James Shapiro responded to Jerry Coyne's criticisms, which Coyne put in the combox, instead of starting another thread, which would have been the polite thing to do. So I didn't realize that Shapiro had responded until just a few minutes ago.
There's an interesting discussion in the combox afterwards. I made a few observations from it:
1) There is some agreement that environmental stress can cause an organism to increase mutation frequency to its genome, in order to solve the crisis.
2) However, are the mutations just random attempts to solve the crisis, like a blind man trying to find his way out of a maze, or does the organism somehow "know" which mutations are more likely to solve the problem?
3) Either way, it still leaves in place Darwin's claim that natural selection decides which variations survive.
4) Why isn't anyone talking about (genetic) drift as an alternative to natural selection? That, it seems to me, is the real challenge to Darwin's claim about natural selection.
Let me add a fifth point:
5) What mechanisms cause organisms to increase their mutation rates? Have these mechanisms been acquired through evolution? Or were they part of the original cells?