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  Topic: Evolution of prokaryote flagella, Links to discussions, webpages, refs< Next Oldest | Next Newest >  
niiicholas



Posts: 319
Joined: May 2002

(Permalink) Posted: May 08 2003,04:58   

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Nic,

With respect to adhesion function, none of the papers show anything different from what I already discussed. In each paper, they talk about the export machine of bacterial flagellum, or pilus.


I don't understand what you are saying here at all.  Here is the point: non-motile cell extensions have function even though they are non-motile.  Some flagella still perform this function in addition to having their motility function.  This function remains even if they have no motors.

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In both cases, we still have the "sea of nonfunctionality" that Dembski's calculation refers to. This is true, even if there are alternative functions all the way to the flagellum


This must set another record for self-contradiction!  If there are alternative functions "all the way to the flagellum" then the "sea of nonfunctionality" either doesn't exist or is crossed by a land bridge.

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, each alternative function obviously requires several parts to function


So?  They function independently from being flagella, that is the point.  Dembski's calculation, like basically all antievolutionary calculations, assume that everything had to come together at once, in one step.  This is how ridiculously low probabilities are reached in calculations.

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so you doing nothing more then what H. Allen Orr objected to:


This is the one quote that you have saying that cooption is unlikely, and it's not even clear what is meant as he's never expanded on these words, discussed the literature on cooption in detail, etc.  Orr himself refers to the change-of-function between swim bladders and lungs in that very review, which sounds to me rather like "half your car's transmission will suddenly help out in the airbag department."  And even if Orr meant exactly what you think he meant, I can cite dozens of other scientists of equal authority who think that cooption is indeed common, because they have written numerous articles and amassed a lot of evidence in favor of it.  For example:

The Origin of "Information" via natural causes

[url=]The Origin of "Information" via natural causes -- citations in the literature[/url]

Co-option/change of function -- Citations of this in the literature

Origins of morphological novelty

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For example, you have the problem of the 6 part export machine. There is no evidence that any subset of this export machine carries out alternative function. And as I stated with the pili, With that you continue to introduce more unselectable steps, the irreducible complexity of the folding of P Pilus, not to mention the sophisticated mechanisms, donor strand exchange and donor strand complementation. The pilus itself is made up of 5 parts, PapK PapA,PapE,PapK, and PapG.


There are lots of kinds of pili based on lots of kinds of transport systems, you keep bringing up  one specialized system (based on a Type I transporter) over and over like it was some kind of talisman.  Type III virulence systems (called Type III pili in some articles, like this the Cornelius and Van Gijsegem paper mentioned earlier).  

It's not very clear, but by repeated mention of the P pilus I assume that you are trying to argue that a pili extension, excluding the export system at the base, would *have* to be made of at least 5 parts in order to function.  But there is no "logic of pili" that requires this -- while a rotary motor must, logically, have at least a stator, rotor, and filament, a simple pili could really be made of one repeated subunit.  Figure 1B of Blocker et al. 2003 (Pubmed) depicts a generalized T3SS where the extracellular extension (pili) is made up of MxiH/PrgI (homologs in 2 different organisms) for the entire stalk and "CaoX?" at the tip, perhaps a cap and/or adhesion protein at the tip (flagellar cap proteins are known to have adhesive functions in some bacteria, if you were interested).  The article says that it is not even clear that T3SS require a cap protein as none has yet been detected.  The online supporing text says that only some T3SS bother to add an additional filament to the top of the needle.

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Furthermore, the pilus doesn't seem to be able to secrete proteins, and the biggest difference between flagella and pili is that flagella are built from the top to the bottom, whereas pili are built from the bottom to the top.


But of course Type III pili secrete just fine out the top.  And archaeal flagella are built from the bottom like some pili.  So there is no problem for pili to secret or be built at the top and no problem for flagella to be built from the base.  I recall pointing this out before in this very thread, but you bring up the argument again as if you didn't have to address the counterargument.

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Now you keep saying things like "I wonder why Dembski didn't take that into account". Now, can you show, in the peer reviewed literature, a paper that shows how natural selection and random mutation, taking all those imaginary homologs and multi-part machines into account with alternative functions, a detailed pathway leading up to the flagellum that Dembski could have worked with. What do we find in the peer reviewed literature?


Dembski hasn't even dealt with the implications of the "imaginary" homologs published in Kojima and Blair, with direct commentary on evolutionary implications, in Biochemistry in 2001.  But Dembski, and you, are arguing that his calculation "sweeps the field clear" of natural hypotheses and that therefore design is the logical conclusion.  This is far more ambitious than simply pointing out that the literature does not yet contain the evolutionary pathway for every molecular system whose mere structure and function have yet to be fully understood.

Even where there is extensive peer-reviewed literature on the evolution of an IC system, e.g. the entire field of evolutionary immunology, neither you nor Dembski has shown any respect for it, despite your respective wild assertions about there being no literature on the evolution of IC systems.

And, no one ever published Dembski's straw-man "the flagellum assembled all at once" model, and yet you and Dembski are treating it as if it's the only conceivable route for natural processes to take.

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We find the evidence that type III systems evolved from the flagellum, and there are good reasons for this. Even taking all these similarities into account, it is quite easy to see how the "sea of nonfunctinality" between each mutli-part machine (especially when proposing a sticky-out thing when in fact it would be useless in a "brownian storm", again the question of minimal function where the actual components don't even matter, it's what those components can do),


Well, I already told you about the diffusion coefficient difference between dead bacteria and bacteria stuck on "tumble" with completely undirected motility, but I guess you won't believe me unless I give you the numbers.  From Berg, 1993, Random Walks in Biology, p. 93:

Diffusion coefficient of a bacterium with flagellum stuck on "run" (rotation is only due to Brownian motion): 2 x 10^-5 cm2/sec

Diffusion coefficient of a normal E.coli bacterium with flagellum doing "run" and "tumble" at normal proportions: 4 x 10^-6 cm2/sec (however, the normal bacterium can bias runs in the right direction to be longer, leading to directional drift, i.e. chemotaxis).

Diffusion coefficient of a bacterium with flagellum stuck on "tumble" is described as "smaller" and that of a dead or paralyzed bacterium it is described as "much smaller".  The number calculated for the dead/paralyzed bacterium is 2 x 10^-9 cm2/sec, so a "stuck on tumble" bacterium is above this but below the number for the non-chemotactic "stuck on run" bacterium.

Even undirected motility, even in a non-smooth-run fashion, appears to improved dispersal capability quite a bit.

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[...] most likely none of these alternative machines will confer a selective advantage until we arrive at the fully functional flagellum. Pure chance events come in full force when you attempt to fortitously have multi-part machines interacting with multi-part machines. It's nothing but a tornado in a junk yard.


No, Dembski's calculation is like assembling a plane by putting a tornado in a junkyard.  But no one advocates that model.  What evolution proposes is (vaguely) more like a "tornado" coming through a junkyard and making various modifications to parts, sometimes linking two systems in some way.  True, most of these go nowhere, but the occasional pairing that is successful can be selected and therefore will persist for another bunch of rounds of modifications and selection, which may eventually successfully pair one double system with another system of one or more parts, etc.  The analogy still sucks but this gives some idea of how many important factors Dembski's random-assembly-all-at-once calculation leaves out.

  
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