Archive for October, 2007

Out of Africa model most likely

By Razib Khan | October 31, 2007 5:57 pm

Statistical evaluation of alternative models of human evolution:

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species ~141 thousand years ago (Kya), an exit out-of-Africa ~51 Kya, and a recent colonization of the Americas ~10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.

I don’t have time to read this paper now, so I hope John Hawks blogs it soon. Obviously I’m curious as to how they explain deep lineages, Bruce Lahn’s Neandertal introgression paper attempted to check for dynamics such as balancing selection.


Donors Choose update

By Razib Khan | October 31, 2007 2:31 pm

OK, last update on this obviously because it is the last day of the month. A few readers really went wild in the last few days (in a good way) and from only 5 donors 508 students were impacted! (check the Leaderboard for the breakdown) Thank you very much! So if you have any spare cash and inclination, please check out the projects I’m sponsoring, this is your last day.


How were the Americas peopled?

By Razib Khan | October 29, 2007 9:58 am

Until recently archeologists held to a model called Clovis First which posited that the Amerindians were descended from Siberian hunters who swept down from Beringia 13,000 years ago and spread rapidly north to south. Findings such as Monte Verde have thrown a cloud over the cleanliness of this hypothesis and there doesn’t seem to be any claimant to the throne at this point.
Geneticists have been weighing in on this topic now and then. Roughly, one line of results seems to suggest that the Amerindians have been resident on the New World for far longer than 10,000 years. Another finding has been that the ancestors of the indigenous people went through a massive population bottleneck and subsequent demographic expansion. It doesn’t seem like geneticists have yielded results with enough precision to decide the matter, but here is another forthcoming study, New Ideas About Human Migration From Asia To Americas:

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Mormonism is illogical, Christianity is not

By Razib Khan | October 28, 2007 11:25 pm

Over at Ross Douthat’s blog, a giggle-inducing comment:

It seems to me that Mormonism is indeed a lot more illogical than mainstream Christianity. It suffers from logical contradictions that Christianity does not- for example, how can someone be retroactively baptized? Why would God say that polygamy was OK for Brigham Young but then not OK anymore after Utah became a state? How do the Gods of multiple universes interact? Most importantly, how is it even logically possible for man to become God? This last bit, about man becoming God, is not just highly offensive to me, it’s also logically incoherent- if God and man are not inherently of unfathomably different kind, then the term ‘God’ has no meaning.

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Woodland Critter Christmas

By Razib Khan | October 28, 2007 6:34 pm

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Who's afraid of nuclear power?

By Razib Khan | October 27, 2007 4:56 pm

Just listened to an interview on NPR with the author of Power to Save the World: The Truth About Nuclear Energy. She mentions how she had a reflexive prejudice against nuclear energy and generally opposed its use because of her environmentalist impulses. That’s not surprising of course, people are terrified of nuclear energy because of its associations.

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The end of capitalist porn?

By Razib Khan | October 27, 2007 1:35 am

youporn.jpgInteresting piece which chronicles the decline in the DVD driven profits of porn companies due to “user generated porn.” Porn is in some ways sui generis, so this is an interesting trend. Check out the traffic of YouPorn vs. Facebook.


Neandertals had red hair! (OK, some)

By Razib Khan | October 25, 2007 1:59 pm

Sometimes science is just too cool! A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals:

The melanocortin 1 receptor (MC1R) regulates pigmentation in humans and other vertebrates. Variants of MC1R with reduced function are associated with pale skin color and red hair in humans primarily of European origin. We amplified and sequenced a fragment of the MC1R gene (mc1r) from two Neanderthal remains. Both specimens have a mutation not found in ~3700 modern humans. Functional analyses show that this variant reduces MC1R activity to a level that alters hair and/or skin pigmentation in humans. The impaired activity of this variant suggests that Neanderthals varied in pigmentation levels, potentially to the scale observed in modern humans. Our data suggest that inactive MC1R variants evolved independently in both modern humans and Neanderthals.

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Four Stone Hearth #26

By Razib Khan | October 24, 2007 3:22 pm

Four Stone Hearth #26.


Contingency & evolution

By Razib Khan | October 23, 2007 8:10 pm

If you like the science on this weblog, I highly recommend Laelaps, Brian Switek’s contribution to the ScienceBlogs network. Where I am more micro and anthro oriented he is more macro and spans the whole tree of life. I’m really glad he’s on ScienceBlogs; Laelaps adds to the diversity in an interesting way.
In any case, I wanted to point to this long post, Troodon sapiens?: Thoughts on the “Dinosauroid”, it mulls over many concepts and evolutionary processes. Brian highlights the alternative views of the paleontologists Stephen Jay Gould and Simon Conway Morris. While Gould emphasized historical contingency and overall stochasticity of evolutionary process, Morris tends to lean toward the power of selection generating convergent adaptations. Some have suggested that Morris’ views are influenced by his Christianity. Brian does note that this tendency toward teleology has correspondences with the talking points of the Intelligent Design movement, but I think it is important to observe that Richard Dawkins has come down on the side of Morris and against Stephen Jay Gould on this question. So the alignments here can be rather confusing to an outsider (some critics of adaptationism argue that the Oxford school of evolutionary biology, of which Dawkins is a representative, owes a great deal to William Paley’s arguments from design, simply substituting the theistic god for the blind engineer of selection).
On a philosophical note, I do think these arguments about contingency and inevitability have to framed within the context of time and space. Assuming enough evolutionary time and a large enough effective population size it is imaginable that contingency and constraint can eventually be circumvented as selection slowly explores every nook and cranny of the adaptive landscape. But of course that is assuming particular parameters; over shorter time periods stochastic forces can be critical in explaining the madness. What is a large effective population? And what is a long time period? There are assumptions often unspecified in these debates between those who argue for contingency and those who argue for inevitability, and I think quite often that results in talking past one another.


Why katz are cute

By Razib Khan | October 23, 2007 5:39 pm

Via Grrlscientist.


Monkeys with bad habits

By Razib Khan | October 23, 2007 5:25 pm

The death of an Indian politician due to a monkey mob is getting a lot of attention. But Ruchira Paul points me to an older story which I think is even more interesting:

They have invaded the prime minister’s office and the Defence Ministry, helping themselves to top secret military files.

Some 250 monkeys have already been relocated by a court order to forests in the central Indian state of Madhya Pradesh.
But many people there are now objecting, saying the animals are bringing with them their hooligan habits learnt in the city and are terrorising rural villages.

Slate has more about the complexity of monkey behavior. We aren’t the only species to facultatively shift our habits in response to opportunities in the environment. Here is a familiar bit, “Female victims might seek protection in a group of men, since monkeys are somewhat afraid of males.” Rember the sexual harassing monkeys?


Why white people are so colorful!

By Razib Khan | October 23, 2007 7:06 am

Another day, and another genome-wide association study. Genetic determinants of hair, eye and skin pigmentation in Europeans:

…We carried out a genome-wide association scan for variants associated with hair and eye pigmentation, skin sensitivity to sun and freckling among 2,986 Icelanders. We then tested the most closely associated SNPs from six regions–four not previously implicated in the normal variation of human pigmentation–and replicated their association in a second sample of 2,718 Icelanders and a sample of 1,214 Dutch. The SNPs from all six regions met the criteria for genome-wide significance. A variant in SLC24A4 is associated with eye and hair color, a variant near KITLG is associated with hair color, two coding variants in TYR are associated with eye color and freckles, and a variant on 6p25.3 is associated with freckles. The fifth region provided refinements to a previously reported association in OCA2, and the sixth encompasses previously described variants in MC1R.

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Bobby Jindal: ignorant genius

By Razib Khan | October 23, 2007 3:09 am

jindal.jpgSome of you know that Bobby Jindal was just elected as the governor of Louisiana. Jindal has an interesting story, he’s the son of Indian immigrants, received degrees in biology and public bolicy from Brown, passed on Harvard Medical School for a Rhodes Scholarship, and took over the Louisiana Public Health System at the age of 24.
He is also a convert to Catholicism, and extremely politically conservative. Conservative blogger Patrick Ruffini had a political orgasm a few days ago in response to Jindal’s victory; and it was typical on the Right blogosphere. I really don’t think that Bobby Jindal winning in Louisiana implies a turn around for the national Republican Party. Nor do I think that he is a trail blazer for brown Americans; very few ambitious browns are going to grow up in the South and convert to Christianity and forgo a medical career because of an interest in public policy. That being said, I think that Jindal’s election does say something about Louisiana.

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"I am condom friend!"

By Razib Khan | October 22, 2007 4:07 pm

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Adaptationism not right-wing!?!?

By Razib Khan | October 22, 2007 3:41 pm

An Empirical Examination of Adaptationists’ Attitudes Toward Politics and Science. You can find a full preprint at Geoffrey Miller’s site. The abstract:

Critics of evolutionary psychology and sociobiology have advanced an adaptationists-as-right-wing-conspirators (ARC) hypothesis, suggesting that adaptationists use their research to support a right-wing political agenda. We report the first quantitative test of the ARC hypothesis based on an online survey of political and scientific attitudes among 168 US psychology Ph.D. students, 31 of whom self-identified as adaptationists and 137 others who identified with another non-adaptationist meta-theory. Results indicate that adaptationists are much less politically conservative than typical US citizens and no more politically conservative than non-adaptationist graduate students. Also, contrary to the “adaptationists-as-pseudo-scientists” stereotype, adaptationists endorse more rigorous, progressive, quantitative scientific methods in the study of human behavior than non-adaptationists.

Some interesting points from the paper:

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By Razib Khan | October 21, 2007 3:54 am

Genetics videos

By Razib Khan | October 20, 2007 2:58 pm

Carl Zimmer interviews Craig Venter (video). They’re talking most genomics and creating life from “scratch.” Also, Esther Dyson talks about the personal genome.


John Hawks' post on Neandertals & FOPX2

By Razib Khan | October 19, 2007 3:43 pm

Please go read it now.


Political views @ ScienceBlogs

By Razib Khan | October 18, 2007 11:37 pm

About a year ago Tim Lambert asked ScienceBloggers to check out a political quiz and collected the responses. 29 of us responded, and below the fold I’ve placed two graphs which display a smoothed out frequency distribution across the two axes generated by the survey. As noted by the author of the quiz the two axes were extrapolated from the empirical variation of responses (their the first two principle components of eigenvectors). They are Left/Right and pragmatism. A more positive value represent Right and and “atheist” or “utilitarian” tendencies on each axis respectively. Remember that the author is British so the respondents and their distribution of responses would have generated an ideological scale relevant to that nation. We’ve doubled the number of bloggers since that original survey, I’d be curious if there’s been any change (I doubt that).

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