It’s nice of Behe to distill the best examples from his book into a single paragraph though:
One big fly in their argument, however, is that they overlook the results from non-laboratory evolution that I give in the book. Every species that has been examined in sufficient detail so far shows the same pattern as seen in lab results. For example, I open the book with a discussion of polar bear evolution. About two-thirds to three-quarters of the most highly selected genes that separated the polar bear from the brown bear are estimated by computer methods to have experienced mutations that were functionally damaging. (Some other reviewers questioned this. I showed why they are mistaken here .) Similar results were seen for the woolly mammoth. Neither of those species evolved in the laboratory. Except for the sickle mutation (which itself is a desperate remedy), all mutations selected in the wild in humans for resistance to malaria are degradative. Dog breed evolution, which has been touted as a great stand-in for selection in the wild, is mostly degradative, and lots of breeds have health problems.
We have the polar bear example again, which I think at best could be described as “ambiguous”. Certainly what Behe says about 2/3rds to 3/4ths of mutations being predicted to be damaging based on the Polyphen predictions has been discredited.
Then we have the example of the woolly mammoth - Behe cites Lynch et al. (2015) for this. In his book, Behe says of this paper:
“Analysis showed, however, that of the approximately two thousand amino-acid residues found to be mutated in mammoths, about five hundred were likely to be damaging.64 Another three hundred changes couldn’t be decided, but a chunk of them too may be damaging. What’s more, a further twenty-six genes were shown to be seriously degraded, many of which (as with the polar bear) were involved in fat metabolism, critical in the extremely cold environments that the mammoth roamed.”
It seems that these figures of “five hundred” and “three hundred” changes being likely damaging/unknown but maybe damaging also come from Polyphen predictions, which are flawed for the same reason as Behe’s claims about the polar bear mutations are. I’m quite surprised how heavily Behe leans on Polyphen predictions to make his case (they form the basis of his top two go-to examples of real-world degradation-driven evolution in nature). It’s also quite telling that AFAIK, Behe hasn’t responded on the subject of the significance of Polyphen anywhere yet, despite writing responses to arguments that included criticisms of his interpretation of these predictions.
I think it’s fair to say that his last example of dog breeds is pretty inane, so that just leaves human mutations that provide resistance to malaria. Worth a new thread to discuss?