Open Thread, 1/31/2016

51Y1vJLRcLL._SX362_BO1,204,203,200_When I was younger I used to follow politics somewhat closely. Every year I would read The Almanac of American Politics. With sites like Politico and Wikipedia there’s really no point. Additionally, I gave up my interest in closely following politics at around the same time (or a little later) I stopped closely following professional sports. To a great extent it was a matter of the opportunity cost, and the fact that I find most of the major camps rather uncongenial to me (e.g., I dislike the multiculturalism which seems embedded within the Democratic party today, and, the militarism which is reflexive for modern Republicans). But I do have one observation to make: the intensity of support for Bernie Sanders and Donald Trump are things I’ve noticed. I’d still bet that neither will win their parties’ nominations, but it definitely makes you wonder.

I’ve been very busy, so no time to really read many books. But I did do some preliminary analysis of 1000 Genomes’ data. Judging from the samples I wouldn’t be surprised if there is more evidence of inbreeding from genetics in the British Bangladeshi community than in the samples from Dhaka. The Gujarati Patel community exhibits somewhat more elevated rates of runs of homozygosity in comparison to Europeans or Bengalis, but the range and median in Pakistani populations is pretty extreme (while South Indian groups do evidence of consanguinity as you’d expect). Also, the ethno-linguistic identity of Pakistani populations is pretty obviously fluid. More on that later….

Daniel Falush is going to draft up a write-up on how to/not to use ADMIXTURE analyses….

debtI’m pretty skeptical of reparations on prior grounds, and have long been so. I read The Debt: What America Owes to Blacks, 15 years ago, and recall it being more substantive that what’s on offer in our day. But, it has crossed my mind recently that cash has been shown to be very effective in development aid contexts. So why not in this situation? Yes, there are plenty of reasons to object, but it strikes me many of the same reasons apply in developed economies as well. It seems that the key for reparations to work and have some “buy-in” is it to be linked to a rollback of positive discrimination in public life. So it’s probably a nonstarter.

The schizophrenia paper. People have asked. Yes, this is a very big deal.

South Asians are not descended from four populations

The above plot I generated using the 1000 Genomes data set. BEB = Bangladeshis from Dhaka, STU are Sri Lankan Tamils, ITU are Telegus, while PJL are Punjabis from Lahore, and GIH are Gujaratis (collected in Houston). These are big categories. The South Indian population sets exhibit some structure in terms of caste; there are a few Brahmins, as well as some Dalits. The Bengalis are strangely coherent for a South Asian population, shifted toward Cambodians. The Gujarati are differentiated between a large number of Patels, and other various groups. To my surprise the Punjabi samples are very diverse.

nihms137159f3To a great extent it recapitulates the results of the 2009 paper Reconstructing Indian Population History. What you see to the left is the “ANI-ASI cline.” Basically South Asians, from Pashtuns all the way to Paniyas fall along a spectrum of genetic distance from West Asian and European populations. A secondary element is that some groups, such as Bengalis and many Austro-Asiatic tribes, are shifted toward East Asians. An old hypothesis of the ethnogenesis of South Asian peoples is that they are a variegated mix of “Caucasoid” populations intrusive to the subcontinent, which was originally inhabited by an “Australoid” element. Malala_and_Freida_Pinto_meet_the_Youth_For_Change_panel_cropped_fridaThough these terms are somewhat archaic, the general point seems to get at something visually clear: some South Asians look nearly Mediterranean in appearance, while others are hard to distinguish from Australian Aboriginals (at least superficially). And of course, most of us are somewhere in the middle.

nihms137159f4The insight of the Reich group was to use Andaman Islanders as a proxy for a primal indigenous population, and infer that the admixture alluded to above consisted of a very West Eurasian-like population, the Ancestral North Indians (ANI), and an indigenous group closer to East Eurasians, though very diverged, the Ancestral South Indians (ASI). Ergo, the ANI-ASI cline. Using the most closely related population to infer the “ghost population,” they were able to infer admixture proportions even though no “pure” ASI group was available as a reference against which they could judge. Clever strategies like this are important, because the reference populations you use to adduce admixture events (or lack thereof) strongly impact the nature of your results. Using simple PCA or model-based clustering, as with ADMIXTURE, one would fix South Indian Dalits and tribal populations as the “purest” aboriginal people. ~100% “Australoid.” And other groups could be modeled as a “Caucasoid/Australoid” mix. But this model was not satisfactory because even low caste South Indian groups were more shifted toward West Eurasians than you’d expect.

Using a statistic called the F4 ratio the they estimated that ANI ranges from 65-75% in the Northwest Indian populations, down to 15-30% in the lower caste South Indian ones. A 2013 paper, Genetic Evidence for Recent Population Mixture in India, attempted to infer an admixture period (two to four thousand years before the present), as well as a possible secondary pulse in some Indo-European groups. This stands to reason today when you note that most Indian groups share the most unique drift trajectory with the ancient Caucasian hunter-gatherer found in Kotias, but a minority, mostly upper caste, are closer to Sintashta steppe culture.

I’m putting this post up because people are asking me about a paper profiled in ArsTechnica, The caste system has left its mark on Indians’ genomes. Actually the 2009 Reich lab paper already concluded this. So what’s the major finding of this paper that makes it unique? We’ll start with the abstract, Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure:

India, harboring more than one-sixth of the world population, has been underrepresented in genome-wide studies of variation. Our analysis reveals that there are four dominant ancestries in mainland populations of India, contrary to two ancestries inferred earlier. We also show that (i) there is a distinctive ancestry of the Andaman and Nicobar Islands populations that is likely ancestral also to Oceanic populations, and (ii) the extant mainland populations admixed widely irrespective of ancestry, which was rapidly replaced by endogamy, particularly among Indo-European–speaking upper castes, about 70 generations ago. This coincides with the historical period of formulation and adoption of some relevant sociocultural norms.

So the two major results which warrant this paper being published are that instead of two ancestral populations, they posit four, and, the admixture between some of these is considerably more recent than in the 2013 paper. I think the first conclusion is wrong, and the second is too strong.

The authors make much of the fact that they have new samples. And their SNP-chip has a high density. But I’m confused why they didn’t integrate the 1000 Genomes data. The paper was received in early July 2015, and I know there was 1000 Genomes data from all the above groups by then. They didn’t even bother to use the HapMap GIH sample, which was definitely there!

Screenshot from 2016-01-26 23:29:21The figure to the right shows the crux of their results. They used ADMIXTURE to break apart the ancestries of their Indian data set into four clusters. Through cross-validation they established that a K = 4 was optimal parameter fit for their data. Two of the populations are previously known: ANI and ASI. But they also find that there is an “Ancestral Austro-Asiatic,” and “Ancestral Tibeto-Burman,” cluster, AAA and ATB repectively. Because they did not use full labels, it can be hard to decipher, but they use this plot to assert that people of the Khatri caste are nearly 100% ANI, while Paniyas are nearly 100% ASI. Additionally, they found several groups which were nearly 100% AAA and 100% ATB.

Long-time readers will see the immediate problem: you can’t use ADMIXTURE like this! There is no guarantee that a group that is 100% actually is in a situation where corresponds to a genuine discrete ancestral population that existed in reality. That is, these sorts of models push a certain number of ancestral populations, and force individuals into being combinations of those. The model is constrained by the data you are putting into it to generate the results. For example, if I took Uygurs and Europeans, and did a K = 2, the Uygurs may form one cluster, and the Europeans another, at 100% levels. But we know from history and other methodologies that the Uygurs are a recently mixed group (within the last 2,000 years). Nevertheless if you tell the package to assume K = 2 with Uygurs and Northern Europeans, then it will place these into two distinct groups. And in fact, the result tells you something real and significant about the relatedness of the individuals in the data…but it doesn’t tell you necessarily anything about the real population history.

There’s a fair amount of evidence that Austro-Asiatic populations in India are not indigenous, nor are they pure. A major hole in this paper is the total lack of acknowledgement that Austro-Asiatic languages are much more common in Southeast Asia, and it seems likely that they were intrusive to India. If so, modern Austro-Asiatic peoples can be thought of us a compound of migrants with the local substrate.

The ATB element is found only in Austro-Asiatic tribes and Bengali Brahmins. That’s reasonable, because both populations exhibit a relationship to East Asian groups. While the Brahmins of South India absorbed a minor element of local Dravidian ancestry, those of Bengal absorbed Tibeto-Burman and Austro-Asiatic, which is found in higher concentrations among Bengalis proper.

To repeat, ADMIXTURE does not necessarily give you real population combinations!!! In fact, populations are to some extent a social construct, insofar as they’re just really collapsing the genetic variation which is the result of a particular demographic and pedigree history. The “ANI” group proffered here is an artifact. The Khatri are not a representative of a pure population which is similar to the ancestral ANI. The Paniya are not 100% ASI, they are just the most ASI. The Birhor are not 100% Ancestral Austro-Asiatic, they are just the most distinctively Austro-Asiatic. The Jamatia are not pure Ancestral Tibeto-Burman; most of these Northeastern tribes have some ANI/ASI admixture. They’re just the most Tibeto-Burman.

Instead of relying on ADMIXTURE so much, they should have also utilized D-stats and f-stats (not as sensitive to drift), as well as TreeMix. I think that would have quickly shown that some of these “pure” groups were mixed.

Second, there is the issue of time-since-admixture. They obtained lower values than the 2013 paper. Why? Because they use source populations (and probably the methodology) which are somewhat different from that earlier work. Honestly if some of these populations are compounds, then it doesn’t make sense to necessarily use them as idealized donors in an admixture event. The AAA tracts are most definitely artifacts in my opinion, since the tracts are the outcome of a previous admixture event.

Finally, the authors allude to a “Southern Route” out of Africa, and, imply that the Austro-Asiatic arrived with this. The best work today suggests that Austro-Asiatic peoples expanded with an agricultural wave ~4,000 years ago, with a locus of origin in the uplands of South China. Therefore, they are not primal. A simple inspection of the map of Austro-Asiatic languages forces one to ask the question of direction of migration.

I offer this critique in the spirit of post-publication review. Perhaps the authors will clarify, as I’m genuinely puzzled by the interpretations they offered.

There was no vast migration of Eurasians into Africa

Last fall while at ASHG this paper came out, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent:

Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5x coverage ancient genome of an Ethiopian male (‘Mota’) who lived approximately 4,500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4,000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6-7% Eurasian ancestry.

Turns out that there was a bioinformatics error which negates the magnitude of these results. Erratum to Gallego Llorente et al. 2015:

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

First, scientists are humans and mistakes happen. So respect that the authors owned up to it. On the other hand, the conclusion never smelled right to many people. I was confused by it. I asked Iosif Lazaridis at ASHG. He was confused by it. I asked Pontus Skoglund. He was confused by it.

Unfortunately the result from the bioinformatics error was emphasized on the abstract, and in the press. In The New York Times:

“The most astonishing thing is there’s quite a lot of backflow in all modern African populations,” Dr. Pinhasi said. He and his colleagues estimate that 7 percent of the genomes of the Yoruba people of Nigeria are of Eurasian origin. In the genomes of Mbuti pygmies who live in the rain forest in the Democratic Republic of Congo, 6 percent of the DNA comes from Eurasians.

Ryan L. Raaum, an anthropological geneticist at Lehman College, part of the City University of New York, called the new study “fantastic” but questioned its conclusions. If people from the Near East moved into Africa, he argued, a drastic shift in the archaeology of the region would logically follow. But no such shift occurred. It is also possible that Eurasian DNA moved into Africa earlier than 3,000 years ago, Dr. Raaum argued. Mota might have simply lived in an isolated community that never encountered people with those genes.

The best way to test the conclusions of Dr. Pinhasi and his colleagues, Dr. Raaum said, would be to gather more DNA from African fossils of the same age. If the researchers are right, they would also lack Eurasian DNA. “Then the argument starts to seem a lot more plausible,” Dr. Raaum said.

A rule of thumb in science is when you get a shocking and astonishing result, check to make sure you didn’t make some error along the sequence of analysis. That clearly did not happen here. The blame has to be distributed. Authors work with mentors and collaborators, and peer reviewers check to make sure things make sense. The idea of massive admixture across the whole of Africa just did not make sense.

If something like this happened to me I’d probably literally throw up. This is horrible. But then again, this paper made it into Science, and Nature wrote articles like this: First ancient African genome reveals vast Eurasian migration. The error has to be corrected.

I’m skeptical “indigenous Arabs” are basal Eurasians

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations:

An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.

This is a good paper. They’ve taken a stab at it, and are very circumspect. But in the end they state that “these two conclusions therefore point to the Bedouins being direct descendants of the earliest split after the out-of-Africa migration events that established a basal Eurasian population.”

To catch everyone up, Lazaridis et al. suggested based on results from ancient DNA that many West Eurasian populations have an ancestry which derives from a lineage basal to all other non-Africans unmixed with this population. That means that the genetic distance of this group to Pleistocene European hunter-gatherers and Pleistocene Australians is the same, while the genetic distance between these two groups is smaller than between them and this population. Therefore they are termed “basal Eurasians,” or bEu.

But it is also important to note that they are a construct. The ancient DNA has not found any unmixed basal Eurasians. This is in contrast to other groups which are used as donor populations: European hunter-gatherers and Siberian hunter-gatherers. About ~50% or so of the ancestry of the Anatolian farmers who were the precursor of the first agriculturalists in Europe derive from bEu ancestry, with the balance consisting of a heritage similar to to European hunter-gatherers. The hunter-gatherers recently discovered in the Caucasus also have this bEu ancestry. Ergo, almost all West Eurasian and South Asian populations have bEu ancestry.

In the paper above, which is open access, the authors found a group of Qatari Bedouin, who seem to have low admixture from Africans or other Middle Eastern groups. Though some preliminary analysis was done with SNP-chips, they went whole genome for most of the work (allowing them to look for rare variants, etc.). I would have been convinced to a great extent if they put a TreeMix graph out which showed that their indigenous Arab population was a good donor to ancient Anatolians along with European hunter-gatherers. But I did not see that. Or they could have done an F4 ratio test showing that the Bedouin were more basal Eurasian than any other modern population. I did not see that.

I did see an F4 ratio test for Neanderthal admixture. I am not confident that their assertions hold. Take a look at the pattern of Neanderthal admixture in the supplements; it’s all over the place. It isn’t in line with the broad patterns found in the latest work out of David Reich’s lab.

There are also some assumptions within the paper which I think are untenable. They seem to be positing a continuity of these Qatari Bedouin within the Arabian peninsula for tens of thousands of years. The divergence of the bEu population, putatively ancestral to these Bedouin, occurred from other non-Africans even before the settlement of Australia, over 50,000 years ago! I don’t think it is likely that the Bedouin were resident in or around the Arabian peninsula for that long.

Finally, there’s some reference to effective population sizes vs. X and autosome. This isn’t a major part of the paper, but I would be skeptical of these sorts of claims. There is a lot of work in this area, and it turns out everything is way more clouded than you might think on first blush.

Overall, good paper. But there’s still a mystery here. The only solution is clearly more ancient DNA from this region.

R. A. Fisher on race and human genetic variation

Youngronaldfisher2In New Creationists a philosopher at Duke recounts his experience when he attempted to explore the implications of group differences in ethics. He stated:

After reading some recent work on the biology of group differences last summer, it occurred to me that as an ethics professor, I should write something about the moral upshot: if there are such differences, what are the consequences for how we should treat one another? Should we support policies that attempt to equalize opportunities only if they produce equal outcomes?

My conclusion was modest: if there are biological differences between groups, and ifas Lee Jussim has argued, some stereotypes turn out to be accurate in part because of correct generalizations about biological differences, these facts should not undermine our commitment to treating one another as moral equals, or to increasing opportunity for all, regardless of group membership.

But I had committed a sin in the eyes of the two referees who read and commented on my paper. I simply acknowledged the possibility of group differences while arguing that whether or not they exist, they should not matter. For having done that, the two journal referees used expletives and exclamation points to give the most venomous and dismissive feedback I have ever encountered. (Needless to say, the paper was not accepted for publication after such hostile comments.)


This is obviously a touchy subject to many reasons. But, the extremely vehement reactions on this topic reveal an aspect of how ideas are policed in our society. Because I have a particular reputation I am privy to viewpoints from many people that they would be terrified to share with others. For example, many young geneticists seem to view the idea that “race is a myth” to be a noble lie.

There are legitimate issues in regards to phylogenetic classification systems. But, the key that many geneticists have noticed is that the lay public makes incorrect inferences from the assertion that “race is a myth.” For example, many people are confused as to why human populations exhibit structure, and one can generate phylogenetic trees. That’s because people translate the idea that race does not exist to one where human population structure is arbitrary and trivial. The conclusion obviously does not follow, depending on your definition of race. But I think one can see how the educated public is coming to these conclusions.

Here’s an article from the year 2000 in Do Races Differ? Not Really, Genes Show:

Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level. But the more closely that researchers examine the human genome — the complement of genetic material encased in the heart of almost every cell of the body — the more most of them are convinced that the standard labels used to distinguish people by “race” have little or no biological meaning.

They say that while it may seem easy to tell at a glance whether a person is Caucasian, African or Asian, the ease dissolves when one probes beneath surface characteristics and scans the genome for DNA hallmarks of “race.”

On the one hand there is an aspect of this article which is almost quaint. Note the references to 80,000 genes and such. But the general spirit captures the modern Zeitgeist well, and it is not dated at all. The idea of race implicit in this piece, and commonly held by the general public, is typological. That is, races are like Platonic ideal forms, and genes and traits are used to explore these ideal forms.

This is false. Races are not like ideal forms. That’s in part because modern human populations are by and large the consequence of massive admixture events between deeply diverged lineages. But, that does not negate the reality that population structure is a robust phenomenon, and, that its consequences are not trivial. My hunch is that some of the eye rolling that I’ve seen when younger geneticists refer to the idea that race is a myth has to do with the fact that population structure is such a big deal for genome-wide associations.

One of the implications of the above passage is that visual inspection allows for a clearer differentiation between individuals from different populations than genetics. This is false. As it happens the groups referred to above are among the most differentiated, as they don’t share common ancestors for ~40,000 years (South Asians on the other hand share ancestry with both “Caucasians” and “Asians” over the last 40,000 years), and are positioned at the extremities of the Afro-Eurasian world island. Genomics actually gives a clearer and more precise picture of population genetic differences.

The problem, if there is one, is that these population genetic differences are not necessarily good fits if one assumes a Platonic model of racial categorization. I think this explains the irritation and frustration with people who are confused as to the ancestral quantification results from firms like 23andMe. The results are true, and robust, reflections of genetic variation. But population groups are reifications, attempting to squeeze human digestible insight from systematic variation at hundreds of thousands of markers whose pattern of differences are a consequence of tens of thousands of years of population history.

Which brings me to the UNESCO statement on the Race Concept. Published around 1950 in a few versions these statements were signals that there was a change in the winds after World War II. Much of today’s conventional wisdom is prefigured in these statements. But if you read the 1952 version much of it is pretty moderate and I think it would be seen as “problematic” by many thinkers today. There are many familiar names (and some not familiar to me) in terms of scientists consulted. E.g., H. J. Muller, Theodosius Dobzhanksy and Ernst Mayr. But for me R. A. Fisher’s comments stood out. I knew he was a dissenter from the statement, but I’m going to cut and paste the whole section from him because I think it’s pretty interesting (and many might agree with him):

In so far as the Statement condemns any defamation of races and emphasizes the appalling nature of the recent abuse of racial theory, it has my full and unqualified approval. I wholeheartedly agree, also, with its explicit and implicit finding that anthropology and racial studies afford no justification for the assumption that members of any particular race are not entitled the enjoyment of all fundamental rights, or for any form of racial discrimination. And I am very glad that, after all the horrors that have been perpetrated, these principles should have been enunciated clearly and publicized widely by an organization of such standing and by distinguished men as the authors of this Statement.

But the Statement also purports to be an authoritative body of scientific doctrines, and this is quite a different matter. Without touching upon the content of these doctrines, and quite apart from whether or not they meet with my approval, I must register my fundamental opposition to the advancing of scientific theses as such, and protest against it.

I recall the National Socialists’ notorious attempts to establish certain doctrines as the only correct conclusions to be drawn from research on race, and their suppression of any contrary opinion; as well as the Soviet Government’s similar claim on behalf of Lysenko’s theory of heredity, and its condemnation of Mendel’s teaching. The present Statement likewise puts forward certain scientific doctrines as the only correct ones, and quite obviously expects them to receive general endorsement as such. I repeat that, without assuming any attitude towards the substance of the doctrines in the Statement, I am opposed to the principle of advancing them as doctrines. The experience of the past have strengthened my conviction that freedom of scientific enquiry is imperiled when any scientific findings or opinions are elevated, by an authoritative body, into the position of doctrines.

A different section of statement relays Fisher’s view of the empirical realities, which would make him extremely unpopular today:

Sir Ronald Fisher has one fundamental objection to the Statement, which, as he himself says, destroys the very spirit of the whole document. He believes that human groups differ profoundly “in their innate capacity for intellectual and emotional development” and concludes from this that the “practical international problem is that of learning to share the resources of this planet amicably with persons of materially different nature, and that this problem is being obscured by entirely well intentioned efforts to minimize the real differences that exist”.

This sort of comment from Fisher makes sense in light of his personality. I’m tempted to think that today he would be diagnosed as being “on the spectrum.” Arguably the most eminent evolutionary geneticist of the 20th century, he also made many original contributions to statistics. But as documented in his daughter’s biography of her father, he was a monomaniacal and selfish person, who lacked many social graces. There is a section in R.A. Fisher: The Life of a Scientist which documents his tendency to engage in arguments with people who shared his general conclusions on a given topic, but where he believed they engaged in fallacious reasoning (in this he seems to resemble Karl Popper). This tendency is clear above. Though he agrees with a broad liberal humanitarianism which looks darkly upon considerations of race, he disagrees with the presumption that these values are rooted in empirical facts.

Finally, I want to quote page 238 of my edition of The Genetical Theory of Natural Selection:

The general consequences of race mixture can be predicted with confidence…Their general character will therefore be intermediate, but their variability will be greater than that of the original races. Morever, new combinations of virtue and ability, and of their opposites, will appear in the mixed race, combinations which are not necessarily heterozygous, but may be fixed as permanent racial characters. There are thus in the mixed race great possibilities for the action of selection. If selection is beneficient, and the better types leave the greater number of descendants, the ultimate effect of mixture will be the production of a race, not inferior to either those from which it sprang, but rather superior to both, in so far as the advantages of both can be combined. Unfavorable selection, on the other hand, will be more rapidly disastrous to a mixed race than to its progenitors. It should of course be remembered that all existing races show very great variability in respect of hereditary factors, so that selections of the intensity to which mankind is exposed would be capable of producing rapid changes, even in the purest existing race.

41PHSZN6AELFisher was writing this in the 1920s. This was near the tail end of the peak of white supremacy across the world. Charles Davenport, the director of Cold Spring Harbor Laboratory, published Race Crossing in Jamaica in 1929. It presented a view where mixed-race children suffered due to crossing between diverged lineages. This was not an atypical view at the time. The man whom Fisher succeeded to a great extent as Britain’s most eminent statistician, Karl Pearson, was a socialist and feminist (Fisher was a political conservative whose views on women were more regressive than Pearson) who also believed that inter-group competition with “inferior races” was a major driver of the evolutionary progress of Europeans. The above passage shows that Fisher’s logical mind internalized Mendelianism and its necessary implications to such a great extent that as early as the 1920s he was already dismissive of the racialism ascendant at the time. But by the 1950s the dominant viewpoint differed, and here Fisher again stood his ground, not changing the things he had written in the later eugenic sections of tGToNS.

Note: R. A. Fisher had some unfortunate views on smoking. See When Genius Errs: R. A. Fisher and the Lung Cancer Controversy.

Open Thread, 1/24/2016

silicon-valleyI watched a few episodes of Silicon Valley at a friend’s house this Friday when I was in the Bay area. I though it was pretty funny. I was at the Googleplex during the day, so it was interesting to see how it influenced the show. But in general I thought the Peter Thiel influenced character Peter Gregory was probably the best thing about the show. Unfortunately the actor who played Peter Gregory died during the first season. (A friend believes that I somewhat resemble the character Erlich Bachman.)

I think Steve mentioned that one unrealistic aspect of Silicon Valley is that the day-to-day action seems relatively detached from the ubiquitous nature of the internet, and the fixation that modern Americans have on their phones. But the reality is that having scenes dominated by characters staring at their phones would probably be quite boring.

You have probably heard about the Free Harvard/Fair Harvard campaign. Here are the detail of how to help:

Thus, anyone holding a Harvard degree who is interested in signing our petitions and perhaps changing the world should email us at, and include your mailing address to obtain a petition for signing. If you can commit to quickly gathering an additional signature or two and also include your phone number, we will FedEx you a petition. The more Harvard alumni signatures all of you can quickly gather, the more likely Harvard will soon become both free and fair.

Alumni here includes both undergraduate and graduate levels. Steve Hsu has part of this too. The deadline is February 1st.

41n4rA-gvoL._SY344_BO1,204,203,200_As many of you know, I have a passing interest in psychometrics. What for me defines a passing interest? Unlike Roman history, for example, psychometrics is not a topic I follow in depth, or closely in any way. I know the basic outlines, and use that make judgments about the nature of the world. The question of where the general intelligence factor comes from in a biophysical sense is not a major concern of mine. Rather, I’m interested in what intelligence can tell us about life outcomes and such. That is, I’m an instrumentalist.

But I’m starting to become a little worried at how much ignorance there is among the intellectual elite on the topic. It is not uncommon for people to be entirely unaware of basic facts, in which case their inferences are derived from false premises. So how to remedy the situation? Arthur Jensen’s The g factor is dense and expensive, so I can’t recommend it casually. Hive Mind has a good introduction, but the topic is ultimately not intelligence as such. So I think I’d recommend Stuart Richie’s Intelligence: All That Matters. Any other suggestions? What is intelligence? by James Flynn is OK, but that’s an older book.

A response to Limitations of GCTA as a solution to the missing heritability problem is now up, Commentary on “Limitations of GCTA as a solution to the missing heritability problem”.

Some refugees are going back to Syria. I suspect there’s an economic angle here. The genuinely poor are probably not going to go back to these countries because being on welfare benefits of some sort in a wealthy country beats being on the margins in a less wealthy country. But many of the middle-class migrants seem to be realizing that they miss their social status when in countries where they are guaranteed to be marginalized for at least a generation, or longer.

51sdHZvYfTL._SX334_BO1,204,203,200_Then there is the issue of cultural differences. I have written a few posts recently about the nature of these sorts of things. Over the medium-term culture is quite malleable and protean. But in a very general sense it does not change very fast in the short term (though specific aspects of culture can change fast). Here is a passage from The Secret of Our Success:

In Iraq, in the aftermath of the American military victory in 2003, many assumed that once freed from the dictatorial oppression of Saddam Hussein and presented with new state-of-the-art political and economic institutions imported from the United States and Europe, Iraqis would rapidly take to these institutions and start acting like people in Ohio. That did not happen, probably in part because new formal institutions and organizations have to fit with people’s social norms, informal institutions, and cultural psychology

One of the major sources of migration to Europe today is Afghanistan. Afghans have very different values from Europeans. To illustrate, here is a story from The New York Times, Flawed Justice After a Mob Killed an Afghan Woman. From the explanation of the video’s context: “Farkhunda Malikzada, a 27-year-old Muslim woman falsely accused of burning a Quran, was killed by a mob in central Kabul as hundreds watched and filmed.”

Let’s unpack the issue here.

1) A woman was killed in broad daylight
2) In the largest most cosmopolitan city in Afghanistan
3) The killing was a matter of mob justice, and by the end young boys are encouraged to throw stones at the dead body in an almost initiatory manner
4) She was killed because she was accused (falsely it turns out) of burning a Koran

Initially prominent political leaders praised the mob justice because they believed the account of her blasphemy. Later there was anger when it came out that she was falsely accused due to a petty squabble.

My point is that hundreds of thousands of men from this particular culture are now living in Europe. It seems implausible that just by drinking European water they would magically become democratic liberals. Though the social context is such that this sort of mob justice is not going to occur in Berlin or Stockholm, it is also almost certainly true that many of the informal and tacit views of these Afghan migrants aligns with the men and boys of Kabul who killed Farkhunda Malikzada.

I was talking recently about how I go about deciding on my “intellectual diet” (similar to the “media diet”) with my friend Carl Schulman. Over the years (I’d probably date the genesis of my habits to when I was eight years old or so) the domains which I explore have varied. I try to balance being focused on issues of particular and personal interest, with an occasional sampling of the parameter space of ideas and topics which are novel to me. There are books I read for really practical reasons. E.g., my friend Joel Grus’ Data Science from Scratch: First Principles with Python (I’m in transition from Perl to Python). There are others I read for professional reasons. An Introduction to Population Genetics Theory. Though I read few genetics books in my field aside from theoretical texts, since the papers are where the latest research is in any case. On the other hand there are topics which have been long-running interests of mine. As is obvious from my Good Reads, I read a lot of history. In particular, Roman and Chinese history. I’ve been doing so since I was about 12 years old. There are other topics, like religion, which I’ve focused on for a while, before moving on when I thought I knew what I needed to know. But occasionally I’ll read something random, such as Alexei Panshin’s The World Beyond the Hill: Science Fiction and the Quest for Transcendence. Most of the time these forays are one-offs, but occasionally I discover a new interest.

Of course the reality is that these sorts of methods and strategies change over time. Between my work and personal life I don’t see much room for reading fiction at this point. But perhaps there will be a time when I’ll go back to that habit.

Some of you now I experiment with things like Soylent. One thing I would like to add though: I think the focus on perfectly optimizing nutritional intake is pretty short-sighted. The reality is almost no one is going to move wholly to meals-ready-to-eat, and variation in the population in nutritional needs does exist. I bring this up because I’m going to try MealSquares soon.

Speaking of food, China Village in Albany, CA, has pretty good Szechuan.

Brian Boutwell and Amir Sariaslan are two accounts on Twitter you should follow. They do a really good job reintroducing the wisdom of behavior genetics into the public discussion.

I find this interesting, because Muslims have never told me that I should change my name. It seems that this is because though my name is operationally Muslim, neither Razib nor Khan are Arabic and explicitly tied to Islamic history. Razib is simply a Bangladeshi variant of the common Bengali name Rajib, which is a variant on the more well known name Rajiv, whose ultimate origin is Sanskrit. And Khan is a Turco-Mongol title, which for various reasons became associated with Muslims in South Asia.

The Day the Mesozoic Died.

How your (sub)cultures’ values are more important than family values

513C5X3UhAL._AC_UL320_SR220,320_As one might expect, the piece that I co-authored with Brian Boutwell, Heritability and why Parents (but not Parenting) Matter, has stirred up some irritation and even anger. Part of this is simply due to the mildly hyperbolic nature of the title. Obviously on some level parents matter a great deal. What we were attempting to get at though is that most parents have far less precise control of the outcomes of their children than they think they do (you do have great control if you beat or starve your children though!). The lack of control is one reason siblings vary so much.

To make it concrete, imagine across the population variation of personality is 30% heritable, 15% accounted for by shared environment, and 55% explained by non-shared environment. The parental effect is captured in the shared environment. When behavior geneticists downplay the role of parents in affecting outcomes, they are doing so because of this value. In this example the proportion explained by the parents’ genetic variation is twice as large as the conscious environmental choices. But, note that most of the variation is not necessarily due to genetic factors!

What is this variation? The short answer is that we don’t know. One hypothesis, promoted by Judith Rich Harris in The Nurture Assumption, is that it is one’s social milieu. That is, peer groups. To my knowledge in the past 15 years there has not been much support for this thesis, suggesting to me that we’re still at a loss to explain non-shared environment. In fact it may just be an intractable stochastic aspect of life outcomes (or if you want to reduce it to biology, developmental stochasticity).

People become uncomfortable with these statistics because they suggest that the most immediate personal control you can have on the character of your offspring is through the spouse you select. Your spouse (or you) may change values over time, but you are not going to change your genes. This is not very congenial with the modern American conservative orthodoxy that crystallized after World War 2 which placed the nuclear family at the center of the culture (basically, fusionism). The rise of “family values” as inoculation against liberal permissiveness is to a great extent predicated on the idea that shared environment is very powerful over the long term. The data just don’t support this proposition.

We can see this when you look through recent history. Some of the response to the Quillette piece emphasized and reiterated that we missed something when we ignore and dismiss the importance of values that parents’ instill in their children. But values are malleable. A whole generation of Southerners grew up in the 1950s and 1960s with racial values taught to them by their parents, and they also grew out of those values as a generational cohort. Or, look what’s happening with gay marriage: …Evangelicals Are Changing Their Minds on Gay Marriage:

The shift is especially visible among young evangelicals under age 35, a near majority of whom now support same-sex marriage. And gay student organizations have recently formed at Christian colleges across the country, including flagship evangelical campuses such as Wheaton College in Illinois and Baylor in Texas.

Obviously this goes back to Judith Rich Harris’ general insight: social consensus and cultural cognition are real phenomena which are enormously impactful. But please remember that this doesn’t necessarily explain non-shared environment, as these sorts of dynamics are forces for conformity and homogenization. When we are thinking about control of outcomes, usually you need to focus on:

– Culture
– Genes
– Parents

In that order. The non-shared environmental variance will still be substantial, but we don’t have a good sense of what’s causing it yet. And we may never. But we can choose a lot of life outcomes by selecting the nation we migrate to, or, by the community with which we identify. For example, if I migrated back to Bangladesh and raised my daughter to be a staunch atheist with a generally liberal-individualist ethos, those values might stick. There’s probably some heritable aspect to my character which makes atheism and liberal-individualism “a good fit.” But, there is a strong chance that my daughter will conform to the milieu in which she grows up, and with which she may identify. The exception to this would be if she found a subculture which insulated her from broader social conformity pressures, and allowed her to develop her worth and identity differently.

I’m not totally sure of the political implications of this perspective in the United States. My own position is that the rhetoric of “family values” on the American Right today has been strongly suffused with an individualist ethos that is common in Anglo-American evanglical Protestantism, and can find its roots in the somewhat atomized nature of Scots-Irish and lowland South culture in the United States. A contrast with this model is that of Mormons, who share values with evangelical Protestants, but whose folkways reflect the more communitarian ethos of New England Yankees and German or Scandinavian peoples. I suspect that the lower divorce rate (and social pathology more generally) among Mormon Americans in comparison to white evangelical Protestants has more to do with the nature of their collective institutions than the individual dispositional nature of believers.

50thversionOn the other hand, this viewpoint does not necessarily support the instincts of modern technocratic liberalism. In general technocratic liberals seem to think that many social ills have a small number of causes, and so are tractable through public policy. Often these causes are pinned down on single institutions (e.g., schools), or, a lack of funds. Recently universal pre-school has been all the rage because of its near magical ameliorative properties. But the social science on that is decidedly mixed. I suspect that universal pre-school as a simple institutional fix is far inferior to the rich civic and social matrix which Jane Jacobs described in The Death and Life of Great American Cities. Not only because organically developed social and civic institutions provide services which pre-school can not replace, but also because a society which gives rise to such institutions is by its nature more healthy and exhibits less anomie. In some ways Mao was right that a true solution toward fixing social ills is a “cultural revolution.”

The tales dead languages tell

smith-devilI’m not sure I believe the methods, but the paper is open access, Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales:

Ancient population expansions and dispersals often leave enduring signatures in the cultural traditions of their descendants, as well as in their genes and languages. The international folktale record has long been regarded as a rich context in which to explore these legacies. To date, investigations in this area have been complicated by a lack of historical data and the impact of more recent waves of diffusion. In this study, we introduce new methods for tackling these problems by applying comparative phylogenetic methods and autologistic modelling to analyse the relationships between folktales, population histories and geographical distances in Indo-European-speaking societies. We find strong correlations between the distributions of a number of folktales and phylogenetic, but not spatial, associations among populations that are consistent with vertical processes of cultural inheritance. Moreover, we show that these oral traditions probably originated long before the emergence of the literary record, and find evidence that one tale (‘The Smith and the Devil’) can be traced back to the Bronze Age. On a broader level, the kinds of stories told in ancestral societies can provide important insights into their culture, furnishing new perspectives on linguistic, genetic and archaeological reconstructions of human prehistory.

Demographic disruption and cultural transformation

ncomms10326-f351IQSePVDRL._SY344_BO1,204,203,200_It has been an open question for historians of the fall of the Roman Empire the extent to which ethno-tribal migrant caused the transformation toward the post-Roman order. In Britain, for example, there has long been debate as to whether the shift from a predominantly Celtic population with a cosmopolitan Latin-speaking patina (at least demographically in terms of origins; I understand there are those who argue that late-Roman Britain was predominantly Latin-speaking), was due to a mass migration of Germans, or more a matter of institutional and cultural defection and conversion. In the early 20th century the model in vogue was predicated on migration. The Welsh and English were perceived by many to be distinct races, with the latter having affinities with the Germanic peoples in blood as well as speech. In the late 20th century the pendulum swung in the other direction. I recall reading Norman Davies’ The Isles in 2000, and he relayed the conventional view of historians of the period that the post-Roman world of Britain saw the conversion through elite emulation of Britons into Saxons (and Angles and Jutes) based on documentary evidence of co-existence and subordination of a Celtic population in early Anglo-Saxon England.

Ten years later Peter Heather wrote Empires and Barbarians to resurrect a moderate migrationism for the post-Roman world. What he was rebutting was the perception that the idea of German folk migrations, which included the movement of women and children along with men, was a post hoc myth. Though even the most extreme cultural constructionist would assent to the proposition that some Germans did migrate into the late Roman world and capture the post-Roman successor states, they usually emphasized that tribal identities were ad hoc, novel and newly constructed, and German identity was highly malleable easily co-opted by aspirant non-Germans. In other words, the Goths, Vandals, and Anglo-Saxons were motley coalitions of opportunists, whose ethnic self-identity was a matter of recent myth.

Some of this is certainly true. Going back to Anglo-Saxon England, Alfred the Great’s early genealogy is littered with names that seem to exhibit a British, not German, provenance. It is not unreasonable that British warlords would on occasion switch sides to maintain their position at the top of the status hierarchy, just as some Visigothic nobles in Spain after the Muslim conquest converted to the new religion and became progenitors of the local Islamic aristocracy.

But we shouldn’t go too far. Last year PoBI finally published their paper, The fine-scale genetic structure of the British population, and confirmed the suggestions of earlier genetic work that a substantial proportion of the ancestry of the contemporary English population derives from Germans. Not the majority, but a substantial minority. In other words, Peter Heather was correct in England. Cultural change was catalyzed by substantial demographic change. There is more and more evidence that in two areas of the post-Roman world where Romanitas faded, with the local decline or extinction of Christianity and Roman speech (whether Latin or Greek), Britain and the Balkans, there was substantial demographic change induced by a migration into Roman territory of Germans and Slavs respectively.

51sdHZvYfTL._SX334_BO1,204,203,200_With that, I submit two open access papers on ancient genomes from Britain: Genomic signals of migration and continuity in Britain before the Anglo-Saxons and Iron Age and Anglo-Saxon genomes from East England reveal British migration history. The plot at the top of this posts shows a striking result: most of the Roman era individuals are genetically least differentiated from the Welsh, and modern East Anglians are the most shifted toward the Dutch. This is exactly the pattern we would expect from archaeology, as the pale of German settlement was along the Saxon Shore.

So genetics tells us that extreme positions of total replacement or (near) total continuity are both false. Rather, the genetic landscape of modern England is a synthesis, with structure contingent upon geography. But, it also shows us that substantial demographic change which produces a genetic synthesis can result in a total cultural shift. Though we may think of elements of culture as entirely modular, with human ability to mix and match components as one might see fit, the reality is that often cultural identities and markers are given and taken as package deals. But, it probably took the transplantation of a total German culture through a mass folk movement to give the Saxons enough insulation from the local British substrate to allow them to expand so aggressively and become genetically assimilative and culturally transformative.

Revisiting the critique of the Nurture Assumption

tnapb4The “nurture assumption” is basically the idea that parents really, really, matter in affecting variation in individual outcomes in their children. Judith Rich Harris famously wrote a book length critique, The Nurture Assumption: Why Children Turn Out the Way They Do, which was published in 1999. I’ve argued that the Steven Pinker’s The Blank Slate is important in large part because it introduced a broader audience to Harris’ conclusions. Though the pattern that she observes, that most variation in outcomes for individuals does not seem to be accounted for by shared environment, that component that is under parental control, is a robust behavior genetic finding it runs against deep human intuitions. This is one domain where political Left and Right share the same sympathies, though the details differ. Many cultural conservatives in the United States impute to parents an almost alchemical power to shape the nature of their children through inculcation. Similarly, cultural liberals attribute the same sort of power to society broadly construed.

If you’ve been reading me for 13+ years you know all this. As a parent these last four years I’ve had to struggle with the nurture assumption myself. For psychological and social reasons the impulse is strong within us. Recently Brian Boutwell has been doing the Lord’s work, so to speak, in Quillette, reintroducing these ideas to a general audience. Now he and I have co-authored the latest installment, Heritability and why Parents (but not Parenting) Matter. I invite you to check it out!