Archive for April, 2009

African genetic structure

By Razib Khan | April 30, 2009 9:03 pm

I’ve been fine tuning Ubuntu all day with goodies and getting drivers to work right, so I missed this paper on African genetics:

Africa is the source of all modern humans, but characterization of genetic variation and of relationships among populations across the continent has been enigmatic. We studied 121 African populations, 4 African American populations, and 60 non-African populations for patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers. We identified 14 ancestral population clusters in Africa that correlate with self-described ethnicity and shared cultural and/or linguistic properties. We observe high levels of mixed ancestry in most populations, reflecting historic migration events across the continent. Our data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations (Khoesan-speakers and Pygmies). The ancestry of African Americans is predominantly from Niger-Kordofanian (~71%), European (~13%), and other African (~8%) populations, although admixture levels varied considerably among individuals. This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies.

In the press the lead author suggests that 13% might be a lowball figure for European ancestry among African Americans (other studies average out in the range of 20%). I’ll outsource my commentary & links to Dan MacArthur, since the exchange rate is good right now….

CATEGORIZED UNDER: Genetics

Religious people support torture

By Razib Khan | April 30, 2009 7:49 pm

John Schwenkler points me to Rod Dreher’s shock that religious people seem to support torture more than the non-religious:

And get this: the more often you go to church, the more pro-torture you’re likely to be!
What on earth are these Christians hearing at church?! Very sad indeed.

John notes:

There are plenty of data showing that Christians’ attitudes toward abortion, contraception, and the rest don’t differ very significantly from those of the rest of society; the real factor, of course, lies in political affiliations, and I have little doubt that most of the relevant findings can be explained in terms of the fact that frequently churchgoing Catholics and Evangelicals are especially likely to identify as Republicans.
“What on earth are these Christians hearing at church?!” asks Rod. Perhaps it’s had something to do with there being a moral obligation to support the GOP in the face of the Democratic menace.

There isn’t any question about torture in the GSS, but there are questions about abortion and the death penalty. I selected 2 with large sample sizes, CAPPUN and ABANY, and checked how they relate to 4 religious identities, Protestant, Catholic, Jewish and None.
So on the Death Penalty:

Do you favor or oppose the death enalty for persons convicted of murder?

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CATEGORIZED UNDER: Politics

Noninvasive Down Syndrome test no go (for now)

By Razib Khan | April 30, 2009 2:57 pm

I blogged about this a few months ago, but Dan MacArthur reports that the firm which was going to roll it out first claims that it doesn’t really work as advertised.

CATEGORIZED UNDER: Biology

Pakistan is already an Islamic State

By Razib Khan | April 30, 2009 2:49 pm

So claims Ali Eteraz:

Most people in the world, including some Pakistanis, live under the illusion that the country is secular and just happens to have been overrun by extremists. This is false. Pakistan became an Islamic state in 1973 when the new constitution made Islam the state religion. Under the earlier 1956 constitution Islam had been merely the “official” religion. Nineteen-seventy-three, in other words, represents Pakistan’s “Iran moment”–when the government made itself beholden to religious law. Most western observers missed the radical change because the leader of Pakistan at the time was Zulfikar Ali Bhutto, a whiskey-drinking, pseudo-socialist from a Westernized family. Those that did notice the transformation ignored it because the country was reeling from a massive military defeat in 1971, which led to half the nation becoming Bangladesh.

CATEGORIZED UNDER: Blog, Religion

Egypt going to kill its pigs?

By Razib Khan | April 30, 2009 2:28 pm

UN says Egypt pig cull real mistake:

The United Nations has called Egypt’s move to cull 400,000 pigs as a precaution against swine flu “a real mistake”.
The Egyptian government ordered the slaughter of the pigs on Wednesday, saying it could help quell any panic in the country that is largely Muslim, who view pigs as unclean.
No pigs in the country have been found with the new strain of H1N1 virus of the so-called swine flu and the World Health Organisation (WHO) says the disease cannot be caught from eating pork that is properly prepared.

I just heard on NPR that urban pigs apparently process a great of the organic trash for the city of Cairo. This overreaction might have some public health ramifications down the road.

CATEGORIZED UNDER: Culture

Drink wine to live longer!

By Razib Khan | April 30, 2009 8:11 am

150px-Red_Wine_Glas.jpgI’m in the mood for a “feel good” story with the past week’s fixation in swine flu. Half A Glass Of Wine A Day May Boost Life Expectancy By Five Years:

The Dutch authors base their findings on a total of 1,373 randomly selected men whose cardiovascular health and life expectancy at age 50 were repeatedly monitored between 1960 and 2000.

Here are the findings:

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CATEGORIZED UNDER: Biology

Spent: Sex, Evolution, and Consumer Behavior

By Razib Khan | April 29, 2009 5:42 pm

31--B9alQzL._SS500_.pngIn the wake of Predictably Irrational, check out Tyler Cowen’s endorsement of Geoffrey Miller’s new book, Spent: Sex, Evolution, and Consumer Behavior. Miller is a good writer, so I’m assuming it will be a page-turner, but he does tend to be “provocative” in all the best & worst ways when it comes to popular science. Evolutionary psychologists have a tendency to make everything about sex & status, but within the field it seems Miller does come off as the “pimp daddy” always talking about the “bling” and “b**tches” as the raison d’être.

CATEGORIZED UNDER: Culture

Post-Cretaceous Dinosaurs

By Razib Khan | April 29, 2009 2:20 pm

New Geochronologic And Stratigraphic Evidence Confirms The Paleocene Age Of the Dinosaur-Bearing Ojo Alamo Sandstone And Animas Formation In The San Juan Basin, New Mexico and Colorado:

…An assemblage of 34 skeletal elements from a single hadrosaur, found in the Ojo Alamo Sandstone in the southern San Juan Basin, provided conclusive evidence that this assemblage could not have been reworked from underlying Cretaceous strata. In addition, geochemical studies of 15 vertebrate bones from the Paleocene Ojo Alamo Sandstone and 15 bone samples from the underlying Kirtland Formation of Late Cretaceous (Campanian) age show that each sample suite contained distinctly different abundances of uranium and rare-earth elements, indicating that the bones were mineralized in place soon after burial, and that none of the Paleocene dinosaur bones analyzed had been reworked.

Here’s ScienceDaily with more:

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CATEGORIZED UNDER: Evolution

Around ScienceBlogs

By Razib Khan | April 29, 2009 12:05 pm

Do you love or hate Cilantro?
K-T extinction debates: cranky “skeptics” or reasonable science?
Modularity and scalability
The elegant logic of dopamine
A Beacon from the Invisible Universe

CATEGORIZED UNDER: Genetics

One New World population expansion

By Razib Khan | April 29, 2009 9:37 am

Haplotypic Background of a Private Allele at High Frequency in the Americas:

Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across 500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the “American Modal Haplotype” (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas.

Some elaboration in ScienceDaily of the logic:

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CATEGORIZED UNDER: Genetics

Jaunty Jackalope Ubuntu

By Razib Khan | April 29, 2009 4:47 am

Installed Jaunty Jackalope with Wubi. Definitely feels like a smoother UI on my Lenovo.

CATEGORIZED UNDER: Technology

Perhaps the pestilence gods are with us!

By Razib Khan | April 29, 2009 2:36 am

Swine influenza, seasonality, and the northern hemisphere:

This history demonstrates the seasonality of pandemic influenza, and suggesta that spread of A/California/09/2009 in the northern hemisphere is not imminent. Based on this regularity, the epidemic in Mexico should be over no later than the end of May. While it is not ‘impossible to see the current contagion spreading in the northern hemisphere over the following months’, it would be unprecedented.

CATEGORIZED UNDER: Culture

Pray the virus away

By Razib Khan | April 28, 2009 10:17 pm

Carl Zimmer points out that Marianne Williamson is making some real strange suggestions in regards to the swine flue in The Huffington Post:

l) Pray it away. Just pray it away, asking God as you understand Him, the Divine Physician, Jesus or whatever other form of divine imagery works for you. Simply ask that it be removed from our midst.
2) Send love to Mexico. Between what’s actually been happening there with the drug wars, plus all the “Mexico is dangerous” thoughts we’ve loaded onto it over the last several weeks, it needs a major dose of love – the most powerful medicine of all – to dissolve the fear thoughts that have produced this flu.

It’s not that surprising that this was published in The Huffington Post, which has some issues with regards to quality control. Remember the Deepak Chopra post on evolution?

CATEGORIZED UNDER: Biology

California swine flu related to Ohio strains?

By Razib Khan | April 28, 2009 10:13 pm

That’s what Sandy at Digital Biology is suggesting from her analyses…. (also see Tara of Aetiology’s response)

CATEGORIZED UNDER: Genetics

The rise of empirical economics

By Razib Khan | April 28, 2009 7:18 pm

In the wake of my post on Predictably Irrational, The Last Temptation of Risk:

THE GREAT Credit Crisis has cast into doubt much of what we thought we knew about economics. We thought that monetary policy had tamed the business cycle. We thought that because changes in central-bank policies had delivered low and stable inflation, the volatility of the pre-1985 years had been consigned to the dustbin of history; they had given way to the quaintly dubbed “Great Moderation.” We thought that financial institutions and markets had come to be self-regulating–that investors could be left largely if not wholly to their own devices. Above all we thought that we had learned how to prevent the kind of financial calamity that struck the world in 1929.

The late twentieth century was the heyday of deductive economics. Talented and facile theorists set the intellectual agenda. Their very facility enabled them to build models with virtually any implication, which meant that policy makers could pick and choose at their convenience. Theory turned out to be too malleable, in other words, to provide reliable guidance for policy.
In contrast, the twenty-first century will be the age of inductive economics, when empiricists hold sway and advice is grounded in concrete observation of markets and their inhabitants. Work in economics, including the abstract model building in which theorists engage, will be guided more powerfully by this real-world observation. It is about time.

The author is an economist, so if this is a caricature, it’s from the inside….

CATEGORIZED UNDER: Culture, History

The genetic architecture of different populations

By Razib Khan | April 28, 2009 2:41 pm

Dan MacArthur has a post, Genetics of complex traits in Europeans and East Asians: similarities and differences:

With those goals in mind, you can expect to see many more GWAS of non-European populations over the next couple of years, and some explicit comparisons of the differing genetic architecture of complex traits between populations. Exciting times for those of us interested in the genetic and evolutionary basis of between-population differences…

This reminds me of A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction:

Read More

CATEGORIZED UNDER: Genetics

Predictably Irrational, behavioral economics in 13 chapters

By Razib Khan | April 28, 2009 9:16 am

predicirrational.pngI first encountered Dan Ariely on the radio show Marketplace, where he offers up little nuggets of research data from the new field of behavioral economics. Because of the individual scale of the research many of Ariely’s findings have some personal finance implications. Consider the pain of paying. This is the finding that when people pay with credit as opposed to cash for dinner, they are willing to spend more. Why? Because credit cards decouple the psychic “pain” of payment from the specific act. The act of deferring reduces our pain at the damage done, and allows consumption with less guilt and discomfort. The big-picture implication of this is obvious when it comes to the credit economy, but for myself I have taken to always paying for frequent small purchases with debit or cash. I do put less frequent large purchases on credit cards on occasion, for example when I buy a plane ticket for a trip months into the future. My reasoning is that I can concentrate in a reflective and rational manner on a few large purchases to a far greater extent than I can on the habitual small weekly food purchases. Monthly automatic cell phone payments for example are naturally a different beast than going to the grocery store; not only are the payments infrequent and regular, but the interval of their expense is predictable (totally predictable if you have some sort of unlimited plan).

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CATEGORIZED UNDER: Cognitive Science, Culture, Psychology

Autoworkers compete for jobs on new reality show!

By Razib Khan | April 28, 2009 8:49 am

OK, it’s from Onion News Network. I really like the touch of the vapid hostess.

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CATEGORIZED UNDER: Culture

Ross Douthat's first column in The New York Times

By Razib Khan | April 27, 2009 10:48 pm

Wondering, what if Dick Cheney had run for President.

CATEGORIZED UNDER: Blog

The two gay-friendly cohorts

By Razib Khan | April 27, 2009 2:56 pm

Matt Springer’s comment that while differences in regards to abortion remain important among the young, but that there no deep fissure in regards to homosexuality, rings true. I decided to look at the same variables as I did below across the years, but limited to the age group 18-30. In other words, each year from the early 1970s to the 2000s you are looking at the opinions of individuals who are in the age range 18-30 during that year. An interesting trend popped up.

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CATEGORIZED UNDER: Culture
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