Archive for May, 2008

Liberals pretend to support black candidates?

By Razib Khan | May 20, 2008 8:08 am

Noam Scheiber points to working paper, SOCIAL DESIRABILITY BIAS IN ESTIMATED SUPPORT FOR A BLACK PRESIDENTIAL CANDIDATE, which attempts to figure out the Bradley Effect by guaging avowed vs. implied support. Mark Blumenthal of Myster Pollster has an interview where one of the authors explains the methodology and touches upon some confusing issues….

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Two new pigmentation papers

By Razib Khan | May 20, 2008 12:33 am

A Genome-Wide Association Study Identifies Novel Alleles Associated with Hair Color and Skin Pigmentation:

It has been a longstanding hypothesis that human pigmentation is tightly regulated by genetic variation. However, very few genes have been identified that contain common genetic variants associated with human pigmentation. We scanned the genome for genetic variants associated with natural hair color and other pigmentary characteristics in a multi-stage study of more than 10,000 men and women of European ancestry from the United States and Australia. We identified IRF4 and SLC24A4 as loci highly associated with hair color, along with three other regions encompassing known pigmentation genes. Further work is needed to identify the causal variants at these loci. Improved understanding of the genetic determinants of human pigmentation may help identify the molecular mechanisms of pigmentation-associated conditions such as the tanning response and skin cancers.

….Taken together, these four regions explain approximately 21.9% of the residual variation in hair color (black-blond) after adjusting for the top four principal components of genetic variation. (Conversely, after adjusting for these four regions, the top four principal components of genetic variation explain 2.6% of the residual variation in hair color.)….

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Incest & delayed mother, an analogy

By Razib Khan | May 19, 2008 11:49 pm

Will Saletan makes an analogy between cousin marriage and delayed (i.e., 40something) motherhood:

If Bittles’ numbers are correct, they substantiate a somewhat embarrassing point made by defenders of cousin marriage. Embarrassing, that is, to all of us good Western folk who turn up our noses at the practice. The British Down’s Syndrome Association has posted a chart showing the risk of producing a baby with the syndrome at various maternal ages. From age 20 to age 31, the risk doubles. From 31 to 35, it doubles again. From 35 to 38, it doubles again. From 38 to 41, it more than doubles again. Each delay multiplies the risk as much as cousin marriage multiplies the risks of all birth defects combined. By age 45, the probability of Down syndrome alone roughly matches the 4 percent cumulative risk of birth defects from cousin marriage.

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Tasmanian Tigers are back!

By Razib Khan | May 19, 2008 7:43 pm

thylacine.jpgOK, the title is deceptive; but the reality is kind of cool in my opinion (you may not share my normative filter; some people prefer the dead). PLOS One is publishing a paper which takes Tasmanian Tiger genetic material, and re-expresses it in vivo in mice! The reasoning for this is pretty straightforward; there are phylogenetic questions which extant lineages can’t always answer. With the emergence of the whole field of ancient DNA extraction and sequencing an entirely new avenue of scientific analysis is opening up. This paper cites the work from last year on Neandertal MC1R; if we’re getting genetic material from remains that are more than 40,000 years in the past, what are the possibilities when it comes to populations of organisms which went extinct more recently? Unfortunately geography is a variable here; the preservation of genetic material is more problematic in moist tropic locales. But I am wondering if researchers could at some point extract enough genetic material from Tasmanian Tiger samples so to generate a rather good replication in terms of physique? I assume there’s already a lot of sequence identity between Tigers and Devils, so perhaps the latter could be the templates? This sort of thing was proposed with dinosaurs and birds. The assumption was that you could just tweak the genes of the latter to produce something resembling the former since they’re not that distantly related, birds are just a branch of the theropods. It seems to me that a Devil → Tiger transformation is lower fruit on the tree….

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Sex, society and science

By Razib Khan | May 19, 2008 8:33 am

Sheril and other science bloggers are talking about the fact that the top 3 in the Intel International Science and Engineering Fair are female. I suppose that means we’ll stop talking about gender disparities in science & engineering? Yeah, I doubt it….
At the same time, this just popped into my RSS, The freedom to say ‘no’: Why aren’t there more women in science and engineering? Controversial new research suggests: They just aren’t interested:

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Food, Folks and Fun

By Razib Khan | May 19, 2008 7:21 am

Via E. Klein, I found out abut a new show on PBS this fall, Spain…on the Road Again, starring Gwyneth Paltrow, Mario Batali, Mark Bittman, and Claudia Bassols. Preview below the fold….

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Marrying your cousin in the USA

By Razib Khan | May 19, 2008 6:14 am

I was IMing with a friend about inbreeding depression and came across a map which shows the laws regarding cousin marriage in the United States….

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Cities of death?

By Razib Khan | May 17, 2008 10:33 pm

As Deaths Outpace Births, Cities Adjust:

This city has passed a grim demographic milestone: More people are dying here than are being born.
What demographers call a natural decrease has been occurring for years in tiny rural towns and in some retirement meccas in the South. But the phenomenon is relatively new in metropolitan areas in the Northeast, the Rust Belt of the Middle West and Appalachia.
Hospitals are closing obstetrics wards and converting them to acute care. Local governments and other social service providers are adjusting to the emergence of entire neighborhoods where the average age is soaring, and private foundations are awarding scholarships to retain students and attract new ones.
In Pittsburgh, public school enrollment plummeted from about 70,000 two decades ago to about 30,000 and continues shrinking by about 1,000 a year.

Here’s the graphic that goes along with the article:

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Firefox 3.0 release candidate

By Razib Khan | May 17, 2008 3:24 pm

Firefox 3 release candidate goes public:

It’s a public preview of the new Firefox code, available in 45 languages, aimed at developers and early adopters to test out the new features. It has an extensive list of known bugs.

On the performance front, the documentation states that applications such as Google Mail and Zoho Office run twice as fast in Firefox 3, compared to Firefox 2, and memory usage has been improved. In addition, bookmarks, history, cookies, and preferences are less susceptible to data loss.

If you are running Firefox, Help → Check for Updates… Or download. Please note that this does break a lot of plugins.


Bonus Katz

By Razib Khan | May 16, 2008 11:10 pm

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By Razib Khan | May 16, 2008 10:12 pm

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By Razib Khan | May 16, 2008 3:04 pm

If you don’t have a spare computer, want to try out a Linux distribution, and are a little intimidated by the details of setting up a dual-boot, check out Wubi. It makes a dual-boot pretty much a “one-click” affair, loading up the Ubuntu distribution via a Windows installer.


Polar bears: a species?

By Razib Khan | May 15, 2008 3:22 pm

Since everyone is talking about the fact that the Polar Bear how become a protected species, I thought I’d point to this cool study, Mitochondrial DNA Phylogeography of the North American Brown Bear and Implications for Conservation. Additionally, check out the figure below….

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When genetic drift = more adaptation?

By Razib Khan | May 15, 2008 9:58 am

I know I’ve posted on this topic before, but I thought I’d revisit it again. You do know that sometimes population bottlenecks can actually result in more variation being freed up for selection? This may strike you as a bit strange; after all, the power of selection to effect phenotypic change is proportional to genetic variance, specifically, additive genetic variance. Population bottlenecks imply a reduction in effective population size, the increase of sample variance across generations, that is, random genetic drift. As population size drops the stochastic change in gene frequencies becames proportionately much greater and alleles rapidly go extinct, or fix, within populations (average time until fixations in generations is proportional to 4Ne, where Ne is effective population size). The homogenizing effect of this dynamic is similar to what might occur with inbreeding, where effective population size is reduced through population substructure, and individuals within the demes quickly become closely related over a few generations. Obviously you know that inbreeding leads to a loss of variation. So how exactly can we extract more additive genetic variance from this? In short, but converting other types of variance….

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Neural Buddhism & the psychology of religion

By Razib Khan | May 14, 2008 10:35 pm

Many people are talking about David Brooks’ new column, The Neural Buddhists. First, I think much respect should be given to Brooks for introducing science into his column; too much punditry today is informed by seat of the pants introspection & anecdote, as opposed to what scholars have uncovered thanks to the funding of the taxpayer. That being said, I think on the specifics there are problems with his interpretation of the literature in the area of neuroscience. Frontal Cortex, Island of Doubt and Evolution Blog have all hit the main points (though I tend to think that Jonah’s reaction most closely reflects my own). I think the idea that neuroscience lends some weight to the validity of mysticism as such is about as plausible as the contention that cosmology buttresses the case for a Creator. These results are interpreted through a filter contingent upon your prior beliefs; for those looking for confirmation of their spirtual or metaphysical beliefs science will no doubt offer it because of the vast sample space of findings and the imperfect mapping of words to the phenomena being described.

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Banana: The Fate of the Fruit That Changed the World

By Razib Khan | May 14, 2008 3:48 am

banana.JPGWhen I was a child in Bangladesh one of my “charming” activities would be to give the local banana seller some unsolicited advice. As he walked down the street carrying his banana-bunch I would shout down from the balcony and tell him which cultivars my family preferred, and that he better get with the program if he wanted our business. What he had on offer was similar to the Cavendish which you encounter in American supermarkets; my family tended to prefer a smaller, sweeter, variety which was often seeded. Despite all the problems (e.g., pathogen load) associated with living in an underdeveloped tropical country, if you had some marginal income the diversity of fruit accessible because of local abundance is something that American supply chains can never recreate.1
In Banana: The Fate of the Fruit That Changed the World Dan Koeppel uses the story of this fruit as the window through which one might examine the intersection of biology, economics, politics and ethics; in other words, modernity. Though the book’s title is obviously a bit hyperbolic, I was surprised to find out that the banana is currently America’s #1 fruit in terms of consumption, not the apple! And of course it is important to note that the plantain is much more than a snack for millions across the world. This reality frames the overarching plot point in Koeppel’s narrative: the fact that a disease is sweeping across banana plantations and the ubiquity of this fruit might be under threat.

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Soul gene?

By Razib Khan | May 14, 2008 2:56 am

Ron Bailey in Reason, The Genetics of Ensoulment:

Advances in stem cell research may be provoking a kind of “God of the Gaps” retreat on the moral status of embryos. People who subscribe to God of the Gaps thinking believe that the hand of God can be seen in those things which science cannot explain. In this case, the closing gaps in the details of molecular biology are forcing pro-lifers into an uncomfortable corner where they have to decide whether or not a cell can be imbued with a soul by turning a single gene on or off.


Richard Dawkins interviewed by 3 Quarks Daily

By Razib Khan | May 12, 2008 10:25 pm

Here. The embed is the best bet if you can view it; the download often fails (server has been slammed?). Only a moderate amount of discussion about religion; Dawkins talks a fair bit about an obscure field, evolutionary biology. Well done.
Via Accidental Blogger.


Ways to skin the cousin marriage issue

By Razib Khan | May 12, 2008 7:33 pm

Another article about cousin marriage in the UK. The issue here is simple; you have a National Health Service which covers everyone, and doctors are noticing that Pakistanis are overrepresented in many cases of recessive diseases. The culprit is probably cousin marriage. Here are two points which are both valid:

‘In our local school for deaf children, half the pupils are of Asian origin though Asians only form about 20 per cent of the population,’ said Ann Cryer, MP for Keighley. ‘I also know of several sets of parents in my constituency who are cousins and whose children are severely disabled. I have no doubt that the mothers and fathers being closely related to each is a key factor.

This last claim is hotly disputed by genetic counsellors and Muslim doctors. They point out that the danger of a child having birth defects if the parents are cousins is double that of other children, which means the risk rises from about 2 per cent in the general population to about 4 per cent when the parents are closely related. A risk of 4 per cent therefore does not make it ‘likely’ there will a genetic problem, as Woolas claimed, say genetic counsellors.

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Browsing biology on the web: NextBio

By Razib Khan | May 12, 2008 10:14 am

Last year p-ter put up a post pointing to useful online tools such as Haplotter. One of the great things about biology today is that so much of the data from genomics is being thrown out there within reach of the plebs. And a lot of value is being added through user interfaces which smooth the connection between you and these databases. So check out NextBio; from the FAQ:

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