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.

Saturday, December 25, 2010

New blogs

The readers of this blog (or at least those that remain) may have been wondering what the authors have been up to as the most recent post accumulates dust on Dechronization's front page (now over a month old, see below). Well, there are two new blogs that myself and Dechronization creator Rich Glor have been contributing to which may have drawn our attention away somewhat from treethinkers.blogspot!
First, Rich has been writing regularly for "Anole Annals" (, which is a great new web-log created by Jonathan Losos and devoted entirely to the wonderful adaptive radiation of Anolis lizards, made famous in evolutionary circles by Ernest Williams and Losos himself. If you find it hard to believe that Anolis can single-handedly sustain a regular web-log, then let Losos, Glor, and regular "Anole Annals" contributors Luke Mahler, Manuel Leal, and Yoel Stuart try to prove you wrong.
Second, I recently started blogging about my R phylogenetic development activities in a separate blog on phylogenetic comparative biology (creatively entitled: "Phylogenetic tools for comparative biology", and located at Since I started programming in R only relatively recently, this might interest both novice users and experienced R junkies alike. It is also designed to complement my newly created beta test version distribution page, which features the R source code for a growing list of R phylogenetics functions and methods that I have been working on.
Please check out these new blogs, but remember to come back to Dechronization because we promise that blogging here will resume here very soon!

Tuesday, November 16, 2010

Morris Goodman (1925-2010)

Morris Goodman, distinguished evolutionary biologist and professor at Wayne State University, passed away last night. Goodman was a pioneer in molecular systematics, known for his early research on primate phylogenetics and the use of phylogenies and ancestral character reconstruction to infer Darwinian evolution of haemoglobin (e.g., 1). Goodman also had important interactions with the founders of the modern synthesis (Mayr, G. G. Simpson, and Dobzhansky) regarding integration of evolution with molecular biology; he even sparred with G. G. Simpson in the 1960s over a revised classification of primates based on molecular data, prompting Simpson to refer to him later as “an old friendly antagonist” (2).

To most practicing systematists, Goodman was best known as the long-time editor and chief of the journal he founded nearly 20 years ago: Molecular Phylogenetics and Evolution. In a prescient editorial published in the first issue of MPE in 1992, Goodman discussed the rapidly expanding body of molecular phylogenetic data and the need to provide an outlet to "help disseminate the results of these molecular studies." Even though DNA sequence data existed for only a few loci sampled from a small number of taxa in 1992, Goodman recognized that "the genie is out of the bottle." Goodman ended his founding editorial noting "We are at the threshold of a new age of exploration that promises to greatly increase our knowledge of the history and ongoing evolution of the ramifying lines of life. It would be gratifying if Molecular Phylogenetics and Evolution became the journal of this age."

Rest in peace, Morris Goodman, no other journal has published more molecular phylogenetic trees over the past 18 years than MPE.

Wednesday, November 10, 2010

Tips for Writing a Systematics DDIG Part 6: The Little Things

One of the best ways to ensure that you don't get a DDIG is to not follow the NSF's guidelines for proposal preparation. There are two sets of guidelines you will need to pay attention to as you prepare your DDIG. The first set of guidelines is DDIG specific and can be accessed via the link under Program Guidelines at the main DDIG page. Carefully read this document (yes, the whole document) and ensure that your proposal adheres to all the rules. I'm told that one commonly overlooked component is the required "Context for Improvement" document, a one page statement that discusses how DDIG funding will permit a student to improve their thesis research and how the student's work relates to research being conducted by their advisor(s). The second set of guidelines you need to be mindful of are included in the NSF's more general Grant Proposal Guide. If you don't follow the formatting guidelines in section B of this guide, your proposal won't even make it to review.

Tuesday, November 9, 2010

Tips for Writing a Systematics DDIG Part 5: Broader Impacts

This is the last in my brief series of posts on preparing a DDIG.

Although often viewed with some mixture of confusion and frustration, a well thought-out broader impacts section is critical to any proposal being submitted to NSF. Are you a cynic who views broader impacts as little more than an obstacle standing between you and your research? If yes, get over yourself. The way you and your science interact with the rest of the scientific community and society at large deserves your attention. That said, expectations for the broader impacts of a DDIG are commensurate with the relatively low amount of funds they involve (relative to the much larger amounts your PI is likely to be applying for). Your PI may be starting a high school science program as part of her grant, but you shouldn’t feel compelled to go to such lengths in your DDIG. What then should you include in your broader impacts? Most proposals include some mention of one or more of the following broader impacts, many of which are likely to be coincident with your primary research objectives.

1. Undergraduate research opportunities (i.e., ‘training’ undergraduates by having them slave away on your project). This is a no brainer. Everybody wins when you get undergraduates involved in your research. This will be all the more convincing if you can include some ‘preliminary data’ showing that you already have experience recruiting and mentoring undergraduates.
2. Dissemination of data and results on the interwebs. You’re going to put your data online anyways, so why not take some credit for it?
3. Conservation significance. Conservation is a noble goal, but try to avoid vacuous statements like “The group I’m studying including some species of conservation concern.”
4. Outreach to the broader community. Often in the form of a museum exhibit or public presentations. Be creative here – visit a school, give a “keynote” at a science fair, etc., but make sure reviewers aren’t left feeling like you’re not going to follow through.

Monday, November 8, 2010

Tips for Writing a Systematics DDIG Part 4: How Much Methodological Detail?

You may feel compelled to give excruciating details of your proposed methods. Done correctly, this can be an excellent way to convince reviewers that you know what you’re talking about. However, space is tight and you can’t be expected to give a completely comprehensive overview of your proposed methods. The most important thing is to convince your reviewers that you understand what you’re talking about and have carefully selected the most appropriate, most sophisticated, and feasible methods possible given the question at hand. If you’re using standard methods (e.g., parsimony analyses in PAUP, Bayesian analyses in MrBayes) its safe to assume your reviewers have at least heard of these methods and the software used to implement them (they’re all going to be practicing systematists, after all). Even with such widely know methods, however, its still a good idea to mention a few specific details to show that you're familiar with the intricacies of your analyses (i.e., which type of search you'll be using in PAUP or how you'll assess convergence of your Bayesian analyses). If your proposal involves relatively new methods, or specialized methods that might not be familiar to other systematists, you should plan on including more detail. Be sure to justify why these methods are the most appropriate for your study, and how they will be used to specifically address the hypotheses/questions framed previously in your proposal.