So an anonymous comment to my last post on Liu and Ochman's paper "Stepwise formation of the bacterial flagellar system" directed me to comments by Nick Matzke over on the Panda's Thumb, which suggest that the L&O results could be an artifact of their methods. I don't have much experience with the methods at the heart of the issue, but it looks like Matzke could have a point. That's what I get for being all triumphalist.
That said, for publication at PNAS, L&O did pass peer review by people who know this sort of work. If Matzke feels he has a solid case, he ought to publish a response (he's previously published on flagellum evolution [subscription], so he should get a hearing), and let the peer review process sort things out. It's also worth noting that L&O are building on a lot of previous work on the evolution of the flagellum (their introduction section sums it up), which has given scientists good reason to think that the flagellum (1) did evolve in a stepwise fashion and (2) was assembled in part from pre-existing components with other functions.