|
Author
|
Topic: Flagellum rotation: Universal joint or not?
|
Jurie
Member
Member # 716
|
posted 12. June 2003 19:25
I just viewed the video entitled "Unlocking the Mystery of Life". It was enormously interesting and stunningly done.
There was one item which was confusing: The depiction of the rotation of the bacterial flagellum. In the video, the rotation was shown with the filament whipping around with the rotation, in orbital fashion.
I have seen a few animations of the flagellum in various other places, one of which showed the motion the same as in the video, while others showed it in a different way altogether: The filament is rotated along its logitudinal axis, like a cork-skrew.
The hook joint is frequently described as a universal joint, also as a U-joint in the movie itself, which has the property of translating a rotational motion around one axis to motion around a different axis not aligned with the first. A U-joint would do this for the flagellum, so the animation with the filament rotating like a cork-screw would be correct.
Furthermore, I can't see how the filament whipping around the axis of rotation would generate a pushing force, while the cork-screw motion case is easy to understand: the filament "screws" through the medium, pushing the bacterium along.
Which is correct?
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 12. June 2003 20:42
Maybe the bacterium was tumbling...
Seriously, I saw the video recently and there are a number of minor inaccuracies such as this. A biggee was the bit where the filament is unraveled into a chain of subunits and the subunits are...amino acids! In other words, they made the amino acids as big as the filament protein (FliC IIRC) should be (when actually FliC is made up of a whole bunch amino acids). Fairly severe scale mismatch there.
Also IIRC there were a number of times when the voiceover was talking about bacterial flagella while the video showed ciliated eukaryotes swimming about (IIRC).
These kinds of things could probably be chalked up to the dangers of handing biochemistry over to a video company and animation shop. (What is really interesting is the similarity between the animation in "Unlocking" and the animation of spaceships in "Babylon 5" -- I kept waiting for the Vorlons to fly in).
More severe problems are (1) all the usual ones surrounding IC and CSI, oft-discussed in this forum and (2) some of the strange DI claims that have gotten attached to the flagellum.
For example, that the flagellum is "water-cooled". This isn't just wrong, it's practically meaningless at the molecular level. The flagellum isn't a heat engine like a car (and if it were, then it wouldn't have the high motor efficiency claimed for it in other DI blurbs).
What's also weird is how numerous IDists are quoted along the lines of "an IC system has to come together all at once because all the parts are required for function" and yet the video then shows the Type III secretion system, which is one common example of a functional subset of parts. They show a bacterium with a nonmotile (motorless) flagellum lying forlornly on the ground and argue that such a state would be nonfunctional, but they ignore their own previous mention of the Type III secretion system (which has just such a functional-but-nonmotile filament) as well as numerous examples of bacteria with nonmotile filaments with other functions.
I suppose that asking that the nonflagellar homologs of the flagellum motor proteins be mentioned would be expecting a bit much, but I can dream...
IP: Logged
|
|
Rompecabezas
Member
Member # 814
|
posted 07. July 2003 10:27
There is indeed every indication that the BacFlag was adapted from an ancestral secretory system (one that would appear to be ancestral also to the type III). Check out the illuminating proposal by Ian Musgrave at the University of Adelaide for a plausible account of the evolutionary development of a system that IDC claims cannot by definiton have had an evolutionary development.
IP: Logged
|
|
Moderator
Administrator
Member # 1
|
posted 07. July 2003 12:48
Rompecabezas,
Your posts are going to need to be more substantial and less polemical to continue at this forum.
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 07. July 2003 19:14
Jurie wrote:
quote:
Which is correct?
I havn't seen Unlocking. However, I have seen some animations that show the flagellum in a whipping motion. Usually when they whip around like that the animation isn't really trying to describe how the bacteria swims but is just showing the different components of the flagellum. AFAIK, they do undergo a passive whipping motion in most swimming/tumbling models.
If the video was showing the bacteria whipping it's propeller it wouldn't be inconsistent with the corkscrew model which is also correct, unless the video specifically attributed the driving force to the whipping motion then that would be inaccurate.
As to Yersinia's post, I can't really comment on voiceovers, since I havn't seen the video.
However I can comment on this:
Yersinia writes:
quote:
For example, that the flagellum is "water-cooled". This isn't just wrong, it's practically meaningless at the molecular level. The flagellum isn't a heat engine like a car (and if it were, then it wouldn't have the high motor efficiency claimed for it in other DI blurbs).
This is quite false. The motor of bacterial flagella involves molecular motion which produces heat, and very likely, the molecular motion of near by water molecules increases as bacteria propel themselves. So "water-cooled engine" is pretty meaningful at the molecular level.
Nic also writes:
quote:
What's also weird is how numerous IDists are quoted along the lines of "an IC system has to come together all at once because all the parts are required for function" and yet the video then shows the Type III secretion system,
Of course they probably meant flagellar function. IC always refers to the "basic function" or "original function".
[ 07. July 2003, 19:16: Message edited by: Nelson-Alonso ]
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 08. July 2003 06:41
Leaving aside IC which has been discussed to death elsewhere...
Rotation: IIRC the flagellum was spinning kind of like a helicopter blade. It was a bit weird. Ah yes, you can see it in the preview hosted online at the Focus on the Family page for the video:
Unlocking the Mystery of Life
Published by: Focus on the Family/ Illustra Media
http://www.family.org/resources/itempg.cfm?itemid=3042
Like I said, though, a minor point; the graphic artists who did the animation can't be expected to know such things...
Regarding the "water-cooled" engine:
Um, Nelson, you do know, don't you, that you don't have to automatically disagree with me, just because it was little ol' ID-skeptical-me that said it. :-)
The molecular world does not work like the common sense world at the human scale. Heat is the vibration of large numbers of molecules. Do you have any idea how quickly heat dissipates for something the size of the flagellum? (assuming that a significant amount of waste heat was produced, which it's not because things such as friction are not factors in the spring-like action of molecular motors) It's on the order of nanoseconds IIRC. There is no danger of overheating, so there is no need for a cooling system, so the flagellum doesn't have one. So how can "water-cooled" be one of the oh-so-spiffy design features of the flagellum?
[ 08. July 2003, 06:45: Message edited by: yersinia ]
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 08. July 2003 18:34
Yersinia writes:
quote:
Um, Nelson, you do know, don't you, that you don't have to automatically disagree with me, just because it was little ol' ID-skeptical-me that said it
How ironic.
Yersinia writes:
quote:
The molecular world does not work like the common sense world at the human scale...There is no danger of overheating, so there is no need for a cooling system,
It's an analogy. Human made rotary engines produces heat due to friction, and water is an excellent medium for transfer of heat, so of course it is used to keep such engines from overheating. Molecular motion is heat. It's not meaningless at the molecular level. For a tiny bacterium in water, heat is dissipated so quicky that any amount of heat generated by the molecular motion of the motor is trivial in terms of overheating.
I have never read any blurb from the DI that states the flagellum has a "cooling system" as a design feature.
[ 08. July 2003, 21:21: Message edited by: Nelson-Alonso ]
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 08. July 2003 21:02
quote:
Yersinia writes:
quote:
--------------------------------------------------
The molecular world does not work like the common sense world at the human scale...There is no danger of overheating, so there is no need for a cooling system,
--------------------------------------------------
It's an analogy. Human made rotary engines produces heat due to friction, and water is an excellent medium for transfer of heat, so of course it is used to keep such engines from overheating.
True for human made rotary engines like car engines, yes.
But the analogy breaks down for molecular motors, because heat production is an utterly insignificant issue, as you admit below.
quote:
Molecular motion is, in fact, heat. It's not meaningless at the molecular level. For a tiny bacterium in water, heat is dissipated so quicky that any amount of heat generated by the various activities of the cell is trivial in terms of overheating.
Wow, two completely contradictory statements in three sentences. The last sentence is exactly my point; so do you now agree that it is incorrect for Scott Minnich in the mysteries video to refer to being "water-cooled" as a design feature in his list of flagellum design features, like the rotor, stator, reversible rotation, etc.?
quote:
I have never read any blurb from the DI that states the flagellum has a "cooling system" as a design feature.
I think that the "water-cooled" claim started with Minnich, who is quoted in the video and in the preview link I posted above. Googling on "water cooled" and "flagellum" gets:
quote:
[Mark Hartwig]
For example, consider the little outboard motor that bacteria such as E. coli use to navigate their environment. This water-cooled contraption, called a flagellum, comes equipped with a reversible engine, drive shaft, U-joint and long whip-like propeller. It hums along at 17,000 rpm.
http://www.family.org/fofmag/pp/a0021018.cfm
[...]
[No Free Lunch blurb, "sponsored by Discovery Institute" listed at the bottom]
The Bacterial Flagellum (e. coli)
Water-cooled rotary engine
Driven by proton motive force
Operates at 6,000 to 17,000 rpm
Can reverse direction within 1/4 rotation
Runs in forward and reverse
Can self-assemble & repair
Only 20 nanometers wide
http://www.nofreelunchbook.com/
[...]
Pro-IC webpage citing an ARN link:
quote:
"Find out why some scientists have called the bacterial flagella the most efficient machine in the universe with its:
1) self assembly and repair;
2) water-cooled rotary engine;
3) proton motive force drive system;
4) forward and reverse gears;
5) operating speeds of 6,000 to 17,000 rpm;
6) direction reversing capability within 1/4 of a turn; and
7) it's hard-wired signal transduction system with short-term memory."
--------------------------------------------------The quote above is from ARN's newsgroup e-mailing from February 2002. A this is part of an advertisement for a video entitled: BACTERIAL FLAGELLA: A PARADIGM FOR DESIGN (click this link for related info: ARN link)
[...]
Various secondary quotes of the above:
From a post discussing science standards (funny):
http://www.emwebhost.com/pipermail/ncdupdate/2002-June/000015.html
Another:
http://www.unityinchrist.com/dinosaurs4.htm
...I found no non-DI derived sources making the claim.
But, if you want to defend the notion that being water-cooled is a design feature of the flagellum, simply because the whole kit-n-kiboodle is immerse in water, be my guest. I've got a compost heap out back with a much stronger claim to being air-cooled than any flagellum has to being water-cooled.
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 08. July 2003 21:16
Nic writes:
quote:
But the analogy breaks down for molecular motors, because heat production is an utterly insignificant issue, as you admit below.
It's insignificant precisely because it's a tiny bacteria in water. There was nothing contradictory in my post.
quote:
I think that the "water-cooled" claim
Of course Nic, you once again change your argument mid-stream. You stated:
quote:
There is no danger of overheating, so there is no need for a cooling system, so the flagellum doesn't have one.
Not the Minnich video, not any DI blurb, contains any statement to the effect that the bacterial flagellum has a "cooling system". There is no specific system that cools the engine of flagella with water, it's just a consequence of it's size. However, there is nothing wrong with the phrase "water-cooled" (it's an analogy). Not even the posts you link to and one you describe as "funny" mention a specific "cooling system".
[ 08. July 2003, 21:25: Message edited by: Nelson-Alonso ]
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 08. July 2003 21:51
Nelson,
Are you seriously arguing that "water cooled" is one of the design features of the flagellum?
I never alledged that anyone used the words "cooling system". I said:
quote:
The molecular world does not work like the common sense world at the human scale. Heat is the vibration of large numbers of molecules. Do you have any idea how quickly heat dissipates for something the size of the flagellum? (assuming that a significant amount of waste heat was produced, which it's not because things such as friction are not factors in the spring-like action of molecular motors) It's on the order of nanoseconds IIRC. There is no danger of overheating, so there is no need for a cooling system, so the flagellum doesn't have one. So how can "water-cooled" be one of the oh-so-spiffy design features of the flagellum?
In other words, if the flagellum doesn't have a cooling system (which you admit it doesn't), how can the claim that the flagellum is "water cooled" be considered a supposed design feature of the flagellum?
I could argue with equal validity that the blood-clotting system is "water cooled".
C'mon, Nelson, isn't it clear that Minnich or someone just got a bit carried away, and that this claim was uncritically copied? The flagellum is still a wonderous little contraption regardless, and the design argument doesn't depend on the flagellum being water-cooled, I'm just trying to correct a little innaccuracy perpetuated in the Unlocking video.
Surely you would agree that the credibility of ID would be enhanced if minor mistakes such as this were corrected, don't you?
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 08. July 2003 21:57
quote:
Surely you would agree that the credibility of ID would be enhanced if minor mistakes such as this were corrected, don't you?
Sure but first you have to show that the phrase "water-cooled" is incorrect. It may be, but I havn't seen any reason why it is. The phrase you used in your previous post critiqued the phrase "cooling system". No DI blurb, no Minnich video, no Unlocking video, contains the statement that one of the design features of the flagellum is that it has a system that cools it through water.
However, saying "water-cooled rotary engine" makes sense. As as I say above,as bacteria swim, the molecular motion of near by water molecules increases.
[ 08. July 2003, 22:04: Message edited by: Nelson-Alonso ]
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 08. July 2003 23:26
Charlie, some nice detective work. Not only is the flagellum an 'outboard engine' but it seems that in some circles it may even been 'water cooled'. What's next?
It does show however that the concept of specification is quite tricky and that, as Sobel argues, one can find a specification for almost anything. One is only limited by one's imagination. I guess we can now have a water cooled flagellum without a system to really cool it. I guess the term water cooled rotary engine meant that the engine was undoubtfully submerged. It surely shows how the term 'water cooled rotary engine' however poorly chosen has started its own life on the web.
Thanks Charlie for your useful contribution to this forum.
[ 08. July 2003, 23:29: Message edited by: Pim van Meurs ]
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 08. July 2003 23:40
I must apologize for making a mistake in a previous post. The time required for the dissipation of heat from proteins is on the order of picoseconds, not nanoseconds.
Discussing the energetics of the F1-ATPase, Yang et al say:
quote:
http://www.pnas.org/cgi/content/full/100/3/874
Although we have focused on ATP synthesis, we note that the results are also of interest for the mechanism of the gamma-subunit rotation during hydrolysis by F1-ATPase. The dissipation of the energy from an exothermic reaction (ATP/H2O to ADP/Pi), which is on the subnanosecond time scale in proteins (45), would be far too rapid to contribute directly to the gamma-subunit rotation, which is on the millisecond time scale.
[and ref 45 says: ]
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=3024159&dopt=Abstract
Proc Natl Acad Sci U S A. 1986 Dec;83(23):8982-6.
Molecular dynamics simulations of cooling in laser-excited heme proteins.
Henry ER, Eaton WA, Hochstrasser RM.
In transient optical experiments the absorbed photon raises the vibrational temperature of the chromophore. In heme proteins at room temperature conversion of a 530-nm photon into vibrational energy is estimated to raise the temperature of the heme by 500-700 K. Cooling of the heme is expected to occur mainly by interacting with the surrounding protein. We report molecular dynamics simulations for myoglobin and cytochrome c in vacuo that predict that this cooling occurs on the ps time scale. The decay of the vibrational temperature is nonexponential with about 50% loss occurring in 1-4 ps and with the remainder in 20-40 ps. These results predict the presence of nonequilibrium vibrational populations that would introduce ambiguity into the interpretation of transient ps absorption and Raman spectra and influence the kinetics of sub-ns geminate recombination.
Proteins cool in picoseconds. There is no heat buildup. So what does "water cooled" have to do with it?
And Nelson, regarding:
quote:
However, saying "water-cooled rotary engine" makes sense. As as I say above,as bacteria swim, the molecular motion of near by water molecules increases.
Do you have any idea what the relative magnitude of (1) molecular motion due to a flagellum swimming is, versus. (2) molecular motion due to the general roiling nature of water at room temperature at this Brownian-motion scale? The proverbial drop-in-a-bucket (not so proverbial, here) doesn't begin to describe it. And yet you wrote,
quote:
So "water-cooled engine" is pretty meaningful at the molecular level.
No, it's not. You'd be on stronger ground describing Behe's mousetrap as "air-cooled", at least there is a little friction going on there.
Behe's mousetrap:
[*] Catches mice
[*] Five+ required parts
[*] Gravity-bound wooden base
[*] Air-cooled spring
Would all of these be reasonable claims to put in a book ad, Nelson?
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 08. July 2003 23:48
Pim,
No, it shows that the descriptions are obviously drawing paralles to car engines. So it uses the term "water-cooled rotary engine". Thats my guess anyway. For example, it only does 1^-19 horsepower. But, because of it's size, that comes out to between 1 and 10 horse power per pound.
[ 09. July 2003, 00:07: Message edited by: Nelson-Alonso ]
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 08. July 2003 23:53
Nic,
How is this:
quote:
Do you have any idea what the relative magnitude of (1) molecular motion due to a flagellum swimming is, versus. (2) molecular motion due to the general roiling nature of water at room temperature at this Brownian-motion scale? The proverbial drop-in-a-bucket (not so proverbial, here) doesn't begin to describe it.
relevant to anything I wrote in my post? None of this contradicts the fact that molecular motion is heat and that the motion of near by water molecules do in fact increase due to bacterial flagellar beating. Bacterial motility involves literally pushing the water molecules out of the way, and not to mention that water is a structure that resists disruption.
[ 08. July 2003, 23:58: Message edited by: Nelson-Alonso ]
IP: Logged
|
|
|
Printer-friendly view of this topic