One New World population expansion

Haplotypic Background of a Private Allele at High Frequency in the Americas:

Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across 500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the “American Modal Haplotype” (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas.

Some elaboration in ScienceDaily of the logic:

Read More

Secular Cycles of the human animal

Quantitative ecologist Peter Turchin’s Secular Cycles is not available for purchase, but you can get a final draft copy online. His previous books, War and Peace and War: The Life Cycles of Imperial Nations & Historical Dynamics: Why States Rise and Fall, prefigure many of the arguments that are fleshed out in Secular Cycles. Turchin’s aim is audacious. The last paragraph of Secular Cycles lays out the vision:

Our concluding thoughts are these. We believe that we showed that it is possible to obtain quantitative empirical estimates for many variables that are needed to test theories of historical dynamics. Furthermore, our models, and the demographic-structural theory in particular, have matured to the point where they can make quantitative and testable predictions. Many of these predictions are supported by the data; others failed, but often in interesting ways that suggest further development of the theory. The historical process is very complex, we have to live with severe data limitations, but nevertheless it is possible to apply the standard scientific approach to the study of history. We are optimistic about the future prospects of History as Science.

If history is any guide Turchin’s optimism is misplaced, and a general theory of historical dynamics will elude us. But the nature of science is that it is exhibits a strong ahistorical* bent and the past can be a weak guide to the future.  If cliodynamics emerges as a respectable field we would expect it to overturn precedent. As someone trained in the former Soviet Union it should be  no surprise I suppose that Turchin would be the one making an attempt to resurrect theoretical history in the English speaking world. An intellectual who was shaped by a Marxist Zeitgeist would be more easily inclined to consider the possibility that history could be formalized so as to produce systems of non-trivial inferential power.

So what makes this latest effort different from the speculations of Arnold Toynbee and Oswald Spengler? First, as a biological scientist Turchin comes the table with a methodological toolkit which is far superior in precision to that available to historians of the early 20th century. From game theory to systems ecology there are many new formal frameworks which can be brought to bear upon human historical dynamics which were not extant in earlier epochs. Secondly, the data sets are far more extensive than they once were due to the prominence of cliometrics, as well as the greater power of traditional fields such as archaeology due to improvements in method. Finally, Turchin’s ambition is constrained to the pre-modern era when Malthusian parameters were ascendant. This is not to say that I do not think that some of his inferences and conjectures have no contemporary salience, but there is no overarching lesson or ideological implication to be derived from his models (in contrast to Marxism).

Nevertheless, I am obviously somewhat intrigued by Turchin’s attempt to add some quant juice to qual questions & observations. I recently read Niall Ferguson’s The House of Rothschild: Volume 1: Money’s Prophets: 1798-1848. Because of the fact that the House of Rothschild was incomprehensibly wealthy at its peak via its involvement in public bond markets there was naturally a whole genre which emerged exposing their power and malice as conspirators at the center of a vast web of influence (see the Age of Metternich). Ferguson does emphasize that the financial interests of the Rothschild’s, public debt, compelled them to attempt to block conflicts between major European powers. But another reality which has nothing to do with the Rothschild’s is that Europe during the early years of the family’s rise was recovering from the Napoleonic Wars, and nations and elites which have experienced sustained and strenuous conflict tend to be wary of future conflicts. In Turchin’s data sets he present evidence that these qualitative cycles are evident in clear generational terms throughout the historical record for regions where we have good records. He also presents a causal motive force behind the explosions of violence which tend to prune military aristocracies. Ultimately one would also want to explore the neurological basis of memory and its effect on how humans make decisions and weight risks, and how long traumatic events can effect behavior, but the gross patterns and the expected period of the recession of violence are also of interest. The point being that despite their wealth even the House of Rothschild might have been accidental players in broader macrosocial dynamics.

* Though operationally it is historical because of the weakness of human cognitive powers.

Perhaps the pestilence gods are with us!

Swine influenza, seasonality, and the northern hemisphere:

This history demonstrates the seasonality of pandemic influenza, and suggesta that spread of A/California/09/2009 in the northern hemisphere is not imminent. Based on this regularity, the epidemic in Mexico should be over no later than the end of May. While it is not ‘impossible to see the current contagion spreading in the northern hemisphere over the following months’, it would be unprecedented.

Western names in China

The Name’s Du Xiao Hua, But Call Me Steve:

Given the nationalism I’ve witnessed in China, I was a bit surprised at how readily Chinese adopted Western names. (Even my Americanized parents were uncomfortable with the idea of me changing my name. They said I could do as I wished when I turned 18, though always in a tone that suggested such an unfilial act would cause them to die of disappointment.) But Duthie’s participants insisted that taking an English name isn’t kowtowing, nor is it simply utilitarian. Rather, it’s essential to being Chinese and achieving Chinese goals. Whereas in the past patriotism was expressed by self-sacrifice, it is now expressed through economic activity. So by working for, say, 3M, Chinese citizens are helping to build up China, and the English names they take on in the process are as patriotic as Cultural Revolution-era monikers like Ai Guo (Loves China) or Wei Dong (Mao’s Protector).

The author is a Chinese American. In Peter Turchin’s model borderlands tend to generate the level of social cohesion necessary for a dynamic civilization-state, while the “heartland” exhibits more anomie and decay. But another aspect of this is that Diasporas often exhibit some element of stasis; as if they enter into a cultural chrysalis. The Chinese case is particularly instructive, as due to the upheavals of Marxism, the Cultural Revolution, and now the unbridled capitalistic ethos, much of traditional China has gone by the wayside. Rather, archaic forms and rites are preserved in the Overseas Chinese communities in Southeast Asia, in Taiwan or even in the United States. Chinese in China naturally have less of a need to assert their “authenticity,” so why not adopt what needs to be adopted?

Pray the virus away

Carl Zimmer points out that Marianne Williamson is making some real strange suggestions in regards to the swine flue in The Huffington Post:

l) Pray it away. Just pray it away, asking God as you understand Him, the Divine Physician, Jesus or whatever other form of divine imagery works for you. Simply ask that it be removed from our midst.
2) Send love to Mexico. Between what’s actually been happening there with the drug wars, plus all the “Mexico is dangerous” thoughts we’ve loaded onto it over the last several weeks, it needs a major dose of love – the most powerful medicine of all – to dissolve the fear thoughts that have produced this flu.

It’s not that surprising that this was published in The Huffington Post, which has some issues with regards to quality control. Remember the Deepak Chopra post on evolution?

The rise of empirical economics

In the wake of my post on Predictably Irrational, The Last Temptation of Risk:

THE GREAT Credit Crisis has cast into doubt much of what we thought we knew about economics. We thought that monetary policy had tamed the business cycle. We thought that because changes in central-bank policies had delivered low and stable inflation, the volatility of the pre-1985 years had been consigned to the dustbin of history; they had given way to the quaintly dubbed “Great Moderation.” We thought that financial institutions and markets had come to be self-regulating–that investors could be left largely if not wholly to their own devices. Above all we thought that we had learned how to prevent the kind of financial calamity that struck the world in 1929.

The late twentieth century was the heyday of deductive economics. Talented and facile theorists set the intellectual agenda. Their very facility enabled them to build models with virtually any implication, which meant that policy makers could pick and choose at their convenience. Theory turned out to be too malleable, in other words, to provide reliable guidance for policy.
In contrast, the twenty-first century will be the age of inductive economics, when empiricists hold sway and advice is grounded in concrete observation of markets and their inhabitants. Work in economics, including the abstract model building in which theorists engage, will be guided more powerfully by this real-world observation. It is about time.

The author is an economist, so if this is a caricature, it’s from the inside….

The genetic architecture of different populations

Dan MacArthur has a post, Genetics of complex traits in Europeans and East Asians: similarities and differences:

With those goals in mind, you can expect to see many more GWAS of non-European populations over the next couple of years, and some explicit comparisons of the differing genetic architecture of complex traits between populations. Exciting times for those of us interested in the genetic and evolutionary basis of between-population differences…

This reminds me of A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction:

Read More