Saturday, September 01, 2007

Adaptationomics

 
Jonathan A. Eisen is an evolutionary biologist with a blog called The Tree of Life. He's also one of the authors of a new textbook on evolution published by Cold Spring Harbor Laboratories [A New Textbook on Evolution]. I'm about to order a copy.

I mention this because Eisen is a pluralist. He's as annoyed by adaptationist just-so so stories as I am. Over on the Dennett on Adaptationism thread I'm encountering commenters who question whether there really are modern scientists who believe in the adaptationist program. I can assure you there are. Eisen has discovered some of them in the field of genomics—he didn't have to look very hard—and he decided to label their approach adaptationomics [Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes]. This is tongue-in-cheek so don't all you adaptationists get your knickers in a knot.

Here's how Jonathan sets up the issue.
For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick - it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.

Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.

And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack Warren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).
Does this sound familiar?

What did the authors say that makes them adaptationists? In order to understand their statement you have to be familiar with their findings. They discovered that the genome of a parasite (Wolbachia) has been integrated into the geonome of their insect host. There are several reasons why this might have happened. It could just be an accident, since these kind of recombinant events occur frequently and most insects don't carry a full complement of their parasite's genome. In other words, it could be junk.

On the other hand, the parasite genome could possibly confer some (unknown) selective advantage on the host. But here's the rub. When the author of the article, Julie Dunning Hotopp, was interviewed for the the Nature News article here's what she said.
You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."
That's a classic adaptationist statement. The result "must be" explained by natural selection. There are no other options. I agree with Jonathan Eisen, this is a fitting recipient of his new Adaptationomics Award.

Congratulations to Julie Dunning Hotopp.

10 comments :

  1. And I am giving out my first award in this to Jack Warren [sic!] and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

    IANAB, but off hand I would assume that this is only a hypothesis. (Based on the individual researchers chosen strategy.) And John Werren now affirms this:

    The basis of my remark about the ~1MB insert into D. anannassae is that I am skeptical that an insertion of this magnitude will be nearly neutral. This is conjecture on my part. We will see if it is correct.

    There is also a missing piece of information in the report. We have indirect evidence that the insert could be strongly deleterious in homozygotes (we have not yet proven that the effect is due directly on the insert itself). [Spelling corrected.]


    FWIW, I think it is irritating when researchers and/or press releases fail to distinguish between results, predictions and hypotheses. And don't get me started on evo psych practices...

    And let me add that even a layman thinks these "hybrids" (seems Wolbachia left fragments in 11 species of the flies and nematodes researched) are pretty @$%! cool.

    You are... a beautiful, beautiful, butterfly. (From Alien: resurrection.)

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  2. ...don't all you adaptationists get your knockers in a knot.

    Ooooh ... painful. And I'm surprised that all the adaptationists are female! :-)

    Serious question from a lay reader - I'd had the impression over the last few years that over-emphasis on adaptation was dying away. Is it making a comeback, or was my impression wrong?

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  3. Julie Dunning Hotopp: "There has to be some sort of selection to carry around that much extra DNA."

    I see nothing wrong with this statement. It sounds like a hypothesis, a hunch, based on her knowledge and experience. She could be wrong, but so what?

    Larry Moran: "That's a classic adaptationist statement. ... this is a fitting recipient of his new Adaptationomics Award. Congratulations to Julie Dunning Hotopp."

    Your ridicule and attempt to publicly shame this particular scientist, and put others on notice that they better watch out, is mean spirited.

    Larry Moran, you should be a be ashamed of yourself.

    Divalent

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  4. anonymous says,

    I see nothing wrong with this statement. It sounds like a hypothesis, a hunch, based on her knowledge and experience. She could be wrong, but so what?

    Not a problem. She is wrong to claim that there's only one explanation. There's no law against being misinformed about basic scientific concepts. I'm just pointing out that error.

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  5. I'm on a learning curve here: I'm not an evolutionary specialist so I'm keeping an eye on this discussion as I'm sure it's cutting edge. (perhaps in more than one sense of the word)

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  6. I am perhaps not quite as fervent an anti-panadaptionist as Larry (I don't think...but I'm close, and I did put myself in the Gould camp in the poll to the left), but I still see the deep, deep problem with Hotopp's statement. She says there "has to be some sort of selection" in this case, and we know that that is not true. It's WRONG. If she'd said there could be some sort of selection, that would have been a more appropriate comment.

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  7. As I tried to say in my original post - their paper is quite good and Hotopp, who was a colleague of mine when I was at TIGR, is an excellent scientist. But the quote of hers is "adaptationomics" in the true sense. We are not ridiculing her, just pointing out that the statement is off base. Since it is in Nature, it is entirely reasonable to point out that there are explanations other than selection.

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  8. While I think I am probably far more of an adaptationist than Larry or PZ the thing that really made me realise the weirdness of adaptionism was hyenas. When you hear about female hyenas giving birth through a pseudo-penis, with the embryo having to negotiate that curve during birth...I really can't see that as being anything other than a side effect of their high testosterone levels, an artefact of some other process (which is, presumably, the product of selection).

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  9. So what is the deal with all this? Does natural selection not exist, or are you just reacting to people who give it too much credit?

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