One frequently reads or hears that Michael Behe's views in his books, Darwin's Black Box and The Edge of Evolution have been refuted. What one never hears is that Behe has responded to all of his major critics, and that they haven't rebutted him. Behe continues making his point in A Blind Man Carrying a Legless Man Can Safely Cross the Street.
Update: There's an interesting debate in the comments section here, featuring one of my favorite critics of ID, Nick Matzke.
My own comment: The discussion of whether amino acid sequence similarity can be explained by convergent evolution is interesting but besides the point. Behe was quite willing to accept the Thornton group’s (non-convergent) evolutionary explanation for the different variety of V-ATPase. The question is whether this exposes a weakness in Behe’s view that the origin of irreducibly complex systems poses a significant challenge to non-intelligently guided evolution.
I think Behe is correct in maintaining that it doesn’t expose a weakness in his view. What Thornton’s group has succeeded in doing is showing how an IC system can become more complex. It does not succeed in showing how an IC system came into existence.
Let’s suppose that only the fungi variety of the V-ATPase existed, and Thornton’s group was able to discover that it arose from a simpler form of V-ATPase. But this simpler form is itself IC. Would they have weakened Behe’s case? Certainly not very significantly. For they still haven’t shown how the simpler IC system came to be.
So I find Thornton group’s work to be very interesting, but not very enlightening to the ID debate.