As I have mentioned before, de novo sequencing of whole eukaryotic genomes may be a thing of the past (or, at least, these whole genome projects won't be getting very much more common). Instead, I proposed that people would use the new high-throughput technologies to sequence parts of the genome they found interesting. What did I propose they'd sequence (based on discussion I'd had with various folks)? The transcriptome, or, essentially, a whole genome cDNA library. This allows for a much higher coverage of the genes in the genome, but sacrifices information regarding non-transcribed…
60 Minutes ran a special on the science of sleep this week. The special included an interview with Scott McRobert about sleep deprivation and mating in Drosophila. So if lack of sleep impacts our appetite, our metabolism, our memory, and how we age, is there anything it doesn't affect? How about sex? Scientist Scott McRobert at St. Joseph's University in Philadelphia is asking that very question, studying fruit flies. McRobert could be seen showing Lesley Stahl a fly in a vial, which he then sucked up in a pooter. He then placed that male, along with a female, in a small dish. Stahl watched…
It's not very funny, but it's about a topic that comes up around here often (groans...). That said, this is something you'd expect to see over at Genomicron, not evolgen. In fact, the guy looks a bit like a young TR Gregory. For the full strip, go here.
The Next Generation Sequencing blog has a post on low coverage of A/T regions with Solexa sequencing. The post is in reference to a paper in Nature Methods on genome resequencing in C. elegans (doi:10.1038/nmeth.1179). Here's how the NextGen Sequencing blog summarizes it: However, it points to a general lack of coverage in A/T rich regions (see figure 2 of the supplementary material) which leaves a number of zero size gaps in the assembly - places where reads sit shoulder to shoulder but simply do not overlap. Having found these problematic A/T rich regions, the authors went back and took a…
I really like the PLoS journals. Their mission -- to make research freely available -- is totally awesome. And, on top of that, the journals publish very interesting research. PLoS Biology is a top notch journal, with papers on par with those in Science and Nature. And the specialty journals, like PLoS Genetics and PLoS Computational Biology, consistently have articles that I find quite attractive. But the website is totally fucked. I can't access most of the articles in PLoS Genetics. Thankfully, the articles are all mirrored on PubMed Central, but it's a major pain to track those down after…
Identifying and cataloging biological diversity is challenging. One way to do go about IDing all the life forms is to sequence a known region of the genome in all those species. This is known as DNA barcoding. An article in PNAS reports on the DNA sequence of a gene found useful for DNA barcoding in plants. In a review of the paper, the following table is presented: DNA Barcoding Genomics Number of species All (or most) One (or few) Number of gene regions One (or few) All (or most) The gist: DNA barcoding results in the sequencing of a single gene in a bunch of species, while genome…
Olivia Judson (aka, Dr. Tatiana) has a blog at the NYTimes website. It's usually a good read, but she has been known to go off the deep end. In this week's entry, Judson posts on how bones are not the only fossils. What other fossils does Judson write about? Genomes. Judson's focus is on genome size. She's clear that differences in genome size are the result of stuff other than genes, but she doesn't want to call that extra stuff "junk". Here's why: I don't like "junk," which suggests the DNA is useless: even if it doesn't hold the instructions for making proteins, it may still serve a…
Apparently, ScienceBlogs is loaded with white people. Hell, the whitest person I know blogs in this very domain. That got me thinking. Sure, we may look white. But are we really white? I mean, really white. So white that we like the stuff white people like. We do have someone who really likes graduate school: And we've got a Canadian: And someone who likes to study abroad: We look pretty white, huh? Well, it gets whiter. We've got a lawyer: A dog owner: Guys who like living by the water: And marathon runner: Man, we're the whitest group of whities I've ever been blinded by when the sun…
Brian Charlesworth has reviewed Michael Lynch's The Origins of Genome Architecture for Current Biology. Charlesworth's review is generally positive, and he agrees that population size may be an important factor in genome evolution. However, he thinks that Lynch overplays the role relaxed selective constraint in small populations plays in the evolution of genomic complexity. Charlesworth argues that sexual reproduction may be partly to blame for some of the features found in the bloated genomes of many eukaryotes. For example, the abundance of transposable elements may be the result of sexual…
One of the drums I beat around here pertains to inferring demographic history using molecular markers (i.e., DNA data). I've been known to go off on people who make claims about ancestral population sizes based on studies of a single locus or gene. You see, studying a single locus only gives you the evolutionary history of that locus. There is no way to untangle the affects of natural selection from those of demography without examining multiple loci. The coalescent is a popular statistical technique used to study DNA sequence polymorphism. Combining bayesian analysis with coalescent theory…
I'm easily annoyed. A lot of things piss me off. Here are the things that irked me today: Fake St. Patrick's Day. A large drinking school schedules Spring Break the same week as St. Patty's Day, and they do it two years in a row. This pisses off the students because it costs them an official drinking day (they'll be drunk on spring break regardless if it's St. Patrick's day). So, the students schedule their celebration of St. Patrick's day for the weekend before Spring Break. There's a few hundred drunk douchebags walking around town in green shirts and stupid hats today. It's goddamn amateur…
Poorly done and over clicked? Rod Page has a post worth reading in which he's "deliberately critical" of the Encyclopedia of Life (EOL). You should be able to visit the EOL at that link. Only you can't, as of two days following the release. You see, they weren't able to handle the 11.5 million hits they received within the first few hours of going live. We're only left to wonder whether this thing will ever get off the ground.
Jonathan Eisen is the new Academic Editor in Chief at PLoS Biology, and he's kicking it off with this editorial. In his editorial, Jonathan describes how he became an Open Access publishing advocate. The header of his article features a short biography with an interesting item: Jonathan A. Eisen is Academic Editor-in-Chief at PLoS Biology. He is also at the University of California Davis Genome Center, with joint appointments in the Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of…
I have an intuition, backed up by absolutely no evidence, that my particular area of interest (evolutionary genetics) has more faculty blogging about stuff related to their research than other fields. This is most likely the result of my interest in those blogs, and, hence, my increased awareness of them compared to blogs of faculty in other research areas. From a quick scan of my blogroll and the feeds I subscribe to, here's a list of research faculty who blog about evolutionary genetics: TR Gregory Rod Page John Hawks John Logsdon Jonathan Eisen Larry Moran That's not a lot of blogs, but it…
Do you ever sit in a boring departmental seminar and scope out the other folks in the room? You'll pick up some odd behaviors. Like the guy picking his nose -- gross! Or the secret couple that can't be open about their relationship because it breaks some university policy sitting a bit too close to one another. Well, here are a few folks that you'll probably see in every departmental seminar: The nodder: This guy affirms every part of the talk with a nod. The background information -- he gets it. The data -- he gets it. The conclusions drawn from arm waving and rampant speculation -- he gets…
Jonathan Eisen's been blogging the Advances in Genome Biology and Technology (AGBT) meeting in Marco Island. Here's what he's written so far: Advances in Genome Biology and Technology Meeting - First Post AGBT Marco Usland Update - Long Live Sequencing Marco Island Evening One - The Strange and the Good More notes from Marco Island/ AGBT Coolest Thing at Marco Island - The Polonator Marco Island sequencing frenzy - are we getting lost in all the data? Marco Island - Saving Some of the Best for Last The second to last post is the best, in my opinion. But there's some interesting points about…
Not Jim or Sam or Sally or Jane. Or Dr. Acula. But how do you refer to your advisor when you're talking to someone else? Do you call him/her "my advisor"? Do you call him/her "my boss"? Do you call him/her "that person I see once every two weeks who provides the money for me to get my PhD"? This is a Sunday unScientific Survey. Leave your answer in the comments.
Paraphyly in Drosophila Many biology students have hands-on experience working with Drosophila melanogaster. This little fly is one of the major workhorses of genetics. It may not be for long. That's not to say people will stop working with the fly, but the fly may no longer be named "Drosophila melanogaster". That's because the Drosophila genus is paraphyletic and should be split into multiple genera. Oh, and D. melanogaster doesn't hold the rights to the name Drosophila. Those rights belong to D. funebris, the first species named in the Drosophila genus. (Christopher Taylor at the Catalogue…
Everyone's blogging about Stephen J. Gould's Structure of Evolutionary Theory (Razib, John Lynch, Laelaps). I'm not. The book's too long, and I'm too busy. But that doesn't mean I can't link to them, and to another review of Gould. The other is Richard Lewontin's review of two Gould books: The Richness of Life: The Essential Stephen Jay Gould and Punctuated Equilibrium. The latter is a chapter in Structure of Evolutionary Theory. Yes, a chapter of a book was released as a book on its own. Lewontin's review of the two books isn't really a review of the two books. It's more of a eulogy or an…
Alex is pissed about science writers neglecting important discoveries in cell biology: Why are cell biology, molecular biology, biochemistry, microbiology never covered in the media? I've spoken to so many science journalists - most of whom have no science training. I've come to the conclusion that the barrier is too high - as a result when it comes time to write about these topics, most science journalists end up writing about "genomes" and "junk DNA". These are easy subjects - sometimes they're discussed within the framework of evolution, but never within the context of "how a cell or an…