Wednesday, July 29, 2009

The Tree of Life

I'm off to a meeting on Perspectives on the Tree of Life.1 (See Perspectives on the Tree of Life: Day One, Day Two, Day Three.)


If you want to follow the real scientific debate on the tree of life then read my earlier posting on The Three Domain Hypothesis especially the one on "The Web of Life."

The basic idea is that there is no strict branching tree of life that accounts for the data during the early stages of life on Earth. The first group of single-cell organisms exchanged genes so frequently that the gene phylogeny looks much more like a jumbled web that a traditional tree.

You should also listen to Ford Doolittle's talk on The Tree of Life. If you have any questions you'd like to ask, post them here and I'll bring them up at the meeting.

This part isn't very controversial. There really are good evolutionary biologists who are questioning the tree of life. It's just part of the gradual undoing of the Three Domain Hypothesis in light of the enormous amount of data refuting it.

What's controversial is the rejection of the very concept of trees in evolutionary biology and that's where the philosophers come in. This meeting has a 50:50 mixture of philosophers and scientists. It's gonna be fun.

Do you remember what was wrong with the New Scientist story last winter? It wasn't that scientists were questioning the tree of life 'cause that part of the story is quite accurate. What upset me was the fact that New Scientist exploited Charles Darwin by tying him to the idea that early bacterial evolution was treelike when, in fact, he knew nothing at all about the subject.

How could he have been wrong when he never wrote a thing about the relationship between various divisions of bacteria and archaebacteria and their affinities with eukaryotes?

The other thing that bugged me was that this story wasn't new but New Scientist played it up as a new discovery.


1. The original title of the meeting was "Questioning the Tree of Life" but it's been changed to more closely reflect the divergent opinions of the participants.

11 comments :

  1. I may be wrong, but I don't think you're characterizing the real scientific debate correctly. It's not Carl Woese's three domains versus rampant HGT. Woese proposed three monophyletic lineages, archaea, eubacteria, and eukaryotes. As you wrote recently, an alternative hypothesis that's been put forward instead of the three domain hypothesis is that eukaryotes are sister to one group of archaea, the so-called eocytes. But the illustration you showed to represent this alternative was also a tree. It's just a different tree.

    Also, Woese himself has argued that in early evolution, gene flow was so rampant that there were no clear lineages.

    My sense is that a better characterization of the debate is that Doolittle and others say that different genes have different histories thanks to lateral gene transfer, versus those who see horizontal gene transfer as more like webs on the branches of the tree of life--that there is a single tree that can accurately represent the phylogeny of all living things.

    I look forward to lots of blogging from you about this conference.

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  2. I'm lucky to have had Doolittle as a prof. at Dal, and thus was exposed to LGT and the tree 'controversy' during my undergrad. This is interesting because I've always sort-of accepted that LGT makes drawing a definitive bacterial/archeal 'tree' unlikely; however, I was surprised at how angered some microbiologists were by this idea when Doolittle gave a talk here at Mac last year. The idea that two strains of what we call E. coli can differ by ~30% of their gene compliments could be scary to someone who studies pathogenesis and is attempting to define such 'species' using the logic of an essentialist.

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  3. If we accept that Darwin's idea of common descent necessitates a single ancestor, by which we of course mean "ancestral population", then we merely need to allow that ancestral eukaryotes, eubacteria, and archaea comprised a single ancestral population.

    We could, for instance, decide that a population becomes dividable at the point where HGT becomes less common than mutation as a source of genetic variation.

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  4. There's an even worse article in this month's New Scientist on the subject of Dawkins's selfish gene hypothesis. The article claims that biologists don't consider it to be the last word on evolution (okay), citing epigenetics (eh?!) and horizontal gene transfer (WHAT?!) and then going on to regurgitate everything that they got wrong in their January issue.

    I'm done with these clowns.

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  5. cont'd

    Having just re-read the commentary online (I'd skimmed it at the bookstore) I find that it's actually worse than I remembered. At no point does Fern Elsdon-Baker actually explain just what is lacking in the selfish gene metaphor, it seems to consist of assertions that various things (among them, bafflingly, gene expression) undercut TSG without ever saying how.

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  6. This just in: Sensationalism used to sell magazines! :O

    I wonder if any religious sorts will protest this process as unnatural "same-sex gene sharing"? Cause...you know...technically it could happen?

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  7. I see you've already written on FEB's piece, sorry for cluttering up this thread.

    This just in: Sensationalism used to sell magazines!

    Addendum: Some readers might be put off when the magazine that they paid for in the hope that it was going to contain useful information turns out to be full of rubbish.

    Didn't the World Weekly News go out of business?

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  8. Addendum: Some readers might be put off when the magazine that they paid for in the hope that it was going to contain useful information turns out to be full of rubbish.

    True, but most reader's of pop magazines don't have the scientific aptitude that the typical reader of this blog does. Thus, they are easily seduced.

    I must point out that epigenetics and other "challenges" to the selfish gene hypothesis are meant as challenges to the gene-centric view of life, not the actually statement that selection acts on genes.

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  9. True, but most reader's of pop magazines don't have the scientific aptitude that the typical reader of this blog does. Thus, they are easily seduced.

    I see no reason to believe this, on the contrary I would expect the audiences for Sandwalk and NS to be quite similar. Indeed, if you browse through the comments on some of the articles you'll find them to be almost as critical of NS as the commentary here. And if people in general are as "easily seduced" as you imply, why do circulation figures suggest a success rate closer to Johnny Bravo than Casanova?

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  10. Ford Prefect, Traveling SalesmanThursday, July 30, 2009 8:04:00 PM

    I never said that people are in general "easily seduced", I simply said that, with regard to scientific matters, the nonscientist cannot discern fact from hype. Of course people are not easily seduced with regard to ordinary affairs.

    You don't take into account that readers of NS who aren't extremely scientifically knowledgeable are less likely to comment. The average Joe, browsing the newsstand, may buy a sensationally marketed magazine, but not take the time to visit a website and discuss it, for pete's sake.

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  11. The average Joe, browsing the newsstand, may buy a sensationally marketed magazine, but not take the time to visit a website and discuss it, for pete's sake.

    What... wait a minute... you mean...

    IT'S STILL 1999?!

    THANK GOD! You'll never believe the nightmare I just had...

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