The follow up article is interesting:

http://whyevolutionistrue.wordpress.com/

What bothers me about Dupré is not so much his bringing to public attention new insights into how organisms work, for that’s a good thing. What bothers me is that, like so many others, he casts these new discoveries as things that throw the theory of evolution in crisis. And that plays into the hands of creationists, no matter how strongly Dupré decries creationism. As an evolutionary biologist—which Dupré is not—I think I’d know if my field was in crisis. Yet I haven’t heard any recent lamentations from my colleagues.