TalkReason provides a forum for the publication of papers with well-thought out arguments against creationism, intelligent design, and religious apologetics.
Exactly the same question has been asked on
the Panda's Thumb blog (see http://pandasthumb.org/archives/2008/05/flagella-real-a.html) by one of the commenters (who signed as Larry Gilman). Perakh provided a detailed reply to that question in the comments section there, so please look it up.