Cilia might be related to the bacterial flagellum, a similar whip-like propulsion devise. But flagella have a very different construction and rotate to help bacteria to swim rather than show the paddling motion of cilia. And the comparative biochemistry of cilia is also almost nonexistent. Nothing is known about variation in cilia design across different groups of organisms, although it undoubtedly exists. Nobody has attempted to relate this variation to differences in function or to reveal hints of the proto-cilium.
Similar problems bedevil many attempts to uncover biochemical evolution.
But there is a bigger problem. Most biochemists have only a meagre understanding of, or interest in, evolution. As Behe points out, for the thousand-plus scholarly articles on the biochemistry of cilia, he could find only a handful that seriously addressed evolution. This indifference is universal. Pick up any biochemistry textbook, and you will find perhaps two or three references to evolution.