Monday, June 6, 2011
Sunday, January 30, 2011
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!
Tuesday, January 25, 2011
Monday, January 24, 2011
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
Saturday, December 25, 2010
First, Rich has been writing regularly for "Anole Annals" (http://anoleannals.wordpress.com/), 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 http://phytools.blogspot.com). 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
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
Tuesday, November 9, 2010
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.