May 2007 Archives

SMBE Talk Accepted

My talk was accepted for the Society for Molecular Biology and Evolution conference at Dalhousie University in Halifax, Nova Scotia this June.—Yea! Prof. Steve Steve will be there to see it. How about you? The talk is entitled “Estimating the rate and length distribution of indels”. According to the current schedule, I will be presenting at 12:15 on June 26 in the “Phyloggenetics: methods and models” session. My fellow Thorne-Lab postdoc, Ben Redelings, is also presenting in the same session.

In my talk, I will be presenting results from my current project which uses an expectation-maximization algorithm with a pair-hidden-markov-model to estimate parameters of an indel evolution model from intron sequences, without the need to assume any alignment is the true one.

Two early results that are important for molecular biologists: 1) a power-law gap model is significantly more accurate than the standard affine gap mode; 2) the indel model appears to be conserved across the mammal taxa that I’ve looked at.

Scientific Atheist

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You scored as Scientific Atheist, These guys rule. I'm not one of them myself, although I play one online. They know the rules of debate, the Laws of Thermodynamics, and can explain evolution in fifty words or less. More concerned with how things ARE than how they should be, these are the people who will bring us into the future.

Scientific Atheist


Militant Atheist


Angry Atheist


Apathetic Atheist




Spiritual Atheist




What kind of atheist are you?
created with

But there is something wrong. There is no way that I am more militant than PZ or Larry.

The Alabama High School Athletic Association has denied a team’s request to schedule a nationally televised football game on a Sunday, citing “Sunday is a day of worship”:

“Sunday is a day of worship,” AHSAA executive director Dan Washburn said when citing the reason for denying Hoover’s application to play an out-of-state opponent.


I wonder if anybody pointed out to Dan Washburn that Saturday is a day of worship as well. Oh yeah, and Friday is a day of worship, but I don’t expect the AHSAA to move high school football to Wednesday’s because Friday is a day of prayer for Muslims.

Heck, everyday is a day of worship for some people. Let’s cancel high school football in Alabama altogether if the AHSAA is so concerned about allowing people to worship.

Email Issues

If you sent me an email over the weekend, it may have bounced. I’ve fixed the problem. Sorry about that.

Cell on Blogs

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In my last year in grad school I got a free subscription to Cell. Cell is a very good journal, but for the most part they didn’t regularly offer articles that pertained to my research interests. Or let me put it another way; I should be reading a dozen of other journals before I read Cell to stay really current with my field: (in no particular order) Evolution, Genetics, AmNat, MBE, PNAS, Science, Nature, Bioinformatics, TREE, Systematic Biology, TPG, etc.

However, this month Cell has an article clearly of interest to me because I’m in it: Scientists Enter the Blogosphere. The leading suspects are all there, PT, PZ, Larry, Bora, etc. They also include the story about Comai and Cartwright (2005):

There is one case (The Scientist 21, 21, 2007) where a scientist blogger ended up becoming a coauthor on a paper thanks to his blog. Back in 2005, Reed Cartwright, a Ph.D. student in genetics at the University of Georgia, wrote an alternative interpretation of published findings about the mutant hothead gene of Arabidopsis (Nature 434, 505, 2005) in his blog De Rerum Natura. Several months later, Luca Comai at the University of California, Davis was publishing a similar interpretation in the journal Plant Cell. When he found out that Cartwright had already “published” the idea in a blog, he offered to make Cartwright a coauthor on the Plant Cell paper (17, 2856, 2005).

Too bad they didn’t link to this blog like they did for others.

The Savannah River Ecology Lab (SREL) is a nearly 60 years old ecological research and environmental education center run by the University of Georgia at the Savannah River Site (SRS), a DOE nuclear facility. The SREL has been operating since the Department of Energy acquired towns, farmlands, and forests along the Savannah River to start the site in 1951. It was operating even before SRS went nuclear.

SREL is a very important biological research station, and one of the few places (perhaps the only one) in which long term and large scale ecological experiments and studies have taken place. There is little comparison to the wealth of data that the SREL has generated for ecologists.

It is therefore not surprising that our anti-science administration in Washington is trying to shut SREL down, in spite of the continued support of SREL by SRS. SRS has obtained funding for the SREL, but unqualified political appointees in Washington are preventing SRS from releasing the funds. Unless those funds are released, SREL will be forced to close its doors by the end of the month.

I’ll post a detailed email that I received below. Please contact your representatives asking for the funds to be released and an investigation into the hold up.

Update: Other Sites on this Issue

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