Mainstream evolutionary biologists are independently arriving at very similar conclusions to Behe’s central thesis.
Researchers at Uppsala University describe the challenge they face — and that standard Darwinian processes had to face.
Swamidass’s response doesn’t address our main arguments, but he indicates he is impressed by what Darwinian mechanisms accomplished in generating chloroquine resistance.
It is important, in evaluating these arguments, that one consider all the evidence: not just the evidence that is consistent. It seems to me that when this is done, the arguments for common descent — certainly in its universal sense — are, at best, inconclusive.
Turning a protein shaped to do one particular job into a protein that does just a slightly different job (which most biologists, including myself, had thought would be as easy as pie) turned out to be much more difficult than expected.