I try to limit the shilling, but since readers of this weblog know what this means: Helix has a sale on kits until the end of the month. The three Insitome products can be purchased for app-only cost ($29.99) as an entrance into the ecosystem. In other words, for $29.99 you can get millions of markers in your exome sequenced, as well as some positions in the rest of your genome. Helix keeps the data, but there will be no kit cost if you see a future app that you want to purchase.
Harvard Office of Institutional Research on Discrimination Against Asian-American Applicants. I will blog about this at some point…and I’ve been making semi-serious/jokey tweets. But people are probably not clear on my “position.” My main irritation about Harvard is the extent of the doublethink that they get away with. Drew Gilpin Faust’s pablum about inclusion and diversity being central values at Harvard is a classic “Shaggy defense”. Faust helms a finishing school for the overclass, and as such accepts the necessity of discrimination when it comes to anointing future overlords. Some hypocrisy is necessary for the ruling caste, but the juxtaposition between “neoliberal” reality of what Harvard is, and the “progressive” rhetoric of it presents to the gullible and ignorant public, is starting to become indecent.
Speaking of overclass, Tim Draper is a third generation member of the capital class, and still defends Elizabeth Holmes.
It is no surprise that I am not excited by the proposal to focus AP History in the United States on the period after 1450. Overall I agree with many of the comments made in T. Greer’s tweet thread. Though I have a concurrent opinion with many history teachers who oppose the change, my opposition is for different reasons. To be frank I don’t care about “showing our black and brown and native students that their histories matter—that their histories don’t start at slavery”.
Though my leanings are toward positivism, that is, I think history is an empirical discipline, even with a potential scientific scaffold, I understand that with finite time and resources your choices are conditional on your viewpoint. When I grew up in the American North the Civil War was taught with facts, but the arrangement and emphasis of those facts were not flattering to the Confederacy. I think objectively this isn’t hard from a modern perspective. But, the fact that some Union regiments were raised in the area where I grew up is certainly relevant
But this old-fashioned biased perspective still gave the nod to the importance of objectivity in some deep way. And though I was an immigrant who was routinely asked “where I was really from”, there was also an understanding that I needed to know this particular Union history, because it was the history which I inherited. It was our history, which set the objective preconditions of the world in which we lived. The sharply critical cast of modern history teaching has its roots in this fundamental understanding. History may often have had propagandistic overtones, in that it inculcated, but the facts still mattered, and sometimes they were at counter-purposes to the narrative (e.g., the Abolitionists were clearly in the minority even in the North; good history teachers didn’t lie about this).
The idea that one’s history, “their” history, is rooted in descent is common sense. But it’s also an idea which brings together frog-Nazis and Critical Race Theorists. Because of the closeness of the past few hundred years, the histories will be contested on the grounds of ideology. All narratives are contested, but emotion and effort vary in the contestation. The way to push through the contestation is to flood the zone with facts, with robust models. But this isn’t feasible for high school students, many of whom simply want to obtain a good AP score so they never have to take a history course again.
Rather, I think history before 1450 is critical not because it is relevant to a diverse student body due to genealogical affinity, but because common human universal themes are easier to perceive in more distant peoples whose actions and choices don’t have as strong a direct connection to the lived present. Consider the Classical Greeks. It is reasonable to assert that the genesis of the West as we understand it has to be traced at least in part to the Ionian flowering of the 5th century, and to Athens in particular. But it is not reasonable to make Classical Greeks a stand-in for modern Europeans, whose Christianity (at a minimum culturally) would be alien, and whose origins are from peoples who the ancient Greeks would term barbarians.
The Classical Greeks are profoundly alien to moderns, rupturing excessive identity, though that didn’t stop 19th century Romantics! Athenian democracy is very different from the modern democracies, with its participatory character and the large class of excluded residents. But Athenian democracy, and Classical Greece more generally, also highlight deep universal aspects of the human condition. It speaks more forcefully to many students because the mental clutter of the past few centuries, and their ideological baggage, are removed from the picture.
Additionally, cross-cultural comparisons of similarities and differences in the ancient and medieval world are useful because they are less overshadowed by the “Great Divergence”, and the post-1800 European breakout. While the world before Classical Greece was one of strange and isolated polities in a vast barbarous world, the world after 1450 points strongly in our mind’s eye to a state where Europe occludes our entire view. The problem is not slavery, because the age of European supremacy saw the abolition of slavery.
Obviously, even the period before 1450 can be fraught. Consider the rise of Islam, and the crystallization of the West as Christian Europe in tension with the rising civilization to the south, and the receding pagan wilderness to the north and east. There are plenty of opportunities for debate, disagreement, and ideological axes to grind. But contrast the same argument around the Arab-Israeli conflict or Sykes-Picot Agreement. The fact is that pushing the past further back into the past muddles modern preoccupations. And that’s a feature, not a bug.
Last week Spencer and I talked about chromosomes and their sociological import on The Insight. It was a pretty popular episode, but then again, my post on the genetics of Genghis Khan is literally my most popular piece of writing of all time which wasn’t distributed in a non-blog channel (hundreds of thousands of people have read it). Thanks to everyone who left a review on iTunes and Stitcher (well, a good review). We’re getting close to my goal of 100 reviews on iTunes and 10 on Stitcher so that I won’t pester you about it.
Of course the reality is that the heyday of chromosomal population genetic studies was arguably about 15 years ago, when Spencer wrote The Journey of Man. I have personally constructed Y phylogenies before…but as you know from reading this weblog, I tend to look at genome-wide autosomal studies. There is a reason that why Who We Are and How We Got Here focuses on autosomal data.
All that being said, Y (and mtDNA) still have an important role to play in understanding the past: sociological dynamics. The podcast was mostly focused on star phylogenies, whether it be the Genghis Khan haplotype, or the dominant lineages of R1a and R1b. Strong reproductive skew does have genome-wide effects, but unless it’s polygyny as extreme as an elephant seal’s those effects are going to be more subtle than what you see in the Y and mtDNA.
About ten years ago I read the book The River of Lost Footsteps: Histories of Burma. Though I have read books where Burma figures prominently (e.g., Strange Parallels), this is the only history of Burma I have read. The author is Burmese, and provide something much more than a travelogue, as might have been the case if he was of Western background. By chance over the past month or so I’ve been in contact with the author, who made a few inquiries as to the genetics of his own family (he came with genotypes in hand). But this brought us to the issue of the genetics of the Burmese people, and their position in the historical-genetic landscape.
The author of The River of Lost Footsteps reminded me of something that’s curious about Southeast Asia: its Indic influences tend to be from the south of the subcontinent. In particular, the native scripts derive from a South Indian parent. Could genetics confirm this connection as well? Also, could genetics give some insights as to the timing of admixture/gene-flow?
In theory, yes.
I had a lot of Southeast Asian datasets to play with, and did a lot of pruning to remove outliers (e.g., people with obvious recent Chinese ancestry). First, comparing them to Bangladeshis it seems that even without local ancestry tract analysis that Burmese and Malays have more varied, and so likely recent, exogenous ancestry than Bangladeshis. At least this is evidence on the PCA plot, where these two groups exhibit strong admixture clines toward South Asians.
But what about the question of Southeast Asian affinities? This needs deeper analysis. Three-population tests, which measure admixture with outgroups when compared to a dyad of populations which are modeled as a clade, can be informative.
Bangladeshis show strong signatures with both Cambodians and Han. This is in accordance with earlier analysis which suggests Austro-Asiatic and Tibeto-Burman contributions to the “East Asian” element of Bengali ancestry. The Burmese always have Han ancestry, with a South Asian donor as well. This aligns with other PCA analysis which shows the Burmese samples skewed toward Han Chinese. Burma is a compound of different ethnic groups. Some are Austro-Asiatic. The Bamar, the core “Burman” group, have some affinities to Tibetans. And the Shan are a Thai people who are relatively late arrivals.
Cambodians have a weaker admixture signature and are paired with a South Asian group and their geographic neighbors the Vietnamese. The Malays are similar to Cambodians but have the Igorot people from the Philippines as one of their donors. And finally, not surprisingly the Vietnamese show some mixture between Han-like and Cambodian-like ancestors.
Further PCA analysis shows that while Cambodians and Malays tend to skew somewhat neutrally to South Asians (the recent Indian migration to Malaysia is mostly Tamil), the Burmese are shifted toward Bangladeshis:
Finally, I ran some admixture analyses.
First, I partitioned the samples with an unsupervised set of runs (K = 4 and K = 5). In this way I obtained reified reference groups as follows:
“Austronesians” (Igorot tribesmen from the Philippines)
“Austro-Asiatic” (a subset of Cambodians with the least exogeneous admixture)
“North Indians” (Punjabis)
“South Indians” (A subset of middle-caste Telugus highest on the modal element in South Indians)
“Han” (a proxy for “northern” East Asian)
The results are mostly as you’d expect. In line with three-population tests, the Vietnamese are Han and Austro-Asiatic. More of the former than latter. There is a minor Austronesian component. Notice there is no South Asian ancestry in this group.
In contrast, Cambodians have low levels of both North and South Indian. These out sample Cambodians are still highly modal for Austro-Asiatic though.
Malays are more Austro-Asiatic than Austronesian, which might surprise. But the Igorot samples are highly drifted and distinct. I think these runs are underestimating Austronesian in the Malays. Notice that some of the Malays have South Asian ancestry, but a substantial number do not. This large range in admixture is what you see in PCA as well. I think this strongly points to the fact that Malays have been receiving gene-flow from India recently, as it is not a well mixed into the population.
The Bangladeshi outgroup is mostly a mix of North and South Indian, with a slight bias toward the latter. No surprise. As I suggested earlier you can see that the Bangladeshi samples are hard to model as just a mix of Burmese with South Asians. The Austro-Asiatic component is higher in them than the Burmese. This could be because Burma had recent waves of northern migration (true), and, eastern India prior to the Indo-Aryan expansion was mostly inhabited by Austro-Asiatic Munda (probably true). That being said, the earlier analysis suggested that the Munda cannot be the sole source of East Asian ancestry in Bengalis.
Finally, every single Burmese sample has South Asian ancestry. Much higher than Cambodians. And, there is variance. I think that leads us to the likely conclusion that Burma has been subject to continuous gene-flow as well as recent pulses of admixture from South Asia. The variation in South Asian ancestry in the Burmese is greater than East Asian ancestry in Bengalis. I believe this is due to more recent admixture in Burmese due to British colonial Indian settlement in that country.
The cultural and historical context of this discussion is the nature of South Asian, Indic, influence, on Southeast Asia. One can not deny that there has been some gene-flow between Southeast Asia and South Asia. In prehistoric times it seems that Austro-Asiatic languages moved from mainland Southeast Asia to India. More recently there is historically attested, and genetically confirmed, instances of colonial Indian migration. But, the evidence from Cambodia suggests that this is likely also ancient, as unlike Malaysia or Burma, Cambodia did not have any major flow of Indian migrants during the colonial period. One could posit that perhaps the Cambodian Indian affinity is a function of “Ancestral South Indian.” But the Cambodians are not skewed toward ASI-enriched groups in particular. And, I know for a fact that appreciable frequencies of R1a1a exist within the male Khmer population (this lineage is common in South Asia, especially the north and upper castes).
As far as Burma goes, I think an older period of South Indian cultural influence, and some gene-flow seems likely. But, with the expansion of Bengali settlement to the east over the past 2,000 years, more recent South Asian ancestry is probably enriched for that ethnolinguistic group.
I’m going to try and follow-up with some ancestry tract analysis….
The latter paper indicates that there were multiple waves to Neanderthal admixture into both Europeans and East Asians. The motivation to do the analysis is that East Asians are about ~12 percent more Neanderthal than Europeans. The authors don’t reject the idea that there was ‘dilution’ of Neanderthal through selection and especially admixture with a “Basal Eurasian” group which didn’t have Neanderthal ancestry. I don’t want to get into the details of the results except for one thing: the preprint confirms a consistent finding over the past eight years that the Neanderthal contribution to the modern human genome is from a single population.
Perhaps it was a small population. Or perhaps it was a large population that had gone through a bottleneck and was genetically not very differentiated. But unlike Denisovans it seems that it was a particular Neanderthal lineage that interacted with modern humans.
Moving back to the “Basal Eurasians,” notice some details of the schematic above. The divergence of Basal Eurasians from other non-Africans was ~80,000 years ago, across an interval of 70 to 100 thousand years ago. The admixture of Basal Eurasians into the proto-LBK population occurred ~30,000 years ago, across an interval of 11 to 41 thousand years ago. Ancient DNA from North Africa indicates that Basal Eurasians were already well admixed well before 11 thousand years ago.
The other dates make sense. 50,000 years for Europeans-Han Chinese, 96,000 years for Mbuti-Eurasians, and 696,000 years for Neanderthal-modern humans.
Ancient modern humans were highly structured. We know this from within Africa. But it seems clear that modern humans who had crossed over the other side of the Sahara also exhibited the same tendency. Basal Eurasians did not mix with Neanderthal populations. I suspect that that might be due to the fact that they were in Northeast Africa. At some point in the Pleistocene a mixing event occurred. This may have been precipitated by drier conditions and human retreat into only a few habitable areas, and the original Basal Eurasian populations may have mixed into other Near Eastern groups, which were part of the broader Neanderthal-mixed populations.
The much-awaited DNA study of the skeletal remains found at the Harappan site of Rakhigarhi, Haryana, shows no Central Asian trace, indicating the Aryan invasion theory was flawed and Vedic evolution was through indigenous people.
“The Rakhigarhi human DNA clearly shows a predominant local element — the mitochondrial DNA is very strong in it. There is some minor foreign element which shows some mixing up with a foreign population, but the DNA is clearly local,” Shinde told ET. He went on to add: “This indicates quite clearly, through archeological data, that the Vedic era that followed was a fully indigenous period with some external contact.”
I haven’t heard anything definitive, but this is what I have heard: that the genetics they could analyze indicates continuity, but none of the steppe element ubiquitous in modern North India (and that there was contamination in the Korean lab). The Rakhigarhi samples date to 2500 to 2250 BC last I checked. That means they shouldn’t have any steppe ancestry if the model of the relatively late demographic impact of Indo-Aryans after 2000 BC is correct.
Basically, the whole article is kind of a non sequitur. I do understand that many archaeologists think there was continuity culturally. And there could have been. But taking into account the genetics of the modern region of India where Rakhigarhi is located, there was a major demographic perturbation after 2250 BC.
A few years ago a reader sent me a copy of Edward Feser’s Five Proofs of the Existence of God. Though I haven’t read that book, I did read a substantial proportion of Feser’s Aquinas: A Beginner’s Guide on a plane trip recently. I’m not a big believer in whole-hog Thomism, but I’ve read some Aquinas before and always admired his incredible intellect. Feser’s treatment seems to be a good introduction to that.
So a friend emailed me and wondered why I’m so hard on R.A. Fisher. To be honest the number one reason is that his own daughter seems to have written a rather unflattering biography when it comes to his personal temperament. That being said, let me pass on E. B. Ford’s R. A. Fisher: An Appreciation.
When it comes to any individual it’s easy to be at some remove from a situation and pass on lies because you don’t know any better. It has certainly happened to me.
Which brings me to what’s happened to someone named Wajahat Ali. He’s a Muslim American (Pakistani) public intellectual who has gotten in trouble with some Muslims because he violated some of the norms of BDS (though he never joined on with BDS as such, it’s become normative in many Muslim circles). To me, there are two curious aspects.
First, the general one that in some cultural milieus lies are very powerful, and became truth. If some people generate enough smoke, other people will assume there’s fire. It’s pretty obvious that the people accusing Ali of being an Islamophobe and Zionist-stooge are either liars or enthusiastic witch-burners. But there’s no huge penalty for making this stuff up, so only “upside” for the accusers.
It is also interesting that Ali contends that some people are finally standing up and admitting they know him, and all the accusations are lies, and they can’t listen to the lies any longer. The implication though is that these people were silent for a long while because they were afraid to stand by him when he was maligned unjustly.
A pretty honest commentary about our society today.
Second, Ali exposes the tacit racial hierarchy which is taken for granted in the Muslim American community. A few months ago a friend of mine who is a liberal (white) academic was saying some negative things about Hindu nationalism in relation to Islamophobia and wondered what Muslim students on campus would think about the tolerance that Hindu nationalist speakers are shown in the United States. My first thought: the only Muslims who care about Hindu nationalists are South Asians. Arabs probably don’t even know anything about Hindu nationalists.
The reality is there is one overwhelming concern of Muslim Americans, and that’s Palestine. To be entirely frank many Arab Muslims don’t give a shit what happens to South Asian Muslims. They’re not as callous to proactively not care. It’s just that it never really comes onto their radar. What matters to them is what is happening in the Middle East.
The converse is not true. South Asian Muslims care a great deal about Palestine. As they should: Arabs and Middle Eastern people, in general, are the center of Islam’s mental hierarchy. Not explicitly so. But implicitly, obviously. In general, Arabs will not listen to South or Southeast Asians, or black Africans tell them anything about Islam. In contrast, non-Arabs will listen to Arabs about Islam (Turks and Persians are a special case, and may not defer as much to Arabs).
Ali’s transgressions led to pretty straightforward observations he was being an uppity Pakistani who should leave Israel-Palestine to Arabs. He doesn’t seem to have been traumatized by this, but that’s because I assume he expected that that would happen. South Asians who don’t defer on these sorts of religious issues will be put back in their place. The mosque in New York I went to as a small child had an ethnic division of labor. The South Asians, mostly Pakistani and Indian doctors, provided funds when needed, and the Arabs ran the mosque and took on adult and childhood religious education.
Back in the day, I used to read Tariq Ramadan’s books to get a sense of what intellectual Muslims think from a moderately conservative viewpoint. Today he stands accused of multiple rapes and admits that he had many affairs. The thing for me to reflect on is that I have no doubt that Ramadan believes in an all-powerful God. And yet he knowingly commits what he believes to be sin (extra-marital sex). And he may have raped women.
One of the major conclusions of Diarmaid MacCulloch’s The Reformation is that Protestantism only captured societies with finality when the most powerful temporal leader pushed for the change from above or maintained the pressure. The “magisterial” Reformation succeeded in those nations where the king or the most powerful aristocrats defended Protestantism and made it their own.
In contrast, in much of Austria, Hungary, and Bohemia, vast territories which had been won over to Protestantism were slowly brought back to Catholicism over the course of the 17th century under imperial direction and force. The process is outlined in Benjamin Kaplan’s Divided by Faith: Religious Conflict and the Practice of Toleration in Early Modern Europe. It was a deliberate campaign to retake ground lost by the Habsburg monarchy and the Catholic Church.
The grinding down of Protestant faith in Hungary left such bitter feelings that Hungarian Calvinists marched with the armies of the Ottomans in the late 17th century during the Battle of Vienna. Even today the center of Hungarian Calvinism is in the far east, which was longest under the protection, neglect and toleration of the Ottomans.
French and Polish Protestants were well represented among the elites and parts of the nobility. Both states offered the Protestants a modicum of toleration, more or less, but in neither instance they did they capture the monarchy. In France, the Protestant Henry IV famously converted to Roman Catholicism, because the monarchy of the French state was tied so closely to the old religion. Polish Protestants, always a minority but concentrated among the upper echelons, slowly lost their position in society over the 17th and 18th centuries, to the point where being ethnically Polish and being Roman Catholic were synonymous. In contrast, the French Protestants suffered a major immediate shock when Louis XIV revoked the toleration and independence that they had enjoyed explicitly. They either had to convert, emigrate, or retreat deep into isolated areas such as the Massif Central.
The maxim adopted in 1555 was cuius regio, eius religio. “Whose realm, his religion.”
But did this really hold? Henry VIII certainly dragged an England that wasn’t entirely comfortable with leaving Catholicism, especially in the north, to Protestantism (though not too far, as the Puritans would learn!). The Scandinavian monarchs transitioned their nations rather quickly to Lutheranism. The Dutch Protestant minority, motivated, concentrated among elite elements, rebelled against their Catholic Habsburg monarch, but rallied under the Protestant House of Orange.
And yet there were other cases where cuius regio, eius religio did not hold. Arguably Henry IV’s conversion to Catholicism illustrates that the monarch was not all powerful…but this case is confounded by the reality that his kingship was conditional on his conversion.
In 1613 John Sigismund of the House of Hohenzollern made public his conversion to Calvinist Reformed Christianity. His Lutheran subjects balked, and did not follow him. Prussia remained a predominantly Lutheran domain with Calvinist rulers for hundreds of years.In 1697 the Wettin House of Saxony converted to Catholicism. While a minority of the subjects of the Hohenzollerns were Reformed Christians, almost no Catholics were present in the domains of the Lutheran Electorate. The overthrow of James II of England in part due to his Catholicism shows that by the latter half the 17th century cuius regio, eius religio did not hold.
The people were self-conscious in having a particular religious identity, and top-down pressure would be met and resisted strenuously.
It is sometimes stated that nationalism and self-identity emerged as late the French Revolution. I do not agree with this. Rather, I agree with Azar Gat’s position in Nations, that nationalism has deep historical and cultural roots. But that does not mean that I believe English self-identity in 1300 is and was the same as English self-identity in 1800. The Gordon Riots of 1780 illustrate how a strident Protestantism had become part and parcel of English national self-identity. In contrast, though there were religious conflicts between the early 16th century (with some rural peasants, especially in the north, retaining loyalty to the Catholic religion) and into the period of the English Civil War, the ultimate outcome seems to have been a matter of mobilizing elites, and up until the overthrow of Charles II retaining the favor of the monarch.
At some point the English monarchy personified the nation. The nation was not simply the extension of the monarch. Anti-German sentiment during the First World War resulted in the switch of their dynastic name from Saxe-Coburg & Gotha to Windsor.
Today in the age of social media we talk about the power of the mob. But it seems like something happened between 1500 and 1750 in much of Western Europe. Nations-states shifted from being syndicates of elite interest groups ad powerful individuals, to becoming expressions of popular will and sentiment. This preceded democracy or liberalism by generations, and it was a gradual process. Mass society and identity emerged. Immovable, with its own will.
And this had happened before historically, from Greek democracies to the Roman republic. Polities were reflections of the public. At some point citizens become subjects, and the populace were simply resources from which to extract rents to fund aristocratic positional contests. The information revolution of the printing press, and economic development more generally, changed the calculus. The past came back.
These sorts of dynamics are universal, cyclical, and playing out to differing extents across the world.
Today we don’t ride horses, so the utility of trousers in that context is gone. It seems that if you work in blue-collar professions and it cold climates trousers are still useful. But is there a reason for men in warm climates in white-collar professions to continue going with trousers as opposed to a simple tunic? Are we just stuck with tradition?
Today on Twitter there was a discussion about why there wasn’t a biography of John Manyard Smith. One reason might be that John Maynard Smith was a pretty nice and congenial fellow. There wasn’t much excitement from what I know.
In contrast, if you read R.A. Fisher: The Life of a Scientist, you get the sense that he was a bit of a dick (the book was written by his daughter). Of course, Fisher was a great scientist, an eminence is both statistics and evolutionary biology. Nevertheless, his irascible personality lends itself to biographical treatment, though rarely hagiographical (a friend is writing a book on Fisher’s life; he too confirms, the guy was a dick).
I say Hamilton was a dope because he was socially awkward, and obviously got himself in trouble through his guilelessness. If he were alive today Hamilton would be in a whole lot of trouble I suspect, except for the fact that he’d be emeritus. Unfortunately, Bill Hamilton died in 2000 due to malaria contracted from field work (or malaria medication).
Yet Hamilton has left us two books where provides autobiographical sketches interleaved between his scientific papers, Narrow Roads of Gene Land: Evolution of Social Behavior, and Narrow Roads of Gene Land: Evolution of Sex (the third volume has biographical sketches from collaborators). In case you are not aware, Hamilton was the originator of the idea of “inclusive fitness.” At the same time, John Maynard Smith was developing “kin selection.” Hamilton distrusted Maynard Smith because of this coincidence, suspecting some sort of scientific fraud (both of them were in communication with George Price at the time).
Narrow Roads of Gene Land: Evolution of Sex was published without revisions to a very long draft of autobiographical sketches because Hamilton had died. It is quite a rambling and sometimes incoherent piece of work because editors couldn’t give any feedback. But it’s fascinating because it’s an unvarnished window into Hamilton’s strange brain.
Of course, the primary reasons to read the three volumes on the scientific papers. I’ve read the famously notationally-inscrutable paper on inclusive fitness published in 1964 many a time. Bill Hamilton had an interesting life and a quirky mind. I’m quite sad that he’s not here anymore.