The Bacterial Flagellum Revisited

The accumulation of small heritable changes within populations over time.

Moderators: Calilasseia, ADParker

Re: The Bacterial Flagellum Revisited

#41  Postby CharlieM » Jun 26, 2010 11:24 am

Larkus:
CharlieM, do you recognize, that Behe's argument, that the Bacterial Flagellum could not have evolved because it is irreducible complex has been refuted?


CharlieM:
If you mean could not have evolved by unguided natural selection, then no.
CharlieM
 
Name: Charlie Morrison
Posts: 1044

Country: UK
Scotland (ss)
Print view this post

Ads by Google


Re: The Bacterial Flagellum Revisited

#42  Postby Larkus » Jun 26, 2010 11:52 am

CharlieM wrote:
Larkus:
CharlieM, do you recognize, that Behe's argument, that the Bacterial Flagellum could not have evolved because it is irreducible complex has been refuted?


CharlieM:
If you mean could not have evolved by unguided natural selection, then no.


This was Behe's claim:
hotshoe wrote:From the horse's mouth:

Behe wrote:In Darwin’s Black Box (Behe 1996) I claimed that the bacterial flagellum was irreducibly complex and so required deliberate intelligent design. The flip side of this claim is that the flagellum can’t be produced by natural selection acting on random mutation, or any other unintelligent process.



So Charlie M can't claim Behe never said it.


And this is, how Behe defined irreducible complexity:
jaredennisclark wrote:His [Behe's] own definition from page 39 of 'Darwin's Black Box' is as follows:

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional [emphasis added, Larkus]. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. (p. 39)


:scratch:


The TTSS is a precursor to the bacterial flagellum.
The TTSS is not nonfunctional.

Listen to Kenneth Miller explaining it:
[youtube]http://www.youtube.com/watch?v=0hW7ddJOWko[/youtube]


Lark
Larkus
 
Posts: 264

Germany (de)
Print view this post

Re: The Bacterial Flagellum Revisited

#43  Postby Rumraket » Jun 26, 2010 2:08 pm

CharlieM wrote:Granted your list of stuff giving the bigger picture shows that life developed into what we see today.

Thanks, atleast you aren't ignoring the evidence that life evolved.

CharlieM wrote:But this does not show that it was some sort of fortuitous accident.

That's where gene-duplications, mutations and geneshuffling enters the picture.

CharlieM wrote:We can observe a human developing from a fertilized egg, this does not mean that there was no plan involved.

Yes, a human being and any given organism will develop from it's DNA.
But CharlieM, the evidence is that gene duplication events, in combination with geneshufflings and random mutations acting on these, are what produce novel lifeforms. It's a matter of putting 2 and 2 together.

We have the evidence that life changed and evolved over hundres of millions of years. You don't deny this.

And we have a mechanism, oberved to produce novel information in the laboratory : Duplication of genes, mutations on duplicated genes and finally gene-shufflings, alltogether, produce new functional protein machinery.

We obser natural selection both in the wild and in the laboratory.

DNA builds organisms, genetic mechanisms change the DNA, natural selection filters the results. The big picture works and I don't see why you would deny it.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13214
Age: 40

Print view this post

Re: The Bacterial Flagellum Revisited

#44  Postby CharlieM » Jun 26, 2010 2:24 pm


Behe via Jaredennisclark via Larkus:
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional [emphasis added, Larkus]. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. (p. 39)


CharlieM:
In the case of the bacterial flagellum the system he is talking about is the flagellar motility system. Its basic function is the motility of the bacterium. Remove the motor and it loses motility, remove the drive and it loses motility, remove the filament and it loses motility. Secretion may be a function of the bacterial flagellar system but its not its basic function according to Behe. Looking at the system, and we can look pretty close these days, I consider it to be extremely unlikely to have assembled itself by unguided natural means.
CharlieM
 
Name: Charlie Morrison
Posts: 1044

Country: UK
Scotland (ss)
Print view this post

Re: The Bacterial Flagellum Revisited

#45  Postby debunk » Jun 26, 2010 2:46 pm

CharlieM wrote:I consider it to be extremely unlikely to have assembled itself by unguided natural means.


Nobody cares if you find it unlikely, it's simply an argument from incredulity.
The beatings will continue until morale improves.
User avatar
debunk
 
Posts: 1013
Male

European Union (eur)
Print view this post

Re: The Bacterial Flagellum Revisited

#46  Postby PhiloKGB » Jun 26, 2010 3:07 pm

CharlieM wrote:In the case of the bacterial flagellum the system he is talking about is the flagellar motility system. Its basic function is the motility of the bacterium. Remove the motor and it loses motility, remove the drive and it loses motility, remove the filament and it loses motility. Secretion may be a function of the bacterial flagellar system but its not its basic function according to Behe.

There is no such thing as a "basic" function. This is teleological thinking.
Looking at the system, and we can look pretty close these days, I consider it to be extremely unlikely to have assembled itself by unguided natural means.

It seems like only in the biological sciences do non-specialists feel they can make statements like this. It's mind-boggling, really.
PhiloKGB
 
Posts: 679

Print view this post

Re: The Bacterial Flagellum Revisited

#47  Postby Larkus » Jun 26, 2010 3:41 pm

CharlieM wrote:

Behe via Jaredennisclark via Larkus:
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional [emphasis added, Larkus]. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. (p. 39)


CharlieM:
In the case of the bacterial flagellum the system he is talking about is the flagellar motility system. Its basic function is the motility of the bacterium. Remove the motor and it loses motility, remove the drive and it loses motility, remove the filament and it loses motility. Secretion may be a function of the bacterial flagellar system but its not its basic function according to Behe. Looking at the system, and we can look pretty close these days, I consider it to be extremely unlikely to have assembled itself by unguided natural means.

Your objection against Ken Miller's refutation of Behe's argument is irrelevant. The TTSS may not have the function of motility, but it has a fuction, that is, it is not nonfunctional.


Lark
Larkus
 
Posts: 264

Germany (de)
Print view this post

Ads by Google


Re: The Bacterial Flagellum Revisited

#48  Postby scruffy » Jun 27, 2010 10:50 pm

]CharlieM:
Well Richard Dawkins called it the Blind Watchmaker and if it isn't unguided you are getting into the realms of teleology.

I thought Goethe had replied to your Monkey Flower example. As he would say, "they have been given a felicitous mobility and plasticity that allows them to grow and adapt themselves to many different conditions in many different places."


You are taking his metaphor way too far. The 'Blind Watchmaker' is simply referring to the fact that evolution has no foresight or purpose, it just is, and it just does. He isn't implying that evolution as a whole is 'random', or 'blind'. Mutations, drift, etc. are all blind, however the natural selection that 'sorts' through these mutations is most definitely not blind. It is selecting based on a criteria, that criteria being the fitness of the animal.

CharlieM:
I am looking at the details while keeping the whole in mind. As you begin to look outward from the half a dozen proteins I mentioned things only get worse for a naturalistic explanation. These proteins need to work together as part of a whole functioning unit in order to be viable. They must be copied in precise numbers, transported to their correct location in sequence and assembled into the right shape, flexibility, strength and position. Thus you have structural proteins, assembly proteins, regulatory proteins and the rest all working together in a precise manner. And many of these proteins have no known homologs.


This is just personal incredulity. Of course we can't give you a step-by-step on how these proteins came together and started working the way they did, but we CAN make direct inferences from other lines of evidence that we do have. It is a mind-blowing example of natures complexity and beauty. You seem to appreciate this complexity, but why look at it and then conclude a designer? Try and find these missing homolog, try and work out just how these proteins are made, contribute to science! Don't reject it because it doesn't hand you all the answers on a silver platter.

CharlieM:
...Looking at the system, and we can look pretty close these days, I consider it to be extremely unlikely to have assembled itself by unguided natural means.


:doh:

CharlieM:
I think you are forgetting about the plan that was put in place when you were conceived, your DNA. You could have all the time and nutrients you wanted but nothing would have developed without your DNA.


Are you implying that DNA was the handiwork of a creator then? Do we really need to get into Abiogenesis, and replicator formation? You're just digging deeper and deeper into nature and hiding behind what science has yet to discover. It's shameful, really.

EDIT: You're coming off as implying that all the beauty and intricacy we see around us was planted via DNA by designer, similar to a gardener planting his seeds to a garden and tending to it every so often.. is this your position? I'm finding it difficult to understand exactly what you DO believe.
User avatar
scruffy
 
Name: Jared Clark
Posts: 361
Age: 30
Male

Country: United States
United States (us)
Print view this post

Re: The Bacterial Flagellum Revisited

#49  Postby Durro » Jun 28, 2010 2:28 am

.
I'll start believing in Astrology the day that all Sagittarians get hit by a bus, as predicted.
User avatar
Durro
RS Donator
 
Posts: 16737
Age: 53
Male

Country: Brisbane, Australia
Australia (au)
Print view this post

Re: The Bacterial Flagellum Revisited

#50  Postby scruffy » Jun 28, 2010 2:54 am

[quote="Durro";p="309289"][/quote]

What the hell is this?
User avatar
scruffy
 
Name: Jared Clark
Posts: 361
Age: 30
Male

Country: United States
United States (us)
Print view this post

Re: The Bacterial Flagellum Revisited

#51  Postby CharlieM » Jun 30, 2010 12:00 pm

Sorry for the delay in replying, I've been away.

PhiloKGB:
There is no such thing as a "basic" function. This is teleological thinking


CharlieM:
I disagree. It may be hard to figure out the basic function of some things but with others it is quite clear and the basic function of the flagellum is motility. We can say ears are for stopping your hat falling over your eyes or for sticking a pencil behind, but I think that the consensus of opinion would be that ears are for gathering sound.

I have been accused of having an argument from incredulity. Well I am skeptical that RM & NS is up to the job, but that is after looking at the evidence. Finding homologous proteins is not evidence for RM & NS, it only suggests common ancestry and even Behe considers that likely.

Irreducible complexity as Behe argues for it stands. The flagellum consists of a motor, a TTSS, a drive, a hook and a propellor. In order to have motility all these parts need to be in place, to be well matched to each other, to be put in place precisely in time and space and to work in unison with other flagella and/or components of the bacterium. And these are far from simple parts.

You can reduce the complexity of the flagellum by taking some parts such as certain proteins away, but take any of the above components away and motility is lost. Even if they all previously performed separate functions in the cell (we have no evidence that this is the case for all the parts mentioned above), then they still have to be matched to each other, assembled and regulated as a functioning whole to perform the task of motility that we can observe.

Jaredennisclark:
...the natural selection that 'sorts' through these mutations is most definitely not blind. It is selecting based on a criteria, that criteria being the fitness of the animal.


CharlieM:
It is blind to the future and, because it only "sees" present fitness, it reduces the variability of the breeding population. Some trait which may be beneficial in a future environment gets weeded out because it is of no present use. So natural selection tends to reduce the variability of the breeding population. A bit like stem cells becoming specialized.

Jaredennisclark:
You're coming off as implying that all the beauty and intricacy we see around us was planted via DNA by designer, similar to a gardener planting his seeds to a garden and tending to it every so often.. is this your position? I'm finding it difficult to understand exactly what you DO believe.


CharlieM:
I do not believe that the beauty and intricacy we see is the result of accidental forces. I believe we can begin to see the whole by studying the parts. Seeing the world in a grain of sand as Blake put it. Every human being starts out with the potential to be a self-conscious being. Not everyone achieves this potential due to circumstances along the way. Nothing is set in stone.

I believe that the evolution of life is the flowering of consciousness. Life develops to produce entities with awareness, and more than that self-awareness. And its not accidental.

Goethe thought of the archetypal plant as being more real than individual plants and he discovered the inter-maxillary bone in humans because of his ability to see the whole in the parts. He did not see humans as being detached from the rest of life.

Saying I believe in God tells you nothing really. It then comes down to defining what we mean by "God". Other than that, what I believe is not important to the argument, but thanks for showing an interest.
CharlieM
 
Name: Charlie Morrison
Posts: 1044

Country: UK
Scotland (ss)
Print view this post

Re: The Bacterial Flagellum Revisited

#52  Postby Rumraket » Jun 30, 2010 1:29 pm

CharliM wrote:I have been accused of having an argument from incredulity. Well I am skeptical that RM & NS is up to the job, but that is after looking at the evidence. Finding homologous proteins is not evidence for RM & NS, it only suggests common ancestry and even Behe considers that likely.

Common ancestry is evidence for evolution. It might not be direct evidence for darwinian evolution, but evolution nonetheless. Evolution in this context simply meaning change over time through succesive generations.

Additionally, homologous proteins IS evidence for mutations. Though it in itself doesn't specify the cause of these mutations or whether they are random or somehow planned. We can agree this far of course.

CharlieM wrote:Irreducible complexity as Behe argues for it stands. The flagellum consists of a motor, a TTSS, a drive, a hook and a propellor. In order to have motility all these parts need to be in place, to be well matched to each other, to be put in place precisely in time and space and to work in unison with other flagella and/or components of the bacterium. And these are far from simple parts.

Yes, behe's definition of irreducible complexity is valid in the sense that if you remove a key part involved in making the flagellum a propulsion system, it will cease to be a propulsion system. This is technically correct.

However, it is irrelevant to darwinian evolutionary theory. Darwinian Evolution predicts that if we take the system apart what we get should have alternative function. And here I don't nessecerily and only mean every indivdual protein, alone. For example, if you remove the propeller(filament) and leave the hook attached to the drive and TTSS, you still have a system that can gather nutrients from the environment, or inject compounds into it. For example the hook, or a pre-hook(before it's function was a hook that transferred torque into the propeller/filament), still attached to the drive and a secretory system, can provide the bacteria with the ability to quickly spray some compound into it's environment... a trick often used by bacteria as a defense mechanism. Many bacteria under physical and chemical stress will eject some kind of ooze that protects it from drying out or from acids, etc. etc. A rotating spraying mechanism will function superiorly to a stationary one(greater volume covered in shorter time, centrifugal force-ejection from the mound of the ejecting system, etc. etc.).

This also happens to fit with the fact that the proteins which are homologues with the propeller(filament) proteins are excreted defensive or virulence proteins. It's not hard to imagine these proteins being ejected from the rotating pre-hook, getting stuck and slowly building a primitive pre-filament. This would already here produce small motility for the bacteria.
Giving the bacteria motility is benefical and would thus be selected for. What is now left is simply selection for mutations that increase the structural strength and rigidity of the hook so that it can properly tranfer torque to the filament without breaking. The Filament is under selection for increased elasticity without breakage.

You see, it's not JUST that we find protein homologues for the parts that constitute the various parts of the flagellum. It's that the homologues are the right type, the types we can reasonably imagine could evolve into what they now are used for in the flagellum.
The filament protein as I described is an example of a part with such a homologue. The homologue is a virulence ejected from a secretory system. If the homologue was some internally used protein in something wildly unrelated to the flagellum or a ejection from a secretion system, you might have had a point. But the homologues fit the model. They are in the right place for their later evolved use in their right place in the flagella.

For example, go to the part about the 3.4. Origin of a type III pilus
http://www.talkdesign.org/faqs/flagellum.html

This is exactly what I mean about not just homologues. The homologues fit with what they evolved into for use in the flagellum. The right place, the right time. This vastly strengthens the evolutionary proposition for the flagellum.

CharlieM wrote:You can reduce the complexity of the flagellum by taking some parts such as certain proteins away, but take any of the above components away and motility is lost. Even if they all previously performed separate functions in the cell (we have no evidence that this is the case for all the parts mentioned above), then they still have to be matched to each other, assembled and regulated as a functioning whole to perform the task of motility that we can observe.

See above.

CharlieM wrote:CharlieM:
It is blind to the future and, because it only "sees" present fitness, it reduces the variability of the breeding population. Some trait which may be beneficial in a future environment gets weeded out because it is of no present use. So natural selection tends to reduce the variability of the breeding population. A bit like stem cells becoming specialized.

The part about possibly future but not currently, use being weeded out is not nessecerily true and this has considerable laboratory support. Most mutations are neutral and will therefore not be under negative selection. If they don't represent a cost to the organism they are not under negative selection. For example, a neutral point mutation in a gene which does not change amino-acid sequence in a transcribed protein will not be weeded out. This can have the potential to later, in combination with an additional point mutation(or gene shuffling or duplication even), result in a change in amino-acid sequence. This change can be positive OR negative, or even both, in varying degrees, depending on the environment. It's really hard to generalize in these hypotheticals. We have no reason to prematurely reject the potential of point mutations, simply on the basis that they are mostly neutral.

Additionally I think you are making the mistake of thinking about evolutionary theory, exclusively as a random point-mutation + selection mechamism.
The most potentiating evolutionary genetic change-mechanism, is that of gene-shuffling.
A genecopying mistake where in the process of replicating a gene, for example, the replication stops and starts over from an earlier point(The Polymerase accidentially "slips" it's grip on the DNA chain and resumes copying, this time from a different position). This can have the effect of resulting in a new gene, much larger and more complex, build from various parts of several other genes. These genes often already had function, that's why they were present. So the new protein being transcribed from this gene has many potential functions, many physically and chemically active sites. This new, potentially highly functional protein didn't arrive slowly from an increasingly impropably accumulation of succesive random point mutation. No, entire functional groups of genes were mistakenly matched together. It is reckognized that this is the most potentiating mechanism in evolution. It is poorly researched and understood, but I hope I have made the underlying concept approachable here. Google it, extremely interesting reading tbh.

Next up is gene-duplications. Again a gene-replication mistake. This time what happens is that an entire gene is copied twice. This serves the purpose of conserving function in the original or the copy, while leaving the other open to possible accumulation of neutral and/or negative or positive mutations, without destroying or altering the original function of this gene. It can also have the function of simply increasing the potensy of the already existing gene. Obviously if there is now two genes making the same protein, twice as many of that protein will be made(not always the case because of gene-interactions in metabolisms bla bla bla). There are many regulatory mechanisms that can affect this relationship but again, gene duplications are a vastly more potentiating genetic mechanism than mere random point mutations.

Lastly, the random point mutations. Yes, it is highly impropable that mere random point mutations will accumulate and produce new novel proteins of great length and benefit, with unique positive function. But in combination with gene-duplications(copying of already functional genes) and gene-shufflings(mixing of functional parts of different already existing and functional genes), the possibilites are innumerable.

EDIT : Edited for clarification and spelling.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13214
Age: 40

Print view this post

Re: The Bacterial Flagellum Revisited

#53  Postby CharlieM » Jun 30, 2010 3:48 pm

Rumraket:
Common ancestry is evidence for evolution. It might not be direct evidence for darwinian evolution, but evolution nonetheless. Evolution in this context simply meaning change over time through succesive generations.

Additionally, homologous proteins IS evidence for mutations. Though it in itself doesn't specify the cause of these mutations or whether they are random or somehow planned.


CharlieM:
I have no problem with this meaning of evolution and I agree that homology is not evidence for either random or planned change.

Rumraket:
For example the hook, or a pre-hook(before it's function was a hook that transferred torque into the propeller), still attached to the drive and a secretory system, can provide the bacteria with the ability to quickly spray some compound into it's environment... a trick often used by bacteria as a defense mechanism. Many bacteria under physical and chemical stress will eject some kind of ooze that protects it from drying out or acids etc. etc. A rotating spraying mechanism will function superiorly to a stationary one.


CharlieM:
From this it sounds to me as though you think of the hook as rotating like a garden sprinkler. It rotates around its central axis while pointing in one direction. A universal joint is not something that would aid the ejection of matter a spinning rigid tube would do that much better. The only thing I've ever seen universal joints used for is to transmit torque through a changing angle of axis. Why would evolution select for a complex mechanical device when a simple fairly rigid tube would suffice.

I've run out of time, will continue this later.
CharlieM
 
Name: Charlie Morrison
Posts: 1044

Country: UK
Scotland (ss)
Print view this post

Re: The Bacterial Flagellum Revisited

#54  Postby Shrunk » Jun 30, 2010 3:59 pm

CharlieM wrote: From this it sounds to me as though you think of the hook as rotating like a garden sprinkler. It rotates around its central axis while pointing in one direction. A universal joint is not something that would aid the ejection of matter a spinning rigid tube would do that much better. The only thing I've ever seen universal joints used for is to transmit torque through a changing angle of axis. Why would evolution select for a complex mechanical device when a simple fairly rigid tube would suffice.


This seems a fairly simple question to me. A rudimentary version of the "universal joint" arises thru random mutation, and now a structure that only served a secretory function can also aid in motility. Further mutations refine the latter function until the structue now becomes specialized for motility only.
"A community is infinitely more brutalised by the habitual employment of punishment than it is by the occasional occurrence of crime." -Oscar Wilde
User avatar
Shrunk
 
Posts: 26170
Age: 55
Male

Country: Canada
Canada (ca)
Print view this post

Re: The Bacterial Flagellum Revisited

#55  Postby Rumraket » Jun 30, 2010 4:31 pm

CharlieM wrote:
Rumraket wrote: Common ancestry is evidence for evolution. It might not be direct evidence for darwinian evolution, but evolution nonetheless. Evolution in this context simply meaning change over time through succesive generations.

Additionally, homologous proteins IS evidence for mutations. Though it in itself doesn't specify the cause of these mutations or whether they are random or somehow planned.


CharlieM:
I have no problem with this meaning of evolution and I agree that homology is not evidence for either random or planned change.

This is not what I meant. I meant homology IS evidence of change, but not WHICH of the two(random or planned).
Now, it just so happens that specific homology is a testable prediction of the theory of evolution. Specific homology in this context of the bacterial flagellum meaning that a protein found in the filament/propeller, should have homology to proteins secreted by whatever relevant secretory transport system secreets them in related organisms. It would obviously be highly confusing if the filament proteins were homologous to proteins found involved in something like a specific carbohydrate metabolism vastly unrelated to flagella or secretory systems.
But this is not the case. All the homologies we find, are homologies where we SHOULD find them. This is the testable prediction, this is what makes the testable prediction make sense and this is why the testable prediction so massively supports the darwinian evolutionary hypothesis for the origin of the flagellum.

CharlieM wrote:
Rumraket wrote:
For example the hook, or a pre-hook(before it's function was a hook that transferred torque into the propeller), still attached to the drive and a secretory system, can provide the bacteria with the ability to quickly spray some compound into it's environment... a trick often used by bacteria as a defense mechanism. Many bacteria under physical and chemical stress will eject some kind of ooze that protects it from drying out or acids etc. etc. A rotating spraying mechanism will function superiorly to a stationary one.


CharlieM:
From this it sounds to me as though you think of the hook as rotating like a garden sprinkler. It rotates around its central axis while pointing in one direction.

Ahh yes I can see how it comes out like that. That was badly worded and the garden sprinkler analogy sounds almost exactly like what I described, lol.
What I mean was simply the ability of a pre-hook, a pilus of some sort(before it was under selection for rigidity for the transfer of torque) to be flexible, to be able to move from side to side. Vibrate? I have a hard time pinning down the word.

CharlieM wrote:A universal joint is not something that would aid the ejection of matter a spinning rigid tube would do that much better.

Well yes, a garden sprinkler would be superior to a vibrating/wiggling device, for the delivery of a compound over a larger area. But natural selection has no foresight, remember? We can come up with a billion intermediates with superior function than what they propably had. We have foresight though :smoke:

CharlieM wrote:The only thing I've ever seen universal joints used for is to transmit torque through a changing angle of axis. Why would evolution select for a complex mechanical device when a simple fairly rigid tube would suffice.

I'm not sure I understand what you mean here.
In any case, I really think you should read that link I gave through carefully. There are several submitted hypotheses for various selective advantages in the individual steps leading to the modern flagellum, and they don't nessecerily involve motility, even at later stages.
Remember the part about the protein homologies being homologues to what we would expect them to evolve from. We find these proteins in the correct places. The proteins of the hook and filaments are homologous to proteins ejected from secretory systems. The proteins of the motor unit are homologous to proteins found in the Tol/Pal machine. Their location in the flagellum is identical to the location wherein we find the Tol/Pal machine on it's own and so on and so forth. The evolutionary model simply makes sense. I honestly don't see these supposedly unreasonable hurdles of extrapolation we have to overcome. The mechanism for the combinations of these molecular machines are duplications and shufflings with positive selection, their later and slower refinement resulting in the modern flagellum is mutation and negative/positive selection. It fits.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13214
Age: 40

Print view this post

Ads by Google


Re: The Bacterial Flagellum Revisited

#56  Postby CharlieM » Jun 30, 2010 7:20 pm

Shrunk:
This seems a fairly simple question to me. A rudimentary version of the "universal joint" arises thru random mutation, and now a structure that only served a secretory function can also aid in motility. Further mutations refine the latter function until the structue now becomes specialized for motility only.


CharlieM:
What would a rudimentary version of a universal joint look like? The forces required to spin the bent tube while keeping it in the required direction are not inherent in the protein structure of the tube itself. As the tube spins the hook proteins orbit the central axis. When they are on the outside of the bend they need to be elongated and when they are on the inside they need to be compressed, but the proteins on the proximal and distal ends of the hook will remain at a relatively fixed length throughout each revolution. How do the proteins "know" when to expand, when to compress and when to retain their length?

I would appreciate any thoughts on how an engineer would go about constructing such a tube. I have my own thoughts on how it could be done but I've never seen any evidence that this is how bacteria solve the problem.
CharlieM
 
Name: Charlie Morrison
Posts: 1044

Country: UK
Scotland (ss)
Print view this post

Re: The Bacterial Flagellum Revisited

#57  Postby Rumraket » Jun 30, 2010 7:24 pm

http://molvis.sdsc.edu/atlas/morphs/flaghook/
I found a nice link about the flagellar hook. Interesting stuff.
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13214
Age: 40

Print view this post

Re: The Bacterial Flagellum Revisited

#58  Postby Rumraket » Jun 30, 2010 7:40 pm

CharlieM:
What would a rudimentary version of a universal joint look like? The forces required to spin the bent tube while keeping it in the required direction are not inherent in the protein structure of the tube itself.

Yes but that's exactly the thing. It doesn't have to serve the function of transfering torque to begin with. Mutations that resulted in this were selected for once a bent joint was in place. In the beginning the "hook" did propably not have the ability to transfer torque without breaking in some way. As the filament developed, and therefore motility resulted, selection for the succesful transfer of torque and thus what resulted in the hook "machine" we see today, were selected for.

The initial, pre-torque-transfering-hook, was propably just a duplicated gene for the secreted protein, making a primitive pilus for better secretion. This is also evidentially supported in that all the proteins secreted by the secretion system, the ones that build the hook, filament and cap, are homologous to each other(in addition to their homologues in secreted virulence and adhesion proteins). Again, the homologues are in the right place, confirming by direct experimental observation the darwinian evolutionary predictions.

As a little side point, I'm learning a lot about the flagellum :)
Half-Life 3 - I want to believe
User avatar
Rumraket
 
Posts: 13214
Age: 40

Print view this post

Re: The Bacterial Flagellum Revisited

#59  Postby CharlieM » Jun 30, 2010 9:43 pm

Rumraket (after linking to Matzke article):
This is exactly what I mean about not just homologues. The homologues fit with what they evolved into for use in the flagellum. The right place, the right time. This vastly strengthens the evolutionary proposition for the flagellum.


Nick Matzke (from article linked to):
In the model, flagellin and all of the proteins of the axial structure – FlgBCFG (rod), FlgE (hook), FlgKL (adaptor), FlgD and FliD (caps), in addition to FliC (flagellin) -- are descended from a common ancestral pilin secreted from the primitive type III secretion system...

Three hypotheses present themselves as to how the ancestral pilus originated: filament-first, cap-first, and modified filament-first. The latter hypothesis combines the best features of the filament-first and cap-first hypotheses.


CharlieM:
Matzke has proposed this model based on his views on how evolution proceeds and this assumes that the type III secretory system is ancestral to the flagellum. I could propose a model based on my understanding of how evolution proceeds in which various bacteria make use of an archetypal plan which contains the "instructions" for making flagellar motility and secretion systems. This plan is expressed variously by different bacteria and sometimes in the same bacterium depending on physical factors. With my plan it doesn't matter which system (type III or Flagellum) came first.

Both our models can fit the observed data. Its our beliefs that determine the model, the data is the same in both cases.

Rumraket:
The part about possibly future but not currently, use being weeded out is not nessecerily true and this has considerable laboratory support.


CharlieM:
I was talking about natural selection on its own. I know things are different when mutations are taken into account. My point was that natural selection cannot create novelty it only removes or lets through what is already there.

Rumraket:
Additionally I think you are making the mistake of thinking about evolutionary theory, exclusively as a random point-mutation + selection mechamism.
The most potentiating evolutionary genetic change-mechanism, is that of gene-shuffling.


CharlieM:
I am not restricting mutations to point-mutations.

Must rush. More later.
CharlieM
 
Name: Charlie Morrison
Posts: 1044

Country: UK
Scotland (ss)
Print view this post

Re: The Bacterial Flagellum Revisited

#60  Postby hotshoe » Jun 30, 2010 11:05 pm

CharlieM:
Please break the bad habit of putting your name before every paragraph which is in your own words. It's very distracting and actually confusing, as the quote function in this forum quite nicely separates out what is NOT in your own words.

We already know your name. More is not better in this case, thanks. :)
Now, when I talked to God I knew he'd understand
He said, "Stick by my side and I'll be your guiding hand
But don't ask me what I think of you
I might not give the answer that you want me to"
hotshoe
 
Posts: 3177

United States (us)
Print view this post

PreviousNext

Return to Evolution & Natural Selection

Who is online

Users viewing this topic: No registered users and 1 guest