Wednesday, May 6, 2009

Dechronization Interviews Rob Desalle

Recently, I sat down at a local watering hole with my colleague, Rob Desalle and we talked about cladistics and the changing field of evolutionary biology. Along the way, Western textiles, horror movies, and a couple of colorful expletives came up…and in the end, he told me it was the most serious conversation we’d ever had.

SP: So, let’s start with the big question: Are you a cladist?
RD: I don’t think I’ve ever been a member of the Willi Hennig Society. But, yes – in the sense that if someone said that I had to only use one method, I would choose cladistics.

SP: Why?
RD: Because I’m a minimalist. There are fewer assumptions in parsimony.

SP: But isn’t that one assumption a rather big one?
RD: Yes, but that big one is easier to track than lots of little ones.

SP: But, you do use other methods, too, right?
RD: Yes, but I don’t do that to test the results of one method against another. I do it to test assumptions. Cladists were among to the first to really examine analysis space, i.e. do sensitivity analysis, beginning with the “Navajo rugs” of Wheeler and then Gatesy’s explorations of alignment space. Then Hillis, Bull, Huelsenbeck, etc. began doing the same thing, but with likelihood. And, we’re seeing a new wave of this now with whole genome analysis. I don’t believe that one should be pluralistic – just because lots of trees agree doesn’t mean you’ve found “the truth.” But, modified pluralism is testing the effects of your assumptions. You could stack your assumptions to give you the answer that you want, but then you’d be no better than the evolutionary taxonomists of the 1950’s.

SP: But, let’s take the opposite view – what do you do if you get a lot of disagreement?
RD: It would tell me that I needed to collect more data. Unless of course I’ve already sequenced the whole genome, then I’m f$@&ed.

SP: OK, let’s talk for a minute about your role as an editor. You’ve been on the editorial board of a huge number of journals right?
RD: I don’t know if huge is the right adjective; but I have been on a few, – Evolution, Molecular Phylogenetics and Evolution, Molecular Biology and Evolution, PLoS One, Conservation Genetics, Ancient DNA, BioEssays, and Mitochondrial DNA. Being an editor is great – you get to see all these papers before anyone else does – and you get to see the field grow and change. But I don’t think it’s the job of an editor to mold the field, per se – just monitor it.

SP: So, from the standpoint of an editor, how has the field of systematic biology grown and changed over the years?
RD: We are more aware of analysis space – and if it hasn’t been looked at in a paper, that really irritates me. Students are more and more sophisticated with respect to their toolkits. In the beginning, I was using RFLP’s and running the very first version of PAUP with IBM cards. Now students are using any number of analytical approaches and a plethora of computer packages. In the old days, you had to just make a tree but now it’s so easy to collect data that you can really think about the questions. Students understand the chemistry less but the algorithms better.

SP: So, what would your advice to students be?
RD: Twenty years ago, I told all of them to learn more biochemistry. Ten years ago, I was saying that they needed to learn more statistics so that they could understand maximum likelihood and Bayesian analyses. But, today, my advice is to learn programming – Perl, R, etc. You need to be able to manipulate your data – move s%#t around on your computer. They need to understand probability, statistics, parsimony, etc, but I don’t think the philosophical ramifications are as important.

SP: You’ve gone from doing population genetics and systematics on Drosophila to being really involved with microbial genomics and phylogenetics. Do you really think a bacterial tree of life is possible?
RD: Absolutely. From some of the work we are doing in the labs here at the AMNH we are finding that reticulation does not necessarily destroy phylogeny as severely as we’ve long thought. Even with horizontal gene transfer, there is a real phylogeny. And even if HGT is widespread, you still need the scaffold. It’s the same problem as lineage sorting in metazoa. I call them the “Freddy” and “Jason” of systematics – but just remember that Freddy died in 1991 and Jason went to hell in 1993 – in other words, these problems don’t obliterate the whole signal.

SP: What are the big remaining phylogenetic questions out there?
RD: Microbial taxonomy, for sure. It’s one of the most important fields. The existing taxonomy is good, but it needs to be done about 3 orders of magnitude better. The other one I would pick would be the nematodes. Taxonomy is like, really cool and important. It’s a real science!

Rob DeSalle is a Curator of Entomology at the American Museum of Natural History. He is affiliated with the AMNH Division of Invertebrate Zoology and works at the Sackler Institute for Comparative Genomics, where he leads a group of researchers working on molecular systematics, molecular evolution, population and conservation genetics, and evolutionary genomics of a wide array of life forms ranging from viruses, bacteria, corals, and plants, to all kinds of insects, reptiles, and mammals. Rob is also Adjunct Professor at Columbia University (Department of Ecology, Evolution and Environmental Biology), Distinguished Professor in Residence at New York University (Department of Biology), Adjunct Professor at City University of New York (Subprogram in Ecology, Evolutionary Biology, and Behavior), Resource Faculty at the New York Consortium in Evolutionary Primatology, and Professor at the AMNH Richard Gilder Graduate School.


Glor said...

Good stuff, thanks guys.

sergios-orestis kolokotronis said...

Just an idea: maybe it'd be useful to add the label/tag "interview" to interviews (great idea, btw), so that readers can find them all in the future (incl. the already posted ones – Sullivan, Felsenstein, DeSalle).


Susan Perkins said...

Done - good idea, Sergios.

Felipe Z said...

Can we, the readers, suggest people we would like to be interviewed here?? who should we contact to suggest some names??

Poletarac said...

How about right here? The blog contributors all receive comment alert emails.

Felipe Z said...

OK. Just to start:
Scott Edwards.
Lacey Knowles.
NSF officer (current or who just left NSF) from the Systematics & Pop. Bio Panels to tell us about proposals, how they see the future of research in these areas, etc.

Glor said...

Thanks Felipe. These are all good suggestions. We'll put these names in the queue. Next up is Brian Moore's interview with John Huelsenbeck. Credit to Luke Harmon for getting the interviews up and running!