There’s an interesting exchange tucked away in some comments at the Pandasthumb on what it would take to provide an evolutionary explanation of the bacterial flagellum:
http://www.pandasthumb.org/pt-archives/001126.html#c34823
[Timothy Scriven writes:]
ID so far hasn’t yet completely jumped the shark, but when the first reasonably detailed model of the evolution of the fallgela (major step by major step) comes out they’ll not only jump the shark but get eaten by it as well. Judging by the progress which has already been made on the problem I’d say their about to leap any moment now. I predict that after the evolution of the fallgela is mapped it will be onto the next organism, then the next then the next and that I think ( or rather hope) may be the end of even public support for the movement.
By the way, I think the first researcher to propose a detailed, falsifiable model of the evolution of the fallgela should receive a nobel prize, anyone else agree?
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http://www.pandasthumb.org/pt-archives/001126.html#c34840
[Nick Matzke responds:]
As much as I would like to agree, given that I wrote this, devising a reasonable model on paper is just a matter of doing the necessary literature research  i.e., actually looking up all of homologies, something no IDist has ever done  and synthesizing it in the context of standard modern evolutionary theory. It’s not a particularly difficult thing to do, it’s just that the number of people who know are sufficiently familiar with both flagellum biochemistry and evolutionary biology is rather small.
Plus, there isn’t a Nobel prize for evolution. There isn’t even a Nobel prize for biology, because old Mr. Nobel didn’t think to endow one.
(And it’s flagellum, singular, flagella, plural. From the Latin word for “whipâ€Â, I think. You get points for creativity with “fallgelaâ€Â, though.)
The point I wish to focus on is Matzke’s claim that the key to explaining the flagellum in evolutionary terms is a literature search of homologies. To see the absurdity of this claim, consider that virtually all human designs these days are put together from components that have appeared in other designed systems (components that are therefore “homologous” to components in preexisting systems). And yet what engineer would think that the problem of solving the design of X is resolved by showing how the components of X are homologous to components making up preexisting systems Y, Z, and W. The problem is not a matter of identifying similar parts, but of coordinating them into n0vel, functional wholes. No literature search of preexisting components will resolve this problem.
Note that Matzke’s additional claim that once the homologies are identified they need to be synthesized “in the context of standard modern evolutionary theory” adds no further insight since this amounts to evolutionary story-telling. The bacterial flagellum is an engineered system and even with all the right components in hand, there is a concept here ( “bidirectional motor-driven propellor”) that needs to be realized. No theory has the specificity to realize this concept. I made this point in my response (go here) to an earlier article by Matzke on the bacterial flagellum.