Reality has a bias against your bias

https://www.youtube.com/watch?v=IjInNxIwfRw

gsi2-chp1-9It has come to my attention that Bill Maher has been making some pronouncements against Islam, and this has resulted fierce blow back from the likes of people such as Reza Aslan. Normally I don’t follow Maher too closely. I used to watch his show, Politically Incorrect, back in the 1990s, and though he had his moments of wit, humor, and insight, by and large his stock in trade was superficial buffoonery. So I generally do not pay attention to him. More recently he’s been espousing views which make him a fellow traveller with New Atheists. As a disagreeable person who enjoys some biting polemic I do appreciate the New Atheists for the role they play in the ecology of ideas. They do not hide behind the post-modern fixation on “tolerance” and “diversity.” But my ultimate judgement about them is that their foundational propositions about human nature are wrong. In other words, I stand with cognitive anthropologists such as Scott Atran as to the roots of religion. Though in the God Delusion Richard Dawkins exhibits some familiarity with this literature, in the end his rhetoric and central thesis seems to take it for granted that religion is a contingent cultural invention, and adherence is a feature of improper implementation of the principles of rationality. My own position, in line with cognitive anthropologists, is that supernatural ideas are relatively inevitable human intuitions given the architecture of our minds, which are far less dominated by the ability to reflexively reason than 18th century rationalists would have believed. The more elaborate specific institutional aspects of religion are also probably rather inevitable given the needs of mass society after the Neolithic Revolution. In other words telling people to stop being stupid probably won’t have the effect that the New Atheists think it should. People are just…well, stupid. I do have to admit that there seems a bit of irony in this, insofar as the New Atheists promulgate a world-view predicated on adherence to the empirical facts, but have the normal human bias to discount those data which conflict with their prior model.

But this is not just an issue with New Atheists. Many who disagree with the New Atheists on the cultural Left seem averse to grappling with the empirical facts when it comes to Islam, where because of the New Atheists’ lack of interest in social conformity they express truths as if they’re the child who sees the naked emperor. Richard Dawkins regularly makes bold and laughable assertions, outrunning his own knowledge base whenever he talks about things not biological. But sometimes those who rebut his claims also outrun the facts in their eagerness to “debunk” his unpalatable views. About a year ago I got into a Twitter conversation with financial journalist Heidi Moore, who basically decided that she had to correct my misguided views about Islam. Though I agreed that Dawkins’ contentions were rather excessively general and deterministic, I believed her own apologia for Islam was based on just as rickety a factual foundation. Somehow in the wake of 9/11 American liberals, and to a lesser extent the mainstream more generally, have transformed themselves into Hujjat al-Islam, or “Proof of Islam,” whenever confronted with “ignorance.” The curiosity here is that yes, their interlocutors are expressing ignorance. But in their rebuttals there is also a great deal of ignorance.

In the exchange above Bill Maher in contrast has clearly done his homework. The majority of the world’s Muslims hold quite illiberal views. Not all Muslims. And there are regions where Muslims hold views in line with Christian societies which have undergone secularization. But overall Pakistan is closer to the central tendency than Bosnia, least of all of because there are nearly 200 million Pakistanis today. You can read the Pew survey which Maher referenced yourself, it’s been out for years.* He’s clearly conversant with the details. The usual rejoinder from liberals out to the mainstream is “but Christians too….” Maher points out that this sort of equivalence is just not plausible. Rather, it’s a ploy. No ex-Christian atheist fears for their life, though they may experience social ostracism.

The flip side of this of course is that some Christian conservatives and New Atheists argue for a Platonic and fixed character for Islam. For the New Atheists this follows from their thin and spare model of religious belief, which derives from elementary axiomatic errors. For many Christian conservatives it is derived from their religious beliefs, which they assume to be true. Islam, being false, is always going to be false. But taking a step back from the perspective of someone who believes all religions are fictions, and accepts a model of more cognitive and cultural complexity, it seems striking exactly how pliable religion itself is. If you read The Northern Crusades (against the pagan Balts) you may be struck by the similarities to the behavior of the Islamic State. And you don’t need to go back nearly 1,000 years, the Thirty Years War is more than sufficient in terms of barbarity. Religions are not special creations of god, they evolved from the history and minds of men.

It is true that not all Muslims present views which make one recoil. The problem is that in places like Pakistan enough do that if you violate the blasphemy law you may be killed rather quickly by those who have a less broad perspective. Even in Turkey, which is on the more liberal side in regards to religion, the ascendant Islamists have conservative views which lead them to chide women laughing in public. Depending on your views of the term “bigot” it is or isn’t bigotry to assert that the majority of the world’s Muslims are deeply illiberal, so it is not entirely surprising that atavistic neo-medieval violence periodically explodes out of the nether regions of the faith. But, it is also critical to question whether Islam is constitutionally so. Being that it is made up, like all other religions, I am quite skeptical of that. So there is hope if one keeps the faith that what goes down must eventually come up.

Does, on the whole, Bill Maher express obnoxious and superficial opinions? Probably, from what I’ve seen and heard. But the evidence above suggests that he’s not constitutionally incapable of honest insight.

* By and large Iraqi Shia are actually rather conservative in the broader Muslim world. I wonder of the low support (relatively) for the death penalty for apostates is a function of the rise of sectarian violence in the mid-2000s, where they saw exactly where a proliferation of takfiris leads.

DNA, history, and genealogy

downloadIn about a week my friend Christine Kenneally will have a new book out, The Invisible History of the Human Race: How DNA and History Shape Our Identities and Our Futures. The scope of the work is pretty diverse, from individual personal stories, to the sorts of grand historical narratives which the Reich lab is spinning from their numerous publications. I had the pleasure of reading early drafts of the work, and what struck me is that Christine does a very good job of making the case for why genealogy is not silly, a common problem that people in the field encounter. Honestly I didn’t give much thought to genealogy until recently, but then I’m one of the people who is rather certain of the near-term genealogy of my family. When your past is more clouded these issues can loom much larger. It’s only silly when you’re confident of your background. The role that DNA can play in constructing the larger portrait is pretty straightforward.

Aside from the human element threaded through the science hardcore DNA junkies won’t find much to surprise. Christine touches base with the usual suspects in personal genomics, as well as those who work in an academic setting. But if you are a more general layperson who is sometimes befuddled by the jargon in my posts, this would be a pretty good taste of the field, and where the “post-genomic era” is leading us all.

We’re at peak haplotype

Credit: Razib Khan
Credit: Razib Khan

Sometimes when I see treatments of the history and development of evolutionary genetics from outsiders I notice how jargon creeps into their descriptions in a way that’s not adding much value. For example, several times over the past year I’ve seen people refer to how one can construct genetic clusters using “haplotypes.” The fact is that haplotypes are not necessary for the construction of genetic clusters; any form of genetic variation will do. Haplotypes can add something of value, but they’re not necessary. Terms such as “haplotypes” or “SNPs” might percolate into broader public discussion, but too often it seems that they’re used like the term Abracadabra!, an incantation.

But it did get to me thinking, how common has utilization of the term haplotype become in the scientific literature? When asking a question like this I did what I usually do: go to Google Scholar and see how many hits I get for a term by year. As you can see the use of the term levelled off in the mid-2000s, as the HapMap took off and became part of the background furniture of human population genomics.

Here’s the raw data….
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Books are best to read with, Jesus told me so

220px-Devil_codex_GigasPeriodically in my Facebook feed I get people posting articles like this, Science Has Great News for People Who Read Actual Books. By “actual books” the author means a physical book, and in particular a codex. Apparently at a conference last month a study was presented where a sample of 50 individuals produced a result where there was more recall of plot points from 30 page story better when reading on a book than an e-reader (N = 25 for each treatment). The report in The Guardian finishes:

The Elizabeth George study included only two experienced Kindle users, and she is keen to replicate it using a greater proportion of Kindle regulars. But she warned against assuming that the “digital natives” of today would perform better.

“I don’t think we should assume it is all to do with habits, and base decisions to replace print textbooks with iPads, for instance, on such assumptions. Studies with students, for instance, have shown that they often prefer to read on paper,” she said.

First, someone who is presenting a huge result based on N = 50 (and a W.E.I.R.D. one at that) has a lot of chutzpah in advising caution at such broad general statements. The only true digital natives today are under the age of 10 when it comes to reading on devices such as the Kindle. These sorts of studies seem keen on reiterating the prejudices of the contemporary median readership. Who cares what median students prefer today? A few years ago MySpace was preferred. I believe that if these studies were going on in the 4th century A.D. then you’d see just how much the well educated Roman preferred the scroll to the uncouth codex (though a well educated Greek slave was probably the most “haptic” and “serendipitous” reading device of all!). The “actual book” is actually an innovation, as widespread utilization of the codex format took centuries to become the norm. The Christian Bible was one of the first books habitually in the codex format, and the spread of Christianity has been credited with the popularization of the codex in relation to the scroll. The point is that a “book” is an abstraction. The codex, scroll, or e-reader, is its concrete manifestation. Perhaps it is true that the codex format is ideally optimized for human comprehension. I suspect not. Humans are much more prejudiced toward their habits than they are optimized toward reading. Humans didn’t evolve with reading.

5dc5c4169There are real problems with the e-reader format. I dislike being unable to jump between pages “naturally” too. But, I’m rather sure that these problems will be solved at some point. The codex has had 2,000 years. Give e-readers at least another 10.

Also, let’s keep it real, the average American does not read very much. The main reason I’ve mostly switched to e-reader format is that I hate having to lug around many books (and I am not a hoarder, I sell/discard books regularly). If the mean number of books read is 12, while the median is 5, you know the distribution isn’t normal. There are many people who don’t read at all, and a few who read a lot. Of those 12 books many are going to be paperbacks. It’s pretty easy to imagine storing a dozen paperbacks. I have a lot of textbooks, as well as academic press books. And I’m on the mild side compared to people who are older or have more of a hoarding habit. I wonder how much an acceptance of the convenience of the e-book formats correlates with people who read too much to not clutter their houses if they stick with the traditional physical formats.

Addendum: If my hardcover books could be compressed somehow so they took up minimal space I might prefer hardcover to e-book. The main thing I would miss is the search features, but I might trade that for being able to jump easily between pages (there are indexes!). I’m not sure that my daughter or son would make the same decision though.

How Turan invented Islam

Credit
Credit

Much of the mythology of the pre-Islamic Persia involves the tension and conflict between Iran and Turan. In modern parlance “Turan” has become synonymous with Central Asia and the Turk, but in its original meaning it involved two groups of Iranian peoples who were distinctly geographically situated. The eruption of the Turkic tribes can be dated to approximately the middle of the first millennium A.D., so they post-date the mythological era of the Iranian peoples, though they coincide with the arrival of Islam to Central Asia. Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane is really the chronicle of the last 500 years of the cultural efflorescence of classical Turan, the ancestors of the people we today term Tajik, as well as nearly extinct groups such as the Sodgians. Though there are numerous ‘call-backs’ to the pre-Islamic era, as well as the requisite scene setting chapters, the heart of the matter occurs during Islam’s Golden Age, in particular of the Abbasid Caliphate. The last few centuries, from the rise of more self-consciously Turkic political actors to the period of Timur, get’s short shrift, and the story is tidied up rather quickly.

k10064Lost Enlightenment is also unapologetically a history of intellectuals. Social, cultural, and diplomatic events serve as background furniture. They’re noted in passing and alluded to, but ultimately they are not the center of the story. They’re for intellectuals to be situated within. The key fact which serves as the cause for a book like this is many are not aware that an enormous disproportionate number of the intellectuals of the Golden Age of Islam were ethnically Iranian and from Central Asia. I say ethnically Iranian, because it is not quite accurate to state they were Persian, because the Iranian languages and ethnic groups differ considerably. Abū Rayḥān al-Bīrūnī was a native of Khwarezm, the Iranian language of which was close to Sogdian, and therefore closer to modern Ossetian. The author observes that because intellectuals from Islam’s Golden Age habitually wrote in Arabic most moderns assume they must be Arabs (perhaps more accurately, the names “look Arabic”, unless they are unrecognizable transliterations). But this is an error of the same class as presuming that because Western scholars utilized Latin as a lingua franca until recently they must have been Latins. A quick perusal of Wikipedia’s entry on the philosophy and science of the Islamic Golden Age will disabuse you of this notion. Though the central focus of Lost Enlightenment is on Iranians from Turan, it is important to remember that many individuals of note don’t quite fall into this exact category but exhibit affinities which might surprise. Though the figure behind the most widespread school of Islamic law, abu Hanifa, is well known to have had his ancestry among the Persians of what is today Afghanistan, ibn Hanbal, founder of the austere Hanbali school (arguably the ancestor of the Wahhabi and Salafi movements) was descended from Khorasani Arabs. In other words, even many of the Arabs had eastern affinities.

41OxoLpuNyL._SY344_BO1,204,203,200_To understand why, you need to realize that to a rough approximation the shift between the Umayyad Caliphate to the Abbasid involved a orientation of the Islamic world away from the Mediterranean world and toward Central Asia, Turan. This is summarized by the reality that the capital shifted from Damascus in Syria to Baghdad in Iraq, but this small distance does not do justice to the shift in mentality. The Abbasids were brought to power by armies and social movements with roots in Khorasan and further north and east. It was in a sense a revenge of the mawalis, non-Arab converts to Islam who were marginalized as second class citizens under the Umayyads. Traditional Muslims sometimes refer to the Umayyads as the “Arab Kingdom” because of the ethnic nature of their polity (evidenced by the fact that there were instances where Arab Christians were privileged over non-Arab Muslim converts). Though the Abbasids were an Arab Caliphate, their ruling culture was much more ethno-linguistically cosmopolitan. Over time the dynasty began to rely more and more upon Turks from Central Asia to man their armies, while the domain of culture and politics was heavily inflected by Iranians and Arabicized Iranians. For a period the caliph al-Ma’mun relocated the locus of the Caliphate to Merv, in modern day Turkmenistan. It is not surprise that al-Ma’mun’s mother was a Persian from Khorasan.

downloadThe culturally Turanian color of the Abbasid world is critical because I think it is plausible to argue that Islam as we understand it emerged during the Abbasid period. On the face of it this sounds strange. Islam as a religion obviously dates to the time of Muhammad, in the early 7th century. Salafi purists would purge all that came after the mid-7th century, the period of the “Rightly Guided Caliphs” (i.e., the pre-dynastic period). But to say Islam was formed in this period is like saying Buddhism dates to the time of the Buddha, in the middle of the first millennium B.C., or that Christianity dates to the time of Jesus down to the writing of the Synoptic Gospels a few decades later. No matter what religionists may aver religions evolve organically through time, and some of their most seminal aspects develop considerably later. Among Christians this is acknowledged by the repeated attempts to recreate “Primitive Christianity,” that is, the Church before it became co-opted by Roman Imperial culture. But even before the conversion of Constantine Christianity had transformed into a gentile religion with Jewish roots, rather than a Jewish sect. The institutional superstructure of the Christian Church and its theological basis were totally transformed by the immersion of sectarian Judaism in the Greek and Roman world (one could say that this is true of both Christianity and modern Judaism!).

In modern Sunni Islam (~90 percent of Muslims) in comparison to Christianity theology plays a relatively minor role in relation to law, shariah. One of the primary bases of shariah are the hadith, the sayings of the prophet. It so happens that the two most respected collections of these sayings for Sunni Muslims were authored by Persians from Khorasan. The author of Lost Enlightenment chalks up the prominence of Turan in the compilation of hadith to the pre-Islamic cultural and religious norms, in particular on the prominent Buddhist tradition of translation and collection. Though never explicit the argument seems to be that this region so essential in the development of Islam as we know it remained religiously plural, with Buddhists, Zoroastrians, Christians, and pagans prominent for centuries, and this cultural background could not but help shape the beliefs and practices of local Muslims, many of them converts. But the connections are often not made concrete, but are more suggestive. For example the connection between Buddhist viharas and the later madrasas. Because the Buddhists of Turan have no modern day cultural descendants it can be quite difficult to comprehend just how prominent this religion was during this period, but it is well known that under the early Abbasids the influential Barmakid family were  relativley recently converted Buddhist functionaries. Rather than the specifics though I think the fixation in Lost Enlightenment on the non-Muslim milieu that persisted in Turan down to ~1000 A.D. is to emphasize that during Sunni Islam’s formative period the religious culture looked east as much as it did to the west, that is, the world of India. The connections between the Near East, Central Asia, and India, are ancient, going back to records of Indian merchant communities settled in Sumeria. It does not take a leap of imagination to wonder if Sufi mysticism may have been influenced by Indian practices and beliefs (some early Sufi mystics do report Indian, or perhaps more accurately Turanian Buddhist, mentors). And there are curious currents in the other direction, “Greek medicine” as transmitted by Central Asians is still practiced in India.

Islamic civilization beginning with Muhammad is at its foundation “West” facing. Muhammad engaged the ideas and thoughts of Christians and Jews, and his foreign travels took him to the margins of Syria. The details of prayer positions among contemporary Muslims reportedly derive from the practice of Syrian monks. The eastern fringe of the Islamic world at its founding was that of the magians, the Zoroastrians, who were also clear influences. But if you accept the proposition that much, most, of Islamic civilization dates to the Abbasids, then your understanding of West and East must shift. Here the West is the world of Persia-verging-upon-Mesopotamia, Iran, and the East is India, and to a lesser extent China. The center is Turan. This is a somewhat tendentious position, but I do think it is defensible, should make us reconsider the genealogy of Islamic culture and civilization.

But one of aspects of Lost Enlightenment that I found irritating is prefigured by the title, and that is the Whiggish attempt to shoehorn Turanian civilization into the stream of ascending scientific and mechanical complexity of the West. I do think it is interesting that Turanians contributed overwhelmingly in the domains of medicine an the natural sciences, and far less to what we might term the humanities. The author argues rather aggressively that this is due to the fact that the environment of Central Asia requires city-scale hydraulic civilization, putting a premium upon the mechanical sciences. I am moderately skeptical of environmentally deterministic arguments, but they are reasonable. What is harder to excuse is harping upon the same thesis so often, as well as showing your own philosophical preferences so clearly. The author, like myself, is biased toward those scholars with a peripatetic method in regards to the natural sciences. Though making the case for Turan’s role in the formation of Islamic orthodoxy, he is not positively inclined toward the anti-scientific legalist orientation ascendant after ~1000 A.D. Neither am I, nor are most Western readers of this work. If al-Biruni is the hero, then al-Ghazali, a Persian from Khorasan, is the villain. This sort of normative typology is not befitting a scholarly work of this level.

Finally, we have to address the fact that today Turan is not what it once was. The prominence in intellectual endeavors indicates a demographic robustness which is hard to see in modern day Central Asia. The short answer seems to be the Mongols. The author argues that the Mongols were particularly destructive in Central Asia, both in the areas of straightforward genocide and destruction of the material basis of Turanian urban society in the form of hydraulic engineering. It seems clear that this period also saw the shift from a mostly Iranian speaking populace, to a Turkic one, as the Turks, long recently dominant politically, became handmaids to the Mongols. Though Lost Enlightenment gives some space to early Turkic attempts at ethnic assertion (apparently they were segregated in Baghdad in the early years), it is a very secondary aspect. But it may be that ultimately Turanian civilization always had a sell-by date, because the geographic parameters for dense civilization in Central Asia are fragile and marginal. Situated at the center of Eurasia, and forcing its populace to engage in ingenious engineering to simply survive, Turan was bound to be a creative force. But its explosion may inevitably have been ephemeral.

You lose-they win & they win-you win

Colossal_octopus_by_Pierre_Denys_de_MontfortProPublica and This American Life have broken an expose of sorts about the spinelessness of the New York Fed in relation to the Wall Street banks which it is enjoined to supervise, specifically Goldman Sachs (which is basically the apotheosis of a Wall Street bank). But this is really all style and no substance: as Daniel Gross points out the New York Fed has always been a creature of Wall Street, there to do its bidding. The reason that this story is worth reporting on is that a whistle-blower recorded some of the meetings between Fed officials and Goldman Sachs, and therefore highlighted just how clear it is that the latter calls the shots for all practical purposes. But we all knew that after 2008. Wall Street socialized its losses, and came roaring back, privatizing the gains which accrued from the easy money doled out by the Fed, as well as the now explicit back-stop of the American government. They know we know, and they know we won’t do a thing about it. Basically it’s like Wall Street punched us in the face, and then sent us a bill for the injury. Also, they demand an apology whenever we besmirch their honor.

There will always be winners and losers, the high and mighty and the low. The key is that it is optimal for the many when the great gain honor through actions which spill over into the public good. The ‘innovations’ of the financial sector, and the bloat that has occurred in ‘inter-mediation’, do not fall into that category. There are only so many gains on the margin of improved allocation of capital. At some point the proliferation of professions meant to smooth the institutions of an advanced society end up devolving into a zero-sum game for finite resources. This is true with bankers and lawyers. Both these are honorable and necessary professions, but when there is a surfeit of both you know that society has gone sclerotic.

downloadThis is why I put my hope in Silicon Valley, and in particular men such as Elon Musk. Musk is as much a megalomaniac as a Wall Street “master of the universe,” but his ambitions and greed for glory drive him to found firms which aim to change the fundamental rules of our civilization. And for the better. It’s not a zero-sum game he is playing; he wants to explode the pie and grab a huge chunk of it. A high-risk high-reward endeavor.

Ultimately to fend off sharks you need killer whales. Our civilization is premised on capitalism, and growth. Without growth elite over-production leads to the rise of zero-sum competition for resources, and the brutal games of greed which led in part to the financial crisis of 2008. The hope is that Silicon Valley and other genuinely innovation sectors of society can hoover in enough talent, creativity, and ego, to change the rules so that the crass an Byzantine machinations that are on display in the activities of the New York Fed become blips upon our near term historical trajectory. In contrast, if we stagnate, except the games to get bloodier and more desperate.

Khorasan is kind of a big deal

k10064Last week the American armed forces attacked a Syrian branch of al Qaeda which went by the name Khorasan. If you read around the web you’ll be informed that the term, a geographic one referring to the lands of Islam’s east, along the fringes of Persia, Central Asia, and western South Asia, is freighted with historical resonance for jihadis whose ideology is strongly inflected by a romantic vision of Islam’s past. By coincidence over the past few weeks I’ve been reading Lost Enlightenment, a book which chronicles Central Asia’s contribution to early Islamic civilization, and therefore a story in which Khorasan looms very large. Of course you don’t need a book length treatment on an obscure historical topic (though I would argue Central Asian shouldn’t be obscure, it is) to understand why Khorasan is important in the imaginations of jihadis. 41OxoLpuNyL._SY344_BO1,204,203,200_To keep it succinct, though Salafis and their fellow travelers idealize the period of the Rashidun caliphs which ended ~660 A.D., the real historical basis of their movement in terms of an idealized period which is not mythological is that of the early Abbasids, after 750 A.D., and especially 800 A.D. And it is under the Abbasids that the motor engine of Islamic civilization shifted to the east, to Khorasan, the source of the armies which fueled their initial victories, and later of the soldiers and intellectuals who solidified their regime. Though Baghdad was the capital of the Abbasid Caliphate, the tendrils of influence and power always led back to the east so long as the polity was vigorous.

These extremist Islamic sects and movements always seem to deal in mythology and the legends of their own past. Though much of the fabric of their reality is fiction, there is often a thin scaffold of historical basis which serves as a skeleton around the narrative. I am not sure how critical it is to understand this scaffold, but it probably wouldn’t hurt. To some extent these radicals seem to speak in an inadvertent code, in that Western audiences as totally lacking in the historical consciousness that is necessary to properly interpret and comprehend considered and conscious semantic choices.

The phenotypic and genotypic

mexicanThe image to the left is the ‘average’ face of a Mexican woman as generated by the University of Glasgow Face Research Lab. Aside from the fact that the face is prettier than the typical human because of the well known tendency of averaging facial features removing unattractive asymmetry it is racially what you might expect, a synthesis of an Amerindian and European face, with an Amerindian skew. But a phenotypic average only tells you so much. Variation is one of the key ingredients in evolutionary processes, and by getting a sense of a population’s variation you can infer things about its past and possible future history. For example, if that variation is heritable, then it is amenable raw material for adaptation. In contrast, if the variation is due to environmental parameters then it is not going to be appropriate input for adaptation via natural selection. In a nation like Mexico we see the full range, from ‘typical’ Amerindian phenotype, to someone who looks to be fully European (with a small minority with visible African ancestry).

But if the phenotype is heritable, then underlying this variation is genotype. The extent that genotype controls the variation is contingent upon heritability. The heritability of behavioral phenotypes is often around ~0.5. But for physical traits such as height or pigmentation the heritability is much closer to 1, on the order of ~0.8 to ~0.9. That means 80 to 90 percent of the variation of the trait across the population is due to variation in the genes. When we code someone as “Amerindian” or “European” or “African” we are assessing phenotypes with a strong underlying genotypic component. A new study in PLOS GENETICS outlines just how this plays out in Latin America, a region of the world which has the virtue of being a living experiment in admixture between different geographic races over the past 500 years.

Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals:

The current genetic makeup of Latin America has been shaped by a history of extensive admixture between Africans, Europeans and Native Americans, a process taking place within the context of extensive geographic and social stratification. We estimated individual ancestry proportions in a sample of 7,342 subjects ascertained in five countries (Brazil, Chile, Colombia, México and Perú). These individuals were also characterized for a range of physical appearance traits and for self-perception of ancestry. The geographic distribution of admixture proportions in this sample reveals extensive population structure, illustrating the continuing impact of demographic history on the genetic diversity of Latin America. Significant ancestry effects were detected for most phenotypes studied. However, ancestry generally explains only a modest proportion of total phenotypic variation. Genetically estimated and self-perceived ancestry correlate significantly, but certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry.

The phylogeographic aspect of this paper is not too interesting to me, as it confirms what we’ve known (e.g., more Amerindian ancestry in northern Brazil, Mexicans are somewhat more Amerindian than they are European, etc.). Rather, the biggest findings are those which relate physical appearance, self-identity, and genetic ancestry. In Europe someone who identifies as “white” is invariably ~99% European when assessed using a genetic method (the ~1% balance is often from Iberia). More precisely, white Europeans are ~99% West Eurasian, since a non-trivial amount of trans-Mediterranean gene flow has occurred, meaning there isn’t a clear boundary between Europe and nearby regions. Similarly, in Sub-Saharan Africa someone who identifies as “black” is likely to be nearly all Sub-Saharan African. This is often not the case in Latin America. That is, those who identify as “white” or “black” often have substantial admixture from other geographic racial groups.

One of the major drawbacks of this study is that it relies on 30 ancestrally informative markers (AIMs). Though this is acceptable in forensics, some of the ancestry inferences made on an individual basis are a touch less accurate than they would be on a dense marker SNP chip (e.g., the 650,000 SNPs used on the HGDP). The modest correlations here are probably a little lower than they would be if the ancestry was more accurately adduced. But in the broad sketch the conclusions are likely defensible. One result which may surprise then is the very modest correlation between physical traits and ancestry. Here’s the quote from the paper:

Regression of phenotypic variation on genetic ancestry (taking Native American as reference) demonstrates a significant effect for most of the traits examined (p-value <10−3 using a conservative Bonferroni multiple testing correction, Table 2). Among the non-facial phenotypes (accounting for sex, country, age, educational attainment and wealth) higher European ancestry is associated with: increased height, lighter pigmentation (of hair, skin and eyes) (Figure S6), greater hair curliness and male pattern baldness. Hair graying approaches statistical significance (p-value 10−2). Higher African ancestry is associated with: increased height, higher skin pigmentation and greater hair curliness. The proportion of phenotypic variance explained by ancestry is highest for skin pigmentation (19%) followed by hair shape (8%) and color of eyes and hair (4% and 5%, respectively) but at most 1% for the other phenotypes.

As I said it could be that the AIMs aren’t quite as accurate as they should be, and are underestimating the ancestral fractions on the individuals at the extremes (e.g., someone who is 100% European is estimated to be 95% European, because the marker set lacks precision). So you might bump up the proportion of variance explained a bit, but likely this still seems way too low to you intuitively. There are a few things going on here. First, skin color is controlled between populations by a relatively small set of genetic loci. This means that in admixed populations the sample variance, the random draw of genotypes across the loci, is going to vary a lot even in individuals with the same ancestry. Because of the relatively small number of large effect loci skin color is a trait which shows a lot of variation within families where ancestry is geographically diverse. And within families, or at least across full siblings, total ancestry is not going to vary that much. Second, for some of the “traits” in question that are being measured there is just a lot of variation within geographic races. It makes sense that ancestry would explain only a small fraction within this pooled data set. And yet people can recognize a set of features which are clearly European or Amerindian or African. I think the answer here is that you are picking up on correlation structure across the traits. A suite of subtle facial contours for example connote “European” in a Gestalt manner, even if quantitatively each contour trait has a lot of variation within a population and overlaps across them.

Where this all “cashes out” though is in the intersection of the sociocultural and biological. Within the paper itself they observe a few trends which would not be surprising. Skin color and hair form are very salient characteristics, and lead individuals to shift their estimates of their own ancestries. Those with lighter skin tend to overestimate their European ancestry fractions, while those with curlier hair overestimate their African ancestry. These are traits which have the characteristics that they are quite ancestrally informative to particular geographic races, and, very visible (unlike, say, Duffy status). Within these data there are also particular patterns which are intriguing and less obvious; those with low amounts of Amerindian ancestry underestimate the fraction, while those with higher levels overestimate it. The details of these patterns are obviously contextual in terms of time and place (e.g., in Henry Louis Gates Jr.’s genealogy specials many celebrities seem to yearn for exotic lineages, which would not be the case in past decades). What is more interesting is that fine grain patterns of variation in genetic ancestry and how they deviate from perceived ancestry can finally allow social scientists to get a better grip on patterns of discrimination (or lack thereof). It is not entirely uncommon in Latin America for full siblings to sometimes be socially perceived to be different races because of the random segregation of salient characteristics. In the aggregate these sorts of cases would allow one to estimate the effect of social perceptions, slights, or advantages. With the genetic dimension one could also ascertain the possibility of group differences, because many subtle characteristics are going to track genome-wide patterns, rather than a few phenotypes which society privileges when sorting people by geographic origin.

Polygyny – maybe it’s agriculture

Citation: Lippold, Sebastian, et al. "Human paternal and maternal demographic histories: 4 insights from high-resolution Y chromosome and mtDNA sequences 5." Methods 1 (2014): 2.
Citation: Lippold, Sebastian, et al. “Human paternal and maternal demographic histories: 4 insights from high-resolution Y chromosome and mtDNA sequences 5.” Methods 1 (2014): 2.

Alexander Kim has already responded in depth to a new paper in Investigative Genetics, Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences:

Results
We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm.

Conclusions
The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.

Comparing male and female demographic histories can be a mug’s game. But if one is appropriately cautious some insight can be gained, and in this paper the authors are appropriately cautious. It isn’t surprising that female effective population sizes are somewhat larger over the long term and across deep history than male ones for our lineage. We’re a mildly sexually dimorphic species, suggestive of possible mild polygyny at best, on average. In other words, males compete, but not that much. Far more interesting to me is what Alexander Kim keys in on:

Among the most interesting inferences is Holocene crash in male Ne, with no clear reflection on the mitochondrial side of things, everywhere but Oceania and America — most dramatically in the Middle East/North Africa:

Not from the Pleistocene
Not from the Pleistocene

As a speculative matter this might reflect the rise of “super-male” lineages that arose with agriculture and mass society. In other words, extreme levels of polygyny are a novel cultural evolution, which could only emerge with the level of stratification and power accumulation in patrilineages enabled by agricultural, or agro-pastoral, societies. Hyper-polgyny might also be correlated with the extreme mate guarding and sexual jealousy which is the norm among many Eurasian societies. The implication here is that many of the “regressive” social practices we associate with “traditional” Eurasian societies are simply cultural retrofits to adapt to new social circumstances enabled by mass society. Liberal individualism as an ethos may not be a novel innovation, as much as the emergence of long submerged instincts which evolved when collective institutions and interests were far weaker as forces in our day to day decision making.