Pharyngula

Uh-oh…poor science alert!

There is considerable interest in a recent paper in PNAS that purports to have found some rather substantial homologies in the proteins that make up the bacterial flagellum. That would be extremely interesting if it were true, but it looks like there are massive methodological problems in the work. Matzke has put up a preliminary criticism; the gang at PT are working on a much more detailed analysis, and if half of what I’m hearing about the paper is true … well, it’s going to be rather thoroughly sunk.

If you are arguing against ID’s favorite example, the flagellum, do not use the data in this paper. It’s about to go kablooieee. Sorry, everyone, but that self-correcting stuff is the way science is supposed to work (and letting error-filled papers make it to press is not supposed to happen, but it does all too often anyway.)


Nick has posted more info — it’s still not the complete argument, but the problem in the author’s interpretation is rather stark.

Comments

  1. #2 Ichthyic
    April 20, 2007

    Echoing Myrmecos, it looks like Nick’s primary complaint is a minor wording mistake about homology in the discussion.

    the author’s use of the single gene model for flagellar evolution is a minor wording mistake?

    that must be one hell of a misprint.

    Nick’s primary complaint seems based on the author’s acceptance of this model without sufficient evidence to support it.

    …and that was just scratching the surface.

    Nick is very well versed in this issue, and is more than qualified to comment on it.

  2. #3 David Marjanovi?
    April 20, 2007

    I pronounce it as a single syllable that starts with the pm/tm/km sound. The mouth only opens during the N. It’s a bit difficult, though.

    Not being used to pronouncing all unstressed vowels the same, I’ve never noticed the similarity… I just like pronouncing abbreviations as words. :-)

  3. #4 David Marjanovi?
    April 20, 2007

    I pronounce it as a single syllable that starts with the pm/tm/km sound. The mouth only opens during the N. It’s a bit difficult, though.

    Not being used to pronouncing all unstressed vowels the same, I’ve never noticed the similarity… I just like pronouncing abbreviations as words. :-)

  4. #5 Blake Stacey
    April 20, 2007

    David Marjanovi?:

    Is your favorite novel Pnin?

  5. #6 David Marjanovi?
    April 20, 2007

    Never heard of Pnin. I don’t read novels much.

  6. #7 David Marjanovi?
    April 20, 2007

    Never heard of Pnin. I don’t read novels much.

  7. #8 Ichthyic
    April 20, 2007

    indeed. I still don’t see where the critics of Nick’s initial analysis have addressed the issue of the single gene model espoused in the paper.

    this seems a blatantly obvious issue, not some semantic misintrepration.

    Nick has studied this issue for years, AND published an excellent review on the subject himself (which was even cited in the paper under the thumb).

    He DOES know what he’s talking about.

    the responses in defense of the paper here seem more knee-jerk than thoughtful, and themselves are likely to lead to the IDers claiming “circling the wagons” than anything in the paper.

    think about that.

    I for one hardly blame the PNAS review process, as I’ve read enough articles in any given journal to know that while the peer review process in general is mare than sufficient, occassionally things slip through the cracks.

    happens with every journal, including science and nature.

    As I stated over on PT, the main thing here will be to hear what the authors themselves have to say, then things will get clearer.

  8. #9 Ichthyic
    April 20, 2007

    uber,

    one reason only:

    it looks at the evolution of flagellum, the flagship of the ID concept of irreducible complexity.

    NONE of them understand even half the actual research that went into publishing the paper, as evidenced by both Paul (whoa nelly!) Nelson in comments to Nick’s post over on PT and William (WD40) Dembski over on UD.

    ergo their commentary so far has actually been more humorous than instructive.

    Nick’s been far more concerned with the actual paper itself than their commentary, but after the dust settles, I’d bet he will circle back to pop their bubbles for them.

    er, not that that hasn’t already been done in several places already, and not that it’s all that difficult or anything.

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