Archive for March, 2012

When little differences matter a great deal

By Razib Khan | March 31, 2012 11:37 pm

In the comment below Clark alludes to the fact that Jonathan Haidt kept reiterating that even if there were differences between populations due to recent evolution, if it was due to selection on standing variation upon quantitative traits then the between group variation would be dwarfed by within group variation. He didn’t quite say it like that, but I’m sure that’s what he meant. For example, there is now evidence that alleles which can explain the small height difference between Northern and Southern Europeans have been subject to natural selection. Most of the variation obviously remains within the groups; you can’t guess that someone is Italian or Dutch just based on their height. There are many tall Italians, and many short Dutch. But on average there are differences between the groups which can be attributed to genes, and those genes seem to have been targets of selection.

This is good as fair as it goes…but small average differences may not necessarily be marginal. That is because sometimes you select from the tails of a distribution. For example, if you want to ascertain which population will produce more N.B.A. players, it is less important that there is a small average differences, so the populations mostly overlap, than that that average difference can result in a large disproportion at the tails of the distributions.

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CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Altruism

Jonah Lehrer, science fiction writer

By Razib Khan | March 31, 2012 10:46 pm

He’s back, and he’s out with a new book, Imagine: How Creativity Works. I am talking of course about Jonah Lehrer, the enfant terrible of cognitive neuroscience. OK, perhaps more Wunderkind. In any case, I was struck by this post on his weblog, The Cost Of Creativity:

There is a serious complication to this triumphant narrative of cliff edges and innovation, however. Because our lifestyle has become so expensive to maintain, every new resource now becomes exhausted at a faster rate. This means that the cycle of innovations has to constantly accelerate, with each breakthrough providing a shorter reprieve. The end result is that our creativity isn’t just increasing the pace of life; it is also increasing the pace at which life changes. “It’s like being on a treadmill that keeps on getting faster,” West says. “We used to get a big revolution every few thousand years. And then it took us a century to go from the steam engine to the internal-­combustion engine. Now we’re down to about 15 years between big innovations. What this means is that, for the first time ever, people are living through multiple revolutions.”

Needless to say, such revolutions aren’t fun. They’re unsettling and disruptive. But they appear to be the inevitable downside of our ceaseless ingenuity, for creativity comes with a multiplier effect: new ideas beget more new ideas. The treadmill is going fast. And it’s getting faster.

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CATEGORIZED UNDER: Anthroplogy, Culture
MORE ABOUT: Creativity

Jonathan Haidt & Robert Wright: crazy delicious

By Razib Khan | March 31, 2012 5:21 pm

Last night I listened to a very long discussion between Robert Wright, author of The Moral Animal, and Jonathan Haidt, author of The Righteous Mind: Why Good People Are Divided by Politics and Religion. If you have been reading my weblog for years there may not be much new, but if you haven’t, then you’ll encounter a lot of novel information, in particular from Jonathan Haidt. I was intrigued by Haidt’s references to evolutionary and anthropology, and I immediately noticed on Twitter that of the 17 people he follows, two are John Hawks and Paul Bloom. John is a friend, and Paul Bloom has been highly influential in my own thinking about cognitive psychology (see Descarte’s Baby). Additionally, many of the other “shout outs” which Haidt makes are familiar to me as well (e.g., Scott Atran, the neo-functionalism of David Sloan Wilson, etc.).

In lieu of a conventional blog post here a list of comments, reacting mostly to Haidt’s various assertions.

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CATEGORIZED UNDER: Evolutionary Psychology
MORE ABOUT: Jonathan Haidt

Post-Neolithic revenge of the foragers

By Razib Khan | March 31, 2012 11:18 am

If I have something to share, why not share it? Over the past few weeks I’ve been ruminating on some of the possible intersections between historical population genetics and anthropology, especially in light of the discussion that I’ve had in the past with Robin Hanson about ‘farmers vs. foragers’. Entering into the record that such a dichotomy is too stark, and only marginally useful (i.e., I think it is important to separate farmers and foragers in to their own sub-classes, as some farmer types may share more with some forager types, and so forth), it may be that after the first wave of the Neolithic expansion the descendants of the foragers “bounced back” in many regions of the world. It does seem that ancient European hunter-gatherers have left modern descendants. They were not totally swamped out. Using autosomal patterns some genome bloggers have inferred the same pattern, and perhaps even a counter-reaction by “Mesolithic” populations which adopted some aspects of the “Neolithic” cultural toolkit.

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CATEGORIZED UNDER: Culture, History

Cultural Folkways in Flux

By Razib Khan | March 31, 2012 10:43 am

A fascinating post over at The Crux, Votes and Vowels: A Changing Accent Shows How Language Parallels Politics. Here’s the section which I might quibble with though:

Labov points out that the residents of the Inland North have long-standing differences with their neighbors to the south, who speak what’s known as the Midland dialect. The two groups originated from distinct groups of settlers; the Inland Northerners migrated west from New England, while the Midlanders originated in Pennsylvania via the Appalachian region. Historically, the two settlement streams typically found themselves with sharply diverging political views and voting habits, with the northerners aligning much more closely with agenerally being more liberal ideology.

But first, here is a map of the dialects in question:

 

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CATEGORIZED UNDER: Culture

Revenge of the herders

By Razib Khan | March 31, 2012 3:29 am

Let me make something explicit: I believe that the model outlined in First Farmers is too simple, and that extant patters of linguistic and genetic variation need to accept the likelihood of multiple population reorganizations across vast swaths of Eurasia within the last 10,000 years. The classic case in point are the Turks. Because of their exotic character vis-a-vis the populations which they displaced and assimilated we can peg rather easily their expansion. Between 0 and 1000 AD they began to make themselves felt across a broad expanse of Eurasia from the eastern fringes of Europe to the western fringes of China, and south toward the world of Islam. Between 1000 and 1800 the Turkic peoples took over much of Eurasia for various periods of time (e.g., the Ottomans, Safavids, and Mughals, were Turkic, while the Golden Horde which imposed the Tatar Yoke were mostly Turkic, not Mongol). It is notable to me that Turkic peoples contributed ~10 percent to the genetic ancestry of modern Anatolians. This is a significant achievement, because Anatolia has been a densely populated seat of agricultural civilization for almost the whole history of agriculture! In Central Asia Turks genetically admixed significantly, to the point of preponderance, with the Iranian substrate.

Why does this matter? Because if it hadn’t happened, and it hadn’t happened in the light of history, I doubt we’d believe it! The Turks were obscure tribes in Central Eurasia 2,000 years ago. There was no anticipating that somehow they would overturn what had been the Iranian world of western Inner Asia, and, that they would break through into the civilized societies of the periphery, to the point of taking them over from above, and assimilating them from below. I do not think the Turks are exceptional in this. It must have happened many times in the past. We just need to open our minds to the possibilities.

CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Turks

The real secret history of the Mongols?

By Razib Khan | March 31, 2012 3:14 am

Thank god for steppe hyper-patriarchy; it’s a model which we can test. Dienekes points me to a paper, The Y-chromosome C3* star-cluster attributed to Genghis Khan’s descendants is present at high frequency in the Kerey clan from Kazakhstan, which is notable for increasing sample coverage of the distribution of “Genghis Khan haplotype.” As you might recall in 2003 a paper reported that a particular Y-chromosomal phylogeny was extremely common in Central Eurasia, and, that it had expanded rather rapidly starting approximately ~1,000 years ago. The natural supposition was that this was connected to the rise of Genghis Khan, from whom male-line descent in particular has become a matter of pride and prestige across the former domains under his rule. Subsequent researchers have supported this finding insofar as the distribution of the haplotype does tend to drop off among the “Western Mongols,” who were for various reasons marginal during the time of Genghis Khan, and whose ruling class were subsequently diminished in part due to their lack of a Genghiside pedigree.

 

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CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Human Genetics

Nature Precedings closes up shop

By Razib Khan | March 30, 2012 5:12 pm

Here’s the announcement:

As of April 3rd 2012, we will cease to accept submissions to Nature Precedings. Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.

Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area.

We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.”

This comes on the heels of Dr. Joseph Pickrell’s first author submission of a preprint. Correlation? Yes. Coincidence? I’ll let you decide.

In other news the existence and flourishing of arXiv puts a whole different spin on “physics envy.” And, just to reiterate, if I post about a paper, and you don’t have access email me and I will send you the paper.

CATEGORIZED UNDER: Genetics, Genomics

How Game of Thrones Should Have Ended

By Razib Khan | March 29, 2012 11:04 pm

I haven’t watched most of the films (or video games, or T.V. shows) being parodied by How It Should Have Ended. But I have read A Game of Thrones. So I’m confused as to why this struck me as rather unfunny, in comparison to most of the others where I have to educate myself on what’s being parodied….

CATEGORIZED UNDER: Culture
MORE ABOUT: Fiction

How culture crashes clines

By Razib Khan | March 29, 2012 12:14 am

The USA has been in Afghanistan for over 10 years now. Like many Americans my own personal preference is that we get out as soon as possible. Because of American involvement we see terms like “Pashtun” bandied about in the media, but there is little further exploration. But politics and international relations are the not focus of this post, at least not politics and international relations in our time. A new paper in PLoS ONE examines the Y-chromosomal patterns as they partition across ethnic groups in Afghanistan. By this, we mean the direct paternal lineage of Afghan men. Additionally, the authors place the results in a broader Eurasian context. The results are not surprising, though they add greater precision and power to our picture because of their sample size. The main downside is that they did not include mtDNA (maternal lineage) or autosomal analysis (the total ancestry, not just the paternal or maternal line).

 

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CATEGORIZED UNDER: Anthroplogy, Human Genetics
MORE ABOUT: Afghanistan, Pashtun

Targaryen genetic load

By Razib Khan | March 27, 2012 11:57 am

I have to point you to this post on royal inbreeding in A Song of Ice and Fire. They reference my post on the Habsburgs. Well done! In any case, one possibility is that the Targaryen lineage may have purged their genetic load through inbreeding. The basic logic is that all the recessive traits are going to be “exposed” every generation, resulting in a far stronger selection coefficient against those alleles than would be the case in a outbreed population (where most deleterious variants with recessive expression are masked by being present heterozygote genotypes).

CATEGORIZED UNDER: Genetics

How income, class, religion, etc. relate to political party

By Razib Khan | March 26, 2012 10:11 pm

Update: There was a major coding error. I’ve rerun the analysis. No qualitative change.

As is often the case a 10 minute post using the General Social Survey is getting a lot of attention. Apparently circa 1997 web interfaces are so intimidating to people that extracting a little data goes a long way. Instead of talking and commenting I thought as an exercise I would go further, and also be precise about my methodology so that people could replicate it (hint: this is a chance for readers to follow up and figure something out on their own, instead of tossing out an opinion I don’t care about).

 

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CATEGORIZED UNDER: Data Analysis, Demographics, GSS
MORE ABOUT: Data, GSS, Politics

The evolution of the human face

By Razib Khan | March 26, 2012 12:58 pm

The face is an important aspect of our phenotype. So important that facial recognition is one of many innate reflexive cognitive competencies. By this, I mean that you can recognize a face in a gestalt manner, just like you can recognize a set of three marbles. You don’t have to think about it in a step-by-step fashion. Particular types of brain injuries can actually result in disablement of this faculty, and a minority of humans seem to lack it altogether at birth (prosopagnosia). That’s why I’ve long been interested in the genetic architecture and evolution of craniofacial traits. I long ago knew the potential range of pigmentation phenotypes for my daughter because both her parents have been genotyped, but when it comes to facial features we’re stuck with the old ‘blending inheritance’ heuristic. The most obvious importance of teasing apart the genetic architecture of craniofacial traits is forensics. It might not put the sketch artist out of a job, but it would be an excellent supplement to problematic eye witness reports.

But it isn’t just forensics. The issue has evolutionary relevance. It looks like that in terms of morphology our own lineage has had a lot of diversity up until recently. I’m thinking in particular of the ‘archaic’ looking humans recently discovered in China and Nigeria, who seem to have persisted down into the Holocene. More generally, humans as a whole have become more gracile over the last 10,000 years. Why? There are two extreme answers we can look to. First, gracile humans have replaced robust humans. Second, natural selection for gracility has resulted in the in situ evolution of many populations over the last ~10,000 years. An interesting aspect of this is that it looks as if many salient traits have been targets of selection, and therefore evolution and population differentiation.

Here the top 10 SNPs which deviate from the overall phylogenetic tree of population relationships in the HGDP data set:

 

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The agricultural "express train"

By Razib Khan | March 25, 2012 11:25 pm

One model for the spread of the agricultural way of life into Europe is of inexorable “demic diffusion” via a “wave of advance” of farming populations met by a land surplus. Conceptually and analytically it’s an elegant model. It’s also fundamentally methodologically individualistic, and so in keeping with the spirit of the age. There’s no need to appeal to higher order social structure or organization, farmers who have a specific cultural toolkit drive the dynamic through endogenous growth in pre-state cultures through the production of large families. This growth washes over the frontier of the advance, and the original locus of the demographic pulse synthesizes across a transect with the indigenous substrate. In the early aughts historical geneticists Bryan Sykes and L. L. Cavalli-Sforza sparred over whether demic diffusion was useful or not as a conceptual framework. Sykes reported chromosomal results which implied that 75 percent of the ancestry of Europeans derives from Pleistocene hunter-gatherers. Cavalli-Sforza’s riposte was that the original model did not specify a particular Paleolithic-Neolithic ratio, but rather characterized a dynamic which emphasized the necessity of migration as a mediator for cultural changes (the two perspectives are outlined in Seven Daughters of Eve and A Genetic and Cultural Odyssey).

 

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CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Agriculture

The upper class is more Republican

By Razib Khan | March 25, 2012 3:31 pm

A few months ago I listened to Frank Newport of Gallup tell Kai Ryssdal of Marketplace that upper class Americans tend to be Democrats. Ryssdal was skeptical, but Newport reiterated himself, and explained that’s just how the numbers shook out. This is important because Newport shows up every now and then to offer up numbers from Gallup to get a pulse of the American nation.

Frankly, Newport was just full of crap. I understand that Thomas Frank wrote an impressionistic book which is highly influential, What’s the Matter with Kansas, while more recently Charles Murray has come out with the argument in Coming Apart that the elites tend toward social liberalism. I’m of the opinion that Frank is just wrong on the face of it, but that’s OK because he’s an impressionistic journalist, and I don’t expect much from that set beyond what I might expect from a sports columnist for ESPN. Murray presents a somewhat different case, as outlined by Andrew Gelman, in that his “upper class” is modulated in a particular manner so as to fall within the purview of his framework. Neither of these qualifications apply to Frank Newport, who is purportedly presenting straightforward unadorned data.

When the “average person on the street” thinks upper class they think first and foremost money. This is not all they think about, but in the rank order of criteria this is certainly first on the list. We can argue till the cows come home as to whether a wealthy small business owner in Iowa who is a college drop out is more or less elite than a college professor in New York City who is bringing home a modest upper middle class income (very modest adjusting for cost of living). But to a first approximation when we look at aggregates we had better look at the bottom line of money. After that we can talk details. And the first approximation is incredibly easy to ascertain. Below is a table and chart which illustrate the proportion of non-Hispanic whites after 2000 who align with a particular party as a function of family income, with family income being indexed to a 1986 value (so presumably $80,000 hear means what $80,000 would buy in 1986, not the aughts).

 

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CATEGORIZED UNDER: Data Analysis
MORE ABOUT: Data, Demographics

The revival of the American city?

By Razib Khan | March 25, 2012 2:37 pm

I’ve never watched Mad Men, but I really can’t help but hear all about the show. One thing that has struck me about the change from then, ~1960, to now, ~2010, is the alignment of quantitative demographic trends with impressionistic cultural ones. The 1970s were a disaster for the old urban order. Below are the top 10 cities by population in 1960 and 2010.

Rank 1960 2010
1 New York New York
2 Chicago Los Angeles
3 Los Angeles Chicago
4 Philadelphia Houston
5 Detroit Philadelphia
6 Baltimore Phoenix
7 Houston San Antonio
8 Cleveland San Diego
9 Washington Dallas
10 St. Louis San Jose

The rise of the “Sun Belt”, housing bubble notwithstanding, is a real and awesome phenomenon. Below the fold I’ve taken some demographic trend data for the top 10 cities of 1960. The first two panels show raw population data. The second two panels show the decade-to-decade change in population in terms of multiples (i.e., 1.2 for 2010 means that the population in 2010 was 1.2 times that in 2000).

 

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CATEGORIZED UNDER: Demographics
MORE ABOUT: Urbanism

No comments please, we've made it through peer review (?)

By Razib Khan | March 25, 2012 12:58 pm

Recently Daniel MacArthur pointed to the vibrant discussion over at Genomes Unzipped on a moderately infamous paper from Science last year, Widespread RNA and DNA Sequence Differences in the Human Transcriptome, asserting that it is “exactly what open peer review should be like.”  This made me wonder, it’s been over five years since Chris Surridge asked why there was so much more commentary on a PLoS ONE paper, By Hook or by Crook? Morphometry, Competition and Cooperation in Rodent Sperm, on blogs than on the paper itself. Has anything changed? The most viewed paper on PLoS Biology, How Many Species Are There on Earth and in the Ocean?, has 9 comments for 45,000 article views. In contrast, Genomes Unzipped has 14 comments for likely far fewer page views. Additionally, if you find the post on the weblog the comments automatically load. Not so with the PLoS Biology paper, you have to click through (yes, I see how this can be a feature, not a bug, but in that case why even bother with comments if you provide an email address for correspondence?)

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CATEGORIZED UNDER: Science
MORE ABOUT: Science

Neanderthals came in all colors

By Razib Khan | March 19, 2012 8:48 pm

There’s a report in Science about a new short paper about Neandertal pigmentation genetics. The context is this. First, in 2007 an ingenuous paper was published which inferred that it may be that Neandertals had red hair, at least based on an N = 2 from two divergent locations. The new study looks at three Croation samples, and reports genotypes which are correlated with a swarthier phenotype in modern populations. But the results are neither here nor there: everyone interviewed in the paper assumes that like modern Europeans Neandertals were a polymorphic set of populations when it comes to pigmentation. There are lots of reasons for this agreement, despite issues one might take with this paper.

The report on the paper in Science has two sections which I want to zoom in on. First, “Nearly 60% of the formula’s predictions matched the subjects’ actual physical appearance, the authors say. The team considers that accuracy rate satisfactory, given the complexity of the genetics behind skin color and other physical traits.” Do you consider 60 percent satisfactory? What curve are you grading on? I’m willing to bet that the reporter didn’t consider 60 percent satisfactory, and neither do I. If you look in the paper you’ll see that their method predicts that a Yoruba in the HGDP sample has blue eyes and red hair. Several of the Papuans are predicted to have blue eyes.

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The collapse of logic & human culture

By Razib Khan | March 19, 2012 9:31 am

Slavery’s last stronghold:

Moulkheir Mint Yarba returned from a day of tending her master’s goats out on the Sahara Desert to find something unimaginable: Her baby girl, barely old enough to crawl, had been left outdoors to die.

The usually stoic mother — whose jet-black eyes and cardboard hands carry decades of sadness — wept when she saw her child’s lifeless face, eyes open and covered in ants, resting in the orange sands of the Mauritanian desert. The master who raped Moulkheir to produce the child wanted to punish his slave. He told her she would work faster without the child on her back.

Trying to pull herself together, Moulkheir asked if she could take a break to give her daughter a proper burial. Her master’s reply: Get back to work.

“Her soul is a dog’s soul,” she recalls him saying.

Consider this. A father in a biological sense leaves his daughter out to die of exposure so as to increase the economic production of the mother of his daughter! Not only that, he obviously considers his daughter an animal. The full article is about slavery in Mauretania, a nation which maintains the practice in de facto form. Because this slavery clearly has a racial character, with a light-skinned population of North African origin enslaving a dark-skinned population of Sub-Saharan origin, there is an obvious “hook” for a Western, and particularly American, audience. But to be fair, if I can use that term, de facto slavery exists in organized form in other parts of the Sahel and Sahara (e.g., among the Tuareg), though the practice is far less pervasive in magnitude.

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CATEGORIZED UNDER: Culture, History
MORE ABOUT: History, Slavery

When independent thought flourishes

By Razib Khan | March 18, 2012 10:09 pm

One of the things I instinctively hated about my “ancestral culture,” that of Bangladesh, is that there wasn’t that great of an emphasis on individual independent thought. Why, for example, was it important never to drink water while you were eating, as opposed to after you were done? The response was simple: that’s the rule. Even if there was a functional rationale, there wasn’t even any pretense at offering a reasoned explanation for why a custom was a custom. It’s just how it was.

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CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Culture
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