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Gene Expression Blog

0879696753 Several people have contacted me about the Aylmer twins, who exhibit very distinct phenotypes. In short, one twin is very fair skinned, to the point of being a redhead, while the other twin has visibly African features and a darker complexion. What caught my attention is that their surname is the same as the middle name of R. A. Fisher. Perhaps they are related in some fashion to the father of evolutionary genetics?

The “science” behind the story is not particularly novel. Rather, for whatever reason the British tabloid press in particular seems to love publicizing variation in phenotypes which are racially coded in mixed-race families. I’ve been talking about “black and white twins” for so long that it’s not something I really wanted to revisit, as there isn’t much novel to say.

But, it is important to note that the media representations of this phenomenon often play a semantic shell game. Though some in the press are not reporting it, is not hard to find out that the black parent in this instance, the twins’ mother, is actually mixed-race. That is, she is about half African in her ancestry. Therefore, though the expected proportion of African ancestry in her daughters is 25 percent, random variation could result in individuals with sharply increased, or decreased fraction. People of mixed African and European heritage who exhibit visible African ancestry are often coded socially as black. But these twins are not “biracial” in a symmetric sense when it comes to genetics, even if they are as it concerns the social construction of racial identity.

One way the science here could be demystified is taking into consideration this important genealogical detail of the mother and making an analogy to populations. The twins can be thought of as backrosses, as their mother is an F1, and the father is a “parental” type (100 percent European). In a genetic trait which is governed by one gene crosses back to the parent population of an F1 can result in a wide range of phenotypic outcomes, depending on the nature of the expression of the alleles. Since human pigmentation is governed by a relatively small number of genes (most of the inter-population variation is probably due to half a dozen loci), some of the same dynamics applicable to monogenic traits in the case of a backcross apply here, though to a diminishing extent. As it turns out in this case the “black” twin invariably has the traits of both African and European populations, just like one of their parents, the F1, while the white twin resembles one of the “parental” populations.

51fULuoOGAL._SY344_BO1,204,203,200_ In the comments below I mention offhand that though on the order of half the genetic ancestry of Latin Americans is European, many salient aspects of their culture are overwhelmingly European (e.g., language, religion, and dress etc.), despite being inflected by Amerindian influences. This is not surprising. Analogies between cultural and biological evolutionary process are useful because one can leverage similarities in terms of formal modeling, but, one can also realize that there are large differences in the dynamics. In particular, cultural evolutionary process exhibit a great deal of horizontal transmission and age cohort effects, and biases in vertical inheritance. Though biological evolution via Mendelian genetics is not a blending process on the fine grain, in the aggregate one inherits half their genetic material from each parent to produce a blended genome. Not only that, but via the law of segregation one exhibits an equal probability of inheritance of one’s parents’ paternal or maternal genetic copies (meiotic drive being an exception to this).

41eQOJU5FBL._SY344_BO1,204,203,200_ On the population wide scale this enforced symmetry between parental contribution has consequences. Between two diverging populations with common ancestry one only needs one migrant between the two per generation to prevent drift apart. The logic is rather straightforward. Large populations require less migration because of reduced genetic drift. Small populations exhibit more drift, but one individual is a much larger proportion of the population, dampening the divergence. This is why between group inter-demic selection (“group selection”) is treated with some skepticism by many biologists; for selection to operate one needs heritable variation partitioned between the groups. That variation is unlikely to accrue between neighboring populations, and it is strange to imagine “competition at a distance” with no interaction (as between inter-continental scale population differences).

The difference with cultural group differences can be traced to the nature of parental inheritance. An individual whose parents speak different languages does not usually speak a language which is a hybrid between the two, which would be the case if a biological analogy with complex traits were appropriate. Rather, they may speak both of their parents’ languages, or even a single one. If the latter, often it is the case that the individual conforms to the dominant culture of their peer group within the population in which they were raised. In this way populations can develop very strong between group differences, which partition groups nearly perfectly due to a high between population differences in trait and marginal within population differences.

As a concrete example in a pre-state society one can imagine endemic warfare between two valleys in Papua resulting in the exchange of women due to raiding and kidnapping producing relatively little genetic distance across them. But the cultural distance could easily be maintained if the children of foreign women careful to adhere to the cultural norms of their paternal heritage, so as to minimize the perception that they are any less “real” members of the group into which they were born. Probably the most famous example of trivial non-functional between group differences that serve to signal in such a manner is the origin of the term shibboleth.

• Category: Science • Tags: Evolution 

605px-5G_IPod_Shuffle.svg In 2008 my friend Michael Vassar, in agreeing with Peter Thiel’s thesis about the decline of innovation, suggested that the only game changing technology of the 21st century so far had been the iPhone. 2008 was young year yet for what we then termed “smartphones,” which my daughter now thinks of simply as the “phone.”* I remember vaguely that my response was that the 21st century was young, and we didn’t know what impacts the new phones would have on our every day life.

IPhone6_silver_frontface One truism has been that the new phones have cannibalized whole sectors. Think maps and watches. This week I realized that it had finally happened to my iPod shuffle, from which I have been moderately inseparable since January of 2008. The morning checklist of what I have on me no longer necessarily includes a shuffle, because as long as I have a power source (as I do at the office) there’s no reason why the phone’s battery life should be an inconvenience.

The 19th century was the age of steam and the train. The 20th century was the age of oil and the automobile. We never really had a nuclear age. But it looks like this century will be the age of electricity and the phone. Though what we mean by “phone” is going to change a great deal, to the point where the term itself will be a curious anachronism. Children in the next generation my wonder why we call them phones in the first place.

* To be fair, in terms of pure telephone utility I think the older flip phones were better as single feature devices than the current smartphones (battery life, robustness, etc.).

• Category: Science • Tags: Technology 

41ncnodwApL._SY344_BO1,204,203,200_Pre-addendum: You can talk about anything in the open thread. End Note

Still reading the second volume of Strange Parallels, Southeast Asia in a Global Context, and it’s hard going. The issue is that the author’s prose is turgid, and I have a very high tolerance for that sort of thing as something of a scholarly book addict. Frankly the total length of the book is partly due to repetition. The upside of that is that you can skim over sections which are reiterated what has come before, but the downside is that you have to do this in the first place. With that in mind I decided to get Inventing the Individual: The Origins of Western Liberalism, after a mention by Steve. I’ve heard about this book for a year or so, and just skimming through it I have to stay it’s an easier read in terms of prose style than Strange Parallels (granted, this was a low bar). But the very title itself highlights why I didn’t prioritize reading this book: a priori I’m very skeptical of scholars who attempt to infer the singular historically contingent origins of a particular contemporary social phenomenon. For example, inventing love, or inventing war, or inventing democracy.

517xvHTM-RL._SY344_BO1,204,203,200_ As an example of what I mean, obviously the modern idea of republics has a great deal to do with the Roman republic. The term itself derives from the Roman example. But the general features which we would highlight as republican were not limited to Classical Mediterranean. Rather, it seems likely to me as societies develop there were attempts to maintain a less autocratic equilibrium in the transition toward complexity and scale, but they invariably failed (the example of the Roman shift from republic to empire is famous, but it is clear in the mythology and text that Mesopatamian civilization in the early Sumerian period was less autocratic and more oligarchic than it was later). A cross-cultural comparison is essential when asserting the sui generis character of any particular phenomenon. For example, if you are interesting the nature of millennarian religious sects, there’s no excuse for you not to know about the Way of the Five Pecks of Rice, a Han dynasty movement indigenous to China (rule of thumb, if you are curious about comparing across cultures, just look at the two ends of Eurasia prior to the Mongols).

41hdiv6SmHL._SY344_BO1,204,203,200_ Finally, there’s the issue of evolutionary and cognitive psychology. I have written at length for over 10 years that many of the individualistic features of modern social existence are probably primal, insofar as the economic growth of the past few centuries in the West has allowed for the loosening or disintegration of mores which evolved organically as cultural adaptations to mass living during and after the Neolithic revolution. Obviously this model has drawbacks, in that there is not a perfect correspondence between the Paleolithic and modern lifestyles. But, I think where it is most evident is in domains of personal choice in regards to sexual partners, where the individual restraint and social constraint of many “traditional” societies have fallen away, to be replaced by individual utility maximization (at least in the short term!). This maximization I think can only make sense in light of the psychological priors which evolved in the context of small groups where pair bonds were an important feature of male-female relations.

In fact, the corporate “organization man” is the true cultural invention. Taking the thesis of Inventing the Individual at face value, it can perhaps be restated more precisely as Rediscovering the Individual. Western liberalism has inflected and interpreted the individual, but it was always there in chrysalis, trapped by the exigences of pre-modern agricultural society. In contrast, topology is a genuine novel cultural invention which has no ancient or prehistoric analog amongst humans.

51ZkgI-fNfL._SY344_BO1,204,203,200_ On a different note, yesterday I listened to an interview with the author of Empire of Sin: A Story of Sex, Jazz, Murder, and the Battle for Modern New Orleans, on the (for what it’s worth, I always listen to the podcasts). The specific details were interesting, but the general arc is pretty straightforward, as it falls into the narrative of the “Nadir of American race relations”. The reason I’m mentioning this is that Robert Wright, author of many books, expressed surprise that race relations in New Orleans got worse during the late 19th and early 20th century. This ignorance surprised me, but even more annoying was his tendency to want to term the segregationist impulse among Progressives who enforced Jim Crow on New Orleans as “reactionary.”51CNKGNNXyL._SY344_BO1,204,203,200_ It seems he couldn’t restrain his Whiggish worldview and acknowledge that in this time and period the modern terms don’t apply very well. Though the nature of increased social complexity and economic growth does lend itself to a Whiggish worldview over the past thousand years or so, history has gone through many epicycles.

If you read a book like The Rise of American Democracy: Jefferson to Lincoln it is hard to deny that between the Founding and the Civil War race relations got much worse over time, and that the inferior status of black Americans became much more explicit in law and social custom. After the Civil War there was a thaw, and then a ratcheting up of racial conflict, tension, and segregation, up until the early 20th century. To term the racial ideology of the United States “reactionary” is entirely misleading, as well as false. Rather, it was a novel cultural concoction which emerged in the 19th century, shaped by the economics of the slave economy and justified by religion, science, and history.

And as it is clear from the interview with the author of the Empire of Sin those progressives who believe that the arc of history is unidirectional, and that they have special insight into its ultimate telos, have often been mistaken. Unfortunately, instead of learning from history most people simply retrofit it into a theory of their own making and preference.

• Category: Miscellaneous • Tags: Open Thread 

200px-IbnWarraqwhyIAmNotMuslim There’s an old joke that people in Alabama can be rest assured that when scholars tote up social statistics there’s always Mississippi to make sure that their state isn’t the last one listed. Sometimes I feel that way when thinking about comparing Bangladesh to Pakistan. Right now it is big news that an atheist blogger has been killed in Bangladesh, presumably by Islamic militants or sympathizers thereof. Naturally people are bringing this to my attention because 1) I was born in Bangladesh 2) I’m an atheist 3) I’m a blogger. But there are some important differences. From what I am to gather this blogger was focused on issues relating to atheism and secularism, and, his core audience was Bangladeshi. I write to a mostly American audience, and religion as a political issue is not a primary focus of mine (as opposed to a scholarly interest). Honestly I am more frightened of dying of a disease than being hacked to death by Islamist radicals if I were to visit Bangladesh, because I’m not that prominent.* Though this is certainly another argument for why I might want to avoid that country. In How The Scots Invented the Modern World the author points out that the last person killed on account of their atheism in the British Isles lived around 1700. Though the killing of Avijit Roy is not quite analogous, because it was a vigilante action, it illustrates the social sentiment broadly in society that blasphemy may be a capital crime in some parts of the world, hundreds of years after this sort of fanaticism abated in the West.

gsi2-chp1-9 Of more interest to me is that there is an atheist movement in public in Bangladesh at all. This is after all a very underdeveloped nation (Pakistan is still more economically developed) which is highly religious. It is also a nation where religious minorities occupy a somewhat precarious position. Nevertheless, against the standard and trajectory of Pakistan Bangladesh is relatively liberal and advanced when it comes to religious liberty from a Western perspective. The chief justice of the Supreme Court of Bangladesh is a Hindu. Unlike Pakistan the Ahmadis receive some official protection. One of the two major political parties, and the one currently in power, has maintained a stronger commitment to secularism in the face of pressure from the religious elements than its socialist analog in Pakistan (though it too has caved to aspects of Islamicization of society since the 1970s).**

The reasons for this difference are multifaceted. It could be as simple as the historical contingency that the United States buttressed the Islamic autocracy of Zia ul-Huq in the 1980s. Though today Pakistan is a byword for Islamic extremism, I tend to be of the opinion that its origins can be understood more as an instance of ‘religious nationalism,’ akin to Revisionist Zionism. The founder of Pakistan had a religious background which would be unacceptable to many Pakistanis today, and his personal piety was minimal. Pakistan initially served as a redoubt in the Indian subcontinent against Hindu numerical dominance, not the catspaw in Sunni radical millenarianism. It was a place where the traditional Muslim elites could take their rightful role as the political leaders, rather than being marginalized as would have been the case in a democratic India. Over time this national identity, of which religion was a part, though never a totality, has become more and more tied in with currents in international Sunni Islamic radicalism (to the obvious detriment of the non-Sunni minorities, including Shia such as the founder of the nation himself).

But this isn’t just a matter of sentiments on high. Rather, the reserves of secularism and tolerance for heterodoxy run deeper in modern Bangladesh than they do in Pakistan. Though >80 percent of both Pakistani and Bangaldeshi Muslims agree that Sharia should be the law of the land, less than half of Bangaldeshis who agree with this proposition believe that those who leave Islam should be subject to the death penalty according to Pew. It is notable that there are people willing to speak the record on video defending the right to Roy expressing his atheism. An English language newspaper in Bangladesh reflects this sentiment. Looking around the web about Pakistani atheism, it seems quite closeted, and columnists who write about it seem to parse their words carefully so as to avoid vigilante attention.

Writing about the modest protests The Guardian notes:

The attacks starkly underline an increasing gulf between secular bloggers and conservative Islamic groups, often covertly connected with Islamist parties. Secularists have urged authorities to ban religion-based politics, while Islamists have pressed for blasphemy laws to prevent criticism of their faith.

It is important to note that despite the groundswell of anger from the usual suspects among Muslims, there is still a strong enough secular liberal intelligentsia in Bangladesh which can speak in favor of someone as religiously marginal as an atheist from a Hindu background. The murder is a tragedy, but the reaction is to some extent heartening, and I hope heralds a future where social conflict can give way to the driving of religion into the private sphere (I think banning religious parties is usually counterproductive, for the record. I’d also oppose banning them on principle even if it was productive).

* Though I checked, and it is interesting that I have more Twitter followers from Bangladesh than Germany, probably on account of my name.

** The Awami League and the People’s Party respectively.

• Category: Foreign Policy • Tags: Bangladesh, Religion 

Citation: Leyk, D., et al. “Hand-grip strength of young men, women and highly trained female athletes.” European journal of applied physiology 99.4 (2007): 415-421.

51bCI-7YlbL._SY344_BO1,204,203,200_ Every now and then there is a debate on who is more “anti-science”, the Left or the Right. I’m not too interested in the details of that, but, a few years ago I expressed my skepticism to Chris Mooney, author of The Republican War on Science, that liberals were somehow reflexively more “pro-science.” I suggested to him, for example, that when it comes to aspects of the biological basis of human behavior, with the exception of homosexual orientation, liberals are highly resistant to accepting any differences across groups because of their adherence to social constructionism. Chris brushed this off, suggesting that the “science wars” were over, and even when it came to evolutionary psychology (broadly construed) the liberal Left had conceded to the best evidence on hand. I was not moved, because I’ve had years of exchange with many liberal Left folk who defy Chris’ assurance to me. This is most notable when it comes to sex differences, which are usually seen as less controversial, and evolutionarily should have some prior expectation due to dimorphism.

To give a concrete example of how far this goes, there are many liberal Left people who won’t even accede to the proposition that men are, on average, stronger in terms of upper body strength than women. A few years ago this came up on social media, where a friend who has a biology background from an elite university, even expressed skepticism at this, when I was trying to get her to be open to behavioral differences between the sexes by starting with something I thought she would at least agree with as reasonable. When I saw the lack of unequivocal acceptance of this point I decided to opt out of the conversation. This was basically face to face with Left

This is not to say that people are totally in denial. Rather, the standard educated tack by those with progressive tendencies kicks in. There are “problematic” terms which need to be “contextualized,” and “difference” needs to be considered as an expression of socially preferred categories and measurement. After the critical theory verbiage is hurled usually sane people want to run out of the room.

But on Twitter recently I saw an article which quantifies the difference in concrete ways. To be honest the difference shocked me. The paper is Hand-grip strength of young men, women and highly trained female athletes. As you can see in the figure above the sample sizes are large. The N = 60 of top female athletes consisted of those who competed in judo and handball, to select for individuals who were already geared toward upper body activities. The very weakest male in the data set of nearly 1,700 males looks to be about at the 20th percentile for average women.


The upshot is that the very strongest female athletes are barely above the median of grip strength for men. The top 75th percentile of female athletes are below the bottom 25th percentile of men. Another way to look at it is cumulative distributions. You can tell looking at this that there is overlap between the two sample distributions. How much? Ten percent of women have stronger grips than the bottom five percent of men. The difference in distributions is big enough that the very strongest non-elite athlete female in the whole data set has a weaker grip than most of the men.

fig4 At this point the intelligent obscurantist will probably make an appeal to something about a confound. But the researchers had a data set of men and women in their early 20s, of a wide range of body types. To the right you see a plot of average grip strength as a function of lean body mass. The further to the right, the more muscular the individuals are. As you can see the more muscular men and women are, the stronger they are. But you can also observe that even the most muscular women can barely beat the least muscular men.

To a great extent I feel like an idiot even writing this post. Who doesn’t know the extent of this biological difference? Well, lots of people at a minimum pretend not to. I’ve interacted with people about genetics for 13 years now. I’m someone who leans to the Right, but I want to think the best of everyone, and really empirical data is my summum bonum. It doesn’t make me happy to know that the flight from reality has gone so far in some sectors. I am aware that most reasonable people on the Left half of the political distribution would have no problem assenting to the facts here. The problem is that a vocal minority who will “problematize” what should be rock solid facts are not marginalized. This group is so loud and fixated on these topics that they begin to shape perceptions. After all, it isn’t every day that a man is going to challenge a woman to an arm wrestling match. And if you watch superhero movies you know that there are plenty of “butt kicking babes” who more than hold their own. But here’s the thing: superheroes don’t exist, movies are made up!

Perhaps these ideas are stronger than I think, because I’ll be honest that I was a bit surprised by the magnitude of the difference. It is fashionable, and defensible, to talk about averages, but these results point to the possibility that on some biophysical metrics men and women exhibit disjoint distributions. In other words, it is reasonable to treat them as distinct and separate categories in near totality.

Mind you, in a population of millions there will be many strong women who can beat many men. But the results from top level athletes should make us aware just how rare these individuals will be. As individuals they are somewhat sui generis. On the whole I am willing to grant the value of individualism on the legal level. Men and women should be allowed to become fire fighters with sex or gender no bar, and honestly I feel the same for volunteer combat troops. There are women who are physically and mentally in the population capable of competing with and besting most men at tasks which they would have traditionally been barred from on account for their sex. But for some traits they are very rare, because sex matters a lot in development. That is a biological fact.

• Category: Science • Tags: Sex Differences 

BIL-2015-LA_T-Shirt-Front-900wide I’m going to the BIL event in a few weeks in Los Angeles. Pretty excited, it’s been literally four years since the last time I went, so it will be cool to catch up. As usual I’m going to be seeing Joel Grus, with whom I began my adventures in blogging in the early 2000s. If you haven’t gone to a BIL before I highly recommend it. To be frank there’s a fair amount of crankery, but also excited ideas. But that’s par for the course when you try and push the boundaries and bring together creative and analytic people together. It’s definitely not a conference for small talk.

• Category: Miscellaneous • Tags: Open Thread 
Distribution of rs17822931 from HGDP

Distribution of rs17822931 from HGDP

Yoshiura, Koh-ichiro, et al. "A SNP in the ABCC11 gene is the determinant of human earwax type." Nature genetics 38.3 (2006): 324-330.

Yoshiura, Koh-ichiro, et al. “A SNP in the ABCC11 gene is the determinant of human earwax type.” Nature genetics 38.3 (2006): 324-330.

I’ve talked about rs17822931 in ABCC11 several times. The reasons are manifold. First, on many traits of interest it exhibits variation across populations in a simple Mendelian (recessive expression) manner. Second, there are suggestive variations in distribution. Third, the traits are kind of interesting without being biomedical. In other words, it’s a cool illustration of pleiotropy and human genetic variation that isn’t going to depress you. If you check out the SNPedia page you note that it is associated with variation in earwax type (wet vs. dry), body odor, and colostrum secretion. This is not the full list, and I’m moderately confident that biologists haven’t hit on all the major phenotypes that this affects variation in.

Until recently I’ve really only been interested in the population genetics of the trait. But talking with a few friends who were molecular biologists I realized I should follow up and dig deeper, and what I found was very interesting. Specifically, as it relates to body odor, which, like it or not is a phenotype of significance in the modern world. The trait happens to segregate within my family. My son is a TT genotype, because his parents are heterozygotes. That means he will exhibit less body odor as an adult. How much less?

In The Journal of Dermetological Science I found Functional characterisation of a SNP in the ABCC11 allele—Effects on axillary skin metabolism, odour generation and associated behaviours. Obviously this is not a journal I read often, but some of the tables are fascinating. The subjects were a few hundred Filipins. This is a population where the allele of interest segregates in intermediate frequencies. So there are many individuals with dry earwax as well as wet earwax, and all the associated traits.

Here are some tables I extracted*:

Mean malodour scores
5 hours 24 hours
TT 2.59 2.6
CT 3.26 3.4
CC 3.21 3.5
Uses deodorant 0.5 0.86 0.97
Does not use 0.5 0.14 0.03

I have no idea how subjective malodour scales work, but the moral is pretty straightforward. Those with the TT genotype saturate at a much lower point. This manifests in daily behavior. There is a fair amount of Japanese data that people who go to the doctor for body odor issues are much more likely to have wet earwax. This data from the Philippines illustrates that individuals with the derived genotype, TT, must be conscious enough of their lack of body odor to forgo deodorant purchases, even though I assume it is normative in the American influenced culture of the Philippines.

1-s2.0-S0923181113003058-gr1But most interesting to me are the chemical differences of the sweat of the different genotypes. They note that there were differences in Nα-3-methyl-3-hydroxy-hexanoylglutamine (HMHA-Gln), Nα-3-methyl-2-hexenoyl-glutamine (3M2H-Gln), and 3-methyl-3-sulfanyl-hexanol-cysteine-glycine between the genotypes. I don’t know much about these chemicals, except that they are “malodour conjugate precursors”. Not surprisingly there’s some difference in the microbial flora of the individuals as a function of genotype.

There have been attempts to understand the selection processes which may have shaped the distribution of the regional variation of this trait, but I’m not entirely convinced of what I’ve seen. Especially when the authors presume that earwax phenotype is in some ways causal (or at least it can give insight to causality, if that makes sense), when it may just be a developmental side effect. A consideration is that some models assume a recessive expression of the trait, which is true for body odor and earwax. But we don’t know if selection occurred that it was on these traits. Because of pleiotropy traits due to variation at a given gene may exhibit different levels of dominance, from full dominance, to additivity, to recessive expression. The target of selection may exhibit a different dominance coefficient than many of the side effect phenotypes (to give you a concrete example, the locus responsible for blue vs. non-blue eye color in Europeans exhibits some recessivity, but it is also responsible for variation in skin color where it is additive).

A 2009 paper using the HGDP data set found evidence of selection on ABCC11 using XP-EHH but not iHS. In other words, extended haplotype differences across populations, but not within them, which often imply sweeps near fixation between populations, rather than ongoing ones within them. To get a better sense of the distribution of the allele I decided to query the SNP in the 1000 Genomes Browser. I invite you to look at the data yourself. The sample sizes start to get pretty large in some of these populations. It is interesting that in West African populations the ancestral variant is nearly fixed, or totally so. The cases where it is not so can pretty easily be hypothesized as due to recent (last 10,000 years) Eurasian admixture. In Europe the frequency of the derived variant is low, on the order of ~10%, but in the Finnish sample it peaks at ~25%. This aligns with patterns in the HGDP data set. African populations tend to be fixed for the ancestral variant, C, while European populations have a low frequency of the derived variant, T, with a cline toward the northeast from the southwest (i.e., peaks in the Russians, lowest fraction in Sardinians). But, Middle Eastern samples in the HGDP data set have European proportions of T as well, though the Mozabites in North Africa do not. The South Asian samples in the HGDP have higher levels of the derived variant than Europeans, intermediate between that group and East Asians. But the 1000 Genomes data results in a thickening of the plot (and, with large sample sizes!). The Bangladeshis are at even a higher fraction than the Pakistani populations. The genotype counts are like so: 12 CC, 54 CT, TT. When I saw this I assumed it was the East Asian admixture, on the order of 10-20%, which might account for the enrichment of T in relation to Pakistan groups. But that is not correct. Here are the counts for Indian Telegus: 20 CC, 49 CT, and 33 TT. And Sri Lankan Tamils: 23 CC, 49 CT and 30 TT. Many hypotheses about the derived variant involve adaptations to cold climates in Northeast Asia. This may still be the case in Northeast Asia, but what you see here is a NW to SE cline of ancestral to derived variant of ABCC11 in South Asia. The Punjabis and Gujaratis have higher fractions of the ancestral variant, as you’d except from the HGDP data.** (the fraction in the Bangladeshi sample might be elevated by East Asian admixture)

The results form East Asian samples in the 1000 Genomes is also illuminating. With sample sizes of around 200 each the Dai minority (related to the Tai people culturally as their antecedents) has a frequency of 56% for T, the Han from Beijing have 97%, the Han from South China are at 86%, the Japanese 88%, and the Vietnamese from the southern region of the country 64%. First, my intuition is that this seems a strange pattern for a allele which was selected on a recessive trait. Rather, it looks more likely for selection on a dominant trait, where the equilibrium frequency remains below 100% because of recessive expression of the unfavored state. Second, the fraction for the Dai seems rather high for the ancestral state. This particular population is sampled from the Mekong region of southern China, as far south as you can go in the nation. This sort of cline correlated with latitude goes a long way to explaining why the thesis often emerged that this variation is somehow related to climate (there is something of a north-south cline in Japan as well).

Where does this leave us? I honestly don’t think we can make a general conclusion about the nature of selection around this variation. To me it looks as it was functionally constrained in Africa. African populations have the derived variant, but those that do can be explained via recent Eurasian admixture pretty easily (e.g., the LWK sample are Kenyan Bantus who have mixed with Nilotic peoples, who do have Eurasian ancestry. The same for the samples from Gambia or Senegal in relation to Eurasian mixed Fula). But once you leave Africa it look as if the constraint was removed, and lots of populations have low frequencies of the derived nonsynonymous mutation. The 2006 paper which focused in on the SNP of interest had Oceanian samples, and the derived variant fraction is too high to simply be a matter of Austronesian admixture. Could it be some form of balancing selection outside of Africa? Who knows. It might be neutral in some areas, under positive selection in others, balanced in a few locations, and under constraint in Africa.

But despite the evolutionary enigma of this locus, the phenotypic correlations keep building up. It’s a classical genetics illustration because of its Mendelian character. In terms of morphology I should emphasize that the body odor related information probably relates to the apocrine glands, which are localized in the armpits and genitals, and also are precursors to mammary secretion glands. Someone who understands these sorts of pathways and how they influence development could probably say much more. I’m sure at some point we’ll be able to answer the big evolutionary questions about this locus, and how it relates to human biological variation, but that will probably necessitate a better catalog of its phenotypic consequences.

Addendum: If you have a 23andMe account, here is the link that will show you your genotype (and anyone else on your account): (be logged in ahead of time).

* I flipped the strand, so converted T to A and G to C.

** To be fair, there was some evidence from Tamils in earlier studies, but two South Indian populations in the 1000 Genomes with high sample sizes nails it.

41WL2k2+47L._SY344_BO1,204,203,200_ Back in the 1990s eggs had an image problem. They are high in cholesterol, so the recommendations for intake were such that many people started avoiding them. Ergo, this commercial from the 1990s trying to convince kids that eggs are not the work of the devil. What was the science behind this? You can read the back story yourself.

But after all these years it turns out that in most people dietary cholesterol is not an issue. Eggs are now back on the menu according to the powers that be. The New York Times notes that it is a “a belated acknowledgment of decades of research showing that dietary cholesterol has little or no effect on the blood cholesterol levels of most people.” Decades. Let that sink in about how stubborn parts of the “scientific” establishment can be.

Science is a human endeavor. And some science is also much harder than other science. The “hard sciences” are different in many ways from the rest. The precision which physics is capable of is never going to be replicated in large domains of biology, of which medicine is the most relevant domain for the public. The issues are even more thorny when it comes to disciplines outside of natural science which manifest scientific aspirations. Here’s looking at you economics!

This is why I don’t like the “because science” meme. It should be “because science, for now.” Or, “perhaps, because science.” There is some science which is tried & tested, robust, and has not only withstood decades or centuries of critique, but yielded incredibly returns in practical domains. Think engineering. Then there are other sciences, such as much of nutrition, clinical psychology, and social science, which is important, but which offers answers which seem contingent on fads and fashions because of the proliferation of studies with low statistical power, or correlations which are ultimately just confounds. So what happens is the science does not shape opinions, opinions shape the science people choose.

On some level we all know this, but it is important to reiterate it. Like democracy science is the best that we have for a particular task. But in many specific instances it turns out to be really crappy. Because it’s hard, and nature is messy. Humility in science is a good thing. So is firmness of conviction, when it is warranted.


61LXo6U7a4L._SY344_BO1,204,203,200_ Reading Strange Parallels, Southeast Asia in a Global Context, I have begun to think about the differences between the eruption of Inner Asian nomads in the early modern period, and in prehistory. The author points out that the arrival of Mughals, and even to a greater extent the Manchu, to the ancient and dense civilizations of South and East Asia did not change the cultural substrate in the main. Yes, Turco-Persian Islamic (“Islamicate”) culture became both prestigious and relatively popular in South Asia. But it was, and still is, a minority tradition set against the indigenous religious system, bracketed under the term Hindu today. In Ching China the Manchu had an even less obvious effect. Arguably they assimilated to the Neo-Confucian mores of the Han elite far more than the Mughals did in India in relation to indigenous South Asian gentry.

The dynamics in this context always need to take into account the numbers of the conquerors in relation to the conquered. The Manchus were less than 1 percent of the population of their domain. The foreign Muslim elites (Turk, Afghan, and Persian, with some Arabs in South India) and their scions were never more than a few percent, at most, of the population of South Asia. These alien elites rested atop an extractive system which predated them (in some cases by thousands of years). It was an institutional arrangement that was useful in terms of subsidizing their lifestyles. China and India were attractive to the nomadic populations beyond the frontier because they were rich with people, and therefore resources which could be deployed in consumption as well as marshaled for war (the Mughals milked India to finance wars in Afghanistan).

There are other cases which are similar in terms of numbers. Both the Magyar and Bulgar incursions into Europe seem to have resulted in an Inner Asian elite acclimating itself on top of a broad mass of peasants, from which it extracted rents. Though the Magyars imparted their name and language upon the populace of Roman Pannonia, genetically their impact has been fairly marginal, if detectable. The Bulgars, who exist only as they contributed to the appellation Bulgaria and Bulgarians, lost their language, and to my knowledge their genetic impact was even fainter.

But there are other cases. Both the Turks and Arabs seem to have more substantial genetic contributions, even if on the peripheries it was very marginal. Vast eras of Central Asia once inhabited by Persian and related Indo-European peoples has become a hybrid zone of sorts between West and East Eurasian peoples thanks to the Turkic migrations. Differences between Muslim and non-Muslim populations in the Fertile Crescent are evident.

Which brings me back to the Indo-Europeans. Even if they were not nomads of a classical sort which emerged later on in history, they seem to have been agro-pastoralists. There is now circumstantial evidence for their impact all across Europe, especially the north and east. There is also likely evidence for substantial Indo-European admixture in India. Herodotus reported 2,500 years ago that India was the most inhabited land on the face of the earth. But was it so 4,000 years ago, during the later stages of the Indus Valley civilization?

I will admit I was not primed to accept the idea of mass replacement of indigenous populations in what would later become the Ecumene by populations form the steppe because of the later record of conquest, which was more a matter of elite replacement, than social turnover. But if the genetic data is correct we need to update our models. If the first farmers of Europe were marginalized by invading Indo-Europeans, could not the same have happened to some extent to the agriculturalists of South Asia, who descended from the people of Mehrgarh? The tension between the interior and littoral in Eurasia is an old one, but it seems to have evolved over time, from one of inter-group competition and meta-population dynamics (read: extinction), to exploitation by Inner Asian steppes of the human resources of the littoral. Social complexity and institutional robustness were the best long term investments for farmer populations against nomads, who always outmatched them in individual skill, and often in terms of the tanks of the ancient world, horses.

• Category: History • Tags: Indo-Europeans 


Many people have read Graeme Wood’s cover story in The Atlantic, What ISIS Really Wants, by now. I have, and I recommend you do so as well. You’ll learn a lot. And there’s much within it that I can assent to without hesitation. It overlaps in key ways with my post from last August, The Islamic State Is Right About Some Things. It does not trade in trite but satisfying demonology (politically correct liberal, or jingoistic conservative) or vulgar Marxist analysis. Rather than fitting ISIS into a fashionable Western ideology or filtering it through an emotional reaction, Wood attempts to sketch the movement out as a phenomenon informed by its own self conception. Before you can grapple with this new beast of our age, you have to take ISIS seriously in regards to the sincerity of its beliefs, and attempt to understand them. Wood does just this. Because of the dangers of going to ISIS territory he interviews those living in Western countries sympathetic to the movement, as well as engaging with scholars who specialize in topics which might shed light upon it. In particular, I think Wood conveys the “camelpunk” aspect of ISIS, a violent version of what you can see across the Gulf monarchies. Like 9780195169263steampunk camelpunk is a mash-up of mores, aesthetics, and technologies, across disparate eras. Anyone who reads science fiction won’t be entirely surprised by the juxtapositions of social media and slavery. Many less creative and historically conscious people live under the delusion that the world that is is the only world that could have been, or that it is the only world that will ever be. ISIS’ vision and reality offer up a window into a startlingly different, and radically objectionable, alternative world.

religionexplained As a descriptive matter the piece in The Atlantic is a tour de force. But there is one aspect where I think it is misleading. Wood seems to imply that ISIS is profoundly anti-modern and neo-medieval. This is certainly their own self image, and superficially their fixations on conquest and slaving seem more fit for the 7th century than the 21st. But like fascism, another ostensibly anti-modern movement, it does not strike me that ISIS actually can be understood except as a reaction against modernity, engaging, assimilating, and co-opting. In a similar vein the attempts of the Amish and some Hasidic Jews to stop time and battle back modern innovation is a deep acknowledgment of the seductive power of modernity. Elements of the program of ISIS may seem medieval and traditional, but as a whole it is a radical movement, which is tearing a fabric in the organic development of modern Islamic tradition across its meany streams, which issue out of the evolution of the thousand year old madhhabs.

But that’s a secondary issue. The main point where I believe Wood’s a exhibits a weakness is in privileging reflection über alles. By this, I mean that as a whole humans are prone to accepting the primary causal role of reflective cognition, of beliefs avowed and rationales offered. We are confident in our conscious self control, despite a robust body of cognitive psychology which implies that much of our cognition is not under the control or constraint of rational faculties. This problem is particularly extreme among intellectuals, the very class which also attempts to understand human phenomena. Through the simple process of introspection and extrapolation intellectuals tend to reduce human action to the outcome of ratiocination, inference from eternal axioms. This is wholly inadequate to a phenomenon as complex as religion. Lutheranism is reduced to theses, Islam to Koran and the Hadith, and Judaism to the Torah. And so forth. Long time readers will know my shtick at this point. Let me highlight the particular sentence which encapsulates the disagreement I have with Wood:

The ideological purity of the Islamic State has one compensating virtue: it allows us to predict some of the group’s actions

3551889 In mathematics truths entail necessary inferences. This is generally not the case with truths in a religious sense. A simple set of distinct beliefs can imply a shockingly wide range of inferences through clever rationalizations, totally unpersuasive to outgroups, and totally persuasive to ingroups. To get a sense of what I’m talking about, observe that denominations still descend from the Millerites. That the Jews responded to their national dispossession in antiquity by blaming themselves, and not the god who had clearly abandoned them. Or consider that in Matthew 24:34 Jesus seems to make a prophecy which was falsified. Of course a little Googling will show that many “literalist” Christians have a ready explanation of what “generation” actually means. Religion is not infinitely pliable, but its adroit flexibility can be marvelous to behold. I recall years ago making the case to an Orthodox acquaintance that Jewish custom of matrilineal descent is clearly a Roman era innovation, as the sons of Joseph by an Egyptian woman were recognized as legitimate. She responded without hesitation that her rabbis had explained that in the “oral law” it was recalled that Joseph’s wife was actually adopted, and her biological mother was a Hebrew. My own supposition is that this tradition is a fiction quickly conceived to give an ancient patina to a novel practice in Roman antiquity. But, it illustrates the ease with which even the most punctilious of religious traditions in terms of text can turn the plain reading of the scripture on its head through interpretation or supplementary traditions and glosses. And that is just the clever elites. The self serving lack of ideological clarity is clear among the foot soldiers. Here’s a story from December in The New York Times of how a young boy joined, and left, ISIS:

Soon, though, he said, “I noticed things I saw that were different from Islam.”

Back home he saw the group inflict severe punishments on men who were caught smoking cigarettes, yet in the camp, he said, he saw fighters smoking. He said he saw men having sex with other men behind the tents in the desert night. And, he said, he was increasingly put off by “the way they are killing innocent people.”

41V-vYSuQrL._SY344_BO1,204,203,200_ The men having sex with men no doubt have a rationalization for their behavior. The details aren’t relevant, the point is that this sort of deviation from expectation is pretty common. If it is so among the foot soldiers, the same sort of hypocrisy and lack of consistency can apply to the elite. Wood argues that ISIS is hobbled strategically by its own millenarian ideology. That its very premises ensure its refutation. True. For now. It may come to pass that there is a parting of the ways at some point within the organization, and almost certainly the suicidal faction is less likely to outlast the pragmatist wing. ISIS is composed of individuals, who exhibit variation in belief and interpretation, even if on the whole they seem rather unhinged.

So where does that leave us? In terms of policy prescriptions I’m not far from Graeme Wood. But, I’m far more open to the possibility that ISIS will mutate, evolve, and adapt. Its ideology is not set in stone, but simply the blueprint for the current era. Like all religions Islam evolves and changes with the times, in unpredictable ways, because it is the aggregate of human actions. If you think we have a good science which would allow to us to predict the future of human actions, I’ve got a bridge to sell you….

• Category: Ideology • Tags: ISIS, Islam 

A Really Bad Week For The Supplements Industry:

What did Schneiderman’s office do? Well, they conducted a scientific study, using DNA sequencing to test the ingredients in six types of herbal supplements, looking at different brands from multiple stores. They tested each sample five times to ensure accuracy. They collected 78 different samples and ran 390 tests in all.

Some of you won’t be surprised that these firms are padding their bottom line by substituting cheap ingredients (e.g., rice powder) in lieu of what’s on the label. But they can game the system this way because of loose regulatory oversight. Meanwhile, there are periodic moral panics about genetic sequencing and typing….

• Category: Science • Tags: Supplements 
OK Cupid results

OKCupid results

And Sarah saw the son of Hagar the Egyptian, which she had born unto Abraham, mocking.

Wherefore she said unto Abraham, Cast out this bondwoman and her son: for the son of this bondwoman shall not be heir with my son, even with Isaac.

- Genesis

41YlHxt+hUL._SY344_BO1,204,203,200_ The above is from a relatively widely circulated post from OKCupid. It has been argued that this post saved the dating website OKCupid, and launched the book Dataclysm. Over five years on the underlying biases have not changed, and if anything gotten more notable. I think the fact that OKCupid has become a more popular service probably explains this. From what I am to understand OKCupid had a more “hip” clientele in the late 2000s in comparison to the big dating sites, so it stands to reason that as its user base increased by many factors it would become more typical. This result is not isolated, but replicated in other surveys in experimental dating situations.

Unsurprisingly much of the male bias in race when it comes to dating comes down to perceptions of physical attractiveness. Once that is “corrected” for, the bias becomes very small. In contrast, this does not occur in women.* You can spin this in two ways. First, women are more racist. Or secondarily, women are less shallow, in that they are fixated on things beyond physical attraction. Though ironically that would definitely include physical appearance as it relates to race.

I thought of this when reading this piece in The Washington Post, Punjabi Sikh-Mexican American community fading into history. What happened is that because of anti-miscegenation laws and bans on the arrival of Indian women Punjabi farmers in the Central Valley of California married Mexican American women. The children had something of a hybrid identity, but are slowly being absorbed into the Mexican American and Punjabi Sikh communities. But this section jumped out at me because it seems an instance of a general pattern:

And when Punjabi women began coming to the United States, the Punjabi-Mexican community confounded them, Leonard said.

“They even kicked out the Mexican women from the gurdwara, even though those Mexican women helped fund it,” Leonard said.

This reminds me of what occurred at Fort Astoria, as the white women arrived the native women and their mixed-race offspring were quickly marginalized. In South Asia the same occurred with the ancestors of the Anglo-Indian community. For reasons of caste and religion they were excluded from assimilating into the native population (pairings between elite individuals, as depicted in White Mughals, differed from the majority of instances where common soldiers and lower caste women made arrangements which resulted in some censure from their respective communities), while the arrival of white women meant that the British men serving in India now had their preferred mating partners, and recreated England overseas in insular enclaves.

There seem to be two stylized extreme positions when it comes to cultural transmission as it relates to sex bias. One model holds that women are the fundamental culture bearers. In the United States for example children are more likely to adhere to the religion of the mother in mixed marriages. But there is another view, illustrated by the Islamic practice where men, but not women, could marry out. This is because it was presumed that culture would be passed down the paternal lineage. Not an unreasonable proposition in a hyper-patriarchal society. In the case of the New World, the mestizo populations clearly inherited language and religion from their male ancestors, but other aspects of their culture are indigenous (e.g., food). Though broad empirical patterns are interesting, the general expectations contingent upon theory are important in light of what we now know about mass migration in ancient history. Skewed distribution of Y and mtDNA seems to imply that migration which can not be modeled as isolation by distance diffusion tended to be male mediated, in the past as it is now. What does the uptake of Neolithic “First Farmer” mtDNA tell us about the dynamic of how the Corded Ware integrated to the local substrate, for example?

* By this, I mean that even when women give high ratings of attractiveness to men of other races, they still do not reciprocate in dating entreaties.

• Category: History, Science • Tags: Culture 

9780195181456The New York Times opinion pages has published an amusingly titled op-ed from Armand Leroi, One Republic of Learning: Digitizing the Humanities. The “one republic” is presumably meant to reflect the dissolution of the “two cultures” segregation, and the rise of a unified scholarly world utilizing the same methodologies and analytical frameworks. E. O. Wilson argued for something similar in Consilience: The Unity of Knowledge over 15 years ago. So why is Leroi publishing this in The New York Times now? I think because “big data” has now come to the humanities. The term “culturomics” was coined in 2010, so the age is young yet. But there’s another aspect to Leroi’s argument, and that is the analytic framework to interpret this data. In the length and technical level of an op-ed in The New York Times there wasn’t much detail, but he states:

But most scholars, I believe, will simply accept quantitative tools for the power that they offer….

Whether the new humanists will accept, or even understand, the rise of a mathematical theory of culture is another matter. It’s being built by biologists, economists and physicists and being published in the unforgiving terms and journals that such scientists read. I hope they do. After all, it seeks to explain the world of human-made things that they know and love.

31PPZ1DeWGL._SY344_BO1,204,203,200_ In the domain of social affairs I presume he’s alluding to the intellectual tradition pioneered by E.O. Wilson & Charles Lumsden, Marcus Feldman & L. L. Cavalli-Sforza, and Peter Richersen & Robert Boyd. These thinkers took as their data cultural variation, and leveraged the formal analytical framework used by evolutionary theorists, to create a discipline which attempts to explain the patterns of variation around us beginning with a few assumptions. Because of the focus on culture this work often can be thought of as a form of theoretical anthropology. But, it has not been that influential. Here is what Cavalli-Sforza said in 2006 when I interviewed him:

4) Moving to, in the interests of frankness, less influential books, in “A Genetic and Cultural Odyssey” Linda Stone & Paul F. Lurquin note the relative lack of response to “Cultural Transmission and Evolution” within the social sciences. You seem to chalk this up in part to the lack of comfort with mathematical methodologies within cultural anthropology. Over the past few years a small group of anthropologists, Peter Richerson, Robert Boyd and Joe Henrich seem to be continuing the attempt to model culture using the techniques that have been fortuitous in the biological sciences. Do you think that we are past the high tide of ‘interpretative’ anthropology and that a more explicitly hypothetical-deductive methodology may come to the fore? [my question]

I entirely agree that the average quality of anthropological research, especially of the cultural type, is kept extremely low by lack of statistical knowledge and of hypothetical deductive methodology. At the moment there is no indication that the majority of cultural anthropologists accept science – the most vocal of them still choose to deny that anthropology is science. They are certainly correct for what regards most of their work. [Cavalli-Sforza response]

I suspect that some of the same attitude is going to apply to the humanities more broadly. “Big data” can at least dampen the tendency to support a thesis with three examples, cherry-picked from literature. But I’m not sure that humanists are going to be happy about the sort of logical analysis which true formalism implies, as people spend more time muddling through algebra than working on a perfect turn of the phrase.

But Armand does note that “the truth of art criticism is not the same kind as scientific truth.” An old fashioned view is that great literature is there to tell us something on a deep normative level, rather than an empirical description of the world around us. In Culture Crash: The Killing of the Creative Class the author argues that one reason many young people refuse to pay for music and see little value in high culture is that the relativistic strain in contemporary academe which is often bracketed under the category “post modern” has totally undermined the idea that art has any intrinsic value. Rather, once it is “deconstructed” as semantic expressions of power relations, or some broader historical force, its sole value is purely semiotic. At which point art, and the critics who rely upon it as the raw material of their enterprise, become totally devalued. Ultimately I think the equivalence of Andy Warhol’s soup can with Michaelangelo’s David made by those who have imbibed a debased Post Modernism is far more dangerous to the long term enterprise of humanistic scholarship than quantitization and formalization.

• Category: Miscellaneous, Science 

Origin_of_Species (1) On Twitter Ryan Baldini asked for a “top 5″ list of evolutionary biologists. Even though this is a sharply delimited list, beyond the top two I think there is going to be debate. As for those, I think Charles Darwin and R. A. Fisher take those stops. Darwin for developing a theory of evolution that was more than purely descriptive in its power (pre-Darwinian theories were not powerful theoretical frameworks, even if they intuited the likelihood of various evolutionary processes). Fisher, for fusing Mendelian genetics with evolutionary biology, and also for being seminal in the creation of population genetics, which is arguably the most elementary system by which one can explore evolutionary processes. But below these top two I think one can go many disparate directions.

For example, Alfred Russell Wallace was there with Darwin as a proponent of natural selection as a mechanism for Darwinian evolution. In fact he was arguably a more staunch pan-selectionist than Darwin himself. Then you have the two other dominant figures in early population genetics, Sewall Wright and J. B. S. Haldane. The debates between Wright and Fisher were influential within evolutionary genetics for decades.

41PHSZN6AEL In the second half of the 20th century it strikes me that W. D. Hamilton and John Maynard Smith loom very large. As in the comparison between Fisher and Haldane, I think there is a difficulty in that both Hamilton and Maynard Smith were very influential and brilliant thinkers, so choosing one seems to unintentionally diminish the other. But for me W. D. Hamilton probably does rank as third on the list, behind Fisher and Darwin. And many do argue that he is their heir (in his biography Hamilton does admit his huge debt to Fisher, though later on in life he also states that he began to view Sewall Wright more favorably). Contemporary with Hamilton and Maynard Smith was George Williams, who made some important conceptual breakthroughs in the 1960s which paralleled Hamilton’s formal endeavors.

Because of the important of population genetics in modern evolutionary biology, I think I’m inclined argue that Wright and Haldane should be in the top five. That leaves only one slot, and I’d give that as I note above to Hamilton, another theorist. This is obviously a biased and subjective list. Others may differ, and I invite you to offer your own ideas.

On another note, despite my moderation policy the comments are beginning to become more frequent here. If you want a response to a comment place it on an “open thread” if it is off topic. I try and respond to queries, but I can’t keep track of it all quite a bit of the time.

• Category: Miscellaneous • Tags: Open Thread 

Citation: Complex History of Admixture between Modern Humans and Neandertals

In 2010 when the Neandertal sequence paper was published the word was that all non-Africans had the same proportion of ancestry from this population, a few percent. Over the past few years researchers have looked closer, and come to the conclusion that that was wrong. In particular, East Asians seem to have ~20 percent greater Neandertal ancestry than Europeans. Why? A simple solution is that there were several admixture events with Neandertals on the way out of Africa as modern humans settled the world. But there are other options, making recourse to standard population genetic theories. So last year in The genomic landscape of Neanderthal ancestry in present-day humans proposed that the higher fraction in East Asians in Neandertals was a function of the weaker efficacy of purifying selection, which removes deleterious alleles from the genetic background, in populations which went through bottlenecks. As you may know, East Asians seem to have gone through more bottlenecks in the out of Africa migration, probably because of several choke points from west to east Eurasia.

Two new papers in The American Journal of Human Genetics seem to suggest that this explanation is unlikely. First, in Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations, the authors use simulation frameworks to suggest that the extent of the bottleneck difference can not account for the difference in ancestry fractions. In other words, there isn’t that much variation in purifying selection. In the second paper the authors explicit test the ‘two pulse’ model vs. the ‘single pulse’ model. To remove the confound of selection they looked at neutral regions, and the difference persisted. Though the authors could not rule out the possibility that Europe received an influx of African-like individuals who reduced the Neandertal fraction in western Eurasian, the three ancestral populations which fused to form Europeans (i.e., hunter-gatherers, first farmers, and the steppe invaders) all had about the same Neandertal fraction. This leaves then the possibility that East Asians received a second dollop of Neandertal ancestry, ergo, the two pulse model.

A few years back Jeff Wall published a paper that showed that the Complete Genomes Gujarati samples were in between the Europeans and East Asians in Neandertal fraction. We know that the “Ancestral South Indian” (AS) fraction of Gujarati ancestry is closer to East Asians than to West Eurasian groups. To me this suggests that the second admixture may have occurred in the eastern zone of the Middle East, seem it seems basal to the eastern lineages of humans.

The topology of the human phylogenetic graph is getting somewhat more complex. But there are diminishing returns. We’re arguing over tenths of a percent now, as opposed to percents. In the near future this book will be probably be closed.

• Category: Science • Tags: Neandertals 



I’m old enough to remember when people were advised by severe-faced nutritionists about the dangers of eggs, all the while being totally unaware of the possible downsides of gorging on high-sugar, fat-free SnackWells cookies. This was the 1980s and early 1990s, when low fat and cholesterol were all the rage. Now The Washington Post is reporting that The U.S. government is poised to withdraw longstanding warnings about cholesterol. It’s a deeply reported story, so read the whole thing. This comes in the wake of research which debunks very low sodium diets, as well Time coming out with articles such as Where Dietary-Fat Guidelines Went Wrong. There are still debates about the details, with some people moving toward a very high fat diet, somewhat as a reaction to past anti-fat excesses I believe.

41ikBliWK8L._SY344_BO1,204,203,200_ A lot of this collapse of the old orthodoxy can probably be traced back to Gary Taubes, at least in the public consciousness (see his The New York Times Magazine piece from 2002). Taubes and company now put sugar into the same category that fat and cholesterol were, though for somewhat different reasons (ergo, the focus on types of calories ingested). But health is not the only concern. Hundreds of millions of people have made their food less savory over a generation because of these false recommendations.

In The Washington Post the article concludes:

“These reversals in the field do make us wonder and scratch our heads,” said David Allison, a public health professor at the University of Alabama at Birmingham. “But in science, change is normal and expected.”

When our view of the cosmos shifted from Ptolemy to Copernicus to Newton and Einstein, Allison said, “the reaction was not to say, ‘Oh my gosh, something is wrong with physics!’ We say, ‘Oh my gosh, isn’t this cool?’ ”

Allison said the problem in nutrition stems from the arrogance that sometimes accompanies dietary advice. A little humility could go a long way.

“Where nutrition has some trouble,” he said, “is all the confidence and vitriol and moralism that goes along with our recommendations.”

41WL2k2+47L._SY344_BO1,204,203,200_ A lot about nutrition is tied up to morality, and our ancient psychological fixations on the “purity” of food. That’s why no matter what people say about veganism, or paleo, or high/low fat/sugar/carb, in terms of its functional health consequences, it’s really about the values that you are projecting in terms of the psychology. And that’s why we tend to get into dietary moral panics so often. Because nutrition has a lot of variables producing an output (weight or overall health) it’s difficult to assess which ones are effecting change. If gunnery specialists were using non-Newtonian physics to land hits on the enemy we’d know pretty quickly that non-Newtonian physics (or at least pre-Newtonian mechanical intuition) just didn’t work. Though heart disease rates have gone down, Americans have become more obese. The signals are mixed. Meanwhile many of us are turning our lives upside down, eliminating or adding food elements on the latest research, which is often overturned or found to be statistically not robust. No wonder many people have started to tune out any health advice from the “authorities.”

Of course there is science, and there is science. Germ theory and epidemiology in relation to viral infections and vaccinations are a robust era of science. Planetary mechanics as well. In contrast many areas of nutritional, medical, and social science remain highly uncertain and low in confidence as to the nature of the results. You wouldn’t get that from the “experts” though. Science is science when they hold forth from on high. Except it’s not.

Addendum: I forgot to mention this, but one clear issue in regards to nutrition is sensitivity to particular individuals and populations. One of the ridiculousness of modern nutrition is how lowest-common-denominator and one-size-fits-all it seems to be. Yes, I’m generalizing here, but I know people with heritable familial cholesterol who were recommended to exercise and avoid eating a wide array by nutritionists even when this condition was already known to run in the family, and, the individuals in question were relatively fit. It was obvious that lifestyle and diet were marginal variables here, but the nutritionists simply could not imagine going off script.

If you have a family history of hypertension and stroke, by all means avoid salt. But it seems that for most of the population the downside risk to flavor is small to non-existent. Apparently the same might apply to cholesterol. And sorry, I think the same also applies to sugar! There are people who are more resistant to metabolic disease. If you enjoined the whole populations to avoid food that 10-25% might gain nutritional benefit, pretty soon that means everyone will eat literally nothing, because we all have different Achilles’ heels.

• Category: Science • Tags: Science 
Fst between ancient European populations
Bell_Beaker_LN 0.020
BenzigeroH_LN 0.021 0.004
CordedW_LN 0.032 0.008 0.007
EHG 0.082 0.041 0.038 0.034
LBK_EN 0.009 0.021 0.025 0.035 0.084
Motala_HG 0.083 0.057 0.053 0.060 0.048 0.093
Spain_EN 0.021 0.028 0.035 0.044 0.092 0.015 0.099
Spain_MN 0.014 0.022 0.026 0.035 0.077 0.016 0.081 0.009
SwedSk_NHG 0.066 0.050 0.048 0.054 0.058 0.078 0.034 0.084 0.074
Unetice_EBA 0.016 0.002 0.003 0.005 0.034 0.022 0.051 0.030 0.023 0.043
WHG 0.073 0.055 0.056 0.070 0.078 0.091 0.053 0.092 0.070 0.050 0.057
Yamnaya 0.054 0.016 0.013 0.011 0.028 0.052 0.063 0.060 0.053 0.062 0.012 0.076

It is often said that the meeting of Europeans and Amerindians in the 15th century is our best taste of what it would be like to meet aliens. The analogy is rather straightforward, as Amerindians were not part of the broad interactions between societies over the Holocene, as they had removed themselves from the scene of action ~15,000 years ago. The interaction resulted in conflict and synthesis. A new people in Latin America arose who were biologically, and to a lesser extent culturally, a compound between two very distinct antecedents. In North America the dynamic was more of replacement and marginalization, often due to organized collective action on the part of white settlers and their political systems.

41ZlHlsdYXL._SY344_BO1,204,203,200_ Above I have again placed a selection of Fst statistics from the preprint Massive migration from the steppe is a source for Indo-European languages in Europe. One must be careful about not over-interpreting these statistics. But, they give a good sense of genetic divergence between two populations, on average (I have uploaded all Fst values in an Excel file). In particular above I’ve focused on the ancient populations in the data set. EN is Early Neolithic, while MN is Middle, and LN is Late. HG is Hunter-Gatherer. I’ve bolded Fst values > 0.05, because to me that’s a pretty high threshold for serious genetic divergence. The LBK brought agriculture to vast swaths of Central Europe. These were the people who encountered the hunter-gatherers who had occupied the continent since the end of the last Ice Age. The genetic distance between these two groups is incredibly high. Between the generic “Western Hunter-Gatherer” population and the LBK the Fst value is 0.091. What does that mean? The Mala are a Dalit (outside the caste system) group from Southern India. The Fst between this group and WHG is 0.11. In other words, not that much greater than between WHG and LBK. The Fst between the Mala and the LBK, two populations separated by a continent and 7,000 years is 0.077, less than between WHG and LBK. The genetic distance between the Mala and the French is 0.051. Considerably less than between the WHG and LBK. The get a sense of how small the values between modern European groups are, the genetic distance between Lithuanians and Sardinians is 0.021. The genetic distance between Belarussians and the English is 0.004, or about 4% of the distance between WHG and LBK. My claim that the contact between the first farmers and the hunter-gatherers of early Europe was one of intercontinental scale interaction is justified by the fact that the genetic distance between Han Chinese and Europeans is about ~0.10, only marginally greater than between WHG and LBK.

These sorts of genetic distances on the ancient European landscape could only be due to massive cultural revolutions which produced demographic shifts which can in no way be modeled as continuous diffusion processes. The Bantu expansion is probably a good analogy for what happened in ancient Europe, it took a little over 1,000 years to traverse the whole continent of Africa, a much larger geographic zone than Europe. But a second issue that we must also focus on are the genetic distances between European hunter-gatherers. One could chalk up 0.078 between EHG and WHG to the fact that EHG has admixture from “Ancestral North Eurasians” (ANE) at a clip of ~40 percent. But even the distance between the Motala hunter-gatherers, who are only 15% ANE, and WHG is 0.053. The uniparental markers are strongly suggestive of a relatively small group expanding to fill Europe after the last Ice Age, they are overwhelmingly haplogroup I for Y chromosomes, and haplogroup U5 for females. So what gives with the high Fst values? This is far higher than any modern intra-European distances. One hypothesis that I think might be viable is that small effective population cranked up the genetic drift in these groups, whose marriage networks were sharply delimited by cultural fractionation as well as ecological constraints which reduced population density outside of narrow specially favored areas (e.g., marine environments). One consequence of excess drift is elevated Fst values, beyond what you might think would be plausible. I’m not specialist in cultural evolution, but my intuition tells me that hunter-gatherer groups can engage in fission rather rapidly, and these divisions may have enforced greater barriers to gene flow to relatively recently diverged groups than is the norm in modern agricultural and post-agricultural societies.

Another issue that comes to mind are future analyses of ancestry tracts and linkage disequilibrium in these populations. The reason I bring this up is the fact that we need to distinguish between genetic differences due to standard workaday isolation by distance, and those produced by pulse admixture events (see Gideon Bradburd’s preprint for more elucidation of this issue). For various reasons outlined in the preprint above I’m convinced that a group like EHG, and later the hunter-gatherers of Scandinavia, did undergo admixture with a very different population during the early Holocene, after their expansion from the Ice Age refugia. But ultimately looking at patterns of this ancestry in the chromosomes as well as estimating a time since admixture would nail the coffin on this likelihood.

Finally, there’s the issue of “Nazi optics.” When word of these results started to percolate last spring a friend who is a prominent human geneticist blurted out “it sounds like the Nazis were right!” By this, he meant that this story of migrations, and demographic turnover, would be much more in place in Europe before World War 2. But there’s an immediate refutation of any attempt to Nazify these results: the Fst statistics made it clear that long term result of the clash of peoples in the early to mid Holocene has been amalgamation. The Bronze Age people of Europe, who gave rise to the historic nations, are the heirs of both the hunter-gatherers long indigenous to the continent, and disparate aliens, who arrived as strangers thousands of years ago.

• Category: History, Science • Tags: Indo-Europeans 
Fst between selected populations
Armenian Bas Cord Czech EHG Eng Fren Gre LBK Lez Lith Sard Sin WHG
Basque 0.017
Corded_Ware_LN 0.023 0.025
Czech 0.011 0.009 0.015
EHG 0.067 0.060 0.034 0.043
English 0.011 0.008 0.014 0.002 0.045
French 0.009 0.006 0.015 0.001 0.048 0.001
Greek 0.004 0.010 0.019 0.004 0.057 0.005 0.003
LBK_EN 0.023 0.024 0.035 0.024 0.084 0.024 0.020 0.016
Lezgin 0.005 0.018 0.017 0.010 0.052 0.011 0.009 0.007 0.032
Lithuanian 0.019 0.014 0.016 0.003 0.043 0.006 0.006 0.010 0.034 0.015
Sardinian 0.014 0.013 0.033 0.013 0.074 0.012 0.009 0.009 0.015 0.021 0.021
Sindhi 0.016 0.032 0.029 0.022 0.057 0.023 0.022 0.020 0.049 0.014 0.028 0.035
WHG 0.086 0.062 0.070 0.056 0.078 0.058 0.058 0.070 0.091 0.082 0.053 0.074 0.087
Yamnaya 0.030 0.034 0.011 0.020 0.028 0.021 0.022 0.026 0.052 0.019 0.022 0.044 0.028 0.076

Update: Nick Patterson writes: Much ancient DNA genotype data is “pseudo-diploid” with just one allele given for a sample at each SNP. If you want to compute F_st values for such data, the easiest way is to run smartpca (see with inbreed: YES set in the parameter file.

The downside is that this option requires at least 2 samples for each population while the default option (inbreed: NO) works on a single sample.

The above table is a selection of F ST values I culled from the preprint Massive migration from the steppe is a source for Indo-European languages in Europe. To get an intuition, the F ST value comparing Northern Europeans and Nigerians is ~0.15 using SNP data. Before I get to the meat of the argument above, let’s take that in for a moment. You see above that the pairwise values between WHG, “Western Hunter-Gatherers,” and the LBK, the first farmer culture of Central Europe, is on the order of ~0.10. That’s about the value between Europeans and East Asians today. We also know that it is possible there was a difference in color between the hunter-gatherers and the first farmers. The meeting of farmer and hunter-gatherer in early Neolithic Europe, and down to the Bronze Age, may best be thought of as analogous to a long term racial conflict and coexistence. Rather than a gradual wave of advance I envisage that the farmers hopped from point to point along fertile stretches of maritime littoral, and pushed their way up into the heart of Europe’s ancient forests by felling the wilderness around the great rivers which issue forth from the uplands. In a world of “isolation by distance” and “clines” this sort of recourse to a term like “race” would be anachronistic, but the model of genetic disruption being reported in these results using ancient DNA strong suggests punctuated demographic transitions across a wide range of localities which would result in biologically and culturally distinct groups persisting for many generations cheek by jowl. Over time admixture resulted in amalgamation, but it was almost certainly a millennia long process.

More specifically, the authors report unequivocally that the arrival of cultures like the Corded Ware in Northern Europe 4,500 to 5,000 years ago was accompanied by massive demographic replacement. Not only were these bands of warriors traversing the landscape, but it was a whole people on the move, men, women, and children. These were akin to the Goths fording the Danube and bursting into a new landscape of conquest. But the lands of the first farmers were not like those of Rome, heavily settled, further human cattle for the steppe agro-pastoralists to extract rents from. The preprint is not clear as to the timescale of the arrival of the eastern genetic influence across Southern Europe, but in the North the conclusion is without nuance or qualification: during the early years of the Egyptian Old Kingdom the lands of the north were being roiled by migration.

admix But in this post I want to turn the focus away from Europe for a bit. In the text they note that “An interesting pattern occurs at K=8, with all the late LN/BA groups from central Europe and the Yamnaya having some of the “light green” component that is lacking in earlier European farmers and hunter-gatherers; this component is found at high frequencies in South Asian populations….” I’ve edited and uploaded a version of the admixture plot. One must be cautious when interpreting these plots, but with all the other information in the paper it is quite informative. As far back as Noah Rosenberg’s 2005 paper, and later on in the blogger Dienekes Pontikos’ analyses, there were suggestions of affinities between a subset of Europeans and South Asians, as well as a connection to the Caucasus. In the F ST results above I note that the Sindhi population is closer to the Lezgins (Northeast Caucasians) and Yamna samples than they are to Armenians. The details are difficult to parse though. Otherwise they would have done so in this monumental paper.

I do want to add one final thing though. It’s been assumed in the past, including by me, that once farmers were established in a locale that future demographic perturbations were unlikely. By this, I mean that farmers are more useful alive to generate economic surplus for incoming elites than they are eliminated. But that is predicated on the idea of a complex specialized society where the elites view all non-elites in an almost Marxian sense of being objects of exploitation. It could very well be that this sort of cosmopolitan globalism only became common in complex societies later, and that in pre-state tribal groups even dense populations did not prevent extermination, because expropriation of vital resources necessary for survival was far more viable an option for these societies than exploitation.

• Category: History • Tags: Indo-Europeans 

Update: The preprint is out. End update

… and also after that, when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.

Genesis, 6:4

A Battle-Axe

A Battle-Axe

An emanation from the one most high…uh, I mean, David Reich, has given his talk at Oxford. Thanks to Jean Manco we have a pretty good report of what he said. The core element seems to be that a paper will soon be published using ancient DNA results to conclude that Indo-European languages came to Europe from the Yamna culture of the Pontic Steppe ~4,000 years ago. Roughly, the argument laid out by David Anthony in The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. Where Reich’s conclusions differ from those that Anthony presented in the book is that this eruption from the Eurasian heartland resulted in a genetic-demographic transformation of Europe ~4,000 years ago. Manco confirms that the genetic data from the ancient sites that Reich’s team has access too indicate that the two dominant Y chromosomal haplogroups in Europe, R1b, and R1a, arrived with the Yamna people. This is not surprising, as previous ancient DNA exhibited a surprising death of these two lineages from both hunter-gatherer and early to late Neolithic populations in Europe. And, recent whole genome sequencing of Y chromosomes indicates that both R1a and R1b lineages across Eurasia have undergone recent explosive demographic expansion on a Holocene timescale (closer to 5 than 10 thousand years). In terms of total genome ancestry it looks as if the transition to Yamna successor cultures in Central Europe (e.g., Corded Ware) was accompanied by substantial genetic turnover. In the initial Corded Ware burial grounds 60-80 percent of the ancestry seems to have derived from the Yamna. The modern Yamna-derived proportion seems to be closer to ~50 percent in a region like Germany.

The Yamna themselves are a compound population, a mix of ancient hunter-gatherer groups (analogous to the modern Karelians), and an intrusive population with Near Eastern affinities, likely from the Caucasus. I am not clear whether the Near Eastern group had “Ancestral North Eurasian” ancestry, but the hunter-gatherers almost certainly did. The 1 to 18 percent “Ancestral North Eurasian” ancestry across continental Western and Central Europe today dates to the arrival of these Indo-European speakers. The very low fractions in Southern Europe, and its near absence in Sardinia, may suggest that the Indo-Europeans were demographically more significant in Northern Europe, even though they were clearly culturally effectual along the northern rim of the Mediterranean, and into Anatolia. In line with the Mal’ta results Manco relays that Reich believes that the R lineages, which are the dominant ones across Indo-European speaking populations from the North Sea down to South Asia, came into Europe via the Yamna, but ultimately derive from an “Ancestral North Eurasian” group.

220px-Yamna-en.svgThere are some phenotypic tidbits in the talk apparently. The Yamna were tall in terms of their genomic potential. Additionally, the very high frequency of lactase persistence may date to their arrival in Europe (there is some lack of clarity here). I doubt the high lactase persistence frequency and genotypes which result in greater final height are together by coincidence. Large people need a larger nutrient pipe, and adult digestion of lactose sugar would enable that.

There are two aspects which are not widely address in this talk. First, what was the exact dynamic of how the Indo-Europeans replaced the original populations? The idea of “demic diffusion” by waves of “demographic advance” promoted by Colin Renfrew seem to gradual and continuous to be responsible for this. This is basically an argument predicated on individual fitness, summed over groups. In this case I suspect that a better analogy may be the future that Genghis Khan had in mind for Northern China before his adviser Yelü Chucai dissuaded him: the North European plain was cleared out of people and turned over to pastureland. Genghis Khan and his Mongols were convinced of the value of Chinese as tax paying peasants, who could support the Mongol elite with their surplus. I suspect in a pre-state society such considerations were less relevant, as the institutional frameworks which would allow for the smooth absorption of subordinate groups were less elaborated, or even non-existent.



In both the Late Neolithic and after the Bronze Age the Reich group alludes to a return of the primal populations which were marginalized by the farmers, and later the Indo-European agro-pastoralists. One way to look at this is that there were larger migrations which were overlain upon the palimpsest. But, I believe one might also consider a model whereby there is ascertainment bias in the sorts of burial sites being explored and sampled, and one might be witnessing a patchy occupation of the landscape by intrusive cultures. For example, the newcomers might monopolize the rich bottom-lands for thousands of years, but huge swaths of the hinterland might be occupied by marginalized and less developed people, who over time drift into the core and become culturally absorbed. Instead of imagining the expansion of these people as purely ones of a vast uniform wave front, it might be better to conceptualize them as penetrating into virgin territory along the optimal avenues of settlement, and producing a patchy archipelago of habitation.

Second, there is the issue that though Reich and company focus on Indo-Europeans and the Yamna culture, the genetics leaves may loose threads that are difficult to tie back up. At ASHG Mait Metspalu express to me some misgivings about the term “Ancestral North Eurasian.” How do we truly know the locus and distribution of this ancestral component across Eurasia ~10,000 years ago? The Kalash of Pakistan exhibit signals of admixture with this group as high as Northern Europeans, so it is not limited to West Eurasia proper. The highest fractions today seem to be found in the North Caucasus, among many groups which are not Indo-European. If R1a was brought by Indo-Europeans to Europe, it is harder to conclude that this was the case in South Asia. Though the frequency of these lineages is higher in the Indo-Aryan North, there are relatively high fractions of R1a even among some South Indian tribal populations. R1b is found in appreciable fractions in Sardinia and among the Basques (one argument for the old idea that R1b was the legacy of European hunter-gatherers!). Obviously some of this could be due to admixture between Indo-Europeans and non-Indo-Europeans. But I think a major issue here is that Indo-European groups were a synthetic population which arose in a world where there were many synthetic populations, with ancient and recent affinities to them. I doubt the “Ancestral North Eurasian” ancestral component was limited purely to Indo-Europeans. So it seems unlikely that the R1 lineages would be purely Indo-European, even if recent expansion of some of their sub-lineages is a function of the Indo-European cultural explosion.

Of course there are only so many ancient DNA samples one can retrieve from a finite number of sites. The age of new genomic discoveries will start to close over the next few years as the paleo-demography inferred will start to exhibit some predictable solidity. That means that a deep knowledge of the archaeology, and what history there is, is essential.

• Category: History, Science • Tags: Corded Ware, Indo-Europeans 
Razib Khan
About Razib Khan

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