Nick Matzke posted Entry 2500 on August 4, 2006 07:49 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2495

Treponema flagellum baseA 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:

Left, Treponema flagellum; Right, Salmonella flagellum
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:

Treponema_flag2.png
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.

Commenters are responsible for the content of comments. The opinions expressed in articles, linked materials, and comments are not necessarily those of PandasThumb.org. See our full disclaimer.

Comment #117035

Posted by Matt on August 4, 2006 11:37 PM (e)

How very like a member of the Darwinist media elite to release this news on a Friday afternoon.

Comment #117043

Posted by mike syvanen on August 5, 2006 1:23 AM (e)

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.

Comment #117108

Posted by apollo230 on August 5, 2006 7:47 AM (e)

There is so much talk about flagella in this ID/Darwinist debate that one can almost say they “propel” the affair!!

Best regards,
apollo230

Comment #117131

Posted by Bruce Thompson GQ on August 5, 2006 9:56 AM (e)

There is so much talk about flagella in this ID/Darwinist debate that one can almost say they “propel” the affair!!

Watching the gyrations of ID proponents respond to scientific data makes one wonder if this new dance craze will be replaced by something more retro or something akin to the western two step. Retro or two step, I have no rhythm.

Delta Pi Gamma (Scientia et Fermentum)

Comment #117133

Posted by k.e. on August 5, 2006 10:17 AM (e)

Apollo said:
There is so much talk about flagella in this ID/Darwinist debate that one can almost say they “propel” the affair!!

Well it certainly propelled Behe to be flagellated for shoddy science and was one of the main drivers of his fall from ID star to notorious infamy in very short order.

Comment #117135

Posted by Brian on August 5, 2006 10:52 AM (e)

When did Behe fall out of grace with the ID community? Did I miss something?

Brian

Comment #117136

Posted by Nick (Matzke) on August 5, 2006 11:08 AM (e)

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.

Which is what I said – the sentence says that the cell wall resides in the space between the membranes.

Comment #117138

Posted by k.e. on August 5, 2006 11:19 AM (e)

When did Behe fall out of grace with the ID community? Did I miss something?

Brian

Well strangely enough he proved the second of Barnum’s Axioms

1. There is a sucker born every minute.
2. There is no such thing as bad publicity.

Ah…I meant that the general public or school board lawyers, if they followed his testimony, would clearly see he was in cloud cuckoo land.

Scientists of course never took him seriously, the DI? …well see number 2 above.

Comment #117141

Posted by Bruce Thompsn GQ on August 5, 2006 11:44 AM (e)

There is so much talk about flagella in this ID/Darwinist debate that one can almost say they “propel” the affair!!

If flagella’s were propellers ID may have flown, but as it is ID will never get off the ground, just taxi around.

Delta Pi Gamma (Scientia et Fermentum)

Comment #117143

Posted by Steviepinhead on August 5, 2006 12:01 PM (e)

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.

Comment #117263

Posted by Bruce Thompson GQ on August 5, 2006 6:06 PM (e)

Steviepinhead argues:

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.

Mine rhymes, if your from the south, and relates to propulsion. Although your metaphor has merit I would work in global warming since the generation of hot air is a critical ID component.

Delta Pi Gamma (Scientia et Fermentum)

Comment #117264

Posted by mike syvanen on August 5, 2006 6:13 PM (e)

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.

Comment #117266

Posted by Steviepinhead on August 5, 2006 7:09 PM (e)

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.

Comment #117292

Posted by apollo230 on August 5, 2006 8:38 PM (e)

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.

Comment #117293

Posted by steve s on August 5, 2006 9:03 PM (e)

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.

Comment #117299

Posted by Michael Suttkus, II on August 5, 2006 10:14 PM (e)

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.

Comment #117307

Posted by Bruce Thompson GQ on August 5, 2006 11:43 PM (e)

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)

Comment #117309

Posted by steve s on August 6, 2006 12:06 AM (e)

Comment #117299

Posted by Michael Suttkus, II on August 5, 2006 10:14 PM (e) | kill

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.

You don’t think so? I wonder if other people agree with you. What do you think possible evidence for ID could be, hypothetically speaking?

Comment #117310

Posted by Shaffer on August 6, 2006 12:08 AM (e)

apollo230 wrote:

Only a good, hard handshake with this ancient carpenter will do!

…at which point God disappears in a poof of logic?

Comment #117333

Posted by Michael Suttkus, II on August 6, 2006 2:34 AM (e)

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.

Comment #117565

Posted by SPAR on August 7, 2006 12:45 AM (e)

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 on HOW 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.

Comment #117602

Posted by Frank J on August 7, 2006 5:14 AM (e)

apollo230 wrote:

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.

Then I’ll make it short and sweet.

The public is already “preadapted” to a double standard that makes the IDers’ job infinitely easier. That is, that science must fill in every last detail before suspicions begin to wane, while any pseudoscience gets a free pass with just a few feel-good sound bites, however misleading.

Comment #117616

Posted by ofro on August 7, 2006 7:24 AM (e)

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)

Comment #117652

Posted by Bruce Thompson GQ on August 7, 2006 11:31 AM (e)

Ofro rightly corrects Bruce:

besides: flagellum (singular) flagella (plural)

You take all the fun out of everything.

In my technical understanding, propellers are used for propulsion in both air and water.

If ID wants to motor around underwater, fine, I guess that too is can be an apt description.

It’s periscope rising above the waves of scientific discourse for a look see, then submerging into the calm waters of its own perception of reality. Believing aspects of itself unseen by those on the surface it rises, but the bulk of the craft remains underwater. But science learned long ago to detect submerged craft and the technology has only improved much to the chagrin of ID.

While the mobility of submerged craft has some tactical advantages in deployment it’s utility is rapidly diminishing with modern technology. Antiquated forms of submerged craft are more frequently seen but it is becoming limited to countries whose scientific abilities are restricted.

Delta Pi Gamma (Scientia et Fermentum)

Comment #117658

Posted by ofro on August 7, 2006 12:21 PM (e)

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.

Comment #117662

Posted by Bruce Thompson GQ on August 7, 2006 12:37 PM (e)

Ofro writes:

[T]he only way to sink intelligently designed submarines in the long run is with continuous and well-presented arguments.

I await intelligently designed experiments and well presented data supporting the conclusions.

Delta Pi Gamma (Scientia et Fermentum)

Comment #117664

Posted by Doc Bill on August 7, 2006 1:01 PM (e)

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.

Comment #117702

Posted by fnxtr on August 7, 2006 3:40 PM (e)

SPAR:

If it is god’s own word though, the question remains who could have done the proof reading.

Not to mention the peer review.

Comment #117743

Posted by Bruce Thompson GQ on August 7, 2006 7:02 PM (e)

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)

Comment #117744

Posted by Nick ((Matzke)) on August 7, 2006 7:17 PM (e)

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.

Comment #117754

Posted by Bruce Thompson GQ on August 7, 2006 9:11 PM (e)

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)

Comment #118282

Posted by Wesley R. Elsberry on August 9, 2006 7:23 PM (e)

Has Lynn Margulis altered any of her claims concerning spirochetes in light of this intracellular flagellar apparatus?

Comment #139609

Posted by Michael Soteria on October 15, 2006 11:27 PM (e)

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???