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Gene Expression Blog

gsi2-chp1-9 It 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, ultimately 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.

• Category: Ideology • Tags: Political Correctness 

download In 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.

• Category: Science • Tags: Genetic Genealogy 
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….

• Category: Science • Tags: Haplotype 

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.

• Category: Miscellaneous • Tags: Technology 

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.

download The 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.

• Category: History • Tags: Islam, Turan 

There’s a lot going on in the world.

• Category: Miscellaneous • Tags: Open Thread 

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.

• Category: Economics • Tags: Finance 

k10064 Last 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.

• Category: Foreign Policy • Tags: History, Khorasan 

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.

• Category: Race/Ethnicity, Science • Tags: Genomics, Latin America, Race 
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:

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.

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.

• Category: Science • Tags: Demography 

Epigenetics is real. But it doesn’t change everything. That needs to be said, because people seem to get the impression that everything is changed. In Trends in Genetics, Serving Epigenetics Before Its Time:

Society prizes the rapid translation of basic biological science into ways to prevent human illness. However, the premature rush to take murine epigenetic findings in these directions makes impossible demands on prospective parents and triggers serious social and ethical questions.

In their efforts to anticipate the eventual human applications of emerging areas of science, scholars of the ethical, legal, and social implications of genetics and genomics sometimes become too speculative to engage the immediate concerns of active scientists and policymakers. However, although evidence-based applications of human epigenetics may emerge in the future, premature epigenetic risk messaging is already here and its content and impact must be understood. The messages in circulation raise ethical and social concerns regardless of whether human epigenetic studies eventually confirm the murine results. Because the prospect for any successful human translation of epigenetic research depends as much on the management of these issues as on further human studies, they deserve close attention by all involved in their design, dissemination, and public consumption.

(the link is ungated)

• Category: Science • Tags: Epigenetics 

854270_w185 I had a long discussion yesterday with an individual who has been reading me since 2003. We talked about lots of things. One issue which perhaps I need to reiterate because it’s implicit is that I dissent to a great extent from the premises which underlay both American conservatism and liberalism. Like American liberals I think the life outcomes of many Americans are not due to their choices simply understood. Rather they are the outcome of chance events, whether it be through social background, or, simple happenstance. Years ago I recall Nassim Taleb complaining that people would read The Millionaire Next Door, and believe that by doing everything those individuals did they too could become millionaires, as if there was no random component to such outcomes. The reality is that some people are in the right place and right time. And, some people are born in the right social positions.

Where I dissent from American liberals is the idea that all of the outcomes in our society, in particular inequality, are due to chance or inherited social position (e.g., race or class privilege). In The Son Also Rises Greg Clark reports on intriguing results which indicate that social competence in heritable. To some extent this is common sense. Personal dispositions are heritable, and some dispositions are more congenial to remunerative activities than others. Though many on the Left (though not all) are willing to acknowledge the arguments in Steve Pinker’s The Blank Slate in the abstract, in the concrete they get very little weight when it comes to social policy. To give an example, for many on the Left we can talk about differences between groups (whether it be cultural or biological) only when all social inequality is abolished. The catch in this though is that any persistent differences may also result in persistent social inequality or difference in outcome.

The_Blank_Slate When it comes to the American Right there are two distinct strands. The first is the child of classical liberalism, to some extent in a more thorough fashion than the American Left. For this element the pidea that capitalism is efficient in allocating resources, and that people receive their just desserts due to hard work, becomes such an all-encompassing narrative that other variables are neglected. This was clearly evident in 2008 when some conservative libertarians kept harping on the “free market” mantra because they literally had no other playbook. I recall specifically someone from the American Enterprise Institute on the radio arguing that bankers should keep their bonuses because that’s how capitalism works, even after the bailouts. When confronted by this he really had no response. He was literally dumbfounded. It is as if the market was the ends of the American political system, and all wealth is the product of the market. Though not as constitutionally hostile to the idea of heritable differences this sort of free market conservatism is not comfortable with the idea that not everyone is born with the same opportunities. The reality is that the liberal Left critique of the nature of the outcomes of a free market is correct in some deep sense, even deeper than American liberals may wish to acknowledge. Some people are born with the genetic deck stacked against them, not just the social one (and of course, as noted above there is a lot of random noise). That undermines some of the moral case for the virtue of the market, since it is not blindly arbitrating the outcomes of our choices, as opposed as sifting based on the accumulated weight of inherited history, some of which is due to the genetic lottery.

51RtznSRTAL The second strand in American conservatism is that of the Religious Right. The problem that it has is most clearly illustrated by the issue of gay rights. Though logically toleration of homosexual behavior and its innate or non-innate nature are not related, the Religious Right prefers that homosexuality be a choice for the purposes of moral censure. That is because though these Christians believe in original sin, they seem to espouse a sort of moral perfectionism where all men are equally endowed with the same sentiments and preferences (those sentiments being debased by Satan or the Satanic influence of culture). As opposed to Homo economicus, these Christians believe in Homo christianus. Though I personally espouse the bourgeois virtues of the Religious Right, their neglect of human diversity in disposition and sentiment leads us down the path of great disappointment, as many will miss the mark. A Religious Right which focused more on social cohesion in a general and collective sense, rather than personal and individual moral perfectionism, probably could produce better results (yes, it does take a village!). But the American radical Protestant model is fundamentally individualistic, and treats each human as equal and similar before Christ. And there I believe is the folly with moral crusades which attempt to turn every American family into the same American family. Such a world never was, and such a world will never be.

The Left looks to the perfect future which could be. The Right looks to the perfect past which was, and could be.

• Category: Ideology • Tags: Politics 

Quanta Magazine has a piece up audaciously titled Evolution’s Random Paths Lead to One Place. It’s basically a review of the research published in the paper Global epistasis makes adaptation predictable despite sequence-level stochasticity. There’s a lot packed into the title. Here’s the important bit from Quanta:

Many biologists argue that it would not, that chance mutations early in the evolutionary journey of a species will profoundly influence its fate. “If you replay the tape of life, you might have one initial mutation that takes you in a totally different direction,” Desai said, paraphrasing an idea first put forth by the biologist Stephen Jay Gould in the 1980s.

The findings also suggest a disconnect between evolution at the genetic level and at the level of the whole organism. Genetic mutations occur mostly at random, yet the sum of these aimless changes somehow creates a predictable pattern. The distinction could prove valuable, as much genetics research has focused on the impact of mutations in individual genes. For example, researchers often ask how a single mutation might affect a microbe’s tolerance for toxins, or a human’s risk for a disease. But if Desai’s findings hold true in other organisms, they could suggest that it’s equally important to examine how large numbers of individual genetic changes work in concert over time.

There’s been a vogue of late for attacking the utility of mouse genetics for medical research. Perhaps studying flies, yeast, and bacteria to understand evolution is also misguided? Interesting research in any case.

• Category: Science • Tags: Evolutionary Genetics 

"Chop-chop square" in Riyadh

“Chop-chop square” in Riyadh

Like Joe Young, the Mormon missionary who becomes involved in the porn industry in the late 90s film Orgazmo, our involvement in the Mid-East is probably going to result in the violation of our purity (yes, that’s only in our self-conception as a nation; we’re mostly definitely only born-again virgins, not the real deal). It’s hard to read anything about the Free Syrian Army which portrays it as anything but hapless, disorganized, if often well meaning and milquetoast (well, when they’re not allying with the Nusra Front and being nasty to Alawites and Christians who support the regime which has been nasty to them). And of course this edition of the coalition of the willing involves our stalwart Western-leaning allies, Bahrain, Jordan, Qatar, Saudi Arabia and the United Arab Emirates. Yes, Bahrain, the sectarian regime dominated by a religious minority which suppresses the majority with foreign forces. Qatar, the Islamists’ number one ally in the Muslim world. The UAE, which is home to the dystopian techno-oligarchy that is Dubai, a glittering vision of the apotheosis of slavery coexistent with post-modernity. And of course there is Saudi Arabia, the only nation in the world which regularly decapitates individuals for capital crimes. Well, except of course the Islamic State if you count that as a state!

I won’t belabor the point. Let’s remember that the Saudi monarchy is quite notably medieval in its practices and institutional arrangement (it abolished slavery in the 1962). Our enemies, Iran, and the Syrian regime, are actually much closer to modernity as we’d understand it using the Saudis as the extreme case. As it is we have to ignore this because the Saudis are our bastards, neo-feudal creeps though they may be. And we’re trusting them to help train the Free Syrian Army? Of the 19 9/11 hijackers 15 were Saudi (a further two were from the UAE, our ally). This is not going to end well. We can’t admit that we’re helping the regime of Bashar al-Assad. Yes, he’s a murdering bastard, but he’s not our bastard.

The Islamic State is a nasty piece of work. Unlike Saddam Hussein’s late lamented dictatorship it also has the ability and ambitions to spread its tentacles of nastiness across the region right now. I won’t shed any tears over the pounding Raqqa is receiving from American cruise missiles. But let’s be clear that almost certainly this is going to benefit our Iranian enemies, as well as Hezbollah. Additionally, the Saudis and their Gulf allies will probably attempt to reshape the Sunni insurgency in their own image, which is not one which we in the West would term “moderate,” let alone free. Let’s go into this with eyes open, and acknowledge that it’s a choice between a bad option, and a worse option.

Shorter: America is on the side of the less evil guys. Go America! Also see this cri du coeur, The Barbarians Within Our Gates.

• Category: Foreign Policy • Tags: Isil, ISIS, Islamic State, Saudi Arabia 

51TpAsC5UlL._SY346_FiveThirtyEight and New York magazine have pieces which look at the prosperity which was the norm in the second half of the 1990s with a soft glow. I was not in the labor market back then, but I recall the excitement, and just how easy it was to get a job for those who wanted one. It seems that these articles reinforce the basic thesis of Tyler Cowen’s Average is Over, looking back to the last golden age for the middle class.

But there’s another angle on this. Would you go back to 1999 if you had twice the income you did today? Probably that depends on your income. But imagine going back to the technology of that era. For many of us the world would be a sluggish and gray place. Cowen would point out that this is not the typical person. But it’s a lot of us, and it isn’t as if smartphones and their various features are low penetration technologies in terms of cultural ubiquity. So a simple apples to apples comparison of income is somewhat misleading. Because of rising demand from China I’m not sure that decreasing expenditures on food is sustainable (though perhaps better GMO would help in that domain). But it does seem to me that public policy is what’s keeping housing prices high, in particular in Blue State urban areas. Make the libertarians happy by getting ridding of rent control. Make the conservatives happy by allowing more sprawl. Make the new urbanists happy by allowing more vertical residential housing.

I think the bigger issue here is not economic, but social. Economic productivity is such that a guaranteed minimum income is probably viable for society. A minority may work so that the majority may eat and recreate. But human psychology is such that it seems implausible that a democratic citizenry can be maintained by passive consumption by those who themselves are not economically productive. Many of these discussions about the passing of the middle class society focus on economic well being, or lack thereof. I don’t think that’s the major issue at all, because economic productivity will continue to increase, at least on the margins, and population growth outside Africa has tailed off. Rather, the larger change will be cultural and social. Even in antiquity when societies were highly stratified the great thinkers understood that social well being rested upon the broad shoulders of the free peasantry, who were the ultimate source of most economic activity. This is very different from the model of stratified societies of the future, where both power and productivity will be concentrated nearer the top of the status distribution.

• Category: History • Tags: Economics 

Obviously colored by my interests.

• Category: Science • Tags: ASHG 2014 

10703498_10102824483928421_3532479251264917335_n (1)

In the Big Apple

I’m very excited to be going to ASHG this year. The last time it was great meeting people like Luke Jostins‘ for the first time (and re-meeting people for the second or third time). Also, the posters and talks gave a preview of things which came out later in the year, so the cost of attendance was certainly worth that. I dig genetics. This time I’m going to be in San Diego, a city that I’ve never been to. Excited to explore a little if I have time. Though despite what I’ve said on Twitter I am not going to Tijuana. But speaking of fun, if any reader knows of after hours parties, etc., I’d appreciate it if you’d hook me up. I’m actually a kind, gentle, and fun person in real life who is not a bad dancer (people seem to think I’m mean and brusque from my internet persona; this has been brought up to me by several people after they’ve met me).

Below are the sessions, etc. I’ll be going to if anyone wants to try and assassinate me in broad daylight (that’s a joke, not an invitation).

• Category: Science • Tags: ASHG 

Credit: A friend of Razib

I’ve been avoiding focusing too much Oxford Nanopore over the past few years. Privately I do ask people smarter than me/”in the know” if they think that the technology is the real deal. The reason for my skepticism is that I remember people being hoodwinked by Pacific Biosciences in 2008. Part of the issue is that biologists want these technologies to deliver, so there’s a bias in terms of how they’re going to be received.

That being said I saw some Nanopore machines recently. I knew they were small. In fact, rationally I knew how small they were. But when they were just there on the counter, like large USB drives, it was hard to take it in. The new Illumina machines aren’t very large. They’re mini-fridge scale. But to see a sequencing machine which you might actually step on by mistake was a bit mind-blowing. It’s as if we’re going from 1970s mainframe technology, where it took up a whole room, to the smartphone era, where a computer fit in your back pocket.

I don’t know if Oxford Nanopore will succeed. But it seems obvious, viscerally so, that someone will, and that we’ll have small portable sequencers which are quite accurate and will generate long reads by 2020. That’s a revolution, but by then we’ll probably take it for granted. Then we can forget about the technology, and focus on the biology and what to do with all the data.

• Category: Science • Tags: Genome Sequencing 
Brawand, David, et al. "The genomic substrate for adaptive radiation in African cichlid fish." Nature (2014).

Brawand, David, et al. “The genomic substrate for adaptive radiation in African cichlid fish.” Nature (2014).

A new paper on cichlid evolutionary genetics in Nature is pretty interesting. It’s open access, so everyone can read it, The genomic substrate for adaptive radiation in African cichlid fish:

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Reading a paper like this makes it very clear to me why organismic information is very critical in trying to understand evolutionary processes. R. A. Fisher was a great scientist, but his attempt to create very general rules for evolutionary processes as outlined in The Genetical Theory of Natural Selection seems quixotic in hindsight. As a professor of mine once said “biology is the science of exceptions.” This is probably one reason that the old 19th century vogue for creating “laws” went into decline; laws are useful only when the exceptions to them are very few. The diversity and specificity of evolutionary biological processes is why I think arguments in the form of dichotomies are in vain. For example, “selectionists vs. neutralists” or those who argue for the primacy of contingency in evolutionary outcomes, or those who favor convergence toward deterministic outcomes. It strikes me that the answer to all these questions must be predicated by the phrase “it depends….”

electr10The story of African cichlids is relatively well known. You have a huge range of phenotypic outcomes which seem to be the result of relatively recent diversification. Not only that, but cichlids look cool. The question though is what can this tell us about evolution? The paper does a lot of genomic slicing and dicing of a few select lineages. Before we knew about genes the nature of transmission in evolution was something of a black-box. With DNA that changed, and now with genomics we can look at how various features differ across lineages and over time. For example copy number variation, coding regions, regulatory elements, and characters more abstruse to those outside of genomics, such as LINEs. Sequencing a bunch of cichlids gets you a publication in Nature, but that’s not the point of it all. The point is what does it tell you about evolution, at least in this case?

Basically it seems that cichlid radiation has occurred due to selection on the natural genetic variation across many loci that already existed in the ancestral lineage. It was easy enough to type, but in some ways this reality is a bit difficult, in that classical models of selection were often predicated on new mutations emerging in the genetic substrate, and rapid sweeps to fixation from the original mutant form. A human illustration of this is lactase persistence, which seems to be due to a change in gene regulation via a new mutation that arose ~5,000 years ago, and quick swept to near fixation across many diverse human lineages. This sort of phenomenon is like striking a hammer at the genome; it leaves a big mark which is easy to detect. In contrast to hard selection, soft selection on standing variation operates across many loci, and rather than a novel genotype in a singular sense produces a change in underlying allele frequencies. In some ways this is more classical Darwinian, but it also generates more work and is not as elegant as a simple model of a hard sweep from a new mutation. But that’s just how it is. At least in the cichlid lineage.

41SWwcvSm6L._SX258_BO1,204,203,200_ Actually, I suspect that’s how it is in many complex organisms. For a human illustration, see The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation. I’m betting that it’s also the norm among our many domestic animals. For example rabbits. A few years ago at a conference Claire Wade reported that the focus on traits and genes with disjoint distributions across dog breeds had obscured the reality that much of the variation in this lineage is still shared, and there is probably a lot of soft selection on polygenic traits going on.

So the near future is in quantitative traits, and natural selection reshaping the variation which is already present in lineages. Perhaps people should start re-reading Genetics and Analysis of Quantitative Traits. And as a weird side effect, if I was interested in such things I bet that the emphasis on selection from standing variation probably supports philosophical monism. All is one. Or something.

• Category: Science • Tags: Evolution 

As you all know by now the eligible electorate of Scotland has voted “No”, against independence. At least 55 percent has. I think that the fact that this has occurred relatively peacefully and in a civilized manner should be edifying to all. Though I do not have great passion on this subject, I am broadly sympathetic to separatist movements within the European Union, as it strikes me that the existence of the European Union itself obviates many arguments for the gains of being part of a larger nation. Scotland though differs from the Catalans in that the United Kingdom is not part of the Euro, and the claims by the Scottish independence camp as to their ability to remain with the pound did strike me as disingenuous. In fact, I found the “Yes” camp ludicrous in terms of their economic arguments, and the “No” camp quite sensible and conservative in the literal sense. I am not particularly sympathetic to social democracy, and much of the pro-independence elite seems to have been arguing that their goal was to transform Scotland into a Nordic welfare state. But economists more sympathetic to the welfare state are also confused as to the cost vs. benefit calculation.

The issue here is that sometimes a cost vs. benefit calculation is not the point. The global elite, high earning cosmopolitans extracting incredible gains from free flow of capital, goods & services, and people, feel the modern nation-state to be simply a device which exists to enact and execute laws which can serve as a framework for the free market. In other words, the nation is a means toward economic welfare. From that perspective Scottish independence seems irrational. But the average Scot is not a part of the global elite. Of course the pensioners and much of the middle class seems to have voted against independence, so one can’t assert that resistance to separatism is just a feature of the wealthy elites. But it does seem likely that a larger proportion of those who voted “No” were voting to keep what they have, rather than looking toward future gains. It wasn’t passion or enthusiasm, but prudence. A bourgeois virtue, which has its points.

But a nation is more than the sum of utils. Would anyone ask that soldiers should sacrifice their lives for productivity gains? Should Britain have yielded to Germany in 1940 because of rational calculations? Or more to the point should the Scots have bowed down before bourgeois, when it seems clear that the odds beforehand were against them? What the global elite seems to not comprehend when facing ‘irrational’ nationalism is that their opponents do not share their premises. In the developed nations of the West there is a sense of ennui due to the lack of motivating spirit. The goal of economic well-being above and beyond basic needs has long been met. Now it is on to the bigger house, the bigger car, and so forth. This rush toward competitive consumption results in short term happiness, but it is often ultimately empty. The cosmopolitan elites may be wealthy in money, but they are also often wealthy in life satisfaction because of the nature of their careers, and the experiences which they can indulge in. They do not comprehend the vacuousness of the lives of the middle to lower classes, because they live lives with verve and excitement. But at some point they will have to face the reality that the 90 percent do not exist purely as means to the ends of the 10 percent. If a system is not sustainable, it will not be sustained.

• Category: Ideology • Tags: Nationalism 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"