Sunday, July 14, 2013

People I Met in Chicago at SMBE2013

I had a great time at SMBE2013 (Society for Molecular Biology and Evolution) in Chicago. Here are some of the people I met. I apologize for not including everyone—I forgot to take pictures of everyone I talked to.

I went to hear Masatoshi Nei give a talk on Monday morning (July 8) during a special session on "Ideas and Thoughts." The title of his talk was "Darwinism and the Theory of Mutation-Driven Evolution." This was the first time I had seen Nei in person and it was quite a thrill. I've been a huge fan ever since I read Molecular Evolutionary Genetics in 1987. That's when I first became aware of the power of population genetics and the importance of mutation and mutationism.



Later on that day, Dan Graur introduced me to Nei and I got him to sign my copy of his latest book Mutation-Driven Evolution. (Eat your heart out, Arlin!).

I met Dan Graur at the reception on Sunday evening and we had many stimulating conversations throughout the week. He's even better in person than the impression you get from The Immortality of Television Sets.

I will be working hard to convince my colleagues to invite him to Toronto as part of the ENCODE tour.

Here's a picture of Dan with his Ph.D. supervisor. Did you know that Dan is an artist? He created the cover for the current issue of Genome Biology and Evolution. He's also a big fan of theatre (plays and musical). I'm told that he knows the scores of all the major Broadway musicals.

I first met John Logsdon when he was in Ford Doolittle's lab and we've hung out at several meetings. You might recall that John's study of sex in snails attracted some attention from Republicans in the American Congress [see Zack Kopplin Defends Science].

Here's an interesting bit of history. Back in 1993 there was an online debate (HMS Beagle) on The Evolution and Origin of Introns. It was stimulated by Ford Doolittle who had just converted from being a proponent of "introns-early" to the correct side ("intron-late"). The Gilbert lab (and allies) defended "introns early" and the participants were Manyuan Long, Bill Martin, and Sandro de Souza. I talked to Bill and Sandro (see below) and they both seem to think their side won the debate. The actual winners, IMHO, were Arlin Stolzfus, John Logsdon, and William Fischer. John knows that his side won and so does everyone who followed the debate. The concept of "introns early" is dead as a doornail. It's one the few examples of a modern scientific conflict reaching a conclusion.

We need more debates like that.

(BTW, Bill Martin is not often wrong. It's good to keep reminding him that he lost this one!)

I met Michael Eisen for the first time. He gave a plenary session talk on "Evolution of Gene Expression and Dosage Compensation in the Early Drosophila Embryo." This is part of a massive study of fruit flies—a study that certainly qualifies as "big science" in my mind. (Michael Eisen usually doesn't like such projects.) You can read all about the work on his blog: New Preprint: Uniform scaling of temperature dependent and species specific changes in timing of Drosophila development. The room was full and you could tell that everyone at the meeting had great respect for Eisen.

Michael is very smart in spite of the fact that I was initially a bit confused by his stance on ENCODE. Here's the correction: THIS Is What Michael Eisen Is Thinking!!!. I think he may be as smart as his brother.

Jim Lake organized and chaired a session on "Large Genome Flows in Early Evolution." Don't be confused by the title; this was about the tree of life and the death knell of the Three Domain Hypothesis.

I've been following Jim Lake's papers since the late 1980's when he first began to challenge Carl Woese and The Three Domain Hypothesis. Lake claimed that eukaryotes arose from within the archaebacteria and are most closely related to Crenarchaeota (formerly Eocytes) [Eocyte hypothesis].


The Three Domain Hypothesis
At first I though he was a bit of a kook (sorry Jim) but gradually I began to realize that it was Woese who was wrong. Today, everyone who works in the field agrees that the archaebacterial component of eukaryotic genomes is more closely related to Crenarchaeota and the Three Domain Hypothesis is dead. The other component of eukaryotic genomes comes from traditional bacteria and eukaryotic cells probably arose by fusion of a primitive bacterium and a primitive eocyte.

Jim is a really kind person and he doesn't gloat over his victory. I think he deserves more credit.

I didn't realize it until this meeting but this is another example of a debate that is effectively over. I wonder how long it will take for textbook authors to remove those ugly, incorrect, three domain trees from their textbooks?

Reed Cartwright runs The Panda's Thumb. The server is in his lab. He has been prominent in the evolution-creation debate since the beginning. We talked quite a few times. Reed was one of the few people who stuck it out until the end of the last day so we had dinner with one of his students at Billy Goat. Cheezeborger, cheezeborger, cheezeborger.

Reed does computational biology. He tries to explain it to me but I have to confess I'm pretty helpless when it comes to that part of evolution. Reed did a post-doc with Dan Graur. It's amazing how many of my scientific friends are interconnected. I wonder why?

Nick Matzke is just finishing up his Ph.D. and will soon be off to a post-doc. He is an accommodationist but I don't hold that against him since he's on the right side of the junk DNA debate.

Nick made up the T-shirts but I don't think they attracted much attention. I have one but I don't wear T-shirts.

Last, but not least, are Sandro de Suza from Brazil and Bill Martin from Düsseldorf (Germany). Recall that they are the two losers (in the introns debate).

I didn't get much of a chance to talk to Sandro de Souza. This was the first time I met him. I did get to talk to Bill Martin. We share a lot of interests and I agree with just about everything he writes. He's on the right side of the junk DNA debate, the right side of the tree of life debate, the right side of the origin of life debate, and, besides, he understands biochemistry. He is very, very, smart. It's a bit scary.

I'm a huge fan of Bill Martin but he gets embarrassed when I tell him that. He is a true curmudgeon, but then, so are many of the other people in this post. I seem to be attracted to them for some strange reason. We need to invite Bill Martin to Toronto. He gives highly entertaining talks.


  1. Lake attended a talk I gave in Berkeley and I met him afterwards. Lovely guy whose work I always appreciated. Nick also came. You should be worried - we seem to move in the same circles...

    1. Some of Jim Lake's work was kind of sub-standard in the past, so I wouldn't accept everything he says just because he says it-- but when he started reporting his stake through the heart of Three Domains, it was pretty cool stuff, and he won that point. The first time I saw him present that stuff, nobody in the audience went "Oh WOW!" although in retrospect, we should have.

      I agree he deserves more credit and more attention to boot. He should get some kind of award for that.

  2. Larry,
    This is a very educational post. Thanks. I hope that you will have time and give us more details on those ideas, theories, debates, and everything else you mention here. In the meantime I am already collecting articles using your clues from this post.

  3. Replies
    1. Yes, I spelled his firt name incorrectly. See Origin and Evolution of New Gene Functions edited by Manyuan Long.

    2. You also wrote "I don't wear T-shits", but I think you should keep it in.

  4. Larry,

    I used to think that you think the three-domain hypothesis is dead because of rampant HGT among prokaryotes but now it seems you are giving another reason, i.e., archaebacterial paraphyly. What is your position now?

    1. It's a little more complicated. There are only about 31 universal genes—most of them are "informational" genes required for replication, transcription, and translation. The tree made from concatenating these genes (The Tree of One Percent) shows that eukaryotes are most closely related to eocytes. In other words, eukaryotes branch from WITHIN archaebacteria.

      One simple explanation is that eukayotes arose from a fusion event, but there are other possibilities that are consistent with the data. The important point is that the original Three Domain Hypothesis is not one of them.

  5. Bill Martin has been coauthoring some of the most interesting papers on the origin of life in recent years.

    1. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.

      Early bioenergetic evolution.

      The origin of membrane bioenergetics.

      Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation.

      This is just a subset I could dig up quickly. Several of his coauthors are similarly involved in the work of course. MJ Russell has an interesting list of papers recently too.

  6. I wish I could attend the meeting. Unfortunately, the fees were too much for me as a student.

    1. Some of us snuck in at the last minute... for free! ;-) (if a conf is nearby, they don't always check for badges; besides, self-respecting academics tend to get too drunk and lose them by the end of a conference...

    2. ) (forgot to close brackets; will drive me crazy.)

    3. It's easy to copy your comment, correct it, post the correct version, then delete the old one. Your sanity will be preserved.

    4. @Psi Wavefunction,

      It was nice meeting you at SMBE2013. Sorry I didn't take a picture. I noticed you weren't wearing a badge! :-)