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All flagellar genes derive from a single gene

A paper published in the Proceedings of the National Academy of Sciences makes the startling claim that all flagellar genes “originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene” (see abstract below). While consistent with Darwinian evolution, such excessive hyperevolution was too much even for the hyperevolutionists at the Panda’s Thumb (go here), who are now distancing themselves from its conclusion. What’s going on here? How could people publish such a ridiculous result, and in PNAS of all places? Let me suggest the following hypothesis: Liu and Ochman, the authors of the piece, are really ID advocates who are pulling a Sokal-style hoax, pushing the envelope to see how extreme they can make their claims for evolution and still get them published. Inspired by Liu and Ochman, I have an article in the works for how the core components of human eye evolved through the successive duplication and modification of a few, or perhaps even a single, precursor gene in a primitive chordate ancestor. I may not be able to get anything published in the peer-reviewed biological literature that’s pro-ID, but something pro-evolution, if sufficiently extreme, is a different matter. Stay tuned.

Stepwise formation of the bacterial flagellar system

Renyi Liu * and Howard Ochman *
Departments of *Biochemistry and Molecular Biophysics and Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721

Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

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15 Responses to All flagellar genes derive from a single gene

  1. “Let me suggest the following hypothesis: Liu and Ochman, the authors of the piece, are really ID advocates who are pulling a Sokal-style hoax, pushing the envelope to see how extreme they can make their claims for evolution and still get them published.”

    Sounds crazy, but really, how far do you have to go to have the extremist faction of the darwin-party reject it? Whether intentional or not, their paper is pro-ID.

  2. Matzke’s reactions

    several of us PT bloggers are reaching the conclusion that this paper is looking worse, not better, after close examination.

    It almost seems like one of our pro-ID guys mangaged to demonstrate how worthless the NAS is on matters of evolution. They were able to sneak such a poorly conceived paper past peer-review. Does not inspire confidence in PNAS.

    Congrats to Liu and Ochman. If they ain’t one of us, they ought to be. Hehehe!

    I like this ID strategy. Submit ridiculously bad pro-Darwin papers. I’m confident ID proponents could publish lots of this sort of muck since lots of this muck is making it through peer review every week!

    But how can such a process be honest? Well, one need only write something like:

    We calculate the mutation rate of nucleotides in protein-x based on the reported ancestral split ……

    This sort of junk passes peer-review every week. One could make a template of it.

    I’m so used to seeing bad stuff churn out through the peer-review system that I didn’t give the paper a second thought.

    But after reading the paper again, it was so bad that it sunk to a new low even by Darwinist standards. I started to laugh.

  3. Let me suggest the following hypothesis: Liu and Ochman, the authors of the piece, are really ID advocates who are pulling a Sokal-style hoax, pushing the envelope to see how extreme they can make their claims for evolution and still get them published.

    I don’t think this is the first time this has happened.

  4. A stealth pro-ID paper by Salvador Cordova

    Solving Protein Sequence Space Topology via Evolutionary Principles

    The topology of functional protein sequences is challenging to estimate because of the difficulty in experimentally testing every possible amino acid sequence. Rather than exhaustive exploration, current methods of experimental estimation explore mutations of selected polymer segments [Axe 2000] and via extrapolation, a topology describing the likelihood of protein function from a random sequence is derived. This paper explores the implication of evolutionary theory to this question. The paper explores what the forgone conclusion of Darwinian evolution rather than experimental techniques will have to say about the density of functional proteins configurations in the the topology of all possible protein configurations….

    Discussion:
    Use of forgone conclusions has paved the way for other theoretical results such as the Origin of Life (OOL), evolution of all genes from a single precursor (Liu and Ochman 2007), and molecular clocks. Here we extend the successful use of forgone Darwinian conclusions over direct empirical evidence….

  5. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria

    What common ancestor to all bacteria? Didn’t Doolittle just get through explaining that there is no such thing?

  6. Michael Behe responds to this same paper, apparently, here:

    http://www.evolutionnews.org/2.....er_se.html

  7. You know, the more I think about it, the more I realize this is a brilliant strategy to promote ID. Like scordova mentions, if IDers could get outlandish pro-Darwin papers past peer-review, it could be more damaging than getting actual ID papers published. What would happen during then next court case if the Darwin side tried pointing to its mountain of peer-reviewed literature as proof and had papers like this stinking up the courtroom? I don’t want the courts deciding any of it, but I really don’t want the courts enslaving us intellectually with atheistic propaganda. What a great paper this is!

  8. What would happen during then next court case if the Darwin side tried pointing to its mountain of peer-reviewed literature as proof and had papers like this stinking up the courtroom?

    Judges don’t even have a high school level understanding of biology. Regarding scientific issues, they reach their decisions based on the testimony of expert witnesses, not an independent examination of the evidence. When expert witnesses conflict, they go with the expert who seems to be the most authorative. Any consensous view is seen as highly authorative.

    That is why the Dover case was such a poorly concieved strategy from the ID perspective. The court room is the LAST place to challenge a prevailing consensous view.

  9. 9
    The Scubaredneck

    They can’t seem to help themselves. The sheep at denialism.com, in agreeing with PT (of course) that the paper is a dog, then go on to say that Mike Behe is still a poopy head for daring to disagree with Nick Matzke (who is the “real” expert, you see) and asserting that this is relavent to ID. It makes perfect sense that Nick Matzke, a trained geographer, would understand such things far better than Mike Behe. It might almost serve as the punchline of a bad joke if they weren’t serious.

    Read all about it

  10. Matzke’s reactions

    several of us PT bloggers are reaching the conclusion that this paper is looking worse, not better, after close examination.

    Of course Matzke doesn’t like this paper. It destroys his story of the evolution of the flagellum by cooption of pre-existing parts.

  11. This is hilarious!

  12. Okay, I admit… I’m confused. Was Michael Behe’s response on the ENV page tongue-in-cheek? Are we just speculating that the paper is a ruse, or do we know that it’s a ruse?

    I mean, it seems ridiculous enough to be a ruse, but then so did John McDonald’s “refutation” of Behe’s mousetrap analogy… and yet he was SERIOUS. (seriously LAME, but serious, nonetheless)

    Spell it out for me, guys.

    Thanks!

  13. I don’t think it’s actually a ruse. I’m not familiar with the authors but I’d bet they were just hoping for uncritical acceptance and instant recognition.

    “Judges don’t even have a high school level understanding of biology. Regarding scientific issues, they reach their decisions based on the testimony of expert witnesses, not an independent examination of the evidence.”

    Jehu, I meant it mainly as a joke, but I think it would pose a problem for Darwinists in a court case if there were papers like this that could be pointed to as evidence for Darwinian dogma and “just-so” storytelling.

  14. I’ve given the paper a brief look. I don’t see what the problem is as far as methodology goes. The authors cite a paper by Pelligrini, et.al., which, it appears, is the foundational paper on a technique called Phylogenetic Profiling. And, apparently, the BLAST program does such profiling. The Pelligrini paper dates from 1998. That’s almost ten years ago. Why didn’t anybody object to this methodology before? I think the problem is that Matzke realizes that what the authors have done is given evolutionary skeptics a tool. The paper suggests that there are about 24 “core” genes that are handed down from the Common Ancestor to all bacterial phyla. This seems to imply that somehow, given that bacteria represent the “first life” on this planet, that 24 genes somehow had to “evolve” before bacteria arose. Well, what form of life does this Common Ancestor represent? And why haven’t we encountered it before in the fossil record? And even if such a CA should be encountered, using the “co-option” method of Matzke and PZMyers, this means that, miraculously, 24 simultaneous “co-options” (or else you have to come up with some selective advantage for each one of the ‘co-options’) took place in a Common Ancestor that we don’t even know existed.

    It’s no wonder Matzke wants to say this is bad science. It’s not bad science; it’s science that’s bad for Darwinism!

  15. This is quite amazing, while I don’t understand the paper I can see the implications.

    I need to learn some more biology, unfortunately I typically view biology as rote memorization…

    Time to crack open that book I bought by Ernest Mayr. :-P

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