Recently in Flagellum evolution Category

Junker_Scherer_2009_edition6.jpgI just came across what is apparently a major online revision to the German creationist textbook Evolution - ein kritisches Lehrbuch, by Reinhard Junker and Siegfried Scherer. The section is section 9.4. There is an HTML summary (original German, google translation) and a 32-page PDF is here (apparently too long for google to translate).

Sadly, while I took German in high school, most of what I remember involves beer-drinking songs, which doesn’t help me out much here. Clearly Matzke (2003/6) and Pallen & Matzke (2006) and perhaps other commentary on flagellum evolution got deep under their skin – most of the chapter seems to be taken up with attempting to refute the evolutionary model for the origin of the flagellum! Regardless, I can tell there are a few issues – they cite the 2003 critiques of the flagellum evolution model by the pseudonymous “Mike Gene”, without noting that several later scientific developments caused Mike Gene to substantially improve his opinion about even the most radical part of Matzke 2003, which was the idea that a good chunk of the flagellum was homologous to the F1Fo-ATPase and relatives. (The original seems to be lost to the internet ghosts, but Ed Brayton blogged it, see: “Mike Gene Admits Matzke was Right”)

Anyway, if anyone knows of a source that can translate PDFs, or if there are any German speakers up for summarizing their main points, it would be interesting to hear if they’ve come up with anything new. I mean, there’s 32 whole pages, so maybe they will actually acknowledge that Luskin & numerous DI sources were wildly wrong about the number of required, flagellum-unique proteins in the flagellum. And actually, it does look kind of like Junker & Scherer are advancing some argument that relies on the idea that the flagellum parts are not unique, but instead were designed to serve multiple independent functions (see Figure 4). How conveniently like evolutionary cooption!

Mark Pallen, author of the Rough Guide to Evolution and expert on Type III Secretion Systems (and producer of the famed Darwin in Dub), has a new blog. He just put up two posts about the third UK Type III Secretion meeting:

Dispatches from the cutting edge of flagellar biology, part 1

Dispatches from the cutting edge of flagellar biology, part 2

Eppur si muove!

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Blogging on Peer-Reviewed Research

The Harvard multimedia team that put together that pretty video of the Inner Life of the Cell has a whole collection of videos online (including Inner Life with a good narration.) Go watch the one titled F1-F0 ATPase; it's a beautiful example of a highly efficient molecular motor, and it's the kind of thing the creationists go ga-ga over. It's complex, and it does the same rotary motion that the bacterial flagellum does; it has a little turbine in the membrane, a stream of protons drives rotation of an axle, and the movement of that axle drives conformation changes in the surrounding protein that promote the synthesis of ATP. It's a molecular machine all right. Makes a fellow wonder if possibly it's "irreducible", doesn't it?

Well, it's not. It can be broken down further and it still retain that rotary motion.

Continue reading "Eppur si muove!" (on Pharyngula)

In the post about my review of Behe’s The Edge of Evolution, many complained that they couldn’t access the full text without a university subscription or paying a huge fee. I have checked Elsevier’s policies on this. Authors are not allowed to post the published PDF to their websites (you have to get that from Elsevier), but they can put up the unformatted, submitted preprint version of their articles, as long as they include the reference and DOI to the published version. So here is the reference: Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, doi: 10.1016/j.tree.2007.09.004.

…and the full text is below the fold. Note that the unpublished version has a few minor differences from the published version. For example, it has more emphases which were kind of my way of jumping up and down on the smoking ruins of Behe’s core arguments in The Edge of Evolution.

Behe review in TREE

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I am pleased to announce that Trends in Ecology and Evolution (TREE) has just put up the article-in-press version of my book review of Michael Behe’s The Edge of Evolution. Here is the reference and link:

Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, DOI.

The DOI link doesn’t seem to be working just yet, presumably that is temporary. And the other link is one of those nasty superlong ones, so if nothing works, go to the TREE website and click on “Articles in Press” to see it (you will have to have a subscription or university access to get the article; I will provide a partial quote below).

Writing this review was challenging. There are a great many things wrong with Behe’s book, and attempting to hit the most important points effectively, with just 750 words to work with, was quite a challenge. For example, there was no way to fit in anything about HIV, even though some really good points have emerged on that front in the last few months. Thanks to the PT crew for a great many helpful discussions, comments, etc. I also had Cavalier-Smith’s (1997) TREE review of Darwin’s Black Box, literally the article that got me into ID criticism in a serious way, to inspire me (despite some flaws in that review).

I tried to make every word count, so it is hard to pick a summary quote, but here is a bit from the middle:

On ERV’s blog we find an article titled Irreducible Complexity Reflects Human Ignorance about Phillip Klebba, Professor of Chemistry and Biochemistry at the University of Oklahoma. It was Klebba’s relentless questions during the Q&A of Dembski’s talk at the Trinity Baptist Church Oklahoma University in Norman Oklahoma which forced Dembski to admit to the level of ignorance that is required for ID.

The Baptist Trinity Church had invited Dembski “to penetrate the university campus with the gospel” (source). After all, what better way to introduce the students to the gospel than through the ideas of William Dembski? Dembski presented a talk titled “Why Atheism is no Longer Intellectually Fulfilling: The Challenge of Intelligent Design to Unintelligent Evolution”. During the Q&A, Dembski found out that the students were not impressed by his arguments. While Dembski may have contributed to the successes of Atheism on the University, he also managed to show to the audience present why ID is scientifically vacuous.

This just in. Current Biology has published a short dispatch piece reviewing the flagellum evolution issue:

W. Ford Doolittle and Olga Zhaxybayeva (2007). “Reducible Complexity - The Case for Bacterial Flagella.” Current Biology, 17(13), R510-R512. July 3, 2007. DOI

I recently expressed some discouragement about the capabilities of blogs for critiquing scientific papers. I still have those reservations, but here is a data point that leans the other way:

A correction to the paper by Liu & Ochman, “Stepwise formation of the bacterial flagellar system,” was just published in PNAS. PT readers will recall that I and others had many problems with the methods and conclusions of this paper (see PT posts 1, 2, 3 for commentary and 4 for comprehensive links). The correction and brief comments are below.

For you flagellum wonks in the audience, an interesting and fairly detailed discussion of some of the science issues and, for lack of a better word, etiquette issues, took place over here at T. Taxus in “JCVI Evolutionary Genomics Journal Club on Liu-Ochman.”

(The discussion is also good for Esperanto wonks.)

The PNAS Early Edition webpage has just posted a series of papers from the December 2006 National Academy of Sciences Sackler Colloquium, “In the Light of Evolution: Adaptation and Complex Design,” organized by Francisco Ayala and John Avise. The series of papers, on topics ranging from color vision to beetle horns, is now available (I will post the list below the fold). Eugenie C. Scott (aka Genie) was invited to speak at this meeting about evolution education and the history of opposition to it, and the speakers wrote papers to be published in PNAS and a forthcoming NAS volume.

Genie brought me on as a coauthor on the paper she was asked to write. This became:

As the discussion over the Liu-Ochman flagellum evolution paper continues, it is clear that I need to do a little more arguing to defend my position. Although some were convinced that skepticism was justified based the previous PT posts (basically: 1. this goes against much prior published knowledge and 2. just look at the obviously different structures), others have defended the paper or at least suggested that the alleged problems are not as overwhelmingly obvious as they seem to me. Two primary lines of argument have been raised. First, some have pointed out, correctly, that the reputation of the authors and journal in question far outweighs the reputation of a blogger like me, so why should readers trust me over PNAS? I will concede the case when it comes to reputation; all I can say is that over the years I have developed some familiarity with the literature pertinent to flagellum evolution, and as I read through the PNAS paper it became apparent that it was going against much of what was already known. This is not necessarily bad if a direct attempt is made to rebut conventional wisdom, but if assertions are made without much evidence of awareness that they go against previous work, that is problematic.

Those who have been following the comments section of the first post on the PNAS flagellum paper, entitled “Stepwise formation of the bacterial flagellar system,” will see that there have been several developments: ScienceNOW at Science magazine has uncritically reported the PNAS paper’s all-flagellar-genes-came-from-one conclusion; Behe and other IDers are getting into the act, although they are so clueless they don’t really even understand why the PNAS paper is problematic; and PZ Myers and I have dropped hints that several of us PT bloggers are reaching the conclusion that this paper is looking worse, not better, after close examination. We will have more on the technical methodology issues in the next few days. For the moment I would just like to offer a simple response to some comments, and a simple but powerful reason that the “all core flagellum genes are descended from one ancestral gene” does not work.

First, the comments. Some commentators have reacted along the following lines: (1) maybe the paper isn’t so bad, just speculative; and/or (2) maybe I’ve misread the paper or its conclusion was poorly worded, and maybe the authors just meant to argue that some of the 24 core flagellar proteins were related, not all 24 proteins.

Unfortunately – and I mean unfortunately because I wish one of these options was true – neither idea is a supportable interpretation of the authors’ views. Have another look at Figure 3 from the Liu & Ochman paper:

Today the prestigious journal Proceedings of the National Academy of Sciences (PNAS) put out an Advanced Online Publication paper on flagellum evolution entitled, “Stepwise formation of the bacterial flagellar system.” The paper is freely available via Open Access. I was initially excited that PNAS had published a paper on this topic, and furthermore that it cited the Pallen/Matzke essay on flagellum evolution, and Ian Musgrave’s excellent book chapter in Why Intelligent Design Fails.

Unfortunately, as I read the paper, my delight turned to concern, and then dismay. The paper makes some potentially useful points and explores new territory in a few areas. But much of it ranges from dubious to just irremediably wrong.

I was recently interviewed by Karl Mogel for his podcast show The Inoculated Mind. Topics include flagellum evolution and Kitzmiller v. Dover, and Casey Luskin’s inability to admit error. Have a listen if you get a chance.

Ode to the Flagellum

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The evolution of the flagellum Youtube video based on Nick Matzke's hypothesis by CDK007

A few weeks back, I posted a rebuttal to the Casey Luskin/Michael Behe interview, which itself rebutted the Pallen/Matzke Nature Reviews Microbiology paper on flagellum evolution.

Over on the hopefully-named “ID the Future” podcast website run by the Discovery Institute, Casey Luskin has posted a short interview with Michael Behe – evidently recorded in-studio rather than over the phone, although, for some reason, Behe sounds like he is sitting in a cave.

Anyway, the topic of the interview is Behe’s response to the Pallen and Matzke (2006) article on flagellum evolution in Nature Reviews Microbiology. As I pointed out on PT last month, among other things, the NRM article showed that the ID advocates didn’t know what they were talking about on the topics of (1) number of required flagellum parts, and (2) number of “unique”, i.e. non-homologous, flagellum parts. These points are obviously important, since the ID advocates themselves have emphasized them repeatedly – almost in hypnotically repetitious fashion, actually – as major reasons that the flagellum could not have evolved gradually.

Carl Zimmer has a post up about his new article in the November 2006 issue of National Geographic. The article surveys recent research on the origin of multicellularity, segmentation, the vertebrate head, eyes, limbs, feathers, flowers, and the new kid on the block…the flagellum! And he even bases it on Pallen and Matzke 2006. Mark Pallen is interviewed – unfortunately there is nothing about the Genomic Dub Collective, but I’m sure that’s destined for ReggaeTimes.

Famed flagellum researcher Howard Berg is also interviewed. Sadly, there is nothing about the ID movement’s frequent claim that one of the spiffy design features of the flagellum is that it is “water-cooled” – a claim which they usually attribute to Berg (googling “water-cooled flagellum” brings up only ID/creationism websites). In my humble opinion, a fish has a far stronger claim to being “water-cooled”, given that the heat-retention capabilities of nanometer-scale molecular system are essentially nil (I read once that the heat energy radiates away dissipates in picoseconds at that scale). Someone should ask him about that some day.

The Nerf Flagellum

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I want one of these for Christmas. Courtesy of Display #1: The Bacterial Flagellum, at the Creation Science Museum of Canada. Watch out, evolutionists, you have been judged on the Hogwash-O-Meter and found wanting! If that doesn’t convince you, just look at the tracks of humans found with dinosaur tracks at Paluxy.

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:

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