Monday, November 01, 2010

Carnival of Evolution #29

 
The latest Carnival of Evolution is up on Byte Size Biology [Carnival of Evolution #29].

Check it out ... there's lots of good stuff from all the best biology bloggers.

Sandwalk readers might be interested in the post by Hannah Waters. She not only defends the "Three Domain Hypothesis" but goes one step further by merging eukaryotes and archaebacteria into a single domain making the "Two Domain Hypothesis"!

Of course we all know that she's wrong but her posting is still worth reading.


11 comments :

  1. You say 'we all know' that Hannah's position is wrong, but frankly, I don't know. I would really appreciate it if you would take the opportunity to educate and convince your readership (even if it is a short comment). Comments like 'we all know' make me feel like I'm the outsider who doesn't get the joke.

    Plus, if you want to say Hanna's wrong, I think it'd be fair to point out on which points you don't agree.

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  2. Hey Larry,

    I'm glad that you still think it's worth reading - but could you please elaborate? I'm happy to engage you, if not for the fun in debate than for learning's sake, but I cannot do so if you don't let me know where you're coming from!

    Plus, as Lucas pointed out, it's a good opportunity for education.

    Thanks,
    Hannah

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  3. On the three 'domain' hypothesis, you may want to take a look at this paper:

    Lienau et al. 2010. The mega-matrix tree of life: using genome-scale horizontal gene transfer and sequence evolution data as information about the vertical history of life


    They recover the three 'domain' tree despite all the LGT "noise" from a whole genome analysis of 166 taxa. Yet, note some funny topology within the Eukarya in that tree.

    @Hannah,

    Larry has a whole series on the subject.

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  4. Check out: The Three Domain Hypothesis.

    All available evidence shows that most eukaryotic genes are more closely related to standard bacteria and not to archaebacteria. All available evidence shows that there was so much sharing of genes during early evolution that it's impossible to define the earliest branches of life.

    The Three Domain Hypothesis died a slow death from 1990-2000 and the final nails were pounded into the coffin in the 21st century.

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  5. Thanks for the paper, Physeter. Will definitely have to check that out.

    I'll have to look through your stuff too, Larry. There's a lot of it though, so it will take some time!

    Just want to clarify - I wouldn't go so far as to say I was defending either hypothesis, but was simply presenting recent research. I'm more of a proponent of a theory that all the microbes were trading genes and other junk around, and some of the combos survived better than others, so that's what we've got. But if scientists continue to publish so much research on the topic, it may be a little presumptuous to call the field dead and the problem solved.

    As I wrote in my post, we people need to categorize. Saying "it was a big mess and now we have life!" isn't enough for us! There is some innate drive to subdivide. That's probably why Woese's model holds such power.

    Anyway, in the future, if you're gonna call someone out on being flat-out wrong, I would recommend to provide some links to evidence. Even if your regular readers will "get it," it's pretty off-putting to the infrequent or new visitor.

    Best to you,
    Hannah

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  6. @ Physeter

    I'm not sure they recover the 3 domains, more like 2. Figure 1 (concatenated AAs) show Eukaryotes buried with the eubacteria, and distinct from Archae. 3 domains not resolved.

    Figure 2 (the mega-data matrix tree) recovers something that makes Archea+eukaryotes a single, distinct group. Whether they are 1 or 2 groups depends on the support of that single node, with small branches leading to Eukaryotes or the Archea. This does not look like the rRNA 3 domain topology, with 3 equidistant clades that are labeled the domains.

    For those without the paper, it looks similar to this tree without as much distance between eukaryotes and archea.

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  7. Oops... the link to "this tree" didn't make it...

    http://en.wikipedia.org/wiki/File:Tree_of_life_1500px_coloured.png

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  8. Hannah says,

    As I wrote in my post, we people need to categorize. Saying "it was a big mess and now we have life!" isn't enough for us! There is some innate drive to subdivide. That's probably why Woese's model holds such power.

    You've identified the two main problems. People need to have simple solutions and that's why they are quick to grasp a simple tree of life and that's why they find it so hard to let go.

    The second problem is Woese. He did a fabulous job of selling his idea. In fact, he did such a good job that even though he has backed off, his disciples continue to promote the original Three Domain Hypothesis.

    But if scientists continue to publish so much research on the topic, it may be a little presumptuous to call the field dead and the problem solved.

    Like so many problems in evolution, there's a disconnect between the real experts and everyone else. Among those whose primary research interest is early evolution, the consensus is that the original Three Domain Hypothesis is not supported. Unfortunately, that word hasn't gotten out to the rest of the community who continue to publish trees that conform to three domains.

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  9. Hannah says,

    Anyway, in the future, if you're gonna call someone out on being flat-out wrong, I would recommend to provide some links to evidence. Even if your regular readers will "get it," it's pretty off-putting to the infrequent or new visitor.

    Did you see the smiley at the end of my sentence?

    I'm sorry you were unaware of the evidence before writing your posting. Stories about the death of the tree of life have been pretty popular lately and most of us have been following them.

    Please read up and get back to me. I'd be happy to continue this discussion.

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  10. Great. I go into all the trouble of editing the Carnival, and Larry gets more comments than I do.

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  11. @The other Jim

    Yes indeed. Well noted!

    Sorry for the late reply, been busy.

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