A paper that just came out in Advance Online Publication section of
Nature,
Murphy et al. 2006, reports the first
in situ structure of a flagellar motor in a spirochete,
Treponema primitia. Such things have been done before, for the bacterial lab rat
Salmonella, but spirochetes are a whole different bacterial phylum, and they have weird flagella. First, instead of the flagella sticking outside of the cell and doing what any self-respecting flagellum would do, the flagella of spirochetes rotate entirely within the periplasm (the space between the inner and outer membrane, which includes the cell wall). You might think that there would be no room for the flagellum to rotate in such a restricted space, or that it would tear apart the membranes -- but intuitions are very unreliable at the sub-microscopic scale. The intracellular rotation of the flagella evidently cause the whole cell to gyrate, moving it through liquid in a corkscrew-like fashion.
But that is not the only weird thing about spirochete flagella. Normal flagella need a P-ring to span the cell wall (made of peptidoglycan) and an L-ring to span the outer membrane. Spirochetes obviously don't need the L-ring, since the flagella don't cross the outer membrane to leave the cell, but the genomes of some spirochetes indicate that they still have the L-ring protein for some reason which remains mysterious. What is surprising, however, is that apparently
Treponema has no gene that identifiably corresponds to the standard P-ring protein, even though their flagella do cross the cell wall. There is a P-ring like structure detected in these images, but what protein codes for it is unknown, and it is also unknown whether or not the structure is homologous to standard P-rings (I believe some spirochetes do have detectable P-ring homologs, if I recall correctly).
Finally, although spirochete flagellar proteins are mostly homologous to "standard" flagellar proteins, the structure published today shows that the rotor and stator structure, even though made with homologous proteins, are significantly modified. Compared to the
Salmonella motor, the
Treponema motor is wider and more robust (perhaps as a form of "down-shifting", to increase power), and sort of squashed down into the lower membrane, perhaps to help the hook complex (the base of the filament) fit within the periplasm:
Portion of Figure 3 from Murphy et al. (2006). Top row: Electron microscope "images" obtained by averaging many individual images. Bottom row: corresponding models of the flagellar structures. The scale is the same throughout, so the relative size differences are real. Bottom Left: model of the Treponema (spirochete) flagellum. Bottom Right: Model of the "standard" Salmonella flagellum. Corresponding structures, presumably homologous (except perhaps the P-ring) share the same colors. Abbreviations: OM = outer membrane, IM = inner membrane, PG = peptidoglycan (cell wall)
The authors say that there is some chance that bowl-shape vs. disk shape is an artifact of the fixation procedure, but regardless, the
Treponema flagellum is further evidence that the idea that there is only one kind of flagellum, implicitly common with ID advocates, is totally bogus.
But, the really cool thing about this paper is the free supplementary video, which you can
download here. Using
cryo-electron tomography, they were able to reconstruct a three-dimensional image of the spirochete and its periplasmic flagella. This is a great way to get an idea in your own heads of where flagella fit into the overall structure of spirochete cells:
A snapshot from the video. The red and white filaments are the flagella.
The video is about 78 MB, and took several minutes for me to download, so use Right-Click, Save as, to download to your desktop before you try to play it.
Reference
Gavin E. Murphy, Jared R. Leadbetter and Grant J. Jensen (2006). "
In situ structure of the complete Treponema primitia flagellar motor."
Nature advance online publication 2 August 2006.
33 Comments
Matt · 4 August 2006
How very like a member of the Darwinist media elite to release this news on a Friday afternoon.
mike syvanen · 5 August 2006
matzke wrote"
"(the space between the inner and outer membrane, which includes the cell wall)."
The cell wall is NOT in the outermembrane. The cell wall is separated from the outermembrane by the periplasm. It probably lies just outside of the inner membrane and is considered integrated with it.
apollo230 · 5 August 2006
There is so much talk about flagella in this ID/Darwinist debate that one can almost say they "propel" the affair!!
Best regards,
apollo230
Bruce Thompson GQ · 5 August 2006
k.e. · 5 August 2006
Brian · 5 August 2006
When did Behe fall out of grace with the ID community? Did I miss something?
Brian
Nick (Matzke) · 5 August 2006
k.e. · 5 August 2006
Bruce Thompsn GQ · 5 August 2006
Steviepinhead · 5 August 2006
To suggest that the flagella-powered ID vehicle has the capability to taxi around is a gross exaggeration--more accurately, still squatting in the lee of a dune at Kitty Hawk, holding a shredded kite in one hand (flag-tail optional), and timidly sticking a finger into the wind with the other.
Bruce Thompson GQ · 5 August 2006
mike syvanen · 5 August 2006
Matzke replied:
"Which is what I said --- the sentence says that the cell wall resides in the space between the membranes."
Hmm so you did. I read it as 'outermembrane, which includes the cell wall'.
Brings to mind Eisenhower's advice to his staff: any written order that can be misread, will be misread.
Steviepinhead · 5 August 2006
Heh. I grew up in the Deep South too, but I still can't quite get "flown" and "around" to rhyme, though I'll admit there are southerners whose vowels are thicker'n molasses.
Now if we just said that the IDists flounder around, we'd be getting closer to a rhyme recognizable in all regions.
Though they still wouldn't be getting anywhere.
apollo230 · 5 August 2006
I have said elsewhere, and will say it again, that ID's abiding vindication will arrive when the reliable, replicable designer detection takes place, and not before. When one posits an intelligence that has been busy for 4 BILLION years, design inferences (however persuasive) are not enough to proof one's case. Only a good, hard handshake with this ancient carpenter will do!
Bona-fide, replicable detection of the designer would give ID an unshakable empirical basis. If this were achieved, there would no more flailing around with flagella. Rather, ID would be riding a Saturn 5!
I hope this statement acknowledging the need for empirical proof (designer detection) is welcomed by all (and to all a good night).
Best regards,
apollo230
P.s. If anyone is inclined to post a lengthy response to this deposition, please kindly note that I may not be available for a long discussion.
steve s · 5 August 2006
apollo, I think it's concievable there could be evidence for intelligent design:
http://www.pandasthumb.org/archives/2006/03/no_wonder_peopl.html#comment-83275
The code-rewrite bunny would be pretty shocking. A hell of a lot better than some fake math by Dembski or Behe.
Michael Suttkus, II · 5 August 2006
The code-rewritten bunny would kill common descent (though, perhaps, only for the bunny), but I'm not seeing how it would particularly suggest intelligent design.
Bruce Thompson GQ · 5 August 2006
Excellent video. The Treponema primita flagella does not traverse the outer membrane and the L ring is missing from the structure, figure 3 of the Murphy paper. This is just one more piece of evidence that the flagella is not an IC structure. Loss of the L ring does not inhibit motility only relocates the flagella to the periplasmic space.
Both FlgI and FlgH (P and L ring) genes are missing in Treponema denticola a related spirokete, so some other unidentified protein has replaced FlgI in Treponema creating the P collar, a potentially homologous structure. Nifty
Delta Pi Gamma (Scientia et Fermentum)
steve s · 6 August 2006
Shaffer · 6 August 2006
Michael Suttkus, II · 6 August 2006
I really don't know. Seeing the rabbit would clearly speak to "something funny is going on", but I'm not sure it would point to any specific funny. I actually cannot think of any other explanation for it than intelligent design, but that's not support.
The example I always use for this is diseases in the middle ages. There were three major theories of disease: Bad smells, imbalanced humors, and supernatural causes. Suppose we disprove two of them, say extensive studies show that sinners get sick at the same rate as non-sinners (disproving the supernatural-based worldview of the MA people), and that people exposed to bad smells don't get sick more often than normal. If I can't think of any other explanation besides imbalanced humors, does that mean imbalanced humor theory is true?
Not in the slightest, of course. From our perspective we see the foolishness because we have thought of another. That's why negative arguments of that sort don't work.
What would speak to ID? Something that can only be accomplished by intelligence, not natural processes... well, you get stuck again having to define EVERYTHING natural processes can accomplish on their own. It's a losing game.
Even replacing "can only" with "would be typically" only helps a little, because the IDer is undefined. Without a specific list of attributes, we can't tell what the designer typically does, so cannot test for those traits in encountered phenomena. Humans alone designed everything from Michael Angelo's David to Jackson Polluck's drizzling paint on a canvas randomly. I defy anyone to come up with a particular trait typical of human design. We make artificial rocks designed to look just like real rocks for pete's sake!
Forensics is probably a good place to start, though. They look into intelligent design all the time, but from the "is typical of" perspective, not "can only be". Of course, they have it easy. Their designers are defined and the situations they're looking in well understood and a bit rigid. ID "theory" can claim none of those things.
SPAR · 7 August 2006
One issue IDists donot touch at all is the technology underlying design. For every man made design one can not only decipher the underlying plan but also elucidate the way how it was actually constructed and what tools have been used for this purpose. Otherwise product piracy would not work. Thus, I am eagerly awaiting ID proponents to publish something onHOW the presumptive designer has built life. If genomes where designed there must be some hint other then IC within the DNA. I am quite willing to learn something about those techniques because they should make my life as a molecular biologist much easier. E.g., we really have problems with the error rate during chemical DNA synthesis, especioally when one needs oligos longer 100 nt.
However, as I am afraid that the outcome of such research is something like "let there be DNA and there was DNA" IDists should stop messing arround and say that they only have one relevant publication. If it is god's own word though, the question remains who could have done the proof reading. Thus, it may not be accepted as a scientic publication by mainstream biologists.
Frank J · 7 August 2006
ofro · 7 August 2006
Bruce Thompsn said:
"If flagella's were propellers ID may have flown ..."
Cute pun, perhaps, but let's be scientifically a bit more precise. In my technical understanding, propellers are used for propulsion in both air and water. And last time I checked, there are bacteria that a flagellum for propulsion, so a flagella are propellers. So by your definition ID may not fly but should be moving around quite nicely. On second thought, maybe you are correct....
besides: flagellum (singular) flagella (plural)
Bruce Thompson GQ · 7 August 2006
ofro · 7 August 2006
OK, you sunk me, and I apologize for being a spoiler (after all, seven years of latin do leave a scar).
The point I was trying to make is that while it is fun to be derisive (I am sure I did that in my "young years"), the only way to sink intelligently designed submarines in the long run is with continuous and well-presented arguments. After all, these posts are not just read by your buddies but also (just maybe?) by the inquiring public.
Bruce Thompson GQ · 7 August 2006
Doc Bill · 7 August 2006
The "intelligently designed" subversible craft appears to be pervious to the torpedoes of argument.
One might say that the ID'ers all live in a Jell-O Submarine.
fnxtr · 7 August 2006
Bruce Thompson GQ · 7 August 2006
Nick, do we get the rest of the story? What about the secretory system in Treponemia? I looked for references and found only this, so they must have something. A scan of the Treponema denticola genome and the COG motility proteins did not list a FlgH or YscC (the type III secretion protein) so what do these spirochetes use to span the outer membrane?
Delta Pi Gamma (Scientia et Fermentum)
Nick ((Matzke)) · 7 August 2006
I am not aware of a nonflagellar T3SS in spirochetes, it would be A Big Deal if such were discovered. That article is interesting, the abstract hints at homologs to something in the T3SS Spa system, I will look it up. Note that the outer membrane ring in NF-T3SS is a secretin and homologous to secretins in many other systems, e.g. Type II secretion -- so merely having that homolog wouldn't prove much.
Bruce Thompson GQ · 7 August 2006
And I was thinking a blast search of the Treponema denticola genome with a Flg- consensus sequence, then sorting by those with membrane spanning regions, and then crossing checking against the smaller genome of T. pallidum. Then looking for relationships with other proteins, but it's to hot outside. Let me know what you find.
Delta Pi Gamma (Scientia et Fermentum)
Wesley R. Elsberry · 9 August 2006
Has Lynn Margulis altered any of her claims concerning spirochetes in light of this intracellular flagellar apparatus?
Michael Soteria · 15 October 2006
RE: Comment #117309
"What do you think possible evidence for ID could be, hypothetically speaking?"
I'm going to assume you consider yourself intelligent. I know... making assumptions can be dangerous. :) Could you make a motor of the same complexity, say even 100 times larger, that would run in that kind of environment, at the same efficiency? Is there any info on the efficiency of this motor??? I've read some are in the 90's%.
I've taken a simple hammer, a piece of wood through a piece of iron, to a class of students and asked them if it could have just "happened" in nature without a designer(which of course precludes intelligence). They readily and correctly answered 'no'. I asked the same question giving greater amounts of time for it to happen. Same answer. Yet here we have something with an incredibly greater amount of complexity, in need of an extremely specific environment, just in the motor, not including the rest of the cell which could equal the complexity of city blocks of factories, yet 'educated' men suggest it just happened by chance???