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Author Topic:   Revisiting the Type III secretion system
Genomicus
Member (Idle past 16 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 1 of 11 (676432)
10-21-2012 12:18 PM


Surprisingly, there has been little discussion on a paper recently published in PLOS Genetics. The paper is titled “The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems.” What’s the big deal about this paper?
A number of ID critics involved in the origins debate have long believed that the bacterial flagellum evolved from the type III secretion system, or that the two systems share a common ancestral system that looked like an export system. For example, the Wikipedia article on the “Evolution of flagella” maintains that:

All currently known nonflagellar Type III transport systems serve the function of injecting toxin into eukaryotic cells. It is hypothesised that the flagellum evolved from the type three secretory system. For example, the bubonic plague bacterium Yersinia pestis has an organelle assembly very similar to a complex flagellum, except that is missing only a few flagellar mechanisms and functions, such as a needle to inject toxins into other cells. It is also a possibility that the flagellum could have evolved from a currently undiscovered system with similar flagellar traits or a currently extinct organelle/organism.

Back in the late 90s and early 2000s, you’d see ID critics arguing that the type III secretion system (TTSS) is a plausible precursor to the bacterial flagellum. At the time, some of the literature hinted towards another possibility: the TTSS may have evolved from the bacterial flagellum. This, then, was the response from ID proponents. When Gophna et al., 2003, published their phylogenies which suggested that the two systems shared a common ancestor, the debate took a different turn. It was now argued that the two systems had a common ancestor in the form of a protein export system. A poster on The Panda’s Thumb had this to say about the Gophna et al. paper:

Clue for the IDers: The TTSS “appearing before the flagellum” is not the only scenario that shatters your flawed and oversimplified arguments about the “designed” origins of the flagellum.

And in 2006, Nick Matzke said:

Back in 2003 I was about 55-45 for the idea that the flagellum came first, but Pallen’s parsimony argument and a few additional small points have moved me about 60-40 for the sister groups idea. There are several specific lines of investigation that could clear this up immensely.

(Note: Mark Pallen’s parsimony argument can be found here: Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective, 2005)

Since 2003, the debate over the origin of the TTSS has been pretty split, with about half the papers saying that the TTSS descended from the flagellum, and the other half saying that the two systems share a common ancestor.

However, the recently published research provides strong evidence in favor of the hypothesis that the TTSS is derived from the bacterial flagellum. Let’s take a look at this a bit closer.

Here’s a quote from the paper:

A decade ago, several studies indicated one single phylogenetic split between the flagellum and the NF-T3SS [75], [79], [81], [82]. This is compatible with three different evolutionary scenarios. The two elements might have independent origins from an ancestral system, or one system might have adapted pre-existing structures from the other system for a new function [61], a process referred to as “exaptation” [83]. Understanding the details of the exaptation process requires an understanding of the direction of the evolutionary events. Current sequence databanks cover a much larger fraction of the prokaryotic world than ten years ago. Phylogenetic methods for dealing with multi-protein complexes have also been improved [84], [85], but these newer approaches have not yet been applied to infer the evolutionary history of T3SSs. The ongoing explosion of partially assembled genomes and metagenomes would also benefit from new tools for the detection and analysis of T3SSs from partial data. We have therefore produced such tools and applied them to genome data in order to determine the evolutionary origins and patterns of diversification of T3SSs.

The phylogenetic analyses of the TTSSs were done in this manner:

1. Maximum-likelihood phylogenetic reconstruction of the ATPase protein that is shared in the flagellum, TTSS, and F- and V- ATPases reveals that the TTSS nests within the flagellar clade. In this phylogeny, the F- and V- ATPases were used as the outgroup, thereby giving the tree a root. Moreover, this tree topology has a statistically significant bootstrap value (84%) in contrast to the two alternative topologies, with 7% and 9% bootstrap support.

2. This result was further supported by a phylogeny built from a larger dataset that included all curated systems.

Also, the study confirmed that the flagellar system has a much broader taxonomic distribution than the TTSS, again suggesting that the flagellar system is more ancient. The researchers also probed into the origin of the TTSS secretin, and found that TTSSs have acquired secretins independently at least 3 times.

Other comments

Some points in this paper that I would like to see improved in future studies:

1. The phylogeny that demonstrated that the TTSS is derived from the flagellum was only built from one protein group: the flagellar, TTSS, and F- and V- ATPases. It should be noted, however, that the TTSS ATPase, SctN, is the most highly conserved TTSS protein (Gophna et al., 2003). Because of the high level of sequence conservation in SctN, and its flagellar homolog, FliI, this protein should be expected to best portray the actual phylogenetic relationship of the flagellum and TTSS.

2. There is no mention of how the results offer a good response to Pallen’s parsimony argument (note: for those interested in the parsimony argument, I would urge you to look it up in Pallen et al.’s paper; in a future post, I may write up a critique of that parsimony argument based on this paper).

This paper is a substantial improvement over Gophna et al., 2003:

1. The study by Gophna et al., which concluded that the TTSS is ancient and did not descend directly from the flagellar system, used four different proteins to construct four different phylogenies. However, their trees were unrooted, which is not good. On the other hand, this study by Abby and Rocha rooted their phylogeny with an outgroup.

2. The bootstrap values for Gophna’s trees are not good, with the exception of one. The Abby and Rocha phylogeny has strong bootstrap support.

3. For phylogeny reconstruction, Gophna et al. used neighbor-joining, which is a distance-based method. Distance-based methods are among the least accurate phylogeny estimation methods, and can lead to incorrect results when lineages diverge at different rates (and it has been suggested that TTSS proteins have diverged faster relative to flagellar proteins). Meanwhile, Abby and Rocha employed maximum-likelihood, which is one of the most accurate phylogeny estimation methods out there.

In conclusion, this study significantly strengthens the hypothesis that the TTSS is derived from the flagellar system. Although we can still expect some of the non-specialists to continue arguing that the TTSS and flagellar system share a common, non-flagellar ancestor, anyone acquainted with the literature should not make such an argument. There is one more important point to make here. If the TTSS descended from the flagellum, then about half of the flagellar proteins lack any precursor homologs. Finally, since the TTSS does not share a common, non-flagellar ancestor with the bacterial flagellum, the TTSS is not evidence that the flagellar system evolved from a primitive secretion system.

Thoughts?

Referrences

1. Abby SS, Rocha EPC (2012) The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems. PLoS Genet 8(9): e1002983. doi:10.1371/journal.pgen.1002983.

2. Gophna, U., Ron, E., Graur, D., 2003. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312,151-163.

3. Pallen MJ, Beatson SA, Bailey CM., 2005. Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective. FEMS Microbiol Rev. 29(2):201-29.

*Note: technically, I should be using the term “NF-T3SS” to indicate which TTSS I’m referring to. In this post, though, read “TTSS” as synonymous with “NF-T3SS.”

Edited by Genomicus, : No reason given.


Replies to this message:
 Message 3 by Taq, posted 10-22-2012 5:59 PM Genomicus has responded

  
AdminModulous
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Message 2 of 11 (676434)
10-22-2012 5:08 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Revisiting the Type III secretion system thread in the Proposed New Topics forum.
    
Taq
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Posts: 7672
Joined: 03-06-2009
Member Rating: 2.5


(1)
Message 3 of 11 (676444)
10-22-2012 5:59 PM
Reply to: Message 1 by Genomicus
10-21-2012 12:18 PM


In conclusion, this study significantly strengthens the hypothesis that the TTSS is derived from the flagellar system.

However, this does not rule out the possibility that the flagellar system evolved from a secretory system that was no the Type III secretory system, or some other system that was not a flagellum. Even more, it in no way demonstrates that the flagellum was designed by an intelligence.

The ID argument ultimately rests on the claim that no flagellum, ever, had a different function with fewer parts. This study does not get ID supporters any closer to demonstrating this claim.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 1 by Genomicus, posted 10-21-2012 12:18 PM Genomicus has responded

Replies to this message:
 Message 4 by Genomicus, posted 10-22-2012 11:00 PM Taq has responded

  
Genomicus
Member (Idle past 16 days)
Posts: 852
Joined: 02-15-2012


(1)
Message 4 of 11 (676458)
10-22-2012 11:00 PM
Reply to: Message 3 by Taq
10-22-2012 5:59 PM


However, this does not rule out the possibility that the flagellar system evolved from a secretory system that was not the Type III secretory system, or some other system that was not a flagellum.

This is a valid point, but possibility should not be confused with what has actually happened in biological history. It is, in principle at least, possible that the flagellum descended from a secretion system that was not the TTSS. But if the TTSS evolved from the flagellum - as this study suggests - then there is no evidence for the view that the flagellum evolved from a secretion system.

Even more, it in no way demonstrates that the flagellum was designed by an intelligence.

For the most part, I agree. However, if the TTSS descended directly from the flagellum, then about half of the flagellar proteins in the "classic" E. coli flagellum lack any homologs that pre-date the system. This means that in order to explain the evolution of this flagellum, you'd have to explain where these parts came from and why we've lost all trace of their ancestors. In short, the discontinuity of the flagellum from the rest of the biological universe has increased IMHO. And discontinuity is often a hallmark of intelligent design, although I strongly disagree with those who think that that's the only criterion needed to infer design.

The ID argument ultimately rests on the claim that no flagellum, ever, had a different function with fewer parts. This study does not get ID supporters any closer to demonstrating this claim.

That's one type of ID argument, and it's basically the "mainstream" argument. I'd also modify it to just say that the flagellum never had a different function, since the number of protein parts can vary among flagellar systems.

This study does support the position that the flagellum never had a different function. If it had turned out that the flagellum nests within the TTSS, then it would mean that the flagellum once functioned as a secretion system.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 3 by Taq, posted 10-22-2012 5:59 PM Taq has responded

Replies to this message:
 Message 5 by Taq, posted 10-23-2012 6:03 PM Genomicus has responded

  
Taq
Member
Posts: 7672
Joined: 03-06-2009
Member Rating: 2.5


Message 5 of 11 (676560)
10-23-2012 6:03 PM
Reply to: Message 4 by Genomicus
10-22-2012 11:00 PM


This is a valid point, but possibility should not be confused with what has actually happened in biological history.

Since possibility is the foundation of Behe's IC argument, it would seem to be very important as it relates to ID arguments. Behe states that IC systems can not possibly come about through incremental changes in a Darwinian fashion. He needs to actually show that this is true with respect to the flagellum.

But if the TTSS evolved from the flagellum - as this study suggests - then there is no evidence for the view that the flagellum evolved from a secretion system.

There is also no evidence that it didn't evolve from a secretory system, or any other functional system, which is the evidence that ID needs.

However, if the TTSS descended directly from the flagellum, then about half of the flagellar proteins in the "classic" E. coli flagellum lack any homologs that pre-date the system. This means that in order to explain the evolution of this flagellum, you'd have to explain where these parts came from and why we've lost all trace of their ancestors.

Given that this sytem evolved deep in the prokaryote tree those homologs may very well be lost to history. As the old saying goes, absence of evidence is not evidence of absence. What ID arguments require is a way of showing that these homologs NEVER existed, and I just don't see how they can acquire this evidence.

I think most biologists will agree that we may never know the exact evolutionary pathways for many of the biological systems we have today. However, our ignorance in no way supports ID. ID needs to be something other than a designer of the gaps in order to have any scientific relevance.

In short, the discontinuity of the flagellum from the rest of the biological universe has increased IMHO. And discontinuity is often a hallmark of intelligent design, although I strongly disagree with those who think that that's the only criterion needed to infer design.

Discontinuities are expected in systems that evolved billions of years ago. Dicontinuity is simply the absence of evidence, not a hallmark of design. What you are constructing is a designer of the gaps.

That's one type of ID argument, and it's basically the "mainstream" argument. I'd also modify it to just say that the flagellum never had a different function, since the number of protein parts can vary among flagellar systems.

I really don't see how that argument works. We can see that the tetrapod forelimb can operate with many different number of parts and still function as a weigh bearing structure in terrestrial environments. However, we also know that it used to have a different function as a fin in aquatic environments.

This study does support the position that the flagellum never had a different function.

How so? The only conclusion that the authors put forward was that the TTSS was ruled out as a possible forerunner of the flagellum. Nowhere did the authors demonstrate that the flagellum had no functional predecessor that was not a flagellum.


This message is a reply to:
 Message 4 by Genomicus, posted 10-22-2012 11:00 PM Genomicus has responded

Replies to this message:
 Message 6 by Genomicus, posted 10-24-2012 6:50 PM Taq has responded

  
Genomicus
Member (Idle past 16 days)
Posts: 852
Joined: 02-15-2012


Message 6 of 11 (676698)
10-24-2012 6:50 PM
Reply to: Message 5 by Taq
10-23-2012 6:03 PM


Since possibility is the foundation of Behe's IC argument, it would seem to be very important as it relates to ID arguments. Behe states that IC systems can not possibly come about through incremental changes in a Darwinian fashion. He needs to actually show that this is true with respect to the flagellum.

I'm not Behe, though, and that's not my argument. The fact of the matter is that it is pretty difficult to demonstrate that a given system could not have plausibly evolved precisely because the human imagination can always imagine scenarios for the evolution of these systems. However, these pathways must be rooted in reality - they must have a historical basis - and thus the finding of pre-cursor homologs is of prime importance.

There is also no evidence that it didn't evolve from a secretory system, or any other functional system, which is the evidence that ID needs.

Demonstrating a negative is notoriously difficult. But let me ask you this question: what kind of evidence would convince you that the flagellum did not evolve from a pre-cursor system?

Given that this sytem evolved deep in the prokaryote tree those homologs may very well be lost to history. As the old saying goes, absence of evidence is not evidence of absence.

Well, if the flagellum did evolve from some kind of secretion system - as has been suggested - then it's reasonable to ask where this secretion system has gone. There really isn't any reason why a fully functional secretion system, distributed in various bacteria lineages, should disappear from the scene of life (and then essentially reappear in the form of the TTSS). You could say that a rapid rate of divergence in the ancestral secretion system erased all trace of homology, but I find that argument of dubious merit. In the first place, such a secretion system would have had an ATPase, and the sequence identities of ATPases in flagella, NF-T3SSs, and F- and V- ATPases, are well conserved. The appearance of homology is not lost among those systems, so why should it be lost in an intermediate system that bridges the gap between the F-ATPase and bacterial flagellum? Basically, the argument that the trace of homology has been lost over evolutionary time only works at a superficial level. When examined more closely, several problems appear.

Discontinuities are expected in systems that evolved billions of years ago. Dicontinuity is simply the absence of evidence, not a hallmark of design. What you are constructing is a designer of the gaps.

Discontinuity is actually often a hallmark of rational design. But keep in mind that that's not the only criterion I'm using to aid in the inference of design. You state that "Discontinuities are expected in systems that evolved billions of years ago." So does Darwinian evolution (note: I simply mean "non-telic evolution" in this context) predict that the flagellum will share deep homology with other systems or not?

I really don't see how that argument works. We can see that the tetrapod forelimb can operate with many different number of parts and still function as a weigh bearing structure in terrestrial environments. However, we also know that it used to have a different function as a fin in aquatic environments.

I don't agree with Behe's overall interpretation of irreducible complexity, so I'm not sure where you're going with this.

This study does support the position that the flagellum never had a different function.

How so? The only conclusion that the authors put forward was that the TTSS was ruled out as a possible forerunner of the flagellum. Nowhere did the authors demonstrate that the flagellum had no functional predecessor that was not a flagellum.

I did not say that this study demonstrates that the flagellum had no functional predecessor that was not a flagellum. I said that this study supports the position that the flagellum never had a non-flagellar function. If the TTSS was found to be the ancestor of the flagellum, then the study would support the idea that the flagellum once had a non-flagellar pre-cursor. But since the TTSS evolved from the flagellum (per this study), then this research supports the idea that the flagellum never had a non-flagellar function.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 5 by Taq, posted 10-23-2012 6:03 PM Taq has responded

Replies to this message:
 Message 7 by Taq, posted 10-25-2012 12:18 PM Genomicus has responded

  
Taq
Member
Posts: 7672
Joined: 03-06-2009
Member Rating: 2.5


Message 7 of 11 (676821)
10-25-2012 12:18 PM
Reply to: Message 6 by Genomicus
10-24-2012 6:50 PM


Demonstrating a negative is notoriously difficult.

Then ID is going to be notoriously difficult to demonstrate since it is based on a negative argument and a false dichotomy.

However, these pathways must be rooted in reality - they must have a historical basis -

That applies to your claims as well.

what kind of evidence would convince you that the flagellum did not evolve from a pre-cursor system?

Evidence of the genomes leading up to the first flagellum and how they did not contain any of the genes involved in the flagellum. However, this evidence is going to be extremely hard to find. Quite frankly, the evolution of any system that early in the evolution of life is going to be nearly impossible to model.

Well, if the flagellum did evolve from some kind of secretion system - as has been suggested - then it's reasonable to ask where this secretion system has gone.

It still could be the secretory systems we see now. There is always the possibility that the phylogenetic analyses are just wrong. These analyses are notoriously difficult in bacteria due to HGT. The fact of the matter is that we do have homologs between the systems.

The second option is that the flagellum evolved from something that is not a secretion system.

You could say that a rapid rate of divergence in the ancestral secretion system erased all trace of homology, but I find that argument of dubious merit. In the first place, such a secretion system would have had an ATPase, and the sequence identities of ATPases in flagella, NF-T3SSs, and F- and V- ATPases, are well conserved. The appearance of homology is not lost among those systems, so why should it be lost in an intermediate system that bridges the gap between the F-ATPase and bacterial flagellum?

The homologies are not lost. They are still there. What the paper at hand is discussing is what nests within what. Also, the intermediate would have existed billions of years ago. ID arguments claim that this transitional did not exist. I dare them to evidence that claim.

I did not say that this study demonstrates that the flagellum had no functional predecessor that was not a flagellum. I said that this study supports the position that the flagellum never had a non-flagellar function.

How does this study support the position that the flagellum never had a non-flagellar function? Please explain. From where I sit, you seem to be contradicting yourself with those two sentences.

If the TTSS was found to be the ancestor of the flagellum, then the study would support the idea that the flagellum once had a non-flagellar pre-cursor. But since the TTSS evolved from the flagellum (per this study), then this research supports the idea that the flagellum never had a non-flagellar function.

False. It only supports the idea that the TTSS was not a predecessor of the flagellum. It says nothing about whether or not some other system was a predecessor.


This message is a reply to:
 Message 6 by Genomicus, posted 10-24-2012 6:50 PM Genomicus has responded

Replies to this message:
 Message 8 by Genomicus, posted 11-01-2012 8:35 PM Taq has responded

  
Genomicus
Member (Idle past 16 days)
Posts: 852
Joined: 02-15-2012


Message 8 of 11 (677845)
11-01-2012 8:35 PM
Reply to: Message 7 by Taq
10-25-2012 12:18 PM


Then ID is going to be notoriously difficult to demonstrate since it is based on a negative argument and a false dichotomy.

You mean some ID arguments are based on a negative argument.

That applies to your claims as well.

Quite right.

Evidence of the genomes leading up to the first flagellum and how they did not contain any of the genes involved in the flagellum.

I'm guessing you're referring to something along the lines of ancestral genome reconstruction, and looking at those ancestral genomes to see if they had any pre-cursors to the flagellum.

Well, if the flagellum did evolve from some kind of secretion system - as has been suggested - then it's reasonable to ask where this secretion system has gone.

It still could be the secretory systems we see now. There is always the possibility that the phylogenetic analyses are just wrong. These analyses are notoriously difficult in bacteria due to HGT. The fact of the matter is that we do have homologs between the systems.

I completely disagree with the argument that the phylogenies may be wrong because of horizontal gene transfer. This study was focused on the phylogeny of the flagellar and NF-T3SS proteins - which means that the estimated phylogenies were protein trees, not species trees, and HGT only becomes an issue when a species tree is trying to be resolved. Horizontal gene transfer is pretty much irrelevant to this since we're talking about the relationships of the sequences, irrespective of the relationships of the organisms from which these sequences came from.

To argue that the phylogenetic analyses are just wrong needs to be backed up by hard data. You might have a case if the estimated phylogeny had weak bootstrap support, or if there was something else that might have plausibly led to an incorrect tree topology. If you don't have anything like that, it really becomes hand-waving to say the phylogenetic analyses are wrong.

The second option is that the flagellum evolved from something that is not a secretion system.

Given that the most plausible evolutionary pathways for the origin of the flagellum invoke secretion systems, this isn't likely. What pre-cursor system do you have in mind for the flagellum, if not a secretion system?

The homologies are not lost. They are still there.

I'm referring to the secretion system homologies that pre-date the flagellar system. In short, as a result of this study, you now need to explain why there isn't any evidence for the pre-cursor secretion system that is thought to have come before the flagellum.

Also, the intermediate would have existed billions of years ago. ID arguments claim that this transitional did not exist. I dare them to evidence that claim.

This is correct: the intermediate secretion system would have existed billions of years ago. However, IMHO this does not explain why all trace of homology of the flagellum with this ancestral secretion system has been effectively lost. Now, as I pointed out in a previous post, the fact that a long amount of time has past can be used as an argument for why the homology has been lost: the sequences have simply diverged so much such that there is no detectable homology. But I critiqued this argument, as well, and explained that upon closer inspection problems appear:

You could say that a rapid rate of divergence in the ancestral secretion system erased all trace of homology, but I find that argument of dubious merit. In the first place, such a secretion system would have had an ATPase, and the sequence identities of ATPases in flagella, NF-T3SSs, and F- and V- ATPases, are well conserved. The appearance of homology is not lost among those systems, so why should it be lost in an intermediate system that bridges the gap between the F-ATPase and bacterial flagellum?

Correct me if I'm wrong, but I don't think you really addressed the above. You simply reiterated that "the intermediate would have existed billions of years ago."

How does this study support the position that the flagellum never had a non-flagellar function? Please explain. From where I sit, you seem to be contradicting yourself with those two sentences.

It's very simple:

If this study had shown that the NF-T3SSs pre-dated the flagellum, this study would support the idea that the flagellum once had a non-flagellar function.

But since this study demonstrates the opposite, the study therefore removes a piece of evidence for the argument that the flagellum once had a non-flagellar function.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 7 by Taq, posted 10-25-2012 12:18 PM Taq has responded

Replies to this message:
 Message 9 by Taq, posted 11-02-2012 11:05 AM Genomicus has responded

  
Taq
Member
Posts: 7672
Joined: 03-06-2009
Member Rating: 2.5


Message 9 of 11 (677887)
11-02-2012 11:05 AM
Reply to: Message 8 by Genomicus
11-01-2012 8:35 PM


You mean some ID arguments are based on a negative argument.

Your argument is certainly teetering close that very thing. Why are you spending so much time trying to show that the TTSS could not evolve? Why not just show how the TTSS is designed without any reference to evolution?

You will notice that when scientists evidence an evolutionary pathway they don't have to mention ID at all. I have been to scientific conferences, and I have yet to see a single scientist spend 9/10ths of his lecture showing how a protein pump required for antibiotic resistance could not have been designed, and then conclude that since it was not designed that it then had to evolve with absolutely no evidence for an evolutionary pathway. It just simply isn't how science is done.

To argue that the phylogenetic analyses are just wrong needs to be backed up by hard data. You might have a case if the estimated phylogeny had weak bootstrap support, or if there was something else that might have plausibly led to an incorrect tree topology. If you don't have anything like that, it really becomes hand-waving to say the phylogenetic analyses are wrong.

Very true. I will look at these a little further.

Given that the most plausible evolutionary pathways for the origin of the flagellum invoke secretion systems, . . .

You are arguing that they are not the most plausible pathway.

What pre-cursor system do you have in mind for the flagellum, if not a secretion system?

Where is your evidence that there was not one?

Correct me if I'm wrong, but I don't think you really addressed the above. You simply reiterated that "the intermediate would have existed billions of years ago."

What is preserved as homology are the functions that were selected for. Functions that were no longer needed will lose homology quite quickly over time. In the TTSS, we may very well see the homology that was kept through selection from the set of functions found in the flagellum that was the ancestor of the TTSS.

If this study had shown that the NF-T3SSs pre-dated the flagellum, this study would support the idea that the flagellum once had a non-flagellar function.

But since this study demonstrates the opposite, the study therefore removes a piece of evidence for the argument that the flagellum once had a non-flagellar function.

Secretion is just one possible non-flagellar function. Ruling out a single secretion system does not rule out all of the other possible non-flagellar functions, including much simpler secretions sytems that are not the TTSS.


This message is a reply to:
 Message 8 by Genomicus, posted 11-01-2012 8:35 PM Genomicus has responded

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 Message 10 by Genomicus, posted 11-16-2012 12:12 PM Taq has responded

  
Genomicus
Member (Idle past 16 days)
Posts: 852
Joined: 02-15-2012


Message 10 of 11 (679918)
11-16-2012 12:12 PM
Reply to: Message 9 by Taq
11-02-2012 11:05 AM


You mean some ID arguments are based on a negative argument.

Your argument is certainly teetering close that very thing. Why are you spending so much time trying to show that the TTSS could not evolve? Why not just show how the TTSS is designed without any reference to evolution?

Well, I'm not trying to show that the TTSS could not evolve. I'm trying to show that based on the new data which indicates the TTSS evolved from the flagellum, the obvious implication is that a large chunk of the flagellum lacks homologs that predate the flagellar system. This, in turn, raises the question of why we are lacking those homologs.

I'm not arguing that because the flagellum lacks these homologies, it must have been designed. To arrive at the design inference for a biological system, we need more than just discontinuity. But discontinuity is one factor that plays a role in the design inference. Think of it like this: we can score our level of suspicion that a given system was designed. If a biological system is discontinuous from the rest of the biological universe, if it displays properties of rational design, if it is strongly analogous to things known to be designed, and if its design shows foresight, then it would be reasonable to be more suspicious that this system was designed than, say, a sloppy, jury-rigged biological feature that has clear homologies throughout the biological universe. This is the approach developed by Mike Gene in his The Design Matrix. Yes, tests would have to be made to definitely infer design, but the design matrix approach allows us to test ID predictions. For example, if we find that the core structure of a molecular machine displays properties of rational design, we could predict further that the (ancestral) sequences of the protein components also display rational design (e.g., they don't have chunks of useless sequence repeats, indels, etc.). Confirmation of that prediction, then, would increase our suspicion of intelligent design.

Given that the most plausible evolutionary pathways for the origin of the flagellum invoke secretion systems, . . .

You are arguing that they are not the most plausible pathway.

But they are the most plausible evolutionary pathways proposed to date, as best I can tell. Whether or not they are actually biologically realistic is a whole other matter, but of all the proposed pathways, the ones involving a secretion system are the most plausible.

What pre-cursor system do you have in mind for the flagellum, if not a secretion system?

Where is your evidence that there was not one?

The burden of proof is on you to provide evidence that the flagellum evolved (inasmuch as the burden of proof is on me to demonstrate that it was engineered). It's very difficult to prove a negative, so it's pretty much a hopeless task to demonstrate that no pre-cursor secretion system ever existed. But what we can do is look at the currently-existing secretion systems, and see if they indeed predate the flagellum. It turns out that all secretion systems that are homologous to flagella are derived from flagella.

What is preserved as homology are the functions that were selected for. Functions that were no longer needed will lose homology quite quickly over time. In the TTSS, we may very well see the homology that was kept through selection from the set of functions found in the flagellum that was the ancestor of the TTSS.

I don't think I quite follow your argument. What we have is a secretion system that is derived from the flagellar export system. Did that export system evolve from a primitive secretion system? Maybe, but there is no evidence for that view. To say that the precursor secretion system (that is, the precursor of the flagellar system) was lost quickly over time seems awfully ad hoc to me. There is no reason why a functional secretion system should be lost across many bacteria lineages, only to be replaced again by the modern NF-T3SSs. Moreover, there is no reason why all trace of homology at the sequence level should be lost. We should be able to find secretion systems that predate the flagellum, but we don't. Why do you think this is the case?

Edited by Genomicus, : Grammar

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 9 by Taq, posted 11-02-2012 11:05 AM Taq has responded

Replies to this message:
 Message 11 by Taq, posted 11-16-2012 4:33 PM Genomicus has not yet responded

  
Taq
Member
Posts: 7672
Joined: 03-06-2009
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Message 11 of 11 (679950)
11-16-2012 4:33 PM
Reply to: Message 10 by Genomicus
11-16-2012 12:12 PM


I'm not arguing that because the flagellum lacks these homologies, it must have been designed. To arrive at the design inference for a biological system, we need more than just discontinuity. But discontinuity is one factor that plays a role in the design inference.

You appear to be talking out both sides of your mouth.

Think of it like this: we can score our level of suspicion that a given system was designed. If a biological system is discontinuous from the rest of the biological universe, if it displays properties of rational design, if it is strongly analogous to things known to be designed, and if its design shows foresight, then it would be reasonable to be more suspicious that this system was designed than, say, a sloppy, jury-rigged biological feature that has clear homologies throughout the biological universe.

Those are all very subjective criteria. Also, we are looking at the modern flagellum which has passed through perhaps 3 billion years of evolution which would have surely increased the effeciency of the system.

But they are the most plausible evolutionary pathways proposed to date, as best I can tell.

It may very well be that the TTSS is not a plausible pathway and new pathways will need to be considered.

The burden of proof is on you to provide evidence that the flagellum evolved (inasmuch as the burden of proof is on me to demonstrate that it was engineered).

Absolutely. However, you do not see me arguing that a lack of a design pathway is evidence that the flagellum evolved. However, you do see ID supporters making those arguments.

There may be systems we will never know the true evolutionary history of. Given the number of systems out there and the limited resources biologists have it is almost a near certainty that this will be the case. Is this where we find the ID argument, in the gaps in our knowledge?

To say that the precursor secretion system (that is, the precursor of the flagellar system) was lost quickly over time seems awfully ad hoc to me.

It is ad hoc, but it is still possible. The deeper we look into evolutionary history the murkier it is going to be.

If the precursor for flagella was a secretory system then the question would just shift to how the secretory system evolved. You would still be using the same criticisms.

Did that export system evolve from a primitive secretion system? Maybe, but there is no evidence for that view. To say that the precursor secretion system (that is, the precursor of the flagellar system) was lost quickly over time seems awfully ad hoc to me.

Do we see the opposite relationship? Do we see strains with a TTSS but no flagella? I don't know off the top of my head, but I wouldn't be surprised to find out that there are non-flagellated strains that have the TTSS. How do we explain that if the TTSS evolved from flagella?


This message is a reply to:
 Message 10 by Genomicus, posted 11-16-2012 12:12 PM Genomicus has not yet responded

  
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