Draining the gods from the world

51CIf5MFrJL._SY344_BO1,204,203,200_In the comment thread below there was a lot of discussion about fantasy literature. This is a topic which I have some opinions, because when I consumed fiction regularly, it was mostly fantasy and science fiction (yes, I’m a nerd). The eruption of Game of Thrones into the popular culture space has brought this classic nerdy genre into the foreground.

Though fantasy is by its nature not of this world, the reality is that some level of plausible coherence rooted in verisimilitude is necessary for it to be broadly accessible and enjoyable. Apparently Robert E. Howard wrote the Conan the Barbarian books partly because he enjoyed writing speculative historical fiction, but didn’t have the time or energy required to become well versed enough in a place and period. Therefore, he created the Hyborian Age as a distant prehistoric epoch which was misty and vague enough that he could let his imagination flow freely while still borrowing heavily from the historical and anthropological furniture of our own universe. Sometimes this can get a little ridiculous. Guy Gavriel Kay’s Sarantine Mosaic books are in some ways historical fiction loosely inspired by the fantasy genre (he’s exhibited this pattern of drawing closely from historical periods and places over the last 20 years)!

And yet most fantasy deviates more strongly from our own universe, creating its own “secondary world” where correspondences to our history and places can be made, but which are more tenuous or speculative. Even in cases where connections are as clear as Guy Gavriel Kay’s work, there are very salient differences which mark the work as fantasy as opposed to fantasy inflected historical fiction. For example, Kate Elliott’s Crown of Stars series draws from 10th century Germany (she states this plainly), but the world is inhabited by various mythological or non-human peoples, as well is being much more gender-egalitarian than our own. I was a little skeptical of the latter part because conventional sexual dimorphism still seemed to hold in Crown of Stars, and that is I believe one of the natural reasons that men in pre-modern muscle-powered societies tend to produce highly patriarchal systems of political organization.

Which gets at the point about verisimilitude: there are stock fantastical aspects of this genre which I can take in stride, but subverting the more banal scaffolds of reality which root the world in something we can relate to bothers me. This is less of an issue in science fiction. I have read works where women take the roles of protectors to men, who conversely dominate the home. But, these works often posited biological changes where females were larger than males. In other words, they exhibited some internal coherency, insofar as the structure of the genre involves subverting and altering the parameters of what we might consider “natural.” In k10063contrast, the fantasy genre often takes us “back” to a world that resembles a static and socially “traditionalist” order, as if to counteract the shocking reality of magic or supernatural beings being normal phenomena which interpose themselves into our existence regularly.

That is why for me religion in particular is an important aspect of the texture of any fantasy work. Religion is important, often even essential and central, to the Weltanschauung of pre-modern humans. In Big Gods the author argues that a transformation of our conception of gods and their role in our lives was critical in driving the emergence of complex societies over the last 10,000 years (others point the arrow of causality in the opposite direction). Even if particular individuals who were leaders in pre-modern societies were personally not pious (e.g., Julius Caesar) the societies in which they were eminent were always suffused with religious sentiment and practice (e.g., Rome).

SilmarillionAnd yet there are two authors who in my mind stand out for giving a “thin” treatment of religious belief and practice in fantasy literature: J. R. R. Tolkien and Ursula K. le Guin. These two authors are very different, very eminent in the field, and, have differing views from me on a range of topics.

I have read widely on Ursula K. le Guin’s opinions in interviews, essays, and notes in her collections of short stories. She is a very political liberal author who has sympathies with anarchism and Daoism. Additionally, le Guin has stated she she is not particularly interested in the “hard sciences,” as opposed to the “soft sciences,” and even evinced a fascination with post-structuralism in one essay! (her father was the anthropologist Alfred Kroeber)

In other words, I have major differences with Ursula K. le Guin in terms of our views and assessments. But overall I’ve enjoyed most of her work. She can get annoyingly preachy on occasion, but le Guin is a great prose stylist, with an ability to be evocative without being pretentious (much of her work is aimed at juveniles and young adults, so that probably necessitates enforced clarity). Because of her liberal politics she enjoys inverting, distorting, or confounding racial expectations. Unlike most of science fiction and fantasy, especially in the period she was writing actively, le Guin’s protagonists are not invariably white males. Despite not being a white male personally I have no major issue with identifying with white male characters (race is not a major personal identity for me). But, because le Guin has non-white/non-male protagonists her works are often situated in worlds that depart from the standard issue fantasy or science fiction settings. And often that’s a good thing.

Her Earthsea novels are epic fantasy, but are strong departures from the typical Nordic backdrop one finds in this genre. Most of the people, and the protagonists which are you meant to identify with, are clearly non-white, with dark brown to olive complexions and dark hair. In contrast, the only recognizably Northern Europe modeled population are marginal barbarians, beyond the limes of the oikoumene, with bizarre folkways and practices. But Earthsea is not a progressive cartoon. Its system of magic is novel and memorable, while its geographic setting is on a world which is characterized by a vast archipelago of islands, rather than on contiguous continents! This is somewhat strange, but not totally fantastical. Consider Majapahit. All of these elements are atypical of classical epic fantasy, but they don’t go beyond the bounds of imagined possibilities, or even plausible realities.

J. R. R. Tolkien couldn’t have been more different. A Roman Catholic who valorized the British bourgeois and supported Franco, his politics are inverted from those of le Guin. An incredible world-builder, Tolkien famously invented the template for epic fantasy. Some writers, such as Terry Brooks, have made very lucrative careers rearranging the plot elements and motifs from Tolkien’s novels. Unfortunately much of fantasy for decades consisted of clones of Tolkien’s work, in part because his world was so lovingly constructed and fleshed out, and also because it was so easy to just generate derivative narratives. This was the standard against which le Guin created her film negative when it came time to world-build.

And yet both authors gave little space to the elaboration of religious phenomena in their pre-modern fantasy! The only conventional theists in Earthsea are the barbaric (white) Kargads. The other inhabitants of Ainur) and God (Eru). These are not entities you have faith in, rather, they clearly exist and are known to exist to all. The antagonists do not disbelieve in the Ainur, they rebel against them. Tolkien himself was a Catholic, and claimed his work was fundamentally Catholic, but many critics are skeptical. Some have suggested because he was very religious in a Christian sense, and well versed in the folkways of the Northern European pagans from whose mythos he drew to construct his world, he was uncomfortable with realistically integrating their religious system into his work. It offended his Christianity to see what were clearly Northern European people practicing false religions. Though le Guin and Tolkien are starkly different in their attitudes toward religion, they ultimately arrive at the same conclusion that a realistic religious system is not congenial to their own preferences or comfort.

I believe their readers are more poor for it, and it detracts from the thick textures which otherwise characterize their worlds.

If maternal stress is a problem, stop stressing pregnant women out!

Screenshot 2016-05-25 01.10.34The title is my response to this article in The Washington Post, Inequality might start before we’re even born. The screenshot to the left is from Twitter, and shows an alternate title. The article is written by a journalist whose work I normally am appreciate of, but when I saw that I started swearing. There’s just no way that that’s nothing but some spurious correlation. But this research is just too sexy not to write up. It has everything. Inequality. Scientific revolution. And some catchy hooks which relate to American culture (sports).

expecting-betterObviously stories like the above are why Emily Oster had to write Expecting Better: Why the Conventional Pregnancy Wisdom Is Wrong–and What You Really Need to Know. Mind you, the fact that Mendelian genetics works as a model should give you a clue as to the reality that epigenetic stress is not ubiquitous in explaining inter-generational variation. But it doesn’t hurt to have a University of Chicago economist step in to rebut the latest well-meaning moral panics.

Here is the reason I am posting this: if you actually believe that mild stress has major long-term impacts, why would the media post a piece that probably induces stress in pregnant women!

Human inequality is not fair: NBA edition

The_Sports_Gene_Book_Cover_2013Interesting piece in The Wall Street Journal, which could have been cribbed from David Epstein’s The Sports Gene (a very good book I might add), NBA Basketball Runs in the Family (if you go to Google News and search for the title it should come up and you can get a free copy):

According to a Wall Street Journal analysis of biographical data on every NBA player, 48.8% are related to current or former elite athletes—defined as anyone who has played a sport professionally, in the NCAA or at national-team level. While other leagues feature notable dynasties—the Manning’s of the NFL or the Griffey’s in baseball—only about 17.5% of NFL players and 14.5% of MLB players are related to other elite athletes, based on a similar study.

The connectedness in the NBA likely comes down to the importance of height in elite basketball. The average NBA player is about 6-feet, 6-inches tall, which is 11 inches taller than the average American male, according to Census data.

As indicated in the piece you aren’t seeing that the 10,000 hour rule is a secret passed down within families. If you are not very tall it is unlikely that 10,000 hours of practice will result in you becoming a professional athlete in the NBA. The article emphasizes that the enrichment of those with relatives who had played in the NBA is far greater than the NFL or MLB, but please note that the average person’s odds of entering any professional sport is infinitesimal. Well, not quite, but the odds are low.

The piece in The Wall Street Journal is valuable for the added data, but there a few conceptual aspects which I’m not satisfied with. Researchers have known for decades that most of the variation in the population in non-malnourished societies in height is due to variation in genetics. 80 percent heritability is conservative. This can lead to some confused intuitions though. The correlation between siblings is high, but not that high, in the range of ~0.50. That translates to an average difference in height of nearly two inches.

41ZhyEU5lGL._SY344_BO1,204,203,200_In other words, parental or sibling success in the NBA is not destiny. On the contrary. Nearly half of current players may have had relatives who played in the NBA, but most of the people who have relatives who played in the NBA did not themselves play in the NBA. But, obviously having relatives is incredibly predictive of much higher than normal odds (orders of magnitude greater!) of becoming a professional.

Why? As noted in the article NBA players need to have an intersection of traits which are very deviated from the norm. The range restriction on height, with “very short” players being mildly above average the human male median, shrinks the pool of potential candidates a lot. Fourteen years ago James F. Crow wrote Unequal by Nature: A geneticist’s perspective on human differences. Crow observes “that whenever a society singles out individuals who are outstanding or unusual in any way, the statistical contrast between means and extremes comes to the fore.” As it happens being a professional basketball player is not just about height; one needs to also be athletic, and exhibit a modicum of agility and skill. At the collegiate level there are many relatively tall players, but most of them do not have the skill level of an NBA player. The best-of-the-best have often been NBA players who combine great height with high skill levels (e.g., Lebron James, Magic Johnson, and Kevin Garnett being examples; Michael Jordan, a few inches shorter than James, had greater skill, but he is close to the NBA media).

The article also illustrates the fact that individual humans often want to attribute their own success to their hard work, or choices their parents made. Many of the players interviewed did not deny the importance of their size and athletic endowments, but emphasized the importance of learned work ethic and competition with family members of similar skill levels and physique. This illustrates two other aspects of quantitative genetics: gene-environment interaction and gene-environment correlation. Obviously these are real phenomena. But are they really relevant for an NBA player?

David Robinson grew up in a middle class family (his father was an engineer). He scored 1320 on the pre-recentered SAT (that puts his IQ well above two standard deviations) and majored in mathematics at the Naval Academy. Robinson’s non-basketball activities were, and are, copious (and not in a Dennis Rodman fashion).

He was not initially very good at basketball in secondary school, but underwent a massive growth spurt in his late teens. Eventually he became a standout basketball player at the collegiate level, and went on to a storied career (after serving some time in the navy). My point with recounting this is that even someone like David Robinson, who had many alternative paths, talents, and opportunities, and evinced no burning desire to become a basketball player at all costs, became a professional. Why? Because his raw talent was clear, and the reality is that becoming a professional basketball players is highly lucrative. The average NBA player earns millions. Even a washout player can earn millions in one year.

So we are at this point moving from the domain of quantitative genetics, to economics. Incentives matter. Millions of young people delude themselves into thinking they have a chance. The reality is that even someone like Jeff Hornacek, perhaps a mascot for those who argue that work ethic can match talent, is not physically typical (he’s 6’4). And, let’s be honest, work ethic matters a lot, but it too is heritable (mediated through conscientiousness). Wheels within wheels….

Open Thread, 5/23/2016

The origin of the white walkers (GoT).

a-game-of-thronesDon’t click the above unless you want a major book spoiler. But the television show Game of Thrones is pushing deep into uncharted territory. And by book spoiler, I don’t mean the reveal about Hodor. Rather, the scene above reveals the origins of the Others, also known as the white walkers.

Or does it? We’re now in a zone where perhaps the show is deviating from George R. R. Martin’s own vision. But I doubt it, because the explanation is actually true to the author’s philosophy when it comes to fantasy. There’s a lot of naturalism, and magic and the supernatural are inferred, and their exact character are difficult to pin down. By this, I mean that in J. R. R. Tolkien the supernatural mythos was well developed, and all understood it to be concretely real in a straightforward sense. Similarly, Robert Jordan and Brandon Sanderson have universes where gods clearly exist and have supernatural agency. George R. R. Martin’s world of grays is more attuned to the mindset of a religious skeptic, to the point of have a fair number of religious nonbelievers as major characters.

One month out now from the Evolution Meeting. Will probably drop in now and then as I’m normally not that far from the convention center.

A bunch of people in the tech scene in Austin are rather upset about the whole Uber/Lyft leaving town thing (honestly, I’ve been hearing about this for 6 months, but like a lot of people I just didn’t believe it would come to this). So there’s one solution, Nonprofit Uber alternative springs from Austin tech minds. Should be up and ready for the Evolution Meeting. So who knows.

Spent the weekend with some out of town friends who are immersed in genomics. Always fun when you can spend a day talking shop in this sort of fluid manner.

Some people complaining again that I’m not nice to commenters. First, these complaints never have any effect. Second, a lot of you shouldn’t comment when you have nothing valuable to contribute to a particular thread. Some of you lack domain specific insight. And some of you are just plain old stupid, even if well intentioned. I hope my irritation that you comment makes you feel appropriately unwelcome.

Speaking of rudeness, Bruenighazi: how a feisty Bernie blogger’s firing explains Democratic politics in 2016. And, Is Matt Bruenig a Populist Martyr? Bruenig certainly seems to behave in a nasty manner in relation to those on his “enemies list.” That probably justified Demos firing him, as that sort of behavior can ruffle too many feathers. But that doesn’t negate the reality that his picking on someone in a position of power, as he did, probably was the immediate cause of what happened to him. Additionally, I’m not going to lie, I exhibit more tolerance towards class-based attacks than I do race/sex/gender stuff, because so often the latter is just signaling and opportunism. I am not on the Left, so I don’t support a lot of Left economic policies, but the logic of self-interest here is at least somewhat logical. In contrast, race/sex/gender identity politics easily devolves into parody.

On the other hand, this massive decline in poverty is despite Left activism against markets.

The ancient scramble for Eurasia


When I wrote the Pleistocene was humanity’s Hyborian age, I meant humanity. For contingent reasons the new genetic sciences of ancient DNA have elucidated the history of northwest Eurasia first. But prior to the Great Divergence Europe was not quite so exceptional. In fact the historian Victor Lieberman wrote Strange Parallels, his macrohistory of Eurasia, to highlight just how similar the trajectories of Western Europe and mainland Southeast Asia were up until the early modern era, when the West distanced itself from the rest. In short, European prehistory updates our priors for the prehistory of us all.

For various reasons having to do with professional responsibilities I look at TreeMix plots quite often. Like PCA TreeMix is great for exploratory data analysis. You throw a bunch of populations in there, and it searches a bunch of parameters which can fit the model. But often the results are weird.

They’re not weird because they’re “wrong.” They’re weird because we’ll forcing data to give us answers, and the model pops out something which is reasonable with the conditions imposed on it. And often we just don’t have the big picture. Statistical inference was indicating strange connections between Native Americans and Europeans for the past decade…but it took ancient DNA from Siberia to resolve the mystery. Europeans and Amerindians exhibit ancestry from a shared common population. In Europe this ancestry is relatively recent, on the order of the past ~4 to 5 thousand years. Statistical genetic inference can tell us our model is missing something, but it can not always specify clearly just exactly what we’re missing.

The image above from a TreeMix plot is hard to make out; click it. But what it will show you are two things which are strange:

1) Gene flow from between the East African (mostly HapMap Masai for what it’s worth) node and Mbuti (HGDP) to the Papuans (HGDP).

2) Gene flow from near the East African node to the point which defines the whole East Eurasian, Amerindian, and Oceanian, nodes.

It would laugh this off, but I see it all the time in TreeMix. I know I’m not the only one. I have no explanation for it. It’s obviously not recent admixture. Rather, there are affinities between populations which we just don’t have a good model for. Knowing what we know about ancient Europe it is mostly likely that these gene flow edges which seem inexplicable reflect prehistoric events which make sense only in the context of population patterns which have been totally obscured over the last 10,000 years. Ancient DNA from China will probably shed a great deal of light on these topics. I predict that the Chinese will exhibit the same discontinuity with their Paleolithic ancestors that modern Europeans do, and the affinities between East Eurasians and some Africans in these TreeMix plots probably is a shadow of a “ghost population” which has been absorbed in Eurasia, and may have contributed to some of the ancestry of a group which migrated back to Africa.

Notes I set TreeMix to check for covariance across blocks of 1000 SNPs. I had 215,000 total markers in the data set (very high quality ones). I rooted it with Mbuti, set 5 migration edges, and ran it 10 times. They all looked the same. Most of the populations are pooled from public sources.

Europe on a finer cartographic scale

In the comments below it seems that most people don’t know about the existence of Eurostat, and the NUTS2 and NUTS3 maps which they generate. They’re really great, insofar as they give you a fine-grained picture of variation within Europe. Sometimes you see how national boundaries matter a great…and in other ways how they don’t.

Above you see a NUTS3 map of purchasing power in relation to the European median. A few things that are salient.

1) France and the United Kingdom exhibit a great deal of wealth concentration around their capital cities.

2) The geographically fragmented and culturally diverse zone from the Low Countries down to Italy’s Po River Valley is seems to be characterized by a large number of economically vibrant cities/regions. The only common variable that I’ve ever been able to point to for this area is that they were under Habsburg hegemony for a very long time.

3) There are zones of poorer nations, such as Spain, which are wealthier than most regions of wealthier regions (e.g., Catalonia is more prosperous than the north of England or rural France across the border).

4) A few of the cities of Eastern Europe seem to be diverging from their host nations.

Below are screenshots of maps I generated from Eurostat, submitted for your comment (remember, don’t be stupid).

Screenshot 2016-05-17 22.41.22

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Screenshot 2016-05-17 22.45.08

Screenshot 2016-05-17 22.46.07Screenshot 2016-05-17 22.46.40Screenshot 2016-05-17 22.47.30Screenshot 2016-05-17 22.48.02Screenshot 2016-05-17 22.48.38Screenshot 2016-05-17 22.49.05Screenshot 2016-05-17 22.49.30Screenshot 2016-05-17 22.49.58Screenshot 2016-05-17 22.50.23Screenshot 2016-05-17 22.50.58

Open Thread, 5/16/2016

51jUZQV3r1L._SY344_BO1,204,203,200_Life has been busy. Very busy. The company I’m working for is ramping up on releasing product…as in on the order of weeks, not months. We’ve already released results to a few early  beta testers, and are taking reservations for orders (basically you are in the front of the line for notification when the orders are being taken, and I’m 99% sure that the turnaround is going to be faster than later on when the analysis pipeline will be crowded).

The details of the test are pretty straightforward, at least for a reader of this weblog. 224,000 markers on the SNP-chip, a reference panel of thousands, with 150 populations. Yes, we have wolves and coyotes, so we should be able to pick up admixture/introgression. It’s mostly a breed focused product at this point when it comes to ancestry, but we’ve got a large number of village dogs in there too. In terms of functional characteristics, the current focus is on diseases, but we’ll be expanding into traits soon. Really there are many directions we could go with this.

Screenshot 2016-05-16 21.20.23I’m making one public plea to Chris Chang of plink to allow us to be able to use his tool without always having to specify that we’re not using a human data set.

The New York Review of Books has a piece up, Who Was David Hume? It’s reviewing Hume: An Intellectual Biography. Of course I purchased it…I could do no other. God knows when I’ll get to read it.

51d1NcqF6rL._SX324_BO1,204,203,200_Speaking of books, I also purchased Patricia Crone’s Pre-Industrial Societies: Anatomy of the Pre-Modern World. Crone is known more broadly in the public for her work in the revision of the history of early Islam, but as a scholar she was much more than that. Her Islamic revisionism didn’t make much of an impression on me, but God’s Rule – Government and Islam: Six Centuries of Medieval Islamic Political Thought, did. She’s a thinker who everyone should have paid more attention to in my opinion, as she was a humanistic scholar in the older tradition, genuinely striving toward the truth as opposed to fixating on the power relations of the present.

200px-TheWayOfKingsAs some of you recall I’m following Game of Thrones now via the internet. The whole idea of a “fork” is somewhat liberating, and, the reality is that I’m not patient enough to wait until Martin completes the series when my daughter is in high school. Speaking of series, I left T Greer of Scholar’s Stage totally dispirited when I informed him that Brandon Sanderson’s The Stormlight Archive is projected to run to 10 books. At his current pace that means Sanderson will complete the series in 21 years assuming that he hits his mark…

Speaking of a long time, this August A Song of Ice & Fire will will be 20 years old! It seems highly implausible to me that George R. R. Martin can wind up all his plot threads in two final books, even if both are 1,500 page monsters. I think we’ll be lucky if he manages to accelerate publication rate again and tie things up in the middle-2020s, when he’s in his late 70s.

A note on comments. If you begin a comment by pointing out some presumed detail of my ethnicity you’re probably getting deleted immediately (I state presumed because 3/4 of the time people are wrong). I don’t prevent assholes from reading what I have to say, but I can make sure assholes don’t leave comments.

How Austin Residents Are Getting Around In A Post-Uber World. Keep Austin primitive?

Eske Willerslev Is Rewriting History With DNA.

Top scientists hold closed meeting to discuss building a human genome from scratch. My prior is to be against closed meetings. Makes scientists seem like they’re part of a cabal.

Interesting map.

Segregation maintains genetic variance

Siblings varyOne of the most curious things to people is that siblings can vary a great deal in their traits. Sometimes, this is not simply due to environment. Height is a predominantly genetic characteristic in terms of its heritability within the population, but the correlation between siblings is only 0.50 in terms of the trait value. The standard deviation in IQ among siblings is only a bit less than the standard deviation among the general population.

And yet with a quantitative trait where most of the variation is due to genes of small effect this seems peculiar. Though genetics is not “blending,” it seems that inheritance should be closer to blending when it comes to thousands of genes combining to account for the variation on one trait.

Andrew Oh-Wilke brings up the objection below:

Because if there are really 5,000-10,000 loci, the law of averages is going to kick in with a vengeance and similarly regression to the mean should be huge, but while IQ breeds fairly true, IQ variation between fairly closely related individuals is often quite significant. If children inherit randomly from both parents and there are really 5,000-10,000 loci that matter, all of which have very small effects, IQ differences between siblings ought to be really, really slight and rare, because the 5,000-10,000 random trials for the large number of low effect SNPs should average out between full siblings almost completely. But, while full siblings are definitely correlated, there are routinely meaningful magnitude sibling IQ differences. When no one inherited factor has an impact of more than say 0.02%, that shouldn’t happen.

Siblings vary

Siblings vary

The short answer is that segregation maintains variance. I allude to this in my Slate piece on grandparents. Siblings may be expected to be 50% identical in terms of their genetic state due to parental contribution, but in reality there is variation around this value. I have two siblings who are 41% identical. The standard deviation around 50% is about 3%.

For the deeper and more explicit formalism in relation to quantitative traits and polygenetic inheritance, you could get a copy of Introduction to Quantitative Genetics (I do recommend this of course). But Alan Rogers published a paper from 1983 which touches upon most of the major issues in a clear manner, Assortative mating and the segregation variance:

Feldman and Cavalli-Sforza (Theoret. Pop. Biol. (1979), 15, 276-307; (1981), 19, 370-377) have emphasized the role of the segregation variance in models of assortative mating for continuous characters. This note examines its behavior in the context of a general additive model. Using known results concerning the effects of assortative mating and selection on genic variance and correlations among uniting gametes it is shown that the effects of these processes on segregation variance will be small if the effective number of loci is large. Thus models in which the segregation variance remains constant are approximate descriptions of the behavior of characters determined by many loci.

Basically he’s saying that contra what some had modeled, segregation variance is rather constant across generations if the genetic variance is on a highly polygenic trait. Naturally this means polygenic traits exhibit segregation variance.

Screenshot 2016-05-15 10.39.25Rogers shows through some algebra that the segregation variance is a function of the additive genetic variance (the first term after 1/2), and, (1 – f). Therefore if f ~0, the segregation variance is about the same as the additive genetic variance, which to me aligns intuitively with why there is roughly the same standard deviation across groups of siblings and the general population in IQ (though the former is smaller than the latter).

Screenshot 2016-05-15 10.45.41Rogers shows that f is a function of variance at the locus (weighted across all the loci) and fi, which is the correlation between uniting gametes. If the correlation between gametes is very high (in the context of this paper he is focused on phenotypes and assortative mating), then variance will naturally be low, as there is not going to be genetic variation at that locus in that individual. Basically, f measures deviation from Hardy-Weinberg equilibrium. In a random mating population then f is small, so the segregation variance and additive genetic variance will be of similar magnitude.

Was the Prophet Muhammad a Jew?

51U-OkDelKL._SX323_BO1,204,203,200_The origins of Islam are fascinating, because the religion is critically important in the modern world, but its genesis within history is surprisingly vague for its first decades. Muslims have their own historiagraphy, and some Western historians, such as Hugh Kennedy transmit this narrative with high fidelity, albeit shorn of sectarian presuppositions and strongly leavened with Western positivist methodologies. His books The Great Arab Conquests and When Baghdad Ruled the Muslim World: The Rise and Fall of Islam’s Greatest Dynasty are rather good in my opinion.

An alternative view is presented by revisionist scholars, who in the process of revising Islamic history tear apart its basic foundations, at least from a Muslim perspective. Their views can be found in works such as The Hidden Origins of Islam. This school of scholars contends that much of Islam’s early history, basically before 700 A.D., is myth-making that dates from the Abbasid period (>750 AD). An analogy here might be made to Republican Rome. The city emerges prominently in history only in the 3rd century B.C., so much of centuries of Roman history which are referred to by later writers are difficult to corroborate. Presumably many of the figures of these earlier periods, such as Cincinnatus, may have been historical, but more often than not it is likely that details of their life served as moral exemplars for republican political leaders.

Similarly, a basic thrust of the revisionists in relation to Islam is that the idea of Muhammad is far more important than the details of who he really might have been. Even the milieu of Muhammad, a desert merchant, may have been manufactured to give him a particular aura. To reduce one line of scholarship to its essence Islam emerged as a national religion of Christian Arabs who had long been on the margins of the Roman and Persian worlds decades after the time of Muhammad. The construction of the Muhammad myth, and relocating sacred sites to a area far outside Roman control and influence (Mecca & Medina), may have been motivated by considerations of distancing from the Greco-Roman and Persian cultural traditions which they were attempting to absorb and supersede.

One aspect of the mythos of Muhammad is that he grew up as a primal monotheist in a pagan land. The revisionists reject this, and suggest that Muhammad was a Christian, in an Arabia where Christianity and Judaism were the dominant elite religions. No doubt there were other religious sects, and the influence of Zoroastrianism was also likely, but organized paganism as depicted in Mecca may have been a propaganda device. There are precedents for this line of thought, some scholars have argued the same for the late survival of paganism in Sweden (in comparison to Denmark and Norway), suggesting that in fact it was a scurrilous attempt by Western Christians to besmirch Eastern Orthodox believers, who were much more numerous in this region of Scandinavia.

I don’t personally take a strong position here. It seems likely that the revisionists go too far, but I do think that a quasi-state paganism in Arabia in the year 600 A.D. is implausible in light of what we know about other regions of the world on the Roman frontier. The dominant forms of religion in Muhammad’s world probably was Christianity, with roles for Judaism, Zoroastrianism, and various gnostic cults. Pagans still remained, but they were likely a marginal residual, not a threatening elite force as depicted in Islamic tradition.

Screenshot 2016-05-15 00.01.48So, with all this historical context in place, it has come to my attention that there are some peculiarities in the male paternal lineage of descendants of the clade L859+, the dominant haplotype among the Quraysh, Muhammad’s tribe. This lineage, L859+ is a clade within haplogroup J1, which includes the famous Cohen modal haplogroup. On the L859+ tree above you see that the Qurayshi’s are a brother clade to ZS22012. This is traditionally a Jewish lineage. None of this “proves” anything, but it’s interesting and suggestive. If the revisionist are right, and Muhammad grew up in a world dominated by Jews and Christians, it would not be implausible if he himself was of Jewish background in some fashion. Or, that Arab Jews and Arab Christians had a fluid and permeable cultural relationship, and both interacted with the large Jewish community of the Middle East of the period, where some Arab Christians descended from Jews.

We are not your Asian American (political) sidekick

Shu_Qi_Cannes_2015Facts are important. But they can be inconvenient. Despite the stream of “think” pieces about “hookup culture” over the past decade there is no evidence that young people today are more promiscuous than in the past. In fact, on the contrary. Young people today are by most measures less promiscuous than past post-WW2 generations, in particular, Baby Boomers. Those articles ultimately are not about the behavior of young people, but the fears, dreams, and nightmares, of a declining Baby Boomer cohort which refuses to go into the sunset quietly. I’m not a Boomer, so I won’t psychonanalyze their motives, but like literature the facts proffered in these essays are a means toward probing deeper issues and questions about the human condition, their generation’s condition and preoccupations, as opposed to being literally true (some of the more recent articles will even admit that the statistical evidence falsifies their premise, but then proceed to suggest there are anecdotal data that lend credence to their premise!).

This applies to other things. Today Quartz put up a piece, If Asian Americans saw white Americans the way white Americans see black Americans, which is not really about Asian Americans at all, but simply uses them as a prop, often in a mendacious manner. First, it gives a nod to the Asian American “Model Minority Myth,” stating that there is “perception that they are high achievers relative to other American ethnic groups.” Get it? There’s a perception. There’s a myth in some scholarly and political quarters that the model minority idea is a myth, founded mostly on assertion (e.g., just stating that it’s a false myth) and slicing and dicing the statistics to emphasize ways in which Asian Americans are disadvantaged in relation to non-Hispanic whites. For example, there is often a focus on the diversity among Asian Americans, ranging from affluent Indian Americans, to groups with more conventional socioeconomic profiles like Filipinos, and finally, those which are somewhat disadvantaged such the Hmong. This is to show that Asian Americans are not a model minority…some of them are struggling. But the logic is not applied to whites! Those who purport to debunk the myth of the model minority would not accede to debunking the idea of white privilege by pointing to the state of Appalachia, and rural white America more generally. Group averages for we, but not thee?

51fMlNGN4lL._SY344_BO1,204,203,200_And yet the Quartz piece engages in some interesting jujitsu by actually reporting the statistics of Asian American advantage vis-a-vis white Americans in the service of a broader agenda of putting whites in their place in relation to their critiques of black Americans. In particular it quotes Anil Dash as saying “If Asian Americans talked about white Americans the way whites talk about black folks, they’d bring back the Exclusion Act.”

This to me is really bizarre, and what I term mendacious: Asian Americans do talk about white Americans the way whites talk about black folks. This sort of thing was a clear subtext of Amy Chua’s Battle Hymn of the Tiger Mother. Many (most?) Asian American kids who grew up with immigrant parents were barraged with assertions about the disreputable character of their “American” (white) friends, and how it was important to keep on the straight & narrow. Immigrants from Asia often perceive white Americans to be sexually obsessed, lazy, and prone to a general amorality and fixation on short term hedonic interests. These are polite ways to condense the sort of attitude many Asian immigrants have toward the white American mainstream, which they worry will absorb and corrupt their children. Dash must know this, as he probably had immigrant parents, or was friends with people from immigrant backgrounds. Most white Americans don’t know this, partly because most white Americans don’t have non-white friends. But anyone from an Asian American background aware of the stereotypes and perceptions.

The tacit misrepresentation of Asian Americans here, not acknowledging that they do engage in the exact sort of behavior you are hypothetically positing they might engage in and so alienate white people, is not surprising. Asian Americans are often simply bit characters in a dram involving broader social and political streams which dominate the American political landscape. For many decades conservatives asserted that Asian Americans were “natural Republicans,” and expressed confusion as to why more were not voting for their party. But this was an empty talking point; over the past generation the Republican party has become the de facto white Christian party, and many Asian Americans are not Christian, and all are not white. Some conservative Christian Asian Americans can identify with Republicans because of their religious ties, but socially conservative Indian Americans, to give one example, naturally have a difficult time identifying with a party which wears evangelical Protestantism on its sleeve as modern Republicans often do. This isn’t rocket science.

Screenshot 2016-05-12 21.34.16On the flip side of this, many liberals erase Asian Americans from the landscape if it does not serve their framework of white privilege. Many people pointed me to The New York Times infographic, Money, Race and Success: How Your School District Compares. The only mention of Asians is this: “Reliable estimates were not available for Asian-Americans.” But my wife pointed out that within the chart itself you still had Asian Americans tabulated! If you check the bubble plots at the top rightyou see schools like Cupertino Union.  It’s 73% Asian American. If you read this blog you know that it irritates me that Asian Americans are routinely elided out of these stories. It’s too regular to be due to a lack of data. It’s because it doesn’t fit the narrative of white privilege and domination. So Asian Americans are edited out of the picture to make it neat and tidy.

Instead of taking reality as it is, in all its complexity and nuance, people attempt to fit the data into a narrative straightjacket. Complexity is a talking point only when confronted with a hypothesis you disagree with. When the data does not cooperate in a simple fashion with your own model, the data conveniently goes unmentioned. In a putatively multicultural America the dominant narrative on the Left side of the cultural and political spectrum is that of a dichotomy between whites, who have privilege, and non-whites, who are oppressed. The black American template, unique, and rooted deeply in the soil of this country, is injected into strange and inappropriate contexts when it comes to people whose ancestors are from Latin America and Asia. White liberals and minorities are assumed to naturally form an alliance against the majority white rump; white liberals because of their moral virtue, and minorities because of their interests. The injustices experienced someone with a name like Raheem Washington, who grew up in the inner city, are rather easy to enumerate. Raheem Washington begins life with some disadvantages. But there is a particular mainstream narrative where someone with a name like Deepa Iyer, who might have elite educations, affluent parents, and a good secure career, has more common with Raheem Washington than their white colleagues at the university that they might work at. And of course, there is the further aspect that often goes unmentioned that someone with the name Iyer is from the top echelons of South Asia’s caste system, and so benefits from thousands of years of privilege! And yet it is common among Indian Americans for literal Brahmins to style themselves PoC tribunes of the plebs, oppressed by white America.

A genuine multiculturalism would actually acknowledge the real empirical texture of this nation’s changing demographics. And, a genuine multiculturalism rooted in fact, rather than vacuous critical theory, would dig deep into the richness of human history, rather than outlining broad sketches where white privilege reigns supreme from Sumer to America. As it is, often liberal multiculturalism is simply an inversion of white supremacist theory. That’s unfortunate, because there are real political debates and values divergences which we can grapple with and debate as a society, but the water is immediately muddied and when the facts are subordinate to an ideological narrative.

* Many of the things I said above can be generalized to the American Right as well, though the particularities will differ.

** I shouldn’t have to say this, but any racist comment isn’t going to be published. That’s not going to stop some of you, but I thought I’d give you fair warning.

Truth is all about money….

Sather-Tower-UC-Berkeley-by-brostad-on-flickrI’ve joked on Twitter that one aim of conservatives should be to defund disciplines whose avowed goals are to espouse a particular ideological viewpoint. Of course “scholars” in those disciplines might dispute the characterization of their chosen fields in such a manner, but the reality is that that’s how they roll. Conservative or moderate viewpoints are considered illegitimate and not worthy of consideration in many of these departments and disciplines. The political spectrum goes from mainstream liberals on the Right to Marxists on the Left. There is no reason that the the “master” should be paying for someone to burn down his house.

Of course these viewpoints are concentrated in the “studies,” which is ironic as many of the scholars in this field don’t study much, as opposed to being activists and ideologues espousing their views at length. Traditional humanities and philosophy are relatively sane compared to Women’s or Ethnic Studies, but I see where Rod Dreher’s reader, a professor in STEM, is coming from when he suggests that “Why Not Close Humanities Departments?”

I was thinking of this when reading this in Nature, Gene variants linked to success at school prove divisive:

The findings have proved divisive. Some researchers hope that the work will aid studies of biology, medicine and social policy, but others say that the emphasis on genetics obscures factors that have a much larger impact on individual attainment, such as health, parenting and quality of schooling.

“Policymakers and funders should pull the plug on this sort of work,” said anthropologist Anne Buchanan and genetic anthropologist Kenneth Weiss at Pennsylvania State University in University Park in a statement to Nature. “We gain little that is useful in our understanding of this sort of trait by a massively large genetic approach in normal individuals.”

Buchanan and Weiss are smart. Money is what fuels research, and without that oxygen further studies may not be possible. At least in the short term. Whole genome sequencing will become ubiquitous soon, so understanding these patterns is going to be a matter of joining a few tables somewhere. Imagine a future where Facebook has your genome as part of your profile; they could glean a lot about human behavior genomics simply by combining genetic states with online browsing and engagement patterns.

74 loci for cognitive development; yes, this is happening

Screenshot 2016-05-11 12.07.21

Screenshot 2016-05-11 12.20.14No time to comment. Yes, the hits with SNPs are cool. But look at all the functional associations and analysis. Some seriously biology in this. Look at the figure from the paper to the left which shows how the genes associated with this SNP hits are expressed in different tissue/types and organs. These are the biggest effect SNPs for years of education in the genome, so it makes sense that they’d way over-expressed in the brain. But it is definitely more convincing to those who might be skeptical a priori (well, it should be more convincing at least).

Genome-wide association study identifies 74 loci associated with educational attainment:

Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals1. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample1, 2 of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.

Social science genomics is a thing….

Behold, Summer Institute in Social Science Genomics:

The purpose of this two-week workshop is to introduce graduate students and beginning faculty in economics, sociology, psychology, statistics, genetics, and other disciplines to the methods of social-science genomics—the analysis of genomic data in social science research. The program will include interpretation and estimation of different concepts of heritability; the biology of genetic inheritance, gene expression, and epigenetics; design and analysis of genetic-association studies; analysis of gene-gene and gene-environment interactions; estimation and use of polygenic scores; as well as applications of genomic data in the social sciences.

The future is not the future anymore.

Open Thread, 5/8/2016

Civil_War_Final_PosterWent to see Captain America: Civil War yesterday at the Alamo Drafthouse. I don’t watch many movies, and I’m not into comic books, but the Marvel films series is one I watch partly for cultural literacy (years ago I got tired of references to The Dark Knight, so I watched them just to get caught up). Also, Alamo Drafthouse really knows how to make a profit on films and distinguish themselves from Netflix in terms of what they offer. Tentpole films are still something you want to go to the movie theater for, but most of the time someone like me is not profitable for the establishment, because I avoid purchasing $4.00 size giant coke’s at the concessions.

As far as the movie, it is hard from where I stand to side with anyone except Captain America, even though if you think about it there are many merits to the position of Tony Stark. I’d probably have been more persuaded by Stark’s consequentialism if it had been motivated by cold calculations, as opposed to an emotionally fraught interaction with someone negatively impacted by the Avengers.

One of the things that kind of annoys me about the Avenger’s films is how much hand to hand combat there is, and lack of acknowledgement at how fragile the human body can be. Recently I got into a bike crash. I’m fine, but I had a lot of bruising which is just healing. I can understand that Captain America can take the hits, but without the suit Tony Stark is a man just like us, while Black Widow at 5’3 putting the smackdown on so many people is kind of ridiculous. But then again, it’s just a movie, and one which had Ant-Man in it, so I’m not taking it too seriously.

41yT8hhOZJL._SX339_BO1,204,203,200_Struck by the importance of ancient Near East in The Shape of Ancient Thought. The Axial Age in the middle of the first millennium B.C. resulted in an efflorescence of ideas which persist down to the modern age. The distribution of these of ideas were geographically distributed across the length of the Old World oikoumene, from Greece to China. The Shape of Ancient Thought is focused on two particular loci, Greece and India. But there is a repeated reference to the primacy of motifs and patterns which seem to have their ultimate roots in Egypt and Mesopotamia. The underlying idea here seems to be that Indian and Greece civilization did not emerge de novo, but rather hoisted itself up on the shoulders of the Bronze Age (the fact that both Indian and Greek writing styles derive from Aramaic roots illustrate this).

I tried to read some more of A New History of Western Philosophy. The author of this book, just like the author of The Shape of Ancient Thought, is on the prolix side. But A New History of Western Philosophy has more boring content in my opinion.

What Makes Texas Texas. Speaking of Texas, Uber and Lyft Are Leaving Austin After Losing Background Check Vote. Uber and Lyft are trying to muscle out and marginal city government, but is regulating ride-sharing really going to be the issue on which defenders of government prerogative are going to stand? Was this the “progressive” thing to do? Apparently some people were frightened by the lack of background checks on Uber and Lyft drivers, and the possibility of sexual assault. Perhaps anyone who uses a public restroom should also get fingerprinted. There’s the principle that corporations shouldn’t dictate to the polity, but in the case of taxi services and local governments, there’s been decades of cozy collusion.

If you leave a comment which tries to hijack a thread into on of your pet issues, I won’t publish it.

game-of-thrones-bookI have long had contempt for the television show Game of Thrones. My contempt was couched in the language of sophistication. Television shows are not as rich in texture and narrative depth as books. In hindsight this seems to have been mostly snobbery. I don’t watch the show as I don’t have HBO, and and I’m not invested in the serial in any deep way, but I am now paying attention to what’s going on since HBO has gone further than George R. R. Martin. And to be honest I am in the camp which believes there is a modest probability that HBO is the only way many of us will get satisfaction in relation to finale of the series.

Also, it is interesting to see clips of flashbacks, as such a young Ned Stark confronts Ser Arthur Dayne. And of course it confirms and foreshadows the final working out of R + L = J. I remember back before the show having discussions on message boards around ~2000, and it as pretty clear to everyone that R + L = J is the most parsimonious model. Not necessarily the right one, but it was always the one you were going to have to bet on. If Martin and the HBO show go in separate directions it would almost be cool. It isn’t as if fantasy and science fiction series haven’t done a bait-and-switch before; Brandon Sanderson did so in Mistborn and that’s how the Dune series ended (the books co-written by Kevin Anderson and Brian Herbert).

This complied version of ADMIXTOOLS runs straight-out-of-the-box on Ubuntu.

000fcb8d_mediumIt would be nice if those you would speculate on genetics constantly in the comments actually bother to know something about genetics. That way it would be easier to understand what you’re trying to say, instead of having to always decrypt your inchoate ramblings. For the purposes of this blog John Gillespie’s Population Genetics would probably suffice. If you are a little more ambitious there are used copies of Nielsen and Slatkin’s An Introduction to Population Genetics to be had for $40. That’s a lot better than $90 used copies of Principles of Population Genetics, and, it is focused on population genomics.

Margot Honecker, unrepentant widow of East Germany’s last leader, dies at 89. She seems to have been quite unpleasant. But her fixation on shaping and determining the thought of the youth is very familiar.

I went to a coffee shop today to work for a while which was basically like being in Portland.

Speaking of the Pacific Northwest, ASHG 2016 is in Vancouver. I plan on going.

I had no idea what the lead singer of Radiohead looked like. He looks like a character out of British Movie.

The 2,000 year selection of the British

Screenshot 2016-05-07 22.23.55

Phenotype selected for

Selection is one of the major parameters which population geneticists investigate. The easiest way to investigate selection is to have omniscience as to the change in allele frequencies over time. If you are a Drosophila geneticist this is feasible, as you control the reproduction of your model organism in the lab. It is obviously much more difficult in natural populations (one reason that I think ecological genetics went into decline for a while is that it is just very hard). And in long-lived species like humans it is really not feasible to “track” change in allele frequencies in real time, as that would take centuries in the least.

So researchers have to make recourse to inferences from patterns of variation in the genome for species like humans, as it allows us to look back into the deep past. The inheritance pattern of Mendelian genetics is such that transmission of variants across the generations can be modeled, and processes such as rapid population growth or positive selection leaves footprints in the genome long after they’ve done their job. So you can test for selection, or population expansion, or bottlenecks, just by looking at patterns that you’d expect being left in their wake. The PSMC method famously infers demographic history of populations by examining variation within a single whole genome!

principlespopulationgeneticsIn regards to selection, which population geneticists are interested in because it is one of the preconditions for the evolutionary process of adaptation, there are many methods of inference from genetic and genomic data. Tajima’s D is an older method which compares different types of diversity across the genome, and popular for those looking more at inter-specific differences. More recently haplotype based tests look for long segments of variants within the genome. EHH and iHS are probably two of the more popular versions of this. Haplotype based methods really didn’t become popular until the middle 2000s because they require a certain density of data which is really “post-genomic” era. Then you have the methods which look for frequency differences between populations, and compare them to the expectation based on patterns across the whole genome (e.g., PBS). Again, these require genome-wide data. More generally the popularity of site frequency based techniques rely on enough data to actually produce a site frequency.

And just as these methods have needs in terms of the raw data necessary to produce viable statistics, they also exhibit different strengths and weaknesses. The haplotype based methods are good at detecting “hard sweeps,” that is, strong positive selection on a novel mutation emerging against the ancestral background. EHH picks up completed sweeps across populations. In contrast, iHS is better at obtaining traction at incomplete sweeps. Though they have good power to detect events on a human microevolutionary scale, think on the order of 10,000 years, they get fuzzy as one approaches the present. Specifically, when iHS detects older incomplete sweeps it may not tell you if the sweep is still occurring, but it probably is. Additionally, they’re not particularly good at picking up “soft sweeps,” where alleles long segregating within the population are driven up in frequency by selection, or polygenic selection where the impact of the coefficient is distributed across the genome.

intropopulationgeneticsFinally, there have been attempts to detect selection using ancient DNA. This a technique which takes a step toward omniscience; rather than inferring from extant variation one can track allele frequency change in “real time” through the record of the DNA. The problem of course is that sample sizes are finite and data quality is often hit and miss.

This is why the preprint Detection of human adaptation during the past 2,000 years, out of Jonathan Pritchard’s lab, has me so excited. Using the whole genome sequence data that has come online over the past few years at large sample sizes they manage to infer selection events over the past 2,000 years among the British! Here’s the abstract:

Detection of recent natural selection is a challenging problem in population genetics, as standard methods generally integrate over long timescales. Here we introduce the Singleton Density Score (SDS), a powerful measure to infer very recent changes in allele frequencies from contemporary genome sequences. When applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past 2,000 years. We see strong signals of selection at lactase and HLA, and in favor of blond hair and blue eyes. Turning to signals of polygenic adaptation we find, remarkably, that recent selection for increased height has driven allele frequency shifts across most of the genome. Moreover, we report suggestive new evidence for polygenic shifts affecting many other complex traits. Our results suggest that polygenic adaptation has played a pervasive role in shaping genotypic and phenotypic variation in modern humans.

Screenshot 2016-05-08 00.35.44The basic logic is not difficult to grasp. Derived alleles (the novel ones which mutated recently) subject to selection tend to alter their local genomic region in predictable ways. In particular, derived alleles subject to positive selection will exhibit shallower genealogies than ancestral neutral variants. Conventional neutral processes result in the birth of mutations and extinction of ancestral variants at regular intervals as modeled by the coalescent process. Some alleles will increase in frequency rapidly, and some more slowly, but it will be a random affair. In the figure above the dark branches are ancestral and red derived. The right panel shows that the coalescence of ancestral and derived are regular and approximately the same for a neutral context (i.e., selection is not targeting the derived variant). In contrast, in the left panel you see that the derived variants have a much shallower coalescence, presumably because of rapid expansion in the population of alleles in the recent past back to a common ancestor.

The SDS needs genome-wide data, as well as large sample sizes. In 2016 you have both, at least for some regions of the world and populations. Comparing SDS to haplotype-based methods they find that the biggest differences in selection in the latter are continental-scale; that is, between Europe and Africa. In contrast, SDS tends to zoom in on intra-European variation, because a ~2,000 year time scale is likely to be localized.

Screenshot 2016-05-08 00.46.28They found lots and lots of selection. The signals around LCT and MHC were not entirely surprising. LCT is almost a positive control for a test of selection. It’s pervasive in Europe, but it was only recently selected, and so there are still ancestral variants around (unlike SLC24A5 which went nearly to fixation in a literal sense). MHC has to do with immune response, and that’s always evolving.

Perhaps more interesting is that the authors detect continuous selection on height and pigmentation in their sample. Why height? I’ve been skeptical of some of the genetic arguments in Greg Clark’s A Farewell to Alms (and have told Greg so), but, recent selection for height does seem to align with his idea that the English were particularly wealth and healthy over the past ~2,000 years. And, it also seems to support the suggestion of elite over-production, as presumably tall men would be more well represented among elites for both nutritional and genetic reasons.

410uvoV1qDL._SY344_BO1,204,203,200_The results for pigmentation are intriguing. Some of the older signals don’t show up (e.g., SLC24A5 and SLC45A2). They’re either fixed, or near fixed, so where are the old haplotypes going to be to compare to? But intriguingly the selection around KITLG and OCA-HERC2 still seems to be occurring! Though the authors associate them with hair and eye color, the extreme tissue specific expression does not mean they have no effect on skin color. In the supplements they note that “In all 14 cases the derived allele is associated with either lighter pigmentation (i.e., lighter hair, skin, or eyes) or increased freckling.” Additionally, they state in the main text that “We speculate that recent selection in favor of blond hair and blue eyes may reflect sexual selection for these phenotypes in the ancestors of the British, as opposed to the longer-term trend toward lighter skin pigmentation in non-Africans, generally thought to have been driven by the need for Vitamin D production.”

At this point reader Sean will probably have a meltdown, and have to go to his natural reflex to core-dump everything on sexual selection he has taken in from Peter Frost for the 1000th time. If he doesn’t control his overwhelming sexually selected urge to repeat himself like a robot I’m going to ban him, as I don’t really want to re-read the same comment again. That being said, I don’t really know how seriously the authors take the idea that pigmentation is sexually selected….

41czavSUnNL._SY344_BO1,204,203,200_I find Geoffrey Miller’s The Mating Mind interesting, but I’m mildly skeptical of the importance of sexual selection in recent human history (as opposed to earlier periods when broad human behaviors became fixed in our lineage). Often sexual selection crops up as a deus ex machina in these sorts of papers (I also don’t see enough variation in reproductive skew to make sexual selection plausible). The reason is simple. Geneticists are good at detecting selection occurring, but far less clear how and why selection is occurring. In this way LCT is an exception.

With all that said, this is an incredible paper. Because of the large genomic data sets in the United Kingdom the preprint focused on the British. But this is the sort of analysis going to expand to all populations in the near future. Genomics will be ubiquitous, as will the tools to make inferences about population history and dynamics.

The Pleistocene as humanity’s Hyborian Age

cave-painting-and-steve-jobsIn my last post I drilled down on just a few of the results in the paper The genetic history of Ice Age Europe (ungated). There are many results which I didn’t really explore, in particular, the finding that there seems to be a gradual decline in Neanderthal ancestry within European populations over time. That’s for a follow up.

In any case, it’s an interesting time to be alive and be interested in these topics.

51OftfuYlSL._SX316_BO1,204,203,200_The epoch we are situated is between an age of ignorance, and one in which we will be overwhelmed by interpretations based on a surfeit of data. The whole genome of the Neanderthal was published in 2010. Today we have many more whole genomes, and probably on the order of 1,000 ancient genomes of varying quality in the pipeline (i.e., some of it is unpublished). Reconstructing the history of humanity from genetic data has transformed from inference from the tips of the phylogenetic tree, to the examining of points deep in the nodes.

This reminds me of an argument that was highlighted in The Monkey’s Voyage between cladists with a background in systematics and paleontologists. The way paleontologists understood evolutionary relationships was to examine the fossil record, and reconstruct trees with putative ancestral forms and their descendants. The cladists asserted that this method relied upon the incomplete and unreliable fossil record, and so was not nearly as powerful as simply looking at extant variation in a more rigorous manner. Though the added rigor of the cladists arguably transformed the field of phylogenetics, as I have suggested before the extremism of the cladists in dismissing whole domains of knowledge and alternative methods has not swept the field.

Personally, I think that is a good thing. But, some of the warnings of the cladists probably need to be considered when taking into account the new results from paleogenetics. The reality is that in many ways there is little difference in terms of the raw data which paleogenetics and paleontology based on fossils provides. For various technical reasons phylogenetic inference from whole genomes of DNA sequence can be much more powerful than analyzing, for example, the teeth of an ancient hominin. Those teeth would give you phylogenetic and functional information. But reconstruction is more robust when you have tens of thousands (or perhaps millions) of variations, which is what DNA gives you. Second, those markers can tell you a great deal more about a variety of functions than simply teeth (I am not denigrating teeth here, as they are very informative!).

Screenshot from 2016-05-07 12:50:12

Extended data table 5

One thing which is more and more clear as more data comes in this that the genetic architecture of pigmentation in modern Europeans is a product of the Holocene, and perhaps even the last 4,000 years. A more sensational way to state this is that the Nordic phenotype may not have been present in appreciable amounts in any population when the pyramids of Giza were being constructed! Of course, there is a major caveat here in that we know that light skin emerges with different genetic architectures, so ancient Pleistocene Europeans may simply have had a different arrangement of functional SNPs. The main caution on this caveat is that pigmentation is a trait that is very well characterized across mammals as a whole, so prediction is much less dodgy than in other traits. If we eventually get enough high quality genomes from Gravettian period Europeans, and they lack derived SNPs across ten major pigmentation genes, then we can be pretty certain that they were in the ancestral state.

Researchers are then literally putting flesh on ancient bones. And yet we still see what we see. Paleogenetics suffers from the same issue as paleontology: skewed sampling. Especially when sample sizes for certain periods and regions are small, our illumination can’t give us a sense of what we don’t know. The genetic history of Ice Age Europe gives us a picture of genetic turnover, but one in which the Goyet sample representative of early Aurignacians turns out be the ancestor of a population which pops back up into prehistory (the Magdalenians) after a long 10,000 year Gravettian interlude. Unless they traveled through a wormhole, it seems clear that this lacunae is a consequence of patchy and biased sampling. As the number of DNA samples increases we’ll get a better sense of how patchy and biased the methods turn out to be, but we’ll never totally abolish this problem. I believe that the same fact explains why many papers see a resurgence of Mesolithic hunter-gatherer ancestry among Neolithic farmers; the former were always there, but they are not being sampled across much of the temporal transect due to spatial patchiness.

As we traverse this period between ignorance and the potential for knowledge, we can start forming conjectures as to the shape of the future. In the comments below Andrew Oh-Wilke suggests that ancient people traveled much further than we might have guessed. I think this is right. In The Monkey’s Voyage the author suggests that in biogeography there has been a move away from vicariance to a somewhat stochastic long distance dispersal model to explain variation. The vicariance model emphasized the emergence of geographical barriers due to geological processes, and the subsequent divergence between two populations due to reduced gene flow. The idea behind stochastic long distance dispersal is basically that a lot of the patterns are due to random freak events, such as a small group of Old World monkeys somehow making it across the Atlantic from Africa, and becoming the ancestors of the whole family of New World monkeys.

F5.mediumThe vicariance model has less relevance for human prehistory, because in most cases we’re not talking about geological time scales. There are exceptions, after a fashion. Berengia and Sahul both harbored populations, and after the sea levels rose groups were isolated on opposite sites of the water barrier. But there was always some contact even after this, because humans can traverse water barriers. There is an analog to the vicariance model in historical population genetics, and that is the isolation-by-distance model of human genetic variation and diversity. The major example is in the 2005 paper Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. This model’s logic is sound. One imagines that humans start at a point in space, and expand outward through a demographic wave of advance, as groups disperse into territory inhabited by archaic hominins, or not inhabited by hominins at all (e.g., the Americas and Oceania). Because this results in a serial founder effect, you see a pattern where populations further away from Africa exhibit less genetic diversity. Additionally, genetic structure in humans can be conceived as as dominated by geographic distance and exhibiting clinal variation.

51t9ODAPTaL._SX366_BO1,204,203,200_What the paper Toward a new history and geography of human genes informed by ancient DNA did was show that the genetic data used to support the isolation-by-distance model of decay of genetic diversity did not have the power to truly show this was the correct model. What David Reich and Eske Willerslev (and others) have shown with ancient DNA (as well as novel methods in Reich’s case) is that 1) population turnover has been relatively common 2) most (all?) modern populations are best thought of as admixtures between ancient lineages, in many cases pulse admixtures that occurred rapidly. Like the vicariance model the isolation-by-distance model was boring and general. It was easy to model, and didn’t engage in special pleadings to historical contingency. In other words, it’s a perfect model to use as null hypothesis. But that doesn’t mean that it’s correct, or, more accurately, captures most of the dynamics.

An example may suffice. Europe is the most well elucidated of the major regions of the world in terms of prehistory. The “standard model”, utilizing simple and generic population genetic demographic processes produces a nice and simple model to fit the data. ~50,000 years ago humans leave Africa, they settle the Middle East/Central Asia. ~40,000 years ago they arrive in Europe. ~10,000 years ago farmers arrive from the Middle East, and expand into Europe from the southeast, with their genetic signal diluting over time to the northwest.

Here is the model, sketchily, informed by ancient DNA. ~50,000 years ago humans leave Africa, and mix with a number of Neanderthals. ~40,000 years ago, they arrive in Europe. ~35-40,000 years ago the first modern Europeans are replaced by another population. This second population is culturally similar to the first, and contributes some (though small proportionally) ancestry to modern Europeans. It is replaced by another population, which does not contribute much to modern Europeans (Gravettians), though populations related to it do. It is replaced by a population related to the first Europeans with descendants (Magdalenians, who are descended in part from Aurignacians, and do not share much drift with Gravettians). Then, the Magdalenians are replaced by Villabruna populations, the very late Paleolithic populations at the tail end of the Ice Age. The Villabruna have mixture from both the Near East, and to a lesser extent East Asia. Or, Villabruna populations were intrusive to the Near East, and possibly East Asia, or there were mediating populations between. It is all somewhat unclear. Then the Villabruna populations, which become Mesolithic hunter-gatherers, are overwhelmed by Near Eastern groups, which have very exotic ancestry unrelated to all other non-Africans (Basal Eurasian). Finally, the Neolithic groups are overwhelmed by populations from the steppe, who are themselves compounds of very distinct elements.

This is a difficult and historically contingent story. It is not neat, tidy, and is a dog of a model. It is not easy to generalize. But, it is probably a model which captures many more of the salient dynamics than the earlier one.

Going forward what generalizations can we take from this? Europe has been well elucidated for historically contingent and biogeographic reasons. But the rest of the world will come into the light of understanding in a similar fashion over the next ten years. One prediction I will make is that inter-group barriers were more powerful earlier in the human past than today, at least in terms of how they were relevant genetically. The emergence of meta-ethnic religions and fictive kinship may have paved the way for gene flow on a massive scale over the past 4,000 years. Additionally, human population density is such that the landscape of habitation is less patchy, and conventional continuous gene flow between adjacent populations is just more feasible. In prehistory human groups thin on the ground may have had organize proactively to exchange mates, perhaps during gatherings which were culturally focused. This might imply that mate exchange was less a function of proximity than cultural affinity.

A pattern of turnovers that we see in Pleistocene Europeans aligns with the idea that socio-cultural boundaries were major fault-lines which were inimical to gene flow. Admixture between two groups in the recent past can occur when one collapses culturally, as occurred in the New World. But it also occurs as a matter of course through proximity, as is the case with the Hui in China. The balance of forces in the hunter-gatherer world may have been toward the former. Patching sampling means we don’t know where the pre-Magdalenian and post-Aurignacian peoples were persisting over the 10,000 years of Gravettian domination, but they were there, biding their time. Any modern understanding of 10,000 years would expect us to lead to massive mixing and gene flow, but that did not seem to occur (some did, but look at the admixture graphs and the Magdalenians are >50% Aurignacian, while the Gravettians are ~0%).

Second, the turnovers probably were partly due to ecological forces. At this stage in history humans were animals whose existence was strongly conditioned on natural vicissitudes. Small numbers of people may easily have gone extinct because of diminished opportunities, and drifted below sustainable levels. Particularly if they weren’t part of a broader network of redundant support, which seems unlikely to have been the case. Agricultural populations still retain a reservoir numerically even after famine. Hunter-gatherers may not have.

Finally, Europe may be a special cases because it is on the frontier of habitation during a phase of glaciation, but it is unlikely to be totally sui generis. The branches of the human phylogenetic tree see to be pruned rather regularly. The genetic history of other parts of the world are likely to exhibit the same pattern of turnover, and relatively recent roots for the demographically dominant group.

The Last Glacial Maximum dictated Europe’s genetic history


The map and chart above is from The genetic history of Ice Age Europe, a new paper in Nature from the Reich lab (the new data has been posted). It illustrates probably the major finding of the paper, using a ~40,000 year paleogenetic transect of 51 ancient DNA samples the authors conclude that there have been at least three major population turnovers/disruptions across Pleistocene Europe. These correspond to three genetic clusters that they’ve identified in their data; the El Mirón, Věstonice, and Villabruna groups. Respectively they are the Magdalenian, Gravettian, and Epigravettian/Azilian cultures. There are also stray individuals which are harder to place, but signal other turnovers. An individual from Goyet that dates to 37,000 years ago and was presumably of the Aurignacian culture, and is somewhat sui generis. But, unlike the ~40,000 year old sample from Romania, and the ~45,000 year old Siberian, Gotye is ancestral to some later Europeans.

Screenshot 2016-05-04 00.23.42The figure to the left is one interpretation of their results. It shows that the Goyet sample contributed substantial ancestry to the Magdalenian culture which  flourished nearly 20,000 years later. But, Goyet did not contribute substantial ancestry to the Gravettian culture, which succeeded it! Rather, the Vestonice cluster which represents the Gravettians has only marginal admixture from other Pleistocene Europeans, but a notable affinity to the Konsteki sample. Intriguingly, Goyet-like ancestry can be found in the Loschbour hunter-gatherer from the Holocene.

This suggests that I was wrong in one of my predictions: I had assumed that most European hunter-gatherer ancestry dates to the Gravettian at the earliest. This is wrong. In fact, this paper suggests minimal legacy of Gravettian peoples as represented by the Vestonice cluster. Rather, earlier peoples have left their mark on modern Europeans via the Holocene “Western Hunter-Gatherers” (WHG) who mixed with incoming farmers.

There’s more. Most of Loschbour’s ancestry is not from Goyet-like groups. Rather, it is from a population with affinities to the Villabruna culture. This to some extent vindicates another prediction I made: that most European hunter-gatherer ancestry would probably date to groups which became established after the Last Glacial Maximum 20,000 years ago. That seems right, as Villabruna-like affinity seems to be the dominant signal in the Mesolithic hunter-gatherers.

700px-Weichsel-Würm-GlaciationSome of the patterns above are perplexing. So at this point, I think I want to drop a conjecture which I think can be inferred from this paper, but probably will have to be explored with future results and analysis: the Villabruna cluster ~14,000 years is a product of a massive expansion of a hunter-gatherer population from the Middle East. The original papers which posited that “Early European Farmers” (EEF) were admixtures between “Basal Eurasians” (BEu) and WHG, at 40% to 60% proportions, were somewhat misleading I suspect. Rather, WHG, the Mesolithic hunter-gatherers of Europe, derive predominantly from an expansion of Middle Eastern hunter-gatherers which had larger populations in the wake of the grueling climatic regime of the Last Glacial Maximum.

The further affinities of Vilabruna make a likely exotic origin obvious. As noted in the paper a Near Eastern, but not BEu, affinity of European hunter-gatherers emerges specifically with Vilabruna, ~14,000 years ago. And, some individuals in this cluster likely exhibit admixture from a population related to modern East Asians. This gene flow is independent of the Middle Eastern gene flow, though I suspect that the Middle Eastern gene flow is simply an expansion of hunter-gatherers from that region, with some absorption of the local substrate. There are other explanations for why this affinity might exist (read the supplements), but other papers have indicated the possibility of this relationship, so it is probably the most likely. The Middle Eastern origin of Villabruna makes more sense of the relationship between it and “Caucasus Hunter-Gatherers” (CHG). Geography they would have been positioned near each other.

These West Eurasian clusters form a very deep clade with the Ma’lta North Eurasian population as an outgroup, with these nested together with East Eurasians, Amerindians, and Oceanians, in comparison to BEu. But if you take a look at the tree, and consider the chronology, it seems that modern Eurasians diversified into several distinct lineages over the course of 5-10 thousand years after the Out of Africa event. Individuals on the ~40,000 year time limit are no more related to all Eurasian groups, perhaps because their lineage went extinct. Ma’lta and the North Eurasians seem to have diverged from other West Eurasians very soon after these two diverged from East Eurasians; there just isn’t that much time to allow for this, but it did happen.

By about 30,000 years ago many of the pieces were in place. Much of the demographic change we see subsequent involve a set of operations to mix and match basic elements. The patchiness and segregation of these populations is probably why ancient DNA, itself spotty and poor and seeing with precision, assigns all of Europe to a particular cluster at a particular time. There were clearly other peoples, but they are not always at accessible archaeological sights, or perhaps they had retreated into the forests as a marginal folk?

There are many other interesting aspects of this paper, such as the Neanderthal admixture. But I’ll save that for another day….

Open Thread, 5/1/2016

51OftfuYlSL._SX316_BO1,204,203,200_I’ve been very busy the past month.

That being said, I made time to read The Monkey’s Voyage. My main interest was driven by the fact that macroevolution and biogeography aren’t scientific questions which I’ve focused much on lately. But, ultimately the book totally convinced me that vicariance doesn’t explain much in terms of geographic patterning of biological variation.

To make it more concrete: the flora and fauna of New Zealand are not relics of Gondwanaland, but relatively recent arrivals due to dispersal. This is in my opinion rather less romantic than the popular view, but the argument and evidence offered in the book are pretty convincing.

The New Yorker has fact-checkers, they should use them

darwin-as-an-old-man-337-450-17The New Yorker has a piece up, Same but Different: How epigenetics can blur the line between nature and nurture, which I think on the balance is pretty good. It introduces epigenetics to a broader audience in a manner that’s more than just a catch-phrase, and, cautions that people shouldn’t over-hype what is a legitimately interesting field of science.

But there’s a major factual problem which I mentioned when it came out, and, which some friends on Facebook have been griping about. I’ll quote the section where the error is clearest:

…Conceptually, a key element of classical Darwinian evolution is that genes do not retain an organism’s experiences in a permanently heritable manner. Jean-Baptiste Lamarck, in the early nineteenth century, had supposed that when an antelope strained its neck to reach a tree its efforts were somehow passed down and its progeny evolved into giraffes. Darwin discredited that model….

It is true that in Neo-Darwinian evolution, the modern synthesis, which crystallized in the second quarter of the 20th century, genes do not retain an organism’s experiences in a permanently heritable manner. But this is not true for Charles Darwin’s theories, which most people would term a “classical Darwinian” evolutionary theory. This is because first, Darwin worked in the pre-genetic era. He did not posit particulate inheritance, and had no genetic model. Second, though it is correct that Charles Darwin’s deemphasized the role of acquired characteristics, he himself was quite open to Lamarckianism in some cases. This openness persisted into the early 20th century, Ernst Mayr started his career as a Lamarckian!

In the least The New Yorker should have had someone with a background in evolutionary biology read the draft. The error is pretty obvious, and easy to fix.

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