If you think that referring to someone’s bad writing as a joke or as pablum is “attack language” then you will have to dramatically reform the expectations for moderation at PS. We all know that’s not going to happen and we all know that isn’t remotely an expectation on this form. So, I’ll leave all the good Christians to discuss flagellar phylogenetics after careful reading of a 15-year-old non-science book by Richard Dawkins. Ignoring you all will save me a lot of time.
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At a certain level of ‘sufficient reason’, the language in question stops being ‘attack language’ and becomes ‘accurate language’. Things that are sufficiently bad can’t be accurately described without sounding like an attack.
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I seriously doubt that is the chief aim of Buggs’s blog post.
The irony of writing this in defense of an article lambasting something Dawkins wrote 15 years ago aside, Buggs’s earlier op-ed piece provides a useful piece of context which allows the reader to better hear the creationist dog whistles contained in his more recent piece.
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Calling evidence “Dawkinsian” is legitimate?
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That the flagellum evolved from the injectisome? Please show evidence that this view is widely held.
Yeah, no. I don’t think so. I don’t think the view is widely held, and I definitely don’t think Dawkins has popularized it. But you’re of course welcome to show that widely held views of flagellum-evolution are derived from The God Delusion.
In my experience, most people got their views on flagellum evolution from Kenneth Miller’s rebuttal to the concept of Irreducible Complexity.
This seems quite confused because it was apparently implied by phylogenetic evidence already back in 2003 when Matzke wrote his article on flagellum evolution, that injectisomes derive from flagella. And it’s still not exactly clear, though a plausible reading of his words, that Dawkins was saying that the flagellum derived from the injectisome. He uses the term TTSS, which can refer both to the injectisome and to the core protein export apperaturs. This whole debacle is a ridiculous storm in a teacup, and serves as just another example of the Dawkins-obsession of ID proponents.
The whole question of the flagellum’s evolution originally arose with Michael Behe’s claim that the system presents an insurmountable barrier to evolution by the structure being irreducibly complex. Finding that subcomponents of the flagellum can function on their own puts a lie to this claim, and while that doesn’t show us (by that alone) how the flagellum did in fact evolve, it shows us a plausible pathway by which it could have. The argument being responded to is that it couldn’t have. That is the purpose of arguing it is IC.
Whether the flagellum is now so widely distributed that it’s gradual origin can no longer shown on a phylogenetic tree is besides the point.
One must also note that the people who are so bent on declaring the flagellum’s evolution impossible, or without evidential basis, have no model of their own for it’s origin, and couldn’t even dream of how to come up with evidence for it.
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I don’t know if that is clear at all. As @Zachary_Ardern points out, we’re using a 14 year old article as a lens to interpret all of Buggs’ current actions through.
But even if Buggs had some nefarious ultimate aim in writing his blog post, how would that affect whether his criticism of Dawkins is correct?
You’re sympathetic to attempts to correct erroneous public statements made by scientists, and you agree that Dawkins’ statements are erroneous or at least highly misleading for an audience unaware of the technical niceties of TTSS terminology. So his statements deserve correction, but someone other than Buggs should have done so?
He could, but that would have been an entirely different, and much weaker argument. Consider the point made in this thread that swim bladders evolved from lungs, not the other way around; saying “lungs could have evolved from swim bladders” is a very different thing than saying “lungs did evolve from swim bladders”.
However, I can see how Dawkins could have been misled by Miller’s article, given that Miller also brings up the injectisome as a “precursor” to the bacterial flagellum.
I don’t want this discussion to devolve into hermeneutics. But here’s an attempt to make things clear: We were talking about a pre-flagellar TTSS. You refer me to Matzke’s TalkDesign FAQ. I go to the section of the FAQ in which Matzke adresses the plausibility of a pre-flagellar TTSS (section 3.2.3), explaining why I don’t think his arguments rise above “might’ve happened”. Whether Matzke himself used “plausible” in a stronger sense than “might’ve happened” is an open question, but I took you to be using section 3.2.3 to argue this stronger point.
No story is being changed; my comments on Matzke’s FAQ have always been directed at how I took you to be using the FAQ.
In your latest reply to me, you write:
But if you think that section 3.2.3 provides the grounds for positing a TTSS ancestral to flagella, why do you object to me evaluating section 3.2.3 in terms of whether it provides grounds for positing a TTSS ancestral to flagella? I feel that we’re talking past each other here.
As for section 3.2.5, the F-type ATP synthase isn’t a TTSS, and rephrasing Dawkins’ argument in terms of the ATP synthase makes for a different and much weaker argument.
I find this less than convincing. The rod-hook-filament structure is located on the outside of the cell, which presents the cell with an engineering problem, as the size of the structure precludes constructing it inside the cell and moving it outside. Instead, the rod-hook-filament is constructed in situ by proteins being transported through the hollow structure and added to the tip as it grows. Given that the TTSS plays a key role in the construction of the rod-hook-filament, it is only to be expected that it is assembled first.
Well your naivete here is not something I can do much about. But you’re welcome to spend a decade arguing with ID proponents.
No, I agree it’s plausible Dawkins might have meant what you take him to write (he really could still be talking about the TTSS at the base of the injectisome and the flagellum, rather than the injectisome), thought even that isn’t really clear.
So what Buggs could have said is something like “depending on exactly what Dawkins meant, it might or might not be correct to say”. And then he could have linked Kenneth Miller’s article to show where Dawkins got his information and how this differs from that interpretation of Dawkins, and said something more about what biologists today hypothesize happened in flagellum evolution.
Instead he made a big deal about how this scenario Dawkins might or might not have intended to convey, is a popular hypothesis that has been falsified and is “no longer suitable for use by science educators and communicators” giving this misleading impression that something false is being taught out there and that apparently Dawkins is at fault for this, and how this leaves us with the flagellum being an “enduring mystery”.
There’s zero evidence that “science educators and communicators” are teaching injectisome-to-flagellum evolution, much less that this ever endured any period of being a particularly popular hypothesis even within the scientific community, and none is given for Dawkins’ supposed influence (“Dawkinsian evidence for evolution”) on these matter.
All of that is obvious spin.
Whatever value of “much weaker” you have in mind, it’s better than the zero models and zero evidence we get from ID.
Yes, and if someone says “they couldn’t” and then you give evidence to show that they could, then repeating the claim that they couldn’t and nobody knows anything and why would anyone ever posit such a thing seems like an exercise in denial.
Miller deliberately puts the word precursor in scarequotes because he’s responding to an argument that says any precursor to the flagellum is by definition nonfunctional. Not because he thinks giving an extant example of a functional T3SS is actually a precursor. And he’s not talking about the injectisome, but the T3SS within the flagellum.
Here’s where Miller is using the word precursor:
The most powerful rebuttals to the flagellum story, however, have not come from direct attempts to answer the critics of evolution. Rather, they have emerged from the steady progress of scientific work on the genes and proteins associated with the flagellum and other cellular structures. Such studies have now established that the entire premise by which this molecular machine has been advanced as an argument against evolution is wrong – the bacterial flagellum is not irreducibly complex . As we will see, the flagellum – the supreme example of the power of this new “science of design” – has failed its most basic scientific test. Remember the claim that “any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional?” As the evidence has shown, nature is filled with examples of “precursors” to the flagellum that are indeed “missing a part,” and yet are fully-functional. Functional enough, in some cases, to pose a serious threat to human life.
That doesn’t appear to me like Miller actually thinks the injectisome is a precursor to the flagellum.
Unfortunately it seems this is largely the basis for having this argument in the first place. What did someone mean by their words, and what should we take from it? You quoted something and then wrote what looked like a response to the quoted material. The response did not make sense as a response to the quoted material, and I pointed this out. Then you wrote instead that you were responding to something else, not what you quoted specifically.
You’ve clarified that you weren’t responding to the quote specifically, but the section more broadly. Okay, fair enough. But what Matzke writes in the sections linked are then the reasons given for positing a T3SS(not an injectisome) prior to the flagellum, not the thing you quoted. I’m happy to let this rest now.
I really don’t see what is so difficult to understand here. There’s a dialectical context, and then there are methods of historical inference in evolutionary biology.
The dialectical context here is that a challenge was put forward. Michael Behe originally claims to have found a principle that makes evolution(of the system in question) impossible, and gives an example of a system he believes conforms to this principle in an effort to undermine public science education in the US. Entirely understandably concerned biologists then try to answer his challenge by showing how the system in question could evolve.
That explains why anyone would even bother making a model for the flagellum’s evolution.
How does one generally try to answer questions about evolutionary origins? There is the phylogenetic method (show changes over time on a rooted phylogeny), ontogeny/assembly (what is constructed first, and what is added later?), pathway-length and gene-order(usually used on things like metabolic pathways, or particular gene operons to show how enzymes catalyzing particular reaction pathways, or genes are added one by one), and the structure-function method (where you try to work out how something works, and how parts of it could work by themselves). These are generally expected to correlate in various ways, and thus allows one to elucidate the origin and evolutionary history of something.
Some times the data is so good you can combine multiple different methods to piece the history of something together, other times much of the data is missing and all you can do is elucidate what could have happened based on the structure you have, without being able to show it on a phylogeny.
The phylogenetic method was not particularly enlightening, because reduced systems appear to generally nest within the flagellum clade and derive from flagella. That means that whatever happened prior to the flagellum’s origin can’t be elucidated by a phylogenetic tree alone. In the absence of phylogenetic data that allows you to extract a history for the flagellum, you go by other data that normally correlates with phylogeny when something with more parts originates. Generally speaking, complex systems originate first from simpler systems incrementally. So instead Matzke employs the other methods, such as assembly order, causal chain of dependence, and structure and functional analysis.
So to move on more specifically, why would anyone posit the T3SS as ancestral to the flagellum, even without a phylogenetic tree as evidence for this inference? Well as you should be able to piece together by yourself by now, when something in evolution consisting of many parts come to exist, it’s usually incrementally/gradually from simpler things with fewer parts. This is so basic and simple an inference it shouldn’t be controversial to anyone but the thickest fundie simpletons. So already there it makes perfect sense to postulate partial structures as precursors to the full thing.
So in analysis of flagellar structures, the T3SS then makes for an obvious choice due to constituting a simpler system, it’s central role in the flagellum upon which the flagellum depends, and it’s ability to function as a useful system on it’s own.
“I don’t know how to refute an incredulous stare.” - David Lewis
Well if assembly order with T3SS before rod-hook-filament in this case is physically necessary, then all the more reason to posit it ancestrally to the flagellum, isn’t it?
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Then let’s use this 2 month old video, which appears to have Buggs [censored] ID claims, instead:
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The more I’m thinking about this interpretation of Dawkins, the more strained it seems.
Dawkins starts out by telling us that the T3SS is “one of several systems used by parasitic bacteria for pumping toxic substances through their cell walls to poison their host organism.” To anyone not familiar with the technical nomenclature on T3SS, there is nothing in this statement that suggests that Dawkins is using the term T3SS to refer to anything other than the injectisome. There is certainly nothing to suggest that by T3SS Dawkins actually means a subsystem present in both flagella and injectisomes.
Dawkins follows this up with a discussion of how the T3SS works, then writes: “The protein molecules that form the structure of the TTSS are very similar to components of the flagellar motor. … 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.”
This argument makes no sense at all if one suppose that Dawkins uses T3SS to refer to a subsystem present in both flagella and injectisomes. Only if TTSS is read as something distinct from flagella does the comparison with the flagella motor make sense.
Finally, Dawkins anchors his argument in terms of what was actually present (not what could have been present) before the origin of flagella: “Evidently, crucial components of the flagellar motor were already in place and working before the flagellar motor evolved.”
Given all of this, I think the most charitable interpretation of Dawkins’ word is the one I am advancing: That as a zoologist by training, Dawkins was not up to date on the technical nomenclature on T3SS (Desvaux et al.‘s paper urging a housecleaning in the nomenclature wasn’t published until 2006, the same year Dawkins’ book appeared), and he used T3SS to refer to something like the injectisome found in extant bacteria.
This understanding of the T3SS is certainly one any non-specialist reading his book (targeted at a lay audience) would have come away with, regardless of what Dawkins intended to convey. That alone makes correcting this false impression a legitimate exercise.
Sure, there are all kinds of things Buggs could have said. The thing is what he should have said. It sounds as if you think that Buggs should not have corrected an incorrect argument (on any straightforward interpretation) without proposing an improved version of the argument.
As mentioned earlier, I don’t know enough about the US education system to know if this claim is correct. I do know that Dawkins’ book is cited in Pallen and Gophna’s paper on the bacterial flagellum and the type III secretion system as a place to find “more extensive discussion of the evolution of complexity, of bacterial flagella and of type III secretion”, which makes it at least plausible that a version of the argument also found its way into an undergraduate course.
And even if the argument only found its way to millions of lay readers, that would not be an argument for not correcting it.
Tu quoque, I believe is the name of this fallacy.
If someone claims that lungs in fact evolved from swim bladders, it doesn’t make the statement true if that person was responding to a claim that lungs couldn’t have evolved. That lungs evolved from swim bladders is still false, even if the overall point the person was trying to make is correct.
It is not clear that Miller is using scare-quotes, as the context is him using actual quotes from Behe. From your own quote from him:
“Remember the claim that “any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional?” As the evidence has shown, nature is filled with examples of “precursors” to the flagellum that are indeed “missing a part,” and yet are fully-functional.”
If “precursor” is in scare-quotes, does that mean that “missing a part” also is? And if he isn’t using those terms in the same sense Behe is using them, then what becomes of his argument?
As for my original claim that Miller brought up the injectisome as a precursor to the flagellum, I worded that more strongly than I now, having re-read Miller’s article, wish I had done. Miller’s phrasing is more careful than Dawkins’, and it’s possible to interpret him as using T3SS to refer to only a subset of the injectisome. But he nowhere makes this distinction explicit, and then there’s this quote:
“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.”
Calling the T3SS “fully-functional” certainly gives the impression that Miller is talking about the whole structure, not merely a subset of it.
First of all, this is a classic overstatement of Behe’s thesis, which wasn’t about irreducibly complex structures being in principle impossible to evolve, but very unlikely. As he writes on page 40 of Darwin’s Black Box:
“Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin’s criterion of failure has been met skyrockets toward the maximum that science allows.”
Second of all, this is the “fake but accurate” defence. Like the incorrect claim that lungs evolved from swim bladers, Dawkins’ (on any straight-forward reading) incorrect claim does not become true, even if he was making an overall point that was correct.
Imagine Jones is accused of a murder that has taken place in New York. You tell me that “Jones was in New York at the time of the murder, as demonstrated by the police report.” I find the report, find the section entitled “Jones’ presence in New York is plausible”, and quote the argument being made in that section: That Jones cannot account for the last 24 hours leading up to the murder, which would have given him ample time to travel to New York and commit the murder. I reply that this argument doesn’t show anything other than the fact that Jones might’ve been in New York, not that he in fact was in New York.
You then ask why I’m responding to the claim that Jones in fact was in New York, when the police report never makes that claim (it only says it’s “plausible”). At my protestation that I was responding to the argument I believed you to be making, you reply that since I was quoting the police report, I must have been responding to the claims made by the report. But I wasn’t responding to the (vague) claim of the police report, but to your (stronger) claim, seemingly backed up by the report.
What I quoted are the arguments from section 3.2.3 (on the plausibility of an ancestral T3SS). If you believe there are some arguments from that section which I have not commented on, I’d be happy to hear them.
As for the other section you mention, 3.2.5 (on the F-type ATP synthase), that does not establish a pre-flagellar T3SS, for the simple reason that the F-type ATP synthase is not a T3SS.
So because complex structures are “usually” constructed incrementally from simpler structures, it must also be the for the flagellum? Using that logic, one would have thought that the first injectisome-like T3SS came from a simpler structure, instead of the more complex flagellum. But that would have been mistaken.
Only if the bacterial flagellum’s immediate precursor was a simpler system. That hasn’t been established outside some principle of complex structures “usually” arising from simpler structures.
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I wonder why you would describe it as a thesis instead of a hypothesis.
Has Behe lifted a finger to test it?
As time increases, the likelihood increases. Correct? Why doesn’t Behe acknowledge time in there?
A quantitative statement that includes no numbers. Given Behe’s pratfalls with misrepresenting the actual data for HIV (by a factor of infinity) and malaria?
In the latter case, we have Behe trying to cast doubts to rescue his claim that K76T and A220S must have occurred simultaneously in 2007 to support his quote mine from a review:
For example, another recent paper (cited by the first) on CQR in Cambodia (5) reported data showing that the mutations K76T and A220S were not necessarily associated with CQR, which is inconsistent with the great majority of other reports.
Versus the data:
https://www.pnas.org/content/111/17/E1759
Fig. 3.
Key mutational routes to CQR PfCRT. These schematics were constructed from the data presented in Fig. 2. The effect of a given mutation on the ability of PfCRT to transport [3H]CQ into oocytes is represented as an increase (green arrow; P < 0.05), a decrease (red arrow; P < 0.05), or no change (blue arrow; P > 0.05). The PfCRT haplotypes of the field isolates (underlined) and mutants are listed in Fig. 2. ( A ) The main mutational routes to PfCRTDd2. The introduction of both 76T and 75E (D32) results in a modest but significant level of CQ uptake and is the foundation of the routes leading to the Dd2, GB4, K1, China-e, and 783 haplotypes. The complete summary of the mutational pathways leading to PfCRTDd2 is presented in Fig. S7. ( B ) Mutational routes to PfCRTEcu1110. This pathway begins with the introduction of both K76T and N326D and leads to haplotypes such as Ecu1110, 7G8, and Ph1.
Krauze, why do you apparently think that someone who misrepresents (not misinterprets) the data this blatantly should be taken seriously as a scientist?
How did you quantify the relative complexities of those two structures?
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It makes no sense to try to correct a misleading claim without providing information on what is actually accurate. Laypeople who read the Buggs article in question might go away with the impression that all what evolutionary biologists (seemingly represented by Dawkins) thought about flagella evolution was wrong, hence, are back to square one, which is far from the truth.
Buggs merely pointed out Dawkins inaccuracy, without providing a more accurate description of the current state of knowledge on flagella evolution. Nothing was corrected.
No, but it seems to be the most likely pathway to the flagella.
I believe he used the word “usually” there to indicate that the evolution of highly complicated molecular systems like a flagella from simpler ones is a plausible route. He wasn’t dogmatic about it.
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What you say here probably makes sense in an evolutionary perspective, not in a design one. Take the example of a house. It is quite obvious that an architect will conceive nearly all aspects of the house before thinking about the foundations. However, when it comes to actualize the plan, the foundations come first, don’t they ?
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But then it’s also true that the first thing that came to exist is the foundations. Thus the foundations really existed prior to the house in time.
After some careful consideration of your argument I have changed my mind. I believe you are correct, that is the most plausible interpretation of Dawkins words. He does appear to have gotten the picture wrong, and I agree that there’s at least nothing wrong with seeking to correct his mistake.
It sounds like you’re saying it’s okay to leave people in the dark.
It would be much desirable when correcting someone to not only point out that what they are saying is wrong, but then to point out what the people from which you got your information are actually saying instead. Particularly when what those people say actually deviate from what you take them to say.
The full section reads:
These ID arguments were discussed – and dismissed – during the recent Kitzmiller versus Dover trial in Pennsylvania [12]. They have also been addressed in print [13]. Given the constraints of space, here we can only briefly outline some of the mechanisms that have allowed complexity to emerge from simplicity and present three case studies in the evolution of bacterial flagella and type III secretion systems. Readers are referred to recent reviews for more extensive discussion of the evolution of complexity, of bacterial flagella and of type III secretion [13–26].
That sentence is followed by a citation of 13 total references. It is unclear which of the mentioned categories The God Delusion (number 19 in the references) is being specifically cited for, but even if it really is cited specifically for it’s discussion of flagellum evolution, honestly, no. It’s not plausible that that one citation to The God Delusion out of 13, the rest of which are more specifically about Type-III secretion and flagella, has ended up forming the basis for a model of flagellum evolution in some graduate course.
That makes no sense as I have made no claim about the truth or rightness of some statement, nor excused wrong behavior based on any perceived failures in other people’s behavior. You made a sort of rhetorical evaluation (that some argument would be weaker if altered), and I responded that it would still be better than none at all. Which is true.
It remains perfectly fine because it shows that a system that does not have those parts still functions.
Yes he does, both very clearly depicted in figure 2 and in the surrounding text. He is very clearly talking about the protein export apparatus at the base of the flagellum.
Sure, and if someone claims there’s just no good reason to think the flagellum had simpler antecedents because you can’t show that on a phylogenetic tree of bacteria, that would also be incorrect, even though it’s true you can’t show that on a phylogenetic tree of bacteria.
That seems to me a distinction without a real difference. Either way Behe seems to suggest that the evolution of the complex system amounts to an event so unlikely it might as well be considered impossible. Whether you argue that on the basis of one big unlikely, or the dwindling odds of many smaller ones, the effect is the same. The IC system is effectively impossible to evolve.
Unfortunately that caveat never made sense. It’s not clear why an indirect route where intermediate steps have different functions would be less likely than a direct route where intermediate steps retain the same function through the system’s evolution. I’ve never seen any calculation that shows this.
Heck, it’s not even clear what is really meant by “direct” and “indirect” route. But this usually comes down to the Texas Sharpshooter Fallacy where the probability any long serious of changes is calculated after the fact. Like tossing a handful of dice ten times in a row and then calculating the odds of that particular series after it has already happened.
What the hell are you even talking about? What you write does not make sense to what you are quoting me say.
False analogy. You did not quote the argument being made for an ancestral Type-III secretion system. You quoted Matzke’s summary characterization of what has occurred to Type-III secretion systems since their origin, not the actual argument for their ancestrality.
The line you specifically quoted which provoked my perplexed response was: “any secretion system that exists will sooner or later get coopted for diverse functions, including virulence, in various lineages.”
That’s not the actual argument. I highly recommend you go back and read your initial post to get back on track because you seem totally lost.
Essentially not that far off, yes. It’s both an inference to the best explanation, and a rather straightforward inductive generalization from our understanding of the origin and evolution of complex structures. They begin simple, and grow more complex over time. And there are other ways of inferring how this occurred than by a phylogeny, though that is certainly the gold standard.
Now this is honestly rather obtuse. I don’t believe you couldn’t reason yourself a few steps further on your own, but okay. I’ll help.
The whole point here is to explain the origin of something complex. How did the complex thing come to exist where before it did not?
If you just push it back to reduction of an even more complex thing, none of the people demanding to know how the complex thing came to exist will be satisfied with that, as they just believe they then have an even greater challenge to be explained.
And generally speaking, even while many complex things came from even more complex things, those even more complex things in turn have evolutionary origins and histories of their own, and invariably in all cases where we can tell, it all goes back to simpler things once we go back far enough.
Be it the physiologies of multicellular organisms, the sizes and interconnections of metabolic networks, developmental pathways, molecular machines, or what have you.
Yes, biologists know (and some of us have spent a lot of time trying to get ID-creationists to understand) that evolution is not just one long unobstructed history of gradual increases in complexity, but that reductions definitely happen a lot too as organisms adapt to different specific ecological niches, and that this is not somehow contrary to evolution. That it is a process that can explain both the increases in complexity, and the reductions.
But what we are being challenged to explain here is the increases in/origin of complexity. That’s what people want to know. How did we go from there not being that impressive looking molecular machine, to there being that molecular machine? If somewhere along the way it got very complex and then a bit simpler again, everyone will just want to know how it became more complex in the first place.
Turns out there’s good reason to think that it was, and I have described the methods by which one can infer that even in the absence of a phylogeny.
Pretty much all of evolutionary biology testifies to this being the ultimate origin of all complex things.
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