Richard Buggs isn’t saying anything about extant structures deriving from each other. He’s referencing Abby & Rocha (2012) showing that the injectisome (aka. the non-flagellar type III secretion system) evolved from a flagellum, not the other way around:
Sure he is. That’s why he’s referencing that Tan et al. 2021 and showing a figure of the extant flagellum and the extant injectisome, to argue that they appear too dissimilar for the depicted flagellum to have evolved from the depicted injectisome.
As he says immediately below the figure depicting the two extant structures side by side:
Examination of these structures shows that the components of the injectisome are far from being “very similar” to the components of the flagellar motor.
And then below the quote from the paper, Buggs writes:
In other words, even parts of the two structures that seem to correspond to each other are very different. Thus, parts of the injectisome could not simply be “commandeered” for the flagellar motor.
If he’s not talking about extant structures, why is he referencing papers and using figures of them?
Yes. And? The extant injectisome is derived from some ancestral flagella much like extant flagella, but that doesn’t mean an ancestral state through which flagella arose were not or could not be injectisome-like(however much) structures, particularly when there are organisms living in the present that do use reduced flagella as their protein secretion systems(see https://www.pnas.org/content/96/11/6456).
I can only repeat myself. Nobody is saying extant flagella derive from extant T3SS, but rather that extant flagella had a T3SS-like ancestral state before they evolved into flagella. That when flagella evolved they passed through an injectisome-like(even if that is not identical with extant injectisomes) state. And that those ancestral flagella in turn diverged into extant flagella and extant, more specialized injectisomes. Quite possibly through further specialization of a structure very much like extant flagellar T3 secretion systems.
Nick Matzke explained all this all the way back in his 2003 article:
Go to the section “3.2.2. Are nonflagellar type III secretion systems derived from flagella?” and read on from there. It is simply not a necessary assumption for the proposed model of flagella evolution that extant injectisomes are phylogenetically basal to extant flagella. It just isn’t, so the continued invoking of this (anticipated) objection persists in meaninglessness.
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Interesting. I assume that means that Buggs accepts the conclusion of this paper. Which would mean that an irreducibly complex cellular machine like the injectisome can arise thru undirected, natural evolutionary processes, and does not require an “intelligent designer.” Has Buggs written about how this paper refutes the central thesis of ID?
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Which is ludicrous, as that’s not how structural biologists find or exclude homology.
Sadly, pretending that someone else is claiming that an extant structure or organism evolved from another extant structure or organism, instead of from a common ancestor, is a staple of IDcreationism.
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Oh and a note about terminology here. Not all papers are exactly consistent on their use of the terms injectisome and Type-III secretion systems. Depending on the source, these may or may not refer to the same thing. As the 2015 Royal Society article referenced by Buggs says:
1. The flagellum and the injectisome share a type III secretion system
Far from being ‘bags of enzymes’, bacteria have evolved to employ remarkably complex structures and pathways to ensure survival and spreading. Two of the most impressive examples of large macromolecular complexes span both membranes of Gram-negative bacteria: the bacterial flagellum, a rotating filament used in chemotaxis, and the injectisome, an injection device used for interkingdom transfer of proteins.
Although these two machineries clearly differ both in overall structure and function, at their core, they both consist of a conserved machinery for protein export, the type III secretion system (T3SS). In the flagellum, the T3SS is used to export the distal flagellar components and build the extracellular filament. Within the injectisome, the T3SS is at the centre of the export machinery and enables both the formation of the extracellular needle and the direct transfer of substrates from the bacterial cytosol into the host cells. While the term ‘type III secretion system’ is often applied to the whole injectisome, we will use it for the export machinery within both systems (and, accordingly, for statements valid in both cases) and use ‘flagellum’ or ‘injectisome’ to specify the respective complete system.
My bolds. When we are talking about the proposed ancestrality of Type-3 secretion systems and/or injectisomes we need to make sure we understand what exactly is being proposed. Buggs is quoting Dawkins, but Dawkins never uses the word injectisome, and exclusively uses the term TTSS(Type three secretion system). And he’s paraphrasing Kenneth Miller, so it’s not exactly clear from Dawkins’ statements whether he’s actually talking specifically about the system employing a flagellin-derived pilus to puncture eukaryotic membranes, or merely referring to the core protein transport apperatues also referenced in the 2015 article quoted above.
Going by Matzke 2003, it’s clear that Matzke is proposing that both functions could serve as hypothetical ancestor states through which flagella evolved, as he shows in his figure 7 that a more injectisome-like structure with a pilus, evolved from a more primitive “mere” Type-III protein secretion system without it.
Edit: Dawkins references Miller, and gives this link in the list of references:
http://www.millerandlevine.com/km/evol/design2/article.html
In this article Kenneth Miller uses this figure when speaking of the type 3 secretion system:
It is now clear, therefore, that a smaller subset of the full complement of proteins in the flagellum makes up the functional transmembrane portion of the TTSS.
Figure 2: There are extensive homologies between type III secretory proteins and proteins involved in export in the basal region of the bacterial flagellum. These homologies demonstrate that the bacterial flagellum is not “irreducibly complex.” In this diagram (redrawn from Heuck 1998), the shaded portions of the basal region indicate proteins in the E. coli flagellum homologous to the Type III secretory structure of Yersinia. . OM, outer membrane; PP, periplasmic space; CM, cytoplasmic membrane.Stated directly, the TTSS does its dirty work using a handful of proteins from the base of the flagellum. From the evolutionary point of view, this relationship is hardly surprising. In fact, it’s to be expected that the opportunism of evolutionary processes would mix and match proteins to produce new and novel functions. According to the doctrine of irreducible complexity, however, this should not be possible. If the flagellum is indeed irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains “by definition nonfunctional.” Yet the TTSS is indeed fully-functional, even though it is missing most of the parts of the flagellum. The TTSS may be bad news for us, but for the bacteria that possess it, it is a truly valuable biochemical machine.
The existence of the TTSS in a wide variety of bacteria demonstrates that a small portion of the “irreducibly complex” flagellum can indeed carry out an important biological function. Since such a function is clearly favored by natural selection, the contention that the flagellum must be fully-assembled before any of its component parts can be useful is obviously incorrect. What this means is that the argument for intelligent design of the flagellum has failed.
So Kenneth Miller does not appear to be speaking about the injectisome (here meaning the T3SS-derived system employing a pilus/needle specifically), but can just as well be understood to be talking about the protein secretion system at the base of the injectisome, like Diepold and Armitage 2015 are.
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Oh I didn’t know this. Thanks for pointing it out.
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Here is a longer quote from Dawkins:
In the case of the bacterial rotary engine, Miller calls our attention to a mechanism called the Type Three Secretory System or TTSS. The TTSS is not used for rotatory movement. It is one of several systems used by parasitic bacteria for pumping toxic substances through their cell walls to poison their host organism. On our human scale, we might think of pouring or squirting a liquid through a hole; but, once again, on the bacterial scale things look different. Each molecule of secreted substance is a large protein with a definite, three-dimensional structure on the same scale as the TTSS’s own: more like a solid sculpture than a liquid. Each molecule is individually propelled through a carefully shaped mechanism, like an automated slot machine dispensing, say, toys or bottles, rather than a simple hole through which a substance might ‘flow’. The goods-dispenser itself is made of a rather small number of protein molecules, each one comparable in size and complexity to the molecules being dispensed through it. Interestingly, these bacterial slot machines are often similar across bacteria that are not closely related. The genes for making them have probably been ‘copied and pasted’ from other bacteria: something that bacteria are remarkably adept at doing, and a fascinating topic in its own right, but I must press on.
The protein molecules that form the structure of the TTSS are very similar to components of the flagellar motor. To the evolutionist it is clear that TTSS components were commandeered for a new, but not wholly unrelated, function when the flagellar motor evolved. Given that the TTSS is tugging molecules through itself, it is not surprising that it uses a rudimentary version of the principle used by the flagellar motor, which tugs the molecules of the axle round and round. Evidently, crucial components of the flagellar motor were already in place and working before the flagellar motor evolved. Commandeering existing mechanisms is an obvious way in which an apparently irreducibly complex piece of apparatus could climb Mount Improbable.
– Richard Dawkins, The God Delusion (Bantam Press, 2006), pp. 131-2; my emphasis
When Dawkins writes that “it is clear that TTSS components were commandeered for a new, but not wholly unrelated, function when the flagellar motor evolved,” which TTSS components is he talking about?
A straight-forward reading would be that he is talking about TTSS components found in those “parasitic bacteria” he just mentioned, i.e. extant bacteria with injectisomes. But as Abby & Rocha (2012) have shown, that claim would be wrong: Instead it is the TTSS components of the injectisome which have been commandeered for a new, but not wholly unrelated, function from the TTSS found in bacterial flagella.
Or is Dawkins talking about the TTSS components of some hypothetical bacteria, existing prior to the origin of the flagellum, having non-flagellar, non-injectisome TTSS’? That is a different and much weaker claim, Matzke’s TalkDesign flagellum FAQ notwithstanding (more on this below).
Incidentally, Coleman et al. have a brand new article in Science, with a rooted bacterial phylogeny and an ancestral reconstruction of the bacterial LCA (Last Common Ancestor), which they estimate as having a flagellum. If this is correct, it would place these non-flagellar, non-injectisome TTSS-carrying bacteria prior to the bacterial LCA. Check it out here:
doi.org/10.1126/science.abe0511
And then there’s this part:
“Given that the TTSS is tugging molecules through itself, it is not surprising that it uses a rudimentary version of the principle used by the flagellar motor, which tugs the molecules of the axle round and round.”
It appears that Dawkins thinks that the TTSS of the flagellum is responsible for generating the rotational movement of the shaft/hook/filament (‘tugging the molecules of the axle round and round’), not for transporting proteins through the hollow structure during the construction of the flagellum. This would also explain why he keeps talking about TTSS as if it was homologous with the flagellar motor.
And again, if by “the TTSS” Dawkins is referring to the TTSS of those extant parasitic bacteria he started out talking about, then it’s function isn’t “rudimentary”, but derived.
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No one is saying that the ancestral state through which the flagella arose “could not be injectisome-like”. I’m certainly not. The question isn’t what could have happened, but what did happen. That extant bacteria use reduced flagella as their protein secretion system is hardly a point against my position.
You link to Matzke’s 2003 TalkDesign flagellum FAQ, in which Matzke hypothesizes a TTSS ancestral to flagella. He claims such a hypothesis is “plausible”, but his argument never rises above “might’ve happened”: He derives a prediction from his ancestral-TTSS hypothesis, explains why it is easy to explain the absence of evidence for this prediction, and then surveys convergent functions of prokaryote secretion system, arguing that “any secretion system that exists will sooner or later get coopted for diverse functions, including virulence, in various lineages.” But why would this give us any grounds to posit a TTSS ancestral to flagella?
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I agree with you that Buggs’ comparison of flagellar proteins with injectisome proteins is not a convincing argument against the flagellum being derived from a non-flagellar TTSS. I think his article would have been stronger if he hadn’t included that comparison.
I think it is entirely possible Dawkins were not aware that injectisomes of parasitic bacteria are derived from flagella, and it is likely he’s talking about the injectisome given the context of parasitic bacteria being mentioned. I have to agree with you there. But I also think the continued obsession about the technicalities of his statements are red herrings(and ends up working against Buggs). The case for flagellum evolution doesn’t rest with Richard Dawkins, and I doubt anyone goes to Dawkins’ The God Delusion for information about flagellum evolution.
But ultimately both statements are wrong, as neither extant structure derive from each other, but from a common ancestor. Now it is clear from phylogenetic evidence that that common ancestor was a flagellum, but you have to be mindful that when you say that “the” injectisome derives from “the” flagellum, no actual extant structure truly represents either of these.
To get any real idea of what kind of flagellum all extant injectisomes derive from would require ancestral reconstruction of the last common ancestor of all injectisomes, and ancestral reconstruction of the nearest nodes in the phylogenetic tree of all flagella. And then structural comparisons made of these reconstructed node systems. It is likely that these older flagella look more injectisome-like, and that ancestral injectisome looks more flagellum-like, than any comparison of extant systems indicate. All extant systems are derived from more similar common ancestors.
Now having to spell that out in a popular press book would be ridiculous. Heck, it would be ridiculous to expect authors of articles comparing flagella and injectisomes to have to spell that out too, as anyone reading the primary literature in molecular evolution must be assumed to be aware (and any evolutionary biologist, of which Richard Dawkins is one, be aware) that extant species, genes, structures, or what have you, generally don’t really descend directly from each other, except on extremely narrow timescales close to the present day. And that as you go back in time on phylogenetic trees where nodes are closer in time, you generally also expect greater similarity.
Specifically injectisomes likely evolved close to the origin of eukaryotes, so would be rather ancient structures by any measure, even while derived from flagella. They have had quite a long time to diverge and specialize from when they first emerged.
Uhm, I don’t see anything factually incorrect in what Dawkins states there. The TTSS(in both Type-III secretion systems alone, injectisomes, and in flagella) consists in part of an ATP synthase, which is the actual “motor” that both generates the torque necessary to spin the flagellum, while also powering the translocation of proteins in all these structures. That ATP synthase is part of the TTSS, so Dawkins is absolutely right to say that the TTSS is both tugging molecules through itself while also tugging the molecules of the axle of the flagellum.
That’s just not true. The entire section entitled “3.2.5. The relationship between type III export and the F1F0-ATP synthetase” argues from numerous observations of functional and structural homologies that such a system likely predates the flagellum itself. This at least gives us ground to think at least some TTSS-parts(the ATP synthase parts) of the flagellum predates the flagellum.
Why should something he doesn’t say gives us ground to posit a TTSS ancestral to flagella gives us ground to think that? He doesn’t say it does. I don’t think it should either.
Glad we agree on that.
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12 posts were split to a new topic: Comments on Buggs: TSS and the Flagellum
I agree with this, and likewise with your previous point that:
My understanding is that Dawkins is a Zoologist, not a Microbiologist, let alone a Bacteriologist. My further understanding, from Rumraket, is that his information derives from Kenneth Miller. My understanding is that Miller is a Molecular and Cell Biologist, so is likewise probably not the original source of this research. That this third-hand information got a little garbled and/or may be a little out of date is therefore not entirely surprising.
If Dawkins’ book were a biology textbook, this might be cause for concern within the scientific community, and possibly warrant some attention from Nature. But it is not even a ‘pop science’ book. It is a book of counter-apologetics. As such, it should arguably be evaluated according to the standards of scientific accuracy in apologetics. And given the outright balderdash I’ve heard of in that field, a bit of garbling does not appear to warrant any substantive attention.
This would appear to leave us with the fact that Buggs is an ID advocate, as the best explanation for his focus on Dawkins comments about the flagellum. The fact that Buggs is likewise not a Microbiologist, let alone a Bacteriologist, so is less likely to be simply concerned about accurate representation of his own field, contributes to this impression.
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But if ID isn’t consistent with the evidence (which it isn’t), there’s nothing left but discussing hearsay. Buggs completely jumps the shark by labeling evidence with Dawkins’s name.
The alternative to harping on what people say would be to test an ID hypothesis, which ain’t gonna happen.
Indeed.
Exactly. Again, false, straw-man claims that something extant evolved from another extant something are an identifying characteristic–an ID, so to speak–of IDcreationism.
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I think I’ve found the source of our disagreement: While you read Buggs’ post as an attempt to discredit the “case for flagellum evolution”, I read it as an attempt at correcting discredited claims about flagellum evolution which have reached a wide audience. As he writes in his first post on Dawkins:
It is with hesitation that I pen a blog post that could be construed as critical of Richard Dawkins FRS. Many members of this Nature Ecology & Evolution Community may have first come to understand the Darwinian mechanism through his lucid prose. His books have sold by their millions and feature on many an undergraduate reading list. School science teachers around the globe teach what they have learned from him. In the public imagination he is our greatest living evolutionary biologist.
But for these reasons it is important to point out where he has erred. Or at least, where scientific progress has discredited his claims. Because of his wide influence, it is in the interests of the public understanding of science that any mistakes he has made should be explicitly corrected. [My emphasis]
It is thus irrelevant whether more nuanced and sophisticated cases for flagellum evolution have been made by other people in technical journals. Buggs’ point is that Dawkins is overstating the case for flagellum evolution, and that his words are reaching a lot of people who will never read those other nuanced technical arguments. That makes correcting Dawkins’ claims a valid exercise.
And Dawkins’ use of the TTSS isn’t a “technicality” or some minor detail in what is otherwise a sound argument. The passage I quoted makes up the total of Dawkins’ case for the evolution of the flagellum. Taking away the “[injectisome-like]-TTSS-to-flagellum” transition leaves nothing behind.
Of course. Extant injectosomes are derived from ancestral flagella.
I suppose it would, but who is demanding that Dawkins does that? None of this has any bearing on whether (extant) injectisomes are derived from (ancestral) flagella.
Torque is believed to be generated by the interaction between the motor/stator complex (MotAB) and part of the C-ring/rotor (FliG); see Santiveri et al. 2020. Neither of these are believed to play a role in the protein secretion of the flagellum. At least not to my knowledge. But I’d be happy to be shown wrong.
Yes, but the F-type ATP synthase is not a TTSS. And citing this in support of Dawkins by calling the ATP synthase parts “TTSS-parts” is just a play on words. We might as well call them “flagellum parts”.
There’s a far cry from Dawkins’ (implicit) claim that an injectisome-like TTSS was coopted into the flagellum, accounting for about ten gene products, and Matzke’s claim that three gene products (FliHIJ) were coopted from the ATP synthase. Dawkins overstates the case, Matzke’s more nuanced and sophisticated argument notwithstanding.
I’m referring to section “3.2.3. An ancestral type III secretion system is plausible”, in which Matzke writes that “a general argument for the plausibility of a primitive type III export system can be constructed on the basis of analogy.” I took you linking to Matzke’s FAQ as you claiming that there were grounds to posit a TTSS ancestral to flagella, which is what Matzke discusses in that section. If you don’t think there are grounds to posit a TTSS ancestral to flagella, I’d be more than happy to let this part of the discussion go.
I read it as an ad hominem attack on Dawkins.
If you disagree, please explain how one can call evidence “Dawkinsian” or “_______ian.” Can you point to a single case of anyone doing so?
Books are not the place to find scientific cases any more. That’s why IDcreationists focus so much on them. 
I would suggest that Buggs is being disingenuous here. I seriously doubt if The God Delusion is on any undergraduate Biology reading list.
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I don’t know enough about the US education system to say whether or not that claim is correct. However, here is an interesting factoid: Mark Pallen and Uri Gophna’s paper on the bacterial flagellum and the type III secretion system (Pallen & Gophna 2007) isn’t (just) directed at undergraduates. In this, they write: “Readers are referred to recent reviews for more extensive discussion of the evolution of complexity, of bacterial flagella and of type III secretion.” Guess which book is among those “recent reviews” cited in this professional scientific paper? Yup; Dawkins’ The God Delusion.
In any case, it is of minor importance if Dawkins’ book is read by undergraduates or “merely” by millions of interested laymen. I doubt Buggs’ blog post is on any undergraduate reading list, and yet, we expect the claims it makes to be correct, and we should consider it a valid exercise to publicly criticize it if it doesn’t. Dawkins’ widely read book shouldn’t be held to a lesser standard.
I don’t agree. While I am generally sympathetic to any endeavor that seeks to correct erroneous public statements made by scientists(and statements by Richard Dawkins are no exception), it is pretty clear Buggs’ aims go far beyond merely getting the view on the relative history of injectisome and flagellum-evolution right. As is typical of ID proponents he is appears to be trying to paint a picture where there is no workable case for flagellum evolution at all, and this is just the latest step in that endeavor.
And it’s just not true that without a phylogeny implying that flagella derive from injectisomes leaves one with “nothing behind”. Dawkins could simply have said what Kenneth Miller said, that the existence of the T3SS both in the flagellum and in related structures provides an excellent rebuttal to the claim that the flagellum being irreducibly complex with respect to the motility function prevents the possibility of it’s gradual evolution.
I believe that I was clearly writing that in the context of Buggs direct flagellum-to-injectisome comparisons, where he works to extract this view that the extant structures have such apparent dissimilarities that their relatedness is cast into doubt.
You are right on that. The motor/stator complex is not involved in protein translocation, that job falls on another part of the TTSS, which like the motor/stator complex can also utilize protons or sodium ions to power the translocation of proteins. It is this part that can also be coupled to ATP hydrolysis.
Now this is just ridiculous I have to say. You first wrote:
“Why would [this] give us any grounds to posit a TTSS ancestral to flagella?” Well I assume by [this] you mean what you quote Matzke write in the sentence immediately before, which is “any secretion system that exists will sooner or later get coopted for diverse functions, including virulence, in various lineages.”
So you quote that, and then ask seemingly rhetorically why that quoted sentence should give us grounds to posit a TTSS ancestral to flagella? But nobody, including Matzke, says it does. Which is why I am perplexed by you quoting that and then complaining about it.
So now you come back after I express this confusion about you quoting something implying it is supposed to serve as an argument for something which it clearly is not, and now you change your story to say you were talking about a different thing instead of the bit you quoted.
But no, I do think there are grounds for positing a TTSS ancestral to flagella, and part of those reasons are argued by Matzke in the section 3.2.3. An ancestral type III secretion system is plausible, and in 3.2.5. The relationship between type III export and the F1F0-ATP synthetase . I think there are more, for example that protein complex assembly order reflects evolution, and flagellar assemply has the T3SS assembled before flagellum-specific parts like rod-hook-filament are added later.
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How is this blog post “a joke”, or “embarrassing pablum”? I think this language of attack is clearly not appropriate for the forum @swamidass
As the majority of flagellar components (something like 34/48) have been inferred to be present in the Last Bacterial Common Ancestor, then I think it will be difficult to infer much regarding something like the T3SS as ancestor of the flagellum (which was a popular hypothesis), on the basis of actual evidence. Feel free to disagree if you like, but try to stick to the science please.
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I agree that more respect is warranted. There is sufficient reason to question Bugg’s argument that there should be no need to use attack language.
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We have to ask why Buggs did not commence his exercise in the ID camp that has produced literature which not only contains scientifically discredited claims, but has a vast audience as well most of whom are unlikely to check the primary literature for findings responsible for the discrediting of tested ID claims like irreducible complexity.
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Whether there is reason to question the argument is irrelevant to whether this kind of exaggerated denunciatory language is warranted. The language is petty and should be unacceptable either way.
In any case I think the point of the post is legitimate and worthy of scientific discussion - a view of flagellar evolution which is very widely held and was popularised by Dawkins (interestingly Prof. Buggs’ great-grand-PhD supervisor), is now obsolete or seems to need to be nuanced to a point where it’s not really supported evidentially.
Also, people dredging up an article that he wrote as a PhD student 14 years ago as proof for what he thinks now strikes me as rather silly. I don’t know what his exact views are, but I was a creationist of some not very well defined sort as a younger person, and my views on this and various other things have changed. Most people’s do over 14 years. It’s best to stick to the science if the aim is to persuade, otherwise any legitimate points will be obfuscated by a fog of irrelevant comments. If the aim is to insult or signal one’s disapproval, then PS is probably not the right place.
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