evolgen | September 15, 2008
I'm currently working my way through John Wakeley's book on Coalescent Theory. (The website has a few pre-publication chapters if you want to take a peek.) In his introductory chapter, Wakeley introduces the concept of gene genealogies. He's careful to point out that, unlike the phylogenies we construct using inter-specific data, we don't actually use intra-specific gene genealogies to infer the relationships of the sequences we've sampled:
Readers used to "tree thinking," which is the subject of Section 1.1, will have little trouble seeing the close connection between gene genealogies and…
evolgen | August 1, 2008About a month ago, we were told that theory is dead. That was the thesis of Chris Anderson's article in Wired. Rather than testing hypotheses using the scientific method, Anderson argues that scientists are merely generating loads of data and looking for correlations and stuff. The article was a bit muddled, but that's Anderson's main point . . . I think.
Well, now the Times Higher Education has published an article by Tim Birkhead in which he argues the opposite (In praise of fishing trips). Birkhead says that the scientific establishment is too attached to hypothesis testing. This means…
evolgen | July 28, 2008
The University of Iowa is hosting next year's meeting of the Society of Molecular Biology and Evolution, SMBE 2009. I usually go to the annual SMBE conference, and I was probably going to attend SMBE 2009. Now I'm definitely going. Why? Because John Logsdon just announced that they'll be hosting a pre-conference meeting on the Evolution of Sex and Recombination.
The Sex & Recombination meeting was supposed to happen this summer, and it was scheduled for the week prior to the Evolution 2008 conference in Minnesota. But mother nature interrupted, and the flooded campus was in no state to…
evolgen | July 26, 2008So, I'm just hanging out here by the side of the water waiting for my lunch. Sure, I could go in the water and get my lunch. But that's not how I roll. I wait patiently for my prey to get within striking distance, and then I attack. So, here I am just hanging out by the side of the water.
Click to enlarge.
There they are. Just a bunch of cichlids waiting to be eaten. By me. Lunch would be good right now. But they won't get close enough. So I'll just hang out here with my jaw agape.
And I can see them. They're not too far away. Maybe one of them will swim close enough to the shore. And then I'…
evolgen | July 25, 2008Last month I mentioned that I had been in Barcelona at the Society for Molecular Biology and Evolution conference. I arrived in Spain early in the morning, and, after I got checked in to my hotel, I went with a couple friends to the Barcelona Zoo. This zoo is famous for housing Snowflake, the albino gorilla who lived at the zoo from the mid-1960s until he died in 2003. They still have an impressive collection of primates despite the loss of the zoo's icon.
Additionally, the zoo has a roaming band of peafowl. The peacocks and peahens have free reign of the grounds, and you'll often see them…
evolgen | July 22, 2008
Randy Olson left a career as a marine biologist (Titleist!) to become a film maker. His first feature project was Flock of Dodos, a movie I enjoyed. His second film is Sizzle, a movie reviewed by lots of ScienceBloggers a couple weeks ago. The gist: a lot of ScienceBloggers didn't like sizzle. Neither did a reviewer for Nature (doi:10.1038/454279a).
I did not request a review copy of the movie because I don't like to diverge much from the main themes of evolgen: evolutionary genetics, manatees, and the douchebag who writes this blog. But some of the recent discussion surrounding Sizzle has…
evolgen | July 22, 2008
All good medicine is evidence based -- that is, diagnoses and treatments are developed via the scientific method. Oftentimes, evolutionary biology is employed to understand human health and diseases. This is known as evolutionary medicine.
Evolutionary medicine is a growing field that takes an interdisciplinary approach toward studying human disease. Tools from population ecology, molecular evolution, comparative anatomy, and many other fields are all integrated with clinical medicine to improve our understanding of human disease and develop new treatments. This approach can be applied to…
evolgen | July 21, 2008We all know that Drosophila are the gayest bunch of gays that ever gayed up genetics. This is especially true when you create mutations in fruitless (nee fruity), "the gay gene". Male flies with mutations in fruitless will try to get it on with other males (e.g., doi:10.1016/S0092-8674(00)81802-4). That's gay!
But fruitless is an old school gene that needs to be fucked up to turn the flies gay (doi:10.1093/molbev/msj070; the first author on that paper is, I shit you not, named Gailey). Drosophila really aren't as gay as they are made to appear in the articles describing fruitless mutants.…
evolgen | July 18, 2008Phylogeny Friday -- 18 July 2008
When they published the initial analysis of the complete platypus genome (doi:10.1038/nature06936), Nature, as they're wont to do, also put out a news item announcing the major findings (doi:10.1038/453138a). That news article included a phylogeny illustrating the evolutionary relationships of various animal species in various stages of having their complete genomes sequenced.
The problem with the illustration: they got some of the relationships wrong. This sparked a letter from Peter Ducey of SUNY Cortland (doi:10.1038/454027d), in which he wrote the…
evolgen | July 18, 2008Until yesterday, there was a span of about two weeks in which this blog laid dormant. I did that on purpose because I didn't want to give you all the blogging you crave. All three of you who may crave my blogging. And I'm guessing not one of those three even noticed the silence. Ah, the joys of insignificance.
Besides being a lazy dick, I actually have a valid excuse for my silence: I was moving. Or, rather, I am moving (my move is not yet complete). Where am I moving? From grad-school to post-doc. It also happens to be a move from one city in the middle of nowhere to another city in the…
evolgen | July 17, 2008
The Creation Museum is located in northern Kentucky, just across the Ohio border from Cincinnati. Answers in Genesis, the folks behind the so-called "museum", claim that their "museum" is within a 6 hour drive of 2/3 of the US population. This is not true -- Kentucky is in the middle of bumfuck nowhere (I'm an expert on cities in the middle of bumfuck nowhere), and most people in the US can't get there in 6 hours.
But the museum is damn close to Cincinnati -- it's in what people would call the "greater Cincinnati area", and it's closer to the so-called Cincinnati airport (which is actually…
evolgen | July 17, 2008Olivia Judson says Darwinism is dead. She's right. Anyone who talks about "Darwinism" or "evolutionists" gets my attention. That's not to say that any use of those terms is incorrect. But they are often used as framing devices by creationists, and those frames get carried over into the lay discussion of biology. You should read her discussion of why we should get rid of Darwinism.
On a somewhat unrelated note, Judson also writes the following:
We'd want to discuss evolution beyond natural selection -- the other forces that can sometimes cause (or prevent) evolutionary change. For although…
evolgen | July 1, 2008Wired Magazine has published an article by Chris Anderson arguing that theory is dead (The End of Theory: The Data Deluge Makes the Scientific Method Obsolete). The argument: with our ability to generate vast amounts of data, there is no need for theory. Now, it's hard to parse what Anderson means by "theory" from the article. But he seems to be arguing that scientists are merely looking for correlations between various parameters, and claiming that's a sufficient analysis. Is it? Well, sometimes, yes, if it's based on a sound theoretical framework.
Deepak Singh has already called out…
evolgen | June 30, 2008There's a post up at Pharyngula describing the concept of synteny in comparative genomics (Basics: Synteny). The definition given by PZ Myers will sound pretty familiar to those of you who have read some of the genomics literature. The problem: it's not quite correct. It's actually the definition that I think most comparative genomics folks would give if they were asked to define synteny. But they keep using that word, and I don't think it means what they think it means. What's the definition? Here it is in PZ's own words:
Synteny is the conservation of blocks of order within two sets of…
evolgen | June 27, 2008Phylogeny Friday -- 27 June 2008
I haven't done a Phylogeny Friday in about a month, but a recent paper reporting a "phylogenomic study of birds" was worth mentioning (doi:10.1126/science.1157704). Now, this isn't phylogenomics as Jonathan Eisen defined it. The bird evolution paper describes building a tree using lots of molecular markers.
I don't have much to say about the new bird phylogeny (I'll let the expert handle the details), but I wanted to post one of the trees for Phylogeny Friday. Here is one of the phylogenies they present, attempting to reconcile their results with those that…
evolgen | June 27, 2008PLoS Genetics has published an interview with Jenny Graves. Graves is one of the leaders in monotreme and marsupial genetics, and has been involved in some of the recent mammalian genome projects, including the platypus genome project (doi:10.1038/nature06936). She is also an expert in the evolution of mammalian sex chromosomes and sex determining genes. However, I'd like to point to a quote in PLoS Genetics' interview of Graves that deals with science education:
So I'm becoming very interested in education, particularly of young children, which is where I think the rot sets in. Science is…
evolgen | June 23, 2008Dak at Fire Joe Morgan asks:
I've been watching a fair amount of SportsCenter / BBTN today, and every two minutes someone mentions that there are "seven teams going for a sweep in an interleague series!", as if this is some sort of big deal. There are fourteen interleague series this weekend. If every match were a coin-flip, wouldn't we expect exactly seven teams to be going for sweeps in the third game of a series?
We'll start by assuming each team has an equal probability of winning each game, and the results of each game are independent. After one game, you're guaranteed that one team…
evolgen | June 18, 2008John Hawks has an interesting post on what it means to be human in which he argues that our "human-ness" (humanity?) is our shared evolutionary history. I like it. But Hawks also writes the following:
It is our history that connects us to our distant relatives, not our genes. Even with a close relative like a twentieth cousin, there is a decent likelihood that you will share no genes at all because of your shared kinship from your most recent common ancestor. By the fiftieth generation, it is a virtual certainty. You are a genetic stranger to your ancestors.
I could share no genes with my…
evolgen | June 15, 2008
If you check the archives of this blog (which I know all of you do on a fairly regular basis), you'll see that I haven't posted anything in over two weeks. Those kind of blog hiatuses can't be good for traffic, but I have a legitimate excuse: I was out of the country. Readers with a keen eye for international architecture will recognize the picture attached to this post. Those without, may not. Either way, I figure I should tell you that it's one of the facades of Sagrada Familia, Antoni Gaudi's best known unfinished church.
Why post a picture of this famous tourist spot? Because I was in…
evolgen | May 30, 2008Phylogeny Friday -- 30 May 2008
Research on animals in under attack throughout the world. Animal rights activists not only stage rallies against animal testing, but they also engage in criminal behavior. They vandalize property, sabotage experiments, and terrorize researchers. How can scientists fight back?
Michael Conn and James Parker have written book documenting the animal rights issue from the scientists' perspective (The Animal Research War). Conn and Parker have also briefly described their position in the FASEB Journal. Here is how they summarize their book:
This book is a personal…