Archive for August, 2009

States which do well educationally, blame Canada!

By Razib Khan | August 31, 2009 2:26 pm

Mike the Mad Biologist points out that Massachusetts, New Jersey, Minnesota and New Hampshire do better on math scores for elementary age students than most of Europe, and are competitive with Asia. Here are Mike’s factors for why this might be:

-Low child poverty rates as measured by school lunch subsidies (a common proxy for poverty).
-Low divorce rates.
-Effective public health departments. MA, NJ, and MN have very good public health systems, and NH has some excellent programs (e.g., electronic syndromic surveillance)
-High incomes. Overall, these are healthy state economies (as good as one can get anyway).
-Educated adult populations.

I’ll add a sixth: they’re all close to Canada. I pointed out last year that being close to Canada also prevents murder. Being close to Canada also persuaded whites to vote for Barack Obama. It even seems to have a salubrious effect on life expectancy. I wonder if American xenophobia can explain the long neglect of the critical “Canada factor” in our social outcomes? And why aren’t Canadians trumpeting the positive social effect of their proximity? Is it because they want to maintain relative advantages and prevent possible overcrowding on the Canadian border? Isn’t it a bit suspicious that Vermont, New Hampshire, Maine and North Dakota are so underpopulated? That Potsdam is dwarfed by New York City?

CATEGORIZED UNDER: Culture

Quest for Antarctica

By Razib Khan | August 31, 2009 4:47 am

Over at Living the Scientific Life an update on the quest to go to Antarctica. Turns out you can “reassign” your vote. Also, if you haven’t voted, please do. Again:

Voting ends at noon EDT on 30 September 2009, and the Official Quark Blogger will travel to Antarctica in February 2010 to blog about the experience, chronicling the action, the emotion, and the drama as this polar adventure unfolds.

CATEGORIZED UNDER: Blog

Hispanics more religious, not that zealous

By Razib Khan | August 31, 2009 4:14 am

A few months ago I pointed out that minorities don’t oppose gay marriage, blacks do. Specifically, there are sometimes assumptions that Hispanics are extremely religious Roman Catholics characterized by very socially conservative views. From what I have seen the data are of much more modest magnitude than what characterizations would suggest, but I thought it would be useful to put some numbers from the General Social Survey up. The years are from 2000-2008, when the “Hispanic” variable was being collected. First I separated into three categories, Non-Hispanics who were not black, which was a 95% white and 5% Asian sample. Then Hispanics (who were 1/3 white and 2/3 “Other”) and finally, blacks. Second, I decided to look at Non-Hispanic vs. Hispanic Roman Catholics. In this sample of Hispanics 2/3 were Roman Catholics.

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CATEGORIZED UNDER: Culture

Chimps, humans, and allopatry

By Razib Khan | August 31, 2009 3:32 am

Thomas Mailmund is going ape over chimps & humans again, Patterns of autosomal divergence between the human and chimpanzee genomes support an allopatric model of speciation. A review of a paper of the same name.

CATEGORIZED UNDER: Anthroplogy, Evolution

Africans, disease, history and ecology

By Razib Khan | August 31, 2009 3:16 am

Interesting review paper on disease and Sub-Saharan African, Neglected Tropical Diseases in Sub-Saharan Africa: Review of Their Prevalence, Distribution, and Disease Burden:

The neglected tropical diseases (NTDs) are the most common conditions affecting the poorest 500 million people living in sub-Saharan Africa (SSA), and together produce a burden of disease that may be equivalent to up to one-half of SSA’s malaria disease burden and more than double that caused by tuberculosis. Approximately 85% of the NTD disease burden results from helminth infections. Hookworm infection occurs in almost half of SSA’s poorest people, including 40-50 million school-aged children and 7 million pregnant women in whom it is a leading cause of anemia. Schistosomiasis is the second most prevalent NTD after hookworm (192 million cases), accounting for 93% of the world’s number of cases and possibly associated with increased horizontal transmission of HIV/AIDS. Lymphatic filariasis (46-51 million cases) and onchocerciasis (37 million cases) are also widespread in SSA, each disease representing a significant cause of disability and reduction in the region’s agricultural productivity. There is a dearth of information on Africa’s non-helminth NTDs. The protozoan infections, human African trypanosomiasis and visceral leishmaniasis, affect almost 100,000 people, primarily in areas of conflict in SSA where they cause high mortality, and where trachoma is the most prevalent bacterial NTD (30 million cases). However, there are little or no data on some very important protozoan infections, e.g., amebiasis and toxoplasmosis; bacterial infections, e.g., typhoid fever and non-typhoidal salmonellosis, the tick-borne bacterial zoonoses, and non-tuberculosis mycobaterial infections; and arboviral infections. Thus, the overall burden of Africa’s NTDs may be severely underestimated. A full assessment is an important step for disease control priorities, particularly in Nigeria and the Democratic Republic of Congo, where the greatest number of NTDs may occur.

Sub-Saharan African has about 12% of the world’s population, so keep that in mind when viewing this table from the paper:

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CATEGORIZED UNDER: Anthroplogy, Medicine

Thirst, Korean vampires at work & play

By Razib Khan | August 31, 2009 3:07 am

200px-Thirstposter.jpgI saw Thirst this weekend, a Korean film about a Catholic priest turned vampire. I was expecting strangeness, but it was really strange. The female lead, Kim Ok-bin gave a pretty good performance that I found very memorable. My friend who I watched the film with wondered if Asians produced really strange films, but my own suspicion is that there’s a selection bias in terms of the types of “foreign films” which arrive to American shores. After all, what’s the comparative advantage of sappy Korean melodramas when we have so many of our own? In regards to special effects driven movies I doubt anyone can compete with Hollywood. So it has to be “art house” productions which trade on pushing the envelope combined with exotic locale. Or at least that’s my working model, would be happy to be informed by those “in the know”….

CATEGORIZED UNDER: Culture

New "language gene"?

By Razib Khan | August 31, 2009 3:01 am

Anthropology.net points me to a new paper, Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impairment:

We analyzed genetic linkage and association of measures of language, speech and reading phenotypes to candidate regions in a single set of families ascertained for SLI. Sib-pair and family-based analyses were carried out for candidate gene loci for Reading Disability (RD) on chromosomes 1p36, 3p12-q13, 6p22, and 15q21, and the speech-language candidate region on 7q31 in a sample of 322 participants ascertained for Specific Language Impairment (SLI). Replication or suggestive replication of linkage was obtained in all of these regions, but the evidence suggests that the genetic influences may not be identical for the three domains. In particular, linkage analysis replicated the influence of genes on chromosome 6p for all three domains, but association analysis indicated that only one of the candidate genes for reading disability, KIAA0319, had a strong effect on language phenotypes. The findings are consistent with a multiple gene model of the comorbidity between language impairments and reading disability and have implications for neurocognitive developmental models and maturational processes.

Right, there isn’t a “language gene” (sorry FOXP2). Language is a complex phenotype dependent on a lot of genes which can be “broken” in a lot of different ways. Though since verbal fluency (or, verbal IQ) varies quite a bit, if not basal verbal competency, there are likely many genes which shape how well we can wield language.
Cite: Journal of Neurodevelopmental Disorders, August 25, 2009, DOI: 10.1007/s11689-009-9031-x

CATEGORIZED UNDER: Anthroplogy, Genetics

Uighuristan as the New World

By Razib Khan | August 30, 2009 10:47 pm

From page 55 of Empires of the Silk Road:

…Archaeology has shown that every location in Eurasia where Indo-European daughter languages have come to be spoken, modern humans had already settled there long beforehand, with the sole exception of the Tarim Basin, the final destination of the people who are known to us as the Tokharians.

I’ve alluded to this before, the unique hybrid aspect of Uighurs probably is due to the fact that the Tarim basin was only recently settled from both the west and east of Eurasia, closing a gap of settlement which might have existed since the Last Glacial Maximum. In this time various genetic differences have built up between humans on either side of this gap, and the Uighurs have not been around long enough to mediate enough gene flow to equilibrate the between group differences.

CATEGORIZED UNDER: Anthroplogy, Culture

Pots, people & seeds

By Razib Khan | August 30, 2009 2:43 am

There’s a new paper in PLoS ONE, Craniometric Data Supports Demic Diffusion Model for the Spread of Agriculture into Europe. That’s fine. There are two extreme models about how farming might have spread in Europe. One model suggests that farmers replaced non-farmers genetically. Another model posits that there was no discernible movement of population, but ideas flowed. Apes are not the only ones who can imitate and emulate after all. Peruvians did not move with the potato, so there are cases of the latter. But the genetic data (see links) seem to imply some non-trivial contribution (for example, greater than 10% of post-Ice Age European distinctive genome content being derived from the Middle East) from Southwest Asia, so one would hope that the skulls would align.
Several years ago the geneticist Bryan Sykes made some waves by suggesting that in fact the majority of the ancestors of modern Europeans were resident in Europe during the last Ice Age. You can read Sykes’ recollection of this episode in Seven Daughters of Eve. L. L. Cavalli-Sforza, who was the geneticist who first attempted to probe this question through biological methods, took issue with Sykes’ characterization of his own position. After all, along a wave of advance one would expect dilution to be operative, so that the Southwest Asian genetic impact would be greater in Southeast Europe than in Northwest Europe. Cavalli-Sforza points out that he did not explicitly claims that the majority of the ancestors of Europeans were Middle Eastern farmers who rode the demographic wave of advance. But, to be fair I think it is correct that many people received this impression in some of his popularizations, e.g., The Great Human Diasporas.
A few years ago I read a bit on the spread of agriculture in Europe. Suffice it to say that the archaeological reality is quite complex, and in some regions there are seems to have been stable mosaic patterns of lifestyles (i.e., islands of agriculture surrounded by non-agriculturalists). Only later in history did the many regions switch wholesale to agriculture despite trading with agriculturalists for many generations (this was the case in southern Sweden). So even more nuanced models positing a uniform wave of advance leave something to be desired, though the stylized fact may be of some utility.

CATEGORIZED UNDER: Anthroplogy, Culture

West Eurasian population substructure + the Baloch

By Razib Khan | August 29, 2009 9:01 am

Dienekes points me to a new paper, European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing Among Diverse European Ethnic Groups. You’ve seen this song & dance before:
Population substructure in Japan
Population substructure of Mexican Mestizos
European population substructure
Genetic Map of East Asia
The genetics of Fenno-Scandinavia
Finns as European outliers
Uyghurs are hybrids
Genetic structure of Eastern European populations
Genetic map of Europe; genes vary as a function of distance
More genetic maps of Europe
Human population structure, part n
How Ashkenazi Jewish are you?
There’s more in the archives. The ostensible reasoning behind all this phylogeography is that in medical studies you want to control for population structure; in other words, throwing a bunch of people together in a big bag labeled “white” may not be optimal. One group of whites, Ashkenazi Jews, exhibit a whole lot of illnesses which are specific to that group. Labeling Jews as whites and using studies which used a non-Jewish populations as informative for Jews can cause obvious issues. The problem likely extends to other groups (e.g., the Quebecois). This particular paper was funded by the NIH, so there has to be a rationale which leads to some sort of human well being medically at the end of the tunnel, at least on paper.
Of course the other reason that these sorts of papers are of interest is that people are fixated upon human genetic relationships. A friend of mine was at a bar the other night and a woman purported to correct him about the nature of the Out-of-Africa movement (from what I can gather she was confused, but that’s another issue). These sorts of studies drill-down to a further level, and so naturally arouse curiosity. Some of the results and interpretations can be fraught because of nationalism; there has been a great deal of controversy and political import over whether modern Greeks are simply Hellenized Slavs, or not. Genetic data can help resolve some of these issues, though perhaps not everyone is looking for a resolution.
Obviously these sorts of papers have returned most of the more important low hanging fruit, but since people have this deep interest in population relationships I assume that there’ll continue to be publications fleshing out the empty spaces on he map, as well as minutiae on the margins. In the discussion the authors observe something which is important:

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CATEGORIZED UNDER: Evolution, Genetics

Northeastern Protestants & Catholics accept evolution

By Razib Khan | August 29, 2009 5:08 am

On a lark I decided to see how Catholics & Protestants broke down in regards to evolution by American region in the GSS. Specifically, I clustered the Census Divisions to create the categories of:
Northeast = New England + Mid Atlantic
Midwest = E & W North Central
South = S Atlantic + E South Central + W South Central
West = Mountain + Pacific
I limited the data to non-Hispanic whites for the question “evolved,” which was asked in 2006 and 2008, so recently. Results below the fold for this question….

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CATEGORIZED UNDER: Creationism

Katz

By Razib Khan | August 28, 2009 3:03 pm

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CATEGORIZED UNDER: Blog

Michael Behe speaks on bloggingheads.tv affair

By Razib Khan | August 28, 2009 1:43 pm

Addendum to my two posts below, here’s Michael Behe’s side. He notes:

…and John emailed back that he himself requested the video to be pulled because people thought he was too easy on me, which was supposedly contrary to that old Bloggingheads spirit. I find that quite implausible (other shows on the site feature discussions between people who agree on many things). Rather, I suspect the folks at the website weren’t expecting the vitriolic reaction, began to worry about their good names and future employment prospects, pictured themselves banished to a virtual leper colony, panicked, and folded.

Behe is correct. The producers do prefer some disagreement (participants refer to this injunction), but it often doesn’t crop up. I would say that the majority of diavlogs don’t exhibit much of an adversarial spirit. The problem was the lack of adversarial spirit and the content, that is, the crankery. When historian of science Ronald Numbers had a discussion with Paul Nelson, a Young Earth Creationist, it was in an anthropological spirit. In contrast McWhorter verged on advocacy.

CATEGORIZED UNDER: Blog

John McWhorter & Michael Behe bloggingheads.tv, 2

By Razib Khan | August 28, 2009 4:04 am

Just a quick follow-up to the previous post, as I finished watching the whole Behe-McWhorter exchange. Notes:
1) McWhorter is an atheist, and implies he’s always been an atheist (or at least not a theist).
2) He’s really impressed by Michael Behe’s arguments, to the point where he might assent to Michael Behe being the Isaac Newton of evolutionary genetics (though his summation of some of the jaw-dropping talking points in The Edge of Evolution leaves me a bit skeptical as to McWhorter’s deep knowledge of basic evolutionary ideas).
3) Part of the issue really has to do with the impenetrability of “scientese.” More clearly, I remember years ago a friend with a legal degree admitting that the Creationist talking point about The Second Law of Thermodynamics would have left him at a loss, as he didn’t have the scientific background to parse such issues. Behe is a much more sophisticated and slick player at that particular game.

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CATEGORIZED UNDER: Evolution

John McWhorter & Michael Behe bloggingheads.tv

By Razib Khan | August 28, 2009 1:14 am

So a friend of mine started IMing me about how crazy the John McWhorter & Michael Behe diavlog was on bloggingheads.tv. I was a bit surprised since there is no such diavlog, either on the bloggingheads.tv website, nor in their podcasts (which is where I usually am made to be aware of them). Well, here’s the story:

John McWhorter feels, with regret, that this interview represents neither himself, Professor Behe, nor Bloggingheads usefully, takes full responsibility for same, and has asked that it be taken down from the site. He apologizes to all who found its airing objectionable.

Beliefnet’s resident Creationist, David Klinghoffer is accusing bloggingheads.tv of “Stalinism”. As it is, I think the explanation about McWhorter’s second thoughts are probably accurate, this wasn’t on “Science Saturday” so the objections made against Paul Nelson appearing are not applicable.
But the video is downloadable at various websites, and so I’m watching it right now. It’s a little shocking to observe John McWhorter being irrationally exuberant at being able to talk to Michael Behe, the author of The Edge of Evolution. Glenn Loury & John McWhorter often joke about being “the black guys” on bloggingheads.tv, with a slight sense of irritation about the role they’ve been boxed into. McWhorter does not show evidence here of being able to break out of that box in the near future after this performance.
Some Creationists are complaining that McWhorter had the video withdrawn because he feared career reprecussions. I doubt that, his bread is buttered by The Manhattan Institute, which is a conservative think thank. Though most elite conservatives are not Creationist, there is no shame in Creationism in the modern American conservative movement. Rather, I suspect the pressure was the more informal one of peer group horror which likely came in via email.

CATEGORIZED UNDER: Genetics

More than a guy in pajamas

By Razib Khan | August 26, 2009 10:58 pm

Dan MacArthur did a lot of legwork in this post on Complete Genomics.

CATEGORIZED UNDER: Health

The Human Family Tree

By Razib Khan | August 26, 2009 2:16 pm

There’s a new National Geographic special out, The Human Family Tree, which readers might be interested in. Next showing is on the 30th. Seems to be an extension of The Genographic Project.
Clips below the fold:

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CATEGORIZED UNDER: Evolution

Tim White, Scientific American, open access to fossils

By Razib Khan | August 26, 2009 3:07 am

Kambiz Kamrani of Anthropology, normally a rather staid blogger, has posted something titled Science Suffers From The Idiots At Scientific American. It’s in reference to this widely circulated editorial, Fossils for All: Science Suffers by Hoarding. I can’t really summarize it, and I think the title certainly does invite you to read the whole post at Anthropology.net

CATEGORIZED UNDER: Evolution

The dog as rat

By Razib Khan | August 25, 2009 9:58 am

Speaking of Richard Dawkins, he’s back to science, in this case an excerpt from his new book, The Greatest Show on Earth: The Evidence for Evolution:

The evolution of the dog, then, if Coppinger is right, was not just a matter of artificial selection, but a complicated mixture of natural selection (which predominated in the early stages of domestication) and artificial selection (which came to the fore more recently). The transition would have been seamless, which again goes to emphasise the similarity — as Darwin recognised — between artificial and natural selection.

Nothing new in the article, which summarizes a lot of the fascinating new research on the evolution & genetics of domestication, particularly in the context of wolves & dogs. But Dawkins is a fluid writer who can weave in scientific data and theory to generate effortless narrative flow. Here lay his comparative advantage.

CATEGORIZED UNDER: Evolution, Genetics

Circumcision to prevent HIV infection in America

By Razib Khan | August 25, 2009 2:11 am

Officials Weigh Circumcision to Fight H.I.V. Risk:

Public health officials are considering promoting routine circumcision for all baby boys born in the United States to reduce the spread of H.I.V., the virus that causes AIDS.

He and other experts acknowledged that although the clinical trials of circumcision in Africa had dramatic results, the effects of circumcision in the United States were likely to be more muted because the disease is less prevalent here, because it spreads through different routes and because the health systems are so disparate as to be incomparable.
Clinical trials in Kenya, South Africa and Uganda found that heterosexual men who were circumcised were up to 60 percent less likely to become infected with H.I.V. over the course of the trials than those who were not circumcised.
There is little to no evidence that circumcision protects men who have sex with men from infection.
Another reason circumcision would have less of an impact in the United States is that some 79 percent of adult American men are already circumcised, public health officials say.

My first thought is that I really would like to see the cost vs. benefit analysis; the United States is not KwaZulu-Natal. The article notes white males tend to be circumcised already, which is interesting because American white male HIV prevalence rates seem to be somewhat higher than British rates (compare & contrast). This is important because while American men are mostly circumcised, most British men are not. The point is not that circumcision has no effect, but that on the margins its return is probably far less when you have a population which is already has low rates of infection. As I have noted before, circumcised South Korea and uncircumcised Japan have the same HIV infection rates, on the order of ~0.1%.
In the United States non-Hispanic white men have the highest rates of circumcision, followed by black men, and then Hispanics. But here are the ethnic-racial proportions of HIV infected individuals in the United States:

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CATEGORIZED UNDER: Health
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