evolgen | March 9, 2006Orac has been reporting on the arson at the Holocaust History Project. He's asking as many people as possible to spread the news and draw attention to the Holocaust History Project as a way of getting back at the people who were trying to silence the Holocaust History Project.
On a more personal note, my grandparents were nearly Holocaust survivors (or victims). They lived in Poland, and had the 'good fortune' to be sent to a Soviet prison in Siberia rather than a Nazi concentration camp. Had events been slightly different, I may not be here.
evolgen | March 8, 2006Kevin White (aka, Mr. Drosophila microarray data) has a paper coming out in tomorrow's issue of Nature. The paper (which is not available on the Nature website yet) compares the expression of over 1,000 genes from humans, chimpanzees, orangutans and rhesus monkeys. From a news write up of the findings:
When they also looked for human genes with significantly higher or lower expression levels, they found 14 genes with increased expression and five with decreased expression. While only ten percent of the genes in the total array were transcription factors, 42 percent of those with increased…
evolgen | March 7, 2006I have been working from home today (mostly grading papers) and watching the World Baseball Classic. This is the first time I've been able to watch a complete game -- the previous games were in Tokyo, which meant they were shown live in the middle of the night. (Note to NBC, you can show sporting events in another time zone live.) Today's game between Venezuela and the Dominican Republic has the energy of a late season game between two teams in the middle of a pennant race. The Venezuelan team is staying with the favored Dominicans. I also plan to watch the USA-Mexico game, and I wanted…
evolgen | March 7, 2006This paper is rather timely considering I just finished reviewing methods for detecting natural selection. Jonathan Pritchard's group has scanned SNP data from three populations (Europeans, East Asians, and Nigerians) for signatures of positive natural selection. The authors used measures of polymorphism to detect natural selection. In their approach, they polarized polymorphic SNPs as ancestral and derived (kind of like a Fay and Wu test) using the other populations as outgroups. In this type of test, high frequency derived SNPs are a hallmark of recent positive selection; the authors…
evolgen | March 6, 2006I have to say, it's kinda cool to have my opinion acknowledged and used to correct an error. It looks like I pull some weight around here (not as much as some folks, but the 100 or so page views a day mean something).
But I ain't done yet. In honor of my dedication to correcting errors in the popular press, I have added a new category called "Science News" to this blog. In this installment, I will point out another error published by Seed. Not all of my posts will be devoted to copy-editing my bosses, it just so happens that they're now one hit away from a trifecta for the day.
This one…
evolgen | March 6, 2006If anyone thinks I have sold out to the Seed Gods, let this be my exhibit A against such opinions. Seed has published a review of Funk et al's ecological divergence and speciation PNAS paper. The scientific content is not all that bad, but it blows the implications of the study way out of proportion. My thoughts are below the fold.
The Seed article uses to the Funk paper to look at the role natural selection plays in speciation. The focus is put on whether allopatric speciation is a neutral process or if it depends on divergent selection in the two different environments. The article…
evolgen | March 6, 2006A very pretty picture (click on the image to make it larger):
Go read what Carl Zimmer and Rhosgobel have to say. For more on the Tree of Life, go here.
evolgen | March 6, 2006Dan Ely sounds a lot like Phil Skell. They both go to the evolutionary biologists at their respective universities and ask them ill-informed questions. They then misinterpret the answers and spread their misnomers throughout the anti-evolution community.
evolgen | March 5, 2006Polymorphism and Divergence
This is the eighth of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The introduction can be found here. The first post described the organization of the genome, and the second described the organization of genes. The third post described codon based models for detecting selection, and the fourth detailed how relative rates can be used to detect changes in selective pressure. The fifth post dealt with classical population genetics methods for detecting selection using allele and genotype frequencies…
evolgen | March 4, 2006All of the ScienceBloggers are taking the quiz to determine which science fiction spaceship on which they belong. The quiz has 48 questions, so I'm not taking it on principle. Also, I don't particularly like sci-fi (or SF, or whatever the hell it goes by these days) . . . and I haven't heard of most of these movies or shows that the ships are from. If it were up to me, I'd be on board the Millennium Falcon if it were captained by Chris Walken with Jack Lemmon riding shotgun.
evolgen | March 3, 2006Today, I will begin a new tradition at evolgen. There are a lot of topics and terms in the biological sciences that sound like something else; many of these fall into the category of double entendre. I'm quite immature, so that kinda stuff really amuses me. Every Friday I'll try to come up with another double entendre for your enjoyment. Reader submissions would be greatly appreciated.
For today's evolgen Double Entendre Friday, I give you the cleavage furrow. Yes, cleavage, as in these things. During mitosis, after all the genetic material is sorted out, the cell splits all of its…
evolgen | March 2, 2006Dudes, here's some stuff around the blogosphere that has caught my eye:
Robert Skipper, a philosopher of biology, knows a whole lot about the history of population genetics. Is he the next Will Provine?
Another philosopher, John Wilkins joins the fight against taxomonic bias.
Razib wants you to bust a rhyme.
evolgen | March 2, 2006I have posted on microbial diversity in the soil previously. Tara pointed out that even though we are just now learning about what ecological factors determine soil microbial diversity, we also have a lot to learn about microbial diversity within the human digestive tract. She asked:
I wonder what a meta-analysis of the diversity of human-associated bacteria would find? For example, we already know that diversity can vary even by location within the colon; we also know that the pH of different areas in the body can vary (due not only to bodily secretions but also other bacterial flora that…
evolgen | March 2, 2006Another molecular biologist has joined the ScienceBlogs army. Go over an say hello to Alex Palazzo at The Daily Transcript. He'll drop some central dogma on you.
evolgen | February 28, 2006
The sixth edition of the Circus of the Spineless is up at Science and Politics. Get your fix of inverts now...
evolgen | February 28, 2006There's a fun article in Nature Reviews Molecular Cell Biology on what distinguishes a good scientific meeting from a not so good one. The author advocates attending small meetings or workshops (under 100 people), which is tough for a young scientist. Small workshops are usually either not well advertised or difficult to get to. The only small meetings that I attend are local meetings, and the only workshops I go to are the workshops that are hosted at larger meetings. For a young scientist, large nation/international meetings allow for the most interaction with the most people in your…
evolgen | February 27, 2006You, me, your pet dog, and any other animal with a backbone are deuterostomes. So are sea stars, sea urchins, and sea cucumbers. During early development you, me, and echinoderms (sea stars et al) are a round ball of cells. The ball of cells invaginates and that opening becomes our anus. This differs from other animals like flies, worms, and snails whose first opening becomes a mouth. A second opening forms later in development, and it becomes our mouth (hence the name "deuterostome", or mouth second). The deuterostomes can be broken into two groups: the chordates and the echinoderms.…
evolgen | February 27, 2006I have a little bit of an infatuation with copy number polymorphism (CNP), which describes the fact that individuals within a population can differ from each other in gene content. Some genes, such as olfactory receptors (ORs), have many different related variants in any animal genome. New copies spring up via duplication events (a type of mutation), so one could imagine that individuals from a single population differ in the number of copies of these genes. In fact, this is the case with any gene or gene family (a group of related genes) in the genome -- there may be duplications…
evolgen | February 26, 2006The Frink Tank has jumped the shark and joined the ScienceBlogs evil empire. If you like your science with a dash of humor (and dick jokes) check them out.
Another blog, Stoat, has come on board. This one's new to me, but it looks like it deals with climate sciences (and no dick jokes).
evolgen | February 26, 2006My advisor received an email from a fairly prominent geneticist regarding some results published by Dobzhansky over fifty years ago. The geneticist had done some back of the envelope calculations and noticed some trends that had been overlooked for a half of a century. We happened to have the animals to replicate the experiments (and I was planning on doing some similar experiments) so my advisor had me perform the crosses. I ended up with a negative result -- I did not see the same trends that Dobzhanksy and colleagues observed. I guess you could say my negative result was a positive…