Posted by Nick Matzke on September 17, 2006 09:51 PM

Anyone who has been a “creationism watcher” for any length of time is familiar with the venerable creationist tactic of “quote mining.” Since creationists, essentially universally, can’t (or don’t want to) deal with actual scientific data pertaining to evolution, they attempt maintain a facade of respectibility by quoting statements from biological authorities. This can take many forms; for example, for the 1987 Supreme Court Edwards v. Aguillard case, the creationist lawyer Wendell Bird, apparently with the help of Paul Nelson, assembled a massive 500-page brief that consisted almost entirely of thousands of quotes from authorities on every topic bearing on “creation science”, from astrophysics to biology to philosophy to religion. This failed to convince the Supremes, but Bird turned his brief into a large two-volume book, The Origin of Species Revisited. Other elaborations on creationist quote-mining include various “Quote Books”, including The Quote Book (1984 booklet, inserted in Creation magazine I believe) and The Revised Quote Book (1990) from Answers in Genesis, the Handy Dandy Evolution Refuter (now online), and Henry Morris’ That Their Words may be used against Them (comes with CD!). Then we have endless collections of quotes on creationist websites, 50 of which were recently surveyed and ranked against the Talk.Origins Quote-Mine Project. Sometimes these quotes evolve and mutate over time (here is an example from Of Pandas and People), and sometimes they even spontaneously generate from thin air, as with this imaginary quote from Clarence Darrow.

You may be saying, “Surely this is a problem, but only famous authorities get quote mined. It would never happen to me!” Think again. On September 5, 2006, an article I coauthored in Nature Reviews Microbiology on flagellum evolution was published on the NRM website as an Advanced Online Publication. Before the ink was even dry – heck, before the ink was even wet, the October issue hasn’t come out yet – Casey Luskin at the Discovery Institute is quote mining it! The mining occured in Luskin’s insta-response to the revised edition Chris Mooney‘s book The Republican War on Science. Check this out:

While intelligent design may be a persecuted minority viewpoint within the scientific community, it is nonetheless receiving increasing levels of scientific support and its proponents continue to publish their research in scientific publications which develop and extend the theory. Meanwhile, Darwinists feel compelled to respond to ID-claims in scientific journals, admitting that their own literature has lacked adequate responses to the ID arguments.[4]

[…]

[4] For a very recent example, see Mark J. Pallen and Nicholas J. Matzke, “From The Origin of Species to the origin of bacterial flagella,” Nature Reviews Microbiology, AOP, published online 5 September 2006; doi:10.1038/nrmicro1493 which writes, “the flagellar research community has scarcely begun to consider how these systems have evolved.”

As if once wasn’t enough, we actually get a two-fer, presumbably just in case the Discovery Institute’s readers missed it the first time around:

Moreover, if there is no scientific controversy, then why are Darwinists responding to the scientific claims of ID-proponents in leading scientific journals such as Science and Nature? One article recently published in Nature Review Microbiology [sic] acknowledges that “the flagellar research community has scarcely begun to consider how these systems have evolved.”[26]

[…]

[26] Mark J. Pallen and Nicholas J. Matzke, “From The Origin of Species to the origin of
bacterial flagella,” Nature Reviews Microbiology, AOP, published online 5 September 2006; doi:10.1038/nrmicro1493.

Wow. Do we get some kind of prize? A plaque welcoming us to the illustrious “quote-mined by creationists” club? [1] I feel a little bit like I’ve joined the big leagues now. [2]

Whipping the Flagellum in the Quote-Mine

This particular variety of quote-mining, which basically argues something like “devastating and dismissive rebuttals of us actually means we are being taken seriously scientifically!”, has been increasingly popular with the ID creationists in the period following Kitzmiller (the DI does the same thing to Chris Adami just after citing the Pallen/Matzke article – maybe their secret plan is to swell my head so much that it pops). Superficially, it’s a no-lose strategy – if no one rebuts the ID nonsense, then they can propagate it with no interference, and if someone gets annoyed enough to publish a rebuttal, well then, there’s a controversy!

The Problem with “there is a scientific controversy!”

The only problem with this is that vicious one-sided pummeling in the scientific literature (well, in review essays at least – Pallen and Matzke 2006, Adami 2006, and Bottaro et al. 2006 were all essays commenting on how the research literature pertains to the social controversy around ID) does not a real scientific controversy make. In a fake scientific controversy, like the one about ID, the scientific community occasionally gets annoyed enough to write an essay commenting on how this or that piece of recent research just happens to destroy a claim that is common in the social controversy outside the scientific community. On the other hand, in a real scientific controversy, both sides produce original research data that indicates one hypothesis or another, and the two (or more) hypotheses are considered sufficiently well-supported that peer-reviewers recommend publication in the research literature. Despite the Discovery Institute list of “peer-reviewed” “articles” that Casey Luskin has been promoting to anyone who will listen – and which actually consists of ragbag of (1) non-reviewed book chapters, (2) “peer-edited” chapters and articles that are evidently supposed to impress us because “peer-edited” sounds kind of like “peer-reviewed” even though it actually means “DI fellows like William Dembski or Stephen Meyer liked the article”, (3) articles that don’t even mention “intelligent design”, and (4) one non-research review article that didn’t even review the relevant literature – they haven’t got anything like that. Judge Jones knew it, Chris Mooney knows it, and deep down the ID movement knows it, as Paul Nelson admitted in print and as Michael Behe admitted on the stand under oath last year.

The First Problem with “[scientists admit] that their own literature has lacked adequate responses to the ID arguments”

Okay, so we have established that kicking the ID movement while it’s down does not equal a scientific controversy. What about the DI’s claim that Pallen and Matzke 2006 shows that:

Darwinists feel compelled to respond to ID-claims in scientific journals, admitting that their own literature has lacked adequate responses to the ID arguments.[4]

[…]

[4] For a very recent example, see Mark J. Pallen and Nicholas J. Matzke, “From The Origin of Species to the origin of bacterial flagella,” Nature Reviews Microbiology, AOP, published online 5 September 2006; doi:10.1038/nrmicro1493 which writes, “the flagellar research community has scarcely begun to consider how these systems have evolved.”

There are several very sneaky things going on here. Now, we meant what we said: “the flagellar research community has scarcely begun to consider how these systems have evolved.” This is quite true, at least in print (I am aware of informal discussions amongst flagellar researchers on the question). Leaving out work not by flagellar/T3SS specialists, there are two major articles on the relationship between flagellar and non-flagellar Type 3 Secretion Systems (F-T3SS and NF-T3SS), some discussions of this work in other papers, many papers documenting the specific homologies of flagellum proteins, and finally Pallen et al.’s 2005 paper that contains a bioinformatics survey of flagellar components and some more extensive discussion of the evolution question. This is actually quite a lot of evolutionary work. But (at least until Pallen and Matzke 2006), no one in the flagellar research community had really sat down and published a survey of all of this relevant data – took a synoptic view of all of the known homologies, for instance – and boiled it down to a basic model for how the flagellum evolved.

But notice sneaky implication #1: the DI article suggests that “Darwinists” [3] have had no “adequate responses” at all to the flagellum argument. But this is not what we said. We said that the flagellar research community hadn’t done much synthetic work producing an evolutionary model. That doesn’t mean that no one had done such work. In fact, just to be clear on this point, we kicked off the article by citing Kenneth Miller’s testimony at the Kitzmiller v. Dover trial:

Kenneth Miller, who appeared as a witness for the plaintiffs, elaborated, in non-technical terms, some of the arguments against the notion that the flagellum is irreducibly complex (see Further information for links to trial material); he and others have also done so in print [1,2]. Crucially, Miller pointed out that the flagellum is modular, in that the T3SS that is responsible for flagellar protein export constitutes a functionally intact subsystem capable of performing a useful function (protein secretion) in the absence of the rest of the flagellar apparatus.

[…]

1. Musgrave, I. in Why Intelligent Design Fails: a Scientific Critique of the New Creationism (eds Young, M. & Edis, T.) 72–84 (Rutgers University Press, Piscataway USA, 2004).

2. Miller, K. R. in Debating Design: from Darwin to DNA (eds Dembski, W. & Ruse, M.) 81–97 (Cambridge University Press, New York, 2004). [Miller’s article, entitled “The Flagellum Unspun: The Collapse of Irreducible Complexity” is online at Miller’s website, along with another one.]

So, not only do we say that Miller successfully made crucial points, we also cite what we think are two very good book chapters (one by PT poster Ian Musgrave) where biologists elaborate the arguments and propose evolutionary models basically similar to ours. (And even if Kenneth Miller and Ian Musgrave didn’t exist, there are other responses to ID arguments that are more general, but still adequate. E.g., it is a valid argument to note that “Biologists don’t yet know everything about everything” does not support “IDdidit.”)

So, sneaky implication #1 about our quote goes down the drain. But if the existing arguments were adequate, why did we write the article? Well, knowing more about a question is always better. As we note just after the above passage,

However, there are additional arguments, which we elaborate below, in favour of viewing bacterial flagella as evolved – rather than designed – entities. (emphasis added)

In other words, Ken Miller’s testimony and the chapters by Miller and Musgrave are great, but there is even more evidence that makes the ID argument flagellum untenable.[4]

Obligatory Trial Detour

To give you a little background on why we saw this was important, ever since my 2003 Big Flagellum Essay (updated!) I have been gathering papers that document homology or inessentiality for flagellum proteins. Even before the trial started, I knew that the common ID talking point – that, apart from the Type 3 Secretion System, “the other 30 proteins are unique” – was just wrong (see my previous PT post on this point). When Scott Minnich wrote in his expert report, “the other thirty proteins in the flagellar motor (that are not present in the type III secretion system) are unique to the motor and are not found in any other living system”, I knew we had a potential scientific “gotcha” that would be scientifically devastating (at least I thought so). You can see this strategy explored somewhat in Minnich’s deposition, where we showed that Minnich didn’t have a clue about the homologies of the flagellum motor proteins, MotAB, to the nonflagellar proteins TolQR and ExbBD (pp. 180-185).

So, during the trial, I lobbied enthusiastically for trying to get this evidence into court somehow. The problem was that any review of homologies would require a lawyer (or Ken Miller) to read into the record passages from a dozen or more articles, and even if this onerous procedure was done, it wasn’t clear that a nonspecialist judge would “get it.” So – proving, by the way, that the plaintiffs had some very good lawyers – we never attempted this particular cross. In the end, Minnich did not the repeat the “30 unique proteins” statement during his direct testimony, and since the expert report is not typically introduced into evidence, there was no strong reason to rebut it. This was the only (very, very, very minor) regret I had in the case.

Readers can now see that while Ken Miller did get the basic points across in court (and they are admirably laid out in the Kitzmiller decision), there is a great deal more that science can say about the evolutionary origin of the flagellum. And that is what is done in the NRM article. Among the points we make:

1. There is no such thing as “the” bacterial flagellum. There are thousands, maybe millions, of variations on the bacterial flagellum. Some of these variations are minor, but others are substantial (I blogged another example recently):

Many new flagellar systems have been discovered through genome sequencing – a trend that is likely to increase with time. For example, over three hundred flagellin sequences were obtained in a single sequencing project that focused on samples from the Sargasso Sea. By even the most conservative estimate, there must therefore be thousands of different bacterial flagellar systems, perhaps even millions. Therefore, there is no point discussing the creation or ID of ‘the’ bacterial flagellum. Instead, one is faced with two options: either there were thousands or even millions of individual creation events, which strains Occam’s razor to breaking point, or one has to accept that all the highly diverse contemporary flagellar systems have evolved from a common ancestor.

2. Within this diversity, bacterial flagella show the same evidence of being subject to the same evolutionary mechanisms as other systems – for example, with vestigiality, internal duplications, duplications of the whole system, modification for different environments, etc.

3. The axial proteins (rod, hook, linker, filament) are all related to each other:

Beyond the common ancestor

Despite this diversity, it is clear that all (bacterial) flagella share a conserved core set of proteins. Of the forty or so proteins in the standard flagellum of S.typhimurium strain LT2 or E. coli K-12, only about half seem to be universally necessary (Table 1). This reduced flagellum is still a challenge to explain, but if one accepts that all current flagellar systems diverged from their last common ancestor (the ur-flagellum), why stop there? All flagellins show sequence similarity indicative of common ancestry (homology). But then all flagellins also share homology with another component of the flagellar filament, the hook-associated protein 3 (HAP3) or FlgL (as is evident from the application of InterProScan to FlgL from E. coli). Therefore, although the ur-flagellum contained flagellin and HAP3, these two proteins must have evolved from a common ancestor in a simpler system that contained only one flagellin-HAP3 homologue. Similarly, six proteins from the rod (FlgB, FlgC, FlgF and FlgG), hook (FlgE) and filament (HAP1/FlgK) show sequence similarities indicative of common ancestry. Therefore, the flagellar rod–hook–filament complex has clearly evolved by multiple rounds of gene duplication and subsequent diversification, starting from just two proteins (a proto-flagellin and a proto-rod/hook protein) that were capable of polymerization into an axial arrangement.

4. Only about half of the proteins of the “irreducibly complex” bacterial flagellum are universally required.

5. Most of the required proteins have known homologs to other proteins, in exquisite contradiction to numerous statements from leading ID advocates (See my previous PT post and the included Table 1).

6. The bacterial flagellum is not the only path to motility, and there are many potential “starting points”:

Although the evolution by random mutation and natural selection of something as complex as a contemporary bacterial flagellum might, in retrospect, seem highly improbable, it is important to appreciate that probabilities should be assessed by looking forward not back. For example, from studies on protein design it is clear that creating proteins from scratch that, like flagellin, self-assemble into filaments is not very difficult. Furthermore, it is clear that there are many other filamentous surface structures in bacteria that show no apparent evolutionary relationship to bacterial flagella. In other words, there are plenty of potential starting points for the evolution of a molecular propeller. Evolution of something like the flagellar filament is therefore far less surprising than it might at first seem. In fact, microorganisms have adopted other routes to motility besides the bacterial flagellum. Most strikingly, although archaeal flagella superficially resemble bacterial flagella, in that they too are rotary structures driven by a proton gradient, they are fundamentally distinct from their bacterial counterparts in terms of protein composition and assembly.

7. There are even some examples of potential “intermediate forms” in modern systems (the NF-T3SS filament EspA is used as an example).

One would think that, especially given #4 and #5, the only responsible thing for the Discovery Institute people to do at this point is to issue a correction and admit that many of their previous talking points about the flagellum – their favorite system – were badly wrong and were due to poor research. But no, what we’ve got instead is quote-mining of Pallen and Matzke 2006 – and, I should add, in the very same document the Discovery Institute continues to cite Meyer and Minnich’s 2003 conference proceedings article (which was the original source of the “30 unique proteins” mistake in Minnich’s expert report) as if it is authoritative.

The Second Problem with “[scientists admit] that their own literature has lacked adequate responses to the ID arguments”

Here comes sneaky implication #2: Even if it were true that we thought that “Darwinists” “lacked adequate responses” to arguments about the flagellum, this would not mean, as the DI article implies, that we thought that science lacked “lacked adequate responses” to “the ID arguments” in general. Research on the evolutionary origin of the flagellum has been starting up in the last few years, but the situation is much different for other biochemical systems. Famously, immune system research has been conducted with a clearly evolutionary, comparative framework for a hundred years, and was quite vigorous even in the 1970s. In the Annotated Immune System Evolution Bibliography, I laid out some of the reasons why, out of Behe’s various “irreducibly complex” systems, the Plaintiffs in Kitzmiller put extra emphasis immune system (although we did address blood-clotting and the flagellum also):

As it happens, there is probably more scientific literature directly on the evolution of the immune system than on the other three systems put together (we can chalk this up to (1) the long tradition of evolutionary and comparative studies in immunology; (2) the age of the discipline (going back to the 1800’s); and (3) the massive amount of medical research money available for studies of the immune system, for obvious reasons). So, while Behe makes various mistakes on the other systems, many also discussed at trial, he is most dramatically wrong about the immune system literature.

And better yet, stunning advances have been made in the last 10 years. Behe found this out to his chagrin at trial, and notably, three of us PT posters wrote an essay for Nature Immunology laying all of this out specifically to head off the Discovery Institute folks when they began trying to rehabilitate Behe’s trial performance. Now, the inevitable has just happened, and yet the DI has yet to even acknowledge the existence of the Nature Immunology article, let alone rebut it. Perhaps they are afraid that some of their readers will begin to realize that the ID movement’s confident claims are not all they cracked up to be. But until the ID advocates actually grapple seriously with the evolutionary immunology literature, they are not even attempting to be serious players in a “scientific debate.”

Our actual point

No quote-mine rebuttal is complete without putting the quote in context. There is really no way to stop between the mined quote and the end of the essay, so, without further ado, I quote the end of the article:

However, the flagellar research community has scarcely begun to consider how these systems have evolved. This neglect probably stems from a reluctance to engage in the ‘armchair speculation’ inherent in building evolutionary models, and from a desire to determine how a system works before wondering how it got to be that way. However, there are several good reasons for adopting an evolutionary approach to flagellar biology. Assignments of homology can provide insights into function, and can provide a framework for interpreting the sequence data in the post-genomic era. The abundance of these data indicates that current studies are looking at the ‘tip of an iceberg’. Recently, genome sequencing revealed that Desulfotalea psychrophila, a sulphate-reducing bacterium from permanently cold Arctic sediments, has the largest of all known flagellin genes, but without a ‘bigger-picture’ view of flagellar biology, we have no idea why. Furthermore, an evolutionary comparative approach fits in perfectly with the current zeitgeist, with its emphasis on evolutionary systems biology.

Notwithstanding the good scientific reasons for new forays in this direction, the lack of a scientific literature on flagellar evolution also has another undesirable consequence – it leaves open the suspicion among members of the public that maybe there is some mystery here, that maybe the ID proponents do have a point. Although all experts in this field agree that there is nothing to these claims, as Wilkins has recently pointed out, in these politically charged times, it is no longer enough to say, for example, that bacterial flagella evolved and that is that. Instead, scientific experts have to engage with a sceptical public.

Scott Minnich speculated in his testimony that studies on flagellar evolution need not be restricted to sequence analysis or theoretical models, but that instead this topic could become the subject of laboratory-based experimental studies. But obviously, one cannot model millions of years of evolution in a few weeks or months. So how might such studies be conducted? One option might be to look back in time. It is feasible to use phylogenetic analyses to reconstruct plausible ancestral sequences of modern-day proteins, and then synthesize and investigate these ancestral proteins. Proof of principle for this approach has already been demonstrated on several NF proteins. Similar studies could recreate plausible ancestors for various flagellar components (for example, the common ancestor of flagellins and HAP3 proteins). These proteins could then be reproduced in the laboratory in order to examine their properties (for example, how well they self-assemble into filaments and what those filaments look like). An alternative, more radical, option would be to model flagellar evolution prospectively, for example, by creating random or minimally constrained libraries and then iteratively selecting proteins that assemble into ever more sophisticated artificial analogues of the flagellar filament. Another experimental option might be to investigate the environmental conditions that favour or disfavour bacterial motility. The fundamental physics involved (diffusion due to Brownian motion) is mathematically tractable, and has already been used to predict, for example, that powered motility is useless in very small bacteria.

The final word

Like Darwin, we have found that careful attention to homology, analogy and diversity yields substantial insights into the origin of even the most complex systems. We close with a quotation from the closing chapter of The Origin of Species that applies as well to a bacterial flagellum as to any other evolved entity:

“When we no longer look at an organic being as a savage looks at a ship, as something wholly beyond his comprehension; when we regard every production of nature as one which has had a long history; when we contemplate every complex structure and instinct as the summing up of many contrivances, each useful to the possessor, in the same way as any great mechanical invention is the summing up of the labour, the experience, the reason, and even the blunders of numerous workmen; when we thus view each organic being, how far more interesting – I speak from experience – does the study of natural history become!”

Just to head off another quote-mine, we did debate whether that last Darwin quote gave an opening to the ID guys (They are terribly bad at analogies. “A ship is designed!” Sigh.). But on balance it seems pretty clear what Darwin is getting at, and most people can tell an analogy when they see one. So the more people that see it, the better.

In Conclusion

That about covers the basic points that need to be made. Once again, we have seen the truth of the dictum that it takes pages to rebut a claim that a creationist can fire off in a sentence or two. But I think that in doing so, we may have an interesting result: assuming the print version of the article comes out on October 1, due to Advanced Online Publication, we have a creationist quote-mining the article at T-minus-16-days, and we have the response of the outraged (co)author at T-minus-14. That’s gotta be some kind of record.

Notes

Note: citations omitted from quotes of the NRM essay.

[1] (Founding members: C. Darwin, T. Huxley. Past president: S.J. Gould. Current co-presidents: C. Woese, S. Conway Morris.)

[2] (A very tiny little bit. I am fully aware that I am an ant among giants.)

[3] “Darwinists”, by which the folks at the Discovery Institute mean “nasty atheist-materialists”, but with which they label anyone who accepts modern evolutionary theory, plus judges who rule against them.

[4] I hesitate to say that ID is “disproved”, since that implies that ID is testable. To head off the common half-baked catcall of “You say is both falsified and unfalsifiable, you are contradicting yourself!” I will spell it out: creationist objections to evolution are testable, because evolution is testable – and the data has shown that the creationist/ID objections have no merit, as was elaborately evidenced during the Kitzmiller trial. However, the ID movement’s “positive” arguments for design are untestable, basically because ID advocates invoke an unconstrained supernatural power to explain everything they don’t understand. This is all quite clearly spelled out in black-and-white in the Kitzmiller decision, but the ID guys still have trouble getting it.