In a list of the most overrated things, we're the Churchills of popular science: Popular science: ScienceBlogs. Politics gets more hits than science, so ScienceBlogs recruits screamers rather than interesting popularizers or important scientists. More here.
So, I missed the three year anniversary of evolgen (it was last Wednesday for those of you keeping score). What does that have to do with police dogs and civil rights protesters in Alabama in the 1960s? Absolutely nothing. But I'm combining two unrelated topics into a single post -- neither of which have anything to do with the American civil rights movement. Or do they? Police dogs attacking black people are as big a part of Alabama culture as nooses hanging from trees in Louisiana. Too soon? Whether it's at a protest march or on a football field, there's not denying it. Anyway, here's a…
Brian at Laelaps has written a post entitled "What's good for the gander isn't always good for the goose", in which he describes some examples of sexual dimorphism in charismatic vertebrates. Studying the phenotypes of these traits is interesting, but what's happening on the genomic level? That is, how do differences between males and females affect the distribution of genes on chromosomes? Many of the traits that are beneficial for males are deleterious in females (and vice versa). For example, male sheep with big horns will mate more and leave more offspring, but females with big horns…
I hate vanity posts -- who the fuck outside my mom cares how I'm doing, and she don't read this -- but I feel somewhat obliged to explain the lack of activity on this unread blog. This is especially important in case my Seed overlords stop by and notice a stark absence of any recent posts and a deficiency in posting regularity over the past couple of weeks. Aside from the few regular visitors, I doubt anyone has noticed the near death of evolgen. That said, here's what I've been up to instead of blogging. I'm in the middle of that clusterfuck known as the last year of grad school. Those of…
Is it just me or does every analysis that looks for over-represented gene ontology (GO) terms turn up transcription factors? It doesn't matter if the study is looking for genes under positive selection or something else. It just seems like transcription factors are enriched in every dataset.
Chad asked a fun question last week, and I just got around to finding it yesterday: What items should be on the list for a scavenger hunt through an academic physics department? Let's now ask: what items should be on a list for a scavenger hunt through a biology department? Taking some hints from Chad and his commenters, here are my ideas to prime the pump: A reagent bottle with a label dating it to the 1980s An out of use fume hood above "the line" A paper copy of a PLoS Journal (they exist) A non-top-heated thermal cycler A Project Steve Steve A journal article used to prop up something A…
What happens when I mention a paper describing two more Drosophila genomes? Well, I get a comment telling me that the 12 Genomes Papers have gone live over at Nature. They have provided a nifty 12 Genomes Portal for us to navigate the articles published by Nature based on data from the 12 Genomes Project. Now, these aren't the only papers published from the 12 Genomes Project -- look for 12 Genomes Papers in the November issues of Genetics (currently not web-available), PLoS Genetics (also not up on the website), and the December issue of Genome Research. The 12 Genomes Papers include two…
The world of genomics is changing. It was initially about sequencing the genome a single representative individual from a particular species. Now, there's a large focus on polymorphism -- that is, sequencing multiple individuals from a single species to study the genomic variation in that species. That's well under way in humans, with HapMap and various other projects designed to generate DNA polymorphism data on a genome-wide scale. That approach has made its way to Drosophila genomics with the publication of a paper describing polymorphism across the entire genome of D. simulans, a sibling…
He's not an atheist! He's found god! This atheist is no more! He has ceased to be (an atheist)! He's found god on his way to meet his maker! He's a deist! Bereft of doubt, he thinks no more! If you hadn't written his book for him, he'd be wandering around a nursing home dribbling spit! His intellectual processes are now history! He's off his rocker! He's kicked his skepticism, he's lost his marbles, run away from reason and joined the bleedin anti-science brigade!! THIS IS AN EX-ATHEIST!!!
During my first semester of college I took an introductory chemistry class from a poet, playwright, and Nobel laureate -- that's all one guy, not three. His Nobel Prize is in chemistry, which made him more than qualified to teach us about acids, transition metals, and the other basics of chemistry. He also advocated a well rounded education, and he required we read The Periodic Table by Primo Levi. In addition to our exams and lab reports, we had to write an essay about one of Levi's short stories. I bring this up because the intro-chem instructor, Roald Hoffmann, gave a lecture last night…
Why is this video so damn funny?
Peer-to-Peer, one of Nature's many blogs, has a post on pseudoscience on preprint servers. The post is in response to a post from another blog (creationists using nature precedings to pre-publish junk science) that pointed out a potentially pseudoscientific article on Nature's preprint server, Nature Precedings (The saltational model for the dawn of H. sapiens, chin, adolescence phase, complex language and modern behavior). The article in question came off as creationist tripe to selena, who blogged about it at Tending the Garden. This brings up a couple of questions. Taking a narrow focus,…
Too funny to pass up: Seeking NIH Geneticist as early (paid) reader of Science/Adventure Novel I'm looking for a one or more readers to vet the science and NIH-specific details of a science/adventure novel. This is a "hard science" book along the lines of Carl Sagan's "Contact," but with certain spiritual elements. The ideal reader would be someone with a graduate level genetics background at the NIH, but who is open to possibilities beyond rigid, scientific reductionism -- -- somewhere between Richard Dawkins and Francis Collins. Willing to consider a reading fee for the right person. If you…
I want to highlight two excellent items related to scientific communication: The first is a post by Tim Lamber on Deltoid in which he reproduces a comment by John Mashey. Mashey provides a very nice description of how scientists should deal with members of the media. Rather than merely berating bad science reporting (as some are wont to do), Mashey suggests some more pro-active ways for scientists to support good science news. The second item is an Editorial in PLoS Biology entitled "When Is Open Access Not Open Access?". In the article, Catriona MacCallum draws the distinction between Open…
Previous entries: Part 1 - Introduction Part 2 - The Backstory Part 3 - Obtaining Sequences Part 4 - Obtaining More Sequences Part 5 - Examining the Outgroups This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 6 of this series (Evolutionary Relationships) can be found below. Evolutionary Relationships While we were probing the outgroup genomes for copies of aldolase genes using TBLASTX (Examining the Outgroups), we discovered that there are two excellent matches to aldolase genes in the honeybee,…
Previous entries: Part 1 - Introduction Part 2 - The Backstory Part 3 - Obtaining Sequences Part 4 - Obtaining More Sequences This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 5 of this series (Examining the Outgroups) can be found below. Examining the Outgroups In the previous post I mentioned that the two outgroup species in our analysis, the mosquito Anopheles gambiae and the honeybee Apis mellifera, have only one copy of the aldolase gene. If that's the case, then it's likely that the gene was…
Remember those prizes I promised if you donated to any of the ScienceBlogs DonorsChoose.org challenges? I described the prize for one lucky donor to the evolgen challenge. Now Seed has revealed what they're giving away to a few lucky contributors to any of the ScienceBlogs challenges. Janet has the lowdown at her blog -- the lucky donors will win either a t-shirt, mug, subscription to Seed, or copy of "The Best American Science Writing 2007". Also, one really lucky donor will win an iPod nano. Go read Janet's post to learn the details. Links: Blogger Challenge progress report (day 11) plus…
Please God, don't let it happen. Please don't let Franky Collins win this stupid award. I don't usually make pleas to you, but, given that this is a matter regarding a man of faithTM, I figured it's a good time to plea to the sky fairy. So, do whatever you can to prevent Congress from awarding Frank the medal. As for my more terrestrial readers, here's the skinny. The Genetic Alliance is petitioning the US Congress to award Collins the Congressional Gold Medal. Why? Because he's in charge of the National Human Genome Research Institute (NHGRI). Now, the NHGRI has done a great job in promoting…
There are two exciting pieces of news about the DonorsChoose.org ScienceBlogs Challenge. First of all, Seed has offered to match all donations by ScienceBlogs readers for the second year in a row. Last year, Seed matched donations up to $10,000, but this year they're willing to match up to $15,000. So, start donating. We're currently 15% of our way to our goal of $1000. Secondly, I have an offer for evolgen readers who donate to the evolgen challenge. When you donate, save your confirmation email so that you can win one of the still unannounced prizes from Seed. In the meantime, if you send…