evolgen | July 1, 2007It'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 also contains many "genes" which are only transcribed into RNAs, but not translated into proteins. All of this has been pretty much accepted by geneticists for a few years.
But rather than putting all of this in the appropriate context, Denise Caruso muddies the waters by overemphasizing the…
evolgen | June 29, 2007After 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 many people discussing both and everything in between in a single 15 minute talk), it's hard to find a better meeting.
I also had the opportunity to meet Rosie Redfield, John Logsdon, Jason Stajich, Reed Cartwright, and Jacob Tennessen. We got together for dinner, along with Professor Steve Steve,…
evolgen | June 27, 2007H.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 chromosome will, eventually, obtain a mutation which decreases the fitness of the organism. Recombination allows for the movement of deleterious mutations off of chromosomes, which decreases the genetic load in a population (because fewer deleterious mutations will fix).
Much of the recent work in…
evolgen | June 23, 2007When 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 everyone is hardcore enough for that -- so we're spending Saturday night in Bangor, Maine. I guess that's probably for the best because it would totally suck if we're already burnt out by the first day of the meeting.
Anyway, for those of you going to the meeting, I'll see you in Halifax. We're planning…
evolgen | 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, but poor vision during day light. These proficiencies and deficiencies in sensory abilities hold for non-mammalian taxa as well.
Olfaction and taste have been well studied in a variety of taxa. Amongst the invertebrates, the genes responsible for olfaction and taste in Drosophila are one of the best…
evolgen | 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 expressed in the developing brain, which lead people to speculate that it played some important role in making humans smarter than chimps (my round-up and stab at speculation can be seen here). Their approach toward identifying those regions is quite simple, but the cause of accelerated evolution in…
evolgen | June 6, 2007Matt'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.
evolgen | 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 at the conference. As you can see, there will be a blogger presence at the meeting.
Are you going to the conference? If you are (whether you're a blogger or not), you should join the SMBE 2007 group on the Nature Network. And if you haven't already signed up for the Nature Network (it's like…
evolgen | June 3, 2007There 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 contribute to the next edition.
evolgen | June 3, 2007Let'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 function of every part of a sequenced genome, but there really isn't a proper definition. In genetics, mapping refers to determining the location of genetic elements, which is different than sequencing. And deciphering has no real meaning.
With that said, check out the newest New York Times article on…
evolgen | June 1, 2007In 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 that, with the availability of the Drosophila grimshawi genome sequence, biologists can now use molecular techniques to understand the genetic changes that give rise to the various pigmentation patterns.
Edwards KA, Doescher LT, Kaneshiro KY, Yamamoto D. 2007. A database of wing diversity in the…
evolgen | June 1, 2007Last 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 inability to communicate science clearly.
It appears that Wade has found a new, yet still incorrect, term for genome sequencing. In an article published today, Wade reports on the 454 sequencing of Jim Watson's genome. Only he reports the Dr. Watson's genome was "deciphered". At least he isn't writing…
evolgen | June 1, 2007For 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.
evolgen | May 31, 2007Late 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 PCRs to work, I'm royally screwed.
As soon as I couldn't get any PCR products, I went into troubleshooting mode. I had just made a new batch of dNTPs, so those were the first thing to get replaced. No dice. I thought there might be something wrong with my water, so I grabbed a new bottle and made…
evolgen | May 31, 2007In 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 that p (and q=1-p) are the same for both discs? But isn't it more reasonable to assume that, while no disc has a perfect p=0.5 probability of landing 'heads', the p's of no two discs are likely to be the same? (Assume, perhaps, that each disc's p is drawn independently from some kind of larger…
evolgen | May 30, 2007The 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 disc in the air. A third player -- a representative from one of the teams -- calls "same" or "different", referring to whether both discs land with the same side (top/bottom or heads/tails) facing up or different sides facing up. If he guesses right, his team gets to choose whether they want to pull…
evolgen | May 29, 2007Amongst 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 lecture exam scores. Does that mean I'm a bad teacher who doesn't explain the material well enough, but grades as if it were explained clearly? Or do I explain the material perfectly fine, but expect too much from my students?
Because I'm such a hard-ass, I often get complaints from my students --…
evolgen | May 28, 2007A 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 studied organisms (ie, ENCODE, which now has Drosophila and Caenorhabditis versions). But the distribution of genomic resources is extremely biased towards a few species. What should those researchers who work on organisms without genome sequences do if they can't solicit funds from the NHGRI?
As…
evolgen | May 27, 2007Given 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. Here's the abstract:
Several recent studies have confirmed that mitochondrial DNA variation and evolution are not consistent with the neutral theory of molecular evolution and might be inappropriate for estimating effective population sizes. Evidence for the action of both positive and negative…
evolgen | May 25, 2007For 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 previously. The take home message: we first thought that hybrid speciation only happened in combination with polyploidy in plants, then we found out that hybrid speciation can also occur without polyploidization in plants, and then we discovered that the same thing happens in animals.
Here's an article on…