It might be good to warn Jacob regarding his repeated and incorrect use of the term “creationism”: he intentionally employs it in a broad-brushing pejorative manner–quite nicely revealing his philosophical ignorance in his weak justification for using it.

Rigorously speaking, “creation” has to do with the before-and-after from nothing to something. (In fact, “before” doesn’t even work here because time is the metric of change.) The Stanford Encyclopedia of Philosophy’s first paragraph in its entry on “creationism” does a fair job in drawing out the important distinctions.

None of the modern empirical sciences can address creationism per se because they study the before-and-after of things already existing: they need to observe and measure something before it changes into something else. It’s kind off amusing to watch atheists flail about looking for an initial target to explain, when there was nothing in the first place. Nothing means nothing: nothing means “no thing”–the privation of beingness itself.

It has turned out that non-coding DNA is far more complex than just pseudogenes. It also includes transposable elements, introns, and highly repetitive sequences (e.g., microsatellites).

Some non-coding DNA is proving to be functional, to be sure. Gene regulation, structural maintenance of chromosomes, alternative splicing, etc., all involve sequences other than protein-coding exons. But this is still a minority of the non-coding DNA, and there is always the issue of the onion test when considering all non-coding DNA to be functional.

According to Gregory, many noteworthy scientists have attempted over the last forty years to explore these functions and ascertain a better understanding of the genome. It’s not exactly stunning that science develops and changes. By the time Mims wrote that letter in 1994, most of the genome was already well on its way to being explored, and we were beginning to have solid ideas about many things that constituted this supposed “wasteland”. By adaptationists, I think he means the people who thought that all of the genes were perfectly conserved by natural selection because they were useful (in other words, it was an assumption that they were overly useful, not simply “junk”). Quote:

It needs to be pointed out again that evolutionary biologists and geneticists held a variety of views on functionality, some claiming that it was all functional, some saying very little (but few, if any, saying it was all totally non-functional). Strict adaptationist (“ultra-Darwinian”) thinking had led many authors to assume that non-coding DNA must be doing something useful or it would have been eliminated by selection long ago. The proponents of the “selfish DNA” approach to non-coding DNA wrote their papers in direct response to this overly adaptationist interpretation and argued that much of it could be explained simply by the existence of mechanisms that put it there, independent of organism-level function. But even they expected that some would turn out to play a role in regulation. At the same time, most researchers for the past half century have noted the link between DNA amount and cell size, which means that total non-coding DNA content is not irrelevant biologically. This could, however, be an effect instead of a function, which is why there has for decades been discussion about this issue.

http://genomicron.blogspot.com/2007/09/junk-dna-let-me-say-it-one-more-time.html

Now what exactly did creationists propose here? Because there is still the very real possibility that the majority of it will not be all that useful. Creationists try to take such a view and claim that it contradicts every new function that’s uncovered, but no: there is room for interesting functions, but what we know about DNA does not appear to support the total usefulness of a genome given discrepencies in size vs. function.

And the accusation that Gregory is quote mining is funny because he says that he is extracting quotes and encourages readers to actually go back into the literature themselves. You, on the other hand, are merely throwing out unsubstantiated claims about scientific beliefs without attempting to back them up at all.

Don’t you just hate that creationist quote-mining?

These showed that the early discussions of these notions did not rule out possible functions for noncoding DNA. Nevertheless, creationists, many science writers, and far too many biologists insist on claiming that noncoding DNA was long dismissed as unimportant because of these ideas.

Where in the world did those foolish creationists, science writers, and “far too many biologists” (as if they would know) get the idea that noncoding DNA was “junk”?

In other words, there was no real period in which noncoding DNA was dismissed by the scientific community, though there was a much-needed shift away from strictly adaptive interpretations in the 1980s.

Translation:
While real scientists continued to investigate the nature of noncoding DNA the evolutionary apologists dismissed it as a nonadaptive artifact of evolution. Now that the real scientists (the far too man biologists?) have discovered that noncoding DNA (an oxymoron perhaps?) does, in fact, have a function the evolutionary apologists are busily quote-mining the literature to substantiate their sudden volte face on the subject. “No, no, no, we never said it was useless junk, we just said it was junk.”

blackwhite- The ability to accept whatever “truth” the party puts out, no matter how absurd it may be. Orwell described it as “…loyal willingness to say black is white when party discipline demands this. It also means the ability to believe that black is white, and more, to know black is white, and forget that one has ever believed the contrary.”

http://www.newspeakdictionary.com/

What did the creationists predict about junk DNA? Did they predict that it would contain evolutionary significance? Did they do any actual research on their own? Anyway, here there are a number of quotes that give wide-ranging opinions from the 1980s. There are about 30 quotes alone throughout the blog, just a sample, but many conclude that more research needed to be done before anything solid could be said. He also gives a more complete history of junk DNA. There is even an article from 1994 that says deeper meanings are clearly embedded in the so-called waste, and it’s leading to a more complete understanding of the genome. More from Ryan Gregory:

In other words, there was no real period in which noncoding DNA was dismissed by the scientific community, though there was a much-needed shift away from strictly adaptive interpretations in the 1980s. Some individual researchers ignored noncoding regions, but there is no gap in the literature other than limits on what could be done in a methodological capacity. The “new” view of noncoding DNA as potentially important has been proclaimed regularly for at least as long as the claimed period of neglect between 1980 and 1994.

Lastly, it should be said that I’m referring to all who believe special creation when I say creationists. I hate saying IDers. How is that misleading? Young earth creationists and old earth creationists, both, unsurprisingly, utilize creationism. When there is a specific theory that denotes very specific research and claims, then you can complain about what I call it.

All chairs are not the same…?

In actuality they’re gradients. Some dogs are like wolves, and there are dogs farther from wolves. In other words, there are only organisms in relation to one another. There is no inherent “dogness” that leads to deleterious effects once gotten away from.

Dogs and wolves are part of the same family of organisms- they are all varietes of dog. The names we give teh different varities of creature are, to some extent, arbitrary, but that does not imply that there is no exxential ‘dogness’ applicable to all dogs.

The interesting cases are the ‘interspecies hybrids’ – are they evidence of diversification within created “kinds” or are they evidence of your evolutionary gradient? Almost all sheep and many goats can hybridize. All dogs can hybridize. Most cattle (including the buffalo) hybridize. Horse, zebra, donkey hybridize. The big cats have been know to hybridize.
http://www.pets4you.com/bobcat.html

However, we do not see cat-dog hybrids or sheep-horse hybrids.

Scientists were so wrong about junk DNA that they were using it to do research on cancer back in 1983 and research on diabetes in 1987.

What conclusion did the evolutionists draw from so-called noncoding DNA? What did the IDers predict. The fact that a few scientists were looking into noncoding DNA, depite the general concensus that was “junk”, is the reason we learned it was useful.

So creationists weren’t even first

And you cannot even get past the misleading use of labels.

Of course, I don’t think it matters how many examples there are, as creationists will always retreat just a step beyond what can be accurately documented and reproduced. The problem with this argument is, as I said before, self-evident. Each organism is a different arrangement of DNA. The argument that these mechanisms for DNA rearrangement and change are deleterious is somewhat defeating. For instance, the dog example presumes that one change, ten changes, a hundred changes, or a thousand changes are all fine. But ten thousand…a hundred thousand…maybe that’s dangerous to the organism. Well how does that make sense? Each organism itself is a different collection of genes. We only use classifications to group like-minded organisms. In actuality they’re gradients. Some dogs are like wolves, and there are dogs farther from wolves. In other words, there are only organisms in relation to one another. There is no inherent “dogness” that leads to deleterious effects once gotten away from. There would have to be good proof and solid research for why such a thing would even make sense. No, there are only different constituencies of DNA. If a poodle can exist, if a golden retriever can exist, if a wolf can exist, then anything in between can exist, as long as it’s a fit creature. Once again, the very fact of fertile hybrids proves this. You’re essentially relying on the unproven definition of “kinds”. But evolution itself is merely change – it works from one generation to the next with no starting point except for the first common ancestor. It’s all minor variations between organisms that are isolated and modified and selected for so that small changes become large changes. You haven’t given a single shred of evidence to the contrary.

Which leads to an interesting question. You seem to be implying that diversification within a species is possible, but then you say that scientists can’t seem to produce evidence of this change and diversification. But there is no evidence for a boundary between species, and it appears possible that incremental alterations can work to make a creature more fit.

It’s false to say that we have no bat transitional forms. There is one that has claws, teeth, and modified limbs and tail like a kind of pre-bat. It’s funny that you quote Gould, though, because he also says this:

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists—whether through design or stupidity, I do not know—as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups.

Fossils are merely snapshots in time. It’s like taking a picture of yourself at ten and again at eleven, but all of the pictures in between were burned. The theory of evolution does not rest on any one series of fossils. Creationists, in fact, are disingenuous here. They themselves have no expectations – if God created organisms that appeared to be transitional forms, well then that’s just God being God. But they expect evolutionists to account for every single fossil. No amount seems to be good enough – even though scientists were able to predict a creature very much like Tiktaalik before it was discovered. Fortunately, there is a lot more to evolution than that. In a moment I’ll discuss why the evidence actually makes the most sense within evolutionary theory.

More pertinently, your inquiry is absurd. You asked me to show you a method of bat evolution (I posted that and about five other things). You never asked me to then prove that evolution must have done it. You asked whether evolution could do something, but when evidence is presented, you switch tactics to say that, well, it doesn’t mean that evolution did do it. To say that a paper on bat evolution assumes evolution is like saying that a paper on germs assumes germ theory. But the purpose of those works is not to produce a treatise on evolution.

Now evolution is buffeted by evidence for common ancestors. The whole point is that, instead of specific fine-tuning, there is evidence of modification from previous organisms. Even the unique organisms can usually be elegantly explained. All creationists can claim is that there only appear to be common ancestors, that God works based on common motifs, but beyond the obvious issue that creationists are co-opting evidence for evolution into their beliefs, it completely ignores the DNA evidence. Once again, there’s a pseudogene in the whale genome that is active in its land-based ancestors but was somehow turned off during its slow modification toward whales. I believe that humans have olfactory pseudogenes that are switched off (so do dolphins, as they obviously have no need of them). The evolutionary baggage that accumulates over long stretches of time seems to speak against special creation. Combined with the mechanisms of change, these things heavily inform the theory.

Scientists were so wrong about junk DNA that they were using it to do research on cancer back in 1983 and research on diabetes in 1987. So creationists weren’t even first, and they don’t get points for being orthogonal to the truth. Ryan Gregory on this topic:

As I have discussed previously, both hardcore adaptationists (if any exist anymore) and creationists have a vested interest in having all non-coding DNA be functional. I believe that real-world variability in genome size argues strongly against such a prospect, but of course it is possible, and this is the point that people like Ohno, Doolittle, Orgel, and Crick made in the 1980s. The important point is that yes, some non-coding DNA is functional at the organism level (as opposed to existing for its own sake or because there is no strong selection against it). And certainly, non-coding DNA has effects at the organism level. But current evidence suggests that about 5% of the human genome is functional, and even the least conservative ENCODE participants (whose primary, and important, objective is to identify the functional elements and their features) are betting that 20% is functional.

In the end, it is obvious that non-coding DNA is the product of evolution whether it all turns out to be functional or not. The cases in which former parasites (transposons) have taken on function at the organism level are a perfect illustration of cooption, which is the same basic process that allows explanations for the evolution of complex structures like eyes or flagella. The research into function of non-coding DNA, which the creationists are eager to cite, can be carried out only under an evolutionary framework — it is meaningless to talk about “conserved non-coding DNA sequences” otherwise.

http://genomicron.blogspot.com/2007/06/junk-dna-gets-wired.html (he gives many more links on his blog)

In regards to the Icons article: it does a good job of exposing Wells, showing where he takes people out of context, fails to cite, or misrepresents the data. If somehow these are distortions of his work, then give a few examples. They give plenty of evidence that outright contradicts Wells, so either they’re misrepresenting things, or their arguments are simply better. Even when they did give one to Wells, Haeckel’s embryos, you failed to list any pertinent scientists who actually believe it. In fact, there’s a much better explanation for embryological development that scientists use to inform their work on things like bat evolution.

P.S. These links are crap. If you can’t get some of them to work, or you need a specific link that I didn’t provide, then I could oblige.

You’ve been calling evolution speculative and no more valid than ID this entire time, but you haven’t backed it up very well.

I suppose that validity is in the eye of the beholder. What would you consider valid evidence?

I asked for proof of the barriers of evolution, but none were provided.

I believe the response was “We don’t know if dog breeders were trying to breed something other than dogs.” and “they’ve only been breeding dogs for a few hundred years anyway.”

If I recall my mention of ongoing and unsuccessful effort to breed novel creature from fruit flies and bacteria was greeted with silence.

I gave an example of prolific evolution that has been documented in nature.

Evolution has not been documented, at best we have observed variation within species i.e. Darwin’s finches or Great Dane and Chihuahua in dogs. Evolution is the “origin of [unique] species” not minor variations within species.

That deliberate deception has been practiced by evolutionists for the better part of 150 years. It has alos been coupled with the straw man that Christian theists believe in the creation of all creatures exactly as they exist today, a demonstrably false statement, although I wouldn’t be surprised if some Victorian divines advocated that herietical notion.

We know it is false because the early church recognized Africans and Asians as human beings, descended from Adam and Eve and capable of receiving salvation. The first African bishop (from Congo) was ordained in the 5th or 6th C. When it became an issue in the middle ages, the church debated and ruled that status of Amerinds as human beings, descended form Adam and salvable. IF all humans are descended from Adam and Eve then only a blind fool would suggest that Christians didn’t believe in variation within created kinds. (BTW – as an aside – the debate over the status of Amerinds became the foundational document for the concept of “human rights”)

You brought up bat evolution, I gave you research.

The earliest fossil bats resemble their modern counterparts in possessing greatly elongated digits to support the wing membrane, which is an anatomical hallmark of powered flight.

Obviously we have a clear line of descent from ur-bats to modern bats. The trouble is… ur-bats look like modern bats, they haven’t evolved.

This absence of transitional forms in the fossil record led us to look elsewhere to understand bat wing evolution.

We have no transitional forms… the perenial problem of paleontology, referred to by the [eminent?] Stephen J. Gould as “the trade secret of paleontology”

http://books.google.com/books?id=yfXJhKmp1wUC&pg=PA263&lpg=PA263&dq=stephen+J.+Gould+%22trade+secret+of+paleontology%22&source=bl&ots=lcrGkiDcWa&sig=lbxvgFdIkqq2vvwLkKJmpp1CMR0&hl=en&ei=qz5pSuSPNoH4sQPyt5mXBQ&sa=X&oi=book_result&ct=result&resnum=1

..so leaving behind the fossil record we go in search of alternatives.

Investigating embryonic development, we found that the digits in bats (Carollia perspicillata) are initially similar in size to those of mice (Mus musculus) but that, subsequently, bat digits greatly lengthen.

A comparative analysis of embryonic development, shades of Ernst Haeckel (whose fraudulent illustations of embyonic development are still defended by evolutionists).

http://en.wikipedia.org/wiki/Ernst_Haeckel#.22Infamous.22_embryo_drawings

Embryos begin with a single cell which develops into a multicellular infant creature through a process of cell division. It is not only unremarkable, but it is a no-brainer, that this process would, at times, produce ’similarities’ in appearance. However, outward appearance masks a finely tuned, highly integrated, and barely understood series of functions beneath the surface.

Together, our results suggest that an up-regulation of the Bmp pathway is one of the major factors in the developmental elongation of bat forelimb digits, and it is potentially a key mechanism in their evolutionary elongation as well.

What the researchers are saying is the “similarity” in mouse and bat digits disappears when the Bmp expression is activated and they speculate (potentially) that the cause of Bmp expression is evolution. It could as easily be said, “…up-regulation of the Bmp pathway is one of the major factors in the developmental elongation of bat forelimb digits, and it is potentially a key mechanism in their design

You dropped the arguments completely when I showed that you were mistaken about the integrated whole of systems and junk DNA.

If you are referring to your rather disorganized defense of “junk” DNA and the desperate efforts of evolutionists to salvage their reputaions from another failed prediction. Yea, I dropped it. My mother told me never to match wits with the witless.

I mean one can do a simple Google search and find a cogent answer to Icons of Evolution.

Yes, I read the talkorigins critique shortly after I read Icons. Despite their vigorous defense of the “unfairly maligned” evolutionists I found their arguments unconvincing. You see, when I went to school (and I had a particular interest in paleontology), they used most of the icons in the biology texts. They are, at best, misleading. Most of them are known to be misleading. Haeckel’s fraud was exposed in 1868 by Ludwig Rutimeyer, but they kept on using them until at least 1970.

In particular probability theory as it pertains to the chemical origins of life.

I thought you had disposed of probability theory as the wrong approach to OOL… perhaps that was David… 8^>

Oh, that’s a comment that brings out my inner snark….but I’ll restrain it.

If you say that religious convictions are on an equal footing, or take precedence over the acceptance of scientific facts, then you have put yourself in the position of opposing some scientific knowledge.

I didn’t say anything of the sort. Religious convictions must match physical reality where those convictions attempt to describe/explain physical reality. You know, Christians believe in the law of non-contradiction too.

But the real question is what should you do when science does not provide the answers you want regarding final causes?

Don’t give up…keep searching for the truth??? If science can help in that endeavor, then I support that effort. If it cannot then I’m content to rely on the other means available to us for obtaining knowledge.

Here’s an example. I have had several knee operations…

Thanks, but this has nothing to do with anything we are discussing.

My question was to explain why the notion of a final cause should be a necessary assumption of biological study. I don’t think you or I have answered that question.

If you rewind the tape you’ll find that I said, “necessary or not, the answers MAY help us”

Now, is it necessary to know this? No. Biological study doesn’t NEED to expand its horizons in order to keep doing what it has been doing. We can stop breaking new ground any time we want and biological studies will keep chugging along just fine.

Does cosmology NEED to study yet another galaxy? No. So why are we doing it?

Well you’ve practically conceded every point as it pertains to biological evolution and the origin of species, so asking me to show my evidence after all of that seems rather pointless…

Okay… you win.

I’m not going to spend a ton of time debating the next two points. By timescale I merely meant the billions of years over which life emerged and evolved (unless you’re arguing that these dating methods are wrong). And by conditions on Earth I simply tried to suggest that there is ample reason to think that things were quite different in that time span. All of these things would be far more in favor of a chemical origin of life than special creation, even without looking at the details.

I never said that God was a myth – that’s kind of a caricature of what I believe and what I think. I have said over and over around here that the God of a specific religion is very unlikely because the religious claims themselves aren’t good enough to warrant belief, and the existence of a non-religious sort of deity is unknown at this time but the answer changes dramatically depending upon how you define this deity. In other words, deism is more likely than religious theism, and atheism is somewhere in there. I say that I live my life as if there was no God, which is a completely different claim.

Anyway, these beliefs are a product of my thinking. I try not to make unwarranted claims. I say that abiogenesis seems likely because the circumstantial evidence points in that direction (in other words, we know the problem, that life probably needed a starting point), and scientists are making progress toward a more competent theory – we’re at a better place than we were ten or twenty or thirty years ago, and I think that we will probably be even closer in the future. It’s not incompatible at all to say that that the evidence hints toward abiogenesis but that we still need more time to work out an actual theory. Again, a big part of the problem is that, unlike evolution, we can’t actually see how things progressed.

The other option is to believe special creation, which doesn’t look at all likely given the competence of evolutionary theory and the inability to actually come up with any solid science. That alone is reason for believing this paradigm (though I suppose that there’s always hope that it will all come crashing down tomorrow, and special creation will stand alone). The two choices are either believe in something that has been discredited in many parts or trust that the science will indeed take its course and reach a better understanding of the origins of life. That, to me, is not a difficult decision. Again, it’s a matter of knowing the problem. It seems to me that the problems of the origins of life are very real, and we need to solve them. On the other hand, there aren’t just problems with special creation – the entire thing doesn’t work.

The “uncertainty is weakness” is a very real point. I’m not going to speak for you, but many creationists aren’t interested in letting the science play out. They’re interested in exploiting incomplete parts of our understanding so that they can buffet their own views.

Your argument about junk DNA seems somewhat of a simplification. For one, it’s not even the case of creationists getting the jump on evolutionists. Biochemist Larry Moran says, “It’s sufficient to remind people that lots of DNA outside of genes has a function and these functions have been known for decades.”

Scientists have been looking at junk DNA long before Mims. Quote: Part of the difficulty in studying junk DNA is that it’s impossible to prove a negative, i.e., that any particular DNA does not have a function.

That’s why T. Ryan Gregory, an assistant professor in biology at the University of Guelph, believes that nonfunctional should be the default assumption. “Function at the organism level is something that requires evidence,” he said.

The idea that scientists somehow missed the boat on junk DNA, I think, frankly, is fictitious. It simply required greater testing instead of catch-all assertions, and our understanding of the human genome in the last fifteen years has been a great boon for this.

Furthermore, of course there are “junk” genes that are useful for various reasons, but there are all sorts of inactivated genes and genes that might seem like evolutionary remnants or products reserved for evolutionary change, thus buffeting the theory even more. On the other hand, I would expect a designer to be efficient, and if he uses a common blueprint (DNA), I would also expect complexity of an organism to be a product of size of the genome. Extra DNA is not proof of a designer. It shows constant change in an organism with inefficient but workable genes. Here is a good article that can explain some of this stuff in more biological terms.

Given what we currently know, there are a few that we can suggest.

1) Life evolved from a starting point.

How do you know? Where is your evidence?

2) The timescale is sufficient.

How do you know? Where is your evidence?

3) Conditions on early Earth seem to be correct.

For which of the more than a dozen hypotheses were conditions correct?

Of course, no one is denying that our current understanding is incomplete,…

No kidding…

…but there are a few problems here with the ID claim. It means that one would have to reject almost all of our current theories for the history of our universe – throwing biological and cosmological evolution out too,

Science is a tentative enterprise which is self-correcting, that’s why it is far superior to the dogma of religion… or so I am told.

even if the evidence highly suggests that such things happened.

“Of course, no one is denying that our current understanding is incomplete,…”

Now no other scientific subject is so charged that one uses the incompleteness of the theory as proof against it.

Someone on here mentioned ice-fairies and refrigerators.

That’s because religion happens to be involved.

See my post on faith and science

Science is a process of investigation and inquiry.

I think I acknowleded that in one of the points above.

Making it an all or nothing, take it or leave it proposition I think is disingenuous.

I haven’t made it an “all or nothing” proposition, I like science and think it is very beneficial. It is the philosphical materialists who have used science as a stalking horse for a philosphical belief that have invented the ’science vs. religion’ superstition.

It’s one thing if the arguments of ID held weight, but they’re rather specious themselves, failing in every possible predictive capacity, so why should I trust ID when it predicts that the origins of life rest with a designer?

At its inception, some ID proponents predicted that a ‘purpose’ would be found for so-called “junk” DNA. It appears that researcher have discovered that “junk” DNA does have a purpose.

“As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science[1] against assuming that ‘junk’ DNA was ‘useless.’” Science wouldn’t print Mims’ letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things: “[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. Design encourages scientists to look for function where evolution discourages it.”

http://stanford.wellsphere.com/general-medicine-article/we-are-not-junk-dna/359769

Compare this with the claims of Professor of Biochemistry Larry Moran dated December 18, 2006

[...]The fact of junk DNA disproves intelligent design and discredits strict Darwinism as well. The IDiots lose twice. Their strawman version of evolutionary biology is wrong and so is design by God.[...]

http://sandwalk.blogspot.com/2006/12/junk-dna-disproves-intelligent-design.html

and the facts as we now know them.

Thus, this discovery in plants illustrates that the link between coding DNA and junk DNA crosses higher orders of biology and suggests a universal genetic mechanism at play that is not yet fully understood.

http://www.sciencedaily.com/releases/2009/06/090606105203.htm

This affirmation of the predictive potential of the ID hypothesis, plus the release of Stephen C. Meyer’s new book, Signature in the Cell: DNA and the Evidence for Intelligent Design inspired Dicovery Institute Fellow, David Klinghoffer to issue the following challenge o his blog.

A Challenge to Intelligent Design-Bashing Regulars on this Blog

[...]If you tell me, “Yeah, I don’t need to read it, I know what he’s going to say” — then you’ve just proven to me that you’re not serious. On the other hand, if you’ll go ahead and read the whole book, including the appendix where he lists and describes 12 ways in which ID is testable,[...]

http://blog.beliefnet.com/kingdomofpriests/2009/07/a-challenge-to-intelligent-design-bashing-regulars-on-this-blog.html

The point is, we think that life came out of simpler chemicals, so we make progress on the question until we find the answer.[italics added]

On what basis do you think that life came out of simpler chemicals? What reason do you have for believing this paradigm?

But that’s not good enough for those who think that uncertainty is weakness.

You can’t have it both ways, Jacob. You appeal to the tentative nature of the scientific enterprise while asserting with dogmatic certainty that God is a myth. I think we can safely ignore the implied ad hominem directed at “those who think that uncertainty is weakness.” because it certainly doesn’t apply to thinking Christian theists.

Gotta go to work now…

Necessary or not, the questions surrounding final causes are interesting and if science can help in some way then I’m all for it.

I have no problem with anyone taking away whatever philosophical conclusions they might from scientific knowledge. The question really is, though, when science does not support, or contradicts, prior philosophical conclusions, what is the proper course?

If you say that religious convictions are on an equal footing, or take precedence over the acceptance of scientific facts, then you have put yourself in the position of opposing some scientific knowledge. I just think IDers cannot simultaneously hold that position and say that they are defending critical thinking and scientific exploration without contradiction.

So your quote above isn’t really a surprising position. But the real question is what should you do when science does not provide the answers you want regarding final causes?

Here’s an example. I have had several knee operations. When the pressure changes, I can often feel my knee ache more than usual. (Sometimes not.) Despite the fact that my knee lets me know (sometimes) when the pressure is changing, I would be a fool to prefer its sensations to the weather report, brought to me by a trained meteorologist, using satellites, doppler radar, other weather data, and a scientific understanding of the forces involved and how they have historically played out. Is the weather report perfect? No. But it’s vastly more reliable and accurate than my knee, every time.

You just answered your own question about necessity that you asked earlier: necessary or not, the answers MAY help us.

My question was to explain why the notion of a final cause should be a necessary assumption of biological study. I don’t think you or I have answered that question. I’m still curious if you can provide me with what you think are the probability arguments for Evolution, and what the bad assumptions are upon which they are based. I still am not sure what it is that you’re going for there.

Preface: some of these URLs don’t seem to link.

Fortunately, some work has been done on bat vision (http://www.ncbi.nlm.nih.gov/pubmed/14660703), digits, and wing (and http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1622783). Furthermore, research has been done on the evolution of the eye, blood-clotting system (per Ken Miller and others), dinosaur to bird digits, and signaling molecules called hedgehog (http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000 146). Some of this is speculative, some incomplete, but investigating genomes is a radically complex business, and what we have to work with isn’t perfect. But the work that has been done is impressive. Darwin’s dictum was essentially “descent with modification”. Starting there, the evidence that we have from DNA and organisms both living and dead is overwhelming. A certain gradient does tend to emerge, as all organisms are merely modified versions of their ancestors. One cannot hope to defeat evolution without addressing this point.

Anyway, I never said anything about giving a free pass to the origin of life. A competent theory will need to emerge. But you used the weasel program, which wasn’t really referring to abiogenesis, and you used examples that could have referred to either. They’re being mixed up because they’re being used interchangably here. Of course, if you can’t even use strict probability on evolution, then how can you use it on abiogenesis, when you know even less about the process behind it, and you base the probability on a current understanding of life that isn’t necessarily applicable? Again, you need to understand the issue well to calculate probability. These probabilities assume that life came together by pure chance. But just like natural selection, it seems likely that there is some concerted process when it comes to the origin of life that makes it much more probable.

Given what we currently know, there are a few that we can suggest. 1) Life evolved from a starting point. 2) The timescale is sufficient. 3) Conditions on early Earth seem to be correct. Of course, no one is denying that our current understanding is incomplete, but there are a few problems here with the ID claim. It means that one would have to reject almost all of our current theories for the history of our universe – throwing biological and cosmological evolution out too, even if the evidence highly suggests that such things happened. Now no other scientific subject is so charged that one uses the incompleteness of the theory as proof against it. That’s because religion happens to be involved. Science is a process of investigation and inquiry. Making it an all or nothing, take it or leave it proposition I think is disingenuous. It’s one thing if the arguments of ID held weight, but they’re rather specious themselves, failing in every possible predictive capacity, so why should I trust ID when it predicts that the origins of life rest with a designer? The point is, we think that life came out of simpler chemicals, so we make progress on the question until we find the answer. But that’s not good enough for those who think that uncertainty is weakness. Part of the problem is that we have no blueprint. With evolution the proof is in the DNA. But we can’t use current life as a model for early life. It’s like looking at a solution and trying to figure out what the problem is. Of course, creationists deny the problem to begin with, but that’s problematic since, again, if the facts don’t support special creation, then you’re merely using an argument from incredulity to deny a naturalistic origin of life.

Anyway, I wouldn’t mind a scientific based argument about the origins of life and where the science currently stands.

One last thing: a common creationist tactic is to act as if evolutionists know that there’s design but actively deny it out of certain commitments to the theory. But Darwin himself said that such arguments are emotional, and intellectually he knows better because the evidence speaks overwhelmingly against specific design. Dawkins says that using teleological language actually produces errors – not that it is beneficial to our understanding of biological systems. It doesn’t help your argument if: 1) special design isn’t intellectually fulfilling and 2) the pattern and answer seeking portions of our brain were actually derived out of natural selection itself, in which case ID would be nothing more than an attempt to look for something that isn’t really there.

I’m not really sure what this means…

And I’m not sure I answered the question, nor am I sure it makes much difference. Necessary or not, the questions surrounding final causes are interesting and if science can help in some way then I’m all for it.

I think it’s conceivable that teleology could inform biology, but I also think that ship has sailed.

You just answered your own question about necessity that you asked earlier: necessary or not, the answers MAY help us. The answers may not help us in the area of biology, but it might help us in other areas. Learning that ID theory is true would confirm to us that some form of intelligence existed before our life existed. If you don’t think science would eat that up, you’re crazy.

To repeat, the science of ID may never become a reality but I’m willing to give them some room to work.

I can only conclude that you are being purposely obtuse or that you are incapable of presenting an argument to support your musings.

I believe my requests for you to support your assertions have gone unanswered. I will let my prior posts here, and your responses to them, stand as a testament to this.

I’m not really sure what this means…

The knowledge we have of the evolutionary process entails the conclusion (or best inference) that final causes are a reality. How so? Because we know that biologists intend (final cause) to study evolution and biologists know they are a result of the evolutionary process

…but I do appreciate your at least trying to answer my questions.

I think it’s conceivable that teleology could inform biology, but I also think that ship has sailed. Without a method for the hypothesis, I don’t see how working the framework of a final cause informs any biological research; it’s just a philosophical conclusion divorced from the scientific practice.