February, 2008: Dan Jones reviews the evidence in New Scientist:
Variants of at least seven T3SS proteins are also found in the flagellum, within a subsystem called the protein export system. This sits within the basal body and funnels replacement flagellin subunits to the filament, using a mechanism remarkably similar to the T3SS. In fact, the two systems are so similar that the flagellar protein export system is now considered to be a subclass of the T3SS (Trends in Microbiology, vol 14, p 157).Such similarities, or “homologies”, are strong evidence that the two systems evolved from a common ancestor – analogous to the way that the arrangement of bones in the limbs of horses, bats and whales reveal their common ancestry despite their very different outward appearance and function. Similar homologies can be seen in the DNA sequences of genes, and in the amino acid sequences and 3D structures of proteins – all are clear evidence of shared descent.
The evolutionary events linking flagella and T3SSs are not clear, but the homology between them is a devastating blow to the claim of irreducible complexity. This requires that a partial flagellum should be of no use whatsoever – but clearly it is. “The T3SS is a useful model of how a ‘partial flagellum’ could function in protein export,” says Nicholas Matzke of the University of California, Berkeley, a prominent defender of evolution and author of a number of academic articles on the flagellum. Miller adds: “The notion that these proteins can only be used in flagella simply falls apart.”