"The Edge of Evolution": Coyne's reply to Behe's reply

Earlier I commented on Jerry Coyne's New Republic article criticizing Michael Behe's new book, "The Edge of Evolution." Behe's reply to Coyne's article is here and Coyne's reply to Behe's reply is here. These are my comments about Coyne's reply to Behe's reply:
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Behe said: Alluding to my participation in the Dover, Pennsylvania court case of 2005, early in the review Coyne writes "More damaging than the scientific criticisms of Behe's work was the review that he got in 2005 from Judge John E. Jones III" . . . . Frankly, it's astounding that a prominent academic evolutionary biologist like Coyne hides behind the judicial skirts of the former head of the Pennsylvania Liquor Control Board.

Coyne said: It's amusing to see Behe attacking me for ad hominem remarks, and then himself engaging in the same tactic by denigrating Judge Jones. He questions whether Jones really understood intelligent design at all, or simply adopted the plaintiff's claims in the Dover case.

The Discovery Institute showed that Jones "simply adopted the plaintiffs' claims" in writing the Dover opinion's ID-as-science section. Jones virtually copied that entire section from the plaintiffs' opening post-trial brief while ignoring the defendants' opening post-trial brief and the plaintiffs' and defendants' answering post-trial briefs. The copying is evident from a side-by-side comparison of the two texts -- word-count comparison computer programs are not necessary and in fact only confuse the issue. There is no evidence that Jones did any independent thinking here. There is no evidence that he even read any post-trial brief other than the one he copied from. To me, the principal issue is not just the copying but is the one-sidedness of the copying. Furthermore, he showed great hostility towards organized religions by saying in a Dickinson College commencement speech that they are not "true" religions -- that alone is sufficient reason to declare a mistrial. I don't understand why Darwinists are willing to touch Judge Jones or the Dover decision with a ten-foot pole. Jones and the Dover decision have been thoroughly discredited. Anyway, it was completely out of line of Jones to rule on the scientific merits of intelligent design -- there is no constitutional separation of bad science and state.

Coyne said: It is important to draw the distinction between Behe and his fellow IDers, lest people mistake ID for a monolithic theory accepted by all its proponents. Behe is one of the few intelligent-design proponents who accepts common descent, macroevolution, natural selection, and an old earth.

That is an unfair stereotype of ID proponents.

Coyne said: Behe argues that the evolution of a single protein-protein binding site requires more than 2 simultaneous mutations -- more like 3-6 of them. He adduces no evidence for this major claim, nor does he give a single example of any case in which two or more binding sites must evolve simultaneously for an adaptation to arise. The reviews by Ken Miller in Nature and Sean Carroll in Science cite several examples of the gradual origin of adaptations via the step-by-step accumulation of point mutations in proteins.

In an adaptation requiring step-by-step mutations, there is no selective advantage for the preliminary steps and so a population possessing just an incomplete set of the required mutations might not be large enough to be likely to proceed to another step by a rare random mutation. Such step-by-step adaptations might be possible in a population of trillions of individuals with very short generational times, like bacteria, but are very unlikely in higher animals that have comparatively small populations and long generational times.

Coyne said: First, as both Dawkins and I point out, if random mutations can't build complexity, how can they possibly have been so effective in artificial selection of plants and animals?

That is begging the question.
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