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November 30, 2010

The naked years: the end of privacy

Filed under: Privacy,Technology,Transparent Society — Razib Khan @ 2:59 am

I do talk periodically on this weblog about the coming ‘transparent society.’ The main reason I bring up the issue is that I think it is probably inevitable, and, I think we’re sliding toward it without even reflecting on it too much. Many people are very surprised at how little time it takes to find information on them in Spokeo and Pipl. Curious about where someone you lost touch with from high school has lived? Go to Intelius.

Rereading David Brin’s original 1996 essay introducing the idea in Wired I’m struck by the fixation on old-fashioned cameras. To me, what people do is almost less interesting than what they’ve done. How much did they buy their house for? Where did they go to university? Did they graduate? Who did they marry? Interestingly, much of this information is offered up freely by the individuals themselves.

And yet what about our genetic code? With the recent 23andMe sale (which continues on, with provisions) I noticed people on Facebook worrying about privacy. Interestingly WikiLeaks has revealed that American diplomats were encouraged to obtain the DNA of foreign notables. Why would they do this? My first thought was that perhaps it would be an easy way to blackmail powerful cuckolds! Though this didn’t seem to cramp Adnan Kashoggi’s style. I assume that powerful individuals don’t have to worry about divulging their disease risks, since they’ll be taken care of. But the reality is that the science is simply not there for a great deal of return when it comes to risk variants. Below is a screenshot of my risks for various diseases from 23andMe as judged from a few single nucleotide variants:

disrisk

First, these are risks assuming a European genetic background. Which I don’t have. So there’s a problem right there, but 23andMe helpfully notes this boldly if you click through. But setting that aside, I know my risks for Type 2 Diabetes are much greater than average. Why? I have a family history of the disease! That’s why I’m obsessed with visceral fat.

The point is that right now family history is a much better predictor of your risks of a given disease than anything else. Not only does this capture missing heritability, but there is a natural correlation between families and environmental risk factors (or lack thereof). Using the breast cancer risk assessment tool it seems that if you have one first-degree relative who has had the disease you double your own odds of coming down with it over a five year period (though the risks over any given five year period are still low). There has been a lot of warranted attention paid to the BRCA genes, but what about the ability of insurers to digitally analyze the obituaries of your relatives and predict your own probability of death and disease?

I’m not saying that one shouldn’t be worried about divulging one’s genetic data. But it’s only a small piece of the puzzle of what we’re losing.

November 29, 2010

Of interest around the web & elsewhere – November 29th, 2010

Filed under: Blog — Razib Khan @ 2:02 am

Goodbye November.

Male Reproductive Problems May Add to Falling Fertility Rates. There’s an implication that there may be epigenetic and developmental reasons for this phenomenon. But check out this quote: “Today, at least one in five 18-25 year old men in Europe have semen quality in the subfertile range.” I’m starting to wonder about genetic load W. D. Hamilton style. If death doesn’t prune the deleterious alleles, perhaps PGD is going to be necessary in the face of rising infertility. Or somatic genetic engineering.

Now a Giant, Google Works to Retain Nimble Minds. I, like every nerd, have friends who work at Google. Great food. Awesome company. Smart people. But I do wonder if the cycle of institutional sclerosis is speeding up. IBM maintained hegemony for decades. Microsoft’s time in the sun really didn’t make it to the 20th year (I think 1990 is a good compromise year to peg the age of Microsoft, though it really got going with Windows 95 and had some juice in the days of MS-DOS. Facebook is already breathing down Google’s neck. This doesn’t mean that Google won’t be profitable, Microsoft is still making bank, and will do so for years to come. But It companies may be more and more ephemeral.

Information overload, the early years. In some ways the internet is, I believe, qualitatively different from previous information revolutions. But the critics really do repeat old & tired arguments, which pre-date the printing press, and go back to alphabetic script in ancient Greece. I assume that cuneiform and hieroglyph elicited the same concerns, but we don’t have records of that.


Children Ease Alzheimer’s in Land of Aging. Developed nations are filled with aging societies where one or two children have to be caregivers for parents. This is the future. We need to deal.

Hybrid vigor and missing genes. Agricultural genetics is really important. There are 7 billion humans, and we depend on plants.

The Rise of the Tao. One thing to remember is that in Taiwan and Singapore Taoism, which is ineluctably associated with the broad term “Chinese folk religion,” seems to give ground to Buddhism and to a lesser extent Christianity with development. So the concentration of the Taoist revival in the hinterlands makes sense.

The Complex Genetic Architecture of the Metabolome. Possible bad news: ” If this pattern proves generally applicable to other species, it could present a significant hurdle to identifying genes controlling metabolic trait variation via genome-wide association studies..”

23andMe $99 sale still going. +$60 subscription fee, but that’s mandatory now.

F.B.I. Says Oregon Suspect Planned ‘Grand’ Attack.

Also, Suspect in Oregon Bomb Plot Is Called Confused. “When you think of someone doing what he did, you think of some crazy kind of guy,” said Mohamed Kassim, 21, a fellow Oregon State student who knew Mr. Mohamud from around campus. “He wasn’t like that. He was just like everybody else.” Actually, most terrorists aren’t crazy. They’re motivated by political beliefs, though naturally specific life situations and dispositions play into their actions. I know it’s PC to say that there’s not a war against Islam, but the reality is that the USA is engaged in several imperialistic ventures which entail tussling with “Team Islam.”

Size of Mammals Exploded After Dinosaur Extinction, Researchers Confirm. Contingency and convergence?

The Real Culprit in Overeating. Not sure if I believe this. We can sense calories?

Fem Hiring Jealousy. It’s been a reported social science finding for a generation that good looking men get more of a wage premium than good looking women. The argument here is that women do the HR screening and penalize good looking women, but not the men. Or perhaps it could just be that men are more concentrated in professions and sectors with winner-take-all dynamics?

Can you provide humanitarian aid without facilitating conflicts? These are complex issues, and I don’t have anything to add.

Dogs Have Bigger Brains Than Cats Because They Are More Sociable, Research Finds. But what about I.Q.?

ADMIXTURE on the shores of the Indian Ocean.

For Google, the Browser Does It All. The article argue that the Chrome OS was designed for the Netbook era which never came to be, thanks to the power of smartphones, and the success of iPads.

Will Ireland Default? Ask Belgium

Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species. “This finding is important because it demonstrates a type of evolutionary change affecting DNA sequence elements critical for gene expression that is currently under appreciated and should be considered when searching for enhancers in related species.”

People Who Donate to Religions Are More Likely to Punish Selfish Behaviour, New Study Finds.

Joel Grus. If you remember him, you’ve read my stuff for a while.

Entitled to an Opinion. Nerd.

Less Wrong. Nerds.

Animals getting fatter too. Really strange.

According to this Isidore of Seville is a descendant of Augustust Caesar! I don’t believe it. Must be errors in the genealogical database. I traced it by starting with Augustus’ great-great-granddaughter Junia Lepida. I suspect what’s going on is that the arriviste Christian aristocratic clans of the early 5th century simply made up connections to older Roman families to burnish their reputations in the face of accusations that they were anti-traditional (because they had rejected the old gods, and often risen from below through imperial patronage of late).

No Romans needed to explain Chinese blondes

uyghurboy
Uyghur boy from Kashgar

Every few years a story crops up about “European-looking” people in northwest China who claim to be of Roman origin. A “lost legion” so to speak. I’ll admit that I found the stories interesting, amusing, if  implausible, years ago. But now it’s just getting ridiculous. This is almost like the “vanishing blonde” meme which always pops right back up. First, let’s quote from The Daily Mail,* DNA tests show Chinese villagers with green eyes could be descendants of lost Roman legion:

For years the residents of the remote north western Chinese village of Liqian have believed they were special.

Many of the villagers have Western characteristics including green eyes and blonde hair leading some experts to suggest that they may be the descendants of a lost Roman legion that settled in the area.

Now DNA testing of the villagers has shown that almost two thirds of them are of Caucasian origin.

The results lend weigh to the theory that the founding of Liqian may be linked to the legend of the missing army of Roman general Marcus Crassus.
Enlarge

In 53BC, after Crassus was defeated by the Parthians and beheaded near what is now Iran, stories persisted that 145 Romans were captured and wandered the region for years.

As part of their strategy Romans also hired troops wherever they had conquered and so many Roman legions were made up not of native Romans, but of conquered men from the local area who were then given training.

250px-Statue-AugustusLet’s start from the end. The last paragraph indicates a total ignorance of the nature of military recruitment during the late Republic. In the year 110 BC the Roman army was composed of propertied peasants. These were men of moderate means, but means nonetheless. They fought for the Republic because it was their duty as citizens. They were the Republic. Due to a series of catastrophes the Roman army had to institute the Marian reforms in 107 BC. Men with no means, and who had to be supplied with arms by the Republic, joined the military. This was the first step toward the professionalization of the Roman legions, which naturally resulted in a greater loyalty of these men to their leaders and their unit than the Republic. Without the Marian reforms Sulla may never have marched on Rome. By 400 AD the legions were predominantly German in origin, and supplemented with “federates,” who were barbarian allies (though alliances were always subject to change). But in 53 BC this had not happened yet. The legions who marched with Crassus would have been Roman, with newly citizen Italian allies in the wake of the Social War. The legions of the Julio-Claudians were probably still mostly Italian, a century after Crassus (service in the legions, as opposed to the auxiliaries, was limited to citizens, who were concentrated among Italians). So that objection does not hold.


But really, do we need the Roman hypothesis? Those big blonde Romans? Here’s one section of the piece: “Archaeologists discovered that one of the tombs was for someone who was around six foot tall.” Because of issues of nutrition the Roman soldiers were notoriously short relative to the Celts and Germans (who had more meat and milk in their diet). Perhaps they had the potential for greater height, which they realized in the nutritional surfeit of…China?

Anyway, there’s a straightforward explanation for the “Chinese Romans”: they’re out of the same population mix, roughly, as the Uyghurs. Before the year 1000 AD much of what is today Xinjiang was dominated by peoples with a European physical appearance. Today we call them Tocharians, and they spoke a range of extinct Indo-European dialects. It seems likely that there was also an Iranian element. The archaeology is rather patchy. Though there were city-based Indo-Europeans, it is clear that some of them were nomadic, and were among the amorphous tribes that the ancient Chinese referred to as the “Rong and Di.” The Yuezhi and Wusun were two mobile groups who left China in the historical period and are recorded in the traditional annals.

Meanwhile, between 500 AD and 1000 AD the Indo-European substrate of the Tarim basin was absorbed by Turkic groups coming from Mongolia. They imposed their language on the older residents, but genetically assimilated them. The modern Uyghurs are a clear hybrid population. In the papers published on the Uyghurs they shake out as about a 50/50 West/East Eurasian mix. But the DODECAD ANCESTRY PROJECT has them in the sample, and here’s how they break down by a finer grain:
uad

Uyghurs are the third population from the bottom. Below them are the Yakut and Chinese. The Yakut are the northernmost Turkic people, and the Turkic element which settled in Xinjiang and assimilated the Tocharians was from the north. The Chinese-like element may simply be that the proto-Uyghurs were already admixed with the Han populations, or, that that element has a geography-conditional cline where the Yakuts are at an extreme. In any case, the other components of Uyghur ancestry are not East Asian. Like many European popualtions the Uyghurs have a West Asian and Northern European aspect, but they lack the South European ancestry. This is important, because it is dominant in both the Tuscans and North Italians.  If the “Roman Chinese” are genuinely Roman, they will have this specific southwest European ancestry, which will put them at a distinction from the Uyghurs.

As it is, I don’t think that’s what’s going on.  On the order of 4,000 years ago the domestication of the horse allowed for the expansion of Indo-European populations from east-central Eurasia across the steppe. Eventually they they also percolated into the underpopulated zones between the taiga and the highlands around the Himalayan massif. I believe that these were the groups which introduced nomadism and agriculture to the Tarim basin, and their genetic and cultural impact was a function of the fact that they simply demographically swamped the few hunter-gatherers who were indigenous to the region.

In the period between 1000 BC and 1000 AD the flow of people reversed. The expansion of the Han north and west, and the rise of a powerful integrated state which could bully, and could also be extorted, changed the dynamics on the steppe and in the oasis cities beyond. The vast swaths of Central Asia which were Indo-European in speech became Altaic in speech. But many of these populations absorbed the Indo-European groups, and came out genetically admixed. A clear residual of West Eurasian admixture can also be found among peoples who presumably never interacted much with Indo-Europeans, such as the Mongols, though at lower levels.

The villagers of Liqian are a different part of the story. Clearly substantial numbers of “barbarians” were assimilated into a Han identity on the northern frontier. In the case of tribes such as the Xianbei and Khitan they even did the assimilating themselves, through top-down sinicizing edits. In areas like Gansu these elements contribute a greater proportion of the ancestry, and just as the Uyghur are Turkic speaking, and yet have equal portions of West and East Eurasian ancestry, so the people of Liqian are Chinese speaking, and have equal portions of West and East Eurasian ancestry.

I find it curious that the piece above didn’t mention Uyghurs at all. No idea if politics was involved, but I won’t be surprised if I get some angry Han and Uyghur comments because of what I’m saying here (I’m not totally clear what these sorts of commenters are angry about really, they’re usually pretty inchoate).

Addendum: East and West Eurasian ancestry seems pretty equitably distributed among the Uyghurs. But the number of genes which code for racially salient traits are far smaller than the total set which can be used to estimate ancestry. So within a large enough population allelic combinations across loci will segregate so that some individuals exhibit a “pure” ancestral phenotype. What colloquially might be termed a “throwback.” This little boy comes strikingly close.

* I am aware of the reputation of this newspaper. Nevertheless, it’s being picked up by the international press and some blogs, so I’m going to address it.

Image Credit: Gusjer

November 28, 2010

Slouching toward transparency

Filed under: Technology,Transparent Society — Razib Khan @ 5:28 pm

In regards to the WikiLeaks story, it seems that:

- The explosive stuff is really a shift from assumed understanding to explicit acknowledgment. For example, that Arab nations are just as terrified of Iran’s nuclear program as Israel.

- The surprising stuff is more funny or strange. More like gossip you wouldn’t have guessed, but isn’t really that significant in the broad canvas of diplomatic history.

Strangely, I sort of think this is of a piece with the recent “Teacher’s Union Gone Wild” videos. Basically, the expectation of privacy is disappearing, on the grandest and most mundane scales. In the latter case, a woman was chatted up at a bar, and recorded for hours on end. Unfortunately for her, she used to the N-word, though not even in a offensive context (follow the link). Who hasn’t run their mouth off at a bar? Make sure you don’t have enemies! Imagine how someone could utilize damaging conversations in office politics. On the grand scale you have problems of coordination across agencies where secrecy and confidentiality are of the essence.


gaysultantConsider the media. I recently was listening to a radio show where Robert D. Kaplan was talking about the enlightened liberal despot of Oman, Sultan Qaboos bin Said al Said. Oman has Hindu temples, due to the existence of a long-standing Indian minority. But of course Kaplan, being a respectable journalist who would not trade in gossip did not mention that the Sultan partakes of liberality himself, as in Oman it is assumed he is a homosexual (he is divorced and has no children as heirs). In a pre-internet period I wouldn’t do so much background checking when it came to politicians and public figures, but now I regularly do so. The personal lives and histories of powerful individuals are often very relevant in assessing how they came to the positions they hold, and the sincerity of their positions.

smartphone
Your life in 30 seconds

This is all almost banal because it has been happening imperceptibly. The WikiLeaks events are notable only in that they’re punctuated gushers. But the TSA wants to see you naked, Intelius can verify your age in 10 seconds, and Zillow can tell me how much your home is assessed and how much you purchased it for. Did you donate to a political party recently? Who are you related to? What’s your social network presence and how much public information do you have dangling out there? Life in 2010.

Image Credit: tomsun

Internet usage by country

Filed under: Culture,data,Data Analysis,Internet,Technology — Razib Khan @ 1:14 pm

In my post below on the rise of China, I ran into the data on internet usage by country again. I was online regularly by the spring of 1995, and it’s amazing to think that there are hundreds of millions of Chinese on the internet now! The World Bank estimates that both China and India have exhibited an increase of internet usage by an order of magnitude from 2000-2010, though from different bases. So while there are ~300 million Chinese users of the internet, there are ~50 million Indians. But who would have guessed that Nigeria has more per capita internet users than India? See below.


Now check out this plot of more advanced economies of internet penetration by % of households vs. income per capita.

Latitudes and continents

Filed under: Climate,science — Razib Khan @ 11:04 am

Thanksgiving in the tropics:

Finally, here are some pictures I took today. It was way too hot and humid when we first got to Taiwan, but now we’re getting some lovely winter weather – Taiwan is about the same latitude as Hawaii :-) It sure doesn’t feel like Thanksgiving or Xmas around here!

One aspect of the East Eurasian temperate zones is that they are far to the south of the West Eurasian temperate zones. Cork, Ireland, at about the same latitude as Petropavlovsk, Kamchatka, and eight degrees further north than Vladivostok!

But since Steve brought up Hawaii, let’s compare highs and lows in Honolulu, and Hanoi, two cities at 21 degrees north. On the literal margins of the tropics:


avehighlow

Taking the end of the age seriously

I am about two-thirds of the way through Why the West Rules-for Now: The Patterns of History, and What They Reveal About the Future, and I have to agree with Tyler Cowen’s assessment so far. The author is an archaeologist, and though a little less shy in regards to general theory than most in his profession, he still seems to exhibit the tendency to focus on thick-detail without any elegant theoretical scaffolding. In some ways it is an inversion of Gregory Clark’s A Farewell to Alms: A Brief Economic History of the World, which manifests an economist’s preference for stylized system-building at the expense of the messy residual. Why the West Rules has added almost no broad-brush theoretical returns beyond what you could find in Guns, Germs and Steel and The Wealth and Poverty of Nations. Though the author has a lot of scrupulously footnoted detail which probably makes Why the West Rules a worthy read.

But this post isn’t a review of Why the West Rules, rather, it’s a lament as to the total intellectual unpreparedness of the West’s intellectual class for the de facto end of the age of white supremacy,* the high tide of which is documented in the final chapters of this book (I skimmed them chapters ahead of time). The de jure end of the age of white supremacy probably spanned the victory of the allies during World War II down to desegregation in the United States in the 1960s. But despite the official end of the ideology of white racial superiority, the white-majority nations of the world were and are objectively superior in metrics such as Human Development Index. On a per capita basis they will remain so for a while longer:

And yet the trend lines are converging between East Asian and developed white Western nations. We are now moving beyond the time when we can talk about ‘the West vs. the Rest.’ There are ~1.3 billion Chinese in China itself, which is approximately the total number of people of white European descent in the world.** In much of Africa China is a rising economic and social presence. There are likely more expatriate Chinese in Africa than there are expatriate whites. Enter “China + any region of the world” into Google, and you’ll come back with plenty of interesting results.

But from what I can tell Westerners, of all colors, are totally intellectually unprepared for the radical shift in geopolitics which is occurring as we speak. Kvetching about China’s trade surplus does not intellectual preparedness make. Most white liberals have an anti-colonialist outlook, and favor the liberation of peoples of color in the face of white supremacy. But this normative framework only makes sense in light of a model whereby white domination and agency are the preeminent considerations in the lives of the people of color. In much of the world that is not necessarily the case anymore. In Australia you have an inversion of the old narrative, insofar as an commodity boom driven by Chinese demand has arguably kept that nation’s economy relatively buoyant!

The white supremacy model (WSM) isn’t only found among white people. It’s very dominant among colored people who reflect on these issues. Indians are haunted by British colonialism. Latin Americans by Yankee imperialism. Middle Eastern Muslims by the Jewish-Western condominium. The Chinese still remember the de facto colonialism which their nation was subjected to after the Opium Wars.

In graphic terms what you have as a model is like so:

europerest

In the late 19th century the whole world became Greater Europe’s playground. Non-European thinkers had to respond to the European challenge. There was no other game in town. To some extent that response continued and elaborated after the collapse of European political hegemony in the 1950s and 1960s; ergo, postcolonialism.

This is probably more accurate today than the old model, and will certainly be more accurate within the next generation:

europerest2

800px-World_literacy_map_UNHD_2007_2008
Because of its population and economic dynamism China will naturally come to rival Greater Europe in its influence and impact on the rest of the world. No other nations besides East Asian ones have shown an ability to match Greater Europe in HDI. The map to the left of literacy rates is I believe a good predictor of potential median HDI and per capita economic productivity ceilings for the next generation or two. South Asia is the world leader in absolute concentrated human misery, both in illiteracy and malnutrition. I think India will be influential and powerful because of raw numbers, but there is no worry that it will be a per capita power. Africa is prospering thanks to the Chinese fueled commodity boom, but it too is low on the human and institutional capital totem pole to leverage its demographic dynamism. Australia is too small in population to be influential. If the trends in its economy remain, that it becomes in large part a commodity source for China, then I think it will be prey to being muscled by the East Asian superpower just as Latin American nations traditionally were by the United States, even without military intervention, because of the asymmetry in economic dependency. Latin American nations like Brazil are populous and on the ‘ascension graph’, but they have problems with wide variance in human capital, just like India.

In civilizational terms we are not going from a unipolar world to a multipolar world. We’re going from a unipolar world to a bipolar world. This means that there must be a revision to our intellectual toolkit. Critics of the West, whether they’re white or colored, still have a superficial understanding of the Dead White Men and their history. Islamic revisionists who make a case for the centrality and superiority of their tradition do so with the West as an explicit or implicit counterpoint. The indigenous traditions of India, Africa, or China, were not relevant to these arguments. Europe was the sun, around with other civilizational planets circled.

Not so any longer. Consider these headlines: China workers killed in Pakistan and Algeria: Xenophobia against Chinese on the rise in Africa. Or Brazil’s huge new port highlights China’s drive into South America. China eyes rail link to Chittagong. A pushcart war in the streets of Milan’s Chinatown. ‘Too Asian’? – Worries that efforts in the U.S. to limit enrollment of Asian students in top universities may migrate to Canada.

This is a different dynamic than the rise of the one-dimensional Arab and Soviet petro-states of the 1970s in a qualitative sense. China and its Diaspora are a full-throated economic counterweight to the two century international geopolitical and cultural dominance of Greater Europe. It is also a different dynamic than the migration of various colored peoples into Western nations after World War II, where these groups are slotted into the lower social and economic rungs, and draw hostility and contempt from some whites and patronizing sympathy and self-interested bureaucratic-managerial concern from others. Japan and the “Asian Tigers” were limited by their demographic modesty when set next to Greater European nations like the United States.

How should people readjust to this world? Obviously following economic statistics and political events are essential to recalibrating with judicious perspective and caution. The world’s intellectual classes, Western and non-Western, have been conditioned to white supremacy for so long that no one remembers a time when it was any different.*** One of the ironies of WSM is that non-whites rarely know the history or culture of other non-whites to the same extent that they know that of whites. In other words, South Asians know their history and that of whites, Africans know their history and that of whites, East Asians know their history and that of whites, etc. (the main exception may be Korea, which was colonized by the Japanese). It’s ironic because the implicit inference of WSM is that non-whites have common interests against the white master race. Though this is admittedly rational because the concerns, values, and motivations of the masters are more relevant than those of other helots. The term ‘master race’ has positive connotations while a ‘the cancer of human history’ has negative ones, but no matter, both indicate that the object of concern is worthy and of note. But the blind-spot in this mode of thinking is that colored people who supposedly have solidarity are totally ignorant of each other’s respective substance.

This was all of purely academic interest until the resurgence of East Asia, and China in particular. It is for example well known that Chinese have a strong racial consciousness. During the Maoist period this was dampened by ideology. China’s objective lack of development for most of the 20th century almost certainly suppressed some of the racial disdain which is an element of Han chauvinism. But the Chinese, like East Asians in general, have a degree of race consciousness which expresses on the surface to an extent that would be surprising and alarming to most whites, excepting perhaps Afrikaners, some white American Southerners, and partisans of nationalist parties in Europe. This predates the modern era insofar as the Chinese have a long history of dehumanizing ‘barbarians’ and looking down on dark-skinned peoples (e.g., see the reports of the legation sent to the Khmer kingdom of Funan, which lingered upon their nakedness and darkness of complexion). But the real genesis of contemporary attitudes may be rooted in the synthesis of Chinese folk attitudes and early 20th century racial anthropology, already evident in the writings of principals in the May Fourth Movement.

Contrary to the Chung Kuo science fiction future history I have no expectation that Han racism will lead to a genocidal war of extermination against the black and brown peoples of the world. Rather, the attitudes in common circulation in China and other East Asian nations must be understood by any politician, diplomat or businessman, who wants to operate in that region. Any dark-skinned South Asian who expects “Asian” fellow-feeling in China may be in for a surprise. Chinese opinions of people of African descent are even more checkered. During the days of Japan Inc. cultural fluency was already seen to be critical, but because China is one order of magnitude more populous than Japan in 30-40 years it will be much more of an international social and economic presence. Interestingly 20% of individuals on the internet are already Chinese nationals, vs. 5% of Japanese (though the difference in penetration rates is 30% vs. 80%).

Where does this leave us? By the end of our lives those of us in early adulthood will live in a bipolar world. China and the West will together be drivers of consumption. When it comes to development aid or investment in poorer nations the West will have a substantive rival. These two will hold up the sky together. With this will come more prominence of Chinese culture, and a necessity for an understanding of that civilization’s history, its values. Though I’m making a pragmatic and utilitarian case for understanding and knowledge here, I do want to enter into the record than an appreciation of the history of the Chinese is an understanding of the history of a substantial proportion of humanity. It is part of our common history, just as Greece and Rome are.

With that, at the end of this post are a list of books which I’ve found useful, and obviously memorable, in trying to understand the shape of the Chinese past, and how the present came to be. Personal preference and bias is obviously operative. The fact that a standalone work on Xun Zi is listed below, and Mencius is not, says a lot about my personal evaluation of the two in relation to each other.

* I use “white” as a compound of both genetic and cultural qualities. So, Turks are not classified as white in this sense, while Ashkenazi Jews are, even though both groups are equivalently white when compared to “reference” populations which no one would deny are white, such as the English, in a genetic sense. So a person of Turkish ethnic origin who converts to Christianity, such as Boris Johnson’s ancestor (originally Bey), can generally be accepted as white because of their appearance. In contrast, someone who has noticeable non-white appearance, a South Asian for example, remains non-white despite their Christianity.

** You can do the back-of-the-envelope pretty easily. Europe, + 0.70 X USA + Canada + Australia + New Zealand + 1/3 Latin America is a good approximation. Of course a substantial proportion of the other 2/3 of Latin Americans have some white European ancestry, but whiteness a privilege which generally comes only through purity of blood, so they can be ignored.

*** I would peg the closing of the previous multipolar world to the second half of the 18th century, though the fact of European dominance did not ripen until the Opium Wars, which illustrated that even the greatest of non-Euroepan powers was ineffectual against European military mobilization.

anlect31RSVQ5XFKL._SL500_AA300_china1
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china3china4china5china6china84china7china9

November 27, 2010

Open Thread – November 27th, 2010

Filed under: Blog — Razib Khan @ 2:16 pm

Hope Thanksgiving went well for Americans. I didn’t gain weight at all, 142lbs as of Friday morning!

Out of curiosity, what fiction do you read?

Also, check out Dienekes post on the ability to generate disjoint clusters in the DODECAD sample set. He asserts that one may now be able to generate extreme fine-scale assessments of likely population assignment from genetic material now. Check out this table; each column after the first two are the number of individuals in a given cluser. The rows are populations. The second column are the N individuals.

Last week’s This American Life had a segment on dog feces DNA fingerprinting. I think this is a good idea.

November 26, 2010

Assorted links related to this weblog

Filed under: Administration,Blog — Razib Khan @ 11:04 am

23andMe kits are discounted to $99 from $499 today.

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Friday Fluff – November 26th, 2010

Filed under: Blog,Friday Fluff — Razib Khan @ 12:09 am

FF3

1. First, a post from the past: Innate social aptitudes of man.

2. Weird search query of the week: ‘evolutionary biologist studies porn.’

3. Comment of the week, in response to The cult of Korea:

Razib, as you say they are literate, but not in a free way. Note that I didn’t say North Koreans were illiterate, just that their ignorance reminds me of places where people are illiterate. The issue isn’t being theoretically able to read but rather being able to find information and be skeptical. I could have made that clearer. After all there are lots of literate fundamentalists who aren’t skeptically literate. However being illiterate in places like Afghanistan or Haiti makes the situation that much worse. Being literate but not reading through choice (as with some Americans) or through restrictions (countries like N. Korea) ends up largely being a difference without much of a difference in terms of results.

Omar, most groups are informed about what they encounter regularly. (Although even there one finds a lot of nonsense – look at water dowsing in the US) Outside of that experience though they are ill informed and typically open to a high level of nonsense. I don’t think indoctrination vs. ignorance really captures what I’m getting at. Someone may be bright but unable to think through issues critically. Of course that can happen here in the US as well. There’s no shortage of urban legends Americans believe. But in places like North Korea, Haiti or many other places the lack of access/ability to read about the world leads to huge problems. The problem is that when leaders try to manipulate the public and enflame them they can quickly lose control precisely because of this problem.

But as you both note, one should distinguish literacy from ignorance.

BTW – I don’t think Cuba is a good analogy to N. Korea. While the US has had a travel ban others have been able to go to Cuba and interact with people widely. (Canadians were quite positively viewed by the Cubans and it wasn’t hard to go on vacation there) Further consumer goods were a little more widely dispersed in Cuba along with telecasts and radio from the US. (I’m not sure how much exposure to S. Korean media N. Koreans have as a practical matter) I’m not playing down Castro and what he did, but I think it gets a mite bit exaggerated in the US. On the other hand N. Korea is a whole other world from what I can tell. Cuba I think most of us would recognize, even if we chaffed under the restrictions in say the 80’s.

4) Are we going through the Great Stagnation?

5) And finally, your weekly fluff fix:
double

November 25, 2010

Eating, and eating well

Filed under: Blog,Diet — Razib Khan @ 12:33 am

turk
Credit: tuchodi

Happy Thanksgiving Day to all the Americans out there. This is a day to loosen the belt a bit, but after the Holidays you probably want to think about slimming back. So, ScienceDaily, Obesity Riddle Finally ‘Solved’, and, Diets with High or Low Protein Content and Glycemic Index for Weight-Loss Maintenance. The upshot seems to be that a high protein-low (refined) carb diet worked best in a large sample of Europeans.

Myself, I was in the 155-165 pound range between 2000 and 2007. 2008-2010 I’ve been in the 140-150 range, and usually closer to the low end than the high. I went from a waist size in the 31-33 inch range to 28-30 range (I wear 28s regularly now). I’m moderately active in that I walk a lot, but I have totally turned away from refined carbs. I am not a religious ‘Paleo’, but I do track glycemic indices and glycemic loads for various foods rather closely. That being said, different people have different biologies. I think that’s important to remember. As a South Asian I have a higher risk for type 2 diabetes, so I’m particularly vigilant about sugar and other variables which increase my probabilities for chronic diseases. If I was a Northern European I might have different priorities, and chill out a little bit about dessert. Life is about trade-offs, and pleasures do often have costs. I am not much of a sweet-tooth, and I’m genetically predisposed to type 2, so my aversion toward sweets is a rather simple calculation. Others may have different outcomes performing the same operations because of different inputs. The answer to a riddle may vary depending on who is asking.

November 24, 2010

We were all Africans…before the intermission

modelhumanQuick review. In the 19th century once the idea that humans were derived from non-human ancestral species was injected into the bloodstream of the intellectual classes there was an immediate debate as to the location of the proto-human homeland; the Urheimat of us all. Charles Darwin favored Africa, but in many ways this ran against the cultural grain. The theory of evolution was birthed before the highest tide of the age of white supremacy and European hegemony, and Darwin’s model had to swim against the conviction that Africans were the most primitive of the colored races. After the waning of the ideological edifice of white supremacy, and the shock it received during and after World War II, the debates as to the origin of humanity still remained contentious and followed the same outlines (though without the charged normative inferences). But as the decades wore on many more researchers began to believe that Darwin was correct, and that the origin of humanity lay in the African continent. First, the deep origin of the human lineage in Africa was accepted, but eventually a more recent expansion out of Africa was argued for by one school. The turning point in these academic disputes was the popularization of the “mitochondrial Eve” theory of the 1980s.

What some paleontologists had long argued, that anatomically modern humans have their locus of origin in Africa, was supported now by research from genetics which indicated that Africans were the most basal clade of humans on a continental scale, so that non-Africans could be conceived of as a subset of Africans. From this originates the chestnut of wisdom that Africans have more genetic diversity than all other human populations combined. By the year 2000 one could say that the “Out of Africa” triumphalism had proceeded to the point where an almost exterminationist model had taken hold when it came to the relationships of anatomically modern H. sapiens, and other groups which had evolved outside of Africa over the past million or so years, such as the Neandertals.

ResearchBlogging.orgBut the theoretical dichotomies were too coarse and absolute as it turns out. A division between multiregionalist phyletic gradualism, where H. sapiens evolved out of its hominin ancestors concurrently on a world wide scale, and a model of rapid expansion of one tribe in Africa to replace all others in totality, may have been warranted in the age of classical genetics and a morphometric analysis, but now we can look at the raw genomic material in a more fine-grained fashion. In fact, we can now look at the genomic patterns of variation among extinct hominins! Though there have long been hints that the expansion-and-replacement paradigm was too extreme from the genetic and morphological data, with the publication last spring in Science of a paper which made the claim for admixture between Neandertals and non-Africans in the range of 1-4% in all non-African groups based on a comparison of Neandertal and modern human genetic variation, one can dismiss absolutist expansion-and-replacement as self-evidently true orthodoxy. But one orthodoxy has no given way to another, and the shock to the old models presented by the data has not resulted in the coalescence of new robust paradigms. We live in a time of scientific troubles, so to speak.

One of the more notable results in the Science paper from last spring was that all non-Africans had about the same admixture in relation to the Neandertal reference genome, ~1-4%. This means from the Orkneys to New Guinea. Because Neandertals were distributed only in the western half of Eurasia this implies that the admixture was an early event. By the time of modern human expansion across Eurasia, Australasia, and the New World, it had become equally distributed across the individuals within the population. Recall the contrast between African Americans and Uyghurs. Among the Uyghurs the ancestral quanta are equitably distributed from individual to individual, but among African Americans there remains substantial intra-population variance. The reason is that African Americans are quite new, an order of magnitude younger than the Uyghurs in a genetic sense, and admixture is still occurring into the African American population from the ancestral groups. The Uyghurs as we known them today genetically are probably ~1,000-2,000 years old (though their cultural origins are both more and less ancient, as a matter of linguistics in the former, and ethnic self-conception as a Muslim East Turkic group in the latter). The implication here is clear: there was a pause in the Out of Africa movement, where the proto-non-Africans mixed with a Neandertal group, possibly in the Middle East, and only began a massive demographic expansion after an unspecified sojourn. A paper from last spring makes this all explicit:

A more likely explanation for the OoA bottleneck is that Eurasia was populated by a larger population that had been relatively isolated from other modern human populations for tens of thousands of years prior to the expansion. The first fossil evidence for modern humans outside of Africa is in the Middle East at Skhul and Qafzeh between 80,000-100,000 years ago, which is at least 20,000 years prior to the Eurasian diaspora. If a population of modern humans remained in the Middle East until the expansion into Eurasia, there would have been sufficient time for genetic drift to reduce heterozygosity dramatically before the Eurasia expansion. This “Middle East isolation” hypothesis provides a robust explanation for the relative homogeneity of European and Asian populations relative to African populations (see Figures 3A-B) and is supported by a recent maximum likelihood estimate of 140,000 years ago for the time of Eurasian-West African population separation . Interestingly, a recent study of the Neandertal genome suggests that the non-African individuals, but not the Africans, contain similar amount of admixture (1-4%) with the Neandertals . The authors suggest that the admixture must have happened between the Neandertals with an ancestral non-African population before the Eurasian expansion. Given the fossil, archaeological, and genetic evidence, the Middle East isolation hypothesis warrants rigorous evaluation as whole-genome sequence data become available.

Now the same group has published a follow up paper in Genome Biology which fleshes out the Deep Time aspect of human evolutionary history by looking closely at the genetic variation of an under-sampled population: South Asians. You may have noticed that the HGDP populations include Pakistani groups as South Asian exemplars. That’s apparently because during the Permit Raj era in India the government was wary of cooperating with the HGDP consortium. But more recently the barriers have come down in India, and one can viably supplement the data sets with Indian Americans. So the GIH sample in HapMap3 consists of Gujaratis from Houston. At ~1.25 billion, or nearly 20% of the world’s population, South Asians are a critical portion of the “big picture” when it comes to world wide genetic variation.

Genetic diversity in India and the inference of Eurasian population expansion:

To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100 kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90-110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans.

First, I want to put into the record that I think there are high enough uncertainties (evident in the confidence intervals in the paper itself) that we need to be careful about taking the divergence times from their results as values we’d bet the house on. Someone with a better knowledge of the fossils (e.g., John Hawks) or controversies about the mutational rates (e.g., Dienekes) can comment on the plausibilities of the dating. But, I think we can infer that there was a time lag closer to a 10,000 years order of magnitude than 1,000 years when it comes to the Middle Eastern sojourn of non-African humans.

The basic method here is that the research group zoomed in on a ~100 kb region of the genome, on chromosome 12, and surveyed their Indian populations, as well as the HapMap3 ones. This is important because the SNPs in the HapMap probably exhibit an ascertainment bias toward variants in European and other more widely surveyed groups. The fact 30% of the SNPs in the South Indian groups seem to not be found among the HapMap populations confirms this hunch. Before digging into the details of the paper, let’s note that the South Indian groups are from the state of Andhara Pradesh, Brahmins, a lower caste group (Yadava), Dalits (Mala/Madiga), and a tribe (Irula). This is a case where even more thorough coverage is necessary. There is some suggestion that South Asian groups have a long history of endogamy and genetic peculiarities, which would limit the usefulness of extrapolations from this sample. Even within the HapMap Gujarati sample there seems to be two clusters when the PCA is used with reference to the European samples.

There are basically three portions of the paper:

- A survey of conventional population genetic statistics,

θ = 4Neμ (Ne = effective population, μ = mutation rate)
π = nucleotide diversity
H = heterozygosity
D = Tajima’s D

- Measures of genetic distance between contemporary populations, Fst and PCA

- Finally, taking the genetic variance from the ~100 kb and plugging it into explicit models of human evolutionary history

Table 1 (I reformatted) shows the genetic statistics by “continent.” Indian includes some Gujarati individuals. They sampled out of the HapMap populations to equalize the numbers.

indiaeur1

euro2Some of these results are striking. The general truism is that Africans are the most diverse population in the world, but some of the South Indian groups are very diverse indeed. Of particular interest though is that some Indian groups are not very diverse at all. What’s going on here? Here you have to look at the specifics of each group. It is likely that South Indian Brahmins are the result of a relatively recent population expansion, with some uptake of other genes through hypergamy. A paper from last year argued that all Indian populations can be modeled as a two-way admixture of different quantities from two ancestral groups, Ancient North Indians and Ancient South Indians. The heterozygosity values may be explained in such a fashion, though the relatively low values for Gujaratis and Andhara Pradesh Brahmins would still surprise. Frankly, I’m just mostly confused by the diversity statistics. Probably the substructure through endogamy and population bottlenecks are obscuring broader dynamics. We can, though, conclude that the idea that all non-Africans are uniformly homogeneous in comparison to Africans may not hold water. Figure 2 above illustrates this by plotting heterozygosity vs. distance from Africa.

Next, let’s move to genetic distance. There’s two ways you can look at this: a summary statistic like Fst, which partitions between and within population variance, and PCA, which visualizes the largest dimensions of variations in the data set. So you have both below (reedited for reasons of space):

EURFINAL

In the generality the results are expected, but there are weird details. For example, the Brahmins from Andhara Pradesh are on the margins, where you’d expect them to cluster with the Gujaratis. The Gujaratis are closer to the Chinese from Denver than Utah Whites? This is a provisional paper, so I’m almost wondering if there’s a typo or coding error here, as I don’t understand how the GIH can be so close to the Tuscans and Chinese from Denver, and much further from the Northern Europeans and Chinese from Beijing. The two European and Chinese samples are rather close in other analyses.

So let’s get to the real deal. The modified Out of Africa model where non-Africans take a “break” after they leave the mother continent:

modelhumanfinal

I’ve mashed up the figures. The models were generated by looking at allele frequencies. They took the variants they found by sequencing the ~100 kb on chromosome 12, which was in a very gene-poor region so as to bias it toward neutrality, and plugged them into a few models in the ∂a∂i program. I’ll jump to the text here:

…the divergence time between African and the ancestral Eurasian population (88-112 kya, CIs: 63-150 kya) is much older than the divergence time among the Eurasian groups (27-39 kya, CI: 20-59 kya). The more recent divergence time and the low migration rate estimates among the current Eurasian populations support the “delayed expansion” hypothesis for the human colonization of Eurasia (Figure 5). Consistent with previous studies…these estimates indicate that a single Eurasian ancestral population remained separated from African populations for more than 40 thousand years prior to the population expansion throughout Eurasia and the divergence of individual Eurasian populations.

549px-Islamic_Adam_&_Eve
Manafi al-Hayawan, Adam and Eve

Take a good look at those confidence intervals. We know that some of those have to be false: the bones don’t lie. From what little I know a very young consensus date for the settlement of Australasia by modern humans is 40,000 years ago. That happens nicely to be their median, but the dispersion toward younger dates is probably not right, unless Aborigines are a separate population who are remnants of an earlier wave of migrants (or the current Aborigines replaced earlier waves). It is also hard to reconcile these dates for the diversification of non-African humanity with very old dates for Chinese fossils which exhibit some elements of modern morphology.

In the broad outlines I think we can accept that the model outlined in this paper may be correct. It would explain the uniform admixture of Neandertal in non-Africans, since they’d need time as a compact population before demographic expansion to integrate the Neandertal genes as part of their genetic background. But before the Neandertal genome came out there were plenty of papers which purported to show how there was no archaic admixture in modern humans, and plenty of papers which did claim there was evidence for such admixture. The point is that these computational models are sensitive to their inputs, and being models they simplify what really happened. In the discussion the authors repeatedly observe that migration between the various non-African demes doesn’t effect the outcome. That is fine, but there is modestly strong evidence that the Indian samples that they’re using are an admixed population of old. That would make me skeptical of claims about dating the separation of “Indians” when Indians are themselves possibly a compound between other groups.

Below is the model presented from Reconstructing Indian population history:

reich

The teens of this century are going to be very exciting when it comes to reconstructing human evolutionary history. You’d be a fool to put bets on any horse at this time.

eurasicansAddendum: I need a term for non-African humanity. So I’m making up one right now: Eurausicans. From Eurasians, Australasians, and Americans.

Citation: Jinchuan Xing, W Scott Watkins, Ya Hu, Chad D Huff, Aniko Sabo, Donna M Muzny, Michael J Bamshad, Richard A Gibbs, Lynn B Jorde, & Fuli Yu (2010). Genetic diversity in India and the inference of Eurasian population expansion Genome Biology : 10.1186/gb-2010-11-11-r113

North Korea vs. South Korea

Filed under: Culture,Data Analysis,Korea — Razib Khan @ 1:13 am

There isn’t a lot of good data coming out of North Korea, but I thought the following charts would be of interest. USA and Mexico included for comparison. In case you don’t know, the South Korea = Republic of Korea, North Korea = Democratic People’s Republic of Korea.

The inevitable social brain

ResearchBlogging.orgOne of the most persistent debates about the process of evolution is whether it exhibits directionality or inevitability. This is not limited to a biological context; Marxist thinkers long promoted a model of long-term social determinism whereby human groups progressed through a sequence of modes of production. Such an assumption is not limited to Marxists. William H. McNeill observes the trend toward greater complexity and robusticity of civilization in The Human Web, while Ray Huang documents the same on a smaller scale in China: A Macrohistory. A superficial familiarity with the dynastic cycles which recurred over the history of Imperial China immediately yields the observation that the interregnums between distinct Mandates of Heaven became progressively less chaotic and lengthy. But set against this larger trend are the small cycles of rise and fall and rise. Consider the complexity and economies of scale of the late Roman Empire, whose crash in material terms is copiously documented in The Fall of Rome: And the End of Civilization. It is arguable that it took nearly eight centuries for European civilization to match the vigor and sophistication of the Roman Empire after its collapse as a unitary entity in the 5th century (though some claim that Europeans did not match Roman civilization until the early modern period, after the Renaissance).

It is natural and unsurprising that the same sort of disputes which have plagued the scholarship of human history are also endemic to a historical science like evolutionary biology. Stephen Jay Gould famously asserted that evolutionary outcomes are highly contingent. Richard Dawkins disagrees. Here is a passage from The Ancestor’s Tale:

…I have long wondered whether the hectoring orthodoxy of contingency might have gone too far. My review of Gould’s Full House (reprinted in A Devil’s Chaplain) defended the popular notion of progress in evolution: not progress towards humanity – Darwin forend! – but progress in directions that are at least predictable enough to justify the word. As I shall argue in a moment, the cumulative build-up of compelx adaptations like eyes strongly suggest a version of progress – especially when coupled in imagination with of the wonderful products of convergent evolution.

Credit: Luke Jostins
Credit: Luke Jostins

One of those wonderful products is the large and complex brains of animals. Large brains are found in a disparate range of taxa. Among the vertebrates both mammals and birds have relatively large brains. Among the invertebrates the octopus, squid and cuttlefish are rather brainy. The figure to the right is from Luke Jostins, and illustrates the loess curve of best fit with a scatter plot of brain size by time for a large number of fossils. The data set is constrained to hominins, humans and their ancestors. As you can see there is a general trend toward increase cranial capacities across all the human populations. Neandertals famously were large-brained, but they exhibited the same secular increase in cranial capacity as African Homo. On the scale of Pleistocene Homo and their brains the idea of the supreme importance of contingency seems ludicrous. Some common factor was driving the encephalization of humans and their near relations over the past two million years. This strikes me as very strange, as the brain is metabolically expensive, and there are plenty of species with barely a brain which are highly successful. H. floresiensis may be a human instance of this truism.

But what about the larger macroevolutionary pattern? Is there a trend toward larger brain sizes in general, of which primates, and humans in particular, are just the most extreme manifestation? Some natural historians have argued that there is such a trend. But, there is a question as to whether increased brain size is simply a function of allometry, the pattern where different body parts and organs tend to correlate together in size, but also shift in ratio with scale. The nature of physics means that very large organisms have to be more robust because their mass increases far faster than their surface area. By taking the aggregate relationship between body size and brain size, and examining the species which deviate above or below the trend line, one can generate an encephalization quotient. Humans, for example, have a brain which is inordinately large for our body size.

And yet there are immediate problems looking at relationships between body and brain size, and inferring expectations. Different species and taxa are not interchangeable in very fundamental ways, and so a summary statistic or trend may obscure many fine-grained details. A new paper in PNAS focuses specifically on various mammalian taxa, corrects for phylogenetics, and also relates encephalization quotient by taxa to the proportion of social animals within each taxon. Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality:

Evolutionary encephalization, or increasing brain size relative to body size, is assumed to be a general phenomenon in mammals. However, despite extensive evidence for variation in both absolute and relative brain size in extant species, there have been no explicit tests of patterns of brain size change over evolutionary time. Instead, allometric relationships between brain size and body size have been used as a proxy for evolutionary change, despite the validity of this approach being widely questioned. Here we relate brain size to appearance time for 511 fossil and extant mammalian species to test for temporal changes in relative brain size over time. We show that there is wide variation across groups in encephalization slopes across groups and that encephalization is not universal in mammals. We also find that temporal changes in brain size are not associated with allometric relationships between brain and body size. Furthermore, encephalization trends are associated with sociality in extant species. These findings test a major underlying assumption about the pattern and process of mammalian brain evolution and highlight the role sociality may play in driving the evolution of large brains.

A key point is that the authors introduce time as an independent variable, so they are assessing encephalization over the history of the taxon. This is clearly relevant for humans, but may be so for other mammalian lineages. The table and figures below show the encephalization slope generated by using time and body size as the predictors and brain size as the dependent variable. A positive slope means that brain size is increasing over time.

Two major points:

- Note that the slope is sensitive to the level of taxon one is examining. A closer focus tends to show more variance between taxa. So, for example, humans distort the value for primates in general. Bracketing out anthropoids paints a more extreme picture of encephalization, a higher slope. In contrast, the lemurs and their relatives exhibit less encephalization over time.

- The correlation between proportion of species which exhibit sociality and encephalization of the taxon is strong. From the text:

Encephalization slopes were correlated with both the proportion of species with stable groups (order R = 0.92, P = 0.005, n = 6; suborder R = 0.767, P = 0.008, n = 9; Fig. 2 A and B) and the proportion in either facultative or stable social groups (order R = 0.804, P = 0.027, n = 6; suborder R = 0.63, P = 0.04, n = 9).

The last figure makes it is clear that the correlations are high, so the specific values should not be surprising. Don’t believe these specific figures too much, how one arranges the data set or categorizes may have a large effect on the p-value. But the overall relationship seems robust.

266px-Alienigena
A highly encephalized “alien”

What to think of all of this? If you don’t know, one of the authors of the paper, Robin Dunbar, has been arguing for the prime importance of social structure in driving brain evolution among humans for nearly twenty years. The relationship is laid out in his book Grooming, Gossip, and the Evolution of Language. Robin Dunbar is also the originator of the eponymous Dunbar’s number, which argues that real human social groups bound together by interpersonal familiarity have an upper limit of 150-200. He argues that this number arises because of the computational limits of our “wetware,” our neocortex. Those limits presumably being a function of biophysical constraints.

One interesting fact though is that the median cranial capacity of our species seems to have peaked around one hundred thousand years ago. The average human today has a smaller brain than the average human alive during the Last Glacial Maximum! (see this old post from Panda’s Thumb, it’s evident in the charts) This may be simply due to smaller body sizes in general after the Ice Age. Or, it may be due to the possibility that social changes with the rise of agriculture required less brain power.

Ultimately if Dunbar and his colleagues are correct, if social structure is the most powerful variate in explaining differences in brain size when controlling for phylogenetics and body size, then in some ways it is surprising to me. After all, it does not seem that ants have particularly large brains, despite being extremely social and highly successful. Clearly the hymenoptera and other social insects operate on different principles from mammals. Instead of
developing “hive minds,” it seems as if in mammals greater social structure entails greater cognitive structure.

Citation: Susanne Shultz, & Robin Dunbar (2010). Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality PNAS : 10.1073/pnas.1005246107

November 23, 2010

The rise of men & the fall of the non-men

Filed under: East Asian,Genetics,Genomics,History,Japan — Razib Khan @ 3:35 pm

Dienekes Pontikos ruminates on the changes in human genetic variation on a world-wide scale over the past 10,000 years based on an MDS plot of East Eurasian genetic variation which he generated. I’ve taken his plot and added geographical labels, so you can see the difference in scale between geography and genetics in terms of distance:

pcaeast

He argues:

What this plot shows, in tangible form, is a picture of mankind’s past: before the invention of agriculture, most humans lived in small tribes, scattered across the world. We can be fairly certain that the action of genetic drift and natural selection would have created a cornucopia of human diversity, with high between-group diversity due to high levels of genetic drift.

Out of all this variety, some tribes of hunters made the transition to agriculture, growing in numbers, filling the areas they exploited, and expanding into new ones. The hunters were on their way to extinction, but new tribes formed at the fringes, those of pastoral nomads exploiting animals to thrive where neither farmer nor hunter could.

In the world of farmers, with growing population densities and expansion came the breakdown of isolates: this led to a further homogenization of the farmers’ gene pool, as different tribes that had adopted the new way of life lost all trace of their past tribal identities and formed new ones based on the common language of the agriculturalists and the new way of life.

With more human bodies in the farming communities, came more novel mutations, and hence more of the raw materials of selection.

Coupled with the new challenges of agriculture, for which man is unaccustomed to, the social challenges of living close to many others in villages, and, later, cities, the cognitive challenges of new symbolic systems of communication, selection further reduced diversity in key aspects of human appearance and behavior, while maintaining it, or even increasing it in others, such as resistance to pathogens.

In western Eurasia this process was pushed to its limits, and there are virtually no nomads or hunters to be found there anymore. Africa was explored by Europeans just in time to find living hunters such as the San and Pygmies still in existence there. A few centuries more, and perhaps they, too, would have beeen absorbed into the mass of expanding farmers.

I pretty much agree with this. Intuitively this seems to jibe with reports of strange looking peoples in the mythologies of many literate civilizations. One plausible explanation for trolls, witches, and fairy-folk is that the human mind is inventive, and perceives mystery and agency all around us. But another seed of these legends may simply be the conventional human tendency to de-humanize other populations. In World War I you saw a perfect illustration of this, as Americans were told that the Germans were “Huns.” This de-humanization occurred despite a substantial minority of Americans being of recent German ancestry at that time, and the Germans and Americans themselves being relatively culturally close (the American colonies were after all ruled by a dynasty of German origin just 150 years before).

495px-AinuManStilfliedBefore the expansion of agricultural peoples within the last 10,000 years perhaps there was more phenotypic diversity than we’re used to seeing around us now. As first-mover advantage allowed for the rapid demographic expansion of some groups into the “frontier” they may have absorbed or assimilated peoples of a far different countenance than themselves. One of the best examples of this seems to be the Ainu. These people retreated to Hokkaido by the historical period, but it seems likely that their near relations, the Jomon, were the indigenous people of the Japanese islands, only driven north or absorbed within the last 2,500 years by rice farmers from southern Korea, the Yayoi. Here’s the received wisdom from Wikipedia:

Direct comparisons between Jōmon and Yayoi skeletons show that the two peoples are noticeably distinguishable…The Jōmon tended to be shorter, with relatively longer forearms and lower legs, more wide-set eyes, shorter and wider faces, and much more pronounced facial topography. They also have strikingly raised browridges, noses, and nose bridges. Yayoi people, on the other hand, averaged an inch or two taller, with close-set eyes, high and narrow faces, and flat browridges and noses….

When European physical anthropologists encountered the Ainu in the 19th century the standard assumption was that these hirsute people without epicanthic folds were a “Lost White Tribe.” Genetic science in the 20th science debunked this inference. The Ainu are an East Asian people, and resemble other East Asians far more than Europeans or other populations. But, their physical appearance clearly was atypical. The reality is that the “typical” East Asian physical appearance is probably a function of the demographic expansion of the Han, and later the Yayoi in Japan.

As the “world became flat” it looks like there was a “winner take all” dynamic at work.

The cult of Korea

Filed under: Culture,Korea,North Korea — Razib Khan @ 2:11 pm

There are currently some scary goings-on in the Korean peninsula. If you have some time, I recommend Inside North Korea from National Geographic. Here’s the final scene. Jump to 5 minutes.

Eurogenes 500K SNP BioGeographicAncestry Project

Filed under: Admixture,Ancestry,BGA,Genetics,Genomes Unzipped,Genomics — Razib Khan @ 12:11 am

Since I have been promoting the Dodecad Ancestry Project, it seems only fair to bring to your attention Eurogenes 500K SNP BioGeographicAncestry Project. The sample populations are a bit different from Dodecad, but again ADMIXTURE is the primary tool. But the author also makes recourse to other methodologies to explore more than simply population level variation. For example, his most recent post is Locating and visualizing minority non-European admixtures across our genomes:

Imagine, for example, a white American carrying a couple of tiny segments of West African origin, from an ancestor who lived 250 years ago, and an eastern Finn with no Asian ancestors in the last 4000 years or more. If we run an inter-continental ADMIXTURE analysis with these two, it’s very likely the American will score 100% European, while the eastern Finn will probably come out around 9% North and East Asian due to really old Uralic influence.

That sort of thing isn’t a huge problem when comparing the genetic structure of populations. Obviously, overall, eastern Finns rather than white Americans are genetically closer to North Asians, and that’s basically what ADMIXTURE picks up. However, if the focus is also on individuals, this certainly can become an issue. Our hypothetical American might be aware of that African ancestor, with solid paperwork backing up their genealogical connection, but he’s pulling his hair out because nothing’s showing up via genetic tests.

So let’s take a look at a real life example of how RHHcounter can pick up segments of potentially recent Sub-Saharan African origin…

euras1
Olivia Munn & Uyghur woman

The basic issue here is that in terms of genomic variation old admixture looks different from new admixture. Someone who is a first generation Eurasian, with a Chinese and European parent, may be about the same ancestral mix proportionally as a Uyghur. They would resemble a Uyghur on STRUCTURE and be placed within that cluster on a PCA chart (this is what happens in 23andMe). But, the Uyghur “Eastern” and “Western” genetic heritage has been reshuffled to a great extent by recombination over the past 1,000-2,000 years. In contrast, a first generation Eurasian will have huge swaths of their genome which are Eastern or Western on alternating strands (from their respective parents). In population genetic language a group of first generations hybrids would be exhibit a lot of linkage disequilibrium (LD). In a panmictic hybrid population LD will decay due to recombination, which breaks apart the distinctive allelic associations inherited from the parental populations.


This is the key to differentiating between the old “Asian” ancestry which sometimes falls out of the genetic variation of Finns at low frequencies, and more recent Asian ancestry. For example, the paleoanthropologist Vance Haynes is apparently a great-grandson of one of the original “Siamese Twins,” Chang Bunker. Chang Bunker was a Chinese Thai, so presumably Vance Haynes would come out to be ~10% Asian, and would be shifted toward the Asian cluster in relation to other Europeans. On the other hand, a closer look at his genome would indicate differences from a Turk who was ~10% Asian, because Vance Haynes’ Asian ancestry has only had three generations for recombination to break apart the original allelic associations which were passed down from Chang Bunker. After only these few generations the genome would still show many segments of clustered ancestry with distinctive sets of markers characteristic of Han Chinese.

Let’s make this more concrete. Below are two “ancestry paintings” from 23andMe. One is of a reference example, a Uyghur woman, and another is of a Eurasian individual. The difference is pretty obvious:

eurasianman

23andmeclusFor the record, 23andMe says that the Eurasian man is 50% Asian, 50% European. For the Uyghur woman, 52% European, 48% Asian. As I indicated above, Eurasian individuals who are projected onto the variation of the HGDP sample tend to cluster with the Uyghurs. In the image to the left the black mark indicates the Eurasian man. The Uyghurs are green. The purple rectangles are Hazaras.

But obviously this is a trivial example. What’s the point of sniffing around for non-European ancestry in individuals whose non-European ancestry is 1) visible, and 2) recent and immediate. No, a bigger question here are claims and suggestions by some white Americans that they have significant non-European ancestry. Usually this is Native American. But in the case of one of the European-origin samples which “Polako” (the principal behind the BGA Project) analyzed it seems there is a suggestion of West African ancestry.

dandonThis individual is Dr. Don Conrad of Genomes Unzipped. In particular, Polako found that there were two nearby segments on two chromosomes which exhibited a pattern of population atypical heterozygosity in Dr. Don Conrad’s genome. Look at chromosomes 7 and 13. Contrast the pattern with my distant paternal cousin, Dr. Daniel MacArthur. He also exhibits points of heterozygosity, but they’re randomly distributed across the genome. It’s old admixture or just noise.

Polako doesn’t make much of Dr. Don Conrad’s results, and neither do I (presumably as Dr. Don Conrad is a member of Genomes Unzipped it’s easy to talk about his results without any of the ethical or moral hassles about confidentiality). On the other hand, unlike Dr. Dan MacArthur, a little utilization of the powers of the interwebs indicates that Dr. Don Conrad is an American. In particular, of recent Midwestern background. Though I’m not a total creep, so I didn’t start poking around Ancestry.com. But after the Pickrell affair I am probably just a touch more hesitant to laugh off peculiar results from these sorts of analyses as simply algorithms-gone-meshugana.

Image Credit: Colegota

November 22, 2010

A positive rate of rate of change

Filed under: Netflix,Technology — Razib Khan @ 8:12 pm

A Cheaper Plan at Netflix Offers Films for Online Only:

Netflix said Monday that it was introducing a subscription plan for customers who want to watch movies only online, underscoring yet another step away from its roots in DVD rentals by mail.

The new plan offers unlimited access to Netflix’s library of streaming movies and TV shows for $8 a month. That is cheaper than virtually all of the company’s DVD plans.

I of course immediately downgraded; I haven’t received a physical DVD from Netflix since circa 2007 (it took me a year to return it because I forgot where I’d left it, and never watched it). But when I’m not feeling so well and can’t focus on anything cognitively challenging Netflix is very convenient. There are plenty of free alternatives on the net, but I’ll pay sub-$10 fees to save some time and headache.

But it does make me reflect on the rapid changes in the area of home entertainment since World War II. Video displaced 8 mm in the 1980s, but VCR’s themselves totally evaporated in the first half of the 2000s. Now the DVD format itself is being superseded, but the internet is replacing the hard copy mode of distribution in general for home film viewing. Netflix is already supposedly 20 percent of peak US traffic.

Also, I just realized that I don’t think I’ve been inside of a specialty “video store” since the early 2000s (most definitely from when I first subscribed to Netflix in late 2004). I have looked in the windows, and from what I can tell these stores are all-DVD format now, and it’s rather strange that I’ve never been inside of a “DVD store” even though I’ve passed so many of them over the years. Have you? Do they still rent video games as well?


Of interest around the web & elsewhere – November 22nd, 2010

Filed under: Blog,Daily Data Dump — Razib Khan @ 12:10 pm

Epilepsy’s Big, Fat Miracle. Two points to note: 1) modern medicine seems to have strongly resisted the ketogenic diet because of ideology, 2) this treatment works, but they don’t really understand why. It shows the importance of empiricism in medicine, but the reality that even an empirical discipline can be shifted by ideology.

Grumpy Kvetching of the Day. One of Sean Carroll’s readers complains about the content he’s posting up. If I ever get one of those blogs where my readers “sponsor” me, then I would listen to this sort of input. You paid for the privilege. Until then, shove it. Anyone who leaves a comment like that would be on my permanent “sh*t list.” I’m not really that disagreeable in person, but in person people rarely make demands on my own time as if such requests are the nature of things. Not so on the internet.

“Operation: Stop Palin” Gets Rolling. I was expecting this to happen some point soon, but my probability that the Republican establishment will be able to crush Sarah Palin is dropping from ~1.0, perhaps moving toward ~0.5. The main issue from what I tell is that the establishment is unlikely to be able to co-opt Mike Huckabee, who is the only other candidate on the horizon that could eat into her base.


Economics & Abstraction. Interesting exchange between Jim Manzi and Karl Smith. The great thing about economics compared to other “social sciences” is the reliance on a common formal language. The bad thing is that the formality hasn’t seemed to be able to remove all these verbal arguments on the margin of what everyone else means.

The most alpha occupations. Sex partners by occupation.

Why are boys’ brains bigger? But the subhead is: “Men cannot multi-task and women cannot read maps – is that a sexist nonsense or scientific fact?” The necessary way to talk about differences between groups today is to make sure that the “privileged group” comes off less flatteringly.

For Russia’s Poor, Blond Hair Is Snippet of Gold. A lot of the world’s wigs and hair extensions are re-purposed Chinese and Indian hair. But with Russians you don’t have to dye their hair necessarily. I believe there’s going to be a premium on that sort of thing because of the importance of authenticity. “Real Blonde HairTM.”

French Professors Find Life in U.S. Hard to Resist. Shocking number: “Of the 2,745 French citizens who obtained a doctorate in the United States from 1985 to 2008, 70 percent settled there, the study found.” It would be interesting to compare international students from various nations and see how many stay in the states and become permanent residents. I predict that the proportion of Chinese and Indian graduate students who remain after receiving their doctorates has been declining, but what about these European nations?

Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. I’m curious if the age at menarche is a quantitative trait. It would be interesting to do cross-species tests.

Ancient mtDNA from Sargat culture. I assume that ancient DNA is going to elucidate population flows in the Asian interior a lot in the coming years. The climate is cold and often dry, so ideal for a slower rate of degradation.

The Parental Non-Equivalence of Imprinting Control Regions during Mammalian Development and Evolution. “Our results support the notion that two independent evolutionary forces have led to the numerical and functional dominance of maternal ICRs: a selective advantage of parent-specific regulation of genes important for the fetal-maternal interface and pressure to avoid the mutagenic environment of the paternal germline.”

Second thoughts on Ireland. Sad. Revenge of Raymond Crotty?

Are We Hardwired to Love Taxes? The main reason I call myself a conservative and not a libertarian is that I believe humans are a communitarian species. This does not make me a social democrat, but it radically alters my normatively biased reflexes. Do note that I am talking about the average human. Myself, I’m still relatively detached from the community of man. I simply don’t confuse my own psychological biases for the average human.

Neanderthals Lived Fast, Died Young. Last paragraph: “Smith and her team, however, hint that forthcoming new studies reveal genetic and brain differences that existed between Neanderthals and members of our species, further heating up the scientific debate.” Someone clearly has inside information.

Vague Assertions of Copyright Infringement. The Financial Times claims you can’t quote any of their text. This sounds as dumb as the argument a few years ago that you’d need permission to link to some web sites. The irony is that these stupid copyright cultures simply mean that people will rewrite what other people say, and probably not give them credit as often. I’m not an anti-intellectual property absolutist, but over the years I’m moved more and more in that direction seeing how it hamstrings real creativity.

Deep Sea News. One of the finest “independent” science blogs out there.

Proofiness: The Dark Arts of Mathematical Deception. Haven’t read it yet, but seems kind of interesting. One datum the author divulged on the radio is that while men overestimate how many sex partners they have, and women underestimate, hooking them up to lie detectors suggests that women underestimate much more than men overestimate!

Strange Parallels: Volume 2, Mainland Mirrors: Europe, Japan, China, South Asia, and the Islands: Southeast Asia in Global Context, c.800-1830. Not a front-to-back read, but dense and extremely well worth it. Synthetic world histories with a scholarly focus are rare.

American Grace: How Religion Divides and Unites Us. I wish the book wasn’t so padded with vignettes. The core data is interesting though.

Less Wrong. If you love Heuristics & Biases you’ll find this weblog of interest. Also, if you’re a 17 year old nerdy virgin and feels isolated from your bestial classmates across the chasm of genuine sentience, you’ll find fellow travelers. You can actually increment the age up to 100 and substitute classmates for colleagues.

Researchers Kick-Start Ancient DNA.

Sleep Program Needed for IT Engineers. A study for this, really?

The flux of genes on the South Seas

Filed under: Genetic History,Genetics,Genomics,Melanesia,Oceania,Papua,Polynesia — Razib Khan @ 12:29 am

poly1
Huli Wigman from the Southern Highlands, Painting of Tahitian Women on the Beach by Paul Gauguin

ResearchBlogging.orgMany demographic models utilized in genetics are rather simple. Yet the expansion and retreat of various demes in post-Ice Age Europe seems to be far more complex than had previously been assumed, though I suspect part of the rationale for the original simplicity was a preference for theoretical parsimony in the face of a paucity of data. The landscapes traversed by our species are rich and topographically convoluted. Not only does the land vary, from plains, to deserts, to mountains, but the climate shifts radically over time and space. In the pre-modern age when humans were more dependent on environmental exigencies these fluxes in ecological and climatic parameters were essential in sharping the arc of human demographic expansion and contraction.

Oceanias_RegionsThis is why a closer examination of the prehistory of Oceania is so appealing: here you have a physical geography which is radically constrained and so reduces the degrees of freedom of human movement and habitation. Unlike Europe, South Asia, or much of Africa, the time depth of the residence of the current indigenous inhabitants of Australia is on the order of 40 – 50,000 years. It seems likely that the indigenous people of the island of New Guinea to the north are from the same original settlement of Sahul, the ancient super-continent which consisted of New Guinea, Australia, and Tasmania. After the initial sweep out to the farthest reaches of what became Tasmania, there was a later push to the east of New Guinea, to the Solomon Islands,~30,000 years before the present. Then nothing for tens of thousands of years. The march of humanity seemed to stand still on the shores of the Solomons, just as the hominin lineage had once been cordoned off from Sahul by the forbidding seas between it and Sundaland, the Ice Age peninsula of Southeast Asia which was later submerged and became the western portion of Indonesia and Malaysia. The stasis was shocked by the Austronesians, a seafaring peoples who seem to have exploded out from somewhere between Borneo and Taiwan within the last 10,000 years, likely just on the margins of written history. The most famous of th Austronesian peoples are the Polynesians, who pushed across the Pacific, and likely even had some tentative contact with the New World. A less well known case is Madagascar, whose inhabitants speak an Austronesian language with clear affinities to a dialect of Borneo. The map below shows rough distribution of Austronesian peoples:

800px-Langues-autronesiennes
Austronesian expansion

Of particular interest for the purposes of this post is the expanse to the east: Melanesia and Polynesia, Near Oceania and Far Oceania. A new paper in Current Biology , Demographic History of Oceania Inferred from Genome-wide Data, examines the genetics of this region of the world in light of history utilizing a ~1 million marker SNP-chip:

We developed a new approach to account for SNP ascertainment bias, used approximate Bayesian computation simulations to choose the best-fitting model of population history, and estimated demographic parameters. We find that the ancestors of Near Oceanians diverged from ancestral Eurasians 27 thousand years ago (kya), suggesting separate initial occupations of both territories. The genetic admixture in Polynesian history between East Asians (87%) and Near Oceanians (13%) occurred 3 kya, prior to the colonization of Polynesia. Fijians are of Polynesian (65%) and additional Near Oceanian (35%) ancestry not found in Polynesians, with this admixture occurring considerably after the initial settlement of Remote Oceania. Our data support a greater contribution of East Asian women than men in the admixture history of Remote Oceania and highlight population substructure in Polynesia and New Guinea.

Like Dienekes I think there’s something off with the dates they’re generating here. The archeology tells us New Guinea was settled by humans 15-20,000 years before this paper finds that they diverged from other Eurasians! We know that Aborigines are the closest to Papuans genetically, so if they separated from Eurasians less than 30,000 years ago, that would mean that the original inhabitants of Sahul were replaced after that period by the current groups. Far simpler I think to assume that something is off with their timing. Below are the primary figures, a frappe bar plot, PCA, and tree 7b which illustrates the most supported pattern of population branching and admixture.

There’s nothing too revolutionary in this paper. Rather, it seems to be an exploratory analysis of Oceanian genetics, a precursor to what may come soon. They can not, it seems, differentiate between the slow-boat and express-train models of the settlement of Polynesia, though the consistent pattern of Melanesian admixture seems to lean toward some form of slow-boat, because that is the theory which emphasizes a longer interaction with Melanesian populations.

800px-Area_of_Papuan_languages.svgI know I emphasized the relative simplicity of Oceania in relation to other parts of the world in terms of interpretation because of the geographical constraints, but even here there are layers and twists in the genetic and cultural bedrock. To the left is a map of the Papuan languages. From what I can tell Papuan languages are actually a negation of Austronesian and other well supported language families. The key is to notice that some parts of Near Oceania, Melanesia, have been shifted toward Austronesian languages, though New Guinea is a general exception to this pattern. Remember that humans did not move past the Solomons for ~30,000 years. Large scale settlement of Madagascar seems to have occurred only with the arrival of the Austronesians within the last 2,000 years (after a likely sojourn in East Africa!). This was a genuine cultural revolution which radically shifted the terrain of the possible. And yet by and large the Papuans resisted assimilation to the Austronesian cultural toolkit, which seems to have been otherwise so successful. Why? The Papuans were well equilibrated to their own local ecology, and the Austronesians had no comparative advantage. Rather, the Austronesians, in the form of the Polynesians, struck out into unknown waters and innovated. They found low hanging fruit by discovering trees which had been neglected.

The second interesting point is the bias toward Austronesian mtDNA, and substantial admixture on the Y lineages from Papuans even among Polynesians. The standard explanation of this is that the Austronesians had some aspect of matrilineal descent and matrilocality in terms of communal fission. I think that the Austronesians are arguably a perfect example of the leap-frog pattern of migration, and yet unlike most continental leap-frogs the genetic signal seems to be stronger on the female than male side. There is some evidence of the same in Madagascar. This indicates to me that the Austronesian maritime expansions were qualitatively different from continental leap-frogs, which often were based on the mobility of men on horses.

As I said, the picture remains broadly the same. But there are some touch ups and clarifications on the margins, and that is worthwhile. And definitely an appetizer for what is to come.

Citation: Wollstein A, Lao O, Becker C, Brauer S, Trent RJ, Nürnberg P, Stoneking M, & Kayser M (2010). Demographic History of Oceania Inferred from Genome-wide Data. Current biology : CB PMID: 21074440

Image Credit: Nomadtales, Wikimedia

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