Intelligent Design Creationists are very fond of this argument. They tell you that there are only two choices when it comes to explaining biology: either Darwinism or Intelligent Design Creationism. If a given feature of the biological world cannot possibly be explained by Darwinism, then God must exist and he must have designed the feature.
Here's Douglas Axe illustrating the false dichotomy on Evolution News & views [Let Science Be the Arbiter: A Reply to James Shapiro].
As an ID proponent, I've put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.This is actually an attempt to get around the charge of false dichotomy by extrapolating from a rejection of Darwinian explanations to any naturalistic explanation. If Axe is truly able to demonstrate that his "data" cannot possibly be explained by any naturalistic means then it follows logically that the only other type of explanation has to be supernatural. But what Axe is really arguing against is a Darwinian explanation and it's only his lack of imagination and arrogance that allows him to claim that no other naturalistic explanation is possible.
There is no crutch here. The aspects of protein structure that appear to preclude a naturalistic origin have been described in detail. If Shapiro or anyone else were to show in detail how these are overcome by a naturalistic mechanism, then my argument would fall and I would let it fall. But the reverse needs to be true as well. Scientists who personally side with naturalism have to be willing to let naturalism fall, as otherwise they would be guilty of using a crutch to prop it up.
As we have seen time after time, the Intelligent Design Creationists do not have a scientific theory or any kind of scientific explanation for biological phenomena. All they have is criticisms of science—criticisms that are usually based on a lack of knowledge. When will we see an ID explanation of protein folding and function?
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I saw Axe's paper where he used chinese characters and simulated an evolutionary process. It was garbage. There are thousands of papers out there on the evolution of protein structure.
I've got some respect for Axe, compared to other ID creationists anyway, simply because he is at least doing actual experimental work vaguely related to evolution. He's putting his money where his mouth is, to some extent, not just basically doing literature reviews and throwing his hands up in the air like Behe. Though, as Larry points out, he's happy to criticise evolution but provides no alternative ID mechanism to be tested.
His work is now largely published in the ID in house journal, Biocomplexity. Essentially (from what I can tell) his work is basically a repeat of the earlier stuff he did that got published in actual proper journals, then with an added ID spin that comes from a paper he wrote attacking Michael Lynch's recent papers:
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.4
Basically, he and Ann Gauger see how one (modern) enzyme can be converted into another. They then apply the population genetics side of things from the Lynch attack and conclude that evolution is impossible. Here's an example:
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1
The details are a bit above my pay grade. What puzzles me is the mechanism. Or lack thereof. Well, I'm not puzzled really, it's fairly obvious why they don't propose one.
SteveF, PZ Myers had very nice takedowns of the Gauger and Axe work you refer to some time ago on his blog Pharyngula. (Multiple takedowns because Gauger, IIRC, replied to his criticisms, to which PZ responded.)
Larry, nice to see you finally catching up with one of the ID criticisms in the judge's opinion in Kitzmiller.
;-)
The facts on Galapagos islands could not convince Louis Agassiz of Darwin's theory (he was a catastrophist). Why should the facts of molecular biology be able to convince a creationist, or if they fail to why should that be relevant? It's simply false to claim that the facts have the power to overthrow personal beliefs. Scientific facts work on a historical scale at which idiosyncratic individuals hardly feature. "Funeral by funeral ..."
One of the problems with those papers by Axe et al. is that they attack known strawmans:
a) nobody is arguing that mutations in cells do a random search through the whole ramdom space of protein sequence.
b) focuses on direct conversions of extant proteins without taking care of ancestral routes
And dismiss wihout explanation true examples of complex evolutionary modifications. Por example Bridgham et al. (2006) or Carroll et al. (2011). The key message of those papers in this context is that mutations do interact and the precise history is important. deleterious mutations can have ulterior advantages, if the carriers are able to survive. You can see this other post in The Loom for an analogy: low frequency cells (mutations) may give rise to ulterior population booms.
Another problem is that Axe tends to minusvalorate some key factors in his postulates. For instance, in orther to support his claim of statistical improbability of evolution he insist in sequence differences. But fail to understand, not to mention explain, how myoglobins and plant leghemoglobins have very similar function AND structure with only a 17% of sequence homology: structure is much more resistant than sequence: there is plenty of space to "play" and founf new functions from new sequences without compromising prior ones.
But the main problem is that he misleads the works of mutations in generating change and thus infravalorate overall change rates. In his calculations he consider that the "mutational space" is the result after selection: only modifications in surviving cells contribute to the "search space". An honest consideration would include in the "searched space" all produced cells in a generation. What selection provides is a way to understand why some changes are preserved and others not.
Well, I think he only really had one critique of their work from what I can recall (and followed it with a description of the Joe Thornton work that Gauger was talking about at the time). FWIW, Gauger responded to Myers:
http://www.evolutionnews.org/2011/10/on_protein_evolution_pz_myers052251.html
One of the main criticisms of their approach was actually made some time ago by Young Earth Creationist:
http://toddcwood.blogspot.com/2011/04/protein-evolution-in-bio-complexity.html
Much of the Axe and Gauger argument seems (to me at least) to rest on the first Biocomplexity article that I linked to above. I think that Myers should also have addressed this for a more comprehensive critique, though I'm not sure how familiar he is with their work and this field in general.
This IDiot seems to have an Axe to grind.
Well, it's a false something.
the reverse needs to be true as well
The reverse being a demonstration of how non-naturalistic means can overcome these 'protein problems'? I'll pull up a chair.
Both demonstrations would, of course, prove little about actual history (though the non-naturalistic one would certainly render me more open to the possibility of ID!). The creation of a protein assessed as a modern protein, either by entirely 'naturalistic' or 'supernaturalistic' means, would not be conclusive. We would need to create one that was functional in the milieu of the first peptide-condensing cell (whatever that was), using only the amino acids available to it, and work from there.
I disagree with just about everything Judge Jones said in his decision. Which criticism are you referring to?
Larry, would you be willing to elaborate on why you disagree with Judge Jones?
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