genetics
razib | July 21, 2007Mike offers his 2 cents on the levels of selection debates. He says:
If it doesn't provide me with testable hypotheses and the conceptual tools to do so, it's just not useful. That's what happened the last go around with this in the late 80s and early 90s. Do the experiments and I'll be interested, because the last time it was a lot of yak and very little data.
Focusing on the "replicators" as opposed to the "vehicles" is so appealing because the former is so easier to grasp on to than the latter.
razib | July 19, 2007Natural polymorphism affecting learning and memory in Drosophila:
Knowing which genes contribute to natural variation in learning and memory would help us understand how differences in these cognitive traits evolve among populations and species. We show that a natural polymorphism at the foraging (for) locus, which encodes a cGMP-dependent protein kinase (PKG), affects associative olfactory learning in Drosophila melanogaster. In an assay that tests the ability to associate an odor with mechanical shock, flies homozygous for one natural allelic variant of this gene (forR) showed better short-…
razib | July 18, 2007Go Ahead, Everyone Talk at Once:
People who can't follow a movie when someone else is talking can blame their genes. The ability--or inability--to listen to more than one thing at once is largely inherited, according to a study of twins. The finding could help scientists better understand disorders that involve problems in auditory processing.
...
"This is the first study to show that [normal] people vary widely in their ability to process what they hear, and these differences are due largely to heredity," NIDCD director James Battey said in a statement. That's important, says Deborah…
razib | July 17, 2007Widely distributed noncoding purifying selection in the human genome (PNAS):
It is widely assumed that human noncoding sequences comprise a substantial reservoir for functional variants impacting gene regulation and other chromosomal processes. Evolutionarily conserved noncoding sequences (CNSs) in the human genome have attracted considerable attention for their potential to simplify the search for functional elements and phenotypically important human alleles. A major outstanding question is whether functionally significant human noncoding variation is concentrated in CNSs or distributed…
razib | July 12, 2007About one month ago Ruchira Paul posted on the ecology around Chernobyl and the surprising bounce back of some taxa. The Economist has some interesting detail about the nature of this revival:
...they found that species which relied on a class of chemicals called carotenoids to tint their feathers fared worse when there was more radioactivity around. Intriguingly, that did not apply to birds that used melanin....
Besides acting as pigments, carotenoids are antioxidants that have an important role in protecting DNA from harm. One of the ways that radiation causes harm is by generating…
razib | July 11, 2007Wired has a blog entry up where they reproduce the text of an email exchange with Bert Hoelldobler, an entomologist who is collaborating with E.O. Wilson on a new book which will argue for the relevance of higher levels of organization in evolutionary processes. In The Cooperative Gene evolutionary biologist Mark Ridley elucidates how multicellular organisms emerge from a coalition of genes all with the same interest because of their imprisonment within the individual (their replication being mediated by the sex gametes). I'm assuming that Wilson & Hoelldobler are going to attempt…
razib | July 10, 2007A commenter below observed that both the Sami and the Finns are cases where females tend to have darker eyes than males. He chalked this up to sexual selection. I was skeptical a priori because 3/4 of the time the variation between blue and brown eyes within the population can be explained by one genetic locus, and this is a region (OCA2) that seems to have been under massive recent selection. Sexual dimorphism tends to emerge slowly within populations because it takes time for modifier loci which express themselves conditionally in response to sex hormones to scaffold the initial gene…
razib | July 10, 2007Someone asked below if the Sami are actually darker than the Finns. Since I've been making this assumption in previous posts I thought I'd check this out. I found this source for the Finnish Sami where they cite a 1936 paper written in German. I've translated the relevant table (hair and skin color) below. The source above also has data on some provinces of central and southern Finland where one presumes the Sami presence is minimal, though I can't vouch for proper calibration of the metrics, I've included the appropriate snippets.
Eye color
Hair color
Light
Mixed
Brown
n…
pharyngula | July 10, 2007We now have a draft of the sea anemone genome, and it is revealing tantalizing details of metazoan evolution. The subject is the starlet anemone, Nematostella vectensis, a beautiful little animal that is also an up-and-coming star of developmental biology research.
(click for larger image)Nematostella development. a. unfertilized egg (~200 micron diameter) with sperm head; b. early cleavage stage; c. blastula; d. gastrula; e. planula; f. juvenile polyp; g. adult stained with DAPI to show nematocysts with a zoom in on the tentacle in the inset; h, i. confocal images of a tentacle bud stage and…
razib | July 9, 2007Over the past two days I've posted about the problems with Vitamin D deficiency that can crop up at high latitudes because of low UV levels. In Civilization Felix Fernandez-Armesto quotes a source stating about the Sami of Finland:
...They are blow-legged from rickets....
The argument I made earlier was that the Sami did not become very light because selective pressure was far weaker upon them than upon the Finns to their south. But this anecdote suggests that rickets is a problem for the Sami. What gives? A little searching led me to this story about the Inuit of Canada:
But as the Arctic…
razib | July 9, 2007Apropos of the recent drift vs. selection debates in regards to the driving forces of evolution, I thought I'd pass on this press release about the pervasiveness of neutral genetic elements. You can read the full provisional paper in PLOS Genetics:
Using sequence analysis and fossil dating, we also show a probable burst of integration of numts in the primate lineage that centers on the prosimian-anthropoid split, mimics closely the temporal distribution of Alu and processed pseudogene acquisition, and coincides with the major climatic change at the Paleocene-Eocene boundary. We therefore…
razib | July 9, 2007In my previous post I highlighted the possibility that extremely light skin might have evolved in Europeans relatively recently due to selection for Vitamin D production in the context of a nutritional deficiency prompted by the shift from a hunter-gatherer lifestyle to an agricultural one. I want to emphasize that the phenotype I was highlighting (skin color) was likely not the only response prompted by this selective force. For example, OCA2 seems responsible for about 75% of the variation in eye color in Europeans:
The TGT/TGT diplotype found in 62.2% of samples was the major genotype…
grrlscientist | July 8, 2007tags: DNA, genetics, blog carnivals
The 16th edition of Mendel's Garden was published today for you to read and enjoy.
razib | July 8, 2007Recently I had some blood work done for a routine check up and it turned out that I had vitamin D deficiency. The doctor explained to me that this is common amongst darker skinned people who live at high latitudes, especially in areas where cloudiness is the norm. That would fit the bill for my own ecological surroundings for these past few years, but I never believed that I would be susceptible to vitamin D deficiency because I perceived myself as someone who got sufficient sun. To the left you see a photo of my foot. I normally wear sandals, so please note the contrast between my exposed…
razib | July 6, 2007Recently a few blogs I follow have been having a back and forth "debate" which seem to recapitulate in the most general sense the "selectionist vs. neutralist" debates of the 1970s.
Three posts from p-ter:
Do phenotypes evolve neutrally?
More on adaptation
Final Thoughts on adaptation
From Larry:
Visible Mutations and Evolution by Natural Selection
Richard Dawkins on Visible Change and Adaptationism
While RPM offers Whither Adaptation?
There are two general responses I have to these sorts of debates. First, their relevance to the "post-genomic era" is something I would question. The…
purepedantry | July 5, 2007Actually that isn't fair. It isn't wrong. The percentage of difference just depends heavily on what you define as a difference.
So argues an editorial by Jon Cohen in the latest issue of Science:
Using novel yardsticks and the flood of sequence data now available for several species, researchers have uncovered a wide range of genomic features that may help explain why we walk upright and have bigger brains--and why chimps remain resistant to AIDS and rarely miscarry. Researchers are finding that on top of the 1% distinction, chunks of missing DNA, extra genes, altered connections in gene…
razib | July 2, 2007Eye on DNA has an interview with a "genetic genealogist." He's a little more enthusiastic about the informative value of these tests than I am, but the interview itself is pretty informative.
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.
razib | July 1, 2007Spencer Wells, author of The Journey of Man, has a write up of The Genographic Project and "Out of Africa" in Vanity Fair. Nothing new or groundbreaking, but you know historical population genetics has come a long way if it's in Vanity Fair. On a related note The Genographic Project has finally yielded a major paper in PLOS Genetics. More method than meat though.
Via Eye on DNA.
evolgen | July 1, 2007It's not entirely obvious at first, but this article in the New York Times is about the problems with gene patents in a world where one gene does not equal one protein. Now, we've known that this model isn't entirely correct, what with alternative splicing and all. Additionally, the human genome also contains many "genes" which are only transcribed into RNAs, but not translated into proteins. All of this has been pretty much accepted by geneticists for a few years.
But rather than putting all of this in the appropriate context, Denise Caruso muddies the waters by overemphasizing the…