Nick Matzke at Panda’s Thumb, what evidence is there that the type III secretion system appeared in nature before the flagellum? If the flagellum coopted the ttss then the ttss must predate the flagellum. The ttss mediates elaborate interactions with plant and animal hosts of the bacteria. The flagellum on the other hand is for locomotion, not parasitic or pathogenic relationships with more complex cells. The flagellum is useful absent more complex organisms in the environment while the ttss is not. It seems to me quite likely that the flagellum appeared in nature before the ttss. Probably billions of years before as the following supports:
J Mol Microbiol Biotechnol. 2000 Apr;2(2):125-44.
Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH Jr.
Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA.
Multicomponent Type III protein secretion systems transfer gram-negative bacterial virulence factors directly from the bacterial cytoplasm to the cytoplasm of a host eukaryotic cell in a process that may involve a single energy-coupled step. Extensive evidence supports the conclusion that the genetic apparatuses that encode these systems have been acquired independently by different gram-negative bacteria, presumably by lateral transfer. In this paper we conduct phylogenetic analyses of currently sequenced constituents of these systems and their homologues. The results reveal the relative relatedness of these systems and show that they evolved with little or no exchange of constituents between systems. This fact suggests that horizontal transmission of the genes encoding these systems always occurred as a unit without the formation of hybrid gene clusters. Moreover, homologous flagellar proteins show phylogenetic clustering that suggests that the flagellar systems and Type III protein secretory systems diverged from each other following very early duplication of a gene cluster sharing many (but not all) genes. Phylogenies of most or all of the flagellar proteins follow those of the source organisms with little or no lateral gene transfer suggesting that homologous flagellar proteins are true orthologues. We suggest that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems.
Update: I found this paper by Scott Minnich and Stephen Meyer to be extremely helpful in understanding the relationship of the TTSS and the flagellum.