Counter arguments:
General:
1. Behe is lazy, Behe is religiously motivated, Behe is afraid of or otherwise against science2. The systems are not really IC
3. The systems are IC but became that way through co-optation
4. The systems are IC but became that way through a complex history which has since been subtracted away (like the arch)
Specific examples:
1. The blood clotting cascade (Russell Doolittle)
Article by Russell Doolittle in Boston Review
cites: "Loss of fibrinogen rescues mice from the pleiotropic effects of plasminogen deficiency", Bugge et al. Genes and Development 9, 794-807.
discussion by Ken Miller in "Darwin's Black Box"Neil Greenspan's article in The Scientist
Michael Ruse's article in Free Inquiry
Behe's interactions with editors of scientific journals related to this example
2. Cilia - Eel sperm flagellum
Ken Miller - audio from Concordia conference3. Eubacterial flagellumcites: J. Cell. Science 1997. 110, 85-94
Ken Miller - audio from Concordia conference4. Mousetrap and opportunism/cooptingScott Minnich - video lecture on Eubacterial flagellum and the Type III secretion system
response by Dembski (and Behe)
Wall Street Journal article by Sharon Begley
article by Minnich and Meyer from Design & Nature II conference
Ken Miller - audio from Concordia conference and web paperJohn MacDonald's diagrams and argumentBehe's defense of the mousetrap analogy
Miller's response to "A mousetrap defended"
Behe's response to Miller's response to Behe's response0
5. Barry Hall's work on the LAC operonKen Miller's discussion in "Finding Darwin's God", M. Behe - audio from Concordia conferenceBehe's response
6. Critical review of Darwin's Black Box by H. OrrReview by H. Allen Orr