support ID as a research project is not necessarily to agree in advance or to expect that it will produce positive results. To expect that it will produce positive results could involve something other than a belief in the supernatural, as Dawkins so charmingly admitted at the end of Expelled.
The supernatural is not synonymous with magic, except to those who are unable to distinguish meanings of words.
Your other two recent comments on the other thread, being quite abusive, have earned you being banned from commenting any further here. I don’t usually ban people so quickly, but then, I did let one of your comments stand. It’s more than you should have expected, considering what else you wrote.
Which proponents aren’t theists? And, for clarities sake, are we talking about “proponent” in the sense of someone who believes intelligent design happened or simply people who think its an idea worth exploring?
I’m more interested in the former. Offhand, I can’t think of any.
I’ve heard statistics of scientists who believe in God ranging from 33% (Pew) to 40% (NCSE, Gallup). Of course, those were scientists in general, but seeing as how the vast majority of scientists also agree with evolutionary theory, I wouldn’t think that it would change the numbers too much. I’ve never seen numbers this low. It almost always tends to range between 35-40%. That’s still lower than the general populace, but it would tend to suggest a very healthy minority that would not let naturalism run out of check.
I still don’t think that the ID arguments are all that great and are instead based on misunderstandings. I think that an argument for unguided process is still the better argument (to the point were Ken Miller, religious himself, says that perhaps man wasn’t the sole possible outcome into which God could instill souls). There are plenty of individuals who tend to be biased, but I also think that science tends to be a self-correcting process. I’d like to think that ID hasn’t made any headway because the arguments just aren’t that great, and they’ve been addressed to death, and I haven’t seen much that would change my mind (which I’m open to the arguments, as I have no commitment to anything for or against a designer).
@david ellis:
I’m thinking of people who support the inquiry into ID, not those who are convinced it’s true. (There’s even a certain sense in which I don’t even commit to its being true, as I have said here before, and wrote again recently.)
So my group would obviously include Bradley Monton. There’s also David Berlinski, of course. There are other unnameds as shown here. Searching on that same site I have also found Jason Streitfield.
My position obviously does not depend on there being a large number of atheists or agnostics defending ID. I can certainly understand and appreciate your being curious about how many or who they are, but I’m sure you can see it’s a side issue.
Jacob, there are several web sites referencing an American Scientist article supporting this number, but the web page they all link to has gone dead. The frequency with which it has been reported on other websites leads me think the numbers are trustworthy.
Don’t miss that Tom’s number is for biologists and the “almost 50%” number refers to all scientists.
Also, I think Tom’s might refer to the so-called “elite” of the NAS.
By the by
http://www.msnbc.msn.com/id/8916982/
http://www.uncommondescent.com/religion/nas-at-85-atheists-lets-bump-it-up-to-100/
I’m thinking of people who support the inquiry into ID, not those who are convinced it’s true.
It’s a bit misleading to call them “proponents” then, without specifying what you mean.
I, for example, support inquiry into just about any claim (including ID, telepathy, reincarnation, xenobiological claims, miracles and a host of other things I consider quite implausible—so long as public money isn’t involved)….but I’d hardly call myself a proponent of ID (or any of the rest of the things mentioned).
There’s a world of difference in being a proponent of X and being a proponent of inquiry into X.
David, try not to be so picky about irrelevancies, would you? I said not all ID proponents are theists. I said the majority of proponents are theists. Both of those are true statements. When I was pressed for details, I supplied details exactly as you just said I should have done. So I did as you requested before you requested it—even though, as I have pointed out, the message of this post does not depend on how many agnostics/atheists support ID in any sense whatever. The message of this post would be valid if all evolution skeptics whatever were theists (which they aren’t).
This is a side issue. There are far more important topics to discuss than this kind of picky nonsense.
Here’s what it conveys: you couldn’t find anything you could dispute in the main point of my post, but you had to find something to disagree with, no matter how irrelevant or picayune, and so you did, and that’s the only thing you care to discuss.
I’d be interested to hear what you think of what I actually communicated in the post, if you think it’s worth sharing.
Philosopher of mind, and ID proponent (?!) Thomas Nagel on ID.
http://philosophy.fas.nyu.edu/docs/IO/1172/papa_132.pdf
Those who have been around this blog long will recognize every argument on either side. If this were on paper my copy would be wet with yellow highlights.
Excellent, Charlie, thanks!
For those who wonder, this was published online August 11, 2008 (http://www3.interscience.wiley.com/journal/121376225/abstract?CRETRY=1&SRETRY=0)
The comment
entertains me with its irony!
If it were not for the “magic” (i.e., that which is beyond science) of consciousness (something that science has no coherent explanation for), and the “magic” of inquiry (again, something beyond science), and the “magic” of language (three times a charm!) there would be no science at all. It would be more accurate to claim that there is no branch of science that is not critically dependent on magic!
Again, I ask, are there ANY nontheist believers in ID (especially ones with credentials in the relevant disciplines)? I understand that this wasn’t what you meant by ID proponents. That issue has been clarified. But I still think this an interesting question in its own right.
If ID promoters have convinced any credentialed atheists it would go a long way toward making atheists without training in the scientific disciplines relevant to the question take notice and look into the issue with more care than they might otherwise be inclined to.
As to my not commenting on other aspects of your article, its simply because I largely agree that we all have biases and, so far as I’m concerned, those who believe in a creator or, for any other reason are interested in it, are more than welcome to pursue ID and attempt to do some good scientific work trying to test ID hypotheses.
Does my not having strong disagreement with you really warrant such harsh commentary on a perfectly reasonable question?
I found this so fascinating I inserted it at the top of the original post. I’m also putting it here so that those who follow changes in the comments will be able to see it.
Update inserted at 5:45 pm, August 1:
There is a group I call “the loyal opposition” who have frequently disagreed with me and other Christians writing here. Of that group, my logs indicate that David Ellis, Ordinary Seeker, Tom Clark, Jacob, Tony Hoffman, and doctor(logic) have visited this blog since I posted this entry. All of them except possibly doctor(logic) visited this entry or the main page which includes it.
It’s fascinating what they have found to criticize here—and what they have not found to criticize. The only complaint that was raised was an irrelevant one, having to do with how accurate it is to say the majority of ID proponents are theists. Jacob had an additional note to add to the discussion, but I don’t think it really amounted to a disagreement. (Bobxxx’s rant was too crazy too count.)
No other dispute has been offered. Considering the post is about “why Intelligent Design is essential to mainstream biology,” I find that very interesting.
Tom, you wrote, “Jacob had an additional note to add to the discussion, but I don’t think it really amounted to a disagreement.” But Jacob wrote, “There are plenty of individuals who tend to be biased, but I also think that science tends to be a self-correcting process.” I think this is a disagreement, and I agree with Jacob, that science is self-correcting and therefore is not in need of ID. Jacob also wrote, “I’d like to think that ID hasn’t made any headway because the arguments just aren’t that great, and they’ve been addressed to death, and I haven’t seen much that would change my mind…” and I also agree with this; and further, I think that far from providing the correction that you would like it to, ID is simply dismissed by the scientific community for the reasons Jacob mentions.
@david ellis:
You asked,
Your not having strong disagreement was not what I was responding to with what you termed “harsh commentary,” and I’m not impressed with your argumentation for suggesting that it was. Your pickiness in pushing on an irrelevant side issue, one which I had already answered, was what I was responding to.
I’m gratified to understand you “largely agree” with the main point of the blog entry. I had not seen your comment when I wrote my 5:45 pm update.
@ordinary seeker:
You write,
Thus isolating evolutionary biology in its massively non-diverse, monolithic mindset and insulating itself from the potentially corrective influences I have suggested would be good for it. Science is a self-correcting process as Jacob rightly said, but only when scientists are allowed (both de jure and de facto, by their culture) to correct it.
Tom, do you honestly believe if there was some great new discovery in the realm of ID, scientists would ignore it?
I think they’re trying to.
And what is that great new discovery? Is it one of Behe’s theories?
Behe has raised some great questions. Seelke, Meyer, Minnich, Marks, and Dembski have too.
Tom:
Be careful: there’s a bit of baiting going on here that is not so much intentional as it is animated by the underlying scientism. The question OS should have asked is, “do you honestly believe if there was some great new MES discovery in the realm of ID, scientists would ignore it?” I to am waiting for a truly MES discovery to come out of ID. But, would I discount ID if they don’t? NO!
To repeat for perhaps the fiftieth time, ID theorists are NOT looking for something physical (like, say, the neutrino when early nuclear physicists could not account for the angular momentum balance in beta decays) but for design. (One does not look for something physical in words when one is trying to understand their meaning.) ID theorist are employing (I believe more or less correctly) information theory, biochemistry, etc., etc., as scientific tools to show “something is there,” but they cannot use these tools per se to interpret the meaning behind the irreducible complexity (among other things) they “see”. (For heaven’s sake, the SETI researchers are NOT looking for EM-radiation or blips on a radar screen: they’re looking for meaning as contained in these material carriers!)
Design is not a physical thing: it is final causality in the mind of the designer imposed upon a material substrate (material cause) to make that substrate meaningful or contain information (formal cause), and this is achieved by some efficient means. Of course, there’s nothing to preclude the efficient cause to be BOTH material and immaterial (our minds impose meaning on ink so that a printer produces meaning symbols on a page).
THIS is where both parties separate: the loyal opposition, as animated by their scientism, does not permit (or only as “subjective”) any epistemological means, methods, tools, or findings that are not utterly MES-bound. They, because of their very, very view of reality (ontological monism), do not admit of anything that cannot be “seen” by the MESs… somewhat foolishly missing the point that it is not the MESs that “see,” but we humans that “see” immaterial verities by means of our capacity to reason. These folks keep on demanding “scientific” proof or evidence, and get none.
The ID side (mistakenly, in my opinion) try to cast non-MES interpretations in terms of the MESs… and fail. The IDers have a “richer” view of reality, but for reasons of science envy or fear or momentum or whatever, keep on trying “to blind me with science”. The IDers have created their own trap: they can’t do it in purely scientific terms (and they shouldn’t!), and yet try to have it taught in science classrooms. But if they admit to the immensity of the project and that it goes way beyond the MESs, they won’t be able to teach the most important (interpretive) aspects of the science classroom. The ID movement has a great idea, but the approach to present it has been wrongheaded from the get-go.
For heaven’s sake, of course there is design in nature! Dawkins and crew are intentionally blinding themselves by their own epistemological self-imposed limitations. It takes an intelligent agent (nous) to see the design behind the material/physical substrate, but that “seeing” is done through reason. There’s such a foul and disingenuous sentiment among the anti-IDers whose inconsistency is blatantly obvious: one cannot claim there is no design in the biological substrate of rational animals like us, and yet claim we humans can design things! The non sequitur is breathtaking!
Tom, I’ve followed the discussion, and it seems that the questions Behe and others have raised have been resolved, and not in favor of ID.
They haven’t been resolved yet. You may think they have, but the work is ongoing. To view it otherwise is sadly simplistic.
For example: Seelke has been trying over thousands of generations to get microorganisms to evolve new structures and functions representing significantly new information. He has not seen it happen yet. Other people say it has happened observably—bacteria in PCBs, for example. Actually there are very few examples, and whether the examples qualify under the criteria is controversial. Let’s grant the most charitable possible interpretation of those few other examples. Do they mean all Seelke’s questions have been resolved, and he has nothing new to discover? How simplistic that would be.
Behe says that multiple simultaneous genetic mutations (more than 2 at once) producing more adaptive phenotypes are vanishingly improbable and have never been observed in nature or the lab. Has that been fully resolved? Has it been fully shown that adaptive changes in phenotypes of higher organisms can be produced with fewer than three simultaneous genetic mutations? I’m aware of the debates on this. How simplistic it would be to say it has all been resolved.
Dembski and Marks are challenging the Avida project and other claimed computer simulations of evolution. Their work is in progress. Should a work in progress be declared “resolved”? How simplistic that would be.
Minnich works on the flagellum. One evolutionary precursor, the TTSS, has been suggested. Is that all there is to say about it? Do you want to be that simplistic?
Meanwhile Holopupenko’s enlarging of the question is very appropriate and important. ID has and will contribute to the MESs, but it has much more to bring to the table than that.
@ordinary seeker
Have you read The Design Matrix? To suggest that the issues raised in such a book have been “resolved” indicates that you haven’t been following the discussion!!
So, what, in your opinion, is the current state of ID? By which I mean: how strong are the arguments for it? Do you simply consider it just something worth exploring or do you think there’s strong scientific evidence in favor of it? And if so, what is it? If not, what arguments or work by ID proponents do you find most compelling?
I’ll frankly admit its not a topic I’ve explored in any depth—I’ve read a handful of articles by ID proponents and, so far, been very unimpressed. But I’m willing to examine the claims of supporter’s of ID as honestly as I can.
I’ve been thinking recently about blogging a chapter by chapter assessment of a book for my blog and ID sounds like a good topic. But if I’m going to do it I want to examine the strongest argument(s) to be found in its favor. What book, books or articles would you recommend?
David:
“do you think there’s strong scientific evidence in favor of it?” is a scientistically-loaded question–you cannot reasonably deny this. You are priveledging MES knowledge over other types of knowledge, and assuming it has no bounds. And, of course, the 800-lb. gorilla in the room is your question itself is not a scientific question.
So, is there scientific evidence to support ID? Yes, but that evidence MUST be correctly interpreted and understood with tools beyond the MESs. If a person limits all knowledge to MES knowledge, then interpretation is impossible. Of course the MESs can’t “see” design: they’re not meant to. Consider the parallel problem in QM: is there MES evidence that nature has inherent “fuzziness” and therefore quantum-level entities are, by the very natures, stochastic? Yes, there is evidence. But the sanity check of natural philosophy exposes why that’s a problematic interpretation, and why epistemological limitations do NOT impose ontological limitations.
Now, to anticipate a possible response: no, I don’t believe Kuhn was completely correct. Just because interpretations of scientific findings come and go through “revolutions” in thinking in NO WAY implies those interpretations somehow actualize the reality they’re trying to understand. One cannot objectively claim that scientific interpretations are subjective… for where does that leave the assertion itself? Dead in the water: it can’t stand up to its own criterion.
Prof. Monton can “see” beyond the rhetoric of the anti-IDers because he’s a philosopher who listens and follows the evidence. He may not believe in God, but he knows there’s something out there… because he “sees” it.
I would suggest any of these:
The Design Matrix by Mike Gene
A Meaningful World: How the Arts And Sciences Reveal the Genius of Nature by Wiker and Witt
The Privileged Planet: How Our Place in the Cosmos is Designed for Discovery by Gonzalez and Richards
The Edge of Evolution by Behe
and though I haven’t read it yet I hear good things about Signature in the Cell by Meyer
You sound like you’ve read it, Tom, with your discussions here and on TT about historic sciences and demarcation.
You’ll obviously find much to agree with.
Thanks, I’ll try to get my hands on at least one of those books. Unfortunately, my college library doesn’t appear to have any of them but I’m sure can get them through inter-library loan (except for the ones that appear to only be published as Kindle etexts).
“do you think there’s strong scientific evidence in favor of it?” is a scientistically-loaded question–you cannot reasonably deny this. You are priveledging MES (David: modern evolutionary synthesis?)knowledge over other types of knowledge….
How so?
How about asking, “… do you think there’s strong scientific evidence that supports sound arguments in favor of it that are also consistent with full causal requirements for the existence of design in nature?” Scientific evidence alone is not a conclusion–scientific or otherwise. To not clarify is to load the question–intentionally or not.
Holopupenko has a habit of using this one abbreviation without always explaining it: MESs=”Modern Empirical Sciences.” MES is the singular or collective form.
My bad.
I’m outta here for possible up to a week or so: new house closing in a week, parent’s weekend at the USNA, getting stuff out of storage, lots of driving.
This really deals with post #16
Opinion masquerading as argument…
This is an opinion, an opinion BTW, baldly asserted without any supporting evidence. Guthermore, it conflates ‘science’ which is a method of studing the world with ‘evolution,’ an interpretation of certain observation and whose veracity is questioned. The statement of an opinion so ambiguously supported hardly qualifies as an objection.
See above
I think that the moon is made of green cheese and, I’d like to think, we could mine it and solve the problem of world hunger.
A mind is like a mouth, the both must open to work.
The mind, like the mouth, opens so that it may can bite down on something solid.
Whatever your opinion may be, there are solid arguments for theism, ID, atheism, evolution, creationism, and nearly every other -ism. To pretend otherwise is to close your mind to any possibilty of learning. I have my sound and reasoned opinion of what is true, but I acknowledge the posibilty that I may be mistaken. The problem with “orthodox” atheists is that they do not entertain, by and large, the possibilty that they might be mistaken. They define those who question their dogma are idiots or charlatans who have forfeited their right to a public hearing. It’s great for protecting dogma from questions, but not so good for learning truth. That’s what Bradley Morton noted about Judge Jones’ decision on ID and ‘science’ so-called.
RE this:
See this; and note also that this bears every resemblance to what the Church is accused of having done to Galileo. All that’s missing is the house arrest.
Holo,
Do I understand you correctly? Are you saying that in order for ID to be a viable scientific theory, the scientific method would have to be changed?
He’s gone for a while, but I think he’s saying that the scientific method as typically understood by materialists, if it excludes a clear and complete philosophical understanding of causation and of natures, should be changed; and that this is true for science itself to be complete. It’s not that science can’t operate at all without this, but that it is truncated. This is the case regardless of what impact it may have on the ID question, because it’s just a better way of thinking about nature and reality.
So yes, in a sense: the scientific method as it is commonly misunderstood needs to be changed to a more correct understanding. Without that correction, ID is not a viable “scientific” theory, but then “science” itself is mis-defined that way, so to say that ID is not a viable scientific theory under that definition is of no consequence. What matters is if ID is a viable scientific theory under a correct understanding of what such a thing is.
That’s my take on Holo’s take. I think he would also say that ID is not a scientific theory; it is a philosophical inference drawn from scientific evidence and from a host of other sources of knowledge besides. I would say it is that, but that it is also a scientific research program drawing on philosophical understandings of design and attempting to find recognizable instances of such design in nature. In other words I agree with Holopupenko, but I think there’s some elasticity in the term, and that it can be applied to two similar but different sets of ideas.
Tom:
(Just before I’m off to rent the U-Haul.)
Actually, no: I would NOT like to see the scientific method changed. It works very, very well for the domain (modern empirical sciences, i.e., MESs) it is intended. I have no clue how OS could conclude I even hinted at that.
What I do think is that OS misses several important things: the scientific method (as we know it today) arose from Medieval Europe with refinements along the way with the underlying intention of formulating a method for exploring the real world limited to the five primary senses. In this way, it removes any non-scientific speculations but it also removes human interference in experiments (hence the adjective “controlled”). The scientific method did NOT arise based on scientific work alone: it arose based on difficult ideas that had to be fleshed out (again, primarily during the Middle Ages) and formulated as principles. ALL of those principles (I have a list I can provide when I return) were based on natural philosophical reflections about the real world. It is those principles that make the MESs possible in the first place. That’s point one.
Point two–most often missed–is that the scientific method is only a subset of the epistemic cycle, i.e., the means by which humans learn about the world writ large, i.e., not just limited to what is “seen” by the MESs. Consider a simple example: as children we eventually learn to not take things from others… usually through a combination of trial-and-error, admonitions, sanctions, etc. Is that MES learning or knowledge? Of course not. Many, many other examples can be provided.
The MESs are the most fundamental form of knowledge to humans. Why? Because we obtain all our knowledge through the senses, and anything that comes through the senses is accessible to the MESs for study. BUT the MESs do not provide the most important knowledge for humans. My favorite example is Iran: we have wonderfully sophisticated technologies (thanks to the MESs) that have provided us with the means to detect weapons of mass destruction in Iran. Great. But can the MESs inform us as to what we ought to do about those weapons once we find them? OF course not. We have wonderful technologies that help us keep people alive for longer. Can the MESs tells us what to do in the case of, say, Terry Schiavo. We have incredible means for destroying people thanks to the MESs. Should we use those means? The MES inform, they do not direct… or, heaven forbid, rule.
My view of the role of ID is to spark people’s thinking in the fact that “something” is really out there, and then to think deeply about it. We don’t need to change the intellectual tools at hand (at least not yet). Rather, we need to use them effectively in concert with all our knowledge and our great ability to reason about the world… and not to be afraid of potential avenues of exploration.
Tom -
Seelke’s experiment was essentially a bid to model irreducible complexity. One mutation happens, multiple mutations don’t, is what he attempted to show by knocking out key genes and seeing if they’d evolve back (regain function). This would be interesting if we’d never observe this happening, which we have, but I call into question his entire experiment. His paper was called What Can Evolution Do? but we must also ask What Would Evolution Do? You can’t have the latter without the former. In other words, any evolutionist will tell you that most changes aren’t viable. Evolution would only seize upon certain directions. So inactivating random genes and expecting them to do what you want to do is very dangerous if one doesn’t have the proper methodology. Jason Rosenhouse points this out:
On the other hand, as Seelke informs us in his PP presentation, it’s not as if the bacteria did nothing at all. He presents a graph that shows that the bacteria evolved to do quite well in their tryptophan limited environment. So evolution occurred, it just didn’t follow the specific trajectory for which Seelke was looking.
And how is any of this a model of evolution, anyway? Did the trpA gene evolve from a functionless precursor that was missing two of its amino acids, which then appeared simultaneously in some ancient population of bacteria? Seelke, fiddled with a genome, and the resulting critters evolved to do quite well in their environment. What’s the news here?
Furthermore, Seelke criticized a similar experiment Barry Hall did on bacteria metabolizability of sugar lactose. Ken Miller gives more details here and offers a rebuttal. Although aimed at Behe, it addresses many concerns.
Behe says that Hall did not wipe out a “multipart system” as I claimed; he deleted just one gene. Well, that’s what I wrote, too. My description clearly and correctly states that Hall started his experiments “by deleting the structural gene for galactosidase,” a single gene. However, I did indeed write that this deletion had knocked out a “multipart system.” Why? Because once the gene was deleted, three components had to evolve to replace its function: First, a new galactosidase enzyme, second, a new lactose-sensitive control region, and third, a new way to switch on the lac permease gene. And, just as Futuyma and I pointed out, that’s exactly what happened – all three parts eventually evolved.
…
Professor Behe may be unimpressed by these mutations, but he’s missing the point. This is how evolution generally works – by minor modifications of pre-existing genes to serve new purposes. He emphasizes that the ebg gene is “homologous ” to the lac proteins and overlaps them in “activity,” but these statements are quite misleading. The pre-existing enzyme activity of the ebg gene is not enough to support the metabolic needs of the cell, and the ebg gene is actually only 34% homologous to the gene whose activity it replaces (meaning that about 2/3 of the protein is quite different from the galactosidase gene whose function it replaces). The repressor (control) gene is even more different, showing just 25% homology to the lac repressor.
Both Behe and Seelke claim that Hall intervened in the experiment using IPTG:
Fourth, he notes that I did not mention that the bacteria in the experiment were supplied with the artificial inducer IPTG. The use of this inducer, he charges, amounts to “intelligent intervention” in the process, thereby invalidating the results as an example of Darwinian evolution. His criticism, once again, misses the point. We cannot even begin such an experiment without deleting the beta-galactosidase gene, and that is necessarily an act of “intelligent intervention.” He does not object to that, of course.
However, when Hall grew the bacteria under selective conditions designed to favor re-evolved galactosidase activity, Behe cried foul. As he should know, and as Futuyma wrote, “… mutation and natural selection in concert are the source of complex adaptations.” All that Hall had done was to set up conditions where the bacteria would survive (although just barely), and would prosper only if they evolved a system to replace the one he had deleted. Behe calls this “intervention,” implying that the investigator had to intervene directly to produce the new system. He didn’t of course. All that Hall did was to use that inducer to set up growth conditions that would ensure that the mutants, if they appeared, could survive to be recovered and analyzed. In short, he screened for mutants, he didn’t produce them as Behe implies.
Behe seems to be unimpressed by a lot of examples. For instance, Richard Lenski ran an experiment, and the microbes gained an ability to transport citrate. Behe downplayed this, even though it took a few different mutations, and said that it wasn’t much for the time given – keep in mind that microbes took hundreds of millions of years to evolve and were on the planet for billions of years. Compared to the five hundred million years since the Cambrian explosion, “simple” life dominated this planet for a very long time.
In a separate incident he also downplayed the evolution of HIV, but HIV has evolved into what we would classify a new species, adapting to individual behavior of humans. Part of the reason it has changed is that those viruses that are not “fit” are irradicated by humans. It’s natural selection accelerated. It took Behe months to admit that perhaps he was wrong about something in HIV called VPU, which he said was totally irrelevant and did not support the idea of evolution in action. You can read about it here and here. They are really in-depth articles, touching on the differences and changes that VPU has undergone, so they should be read. Of course, Behe still contends that most changes are destructive, which isn’t an affront because they are, and that they’re not that significant of changes, even though it interacts with a different binding site and causes large scale changes in its hosts. Ralph Seelke, incidentally, claims that the effectiveness of cocktail drugs in HIV demonstrates the inability of evolution, which I’m not sure what he means. Even if he’s correct, it merely proves that they can’t undergo massive mutations all at once, but that much isn’t necessarily true: cocktails are effective but not the end all be all treatment. HIV can change and adapt in response to cocktails. Usually this comes at a hit to reproduction rates, but as long as the selective pressures remain, it may undergo compensatory mutations and become more fit than ever.
Keep in mind we’ve only been doing a few decades of work, which is nothing in evolutionary time. If one moves the goalposts back just a little and defines something in their own way and not necessarily what evolution truly purports, then of course you’re not going to be satisfied. Fortunately, some good work has been done and buffets the evidence for common descent, which is overwhelming in and of itself. I think that addressing the inefficacy of ID also addresses the question of bias, which was the point of this topic. If evolution is completely solid science, then nothing else necessarily matters. And like I was going to say in the other topic, it too wouldn’t necessarily matter who the proponents of ID were if the were using facts and logic correctly, but I don’t think they are, which I think says something about their mindset. Not that they’re necessarily biased, but that there’s a correlation between the two. If ID isn’t a good belief, then what reason would atheists have to accept it? And that’s why they’re not on board.
Lastly, I see now that the article in the original post says “eminent” biologists, but no criteria is given for who these people are. Interestingly, most of them also think that religion itself is a sort of adaptation of evolution (the paper can be found here). Anyway, these people would still seem to make up only a small minority of scientists, but the anchor of your post relies on scientists in general. If plenty of them are still religious, then it’s hard to call bias. There was a Gallup poll sometime ago that concluded 95% of all scientists agreed with evolutionary theory and over 99% of scientists in the credible biological fields did. That would mean that whatever subset of scientists you’re looking at, whether religious or not, you’re still going to find overwhelming support for evolution.
Dave -
Solid arguments? You haven’t presented any. You keep dropping them when I offer substantive rebuttals. I’d really love to debate, but for whatever reason it’s not sustained. Would you really change your mind if better evidence was presented? Frankly, I don’t think that one can cling to Icons of Evolution and yet claim he gave both sides equal opportunities.
Holopupenko has a habit of using this one abbreviation without always explaining it: MESs=”Modern Empirical Sciences.” MES is the singular or collective form.
Ah, thank you, that makes much more sense in this context. As to his question:
“do you think there’s strong scientific evidence in favor of it?” is a scientistically-loaded question–you cannot reasonably deny this. You are priveledging MES knowledge over other types of knowledge, and assuming it has no bounds. And, of course, the 800-lb. gorilla in the room is your question itself is not a scientific question.
Its scientism to ask if there’s good scientific evidence in favor of a hypothesis its supporters regard as scientific?
If so, then lock me up, I’m guilty as charged. Even if I’m not as philosophically naive as to think, as Holo seems to imply I believe, that science has no philosophical underpinnings. Indeed, as a lover of both science and philosophy I see no problem in this (though Holo likes to ignore it—its not convenient when one is trying to accuse others of scientism).
My view of the role of ID is to spark people’s thinking in the fact that “something” is really out there, and then to think deeply about it.
That sounds suspiciously like an endorsement of “god of the gaps” thinking.
Tom,
I glanced at this post yesterday but didn’t read it entirely yet. I still haven’t had the time to yet. I also see that there are 42 comments in the approximately 24 hours since you posted.
Sheesh. Sometimes a pause is because it’s a beautiful summer day, some of us have kids, and there are other things to do.
Hi Jacob
Aside from the fact that evolution is random mutation, so inactivatin random genes to observe the consequences is precisely the correct method to test evolution, you have insinuated a rather curious anthropomorphism – that “Evolution would only sieze upon certain directions.” Evolution is a mindless (undesigned) a-teleological (purposeless/goal deficient) process.
Perhaps it is my own undesigned and goal deficient mind, but I find evolutionary apologetics filled with unwarranted assumption and ambiguous language. It is difficult not to believe that this assumption and ambiguity is the deliberate “stock in trade” of many evolutionists.
On the merits of which we both disagree. I say ‘solid’ you say ‘substantive’ and ne’er the twain shall meet. I dropped the discussion when I understood that, in your mind, there can not be any argument that could contradict evolution.
I don’t know. Having changed from a dogmatic evolutionist to a ‘creationist’ I am not convinced the theory has enough compelling evidence to sustain it in the free market of ideas – and see little reason to expect any change in this condition. In fact, I think such incidents as Kitzmuller and other legal action on the part of atheists demonstrate their own lack of confidence in the merits of evolution. I share the confidence of Milton… Let the free exchange of ideas and open debate settle the matter.
Silly rabit… I don’t cling to “Icons of Evolution” – I read the book and found his arguments were substantial and compelling as far as they went, and they only went so far as to reveal that many of the iconic examples of evolution were simply that, icons.
I was taught from text books that used many of the icons he identified. I, like you, never considered the possibility that the proofs they illustrated were less observed than induced – that is their proof depends upon certain assumptions which have not been, and perhaps can not be, observed. Now, here is nothing inherently wrong with induction, but induction is interpretive, and interpretation is conditioned by philosophy.
And by what strange quirk of mind do you suppose that Wells should ‘give both sides equal opportunities’? He presented his thesis. It’s open to rebuttal (and I have read several rebuttals). The rebuttals do not ‘give both sides equal opportunities’ and mainly accuse Wells of ‘misrepresenting’ that which I know from my own personal experience in the use of biology text books that he did not misrepresent.
The fact that a student entering college as a biology major is then informed that some of the iconic images of evlution in action are inflated (at best) illustrations of the theory and shouldn’t be taken literally does not mitigate their deliberate use for the purpose of indoctrinating students in elementary and secondary schools where they are taught as factually correct.
Random is not the same as purposeless. Mutations may be random, but natural selection is not, and thus evolution as a process is not. I often find that it’s the ID arguments that confuse this language and make it ambiguous. It’s an important distinction because it’s for this reason that many in the ID community just expect certain processes and functions to come out randomly. Miller explained why Hall’s experiment was justified in that it modifies previously existing genes and selects what’s beneficial. Seelke devotes a single sentence to the fact that his experiment didn’t produced two successive mutations but never tells us why, even though he appears to say that it should happen due to sheer probability. In some experiments it actually deleted a gene.
The irreducible complexity argument is only correct in the sense that you can’t reduce functions in certain ways. The quote from Rosenhouse is apt because the experiment only works if the way in which Seelke inactivates genes and expects them to evolve again is the only way that these genes could evolve. The criticism here is that he’s ripping out parts in a different way than they were manufactured. In this case, evolution can only manufacture something in certain ways, but it can be destroyed in any which way. Certain conditions need to be met (the genome needs to be in a certain state) in order for something to evolve, which means that evolution does seize upon these conditions, taking them in certain directions, and these are not the conditions that Seelke is using in his experiment. Imagine a gene at the time necessary for evolution being turned off later or a gene that used to have a different function. It would invalidate things, as Seelke is removing things wholesale. So when we see something evolve in nature like HIV, it’s not surprising that they take advantage of multiple mutations. Besides, you haven’t really explained whether you agree with an experiment like Seelke or think that evolution is possible to a certain extent.
It’s strange that you’d call for the debate of ideas and yet dismiss almost all of my arguments without engaging many of them. I’ve attempted many times to explain that there is nothing between organisms that prevents change (you still haven’t offered reasons why change can’t happen), examples of changes in organisms, research done on the evolution of certain features (you instead stated that such things don’t prove evolution, which wasn’t the point at all), and the fact that features exist in nature without the benefit of others that you claim would make them irreducibly complex systems. Maybe I think that evolution can’t be contradicted because you haven’t actually contradicted anything (especially when I ask for evidence or experiments over and over and don’t receive any – Tom at least provided one). Your silence is tantamount to one who proves nothing and yet still thinks that he has a case. Much more educated people than me in the field of biology have repeatedly addressed the ID arguments. After all of that, if it still looks like they lack confidence (even though oftentimes they’re quite smug, which many IDers try to call them out for), then I question the criteria you’re using. I was not always an evolutionist, so it’s useless to say that I’d never change my mind. But I changed my mind because I began to understand evolution better. It seems that you fail to understand evolution in spite of all of your research. And yes, I do question how far you’ll try to go to discredit evolution when you try for three or four posts to show that evolutionists were against junk DNA, making explanations up that I then showed were mistaken. I’m sure you really believe that the arguments against evolution are so substantive that evolution looks like a tough pill to swallow, thus seeing challenges to evolution where they don’t exist. That is not a question of commitment but a problem in thinking. The lack of a hybridized dog-cat is evidence against evolution? I showed why evolution wouldn’t ever predict such a thing but received no reply, so what do you want me to do? Really. All I want are things that contradict what I’m saying. If you can show me why they should be considered, then I’ll consider them.
Your claim that textbooks indoctrinate school children is incoherent. Many of these examples, such as Haeckel’s embryo, do little to actually improve the case of evolution since often there is a better theory or different explanation out there (many biologists will argue that embryology is still a powerful argument for common ancestry). In some cases, like the ape to man image, it actually leads to a detrimental understanding of evolution (since, if evolution did purport to evolve organisms in a straight line, then it would be very wrong indeed). What evidence is there to suggest that these textbooks are anything more than mistakes or misunderstandings? Even worse, most of the examples that Wells gave were simply wrong on his part. If not, then point to specific examples from the Talk Origins article. We can debate them. It’s easy to think that biology textbooks are wrong when one incorrectly thinks that a given part of them wrong.
Hi Jacob
Random is not the same as purposeless. Mutations may be random, but natural selection is not, and thus evolution as a process is not.
Come on… random means without purpose or design [intent]. “proceeding, made, or occurring without definite aim, reason, or pattern.”
‘Natural selection’ is an acknowledged tautology – survival of the fittest defines ‘fit’ as those who survive. The newer paradigm, introduced after survival of the fittest fell into disrepute, is reproductive fitness which is also tautological.
Furthermore, natural history is replete with examples of randomly occurring natural catastrophes which have ‘selected’ [extinguished] entire classes of organisms without regard to their ‘fitness’ however we define fitness. Worldwide extinction events or localized extinction events are equally random [without purpose].
http://findarticles.com/p/articles/mi_7051/is_2_12/ai_n28127232/
Evolution does not occur in any particular direction (alinear) nor does it proceed to any particular goal [purpose] (ateleological).
I often find that it’s the ID arguments that confuse this language and make it ambiguous.
I often find that it’s the [evolutionary] arguments that confuse this language and make it ambiguous. ID disambiguates the language and calls the evolutionary bluff.
…In this case, evolution can only manufacture something in certain ways, but it can be destroyed in any which way…
Evolution is a destructive process, it does not manufacture, nor does it have any goal or any direction. Random change in the genetic code will result in death or survival. Those that survive are the ‘fit’.
This is why the laws of probability are applicable, despite your objections in a previous thread to the use of them. There are X number of possible combinations which are randomly generated. This could explain why “Seelke devotes a single sentence to the fact that his experiment didn’t produced two successive mutations but never tells us why, even though he appears to say that it should happen due to sheer probability.” Seelke understands the theoretical mechanism of evolution (random mutation) and the likelihood of any particular mutation occurring (the laws of chance) and was disapointed because, while the particular sequence of mutations he expected was theoretically probable, it did not occur in practice.
…I’ve attempted many times to explain that there is nothing between organisms that prevents change (you still haven’t offered reasons why change can’t happen),…
I think what this means is that you have asserted that there is no theoretical reason that [for example] an ‘ape-like creature’ couldn’t evolve into a ‘human-like creature’. If we assume, for the purpose of this example, that evolutionary theory is plausible, then there is no theoretical reason that an ‘ape-like creature’ couldn’t evolve into a ‘human-like creature’.
The question is, do we have any justification for assuming that evolutionary theory is plausible.
examples of changes in organisms, research done on the evolution of certain features (you instead stated that such things don’t prove evolution, which wasn’t the point at all), and the fact that features exist in nature without the benefit of others that you claim would make them irreducibly complex systems.
I realize we are talking past each other in this (quite likely) unresolvable dispute. You assume (as did Darwin) that because we can breed long haired dogs and short haired dogs or large dogs and small dogs ([trivial] changes in organisms) (or Darwin’s observation about pigeons) that it is legitimate to extrapolate some new creature that we might call the ‘post’ dog or ‘uber’ dog which is no longer a dog, but something new. I challenge you to demonstrate any such change, but it cannot be demonstrated since it has never been observed. You offer trivial change such as antibiotic resistance in bacterial strains or trivial changes in HIV – both the bacteria and the HIV remain classified as same bacteria or as HIV. The title of Darwin’s book is “The Origin of Species” not “An explanation of trivial change within species.”
This is another evolutionary tactic, well documented in the Scopes trial, of conflating trivial change with the macro-change required by the theory and then using the trivial change as “proof” of the macro-change. If I recall correctly, one of the ‘expert’ witnesses for the defense argued that the development of the egg to adult was ‘evolution’. Granted, it is ‘evolution’ in the broad sense of the word, but it certainly is not what is meant by evolutionary theory.
http://www.etymonline.com/index.php?search=evolution&searchmode=none
Hello Jacob
Many of these examples, such as Haeckel’s embryo, do little to actually improve the case of evolution since often there is a better theory or different explanation out there…
I recall specifically learning about Haeckel’s embryos in biology and the altered drawings were presented as essentially correct, proof of the validity of evolution. This was in 1970 despite the fact that the alterations had been exposed nearly 100 yrs before and Haeckel had confessed to altering them.
http://scienceblogs.com/pharyngula/2007/02/wells_and_haeckels_embryos.php
And this is from the poisonous pen of P. Z. Myers whose idea of tolerance includes the desecration of the Catholic host to revenge an alleged medieval injustice.
http://scienceblogs.com/pharyngula/2008/07/the_great_desecration.php
http://en.wikipedia.org/wiki/Host_desecration
No doubt Myers would reject outright any ‘mitigating justification’ I might offer for the excesses of medieval Catholicism. Perhaps he would consider any such mitigation nothing more than a defense of bigotry and further evidence of religion inspired bigotry.
Given his temperament and his usual response to anything which questions the validity of evolution I think his grudging admission to the veracity of Wells’ exposition of Haeckel is significant. I don’t think Myers wouldn’t have done so had he any hope of denying the obvious. As it is , he still offers a ‘mitigating justification’ for perpetuating the usage of Haeckel’s drawings.
… could be construed as evolution inspired fraud?
Jacob,
All genetic variation in individual organisms is produced by random processes. Change in populations is produced by random processes plus natural selection.
You are correct in saying that NS is non-random. Note what NS does, however. Even in populations it creates nothing. It invents nothing. It is a conservative, not a creative force. It is what allows certain randomly produced variations to be kept for future generations. NS can’t take a population anywhere except for where some random variation(s) in individuals has dug a rut for it to go. It can identify the most successful ruts and send a population that direction, but it can’t dig one of its own, not even as deep as a worm-track.
Switching metaphors, the engine that drives evolutionary change is not NS. NS is the most conservative force in all of natural history (it’s also the most tautological, so I use the word “force” advisedly).
So don’t overstate the non-randomness of evolution. All of the variation in individual organisms is random (on NDE), and NS is absolutely, 100% dependent on those unguided, purposeless variations for every bit of its work. It never came up with a single idea on its own, and it never will.
Dave -
The difference between random and purposeless in this context is very important because it’s the difference between using random probability, such as many in the ID community would like to use, and understanding the processes of evolution and how it selects what is appropriate. No one claimed that it’s the only force working on survival. An organism could fall out of a tree or be eaten by a predator. But the differences are obvious. Mutations are kind of like an independent event that cannot necessarily be predicted except for sheer probability (as far as I’m aware). Selection is qualitative. Some functions have better chances of surviving and being passed down. It’s advantageous and predictive. Survival of the fittest must be looked at in this way:
“Survival of the fittest” is a poor way to think about evolution. Darwin himself did not use the phrase in the first edition of Origin of Species. What Darwin said is that heritable variations lead to differential reproductive success. This is not circular or tautologous. It is a prediction that can be, and has been, experimentally verified (Weiner 1994).
…
The fittest, to Darwin, were not those which survived, but those which could be expected to survive on the basis of their traits. For example, wild dogs selectively prey on impalas which are weaker according to bone marrow index (Pole et al. 2003). With that definition, survival of the fittest is not a tautology. Similarly, survival can be defined not in terms of the individual’s life span, but in terms of leaving a relatively large contribution to the next generation. Defined thus, survival of the fittest becomes more or less what Darwin said, and is not a tautology.
Ecosystems are at the sway of systematic upheaval, which is why so many species go extinct, and that’s what evolution predicts. None of anything you’ve said up to this point actually works against evolution. All of this is readily known and accounted for by the theory. You’re simply conflating and misunderstanding terms. For instance, selective pressures have been well documented and understood. Considering that you keep changing your arguments, such as with the junk DNA bits, you can hardly call anyone out for being unclear and confusing.
Futhermore, you’re cherry-picking what you don’t like from my post. The modification of previously existing organisms is one of the cornerstones of evolution, as Miller pointed out. Because the genome is already in a certain “state”, the change that gives it a better chance will tend to be selected for. In the Hall experiment the necessary changes occured. But if you start ripping out the machinery, then you might be ripping out the genes that would allow this necessary change. I question how much Seelke understands this, considering he was incorrect about HIV. The multiple mutations there would appear to invalidate his entire experiment, thus throwing into peril his methodology. So are you going to criticize the Hall experiment? Are you going to address the specific changes in HIV? Without talking about these, you’re implicitly admitting that we have observed change. But if these these examples can be criticized, as Seelke and Behe at least try to do, then I would need to provide something more.
You do address HIV but in a vague way. HIV, for all intents and purposes, is a new species. In fact, there are two different strains of it and a good dozen different subspecies. It’s changed to the point where totally different treatments have to be used on each, and they have adapted to specific environments. Of course, I suppose that the goalposts will be moved a little farther so that I have to demonstrate changes between orders and famlies, which isn’t possible since it would take longer than we could document. That’s why there are two additional arguments. 1. Yes, whether there are any theoretical limits to evolution. Now, given that these arguments for beneficial changes are indeed correct to the point where different species and subspecies have emerged, it stands to reason that there is nothing stopping them from changing into another species and another species and another species. In other words, because we’ve established a mechanism for change, the macro becomes no different from the micro – it’s just a lot of micros strung together. This definition is clear. The hybrid argument was an attempt to show this – you can typically breed two similar species because their genomes are compatible, which speaks to incremental change. The farther the change is, the less likely two animals are to breed. But if there is a difference between micro and macro, then it can’t just be assumed – there needs to be a specific theory. You’re trying to place the burden of proof on me to establish change, which I have attempted to do quite specifically, but you’ve only vaguely tried to establish some limits to evolution (I still don’t even know if you’re advocating evolution as a destructive process or limited evolutionary change). 2. Luckily, we don’t have to assume anything about limits. The argument for descent with modification rests within the genes. I’ll use the whale example again until it’s addressed: whales have genes from land-based mammals that appeared to be either modified or inactivated. Either evolutionary theory is true, or evolution merely looks true, in which case I question the intentions of the designer.
Myers’s article was not some tacit admission that ID has something to offer – in fact, evolutionists have excoriated Haeckel’s embryo long before there even was ID, as Myers rightly points out. Myers attacks Well by basically saying that compared to the mistakes in Icons, Haeckel’s embryo is a pittance. Nothing in his article really supports your interpretation. Embryology does point toward evolution, so Haeckel’s embryo offers little, and its appearances in textbooks are probably due to typical human error. You’re just trying to find something to pin on evolutionsts. Again, are you going to defend the rest of his book?
Tom -
Fundamentally, yes. There’s a lot more to it than that (differences of mutations, interaction of genes, conservation within the genome, etc), but you didn’t address the most important point: given this process, is evolutionary change still possible? That’s the entire point of criticizing Seelke’s approach and using the examples I did. If we add enough time, then all changes seem possible, and it’s natural selection that seizes upon what happens to work. There was a debate about Dawkins’s weasel program in the other thread. Basically, it’s a program that attempts to show that a random process would take all of the time since the Big Bang just to pick out a sentence, whereas it would take only a lunchbreak with the addition of some selective force. As Dawkins notes, the lunchbreak thing isn’t necessarily important, only that the length was vastly reduced. His program wasn’t totally analogous but tends to illustrate how important the mechanism is. If you think about it in its raw form, then it does seem impossibly random, but we have specific examples of organisms responding to environmental pressures quite quickly, such as when the human genome undergoes some change in response to microbal invaders, which means that the process works and is decisive. The sheer number of changes that occur makes them likely in some cases, so natural selection can act upon them.
A repetitive and scattered hodge-podge, an unorganized gathering of some of my thoughts on the goat-getting “evolution is anything but random” red herring for anyone who cares …
I can’t see this as anything but a dodge to avoid the implications of the obvious math – neither OOL nor evolution has the resources, time -wise or materially, to have accomplished what the theory asks of ateleological, chance-driven processes.
From the start the claims have been infused with this metaphysical component but they fail the empirical test. To Darwin (who never said “random”, we’re assured) variation was “spontaneous”. And he defined this for us, using his metaphysical requirement ( a presupposition, not a conclusion) of the theory, as being unguided and without foresight.
But unguided variation culled by the blind forces of nature (by the way, how does NS, the blind processes on an unremarkable pale blue dot, created by random processes itself, somehow remove “random” from the equation?) is seen as impotent. Whether you call it spontaneous or random, it doesn’t work.
Since this is obvious, men like Dawkins tell us “oh, but evolution is ANYTHING but random”. Although he still claims that genetic variation is “random with respect to fitness” (which the atheist materialist must insist on, but, of course, is against the evidence) he says that evolution itself is GUIDED. Guided by what, one asks. By Natural Selection.
But what determines Natural Selection? Well, which genotypes survive or not, replies Dawkins. But, of course, that differential survival IS Natural Selection – you’ve argued in a circle.
Generally when you say this to an evolutionist they will just retort “oh, you’re ignorant of what modern evolutionary theory says”.
But Will Provine isn’t ignorant, and here’s what he says, very much counter to Dawkins.
His Cornell colleague, Allen MacNeill says many things that I like hearing from an evolutionary biologist; he tells us that neo-Darwinian evolution is dead, that NS is not the engine of evolution (and, in fact, sometimes even goes so far as to tell us, with his friend Will Provine, that NS does nothing), that the engines of evolution are actually the engines of variation (of which we are only now getting an understanding — notice that this means we are only now getting started understanding evolution, in MacNeill’s estimation), that there is a real difference between micro-macro evolution, that genetic changes can be the result of phenotypic changes, etc., for instance.
I even like the current admission that the word “random” is not accurate and doesn’t mean quite what it is intended to convey. As was the case with Darwin’s “spontaneous variation” the point is, as MacNeill has said, that variation has no foresight. Since the randomness claim has failed the mathematical test over and over again, and biologists have had to resort to saying that because of NS (which does nothing) evolution is “anything but random”, the word “random” is going out of favour; it just is not empirically sustainable.
What MacNeill and others mean is “without foresight”. Of course, this is a philosophical assertion, and not an empirical observation.
But, is it true that evolution is “anything but random”?
Not according to recent textbooks, including this one quoted by Anika Smith in a CSC article.
Now why are they emphasizing the randomness of evolution, when Richard Dawkins has made it plain that, due to the fact that evolution is guided by Natural Selection, it is not random? Because, as always, they are making a metaphysical statement and have tried to pass it off as science. The philosophy is never far below the science.
They want us to know that there is no guide and no purpose to the “random with respect to fitness” mutations. But they need the Dawkins hedge because, mathematically, a random, stochastic, process cannot result in the increasing information and the diversity of life on Earth. So, when this is demonstrated we are told that “evolution is not random, you misunderstood”, but as long as this fact is not pointed out they can merrily go about their metaphysical propagandizing.
So the current crop will now pretend that they don’t call evolution “random”.
But they cling to this new pretense only because, as far as evolution goes, “randomness” is a failure.
What they will not admit is that the opposite of the version of “random” which has failed is “directed”. “Undirected” evolution is a bust.
When they do admit that they called evolution “random” they now pretend that the opposite of this “random” is “predictable” – yet another obfuscation by equivocation. But that was never the “random” they meant (as seen above with Darwin and MacNeill)
Here’s what they really meant:
Professor Douglas Futuyma, in his biology textbook Evolutionary Biology, states: “By coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of life processes superfluous.”
So why did they say “random” all these years? Because they were making a metaphysical claim. They were, in fact, claiming that evolution is unguided, undirected and unplanned (they weren’t saying “it’s unpredictable”).
There is no scientific way to know this and it is merely a philosophical position – but it is the Darwinist’s position. And when busted, as always, the back-peddling begins.
Darwin himself talked about variation being “natural”, “innate” and “apparently spontaneous” throughout Origin…. He was, of course, telling us that it was following no plan, that it was not orthogenic or teleological. And his mantle has been carried ever since.
Darwin faces Mivart’s criticism here:
There can be no “variation in all directions” and no comparison of beneficial, deleterious and neutral variations if variation is not, in fact, random-with-respect-to fitness.
But his point always was that there was no guidance or purpose to the variations – this is a metaphysical point and not a scientific one.
At CSC Casey Luskin has highlighted the latest case.
Just to make sure you aren’t bringing any kind of purpose or teleology into evolution, Ayala explains that an evolutionary account “does not necessitate recourse to a preordained plan, whether imprinted from the beginning or through successive interventions by an omniscient and almighty Designer.” Ayala isn’t saying that this “preordained plan” might exist, for he is adamant in saying that “Biological evolution … is not the outcome of preconceived design.” Ayala concludes that Darwin completed a “conceptual revolution” that “is nothing if not a fundamental vision that has forever changed how mankind perceives itself and its place in the universe.”
Now how on earth would Ayala know all that?
Luskin also recently repeated, and expanded the Kenneth Miller evidence on this subject:
You’ll also recall the Weisel 38:
Tom,
This is a reply to your last comment to me in the most recent Monton posting – I am posting it here becaue it appears that the discussion has spilled over.
Okay. But Evolutionary theory is not chess, and although it’s far more probable than a teacup in the universe it does resemble the teacup in that it could retreat to the position of the infinitesimally small probability. I don’t care to defend it on those grounds, but when I see the sometimes ridiculous lengths ID proponents will go to concoct their deductive arguments I think the point is worth raising.
That’s not quite what I said. I said that “I was trying to talk about ID’s need to clear the minimum hurdle of scientific acceptance. In my opinion, it does not rise to the level of rain dancing in this regard.”
I will try to re-explain the problem in this way: The Theory of Rain Dancing is not true. We know this because the Theory of Rain Dancing is something for which it is easy to imagine a hypothesis: if the rain dancer dances, rain will soon follow. Control, test. Repeat.
The problem with ID isn’t that it fails to prove its hypothesis; it fails to even offer a hypothesis. Its only hypothesis appears to be: Evolution doesn’t explain everything. This provides no positive, inductive proof on its behalf. All it does is make a deductive argument against some supposedly weak area of Evolutionary Theory, then assume it can skip the part where evidence in its favor needs to be provided in order for it to prevail. This might be adequate for some philosophers, but it fails to raise itself to the level of the MES’s, let alone underdetermine something so wildly productive as Evolutionary Theory.
I raise these issues over and over again because I think it’s worth noting that you, on one hand, declare the correct theistic position to be pro-science, and yet that a theist such as yourself advocates that basic scientific standards (such as the expectation that a scientific theory actually contain a working hypothesis) be altered in favor of your pet philosophy.
I haven’t read everything in this new posting, but I did notice this from one of your comments:
But it is unclear to me with the above if you are summarizing what you thought Holopupenko’s thinking was, or noting where it aligns with your own. I do find the above statement to be clearly belligerent toward the MES’s in a way that you (hopefully) do not comfortably endorse, so I’d ask to see if the statement above needs to be clarified.
Looks like I’m late to the party. (I only just saw the post. And I haven’t read the comments.)
I think you’re right, Tom. Whether one is a theist or an atheist per se doesn’t have much to do with it.
A few points:
1) You might be assuming that it was atheism and agnosticism which led people to becomes scientists, rather than the science leading people to atheism or agnosticism.
As I’ve said numerous times, there are a lot more ways to design a world than there are to evolve it. This is why descent, common descent, common composition, etc. overwhelmingly confirm unguided evolution. It’s possible that there’s design in the gaps somewhere, but it’s extremely unlikely. That means that if a god does exist, he’s almost certainly not the kind of god who cares about us.
(BTW, the free will argument for God hiding himself seems silly. Surely, he would be more rational to appear obvious to us, but hide the consequences of disobeying him. Of course, this provides no solace for theists who desire universal justice.)
2) Historical sciences are predictive. They’re messier than physics, but they’re still predictive.
If you find some sharp flints, they might be designed or they might not be. If they are designed, we expect to find a bunch of other things. First of all, we expect to find traces of the designer (bones, etc.). We expect the designer to have the ability to manufacture the flints. We can test this by manufacturing flints with naturally occurring rocks, etc. We expect the flints to have been used to cut things, and so we expect to find things that appear to have been cut by flint, e.g., bones that have been stripped by flint.
Same thing goes for SETI. We assume that there are aliens, and that the aliens have limitations. They are physical beings with limited energy. Consequently, they will have to rely on regular, narrow-band transmissions because all-band requires too much energy over interstellar distances.
In principle, ID could do the same, but we know that in practice it won’t. ID advocates believe the designer is God. They don’t want to talk about the designer because nothing is useful to God, God has no limitations, and so God makes no predictions. Even SETI makes more predictions.
3) The DI’s goal is not an honest one. Their goal is to turn science into a he-said she-said affair. They bring not one shred of evidence against evolution. All they can say is that science hasn’t explained everything yet. Well, that’s not good enough. There’s no difference between them promoting ID because evolution hasn’t explained everything and someone promoting intelligent falling because we don’t know everything about gravity (quantum gravity, anyone?). The predictive theory of gravitation is not in jeopardy just because we haven’t filled in all the gaps yet. Should physics open its doors to astrology and intelligent falling? Well, the reason the DI doesn’t promote these things is because it doesn’t meet their ideological goals. ID does meet their ideological goals, and that’s why it’s an issue.
4) ID doesn’t have an explanation for origins. You know why.
Suppose a bunch of roses magically appears on my desk. Suppose I propose that the appearance of the roses out of thin air was caused by the quarter I dropped on the floor 15 minutes earlier. However, I can’t describe any mechanism, and I won’t commit to saying that dropping more quarters will make more roses appear. Am I really “explaining” the roses with my quarter “theory”?
No. I’m just stating two brute facts, events A and B, and assuming a third brute fact that A caused B, just this once in the entire history of the universe. No prediction, no explanation. (There’s no difference between a brute fact and an ontologically random fact.)
For the TC history buffs and newbies … watch what happens to DL, his explanations, his “predictions” and his ideas about God and predictions:
http://www.thinkingchristian.net/C246305481/E20061111083055/index.html
Charlie -
That Provine quote seems horribly mangled. In fact, within his book he was replying to a simple statement: Natural selection was the primary mechanism at every level of the evolutionary process. After he contends that natural selection does nothing, the most important thing he had to say was cut from that quote:
Natural selection is the necessary outcome of discernible and often quantifiable causes. Some of these causes produce heritable differences between individuals of most populations, and between populations. The possible production of offspring is immense in any species and a “struggle for existence” occurs. A complicated demographic process follows, resulting in organisms adapted to their environments, as long as the environments don’t change too rapidly. Otherwise, the same basic set of causes results in extinction of the population. Understanding natural selection as the result of specific causes requires the researcher to understand ecological settings, life histories, and development in relation to differential leaving of offspring.
In his estimation, natural selection isn’t a mechanism in and of itself. It doesn’t have the power to do anything (which makes it even odder that Seelke would expect something from his experiments). Instead, natural selection is a series of complex genetic and environmental causes:
Natural selection does not shape an adaptation or cause a gene to spread over a population or really do anything at all. It is instead the result of specific causes: hereditary changes, developmental causes, ecological causes, and demography. Natural Selection is the result of these causes, not a cause that is by itself. It is not a mechanism.
One can debate his exact ideas, but one can certainly see that he calls for a more detailed, nuanced explanation of variation – not the abolition of natural selection. This would align with the idea from my last post that there are specific metrics involving the component of heritability – thus it’s not circular. Allen MacNeill echoes Provine here:
Creationists and supporters of Intelligent Design Theory (“IDers”) are fond of erecting a strawman in place of evolutionary theory, one that they can then dismantle and point to as “proof” that their “theories” are superior. Perhaps the most egregious such strawman is encapsulated in the phrase “RM & NS”. Short for “random mutation and natural selection”, RM & NS is held up by creationists and IDers as the core of evolutionary biology, and are then attacked as insufficient to explain the diversity of life and (in the case of some IDers) its origin and evolution as well.
Evolutionary biologists know that this is a classical “strawman” argument, because we know that evolution is not simply reducible to “random mutation and natural selection” alone. Indeed, Darwin himself proposed that natural selection was the best explanation for the origin of adaptations, and that natural selection itself was an outcome that necessarily arises from three prerequisites:
• Variety: significant differences between the characteristics of individuals in populations);
• Heredity: genetic inheritance of traits from parents to offspring; and
• Fecundity: reproduction, often resulting in more offspring than are necessary for replacement.
Given these prerequisites, the following outcome is virtually inevitable:
• Demography: some individuals survive and reproduce more often than others, and hence their heritable characteristics become more common in their populations over time.
As I have already pointed out in an earlier post, the real creative factor in evolution isn’t natural selection per se, it’s the “engines of variation” that produce the various heritable characteristics that natural selection then preserves from generation to generation. According to the creationists and IDers, the only source of such variation is “random mutations”, and so there simply isn’t enough variation to provide the raw material for evolutionary change.
He goes on to list 46 sources of variation. Elsewhere he says this:
Ever since Darwin, the primary “engine” of evolution has been considered to be natural selection. However, if one takes a closer look at this, it is clear that natural selection is not an “engine,” it is an outcome. If evolution is defined as change in the characteristics of the members of a population over time and natural selection is defined as unequal non-random survival and reproduction (or, more parsimoniously, differential reproductive success), then the underlying cause of the changes that are differentially preserved over time is the real “engine” of evolution by natural selection.
Of course, the ID argument uses an admission of the theory’s shortcomings (all theories have shortcomings) and tries to stake it out as some sort of tacit statement of evolution’s inefficacy. This is not true. More from MacNeill.
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 “modern synthesis” is dead – long live the evolving synthesis!
What he does is hail the “evolution” of evolutionary theory because our understanding is constantly growing. This is a great thing for MacNeill, not a bad thing. I know that you’ve at least given kudos to MacNeill for admitting this (and have talked about many of the articles I’m quoting), but I think you’ll find that most biologists worth anything are quite sober when it comes to evolution. PZ Myers:
There are a number of reasons why the current theory of evolution should be regarded as incomplete. The central one is that while “nothing in biology makes sense except in the light of evolution”, some important disciplines within biology, development and physiology, have only been weakly integrated into the theory.
…
One unfortunate problem with discussing these issues in venues frequented by lay people is, you guessed it, creationism. Any criticism of a theory is seized upon as evidence that the theory is wrong, rather than as a sign of a healthy, growing theory. The Neo-Darwinian Synthesis is not wrong, but neither is it dogma. It was set up roughly 70 years ago with the knowledge that was available at the time, and it is not at all surprising that the explosion of new knowledge, especially in molecular biology, genetics, and developmental biology, means that there are radically different new ideas clamoring to be accommodated in the old framework. The theory is going to change. This isn’t cause for creationists to rejoice, though, because the way it is changing is to become stronger.
This is the attitude that many of them take. Even if MacNeill is correct in his assertion, saying that the modern synthesis is dead is like saying that Newtonian gravity died with Einstein. The old is not enough, and there needs to be something new. He does not seem to be advocating a completely different understanding of evolution, as many of his thoughts on evolution are quite in line with modern thoughts that have been advocated for decades. He says it’s insufficient for dealing with certain things, which means that it needs to change, but that’s good and healthy.
Now, of course, it’s clear that the evolution of organisms is dependent on many factors. Here, I think, is where the confusion of terms comes from. The events that would lead to evolution are unplanned, and one may consider those random, but that’s not what many are referring to, I believe. They’re saying that the way in which the genome itself is molded is decidedly not random. There will always be a “direction” because evolution is about change, and there is always change. It takes an understanding of these circumstances that mold change, as Provine says, to understand what will be favored. It’s predictive in that way. This is an important distinction: there is no such thing as favor in true randomness. One event is as likely as any other. But, obviously, aspects of organisms are favored. That’s usually what people mean, despite the difficulties of language. MacNeill himself seems to suggest that evolution is more about “exaptation” – building away from non-functionality or previous functionality – not adaptation. If one automatically assumes that random means purposeless, then the source of the equivocation becomes obvious, but I think about it more in terms of likelihood.
I’d also say that the assertion that evolution is unguided (or “goal-less”) is more than a philosophical supposition. The two (guided or unguided), we’d suppose, would look quite different, and the evidence of genetics suggests an unguided process that produces mistakes and imperfections and inefficiencies and waste. It doesn’t look like there’s any forethought there – only what can be used as evolutionary fuel in the present. Now there’s always the possibility of a guided process masquerading as an unguided process, but we see evolution happening even today, so to the best of our knowledge it looks like an unguided, natural process.
What I think from all of this is that there are massive confusions of terms (I even tend to use NS as a kind of catch-all), and that’s somehow pinned on biologists as obfuscating and equivocating. But you’re going further and somehow making this a referendum on evolution. Like most ID arguments, the very people that are quoted in order to make evolution look inept are actually quite coherent in their thinking and will tell you what evolution is and why it’s so strong. And then there are the actual examples that have been debated, which, if true, lends a ton of credence to the idea of changes in organisms over time.
Hi Jacob,
Appearances can be deceiving.
You confirm it yourself:
NS is an outcome, not a cause.
NS is a result, not a cause.
You say:
No, this is mangled. Provine has clearly said, as repeated by MacNeill and in your own quotes that NS is not a cause and it is not a series of causes.
You show the clear contradiction as you quote Provine immediately after:
Two times, it is the result of causes.
If this reading came from my comment then the mangling is again yours.
Later you quote both Darwin and MacNeill in support of my citation:
You complete my thought by continuing to quote MacNeill:
The causes of the changes, the Random Variations are the engine – NS is not. NS does not cause variation, it is the result of many factors which preserve some variations and destroy others. And, as Gould has shown us, that preservation itself is contingent, staggering, undirected, non-linear …. random.
This is a strawman that MacNeill erects everywhere he goes. It is not only a strawman, but it is a lie. Time and again he is corrected when he pretends to think that by RM his opponents are referring only to random single-point mutations and he is lying when he pretends that evolutionary biologists themselves do not use this exact terminology; in my quotes, for instance. He is obfuscating when he pretends that non genetic factors in heritability, which he believes in and which he claims make NDE obsolete, somehow argue against the ID position, i.e., he accepts that the failure of the paradigm is true but because he wants to dismiss ID he pretends that he is the only one who sees it and that his patch is the only solution.
Lee Spetner did a great job in Not By Chance of discussing why the other “engines of variation” appear to be guided and nonrandom, and why this argues for a guided evolution.
You then go on to tell me that MacNeill still believes in some kind of naturalistic evolution. That wasn’t the point though. The point was that NS does not eliminate “randomness” from evolution. As I said, to admit that evolution by chance, by any unguided mechanisms of genetic change, fails empirical and mathematical tests, and then to try to disguise the randomness inherent (philosophically necessary) by waving NS at it is fallacious. Culling does not solve the information problem of an unguided process. This “evolution is not random” mantra is the equivalent of “only creationists us the term micro-evolution” or MacNeill’s “RM/NS is a strawman”; it is intended to hide the debate behind a cloud of words and to imply ignorance on the part of the person using the terms.
Both fail. When randomness is an expression of likelihood it fails the math test. Thus, Dawkins’ claim that it is “anything but random”. What the term means, and has always meant, as evidenced by my cites from Darwin to MacNeill to the Weisel 38, is that it is without purpose.
1) “Evolution” has always been a metaphysical position, thus its reliance upon randomness as meaning ‘unplanned, unguided’. It was a philosohical claim long before it was ever a scientific hypothesis.
2) This type of randomness is not an empirical finding.
3) The term is couched in meanings regarding likelihood and probabilities.
4) As such it cannot create the information or forms that it has to have – time and resources have perpetually been against the claims. Mathematicians, physicists, and geneticists have exposed the problem from the beginning.
5) Randomness, as a failed probability claim, is then supposedly erased by NS.
6) It can’t be. NS is not a force and is nothing but a result of other random processes and cannot solve the information problem.
7) Randomness is then claimed to mean merely “unpredictable”. However, as seen above, that was never its intended use. If that were its real meaning it would never have been used and, in fact, the genetic factors are not unpredictable.
You have tried to argue that the guided/unguided argument is not necessarily a philosophical question but you’ve summed up with a bare philosophical assertion. It does not, to the best of our knowledge, look like an unguided process. It looks very much like a guided one.
Not so. I made this a referendum on the fallacious claim that by reference to NS one can say that evolution is not forwarded as a theory of randomness.
Nobody disputes change over time. This is another equivocation on the word evolution. The strongest, most strident YEC believes in change over time.
This is a question of, as MacNeill puts it, the engines of variation. And though he presents those engines as purposeless, the evidence does not support this.
Tony:
You wrote,
Several comments:
One, ID does provide positive, inductive evidence (I’m sure you didn’t really mean to write “proof”!) on its behalf: information in the genome and cosmological fine-tuning, to name two of them.
Two, ID’s argument is not “evolution doesn’t explain everything.” That would be unreasonable. Rather it is, “evolution doesn’t explain enough.” It leaves too many questions unanswered, and possibly (this is part of ID’s empirical project to ascertain this), unanswerable. If evolution doesn’t explain enough of what we see in nature, then it is not strong enough to support the confidence placed in it.
Three, there is no third option on the table. P(ID) + P(Evolution) = 1. If the probability of evolution’s being true decreases, then the probability of ID’s being true increases, unless some third explanation for the species comes to light. Therefore evidence against evolution can be evidence for ID.
Of course everybody recognizes that “evidence against evolution” may in some cases be more accurately understood as “evidence against current understandings of evolution, to be corrected by more advanced understandings of evolution.” But to assume that this is always the case, and that evidence against evolution as we currently understand it could never be evidence against evolution period, is to beg the question or to rest faith in the promissory note of future science. I emphasize the word faith.
Four, P(ID) +P(naturalistic origin of life) = 1 for the same reason. If the probability of a naturalistic origin of life is low, then the probability of ID is high. At this point there is no experimental or theoretical reason to suppose that the probability of a naturalistic origin of life is very high at all.
Five, as I have written elsewhere, the demand for an ID hypothesis must take into account the fact that if the design was accomplished by God, then the mechanism of design is not going to be entirely susceptible to scientific observation or evaluation. Often when an hypothesis is demanded from ID, it is expected that it would be in terms that are 100% susceptible to scientific observation or evaluation. That demand, however, calls for ID be defined in terms by which it would contradict itself (for those, like myself, who take it that the designer is God). It is a logically illegitimate demand.
Therefore ID is not a purely scientific enterprise. It is a scientific/philosophical/theological enterprise. For those who consider it necessary for all knowledge that it be scientific, this will seem wrong, inadequate, or impossible. I simply reply that not all knowledge is scientific, and it is wrong to expect it to be.
So am I expecting “that basic scientific standards be altered in favor of my pet philosophy”? No. I’m expecting that science do what science can do, and that it not be expected to do more than it can do. As far as ID is a scientific enterprise, it must be carried out by good scientific methods. But that is not the whole story for ID. I have written an extended discussion about this previously.
“The correct theistic position is pro-science,” you represent me as saying, and you are right. The correct theistic position is also pro-philosophy, pro-theology, pro-history, pro-art, pro-literature, pro-logic, pro-reason, pro-spirituality…. (provided that all of those are carried out with excellence and that they all mutually inform one another).
Charlie -
Perhaps I wasn’t making myself clear, but I intended to imply that NS is the result of these factors. No mangling necessary. Just unclear language, which, incidentally, is the whole point here – biologists don’t evoke NS as some sort of empty phrase but already explore the causes of selection. I pointed many of them out in this thread, so my points themselves relied on this distinction.
Furthermore, my intention in quoting MacNeill was not to talk about his strawman comment (I’ve seen Behe and others make the distinctions before). I thought that perhaps you’d argue against it, but I didn’t think that it was that important, and I wanted quote the “engines of variation” bit in its entirely. I’m not sure why you’re quoting people who don’t at all contend that change is totally random, though. I know you’re trying to define NS here, but it’s kind of strange to use them to agree with their definition but disagree with their implications (which shows the dangers of quote-mining).
Anyway, I hope that clears a few things up. But some of your statements seem rather vague to me. What empirical claims? Now, by evidence for change over time I meant the usual evolutionary claims, which are different from most ID claims. More specifically, I’ve been arguing that there are examples that show clear unguided selection of new functions, and many of these Behe has attempted to downplay as insignificant. I was hoping that we could discuss those.
Secondly, the math. As far as I’m aware, you can express mutations in terms of sheer probabilities, but the number six on your list is the weak link. The most basic problem here is that I don’t think it’s appropriate to describe NS as random. Arbitrary, perhaps. A function selected for in one situation may not be selected for in another situation, but this only effects the probability of certain functions, which doesn’t even matter because evolution has no end goal, and not the probability of selection occuring. Selection will always occur. Thus, the probability of selection occuring will always be high. For instance, the chance of a human-like organism emerging is incredibly low because different genes will be selected for if you rewind the entire thing and do it over. But something will always emerge. Selection preserves and promotes (sometimes to the degree that common motifs are conserved for millions of years), which, by definition, effects probabilities dramatically. That’s why someone like Dawkins would claim that ultimately evolution is not random because all changes must be syphoned through selective criteria. Anyway, who questions all of this? Most of the opposing arguments I’ve seen that use probability have fundamental problems and have been addressed legitimately by biologists and mathematicians both (for instance, Dembski has been largely discredited).
You have tried to argue that the guided/unguided argument is not necessarily a philosophical question but you’ve summed up with a bare philosophical assertion. It does not, to the best of our knowledge, look like an unguided process. It looks very much like a guided one.
I know that your entire argument has been an attempt to prove that evolution cannot be unguided, but my point here was totally distinct from that. In other words, assuming that we haven’t yet totally resolved the question of the mechanisms of evolution and their probability, what other evidence is there to suggest whether the process is guided or unguided? So what I’m saying is that there is indeed evidence within the genome to suggest that evolution wasn’t guided, and it would have to be made to look like it was guided. Given all of the inactivated genes, one could probably argue for unguided evolution and the efficacy of selection in the same breath.
Hi Jacob,
For the same reason I quote evolutionsists against certain aspects of the theory even though they aren’t IDists or Christians – hostile witnesses make better witnesses. And it’s irrelevant to the point I was making whether or not MacNeill believes that RM is totally random. And, by his definition, which I’ve pointed out, he does think mutations are totally random. That is because he thinks “random” should be taken to mean “without foresight”. Of course, his science is a metaphysic when he determines this.
Quote-mining is dangerous. It’s also dishonest and it’s also an inflammatory and impolite charge to make.
Sorry, I’m not going to debate the whole of evolutionary theory here. I made my point – NS does nothing to remove the randomness from evolutionary theory and “randomness’ is a metaphysical presupposition.
Very high, indeed. In fact, it is 1.
I haven’t seen the empirical studies that back this one up but I know Gould would agree with you.
No, you’ve missed my entire argument. My entire argument is that claiming that variations are preserved unequally does not eliminate the randomness from evolutionary theory, that it is still a theory of randomness and chance, and that this is a metaphysical claim, not an empirical finding.
As to the weak linkness of my #6:
A cull does not add or increase information. It does not create.
This (at least the first half) is much better than your previous claim that to the best of our knowledge the process looks (empirics) unguided (metaphysics). Yes, there is evidence of evolution being unguided. But evidence is in the eye of the beholder.
If there are inactivated genes they are, coincidentally, able to be re-activated. This is evidence of efficient design and manifests itself time and again. The genome has remarkable regulatory capabilities.
And as ENCODE shows us, as comes out daily, and as you’ve seen in your discussion with Dave, there is good evidence that the much of or the entire genome is transcribed and functionally necessary. Of course, while evolutionists are busy trying to deny that when they called junk-DNA ‘junk’ they are just as busy now trying to pass the transcribed RNA off as junk. And, at the same time as they point to this “inactivation” as evidence for unguided evolution they also claim that they didn’t really think the theory was predicting “junk” at all.
Maybe Dave is interested. I know the guys at Telic Thoughts and Uncommon Descent would enjoy listening to you. As for me, right now, I have made my points and don’t intend another round on the evolution merry-go-’round.
Tony and I had a chat about Behe and the supposed disproofs of his claims a while back, which you all can peruse though, if you’d like.
http://www.thinkingchristian.net/2009/01/is-religion-adaptive-its-complicated-scientific-american/#comment-11315
HOw about
http://www.richardsternberg.org/pdf/sternintellbio08.pdf
On your side you can have a look at Fodor. Or Kaufman http://creationevolutiondesign.blogspot.com/2007/11/poe-bibliography-k.html
The fact that people question all of this is evidenced by the mere existence of theories like self-organization, neo-Lamarckism and evo-devo.
No junk RNA either.
http://www.evolutionnews.org/2009/03/nature_paper_shows_junkrna_goi.html
Jacob,
Charlie’s discussion of junk DNA is misleading.
Junk was a term coined to refer to non-coding regions, and most of DNA is non-coding. Obviously, we now know that SOME of the non-coding regions are regulatory. However, this doesn’t mean there’s no “junk”.
If you simply define junk as non-coding, it includes a lot of important functional stuff. You can’t delete all the non-coding stuff and get a living animal.
However, if you define junk as stuff you can delete and not see any problems, then there’s still a whole lot of junk. Quite possibly more than 50% of our DNA is this sort of junk.
So, let’s hear it from the ID folk… If we’re designed, how much junk should there be? 0%? 50%? 90%?
Suppose that junk is an important source for new genes or new regulatory mechanisms. Is it then not junk? That would be a pretty peculiar definition of junk. If you delete the junk, we might be marginally less adaptive over the span of many generations. However, humans aren’t doing a lot of evolving at the moment. We control our environment to suit our existing genes and regulators. An ability to evolve more genes over hundreds of generations is not very useful for modern humans. IOW, it’s still junk.
Besides, for less-intelligent species, wouldn’t the percentage of maintained junk be something that would be adaptive, and, hence, selected for in most of our ancestors?
Jacob, sounds to me like you have a good understanding of the NS mechanism and why it isn’t random.
Oops. I meant
Charlie,
Remember the time you said that, if neo-Darwinian evolution were true, all the lions in Africa should have eaten all the antelope and wildebeast by now? That was funny.
Hi DL,
No it’s not.
It was very rudimentary though, I’ll admit.
Meaning only that it is not translated into proteins.
Read the Sternberg.
It’s likely that all of the DNA is transcribed. And yes, at times we can do without many of the products of this RNA but, read the Sternberg, it is very unlikely that this RNA is junk either.
A better question, since you are contending that junk DNA is a prediction and is evidence of evolution (thus, junk DNA … contra the modern apologists, IS junk), would be this: how much junk do you need to evidence evolution? It used to be 98% (required by theory before any investigation). Now it’s 50%. When will you have lost enough evidence? Ever?
Of course not. As with vestigial organs and “randomness”, when our ignorance is erased and the evolutionary claims proven wrong evolutionists will just rewrite history and tell us that they never said junk DNA was evidence (as they’re doing, you’re just a little late to the party).
Nice evidence there of selective removal of undesired qualities. A perfect example of why intelligence (there, don’t say I never complimented you) is required – as in Darwin’s analogy, animal husbandry. Now perform a cull by chance.
Yeah, that was real funny DL. In fact, it’s such a laff riot that I linked to the discussion already. You should go read your LIES on that thread again and reel in embarrassment.
Enjoy.
Charlie -
I’m honestly wondering this. Suppose that evolutionary theory is true. If not randomness and chance, then what would you call a theory that relies on copying errors and factors that might or might not be present at a given moment? I honestly can’t tell if this argument is supposed to be some kind of affront to evolution or just inquiring about the nature of the processes that allow it to occur. ID arguments are so hard to track because there are so many different versions of it. And, regarding empirical claims, if we saw some form of evolution in action today, how would that effect your argument?
Information can increase. As far as I’m aware, we’ve documented it. Of course, I’m talking about an increase to the size of the genome. New “functions” are a different matter and require only a change in the genes.
What about inactivated genes makes them efficient? Many of them are discarded or half-deleted. They may be reactivated if they prove useful, but if you want to infer design, then there doesn’t seem to be much rhyme or reason to any of it. I mean, it’s not like we have waves of backup genes from our evolutionary history that are perfectly preserved because of some potential future use. Any genes could be useful given a specific circumstance, but what we see is that certain genes may or may not be there in the genome, and the reasons aren’t efficiency and usefulness.
Ryan Gregory on ENCODE:
A large fraction of the sequences analyzed, both in introns and intergenic regions, appears to be transcribed. However, most of this DNA is not conserved and there is no clear indication of function. It could be that the transcripts themselves play a functional role or that the process of transcription but not the transcripts per se contributes an important effect. It could be that the regions they examined, which were typically gene-dense, included transcribed introns (no surprise) plus longer-than-expected regulatory regions such as promoters near but outside of genes (e.g., Cooper et al. 2007), but that on the whole the long stretches of non-coding DNA in between genes are not actually transcribed. Or, it could be that transcription in the human genome simply is very inefficient. For example, the data in this study suggest that 19% of pseudogenes in their sample are transcribed, even though by definition they cannot encode a protein and are unlikely to play a regulatory role. It also appears that in other groups, e.g., plants (Wong et al. 2000), there is lots of intergenic DNA that is not transcribed, which may indicate that this is a process unique to mammals and is not typical of eukaryotic genomes.
Looking at a broader scale, we must bear in mind that about half the human genome consists of transposable elements. Some of these clearly do have functions (e.g., in gene regulation), but others persist as disease-causing mutagens. It could be that a large portion of these have taken on functions, but this remains to be shown. We are also left with the question of why a pufferfish would require only 10% as much non-coding DNA as a human whereas an average salamander needs 10 times more than we do. The well known patterns of genome size diversity make it difficult to explain the presence of all non-coding DNA in functional terms, even as there is growing evidence that a significant portion of non-coding DNA is indeed functionally important.
It should be said that “evolutionsts” have been exploring the regulatory capabilities for decades.
It’s also dangerous to use the word “they” here. There were a lot of different views on junk DNA (actually, the entire word originated to explain a very specific kind of non-coding DNA). There were some who said that it was all preserved because of complete usefulness, but most were trying for a more nuanced view, which has grown quite a bit as more evidence reveals itself. It’s the evolutionists (read: the overwhelming percentage of biologists) doing the research. The evolutionists have been trying to find the answers here since the 50s and 60s. Even if they had different opinions, it’s difficult to say that it was ever dismissed. And there is still a very realistic view on it. I think it’s disingenuous how ID claims every new hypothesis as a victory. It’s a victory for science. Since most biologists never stood in the way in the past, it’s strange to say that they’d stand in the way now. The views of these biologists are always changing, but it’s tough to calculate straight percentages because it depends upon the metric (that 98% figure was always traditional coding DNA, so it still generally stands). Like vestigal organs, the argument isn’t that they don’t do anything. The argument is that there are remnants everywhere – some may be useful, some may do something, some may have done something or could do something yet. But it’s much more unwieldy and complex than it should be if it’s the product of intelligence.
Hi Jacob,
Question begging. Who said that errors equal evolution? The genome is designed to repair, and is highly efficient in doing so, the so-called errors (MacNeill’s RM). These base substitutions do not and cannot lead to evolutionary change. The changes that might, inversions, jumping genes, etc, are highly coordinated with a suite of specific enzymes required to cut them in, and then back out of genes. This is design, not error.
On the other hand, entropy being what it is, the genomes are likely suffering some degradation as some of the base pair errors get by, but this damage is not the stuff of positive upward evolution.
This is more evolutionary question-begging.
Genes that resemble portions of other genes are not half-deleted because somebody proposes they might be. When we see how often genes are turned on to perform specific functions when the time is right, and even when the environment demands it, it is just a repetition of the same vestigial argument from ignorance to keep making these claims – especially as daily the evidence for such waste is evaporating.
What was my argument, again?
“Only a change in the genes”. That sounds simple. But then you also require that a useful, foldable protein happens to be associated with this merely changed gene, and that there be a function for that useful, unique, 3-dimensional protein to fulfill. Again, sounds more like design than chance.
I have some trouble with this sentence but it looks quite philosophical and question-begging at the end. Lots of genes may not be in the genome. But very often what was thought to be “not a gene” becomes a “gene” when we realize that it is either activated for a purpose later, essential as a regulator for a previously unknown function, part of a “gene” found elsewhere on the chromosome, or even on a distant chromosome, etc..
Face it, the ignorance level is way to high, and we are at the very beginning of this exploration; an exploration which only shows greater and greater function, and deeper codes and more information every day. And yet Darwinists will cling to every last vestige of “junk” and “uselessness” (the same thing) as evidence of “no design” until there is nothing left – and you call IDists disingenuous.
Talk about gaps arguments.
If they stuck to science, left the philosophizing out of it and quit trying to pretend that science could possibly give them anti-design arguments then we wouldn’t even be having these discussions.
They can be reactivated when the time is right and are not being wasteful when the time isn’t.
Did you notice that while you claim that junk DNA is not junk DNA on one thread you are still making arguments for its junkiness and you even quote a guy in your ENCODE rebuttal (?) hoping that it still is? And all he has are hypotheticals, questions begged by definition (pseudogenes may be without function by definition, but by empirical observation they have function) and arguments from ignorance.
I do like his ending, however:
That’s right, growing evidence for functionality, diminishing evidence for waste.
Maybe, but in the face of ignorance it is still claimed, as in your report on ENCODE, that just maybe, some of it is still useless and that would then be evidence for our theory. I ran into this on MacNeill’s blog a couple of summers ago when the redoubtable PvM got all excited because a pseudogene which was reported to have function was again determined no to have function. He spread that story from blog to blog. Why? Because junk = evolution. One really would think then that not junk = not evolution.
The same way Darwinists do. When we don’t know how it happens it’s random, when we don’t know what it does it’s junk/vestigial, when we propose some kind of mechanism yet to be explicated/rebutted it’s proof. If junk DNA isn’t junk then it’s not evidence of a wasteful, blind, random process. Darwinists can’t keep admitting that it’s not junk and claiming that it is without being disingenuous.
The 98% was NON coding, and it still is – when coding means transcribed -> translated -> protein.
But the very things claimed as useless, yes, useless, like pseudogenes and transposons are found to be useful, bit by bit, piece by piece, until we are at a point where many are saying none of it is useless. Some keep hoping though. And, as I said earlier, as the hope for junk DNA dimnishes they just move it over and hope for junk RNA.
But actually, that was the argument. The word “useless’ comes to mind over and over again.
New Scientist, via Creation Evolution Headlines.
http://creationsafaris.com/crev200709.htm#20070912a
http://www.evolutionnews.org/2007/06/will_darwinists_try_to_pull_a.html
Richard Dawkins thought that not being translated into protein meant not being used:
http://www.abc.net.au/science/news/stories/s594118.htm
Describe frustration… taking several hours to write a post only to have it vaporize when clicking the submit key. In the immortal words of Charlie Brown.. “Aaargh!”
Tom,
Just a few comments on your last post.
Hmm. Cosmological fine tuning is a philosophical argument, and is about as post hoc as it gets. If you can explain to me how cosmological fine tuning is inductive, I’m all ears.
“Information in the genome” sounds like something, but I don’t know what you mean. Again, to be clear, I’m looking for evidence found through induction – as in, “if things were designed (and not the result of evolution), then we would expect to find this, which is different than something that would occur were it to have developed through evolutionary means.” (I did say “proof” and not evidence because I was trying to convey the sense of how a positive, inductive test would help confirm the argument for ID.)
Do you have a definition for “enough” as it pertains to when scientific theories are acceptable? Do you apply this same definition of “enough” to ID? What about all the overwhelming number of things that ID does not explain, like bad design, extinctions, the origins of the designer, etc.? This does seem like your caviling.
I’ve never understood this kind of Plantinga “only game in town” argument. For one, there’s Unintelligent Design. There’s Probabilistic Design. Not to mention pure Unguided Randomness. Designating ID as some kind of vacuum cleaner recipient of everything unexplained, especially when there are a whole slew of groups who can’t agree who the Designer might be, seems a tad hasty. Lastly, I’d rewrite the formula above to read P(Unexplained) + P(Evolution) = 1, because, per my chief complain here, ID doesn’t actually explain anything.
At first this seems more reasonable to me then 3 above, but then I don’t understand why you wouldn’t include (P)Panspermia, a (P)deistic creator who initiated the universe but didn’t design it per se, etc. I could also add that at this point there is no experimental or theoretical reason to suppose that the probability of an intelligent designer is very high at all, which I think if we were to accept your formula would have the exact opposite outcome of what you intend. (I don’t, however, think this would be acceptable way to conclude that Evolution is probably correct; I prefer Evolution because it explains and predicts so much, not because ID explains and predicts so little.)
This is quite an understatement. Actually, instead of it not being “entirely susceptible,” I’d say that no one has shown how any mechanism of design by God is at all susceptible to scientific observation or evaluation. If someone had we’d have a hypothesis and could go about seeing what ID can provide to us in terms of scientific knowledge.
It seems clear to me that one cannot be, despite your claims, both pro ID and pro science under the definitions you have given. Of course, that is only my conclusion from what you have written – I’ll leave it for any others who might read here to come to their own determination on that topic, as I imagine we’ve both stated our positions to the best of our abilities.
@Tony Hoffman:
I’m not at all sure how to respond to your latest. It’s filled with strange assertions.
Like, for example, “Cosmological fine tuning is a philosophical argument.” Cosmological fine-tuning is a scientific argument in favor of design. It just is. Of course it has a philosophical element. So does quantum mechanics, Newtonian physics, neo-Darwinian evolution, and the value of avoiding transfats. I mean, to call for an argument that is not philosophical is to call for an argument that is not an argument.
Or that it “is about as post hoc as it gets.” So is every other explanation for fine-tuning, especially the multiverse. So, are we supposed to run an experiment on the birth of some other cosmos?
Or, “I did say ‘proof’ and not evidence because I was trying to convey the sense of how a positive, inductive test would help confirm the argument for ID.” I think everyone knows that a positive inductive test would help confirm the argument for ID, if such a test could be devised in a way that did not undercut what ID actually affirms. (I wrote about that in point five in that last comment.) In the meantime, what’s wrong with evidence in favor of ID? Does it have to be proved right out of the gate? Do we have to start at the finish line?
Or this:
First you’re complaining that ID calls for a philosophical argument, then you’re saying bad design is an argument against it. “Bad design” is a theological argument. (David Heddle dealt with a closely related point just a few hours ago.) My theology can explain what you call “bad design.” But if I introduce my theological argument to answer your theological argument, you’ll blow the whistle on me for using theology. I’m blowing the whistle on you first.
The same goes for extinctions. Do you have a non-theological reason to suppose the designer would not want extinctions?
As to the origin of the designer, that’s very basic. But it’s also theological. Again. The explanation is that God’s being is necessary. Any argument you raise against that is going to be philosophical or theological.
Now, ID does have a component to it that is more purely focused on the empirical. I explained that in the blog entry I linked to last time. But ID as a research program in its entirety includes more than that, and that’s okay. Life is more than empirical.
Then there’s this:
Unintelligent Design is a contradiction in terms. Probabilistic Design probably is too; I’ve never heard of it. Unguided Randomness won’t get you life and all the species by any method that has been proposed except for evolution. I think you’re spouting nonsense by suggesting these are alternatives to evolution or ID. If not, then kindly fill me in on what they mean.
And this:
Sure it does. Taken as a complete empirical/philosophical/theological program, it explains where life came from. Isn’t that something worth knowing?
As to probabilities of panspermia, I see that as a non-starter; it just puts the same problems we have here out somewhere in space. A deistic non-designer is no different from evolution, for without design, there is no explanation for the origin of life.
Huh?
I stand in astonishment at the hubris of people who pronounce that every theistic argument, every historical evidence, every experiential testimony of millions and millions of people, every documented miracle (I know of one locally here where a doctor at the Portsmouth Naval Hospital canceled a foot amputation following prayer, just in the last two weeks), all taken together, amounts to “no … reason to suppose that the probability of [God] is very high.”
Look, Tony, at least be intellectually honest and say you think the arguments are insufficient or something. This business of “no … reason” is ignorant and/or foolishly proud of one’s own absolute knowledge of everything in the world.
And then there’s this:
I love it when people go complaining that they can’t figure out the “mechanism” God used, as if they think that’s part of the God theorem, that he turns levers and wheels and makes things happen in the non-physical realm. Surely you can think on a more sophisticated level than that!
And here’s the nub of it all:
“Scientific knowledge” is the only kind you’ll accept, and that’s just wrong. It’s philosophically, rationally, and even scientifically naive.
I’m not pro-scientism, which is what I think you have in mind when you say pro-science. Scientism is the obviously incorrect but altogether too widespread notion that knowledge must be scientific.
Hi Dave,
That is very unfortunate. I hope you can recreate it. I know it never seems the same the second time around.
What’s really frustrating is when it happens the second time. “… fool me twice, shame on me…”
Friendly suggestion: For lengthy posts, it’s good practice to work in your favorite word processing program such as MS Word instead of directly in the comment box. Then when satisfied, copy/paste your work to leave your comment. Not only does MS Word auto-save your work every few minutes in case of a crash, it also helps with grammar and spelling! (that is, if you need the help like certainly do!)
Back to the subject at hand….I’ve followed the ID arguments and counters for a few years now and have read some of the books Mr. Gilson recommends above. Behe’s Edge of Evolution I thought was very convincing. Not as a positive argument for ID per se, but as a successful skeptical threat to Darwinian Evolution.
I agree with the opponents here regarding ID–that it’s lacking a proper set of scientific evidences in order to make a positive claim. But, they don’t have to prove ID as an alternative theory to Evolution in order to have value. Instead, they can prove Evolution *false* (or at least partly so, or probably so) and still have an enormous impact on our knowledge and bring us closer to accurate understandings of our origins.
As a Network Engineer, oftentimes I’m asked to troubleshoot a problem. Sometimes there’s no evidence to suggest what the problem is. But plenty to suggest what the problem *isn’t*. And that information has tremendous value. And I’ve become increasingly convinced, by the works of Behe and others that they’ve brought forth substantial evidence to falsify Darwinian Evolution—even if they haven’t made much headway offering positive evidence of a competing theory.
To the skeptics: Read Behe’s “Edge…”. At the very least you will find that it shows that some in the ID community are *doing* science in order to support their *philosophical* theory. And, that science might just convince you, as it has me, that Darwin was *probably* wrong.
But, they don’t have to prove ID as an alternative theory to Evolution in order to have value. Instead, they can prove Evolution *false* (or at least partly so, or probably so) and still have an enormous impact on our knowledge and bring us closer to accurate understandings of our origins.
What ID argument(s) do you find most convincing in this respect? Everything I’ve read from ID proponents has been endless variations of the argument from incredulity—nothing that even begins to reduce the plausibility of undirected evolution.
To those supporting ID: what books have you read criticizing ID arguments?
Hello David
Everything I’ve read from ID proponents has been endless variations of the argument from incredulity—nothing that even begins to reduce the plausibility of undirected evolution.
I think it is safe to say that you haven’t read much. You probably haven’t read much from the pro evolution side either, since the many evolutionist in their more candid moments, admit their bewilderment over the mechanism of evolution.
Have you actually read any books explaining the ID hypothesis?
BTW thanks for the tip about the word processor, I know I should do that, but I get caught up in the moment. This time I forgot to copy the post before submitting it and the rest, as they say, is history…”
I’ve read The Origin of Species and Descent Of Man (several sections many times), most of Dawkins, Hens Teeth and Horses Toes and Wonderful Life by Gould, several books by Paul Davies, several books by religious people like Steven Unwin who believe in God but don’t like ID ( I can’t even recall how many of these there are … the majority, for sure) and countless articles that my atheist interlocutors on these sites have thrown my way to disprove ID, from Miller, to Coyne, to Shallit, etc. as well as the dreaded talk.origins and Panda’s Thumb sites and their like and checking out the critics at UD and TT. I’ll admit to spending little time with the esteemable Dr. Myers, though.
I also took all my sciences and maths through highschool and at a post-secondary level where, of course, the arguments were all pro-RM/NS and anti teleology.
It’s not like you have to go looking for the critics.
On the pro side, I’ve read Dembski, Behe, Meyer, Gonzalez, Strobel, Flew, etc.
I have hundreds of books within reach right now, but maybe only a dozen or so on this topic in particular, and many. many hundreds of articles on my hard drive and in my bookmarks.
And I don’t even really care about the debate (saith my mouth).
If he is interested in answering the question wait until you see Tom’s list – or you could peruse his blog.
I’ve also read the Bible many times, including 3 times through in the past 15 months and am well into it again.
You probably haven’t read much from the pro evolution side either, since the many evolutionist in their more candid moments, admit their bewilderment over the mechanism of evolution.
Not knowing things about the “mechanism” of a phenomena is hardly evidence against the phenomena.
For example, one may not know the mechanism behind solar flares while having more than adequate evidence they actually occur.
As to my own reading, I used to be a creationist (a very long time ago). At the time I began doubting my religion’s creation story I read quite a lot of books from both sides (don’t ask me to name them, this was over twenty years ago). Even as a Christian (at that time), it wasn’t difficult to see that the creationist books depended on the scientific illiteracy of their audience. The arguments were simply horrible and more than a few times flatly ridiculous (and this was my reaction as a Christian, not an atheist).
Have you actually read any books explaining the ID hypothesis?
As I said earlier, no. I’ve read some articles and essays by prominent ID proponents, that’s all. My in depth study of the evolution vs creation issue took place before the ID movement had been kicked off. I asked earlier what would be the best ID books to read. The ones who make the best case for it. Tom gave some good suggestions. What’s your opinion? What are the best ID books?
I’ve read The Origin of Species and Descent Of Man (several sections many times), most of Dawkins, Hens Teeth and Horses Toes and Wonderful Life by Gould, several books by Paul Davies, several books by religious people like Steven Unwin who believe in God but don’t like ID….
Good, its a shame but so many of the people I encounter who defend creationism or ID haven’t bothered to read anything about evolution that wasn’t written by someone who doesn’t believe in it.
Hi davidellis,
I think you’re right. But I noticed another interesting phenomenon a long time ago: while I was repeatedly called ignorant because I am skeptical of evolutionism (and ignorant I am – as I’ve said before, if a biologist decides to bluff me I will have little or no response to her) those with far less exposure to the theory than I have are considered well-informed merely because they believe in it. There are several on this site right now reading this who fit that category. One pompous fellow with a name quite well known on the blogs had to even go scrambling back to AtBC to confirm with his fellows that scientists really are finding uses for junk DNA at the same time that he was comparing my intellect to that of a 12-year -old (which I don’t deny, but I’m pretty sure he meant it as an insult).
More on that note, with maybe one exception (no, two exceptions), just about every conversation I’ve had in real life with an atheist questioning my beliefs has started with a rebuttal like ‘well what about science?’ or ‘what about evolution’ or, my favourite ‘I only believe what I can see…’. This from people who know nothing about science or evolution and less about the Bible and God.
I also forgot to mention that I’ve also spent probably a dozen hours reading each of Huxley and Haeckel, and longer still on Darwin’s letters and notebooks (online, of course).
On my side I also forgot Philip Johnson, who gets an undeservedly short shrift these days and maybe my favourite book on the subject, Wiker and Witt’s A Meaningful World.
Enough bio for today … thanks for asking.
Greetings Mr. Ellis,
Since you asked, I would recommend Behe’s “Edge of Evolution” to start with first. It’s a refinement of his earlier works and in it he doesn’t discount Evolution entirely, he makes the case that it can only do so much. What you’ll appreciate, is that he doesn’t do this with an argument from incredulity or ignorance. You may not be convinced, but you seem decent and honest enough a fellow that I’m *certain* you will come away from that book having been intellectually challenged and at the least you’ll be well armed to defend your own position against a serious work—not the “creationist” stuff you’ve frowned upon in your past readings.
To your other question—it doesn’t matter whether or not I (or others) have read the critics of ID. You have admitted your own gap in modern knowledge on the subject. It’s up to *you* to fill the gap you admit you have on the subject before you can be justified in offering your own critiques of the subject. Until you have, any critique you might offer would be completely unwarranted.
As an aside—in my experience I’m often enticed to read the critics *before* I read the work they’re criticizing (on any subject, not just ID), and worse, I’ve become so convinced that the critic was *right*, that I never even bothered to get around to read the source!!! I think it’s some weird human nature thing many of us suffer from. Then one day I decided that that was pretty stupid. I should read the source first, and *then* the critics. And when I did, I was surprised to learn that often (not always) the critics had obviously never read the source themselves!! Do you ever suffer this weird habit too? I’ve gotten better, but I still fall into that on occasion, much to my own detriment.
Proverbs 18:17
Most of Wiker’s “A Meaningful World” is available on googlebooks as a free preview.
http://books.google.com/books?id=AyWMnrcuyv0C&printsec=frontcover&dq=benjamin+wiker#v=onepage&q=&f=false
The book was so facinating I read it through twice – something I rarely do with any book.
And this is “Moral Darwinism”, also by Wiker, which traces the history of evolutionary thought from ancient Greece to the modern West.
http://books.google.com/books?id=n27AG9eyq3gC&pg=PA1&dq=benjamin+wiker#v=onepage&q=&f=false
Tom,
I went through and responded to your last set of comments to me.
No. I think you are confusing the use of premises that use scientific data to form a deductive argument from a scientific, inductive argument. A scientific argument that uses induction takes existing data and hypothesizes an explanation and performs a test that confirms or does not confirm the hypothesis. There is no test to perform on a universe that already supports life to confirm that it is indeed fine tuned to support life. (I think it’s such a tautology that I find it hard to take seriously as a philosophical argument, but that’s a separate issue.)
So I have provided an explanation why cosmological fine tuning is not a scientific argument. Please feel free to disagree with me, but if you do so please provide an explanation of why you think so. (Here’s another way to look at it: if I were to say that studies on the effectiveness of prayer and research on evolution etc. were scientific arguments for naturalism, you should rightly correct me. My data may be gathered scientifically, but my argument would not be scientific because I haven’t offered a hypothesis for how I can test that Naturalism is true, only offered scientific evidence upon which I base my philosophical conclusion.)
I haven’t said that science doesn’t have a philosophical element. But the fact that science relies on some philosophical assumptions does not mean that a scientific (inductive) argument is identical to a philosophical (deductive) argument.
To repeat, I am only asking that if ID proponents wish for ID to have its conclusions accepted on an equal level as those of the other modern empirical sciences, it should make a scientific case – provide a hypothesis, and test it. The fact that this expectation –that basic scientific standards be met — is somehow considered out of bounds by ID proponents is bizarre.
I don’t consider the multiverse a scientific theory. Someday it may be. Until then, I hold it in the same regard as ID – a provocative and interesting idea, but one that I don’t place much confidence in.
There’s nothing wrong with evidence in favor of ID per se. But until that evidence is used to form a working hypothesis for ID, it is not scientific evidence for ID. Until then, ID is not science. It’s just another idea. (I keep on saying this over and over because you keep on writing about the aspect of ID that is scientific. To be clear, I hold something like the multiverse idea in the same regard, and I would be just as persistent with the multiverse proponents if they wanted their idea considered a science.)
I have never complained that ID calls for a philosophical argument. I have asked for proponents who claim that ID is a scientific enterprise to provide a scientific argument – a workable hypothesis. I think I have been clear on this point throughout.
I was pointing out that evidence of bad design is evidence that should be considered when forming a hypothesis of ID. (Why Bad Design is considered a theological argument I don’t understand.)
And you’re right that I am not interested in theological arguments for ID. I am interested in scientific and philosophical ones, because I am interested in how ID intends on conducting science.
Extinctions are a piece of data that both Evolution and ID should account for. If you can only provide a theological explanation, then it is not relevant to our discussion about how ID intends to conduct science.
Same as my last sentence above.
I remember you provided a link to that blog entry awhile ago, and I read it diligently then. It is one reason why I am familiar with your views on ID. For the record, it does not provide any substantive information on how ID is going to conduct science.
Yes, life is more than empirical. But science is something that is accessible to everyone. That’s what has made is so effective and productive in terms of expanding our knowledge. If you have access to some non-empirical experience that can be tested and provide the reliability of our empirical data, then there is no reason why science would not incorporate this. But the ID proponent needs to show how this data is accessible.
Anyone who’s seen the Pontiac Aztek knows that Unintelligent Design is not a contradiction. By Probabilistic Design I meant a deistic God who established initial parameters but does not guide every single thing. By Unguided Randomness I mean pure randomness, as in the 747 flying together by itself. (Although the probability of this occurring is admittedly insignificantly low, the possibility of a multiverse raises the odds to worthy of consideration in your formula. Why should we even suppose a multiverse? For the same reasons that it is supposed that the physical constants are all arbitrary and unrelated in the cosmological fine tuning argument – because we don’t know otherwise.)
(By the way, I just remembered that you did not provide an answer to my question regarding how “information in the genome” provides us with positive, inductive evidence.)
“ID doesn’t actually explain anything,” was poorly written by me. I’d ask to amend this to ID doesn’t explain anything scientifically, and offers philosophical arguments based on weak premises. In the above, I wonder if you’d like to reconsider theology as being part of what makes ID complete, as I believe that some ID proponents have gone to some lengths to deny this.
Well, panspermia does increase the odds of OOL being natural – the larger the universe, the longer it exists, etc. Okay on deistic non-designer being the same as evolution. But saying that “without design there is no explanation for the origin of life” is a double stretch. There are (experimentally unproven) explanations for the natural origins of life. They offer explanations, albeit deductively implausible ones. And the second stretch is that we run into the same problem as I mentioned above with your assertion that design is an “explanation for the origins of life.” At the most, I would say ID proposes that life is unexplainable through naturalistic means. I think that calling this an explanation stretches the definition of the word “explain” beyond its breaking point.
Well, those were your words I echoed above. (You: “At this point there is no experimental or theoretical reason to suppose that the probability of a naturalistic origin of life is very high at all.”) I find it equally remarkable that you would make your original statement, seeing as how ID fares worse than naturalism for its experimental (none) and theoretical reasons. Naturalism has at least submitted hypothesis that could theoretically be proven regarding the natural origins of life. ID has not.
My statement above is a completely unremarkable thing to say. Despite all your protests you have not answered the fundamental question – how is it that ID proponents expect ID to provide knowledge to us in a way that is commensurate with the modern empirical sciences. If you cannot do this I simply recommend that you identify ID for what it is – an interesting idea that has yet to demonstrate how it can be scientifically useful. (Like I said, this is how I would define the idea of a multiverse – this is not an anti-religious bias on my part.)
You have mischaracterized my argument. I think that would be clear on any reading of our discussion.
To your other question—it doesn’t matter whether or not I (or others) have read the critics of ID. You have admitted your own gap in modern knowledge on the subject.
I didn’t say I was ignorant of modern ID arguments—only that I’ve not read any of the ID books.
I’ve read many articles by ID proponents and when they present bad arguments with readily apparent flaws in short form I have little reason to expect their books to make good arguments.
But, yes, I’d be interested in reading at least one of the books—if for no other reason to blog about it. Thanks for the suggestions.
I am a fan of both Dawkin’s The Selfish Gene and of The Blind Watchmaker. I think the Blind Watchmaker is an excellent explanation of Evolutionary Theory, and The Selfish Gene is simply one of the most intellectually stimulating books of the last 50 years.
I’ve read Origin of Species and Descent of Man, but I think they (especially the latter) are more historical documents than primers on Evolutionary Theory.
As for ID books, some of them are largely online on google.books — I know that you can read a lot of Behe’s Edge of Evolution there, for instance.
Charlie -
It’s hardly question-begging when I’m asking the question. I’m merely trying to find out where you have difficulties with the theory. Your post here is more informative, but it still hasn’t answered some key questions.
It is true that the DNA tends to repair itself, but there’s a difference between damage and mutations. Many types of mutations generally cannot be repaired, as I understand it (although damage can lead to mutations). Mutations do happen, obviously, because we witness them all the time, showing that the rate of mutation is still pretty high (which, once again, is why we must look at the empirical evidence). If these are discounted, then some of the more complex elements would look unlikely, but evolution itself, were it to happen, is meant to explain this complexity. Your entropy point might be true if errors were nothing but damage, but they’re not.
“Only a change in the genes”. That sounds simple. But then you also require that a useful, foldable protein happens to be associated with this merely changed gene, and that there be a function for that useful, unique, 3-dimensional protein to fulfill. Again, sounds more like design than chance.
Sounds like design is practically a non-argument. Can organisms gain new functions, or can’t they? It doesn’t matter how complex it is. It doesn’t matter what it looks like. Even Behe will admit some different functions can arise: the real question is, are they the fuel of evolutionary change over long tracks of time?
The topic of Junk DNA will occupy the rest of this comment.
First, there is something very wrong with the Christian de Duve quote. It wasn’t even his! He was quoting Dawkins. Excerpt from his book:
To quote Dawkins: “The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”
Which he responds to by saying: This imaginative concept does not explain the striking differences in DNA economy practiced by prokaryotes and eukaryotes, nor the fact that, albeit with wide variations (remember the salamanders), the proportion of “junk” DNA in the eukaryotic genome tends to increase with increasing evolutionary complexification. The Discovery Institute can’t even get that right. On the contrary, this particular chapter from which the quote originated is called The Virtues of Junk DNA and posited many interesting ideas about introns and split genes, but as he pointed out, the entire idea of selfish DNA remains a possibility:
It is thus possible that eukaryotes carry “selfish” DNA from generation to generation because the advantage of getting rid of it is not sufficient to drive natural selection. On the other hand, the possibility that this DNA plays a role, for example, in chromosomal structure, or in some other unknown way, cannot be excluded.
This is a popular view. Even Mattick, who, incidentally, represents one opinion, an opinion that is quite vociferous and must be placed within context, nevertheless only puts the “betting line” of useful elements at 20% of the possible functional elements of DNA. The interesting thing about the 20% figure is that Comings (and others) used a similar figure of 20% back in 1972, so far from being some sort of radical, his view isn’t that uncommon. Furthermore, Mattick’s assertion of “sweeping things under the carpet” seems rather strange based on quotes like this from 1986:
Many biologists were unhappy with the idea that much of the DNA might have no function, says Loomis. “There is a very strong feeling that if a molecule, or any kind of biological structure, exists, then it must be serving some kind of selectively advantageous purpose. I disagree with this viewpoint very strongly.” Loomis prefers to turn the question around. “We should ask, ‘what is the selective advantage of getting rid of a particular structure?’ This is not common thinking.”
Or from 1988:
At least some proportion of the DNA in the genomes of most organisms is in the form of these so-called middle repetitive sequences, ranging from 3% to as much as 70%: typically, the bigger the genome, the more repetitive DNA. There is a long tradition in biology that, seeing structures as extensive as these, argues that there must be a functional explanation for them.
Or from 1982:
The truth is, however, that the functions of the large and motley collection of repeated DNA families are proving particularly resistant to elucidation. Putative functions are many, including, variously, involvement in chromosome pairing, control of gene expression, processing of messenger RNA precursors, and participation in DNA replication. So far none has been established, save for the single exception of a small family that gives rise to 7S RNA, a molecule that recently was serendipitously discovered to be an essential component of a particle that mediates the secretion of proteins from cells.
…
Some repetitive DNA will undoubtedly be shown to have a function, in the formal sense; some will likely be shown to exert important effects; and the remainder may well have no function or effect at all and can therefore be called selfish DNA. Repetitive DNA constitutes a substantial proportion of the genome (up to 90 percent in some cases), and there is considerable speculation on how it will eventually be divided between these three groups. Current bets would put a small fraction in the function category, with distribution of the rest rising steeply through the effect and selfish categories.
…
One observation that might be taken as evidence of function in repeated sequences is the frequency of transcription into RNA. A significant proportion of nuclear RNA contains transcripts of repeated sequences, although 90 percent of this is lost in RNA processing and exit to the cytoplasm. Davidson and his colleagues have shown that in sea urchin the spectrum of repeat families that are transcribed changes during development, an appealing argument for some regulatory function. Most intriguing, however, is the discovery that only a small proportion of any repeat family is ever transcribed. “Most members appear to be quiescent, which must make you cautious when isolating samples in search of their function.”
…
It is clear that, from their abundance, their unusual structure, and their frequent transcription, dispersed repetitive DNA families cannot be ignored. But it is equally clear that for the most part they, like their tandemly repeated relatives, remain a phenomenon in search of a function.
All of these appeared in Science magazine, which means that a strict adaptionist view was quite prevalent. Some people overestimated, some underestimated, some gauged wrongly (everybody can be wrong, even Mattick). This is not new. Like I said, science is a process of self-correction. It was open-minded enough to incorporate what was proven. Funny enough, Mattick was mentioned in a 1994 article, before the Scientific American quote you brought up.
“[Mattick's] idea is very interesting indeed,” says evolutionary geneticist Laurence Hurst of Cambridge University, England. “And it’s perfectly testable.” For example, he says, Mattick’s model predicts that certain genes, like regulatory developmental genes, that must be finely controlled, will likely bear intron-encoded regulatory RNAs.
The article is about geneticists and scientists at large coming to a better understanding of DNA at that time (which, again, isn’t entirely accurate since I also quoted articles going back decades that reveals geneticists were already uncovering regulatory capabilities, long before ID made it some sort of point). 1994 was also the same year that Bruce Alberts wrote his textbook, which shows that, even if he had been wrong, nothing was standing against the research that revealed the truth of the matter.
Sydney Brenner seems to echo the sentiment that there was a strong belief amongst some evolutionists that everything has a function:
There is a strong and widely held belief that all organisms are perfect and that everything within them is there for a function. Believers ascribe to the Darwinian natural selection process a fastidious prescience that it cannot possible have and some go so far as to think that patently useless features of existing organisms are there as an investment for the future.
Of course, he defines junk as excess DNA, and that’s the issue here. We are finding a lot of interesting functions, but many of the same geneticists finding these functions also seem to conclude that there is excess DNA. One can believe that there is useless DNA, inefficient DNA, and a lot of DNA that contains interesting, nuanced functions all at the same time without being wrong, so that distinction has to be made. “Most DNA is excess” vs. “a lot of them have functions” are compatible claims. Otherwise it’s going to look like someone is disingenuously claiming competing ideas, when in truth both ideas work together. This equivocation fuels misunderstandings and bad arguments. Furthermore, many proclamations of excess DNA are not made because we don’t understand the functions. Actually, we do understand many different genes, and they do appear to be excess. Buffeting this view are a few experiments in which long portions of DNA were cut, and the organism did not appear to be effected: not in its development or gene regulation or in any such way (though the possibility was never discounted that they could be compromised in the wild). This in turn buffets the obvious fact that size of the genome is not strictly proportionate to the “complexity” of the functionality of an organism.
Did you notice that while you claim that junk DNA is not junk DNA on one thread you are still making arguments for its junkiness and you even quote a guy in your ENCODE rebuttal (?) hoping that it still is? And all he has are hypotheticals, questions begged by definition (pseudogenes may be without function by definition, but by empirical observation they have function) and arguments from ignorance.
What is this “it” you’re referring to? “It” is clearly not a single, catch-all function for the entire genome because from the start I’ve advocated a more nuanced view that parts of the genome are there for all sorts of different reasons: some coding, some regulatory, and some baggage. Likewise, the entire term “junk DNA” is somewhat useless because it’s used in so many different contexts.
Anyway, your attacks on Gregory are sort of strange. While a lot of this is merely hypothetical on both sides, there is also a lot that we can postulate. To be fair to Gregory, he does conclude that while many of these genes have no fitness function, their absence could have a detrimental effect (in terms of physical spacing or structural arrangement). But his “gene-dense” comment could prove to be correct; they looked at only 1% of the genome (and not all of those were even transcribed). You also misused his last sentence. He says that even though we’re finding uses, it seems unlikely that much of it will be terribly useful. These uses, by the way, were long suspected:
“We all suspected there was interesting stuff going on in these regions [between genes], and sure enough there is,” says bioinformatician Ewan Birney of the European Bioinformatics Institute near Cambridge, England, a member of the project’s computer analysis team.
Gregory cites studies done in 2000, but a quote I introduced earlier in this comment showed that speculation went back even further. It should be said that the entire ENCODE project rests on the structure of evolutionary theory and the “belief” that organisms evolved.
As for pseudogenes, some of them are useful, but one scientific paper that explored these uses prefaced it by saying that the vast majority of pseudogenes do nothing. So when 19% of pseudogenes appear to be transcribed, that would include useless ones. Here’s an explanation from PZ Myers:
We know that most pseudogenes are useless junk, because we can compare them directly with functional copies in other organisms. We can see stop codons in the middle of them, or frameshift errors, or deletions or insertions. I gave an example of a pseudogene equivalent in English text here — isn’t it clear how we can look at the functional copy and the garbled copy and see the difference?
What we observe fits with what we would expect, too. If a mutation planted a stop codon in a gene, for instance, we wouldn’t expect the wreckage to magically disappear in the next generation. It would just sit there, accumulating further random changes that are not selected away, and would slowly erode away into the background noise. When Carroll says that a gene is lost, he does not mean that every last shred of its sequence is whisked away, but that it is no longer transcribed or no longer produces a transcript with any function.
Here is one such pseudogene from Larry Moran. So no question-begging required. While many can be used as evolutionary fuel, the whole point is that prior functions have fallen out of favor and have begun to be mangled by random forces.
Hi Jacob,
I’m sorry if I haven’t answered your key questions, Jacob, but like I said, I’m not about to debate the whole of evolution with you or put hours into this blog now. I’ve made my points clearly and am not going to chase around everything you’d like to talk about. I’ll have a glance over this massive comment of yours and see if their is anything germane to my points but I will tell you now that my time is limited and I’m not going to keep at this for long.
Pretty high? Everything’s relative, I guess.
Not sure what your point is differentiating between damage and mutations.
The bulk of all mutations, visible and invisible, expressed or not, are deleterious to the organism. See my conversation with Tony as linked previously.
The few that are beneficial are almost always beneficial only because they cause a loss of function – they are not improving the genome or the organism. Making it more fit for a given environment by losing information – as demonstrated by empirical investigation – will not lead to the kind of evolution the theory demands. This is obviously the case even if you look only at friendly fire – this is why MacNeill gets upset every time he gets near a RM/NS argument – it’s more and more well-known that copying errors, the most common and most plausibly “random” mutations, can not do the work required.
The question is, what is the nature of the new function and how is it acquired? By breaking a pump? Yep. By blocking an uptake site? Yep. By destroying inhibitors. Uh huh. That does not lead to evolution. Evolution has to MAKE these this things, not break them
I’m about halfway through your quotes on Junk DNA and haven’t found the point yet. You seem determined to prove that at one point not everyone always thought that all Junk DNA was useless. That’s all well and good. My point is that it isn’t useless and isn’t evidence for random trial and error and junk it evolution. You keep showing that biologists agree with this by saying it wasn’t really thought to be junky junk, or you can keep trying to slip back in the other door and say it is junk and that it demonstrates RM/NS evolution. You show guys who think that maybe some of it has a use and that the rest is still likely junky useless junk. So what?
Either way, you’re arguing against yourself and not me.
Against whom are you supposed to be arguing here? Maybe I should make myself clear – scientists do good work and are probably good people.
But when people claim “Junk” DNA is useless, left-over, fossilized evidence for trial and error random mutations they are arguing from ignorance and their arguments are being erased by empirical findings – regardless of whether some evolutionary biologists considered function before it was common knowledge.
Whatever else impresses you about the Junk DNA argument you are only entertaining yourself.
But whether their claims are compatible or not, they are arguing from ignorance and against evidence when they refer to it’s excessiveness and uselessness. And when it is claimed as evidence for evolution by random mutation it is disingenuous and is making the same leap from hypothesis to fact that you were accusing ID supporters of doing.
Indeed. You can’t test a knockout in a single environment, in vitro, and claim that nothing necessary was lost. Genes turn themselves on and off in different environments, under different pressures and with different cues. This is like pulling the starter motor out of a running car and saying “look, it was superfluous, the car runs just fine…”
But when it’s used in the context of being useless baggage that evidences RM it is an argument from ignorance and it is not holding up well to observation.
The pre-testing estimation was 99% junk. Now the best you’ve got is 50% and more likely much closer to 0 % What percentage is actually the one that evolution predicts such that you’ll be able to use it as evidence when the dust finally settles?
Attacks?! Oh my! Do apologize to Gregory for me.
Hypotheses and postulations are not evidence.
Could be. And he could be wrong and people could be misusing his postulations as evidence for useless junky DNA.
No, I used it properly.
No, he said ” even as” and he says that it’s difficult to describe them in terms of function. Of course, he is speaking from the position now of our incomplete knowledge and ignorance, and from the position of a person looking for reasons to claim there is still much junk in the DNA.
I used it exactly as I wanted and exactly as he meant –
“there is growing evidence that a significant portion of non-coding DNA is indeed functionally important.”
The evidence is growing. That means the evidence for it’s lack of function is shrinking. Exactly what I said, exactly what I meant, and exactly the right use of his words. Please quit pretending to know a thing or two about quote-mining when this is how you read. If I say A and B and somebody quotes me as having said A that is an accurate quote.
Next you spend more time trying to convince me that uses have been suspected for some “junk” DNA by some people all along. This is a waste of our time.
Should it be? Well then kudos. But unfortunately for your argument this does not put their evidence off-limits for somebody who doesn’t believe in blind, unguided, mindless evolution. Nobody wanted Crick and Watson to use their evidence about DNA either, but they did.
Oh, more junk=useless again. We already know this is the claim. But for some reason you insist on arguing both sides and claiming evidence both coming and going.
As for “the vast majority” your preface is premature and, again, against the evidence.
http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.37.040103.103949?cookieSet=1&journalCode=genet
Oh, before you point it out, yes, the authors above believe in evolution, too.
http://www.reasons.org/design/bad-designs/are-pseudogenes-junk
Compare the last sentence to the first.
Stephen Meyer, Signature In The Cell:
page 407
More on transcribed but not used junk RNA,
http://www.sciencedaily.com/releases/2008/02/080205115800.htm
Like Gregory said, we just keep finding function.
Oh, and thanks for pointing out that Christian de Duve was quoting Dawkins when he said:
But something about your reference to what Christian said made me think that perhaps he was quoting Dawkins without approval.
Interestingly, thanks to your extended quote, he also had this to say about junk DNA in that same chapter, with a not-so-handy link:
http://books.google.com/books?id=N-qMzmNYCqAC&pg=PA223&lpg=PA223&dq=This+imaginative+concept+does+not+explain+the+striking+differences+in+DNA+Christian+de+Duve&source=bl&ots=tEL57YOhMf&sig=1cvp8Mc1eeabq08ltugo8WWaMMQ&hl=en&ei=dyJ6SuW0DYnEsQOYir2lDw&sa=X&oi=book_result&ct=result&resnum=1#v=onepage&q=&f=false
Although he is usually careful to say “apparently useless” and says we can’t just exclude the possibility that junk DNA plays some role he is not disagreeing with Dawkins and only goes on to talk about the junk DNA as though it is, indeed, useless.
In fact, though, I am more than grateful for your pointing out this piece. De Duve kindly discusses how a single gene can be split up into several segments on the chromosome [as it can also be spread out over different chromosomes]. They then undergo “intricate processing” after transcription, are taken apart and respliced into “mature RNAs [which can then make up to thousands of proteins from a single "gene", depending upon the cell's needs]. It was an utter surprise to find these split genes. The splicing is “honed … to a remarkable degree of precision” [by "evolution", of course], gaining substantial advantages, due likely to exon shuffling, maintaining their capacity to innovate.
Once again, precision, expedience, advantage … design. What looks like bungling at first turns out to be highly advantageous.
This is why evolutionists don’t get to keep the data all to themselves and they can be quoted even by people who disagree with their overall paradigm or interpretive framework – because evidence speaks to different people in different ways.
As I started out, just waving “evolution” or “natural selection” at complexity, intricacy, precision, etc., doesn’t solve the problem.
Tony, when I read this from you,
… I had to wonder, “where in the history or philosophy of science is it written that deductive arguments using scientific data are more scientific than inductive arguments?” Could you help me with that, please? I’ve done a bit of reading on the “demarcation problem,” wherein the attempt is made to find the line of demarcation between science and non-science. The attempt has been generally unsuccessful in the first place; but I don’t recall that criterion even been discussed as a possible one.
Nor, in response to something you said later, is it written anywhere that a deductive argument is a philosophical one, or that a philosophical argument is a deductive argument. Inductive arguments can also be philosophical (or historic, or literary, or scientific, or forensic…)
First, as I just said, the manner in which you determine it not to be scientific doesn’t seem to be valid. Second, I have the support of a lot of scientists saying that fine-tuning means either multiverse or design. There’s a definite scientific case to be made that it entails either one or the other. There is also this from physicist David Heddle.
So we have (a) an argument based on scientific data, which (b) is not disqualified from being scientific just by being a deductive argument, and which (c) is regarded as a scientific argument by scientists. That’s my explanation of why I think the cosmological fine tuning argument is scientific.
Now let me turn around and add, “so what?” As I have asked repeatedly here and also on Telic Thoughts, does an argument have to be “scientific” to be valid? Of course not! That’s too easy, really: for no argument supporting that belief could be a scientific one; so if it were true, it would have to be false. It is self-defeating.
The cosmological fine-tuning argument is a scientific and philosophical argument; and that’s okay.
To rule out deductive argumentation from science is bizarre.
Behe has provided a hypothesis and tested it, by the way. And Meyer makes a strong case in his most recent book that the logical basis on which he infers intelligence is as strong as that on which Darwin inferred random variation and natural selection.
I’ll quote Monton again:
(Or feel free to acquire the book and read it for the first time.) ID can be pursued as a matter of knowledge whether or not it is purely scientific (if such a thing as “purely scientific” exists, which it doesn’t).
It has been done. I’ve been clear on this now, too, I hope.
It’s because it assumes that the Designer would only do what we regard as Good Design. It draws upon your opinions or belief regarding what the Designer is or should be. It discards Christian theological answers to the same question.
ID can account for extinctions easily: species die off because all their members, all the organisms of that species, die. Is that hard? ID is a theory of origins. It says nothing for or against endings. It doesn’t need to, because enough is said just by noting that sometimes every member of a species just dies.
(I had assumed you were making a theological argument against extinctions there, because you had juxtaposed it with your clearly theological argument with respect to Bad Design, and because others have thought there was a theological argument with respect to extinctions. I may have been wrong: perhaps you were not doing that there.)
Now here you get weird again, Tony. The first quote is from me, which you quoted and then answered as follows:
Your last sentence was, “If you can only provide a theological explanation, then it is not relevant to our discussion about how ID intends to conduct science.” Here’s what’s weird about it. You had asked earlier,
I think you’re saying that any explanation of the origin of the designer must be scientific, and that a theological explanation makes ID non-scientific. First, that’s ridiculous. There is no scientific explanation for the ultimate origin of the universe or of reality on any theory whatsoever. Second, if the Designer is thought to be possibly God, yet you rule out theological discussion about Him, that’s like saying it’s okay to discuss science as long as we don’t talk in terms of empirical evidences or inferences. It’s outlandish.
Third, and most importantly, I don’t care if ID is purely scientific. That part of it which is scientific is scientific, that part of it which is philosophical is philosophical, and that part of it which is theological is theological. I don’t understand why you yourself care whether it is purely scientific. There is no reason to suppose that all knowledge is scientific. There is no reason, either, to suppose that a research program that has a philosophical/theological element cannot also have a scientific element, or that the scientific-ness of its scientific element is diminished by its being associated with elements of other disciplines.
For the record, that was not its purpose.
Your scientism is showing through ever more clearly. ” If you have access to some non-empirical experience that can be tested and provide the reliability of our empirical data, then there is no reason why science would not incorporate this.” You’re saying that if I have access to some non-empirical (read: non-scientific) data that is as reliable as science, then science can incorporate it (make it scientific). Or, if I can make my non-science into science, then and only then is it knowledge. Only science is knowledge. Hogwash.
If you deny that’s hogwash, then you must deny it scientifically or you contradict yourself. I invite you to the challenge.
Was that intended to be cute? If not it rises not even to the level of sophistry, and it certainly is no rebuttal to my point.
That’s intelligent design.
Nobody believes that is possible, not even on the multiverse theory. Not unless you really believe that the infinite multiverse shows that everything that is not logically impossible must happen somewhere in some universe. On that, see here for the absurdity it leads to.
Scientism oozes from your argumentation.
I have nothing to reconsider. The total package of ID does call for considerable information from theology. The scientific component does not, but the total package certainly does.
Deductive? Can you use that word in a scientific discussion? (Of course you can! But I thought you had said it was ruled out.) Anyway, you understate just how implausible. At this stage of research they are so implausible as to render false your first sentences, “there are … explanations for the natural origins of life.” Actually there are none at this point.
Tony, you’re being hardheaded here. I mean it. ID’s scientific element does not explain the origin of life, you’re right, but the total program says that there is a designer that explains the origin of life.
You’re saying that’s a hard stopping point. It doesn’t explain it all, so it doesn’t explain everything. How about seeing it as a door opening to further exploration? If we discover that there’s something we don’t understand there, does that mean we should slam the door shut? Does no explanation count for anything if it is not naturalistic? Then the search for our origins is the search for the most plausible naturalistic explanation, whether it is true or not. It is (as Monton argues in his book) no longer a search for what is true. It is a search for what works best under naturalism, and if there is any evidence that naturalism is insufficient, set it aside, because we’re only searching for what works best on naturalism.
That’s about the only sensible thing you’ve said in this whole comment. That’s what I’ve always said about ID. I would add that it is interesting enough that it is worth seriously pursuing, and interesting enough (worth pursuing enough) that all the efforts that have been mounted against it are damaging to the progress of knowledge and yes, to the progress of science.
Would you please show me, then, how I should regard your attitude as anything other than scientism?
And, since you linked to Larry Moran, let us enlist him for the very point I came in to make.
http://sandwalk.blogspot.com/2008/12/testing-natural-selection-part-1.html
My point:
Natural selection, a result, not a force, is caused by random, uncaring, undirected, blind occurrences which cause differential survival.
It cannot remove the randomness from evolution.
Larry Moran, a pluralist, does not deny that it exists, and is responsible for adaptations HOWEVER, he believes it is negligible.
First, he doesn’t believe that evolution has adapted creatures so finely to their environments that it could not have occurred at random (see, we disagree, and yet I’m citing him to my advantage).
So the circle is complete.
Natural selection is not even universally seen as the dominant mechanism (or, better, result of many different factors) in evolution. Therefore, according to professional, evolution-believing biologists, random mutations are not coupled to drive evolution to a selective ratchet which is “anything but random”, but rather, it is coupled to another random process – random genetic drift.
Evolution is not anything but random. Rather, it can be nothing but random.
And, once again, the reason Dawkins et al want to say it is anything but random is because randomness will not get the job done.
The nice thing about the different varieties of evolutionary theory is they are so often mutually-refuting.
Hi Jacob
Responding to your post #41 regarding mutations and evolution.
Behe seems to be unimpressed by a lot of examples. For instance, Richard Lenski ran an experiment, and the microbes gained an ability to transport citrate. Behe downplayed this….
In a separate incident he also downplayed the evolution of HIV, but HIV has evolved into what we would classify a new species, adapting to individual behavior of humans….
1) I don’t agree with Behe on a lot of his theorizing because I am of the opinion that he is a little too much of a reductionist (I believe I made the same comment somewhere else).
2) Given the above, I have only read one of Behe’s books, “Darwin’s Black Box”.
3) The reason Behe downplays these results is because they are insignificant.
In the case of Richard Lenski, he has reportedly been running evolutionary experiments on e coli for somewhere between 20,000 to 40,000 generations. In that time frame one batch developed the capacity to metabolize citrate.
Sounds impressive, but what happens when we express that in people years? 20,000 generations (NB: I took the lowest number) in human terms is @ 400,000 years at 20 yrs to a generation. That is, it took 20,000 generations for an isolated, inbreeding population to develop one new ‘function’. Inbred populations exhibit an increased tendency for latent mutations to be reinforced, usually with disastrous consequences – that’s why we don’t marry our sisters. This is the reason why S. J. Gould and M. Eldridge postulated punk-eek, isolated population, quick mutation, new phenotype. In this case there is no new phenotype, just a new appetite.
In the case of the “missing HIV mutation” –
An incorrect assertion. I could see nothing on the Amazon blog that remotely fitted the description that Dr Behe ‘admitted, to be wrong’.
Here is a list of research articles that show the VPU in subtype M HIV-1.
1) A novel gene of HIV-1, vpu, and its 16-kilodalton product
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=3261888&ordinalpos=30&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
2) Genetic organization of a chimpanzee lentivirus related to HIV-1
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=2188136&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
3) The HIV-1 Vpu protein: a multifunctional enhancer of viral particle release
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=12941395&ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
4)The human immunodeficiency virus type 1-specific protein vpu is required for efficient virus maturation and release
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=2404139&ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%E2%80%9D
5) The Vpu protein of human immunodeficiency virus type 1 forms cation-selective ion channels
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=8794357&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%e2%80%9d
6) Drug-protein interaction with Vpu from HIV-1: proposing binding sites for amiloride and one of its derivatives
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17082882&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%e2%80%9d
7) Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=8946945&ordinalpos=15&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%e2%80%9d
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16699598&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%e2%80%9d
9) Vpu-mediated CD4 down-regulation and degradation is conserved among highly divergent SIV(cpz) strains
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15823605&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%e2%80%9d
10) Molecular characterization of the HIV type 1 subtype C accessory genes vif, vpr, and vpu
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17331040&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%e2%80%9d
11) Identification of a region within the cytoplasmic domain of the subtype B Vpu protein of human immunodeficiency virus type 1 (HIV-1) that is responsible for retention in the golgi complex and its absence in the Vpu protein from a subtype C HIV-1
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=15929700&ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum%e2%80%9d
This is a bit of ‘elephant hurling’, providing a list of references that would ‘snow’ many into just accepting the assertion without further question. Most would reason that no one would provide references that don’t actually back up the claim made. It’s a bluff, basically.
Reference 9, a 2005 paper, actually shows that the supposedly novel Vpu activity in HIV-1 (based on the title (?!) of Reference 1, which dates from 1988) is not confined to HIV-1, but is present in SIV (the ape / monkey form of the virus):
‘Human immunodeficiency virus type 1 (HIV-1) along with simian immunodeficiency viruses from chimpanzees (SIV(cpz)) and three species of Old World monkeys from the genus Cercopithecus have been shown to encode a Vpu protein.’ [Abstract]
All four different isolates of SIV that were investigated expressed a version of the Vpu protein. So where is the evidence that this is even a new protein, peculiar to HIV-1
http://creation.com/an-information-gaining-mutation-in-hiv
From Behe’s blog
http://www.amazon.com/gp/blog/post/PLNK36ZEH0HZZXVX4
Regarding the time it took Behe to respond to Ms. Smith, after reading her letter I’m not surprised. As Behe writes in his (belated) response.
If I received a letter written in the style she so proudly displays I would dump it in the trash bin on general principle. Why do so many evolutionists adopt such an ill-mannered and beligerant style?
Charlie -
Well, they are “relatively” high, high enough so that, as far as I’m aware, any conservative estimate of mutation rates and useful mutations would produce big numbers given individuals over time.
I also believe that many deleterious mutations are still distinct from other kinds of damages because repair enzymes don’t recognize simple changes to base pairs (although some mutational changes can still be repaired). It’s tough to tell, as I’ve read conflicting information. But obviously quite a few mutations make their way through, deleterious or otherwise, so the point is that changes do occur and are not screened out. You made it sound like mutations are screened out. Otherwise there’s no point in bringing up repair. Anyway, I’d like to see this empirical investigation. People who actually seem to do the research disagree. By the way, the Lenski experiment is interesting because it addresses this concern and one you had spoken about before (whether evolution can be “rewound” and found to be random). Lenski allowed bacteria to divide for however many generations, freezing them every 500 generations or so. Eventually they developed the ability to transport citrate. When he went back and redid the experiment before a specific generation with previously frozen bacteria, the citrate using capability did not develop. This means that a random mutation had developed around a certain generation, and this led to further mutations, which could then be rewound to that point so that the citrate ability could reemerge with various degrees of success. All in all it took three separate mutations, which, according to Lenski’s word, suggests historical contingency based on random occurrences (which is why I’ve been saying, by the way, that you can’t rip out random machinery and expect a regain of function because it’s contingent on its own history). It would seem to at least counter Seelke’s assertion (that anything requiring multiple mutations are impossible), which is funny because he criticized the Lenski experiment years ago for not producing such an occurrence. I’ve only seen one of Behe’s responses, but it’s kind of baffling, as he seems to take it as a victory for his view without providing much of an explanation. I presume he means that subsequent mutations require greater and greater time and odds, but in this case it only took three mutations to reach a sort of selective “plateau”. From there it would be free to change again. His view would only be interesting if there was absolutely no selective advantages conferred upon the intermediate steps between two very distant functions (or at least no reason to conserve them). Lastly, I don’t believe that Lenski has actually found out where the mutations occurred, but some are claiming that it could have been a loss of information that caused this change, which is dubious, as it wouldn’t appear that way, but even if true, it’s not like gain of information mutations have never been observed and discussed thoroughly. (Handy diagram for the latter)
Anyway, I can only assume that most of your quotes about junk DNA have been an attempt to show that scientists underestimated it all in the past. That’s what it seems to me since you had Mattick discussing how scientists held research back and Alberts getting the introns wrong and Dawkins underestimating things. What I’m saying is that while not all of the functions have been well understood, many of them have been postulated for decades. You ask what was the point in showing that, but then you quote Stephen Meyer, who once again mischaracterizes the argument, taking a few functions, finding a quote or two from biologists, and saying, see, they were against this. But you haven’t actually provided any reason for anything. Your assertions are purely hypothetical, whereas biologists have been postulating and testing for decades and have given many reasons why we shouldn’t expect complete functionality from everything. I already explained what the 98% figure is referring to, thus it’s not applicable here, but I would like to know where you keep getting that 50% figure. Like I said, a lot of upper estimates seem to be around 20%. This is a very important point. Biologists who in the past have been on the cutting edge of genome research, sometimes well ahead of others in their field, are still capping the number relatively low. In other words, many biologists for decades have been predicting the functions that we’re still finding, but they are now not predicting that we will uncover a function for everything because they have good evidence that not all genes are totally useful. This is a distinction you still haven’t quite completely made. One can believe in useful DNA and partially useful DNA and useless DNA all at the same time. Showing plenty of the first two does not exclude a belief that a good percentage of it falls into the last category.
Just to point out why you’re equivocating arguments: Francisco Ayala, the guy who wrote, We describe some unexpected features of pseudogenes in diverse organisms that are inconsistent with the traditional view (of junk DNA), conferring upon many of them uses and advantages, also says this: The design of organisms is not intelligent but imperfect and, at times, outright dysfunctional.
All of these people you’re quoting say nothing about which you contend. They have conservative estimates, and then you’re extrapolating that over the remaining 50% or 80% or even 90% of the rest of the genome without any reason for doing so.
Worse, the Zheng/Gerstein article, which Fazale Rana links to, says nothing radical. It suggests that “some” transcribe and a “few” might have biochemical roles, thus showing the necessity of more nuanced terminology. Both Zheng and Gerstein were a part of ENCODE, which also happened to find that most pseudogenes were being preserved neutrally, and the fraction that were under selection weren’t necessarily the ones being transcribed. Even Ayala and Balakirev said that some pseudogenes that do not gain functions will become subject to disabling mutations, which is what Myers and others postulate firmly, as we can compare them to functioning genes. The point here is that they have not only fallen out of favor, but undergone changes with no selective criteria, thus elucidating an evolutionary picture. Otherwise they’d have to be put there by a designer so that they could be mangled (or were mangled already), remarkably pointing toward some evolutionary ancestry that supposedly didn’t happen.
Lastly, regarding Duve, scientists just don’t wave the magic wand of selection and expect complexity to happen. In fact, research done on the evolution of individual genes and functions is incredibly rich. Here’s one.
Dave -
I’ve always been hazy on this, but wouldn’t the sheer number of generations be counterbalanced by the short life expectency, and thus you can’t directly compare generations? In other words, all of the cell cycles and transcription issues within the human body would still be enough to produce an ample number of mutations to fuel evolution in a given amount of time. A given bacteria population might be able to confer evolutionary advantages quicker due to the short generation times relative to its own small space, but there are also other differences in mutation rates and genome size and, of course, sexuality, which changes things.
Behe did concede something, though he doesn’t give much up:
Yes, I’m perfectly willing to concede that this does appear to be the development of a new viral protein-viral protein binding site, one which I overlooked when writing about HIV.
Anyway, that’s unimportant. One of the sites I had linked to earlier already addressed the concern that Vpu is found in SIV (by the way, since evolution states that new functions are built on pre-existing genes, this idea is perfectly in line with the theory and expected):
Ah, Michael Behe, you might try to talk your way around Vpu now (though you were evidently unaware of its existence moments ago) by insisting that it is not *new* new. “Sure it’s new in chimpanzees, but its not *new* in HIV-1!” Sorry, you’ll find no escape with that limp-wristed, ad hoc parry. SIVcpz Vpu and HIV-1 Vpu act in different ways, biochemically, which is predictable enough when you do something as simple as comparing amino acid sequences. For instance, if you compare a laboratory strain gag to SIVcpz gag, you get a similarity of ~75%.3 Not too shabby. On the other hand, if you compare the subunit portion of env (the gene I use to create phylogenetic trees because it’s the most variable between viruses) you get an AA similarity of only ~59.5%.
The amino acid similarity between HIV-1 Subtype B Vpu and SIVcpz Vpu is ~37%. Ah but that study was published in 1990. Perhaps things are different now? I found the AA sequence of NL4-3 (lab standard Subtype B) and several recently entered SIV cpz sequences at the Los Alamos National Laboratory HIV Sequence Database4 – I got the same numbers. Highest was ~39% AA sequence similarity.
Turns out a LOT of evolution has been going on in HIV-1 since it was transferred to humans 50-60 years ago. What are the biochemical implications of these differences?
In humans, there are two functions of Vpu5 – one is inducing the degradation of CD4 molecules. CD4 is the host cell receptor HIV needs for infection. Removing CD4 from the cell surface prevents superinfection (more than one virus infecting the same cell) and helps prevent newly released viruses from turning around and infecting the same cell (also prevented by an HIV maturation step involving protease). To put this the simplest way possible, Vpu involves the evolution of at least two protein-protein interaction sites – one to interact with CD4, one to interact with the pathway that degrades the CD4.
The second function is to act as an ion channel in the host cell plasma membrane.6 Five Vpu proteins come together to form a Na+K+ viroporin.7 This has been shown to assist in particle release, making the cell charge more conducive to the release of new particles. This involves the evolution of more protein-protein interactions – the individual Vpu proteins must interact to form the pentamer, plus an action site that can be used to block ion flow.8
Viroporin capabilities have not been found with SIVcpz Vpu. Knowing what we know about Vpu, this is not surprising. If you scramble the transmembrane region of HIV-1 Vpu (the portion responsible for the ion channel formation), viral release is crippled.9 And when you compare AA homology between SIVcpz and HIV-1 Vpu in the transmembrane region is unremarkable (roughly two) – that’s as good as a ‘scramble’. So theoretically, ion channel formation evolved in HIV-1 when it infected humans to overcome a species specific and cell specific host factor.10 Though the list of viroporins discovered is continually growing, the evolution of a viroporin de novo is not menial task.
This seems like a pretty significant biochemical change in HIV-1, to me.
But the ‘pathetic’ evolution doesn’t stop there. The feature both Vpus have in common, CD4 degradation, is carried out in completely different ways. HIV-1 Vpu requires two casein kinase II sites. You could almost call it irreducibly complex – if you dont have both CKII sites, CD4 isn’t degraded. Yet some SIVcpz Vpus have only one CKII site, and instead utilize a simple string of negatively charged amino acids in place of the second site.11 Different ways of performing similar tricks with totally different amino acids. I think that’s biochemically significant as well.
And HIV-2 doesn’t even have Vpu. Once again, that “very little” has produced two different strains of HIV with dozens of different subtypes and a strange penchant for evolving and resisting treatments. This “unguided” process has managed to elude a supposedly intelligent agent: us. Sure the mutation rate is fast, but that explains why HIV-1 and 2 have changed so much in only the blink of the evolutionary eye (I believe that in some spots they share something like 60% similarities). Numbers like 50% or 60% or 70% are impressive given the fifty year time frame. I believe that we have more in common with many mammals in some parts of our genes.
Hi Charlie
“Read the Sternberg.”
I finally finished reading his essay. It’s very good. An interesting excursion into the consequences of non-conformist thinking.
http://www.richardsternberg.org/pdf/sternintellbio08.pdf
Thanks for the link. I can’t help but feel sympathy for his experience, but at least it illuminates the intellectual straightjacket that scientism has imposed upon free inquiry and independent thought.
Hi Jacob
I’ve always been hazy on this,…
That makes two of us 8^> – I am also not particualrly interested in Behe. I consider his thesis on line in a preponderance of lines of evidence that contribute to my skepticism about evolution.
…but wouldn’t the sheer number of generations be counterbalanced by the short life expectency,…
Reproduction, specifically differential reproduction or changes which happen in the process of reproducing, are the theoretical engine of evolution. Natural selection is a ‘sorting mechanism’ which eliminates the ‘unfit’. Each duplication (generation) of an individual (theoretically) has the potential to produce a new ‘function’. The reason e coli (and frutit flies) is popular for these experiments is the short ‘generation’ time – the short reproductive cycle. You can produce many generations in the time it would take for one mouse or dog generation, let alone one human generation.
…and thus you can’t directly compare generations?
Because evolution relies on differential reproduction you can only compare generations. The reproduction event is the critical stage wherein a ‘new’ organism is constructed. That new organism is built on the pattern of the parent organism(s) + any mutation event.
In other words, all of the cell cycles and transcription issues within the human body would still be enough to produce an ample number of mutations to fuel evolution in a given amount of time.
Cell cycles and transcription issues in an organism as complex as a human (or any multicellular organims) would likely instantiate as a cancer or other cellular malfuntion. It is highly unlikely that an existing organism could transform itself into a different organism, however, genetic a genetic mutation in the parent(s) could be passed on to the offspring which would be constructed according to a different pattern.
A given bacteria population might be able to confer evolutionary advantages quicker due to the short generation times relative to its own small space, but there are also other differences in mutation rates and genome size and, of course, sexuality, which changes things.
Even so, with NS acting to ‘conserve’ existing structure the potential for catastrophic failure from any change is far higher within the highly integrated multicellular organism. Any change must allow the organism to survive long enough to reproduce if it is to be considered adaptive.
…This “unguided” process has managed to elude a supposedly intelligent agent: us…
Here you go again… You assume that the changes exhibited by HIV are “unguided”, you presuppose the answer to the very question under debate. The very same potential to adapt could be inferred as a designed capacity to respond to environmental changes. There is also good evidence that distribution of such adaptaions are enhanced by stressing the organism (introducing poisons) or that many so-called adaptations are commonplace in a minority sub-population of the organism which, through the introduction of poisons to kill the majority population, reproduce to fill th gap and end up as the majority population in the stressed environment. Quite often, as in the case of Darwin’s finches, the population will revert to type when the environment normalizes.
Sure the mutation rate is fast, but that explains why HIV-1 and 2 have changed so much in only the blink of the evolutionary eye (I believe that in some spots they share something like 60% similarities).
There are a couple of problems with this idea.
The first problem is that HIV is a virus. A virus is (technically) not a living organism (althought the lines between life and non-life are confused). Viruses are parasitic and cannot reproduce without hijacking the cellular reproduction functions of a “living” organism. Because the virus uses reproductive functions that are not properly its own, there may be a higher incidence of mutation within the larger, apparently fixed, pattern which identifies it as HIV.
http://www.tvdsb.on.ca/Westmin/science/sbi3a1/Bacvirus/Virusrep.htm
The second problem is that time is not the main factor in evolution, and the failure to make this distinction is one of the errors in evolutionary thought. The main factor is differential reproduction (generations). I don’t know the frequency at which HIV reproduces, but I suspect it would be far closer to the reproductive cycle of e coli than humans. Many hundreds of thousands of generations in the single life of a human.
http://aids.about.com/cs/aidsfactsheets/a/hivlife.htm
Numbers like 50% or 60% or 70% are impressive given the fifty year time frame. I believe that we have more in common with many mammals in some parts of our genes.
Just a short jaunt back to Behe’s blog…
http://www.amazon.com/gp/blog/post/PLNK36ZEH0HZZXVX4
Far be it from me to claim that this is enough to thoroughly refute the theory of evolution. As I wrote above, it is one link in a chain of evidence, the sum of which leaves me very skeptical about evolution as an explanatory model.
Hi Jacob,
Oh boy, you sure do like to talk everything to death, don’t you?
“Damage” from external or endogenous sources can be repaired by enzymes, and “damage” from copying errors can be repaired by enzymes.
If I made it sound like errors never made it through, or that there were no such thing as mutations then either I communicated badly or you misread. This entire conversation about RM/NS would be kind of funny if I were contending there were no such thing as mutations, don’t you think?
Regardless of whether we want to call the rate high or low (I call it low http://www.ncbi.nlm.nih.gov/books/bv.fcgi?tool=bookshelf&call=bv.View..ShowSection&searchterm=repair&rid=cell.section.1023) we can infer what the rate(s) is(are).
Yes they do. Wiki misstates this.
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?tool=bookshelf&call=bv.View..ShowSection&searchterm=repair&rid=cell.section.1023
Same link as above, don’t follow it twice.
(By the way, it’s written by an evolutionist.)
I do see your point about “mutations” though, and I was sloppy. Yes, if the substitutions, changes, damage, are not caught and corrected and become a permanent feature they are often referred to then as mutations – I was talking about the spontaneous alteration itself as the mutation – which can be corrected before becoming permanent.
You did the same.
I think I didn’t talk about rewinding, I merely mentioned that Gould would agree with you and I’ve seen no evidence for your metphysical claim that humans would not “evolve” if we were to do tis all again.
I didn’t talk about Lenski, either.
Your primer doesn’t add anything to the conversation about Lenski.
As I continue I wonder am I reading the right comment? What does Seelke have to do with our conversation? And Behe? Again, who are you talking to?
Do you have these arguments already saved and you’re just cutting and pasting from your files regardless of what I say?
Anyway, indeed. You could assume this or read my very stated purposes.
They counter your implication that junk never = useless. That’s very often what people meant, especially people like you who claim that junk is evidence of unguided evolution.
My recent cites also counter your recent claim that the “vast majority” of pseudogenes are useless.
I got that and have commented on it several times.
I quoted Stephen Meyer to further emphasize the degree of uses for junk DNA as you keep trying to forward two arguments: 1) that people always knew Junk DNAhad uses and 2) there’s still useless Junk DNA.
You don’t seem to know what words mean when you comment on the quality of arguments. Meyers didn’t ‘mischaracterize’ anything and he clearly shows that there are prominent ID critics who still use this argument (as of last year).
I quoted Meyer showing that all kinds of “junk” DNA has uses, one quarter or more of the genome is made up of retrotransposons, for instance, and Meyer’s notes show that retrotransposons and ERVs, are being found to have function. The other link shows that “useless” introns may universally have a function. One cite estimates 50% (and wait until we know more) of pseudogenes are transcriptionally active. Another that when pseudogenes are suitably investigated they are found to have function. The other that even if DNA is transcribed to RNA that is not translated (the last resort for Junk proponents) even this RNA is being found to have essential function. Each point adds to the other.
Any reason for anything? Purely hypothetical? To what are you referring?
Please say something that is both relevant and clear. Actually, don’t, it’s ok.
So is that your figure then? The very important 20% is evidence for blind watchmaker evolution?
Again you are mistaken. I acknowledged your distinction last time you made it. But you seem to have missed the distinction I made; which is that it doesn’t matter and continues to be irrelevant.
There will be virtually no useless junk when all is said and done – and that is the way research is going (if you add it up I’d say we are there now).
You seem to think now that 80% is a good number. You are clinging to the Junk DNA argument because you really do think this talkOrigins argument is evidence for your materialistic evolution and in so doing you keep making the point for me again and again – opponents of teleology have long said that Junk DNA is absolutely useless and that it evidences evolution.
Wait, please listen.
Some biologists thought not all Junk DNA was useless, but that some (lots, most) of it was.
Some biologists thought there was less useless DNA than others did.
This is irrelevant. Please, I’m not arguing that biologists were wrong, biased, stupid, incompetent, evil, left-handed, cross-eyed or anything.
I am saying:
1)it is disingenuous to say that nobody thought the vast majority of DNA was useless (many, including you, still do)
2) the supposed uselessness of the vast majority was used as an argument against teleology.
3) the vast majority is not useless. It is not evidence against ID and is an argument from ignorance. Lack of evidence/evidence of lack, and all that.
Your evolution predicts the vast majority of DNA to be useless junk (not just something we called junk but can later say we didn’t mean was really junk).
My teleology predicts the vast majority is not junk. I made this (what I thought to be risky) prediction 4.5 years ago on many a blog and am excited to see it is coming to fruition. Then again, Dembski made it ten years ago, so, big whoop on me.
This is not an equivocation and you fail every time you try to cast arguments in a negative light. Why don’t you just stop?
It doesn’t matter an ounce what Ayala’s overall impression is of ID or design – what matters is the data. He doesn’t have to believe the design is good or real, or that all pseudogenes are exactly useless (what, though, does he mean by the “traditional view (of junk DNA)” do you think, when he contrasts it to a view of pseudogenes that have uses and advantages?).
In fact, you bolster both of my arguments here again, that 1) you can’t pretend that Junk never meant “useless” as Ayala shows us that was the traditional meaning and 2) that the “Junk” is disappearing.
They say exactly what I contend they say.
What does it matter to you whether the “functional” DNA is 20%, 50% or 90% of the total? Are you for sure settled on 20%? Can’t you accommodate 50% as easily as 20%? I bet you can.
Here’s one I linked to earlier.
http://www.nature.com/nature/journal/v458/n7235/pdf/nature07672.pdf
Almost all DNA is transcribed and almost all RNA shows signs of function.
I think that’s exactly what they do when they claim, as Dawkins does that “evolution is ANYTHING but random because the random variation is GUIDED by natural selection.”
But, in fact, the magic wand of “selection” doesn’t do anything as 95% of our genome shows no sign of selection [ENCODE] and as Moran argues, selection is not a significant factor in evolution.
Or, again:
http://creationevolutiondesign.blogspot.com/2007/11/poe-bibliography-k.html
It can’t very well increase complexity and erase the randomness of random evolution when it is insignificant and when it is, itself, a stochastic process.
So, as you lamented over ID, we just have too many versions of evolution to be running around claiming fact, fact, fact! and making such wild arguments from ignorance as to say that every undiscovered purpose is equal to no purpose and is evidence for your metaphysical claims.
So, Jacob, I’m sorry, but we are done here.
You’ve done nothing to argue against my point. You’ve introduced rabbit trail after rabbit trail. You insist on misreading and then trying to moralize about my points. You’ve accused me of quote-mining and don’t exercise the least bit of discernment in this. You aren’t getting the most basic of points. You are arguing both against yourself and some phantom of your creation.
And I have better things to do.
The last word is yours.
Hi Dave,
You said:
…
Behe:
Edge Of Evolution
{my italics]
Thanks Charlie
I guess that answers that question. Who’d a thunk it 8^>.
My pleasure, Dave.
Peace
I think it’s good to take another look at the claimed efficacy of randomness etc. in how life developed, but: it we accept the fossil record and rough time line, and if creatures were born (broadly speaking) of other creatures (once there was life to begin with – another question!), then the later creatures had to evolve from the earlier ones. Maybe something special happened, but they still came from ancestors who were different from them over a long time scale. So I guess most of you are not YEC and accept the time scale and the changes. You would expect to see the same scenes cruising back in a time machine – so what was different about what happened, versus as imagined by an orthodox evolutionist?
(BTW, I know David Heddle and surfed from his He Lives. I follow the “anthropic design” idea, which says the way the universe works is “intentional” but not necessarily ever “meddled with” once it’s here. AD is not ID AFAICT, because ID looks at whether the universe, as is, could have produced life even if cleverly designed from the outset. Dave’s talk on the fine-tuning of physical laws and how unlikely the universe would be so convenient in properties for life, is classic.)
Hi Neil,
re. ID and “meddling”:
Edge Of Evolution
OK… I’m pretty much on board with the “extended fine tuning” idea. In fact, I have that “So and so stole my lines” experience when I read:
One simply has to envision that the agent who caused the universe was able to specify from the start not only laws but much more.
Note that the media, even “quality” outlets tend to ignore such subtle implicit design views. They’d rather show the battle between hard-core atheists and YECs. That plays into their narrative of the struggle between poles, etc. It’s unfortunate. I think many people could be attracted to the “center” as described above in Behe’s The Edge of Evolution. That work also seems to have been misrepresented as “pro-meddling” in outlook, despite the import of the above excerpt. (Following typical political practice, where liberals become Marxists and conservatives become fascists or racists etc. on the basis of hints and exaggerations.)
PS: I kid you not, my Captcha phrase was “prejudiced reopened.” I am symbologically coincidotropic.
Hi Neil,
I appreciated your open-minded comment and your observation on the media.
This pdf takes a bit of reading, but since I was hyping it up-thread I’ll point it
out to you as another look at non-meddling design.
It’s a little long and maybe a few steps beyond mainstream, but very thought-
provoking.
http://www.richardsternberg.org/pdf/sternintellbio08.pdf
saith Captcha
tadpoles homestyle
(yum!)
Charlie -
You just asked in your last post: The question is, what is the nature of the new function and how is it acquired? You went a step further, claiming that empirical evidence was on your side. Demonstrating otherwise would clearly be important, so I provided a few examples that evolution is effective and spontaneous while trying to anticipate all counter arguments in advance. Do you even know what we’re arguing about here? You keep asking me for evidence and tell me that I’m the crazy one.
It actually wasn’t Wikipedia where I read that repair enzymes don’t always effect mutations, but I suppose that it doesn’t matter to debate it. By the way, that mutation rate doesn’t seem so bad when you give it context: http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/cell/ch6f32.gif
With junk DNA you’re trying to have it both ways. You’re quoting the people doing the research in order to say that growing parts of the DNA are active and useful and that the uselessness is quickly disappearing, but these same people are also saying that there are parts of the DNA that simply aren’t useful. Meyers is using this specific tactic. He’s taking a rather mundane conclusion, that most DNA is useless, and then finding a series of uses, uses that scientists have known about and take into account when they make such statements. But the assumption of Meyers that it is basically all useful, and that is not based on current science. So this list is based on a misconception:
1)it is disingenuous to say that nobody thought the vast majority of DNA was useless (many, including you, still do)
2) the supposed uselessness of the vast majority was used as an argument against teleology.
3) the vast majority is not useless. It is not evidence against ID and is an argument from ignorance. Lack of evidence/evidence of lack, and all that.
My point has never been that nobody thought most DNA was useless. My point has been that many still think that most is useless even when they are uncovering missed functions. When they do find surprising uses, like in pseudogenes, it’s because a lot of it are not necessarily active toward the efficacy of the organism, and so these exceptions would require a much greater look. Take the nature.com article (which I didn’t see in any of your previous comments, unless it was an HTML hyperlink, and it didn’t say anything about most RNA, but that most of what they found was being conserved and only about 100 were validated for function).The reason they didn’t find it at first is because it’s small (1600 thus far) and difficult and hidden amongst a lot of different stuff. Because of this, different metrics have to be used to find them. Quote from one of the people behind that study:
“The challenge in finding these lincRNAs is that they have been hiding in plain sight,” said John Rinn, a Harvard Medical School assistant professor at Beth Israel Deaconess Medical Center and an associate member of the Broad Institute of Harvard and MIT. “The human and mouse genomes are already known to produce many large RNA molecules, but the vast majority show no evolutionary conservation across species, suggesting that they may simply be ‘genomic noise’ without any biological function.”
The entire difficulty and the reason they’re finding them is based upon the idea that they have to be sifted out amongst the rest, that much of it is noise and the gems have to be uncovered by a fine tooth comb.
The vast majority wasn’t my claim, by the way. The terminology came from a particular citation, and it was in reference to pseudogenes. To illustrate, there are other papers on pseudogenes that say up to 80% are decayed gene copies that have accumulated nonsense or frameshift mutations in neutral evolution (ENCODE again), that they’re genetic fossils, and perhaps that some are actually failed horizontal transfers. One of your defenses here is to quote a paper that says “often” functions are found, but do you have any specific claims from the paper about the amount of functional pseudogenes, one that would counter the non-functional ones we have found? You’re throwing a paper out with an ambiguous term but with absolutely no specifics. (It also depends upon how you define it – some would say that if they are active, they shouldn’t be considered as strict pseudogenes) Anyone can often find things in junk; that’s not an argument about it as a totality. It’s hard to claim that we’ll find a ton of uses here when much of it isn’t transcribed, and much already is shown to be functionless. Even Ayala argues that pseudogenes may not be selected for, which, as ENCODE will tell you, is true for many of them. They may be selected for with new functions, and they have the potential for becoming new genes, and this does not seem to contradict the fact that many change and gather “dust”, so to speak, because there’s no reason to clean them up (some don’t have promoters, most are inactivated). The point is, this is a lot of hypotheticals based on one abstract. I want to debate something more concrete from the paper. And clearly Ayala is stating his conclusion based on the facts. That there are sections of dysfunctional genes is a claim of fact. He must be saying it for a reason. So there probably won’t be a dramatic shift of thinking here – and instead an incremental restoration of a more nuanced view.
I kind of tried to make this my larger point, that it’s not just the stuff in our genomes but whether the current arrangement of our genome is even the best or most efficient way of expressing it. There are competing claims here, and they can generally be tested. A designer would try to be efficient (and one can argue that a perfect designer would be perfectly efficient). But current evolutionary theory seems to say that things would be cobbled together from various parts or perhaps even detritus. So the final tally ends of this “non-essential DNA” is only part of the point. Like Gregory said, it could be 50%. It could be more. I’m using 20% because that numbers has come up several times amongst scientists. The larger point is that there are large sections of redundant and mangled and cobbled together DNA that speak far better to current evolutionary theory over long periods of time. It could be the minority; that it’s larger is better, but their mere existence says something. I’ve said this twice, but it hasn’t really been addressed.
Furthermore, ERVs and retrotransposons both seem to point toward evolutionary descent. Some can be used as promoters or alternate promoters or regulators, but expression patterns can be minor or subtle. Ryan Gregory on ERVs: Not only is only a small fraction likely to be involved in gene regulatory networks such as that of TP53, others are clearly maladaptive from the perspective of the host genome. Many TEs aren’t active. I didn’t respond to the intron article because I didn’t think that it was important to pull apart every single function. What does it say about the introns involved? What does it say about the potential for other introns? I believe that some of them are unusable. And despite saying that 50% could be transcribed (ENCODE seemed to say 19% – both aren’t huge), Zheng and Gerstein still said that “few” were biochemically active.
So just to reiterate my two points here: 1. It is because these biologists say that there are large sections of useless DNA that we should take it seriously. 2. The useless or inefficient sections that are there, whether small or large, are evidence of evolutionary descent. Every researcher and biologist you quote will say this. Perhaps I’m not making the difference between these two points clear. More specifically, your list has failed. 1 isn’t true because I didn’t claim that. 2 isn’t true because nearly any biologist will tell you that the genome does point against ID. 3 fails because much of it is still not essential, and any essential genes we do find are like gold in the mountain.
Lastly, genetic drift: I think that things do tend to become fixed in populations over time, so, as Moran points out, speciation can occur due to genetic drift alone. For every allele that’s fixed, it’s one more separation from the previous generations. There is also purifyng selection to consider. And there are studies that suggest neutral mutations are quite likely to lead to beneficial changes:
Overall, experiments have now demonstrated two clear mechanisms by which neutral genetic drift can aid in the evolution of protein functions. In the first mechanism, neutral genetic drift fixes a mutation that increases a protein’s stability [24,25,55], thereby improving the protein’s tolerance for subsequent mutations [26-28], some of which may confer new or improved functions [28]. In the second mechanism, which was the focus of this work and the recent study by Tawfik and coworkers [44], neutral genetic drift enhances a promiscuous protein function. This enhancement poises the protein to undergo adaptive evolution should a change in selection pressures make the promiscuous function beneficial at some point in the future.
And
Neutralism and selectionism are extremes of an explanatory spectrum for understanding patterns of molecular evolution and the emergence of evolutionary innovation. Although recent genome-scale data from protein-coding genes argue against neutralism, molecular engineering and protein evolution data argue that neutral mutations and mutational robustness are important for evolutionary innovation. Here I propose a reconciliation in which neutral mutations prepare the ground for later evolutionary adaptation. Key to this perspective is an explicit understanding of molecular phenotypes that has only become accessible in recent years.
I’ve been aware of genetic drift; it’s something I consider, though I’m not quite on the same level that Moran is (though to be fair, he bases on a lot of it on the fact that creatures are only partially adapted to their environments, and many things effect the organism neutrally). The one thing he says that really intrigues me and makes me want to do more research is that any given change amino acid nominally effects function. But then I’m kind of confused why you’d insist that evolution is random and yet completely ignore an experiment like Lenski’s, which shows selection occurring after at least three steps. We do need to get out of the realm of the theoretical and look at the evidence. It’s also strange to say that most of the genome isn’t under selection when we’ve been discussing a perfectly valid reason why it wouldn’t be, and Moran does say that selection does lead to adaptation, so it still must be significant.
I know that we’re talking about each other, and both of us have failed to state our main points often, but I would like to continue this. I was actually hoping that this comment would be more expansive. I had more to address. That will have to wait until later, if we continue, as will a response to Dave’s comment.
Hi Jacob,
I guess I’ve partially lied.
While you can continue to have the last word as you go hither and yon and pursue your expansiveness I will correct you on one point of fact, answering your question on the Ayala paper:
It was your claim – you used a cite to make the claim and continue to make the claim.
Yes.
http://books.google.com/books?id=tJeZC885-OcC&pg=PA177&lpg=PA177&dq=pseudogenes+are+not+junk&source=bl&ots=at3Bo46YbT&sig=IoMl4vTqMC-ZxKCrcpkS1pBakoU&hl=en&ei=7P58So2FGZGANtL7geoC&sa=X&oi=book_result&ct=result&resnum=2#v=onepage&q=&f=false
Pseudogenes Are Not Junk
Balakirev and Ayala
Once again, non-function, especially of the vast majority, is an argument from ignorance.
To save you trouble, yes, Ayala believes in evolution.
The evidence is that pseudogenes are not useless, Ayala’s interpretation of what this means is his own.
Charlie, thanks for the link. I haven’t had time to digest it. Meanwhile I found an interesting link (forgive if already put here, my mind plays such tricks) to a critique of critiques of ID (more or less):
http://www.arsdisputandi.org/publish/articles/000191/article.pdf
- cities Slacker! (Made me think of the cute film “City Slickers.”)
Hi Neil,
Thanks. I’m skimming this piece right now and do appreciate it.
My hat remains off to you.
Nothing interesting in my captcha this time.
I said that the phrase wasn’t mine, meaning that it didn’t originate with me (but anything I’m claiming is a result of their work), so I’m saying that you’d have to take it up with the paper itself and the others. But then again, I still don’t think that you’re addressing the very reason why non-essential DNA was brought up in the first place. What I said is that such things are better evidence for evolutionary descent. The first quote of yours points that out. They are available for functional evolution. Non-neutral constraints seem to cover much of the paper, however. One of the points is that pseudogenes conserve sequence similarity of about 90%, which is true (on average processed pseudogenes have about five frame disruptions, and about a thousand others have ten plus), but then ENCODE says this:
The overall sequence decay rate of pseudogenes is very similar to that of neutrally evolving DNA. The nucleotide sequence identity between human pseudogenes and their orthologs indicates apparently that the majority of pseudogenes experience no evolutionary constraints, as their sequence decay pattern is not much different from that derived from fourfold degenerative sites, at least within the lineage of mammals (Fig. 5A Figure 5.). We subsequently analyzed these 201 pseudogenes and the corresponding MSA data using the program phastOdds (Siepel et al. 2005), which computes the log odds ratio of the probability that a sequence fragment fits a model of “constrained” versus “neutral” evolution. The result supports that the evolution of pseudogenes as a group is better described by the neutral model, but it suggests that a few pseudogenes (mostly nonprocessed ones) may have experienced evolutionary constraints in certain periods of their evolution (most likely as genes) (Fig. 5B Figure 5.).
Pseudogenes are often non-functional because they lack promoters or other regulatory elements. And only some of them transcribe. Of course, as ENCODE points out, the transcriptional levels in these few are of a similar caliber of antisense RNA and other such things, so some functions cannot be ruled out. Neither is conservation an end all be all sign of function, although transcribed and conserved “pseudogenes could be good candidates with biochemical functions”. Ayala and Balakirev seem to be slightly cheerier about the situation, as the most promising thing they say is that some functionality has been observed in cases that have been suitably investigated, but they also say that some pseudogenes have completely degraded toward non-functionality. Perhaps they are talking about the many pseudogenes that have exhibited characteristics in between those of fully functional genes and degenerated genes. Their one example (beta-Esterase from Drosophila, as they did the research on it) is one that shares both: it has eleven premature stop codons and a high structural divergence, but some alleles produce a catalytically active esterase; however, I don’t believe that an actual function has actually been confirmed, so it still remains unknown, even with investigation, besides, perhaps, an ability to recombine with the expressed gene (this paper from 2006 says that functions in humans have never been documented but exist over an evolutionary timescale; I don’t know how true that is). There are a few things to take away from this. 1. Any functions that are present are co-opted by evolution, speaking to a process that uses what it can in the moment without necessarily the intelligence of a designer or engineer. What intelligence would use moth-eaten and partially degenerated genes? 2. We know of functionless genes or at least genes that would not appear to have any function based on obvious issues of transcription and conservation. It doesn’t matter how closely we look at them because many are quite degraded, as even Ayala and Balakirev will tell you.
This does not contradict what I said in my previous comment. There are pseudogenes that are not selected for, parts that gather dust, and parts that are dysfunctional. Things can be found in “junk”. Like Brenner and others have said, there is a distinction between junk and garbage. Garbage is thrown away. Junk accumulates. I’ve said from the start that there are potentially useful ones. Yes, I still think that the most of them will probably prove to be dysfunctional. Pseudogenes are, at the very least, defined by nonsense mutations and seem to be under few constraints to preserve what’s left, and many wouldn’t appear to actually do anything because they cannot be transcribed. But the larger point is that they would appear to demonstrate evolution. I’ve pointed this out numerous times. Even if there are functions, would they be the best way of carrying them out?
I still find it odd that you would ask about the acquirement of new functions and yet tee off on me when I want to talk about it. I also think it’s strange that you would post something about the resplendence of transcribed RNA that shows nothing of the sort and then fail to respond to that. I would really like to talk about genetic drift, though. That topic is eminently fascinating. But you quoted Moran without asking why he would believe that functions would emerge due to genetic drift (although he does say that natural selection would give rise to adaptations).
Hi Jacob,
You wrote a lot of words when all you meant to say was
1) ‘you’re right, contrary to what I said it was my claim [not "phrase"], even though I said it wasn’t’
and
2) ‘you’re right, evolutionist Ayala says that most pseudogenes are not useless – therefore you have ‘taken it up’ with the paper from which my claim came.’
Oh, and …
3) ‘I have a theological argument – bad design = no design.’
—–
It doesn’t matter why Moran (or Lynch, or Kauffman) thinks drift => evolution.
What does matter is what I’ve said, and demonstrated, from the word “go”.
And that is that this:
is a meaningless red-herring.
Taken at face value it claims/admits that mutations are random so there is no point debating whether or not they are for these purposes.
But natural selection, adaptiveness, etc., is not ‘not-random’, it is not a force and, whatever else it is, by the claims of professional, peer-reviewed biologists, and population geneticists, it is not the dominant or even necessarily a very important factor in evolution ["Thus at the molecular level, at least, random genetic drift must be the dominant mechanism of evolution."- Moran]
Whatever it is, its “not randomness” cannot convey “not randomness” to evolution.
Another irrelevant little sidestreet from you “(although he does say that natural selection would give rise to adaptations).” He does indeed. And what he’s saying is that “adaptation” does not explain most physical features.
This comment demonstrates again why your desires to debate everything you find fascinating about evolution are a waste of my time and why I will limit my responses to you.
I have not disavowed myself from that phrase (The more you keep picking stupid things apart, the more I’m just going to keep doing it). But surely even you can tell that I’m trying to make the distinction between an unsubstantiated claim and one that comes straight from the mouth of researchers. The rest of my post was an attempt to back that up by addressing the Balakirev and Ayala paper directly with up to date research (lack of transcriptions, neutral selection, and some mangled genes), and you can’t really just address one disparate paper with another anyway. One has to address why they’re disparate. Why do they appear to disagree? Why are active pseudogenes likely or unlikely to be found? Have we found any clearly functional ones in the human genome? No matter how much you quote the paper, which was quite hypothetical in its own right, your point won’t work here if we aren’t finding functions or know that we won’t find functions.
By the way, it’s interesting that in a book Ayala co-authors he says:
Much of the junk DNA might not be functional at all, but some sequences, such as those encoding the miRNAs mentioned above, play a role in regulating the transcription or translation of other DNA sequences.
More:
“The design of organisms is not intelligent, as it would be expected from an engineer, but imperfect and worse: defects, dysfunctions, oddities, waste, and cruelty pervade the living world,” Dr. Ayala stated in a preview of his speech, “Darwin in the History of Ideas: From Natural Theology to Natural Selection.”
Furthermore, it wasn’t just an argument for bad design (compared to your original statement that it’s quite efficient, this itself would be a large change). It was an argument that everything we see is much better explained with how current evolutionary theory works. In other words, it has explanatory power. It can tell you how it got there: the processes have been well studied and documented. When such a thing comes into focus, we don’t necessarily need a designer to explain how the genome turned out like it did. It’s best explained via evolutionary theory.
It would also appear that ID shares something in common with pure adaptationists.
Lastly, there are several issues underlying the genetic drift problem. 1. It was the “dominant force” part that I was hoping to debate. There are a lot of people on both sides of the issue who have their own arguments. It’s useless to conclude anything until this point is discussed. 2. The reason why he says that many features are not adaptations is that many of them do not effect survival and reproduction, and thus they are not subject to selection. For instance, one of his arguments: is two horns necessarily better for survival than one? Would natural selection apply here? He is not making the act of natural selection any less; he is asking whether it’s truly applicable to most situations. 3. I’ve already said that randomness is involved, particularly at the genetic level (and sometimes in what becomes fixed in a population), but as Moran rightly points out elsewhere, it’s probably not completely apt to describe a complex, nuanced theory as either random or non-random, and I think that I’m seeing his point here. He’s essentially saying when it doesn’t matter, it doesn’t matter, and organisms don’t have to be perfectly adapted anyway (or simply can’t adapt). My intention in making that comment was to say that genomes naturally organize themselves into something that would build a functional organism, which is still quite true, as positive selection still happens and negative selection is prolific even in genetic drift, but I didn’t consider neutral selection on a phenotype level as big of a factor as it probably is. 4. If the contribution of something like genetic drift can still lead to the evolution of organisms over time, then why is that not worth discussing? Your original point was that evolutionary theory cannot really be accomplished. 5. That natural selection isn’t a strict mechanism in its own right doesn’t mean that it’s somehow less powerful. If something leads to a fitter creature, then it’s a very real effect. Even these “pluralists” will tell you that there are many things that would be selected for (Daniel MacArthur uses the example of the signal around a lactase gene).
Everything seems to be irrelevant with you. Examples? Irrelevant. The way in which transcription levels and conservation effect the argument of the potential functionality of pseudogenes? Irrelevant. Instead of dismissing it out of hand, you could point out the distinction (even though I’ve read his post) and discuss adaptation’s place in evolution, because it bears a significant effect on this topic.
Hi Jacob,
For the most part, see my comment #107 as an answer to your #108.
I only think irrelevant things are irrelevant, i.e., those having no impact on the argument.
That Ayala quote wasn’t much, was it? “Much” junk DNA “might” have no function? Is “much” the “vast majority” as you’d claimed? Is “much” closer to 20%, or 80%?
By the way, he also says in that broad sweep of a book that mutation rates are “low”. So what does that tell you?
And again you demonstrated that Ayala is an evolutionist. Did you not find it sufficient evidence when I first quoted him?
But thanks for clearing that up anyway.
Here’s more on pseudogenes. These are not quotes of Ayala but his paper is referenced.
http://www.truthinscience.org.uk/site/content/view/277/65/
re your debate against yourself in your second last paragraph:
By your statement and in agreement with Dawkins, mutation is random, Moran says that random genetic drift is the dominant feature of evolution, that NS itself, though not an important factor for most features, is stochastic.
Other than the question-begging attribution of self-organization to the genome and switching to yet another version of the theory we have nothing here to bolster the Jacob/Dawkins conclusion that because Natural Selection guides evolution evolution is anything but random.
Tom,
Sorry it’s take me so long to get back to your last comment to me.
You wrote:
Well, I didn’t say that. I also wonder if this is a typo (if you meant to switch inductive and deductive above), because if anything I am arguing for something along the opposite – that the proper way to distinguish scientific arguments from other types of arguments is that scientific arguments offer a workable hypothesis – that they employ induction to test and verify or falsify their conclusion. I have been trying to argue that when an argument fails to offer this, that argument should not properly be classified as scientific.
Okay, and thanks for responding directly to my argument. But here are the problems I see with your argument:
a) an argument based on scientific data is not the same thing as a scientific argument. Here’s a quick example of why: Let’s say that I argue that I am the ultimate me. As evidence for my argument, I present, me. We can weigh me (scientifically), scan me (scientifically), and conduct tests on me (scientifically). But all of these scientific tests do not make my argument scientific. That’s because I think it’s not only the use of scientific evidence that makes an idea scientific, but the argument itself allowing for scientific data to falsify or verify the claim.
b) “[an idea] is not disqualified from being scientific just by being a deductive argument,”
To repeat, I contend that without a workable hypothesis an argument itself is not truly scientific. (You may call this scientism, but I think it’s more a case of applying consistent standards to definable words.) One can arrive at an idea any way one wants to; but scientific ideas are differentiated from other ideas by offering testable hypotheses. To assert otherwise is, I still believe, to redefine the word “science” beyond its modern definition.
c) an idea being regarded by some scientists as scientific is just an appeal to authority. Lots of scientists believe lots of whacky things. Clearly, that does not make everything a scientist believes “scientific.” I am interested in the argument that makes some scientists regard the cosmological argument as scientific. (If you don’t agree with this, then I will simply assert that lots of scientists do not consider cosmological fine tuning to be a scientific argument.)
Fortunately, I don’t rule out deductive arguments from science. And I’m not making such a claim.
and
Why is there such a consistency between the assertion among ID proponents that ID has provided a workable hypothesis and the complete failure to provide that hypothesis? Why does it seem like the hypothesis for ID is the biggest secret in science, especially among its proponents?
For the record, you have been anything but clear on this. You now say ID has provided a workable hypothesis (and now that it has already been tested), that that you’ve made this clear to me somewhere. But you have still not actually told me what it is, or provided a clear link to where it is stated. This remains a pattern here and elsewhere that has yet to find an interruption.
@Tony:
You’re right, Tony, and thank you, I did switch the words. I knew you were arguing against deductive arguments being scientific arguments.
Now, there are two problems with this:
One, there is no “proper way to distinguish scientific arguments from other types of arguments.” Some obviously non-scientific arguments, related (for example) to English literature, history, philosophy, etc., may quite certainly offer workable hypotheses to test or verify their conclusions. And not every scientific argument does this. One could argue how many animal phyla there are. That would be a scientific discussion but not testable in the way that you say. Another one, more germane to the current debate, would be uniformitarianism. Darwin himself said that in interpreting evidences from the remote past, we must assume that biology acted then in ways consistent with the way biology acts today. That is, I think, a scientific (and also philosophical) argument. It is probably not empirically testable. (There are empirical means by which it is shown that the speed of light has always been the same that it is now, but that’s a different story, because if I understand correctly, these tests are based on currently visible characteristics on earth of “old” light from many light-years away.)
Larry Laudan has shown quite convincingly that all demarcation criteria for science suffer the same pair of defects: they can be applied to other fields that are clearly not science, and they do not universally apply to all science. So there is no “proper way to distinguish scientific arguments…” in the way you seem to say that there is.
Second, and less importantly, your use of the word “induction” seems strange here. To offer a workable, testable hypothesis is not necessarily to use inductive argumentation. Why couldn’t a hypothesis be a deductively testable hypothesis, or an inductive/deductive hypothesis? Kepler’s planetary laws, or Hubble’s interpretation of redshift, would be examples of deduction implied to something known by induction.
Of course you are right about this:
But your counterexample misses on the words “based on.” This is an important but fine distinction. In your counterexample you mention data that can be used while someone is talking about “me,” and “the ultimate me,” but the data you mention would not be used as the basis for an argument for “the ultimate me.” I’m not sure what such an argument would be based on, of course, since it’s a rather nonsensical thing to talk about anyway. If it were based on anything, it would be perhaps the Law of Identity.
So I would state it this way: “An argument that mentions scientific data is not necessarily a scientific argument, but an argument whose conclusions are based on scientific methodology or scientific data is probably a scientific argument.”
I would not call that scientism. It’s only scientism if you state (as you have certainly implied previously) that “without a workable hypothesis an argument itself is not truly scientific, and its outcome is therefore not knowledge in any reliable sense.” Scientism is I(roughly) he view that there is no reliable knowledge except scientific knowledge.
I would not call it scientism, but I would say it’s not entirely true, because of, for example, scientific arguments relating to classification, which may not be testable by inductive means.
Thank you. Let’s just drop the idea, then, that evolution has carried the day simply because lots of scientists regard it as scientific. Same with global warming, and the idea that AIDS is caused by a virus. Or that El Niño affects North America’s climate, or that earthquakes are caused by continental plates grinding together.
You say,
You had written earlier,
You also said,
And this:
I took that to mean you were ruling out deductive arguments from science. If I took that wrong, then I would like to know what part you think deductive arguments have in science, so I can understand you more accurately. (The second quote here is one place where I have seen in you what appears to be scientism, by the way. I’ve already pointed that out.)
Behe has hypothesized that there are at least some instances of irreducible complexity in nature that are in principle unexplainable by Darwinian approaches (except on the basis of accepting unreasonably extreme improbabilities); he has hypothesized that there is an “edge” to evolution such that (a) for at least some transitions between species over the course of natural history, multiple simultaneous advantageous genotype mutations/variations would be required, and (b) laboratory and field observations (induction) show that multiple simultaneous advantageous genotypic mutations occur at frequencies much too small to explain the variety of life that exists. Seelke has hypothesized that populations of microorganism will show no signs of evolving to new species within a reasonable number of generations, despite being given the greatest possible opportunity to do so under laboratory conditions.
ID is also supported by inductively generated observations that the fossil record has failed to meet the predictions made by Darwin and his contemporaries that the gaps then existing would be largely filled in by new discoveries. The hypothesis that could be made now (and was made by creationists at least 50 years ago) is that this will continue to be the case over time.
There is a perfectly valid deductive/inductive argument to be made, which I have already stated:
A. There are only two explanations for origins that are currently on the table: Evolution (in some form) and Design (in some form). (This is a fact of the field as it stands.)
B. Therefore, unless a third explanation is put forth, P(Evolution) + P(Design) = 1. (You argued against this earlier, but all your third options turned out either to be self-contradictory or else Evolution or Design in some form or other).
C. Therefore any finding, inductive or deductive, that decreases P(Evolution) increases P(Design).
D. Thus from (C), the case for design can be made in part by making a case against evolution.
Finally, evolution rests on a philosophical substratum as much as does Design. (Stephen C. Meyer makes this case.) As noted above, Darwin had said that past (historical) processes in nature must be assumed to have occurred by processes that are consistent with processes we see in operation today. We should not assume that nature did things eons ago that are fundamentally different than what we see happening today. There is undoubtedly information in nature (the genome). Today we see information coming from one source and one source only: mind. Why not take the uniformitarian view here?
Hi Jacob
Furthermore, it wasn’t just an argument for bad design
You might want to consider the following article, which deals with the question from an aesthetic perspective.
The Gods Must Be Tidy!
http://www.touchstonemag.com/archives/print.php?id=17-06-025-f
Dave, thank you for the link to that article. It’s excellent.
Tom,
At this point I don’t know what else to say. On the one hand you continue to argue that…
While on a subsequent posting you provide a quote from Heddle that you seem to endorse by saying that he has beaten you “with all the best responses”:
David Heddle’s quote is my argument exactly. I don’t see how you can disagree with me here, and commend his statement elsewhere.
That lots of biologists regard Evolution as scientific is only evidence against the charge that there is a real controversy in the biological sciences about the Theory of Evolution. Since we are not talking about a controversy among scientists, but about an argument itself, citing authority would be a fallacy to the argument.
(1) Without some way to test this positively it is speculation, not a hypothesis.
(2) Again, this is not a hypothesis but a conclusion whose premises need to be tested.
(3) And it ends not with a test for ID, but an attempt to falsify Evolutionary Theory.
This suffers from the same flaw mentioned in (3) above.
Regarding your formulation of the deductive/inductive argument for ID, thanks for that — I see now what ID proponents are driving at. But this formulation doesn’t offer nor test its own hypothesis, but tests another theory (Evolution, or some component thereof) in an attempt to falsify that theory and, by its reasoning, somehow claim validation (without positive testing of its own) by default. David Heddle and I seem to agree that this is inherently unscientific.
So we still don’t have a hypothesis and test for ID, but a deductive argument whose only test is based on the faulty premise that some unexplained phenomena by a version of Evolutionary theory is sufficient evidence for ID’s acceptance.
Regarding this…
You have constructed a misleading argument because we are talking about ID’s supposed validity as science. When comparing scientific theories the question isn’t what inductive or deductive findings do the theories fail to explain, but which theory better explains the data.
I do think the formulation betrays an impulse on the side of the ID proponents — that while they say they are interested in promoting science, by their own stated logic the only way they can promote the acceptance of ID is by trying to destroy the science that is Evolutionary Theory. Things do make a lot more sense when drawn in that schematic light.
Assuming that you are still promoting the idea of ID ultimately conducting science, the question should be: how can ID be hypothesized (and tested) so that it will increase our scientific knowledge? I think any other question fails to help raise ID to the level of science.
@Tony Hoffman:
No, his quote is about a different topic than yours. Let’s make the distinction clear. You said that an argument that does not include a testable hypothesis is not a scientific argument. David said that an hypothesis that is not testable is not a scientific hypothesis. You were talking about how one can (allegedly) tell a scientific argument from a non-scientific argument; he was talking about how one can tell a scientific hypothesis from a non-scientific hypothesis. “Hypothesis” is a far more unitary construct than “science,” and therefore it is considerably easier to define. Whether it is or not, though, the fact is that the problem of defining one is not identical to the problem of defining the other.
I recommend you not argue the point about the demarcation problem with respect to science. It’s a very, very well established finding in the philosophy of science. I’m not presenting you with any original (or even controversial) thinking on the topic.
I’m lost now, and I don’t think I’m the one whose compass is spinning wildly. First, I think your statement is completely wrong. The vast majority of biologists regard Evolution as scientific, and surely this is evidence that Evolution is scientific. It would be evidence that Evolution is scientific even if there was no controversy over whether there was a controversy (sorry I had to be repetitive there).
Second, I can’t figure out any more why that point even matters. Could you tie it in to the main point of the discussion, if it actually has a place there, please?
Regarding Behe, you wrote,
1. Without some way to test it positively? But he does have a way to test these things (it’s plural, by the way). Yes, its premises can be tested, but that just means it’s not a simple, unitary theory, as easily demonstrated as, say, Kirchoff’s Law. Neither is evolution. Evolution’s premises need to be tested, too. In fact, part of what Behe is doing is testing evolution’s premises. As for (3), I’ve answered this twice already. That which decreases the probability of evolution’s truth increases the probability of ID’s truth, as far as we know right now.
Wrong. It provides evidence for ID through elimination, not by default. And there is a positive aspect to it anyway, which is that what we know about information is that it comes from minds.
As to this:
I am about ready to give up on you. If there is scientific evidence against the truth of evolution, then that scientific evidence is science. Add that to the fact that there is no other proposal on the table besides ID, and you have evidence for ID that is scientific evidence. If there is scientific evidence for ID, then I don’t care whether you call ID “science” or not; I’m content with whatever non-tendentious label you put on it, while we keep using science to test theories related to ID, and while we also keep in mind the philosophical and theological adjuncts to that work.
And there you have a marvelous example of tendentiousness. ID is not trying to destroy science. It is trying to test (and prove wrong) a scientific conclusion. If that is destroying science, then science is destroying science everywhere, every day.
You’re thinking way, way, too small here. Suppose Behe is correct in saying there is an edge to evolution. Suppose research bears him out. Does that not increase our scientific knowledge? Suppose Seelke finds that organisms never evolve to gain significantly new genotypic or phenotypic information, even under the most favorable circumstances. Does that not increase scientific knowledge? Suppose we conclude at the end of the day, by means of scientific knowledge, that evolution is wrong. Does that not increase scientific knowledge, by way of erasing falsehoods? Suppose we decide that means there is an Intelligent Designer. That’s jumping from science to philosophy and opening the door to theology. That probably doesn’t increase scientific knowledge, but it does increase knowledge. And knowledge is the point of science (and of much more than science), after all.
Here’s a summary simplification and clarification about evolution (in the broad sense): Working off the idea (and reiterating some others’ points) above that there are basically two ideas in play : 1. It all happened from natural processes (but still with room to ask, WITSION, why these laws like life-friendly 1/137 FSC etc.) or 2. “Something” acted to induce outcomes. Well, if someone can find reasons for natural processes having a hard time producing what we now find, that would be implicit support for some sort of ID since “what’s left” more or less. IOW, it isn’t necessary to have a strictly and clearly formed “theory” about that or what it was, since it is basically the rough consequences of negation of the first idea. About right?
That doesn’t say whether there are indeed such grounds for doubting what nature can do. I find arguments that such and such couldn’t happen naturally, irreducible complexity etc. to not be plausible on “inherent logical grounds” alone. I think, it depends on what kind of universe you start with – how “clever” is that universe? I’m inclined to support “original cleverness” in the anthropic fine-tuning and even extended FT that steers things in specific ways (still not “intervention” – but REM that indeterminacy makes the idea of what had to happen, or not; problematical.) In any case, whether the universe could have produced all this as is, or not, is at least a game question in principle.
Man, I like that eighth note in your sig. It cheers me up immediately.
How’s this, Charlie?
I was laughing as soon as I opened the main page.
If anybody gets triplets on here I’ll be positively giddy.
In a manly way, of course.
By the way, for the ID supporters I now recommend Benjamin Wiker’s The Darwin Myth. I read it today and, although not a compendium of new info, it makes many of the arguments we’ve worked out here; including on Darwin’s failed view of morality and the evidence seen by his fellow scientists – among them those better trained and every bit as familiar with the evidence – of ‘a Power’, an ‘Overriding Intelligence’, ‘theistic evolution’ and, of course, God.
They also knew that the problems with his theory included the insufficiency of natural selection, the philosophical imposition of naturalism on science and the weak theology implied in his arguments.
For pointing these problems out G.J. Mivart, a student of Huxley’s, a biology professor and MD, with philosophical and theological training well beyond Darwin’s, was blackballed by Darwin and his friends in scientific society.
Cell video
I’m sure most here would enjoy listening to Dr. Stephen Meyer talk about ID and his new book during the first 2 hours of the Aug 9th STR radio show with Greg Koukl. Direct link to the mp3 file is here.
I listened to it today on the plane and really enjoyed it – particularly the 2nd hour.
If someone already commented on this then I apologize. I haven’t been able to keep up lately.
Charlie -
I don’t want to dissect the meaning of ambiguous words, but it’s at least telling that the first Ayala statement was qualified with the fact that some of the junk DNA might have functions, indicating that most of it doesn’t. Keep in mind also that he seems to be talking about junk DNA in its totality, not just pseudogenes, which themselves were merely mined for hypothetical functions in the Ayala/Balakirev paper. It’s been six years since it was published, and in spite of all of the pseudogenes throughout the species, we still only have a lot of conjecture and some functional ones, which typically must be found amongst the functionless ones (the same reason, if you’ll recall, John Rinn and fellow researchers had such a tough time finding lincRNAs). Your new article doesn’t change much of the equation, as it points out that there are still “broken” pseudogenes. It brings up the ENCODE paper as support, which itself concludes that most pseudogenes don’t appear to be transcribed or highly conserved. It’s those reasons that would seem to dissuade function on a broad scale. Otherwise I’ve said from the beginning that there probably are some that have retained functions. I’m not going to disagree when you show me very specific examples of pseudogenes that point toward functionality.
I also wanted to get back to the knockout examples: the timing of transcription wouldn’t have effected them, as the entire lifespan of organisms have been tested. I would also not expect a finely honed organism to endure the deletion of millions of base pairs so readily. I admitted that it wasn’t overwhelming evidence, as there are possible explanations, but it’s another thing to consider along with the size of genomes not correlating with the “complexity” of the organism, the sheer redundancy, and all of the mangled genes that we have found.
The second Ayala quote was an attempt to highlight the word “waste”. It had nothing to do with him being an evolutionist, but that, despite your insistence, he apparently thinks that there is enough evidence of waste to conclude that life was not intelligently designed.
Regarding the article: I would certainly question the employment of CSI, which has been criticized for all of its obvious flaws, but the more pertinent point here is that any design would have to be made to look like evolution occurred, that certain genes are in different levels of deterioration, some co-opted for certain functions, some totally functionless, and this seems to chafe against the idea of the designer that most in the ID movement posit. These facts fit in better with what we’ve documented from unguided evolution. The broader criticism of the paper is an extension of that argument: it’s not just that there are common motifs throughout organisms, but that these organisms look like they were “assembled” by a process over time in that newer models build upon the pre-existing models by adding or deleting or modifying. A designer wouldn’t feel the need to suddenly inactivate certain genes unless he was under serious constraints; otherwise he would have the foresight not to include the gene at all.
Mutation rates are low, but they add up over time and populations. Refer to that graph from the article you linked to that attempts to show the rate of change for certain proteins over divergence through evolutionary time.
Lastly, you only seem to want to debate when it’s convenient for you. You talk about NS, but you seem to think it’s irrelevant when I try to talk about the place adaptations have, and when I want to discuss the dominant force in evolution, the question is completely ignored. You cling to Moran without actually discussing what would make him correct, and even worse, you haven’t really entertained the possibility that evolution can readily work despite this. I perceived two arguments in your original post: that “unguided” is a metaphysical claim (though still contingent on evolution occurring) and that evolution simply cannot happen. For the latter, you brought up an unsupported mathematical claim, but Moran will tell you that genetic drift guarantees that evolution will occur (and at the same rate throughout time) because neutral genotypes are constantly becoming fixed and “leading” populations down certain evolutionary roads. You also brought up an argument that NS doesn’t actually do anything, even though we’ve actually seen it occurring (which you still refuse to discuss, for whatever reason).
Dave -
I was trying to convey the fact that mutation rates are contingent on the number of cell cycles but that selection occurs based on reproductive cycles and age, which you pointed out, but I was also trying to say that there are also many other factors in play, such as sexual reproduction that would act as its own sorting mechanism, that would alter comparisons between the evolution of multi-celled organisms and single-celled organisms. Some studies of nucleotide substitutions reveal that change of “long-lived” organisms is not out of line with what would be expected under evolution.
Furthermore, the question under consideration, at least as far as I’m concerned, isn’t that organisms were designed with the capacity to change. Even if true, the change itself would still be unguided, like designing a computer program and letting it go (which many people have done to test “unguided” evolution). So unless you meant something different, that isn’t necessarily an argument against evolution. That something changes in such a way as to appear to confirm the process is good evidence for evolution.
I believe that Darwin’s finches reverted because that allele still existed in their population, and they were merely responding to fluctuating environments. Or sometimes there can be a back mutation. Neither means that an organism can’t change irrevocably. Certain things can become fixed in a population or change just far enough that it’s greatly modified.
I already noted that viruses mutate faster, but we also wouldn’t expect a human to change that quickly within fifty years either. It typically happens over a much longer scale. Viruses are just evolution in overdrive.
I don’t think that Behe’s response is entirely adequate because there are large structural differences between the two which confer different functions altogether, as my previous quote pointed out. It’s these new functions that make the differences large and why it would be considered a large evolutionary leap (again, HIV-2 uses something different altogether).
I did miss one of your arguments in this comment: that highly integrated structures have difficulty changing. I plan on getting to that later.
Hi Jacob,
That’s right, he did. I’m glad you brought that up because I didn’t want to be persnickety about it.
So not only has he weakly said that “much” “might” (very ambiguous, you are right, quite non-committal) be useless, he was also talking about junk DNA itself, not pseudo-genes in particular.
So, as I said, this is not much of a counter to his statement that most pseudogenes may very well have function.
Ayala thinks maybe most.
Very good. Since there are more all the time I suggest you keep your eyes peeled.
But notice that expression of the pseudogene varies. Here it varies with age. We also know that genetic expression varies with environmental conditions, so we can’t just look at an organism en vitro and then argue from ignorance that a knock-out didn’t seem to do anything. When the first functional pseudogene was found accidentally in mice it cause only 80% death in the line. Obviously it was functional even though 20% seemed unaffected. What if it were functional and only 79% died. Or 50% Or 10%. It would be less and less likely that its function would be detected, but it would still have had function.
The argument from ignorance is a weak one.
We already know he’s an evolutionist and that he must point to something as evidence. In this case it’s a theological argument and one from ignorance as well. But it doesn’t undo his allowance that one could conclude from the evidence that most pseudogenes are functional – esp. since he wasn’t talking about pseudogenes.
Good, I thought they were low as well.
You got that right. It;s not convenient for me to chase you all around the interwebs parsing every claim and paper you find. I make simple points, tell the truth, and defend my claims. I’m not going to debate all of evolution just because you find it fascinating. There are many places for you to fulfill your desires there but don’t look to me.
As it should be. My point is simple and truthful – professional, evolution-believing, not-ignorant biologists think adaptation (correlated with NS) is insignificant and not the dominant factor in evolution.
Thus, on their view it is impossible thatNS has removed the randomness from evolution and Dawkins (et al) cannot claim this as fact as though anyone who disagrees with his slogan is ignorant..
Easy peazy. Convenient as can be.
This is why it is useless to talk to you and would be very inconvenient to waste my time on every issue you’d like to chat about; you still don’t do well at reading what I’m saying. I have not disputed that “evolution can work”. I’ve been pointing to evolutionists (they believe it can work) to make my points.
While I cling to Moran it would be highly arrogant of me to think that Jacob and Charlie, can, in the back pages of Tom’s blog, settle the question of whether or not Moran is correct. Say we hash it out, then what? Are you going to send our discussion to Nature and show them that we solved the the debate that doesn’t exist, and that Orr and Moran, or Dawkins and Kauffman can just settle down and agree now?
Or, could we not say that there are two opposing viewpoints and you can’t claim one opinion as “fact” and ignore the other?
What you do get right is that I contend, and support with detailed argument, that the real intention of the word “random”, from before Darwin and all the way to the present, is to convey a metaphysical point. You can refer back to my original comment for the rest of it.
Oops, cut this out.
To find functions for pseudogenes sometimes you have to look in specific tissues and cells.
http://www.biomedcentral.com/1471-2164/9/165
Tom,
Okay. It was never my intention to argue for universal adoption of my definition of what constitutes a scientific argument, just to establish a point of agreement between us so that we can proceed; I am trying to define a point where ID differs intrinsically from the other MES’s. I think there is a difference that is (no pun intended) material – and that we can’t properly call ID “science” because of this difference. Without an agreed upon working definition between the two of us, however, I don’t see how this argument can go forward.
Okay. I’ll concede this for now but I don’t think this is at the heart of our disagreement.
Well, another problem with the P(Natural Explanations) + P(ID) = 1 is that it should be written like this: P(Natural Explanation) + P(Natural Ignorance) + P(ID) = 1. In other words, you have set the table to unfairly assign ignorance of natural mechanisms to be assigned to P(ID). Of course, another problem is that there is no set definition of what portion of parts constitute the totality of 1 – is the OOL worth ½, 2/3rds? How much is each fossil gap worth? And what does ID claim to share from the current Theory of Evolution? The ID scientific formulation might initially look good on paper, but is any of it really definable in a way that allows for scientific inquiry to proceed?
Here’s another way to look at it: say that there is an Event A such only one person (Ms. Explanation) in the world witnessed Event A. Some portion of the all the people who could have witnessed event A, let’s say half, then die.
Two of us are given the job of explaining Event A. It is my job, as Mr. Science, to find out if there is a Ms. Explanation who witnessed Event A who is still alive. My job is also complicated by the fact that everyone I interview will say that they were the witness, so I must vet their claims to see if they match what I know about Event A. But that’s my job, as Mr. Science.
It is Mr. ID’s job to show that the way that Event A occurred it could not have had a witness so that I will stop wasting my time and become a productive member of society.
According to the argument for ID that you have detailed above, every person I find who turns out not to be Ms. Explanation is valid evidence that Event A could not have a witness. In fact, it is only evidence that that person is not Ms. Explanation.
That is the situation that ID has painted for itself. Rather than saving me a lot of time and explaining how Event A occurred means it could not have been witnessed by anyone, it has chosen to use the current results of my assigned task as evidence for a fallacious argument; that my failure to have yet identified Ms. Explanation demonstrates that Ms Explanation never existed. Even if I never find Ms. Explanation, we cannot conclude what ID has been assigned without resorting to fallacious logic.
I have no problem with Mr. ID’s assigned task above, and I wont’ rule out that it could be done scientifically. But broad demarcation disagreements aside, I still have trouble seeing how noting data to fortify a fallacious argument can be considered scientific.
I bring it up because you seem to still be citing for your argument the fact that some scientists think that the cosmological fine tuning argument is science, and I think that this is fallacious (for the same reason that lots of scientists think that Evolution is scientific does not mean that Evolution is scientific). If a thing is scientific, it should be because it conforms to a definition of science, not because it has adherents.
I have tried to define science in order to show where I think ID falls outside its line. I think that this disagreement is doomed to a stalemate unless you are willing to provide a definition of science and how it is that you think ID conforms to that definition.
I hoped my earlier re/summary of the issue would do more good, but maybe I should sharpen the point. Sure, having trouble finding a way for know natural processes to lead to X could be loosely lumped as “ignorance” rather than a specific alternative. Re:
In other words, you have set the table to unfairly assign ignorance of natural mechanisms to be assigned to P(ID). OK, worth pointing out. However: if you call it all “natural ignorance” then you are making the same mistake in reverse: imposing an assumption on what’s left – that it has to be some natural process we didn’t understand rather than “something else.” Of course we find ourselves unable to imagine how some things happen, but they do anyway without “meddling.” One possible example is some kinds of superconductivity. That doesn’t prove everything must be like that either. Something “rigging” things is a “logically possible world” and thus fair game for investigation.
I think some critics are saying, they have arguments for it being hard for the material beings in the context supposed, to end up so well speciated with this or that traits given what we know or think we know. Imagine oceanographers finding “blocks” on the sea floor (“Bimini Road” an actual example?) and wondering if natural processes could have made them – or was it people? It would be silly to say it was unscientific to even look the blocks over to see whether it made sense for them to have formed naturally. The data, such as cut marks or odd ingredients, that showed artificiality are not “unscientific data” and presenting the conclusion the blocks were made would not be a priori “unscientific.” If some oceanographers got into the habit of looking for such structures, it would neither:
1. Be unscientific for them to look, examine features, and draw conclusions.
2. Their sub interests and activities wouldn’t have to be a special “scientific theory” if defined through negative result: finding difficulty of being naturally formed.
There is a difference though, in that those concluding something was “man made” would at least have other examples in the category and knowledge of how people cut rocks, etc. But there could in principle be artifacts found that are not built by human intelligences (but still “creatures.” In any case, the more abstract notion is just looking at structures and finding it hard to explain their being formed by “what just happens” – leading to speculation of some alternative. That is a valid deduction through negation. It isn’t a special category of science, or theory, or unscientific process per se to get the first part done. It is wondering about the alternative as such that presents a problem.
I don’t yet know of convincing arguments that the universe didn’t have it in itself to produce what happened. I even prefer the “cleverness” of adequate anthropic fine-tuning in advance, to any one/thing working on the scheme in progress. Yet I don’t assume I have to be right. It is important to properly frame issues. Also, theories of how evolution work have to be challenged anyway to weed out false notions (such as maybe, piling up of single-point mutations was the input to NS instead of more complex processes.)
BTW, bobxxxx is wrong to assume an person with interest in some kinds of ID had to be a theist. Likely, but no logically necessary.) It could be that anthropic principles are part of the same conceptual basis, “logos” in the broader sense, whether there is “a being” thus represented or not. I don’t know if that should still be called “supernatural.” I mean, is “everything” that isn’t material, “supernatural”? If so that would include mathematical entities like the series of decimal digits of pi, the complex numbers, the aleph series of infinities, perfect geometric shapes, conceptual worlds “that don’t really exist” etc. BTW read up on “modal realism” if you want to be stunned about the issue with “realness.”
@Tony Hoffman:
I’m essentially in agreement with the first portions of your comment, except I think you say to readily, “this was not at the heart of our discussion” about things that earlier seemed quite important to you. But that matters little.
That’s not what at all what the probability equation was about. It was for the purpose of showing that whatever decreases the probability of evolution as a true explanation, increases the probability of design as a true explanation. There is no P(Natural Ignorance) explanation. Natural Ignorance may describe our current state of affairs with respect to knowledge of origins, but by itself it does not affect the probability of either evolution or design. Design arguments are not, contrary to some false opinions, arguments from ignorance.
The only way you can rebut the probability equation I’ve offered is to suggest a viable third alternative x, such that P(Natural Explanation) + P(ID) + P(x) = 1; where x is a serious candidate for an explanation of how life came about.
After all these decades of research and study, there does not seem to be any x in the offing, so I would consider P(x) to be quite low at this time.
Again, the purpose of the probability argument was not to assign values. It was to show that a negative case against evolution can rationally, legitimately, be considered a positive case for ID.
Yes, it is. I could elaborate but that would be repeating things I’ve said more than once already here.
Funny, you’re the one who earlier argued that science was inductive, not deductive. Every person you find who turns out not to be Ms. Explanation increases the probability that there is no Ms. Explanation. That’s the kind of thing I’m talking about.
This is also a misrepresentation on two levels. The probability argument I have given you is not the only kind of work being done in ID research. There is research that is essentially seeking to “save you a lot of time and effort” as you have said it should do. Second, my probability argument was never intended as anything but a probability argument. It was not presented to you (as you have falsely put it here) as a demonstration of ID’s case. The word “demonstrate” (as used in argumentation) usually applies to a result that is deductively certain, which I never claimed. Now, in the long run, if ID’s probability arguments against evolution succeed in showing a very, very low probability for Evolution, then this would be something like a near-demonstration of ID’s case, of the probabilistic/inductive sort. And if you visited every possible evidence in the entire world and you found there was no Ms. Explanation, that would be the same.
There is no fallacious argument here, in other words, as long as you understand properly what is being argued.
The best definition of science to come out of Laudan’s work on the demarcation problem may be this: science is what scientists do. We all know it when we see clear cases of it, we all know that some things (like music, history, horseback-riding) are not science, and there are some things in the middle for which it’s hard to categorize things. For the most part we know science and non-science when we see it, though. And there is apparently no “definition of science” that works universally, so we can’t test whether something is science or not on that basis.
Since when did your assertion—that ID is not science—become mine to disprove? I think it behooves you to prove your point, since you’re the one who wants to make it. We’re at a stalemate because you can’t show that ID is not science, but you don’t want to admit that it might be. I’ve shown that ID uses scientific methods (in addition to philosophical and theological reasoning, as I’ve emphasized repeatedly), and that where it applies scientific methods to the study of nature, in that aspect of its work it is science. If you think that studying HIV mutation rates, or the protein components of the flagellum, or the DNA code, is not doing science, then you have a pretty lonely position to defend.
Hi Jacob
I did miss one of your arguments in this comment: that highly integrated structures have difficulty changing. I plan on getting to that later.
Thanks for your thoughtful response. I am beginning with the part you didn’t have the time to address now because your comment inspired a thought process which may have bearing on our discussion. Previously I offered the following hypothesis (guess) regarding mutation rates in the HIV virus. Charlie later confirmed that my hypothesis (guess) was accurate to a degree which I had not suspected when I offered my hypothesis (guess). 8^>
This is not about mutation rates per se but about “highly integrated structures”. When I offered my hypothesis (guess) regarding the mutation rate in HIV I deliberately couched it in terms which implied overall structural stability.
Despite its extremely high mutation rate there must be a regulatory mechanism which preserves overall stability within the structure of the virus or we would could no longer identify the mutated virus as HIV.
If we use the analogy of a building, we might suggest that a virus is like a garden shed. There is a frame, and a roof, and walls, placed according to a particular design, which identifies it as “garden shed HIV”. The influenza virus is similar in complexity but different in design, which identifies it as “garden shed, type influenza”. And so on…
We can take “garden shed, type HIV” and paint the walls, or install hangers on the walls, maybe even construct a lean-to on one end but, unless we tear it down and reframe it, it will always be “garden shed, type HIV”. That’s why the high mutation rate of HIV is significant. As high as that mutation rate is, it remains HIV.
If we then extrapolate the high mutation rate of HIV, an oraganism (virus) so “simple” that it cannot reproduce on its own and whose integration level is analogous to a “garden shed”, to a more highly integrated structure such as a bacterium which might be analogouos to a “one bedroom bungalow”, we can see where evolution might run into some difficulties. The mutation rate in “one bedroom bungalow, bacterium” is much lower than “garden shed, HIV” and the functions are much more highly integrated. This means fewer changes overall, and a higher probability that any particular change would be deleterious.
H-e-l-l-ooo….?
To simplify and follow up, it is OK in the analogy for a geologist to note “artificial origins” but not to go deeper “as a geologist” and think, is this done by Romans or Vikings? etc. (Hence, not for the biologist, “as a biologist”, to think “God” did it…) But that doesn’t mean that no one should think such thoughts, just someone acting in a different capacity. And interdisciplinary effort is a good thing.
How now Mr. Dembski. It seems William Dembski’s course outline has stirred up more than a little controversy among the opponents of ID.
Included in the commentary is the following quote from C. S. Lewis;
http://www.uncommondescent.com/education/dr-dembskis-students-coming-to-a-hostile-website-near-you/
http://scienceblogs.com/dispatches/2009/08/dembskis_rigorous_coursework.php
http://www.uncommondescent.com/education/the-intellectual-equivalent-of-spray-painting-graffiti/
Dembski makes this observation;
And has offered this compromise…
re: adaptations
http://darwins-god.blogspot.com/2009/08/how-evolution-created-evolution.html
I like hearing scientists speculate (informal hypothesis) about why something occured. I like it because sometimes it demonstrates what ID theorists point out regularly: that an hypothesis can be considered scientific [and not be banned from being discussed in the classroom
] even if it lacks a way to empirically test/confirm/falsify the hypothesis.
The most recent example of this is the planet WASP-17, which orbits its star in the wrong direction. What’s the informal scientific hypothesis for the backward motion?
“WASP-17 likely had a close encounter with a larger planet, and the gravitational interaction acted like a slingshot to put WASP-17 on its odd course, the astronomers figure.”
As I layman, I think the astronomer’s informal hypothesis is reasonable despite the fact they will never be able to test/verify/falsify a formal version of the hypothesis by directly reproducing the results. They may be able to observe the hypothesis in action sometime in the future (strengthening their case), but that is not the same as proposing an empirical test to verify/falsify.
Why is it a reasonable scientific hypothesis? Because we see objects in space today alter the trajectory of other objects so it’s not unreasonable to think this occured in the past.
But what if the astonomer’s hypothesized that an intelligent being caused the backward orbit? I think that is not a reasonable scientific hypothesis because we don’t see intelligent beings altering the trajectory of planet-sized objects today so there’s no reason to think it occured in the past.
What can we say about the ID hypothesis as science? We may never be able to empirically test/verify/falsify the hypothesis by directly reproducing the results. Is it still a reasonable scientific hypothesis? I think it’s reasonable because we know today that intelligence can create information so it’s not unreasonable to think this occured in the past (information in the cell). It’s the same line of reasoning the astronomers are using – applying today’s knowledge of how the universe works to the past.
SteveK, it seems you appreciate that ID is basically an argument from negation. If the examiner can eliminate (or cast serious doubt on) one idea (the evolution of advanced beings like people can proceed over millennia from chemicals), then it brings up the question, “what else is responsible”? They have failed to convince me the universe can’t do that by itself, but I don’t object to people making an honest effort to look into it. (Note, the question of “by itself” is not perfectly clear anyway.)
Some people in ID are motivated to reconcile literally interpreted Bible passages with natural findings. For me, that isn’t at issue since I much utilize higher criticism. I myself more favor the idea of anthropic pre-design. That means, “Something” made the nature of the universe so “clever” that life could develop and evolve.
An argument from negation? I don’t know about that. It’s an argument from applying today’s knowledge to the past by assuming the universe worked the same back then.
You might disagree with my argument and give me a different argument to support a different conclusion, but you can’t say my reasoning is invalid.
Tom,
Sorry I haven’t replied yet; I drafted a reply then lost it. Not that you’re eagerly waiting, but I do want to reply to your last. I should be able to get to it this weekend.
I drafted a reply then lost it.
I sympathize. It’s a frustrating experience.
Charlie -
Sorry for the very long delay. Addressing this is probably pointless now, but I’ll try anyway.
Pseudogenes are still a minor part of the genome, and since we were, in part, talking about junk DNA at large, it’s just as pertinent, if not more so, to say that this large majority of the genome perhaps is non-essential. It seems to me that such a fact would be a far bigger blow than if we were talking about just pseudogenes by themselves. We can snipe back and forth about ambiguous language, but, first, I’ve already produced multiple reasons backed up by even the most generous geneticists for why most DNA is “junk”, and second, it’s strange to use ambiguity in an argument when you keep harping on a paper that says we may find some functionality (which ones are even worth investigating for function? why investigate ones we already know won’t have function?) in a small subsection of the genome and since haven’t found much evidence that most are even active. You haven’t found any leading geneticists or biologists whose conclusions aren’t that our genome makes the most sense underneath the light of evolution (genetic variability, evolutionary fuel, gene duplication, gain of some functionality, etc) and who don’t think that huge sections of the genome, if not most of the genome, lacks a normal function. All you’ve managed to do is cherry pick quotes from ID proponents who are cherry picking functions themselves with no context or biologists with the most generous of views on junk DNA but who still basically agree with me because they know that there’s such a thing as evolutionary remnants left over (and, as I hinted at earlier, a lot of RNA is actually thrown away by the cell).
In fact, that some such genes go on to gain new functions is a boon to evolution; it’s a process of destruction and creation. There is no real proof of creation and then destruction or even an inefficient designer (or one who looks inefficient); both processes are intertwined into one scheme.
Furthermore, I admitted from the start that such mouse experiments can’t detect the reason why they were relatively unaffected. But you’re leaving out the rest of the argument: if we have reason to think that there’s such a thing as junk DNA, then the explanation is obvious. Things like the onion test and known redundancies and dilapidated genes supply us with the reasons; thus, when they’re removed, they wouldn’t have a big effect. It’s not telling us anything but confirming what we already know. Otherwise effects would have to be incredibly subtle, and that leads to other problems. For instance, I question the efficiency of the genome (that’s a lot of DNA to use for incredibly specific circumstances), and it further degrades the IC argument. If you can remove a lot of DNA and have the organism function on certain levels, then it can’t be that irreducible. I would like to know what mouse experiment you’re talking about, though.
At the end, you have no real reason to be so optimistic. You cite paper after paper that only base findings on the fact of evolution and claim that they’re finding gems in spite of the detritus surrounding them. We’re only making discoveries in small increments; going through everything with a fine-toothed comb. You’ve managed to pick out individual functions while ignoring this larger issue and have clung desperately to a paper about a small part of the genome that still hasn’t been substantiated in even its most generous interpretation. You’ve failed desperately at what you set out to do. I’m not arguing this because it’s favorable to evolution. If the findings supported it, I could easily be an ultra-adaptationist who would still say that the composition of our genome makes the most sense because of evolution.
Lastly, you started this argument by saying that the randomness of evolution made it unfeasible. Your words were that it doesn’t work. I’m trying to show how, despite any “randomness”, it is feasible. How is that not relevant? You’ve managed to ignore many salient points under this guise because it’s not convenient for you. For instance, you’ve ignored just about any argument stating that genetic drift isn’t true randomness in the sense that the ID argument uses it as (that it’s like hitting any one part a dart board, all parts being equal). If most changes are still deleterious, then most changes are selected against with genetic drift because negative selection is occurring. So functional organisms are still resulting (and as Moran points out, at a constant rate). Second, that’s a very big (and I think unwarranted) interpretation to say that anyone thinks that NS is insignificant. It’s not hard to imagine how many features would be selected for. In fact, much of our basic body structure and organs have been preserved for hundreds of millions of years through selection. One might even say that much of the big evolutionary innovations or changes have to be selected for. There is a lot that’s more inconsequential: a flatter nose, for instance. But NS is a huge part of evolution. Now, what’s more interesting is discussing NS at the genetic level, as Moran indicated, but for some reason you’ve yet to discuss it or talk about real-world examples. It’s hard to call it irrelevant when this is exactly what Moran talked about.
Dave -
I can only imagine that you meant this, but it hasn’t remained HIV. It came from SIV. Anyway, your analogy misses a few key points. 1. Much of life is built using a similar “blueprint”. Multi-celled organisms have been constructed on the basis of single-celled organisms. Once a backbone came into being, it never went away. Many organs still subsist except in fine details. 2. Destruction is a very real facet of evolution. Just as certain parts of a building can be torn down and rebuilt, so can parts of an organism. 3. Neutral mutations may translate the same way but can lead to even bigger changes later on. 4. Changes can happen behind the scenes where it wouldn’t necessarily effect the organism in huge ways.
And if HIV is developing completely new abilities, then what’s stopping the next change? And the next change? It came from SIV. Therefore, can’t it become something else? The genome isn’t degrading, clearly. Every adaptation to a new environment means that it breaks away from the pre-existing, and every step along the way looks to be just as viable, if not more so. How integrated could it be if both versions of HIV have changed irrevocably in functions, adding new binding sites and such?
Furthermore, some experiments have been done on more complex organisms. Some individual genes can be altered; not on a large scale, not all at once, of course, but small ones, yes. At the heart, it’s basically the IC argument, which, again, how integrated is a feature when it can exist a thousand different ways? And that leads us back to the argument of all the work that’s been done to document the possible evolution mutation by mutation of certain things.
Tom,
I said I’d repost here but I ran out of time and had some other problems. My apologies for not posting within the normal time frame of a discussion — I was torn between failing to reply when I said I would and the impoliteness of following up too long afterward. Anyway, this was approximately what I had been working on for a reply before I managed to lose it.
Regarding this, I don’t strictly agree because anything that decreses the probability of Evolution being the true natural explanation could, in truth, increase the probability of a new (natural) theory – what I called P(Ignorance). In that case, the equation as written does not account for all factors that total 1, and a decrease in the probability of Evolution would not automatically result in an increase in P(ID).
Well, I’d rebut your probability equation by saying that this is gaps reasoning, and that the history of science is rife with those who have espoused it looking, in hindsight, to be only shortsighted. It’s not proud company.
You continue to misrepresent what I have said. The last time you falsely accused me of this I wrote:
I don’t know how to say it any more clearly. I am not ruling deduction out of science (that would be absurd), I am trying to say that at some point a testable hypothesis (induction) has to be developed for something as broad as theory to be considered scientific. (As explained above, I don’t accept the argument that trying to find some gaps in a version of Evolutionary theory or other natural explanation is equivalent for a testable hypothesis for ID.)
I think we’re at a stalemate because when I try to offer ways in which I think ID fails to raise itself to the level of the modern empirical sciences you say things like:
Well, without a point of demarcation for science then it makes sense that nothing can be unscientific. I think your recommendation is a shame, because as frustrating as the discussion may for those who try to define it I think the discussion could have been productive.
I don’t really know what to make of this. I don’t know what you mean by a “deductively testable hypothesis, or an inductive/deductive hypothesis” or “examples of deduction implied to something known by induction.” Kepler’s planetary laws were the result of his arriving (whatever kind of thinking he did it) at a hypothesis – as I understand it he was the first to explain planetary movement as elliptical rather than circular. His hypothesis (and the math he developed to calculate it) can be tested inductively through the prediction of future planetary orbits, through the discovery of new planets, or launching artificial satellites. (I don’t have any idea how you would propose that we test Kepler’s laws deductively.) And his laws gained acceptance not by running further tests that demonstrated the explanatory deficiencies of whatever theories of planetary motion were current at the time (as ID proponents would have us do to adopt their theory), but by testing his hypothesis. I’m not sure what similarities you might see between Kepler’s laws and ID, but their difference appears material to me along the lines I have been arguing.
I refer you to Heddle’s comment quote previously – a hypothesis which cannot be tested is inherently unscientific. What you quote above concerning Behe are not hypotheses – they are speculations about a scientific theory without a testable hypothesis. This has been a problem for Behe and ID from the start and it remains.
What Behe and Seelke both do give us are scientific arguments that criticize a version of Evolution that it appears few biologists except for ID advocates actually adhere to. I’ll give you that, and to the extent that they encourage any greater understanding and examination of biology then I’m all for it. But what they don’t appear to do is provide a hypothesis for testing for ID. And without that they are just like all other biologists working on Evolution – some great, most competent, and some just bad. But calling them ID scientists would, I think, be like calling them Democratic scientists, or baseball fan scientists; the nature of the work they do in biology is based on Evolution, and affects ID to the same degree it affects the Democratic party or baseball.