Thursday, May 22, 2008

The Tree of Life

From RNA to Humans: A Symposium on Evolution is the title of a meeting held at Rockefeller University on May 1st and 2nd.1 The entire series of lectures is available online at Evolution.

There are several interesting talks but the one that you need to listen to, in my humble opinion, is the talk by Ford Doolittle on Barking up the Wrong Tree: The Dangers of Reification in Molecular Phylogenetics and Systematics. Ford Doolittle challenges the common belief in The Three Domain Hypothesis and Norm Pace's idea that the term "prokaryote" is no longer useful. (Norm Pace is Carl Woese's bulldog.)

Furthermore, Ford Doolittle challenges the very way we think about phylogeny and the tree of life. If you want to keep on top of the current controversies in the field of molecular evolution then this is an excellent way to begin. Ford allies himself with Stephen Jay Gould and against Richard Dawkins. You may not agree with him but it is extremely important that all evolution supporters become aware of the controversy.

1. An unfortunate choice of title. Why not "from RNA to E. coli" or, better yet, "from RNA to modern organisms"?

[Hat Tip: Panda's Thumb]


  1. haha, i juts watched that some minutes ago.
    It'interesting what he says, that surnames can cluster but we actually aren't ever the tip of a branch, but the result of sexual fusion.

    The interesting thing is that this does not undermine at all the evident clusterings of molecular an morphological phylogeny of sexual animals.

    I have been thinking also about species hybridization, there has been more going on than we thought for sure, and it seem a pretty ubiuitous form of sepciation of flowering plnts. But while this can certainly be a problem when deciding the phylogentic relationships between a few closely related species, the fact remains that molecular and morphological phylogenies will still provide string support for the basic groups or "clusters" of plant phylogeny.

  2. Wow, there are some really interesting talks in this series! I assume that we're on the cusp of being able to 'attend' these types of conferences from the privacy of our own homes.

    I took Dr. Doolittle's molecular evolution class when I was in my undergrad at Dalhousie, and he spent a lot of time going over these concepts. He actually gave a similar talk ~6 months ago here at Mac, where he emphasized our reification of the 'tree of life' - which some attendees were quite resistant to admit.

    The results coming out of lateral gene transfer (LGT) studies are quite illuminating. For example, it seems that some extremophiles have inherited their way of life by LGT rather than descent. It poses all kinds of challenges for figuring out relationships, but why did anyone think it was going to be simple in the first place?

  3. I feel that doolittle exaggerates a little. hw thinks some peopel are worng in wanting a tree and artifically imposing that apttern on anture. OK. We got it. he spends to much time characterizing his opponents like this.I dont think it makes his evidence more
    compelling...looks more like he's trying to "force" it on you. Not good. For Doolittle.
    I mean, even if there is no strong molecular clustering,it still seesm we can charcterize groups of bacteria, and why should not sat least some of this similaruty reflect common ancestry? Is Doolitltle telling us there is no such thing as the bacterial clade?
    He seemed willing to throw away the notion of species, too.

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  5. Thanks, Larry!
    I was aware of the LGT controversy, but it is nice to hear the big shots selling their ideas. Here are two links adding beef to the disput:

  6. I have problems to understand why it would be wrong to hug at least some trees. I would strongly agree though to superimpose all the data like symbiosis, LGT and duplication events on the t r e e s and if there is a method to do it differently today I would welcome it. Any hints?
    Furthermore, I can see that there is a problem with bacterial phylogeny concerning assertion of deep branching clades but is it the same if you investigate betaproteobacterial phylogeny. There might be a core of genes that tell you how to superimpose the LGT events on the tree. Those could actually be additional markers, right?

  7. what do you think about this metaphor:

    there is a house in a city that has been there for 400 years (I come from europe ;)). This house was refurbished at least 40 times, parts were added and parts were demolished. But then, in world war II it got hit hard. The people rebuild it (since it was not totally destroyed) with parts from other houses nearby.
    the basement never got changed. though if the person living 400 years ago could enter the house he would immedeately recognize it as his (entity) house and former owners of the destroyed houses nearby would never think this is their house. Am I off the track?