Towards a Hypothesis of Molecular Design

Does an evolutionary model for the origin of the ur-flagellum predict that all the proteins diverged from their homologous counterparts at about the same time or that their divergence times are significantly different, depending on the amount of modification that would be needed to incorporate them into the flagellum? In my humble opinion, the answer to this question is obvious: there is no prediction here from an evolutionary perspective. The evolutionary model could only explain these observations, but it does not predict them. On the other hand, the molecular design hypothesis logically leads to the specific predictions described in the OP.

That is correct. The broad thesis that life was somehow designed doesn't predict the specific cases described in the OP. However, the molecular design hypothesis does make those predictions, and while you can formulate an evolutionary model that makes those same predictions, that evolutionary model runs into difficulties, as detailed in my response to bluegenes (message 12).