niiicholas
Posts: 319
Joined: May 2002
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Another fun new post:
http://www.iscid.org/ubbcgi....#000061
Well, how fast the tides turn. Earlier in this thread, I had quoted Blocker et al.:
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The similarity of the beta subunit to FliI is something like 33% which is highly statistically significant, well above the ambiguous level:
[QUOTE]
How might these ATPases catalyze processive protein export? Spa47 (the Shigella FliI homolog) shares 33% amino acid identity with the beta-subunit of F1-ATPase. Proteins with >30% sequence identity have a high probability of sharing similar structures (69). Active F1-ATPase is a heterohexamer consisting of alternating alpha- and beta-subunits with a gamma-subunit inserted in a central channel where it rotates during the catalytic cycle (70). No equivalent of the alpha-subunit of F1-ATPases is found within flagellar or TTSS-encoding operons, so we assume that the type III export motor is a homohexamer. When modeled on the F1 structure, Spa47 fits at the inner membrane base of our NC structure (Fig. 3). It would contain a central channel aligned with the one found within the NC and of similar diameter to it, through which the proteins could be secreted (see Supporting Text).
Source: Blocker A, Komoriya K, Aizawa S. Proc Natl Acad Sci U S A 2003 Mar 18;100(6):3027-30. Type III secretion systems and bacterial flagella: Insights into their function from structural similarities. http://www.pnas.org/cgi/content/full/100/6/3027
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...the assumption of homology seems to be confirmed by the fact that the resulting protein complex fits well into their model of T3SS structure.
[/QUOTE]In this quote they:
- 1. Note the statistically significant sequence similarity between FliI/Spa47 and beta-F1-ATPase
- 2. Based on this evidence of homology, make a prediction about the structure of Spa47, and
- 3. Test it by placing the inferred structure into the base of the T3SS (width and configuration derived from electron microscopy etc.) and
- 4. Note that it just happened to fit, even though it was perfectly possible that the structures would have been the wrong size to fit. This strengthened the inference of homology.
This is what Nelson apparently disputed:
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Although the point of FliI homology seems moot upon careful reading of the paper you cite:
Source: Blocker A, Komoriya K, Aizawa S. Proc Natl Acad Sci U S A 2003 Mar 18;100(6):3027-30. Type III secretion systems and bacterial flagella: Insights into their function from structural similarities.
I read the paper last night, and it seems you are quite wrong about this. There is no evidence for a Spa47 protein complex, a fliI that is homologous to the b subunit of the F-ATP synthase. What is shown in green in fig 3 in the paper is only an imaginary model of Spa47 based on the F1 structure and that model can be successfully docked to the real NC outline where they would imagine it would have to sit to pump secrete proteins into the channel. The evidence here is pretty weak.
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...much like your Spa47 blunder...
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Everytime you show me a list of citations, the first few turn out to be a wild goose chase, as with the Spa47 paper.
[...]
Nic, there is no such thing as a protein complex of Spa47. It's ficticious, imaginary, like Santa Clause, the Easter Bunny, Pumpkin Head, the Matrix, X-men, spider-man, super-man, echo and the bunnymen(actually they exist). It's made up. Of course it fits, the whole thing is imaginary. How can it be a confirmed prediction? Once the post-doc finds it (or something like it) then the prediction that the model makes can be confirmed.
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The question is important, because if homology is conceded, then Nelson can no longer claim that there is no evidence for cooptable structures preceding the IC structures like the flagellum (e.g. in this thread), and he can no longer defend Dembski's calculation as actually taking into account the evidence for precursors:
| Quote | | As I already showed, Dembski's calculation is not like assembly a plane through a tornado in a junkyard. It is precisely attempting to find a forward-chaining of events that would have selection as the driving force all the way up mount improbable. |
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I raised (here) other examples of important facts that Dembski calculation didn't take into account, for example ExbBD-MotAB homologs, internal homologies of the axial proteins (rod-hook-linkers-filament), and analogies showing how various intermediate non-flagellum stages could still be functional.
Much of the thread was spent debating these various points (people can judge for themselves). In my opinion it is clear that Nelson's ID reasoning led him astray repeatedly:
- 1) For awhile he argued strenuously ("near certainty") for the external-proton-channel model of MotAB's motor mechanism. Evolutionary considerations and homology with ExbBD indicate an internal channel, and in fact all of the most recent papers appear to now endorse the internal channel model.
- 2) Nelson argued that "simple" pili had to have 5 parts in their extracellular filament, but the Hrp pilus apparently has only 1-2
- 3) Nelson argued that nonflagellar filaments had to be assembled from the base rather than the tip, but this was also disproven by the Hrp pilus and other Type III pili.
- 4) Nelson argued that the distribution of ExbBD was more restricted than the distribution of MotAB, indicating that ExbBD was derived, but the existence of ExbBD but not MotAB in cyanobacteria and archaea disproved that.
- 5) Was his assertion that the evidence was weak for the homohexamer model for FliI/Spa47. And yet, the Blocker et al. proposal, clearly based on common evolutionary reasoning, appears to have won out here also.
But now we have Nelson saying that he wasn't expressing doubts, and Mike Gene saying he wished he'd predicted the homohexamer model, and Nelson saying "what Mike Gene said"!
(even though MG's flagellum essays were clearly the source of Nelson's claims #1 and #2, perhaps #3, and IIRC MG tried out #4 on ARN a few months before Nelson tried it here!
I'm not sure we could have a clearer case of ID thinking consistently leading to the wrong answers on a variety of specific empirical questions.
[edits for format etc.]
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