Cilia might be related to the bacterial flagellum, a similar whip-like propulsion devise. 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. 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. Behe is good at exposing the paucity of evolutionary thought in the field of biochemistry. So what we have here is just the latest, and no doubt not the last, attempt to put God back into nature.