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March 27, 2017

Adaptation is ancient: the story of Duffy

Filed under: Duffy allele,Duffy antigen,Genomics,History,Malaria — Razib Khan @ 10:06 pm

Anyone with a passing familiar with human population genetics will know of the Duffy system, and the fact that there is a huge difference between Sub-Saharan Africans and other populations on this locus. Specifically, the classical Duffy allele exhibits a nearly disjoint distribution from Africa to non-Africa. It was naturally one of the illustrations in The Genetics of Human Populations, a classic textbook from the 1960s.

Today we know a lot more about human variation. On most alleles we don’t see such sharp distinctions. Almost certainly the detection of these very differentiated alleles early on in human genetics was partly a function of selection bias. The methods, techniques, and samples, were underpowered and limited, so only the largest differences would be visible. Today we often use single base pair variations, single nucleotide polymorphisms, and the frequency differences are much more modest on average. Ergo, the reality that only a minority of genetic variation is partitioned across geographic races.

Why is Duffy different? Obviously it could be random. Assuming you have a polymorphism, you’ll get a range of frequencies across populations, and in some cases those frequencies which map onto different geographic zones just by chance. Imagine constant mutation, and high structured bottlenecks. You could get a sequence of derived mutations fixing in populations one after the other, just by chance.

This is probably not the case with Duffy. I’ll quote from Wikipedia:

The Duffy antigen is located on the surface of red blood cells, and is named after the patient in which it was discovered. The protein encoded by this gene is a glycosylated membrane protein and a non-specific receptor for several chemokines. The protein is also the receptor for the human malarial parasites Plasmodium vivax and Plasmodium knowlesi. Polymorphisms in this gene are the basis of the Duffy blood group system.

Malaria is one of the strongest selection pressures known to humanity. The balancing selection which results in sickle-cell disease is well known even among the general public. But the likely selection pressures due to the vivax variety are well commonly talked about, partly because they don’t as a side-effect induce a serious disease. Duffy may be canonical if you are a human population geneticist, but it is of less interest more generally.

But a recent paper in PLOS GENETICS shows just how dynamic the evolutionary genetic past of our species was, through the lens of the Duffy system, Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans. Here’s the author summary:

Infectious diseases have undoubtedly played an important role in ancient and modern human history. Yet, there are relatively few regions of the genome involved in resistance to pathogens that show a strong selection signal in current genome-wide searches for this kind of signal. We revisit the evolutionary history of a gene associated with resistance to the most common malaria-causing parasite, Plasmodium vivax, and show that it is one of regions of the human genome that has been under strongest selective pressure in our evolutionary history (selection coefficient: 4.3%). Our results are consistent with a complex evolutionary history of the locus involving selection on a mutation that was at a very low frequency in the ancestral African population (standing variation) and subsequent differentiation between European, Asian and African populations.

Why is it that regions of the genome subject to selection due to co-evolution with pathogens are hard to detect in relation to selection? My response would be that it’s because selection and adaptation are always happening in these regions, constantly erasing its footprints in these regions of the genome.

You may be familiar with the fact that the major histocompatibility complex (MHC) are some of the most diverse regions of the genome. That’s because negative frequency dependent selection makes it so that rare variants never go extinct, as the rarer they get the more favored they are.

Many classical and modern techniques of selection require less protean dynamics when it comes to the model which they attempt to detect. Basically, many of the standard selection detection methods are looking for a simple perturbation in the pattern of variation that’s expected. A strong powerful recent sweep on a single mutation is like the spherical cow of evolutionary genetics. It happens. And it’s easy to model and detect. But it may not be nearly as important as our ability to detect these “hard sweeps” may suggest to us.

In contrast, if selection targets a larger number of independent mutations, then you get a “soft sweep,” which is harder to detect, because it is no singular event. Complexity is the enemy of detection. As a thought experiment, if you selected for height within a population you may catch some large effect alleles that would leave strong signals, but most of the dynamic would leave a polygenic footprint, distributed across innumerable genes.

The Duffy locus is somewhat in the middle. The authors distinguish between selection on standing variation (the allele frequency is higher than a single new mutation within the population) and a soft sweep, where multiple variants against different haplotypes are subject to selection. Their models and results strongly support selection on standing variation for the FY*O variant, and perhaps selection for the FY*A variant.

These selection events were very old, and very strong. Selection coefficients on the order of 4% are hard to believe in a natural environment. Curiously the coalescence times for the haplotypes some of these alleles indicate that selection was contemporaneous with the emergence of modern humans out of Africa, about ~50,000 years ago. From their sequence data analysis the different alleles have been segregating for a long time in the collective human population, and powerful sweeps fixed FY*O in both the ancestors of the Bantu and Pygmies before they diverged from each other. In contrast the Khoisan samples suggest that FY*O introgressed into their population from newcomers, while variants of FY*A are ancestral.

The big picture here is that selection is ancient, that it is powerful, and it was a dynamic even before our species diversified into various lineages.

If you read the paper, and you should, it’s pretty clear that a lot of the adaptive story was suspected. It’s just with modern genomics and fancy ABC methods you can put point estimates and intervals on these hunches. But another issue, as they note in the piece, is that we have a better grasp of African population structure today than in the past, and this allows for better framing.

But it is here I have some caution to throw. At one point citing a 2012 paper the authors suggest “The KhoeSan peoples are a highly diverse set of southern African populations that diverged from all other populations approximately 100 kya.” I can tell you that some credible researchers who have access to whole genome sequences and have been looking at this question peg the divergence date closer to 200,000 years. Some of the issue here is that you need to decompose later gene flow, which will reduce the distance between populations. Easier said than done.

The genetic prehistory of the African continent is almost certainly much more complex than what is presented in the paper, largely due to lack of ancient DNA within Africa. Northern Eurasia turned out to be far more complex than had earlier been guessed…and it is likely that Northern Eurasia has had a simpler history because of its much shorter time of habitation.

If I had to guess I suspect that the ancestors of the Khoisan as we understand them were a separate and distinct group who diverged between ~100,000 and ~200,000 years ago from other extant African populations. But I suspect our clarity is very low in relation the sort of structure which eventually resulted in the shake-out of only a few large groups of Sub-Saharan Africans aside from the Khoisan.

Citation: Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans.

January 6, 2013

Rome: who we were and who we are

Filed under: Bryan Ward-Perkins,Fall of Rome,History,Late Antiquity — Razib Khan @ 5:52 pm

Bryan Ward-Perkins in The Fall of Rome: And the End of Civilization spends a great deal of time on the archaeology of the Classical and post-Classical world. But, he also devotes only somewhat less space to the historiography of the study of the Roman Empire, and Late Antiquity. That is because the study of the past is not just the study of the past, but it is the study of the concerns and values of the present. We look through the dark mirror to the past, and in it we see our own outlines. Similarly, science fiction which purports to be a projection of the future is often nothing much more than a retelling of the present in shinier garb. This reality of history, its reflection of the prescription of the present despite the conceit that it is a description of the past, needs to be kept in mind. It is not a failing which pollutes the whole enterprise, it is a reality which must inform our interpretation of it. The study of Rome is a study of what humanity was, but it can not help but also reflect and define what we wish to be, by comparison and contrast.

But before I go on, a minor mea culpa. After further research and correspondence I believe that I extrapolated too far from lead concentrations in Greenland ice caps in a previous post. Though I still believe that it is a good reflection of the decline in proto-industrial vigor in the Western world, I do think that distance from China means that we do not have a good gauge on any comparisons between 0 AD and 750 AD (the later date being the apogee of the Tang). Though I do note that world population estimates seem to be somewhat lower for 700 than 0. But these are not precise estimates, so they need to be taken with a grain of salt. Chinese census records indicate that Tang population was higher than that of the Han, while it seems plausible that the Arab Imperium of the 8th century resulted in a higher population for the regions under its purview than during antiquity. Therefore to make the “math work” one can reasonably assume that the population in Europe was far lower.

Additionally, to clarify my points from the previous post, I was presenting a description of the decline, not any allusion to the causes of the fall. And, my argument was that the rate of decline was far greater after the fall of Rome, not that there was no decline from the Principate to the Dominate. Though my opinions are not particularly well informed or strong, I would hazard to bet greater per person production during the Antonine period of the mid-2nd century than the relatively quiescent epochs of the 4th century. My argument is simply that in terms of economic production the 4th century resembles the 2nd far more than it does the 6th in the Roman West. The world of Procopius was further from that of Constantine than that of Constantine was from that of the Antonines, despite the fact that Justinian’s Byzantium perceived itself to be (and rightly) simply a continuation of antique Rome.

The argument of The Fall of Rome which is powerful and persuasive as a description is fundamentally a material one. Political unity within the Roman Empire decreased the fixed costs of production (e.g., no need for city walls, no political boundaries imposing extortionate levels of duty, etc.). Rome was the Western world’s first free trade zone where military conflict was ended by the imperial monopoly on force. This resulted in gains in wealth due to the economies of scale and classic Smithian productivity increases through specialization. Ancient Rome was not a consumer society characterized by eternal expectations of growth, but neither was there an expectation of collapse and regression (e.g., “The Eternal City”). I find the Malthusian logic of biology powerful in that greater  productivity should be swallowed up by population increase, so that over the long term average well being for most humans has been approximately the same (increased aggregate wealth coexisting with the same per capita wealth). But there are many qualifications within that statement; the long term may actually have been longer than the course of the empire, suggesting that Rome never attained Malthusian equilibrium.

To support his proposition about material prosperity Bryan Ward-Perkins recounts the quality and number of pots and amphorae, as well as extensive archaeological evidence of a dense network of cities all across the Roman Empire. And though the average Roman peasant did not avail themselves of the consumption of the broad upper orders, they were at least free of the fear of marauders and enslavement by foreign peoples. One might respond here that they were subject to grueling taxation, but this is fundamentally a different argument. Modern examples seems to imply that high taxation is preferable to an anarchic order of no taxation and no services (e.g., Afghanistan). Bryan Ward-Perkins makes a compelling case in The Fall of Rome that the economic and political order of the Western Mediterranean and Northwest Europe regressed back to a pre-Iron Age level of complexity in the two centuries after the fall of Rome! In other words, the “Dark Ages” saw the unraveling of a set of organically developed norms and connections which had matured from the 5th century B.C. onward. A 1,000 year old civilization expired, as defined by the innumerable threads which had bound together the Western Mediterranean, Gaul, and Britain.

But there looms over this argument aspects which are just not material, but also normative. When alluding to literacy we obtain here a case where the material and normative intersect. By various means Ward-Perkins argues that rates of literacy were far higher during the period of the Roman Empire than after. It is famously well known that across the centuries of Rome it was not until 518 that an Emperor donned the purple who may have been illiterate (Procopius is not entirely reliable on matters factual when it comes to the family of Justinian!). In contrast, Dark Age princes such as Charlemagne were often illiterate. The most evocative and persuasive component of the argument in regards to penetration of literacy is that graffiti and casual scribbling are legion from the Roman period, but far rarer afterward. There is even documentary evidence that most priests during this the Dark Ages were functionally illiterate, with a substantial minority being totally illiterate (i.e., they could not sign their own names to documents).

Marcus Aurelius

So what that 10% of Western Europeans in 400 may have been functionally literate, while only 1% in 700 were? The “what” is that the penetration of literacy allows for a critical mass to develop for a particular form of cultural discourse. A fundamental aspect of the Classical World is that it developed out of a world of citizens. This does not mean that it was a democratic world. Rather, it means that a broad expanse of the populace was vested in the political order, whether in an Athenian democracy, Spartan oligarchy, or Roman republic. Only 100 years into the Empire were emperors actually called Emperor. Rather, they were Princeps, “First Citizens.” The false conceit of the Roman Empire was that it was a restoration of the republic. Rome never had kings, and the slide toward explicit and formalized autocracy and despotism was gradual. The early republican army was one of freeborn citizens, and even after the Marian reforms which opened up the army to the proletariat the Roman legions were draw from the citizenry. Between the era of Augustus and the 3rd century the military became progressively less Italian, but it remained Roman, with only auxiliaries derived from barbarian people who were not citizens (after Caracalla granted citizenship to all freeborn Romans barbarian would mean someone from outside the imperial frontiers).

This alien world of emperors, slaves, and gladiatorial battles was nevertheless populated by familiar figures. There were philosophers and civil servants, city councils and a professional army paid in coin or salt. What was fundamentally alien is that it was ‘pagan.’ This is to some extent a catchall term which developed relatively late in history (in the Greek-speaking world pagans were termed ‘Hellenes’), but it reflects the view that the old religion of the West was alien in a deep manner from what came after. Until recently faiths like Christianity, Judaism, Islam, Buddhism, and Hinduism were termed ‘higher religions.’ Today such judgmental terminology is less common, and they might be classed together as ‘institutional religions,’ or more more colloquially ‘organized religions.’ Often the term pagan is used to encompass the faiths outside of the Abrahamic religions, but because of the pejorative connotations of pagan this is probably not advisable.

The critical aspect which I think needs elaborating here is that in regards to the relatively seamless coherency and integration of all aspects of religiosity, high and low, and ritualistic, mystical, and philosophical, there is a qualitative difference between the institutional religions, and the older traditions. The ancients had ethical philosophy, they had rites, and they had mystical and ecstatic communal worship. What they often did not have was an organized system which packaged all these aspects together. If Constantine had fallen at the battle of Milvian Bridge then the West may not have become Christian, but it would not have remained pagan in a way which we understand it. The exact nature of the organic development of an institutional religion varies across civilizations, but it seems that a complex culture invariably demands a religious system which binds together various sentiments across elements of society. This is clear in the rise of solar religion in the late 3rd century, and points to the fact that in the 1st millennium all civilizations were moving toward a system where an institutional religion with metaphysical grounding anchored and gave legitimacy to the body politic.

But is this enough to differentiate us from the Romans and align ourselves with what became Christendom? Bryan Ward-Perkins observes that the study of Late Antiquity is rife with a fixation on cultural change in the domain of religion, with a neglect of the material and  political dimensions of life. In particular there is much attention paid to ascetic religious figures who were instrumental in transforming Roman Christianity into Medieval Christianity. Granting the materialist argument (which even the doyen of Late Antique studies, Peter Brown, seems to do in Through the Eye of a Needle), are the cultural changes of Late Antiquity which make the world of Europe more familiar stark enough to make that age truly the seedbed of recognizable modernity?

Charlemagne receiving homage from Saxons

It is critical to note that Late Antiquity lives on genealogically. The modern British royal family can trace descent back to at least the 8th century kings of Wessex. The dispossession of the Roman elites was such that despite the persistence of eminent families with roots in the late Classical period across Europe at the local level it is difficult to validate any European royal genealogies before the early Dark Ages. The modern nation-states of Europe also date back in their embryonic sense to this period. And critically one must distinguish between the Dark Ages from the High Medieval period. The latter phase saw a reemergence of social complexity, in particular in northern France, southern England, and the Low Countries. The Aristotelian Renaissance illustrates that after 1000 A.D. Western Europe began to rouse itself from its intellectual slumber.

But all that notwithstanding for me the critical aspect to emphasize is that the Germanic elites of the post-Roman Western European world were fundamentally military gangs; warlords and their underlings. This is not atypical. Rather, this is the normal state of pre-modern societies. And in this way it is fundamentally alien to the modern sensibility. The lords of the post-Roman world were of the same category as anax of Mycenaean Greece. Their profession was war, and their cultivation was of the sword. Though the Roman world was militarized, in fact most of the Imperial expenditure was on the legions, its elite was fundamentally civilian in orientation. Roman aristocrats were often military leaders, but more universally they defined themselves as being cultured and refined in relation to the common. No Roman could rise to a status of prominence without being literate, and the established nobility was educated in classical literature and rhetoric. This is not entirely surprising, as for several centuries the Roman world was characterized by peace, and high status was not likely to be won through feats of martial prowess. A similar process seems to have occurred in early modern Europe, as the military elites who were often the descendants in spirit if not genealogy from the post-Roman Germanic warlords began to cultivate their manners and fashions to signal their gentility. Part of this is due to the same decline in violence which characterized the Roman world. But it is also perhaps a response to the rise of firearms, which made aristocratic cavalry vulnerable on the field of battle. The civilian orientation of the Roman aristocracy is similar in many ways to that of China, where dynasties founded by generals nevertheless marginalized the military over time.

All of the above is why I state that my agreement with Bryan Ward-Perkins’ contentions are to some extent normative. I feel that a brutal Classical Roman autocrat such as Marcus Aurelius is more modern than a brutal Dark Age autocrat such as Charlemagne. Then again, some of Aurelius’ self-serving thoughts are preserved for us in his Meditations, while Charlemagne was an illiterate whose character is filtered through chroniclers. Charlemagne may have been the defender of Roman Christianity, but he was an exemplar of Romanitas in the same manner that the Democratic Republic of Korea (North Korea) is democratic (for example, he was an open de facto polygamist). The American republic was founded as a republic. Granted many of its institutions evolved organically from English common law tradition, but it is clear that the injection of ancient political theory revitalized the organization of Western nation-states. The Napoleonic Code draws inspiration from the rediscovery of Roman law. Ultimately it strikes me that the modern world manifests many of the structural features of the Roman world, with the Dark Ages being an unwinding from which the West only slowly recovered. Your mileage may vary, but that says more about differences in values among contemporaries, than it truly does about the factual assessment about the shape of the past.

January 2, 2013

When Rome fell civilization did decline

Filed under: Antiquity,History,Late Antiquity,Roman History — Razib Khan @ 9:37 pm

Before the Holidays I mentioned that I was rereading Bryan Ward-Perkins’ The Fall of Rome: And the End of Civilization. Why do I hold this book in such high esteem? Because of figures such as the one to the left. Granted, this chart is not from The Fall of Rome, but that book has an extensive bibliography which drew me to research on long term trends in pollutant concentrations. What you see illustrated are variations in the concentration of lead in ice cores from Greenland. Why is lead so important? Because it is a noxious byproduct in various primitive metallurgical processes. The basic thesis that Ward-Perkins fleshes out in great detail in The Fall of Rome is that the material basis of European life suffered a sharp regression after the collapse of the Roman Empire. In short the fall of Rome was the end of civilization, and what came after was coarser and more elementary in character. This may seem “common sense,” but it is actually a matter of some dispute and debate in the academy.

When discussing this issue there are two primary objections which always seem to come to the fore. First, after the de facto collapse of the West Roman imperium in the first half of the 5th century there were other societies of importance and grandness on the historical stage (see The Inheritance of Rome, When Baghdad Ruled the Muslim World, and China’s Cosmopolitan Empire). Far to the east of faded Rome Tang China’s glory waxed in the nadir of the European regression between 600 and 750. More well known to Westerners, the same period saw the apogee of Arab Islamic civilization. But the data above indicate that the industrial production of these two polities did not match that of the period around the peak of the Roman Empire. I refer here to period, because of course the Roman Empire flourished at the same time as Han China, and Sassanian Persia. The collapse of the 5th century was not a collapse of civilization as such, but of the western terminus of the oikoumene. And this decline was not compensated for by greater vigor in the Islamic center, or Chinese east.

Marcus Aurelius, 2nd century

A materialist perspective has the elegant attribute that it is less malleable in the hands of those with stylistic polish and the will and skill to engage in selective massaging of sources. I can assert plausibly I think that that the classical civilization which produced Thucydides, and later Polybius, Tacitus, and Ammianus Marcellinus, was superior in the fineness of its high culture than that in which Jordanes or the Venerable Bede flourished. But if an individual is clever, erudite, and set in their proposition, it will be impossible to definitively refute someone who holds that 8th century Anglo-Saxon England was no less cultured than 5th century Athens or 2nd century Rome. And if the exposition of the counter-intuitive position is placed in the hands of a cunning sophist, and the one who endorses common sense is plain and less learned, then the battle is already lost before it is begun. Terms like “superior” and “cultured” are slippery, and the whole enterprise of grading societies is held in bad odor in our age. A barrage of facts curated with intent to support a preposterous thesis can overwhelm simple sincerity. But the quantitative consequences of material production are not as contextualized or easily problematized. It is simply fact that proto-industrial production in the post-Roman world had regressed, and with it an array of material comforts and minor luxuries vanish from the record or become very rare. The dull can defeat the sly simply by pointing to the angle of the line on a chart.

A broader and more fundamental issue is that one must question how one judges the rise and fall of civilizations and society. From an orthodox Muslim or Christian perspective the collapse of Rome in the 5th century was an unfortunate incident, but ultimately secondary to the reality that the western half of the civilized world was to soon to be permeated by the presuppositions of their respective religious creeds. St. Augustine’s The City of God is only the most extended and thorough of many contemporaneous Christian apologetics which purport to explain the peculiarity of the collapse of the civilized (i.e., Roman) world just as the old pagan high traditions were finally superseded by Christianity. This is why I say that I find The Fall of Rome persuasive for partially normative considerations. Though I am willing to grant the superiority for various reasons of Christianity or Islam over the animistic primal religion of Republican Rome, or the Mystery Cults of the High Empire, I weight the extinction of industrial production of pottery and the reversion to localized barter economies as of greater consequence. Matter is more critical necessary precondition for civilization than mind. I doubt that Tacitus was anymore brilliant than Bede, but the former shone with more absolute greatness of the cultural capital which he could mine and leverage. The withering of the Christian church in the Balkans and England is a testament to the fact that higher religion themselves are preconditioned on a minimal level of social complexity and organization. It seems likely that by the 5th century Christianity succeeded in spite of the collapse of the West Roman Empire, not because of it. Rather than being a minor problem of history, the disturbance of the Roman order was a disaster for institutional Christianity, from which it only slowly recovered, still maintaining its original Roman outlines despite the Germanic interlude.

There are often debates as to whether fields like anthropology or history are humanities or social sciences. The truth is almost certainly both. In many ways I find archaeologists, particularly those of prehistory, theory-poor. Rather, what theory they attach to their wealth of material remains seems to be imbibed from the spirit of the times. Before World War II they were keen to illustrate the congruence of their material results with a migrationist narrative, while after World War II they rejected such models. But though archaeology can often tell us little directly in and of itself about the creators of a material culture, the flux of that material culture can tell us a great deal about aspects of that given society’s material workings. Technology is predicated on basic laws of nature, and those laws of nature produce constraints in the possibilities. Though it is possible in theory that Europeans between 500 and 1000 AD developed complex social systems which were also more ecologically friendly than those of antiquity (so as to generate less pollution in the material record), a more parsimonious explanation seems to me to be that in fact those societies were simpler, and that the order and institutions necessary for large scale proto-industrial production which had evolved organically from 1st millennium BC down to the Roman era had disappeared. This is simply not a matter of discourse, dialogue, debate, or contexualization. It is.

December 23, 2012

History as intellectual hydrography

Filed under: History — Razib Khan @ 1:26 am

One of the great aspects of owning a Kindle has been that I have been able to load it with cheap copies of “classics.”* As it happens I had physical copies of many of these works, but often it became difficult to keep track of various books in even my modest personal library. Generally scientific references were placed prominently, and I made use of them often, and so always was able to mark exactly where they were. But when it came to Nicomachean Ethics or The Critique of Pure Reason, I would proactively seek them on only rare occasions. Now with a compact and well organized personal digital library I find that I revisit the ancients much more often to engage with them in dialogue. Here I recall what Niccolò Machiavelli once asserted:

When evening comes, I return home and go into my study. On the threshold I strip off my muddy, sweaty, workday clothes, and put on the robes of court and palace, and in this graver dress I enter the antique courts of the ancients and am welcomed by them, and there I taste the food that alone is mine, and for which I was born. And there I make bold to speak to them and ask the motives of their actions, and they, in their humanity, reply to me. And for the space of four hours I forget the world, remember no vexation, fear poverty no more, tremble no more at death: I pass indeed into their world.

Meghna River

I am far too much a Whig in instinct to agree with this sentiment without reservation. When I trudge through the extended diatribe that is City of God I cannot help but scoff at St. Augustine’s screed, 1,600 years on. And yet this contempt instills in me a sense of deep humility, for surely generations future will look toward our own orthodoxies and sneer and laugh. We are all embedded in our own presuppositions, and the ecology of ideas which nourish our prejudices, for good or ill.

It is as if we are an element of a broad and powerful river, flowing through familiar territory. If you asked a stream of the river to describe its place in the context of the whole, it would be at a loss, because the river is one, and as a category is indivisible. But step back, rise up, and you can see the topography and the overall course of the flow, from headwaters down to the floodplain. Similarly, ideas have history, and people have history, even if they are not aware of that history as it flows past them.

Human cognition is such that there is a strong bias to imagine that we are idealized rationality machines, who derive our own positions by force of our free will. But the reality is that much of our cognition is socially and historically contingent. This does not mean that beliefs are arbitrary, but, they are flexible and strongly shaded by context. The folly of the most brilliant of ancients brings home to us the reality that pure force of mental acuity can not break free of the shackles of history. What follies do we adhere to? What positions are we “evolving” toward at this very moment?

During a typical day my own interactions are with young people of a very precise and specific technical bent. There is no lack of cognitive processing power, but when conversation drifts away from areas of deep technical fluency, then St. Augustine begins to strike me as a man of objective ahistorical clarity. The technics of the modern age are humans who sustain our civilization, but they often lack background or interest in the human past, or a more expansive view of the present. There is a very definite poverty of imagination in regards to the range of human opinion, and a conceit that the shape of the world is as precisely defined as the arc of planetary motions.

Whereas before I had held to the position that a minimal level of liberal classical education was critical in tying together the higher orders of a social system through a common set of narratives and frames, today I believe that a canon is essential to allow people at any given moment to see that human experience is broad, and that we are all creatures in a specific time and place. I cannot help but wonder if the occasional outbursts of extreme relativism which issue out of the academy may simply be a function of the inability of narrowly trained moderns to comprehend that one can hold onto one’s values and views, while at the same time appreciating differences of perspective. It may be to difficult to withhold ill will across the chasms of contemporary partisanship, but surely one must acknowledge Aristotle’s brilliance and his folly!

* You may wonder why I would pay even a nominal fee when these are public domain. My personal experience is that a minimal amount of commentary and attention to formatting is worth a few dollars.

October 8, 2012

Ancient DNA and Sumerians

Filed under: History,Sumerians — Razib Khan @ 6:49 pm

A few months ago someone asked me (via email) which populations I would love to get typed (genetically that is). There is one population which did not come to mind at the time: the Sumerians. Why? Because these are arguably the first historic nation. The first self-conscious ethnic group which operated by the rules which we define as the fundamentals of literate civilization. Strangely, they are an ethno-linguistic isolate. My own assumption until lately has been that this is not too surprising, in that prior to the rise of expansive civilizations (Sargon of Akkad) there was much more linguistic and ethnic diversity than we currently see around us. Or, was evident even in the early Iron Age. In other words, the ancient Fertile Crescent may have resembled the highlands of Papua, with Hurrians, Akkadians, Gutians, Elamites, Sumerians, etc., all speaking mutually unintelligible dialects which diverged very far back in the mists of antiquity.

I am no longer quite so sure about this model. That is largely due to the possibility that there was a great deal of demographic change between the Mesolithic and the Bronze Age, with successive waves ...

September 17, 2012

The great Eurasian explosion

Filed under: Genetics,Genomics,History,Prehistory — Razib Khan @ 8:38 pm

Dr. Joseph Pickrell has updated his preprint, The genetic prehistory of southern Africa, with some more material on the Sandawe. I’ve explored the genetics of the Sandawe a bit using ADMIXTURE, so I jumped straight to the section on ROLLOFF:

…To further examine this, we turned to ROLLOFF. We used Dinka and French as representatives of the mixing populations (since date estimates are robust to improperly specified reference populations). The results are shown in Supplementary Figure S22. Both populations show a detectable curve, though the signal is much stronger in the Sandawe than in the Hadza. The implied dates are 89 generations (2500 years) ago for the Hadza and 66 generations (2000 years) ago for the Sandawe. These are qualitatively similar signals to those seen by Pagani et al. [65] in Ethiopian populations. There are two possible historical scenarios that could lead to these signals: either the Hadza and Sandawe both directly admixed with a western Eurasian population about 2,000 years ago, or they admixed with an east African population that was itself admixed with a western Eurasian population. The latter possibility would be consistent with known east African admixture into the Sandawe [16] .


Pagani et al. refers to the paper Ethiopian Genetic Diversity Reveals Linguistic ...

September 4, 2012

The Alawite analogy

Filed under: History — Razib Khan @ 10:59 pm

Analogies exist to convey information. But too often all they do is add rhetorical flourish. For an analogy to have power there needs to be a genuine mapping of the structure of the source and target. And perhaps more crucially your target audience needs to understand the structure of the source well enough to map it onto the target. You can’t get insight from a foundation of nothing.

A story in The New York Times suggested to me one avenue by which to communicate the particular nature of the relations in Syria between ethno-linguistic groups. Syrian Children Offer Glimpse of a Future of Reprisals:

The roots of the animosity toward the Alawites from members of Syria’s Sunni Muslim majority, who make up about 75 percent of the population, run deep into history. During the 19th-century Ottoman Empire, the two groups lived in separate communities, and the Sunni majority so thoroughly marginalized Alawites that they were not even allowed to testify in court until after World War I.

As has been noted elsewhere the Alawite identity as Shia Muslims is to some extent an artifact of modern circumstances (i.e., the alliance with Iran which dates back to the 1970s). But, it does ...

August 26, 2012

America, these are (some) your graduate students

Filed under: academia,History — Razib Khan @ 7:19 pm

If you haven’t, you should check out The Shadow Scholar, The man who writes your students’ papers tells his story. This is the conclusion:

“Thanx u so much for the chapter is going very good the porfesser likes it but wants the folloing suggestions please what do you thing?:

“‘The hypothesis is interesting but I’d like to see it a bit more focused. Choose a specific connection and try to prove it.’

“What shoudwe say?”

This happens a lot. I get paid per assignment. But with longer papers, the student starts to think of me as a personal educational counselor. She paid me to write a one-page response to her professor, and then she paid me to revise her paper. I completed each of these assignments, sustaining the voice that the student had established and maintaining the front of competence from some invisible location far beneath the ivory tower.

The 75-page paper on business ethics ultimately expanded into a 160-page graduate thesis, every word of which was written by me. I can’t remember the name of my client, but it’s her name on my work. We collaborated for months. As with so many other topics I tackle, the connection between unethical business practices and ...

August 16, 2012

Cultures & genes: Paleolithic to the Neolithic

Filed under: Anthroplogy,Genetics,Genomics,History — Razib Khan @ 10:23 pm

Spatial linguistic variation Spatial genetic variation Temporal linguistic variation Temporal genetic variation Paleolithic Very high High Moderate-to-high Moderate-to-low Neolithic Moderate Moderate-to-low Moderate High Bronze Age Moderate-to-low Low Moderate Moderate-to-high Iron Age Low Low Moderate-to-low Moderate Modern Age Very low Low Low Moderate-to-low

In the comments below I posited a scenario to explain a strange inference from a paper from a few years back, Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude:

Population historical models were estimated (8) from the two-dimensional frequency spectrum of synonymous sites in the two populations. The best-fitting model suggested that the Tibetan and Han populations diverged 2750 years ago, with the Han population growing from a small initial size and the Tibetan population contracting from a large initial size (fig. S2). Migration was inferred from the Tibetan to the Han sample, with recent admixture in the opposite direction.

2,750 years would place the divergence of modern Tibetans and Chinese a few hundred years before Confucius. In fact, it would technically post-date the first historically attested Chinese writing, from the Shang dynasty. This result was pretty incredible, though one of the main authors believes it is a reasonable estimate. There are many ways you can explain this sort of divergence time, but one way which I elucidated below is rather simple. Imagine, if you will, a large set of populations which are ...

Rise of the planet of the Indo-Europeans

Filed under: Anthroplogy,History,Indo-Europeans — Razib Khan @ 9:00 am

In response to my post below a friend emailed me the above sentence. As I suggest below it sounds crazy, and I don’t know if I believe it. But here’s an abstract from the Reich lab from June:

Estimating a date of mixture of ancestral South Asian populations

Linguistic and genetic studies have demonstrated that almost all groups in South Asia today descend from a mixture of two highly divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners and Europeans, and Ancestral South Indians (ASI) not related to any populations outside the Indian subcontinent. ANI and ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago, but the date of the ANI-ASI mixture is unknown. Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago. Some mixture may also be older—beyond the time we can query using admixture linkage disequilibrium—since it is universal throughout the subcontinent: present in every group speaking Indo-European or Dravidian languages, in all caste levels, and in primitive tribes. After the ANI-ASI mixture that occurred within ...

August 15, 2012

The Age of Heroes

Filed under: Culture,Genetic History,Genetics,History — Razib Khan @ 5:42 pm

Sometimes when you read reviews or papers you need to look very closely at what people say in a tentative speculative fashion. That’s because though the prose may be as such when read plainly and without context, you often have more prior information as to the background of the authors. In other words, assertions which literally seem cautious are actually foreshadowing likely probabilities down the pipeline, because the authors are not distant third-party observers, but active participants in the production of new insights. I think that’s what’s going on in a new paper in Trends in Genetics, The genetic history of Europeans:

Future research should also reveal the effects of post-Neolithic demographic processes, including migration events, which preliminary data suggest had a major impact upon the distribution of genetic variation. These include events associated with Bronze Age civilizations, Iron Age cultures, and later migrations, including those triggered by the rise and fall of Empires. Challenges remain in being able to sequence aDNA routinely from serial samples in the range of megabases, and in the development of software that allows spatially-explicit simulation of genome-scale data, but advances in these areas are now a weekly occurrence and the stage is set for ...

August 12, 2012

And you shall find the light & the truth

Filed under: David Barton,History — Razib Khan @ 9:57 am

John C. Calhoun – religious liberal

I’ve been expressing my pessimism about the state of contemporary intellectual discourse, but it’s time to spotlight something which should make us optimistic. For years David Barton has been promulgating the falsehood that the Founding Fathers were nearly all evangelical Protestant Christians, and therefore this nation was founded as a Christian nation as understood by modern evangelical Protestants. Barton’s influence through the network of conservative evangelical churches is powerful. I’ve encountered people who repeat Barton-lite “facts” who no longer have any connection to conservative evangelical culture simply because that’s all they’ve ever been made aware of.

But it seems that Barton has finally gone a step too far. Conservative Christian historians have started to counter his fabulism, to the point where his publisher is now withdrawing his ironically titled book The Jefferson Lies: Exposing the Myths You’ve Always Believed About Thomas Jefferson. Such revisionism is just too bald for even the most sympathetic to Barton’s worldview. Jefferson was famously the Founder who produced a bowdlerized Bible, and presumed that the future of Christianity would be in a heretical Unitarian ...

August 11, 2012

Hindus invented the missionary religion

Filed under: History,Religion — Razib Khan @ 4:31 pm

A comment below:

To be honest with you, being of a Hindu background I’ve never ever understood the concept of conversion. It seems so alien to me and seems to be prevalent only among the monotheistic religions, to me it seems to be a sort of rejection of the other.

Two qualifications. First, by “Hindu,” I mean Hindu-as-Indian, not Hindu as the set of native Indian beliefs which matured and crystallized under Turco-Muslim and British Christian hegemony. Second, inventing a missionary religion is like inventing the hypertext link or “one-click purchasing.” Someone was going to invent this. People of “Hindu background” seem to routinely forget that the first non-tribal religious system with universalist aspirations arose on the soil of India, Buddhism. This makes some sense because most people don’t know any history.

Below is a map which illustrates the nations which the Indian king Ashoka reputedly sent missionaries. One does not need to take this literally in all the details. Rather, it does establish the likelihood that Buddhism, which was a native Indian tradition, sent out missionaries across much of the civilized world centuries before Christianity in any form existed. In fact, it is almost certainly the case that Buddhism was a presence within China proper when Christianity was still self-consciously a Jewish sect, in the 1st century.

Of course, it must not be denied that Hinduism as a recognizable religious tradition has engaged in proselytization. The Cham Hindus of Vietnam and the Balinese are both relics of a vast domain of Southeast Asian Hinduism, which stretched from Cambodia south to Java.


August 9, 2012

Historical Dynamics & contingent conditions of religion

Filed under: Anthroplogy,History — Razib Khan @ 11:39 pm
Below is a long essay I wrote four years ago which I’m reposting. It may be a useful guide for readers who are not aware of my various non-genetic interests….

Peter Turchin’s Historical Dynamics: Why States Rise and Fall showed up a little sooner than I’d thought it would, and it was an even quicker read than War and Peace and War: The Rise and Fall of Empires (see review). There isn’t really anything new verbal in the more technical treatment, but the book is about half the length because so much of the text was condensed into simple differential equations and figures which displayed the results of simulations. The figure to the left was one that I found particularly interesting, the differential equations which this is based on are:

dA/dt = c0AS(1 - A/h) - a

dS/dt = r0(1 - A/[2b])S(1 - S)

Where A = area, c = state’s resources translated into geopolitical power, r is the growth rate, h is the spatial scale of power project, a is the geopolitical pressure from the hinterland and S is average polity-wide level of collective solidarity. You can find the elucidation of the details of the simulation in the appendix of Historical Dynamics.

Turchin was obviously pleased with how similar the dynamics of area of polity vs. time were in the simulation to what the ...

July 27, 2012

We are all Anglo-Saxons now

Filed under: Anglo-Saxon,History — Razib Khan @ 10:21 pm

I’m kind of wary of getting into political debates at this point because it’s not my primary interest (additionally, people with stronger political views often end up willfully misrepresenting me because they think I’m taking specific sides, even if they actually guess my preferences incorrectly!). But the whole Mitt Romney-Anglo-Saxon heritage kerfuffle has now gotten under my skin. What prompted my agitation is a post over at The Atlantic by Max Fisher, Sorry, Romney: Neither America Nor the U.K. Are ‘Anglo-Saxon’ Countries. There are two dimensions to this, the positive and the normative.

Most of you are probably aware of David Barton, the conservative Christian scholar whose bread and butter is a revisionist history of the United States which rewrites the past into a fiction to serve his own political ends, in a manner which would make Michel Foucault proud. But believe it or not conservative Christians are not the only group wont to rewrite the past to serve  their own contemporary political preferences. In the case of Max Fisher what you have is a conclusion in search of support, and so our enterprising young man went out looking for it in classic hack style. Reading through ...

July 22, 2012

British class differences persisting down centuries?

Filed under: Anthroplogy,Genetics,History — Razib Khan @ 10:01 am

People with Norman names wealthier than other Britons:

Research shows that the descendants of people who in 1858 had “rich” surnames such as Percy and Glanville, indicating they were descended from the French nobility, are still substantially wealthier in 2011 than those with traditionally “poor” or artisanal surnames. Artisans are defined as skilled manual workers.

As Steve Sailer observes strict adherence to surnames on a mass scale post-dates the Norman invasion by centuries. So the headline is pretty sensational. But I went and read the original working paper, and there is no mention of Norman or French names! The author of the piece in The Telegraph is probably right (i.e., a casual reading of history will show that Norman names are enriched in the English elite), but this is clearly another case of one having to be careful of the details when it comes to British media.

But the results in the paper are interesting enough. The biggest finding is that regression toward the mean is far less using this 200 year data set than might be extrapolated from modern 2 generation data sets. Another reason to be skeptical of economists waxing grandly on all they know from the ...

July 20, 2012

The many Americas

Filed under: History — Razib Khan @ 12:25 am

One of my main hobbyhorses is that in the United States today the identities of race and religion get so much emphasis that it is easy forget the divisions among white Anglo-Protestants which persist, and to some extent serve as the scaffold for the rest of American culture. This is why I recommend Albion’s Seed and The Cousins’ Wars to anyone interested in American history. Often these realities of American “dark ethnicity,” the divisions between Yankees and Low Country Southerners, Scots-Irish and the people of the port cities of the Northeast, get conflated with issues of class. Class is a major dimension, but it is not the only one. For example, the people of Appalachia are poor, but they are not Appalachians because they are poor.

These issues of dark ethnicity rooted in “dark history” can crop up in the strangest places. For example, in The New York Times Magazine, Greg Ousley Is Sorry for Killing His Parents. Is That Enough?:

Greg remembers his early childhood being a content one — long afternoons spent tramping through the surrounding woods with his friends, family vacations to the Indiana Dunes on Lake Michigan and to visit the extended Ousley clan ...

July 19, 2012

Iranian religious distinctiveness is not primal

Filed under: History,Iran,Shia — Razib Khan @ 1:03 pm

Dienekes has a discussion up of a new paper on Iranian Y-chromosome variation. My post isn’t prompted by the genetics here, but rather a minor historical note within the text which I want to correct, again, because it isn’t totally minor in light of contemporary models of the uniqueness of Iranian (specifically Persian) identity in the Middle East:

Persian identity refers to the Indo-European Aryans who arrived in Iran about 4 thousand years ago (kya). Originally they were nomadic, pastoral people inhabiting the western Iranian plateau. From the province of Fars they spread their language and culture to the other parts of the Iranian plateau absorbing local Iranian and non-Iranian groups. This process of assimilation continued also during the Greek, Mongol, Turkish and Arab invasions. Ancient Persian people were firstly characterized by the Zoroastrianism. After the Islamization, Shi’a became the main doctrine of all Iranian people.

As Dienekes observes I’ve objected to this confusion before:

For example, it is routinely unknown that before the Safavids Iran was a predominantly Sunni domain. This is not to deny the presence of Shia within the borders of modern Iran, but aside from periods of state patronage (e.g., the Buyids) the status of Shi’ism was as ...

July 17, 2012

Identity by descent & the Völkerwanderung

Filed under: Demographics,Europe,Europe history,History,Völkerwanderung — Razib Khan @ 8:07 pm

Early this year I received an email from Dr. Peter Ralph, inquiring if I might discuss some interesting statistical genetic results from analyses of the POPRES data set which might have historical relevance. I’ve been excitingly waiting for the preprint to be made public so it could trigger some wider discussion. I believe that the methods outlined in the paper perhaps show us a path into the near future, where we might gain a much sharper perspective upon the recent past. So it’s finally out, and you can read it in full. Ralph and Dr. Graham Coop have posted put it up at arXiv, The geography of recent genetic ancestry across Europe. The paper uses ~500,000 SNPs from the POPRES data set individuals, and looks at patterns of identity by descent as a function of geography. By identity by descent, we’re talking about segments of the genome which are derived from a common ancestor. Because of recombination the length of the segments can give us a sense of the date of the last common ancestor; long segments indicate more recent ancestry because fewer recombination events have ...

July 15, 2012

Continuing the search for Indo-Europeans

Filed under: History,Indo-Europeans — Razib Khan @ 1:53 pm

Dienekes P. is often rather laconic in commentary on the papers he links to, but of late he has “come out of his shell.” He has two posts which are important “weekend reading”:

- Population strata in the West Siberian plain (Baraba forest steppe)

- Hints of East/Central Asian admixture in Northern Europe

I freely admit that much of the conjecture here is above my pay-grade in terms of evaluation. But I do think it’s important think through. My “gut” tends to lean toward a “revenge of the Mesolithic” scenario promoted by some of Dienekes’ critics, but I don’t have a strong position.

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