evolgen | May 28, 2008Francis Collins, head of the National Human Genome Research Institute (NHGRI), will be stepping down from that position in August. Collins has overseen the sequencing of the human genome, the HapMap project, the ENCODE project, and many other large advances in genomics. The NHGRI has had a major impact in the field of genetics while Collins was at its helm.
Collins also has a history of putting his foot in his mouth -- not that it's a bad thing to do so (lord knows my foot's spent more time lodged in my face than on the ground). He's been incorrect about morality and human evolution, to name…
evolgen | May 28, 2008Chad's in town for the DAMOP meeting. What that means isn't all that important in the grand scheme of things. But it did give us a chance to have a blogger meet-up. So, I grabbed Professor Steve Steve and Kevin (of Deep Sea Nudes and the Unimportant 95%), and we met Chad for some dinner and beers.
Kevin's posted another version of the picture.
evolgen | May 27, 2008
In his classic book from 1976, The Selfish Gene, Richard Dawkins introduced the concept of the meme. Basically, a meme can be thought of as a cultural gene -- an idea that is transmitted in a population.
This being Dawkins, memetics has a certain adaptationist flavor to it. The Selfish Gene introduces evolution from the gene's eye view. But Dawkins is a staunch advocate of natural selection as the primary driving force behind evolution. The debate over the role of natural selection in evolution has been carried out using empirical data, theoretical modeling, and philosophical arguments. I…
evolgen | May 22, 2008
On Tuesday night, the National Basketball Association (NBA) held their annual draft lottery. In the draft, each team is given the opportunity to select a few players that have declared themselves eligible for the draft (either after completing at least one year of college in the United States or being from another country and over 18 years old). The order of picks in the NBA draft is determined with a goal of awarding earlier picks to teams that performed the worst the previous season. However, rather simply giving the worst team the first pick, second worst the second, etc., the NBA takes…
evolgen | May 21, 2008I recently chastised Harold Varmus for equating open-access publishing with pay-to-publish. While open-access journals do tend to have higher author charges than pay-access journals, many journals make money from both author charges and subscriber charges. That is, they are pay to publish and pay to read.
A letter to Nature this week challenges the idea that open-access publishing is good for the developing world by assuming the same fallacy as Varmus (doi:10.1038/453450c). Raghavendra Gadagkar, of the Indian Institute of Science, argues that the pay to publish model prevents underfunded…
evolgen | May 20, 2008My advisor has recently got me listening to Whad'ya Know. My first reaction: It's like Wait Wait...Don't Tell Me! Only not as funny, not as interesting, and not as good. I've been downloading the podcasts for the past couple of weeks, and I'm not sure whether I'll keep subscribing in iTunes.
I'm only bringing this up because last week's episode contained a very egregious example of someone knowing just enough biology to get themselves in trouble. The sad part was that the person should have known better. Why? She teaches biology at the university level.
What happened? At the midpoint of the…
evolgen | May 14, 2008I can officially claim myself as a member of the ivory tower elite. At least, that's what they tell me.
evolgen | May 4, 2008Kevin has posted the newest Circus of the Spineless at Deep See Nudes News. Go get your monthly fix of inverts.
evolgen | April 25, 2008Duh! That's Obvious, Edition
Take a look at this mastodon skeleton:
Does it look like anything you recognize? Perhaps a large terrestrial mammal with big tusks. If you said "elephant" you win. The prize: nothing.
That is half of the conclusion from a recent paper in Science (doi:10.1126/science.1154284). Really. The other half: birds and dinosaurs are pretty closely related. Or, more specifically, birds and Tyrannosaurus rex -- THE COOLEST MOST AWESOMEST OF ALL DINOSAURS EVER!! -- are closely related. And, for this, they get a Science paper.
Now, the way they did this is pretty damn cool…
evolgen | April 23, 2008Brian Charlesworth wrote a review of Mike Lynch's The Origins of Genome Architecture, in which Charlesworth argues that sexual reproduction can explain many of the features Lynch claims evolved under nearly neutral processes (doi:10.1016/j.cub.2008.01.008). Not to be left out of the party, Deborah Charlesworth has chimed in with her opinion, and it's much more critical of Lynch than her husband's (doi:10.1017/S0016672308009282). The main thesis that Lynch has been presenting in both this book and some of his recent papers is that many features of eukaryotic genomes (introns, complicated cis…
evolgen | April 22, 2008The Drosophila genus is paraphyletic. That means there are species nested within the phylogeny of the genus that belong to other genera. Or, in other words, there are species descended from the most recent common ancestor (MRCA) of all Drosophila species that belong to different genera. If that doesn't make sense, just look at the tree.
A paraphyletic genus is a no-no in taxonomy. There are two ways to deal with the problem. First, the genera nested within the Drosophila phylogeny can be redesignated into the Drosophila genus. That's not going to happen because the genus is too freakin' big…
evolgen | April 21, 2008Someone was asked something along these lines by a member of some legislative body:
How will your research help protect this country?
That someone replied with something like this:
It won't, but it will keep this country worth protecting.
The exact wording in those quotes probably differ from what was actually said.
This isn't a rhetorical question, nor is it an exercise in trivia. I don't know who said it, what the exact context of the quote was, or whether this was actually said by anyone, anytime, anywhere. So, if you know of the exact quote, who said it, and where it was said, please…
evolgen | April 21, 2008
The creationist movie that everyone* is talking about came out was released this weekend. Early reports have Expelled coming in 9th nationally in weekend gross, with about $3 million. That's a lot of money, and you can color Randy Olson freakin' impressed. However, put in the context of what the producers were expecting, it's not so good.
That doesn't stop Randy from pulling at Matt Nisbet and touting how awesome the creationists are and how shitty the "evolutionists" are. Fucking "evolutionists"! I'm gonna go off on a rant here, but, before I do, allow me to point out the beautiful irony…
evolgen | April 20, 2008Last year, Craig Venter became the first single person to have his genome sequence published (doi:10.1371/journal.pbio.0050254). That genome was sequenced using the old-school Sanger technique. It marked the second time the complete human genome had been published (which led to some discussion as to whether the publication deserved to be published in a high profile journal like PLoS Biology), and the first time all of the sequence came from a single individual.
This past week, Nature published the second complete genome sequence of a single individual (doi:10.1038/nature06884). Like Venter,…
evolgen | April 19, 2008It's funny because some people think both groups are wrong:
Originally from Tom the Dancing Bug.
evolgen | April 14, 2008I think I'm cursed. Or I have bad luck. Or conference organizers think I'm a morning person. Alright, so maybe I really am a morning person. But that's besides the point. Because it sucks to give a talk on a Saturday morning. Saturday mornings should be reserved for things like Belgian waffles, homemade hash browns, made to order omelets, and mimosas. Not for 12 minute talks about my research. How much can you fit into a 12 minute talk? Not much. And you end up speeding up at the end when you realize you've got about 1 minute to make it through four slides. It's either that or go over 12…
evolgen | April 13, 2008Harold Varmus is one of the most high profile advocates of open access to biomedical research. As one of the cofounders of the Public Library of Science (PLoS), he has played an important role in making published results freely available to all. And he's a Nobel Laureate, which ain't too shaby either.
Varmus was interviewed by Ira Flatow for NPR's Science Friday program about the NIH's new policy requiring that research publications presenting results funded by the NIH be deposited in PubMed Central (the NIH's free online archive of biomedical journal articles) within a year of publication.…
evolgen | April 11, 2008Drosophila Are Not Fruit Flies Edition
As I have mentioned before, Drosophila are not fruit flies. Tephritids are fruit flies. Drosophila feed on rotting fruit, while true fruit flies feed on fresh fruit. That makes true fruit flies agricultural pests. Drosophila, on the other hand, are connoisseurs of the finer things in life -- wine, beer, cheese, and the like.
In addition to rotting fruit, Drosophila also feed on mushrooms and crabs. Yes, crabs. Well, they don't actually feed on the crabs, just like they don't actually feed on the fruit. The flies and their larva are more interested in…
evolgen | April 9, 2008PLoS Biology's press releases have taken another step toward being dismissed as "crap" by people who know jack shit about evolution, thanks to a new press release published last week.
It starts off like so:
Evolution has taken another step away from being dismissed as "a theory" in the classroom, thanks to a new paper published this week in the online open-access journal PLoS Biology.
And goes on like this:
As all students of Darwin know, evolution occurs when there is variation in a population; where some variants confer a survival or reproductive advantage to the individual, and where the…
evolgen | April 8, 2008Us dudes are always accused of thinking with our dicks. Perhaps it's because the genes expressed in our brains are similar to those expressed in our 'nads:
Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division.
The authors of the paper allege that their result has something to do with speciation. They even claim, "Brain is the most important tissue in…