Monday, December 25, 2006

Science Blogs listed on the OMMBID blog

The OMMBID (Online Metabolic and Molecular Bases of Inherited Diseases) blog has published a list of science blogs and related websites. It's nice to have been included. When I get some time I will browse that list and update my own lists of favorites on Connotea and my summary page.

Tuesday, July 11, 2006

Shared bookmarks for the literature -- what to do?

After some initial skepticism, I agree that "social bookmarking" is nice. It's very useful to put bookmarks to the literature online and see what articles others have cited, and the old approach of journal-specific browsing (associated with hard-copy volumes, but also including eTOCs) is certainly outmoded. I'm experimenting now with (as both ongenetics and RNAinfo) and Connotea. An RNA Society survey generated a few votes for CiteUlike, which looks great, although it is not easy to get it to accept an article from PubMed (in order to get the correct URL active you have to select the article you want from a list; if it is only result of your search, PubMed continues to display the URL for the search). A user named Cortel has lots of relevant citations, so I may continue to keep track of him, whether I settle on CiteUlike or not. I also created my parallel blog, "Quick Notes on Genetics," primarily with the idea of citing articles, and I keep a list of especially relevant articles tied to my lab's web page (the Mount lab reading room). Finally, it's worth mentioning the Faculty of 1000 in this context. This is all way too much. It's not clear what I will settle on, but most of these will be forgotten once I stop exploring and develop a routine for finding and sharing the articles that interest me.

Friday, May 12, 2006

The genetic architecture of complex traits: significant differences can involve noncoding DNA and can be epistatic

Clark et al., in "A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture," describe a significant QTL residing in noncoding (and largely repetitive) DNA far upstream of the affected gene (PubMed, Nature Genetics). I am reminded of the graduate genetics course given by Michael Freeling that I sat in on while a postdoc at Berkeley (in 1984, while studying the effects of transposable element insertions on gene expression in Drosophila in Gerry Rubin's lab). He emphasized epigenetic phenomenon and truly expected that novel molecular mechanisms (such as transposon instability) would reveal "a molecular clock that really ticks." From his web page it looks like he's continuing on the same tack today.

A paper in the previous month's issue of Nature Genetics (Carlborg et al., "Epistasis and the release of genetic variation during long-term selection," PubMed, Nature Genetics) reported a genetic network of four interacting loci affecting chicken growth ("Growth4, Growth6 and Growth12 had a significantly larger effect on growth in homozygous Growth9 individuals than [others]"). This kind of genetic interaction is precisely what any developmental geneticist would expect, yet breeders and population geneticists often cling to simple linear models. This paper will certainly help, not least of all because it involves a method for the detection of epistatic QTLs.

Wednesday, March 08, 2006

From HapMap to selection map

It was the article by Nicolas Wade in the New York Times ("Still Evolving, Human Genes Tell New Story") that alerted me to the new article in PLoS Biology by Voight et al. ("A Map of Recent Positive Selection in the Human Genome", from Jonathan Pritchard's group at the University of Chicago). I've been anticipating a list of human genes under selection for some time, and it's exciting to see this published. This paper, perhaps more than any other, marks the transition to a new and controversial era in genetics. On the positive side, we're going to learn a lot very quickly about the genetics of human differences. This will provide many benefits and engage curiosity in satisfying and useful ways.

On the other hand, the uncritical acceptance of results that are statistical in nature (and have a real possibility of being wrong) is disturbing. A recent visitor to Sarah Tishkoff's lab (Jeff Jensen, from Cornell, where he works with Aquadro and Bustamonte) gave a talk about the statistical problem of distinguishing selection from certain demographic phenomena that made me think the interpretation of selection maps is going to be extremely uncertain. It is surprising that none of those issues were addressed in Wade's article, especially so because the New York Times typically fills their science articles with quotes from others in the field. I felt the same unease a few weeks ago when watching a PBS documentary "African American Lives," in which famous African-Americans were given overly specific information about their ancestry without appropriate statistical disclaimers.

I suppose that we will all be talking a lot more about selection and race with my friends who are not geneticists, and putting a lot more population genetics into my graduate genetics course. Clearly, the idea that population genetics is passé is now passé.