evolgen | August 14, 2007Peter Lawrence has an opinion piece in Current Biology on the problems with evaluating scientists, amongst other things. He hits upon a few important points, including journal impact factors, the cost of high risk research, hyping up publications, and networking with the right people to improve your publications. One passage was quite salient given a private discussion I've been having with some folks:
Fourth, there is the way that science is done and papers are authored. These measures are pushing people into having larger groups. It is a simple matter of arithmetic. Since the group leader…
evolgen | August 13, 2007King and Wilson are the bee's knees for all the kids who want to hype the effect of gene expression divergence between humans and chimps. The argument boils down to a few points: humans and chimps are mad different, their protein sequences are mad similar, therefore expression of the proteins must be important for those phenotypic differences. There are some people who point out that looking at straight sequence divergence between orthologous sequences neglects the importance of copy number differences between species.
In a channeling of King and Wilson, a new paper looks at differences in…
evolgen | August 12, 2007
Wow, posts at evolgen have been few and far between. A damn, dirty manuscript is to blame. I keep trying to get it write itself, but the sucker refused to oblige. Maybe it would help if I could finish the data analysis.
But enough about me. Let's talk about me Steve Steve. The last time Professor Steve made an appearance on evolgen we were on our way back from the Fly Meeting (the other Fly Meeting posts can be found here: 1, 2, 3). After we got home, Steve Steve visited our lab, and I got a few pictures of him posing with Charles Darwin and hanging out in the fly room. You can see them all…
evolgen | August 2, 2007One of the primary hypotheses of Sean Carroll's model of evo-devo is that cis-regulatory elements (CREs) are the primary drivers of morphological evolution (see here). This hypothesis is controversial in the evolutionary genetics community. Because it's hard to examine the effect of CREs on phenotypes at a genome-wide scale, the problem must be reduced into smaller elements. One such element that has been the subject of previous studies is the role of cis and trans mutations in the evolution of gene expression. I have previously discussed some results that shed light on this issue. The basic…
evolgen | July 22, 2007Mark Liberman at Language Log has been posting on genetics recently. A couple of days ago he tried to track down the origins of the components of the gene name BTBD9. The letters and numbers in the name stand for complex-tramtrack-bric-a-brac-domain 9, which are hijacked from Drosophila nomenclature. Liberman then tries to figure out the origins of the names tramtrack and bric-a-brac using FlyNome (a cool webpage that I hadn't seen before) and FlyBase. In the end, he couldn't track down the (clever) story behind either one.
I was amused by that post, and I was further impressed by Liberman's…
evolgen | July 19, 2007Bill Hooker has taken Nature editor Maxine Clark to task for her claims about the open access status of the online features offered by the Nature Publishing Group. Maxine points to the various free online services offered by Nature -- including Nature Precedings, Nature Reports, Nature Network, Scintilla, and the journal Molecular Systems Biology -- in claiming that Nature has "many open access projects and products". Bill disagrees. You should read his entire post, but the punchline is that Clark is redefining Open Access to fit Nature's model and to be used as a marketing device.
A big…
evolgen | July 18, 2007
Remember that new species of leopard that was "discovered" earlier this year? Well, it wasn't really discovered so much as recategorized as a unique species (it was originally discovered in the early nineteenth century). That's a picture of it on the right if you don't remember.
Anyway, there's an Editorial in PLoS Biology arguing that we're creating too many damn species. We're not really "creating" them, mind you, but categorizing what were previously subspecies as distinct species. The authors of the editorial think that this is getting out of hand; they're taking the lumping position in…
evolgen | July 16, 2007
Mike Lynch has been getting a fair bit of hype recently for his nearly neutral model of genome evolution (see here and here). The nearly neutral theory riffs off the idea that the ability of natural selection to purge deleterious mutations and fix advantageous mutations depends on the effective population size of the population in which the mutations arise. From here, the nearly neutral theory predicts that more slightly deleterious mutations and fewer slightly advantageous mutations will fix in small populations compared to large populations (see here and here for previous posts on this…
evolgen | July 15, 2007I've recently come across two articles on junk DNA. The first one, from New Scientist, includes a pretty thorough coverage of recent studies that have identified functions for non-protein-coding regions of the human genome ("Why 'junk DNA' may be useful after all"). The article is set up as if it will present the demise of junk DNA, but it paints the accurate picture that a large portion of the human genome is non-functional. And TR Gregory like the article too.
The second article tries to do that, but fails. It's from The Scientist and entitled Junk Worth Keeping: Is it time to retire…
evolgen | July 12, 2007The American Institute of Biological Sciences has posted talks from their meeting on Evolutionary Biology and Human Health. Not only have they provided audio and video of the talks, but there are also transcripts and slides that go along with the talks. Very cool.
evolgen | July 11, 2007Bad tests for natural selection are bad at detecting selection.
Austin Hughes has published a fairly critical review of some methods used to detect natural selection in protein coding sequences. His attack on current methods for detecting natural selection is threefold. First, he claims that comparing non-synonymous to synonymous substitutions (see here) does not allow one to differentiate between adaptive evolution and relaxed selective constraint. Second, he argues that comparing polymorphism and divergence of synonymous and non-synonymous sites (see here) does not allow one to…
evolgen | July 10, 2007Dave wants to know whether we biologists have physics envy, as the physicists often claim. I'm quite happy being a biologist and I wouldn't want to study physics, but there are certain skill sets I wish I had. My envy is not for the questions other fields address, but for the tools other people in my field have at their disposal.
Enough with the foreplay; here are my answers to Dave's three questions:
What's your current scientific specialty?
Evolutionary genetics, in general. Specifically, the molecular biology and evolutionary dynamics of genomes.
Were you originally pursuing a different…
evolgen | July 9, 2007I thought I had come to grips with evo-devo. Then along come Hopi Hoekstra and Jerry Coyne to call shenanigans on Sean Carroll's model of evo-devo. This is nothing new for Coyne, but I can't recall Hoekstra ever getting involved in the debate before now.
Before we get to Hoekstra and Coyne, let's allow Carroll to describe evo-devo in his own words. His most recent summary of the evolution of transcriptional regulatory regions can be found in this paper from a recent National Academies Sackler Colloquium. Here's how he and his colleagues explain the importance of cis regulatory regions (CREs)…
evolgen | July 8, 2007I'm fucking sick of blog memes. Not only do I find online surveys totally lame, I also never get tagged. Boohoo, nobody likes me. Now, John Logsdon orders me to tell you eight things about me. I'm only doing this 'cause we had dinner together last week. Here are the rules:
We have to post these rules before we give you the facts.
Players start with eight random facts/habits about themselves.
People who are tagged need to write their own blog about their eight things and post these rules.
At the end of your blog, you need to choose eight people to get tagged and list their names.
Don't forget…
evolgen | July 8, 2007I've got far too many tabs open in my browser window, and I gotta blog them ASAP so that I can clean up the ol' computer. Here are a few things I've been meaning to blog, in list form:
Nature Genetics has published an issue devoted to structural variation in genomes. There appears to be a bias toward human genomes, but it's cool nonetheless. Also, I'm pretty sure all the articles are FREE ACCESS.
The most recent issue of Molecular Ecology has a bunch of articles on the genetics of speciation. There's also an article on the genetics of pigmentation variation in Drosophila melanogaster.
Peter…
evolgen | July 8, 2007The sixteenth edition of Mendel's Garden (the genetics blog carnival) has been posted by Hsien at Eye on DNA. If you'd like to host an upcoming edition of the carnival, you can sign up for the October, November, or December edition by emailing me (evolgen[at]yahoo[dot]com).
evolgen | July 6, 2007This week's phylogeny takes a look at the green portion of the eukaryotic tree. These are the eukaryotes capable of photosynthesis. Eukaryotes first obtained the ability to perform photosynthesis when a eukaryotic cell absorbed a photosynthetic cyanobacterium. This was followed by a few subsequent horizontal transmissions of the endosymbiont between unrelated eukaryotic lineages. Although eukaryotic chloroplasts can trace their origins to a single endosymbiosis, they don't share that organelle based on simple common descent.
Green plants -- one of the photosynthetic eukaryotic lineages --…
evolgen | July 5, 2007Last month's issue of Evolution (aka Evolution Int J Org Evolution, aka Evolution (Lawrence Kansas), aka some other confusing way of referring to the journal published by the Society for the Study of Evolution) contains two articles on teaching evolution. The first is on creating museum exhibitions to showcase evolutionary biology. The article focuses on Explore Evolution, a project in which multiple museums in the midwestern United States put up permanent exhibits about evolution. The exhibits encourage problem solving to understand how evolution works and have multiple examples from diverse…
evolgen | July 3, 2007In a post at the Panda's Thumb, Ian Musgrave cites this paper by Bakewell et al claiming that 154 genes out of 13,888 surveyed show evidence for adaptive evolution in humans since the divergence with chimps (this is the "chimps more evolved than humans" paper). Ian brings this up in a discussion of Haldane's dilemma -- which is only a dilemma to creationists (biologists are more interested in his sieve and his rule) -- but he cites the paper as an authority on the amount of adaptive evolution in humans. A discussion of adaptive evolution in human genes would be incomplete without mentioning…
evolgen | July 1, 2007The tenth edition of Gene Genie has been posted at Genomicron. Given that TR Gregory is an evolutionary geneticist based in Canada, one is left to wonder why he didn't attend the SMBE meeting. I know Larry Moran was at his daughter's wedding, but what was Gregory's excuse?
Also, the next edition of Mendel's Garden will be hosted by Hsien at Eye on DNA. If you have anything to submit, you can use the blog carnival submission page.