I always make a point of telling my students about the fatal problem that type III secretion poses for Michael Behe's use of the bacterial flagellum as an example of "irreducible complexity" (discussion here).
Today I came across a paper (here) by Joe Felsenstein that was new to me, which deals with the other intellectual force behind Intelligent Design, William Dembski. In classic Felsenstein style, he restates the arguments in a way that starkly reveals their problems. His analogies are simply fantastic. It's very well written, and a must read for anyone interested in bioinformatics.
