evolgen
Archives for August, 2007
I’M IN UR GENOME, ADAPTING UR HOST-SYMBIONT RELATIONSHIP
Posted by RPM on August 31, 2007 Eukaryotic genomes are chimeras of sequences from many different sources. There are the genes responsible for the normal functioning of the host, but there are also transposable elements (TEs), sequences from mitochondria (numts), and endogenous retroviruses (ERVs). In addition to those examples, other symbionts also infect eukaryotes and leave traces of their presence in the…
Sorting the Pancakes that Make up a Genome
Posted by RPM on August 31, 2007 Genome rearrangements are fast becoming one of the most interesting aspects of comparative genomics (I may be slightly biased in my perspective). We have known for quite some time that genomes of different species (and even within species) differ by inversions of their chromosomes (this was first studied in Drosophila). In fact, some of the…
Michael Ashburner on Open Access
Posted by RPM on August 30, 2007 BioMed Central has posted videos of interviews of some notable scientists. Included is a video of friend of evolgen (and enemy of Prof. Steve Steve) Michael Ashburner espousing the virtues of open access. Ashburner was a signatory on the letter to Science encouraging publishers to make their journals publicly available. He also walks the walk,…
In Vino (Genome) Veritas
Posted by RPM on August 30, 2007 A group of researchers from France and Italy have sequenced the genome of the finest grape varietal, Pinot Noir. The genome has hallmarks of ancient triploidization, shared by other dicotyledons, but there is no evidence for recent polyploidization. That meant sequencing and assembling this genome is easier than doing so for other agricultural plants that…
Stealing from Other Schools
Posted by RPM on August 29, 2007 That’s the poster for the upcoming football season at Penn State. It’s purpose is both utilitarian (it’s got the schedule of games printed on it) and motivational (it’s supposed to get you all geeked up for the upcoming season). This year’s poster is using the slogan “FIGHT ON!”, and I bet someone in the athletic…
Two Posts on Publishing
Posted by RPM on August 26, 2007 Why should advisers encourage their students to publish? For the answer, read this post by TR Gregory. Why is the publishing industry afraid of open access? I can’t answer that question, but I can point you to the evidence for their fear: it’s right here. Jonathan Eisen points out why PRISM, the anti-open access lobbying…
Zombie Labs Eat Brain Genes
Posted by RPM on August 25, 2007 Remember the story about how we inherited the gene that gives us human brains from Neanderthals? The genetic data that were used to reach that conclusion (or a slightly less over-the-top conclusion) were part of a couple of other studies that identified signatures of adaptive evolution in genes involved in brain development. Those results were…
Junk on Cancer
Posted by RPM on August 23, 2007 The University of Michigan has put out a press release entitled: Bits of ‘junk’ RNA aid master tumor-suppressor gene With a title like that, how could I not blog the hell out of this bastard? I mean, they even put the scare quotes around “junk”. Like that — like I just did. Amazing! The story…
Confusion Regarding Long Author Lists
Posted by RPM on August 21, 2007 Nautilus, Nature‘s blog for authors, has a guest post by Robin Rose on long author lists, entitled “What’s an author?”. The post is representative of a certain brand of curmudgeonliness mixed with a dash of either ignorance or naivete. Rose has seen author list with more than 20 authors, and he’s confused. Did each author…
Selective Constraint on Ultraconserved Elements
Posted by RPM on August 20, 2007 There’s been a lot of recent interest in sequences that are highly conserved between humans and other mammals (and even other non-mammalian vertebrates). These sequences are thought to be under purifying selection, which prevents the accumulation of substitutions after two evolutionary lineages diverge. We cannot rule out, however, that the sequences are conserved by either…