What's a gene chip? Well, it's not a gene chip, that's for sure. It's a microarray. It has various parts of a genome arrayed on a small chip. The parts of the genome you put on the chip depends on what you're interested in studying. You then take some DNA you're interested in and apply it to the chip. If a DNA sequence matches a sequence on the chip, it hybridizes to the part of the chip with the matching DNA sequencing. You then use a special technology to visualize which parts of the chip have DNA hybridized to them. This technology can be used to differentiate between different single…
While much of the research in evolutionary biology is purely academic in nature -- designed for the purpose of understanding the biology of a system rather than for immediate human benefit -- there is some research that yields immediate practical uses. One research area that is particular fruitful in this regard involves applying evolutionary theory toward combating infectious disease agents. The metaphor of an arms race is often used to describe the evolutionary dynamics of parasites and their hosts. This true for the naturally evolved reactions in hosts, but also for human engineered…
Let's pretend this never happened: Those are the Scientists for Better PCR, complete with their own wanna-be Boss. Because when you need to find out who the daddy is, you turn to PCR.
John Timmer has a must read post on the coverage of science in the New York Times editorial pages. The science section of the NYTimes is probably the best in the country. Carl Zimmer leads the way, and there are many other solid science writers published by the NYTimes. Even Nicholas Wade, who has a known diction problem, manages to produce some pretty good articles. This excellence in science reporting does not extend to the opinion pages. From Behe's article on Intelligent Design to Sam Brownback writing about evolution to a questionable piece on fMRI and politics the track record on the…
There's a large element of "chance" in all biological systems. Whether it's a biochemical process within a cell, the movement of cells throughout an organism, or the evolution of the those organisms, stochasticity plays a large a part in biology. Unfortunately, this is often missed by most students of biology -- either because they fail to grasp the concept or it is never even presented to them. Yann points us to an article in PLoS Biology on teaching students how to appreciate the importance of randomness (I prefer to call it stochasticity) in biology: Klymkowsky MW, Garvin-Doxas K (2008)…
Matt Nisbet thinks that Francis Collins should be the next presidential science advisor. He does this after rejecting excellent popularizes of science, such as Neil deGrasse Tyson and E.O. Wilson, on the following grounds: Most science popularizers such as Wilson or Tyson don't have the years of government experience to understand the machinations of Federal science policy. Moreover, they have a paper trail of strong opinions on issues that might make appointment politically tough. I'm not sure what exactly those issues upon which they have strong opinions are. Is it that they're both…
I can't draw for shit. And I've got crappy penmanship to boot. All in all, I don't end up with aesthetically pleasing creations when I put pen or pencil to paper. So it's ironic that my one blog post selected for the 2007 edition of the Open Lab is a comic that I made. It's called The Lab Fridge, and it's a play off of a PhD Comic. Thankfully, I had Illustrator at my disposal in creating the comic. I don't think it's my best post of the year, but it is the best (and only) comic that I drew this year. For those of you looking to make it into Open Lab next year, go for one of the niche…
Can positive selection drown out neutral evolution? That's what John Hawks claims in response to my post on accelerated evolution. Hawks points out that, rather than looking at the neutral fixation rate (which is equal to the mutation rate, u), we should be more interested in the average time to fixation of a neutral mutation (the product of 4 times the effective population size, 4Ne). On the time scale he's looking at (40,000 years), neutral evolution shouldn't really matter because Hawks says that the Ne=100,000, which makes 4Ne>40,000. Therefore, the majority of new mutations that arose…
Historical Inaccuracy Edition A lot of us who work in well established biological systems take for granted how those systems were first discovered or established. Sometimes this involves the choice by an individual to begin studying development using a small worm. Other times it's the fortunate discovery of visible chromosomes allowing for physical maps of genomes to be constructed decades prior to genome sequencing. Or it could be the fortuitous choice of a taxon to use a model system for molecular evolution. This post deals with that last scenario, specifically the Drosophila melanogaster…
There's been a whole lot of hype around the Hawks et al. paper describing a recent burst of adaptive evolution in the human genome. The problem is a lot of people are conflating accelerated adaptive evolution with accelerated evolution. Take this for example: 12/11: Accelerated Human Evolution In recent years, humans have evolved at a much higher rate than previously thought, according to a new paper in PNAS. By analyzing genome variations, researchers found that the rate of human evolution was fairly stagnant until about 50,000 years ago, and then--because of larger populations, climate…
For those of you interested in recent adaptive evolution in some insignificant bipedal primate, John Hawks and pals have published a paper in PNAS describing something you'll find interesting. Of course, if you're interested in such things, you already know that. Here are some links related to Hawks et al. paper: The Hawks et al. paper presents data to suggest a recent burst in adaptive evolution along the human lineage. The reason for this burst is an increase in populations size, allowing for more beneficial mutations in the species. Eventually, the paper itself will be available here.…
Are you bothered by the total disregard for science shown by some US presidential candidates? Mike Huckabee does not heart evolution. Other candidates aren't saying much. Would you like to see where the candidates stand on various science and technology issues? Sheril and Chris at the Intersection have put together a campaign for a Science Debate amongst the presidential candidates in 2008. They have the support of many top notch scientists and science advocates. You too can sign on if you agree with the following statement: Given the many urgent scientific and technological challenges facing…
The Scientist blog reports that a representative of the National Science Foundation (NSF) was at the annual meeting of the America Society for Cell Biology (ASCB). The NSF representative pointed out a couple of things things: If your proposal describes research designed to find a cure for some disease, the NSF will not fund it. Well, duh! The NSF is about funding basic research. If you want to cure diseases, go ask the National Institutes of Health (NIH) for money. Research about human diseases and human health are not fundable by the NSF. If your lab is well funded, don't expect the NSF…
There are two recent genetics related posts on other blogs that evolgen readers might find interesting: First, check out Query Gene (via ScienceRoll). This web-ap allows you to couple a nucleotide blast search with a Google search for a term related to your blast query. Here is how the creators describe it: Query Gene is a web-based program that searches for information about genetic sequences on the web. It is distinctive because it is not limited to a single database, but instead captures genetic information on the entire Internet using Google. Query Gene works by taking a gene sequence in…
I previously described where in a genome we would expect to find sexually antagonistic genes. Briefly, depending on whether a gene is male-biased or female-biased and whether beneficial mutations are dominant or recessive, we can predict whether these sexually antagonistic genes will be on X chromosomes or autosomes. As I mentioned in that post, the theoretical results can only be translated into realistic predictions if we have reliable estimates of the relevant parameters. We do not have such estimates, but we can study the distribution of sex-biased genes throughout genomes. The results…
Not all animals must have sex with another individual to produce perfectly viable offspring. And neither do humans, thanks to technological breakthroughs in artificial insemination. But what about those critters that do not require masturbation and meat basters to produce babies sans contact with another individual? Remarkably, this is quite common in the animal kingdom, although different animals go about doing it in different ways. Caenorhabditis elegans, the roundworm that has become a popular model in developmental biology, lives in populations made up almost entirely of hermaphrodites.…
BioMed Central advertises itself as "The Open Access Publisher" (see their logo floating next to this text). They publish a lot of journals, but I think the Public Library of Science (PLoS) has the lead when it comes to being THE open access publisher. That's because everything published by PLoS is Open Access -- it's free to read, distribute, and reproduce, provided there is proper attribution. BioMed Central, not so much. That's right, BioMed Central, The Open Access Publisher, publishes paid-access articles. In fact, it publishes entire journals that are not open access. That includes…
PLoS ONE has recently published a paper entitled "Beyond the Gene" by Evelyn Fox Keller and David Harel, in which the authors take a stab at the long standing question: What is a Gene? Because this is such a big picture question, the appropriate discussion of the paper would involve a synthesis of what they authors wrote, what has previously been written, and what I think about all of that. I'm not going to do that. I'm too lazy and too stupid to do that. Instead, I'm going to read the paper and live-blog it. This one's for you, Bora. Quick tip: If you're planning to read an entire paper,…
John Hawks linked to a wiki with information on cultural anthropology job searches. If you poke around the website, you'll find a list of such wikis for many different academic disciplines. Of interest to evolgen are the Biology Jobs Wiki and the Ecology/Evolution Jobs Wiki. If you're currently on the job market, consider contributing information to these wikis. Do you know of any other academic job wikis for biologists? If you do, link to them in the comments.
I came across two press releases yesterday, entitled: Entire Yeast Genome Sequenced and University of Toronto scientists map entire yeast genome Upon reading the first, I thought, hasn't the entire genome of Saccharomyces cerevisiae already been sequenced? And haven't other yeast genomes been sequenced as well? What in the world could they be referring to? Did yet another yeast species gets its genome sequence? Does that really warrant a press release (sorry Jason)? And the second made me think that the person in charge of titling the press release decided that genome sequencing is synonymous…