Razib Khan One-stop-shopping for all of my content

July 31, 2010

Open Thread, July 31st, 2010

Filed under: Blog,Open Thread — Razib Khan @ 3:29 pm

The usual. Links, questions, etc.

July 30, 2010

Daily Data Dump – Friday

Filed under: Blog,Daily Data Dump — Razib Khan @ 12:02 pm

Have a good weekend.

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

‘Petite’ woman thrown off plane to make way for obese teenager who needed two seats. The source is a British tabloid, so take with a healthy dose of skepticism. But the general issue of obese people and airline flights is something that the obese and non-obese have to confront regularly. As a non-obese person I’ve had the discomfort of obese people using my own space as “overflow” to become more comfortable. The weirdest thing that has happened to me was on a trans-Atlantic flight where an obese man came and sat next to me in what had been an empty seat. Thirty minutes before the flight landed he went back to his seat, so I got up and saw where he’d come from, and it seems that he was sitting next to another obese person. It must have been uncomfortable for both of them, but still. Looking around there were a few other empty seats on the flight, but I was the slimmest person adjacent to any of them, so I strongly suspect that I was “targeted” for my co-passenger’s comfort. It must really be stressful to be obese on a long flight, but I really hate being penalized for being thin enough that I don’t “use” all my space.

The rich are different from you and me. One issue is that if there’s a huge wealth differential between two people there’s always the tension of the poorer person asking the wealthier one for money at some point. It makes wealthier people more guarded and less compassionate because they’re no longer in a plausible situation of reciprocity. They start seeing everyone as a utility maximizing rational actor trying to work an angle. Those with relatives in poor countries probably know what I’m getting at in terms of how fiscal imbalances distort personal relationships.

What Makes Humans Unique ?(III): Self-Domestication, Social Cognition, and Physical Cognition. Humans, the self-domesticated animal? Or perhaps some humans domesticated others?

Did emotions evolve to push others into cooperation? Rationality is bounded by emotion. Proximate individual behavior dictated by general intelligence is one dimension of humanity, but heuristics grounded in non-rational elements of cognition are evolutionarily informed and ecologically useful (or were).

Koreans, not quite the purest race?

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

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

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

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

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

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

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

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

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

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


And here’s a detailed breakdown of samples:


One point to note is that there seem to be some mixed-nationality individuals in the sample; Korean-Japanese, and Korean-Vietnamese. Here’s a MDS plot showing the relationship between the various East Asian groups:


And Structure (remember K = putative ancestral populations which contribute quanta to the genome of individuals):


I think it is important to note that their Chinese samples were all north Chinese; Beijing and Manchurian. Fujianese and Cantonese would span the Vietnamese and Chinese cluster. The outliers are probably due to the moderately cosmopolitan nature of the Beijing HapMap sample. The Han Chinese are less diverse than Europeans as a whole, but not inordinately so (using pairwise Fst’s a measure). There is an asymmetry when talking about China and any other East Asian nation because it is feasible that Han groups from various regions of China are more genetically similar to non-Han groups which are geographical neighbors. This is what L. L. Cavalli-Sforza found in History and Geography of Human Genes. The northern Chinese clustered with northern Asians, while the southern Chinese clustered with Southeast Asian groups. There have been conflicting results since that initial finding, but I think that points to the sensitivity of some of the inferences to the geographical and linguistic biases of sampling (different dialect groups in Guangdong may be very genetically distinct).

With all that said it’s pretty clear from the above figure that the Japanese and Korean samples are close enough that you need to zoom in on them specifically. So here you go:


KB_Japanese = Kobe Japanese. In the paper itself they’re testing a few historical hypotheses. So I’ll leave it to them for the interpretation:

The gene flow events of the three selected models for SW, MW and SE Korea can be assessed using the genome map. The populations in Model I (SW Korea) are closer to Mongolians than are the other two regions in the genome map (Fig. 2B). Historically, some of the loyal families and their subjects in the Goguryeo Empire moved to this region and formed the BaekJae Empire in BC18-22. This region also showed connections with populations in Tokyo (JPT), as illustrated in Fig. 4. Certain outliers in Model II (SE Korea) display some similarity to the people of Kobe, a port city near Osaka, indicating that there may have been links between the two regions. In addition, considering that the SE Korea region has some connections with Siberian lineages, with respect to grave patterns and culture, it is possible that the outliers in the GU and Kobe (KB) populations could be of Siberian lineage. On the other hand, the GR and US populations showed average signals in the Korean Peninsula. Historically, the Kaya Empire, with its southern lineages, was formed in the GR region and then the Shilla and Kaya Empires became united around AD532. Very recently, the US region became one of the rapidly developing regions, and people from other provinces moved to this region. This might explain why it shows an average signal in South Korea. Model III (MW Korea): the Middle West area formed a melting pot in the Korean Peninsula because populations moving from South to North, North to South, and from Eastern China, including the SanDung peninsula, to the Middle West in Korea all came together in this region. In the genome map, the signals for MW Korea are also close to those for Peking (CHB) in China. The overall result for the Korea-Japan-China genome map indicates that some signals for Mongolia and Siberia remain in SW Korea and SE Korea, respectively, while MW Korea displays an average signal for South Korea.

The connections between coastal southern Korea and the western islands of Japan are well known. It seems like that the Yayoi people, who probably contributed the preponderance of the ancestry of modern Japanese, arrived in Kyushu approximate ~2,500 years ago. And were originally a group within the Korean peninsula. Over the past 2,000 years Korea has gone through a process of ethnic-linguistic homogenization during the ethnogenesis of the modern Korean nation, but it seems possible that the original group(s) which gave rise to the Yayoi existed in southern Korea to facilitate contact between the islands and the peninsula into the historical era.

Citation: Jung J0, Kang H, Cho YS, Oh JH, & Ryu MH (2010). Gene Flow between the Korean Peninsula and Its Neighboring Countries PLoS ONE : 10.1371/journal.pone.0011855


Filed under: Blog,Katz — Razib Khan @ 10:54 am

(click image for larger view)

July 29, 2010

Finland, still going its own way

Filed under: Finland,Genetics — Razib Khan @ 11:16 pm

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


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

Reader survey results: politics

Filed under: Blog,Reader Survey — Razib Khan @ 10:38 pm

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

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

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


Median – 8
Mean -7.4
Standard Deviation – 2.48


Median – 5
Mean -5.01
Standard Deviation – 2.74

The correlation between social and economic liberalism was 0.37. Here is a chart which illustrates the different distributions:


I’ve smoothed a bit, but it’s clear that while there’s several modes in the economic liberalism distribution, there’s a strong liberal slant on social issues. Not that surprising. But I wanted to look at the combinations, so I created some bubble plots. The size of the circle is proportional to the weight of the particular political combination within the set (or subset).

First, the whole data set.


You see four quadrants. The plural majority of readers are liberal, followed by libertarians, then conservatives, then populists. Remove the centrists (those who selected 5 on either social or economic responses) and summing up the numbers in the quadrants, here are the percentages:

Liberals – 40%

Libertarian – 28%

Conservative – 11%

Populist – 3%

(the rest are in the borderline zones)

Now let’s look at the subsamples and how that impacts distribution.


Female readers tend to be more liberal.

I’ll just leave you with the rest of the bubble charts with minimal comment. But if you want to know something about the data, ask in the comments. Doing the analysis isn’t usually that hard, but I don’t know what people want to know (virgins are young, but not different than the rest of the readership).

ResearchBlogCast #11

Filed under: Blog,ResearchBlogCast — Razib Khan @ 12:07 pm

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

Daily Data Dump – Thursday

Filed under: Blog,Daily Data Dump — Razib Khan @ 8:19 am

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

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

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

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

Study says Amish expanding westward. Amish future!

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

The Anglo Revolutions

Filed under: History,Replenishing the Earth — Razib Khan @ 2:20 am

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

And yet one can go too far in emphasizing this component of 18th century America. One hundred years ago, in 1910, the Zeitgeist was very different from that of today. The American founding was seen as a project of the unfolding arc of evolution, the fruition of the genius of the Nordic race. In this reading America was a fundamentally white Protestant republic rooted in the supremacy and domination of the white race over the colored races. Again, this goes too far, and reframes the late 18th century American elite as proponents of a scientific view of racial competition which derives in part from a post-Origin of Species inflected perception of the nature of things, and the rising tide of white supremacy which peaked in the years after 1900 with the apogee of colonialism. Certainly the American founders would have been understood to be racist today, but as outlined in works such as What Hath God Wrought: The Transformation of America, 1815-1848, the reality is that an explicitly race-based republic crystallized in the first half the 19th century in North America with the rise of democratic populism. As states removed property qualifications for voting, they enacted racial bars which had not existed prior. It is an interesting comment on the complexity of changing norms in this period that Martin van Buren’s vice president, Richard Mentor Johnson, was known to have had a common-in-law wife who was mixed-race (and two daughters by her whom he acknowledged). Van Buren’s Democratic party was the primary driver of “white male suffrage,” which expanded voting rights to those males who were without means, but barred voting rights in many states from non-whites. It helped transform the self-conception of the American republic to that of the American democracy. These two dynamics, the broadening of suffrage to most American males, combined with a more explicit and legally sanctioned commitment to white supremacy, causes interpretive tensions for 20th century American liberal historians. This seems clear in works such as Arthur Schlesinger Jr.’s The Age of Jackson, which attempted to trace American liberalism back to this period. So it is somewhat uncomfortable for him that it was among some of the older aristocratic conservative Federalists that one could find objection to a binary republic where color was one’s passport to equality. This is not because the conservatives favored racial equality as such, but rather preferred a more complex hierarchy and a set of values which included race, class, education and breeding, as the judge of a man. Such old republic conservatives may not have accepted a black man as an equal on the grounds of race, but they may not have acceded to the contention that all white men were superior in nature to all black men. They would not have necessarily fallen under the class of whites which Malcolm X referred to in regards to their attitudes toward blacks with education. David Cannadine covers the same attitude on race among the British masses in Ornamentalism, but in this instance the aristocracy managed to retain more cultural influence, and race did not overwhelm class. The maharajahs of India may have been black, but they were still aristocrats who were of a particular elevated station which demanded respect, if not necessarily deference.

All this is to highlight the fact that we perceive of history is filtered through the light of our normative frameworks, and in the process we miss much of what once was. Modern perceptions of white American racism are so strong that I suspect Richard Mentor Johnson’s private life would surprise us. As would the fact that Herbert Hoover’s vice president was nearly half Native American in ancestry. This is the sort of thing which I refer to as the “dark matter” or “dark history,” dynamics and phenomena which echo down to our age, but are forgotten because of the presuppositions which we promote today because of ideological preferences.* In the context of the United States of America one of the most important and overlooked threads of dark history are the separate Anglo-Saxon streams of settlement in the American colonies prior to independence. As outlined in Albion’s Seed: Four British Folkways in America they were the Puritans of New England, the southwest British gentry and their retainers in the lowland South, the Scots-Irish in the American uplands, and finally, the polyglot mix of Midlanders and other Europeans in the Middle Colonies. The thesis is that these patterns can explain much of the details of American history after the Revolution, and down to the present day. I have suggested that differences between Mormon and Southern white political conservatism can be traced back to different attitudes toward communitarianism on the part of New Englanders and Southerners. Mormonism was at its root a Yankee religion, with most of its early acolytes and followers derived from New England or Greater New England (western New York and the Western Reserve of Ohio).

This sort of detail of distinction is lost in our discussion of American ethnicity. The idea that whites, or at least “non-ethnic” whites, “have no culture,” gets at the root of it. What is assumed, what is background, what is default, is not deemed worthy of history. When it comes to Anglo history and culture the commanding heights remain of interest, William Shakespeare, the King James Bible, the Magna Carta, etc. But much of the more mundane detail is of little general interest compared to the more salient identities of race, religion, and such. I believe this causes real pragmatic problems. White Angl0-Americans from the North may find Southern whites of an alien kind, lacking community spirit, belligerent, but they have no essentialist explanation which can explain this as a product of a different historical experience, because this aspect is not emphasized in our minds. But the greater propensity to violence by Southern whites was noted by Northerners as far back as the 1840 Census, where the data were fertile fields from which Northern polemicists drew in frame their attacks on the morals and character of the Southern states. Northern whites may seem to be liberals driven to bizarre and irrational flights of fancy to Southerners, but this is nothing new, as far back as the early 19th century Southern observers noted the Northern fascination with “-isms.” Many of the deep chasms in American history go far back indeed, and impact those of us whose families arrived far later. As a South Asian whose formative understanding of American history was derived from a Northern perspective, it is peculiar to talk to South Asians who grew up in the Deep South who have a more “nuanced” view of the Civil War (taking my hat off of objectivity, the descendants of those who arrived in the South after the Civil War, and are not black, do not always understand that the Southerners were traitors, and that the side wearing blue were the Good Guys).

But why be Americo-centric? We can widen the canvass out far more. America was not the only settler society. Canada, Australia and New Zealand were also settled by British. South Africa and the highlands of Kenya were also settled by the British. The differences and similarities between the British settler societies can tell us a great deal about the history of the English-speaking people, and therefore the history of the world up to this point. That is the subject matter of Replenishing the Earth: The Settler Revolution and the Rise of the Anglo-World, 1783-1939. This is a history of migration, of migrants, and of the rise of the Anglo-Saxon civilization. Numerically in 1780 there were 12 million English speakers. In 1930 there were 200 million! Obviously not all of that was due to demographic growth, but much of it was. In New England we know that the vast majority of the ancestry of the hundreds of thousands who were alive on the eve of the Revolutionary War were descended from the 20,000 or so who arrived in the 1630s. The fecundity of New Englanders was legendary in the 19th century, as they spilled out of the east and overran western New York, and later the Great Lakes region. This was the long boom of the Anglo peoples. But it was also the era of the busts. And it was the era of equilibriums.

The core thesis of Replenishing the Earth is that the rise of the Anglo societies has been characterized by a series of booms, busts, and often-times recoveries from those busts as regions and populations settle into a quiescent phase. In this the author, James Belich, suggests that the Anglo people prefigure the dynamics which are operative in the world today, the post-Malthusian reality of presumed & expected economic growth, of sunny futures, and a Whiggish sense of the possibilities of what could be ,what will be. He describes nothing less than a revolution of imagination, which subsequently drove the material changes we see around us.

A bigger context which hangs over this are debates about the economic lift-off (sometimes termed the “Industrial Revolution”) which has characterized much of the world over the past 200 years. The noncontroversial part is this: some societies over the last 200 years have developed to the point where they are not characterized by uniform subsistence, and have some level of mass affluence. Before 1800 no society had mass affluence, and all societies were Malthusian. Yes, wealthy people existed, but generally they lived off the labor and output of the productive masses, who managed to barely get by. In Replenishing the Earth the author notes that some economic historians believe that all of Europe as a whole engaged in this lift-off simultaneously, while others suggest that Britain was first, with Belgium second. He favors the idea that Britain was first, and that other European societies were later additions to the club of wealthy nations. Like Greg Clark in A Farewell to Alms James Belich indicates that there was something special about Britain, and England in particular, and like Clark he rejects purely institutional explanations. Additionally, he also seems skeptical of the idea that England’s position near North America (resources and land) along with its strategic coal reserves can be the total explanation for its lift-off. Though the description of the phenomena which led to the Anglo-world is crisp, a series of booms, busts and static phases in sequence, the root of the historical dynamic seems rather vague. The best I can come up with is that the English were the first society to reconceptualization the possibilities of the future, and engage in settlement activities which might seem irrational or foolhardy in the past.

The extent of the booms shocked even me, in part because I was only aware of the American experience. In Replenishing the Earth there is a distinction between incremental endogenous growth (e.g., New England in the 17th and 18th century), and explosive booms driven by exogenous migration (e.g., New England in the 1840s and 1850s). I had not thought in detail about the difference between these two, but the distinction is important in hindsight. One of the more surprising things to me about American history before the independence of the colonies and the emergence of the United States of America is that it was not always easy to draw migrants to the New World. Now, one might not be surprised during the initial decades, but throughout the 17th century the flow of migration was halting, and generally low. The massive burst into New England in the early 17th century was famously driven by religious conflict in England, as an anti-Puritan faction was ascendant. Much of the migration actually reversed with Oliver Cromwell’s victory, as many Puritans removed themselves back to the motherland, but enough remained to serve as the core of a growing set of colonies who slowly pushed themselves into the frontier through native population growth. The situation in Canada was famously more difficult, as attracting settlers was nearly impossible. Part of the reason was probably that unlike Great Britain the French banned the emigration of religious dissenters. The large enterprising French Protestant minority in the 17th century probably would have left for the New World if they had had liberty to do so, but settlement in Canada was limited to Roman Catholics. As it is, many French Protestants settled in the British colonies. Franklin Delano Roosevelt’s mother was from such a French Protestant family. They had settled in Calvinist New Netherlands early on.

After independence, and to a lesser extent in the decades before independence, many immigrants did come to the United States. But note how variant the numbers were by year.


Many of these variations correlate with economic booms & booms. But one of the most fascinating hypotheses proffered in Replenishing the Earth is that migration and population growth often preceded economic booms we read about. An example of this is the California Gold Rush. The author asserts that migration had already increased in the years before, and that the resource driven attraction only emerged after the initial stream had become established. It seems here that he’s positing a sort of positive feedback loop: more people results in more opportunities and perceived opportunities. In the case of asset speculative bubbles these gains may be illusory, but when it comes to concrete natural resources the increased population naturally has a better prospect of detecting or utilizing them. Once mines are discovered a chain reaction can occur whereby word gets back, and a massive wave of migration ensues. But even here quite often the migration will continue after resource exhaustion. California may have run out of gold, but its climate and population was such that other economic activities filled the vacuum. California firms raised fruit and created a demand for orange juice in the rest of the United States once transportation and preservation were up to snuff through a proactive marketing campaign.

It is here that the rise of an Anglo international order is critical. The colonies in North America, Australia, New Zealand, and lesser extent South Africa, were dependent on the mother to buffer them during the collapse, and support their faltering economies through export oriented growth. The United States was an empire in itself, so that California could look to New York and the east as its own motherland. There is a fair amount of economic literature that in reality colonies do not usually pay for the home country. Rather, quite often the colonials depend on the military power, and economic demand pull, of the motherland. Prominent colonial lobbies emerge and engage in an ideological, nationalistic, appeal to the tax-payers of the motherland. It is often said that much foreign aid today is a transfer from the middle classes of developed nations to the elites of developing nations, and in some ways this is analogous to what is argued for colonies. Speculators, promoters, and incipient elites are strongly invested in as much transfer of wealth from the mature motherland to the frontier. During the first age of globalization around 1900 the United States was a debtor nation which absorbed a great deal of cash from the United Kingdom. This illustrates that even despite the fact that the USA was no colony, ties and affinities of nationality, combined with the idea of explosive returns during boom times, attracted British investors. Apparently the econometric literature indicates that in fact British investors would have done better investing in the home country, rather than in the USA or the colonies.

In Replenishing the Earth the argument is repeatedly made that these national affinities, ramping up of pre-industrial technologies and industrialization, and a particular shift toward an expansive, dominionist ideology, all aligned together to produce an Anglo breakout.  Other nations had had extensive colonies, and even non-trivial settlement, such as Spain. But all had stabilized at a far lower, less explosive stationary state. It may be that England’s growth was a matter of happenstance, that the technological and ideological conditions were not ripe during the age of Spanish colonial expansion for them to transform their domains into anything more than a pre-modern empire, such as the Romans, Arabs, and Chinese had had. Incremental, ideologically dominant, but not explosive and revolutionary.

But revolutions come to ends. The most surprising fact I encountered in Replenishing the Earth was that in 1890 Melbourne was the second largest city in the British Empire, after London, with 500,000 people! This was at the peak of a massive speculative boom, right before a bust. Over the next 50 years Melbourne grew only another ~50% in population! During boom-times prognosticators asserted that Australia was destined to have 100 million by 1950. That New Zealand was destined to match the mother country in population within two generations. These hopes were dashed by reality. It seems clear that Australia had ecological limits which were reached, as agriculture could only be so productive in the Murray-Darling basin. Britain’s own demographic expansion abated, so it could no longer provide so many migrants. And so forth. Linear projections fail more often than not. The future is full of surprises.

For me one of the interesting points was reading about past manias and bubbles, engendered in part by more efficient information technology, expectations of constant future growth, etc. It is likely that much of the Replenishing the Earth was written years ago, but many of the English-speaking nations went through irrational property bubbles in the 2000s. The USA and Britain predictably shared home-related television shows. James Belich warns repeatedly about excessive reliance on rational choice theory, and the assumption that the market price is an accurate reflection of all information. History repeats itself over and over, the information is clear in the record, and yet human optimism overcomes. To some extent this optimism, Whiggish, may have been necessary to sustain the economic productivity growth. But in some sense it was profoundly irrational, as all of human history teaches that one can never escape the iron laws of natural constraint.** Once the first boom-bust cycle occurred, the pattern was set in motion. Fortunes were to be made and lost, and those who had relocated, migrated, and uprooted themselves, were far more likely to do so in the future, or inculcate in their offspring the ideology whereby such migration was acceptable, expected, and meritorious.

Finally, the rapid change, and the stasis, in culture, economics and political order, makes me thinl of biological analogs, in particular evolutionary ones. We hold it as a matter of faith that nature is real, that in some sense the laws of the cosmos are bound as one, with each specific instantiation a reflection of some underlying principle. The peculiar similarities which a macroeconomist may feel when reading R. A. Fisher’s The Genetical Theory of Natural Selection is one case. The rise and fall of frontiers, with epidemics of manias, the cycles of enthusiasm, migration, and population growth, remind one of the shape of Lotka-Volterra equation. Replenishing the Earth may be a dense work of economic and cultural history, but in some very important ways it gives us a window into general phenomena which percolate through the order of things.

* Here’s a case of inversion: in the early 20th century ideologues turned the roots of all civilizations into examples of Aryan/Nordic superiority. Today from what I can tell the mainstream sentiment is to not comment or inquire too deeply into the Afrocentrist fiction that St. Augustine, Hannibal or Cleopatra were black. A fiction which from what I can tell has spread widely within the African American community. How the pendulum has swung!

** I understand that some readers feel we are facing those laws now, fair enough. The point is that much of humanity had nearly a 200 year respite, which is not trivial.

July 28, 2010

Daily Data Dump – Wednesday

Filed under: Blog,Daily Data Dump — Razib Khan @ 10:02 am

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

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

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

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

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

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

Investing in a nanny state for social returns

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

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


Intuitively we understand this. Through experience we know of this. There are individuals with high intellectual aptitudes who lack self-control. Who do not succeed in life because of poor life choices. There are individuals with mediocre intellectual aptitudes who achieve a certain amount of comfort and prestige in their life because of their rock solid focus on their goals. By analogy an old under-powered computer with Ubuntu installed on it running Open Office will still perform at a higher level in achieving productivity goals than a high-powered computer which is loaded with Windows riddled with spyware and mostly running games which require a lot of computational muscle power beyond the specs of the box.

My main question is one of interpretation: is the change in non-cognitive skill portfolio due to intervention at a “critical period” in a neurobiological sense? The authors make explicit analogy to language. If children are exposed to a language before the age of 12 they generally can learn and speak it without an accent with marginal effort. Severely abused, or in rarer cases “feral children,” who are not exposed to language at all in their formative years, may remain unable to speak fluently in any language for the rest of their years after recontact with mainstream society. This is likely a function of the biological aspect of language acquisition and learning. Or at least that is the contemporary consensus.

Does this apply to non-cognitive skills? I am moderately skeptical, though my attitude here is provisional at best. Through the pre-prints the authors take a methodological individualistic perspective. Individuals invest in their skills, and the earlier they invest in their skills the more positive feedback loops can emerge so that their skills can mature, extend and sharpen. There’s clearly something to this. But the focus on family environment and such in the paper makes me a touch skeptical. There is a large behavior genetic literature which suggests that family environment, “shared environment,” is not very predictive of long term outcomes. Rather, “non-shared environment” explained about 1/2 of the outcomes for many behavioral traits (the balance is genetic variation).

In The Nurture Assumption Judith Rich Harris argued that the non-shared environment really referred to peer groups. Again, the analogy to language is illustrative. Children do not speak with the accent of their parents, they speak with the accent of their peer groups. There is an exception to this: autistic children (or, children who consciously want to have a particular affect). Though I was not explicit, this is the sort of dynamic I was indicating when I suggested that culture matters in saving. Different cultures have different norms, values, and frameworks in which you can express your personality predispositions. In genetic terminology I’m talking about a norm of reaction.

Quickly skimming through the original paper which Jonah Lehrer’s post was based on (and skipping over the guts of the economic modeling) I was unclear if there was a long-term peer group effect, as they didn’t seem to explore this possibility. Perhaps instead of a critical period in a neurobiological sense, what we’re seeing here is the emergence of specific peer groups which reinforce and buffer individuals in decision making and goal setting? Perhaps the original intervention resulted in the emergence of a new subculture within the low SES black community of Ypsilanti, Michigan?

Life outcomes can vary a great deal based simply on social norms.


In terms of the bottom line this may not change the policy conclusion that much. The operational outcome of a given policy may be the same even if the means by which the outcomes are realized differ. That being said, I probably does matter on the margins if the effect is due to individual level biological changes vs. group level norm shifts when it comes to details of policy formation.

Image Credit: CDC

July 27, 2010

Daily Data Dump – Tuesday

Filed under: Blog,Daily Data Dump — Razib Khan @ 3:31 pm

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

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

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

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

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

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

Summer books, what’s readable?

Filed under: Blog,Books — Razib Khan @ 2:08 pm

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

So what are you reading? What would you recommend? Over the years I’ve noticed I don’t read much science in book form; I much prefer papers. But since I don’t read physics or chemistry papers that means I haven’t recharged my familiarity, at least on a superficial level, with these fields in years. So I plan to a hit a few popular physics books at some point summer. And I’m always up for economics, world history, international affairs, cognitive psychology, etc.* I suspect I’ll avoid fiction until George R. R. Martin gets his next book out, but that might mean I’ll avoid fiction for a long time.

* In my short-term stack The Sea Kingdoms: The Story of Celtic Britain and Ireland, Lives of Confucius: Civilization’s Greatest Sage Through the Ages, Superfusion: How China and America Became One Economy and Why the World’s Prosperity Depends on It and The Invisible Gorilla: And Other Ways Our Intuitions Deceive Us. In my medium-term “must-read” queue, How Pleasure Works: The New Science of Why We Like What We Like and Shall the Religious Inherit the Earth?: Demography and Politics in the Twenty-First Century.

Snap, phenotype, genotype and fitness

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

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

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

A major conundrum in biology is why hybrids between species display two opposing features. On the one hand, hybrids are often more vigorous or productive than their parents, a phenomenon called hybrid vigor or hybrid superiority. On the other hand they often show reduced vigour and fertility, known as hybrid inferiority. Various theories have been proposed to account for these two aspects of hybrid performance, yet we still lack a coherent account of how these conflicting characteristics arise. To address this issue, we looked at the role that variation in gene expression between parental species may play. By measuring this variation and its effect on phenotype, we show that expression for specific genes may be free to vary during evolution within particular bounds. Although such variation may have little phenotypic effect when each locus is considered individually, the collective effect of variation across multiple genes may become highly significant. Using arguments from theoretical population genetics we show how these effects might lead to both hybrid superiority and inferiority, providing fresh insights into the age-old problem of hybrid performance.

There are various ways one presumes that hybrid vigor could emerge. One the one hand the parental lines may be a bit too inbred and therefore have a heavier than ideal load of deleterious alleles which express recessively. Since two lineages will likely have different deleterious alleles, crossing them will result in immediate complementation and masking of the deleterious alleles in heterozygote state. Another model is that two different alleles when combined in heterozygote state have a synergistic fitness effect. We generally know of heterozygote advantage in cases where there’s balancing selection, so that one of the homozygotes is actually far less fit than the other, but the fitness of the heterozygote is superior to both homozygotes. But that is not a necessity, and presumably there could be cases where both homozygotes are of equal fitness, but the heterozygote is of marginally greater fitness.

As for hybrid inferiority, a simple model for that is that lineages have co-adapted complexes of genes which are enmeshed in gene-gene networks. These networks are finely tuned by evolution and introduction of novel alleles from alien lineages may lead in destabilization of the sensitive web of interconnections. This model taken to an extreme is a scenario whereby speciation could occur if two lineages become mutually exclusive on a particular genetic complex which is “mission critical” to biological machinery (imagine that the gene involved in spermatogenesis is effected).

These stories are fine as it goes, but they do have something of an excessively ad hoc aspect. A little light on formalization and heavy on exposition. In this paper the authors aim to fix that problem. To explore genetic interactions in hybrids, and how they effect gene expression, they selected the genus Antirrhinum as their model. These are also known as “snapdragons.” Like many plants Antirrhinum species can hybridize rather easily across species barriers. They observe the effect of taking genes from a set of species and placing them in the genetic background of another. In particular they are focusing on A. majus, hybridizing it with a variety of other Antirrhinum species, as well as introgressing alleles from the other species onto a A. majus genetic background (so an allele on a specific gene is placed within the genome of A. majus).

Just as they focus on a specific genus of organism, so they also focus on a specific set of genes and the molecular and developmental genetic phenomenon associated with those genes. The genes are CYC and RAD, which are located near each other genomically, with CYC being a cis-acting regulator of RAD. In other words, CYC modulates the expression of RAD which is on the same chromosome.  Variance in gene expression simply defines the concrete difference in levels of protein product. Mutant variants of CYC and RAD, cyc and rad, are created by insertion of transposons. Insertion of transposons can abolish gene expression, resulting in removal or alteration of function. What is that function? I’m rather weak on botanical morphology, so I’m going to be cursory on this particular issue lest a reader correct me strenuously for misapplication of terminology. So I’ll show you a figure:


I added the labels. C is basically what majus should look like, while G is a totally “ventralized” mutant. B and F approach wild type, but the other outcomes are more mixed. Note the genotypes in the small print. Table 1 measures the expression levels of the gene product for the various genotype:

journal.pbio.1000429.t001 (1)

Look at the first row; mutant variants of CYC which are nonfunctional reduce normal copies of RAD down to 20% levels of gene expression. That’s because CYC is a transcriptional regulator of RAD. The process is not reversed. RAD lacking functionality does not impact CYC (last row). Finally, the heterozygote states does result in reduced dosage of the gene product. Though the phenotypes might be closer to wild type than the mutant, the molecular expression of the gene is substantially changed. This is one of the issues which is always important to remember: the extent of dominance exhibited by a sequence of phenotypes consequent from a particular genotype may vary dependent on which phenotype you are a highlighting. On a molecular level there is incomplete dominance. Additive effects. On the level of exterior morphology there is more perceived dominance. This is not even addressing the issue of pleiotropy, where the same gene may have dominant and recessive expression on two different traits simultaneously in inverted directions (i.e., the recessively expressed allele in trait A may be dominant in B, and vice versa).

Figure 1 shows the different allelic expression levels in hybrids of Antirrhinum species. But what about the impact of the combinations on phenotype? I’ve reedited figure 4 so it fits better on this page:


July 26, 2010

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

Filed under: Culture,Economics,History,Linguistics — Razib Khan @ 2:51 pm

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

From Wikipedia:

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

The origins of Indonesia are complex. Though the islands of maritime Southeast Asia were long part of the Dutch “sphere of influence,” true direct rule came to much of the archipelago only in the early 20th century. Before that local identities were paramount, whether it be Javanese, the various ethnic groups in Sumatra or Sulawesi, and of course the culturally more distinctive peoples to the east on the island of New Guinea (the pre-modern precedent for an Indonesian state is Majapahit, but like the Dutch colonial empire for most of its history, Majapahit directly controlled and influenced only a small proportion of the archipelago).

I think the complexities and peculiarities of Indonesian history before the rise of the nation-state can be illustrated by Blambangan in eastern Java. This kingdom was deeply influenced by, and to a large extent a cultural satellite of, Bali. As such it was the last major Hindu polity within Java in the 18th century (though isolated communities managed to avoid Islamicization, all Javanese political entities had switched to Islam as their state religion except Blambangan). The VOC, the Dutch East India Company, participated and encouraged what was notionally religious war, a jihad against Blamgangan. The Dutch collusion with Muslim religious enthusiasm was purely a matter of self-interest, as the rulers of Bali were major impediments to VOC hegemony. With the fall of Blamgangan this last region of Java was subject to Islamicization and most of the population converted.

The point of recounting this episode is to show that prior to the construction of Indonesian identity after World War II the ties which bound the archipelago together were very loose. Some regions, such as Aceh, had been Muslim for nearly one thousand years. Java, the demographic and cultural heart of the archipelago had switched to Islam far more recently, and retains a strong pre-Islamic stamp to its culture (e.g., Hindu epics remain popular in Java, while the Javanese elite has not repudiated its own mystical tradition which pre-dates Hinduism and Islam). And finally, the eastern islands were only marginally influenced by the Indian and Islamic trends which were prominent in more populous western islands, and their population converted to Christianity during the colonial period. Many Ambonese, who feared Javanese Muslim hegemony in Indonesia because of their support for Dutch rule were relocated to the Netherlands.

Abstract principles such as Pancasila and concrete policies such as the promotion of Bahasa Indonesian, which was already an interregional lingua franca analogous to Swahili, were seen as critical to cementing national cohesion. Despite the national motto of Indonesia, loosely translated as “unity in diversity”, the post-World War II period has seen the spread of a unifying national language, and a deeper connection among many of the nation’s Muslims with international-normative Islam. The rise of santri Islam as Islam qua Islam in Indonesia, and the decline of local Muslim traditions which are strongly inflected by Dharmic and indigenous religious influences, is part of the cultural revolution in uniform manners.

Indonesia’s conundrum is simply a more extensive and contemporary manifestation of what many European nations faced centuries ago. When France was declared a republic some estimate that only 1/3 of the citizens spoke standard French. The proportions of Italians and Germans who spoke the standard national languages may have been even smaller (in the case of Italy I have seen estimates of less than five percent speaking Italian at the founding of the Italian nation-state!). The period of the Wars of Religion in the 17th century may have pushed theological motivations to the back-seat in the game of kings, but it is important to note that religious homogeneity increased due to the migrations compelled by the conflicts, as well as subsequent expulsions in France, and persistent legal and social disabilities for Roman Catholics in England. The emergence of Germany in its modern form, which did not include the Austrian domains, was driven in part by considerations of religious and ethnic homogeneity (the Austrian lands included many more Magyars and Slavs, and would have resulted in Catholic demographic majority, as opposed to a overwhelming Protestant dominance in the Prussian-dominated “Little German” state).

In A Study of History Arnold Toynbee introduced the concept of “still-born” civilizations. The Christianity of the Church of the East, which grew out of the Christianity of the Sassanid Empire, is a perfect illustration of the type. On the eve of the Islamic conquest of Persia there was a vibrant Christian community, which in some ways was engaged in a rivalry with the Zoroastrian state religion. It had pushed beyond the frontiers into Central Asia, to the point where it managed to persist even after the collapse of the Sassanids in the face of the Arab conquests. In the early 13th century many of the Turkic and Mongol tribes of Central Asia were Christians in the tradition of the Church of the East, including one of Genghis Khan’s daughter-in-laws (the mother of Kublai and Hulagu Khan). But this Christian tradition never gained the prominence, the embeddedness within steppe society, to become a religious monopoly and spread its wings with the rise of the Mongol Empire. Though many of the Mongols were sympathetic to Christianity, none of the great leaders died as Christians (though some were baptized at some point in their life), and the Mongol Empire was religiously pluralistic. Without this state support Eastern Christianity did not bloom, and became a minority sect in the lands of Islam and South India, fading away in Central Asia and China after the decline of the first Mongol Empire.

With the rise of the idea of the nation-state, modern communication, and the models of European states in their generation of cohesion via both top-down and bottom-up processes, you are seeing I suspect both the flowering and still-birth of new national complexes bound together by common language. Both India and Pakistan have attempted to forge a national unity with a South Asian language, overlain atop the preexistent diversity. Pakistan privileged Urdu, the traditional language of upper class Muslims throughout the subcontinent, as well as the day to day language of the Muslim population of the Gangetic plain excluding Bengal. At independence only a small minority of the population of the state spoke Urdu as their native tongue, but while in the western provinces there was acceptance of the necessity of Urdu as a link language, in the east Bengalis objected, and the rejection of Urdu became one of the symbolic aspects of conflict which led to the emergence of Bangladesh.* India has not had the same faction due to language, but standard Hindi plays the same role that Urdu does in modern Pakistan. And yet over 60 years since independence English remains commonly used as an elite language among a segment of the upper classes. Hindi is not understood in much of southern India, but since this region is demographically inferior to the north, as opposed to Bengal, which was demographically superior to West Pakistan, the tensions are not of the same magnitude. Additionally, English serves as a prestigious alternative lingua franca for Indians with a weak or nonexistent command of Hindi. Over the long term Hindi may suffer the same fate of Nahuatl and Quechua after the Spanish conquest. Because of the superior communication technologies, as well as the more persistent and powerful integrative institutions introduced by the Spaniards, the language of the fallen pre-Columbian empires actually spread in the centuries leading up the independence of Mexico and Peru from Spain, at the expense of local languages. Only in the modern period has Spanish started to marginalize the elite native languages.  Why the change? In The Rule of Empires the author notes that the Peruvian highlands in the centuries after the Spanish conquest was dominated by a local indigenous elite who served as intermediaries between the authorities of the Crown based out of Lima and the vast Andean peasantry.  With the rise of international trade, the collapse of the Spanish Empire and greater national integration, and globalization writ large, the power and attraction of such sub-national elite identities faded. Quechua or Nahuatl may have been lingua francas in segments of the Spanish Empire, but Spanish opens up much more of the world to aspirants for status, power and wealth.

It is cliche today to say that the “world is flat,” and that globalization is inevitable. There was famously another period of globalization before World War I, and it took 50 years after its collapse for the engine of international integration to slowly start up. But assuming that globalization and an international political economy is inevitable I wonder as to number of languages which we will stabilize at. Consider religion. Since the rise of Islam there really hasn’t been another great international religious revolution which has given rise to a global civilization. The fracturing of Western Christianity into Protestant and Roman Catholic domains are the closest analog, but do not rise up to the same level of impact (the shattering of the Western Christian commonwealth with the rise of Protestantism was healed in large part by the marginalization of religion in the public realm after the Enlightenment and the acceptance by most Christian groups that religious monopolies enforced by the state were no longer feasible or moral). There are really only four religions of civilizational import, Islam, Christianity, Hinduism, and Buddhism (Judaism is culturally influential, but there is only one Jewish nation, so no Jewish bloc could emerge). Why so few religions, and why such religious homogeneity so early in relation to language? I think this is because world religions are the concern of elites, whose numbers are small, and whose information networks were much more globalized in the pre-modern era than that of the masses. A “republic of letters”, or peregrinations of men such as Ibn Battuta, are only relevant for tiny elites in a pre-modern era because of economic constraints. No longer today; every man is a potential prince of letters with mass literacy and the internet. If the international dynamics which were long operative with world religions are now operative with languages, then will we see the world winnowing down to half a dozen languages? Right now linguistic diversity experts the focus on the small-scale societies and micro-languages hovering at the point of extinction, but over the next century much of the change might occur in the “middle-weight” category. Languages which rose to prominence in the era before globalization as regionally prominent mediums, but which lack comparative advantage set next to global languages. Bahasa Indonesian for many families is a new language, of only the past few generations, so its sentimental value should be relatively shallow. It is a utility, and when a newer utility offers superior services for a cheaper price, why not switch? Well, sometimes the government imposes monopolies and shields native firms. So we’ll see.

* My parents grew up in the united Pakistan, and do recount the imperiousness of Urdu speakers in Bengal during that period. For example, Urdu speakers would demand the best positions on a buses, and berate drivers in Urdu (who likely did not have a good grasp of what they were saying) when their demands were not met. Though both know Urdu, I definitely get a sense that their experiences during this period left them with little sympathy for the idea that Urdu should be the common language of South Asian Muslims.

Daily Data Dump – Monday

Filed under: Blog,Daily Data Dump — Razib Khan @ 11:33 am

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

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

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

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

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

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

Saving is heritable, but culture matters a lot

Filed under: Behavior Finance,Behavior Genetics,Finance — Razib Khan @ 9:58 am

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

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

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

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


That’s the median savings rate in the USA.

There’s not enough time to explain this sort of volatility as the result of changes in gene frequencies. Some of the trends, as the recent increase in savings, have easy contextual explanations. The point is that individual dispositions express themselves within an environmental context, and culture is such an environment. This is why we have to be careful about the high heritabilities of obesity. Your genes may indicate how high your masts are going to be in the flotilla, but the rising and falling of the tide are going to have a huge absolute impact on the position of the whole constellation of ships.

Image Credit: Wikimedia

A Replicated Typo empire

Filed under: Uncategorized — Razib Khan @ 8:44 am

Just want to note that GNXP contributor bayes has transformed A Replicated Typo into a fascinating group weblog. Feed here.


Diseases of the Silk Road

Filed under: Disease,Genetics,genome-wide association,Genomics,GWA,Health — Razib Khan @ 7:42 am

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

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

Behçet’s disease is a chronic systemic inflammatory disorder characterized by four major manifestations: recurrent ocular symptoms, oral and genital ulcers and skin lesions1. We conducted a genome-wide association study in a Japanese cohort including 612 individuals with Behçet’s disease and 740 unaffected individuals (controls). We identified two suggestive associations on chromosomes 1p31.3 (IL23R-IL12RB2, rs12119179, P = 2.7 × 10−8) and 1q32.1 (IL10, rs1554286, P = 8.0 × 10−8). A meta-analysis of these two loci with results from additional Turkish and Korean cohorts showed genome-wide significant associations (rs1495965 in IL23R-IL12RB2, P = 1.9 × 10−11, odds ratio = 1.35; rs1800871 in IL10, P = 1.0 × 10−14, odds ratio = 1.45).

And, Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with Behçet’s disease:

Behçet’s disease is a genetically complex disease of unknown etiology characterized by recurrent inflammatory attacks affecting the orogenital mucosa, eyes and skin. We performed a genome-wide association study with 311,459 SNPs in 1,215 individuals with Behçet’s disease (cases) and 1,278 healthy controls from Turkey. We confirmed the known association of Behçet’s disease with HLA-B*51 and identified a second, independent association within the MHC Class I region. We also identified an association at IL10 (rs1518111, P = 1.88 × 10−8). Using a meta-analysis with an additional five cohorts from Turkey, the Middle East, Europe and Asia, comprising a total of 2,430 cases and 2,660 controls, we identified associations at IL10 (rs1518111, P = 3.54 × 10−18, odds ratio = 1.45, 95% CI 1.34–1.58) and the IL23R-IL12RB2 locus (rs924080, P = 6.69 × 10−9, OR = 1.28, 95% CI 1.18–1.39). The disease-associated IL10 variant (the rs1518111 A allele) was associated with diminished mRNA expression and low protein production.

Observe that the SNPs differ between the two studies. Here are the tables which show the SNPs, their odds ratios and statistical significance for the first and second paper respectively.



In the second paper they actually did an analysis of the effect of the disease associated allele at one of the SNPs, rs1518111. The A allele is disease associated.


Finally, the last paragraphs to the two papers:

We report here a GWAS identifying two new susceptibility loci for Behçet’s disease; these loci include interleukin and interleukin receptor genes, which are central in immune response. The quantitative alteration of these cytokines (and others in the same cascade) could help explain in part the complex pathophysiology of Behçet’s disease and suggest new therapeutic avenues.


In summary, we report a GWAS and meta-analysis identifying common variants in IL10 and at the IL23R-IL12RB2 locus that predispose to Behçet’s disease. Our study also supports the association of HLA-B*51 as the primary association to Behçet’s disease within the MHC region and reveals another independent MHC Class I association telomeric to HLA-B. Expression studies indicate that the disease-associated IL10 variants are associated with decreased expression of this anti-inflammatory cytokine. This may suggest a mechanism, possibly in concert with commensal microorganismsthat results in an inflammation-prone state that increases susceptibility to Behçet’s disease.

The relationship to commensal microorganisms may be pointing to a major reason why the frequency of the illness seems to decrease as one moves north. This could be a case where genetically susceptibilities toward expression of the illness interact with environmental factors. One could imagine, for example, that the harsh cold and light population of Inner Asia may have incubated particular susceptibilities which never manifested themselves because of the environment. But with the shift toward the denser and moister climes of western and eastern Eurasia the combination of genes and environment resulted in the emergence of the disease.

With that said, again, I’m curious as to the nature of the SNPs, and the phylogenetics of the disease causing mutations. Do they derive from common mutants? Implying then that common ancestry via the Silk Road was critical. If the genetic variation around the mutants implies common descent then the Silk Road may have been critical in the spread of the risk alleles, but it would still be an open question whether they flowed from east to west or west to east, contingent on patterns of genetic variation. Or, are they independent mutations? Perhaps they’re side effects of adaptations?

Citation: Remmers EF, Cosan F, Kirino Y, Ombrello MJ, Abaci N, Satorius C, Le JM, Yang B, Korman BD, Cakiris A, Aglar O, Emrence Z, Azakli H, Ustek D, Tugal-Tutkun I, Akman-Demir G, Chen W, Amos CI, Dizon MB, Kose AA, Azizlerli G, Erer B, Brand OJ, Kaklamani VG, Kaklamanis P, Ben-Chetrit E, Stanford M, Fortune F, Ghabra M, Ollier WE, Cho YH, Bang D, O’Shea J, Wallace GR, Gadina M, Kastner DL, & Gül A (2010). Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with Behçet’s disease. Nature genetics PMID: 20622878

Citation: Mizuki N, Meguro A, Ota M, Ohno S, Shiota T, Kawagoe T, Ito N, Kera J, Okada E, Yatsu K, Song YW, Lee EB, Kitaichi N, Namba K, Horie Y, Takeno M, Sugita S, Mochizuki M, Bahram S, Ishigatsubo Y, & Inoko H (2010). Genome-wide association studies identify IL23R-IL12RB2 and IL10 as Behçet’s disease susceptibility loci. Nature genetics PMID: 20622879

Reader Survey, summer 2010

Filed under: Blog,Survey — Razib Khan @ 2:51 am

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

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

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

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

Female Male
How long have been reading Gene Expression(s) regularly?
No more than 4 weeks 9 3
1 to 6 months 19 12
6 months to 12 months 14 12
1 to 2 years 16 26
2 to 4 years 29 27
More than 4 years 13 21
What is your highest educational level attained?
Did not complete secondary school 1 1
Secondary school 0 1
Some post-secondary education, incomplete 6 8
Post secondary education, but not a university degree holder 9 8
University degree holder 32 31
Masters degree 18 18
Professional graduate degree (law, medicine, etc.) 6 12
Graduate degree (science, humanities, etc.) 28 21
What is your subjective socioeconomic status?
Lower class 1 5
Lower middle class 15 14
Middle class 54 43
Upper middle class 28 33
Upper class 1 5
What is your belief about the nature of God?
I believe in theistic God(s) 14 10
I believe in deistic God(s) 6 5
I believe in a Higher Power 8 6
I am skeptical of the existence of God(s) 14 24
I do not believe in the existence of God(s) 58 55
What is your racial identity?
European ancestry (white) 70 85
East Asian 2 2
South Asian 4 4
Southeast Asian 3 1
African ancestry (black) 1 1
Middle Eastern 4 2
Mixed 8 4
Other 8 2
Which of the following characterizes your general politics:
Far Left 4 3
Left 30 12
Center Left 19 18
Center 10 5
Center Right 11 11
Right 6 16
Far Right 1 4
Libertarian 16 25
Other 1 5
Do you consider yourself sympathetic to transhumanism?
No 28 38
Yes 19 16
No idea 18 19
Don’t care 35 27
Have you ever had sexual intercourse?
Yes 91 85
No 6 13
? 3 1
Personality type in terms of shyness you are:
Very extroverted 0 1
Extroverted 6 7
Somewhat extroverted 15 18
Somewhat introverted 48 39
Introverted 28 27
Very Introverted 3 8
Attitudes toward abortion:
Support abortion rights on demand 49 40
Support abortion rights, but with some constraints 37 43
Support ban on abortion, but with some exceptions 6 13
Support ban on abortion 8 4
Have you taken calculus?
Yes 82 82
No 18 18
Race is:
A social construct, not a biological reality 18 9
A biological reality, not a social construct 9 20
Both a social construct and a biological reality 73 72
IQ measures:
Something real which we refer to as intelligence 32 67
Ability to take a particular type of test 44 19
Who knows? 24 14
What is the heritability of IQ among groups in the West which are middle class and above?
Less than 0.3 6 4
0.3 to 0.5 23 19
0.5 to 0.7 43 47
More than 0.7 29 30
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