genetics
razib | October 7, 2008Yesterday I attempted to rebut Steve Jones' ridiculous contention that evolution is going to stop in the modern West. Sometimes it is difficult to really know when to start, especially when your interlocutor seems to be in "incoherent spray arguments mode." Some of the commenters also noticed the internal lack of consistency in the model which Jones was putting forward. But saying it is a model is being overly generous. In short, Jones' most solid (that is, least vague) claim is that reduction in the number new mutations being added to the population every generation is decreasing because…
razib | October 6, 2008Yann commented on a new paper, Association of the SLC45A2 gene with physiological human hair colour variation:
Pigmentation is a complex physical trait with multiple genes involved. Several genes have already been associated with natural differences in human pigmentation. The SLC45A2 gene encoding a transporter protein involved in melanin synthesis is considered to be one of the most important genes affecting human pigmentation. Here we present results of an association study conducted on a population of European origin, where the relationship between two non-synonymous polymorphisms in the…
evolgen | October 6, 2008
I will be hosting Mendel's Garden #25 at evolgen. That's right: the carnival is back! Mendel's Garden is the original blog carnival devoted to genetics. Submit your genetics related posts to evolgen[at]yahoo[dot]com.
Because Mendel's Garden has been dormant for the past few months, I'll be accepting posts written from March through October. So, dig through your archives to find something good, and shoot me an email.
clock | October 5, 2008The October issue of the Journal of Biological Rhythms came in late last week - the only scientific journal I get in hard-copy these days. Along with several other interesting articles, one that immediately drew my attention was Clock Gene Wikis Available: Join the 'Long Tail' by John B. Hogenesch and Andrew I. Su (J Biol Rhythms 2008 23: 456-457.), especially since John Hogenesh and I talked about it in May at the SRBR meeting.
Now some of you may be quick to make a connection between this article and its author Andrew Su and A Gene Wiki for Community Annotation of Gene Function, published…
razib | October 5, 2008Think Gene has a new digg-like site up, news.thinkgene.com. Worth checking out.
razib | October 3, 2008Photo credit: Robert Hanashiro, USA TODAY
It is the norm today to discuss race as a social construct. Less fashionable is it to explore race as a biological concept. When there's no up or downside and the discussion is abstract I think most people can get away with benign neglect in regards to the second; but when your health is at issue people's ears perk up. The HapMap. Here's the first paragraph in Wikipedia on the HapMap:
The International HapMap Project is an organization whose goal is to develop a haplotype map of the human genome (the HapMap), which will describe the common…
edyong | October 1, 2008
The world is currently home to 6.5 billion people and over the next 50 years, this number is set to grow by 50%. With this massive planetary overcrowding, Band Aid's plea to feed the world seems increasingly unlikely. Current food crops seem unequal to the task, but scientists at Texas University may have developed a solution, a secret ace up our sleeves - cotton.
Cotton is famed for its use in clothes-making and has been grown for this purpose for over seven millennia. We do not think of it as a potential source of food, and for good reason. The seeds of the cotton plant are rife with…
gregladen | September 29, 2008An article just out in PLOS Biology explores one of the most important, but also difficult to observe, phenomena related to DNA regulation.
Figure 1 from the paper: "Atomic Force Microscopy of Lac Repressor-DNA Complexes (A) Schematic structures of biotin (bio)- and digoxigenin (dig)-labeled DNA constructs with one (O-539 and O-349) or two (O-153-O and O-158-O) ideal lac operator sequences (white bars)... (B) AFM image of molecules adsorbed to a mica surface ... (C) Scatter plot of the DNA arm contour lengths in repressor-DNA complexes....(D and E) Left: projection images of two…
gregladen | September 29, 2008Human societies tend to be at least a little polygynous. This finding, recently reported in PLoS genetics, does not surprise us but is nonetheless important. This important in two ways: 1) This study uncovers numerical details of human genetic variation that are necessary to understand change across populations and over time; and 2) the variation across populations are interesting and, in fact, seem to conform to expectations (in a "we don't' really care about statistical significance" sort of way, for now) regarding human social organization.
Before examining the paper, we should…
pharyngula | September 29, 2008This is a very simple, lucid video of Spencer Wells talking about his work on the Genographic Project, the effort to accumulate lots of individual genetic data to map out where we all came from.
I've also submitted a test tube full of cheek epithelial cells to this project, and Lynn Fellman is going to be doing a DNA portrait of me. I had my Y chromosome analyzed just because my paternal ancestry was a bit murky and messy and potentially more surprising, and my mother's family was many generations of stay-at-home Scandinavian peasantry, so I knew what to expect there. Dad turned out to be…
razib | September 29, 2008Another paper with another technique to detect positive selection in the human genome, Identification of local selective sweeps in human populations since the exodus from Africa:
Selection on the human genome has been studied using comparative genomics and SNP architecture in the lineage leading to modern humans. In connection with the African exodus and colonization of other continents, human populations have adapted to a range of different environmental conditions. Using a new method that jointly analyses haplotype block length and allele frequency variation (F(ST)) within and between…
razib | September 27, 2008There is some buzz recently about a lawmaker in Louisiana, John LaBruzzo, who is proposing to pay poor women to be sterilized. His logic seems naively reminiscent of Thomas Malthus. It any case, I will admit that I'm generally skeptical of the efficacy of these sorts of programs. But I think government sponsored eugenical projects are I think besides the point and miss the bigger picture.
2 years ago I reviewed a paper by Armand Leroi, The future of neo-eugenics. 2 years is ages in genome-time; it keeps getting cheaper. Notwithstanding the current low returns on investment in the…
razib | September 27, 2008R. A. Fisher and the Adaptive Landscape:
...My own interpretation is that Fisher was sceptical about the value of the landscape concept as such, because both environmental and genetic conditions were too changeable for the metaphor of a 'landscape' to be useful. For Fisher the question of the 'shape' of the landscape therefore did not arise as a major issue, and he had no need to take a firm view on it. I discuss this interpretation below the fold.
Read the whole thing.
Related: R. A. Fisher and Epistasis, Notes on Sewall Wright: Population Size, Notes on Sewall Wright: the Measurement of…
razib | September 27, 2008Earlier I reviewed a new paper which made some species-wide grand claims about the nature of human demographic dynamics. Specifically, as it relates to the ratio and reproduction of males and females over time. But to me some of the less ambitious but more specific work in this area where demographics, anthropology and genetics intersect are nearly as interesting.
From example, look at this figure:
This distribution shows the confidence intervals estimated from genetic data in relation to sex-specific migration rates. Granted, as noted in the paper, Molecular analysis reveals tighter…
razib | September 26, 2008PLoS Genetis has a neat paper up which clarifies something which we kind of already knew, Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity:
Like many primate species, the mating system of humans is considered to be moderately polygynous (i.e., males exhibit a higher variance in reproductive success than females). As a consequence, males are expected to have a lower effective population size (Ne) than females, and the proportion of neutral genetic variation on the X chromosome (relative to the autosomes) should be higher than expected under the assumption of strict…
razib | September 25, 2008Dienekes points me to a new paper, Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies:
....Here, we examined Japanese population structure by Eigenanalysis, using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster…
razib | September 23, 2008A few weeks ago I had a post up, Down syndrome and abortion rates. Today I noticed a variable in the GSS, GENEABRT, which gives responses to the following question:
1567. Suppose a test shows the baby has a serious genetic defect. Would you (yourself want to/ want your partner to) have an abortion if a test shows the baby has a serious genetic defect?
I decided to check the responses for different demographics of course. The table are below the fold, but there seems to be a trend with people with more education, less religion and more liberalism being more prone to being inclined to…
razib | September 21, 2008Carl Zimmer has a post up where he points to a piece he just wrote for Scientific American, Searching for Intelligence in Our Genes. Here's the major point:
Intelligence tests do identify a difference among people that has predictive power, and that difference can be linked-in part-to differences in people's genes.
The news about intelligence is that now scientists have new tools for probing intelligence, from brain scans to gene chips that can search for variations in half a million genetic markers at a time. But so far, those tools are yielding some pretty scant results. For example, just…
grrlscientist | September 20, 2008tags: political views, politics, physiology, threat response, psychology, philosophyfight or flight, nature versus nurture
Most Americans have been actively engaged in the frustrating sport of arguing about politics, which often leads to the common refrain; "You just don't get it!" So this made me wonder why people who seem to have similar life experiences can end up with such dramatically different personal philosophies -- philosophies that ultimately affect their political views and voting behavior. Apparently, I am not the only one to wonder about such things, because a paper was just…
purepedantry | September 17, 2008An Israeli town has come up with an aggressive method to fight uncollected dog poop: DNA IDing the "originator."
An Israeli city is using DNA analysis of dog droppings to reward and punish pet owners.
Under a six-month trial programme launched this week, the city of Petah Tikva, a suburb of Tel Aviv, is asking dog owners to take their animal to a municipal veterinarian, who then swabs its mouth and collects DNA.
The city will use the DNA database it is building to match faeces to a registered dog and identify its owner.
I am as disgusted with the stray poop as the next guy, but this seems…