Nick Matzke’s TTSS to Flagellum Evolutionary Narrative Refuted

_{August 15, 2008

Intelligent Design}

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Nick Matzke’s problematic evolutionary narrative of the Type Three Secretory System (TTSS) into the bacterial flagellum quickly made it into a peer reviewed journal while the response from the ID camp took two years longer. Our position, which I mentioned several times in the past, was that the flagellum preceded the TTSS in nature and thus the TTSS represents a devolution from flagella rather than flagella being evolved from a TTSS. Nick had it ass-backward. No surprise there. Devolution is much easier than evolution, Nick. Always look for devolutionary explanations first. I’d like to say that devolution being far easier than evolution is something that ID predicts but alas, it’s predicted by nothing more than common sense. Of course ID is predicated by common sense too so there is that kinship to consider.

The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes

Molecular Biology and Evolution 2008 25(9):2069-2076
doi:10.1093/molbev/msn153

The evolution of the flagellar assembly pathway in endosymbiotic bacterial genomes

Toft C and Fares MA

Department of Genetics, Smurfit Institute of Genetics, University of
Dublin, Trinity College, Dublin 2, Ireland.

Genome shrinkage is a common feature of most intra-cellular pathogens
and symbionts. Reduction of genome sizes is among the best-characterised
natural strategies adopted by intra-cellular organisms to save and avoid
maintaining expensive redundant biological processes. Endosymbiotic
bacteria of insects are examples of biological economy taken to
completion because their genomes are dramatically reduced. These
bacteria are non-motile and their biochemical processes are intimately
related to those of their host. Because of this relationship, many of
the processes in these bacteria have been either lost or have suffered
massive re-modelling to adapt to the intra-cellular symbiotic lifestyle.
An example of such changes is the flagellum structure that is essential
for bacterial motility and infectivity. Our analysis indicates that
genes responsible for flagellar assembly have been partially or totally
lost in most intra-cellular symbionts of gamma-Proteobacteria.
Comparative genomic analyses show that flagellar genes have been
differentially lost in endosymbiotic bacteria of insects. Only proteins
involved in protein export within the flagella assembly pathway (type
III secretion system and the basal-body) have been kept in most of the
endosymbionts whereas those involved in building the filament and hook
of flagella have only in few instances been kept, indicating a change in
the functional purpose of this pathway. In some endosymbionts, genes
controlling protein-export switch and hook length have undergone
functional divergence as shown through an analysis of their evolutionary
dynamics. Based on our results we suggest that genes of flagellum have
diverged functionally as to specialise in the export of proteins from
the bacterium to the host.

Comments

Kevin Parker said (#1) -- In the recent Dover trial, and elsewhere, the ‘Intelligent Design’ movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Nothing is clearer here than the fact that these scientific questions do not belong in the courts.Larry Fafarman_{August 19, 2008
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But the TTSS is also IC. IOW using the TTSS to help explain the BF is BS. Also once you start re-arranging the TTSS to get a BF there will be a time when the TTSS doesn't function as such and the reconfigured part does not have any function at all. Also both Pallen & Matzke appear to be ignorant of the "designed to evolve" part of ID. IC does NOT say that the system in question could not have evolved. It just questions and rightly so, that the evolution occurred via culled genetic accidents.Joseph_{August 18, 2008
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Interesting, but it still seems to support Ken Miller’s assertion (via the mousetrap analogy) that the bac flag is not irreducibly complex rather than Behe’s assertion that it is. What does Behe say?
What he's been saying for years yet Darwinists like you studiously ignore... https://uncommondescent.com/comment-policy/put-a-sock-in-it/
It is certainly true that evolution predicts only minor changes from generation to generation - but when you look at the cumulative effect of hundreds of millions or billions of replications then those many, many changes can incrementally lead to large changes. You cannot simply stack small changes and–boom–you got something complex. That is not how it works in reality. A series of small changes have to come about independently, each having positive selective pressure, and then indirectly come together to form a new whole. This is called an Indirect Darwinian pathway. The reason a Direct Darwinian pathway is not an option is due to Irreducible Complexity since a Direct Pathway requires that a component have positive selective pressure for its function every increment. Darwinists do not like to tacitly admit that IC is a factor but that is why all current research is now directed upon Indirect Darwinian pathways. Unfortunately for Darwinists, that type of scenario is essentially relying on serendipity. One of your fellow Darwinists was nice enough to admit this is not the case here on UD: One of the central tenets of the modern synthesis of evolutionary biology as celebrated in 1959 was the idea that macroevolution and microevolution were essentially the same process. That is, macroevolution was simply microevolution extrapolated over deep evolutionary time, using the same mechanisms and with essentially the same effects. A half century of research into macroevolution has shown that this is probably not the case. -MacNeill What types of life are Irreducibly Complex? Or which life is not Irreducibly Complex? It’s not life as a whole. Mechanical components of all life are Irreducibly Complex (IC). Not all components are IC nor do they qualify as Complex Specified Information (CSI). The question is whether unguided Darwinian processes (RM+NT, lateral gene transfer, symbiogenesis, reliance on hox genes, whatever) can produce IC and/or CSI components via Indirect Pathways. Unguided Darwinian processes perhaps are capable of producing components that are composed of 3-6 parts. But for comparison the flagellum is composed of 41 parts and the most observed we’ve ever heard of is 2 or 3. Again, part of ID research is determining the limits of unguided Darwinian processes. Agreeing that there are beneficial mutations and limited instances of small changes is in no way a threat to ID or an admission of some sort we have been saying this for years to deaf ears. An IC machine cannot, by definition, be the result of a direct Darwinian pathway. Direct means that the steps are selected for the improvement of the same function we find in the final machine. IC makes a direct Darwinian pathway impossible. So, only two possibilities are left: either sudden appearance of the complete machine (practically impossible for statistical considerations), or step by step selection for different functions, and with the target function COMPLETELY INACTIVE for natural selection. This is a point that Darwinists tend to bypass. Darwinists may believe in indirect Darwinian pathways, because it’s the only possible belief which is left for them, but it’s easy to see that it really means believing in impossibilities. There is no reason in the world, either logic or statistical, why a complex function should emerge from the sum of simpler, completely different functions. And even granted that, by incredible luck, that could happen once, how can one believe that it happened millions of times, for the millions (yes, I mean it!) of different IC machines we observe in living beings? The simple fact that Darwinists have to adopt arguments like co-option and indirect pathways to salvage their beliefs is a clear demonstration of how desperate they are. In the Flagellum Behe Ignores that this Organization of Proteins has Verifiable Functions when Particular Proteins are Omitted, i.e. in its simplest form, an ion pump. I note you refer to the ion pump. An IC machine cannot, by definition, be the result of a direct Darwinian pathway. Direct means that the steps are selected for the improvement of the same function we find in the final machine. The very fact that you even attempt to make this argument showcases that your comprehension of IC is in error! Behe discusses this common argument in more detail here: http://www.discovery.org/scripts/viewDB/index.php?command=view&id=1831 Here’s how Ken Miller phrased this poor argument: “The very existence of the Type III Secretory System shows that the bacterial flagellum is not irreducibly complex.” Reference my last comment to see why he completely misunderstands ID and why finding homologs doesn’t threaten ID. Finding the reuse of code is a prediction of some ID-compatible hypotheses. Years ago, Darwinists were SURPRISED (as usual) when they found the code to be this way. Now an Indirect Darwinian pathway for the flagellum would not only require that the code for various components come together (be co-opted), but that the code regulating that code be modified, the location/orientation be precise, modifications be made to the original code for these components, and that new code be generated. The reason new code is needed is because not all the components in the total system may have homologs or functions separate from the whole. For the flagellum there are currently 17 unique proteins with no known homologs (by the way, the T3SS and the subsystem in the flagellum are similar but not exactly the same; Behe is researching protein binding sites to see if there are limitations that may make indirect pathways not just unlikely but impossible). Then of course there are the external systems for controlling the usage of the flagellum…kinda useless to have an outboard motor but no way of using it. Never mind overcoming the pleiotropic nature of this code, since making these changes can and will often have adverse effects. As in, in order to have positive selection the changes being made not only have to pull together a functional flagellum but they can’t have a negative effect that is worse than the positive of having the functional flagellum. Invoking exaptation like a magic wand won’t help you here. Now Behe certainly wouldn’t deny exaptation in general since he accepts universal common descent and this deals with a system being modified to deal with different environments. An example would be bird feathers, which are said to have evolved for temperature regulation and then later evolved for flight. But that still doesn’t provide a mechanism for this evolution. Finally, we have been discussing the supersystem of the flagellum this whole time but we have neglected to focus on the subsystems. In its own right, the T3SS is fairly complicated, being comprised of 11 proteins. The problem Darwinists face is that Darwinian mechanisms have never been shown capable of even producing a system like the T3SS, never mind the full flagellum.
A recent conversation on UD where the hypothetical indirect pathway of the bacterial flagellum is discussed: https://uncommondescent.com/intelligent-design/chance-law-agency-or-other/#comment-289741 The end of this conversation puts the problem in perspective: https://uncommondescent.com/intelligent-design/chance-law-agency-or-other/#comment-290187 Other major points: https://uncommondescent.com/evolution/behes-multiple-mutations-needed-for-e-coli/#comment-290408 https://uncommondescent.com/intelligent-design/chance-law-agency-or-other/#comment-289702 https://uncommondescent.com/philosophy/id-and-catholic-theology/#comment-212175Patrick_{August 16, 2008
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PAV
then insects came along and, with the endosymbiotic relationship established, the flagella no longer needed those genes, and so, out of economy, eliminated them (this is one explanation for the putative “elimination”). Thus, the need to export proteins via the TTSS arises after the flagella have formed, not on the way to the formation of the flagella. This severely weakens Matzke’s argument
you may be surprised how fast down regulation of flagellar genes through adaptive mutations occurs in E. coli "front loaded" into gnotobiotic mice. From the paper:
SG colonies forming bacteria, undetected in the initial inocula, appeared in the feces within two days, and reached a prevalence of 90% within seven days (Figure 1B). Their phenotype remained stable when grown in vitro over many generations, indicating that it was heritable and may result from the rapid in vivo selection of mutation(s). [...] While no mutation was detected in LS clones, all SG clones displayed a different missense point mutation, seven located in envZ, and one in ompR (Table1). The independent systematic and rapid selection of mutations in the same genes under identical experimental conditions is evidence for a strong selective advantage of the mutants during gut colonization [1].
BTW, the adaptive mutations can not be qualified as "Devolution" because
Importantly, the selected mutants did not exhibit the same motility phenotype as null mutations, since strains deleted for envZ, ompR or both kept the wild type LS morphotype (Figure S1). The membrane receptor kinase-phosphatase EnvZ forms a two-component pair with its cognate response regulator, OmpR, that enable cells to sense external changes of osmolarity [13]. The native receptor exists in two active but opposed signalling states, the OmpR kinase-dominant state and the OmpR-P phosphatase-dominant state. The balance between the two states determines the level of intracellular OmpR-P, which in turn determines the level of transcription of the many target genes [13]. One important bacterial function controlled by OmpR is motility, as OmpR regulates transcription of the flhDC operon, the master regulator of flagellar biosynthesis [16]. Several mutations identical to those selected in vivo during colonization were previously shown, by in vitro mutational analysis of EnvZ activities, to switch on the EnvZ kinase-dominant state [17,18] (Figure 2), resulting in increased levels of phospho-OmpR and repression of the flhDC operon [16].
(emphasis mine)sparc_{August 15, 2008
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RobertC: Bacteria existed for over a billion and a half years before insects came along. IOW, the bacteria needed the flagella; then insects came along and, with the endosymbiotic relationship established, the flagella no longer needed those genes, and so, out of economy, eliminated them (this is one explanation for the putative "elimination"). Thus, the need to export proteins via the TTSS arises after the flagella have formed, not on the way to the formation of the flagella. This severely weakens Matzke's argument.PaV_{August 15, 2008
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Not that it will get posted, but: I think the paper clearly SUPPORTS Nick Matzke's hypothesis. This paper shows flagellar genes, in the absence of need for a flagella (non-motile bacteria), can diversify and contribute to protein export. It provides a functional link between the flagella and Type III secretion systems-which might have been lacking before. It does not attempt to construct a narrative for the evolution of the Type III secretion system. So, if we accept both papers on face value-it has been shown Type III secretion systems and protein export are related. Matzke shows a potential route by which ancestral proteins evolved into each. This paper shows that in non-motile bacteria, certain "ex-flagellar" proteins can adopt a role in protein secretion.RobertC_{August 15, 2008
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Interesting, but it still seems to support Ken Miller's assertion (via the mousetrap analogy) that the bac flag is not irreducibly complex rather than Behe's assertion that it is. What does Behe say?terry fillups_{August 15, 2008
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Although Nick Matzke’s problematic evolutionary narrative of the Type Three Secretory System (TTSS) into the bacterial flagellum never (AFAIK) made it into a peer reviewed journal
From "A Guide to Nature Reviews Microbiology"
Peer review Our review-type articles are subject to rigorous peer review. The purpose of peer review is to ensure that our articles are balanced and accurate. Authors are encouraged to express their opinions, but a clear distinction is made between generally accepted views and more personal perspectives.
Fixed it. Thanks. -ds sparc_{August 15, 2008
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"....and speculate as to how an experimental programme focused on this topic might look." KWP, why this post (#1)? I don't have access to the full article, but it seems clearly presumptuous that a Darwinistic process must somehow be responsible for the irreducible complexity of the flagellum. This seems remarkably tentative and predicated on the usual Darwinist assumptions. Has there been an "experimental program", and have there been any results?magnan_{August 15, 2008
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Having had many discussions with naturalistic evolutionists and reading their blogs, they'll probably say this was just a study of evolution not ID. "Where are the words 'Intelligent Design,' and 'Irreducible Complexity.'?"parapraxis_{August 15, 2008
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Nat Rev Microbiol. 2006 Oct;4(10):784-90. Epub 2006 Sep 5. From The Origin of Species to the origin of bacterial flagella. Pallen MJ, Matzke NJ. Division of Immunity & Infection, Medical School, University of Birmingham, Birmingham, B15 2TT UK. m.pallen@bham.ac.uk In the recent Dover trial, and elsewhere, the 'Intelligent Design' movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look. Fixed it. Thanks.KevinWParker_{August 15, 2008
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