The Edge of Evolution, as seen by Dave Ussery and BioLogos
In his next installment Professor Ussery complains that I wasn't enthusiastic enough in my chapter "What Darwinism Can Do." As an example of common descent I pointed to Baker's yeast, for which there is good evidence that sometime in the past its genome duplicated. But I also noted that other yeasts with unduplicated genomes have done fine for themselves. The point was that gene or even whole genome duplication is not the powerful tool that Darwinists often claim. That point passed over Dave's head. His main comment on the book's next chapter, "What Darwinism Can't Do" is to tell the reader to search PubMed for the words "cilium" and "evolution." One gets lots of papers that contain both those words, he assures us. He naively assumes that means progress is being made on how the cilium could have arisen by a Darwinian mechanism. Ussery is simply wrong. Most of those papers have nothing to do with how the cilium evolved. Others contain interesting studies of which ciliary proteins are similar to which other proteins (which at best concerns only the topic of common descent) as well as vague, speculative scenarios, but none of the papers describes in testable detail how a structure like the cilium could have arisen step-by-step by a Darwinian mechanism. Dave's argument might be dubbed "The Argument from Personal Credulity" -- because he and others believe the cilium could arise by Darwinian means, it must have done so, and any paper that agrees it happened must contain strong evidence that it did happen. Credulity, however, is not ordinarily considered a scientific virtue.
Consider this -- if it remains a longstanding mystery how "complex features in proteins that require two or more mutations" could evolve, as Eugene Koonin claims, how could we possibly know how a structure like the cilium, with hundreds of different proteins, might evolve by Darwinian means? Talk about straining at a gnat and swallowing a camel. The short answer is that Dave's (and other Darwinists') imaginations supply gauzy ideas that take the place of hard data and experiments.
In his fourth installment Professor Ussery discusses chapters 6 and 7 of The Edge of Evolution ("Benchmarks" and "The Two Binding Site Rule"). The only point he has to make about chapter 6 is that, gee, Richard Dawkins solved the problem of coherent, multiple, evolutionary steps in his book Climbing Mount Improbable. All a Darwinian process has to do to build a complex, interactive machine like a cilium, you see, is to take the gradual, gently-sloping side up Mount Improbable instead of its sheer-cliff face. Dave is so trusting it never occurs to him that, while we see the sheer face, the gentle slope appears only in Dawkins' imagination. The point of The Edge of Evolution was to argue that experimental evidence does not support Dawkins' metaphor. No evidence has since been brought to the table to show otherwise.
In his comments on Chapter 7 Dave again shows a very peculiar understanding of the benefits of mutation. I suspect that since he is in the Center for Biological Sequence Analysis and studies mutations for a living, he must somehow think that the more mutations there are, the more he can analyze, and the better it is for him and the organism too. That's the only explanation I can come up with for his discussion of how good it was for one of Lenski's bacterial lines to turn into a mutator strain (in which the repair function of DNA polymerase is broken and the bacteria accumulate orders of magnitude more mutations than they normally do). He seems not to wonder why E. coli in the wild keeps a much lower mutation rate if it would be beneficial to have a higher one. For his last point he shows a figure comparing the genomes of different strains of E. coli, and commenting that many of them are missing large chunks of DNA that are found in other strains, which he thinks are coding for molecular machines. Perhaps they are. But what evidence does he give that they were not initially present and then lost from the strains that are missing them? And what evidence does he give that any of the molecular machines arose by a Darwinian mechanism? None and none, respectively.
Unfortunately, like many (not all) Darwinists, including many (not all) theistic-evolutionist Darwinists, Professor Ussery simply assumes the points at contention and appears utterly incapable of stepping back from his assumptions.