Archive for July, 2010

Open Thread, July 31st, 2010

By Razib Khan | July 31, 2010 4:29 pm

The usual. Links, questions, etc.

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Daily Data Dump – Friday

By Razib Khan | July 30, 2010 1:02 pm

Have a good weekend.

Death of A Language. Since I started being more pro-active about my general lack of respect for modern American cultural anthropology I’ve gotten a lot of response. On the specific question of whether linguistic diversity is inversely proportional to economic growth, I’ve gotten some mixed-responses, and find all the conclusions inconclusive (I’ve had some r-squared results sent to me privately). Here’s A Replicated Typo reviewing a paper which tentatively supports my theoretical inference empirically. As I said, looking at the correlations are now in my “stack” of “TO-DO”‘s. But more broadly the normative gap between myself and my critics remains. So in the post I point to here, the author paraphrases a linguist as saying: “The languages spoken on the islands are considered to be almost 70,000 years old and are theorized to have African roots.” My comments about this sort of stuff are dismissive, and this experience only reinforces my disrespect for the “discourse” which linguistic anthropologists are introducing into the public domain. There are intellectual reasons to be interested in linguistic isolates not part of the big language families (e.g., Semitic, Indo-European, Niger-Kordofanian, etc.), but no language is “70,000 years old.” The Andaman Islanders are not black-skinned elves, immortals who brought their culture in toto from the ur-heimat of Africa, genetic and cultural fossils who have been in total stasis. Cultural anthropologists presumably understand that all humans are equally ancient, derived from African ancestors, and that all languages and peoples are African (or at least 95% so within the last 100,000 years), but their communication to the public confuses the issue and presents some groups as “pristine.”  As it is, Andaman Islanders have a major issue with high mortality levels due to being exposed to Eurasian pathogens. Language death is a relatively secondary issue for a group which had to be forcibly separated from Indian settlers in the 1960s for their own survival as a biological group.

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Koreans, not quite the purest race?

By Razib Khan | July 30, 2010 12:30 pm

ResearchBlogging.orgPLoS One has a paper out on Korean (South) population genetics and phylogeography, Gene Flow between the Korean Peninsula and Its Neighboring Countries:

SNP markers provide the primary data for population structure analysis. In this study, we employed whole-genome autosomal SNPs as a marker set (54,836 SNP markers) and tested their possible effects on genetic ancestry using 320 subjects covering 24 regional groups including Northern ( = 16) and Southern ( = 3) Asians, Amerindians ( = 1), and four HapMap populations (YRI, CEU, JPT, and CHB). Additionally, we evaluated the effectiveness and robustness of 50K autosomal SNPs with various clustering methods, along with their dependencies on recombination hotspots (RH), linkage disequilibrium (LD), missing calls and regional specific markers. The RH- and LD-free multi-dimensional scaling (MDS) method showed a broad picture of human migration from Africa to North-East Asia on our genome map, supporting results from previous haploid DNA studies. Of the Asian groups, the East Asian group showed greater differentiation than the Northern and Southern Asian groups with respect to Fst statistics. By extension, the analysis of monomorphic markers implied that nine out of ten historical regions in South Korea, and Tokyo in Japan, showed signs of genetic drift caused by the later settlement of East Asia (South Korea, Japan and China), while Gyeongju in South East Korea showed signs of the earliest settlement in East Asia. In the genome map, the gene flow to the Korean Peninsula from its neighboring countries indicated that some genetic signals from Northern populations such as the Siberians and Mongolians still remain in the South East and West regions, while few signals remain from the early Southern lineages.

I can’t comment too much on the inferences they make from the results because I’m not familiar with the geography of South Korea, or particular historical details. But more generally the genetics of Korea are of particular interest for social reasons:

South Korea is one of the most ethnically homogeneous societies in the world with more than 99 per cent of inhabitants having Korean ethnicity…The Koreans call their ethnic homogeneousity of their society using the word, 단일민족국가 (Dan-il minjok gook ga, literally means the single race society.)

Korean racialism has recently gotten the spotlight in works such as The Cleanest Race: How North Koreans See Themselves and Why It Matters, articles in The New York Times about South Korean prejudice against dark-skinned people, and the rise of mixed-origin Koreans nationals due to the large number of Vietnamese brides in rural areas. Here’s an interesting comment on South Korean race consciousness, Western Mixed-Race Men Can Join Military:

Western mixed-race men can join the military beginning next year.

Currently, Asian mixed-race men, dubbed “Kosians,” are subject to the country’s conscription system, but “Amerasians” or “Eurasians” are exempted from the mandatory service.

The parliamentary approval of a bill proposed by Rep. Yoo Seung-min of the governing Grand National Party has paved the way for them to join the military.

Western mixed-race men, who have distinctive skin colors, had been exempted because they could have experienced difficulty mixing with Korean colleagues in barracks, the defense ministry had said previously.

The article was published in January of 2010. And that’s not the weirdest idea to come out of the Korean peninsula. With all that in mind, the distinctiveness, or lack thereof, of the Korean nation as adduced from scientific genetics is of particular curiosity, as it is a clear example of the intersection of science and culture. First, here’s the figure which shows where in Asia & South Korea they got their samples from:

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CATEGORIZED UNDER: Genetics, Genomics

Katz

By Razib Khan | July 30, 2010 11:54 am

(click image for larger view)

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Finland, still going its own way

By Razib Khan | July 30, 2010 12:16 am

Dienekes points to a new paper which highlights genetic variation in Fenno-Scandinavia (or in this case, Finland, Sweden and Denmark). A two-dimensional plot with the variation is pretty illustrative of what you’d expect:

leunordicdb

Finns are genetic outliers in Europe, to some extent even in comparison to Estonians, who speak a very similar language. But, I wonder if the situation will change a bit when we have more samples from Finnic populations of northern Russia. Remember that the nature of these representations is sensitive to the variation which we throw into the equation in the first place.

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Reader survey results: politics

By Razib Khan | July 29, 2010 11:38 pm

Since the reader survey is topping out in response, I though I’d report some of the results. Since I’ve been doing these surveys my readership has exhibited a few patterns, and I was curious as to any changes since moving to Discover. Not too much has shifted. Instead of 15% female, as was the case for years, the readers are now 25% female. It looks like ~10% of the readers know this website only through Discover. Feel free to browse the results yourself.

I think the most interesting aspect for many is the political diversity. Generally the readership is split between Left liberals and libertarians. Though there are a small number of conventional conservatives, it is very rare to find those who are socially conservative and fiscally liberal. These “populists” tend not to be as intelligent as the other combinations, and so I suspect that’s why they’re not well represented on the web, among my readership, or the political elite of the United States in general (for what it’s worth, I’ve been moving in a more populist direction over the years, starting from a libertarian stance).

First, a few summary statistics. I asked readers their index of liberalism, with 0 being as conservative as possible, 10 as liberal, and 5 in the middle. I asked on two dimensions, social and economic.

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ResearchBlogCast #11

By Razib Khan | July 29, 2010 1:07 pm

ResearchBlogCast #11: Using The Genome To Identify Species. Check out Kevin Zelnio for more details. We also talk about the ScienceBlogs kerfuffle a bit at the beginning.

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Daily Data Dump – Thursday

By Razib Khan | July 29, 2010 9:19 am

If you are a regular reader, and have not done so, please take the Summer 2010 Gene Expression survey. N = 300, so I’ll stop buggin’ now and start posting results in the next day or so.

Ancient iceman’s gene map underway. Does anyone have any inside dirt on Otzi? His mtDNA was an outgroup to any modern Europeans, but we know that there’s sometimes a disjunction between mtDNA and autosomal results.

Protecting consumers from their own genetic data will come at a cost. Regulations have costs. Sometimes those costs are worth it (and result in long-term gains due to buffering of short-term volatility and such).

Vitamin D Deficiency Linked to Arterial Stiffness in Black Teens. There has been some concern about supplementation in colored people based on studies with whites, so this is important. Many people with darker-skins, including me, have been diagnosed with vitamin D deficiency and have started to take supplements. Anecdotally many of us report a decrease in respiratory infections and such. But it will be good when we have more rigorous studies.

Study says Amish expanding westward. Amish future!

Ancient DNA Identifies Donkey Ancestors, People Who Domesticated Them. Any surprise that domestication was a bottom-up, not top-down affair? Command economies are good at increasing factor inputs, but not necessarily driving innovation.

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The Anglo Revolutions

By Razib Khan | July 29, 2010 3:20 am

51TZ-cnJTrL._SS500_Over my lifetime in the United States there has been a shift toward a set of values which emphasize diversity, understood as being expressed along a few particular parameters: racial, sexual and ethnic. Part of the project is obviously concrete: increased representation of various segments within American society at the commanding heights of institutions and in positions to operate levers of power. But part of the project is intellectual and didactic. In the domain of history the past is reshaped and mined to create myths which serve as foundations for our understanding of how we got here, and why we value what we value. It is true that some reject the Founding Fathers as “Dead White Males,” and repudiate the history of the United States, and damn America. But others see in aspects of the founding project, and in the lives of the founders of the American republic, the roots of the modern liberal democratic order. Even the progenitors of multiculturalism. I would say that the latter position, of reappropriation and reinterpretation, is the dominant mode. But it is clearly myth-making. Those who repudiate the foundation of the American republic as a project of white supremacy, Eurocentrism, and ethnocentrism, have a great deal of reality to draw upon. The personal correspondence of men who were self-identified and perceived radical liberals for their time, such as Thomas Jefferson, attest to this reality.

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Daily Data Dump – Wednesday

By Razib Khan | July 28, 2010 11:02 am

Another reminder, if you are a regular reader, and have not done so, please take the Summer 2010 Gene Expression survey.

Assortative mating, regression and all that: offspring IQ vs parental midpoint. Very sad: “For n = 3 (parental midpoint of 145) the mean for the kids would be 127 and the probability of exceeding 145 less than 10 percent.”

On individuality, stochasticity and buffering. I think this is relevant at higher levels of organization than cell biology as well.

How far will the homeownership rate fall? This is not necessarily a disaster. People are less rooted, but that means there is more fluidity in labor mobility.

Get a Blazing-Fast Computer for Free. I’ve been using Ubuntu (dual boot) for years. I think perhaps it is ready for “prime time” in relation to ease-of-use for your grandmother. At least if she likes to perform BIOS upgrades!

Social Relationships and Mortality Risk: A Meta-analytic Review. We’re a social animal. I think that the methodological individualism at the heart of American politics, liberal, libertarian, and conservative, may not be rooted in human nature. Not that there’s anything wrong with that. But good to know.

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Investing in a nanny state for social returns

By Razib Khan | July 28, 2010 10:13 am

Jonah Lehrer has a post up, How Preschool Changes the Brain over at Frontal Cortex. He reports on a paper, Investing in our young people, which has been around for about 5 years. The top line of it is this, an investment in a $2,500/year (inflation adjusted) pre-school program in the early 1960s seems to have been effective in improving the life outcomes of at-risk low SES young black Americans tracked over their lives up to the age of 40. Their measured I.Q.s were not initially high, 85-75, 15th to the 5th percentile (though the median black American IQ is ~85, so not so low within ethnic group). They did gain an initial I.Q. boost, but like most of these programs that boost disappeared over time. But in terms of their non-cognitive skills there remained an appreciable effect which impact their life outcomes. What were these non-cognitive skills? To me they resemble classical bourgeois values rooted in low time preference. Willing to be a “grind,” work hard and forgo short-term pleasures and not cave in to impulses with short-term gains and long-term costs.

Here’s a figure from the paper which I’ve reedited with labels:

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CATEGORIZED UNDER: Behavior Genetics

Daily Data Dump – Tuesday

By Razib Khan | July 27, 2010 4:31 pm

First, if you are a regular reader, and have not done so, please take the Summer 2010 Gene Expression survey.

A horse is a horse, of course of course. Horses, like dogs, may be able to “read” human cues. In general intelligence dogs are less intelligent than wolves, but geniuses at this. In fact before this highly provisional finding they were the only non-human species able to engage in this sort of behavior. Horses are less intelligent than donkeys, but I wonder if they’re more intelligent in this domain than donkeys. Donkeys are more like cats, and horses more like dogs, if we’re going to do analogies. The latter have a much tighter connection with humans. From the perspective of aliens I wonder if humans their co-evolved organisms (dogs, horses, chicken, wheat, rice cow, pig, etc.) are like a movable ecosystem.

Thirteen new sample sets make their debut on the population genetics scene (Xing et al. 2010). I agree with the skepticism of the interpretation of the hypothesis that the ANI were Middle Eastern, for what it’s worth.

Human Induced Rotation and Reorganization of the Brain of Domestic Dogs. If humans can induce this sort of evolution of dogs, why not on themselves?

Leak May Hurt Efforts to Build War Support. I thought that was the point?

Learning Multiple languages from Multiple teachers. Looks like there are different “equilibrium states.” So what shocks societies from state A to state B?

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Summer books, what's readable?

By Razib Khan | July 27, 2010 3:08 pm

Danny reminded me that I still hadn’t read Empires of the Word: A Language History of the World. Since I know him a bit (at least internet “know”) I’ve decided I can’t put it off any longer, and I’ll tackle it soon. I just finished two books, Replenishing the Earth: The Settler Revolution and the Rise of the Angloworld, 1783-1939 and The Secret History of the Mongol Queens: How the Daughters of Genghis Khan Rescued His Empire. I can recommend the first, but not the second. Since I will (or plan to) review Replenishing the Earth, I won’t say more about it here. The Secret History of the Mongol Queens was written by the author of Genghis Khan and the Making of the Modern World. The author is a bit on the pro-Mongol side (he always ends up making Genghis Khan a benevolent warlord!), and his writing style doesn’t have the density which I prefer in these sorts of works, but Genghis Khan and the Making of the Modern World was a serviceable book. The Secret History of the Mongol Queens on the other hand is too sensational, and it seems rather obvious that the source material was much thinner than for Genghis Khan and the Making of the Modern World (he admits as much repeatedly), so he had to include a lot of apocryphal material, with caveats, to fill it out. I much preferred The Cambridge History of Inner Asia: The Chinggisid Age, which I read earlier this summer. A naturally more turgid work without a central narrative (each chapter was written by a different academic), but lots of dense data.

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Snap, phenotype, genotype and fitness

By Razib Khan | July 27, 2010 1:19 pm

Snapdragon,_smallOne of the main criticisms of the population genetic pillar of the modern evolutionary synthesis was that too often it was a game of “beanbag genetics”. In other words population geneticists treated genes as discrete independent individual elements within a static sea. R.A. Fisher and his acolytes believed that the average effect of fluctuations of  genetic background canceled out as there was no systematic bias, and could be ignored in the analysis of long term evolutionary change. Classical population genetics focused on genetic variation as abstract elementary algebras of the arc of particular alleles (or several alleles). So the whole system was constructed from a few spare atomic elements in a classic bottom-up fashion, clean inference by clean inference. Naturally this sort of abstraction did not sit well with many biologists, who were trained in the field or in the laboratory. By and large the conflict was between the theoretical evolutionists, such as R. A. Fisher and J. B. S. Haldane, and the experimental and observational biologists, such as Theodosius Dobzhansky and Ernst Mayr (see Sewall Wright and Evolutionary Biology for a record of the life and ideas of a man who arguably navigated between these two extremes in 20th century evolution because of his eclectic training). With the discovery that DNA was the specific substrate through which Mendelian genetics and evolutionary biology unfolded physically from generation to generation a third set of players, the molecular biologists, entered the fray.

The details of genetics, the abstract models of theorists, the messy instrumentalism of the naturalists, and the physical focus of the molecular researchers, all matter. Through the conflicts between geneticists, some arising from genuine deep substantive disagreement, and some from different methodological foci,  the discipline can enrich our understanding of biological phenomena in all its dimensions. Genomics, which canvasses the broad swaths of the substrate of inheritance, DNA, is obviously of particular fascination to me, but we can also still learn something from old fashioned genetics which narrows in on a few genes and their particular dynamics.

ResearchBlogging.orgA new paper in PLoS Biology, Cryptic Variation between Species and the Basis of Hybrid Performance, uses several different perspectives to explore the outcomes of crossing different species, in particular the impact on morphological and gene expression variation. You’ve likely heard of hybrid vigor, but too often in our society such terms are almost like black-boxes which magically describe processes which are beyond our comprehension (hybrid vigor and inbreeding depression freely move between scientific and folk genetic domains). This paper attempts to take a stab at peeling pack the veil and gaining a more fundamental understanding of the phenomenon. First, the author summary:

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CATEGORIZED UNDER: Evolution, Genetics

The rise (and fall?) of second-tier lingua francas

By Razib Khan | July 26, 2010 3:51 pm

The New York Times has an interesting piece, As English Spreads, Indonesians Fear for Their Language. It is dense with the different strands of this story. Basically, upper and upper middle class Indonesians are switching from Bahasa Indonesian to English to give their children a leg up, and are sending their children to English-medium schools. Because these children have a weak command of Indonesian some authorities are fearing for the cohesion of the Indonesian nation. Though the piece alludes to other languages in Indonesia, such as Javanese, it does not emphasize the fact that the widespread knowledge of Bahasa Indonesian was the outcome of a top-down project of nation-building, and that that language is the native tongue of only a minority of the citizens of Indonesia!

From Wikipedia:

Whilst Indonesian is spoken as a mother tongue (first language) by only a small proportion of Indonesia’s large population (i.e. mainly those who reside within the vicinity of Jakarta), over 200 million people regularly make use of the national language – some with varying degrees of proficiency. In a nation which boasts more than 300 native languages and a vast array of ethnic groups, the use of proper or ‘good and correct’ Indonesian (as opposed to Indonesian slang or regional dialects) is an essential means of communication across the archipelago. Use of the national language is abundant in the media, government bodies, schools, universities, workplaces, amongst members of the Indonesian upper-class or nobility and also in many other formal situations.

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CATEGORIZED UNDER: Culture

Daily Data Dump – Monday

By Razib Khan | July 26, 2010 12:33 pm

Hope the heat is treating you well (if you live in the northern hemisphere). If you are a regular reader and haven’t taken the summer 2010 reader survey, click here.

Cultural Diversity, Economic Development and Societal Instability. A post which addresses some of the issues emerging out of my comment about the relationship between linguistic diversity and economic growth. I’ll have more to say about this later…but I want to reiterate that my assumption as to the direction of correlation and conjecture as to the nature of causation is secondary. I’m really rousing myself from avoiding with engaging a particular “discourse” because of the intellectual exhaustion which ensues. Cultural anthropology is too important to leave to the….

Where are the Libertarians at Netroots Nation?. No idea where the causation is, but my personal experience as a libertarian-leaning individual (though less so as the years go by) among liberals is that I’m classed as a “Neandertal conservative” by my intellectual and moral superiors. Of course libertarians generally have the same attitude toward social conservatives, but a modus vivendi has developed between the two subculture which allows for collaboration despite personal distaste (in fact, liberals and libertarians tend to socialize more in urban areas because of shared cultural values, which I think may explain part of the issue: they know each other too well, and the differences are magnified!)

New Orleans’s Gender-Bending Rap. “Sissy bounce.”

Britain Plans to Decentralize Health Care. Violation of O’Sullivan’s Law?

The Moral Naturalists. Much more over at Edge. Our moral nature does not entail the moral systems upon which agree, but, it is a starting point for any realistic discussion.

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Saving is heritable, but culture matters a lot

By Razib Khan | July 26, 2010 10:58 am

The nature and character of your financial decisions is shaped by your genes. That shouldn’t be too horrible. Many decisions are the outcome of a combination of heritable and non-heritable predispositions. But I have to honestly express a bit of alarm at this segment I just heard on Marketplace, There’s only so much you can teach your kids. Here’s the subhead:

For better or for worse, kids take after their parents — but studies show parental influence only goes so far when it comes to how your children will handle money.

I’m not one to be worried about “genetic determinism” (usually just an insult which describes very few scholars), but this is a bit ridiculous. First, the primary research, of which you can find a pre-print online, seems to indicate that around ~30% of the outcome of financial decisions are heritable. That is, that ~30% of the variation in financial decisions within the population can be accounted for by variation in genes within the population. Additionally, there’s some context missing. The researcher expresses surprise that monozygotic twins converge in behavior as they age, and that parental influence tends to wear off as people leave the home. I don’t know if the researcher was taken out of context, but this is a totally unsurprising result. Over time shared home environment, what your parents model and teach you, tends to wear off, and gene-environment correlation increases the correspondences between particular genetic makeups and behaviors (i.e., identical twins resemble each other more at maturity than in their youth). For most behavioral traits heritability increases with age.

But the problem that microeconomic analyses like this create is that they confuse the public as to the relevance of charts such as this:

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CATEGORIZED UNDER: Behavior Genetics

Diseases of the Silk Road

By Razib Khan | July 26, 2010 8:42 am

behcetprev1Nature has two papers out about something called “Behçet’s disease.” It has apparently also been termed the “Silk Road Disease”, because of its associations with populations connected to the Central Eurasian trade networks.Though described by Hippocrates 2,500 years ago, apparently it was “discovered” only in the 20th century by a Turkish physician. The reason that that might be is obvious; the prevalence of Behçet’s disease is far higher in Turkey than any other nation. Two orders of magnitude difference between Northwest Europeans and Turks. East Asian populations are somewhere between Europeans and Turks, while the coverage of Inner Asia itself is thin (the first case diagnosed in Mongolia was in 2003). Additionally, the relatively similar frequency in Morocco and Iran, despite the latter nation being strong influenced by Turkic migration (25-30% of Iranian citizens are ethnically Turk), and the former not at all, leads to me wonder if there may be convergence or parallelism, rather than common ancestry, at work (or, more likely, a combination of both). The relationship between Morocco and Japan to the Silk Road in a direct fashion is tenuous at best. These were two polities which managed to be just outside the maximum expanse of Turanian empires. The Japanese famously repulsed the Mongol invasion ordered by Kublai Khan, while the Arab rulers of Morocco never fell under Ottoman control.And the early documentation by Hippocrates makes me wonder at the frequency of the disease in Greece itself. Greeks presumably contributed to the ancestry of modern Anatolian Turks, but it is far less likely because of the nature of the Ottoman system that Turks would have contributed to the ancestry of Greeks. I can’t find prevalence data for Greece, but it may be an open question in what direction the disease spread along the Silk Road.

ResearchBlogging.orgBut studies like these are nice because they are steps to overcoming one of the main issues with genome-wide associations: they use a narrow population sample, and so are not of necessary world wide relevance. Remember that even if a risk allele is not the direct cause of the disease, if it is closely associated with that alleles which are, it is of diagnostic utility. At least within that particular population. This study used groups from western and eastern Eurasia to check the power of particular single nucleotide polymorphisms (SNPs) to predict disease risk. First, Genome-wide association studies identify IL23R-IL12RB2 and IL10 as Behçet’s disease susceptibility loci:

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CATEGORIZED UNDER: Genetics, Genomics, Health

Reader Survey, summer 2010

By Razib Khan | July 26, 2010 3:51 am

So that reader survey that I mentioned last week is done. I’m mostly interested in seeing the changes since I’ve moved to Discover from ScienceBlogs. I assume that the standard 85% male readership has shifted somewhat toward more balance, but I don’t know. Many of the basic demographic questions (sex, race, age, etc.) are the same, but I swapped out ones I usually ask with others. At this point I’m rather sure that a huge proportion of the readers of this weblog are introverted nerds, so I’m not going to ask about personality type and what not. I took some reader suggestions, so there are questions about what you read, as well what your somatotype is. I converted the political question to a 0 to 10 scale that I wouldn’t have to recode if I did a scatter plot, and also so that it’s a little more fine-grained.

As usual all questions are optional. I timed it and should take you 5 minutes max, though I guess I can’t account for lack of clarity in prose. If you don’t see your exact response, but want to respond, I think it is totally fine to give the closest equivalent.

To take the survey, click here. After you’re done it’ll bring you back to this website. You can review results here.

Below are percentage breakdowns of last winter’s survey by sex.

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Reader survey results: Science vs. social science vs. humanities

By Razib Khan | July 25, 2010 11:51 am

About six months ago I did a survey of the readership of my two Gene Expression blogs (before moving to Discover). The N was around 600. You can view the raw frequency results here. One of the issues which I was curious about: did the disciplinary background of readers have any major correlates with responses? So I created three categories from the data on disciplines:

-Science
-Social Science
-Not Science

Social science had its own section, but for science I amalgamated those who studies Math, Engineering, Natural Science and Medicine. The balance were under “Not science.”

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MORE ABOUT: Reader Survey, Survey
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