evolgen
Posts by this author
July 1, 2007
It's not entirely obvious at first, but this article in the New York Times is about the problems with gene patents in a world where one gene does not equal one protein. Now, we've known that this model isn't entirely correct, what with alternative splicing and all. Additionally, the human genome…
June 29, 2007
After driving through the night, we got home from Halifax this morning. The SMBE meeting was excellent as usual, and I agree with Dan Hartl that it's the best meeting for evolutionary genetics. With excellent talks and posters on topics ranging from population genetics to comparative genomics (and…
June 27, 2007
H.J. Muller is famous for (among other things) his argument for the evolution of recombination involving the purging of deleterious alleles (dubbed Muller's Ratchet). In a nutshell, Muller observed that, in the absence of recombination, deleterious mutations will fix in populations because every…
June 23, 2007
When this post appears, I'll be on the road to Halifax for the SMBE meeting. That's right -- on the road. As in an 18 hour drive. I'm not doing it alone, mind you. It's me and ten other grad students and post-docs packed into two vans. And we're not doing the whole thing in one stretch -- not…
June 22, 2007
Sensing and reacting to one's environment is necessary for survival. Different species have different expertise in regards to how they sense their environment. Humans, for example, have reduced olfactory abilities relative to other mammals, but excellent color vision. Cats have good night vision,…
June 16, 2007
Last year, Katie Pollard and colleagues published a couple of papers in which they identified regions of the human genome that had recently undergone an acceleration in their rate of evolution and characterized the expression pattern of an RNA gene located in one of those regions. The RNA gene is…
June 6, 2007
Matt's posted the newest edition of the Tangled Bank (the original science blog carnival) at his Behavioral Ecology Blog. There's a link to a post on Mike Lynch's anti-adaptationist paper in PNAS and another to a post by Pedro's on protein evolution.
June 5, 2007
This year's meeting of the Society for Molecular Biology and Evolution will take place at Dalhousie University in Halifax, Nova Scotia (conference webpage). I'm going, and so are Reed Cartwright and Jason Stajich. Additionally, Rosie Redfield and John Logsdon have each been invited to give a talk…
June 3, 2007
There are two genetics blog carnivals available for your perusing today. First is Gene Genie hosted by Hsien at Eye on DNA. The second is Mendel's Garden, over at The Daily Transcript. Hsien will also be hosting the next edition of Mendel's Garden. Visit the Mendel's Garden webpage if you'd like to…
June 3, 2007
Let's go through the basics again. Cracking the genetic code refers to figuring out how DNA encodes the information to make proteins -- that was done decades ago. Sequencing a genome does not mean that you have decoded the genome; presumably, decoding a genome would mean you've figured out the…
June 1, 2007
In a new article in PLoS ONE, a group of researchers led by Kevin Edwards present a collection of images of Hawaiian Drosophila wings. Here's one figure from the paper showing the evolutionary relationships of a bunch of different clades and some representative wing patterns:
The authors point out…
June 1, 2007
Last year, New York Times science writer Nicholas Wade wrote a few articles in which he referred to genome sequencing as "decoding". I chastised him for his poor use of terminology, was pleasantly surprised when he began to correct himself, and then realized that he would never overcome his…
June 1, 2007
For some reason, John Hawks thinks my disc flipping calculations have something to do with population genetics. He extends it to FST, which is just plain ridiculous. There is nothing about binomial sampling that can be related to popgen theory. Nothing.
May 31, 2007
Late last week, my PCRs stopped working. One day I was able to amplify DNA from multiple different templates using different primers, and the next day I couldn't. This is a major setback for me -- a huge chunk of the remaining work I need to complete for my PhD involves doing PCR. If I can't get my…
May 31, 2007
In yesterday's post, I argued that, when flipping two unfair discs (or coins), there is a greater chance that both discs will land with the same side up than different sides up. As pointed out in the comments, I was assuming that the probability of heads is equal for both discs:
Aren't you assuming…
May 30, 2007
The beginning of many Ultimate (nee, Frisbee) games is marked by flipping discs to decide which team must pull (kick off) and which goal each team will defend at the start of the game. This is sort of like the coin flip before an American Football game. Two players -- one from each team -- flip a…
May 29, 2007
Amongst the other TAs and the lab coordinators in my department, I have a reputation of being a tough grader. At the end of the semester, when the course admins calculate grades, my students invariably get a few points added to their lab scores -- this is done to bring lab scores more in line with…
May 28, 2007
A couple of weeks ago I suggested that the National Human Genome Research Institute (NHGRI) would no longer be funding de novo genome sequencing projects via white papers. They appear to be shifting their focus to resequencing projects to study variation (ie, this) and take a closer look at well…
May 27, 2007
Given the amount of attention I devoted to the effect of selection on the relationship between mitochondrial DNA polymorphism and population size (see here, here, here, here, here, and here), it's only appropriate that I link to this article by Meiklejohn, Montooth, and Rand on selection on mtDNA.…
May 25, 2007
For some reason, I have been collecting links to articles involving hybridization. That, on its own, would call for a massive link dump, but a recent news item makes for a nice contrast. First, the hybrids:
Where better to start than this review of hybrid speciation -- a topic I've discussed…
May 17, 2007
I'm working on a few graphs for a presentation. In a previous incarnation, I distinguished two partitions of my data using the colors red and green. This made sense intuitively (the red ones had something broken, and the green ones were a-ok), but I realized that people with red-green…
May 17, 2007
Keith Robison, at Omics! Omics!, asks and answers the question, "What math courses should a biologist take in college?" His answer: a good statistics course is a must (one where you learn about experimental design and Bayesian statistics), and a survey course that covers topics like graph theory…
May 16, 2007
There's an interesting post over at Statistical Modeling, Causal Inference, and Social Science on calculating probabilities. Traditionally, if you observe a certain number of events (y) in some number of trials (n), you would estimate the probability (p) of the event as y/n. To calculate the…
May 14, 2007
The Canadian research organization Genome BC has unveiled a science education website, Genomics Education. One of the features of the website is Floyd the Fruit Fly, who, we can only presume, is some sort of cartoon drosophilid. Or maybe he's a tephritid, but I highly doubt it. When you hear "…
May 14, 2007
Paul Erdos was an extremely prolific and mobile mathematician who has left a legacy in academia in the form of the Erdos Number -- a count of your "academic distance" from Erdos. Anyone who published a paper with Erdos has an Erdos number of one (Erdos, himself, had a number of zero), people who…
May 13, 2007
Have you heard of the Encylopedia of Life? If not, get out from under the rock, dude. Seriously. The hype machine has been going at full steam. This is supposed to be a database of all known species of organisms on earth. It's the incarnation of E.O. Wilson's call for a database of all species. It'…
May 10, 2007
Rick at My Biotech Life is organizing all the genetics feeds into a single Feedburner feed. The DNA Network is a collection of feeds from sites that blog on genetics. You can subscribe to the DNA Network Feed to get the web's best genetics content delivered to your newsreader. If you would like to…
May 10, 2007
Nothing captures life in the academic sciences quite like Piled Higher and Deeper. In yesterday's comic, Jorge Cham shows us the disgusting innards of the lab/office fridge. Now, Jorge is a physicist engineer, so his fridge is the one where you're supposed to store your food and drinks. When a…
May 9, 2007
For the past decade, when a research community wanted to sequence the genome of their favorite species, they submitted a white paper to the National Human Genome Research Institute (NHGRI). Despite its name, the NHGRI funds genome sequencing projects of not only non-human mammals, but also non-…
May 8, 2007
Trevor has posted the newest edition of Mendel's Garden at Epigenetics News. Go check out the best genetics blogging of the past month.
Also, we need hosts for the upcoming editions. If you'd like to host the June, July, or August editions, please email me (see the contact tab at the evolgen…