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 Gene Expression Blog

genome-sequencing-graphic-online

The chart is from an article in Nature. But the source is NHGRI. It illustrates that between 2008 and 2012 genomics as a field crushed Moore’s law. Then there was a leveling off between 2012 and the middle of 2015. Illumina had a quasi-monopoly for that period and sequencing costs did not decrease too much. But something changed in the past year. As you can see it’s as if we’re back in 2008, or at least we see hints of the beginning of another major crash. I assume part of this is that Oxford Nanopore is finally starting to present a possible future of a disruption of Illumina’s dominance. Though that’s still a very speculative possibility.

But second, Illumina itself sees sequencing as a commodity service, and is pushing the price point down to get more data out there. Sort of like IBM transitioned from being a company that sold you big metal boxes, to a company where big metal boxes were part of an ecology of services that you purchased, Illumina is imagining a future where the sequence is just the first step, and not a very remunerative one at that.

To take a step back, we’ve gone from the 1990s, where the human genome cost about $3 billion dollars to sequence, to today where small firms like Full Genomes are pushing $1,450 high quality whole genomes to consumers. Veritas is gone even lower, though it seems that they’re limiting the supply right now.

It’s easy to be pessimistic. But there is reason for optimism about the power of technology.

 
• Category: Science • Tags: Genomics

340px-Codex_Gigas_devilThere has been extensive discussion online about the fact that the character of Ramsay Bolton on the HBO television show Game of Thrones was irredeemably psychopathic, cruel, and so ghoulishly sadistic as to be a cartoon of evil. But as a reader of the books I’ve generally shrugged off these complaints, because the character is even more perverse on the page than the screen. If you don’t believe me, this article in Vulture lays it out comparatively. It isn’t just that Ramsay kills people, most of the “nobility” in George. R. R. Martin’s world are butchers. It is who and how that is more shocking. For Ramsay killing is not simply a means, but an ends.

Screenshot 2016-06-20 20.31.42 Not only is the book Ramsay even more inhumane than the television Ramsay, but he doesn’t exhibit an incongruity between his physical appearance and his behavior, as he does on the television show. That is, while the actor who plays Ramsay is handsome, in the books he described as not not physically attractive at all.

All this in and of itself doesn’t raise eyebrows. George R. R. Martin doesn’t write characters who are boy-scouts. He admits to preferring shades of gray. But Ramsay is no shade of gray. Who then is the equivalent to Ramsay? It seems that in this case Martin’s world is somehow unbalanced.

 
• Category: Miscellaneous • Tags: Game of Thrones

18925629._UY200_ The show runners of Game of Thrones (the HBO television which will actually complete its run under its original creators) admitted that they patterned part of the battle in yesterday’s episode on the Battle of Cannae. This was obvious to me, as I was actually thinking that the Boltons were exhibiting something similar to the Carthaginian double envelopment. Pretty cool synthesis of a callback to The Two Towers, as well as integrating real history.*

If you want to read a great description of Cannae, I’d recommend Adrian Goldsworthy’s The Punic Wars.

* Somewhat anachronistically, as the phalanx formation was used by the Romans, and perhaps not the Carthaginians.

 
• Category: History • Tags: Game of Thrones

The genetics of an early Neolithic pastoralist from the Zagros, Iran.

The genetic structure of the world’s first farmers.

Busy at the Evolution Meeting.

 
• Category: Miscellaneous • Tags: Open Thread

If you aren’t following the New Real Peer Review, you should. Endless enjoyment. What happened to the “old” Twitter account? The Daily Caller has an article about it, Social Justice Warriors Declare Battle On Colleague For Exposing Their ‘Research’. Aristotle may be a dead white male, but he had these people dead his sights:

Hence it is evident that the state is a creation of nature, and that man is by nature a political animal. And he who by nature and not by mere accident is without a state, is either above humanity, or below it; he is the ‘Tribeless, lawless, hearthless one,’ whom Homera denounces—the outcast who is a lover of war; he may be compared to a bird which flies alone.

Scientists are political too. But their object of study is real, and imposes the ultimate veto, that of the truth test. Critical Theory in contrast is fiction, and of a socially destructive rather than edifying sort.

 
• Category: Ideology • Tags: Humanities

Vox has a post up, This comprehensive Targaryen family tree explains Game of Thrones’ most complicated dynasty. I don’t really know if the family tree explains much, but it’s interesting. It does highlight two important dynamics which are probably important.

Screenshot 2016-06-14 22.51.18 The Targaryen’s are notoriously inbred. The rationale for this is that their affinity with dragons is a heritable trait, and that is the basis of their power (or it was before all the dragons died, at least until Daenerys brought them back). If they mixed their genes with outsiders presumably they would dilute that ability. Of course that doesn’t take into account selection for the trait, which would diminish any dilution through outbreeding.

As you can see Daenerys’ parents and grandparents were full siblings. Using a pedigree method her Wright’s coefficient of inbreeding would be 0.375. For a point of comparison, the child of parents who were full siblings, but whose own parents were unrelated, would have a coefficient of inbreeding of 0.25. The terminal individual in the genealogy of the Spanish Habsburgs, often cited as a case study of how inbreeding can lead to the extinction of a lineage through sterility and imbecility, had a Wright’s coefficient of inbreeding of 0.254. Something really doesn’t add up in terms of the viability of the offspring of the Mad King and his sister-wife (to get a sense of what multi-generation inbreeding might do, please see the Colt family). But then, it’s fantasy, and genetics is one area where George R. R. Martin’s gritty verisimilitude gives way to flights of fancy.

a-knight-of-the-seven-kingdoms-jpg A second aspect of the generation which Daenerys is a member of is that they are not very Valyrian in terms of their ancestry. More precisely, they are at most ~1/8th Valyrian.

This might surprise some, as the incestuous and closed-off nature of the Targaryen’s plays a huge role in the backdrop of George R. R. Martin’s novels. But incestuous marriage is actually a resurrected custom of the previous two generations before Daenery. Her great-grandfather, Aegon Vth, “Egg” from the novellas, was the result of two generations of outmarriage (so he was outbred). This pattern of outmarriage was not a conscious shift in the mores of the Targaryen royal house, but happenstance. Aegon’s father and grandfather both came to the throne because other senior claimants died. They were not expected to become kings. Aegon’s mother was a Dayne, while his paternal grandmother was a Martell. He himself married Betha Blackwood (a family of First Men background which still worships the old gods). Therefore, Daenery’s two grandparents were both 1/8th Valyrian, her parents were 1/8th Valyrian, and she is 1/8th Valyrian (at least that’s the expected value).

 
• Category: Miscellaneous

Screenshot 2016-06-13 18.15.37

Just been notified that there’s an update to Admixtools GitHub. Also, of interest to some: “This contains a public domain version of qpGraph, using the GNU subroutine library (gsl).” You can find example data the Reich lab website.

(related note, also might check out Alicia Martin’s GitHub, it has a lot of local ancestry stuff)

 
• Category: Science • Tags: ADMIXTOOLS

51u0BtDlYJL._SX329_BO1,204,203,200_ Pretty happy about the quality of comments on my post There Is No Exception in Islam. Compare to the quality of comments on the Reddit thread for the same post. Thanks to Shadi Hamid for pointing to the post on Twitter.

One thing on comments. The space of things that someone knows about is finite. But if you talk about something I know about, and are clearly bullshitting, that’s not going to be good for your future commenting on this website in terms of my supervision. For example, if you want to talk about the Reformation and early modern Europe, you better have more than Google and Wikipedia under your belt. For example, you should at minimum have read a survey such as MacCulloch’s The Reformation, and hopefully more specialized works such as Divided by Faith: Religious Conflict and the Practice of Toleration in Early Modern Europe.

Here’s a Bloggingheads.TV interview with Shadi on the book.

Some readers may not know this, but the philo-Hellenic thread prominent in Islam’s first few centuries persists to this day, but within the Shia tradition. Ayatollah Khomeini for example studied Aristotle and Plato with appreciation. This Greek inflection becomes very prominent among Ismailis.

14726 As I’ve stated before, Buddhism and Islam on the Silk Road, was a quick read. It was fascinating to read about how the spread of Islam into Central Asia and India elicited a reaction from Buddhists, who produced prophecies of apocalypse and counter-reaction (Zoroastrians did the same in the 8th and 9th centuries). One dynamic only cursorily explored is the centuries long flirtation of Mongol peoples with different world religions, before they settled on Tantric Buddhism. I did not, for example, know that the Oirat had had decades of leadership by individuals who were clearly Muslim (e.g., a leader whose name is Mahmud is recorded), before they finally converted to Buddhism en masse.

But more fascinating if you go back further is that the peoples of Mongolia had flirted with Christianity in the form of the Church of the East for centuries (the Church of the East is prominent within the family of Genghis Khan). One hypothesis, which seems plausible at first blush, is that in a competition between an Abrahamic religion and a Dharmic one, the Abrahamic one will inevitably win. The spread of Islam eastward on the Silk Road is clear evidence of this; it began at Kashgar around 1000 and completed at Turfan around 1400. But conversion of Mongolic and Manchu peoples to Buddhism in the middle of the second millennium after centuries of dabbling solidified the distinction between the Inner Asian Muslim and Buddhist blocs. But the lines we see as so clear and distinct (and inevitable) today were very different before 1500.

Currently I’m almost done with Valerie Hansen’s The Silk Road: A New History. It should probably be subtitled A New Archaeology, since its focus is on the earlier period when texts are few and far between, but excavations are copious. One interesting thing that Hansen mentions is that Zoroastrian Sogdians in China seem to have developed on a different track from Zoroastrians in Iran. In particular, the shift toward a monotheistic conception of Zoroastrianism is far less in evidence the Sogdian form prevalent on the eastern end of the Silk Road. Again, this parallels later tendencies toward divergence of Islam within China (which has been rolled back by the spread of world-normative Islam more recently; see the Dao of Muhammad).

Evolution of resistance against CRISPR/Cas9 gene drive.

Haplotype block dynamics in hybrid populations.

Human germline mutation and the erratic molecular clock.

I’ll be at the Evolution Meeting next weekend.

 
• Category: Miscellaneous • Tags: Open Thread

51+k4ZOOrlL._SY344_BO1,204,203,200_The Wall Street Journal has a piece up, The Greek Hero at the Gym, which is adapted from a new book, Lift: Fitness Culture, from Naked Greeks and Acrobats to Jazzercise and Ninja Warriors. A lot of the argument seems straight out of the kind of things I’ve heard from friends involved in CrossFit. Much of the piece disparages machines:

By contrast, traditional gym movements are geared to the lowest cognitive denominator: bicep curls, crunches, reading Us Weekly while plying the elliptical. Weight machines, by design, entirely remove skill from the equation: They are intended to offer the untaught user a way to lift.

I think machines are fine for some people. I have a friend who likes to work out on machines in a solitary fashion, and that’s what’s sustainable for him. It’s definitely better than nothing. For me, the transition to body weight exercises has been transformative in terms of maintaining a basal level of fitness. I work a lot so getting to the gym is not something I’ve found time for in a while, but I regularly do pull ups before work and when I come home. In fact I have my pull up stand right next to my front door so that I see it every day.

Screenshot 2016-06-11 20.00.25 It is interesting that the author focuses on the ancient Greeks and their body ideals. In the 1980s, as noted in the piece, there was a focused on extreme size, as you might find among body builders, especially in action films. Today the focus is on a lean look.

In past decades there wasn’t as much focus on fitness in American culture. I think part of this probably had to do with the fact that so many people worked on the farm. They engaged in physical labor as a matter of course. And there are cross-cultural differences as well. Traditionally the civilian Chinese elite class avoided strenuous exercise. In contrast, the militarized ruling classes of Greek and Rome idealized a more rugged physique.

And of course the United States has a schizophrenic attitude on this issue. There is a whole cult of fitness, where few manage to hit their targets, but most aspire to. And then there is also a movement toward “body acceptance,” which is basically a backlash.

 
• Category: Miscellaneous • Tags: Exercise

Several years ago there was a famous exchange between Ben Affleck and Bill Maher & Sam Harris on the nature of Islam. In response I published a post titled “ISIS’ Willing Executioners”. The overall point was that Affleck’s comments were not informed by the nature of Islam or Muslims, but broader political currents. As for his interlocutors, Bill Maher and Sam Harris, I think they were making a better faith effort to engage with the facts, though they too came up short. The primary reason that I give them more credit than Affleck is that I think to some extent their anti-Islamic talking points were counter-narrative toward their preferred ideology, which was on the Left-liberal end of the spectrum. Though a general contempt or disdain for religion is not necessarily a problem among American Left-liberals, for various reasons Muslims have become a “protected class” subject to prejudice from the ideological opponents of Maher and Harris’ normal fellow travelers.

41XeU3O2hiL._SY344_BO1,204,203,200_ As an intellectual Bill Maher is not a serious thinker, so there isn’t much point in engaging more deeply with his ideas. His anti-Islamic stance seems to derive from relatively old-fashioned anti-religious sentiments, which are socially acceptable among American Left-liberals so long as their targets are white Christians (“punching up”) but more “problematic” and perhaps even “Islamophobic” when the invective is hurled at Muslim “people of color” (all Muslims here being tacitly racialized as nonwhite).

Sam Harris is a more earnest individual, who clearly isn’t just parlaying a schtick into profitable provocation. I respect Harris for expressing the courage of his genuine convictions so often, instead of sanitizing his conclusions because of broader ideological commitments. That is, many Left-liberals today consider themselves “allies” of Muslims, and so tend to avoid making comments which might seem “Islamophobic”. In Left-liberal parlance ally has specific connotations: it indicates a person who has privileges, but still supports social justice for others who may be marginalized. Terms like “social justice” and “marginalized” also have rather precise meanings in terms of the theory of what they are, and the instances concretely of who may be marginalized. Rather than recapitulating the lexical subtleties of the progressive avant-garde I simply will state that a quick bit of research will clear up any possible confusion. Muslims, as marginalized people, are now considered part of a broader coalition on the progressive Left. This can be made clear for example when illustrations of “women of color” will often include one woman in a hijab (e.g., this website devoted to queer and trans issues displays a picture with three women in a tough pose, and one of them is a hijabi).

Harris, taking logical inference a bit too seriously, would probably ask about the propriety of the message it sends to display a woman in a hijab as if they are doing something meritorious, as that might strike him as anti-feminist in a traditional Left-liberal framework. And I have met progressives who agree with Harris privately in relation to a skepticism of valorization of the folkways of Muslims, but because of the broader coalition in which they are participants, they hold their critique (more concretely, they don’t want to be accused of being racist and Islamophobic). But, I suspect most people are like Ben Affleck, and genuinely believe that there is not a problem with the perpetuation of a stable multicultural society which includes large numbers of mainstream Muslims (e.g., many hijabis), as well as “sex positive” radical feminists, and queer theorists.

Sam Harris would probably respond that these people don’t take Islam seriously on its own merits, and that Islam is fundamentally and constitutively at odds with tolerance of gay people and a liberal attitude toward the rights of women. Though I disagree in the firmness and definitiveness of Harris’ conclusions, I do agree that people like Ben Affleck, and frankly most Left-liberals who might fall back on the term Islamophobia, don’t actually take Islam, or religion generally, seriously. This explains the rapid and strident recourse toward a racial analogy for Islamic identity, as that is a framework that modern Left-liberals and progressives have internalized and mastered. The problem with this is that Islam is not a racial or ethnic identity, it is a set of beliefs and practices. Being a Muslim is not about being who you are in a passive sense, but it is a proactive expression of a set of ideas about the world and your behavior within the world. This category error renders much of Left-liberal and progressive analysis of Islam superficial, and likely wrong.

51qwSfB3NBL._SY344_BO1,204,203,200_ But just because Sam Harris has the “right enemies” does not mean that he is right. Though I don’t believe Harris is engaging in sophistry or posturing toward some ideological ends, which is the case with many progressives as well as those on the social and political Right, I do think he is wrong in many details of his model of religion and Islam in particular. Unlike Ben Affleck and many progressives Sam Harris actually engages in ratiocination scaffolded by facts, rather than emotions derived from political commitments. But there are weaknesses to Harris’ methods, and his grasp of facts for his rationality engine to operate upon can sometimes be lacking (this is unfortunately a general problem with being a dilettante, which I would know, but it also doesn’t excuse people from taking Harris too seriously on topics where his command of the subject is outrun by his ambitions).

To get a genuine understanding of a topic as broad and boundless as Islam one needs to both set aside emotional considerations, as Ben Affleck clearly cannot, and dig deeply into the richer and more complex empirical texture, which Sam Harris has not. Islamic Exceptionalism: How the Struggle Over Islam Is Reshaping the World by Shadi Hamid is a genuine attempt to tackle a big issue with cold analysis and making recourse to a broader range of academic sources than Harris is wont. Hamid is a relatively well known figure, so his personal cards are on the table. A self-identified Muslim, and from what I can tell a Western liberal, he nevertheless arrives at a conclusion that Islam may be fundamentally and constitutively incompatible with the conventional Western liberal understanding of the relationship between the polity and faith.

18730593 One of the most obnoxious memes in my opinion during the Obama era has been the popularization of the maxim that “The arc of the moral universe is long, but it bends towards justice.” It is smug and self-assured in its presentation. Though in some sense over the long term I am broadly persuaded by it, too often it becomes an excuse for lazy thinking and shallow prognostication. Though there are broad trend lines in history, there are also cycles which oscillate around those lines. In those oscillations are consequences for human lives that can not be dismissed by asserting that the trend nevertheless remains. The cognitive psychologist Pascal Boyer has a saying which basically states that a theory gives you information for free. Modern Western liberals have a particular idea of what a religion is, and so naturally know that Islam is in many ways just like United Methodism, except with a hijab and iconoclasm. But a Western liberalism that does not take cultural and religious difference seriously is not serious, and yet all too often it is what we have on offer. This transcends the political divide, as before the Obama era we were given to thinking that the invasion of Iraq would result in Jeffersonian democracy, because George W. Bush had a particular model of the nature of man and what he craves (“freedom” and “liberty”), and from that he drew conclusions.

On both the American Left and Right there is a tendency to not even attempt to understand Islam. Rather, stylized models are preferred which lead to conclusions which are already arrived at. Islamic Exceptionalism is worth paying attention to because he frankly admits the problems of this line of thinking. Or, more honestly, he admits that this is a problem in the first place! In a piece at The Atlantic (which is based on a passage from Islamic Exceptionalism) he states:

To say that Islam—as creed, theology, and practice—says something that other religions don’t quite say is admittedly a controversial, even troubling claim, especially in the context of rising anti-Muslim bigotry in the United States and Europe. As a Muslim-American, it’s personal for me: Donald Trump’s dangerous comments on Islam and Muslims make me fear for my country. Yet “Islamic exceptionalism” is neither good nor bad. It just is.

 

This is a commendable viewpoint in our world, where too often “problematic” conclusions get swept under the rug or explained away. From what I can tell reading Islamic Exceptionalism many of the conclusions that he comes to are not his preferred conclusions as an American Muslim. But, they are is best guess as political scientist. This is how a scholar should behave, though too often this is not how scholars do behave.

In some ways the model of Islam and religion that Shadi Hamid believes is most informative for our world is rather like that of Sam Harris, despite wide differences in details and a general shift in emphasis. Out of all the religions in the world Harris believes that Islam is fundamentally exceptional. And Hamid agrees with him. I will state here that at the end of the day I disagree with both Harris and Hamid. But, we all begin with the same proximate empirical universe, where we an agree on some general facts. This is where we differ from someone like Ben Affleck, who probably finds reality rather “gross.” To get a sense of Affleck’s engagement with facts, consider his attempt to suppress the fact of his own slave-owning ancestors:

After an exhaustive search of my ancestry for “Finding Your Roots,” it was discovered that one of my distant relatives was an owner of slaves.

I didn’t want any television show about my family to include a guy who owned slaves. I was embarrassed. The very thought left a bad taste in my mouth.

Gigi_Hadid_2016

Not your typical Muslim

It’s fine to be embarrassed by reality. But you still need to face up to reality. Where Hamid, Harris, and I all start is the fact that the vast majority of the world’s Muslims do not hold views on social issues that are aligned with the Muslim friends of Hollywood actors. This is trivially obvious to anyone who digs (so obvious that even Bill Maher cites these data, they’re so easy to find). Before the Green Revolution I told people to expect there to be a Islamic revival, as 86 percent of Egyptians polled agree with the killing of apostates. This is not a comfortable fact for me, as I am technically an apostate.* But it is a fact. Progressives who exhibit a hopefulness about human nature, and confuse majoritarian democracy with liberalism and individual rights, often don’t want to confront these facts. Their polar opposites are convinced anti-Muslims who don’t need any survey data, because they know that Muslims have particular views a priori by virtue of them being Muslims. These people would miss out on the fact that 5 percent of Turks agreed with Egyptians on apostates.

There is a glass half-full/half-empty aspect to the Turkish data. 95 percent of Turks do not believe apostates should be killed. This is not surprising, I know many Turkish atheists personally. But, 5 percent is not a reassuring fraction as someone who is personally an apostate. The ideal, and frankly only acceptable, proportion is basically 0 percent. In the aughts the Turkish example was given as a case study in moderate Islamism. The regime of Recep Tayyip Erdoğan was genuinely more liberal than other Islamists. During the Green Revolution he went to Tunisia and stated:

“Turkey is a democratic, secular and social state of law. As for secularism, a secular state has an equal distance to all religious groups, including Muslim, Christian, Jewish and atheist people,” Erdoğan said during a visit to Tunis, the place where the wave of pro-democracy revolts sweeping the Middle East and North Africa began late last year.

Obviously things have changed in the last few years, as Erdogan has taken a more authoritarian tack, and Islamism in more muscular form is ascendant. Nevertheless, the very idea of accepting atheists is taboo in most Arab countries, including Tunisia, which shows how far beyond them Turkey is in a classical Western reckoning (though there are conflicting reports, Ataturk himself, the founder of the modern Turkish state, may personally have been an atheist).

Harris would give a simple explanation for why Islam sanctions the death penalty for apostates. To be reductive and hyperbolic, his perspective seems to be that Islam is a totalitarian cult, and its views are quite explicit in the Quran and the Hadith. Harris is correct here, and the views of the majority of Muslims in Egypt (and many other Muslim nations) has support in Islamic law. The consensus historical tradition is that apostates are subject to the death penalty.

But Hamid adds some nuance to this picture. He seems to argue that attitude toward apostasy falls out of a broader program of Islamic civilization which goes back to the foundations of the religion. Engaging with scholarly works, such as Ancient Religions, Modern Politics: The Islamic Case in Comparative Perspective, Islamic Exceptionalism argues that the Muslim Weltanschauung has an integrated role for religion in the political order baked into its cake. To refer back to an old saying, Muhammad was his own Constantine. Islam arose and exploded with the rise of its empire. In contrast, Christianity developed slowly as a marginal sect, and later a religion among religions, in the Roman polity. Its eventually victory in the 4th century came to some extent at the sufferance of Roman elites who had their own traditions and customs which the Church had to make peace with. Render under Caesar what is Caesar’s.

614cyv0xnJL._SY344_BO1,204,203,200_ There are several problems with this thesis. As a believing Muslim Hamid talks about how alive the Salafs of early Islam are to modern Muslims. These are the first few generations of Muslims who remembered Muhammad personally or well well acquainted with those who did. They were the people who lived in the world before Islam became embedded within a profane state, that of the Umayyads, who transformed the polity into a hereditary monarchy. Reviled by the Shia for their role in the murder of the family of Ali, and ignored at best by the Sunni who look more to the traditions crystallized under their Abbasid successors, the Umayyad are a sort of historical cordon sanitaire between the centuries when the streams of modern Islam matured and elaborated, and the age of the Salafs.

There is a small problem with this narrative: it may be wrong. The story of Christianity is rather well known, and well disputed, in the public arena. There is a large body of scholarship which contends that orthodox Christianity, rooted in the Athanasian creed, developed organically over the centuries after the life of Jesus. Though many Christians would disagree, many scholars argue that aspects of Christianity which Christians hold to be fundamental and constitutive of their religion would have seemed exotic and alien even to St. Paul. Similarly, there is a much smaller body of work which makes the same case for Islam.

51nf9+uTZwL._AC_UL320_SR212,320_ A précis of this line of thinking is that non-Muslim sources do not make it clear that there was in fact a coherent new religion which burst forth out of south-central Arabia in the 7th century. Rather, many aspects of Islam’s 7th century were myths which developed over time, initially during the Umayyad period, but which eventually crystallized and matured into orthodoxy under the Abbasids, over a century after the death of Muhammad. This model holds that the Arab conquests were actually Arab conquests, not Muslim ones, and that a predominantly nominally Syrian Christian group of Arab tribes eventually developed a new religion to justify their status within the empire which they built, and to maintain their roles within it. The mawali (convert) revolution under the Abbasids in the latter half of the 8th century transformed a fundamentally Arab ethnic sect, into a universal religion. Robert Hoylands’ In God’s Path: The Arab Conquests and the Creation of an Islamic Empire presents this viewpoint. In contrast, Hugh Kennedy’s Great Arab Conquests presents a traditionalist view, which accepts the conventional Islamic framework in its broadest outlines (I recommend both, though Kennedy is the better prose stylist).

I was struck that in Islamic Exceptionalism Hamid observes that because so little is known about Jesus’ life there is a live debate about the historical Jesus. I agree there is little known about the historical Jesus (with even Josephus being asserted to be later interpolation by some), but this is not what believing Christians would contend. I only bring this up because here the shoe is put on the other foot. The fact that Hamid can entertain these views, along with revisionist** works such as Reza Aslan’s Zealot: The Life and Times of Jesus of Nazareth, is a function of the history of Christianity and its relationship to the West, not something natural to Christianity itself. The debate about the historical Jesus only emerged when the public space was secularized enough so that such discussions would not elicit violent hostility from the populace or sanction form the authorities. T he fact is that the debate about the historical Muhammad is positively dangerous and thankless. That is not necessarily because there is that much more known about Muhammad than Jesus, it is because post-Christian society allows for an interrogation of Christian beliefs which Islamic society does not allow for in relation to Islam’s founding narratives.

The early portion of Islamic Exceptionalism that goes back to the first centuries of Christianity and Islam is to use an overused word highly “problematic.” It isn’t that Hamid makes incorrect inferences, it is simply that the chain of inference are so rapid fire, and proffered as fait accompli, that it is difficult to keep up with them and evaluate their likelihood. Assertions that seems plausible from one angle are highly disputable from another. For example, he suggests that because Jesus is divine he does present himself as a model in the same way as Muhammad, who was a man. The problem with this assertion is that the standard Christian thesis is that Jesus is both divine and human, and that it is his incarnation into the human flesh that allows him to be relatable. As an atheist I honestly don’t even know if any of this has any content, though I understand that religious people find these sorts of assertions substantive. My point is that most of the arguments in this portion of the book can be easily flipped on their heads by deeper or alternative analysis.

Hamid’s description of Christian soteriology is very superficial, in a way that I think misleads if you take this sort of analysis of religion seriously. I happen to believe that this sort of analysis doesn’t add much value, so I don’t hold it against Hamid. But a presupposition of Islamic Exceptionalism seems to be that there is a deep and fundamental essence to religions in their ideas and foundations, so one must critique his arguments on their own terms. Consider this passage:

If salvation is through Christ and Christ alone, then there is little need for the state to regulate private and public behavior beyond providing a conducive environment for individuals to cultivate virtue and become more faith to Christ. The punishment of sins is no longer a priority, since Jesus died for them. In start contrast, whereas theologians like Martin Luther fashioned a dialectic between faith and good works, these two things are inextricably tied together in Islam….

This is just an unfortunate caricature of the majority of Christians’ views on salvation and works. Not to belabor the point, as an atheist who is skeptical of a lot of religious “analysis,” many of these distinctions that you see in probing these topics strikes me as similar to philosophizing about the number of angels on the head of a pin. But, if you believe these constructs have material consequences in this world, then you need to relay them correctly. A simple reading of this passage would suggest that all Christians are slouching toward antinomianism
.

Similarly, one could argue that Islam also slouches toward antinomianism
because predestination is the dominant view within the religion. Obviously this isn’t true. Neither Muslims nor Christians are antinomian in their behavior.

in-gods-we-trust-the-evolutionary-landscape-of-religion-evolution-and-cognition-scott-atran-complete-book-1-638 As I observed above, Hamid cites Michael Cook’s Ancient Religion, Modern Politics, to contend that ancient beliefs, forms, and models, echo down the generations and constrain the shape of the present. Having read Cook’s book I can say it’s interesting, but its argument for why textual constraint and ancient precedent matter are not particularly convincing. In fact, he comes close to asserting it as common sense.

I take a different view. When it comes to understanding religion you need to start with psychology. In particular, cognitive psychology. This feeds into the field of evolutionary anthropology in relation to the study of religion. Probably the best introduction to this field is Scott Atran’s dense In Gods We Trust: The Evolutionary Landscape of Religion. Another representative work is Theological Incorrectness: Why Religious People Believe What They Shouldn’t. This area of scholarship purports to explain why religion is ubiquitous, and, why as a phenomenon it tends to exhibit a particular distribution of characteristics.

What cognitive psychology suggests is that there is a strong disjunction between the verbal scripts that people give in terms of what they say they believe, and the internal Gestalt mental models which seem to actually be operative in terms of informing how they truly conceptualize the world. In Theological Incorrectness the author draws upon his field work in Sri Lanka and narrative interviews with religious people which don’t elicit reflexive scripts to get a sense of the internal beliefs which might shape their behavior. Though Hindus, Buddhists, and Muslims, all agreed that they had very divergent views, what the author founds is that their mental model of gods(s) were very similar. The Theravada Buddhism of Sri Lanka may notionally reject the idea that Lord Buddha is a god, but he for all practical purposes fills in the role of a god. Similarly, Muslims may aver that their god is omniscient and omnipresent, but their narrative stories in response to life circumstances seem to imply that their believe god may not see or know all things at all moments.

The deep problem here is understood bt religious professionals: they’ve made their religion too complex for common people to understand without their intermediation. In fact, I would argue that theologians themselves don’t really understand what they’re talking about. To some extent this is a feature, not a bug. If the God of Abraham is transformed into an almost incomprehensible being, then religious professionals will have perpetual work as interpreters. Some religious groups, such as Mormons, even point out that their own idea of the godhead is more concrete and less philosophical, so actually makes more coherent sense.

Which brings me to the issue of the Quran and the Bible. There is extensive discussion in Islamic Exceptionalism about the fact that the Quran is the literal Word of God (the recitation by Muhammad), while the Bible is inspired by God, but by and large is not in the voice of God. The standard thesis being proffered is that this means there is less flexibility in Islam, because all Muslims are by nature in some ways fundamentalists.

First, for the vast majority of history most Muslims and Christians have been illiterate. They could not read their scriptures. Second, even today most Muslims can not read the Quran. Most Muslims do not speak Arabic. Second, from what I have been told the Classical Arabic in the Quran is impenetrable to most Arabs. The point isn’t to understand, the point is that they are the Word of God, in the abstract. When I memorized surah Fatiha I was told the meaning of what I was reciting almost as an afterthought (though some of the terms are rather transparent from other concepts). The power of the Quran is that the Word of God is presumably potent. Comprehension is secondary to the command.

Second, Hamid admits the importance of the reality that Islam, like Judaism, and unlike Christianity, is an extensively orthopraxic religion. Though there is much talk about theology in Islamic Exceptionalism, it is more as a general catchall term than technical theology, because this is a domain where Christians have devoted a lot more resources than Jews and Muslims, whose ideas of God are relatively shorn of Greek philosophical sophistication (the Ismaili sect has a sophisticated Neoplatonic cosmology, but they are the exception not the rule). In contrast, Christians have neglected elaboration of religiously informed laws, while Jews and Muslims have developed an enormous corpus.

Aside from some radical Protestant sects religious professionals in the Christian tradition engage in extensive sacramental and liturgical activities. In the pre-modern era the Christian church had a role in collective social salvation through these activities, which it performed for the whole community. In contrast, Judaism and Islam have a quasi-clerical professional class whose roles are often focused upon legal matters, public and personal. In Judaism these are the rabbis, while in Islam they are the ulama. Historically, and even in my own generation, my family has had individuals who are members of the ulama. From what I have seen and heard there is little discussion about the details of the nature of God. Rather, the workaday consists of instruction in memorization of the Quran and elaboration of proper behavior and ritual.

Hamid to some extent discounts the analogy with Judaism for Islam in terms of political insight because after the decline of the Herodians Jewish states were few and far between. Jews had to respect the law of the land in which they lived, to the point where this became a maxim. But I think this example is illustrative, because of the family similarities between Judaism and Islam when it comes to a focus on orthopraxy. Judaism has a deep and rich history of political action and engagement, from the prophets, judges, down to the kings. After the fall of the House of David Jewish monarchies rose several times, and the Herodians themselves were the products of a forced conversion by the Hasmoneans.

And yet after two failed rebellions in antiquity Judaism became relatively quiescent. Hamid asserts that the modern Jewish state of Israel is fundamentally secular in a way that Islamic states are not. I am not entirely convinced by this. First, the secular Ashkenazi elite are now a minority of the population, though at founding they were the overwhelming majority. The Haredi population is growing, and there is a large body of Sephardic Jews for whom Jewish religious identity is stronger than for the Ashkenazi. Finally, the “national religious” block of non-Haredi religious Jews have contributed many of the individuals engaged in religious-ethnic motivated political violence. Some radical Jews even term the Palestinians Amalekites.

This was pregnant within Judaism. It simply needed the proper social context.

In terms of the historical and religious narrative Islamic Exceptionalism naturally argues that Muslims are the exceptions. I take exception to this. Rather, I think the Western liberal model based on a creedal Protestant church is the exception. In The Impossibility of Religious Freedom, the author, a lawyer, argues that America’s regnant ideology of church-state separation only retains coherence if one posits religion qua religion is fundamentally similar to creedal Protestantism. The authors shows that recent emergence of liturgical and orthopraxic traditions has been causing more issues with accommodatio, as authorities have to pick and choose what they will, or won’t, accommodate. The history of American Roman Catholicism and American Judaism are to a great extent the Protestantization of these religious traditions enforced by a dominant and xenophobic Protestant ascendancy in the 19th and early 20th centuries. Now with the emergence of multiculturalism and the decline of normative Protestantism religious traditions which take a different view of the essence of what religion is are now beginning to flourish and multiply.

k10063 Historically all political units have exhibited a sacral dimension. Some cognitive anthropologists now argue that in fact powerful supernatural agents, active gods, were essential to the emergence of larger social and political units. King James may have asserted “no bishop, no king”, but perhaps it is more general and primal. “No god, no tribe” (or the inverse, “no tribe, no god”). The relationship in the detail between religion and polity differed in various civilizations. In ancient China by and large the elite tolerated pluralism so long as cults were not socially disruptive and political active. But the state was not secular. The emperor was the Son of Heaven, the axis mundi between Heaven and Earth. In India kings became the cakravartin, the universal ruler through whom the wheel of the dharma moves. The Christian East Roman emperors were the vice-reagents of God upon earth, while the last emperor to be deified was Anastasius, a century and a half into the period of Christian emperors! The rulers of Egypt were gods, while those of Mesopotamia began as priest-kings.

In Jay Winik’s Great Upheaval there is extensive discussion of the controversy after the independence of the colonies from Britain that the federal government did not have a state religion. The original settlers were by this point not a particularly churched people, and free thinking was common, from top to bottom. But never had there been a state in the history of the world which disavowed the need for favor from the gods. In The Godless Constitution the authors argue that the lack of a national religion was quite conscious, and a radical move on the part of a coterie of founders.

If we were to rewind history what would it look like? Is the arc of the moral universe always going in the same direction? I don’t know. Perhaps secular Western liberalism wouldn’t have developed the way it did. My overall argument in this section is that the prior for historical contingency is still very strong.

The reality is that most of Islamic Exceptionalism has nothing to do with all the details above. There are chapters devoted to Turkey, Egypt, Tunisia, and ISIS, as case studies. The authors personal experience and history, as well as his academic background as a political scientist come to the foreground. There is extensive interlacing of journalistic narrative and reportage with citations of the scholarly literature on Islamism and democratization.

The theoretical scaffold here is not too surprising or novel, as the author himself admits, though it may be to Americans. In short, liberalism and individualism do not always go hand in hand with democracy. The examples from American history are legion. The rise of the Democratic party and universal white male suffrage resulted in a curtailment of the political rights of black Americans. In England when the elite wished to grant Roman Catholics more rights, the populace of London rioted. In 19th century Prussia the extension of suffrage out of the high bourgeoise to the rural population increased the base of conservatives, because the rural population looked more favorably toward their traditional aristocratic leaders and were more socially conservative. As the American political system has become more populist, expressions of religious piety and adherence among those in high office have increased.

In Islamic Exceptionalism Shadi Hamid presents Tunisian and Egyptian Islamists in a relatively sympathetic light. He observes that in some ways the secular population is more intolerant, because they fear the rise of illiberalism due to democratic will. Americans do not have the language today to process this, but what Hamid is alluding to is simply what in an earlier era would be the “mob.” Economic, social, and political, development expands suffrage and distributes power. This moves it outside of central elite control, and human nature is such that inter-group competition often emerges as old elites and arriviste proto-elites clash.

Hamid’s contention seems to be that if democracy is going to come to the Arab Middle East in the near future then it must make peace with the pious majority. He has no grand solutions, but definitely offers a diagnosis. Though liberalism has percolated through Western society, I would point out that the expansion of suffrage was almost always met with the diminishment of the liberal faction to becoming a “third force,” as a more populist party took its spot in opposition to the conservatives.

The final issue that I want to touch on is addressed somewhat in the book, but gingerly, and without great attention. The work is titled Islamic Exceptionalism: How the Struggle Over Islam Is Reshaping the World. But the focus is on the core Middle East of Arab countries, and Turkey. About 25% of the world’s Muslims are Middle Eastern. About half the world’s population of Muslims live in South Asia and Indonesia (~700 million). There is some discussion of the nature of Islamic identity and piety in these nations, but no great depth of analysis. For example, there are some data which suggest that Indonesians want more mixing of religion with politics than people in the Middle East. Hamid suggests that this shows some underlying essence of the Islamic polity. But Indonesia is a very strange case, it is a nation where conversion from Islam to Hinduism or Christianity is not entirely uncommon. A large number of Muslims in East Java maintain a religious identity which is highly synthetic, and tacitly supported by their local ulema. In Bangladesh, you have a society where Islamic and non-Islamic identities are at rough parity. This is in strong contrast with nations like Egypt and Turkey, for whom the past 1,000 years are hard to discuss without addressing Islam directly and copiously.

This book posits explanations for the nature of Islamic polities, but the reality is that this only even applies to the core Islamic nations which were part of the Abbasid caliphate. Islam’s role in maritime Southeast Asia or South Asia was far different than in the core Islamic lands, as it was contested and its period of ascendancy curtailed.

To a great extent let me gloss over the majority of the book that is focused on political and social facts in the Islamic world today. The reason is that I don’t disagree with the facts. That is the best thing about Islamic Exceptionalism, it will put more facts in front of people who are fact-starved, and theory rich. That’s good.

But how those facts came about, and why, that is a different matter. The Islamic world is here. And it will be difficult to move it elsewhere. By making it seems as if being here is inevitable, Hamid seems to be arguing that moving it to a different equilibrium will be exceedingly difficult. But if you posit that modern conditions are historically contingent and labile, then the future is less predictable. I am come not to bring answers, but the cloud of confusion.

* I have never been a big believer in Islam, but since my father is a believing Muslim, by most sharia definitions I’m an apostate.

** Aslan’s views are not new, but derive from an older scholarly tradition of Jesus as a political radical, which today is generally out of favor.

 
• Category: History • Tags: Islam

Lake_Washington_Ship_Canal_Fish_Ladder_pamphlet_-_ocean_phase_Chinook
440px-07-03-23RedWolfAlbanyGAChehaw Years ago I had a long phone conversation with a journalist about the origins and natural history of the red wolf. The reason was that I had casually mentioned that there was genetic evidence suggesting that the red wolf is a stabilized hybrid between gray wolfs and coyotes. That was 2007, if I recall correctly. It’s gotten more definitive since then, as canid genomicists are starting to be convinced that red wolves are a species which emerged as a synthesis between gray wolves and coyotes. Nevertheless, it also seems true that the red wolf has ancient morphological roots. That is, you can find fossils which resemble red wolves very far back in prehistory.

hqdefault And it’s not just red wolves. There’s a melanic form of the gray wolf in North America, the visually arresting black wolf. It turns out that this morph is due to introgression from domestic dogs, and more specifically, the dogs brought with Amerindians ~10 to ~15,000 years ago. If you look at on a genome-wide scale these melanic wolves are not admixed. It’s just that there is a small portion of their genome with a novel variant that increased in frequency and moved from one “species” to the next.

This is just prologue. I’m a geneticist, and these are just interesting facts to me. But these genetic facts translate into policy implications. E.g., is the red wolf a species or not? If the gray wolf is protected, should there be culling of the melanic variant, which exhibits a phenotype introgressed from dogs? 51D2RoDDkXL._SX329_BO1,204,203,200_ In the United States this all goes back to the Endangered Species Act. And the problem at the heart of this piece of legislation is that species are not a clear and distinct concept. As taxonomic ranks go species makes the most coherent sense, but there are many different species concepts, and different groups of scientists have different preferences (e.g., evolutionary geneticists tend to prefer the biological species concepts because it works well for their model organisms and is useful in testing particular hypotheses related to evolutionary genetics, while phylogeneticists unsurprisingly prefer the phylogenetic species concept!).

Population geneticists tend to give rather nuanced characterizations of a given species when asked. This is not a useful trait in the eyes of lawyers or politicians. Population genomicists often give an even more gnarly picture! (see: red wolf) There are more things in heaven and earth than are dreamt of in our pre-genomic philosophies.

sushi-621415_960_720 Several months ago I saw a draft of a preprint which would be posted soon speaking to many of these issues. The species in question was Pacific salmon (which, to be clear, is a very distinct lineage from Atlantic salmon!). Using genome-wide methods the results implied that populations of research interest are genetically similar even if they exhibited some distinct phenotypic differences (or, more precisely, these are cases where geography dictated genetic variation, as is a good null hypothesis). In relation to “conservation” if the goal was conservation of genetic variation, then focusing on specific phenotypes may not be relevant because the whole population range presumably had the viable extant variation.

But the devil is in the details. Here’s the preprint, The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation:

…Here we use genomic methods to investigate the evolutionary basis of premature migration in Pacific salmon, a complex behavioral and physiological adaptation that exists within highly-connected populations and has experienced severe declines. Strikingly, we find that premature migration is associated with the same single locus across multiple populations in each of two different species. Patterns of variation at this locus suggest that the premature migration alleles arose from a single evolutionary event within each species and were subsequently spread to distant populations through straying and positive selection. Our results reveal that complex adaptive variation can depend on rare mutational events at a single locus, demonstrate that CUs reflecting overall genetic differentiation can fail to protect evolutionarily significant variation that has substantial ecological and societal benefits, and suggest that a supplemental framework for protecting specific adaptive variation will sometimes be necessary to prevent the loss of significant biodiversity and ecosystem services.

The method here was using Rad-seq, which is pretty cost-effective for non-model organisms. Depending on the confidence you want for the genotype calls (this was done with ANGSD) you get hundreds of thousands of variants back. This is a huge improvement over publications where the fate of a species (or “species”) comes down to a few dozen microsatellites. The form of genomic analysis that that is prominent in this paper is looking at variation in the site frequency spectrum (sfs) and genetic diversity statistics (a lot of other statistics fall straight out of sfs).

Screenshot 2016-06-05 02.41.04 The phenotype that was being investigated was migration timing. Remember, salmon tend to migrate at around the same time so that runs can form the huge masses which allow for mating between males and females. You’ve seen the same documentaries as I have.

Premature migration occurs in some regions of the Pacific salmon distribution, and it is important for various reasons outlined in the introduction (I’ll spare you the ecological details and leave it to your interest in that sort of thing). So comparing premature vs. normal migration timing there was a real obvious hit for likely selection around GREB1L. Apparently this gene is well known to be implicated in behavior shifts (for humans it seems to be related to breast cancer, but there’s an ascertainment bias for medical traits in the literature). One thing really obvious is that for salmon who migrate upstream early the region around GREB1L is cleaned up so that there isn’t much genetic diversity. This is a hallmark of a recent positive selection sweep.

More specifically, they found that there seem to be selection events around GREB1L in both steelhead and chinook salmon (two species of Pac salmon that diverged 10-15 million years ago), and, that these occurred independently once in each species. Because in the steelhead the site frequency spectrum differed across populations with the premature migration it seems likely that the sweep is at differences stages (or occurred earlier or later). The likelihood then is that a single mutational event has been moving between populations across the coastal groups within a species.

As someone interested in evolutionary dynamics of connected populations this is fascinating to me on an abstract level. Instead of a welter of numerous segregating variants it seems that the mutational events are rare enough in concert with strong selection for this particular morph, so that one variant becomes dominant quickly. But what does it mean for conservation?

Here’s the beginning of the abstract, which I chopped off earlier:

The delineation of conservation units (CUs) is a challenging issue that has profound implications for minimizing the loss of biodiversity and ecosystem services. CU delineation typically seeks to prioritize evolutionary significance and genetic methods play a pivotal role in the delineation process by quantifying overall differentiation between populations. While CUs that primarily reflect overall genetic differentiation do protect adaptive differences between distant populations, they do not necessarily protect adaptive variation within highly connected populations. Advances in genomic methodology facilitate the characterization of adaptive genetic variation, but the potential utility of this information for CU delineation is unclear….

And now, the last sentence of the discussion:

Taken together, our results demonstrate that conservation units reflecting overall genetic differentiation can fail to protect evolutionarily significant variation that has substantial ecological and societal benefits, and suggest that a supplemental framework for protecting specific adaptive variation will sometimes be necessary to prevent the loss of significant biodiversity and ecosystem services.

Let’s go back to the red wolf for a moment, Should Red Wolves Be Allowed to Mate With Coyotes?:

… Robert Wayne, a geneticist at U.C.L.A., thinks the red wolf is itself a hybrid. When officials captured what individuals they could find in the 1970s, the beleaguered animal already had coyotes among its ancestors, Wayne says. He argues that red wolves should be allowed to mate with coyotes — that natural selection should sort out the question of what animal is best for that landscape.

The case here with salmonids and wolves are not analogous. It strikes me that many of the features of the red wolf are the outcome of genome-wide admixture. E.g., the morphometric properties of the red wolf are between those of the gray wolf and the coyote. The ancient evidence in the paleontological record of the red wolf is probably a function of the fact that red wolves are easily recapitulated out of the genetic reservoir of gray wolves and coyotes. Let me be honest: we could create the “red wolf” de novo if the current populations went extinct.

In the case of the salmonids the dynamics are somewhat more complex and simple at the same time. It is simple because the genetic architecture for a complex behavior is very elegant. One locus, with presumably a single allele. If there were many numerous segregating variants than one would have to think that the mutational target is large (e.g., lactase persistence in humans exhibits this). But there aren’t. The authors suggest then that mutation itself may be a rate limiting step in diversification, so that if the endangered premature migrating salmon are extirpated they may not ‘naturally’ reemerge out of the genetic background of the more numerous conventional phenotype (at least within the normal scope of a human lifetime). Though there are heterozygotes their data may be selected against. It seems that there are probably two stable states in terms of behavior, encoded by homozygote genotypes (this is a preprint, so to me it begs the question as a critique: how are the initial heterozygotes eventually reproducing enough to produce homozygotes?).

The ultimate moral of the story is that to make informed decisions in the area of conservation biology in the future one needs to sequence individuals of the organism of interest with reasonable good geographic coverage. A single summary statistic, whether it be of genetic diversity, or population structure, is not going to be the end of anything. Rather, one has to frame the ends of the policy (e.g., are there ecological morphs which are deemed worthy of protection?), and then laboriously decompose the data as population geneticists would, focusing on structure and parameters of allele frequency change like selection and drift.

Citation: The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation, Daniel J Prince, Sean M O’Rourke, Tasha Q Thompson, Omar A Ali, Martha Arciniega, Hannah S Lyman, Ismail K Saglam, Anthony J Clemento, Thomas J Hotaling, Andrew P Kinziger, Adrian P Spidle, John Carlos Garza, Devon E Pearse, Michael R Miller, bioRxiv 056853; doi: 10.1101/056853

 
• Category: Science • Tags: Genomics

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14726 Reading Buddhism and Islam on the Silk Road. It’s a quick read. Not because it is not scholarly, it is scholarly. But unlike The Shape of Ancient Thought is relatively economical in its prose (to be fair, The Shape of Ancient Thought covers more ground). Also you probably benefit from reading Beckwith’s Warriors of the Cloisters and Starr’s Lost Enlightenment essential complements. The author is a scholar of Buddhism, so a Buddhism and Islam on the Silk Road has a somewhat superficial treatment of the Muslim side from what I can tell. The most interesting stuff so far has been the tendency for Muslims to “Orientalize” the “Other”, in the exact same way that postcolonial theorists assume is some sui generis characteristic of Western civilization.

Just 5% of Indian marriages are inter-caste: survey. This only a little lower than the proportion of interracial marriages in the USA (though Hispanic to non-Hispanic does not get tabulated in this, and so is somewhat a slight underestimate).

If you spend time on the internet you can find “Game of Thrones Spoilers” websites. Some of them seem to have sources from extras or people working on set. This is what George R. R. Martin’s tardiness has wrought: he’s now being scooped by the HBO versions of Reality Steve. Go to Google News and type “Game of Thrones,” and you can find out a lot of what will probably happen in the next book.

I still have no idea how Martin is going to unwind his narrative in even two 1,500 page books. 90% chance if he finishes the series that there are more books to come, especially if you imagine the “last book” is split out into a part 1 and part 2.

Thinking about George R. R. Martin’s Weltanschauung I’ve always had a lot of issues with the role that prophecy plays in his universe. It just doesn’t seem to make sense. But now I have a theory: all prophecies in in the world of A Song of Ice and Fire come from one being, outside of the normal flow of time and space. That being is incarnated in the books as Bran.

Dogs may have been domesticated more than once. I believe this is wrong. Though the process we call domestication probably occurred several times in wolf lineages, almost all the ancestry of modern dogs descends from one single divergence event from a wolf lineage (now extinct). The issue is that the divergence is almost certainly considerably older that 15,000 years ago. The Amerindians had dogs. They separated from other human groups ~15,000 years ago. I’d take the origin of domestic dogs from wolves some time before the Last Glacial Maximum. If that is true, then there is probably a lot of old population structure that came down to the Holocene, some of which was erased. Similar to the story for humans.

I think we’re in a recession. The last time I wondered about this was in May of 2007.

For UCLA shooter Mainak Sarkar, sudden rage after years of intense academic studies. Well, I’m glad it’s not a white guy. Wouldn’t see the end of Twitter and Facebook posts from people on how white men are dangerous and stuff (my maternal grandfather’s family surname was Sarkar).

An addendum to my post from yesterday, It All Began at Eden. I have a tentative hunch that between-group pairwise Fst was far higher in the past than the present as a function of geography. Basically, cultural distinctions where harder and sharper, and trade and commerce less prominent, so there was less gene flow between neighboring groups. That to me is a possible reason that the ‘blow up’ effect of farmers in the ancient Near East may have resulted in very different streams hurtling toward different antipodes of Eurasia….

Screenshot 2016-06-04 22.40.51Comments at Eurogenes interesting. Hints of new ancient DNA papers. Will probably see some posters/presentations at ASHG in Vancouver this fall….

My wife saw my Edge on the table with its case off, and commented on how pretty it was. I only bring this up because I’ve been thinking about this recently. On the one hand I spend money on a higher end phone which has a sleek form factor, but I put it in a clunky case to prevent it from being damaged, and even then there are cracks here and there. I assume in the near future some phone maker will figure out a way to make the screen a little more robust?

The Evolution Meeting in Austin is literally a little more than a week away. I’m pretty excited. Yes, the $ won’t flow like at ASHG, but I’m genuinely curious about evolutionary biology beyond genetics.

 
• Category: Miscellaneous • Tags: Open Thread

320px-Tigress_at_Jim_Corbett_National_Park This isn’t a good time to be into charismatic megafauna. Mostly due to habitation destruction the numbers are not going in the right direction. There has been a precipitous decline in the number of lions over the past 20 years. This is probably a good thing for rural Africans, but ideally I envisage a future where most agricultural work will be so high productivity that cities will suck up a lot of this labor (even in the United States economic growth is in a few large urban areas).

But I happily note that this year we seem to have hit the bottom (hopefully) for the number of tigers, World’s wild tiger count rising for first time in a century:

The world’s count of wild tigers roaming forests from Russia to Vietnam has gone up for the first time in more than a century, with some 3,890 counted by conservation groups and national governments in the latest global census, wildlife conservation groups said Monday.
The tally marks a turnaround from the last worldwide estimate in 2010, when the number of tigers in the wild hit an all-time low of about 3,200, according to the World Wildlife Fund and the Global Tiger Forum.

India alone holds more than half of them, with 2,226 tigers roaming reserves across the country, from the southern tip of Kerala state to the eastern swamps in West Bengal, according to its last count in 2014.

This is down from ~100,000 in 1900, with declines pretty much every year. Part of this is probably basic economics: the last refuges of tigers are probably the most marginal for farmland. Additionally, economic development and cultural changes are probably having some effect. But the census here is very small. And there are genetic concerns if you look at the sizes for some nations:

Bangladesh, 106; Bhutan, 103; Cambodia, 0; China, more than 7; India, 2,226; Indonesia, 371; Laos, 2; Malaysia, 250; Myanmar, no data available; Nepal, 198; Russia, 433; Thailand, 189; Vietnam, fewer than 5.

For a large mammal a bottleneck of ~100 is probably not a major genetic concern, though some of these populations have been through many decades of small population size. But in terms of sustainability 100 is too close to the edge, so that a low population year might result in some genetic problems, which would result in more problems down the line.

 
• Category: Science • Tags: Conservation, Genetics

620px-Agry(ararat)_view_from_plane_under_naxcivan_sharurIt all began in the hillocks to the north of the plains of modern Syria and Iraq. Agriculture that is. Or more precisely, the West Eurasian package which would wash all the way to the Atlantic, and deep into Eurasia, and in innumerable ways influence most human societies. The standard model until recently was that this was a cultural, rather than genetic, revolution. That is, the idea of agriculture took root among people as they emulated their successful neighbors. An analogy here can be made to writing. Early Egyptian forms of what became hieroglyphs much more resemble Mesopotamian cuneiform than they later did. The idea of writing was critical, to the point where we know that it occurred at least one other time (East Asian writing may have been independent, there is debate about this).

51IZQjMbVlL._SX346_BO1,204,203,200_ But there’s a crucial difference. Writing is complex, but the idea is simple enough, symbolic representation of language, that one can imagine imitating it. Additionally, originally literacy was a monopoly of a small class of scribes. One can imagine that these people were highly skilled and perhaps initially mobile, but they made little demographic impact among the polities which they traversed. Agriculture is different. It is not just a technology, but it is a lifestyle. One of the insights of Peter Bellwood’s First Farmers is that the there aren’t too many instances of modern ethnographic instances of hunter-gatherers or nomadic populations happily settling down to the farmer lifestyle. The work of cultural evolutionists more recently reinforces the fact that there is a great deal of tacit norms which are both functionally critical toward many traditional lifestyles, and, whose utility and contingent integration are not reflectively understood by those who practice a given lifestyle.

That’s just a way to say that many people do what they do because they’re going through the motions of traditions which they have internalized over their whole life, and they couldn’t even tell someone else in any rational way why they were doing what they were doing. If you were trying to imitate them you’d probably discard a lot of functionality without understanding its importance to the whole system.

So how did farming spread? It didn’t, farmers did. Endogenous population growth in the simplest formulations resulted in a natural replacement of hunter-gatherers with farmers. More recently works such as War Before Civilization have convinced me that early agriculturalists engaged in a lot of inter-group competition. In other words, it wasn’t just passive demographic replacement, but proactive expansion of clans, tribes, and confederacies into the “empty frontier.” This makes more sense of the reality that ancient DNA is witness to quick rapid disruptions, and later equilibration (perhaps as residual hunter-gatherers slowly become assimilated to the new society which is more self-confident in itself).

An implication of this model is that the chrysalis of later genetic and cultural variation was already preexistent rather early on. That is, if you looked at the ancient Near East, where several communities stumbled upon agriculture, perhaps in concert, you will see in these the “womb of nations.” The idea struck me as crazy when the blogger Dienekes Pontikos presented it in the late aughts based on patterns in admixture analyses. It strikes me as far less crazy after half a decade of ancient DNA. Now in the comments David points me to an abstract at SMBE which shows this all coming to a head:

The shift from hunter-gathering to food production, the so-called Neolithic Revolution, profoundly changed human societies. Whilst much is known about the mode of spread of people and domesticates into Europe during the Neolithic period, the origin of this cultural package in the Ancient Near East and Anatolia is poorly understood. By sequencing the whole genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, we show that the eastern part of the Ancient Near East was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus but distinct from the Neolithic Anatolian people who later brought food production into Europe. Despite their key role in developing the Neolithic package, the inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting they were somewhat isolated from other populations in this region. Their high frequency of short runs of homozygosity, comparable to other early Neolithic farmers, suggests that they overwintered the Last Glacial Maximum in a climatically favourable area, where they may have received a genetic contribution from a population basal to modern Eurasians. Thus, the Neolithic package was developed by at least two genetically-distinct groups which coexisted next to each other, implying a degree of cultural yet little genetic exchange among them.

As I’ve said before, the the hunter-gatherers of the Caucasus share a lot of drift with South Indians. I’m betting that the woman from Ganj Dareh is part of the root population of what later became the dominant contributor to “Ancestral North Indians,” as well as the major vector of “Basal Eurasian” into the Yamnaya people.

Addendum: This site is very close to ancient Elam. This nation has been very speculatively associated with Dravidian languages. The Copper Age commercial ties with the Indus Valley Civilization in the Persian Gulf may be less surprising if many of these routes dated back to the early Neolithic expansion.

 
• Category: Science • Tags: Genetics, History

Screenshot 2016-06-03 12.15.55

51OftfuYlSL._SX316_BO1,204,203,200_The Monkey’s Voyage is a book I’ve spotlighted before. Probably the main reason is that it highlights the importance of migration/dispersion on an evolutionary timescale. That is, change is the norm, and turnover is ubiquitous. The Tuatara is the exception, not the rule, when it comes to the biogeographic diversity of New Zealand.

As I’m not particularly focused on macroevolutionary dynamics, I’ve taken a microevolutionary lesson. That is, attempts to understanding variation within species. Updating one’s priors with the above the finding that Palearctic wolves descend from a core founder population which flourished after the Last Glacial Maximum is a lot less surprising. Wolves have been around a lot time, but meta-population dynamics and local extinctions may be the rule.

The same probably applies to another Ice Age megafauna, humans. For a long time it was something of a mystery why macro-haplogroup M, so common in South Asia, East Asia, the New World and Oceania, had no presence it Europe. Turns out it did, at least during the Pleistocene. Some of this is is just drift acting on smaller effective population size of uniparental markers. But, we know now some of this was population turnover.

This explains my casual comment below that I think “Ancestral South Indians” may have origins outside of India itself. My theoretical expectations have just shifted over time. Imagine that you have population X in a constrained geographic region. It is divided into two components, X0, at 50%, and X1 at 50%, while X1 is just the remainder after you remove X0. When you look at worldwide variation you see that X0 is modal in the region in question that you are focusing on. From this can you conclude that X0 is indigenous to/originates from this region?

I don’t think that that is necessarily true for a variety of reasons. More concrete, if you looked at ancient DNA 5,000 years before the present in the region I think X0 is probably likely to be dominant. 10,000 years before the present though I’m sure. At 20,000 years before the present I’d be skeptical. Finally, at 40,000 years before the present I’d think continuity is unlikely.

That’s the theoretical/abstract reason why I think ASI are likely to be intrusive to India. But there’s a concrete reason. The table above is from a preprint, Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. What you see is that the coalescence for M lineages, which are the modal haplogroups in South Asia, seem higher to the east than in South Asia itself. The authors take that to suggest M probably diversified in Sundaland and even Sahul before it became prominent in South Asia.

A few caveats. First, the paper is quite uneven, and there’s a lot of talk about “Out of Africa” routes which I think are neither here nor there (Y/mtDNA work isn’t going to resolve this issue, ancient DNA is). Second, these coalescence dates aren’t “proof” of anything, they simply make the case for shifting priors. Finally, the differences between South Asia and Southeast Asia are modest, suggesting that there was a very large effective population of females in both areas. In all likelihood there were multiple waves of migration west…and east, during the Pleistocene (some of the M in Northeast South Asia is almost certainly very recent Holocene gene flow from Burma).

 
• Category: Science • Tags: Genetics, History

57348Like you, I am waiting on the Rakhigarhi DNA results. Whatever they come back with is going to definitely impact the textbooks. But until then, I thought this paper in Scientific Reports was interesting (sort of), Oxygen isotope in archaeological bioapatites from India: Implications to climate change and decline of Bronze Age Harappan civilization.

I say sort of because 1) a lot of archaeology is impenetrable to me 2) everything is about climate change. What is interesting to me is that these researchers seem to favor an old date for origins of the Harappan civilization within India. Here’s the relevant section:

At Bhirrana the earliest level has provided mean 14C age of 8.35 ± 0.14 ka BP (8597 to 8171 years BP8). The successive cultural levels at Bhirrana, as deciphered from archeological artefacts along with these 14C ages, are Pre-Harappan Hakra phase (~9.5–8 ka BP), Early Harappan (~8–6.5 ka BP), Early mature Harappan (~6.5–5 ka BP) and mature Harappan (~5–2.8 ka BP8,17,18,20,34).

Setting the Hakra culture to the side, Early Harappan at 6,000 BC suggests to me that the demographic parameters which led to the creation of the ANI-ASI genetic complex may already have been present then. If, the ASI are intrusive to the subcontinent it may even be that the Early Harappan were more West Asian than the final late stage Harappans.

 
• Category: History, Science • Tags: India

panam-09-backYears ago when I was noticing specific population genomic estimates I asked a friend about the confidence intervals, and how much to trust the values therein. One thing he mentioned offhand is that linkage disequilibrium based estimates of time since admixture often seem to give a relatively low figure in terms of generations. When it comes to non-human organisms in the field one doesn’t know always the demographic history, but with humans we have better records, and I too have noticed that the dates seem extremely skewed toward the recent. Part of this is accounted for by the dodge that these estimates are often sensitive only to the last pulse of admixture. But even then….

A new preprint discusses in detail why this occurs, The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium:

Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of non-random mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating. We derive closed form formulae for LAD under an assortative-mating model with and without migration. We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. We also present the first evidence of ancestry-assortment in African Americans and examine LAD in simulated and real admixed population data of African Americans. We find that demographic inference under the assumption of random mating significantly underestimates the number of generations since admixture, and that accounting for assortative mating using the patterns of LAD results in estimates that more closely agrees with the historical narrative.

The intuition isn’t that difficult. Assortative mating in this case often means that within population there are going to be correlations of segments of genomic ancestry which are the patterns you are tracking to infer backward the initial admixture. The dynamic of the mating, random or not, is going to effect the shape of decay over time. If you see more dense local ancestry tracts in individuals because of positive assortative mating, you may confuse it in your model for very recent admixture.

This sort of thing crops up in all sorts of models. Assortative mating within a population may lead to higher heritable transmission of a trait across generations than you might expected. Many of the model based clustering algorithms which generate the bar plots now ubiquitous in admixture analyses assume Hardy-Weinberg Equilibrium in one’s populations.

 
• Category: Science • Tags: Genomics

91I3cXu7PxL One of the most surprising things that I encountered when reading The World of Ice & Fires is how many noble houses outside of the North still claim paternal descent from the First Men. Reading the books I had no idea the extent of it. For example, the Blackwood house of the Riverlands worship the Old Gods of the First Men, so their derivation from this group made sense. But I had no idea that House Dayne, House Royce, or House Westerling, descended from the First Men. And that’s not the least of it. When Aegon I conquered the Seven Kingdoms of Westeros, four of these lands were ruled by houses directly descended down the male line from the First Men (the Lannisters descend from the First Men through their maternal line).

Here are the list:

- the Starks, you knew this.

- House Greyjoy, of the Iron Islands and portions of the Riverlands. They descend from the legendary Grey King, rather than a specific semi-historical individual, as the Andal families do. Though culturally diverged it seems likely that the people of the Iron Islands are part of the First Men migration.

- House Gardener. These were the kings of the Reach. After they were exterminated by Aegon I the Tyrells took their place as the preeminent house of this region. They descended from Garth the Greenhand.

- House Durrandon. These were the kings of the Stormlands. Robert Baratheon’s ancestor married the daughter of the last king.

Gardener and Durrandon were both culturally assimilated to Andal folkways obviously (the legendarium even states when the kings converted to the Faith of the Seven). But the fact that these two dynasties persisted after the Andal cultural revolution is rather peculiar to me. The Lannisters were Andal kings of the Westlands, but their name is from the First Men (a male Andal lord who married into the house adopted the name when there wasn’t another male heir). In the Riverlands the Tully house was preeminent, but there were no kings. The Martell princes of Dorne were Andals on the male line, but famously they intermarried with the Rhoyne people and became culturally amalgamated so that it is hard to describe them as prototypical Andals. Finally, the Arryns of the Vale are classical Andal kings, and they are described as “oldest and purest line of Andal nobility.” That would be strange to note if it were not for what I describe above.

George R. R. Martin has admitted that he’s making things up as he goes along to satisfy fans. Though he might have known Hodor’s fate as far back as 1991, I doubt he knew the genealogies of the noble houses, or their ethno-religious backgrounds. Rather, people kept badgering him, and he responded, and when he stated something in print/web it became canon. So here we are.

 
• Category: Miscellaneous • Tags: Fantasy

I call the guy above “the rabbi of the geeks.” The depth and nuance of his analyses are incredible. (I don’t watch the non-GoT commentaries from him because I have no idea what he’s talking about)

51NWscXxuDL._SX327_BO1,204,203,200_ I recently read Shadi Hamid’s Islamic Exceptionalism: How the Struggle Over Islam Is Reshaping the World. It’s a quick read, at 300 pages, though it traverses the gray land between being academic and aimed toward a popular audience (Hamid’s political science background informs his analysis, and I’m pretty sure I missed some stuff in there since that isn’t my background). I will be posting a very long reflection/review on the book and its topic closer to its publication date (I got a review copy). More precisely, a post will go up on June 6th. But before that I thought I would commend that you check out the book if you are broadly interested in the topic. Hamid engages with facts and managed to display a fair amount of epoché, whereby his own personal religious and political commitments are set aside long enough for there to be some genuine analysis. Unfortunately, this is a rare thing in our day and age. My main disagreements with the book are theoretical, conceptual and semantic, rather than descriptive. More to come on this.

51OftfuYlSL._SX316_BO1,204,203,200_ With some hindsight I have to say that The Monkey’s Voyage is an important book. It is far more influential in my thinking a month out than I would have thought before I picked i up. By and large I hold to the scale independence of evolutionary processes, but to a great extent that has resulted in me ignoring macroevolutionary processes and fields. In hindsight this was short-sighted of me. I’ve already started integrating the insights from The Monkey’s Voyage into my mental models. In particular, the reality that geographic distributions of populations are highly dynamic, and turnover is ubiquitous. Yes, The Monkey’s Voyage focuses on macroevolutionary time scales, but I think it’s a general dynamic with relevance for microevolutionary (and historical) scales as well.

Nick Denton, Gawker Founder, Assails Peter Thiel as ‘Vindictive’ Foe. Last summer I was approached by lawyers working with potential plaintiffs against Gawker. I didn’t join because 1) I wasn’t sure there was any merit to my case (I’m a “thought criminal” so of course The New York Times didn’t want to be associated with me!) 2) I’m a person with a lot of other things going on aside from my media “career” (which for obvious reasons didn’t ever get started anyway) so it wasn’t too big of a deal for me personally 3) Gawker and the media-industrial complex are powerful and might be able to destroy other aspects of my life which actually are important to me in a deeper way if they wanted to come after me.

thielbinb The media are flipping out right now because of the “injustice” Peter Thiel has wrought upon Gawker. The reality is that the media commits blatant ethical and moral violations against private individuals all the time, they are simply “little people” who are collateral damage in the battle for “justice.” You have to break some eggs to make an omelette, right?

When journalists are treated the same way they treat others they often become very angry. Journalists, like lawyers, think they have a noble calling, so they want their profession insulated from being attacked or diminished. That is human nature. Most of the rest of us are less than sympathetic. Journalists have an important job. Often it is difficult. It is important. But sacred? Nothing’s sacred. That’s what you learn by consuming the media today (also, my minimal interactions with journalism have made it clear to me that it’s a biased and selectively outraged field; you knew that, but I can confirm that).

51fGEWZ08UL._SY344_BO1,204,203,200_ At about the same time the lawyers for Hulk Hogan contacted me I was clued in to the fact by someone else that Peter Thiel was obviously working to destroy Gawker, and that it was a long game for him. If someone like me, who spends most of his days thinking about site frequency spectra and the role of inter-group conflict in multi-level cultural selection (to give two interests of mine), knew that Thiel was involved last year, it had to be widely known among many. I can’t believe Denton didn’t know, unless his social circle is that insulated or he’s alienated so many people that they wouldn’t think to give him a heads up (in 2006 when Denton started talking about the possibility about outing Thiel apparently Thiel told Denton to not do that unless he wanted Thiel to come after him). The idea that this was some huge secret and nefarious plot is ridiculous. Peter Thiel is smart, why would he have told many people what he was up to if secrecy was important?

This TPM piece on Thiel, The Eccentric Tech Billionaire Behind The Gawker Suits Has Some Curious Ideas, illustrates why some of us have so little respect for the “nobility” of journalism. Peter Thiel does not subscribe to the latest 95 theses promulgated by the committee to promote social justice. No shit? Neither do a lot of people.

All men must die. If you are a progressive the day will come where you have to confront whether you will let #TeamProblematic dictate your thoughts down to every detail. I know that many of my liberal/progressive friends privately roll their eyes and go along because of team spirit, but all unsustainable things must come to an end. Though the long game can be long indeed. In any case, no surprise, #ImWithPeter.

There will be a short pre-recorded segment on the company I’m working for on NBC’s Today Show between 8:00 AM and 9:00 AM tomorrow (Monday the 30th). About three minutes. Fun fact: I did the genotype calling specifically on the dog being profiled! Also, we’re selling kits on the website now. Standard on the order of one month turnaround.

51B5+P66c6L._SY344_BO1,204,203,200_ A reader mentioned Lord Dunsany in the extensive comments below (not totally surprising that I have a lot of fantasy geeks in my readership). As I’m something of a philistine I had no idea who Lord Dunsany was. So I looked him up. Well, I noticed that King Elfland’s Daughter was available for 99 cents as an e-book, so I got it. Quite interesting so far, especially with the archaic prose. The reader who brought it to my attention contended that Dunsany lay at one of the spectrum, with the other end defined by someone like George R. R. Martin. Seems about right so far. I don’t have much time to read fiction, but it seems worth exploring this a bit further.

9789814414012 On Twitter I saw a reference to Buddhism and Islam on the Silk Road. I read a bunch of pages (actually parts of many chapters) on Amazon. It won’t be everyone’s cup of tea, but I purchased it. Recommended, though I haven’t read much of it since I was spending the last few days reading Islamic Exceptionalism. This is an interesting topic though. As some of you know I am more and more convinced that aspects of Buddhist institutional structure were laundered into Islam by Central Asian ulema in the 9th century.

Someone asked me to comment on this, A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa:

While Phoenician culture and trade networks had a significant impact on Western civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa.

518F-qjf9rL._SX323_BO1,204,203,200_ We should be careful about making such strong inferences from mtDNA lineages when the geographic distance wasn’t that great. But, several years ago I read Adrian Goldsworthy’s The Fall of Carthage. It’s a good book, and worth reading at least for its description of the Battle of Cannae. There’s a reason we remember Hannibal. He was seriously bad-ass. Additionally, his family, the Barcids, had somewhat of a cosmopolitan background. Not too surprising in light of the cultural melange which Carthage had become (it had its own Senate, and seems to have been strongly influenced by Hellenistic culture). So, if I recall correctly one of Hannibal’s female ancestors may have been a Greek woman from Sicily. It light of this sort of fact we should not be entirely surprised if people in Carthage had typically European mtDNA lineages (in fact, because of Greek colonial expeditions were extremely male biased Hannibal likely had a native Sicilian mtDNA, if that woman was part of is unbroken maternal line).

Spontaneous mutations and the origin and maintenance of quantitative genetic variation. Out of Trudy Mackay’s lab (she’s the co-author of the later editions of Introduction to Quantitative Genetics). Great to see prominent professors publishing in a place like elife.

Geneticists and historians need to work together on using DNA to explore the past. More precisely:

Other efforts to get geneticists and historians speaking the same language are under way. A consortium led by ancient-DNA researcher Hannes Schroeder, at the University of Copenhagen, recently won a €1.2-million (US$1.3-million) grant for a collaborative research project called CITIGEN to make his field more accessible to historians and other humanities scholars. Like Geary, Schroeder worries that historians will be left behind if they fail to incorporate genetics into their research. “The train is running, and you jump on it or you miss it,” says Schroeder, who is also involved with an effort using ancient DNA to study the transatlantic slave trade.

Neanderthals built cave structures — and no one knows why. This stuff is getting crazier and crazier.

In ‘Game of Thrones,’ it’s time to start rooting for the White Walkers. Not really. But there is some logic to it. The “nobility” of Westeros seems so depraved, the White Walkers strike me almost like the medieval idea that the Mongols were the scourge of God.

 
• Category: Miscellaneous • Tags: Open Thread

Mohenjo-daro_Priesterkönig At the Eurogenes blog there has been a lot of analysis of South Asian genetic history in light of ancient DNA recently. Part of this is probably due to the fact that “Euro” genes (that is, the genetic history of European peoples) are now understood to be inextricably tied to demographic pulses and shifts which are deeply rooted in Eur asian cultural revolutions over the past 4 to 10,000 years. Only a very small fraction of the ancestry of modern Europeans dates to the period before the Last Glacial Maximum ~20,000 years ago; at least according to ancient DNA. And most of the ancestry is conditional on events which occurred during the Holocene, the past 10,000 years.* To give a sense of how recent all this is, when the first cuneiform tablets were being written, the demographic-genetic revolution which was to begin the transformation of Northern Europeans into what we now know as Northern Europeans had not completed itself, and in many regions not even begun (e.g., the Swedish-Battle Axe culture begins in 2800 BCE, several hundred years after the earliest writing in Sumerian).

Screenshot 2016-05-28 16.24.36 They say you need two hands to clap. And India is the other hand that we have now when comes to understanding this process. There’s now a lot of circumstantial evidence to tie Indians to Europeans in moderately complex ways. To the left is a figure from the supplements of Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. You see that the phylogeny of R1a in South Asia really is a burst. There’s just not that much genetic difference between all of us South Asian R1a males, irrespective of region and caste. We’re pretty much all on a particular branch, Z93. Rare outside of South Asia today (it is found in the Altai and in Central Asia), it has been discovered in ancient males from the Srubna culture of eastern Ukraine ~4,000 years ago. In Europe R1a is found mostly in Northern Europe, and especially Eastern Europe. And yet if you look further up in the supplements you see that for haplogroup J2 most of the males are partitioned between South Asians and Southwest Europeans. Additionally, the two large branches of J2 have both South Asians and Southwest Europeans, suggesting that divergence in J2 predates the arrival of J2 bearing males to South Asia and Southwest Europe. Finally, unlike R1a you can see visually that the phylogeny of J2 is less explosive; there are more clean sequences of mutations to differentiate the various branches of this patrilineage. J2 is common, but it did not undergo nearly the same burst as R1a. It’s prevalence is due to more continuous and gradual demographic processes.

51IZQjMbVlL._SX346_BO1,204,203,200_ What does this mean? Various genome bloggers have been arguing since the late aughts that there seem to be two West Eurasian admixtures into South Asia, who are clearly a compound of West Eurasians and non-West Eurasians. This was supported to some extent by the 2013 publication of Genetic Evidence for Recent Population Mixture in India, which found evidence for more than one admixture event in a subset of populations. Then, ancient DNA from the Caucasus added more evidence, Upper Palaeolithic genomes reveal deep roots of modern Eurasians. If you dig deep into the paper you see that Indian populations which are likely to be due to one(ish) admixture event are best modeled as a synthesis between the Kotias Caucasus hunter-gatherer and a non-West Eurasian population (i.e., Ancient South Indians or ASI). But some groups, such as high caste North Indians, seem to be better modeled with ancient Eurasian steppe groups as the source population (these groups themselves have ancestry from a Kotias-related/descended group).

In 2016 the ultimate judge is going to be ancient DNA. In the next year or so I think it will tell the tale that we’ve been hearing in the winds of modern contemporary genetic variation. What I think is that it will confirm part of the narrative and model pushed forward in First Farmers, Peter Bellwood’s book from the middle aughts. The Dravidian languages were brought to India from West Asia in the early-to-middle Holocene by agriculturalists descended from or related to the hunter-gatherers of the Caucasus. They mixed with indigenous hunter-gatherer populations, and gave rise to the first people we would recognize as modern South Asians genetically. Eventually they built what we term the Indus Valley civilization. The relatively evenness of this mix between West Asian descended Ancestral North Indians (ANI) and ASI across South Asia is due to the fact that much of the subcontinent was sparsely populated, and the farmers demographically overwhelmed the indigenous groups. The fact the non-Brahmin upper and middle castes are genetically somewhat different from tribal populations and Dalits in South India is probably due to the fact that the indigenous populations were absorbed at the lower levels of the nascent civilization.

The arrival of Indo-Europeans may or may not have been an “invasion” in a classical sense, but it was highly disruptive. The phylogeny of R1a in South Asia is strongly indicative of an incredible reproductive advantage for males bearing this haplogroup. In fact, R1a is more expansive than Indo-Aryan languages, and is found across language and caste, including among tribal populations. Previously this was argued as a reason for why R1a in South Asia must be old and indigenous to South Asia. Next generation sequencing of the Y chromosome has looked closely, and that is unlikely. The expansion of R1a, and the South Asian branch, is very recent. It hints at cultural processes of male domination and elite diffusion of lineages which we do not have a good theoretical grasp of at this moment.

But this is not the end of the story. I have spoken only of West Eurasians. What of the other half of the ancestral glass, the ASI? I have not explored this literature in detail, but there is now suggestive evidence I believe that ASI themselves may have been intrusive to the subcontinent, perhaps as hunter-gatherers migration out of Pleistocene Southeast Asia. The closest modern population to the “pure” ASI ghost group are the Andaman Islanders, and they arrived where they are today not from the Indian subcontinent, but from Burma. There is now a modest amount of evidence through various angles that the ancestors of the Munda people of South Asia must have arrived as part of the Austro-Asiatic agricultural migrations from what is today interior South China. They are not primal. There is no reason to think that that this was the first eruption of humans from this region into South Asia. Those with more understanding of paleoclimatology need to weigh in, but it may be that in the drier conditions of the Pleistocene South Asia had a naturally smaller population than Southeast Asia, so that the latter was always going to be a source and the former a sink, in terms of demographics.

In any case, if the model fits, eventually a preprint you must submit. I think the age of speculations will give way to the age of understanding, though I have no inside information at this point….


* To unpack this, take a conventional idea of Europe today, bounded by Gibraltar on the southwest, the Bosporus on the southeast, and in the far east the Urals and far southeast the Caucasus. The majority of Southern European ancestry seems to derive from Early European Farmers (EEF), and these almost certainly are from Anatolia. In Northern Europe the ancestry is a compound of EEF, Indo-Europeans from the east, and probably residual hunter-gatherers (some researchers believe nearly all of the hunter-gatherer ancestry in Northern Europe is actually from the Indo-Europeans and EEF, with no true relic populations by 5,000 BC). Of the original Yamnaya Indo-European ancestry, the ~25% or so that is Ancestral North Eurasia (ANE) probably is extra-European in provenance. Specifically, a migration out of central Siberia or thereabouts. Nearly half of the remaining is similar to EEF, but we now know it is likely derived from a different Near Eastern farming populations which descend in part from hunter-gatherers from the Caucasus. The balance is from indigenous European hunter-gatherer ancestry which amalgamated with ANE. This last portion is indigenous to Europe broadly construed before the Holocene. I haven’t done the detailed math, but it seems difficult then to imagine a scenario where anything by a minority of the ancestors of modern white indigenous Europeans actually lived in Europe during the late Pleistocene.

 
• Category: Science • Tags: Genetics, India
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 http://www.razib.com"