evolgen | December 9, 2006There are certain scientific disciplines that are well represented in the blogosphere. Bioinformatics comes to mind. As does physics. But these are computer savvy people who probably spend quite a bit of time hooked up to the interwebs. How about scientists that need to get their hands dirty? Like ecologists.
Does anyone know of any good blogs by ecologists about ecology? Not conservation or environmentalism, but ecology. Like population dynamics, landscapes, nutrient cycling, predator-prey interaction. I've got a couple in mind, but I want to hear your suggestions.
And if you're an ecology…
evolgen | December 8, 2006My university has been hosting panel discussions on science, religion, and teaching. I missed the first installment, which consisted of faculty members from science and humanities departments and a local clergyman. The second discussion was led by four students from a course cross listed in Science and Technology Studies and Philosophy. The topic of this discussion was teaching science and religion, but the discussion often strayed to the intersection of science and religion in general. It would have been nice if they stayed on topic. I, however, can't hold much against them, as I once took a…
evolgen | December 7, 2006The five nurses and one doctor (the Tripoli Six) accused of infecting hundreds of patients with HIV in Libya are awaiting the verdict of their trial, expected to be handed down on December 19. The second trial concluded on November 4 -- the original guilty verdict was overturned. I previously mentioned that the molecular evidence (DNA sequences from HIV taken from the patients) did not support a guilty verdict. Nature has published the results of an analysis of those DNA sequences that suggests the doctors were not responsible for the HIV infection. A description of that evidence is below the…
evolgen | December 7, 2006Circus of the Spineless #15 has been posted at Words & Pictures. Go check out the best invertebrate (cough, paraphyletic taxon, cough) blogging from the past month or so.
evolgen | December 5, 2006A few weeks ago PNAS published a paper on the evolution of snake sex chromosomes. The authors compare snake sex chromosome evolution with that of mammals and birds. Given my passing interest in sex chromosome evolution, I decided to check it out.
Snakes use sex chromosomes to determine the sex of their progeny. Sex in other reptiles, such as crocodiles, is determined by the temperature at which the eggs are incubated. There are two main types of sex chromosome systems in vertebrates: XY and ZW. Most mammals, some fish, some reptiles, and some amphibians use the XY system -- males are…
evolgen | December 4, 2006The funniest lab accident?
There was the time I spent an entire day trying to make electrophoretic gels using distilled water instead of buffer. The agarose suspended fine in the distilled water, but I couldn't get it to solidify. I kept remaking the agarose solution and never got anything worthwhile. The next day, I asked a lab mate what I was doing wrong. I found out and felt damn stupid.
And just last week the autoclave leaked. A brown liquid covered the floor. It was real funny while I cleaned it up.
Or how about the time I mouth pipetted ethyl methanesulfonate . . . NOT!!
evolgen | December 4, 2006We usually think of speciation as a bifurcating process -- a single lineage splitting into two. The relationships of those species can often be determined using DNA sequences. But we know that there are exceptions, like horizontal gene transfer in bacteria. And hybrid speciation in plants. These exceptions often interfere with our ability to reconstruct the evolutionary relationships of those species.
Hybrid speciation occurs when two species produce hybrids that are both fit and capable of becoming reproductively isolated from the two parental species. The new species will often exploit a…
evolgen | December 4, 2006
The ninth edition of Mendel's Garden has been posted by the collective of Oregon State grad students known as Salamander Candy. Go read the month's best genetics blogging.
evolgen | December 3, 2006Sandy has declared her love for all things "-omics". She even came up with a nifty table to define a bunch of omes. It's like she's created a list-o-omes-eome.
Snark aside, here's why she likes omes:
I like "ome" [see, I told you she would tell us why she likes omes] because it simultaneously gives us more precise definitions for fields of study, while making a distinction between the reductionist view of biology, that was so popular when I was in graduate school, and the more global-omic-view that's been emerging of late. When I grew up, we were mired in the one gene - one enzyme rut.
As a…
evolgen | December 2, 2006The USC offensive line sucks.
Lane Kiffin and Steve Sarkisian suck.
Absolute failure.
When you play against a speed defense, you run right at them. You attack them. You make them overrun and overplay. You don't run slow developing plays.
And when you play against a young, crappy QB who likes to run the football, you hit him hard -- real fucking hard -- early. You make him question his ability to play the game. You make him question his skill level. You make him question his manhood. You don't wait until the 4th quarter to kill the motherfucker. You don't get a 15yd. personal foul by tapping…
evolgen | December 2, 2006In the sake of fairness, it's worth reporting that mitochondrial DNA (mtDNA) may not be as flawed as previously thought (see the original paper here). I spent a bit of time earlier this year barking about how mtDNA is a less than stellar marker for inferring demography because it's subject to recurrent selective sweeps which wipe out all signatures of demographic history. Thanks to Dr. Rob, I revised my position to take into account the effects of population size on selection.
If mtDNA mutations are only weakly advantageous, then they should only be under selection in large populations (this…
evolgen | December 1, 2006What if some phylogenies were simply irresolvable? That is, what if, no matter how much data we collected, it would be impossible to reconstruct, with a high level of certainty, an accurate representation of the tree of life? That would suck. A lot. I have mentioned how this can result from long branch attraction or lineage sorting. But are there any taxa where this appears to be a major problem?
Antonis Rokas and Sean Carroll have published an essay in PLoS Biology that addresses the issue of bushes (or irresolvable nodes) in the tree of life. They point out four clades in which no single…
evolgen | November 30, 2006Dr. Joan Bushwell (not her real name) has hurled some poo at the -omicists. You know, those people who attach -omics to everything and act like they've come up with a brand new research discipline. I imagine them making the "guitar player changing chords" face (go to 1:09 in this video) when they coin a new "ome".
As one last hurrah for omeomics, Doc Bushwell coined the meme-ome. That would be a collection of all the memes floating around the blogosphere. Or is it all memes everywhere? Who knows? But it is the perfect congruence of two terms that have worn out there welcome.
And systems…
evolgen | November 30, 2006Last week I linked to Carl Zimmer's take down of Casey Luskin. Notice how the text containing the link to Carl's post says "Casey Luskin". It's called a Google bomb -- we're trying to make Carl's post the number one search result when one enters Casey Luskin as a query in Google. It only works if a bunch of people link to Carl's post like this: Casey Luskin.
As of November 29, 2006, Carl's post is the 22nd result when you Google Casey Luskin. That puts him on the third page. In fact, Carl's post ranks behind a post from Afarensis and one from Migrations that both link to Carl's post (and both…
evolgen | November 29, 2006If you're getting near finishing your PhD (within a couple of years or less), check out this article from PLoS Computational Biology. It offers ten suggestions to consider when searching for a post doc. The suggestions are not comp-bio specific, but I'd be interested in hearing if people have other ideas. I've definitely been thinking about post docs, but I have no concrete plans as of yet.
evolgen | November 29, 2006
A bunch of grad students at the European Molecular Biology Laboratory (EMBL) are organizing an online symposium in the Life Sciences. They've got a list of speakers and you can upload your own presentation. The conference runs from December 4-8, but I'm not sure how exactly this virtual conference works. If you're interested, check out their website and read what other people have to say.
(Via Public Rambling.)
evolgen | November 29, 2006A couple of years ago, one of the rear tail lights went out on my car. I'm kinda handy with tools, so I figured it would be an easy fix. I poked around in the trunk area with my screw driver, removing every screw within spitting distance of the lamp. I tugged on the lamp in every possible direction, but the sucker wouldn't budge. Just because I could sequence DNA or parse a genome into the interesting bits and discard the boring stuff, didn't mean I could perform simple maintenance on my car. I admitted defeat and had the lamp fixed the next time I brought my car in for an inspection.
Why did…
evolgen | November 28, 2006Everyone's jumping on this meme, but I'm not gonna do it. Ooops . . . Looks like I just did it. Anyway, blogging's been light recently. Hopefully I can get my act together and have some posts up later this week. And by "get my act together" I mean procrastinate from doing real work by writing blog posts.
They're also all doing this meme. Turns out, I'm a "SoCal surfer". Makes sense -- I grew up a few blocks from the ocean. Of course, it could be worse. I could have grown up in Huntington Beach. Then I'd really sound like Spicoli.
What American accent do you have?Your Result: The West
Your…
evolgen | November 24, 2006Remember Maciej Giertych? He's the Polish representative to the European Parliament who wants creationism taught in schools alongside evolution. And he's got a degree in tree physiology, but he claims to be a population geneticist. Anyway, his letter to Nature made it seem like Poland has this big problem with creationism. Boy was I mislead.
It turns out the problem isn't just localized to Poland; it's spread throughout Europe. Nature reports that creationists in Great Britain, using the name Truth in Science, are trying to undermine the teaching of evolution. And Letizia Moratti, the former…