Monday, June 6, 2011

Applications for our r-workshop are still being accepted - please apply by June 15!

We are pleased to announce an intensive short course on using R to perform comparative methods to be held in Santa Barbara on July 31-Aug 5, 2011. This course is funded by the National Science Foundation, and a number of stipends to cover or defray travel, room, and board are available to qualified students and post-docs. Topics covered will include an introduction to the R programming language, tree manipulation, independent contrasts and phylogenetic generalized least squares, ancestral state reconstruction, models of character evolution, diversification analyses, and community phylogenetic analysis. Course instructors will include Luke Harmon, Mike Alfaro, Todd Oakley, and Dan Rabosky.

If you are interested please submit your CV along with a short (maximum 1 page) description of your research interests, background, and reasons for taking the course. Admission is competitive, and the best applications come from students with data sets to analyze. International applicants are welcome. Applications should be submitted online at by 15 June 2011.

Luke Harmon and Mike Alfaro

Sunday, January 30, 2011

Nabokov in the pulpit: the story of dead man's gulch

There is a great NY Times article about Vladimir Nabokov by Carl Zimmer. This article, which links literature, taxonomy, and biogeography, is definitely worth a read. Nabokov is best known as the author of Lolita, a story made even more famous by Stanley Kubrik’s film. As Zimmer points out, Nabakov was also the curator of lepidoptera at the Museum of Comparative Zoology at Harvard, a position now held by Dr. Naomi Pierce. Pierce just published a paper vindicating an old hypothesis of Nabokov (Vila et al. Proc Roy Soc B online early). There have also been a lot of interesting blog comments related to Zimmer’s original article (for example here at Bioephemera and here at Denim and Tweed).

This story of Nabokov reminded me of a striking experience I had last year on a trip to visit my family in the midwest. On the plane ride home, I read a copy of Sean Carrol’s book Endless Forms Most Beautiful. The book has a section about Nabokov, highlighting his work on butterfly evolution.

I was thinking about this book while I sat in the hard wood pews of our Lutheran church that Sunday. The pastor had just begun his sermon, a discussion of selfishness. The sermon caught my attention when the pastor mentioned Nabokov. He told a version of the following story (cribbed from the internet - see below).

You’ve heard of Dead Man’s Gulch? It was named because of the perseveration of a novelist named Vladimer Nabokov, who visited the poet and publisher James Laughlin at his home in Utah. Nabokov was an ardent lover of butterflies, always wandering landscapes wherever he visited to add to his collection. Laughlin told the story that Nabokov, while visiting his house, went looking for butterflies. When he returned at dusk, he told Laughlin that during a hot pursuit of a butterfly over Bear Gulch, he heard someone groaning down by the stream. “Did you stop and check it out?” asked Laughlin. “No,” Nabokov replied, “I had to get that butterfly.” Sure enough, the next day a prospector’s body was discovered there and it was renamed, in Nabokov’s honor, Dead Man’s Gulch.

-- from Preposterous! The Sinning Christian, by Siegfried S. Johnson

It turns out that pastors and priests draw some of their sermon ideas from the web - I found sermons very close to the one I heard that Sunday on Johnson’s page, but also here, here and here. When attribution is given, the anecdote is credited to Clifton Fadiman’s “The Little Brown Book of Anecdotes,” published in 1985. I can find no reference to this story anywhere outside of Fadiman’s book and thousands of online sermon links.

I think that Nabokov is a useful symbol in today’s church for two reasons. First, he wrote Lolita. I can only suppose that many churchgoers disapprove of this book, even if they haven’t read it. Second, the story ties this morally questionable author to evolutionary biology, effectively making it a parable of the “dangers” of modern science.

I really doubt that this story is true. But tying evolution to questionable morals is an old goal of those who seek to undermine the foundations of science. I thought that this was a particularly good - and timely - example.

Ed: Spelling corrected, thanks!

Twitter: @lukejharmon

Tuesday, January 25, 2011

Great blog to visit - including interview with Rosie Redfield

The blog "The Molecular Ecologist" has a number of great posts - everyone should go check it out. This blog is great because the posts have been more in-depth than typical blog posts. For example, Dilara Ally has posted a nice series of essays about the promises and perils of next generation sequencing (example), Brant Faircloth posted a how-to for finding homologous genetic regions, and Tim Vines has been posting about the journal industry and other things.

Recently Dr. Ally has posted part I of a two-part interview of Rosie Redfield, a scientist at UBC known for her innovative work on bacteria. The interview touches on the recent controversy about "arsenic-based life," where Dr. Redfield's blog played a key role in an international debate - and sparked a remarkable and disturbing response from NASA.

Anyway a blog worth reading.


UPDATE: Part II posted here.

Monday, January 24, 2011

Felsenstein's phyloseminar

Joe Felsenstein just gave a really nice talk at phyloseminar. If you missed it live, the talk was recorded and will be archived.

I liked the talk because it gave us some hints about the future of comparative methods. Often it takes the field of comparative biology 20 years to catch up with Joe, but perhaps this time we can shorten the interval a little bit.

The talk included discussion of inferring the evolution of geometric shape on trees, placing fossils on phylogenies using likelihood, and applying threshold models to comparative data. Everything was placed in an historical context, which was nice. I particularly appreciated funny snippets about an argument between Felsenstein and Bookstein, Felsenstein's take on the famous Wright "guinea-pig-as-blackboard-eraser" story, and a really interesting idea about QTLs. The above image is from the movie G-Force - it's terrible, please promise not to watch it.

Felsenstein concluded with two crucial points. First, we're witnessing what he called a "grand reunion" of quantitative genetics and statistical comparative methods - fields that have remained too separate for too long. I will make a similar point in my talk. Second, you need more tips! New comparative methods are data-hungry and even 100 taxon trees can be barely big enough for some methods.

My phyloseminar is up next on Feb. 24 - please tune in! Also I've started a twitter account @lukejharmon.

Friday, January 21, 2011

Phyloseminar - new series on comparative methods

I wanted to put in a plug for Phyloseminar, which is an online seminar series. You can hear spectacular talks from the comfort of your office / home / wherever!

Phyloseminar is starting a series on "Macroevolution and phylogenetics," featuring talks from Joe Felsenstein, Brian O'Meara, and me. The first talk is coming right up on Monday Jan 24 (see homepage for the time). Joe Felsenstein will be presenting "What poultry breeders and guinea pigs have to tell us about statistical nonmolecular phylogenetics" (a spectacular title, right?). Don't miss it.

You can also listen to archived phyloseminars on alignment, gene tree - species tree concordance, and infectious disease.