Evolutionists propose that irreducibly complex systems can arise by
co-option of parts from other existing systems. But approximately
thirty of the proteins needed for the bacterial flagellum are unique to
it; closely similar proteins are not found in other living systems.
Thus, there is apparently no place they could have been co-opted from.
The claim is simply false. Of the twenty proteins in the archetypal
Salmonella bacterial flagellum which appear to be required in all
bacterial flagella, only two have no known homologies, that is, are
"unique". It is at least plausible that homologies for those will be
discovered later. At least nine flagellar proteins are homologous to
proteins of the Type-III secretion system (T3SS), suggesting the two
evolved from a common ancestor. Regardless, the existence of many
homologous proteins shows that the parts of the flagellum can
function for purposes other than motility (Pallen and Matzke 2006).
There is no such thing as "the" bacterial flagellum. There are
thousands, perhaps millions, of varieties among different bacteria,
not to mention other very different kinds of flagella on
archaebacteria and eukaryotes. The Salmonella flagellum, for
example, has 22 additional proteins which some other bacteria lack in
their flagella. Do design proponents suggest that each was a
separate creation, or did they evolve? (Pallen and Matzke 2006).
Pallen, Mark J. and Nicholas J. Matzke. 2006. From The Origin of
Species to the origin of bacterial flagella.
Nature Reviews Microbiology, Sept. 5 (epub. ahead of print).