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Claims about evolution of flagella
Claim: "[T]he proteins in the motor are older than those in the pump"
Explore Evolution again misleads readers. This issue is currently debated within the community of flagellum researchers (reviewed briefly in Pallen & Matzke 2006), and about half the papers go each way. The definitive study has not yet been done. Even if it turns out that the type 3 secretion system is derived from the flagellum, it will still prove that (a) Behe was wrong that reduced subsets of "irreducibly complex" systems "are by definition not functional", and (b) that a subset of flagellum parts has a plausible function different from motility. Furthermore, only the ID advocates think that the type 3 secretion system is the only known relative of the flagellum: the actual scientific community, in contrast, knows of several others.
Claim: The pump only accounts for 10 of the 30 proteins
This is yet another claim copied straight from the ID literature. Here are several previous examples:
It follows that the TTSS does not explain the evolution of the flagellum (despite the handwaving of Aizawa 2001). Nor, for that matter, does the bacterial flagellum explain in any meaningful sense the evolution of the TTSS. The TTSS is after all much simpler than the flagellum. The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.
With the bacterial flagellum, you're talking about a machine that's got 40 structural parts. Yes, we find 10 of them are involved in another molecular machine, but the other 30 are unique! So where are you going to borrow them from? Eventually you're going to have to account for the function of every single part as originally having some other purpose. So you can only follow that argument so far until you run into the problem of you're borrowing parts from nothing.
Miller's scenario faces at least key three difficulties. First, the other thirty or so proteins in the flagellar motor are unique to it and are not found in any other living system. From where, then, were these protein parts co-opted?
Additionally, the other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system. From whence, then, were these protein parts co-opted?
With regards to the flagellum at least 2/3 of the parts are not known to be shared with any other structure therefore might not be even a sub-part of another system at all.
In the Unlocking video, Scott Minnich stands in his microbiology lab and quietly assesses the Darwinian TTSS scenario. Yes, he says, it is remotely possible that the TTSS injector came first, and he affirms that its ten proteins do seem to parallel or match the core proteins of the flagellum. But that's where you bump into a huge problem. Where did the cell find the other thirty or so proteins to build incrementally from the TTSS all the way to a rotary-motor flagellum? You come to the point where you are borrowing from nothing, and the plausibility of the scenario fades quickly.
The ID proponents are all telling the exact same story as Explore Evolution. (The difference between 20 or 30 unique proteins depends on whether or not regulatory proteins are included.) And they seem terribly confident that they know what they are talking about. After all, the flagellum is the "icon of ID," the ID movement's flagship example of something that could not have evolved, and must have been intelligently designed instead. Explore Evolution repeats the talking points almost word-for-word, with the only difference being that the "intelligent design" conclusion is tactically left out. Scott Minnich seems to be the original authority for the claim, and he is a published researcher on type 3 secretion systems. Furthermore, Minnich made the same claim in his expert report for the Kitzmiller case. As a named coauthor of Explore Evolution, he presumably checked or edited this section of the textbook, if he made any substantial contribution to the book at all.
Apart from dishonestly pretending that Explore Evolution is not making an ID argument here, the only problem with the "20+ proteins are unique to the flagellum, where did they come from?" argument is that it is wildly, hopelessly, false, and is obviously so to anyone familiar with the actual scientific literature and data on the subject. Pallen & Matzke (2006) reviewed the evidence on this specific point and published a table listing all 42 "standard" flagellar proteins (structural and regulatory) in the most-studied lab strains of E. coli and Salmonella typhimurium.
Here is a summary of the table published in Pallen & Matzke (2006) (the table is freely available online here):