The beginning of the end of Game of Thrones and the hanging thread of A Song of Ice and Fire


Even if marginally, A Storm of Swords is the highest rated of George R. R. Martin’s books on Amazon. In the judgment of many people, which includes me, it is the best of his books. It was also the highpoint of interest in the series. For various reasons, it was published several months earlier in the UK than in the USA. So I special ordered the UK edition and received it in June of 2000, about 1.5 years after I began reading the series in the last weekend of January 1999.

Since I began writing this blog, in 2002, I have written now and then about my interest in the series, and frustration and patience with the delay in the books being published. The first three books were published in 1996, 1999, and 2000. The fourth book came out in 2005. The fifth, 2011. We’re now eight years along, and Martin is still working on book six.

For the longest time, I had no interest in watching the television show, since the books were far ahead of them, and I planned on watching the HBO series after George R. R. Martin wrapped up A Song of Ice and Fire. I had long assumed that the penultimate book would be published ~2016 so that the gap between the end of the HBO series and the novels would not too drawn out. Obviously, that did play out.

With the show Game of Thrones to conclude this year, there is a bittersweet aspect to those of us who have been reading the books for nearly a generation. There has been something of a “fork” so that many details of the show now differ from the books, and the HBO series, in fact, outrun Martin’s writing so much last year that much of the storyline was somewhat improvised. But the conclusion is said to be broadly the same between the television series and the book. Which means if and when we read the books we’ll know where it ends.

Open Thread, 03/05/2019

Thanks to everyone who has gotten a membership. Still working out a few kinks and trying to enable yearly billing and Papyal (I’m messing up something on the Paypal API). Since someone asked, here is my Patreon for the Brown Pundits podcast.

Speaking of that, I’ll be posting a conversation with an Indian middle-class Dalit soon (already posted for patrons), as well as interviews pending for Thomas Chatterton Williams and Shadi Hamid.

The Insight will have Alicia Martin on this week, and then Lara Cassidy on Irish genetic history, as well as something on historical linguistics by Asya Pereltsvaig. Yeah, we’re preloaded for the next month! Then the current plan is to talk about deep ancient structure in our complex species.

I’ve been thinking about Twitter, comments, papers, books, and blog posts recently. And the audacious argument in Christopher Beckwith’s Warriors of the Cloisters: The Central Asian Origins of Science in the Medieval World. Beckwith renames what we know as the scholastic method as the “recursive argument method.” His contention is that this method developed in the viharas, colleges, of Central Asian Iranian Buddhism before the rise of Islam. With the conversion of these Buddhist peoples to Islam, their intellectual traditions were assimilated into the Islamic one. While the vihara became madrassas, which spread from the Islamic east to the west, the disputation techniques were never fully integrated into Islamic civilization, even though Central Asian Iranians such as Avicenna continued the tradition. Eventually, the tradition did take root in the Latin West, being transmitted by Islamic civilization.

Here is the Wikipedia definition of scholasticism:

Scholasticism is not so much a philosophy or a theology as a method of learning, as it places a strong emphasis on dialectical reasoning to extend knowledge by inference and to resolve contradictions. Scholastic thought is also known for rigorous conceptual analysis and the careful drawing of distinctions. In the classroom and in writing, it often takes the form of explicit disputation; a topic drawn from the tradition is broached in the form of a question, opponents’ responses are given, a counterproposal is argued and opponents’ arguments rebutted. Because of its emphasis on rigorous dialectical method, scholasticism was eventually applied to many other fields of study.

Scholasticism is basically enforced nerdiness. Beckwith argues that modernist humans have abandoned this tradition, and he argues that postmodernism is really just a form of late-stage modernism. While in scholasticism the method and substance of the argument are critical, in postmodernism the individual who is making the argument is arguably even more important.

If a wealthy white male and a poor black woman entered into the argument as to whether “income inequality was bad for society,” we (post)moderns would place a great deal of weight upon who the disputants were, no matter the substance of their arguments.

The recursive argument technique is thorough, exhaustive and requires space. One can see scholasticism playing out in the form of a book-length argument, or in an extended paper. But it is almost impossible to imagine that its well-structured method could be format could be fitted to the comments of an article or blog post, let alone Twitter.

Twitter, in particular, is extremely well suited for a who/whom style of argument. Aside from threading it lacks the ability to structure arguments in a complex manner, and, its 280 character limit enforces a level of brevity at the single tweet scale. Deep substantive disagreements are almost never hashed out on Twitter because the platform does not have the capacity, goodwill or no. Rather, short rhetorical bursts and quips are optimized to lift the spirits of conferences in fellowship, ostracize heretics, and demonize the opposition. The laconic sophist is the ideal user of the platform.

Linkage disequilibrium in subdivided populations. Nei hath spoken.

Statistical Thinking from Scratch: A Primer for Scientists. Coming this summer, something new for your dead-tree collection.

Hierarchical clustering of gene-level association statistics reveals shared and differential genetic architecture among traits in the UK Biobank.

Ant collective behavior is heritable and shaped by selection.

Testing for correlation between traits under directional evolution.

Constraint-based analysis for causal discovery in population-based biobanks.

H.I.V. Is Reported Cured in a Second Patient, a Milestone in the Global AIDS Epidemic.

Theranos: How a broken patent system sustained its decade-long deception.

Interesting how similar his take is to some moderns:

Medicare should stop blocking access to next-generation sequencing for people with hereditary cancer.

PARASITES MEDIATE CONDITION-DEPENDENT SEXUAL SELECTION FOR LOCAL ADAPTATION IN A NATURAL INSECT POPULATION.

Will be reading This View of Life: Completing the Darwinian Revolution soon. Hope to have the author on the podcast at some point.

Very heartened to see the author of This View of Life: Completing the Darwinian Revolution, David Sloan Wilson, rejecting attempts to smear and taint Bret Weinstein with guilt by association. Wilson expressed an old-fashioned liberal sense of fair play and decency which seemed totally out of place in a place like Twitter.

Some of the idiots on Twitter once asked me “I wonder how it makes you feel that Ann Coulter retweeted you” in relation to a tweet that “blew up” (I don’t remember what it was). Now Illan Omar is having her words retweeted by the froggish sect for obvious reasons. How does it make her feel? I assume whatever her feelings are they are sincere and deeply felt, and whatever agreements frogs might have with her is neither here nor there to her. At least she cares about the substance of her beliefs, whether you think they are good or bad, not vague posturing associations.

The cult of feeling and naked emotive reflex reigns supreme today. Reason, for ill or goodwill, is at least bracing in its clarity.

The game is on. Let the disputes begin!

Very ancient ghosts in the African genome

The above figure is from a preprint (updated from last year), Recovering signals of ghost archaic introgression in African populations. But to truly get a sense of this preprint, I would highly recommend you read the supplementary material. And, to be honest, a publication from 2007, The Joint Allele-Frequency Spectrum in Closely Related Species, as the core of the method used in the preprint is developed in that paper.

Here is the abstract:

While introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. Using 405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations that recover about 482 and 502 megabases of archaic sequence, respectively. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day African populations.

To get a sense of how much work went into this preprint, really do read the supplementary material. The step by step analysis convinced me pretty thoroughly that these results are not due to straightforward errors in the genotypes and classifications of the genotypes. Such things do happen, so it was nice to see them be very careful about that.

The key point is that the distribution of the conditional site frequency (CFS) spectrum in West Africans does not align with theoretical expectations. The condition here being the state in the archaic outgroup, generally the Vindijia Neanderthal. The authors ran a bunch of simulations and models and found a subset that could produce the CSF they see, the u-shaped distribution. It is represented by the graph you see at the top-right. Basically, a scenario where a diverged archaic lineage which diverged from the other human lineages before the Neanderthal-Denisovan lineage left Africa contributed to the ancestry of West Africans within the last ~100,000 years (the most likely time is ~50,000 years ago).

This is not a new finding at the highest level of generality. Jeff Wall has been beating this drum for nearly 15 years. For example, Genetic evidence for archaic admixture in Africa.

What has changed is that whole-genome sequencing, including high-quality sequences of ancient hominins, has allowed for a more robust exploration of the topic. The analysis of site frequencies was really not useful 20 years ago without genome-wide data. More data has allowed for more subtle methods.

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The blood on brown hands is a legacy of all of history

Yesterday I put up a tweet which went a bit viral (I won’t embed since it has a vulgarity). It was the result of my frustration with a very liberal Indian American who was using unfortunate tensions in the Indian subcontinent to attack “white supremacy.” My frustration was due to the reality that a major conflict between India and Pakistan would not just impact India and Pakistan, though that is dire enough. In a globalized world, a war involving the world’s fifth largest economy, situated athwart the southern flank of Asia, would impact many people outside of the subcontinent. In the midst of this, the fact that someone was using this to promote their own ideological hobbyhorse was offensive to me.

But the construct of “white supremacy” was presented specifically in the context of a particular history with the British. That is, British policies in the 19th and early 20th centuries laid the seedbeds of conflict between Hindus and Muslims, along with the tortured borders of the partition of the Indian subcontinent in 1947. This is a complicated issue. It is simply manifestly true that the British administered most of the Indian subcontinent from the beginning of the 19th century down to 1947, to various degrees. And, the British were at the center of defining and delineating the borders and divisions which frame the current tensions within the Indian subcontinent.

And yet, the reality is that I believe all these were contingent. That is, imagine an alternative history where the Sepoy Mutiny succeeded in winning independence for several states within the subcontinent, even if the British also retained some of their territories. Presumably, when the British receded, more independent states would emerge. Would the subcontinent be one of amity and low tension, with the much milder historical footprint of the British? In such a timeline the Amritsar Massacre may never have happened (I presume the British would be more likely to retrench to the coastal areas to the east, south, and southwest).

I don’t believe that that is so. Since I am not Pakistani I did not know what the “Two-Nation Theory” (TNT) was before I ran the Brown Pundits weblog. Basically, this is the idea that the Indian subcontinent has within it two religious nations, the Hindu and Muslim. This is not a theological assertion as much as an ethno-sectarian one. The founder of Pakistan, Muhammad Ali Jinnah, was not a devout Muslim. His personal mores were more that of an upper-class Brit (he enjoyed his whiskey). But, his ethnocultural identity was clearly that of an upper-class Muslim. As a lawyer, he defended a man who killed a Hindu who the man believed had blasphemed against Islam. Jinnah’s defense was motivated by his communal loyalty. Even if he himself was not pious, the offense was against the Muslim nation, and he stood with the Muslim nation.

This highlights the fact that the 1947 partition was not driven by the all-powerful British, but also native Indian groups. Though the British, as imperial rulers, implemented the specifics, the underlying demand was from the Muslim League, with the tacit acceptance of many Hindus who were happy to remove a substantial proportion of the subcontinent’s non-Hindu population into another state (some extremely religious fundamentalist Muslims actually opposed partition, since their goal was to convert the whole subcontinent, for which a united India would have been more efficient!).

If you had asked me at a younger age my unconsidered opinion would have been that India should have stayed united to avert the bloodiness of the partition, whose death toll is estimated from the hundreds of thousands to millions. But upon further reflection and thought, I think the TNT captures the essential fact that the Muslim upper-class of Northern India would never be able to reconcile itself well with secondary status within the state, and, with ~25% of the population being Muslim, would always have a huge vote bank so that they could not be ignored. Perhaps a confessional state with a divided balance of power such as Lebanon could have been attempted, but I doubt the Lebanese solution would scale to a polity which covered the whole Indian subcontinent. A more feasible scenario might be a confederation.

The separation of East Pakistan, what became Bangladesh, within a generation of the partition, actually proves to me the point about the Muslim upper-class of Northern India and its general attitude toward power-sharing. Though the Muslim League was quite successful in East Bengal before the partition due to the salience of religious divisions in the region, with the emergence of a Pakistani state the party became the instrument of an elite whose cultural focus was on the northwest of the subcontinent. These were people who saw themselves, quite often genealogically in a valid sense, to be heirs to the Mughal tradition. They dreamed of the time when they had been part of the dominant ruling class (albeit, often subordinate to Turks and Persians).

This was quite separate from the Muslim Bengali identity, which existed more at an equipoise between an Islamic self-consciousness and a Bengali one, which connected them culturally in a deep sense to the Hindu Bengalis who resided across the border in India. The Muslim elite of West Pakistan saw the Bengalis of East Pakistan, even when Muslim as the majority were, to be a culturally and racially inferior group. Culturally inferior because of their embrace of a Bengali high culture which was originally pioneered by Hindus such as Rabindranath Tagore, and racially inferior because they were a smaller and darker-skinned people, who could clearly not make the pretensions toward non-Indian West Asian ancestry common among the post-Mughal Muslim elite.

Now, imagine this same elite having to deal with the Hindu elites of a united India!

What this shows is that the cleavages that exploded into violence in 1947 with the partition were long pregnant within India, before the British ever arrived. The reason I have no patience for the constant indictments of the British is that South Asian elites had their own agency, and their own history, long before the British became the major power in the subcontinent, and retained that agency after. First, one has to remember that the British domination of the subcontinent in a sense we’d recognize it probably dates to the defeat of the Marathas in the Second Anglo-Maratha War of the early 19th century. This puts British rule across much of the subcontinent at 150 years, and even then many of the Princely States administered themselves.

Obviously, India has a history before the British period and that history as preserved and maintained amongst its ruling elements continued down into the British Raj and reemerged after the independence of India and Pakistan. From the period after the emergence of the Delhi Sultanate in ~1200 to the decay of Mughal power in the early 18th century, Turkic conquest elites espousing the faith of Islam were the dominant ruling class of South Asia.

To be sure, not all of them were Turkic. Many were Iranian, Afghan, or Arab, and some were slaves from the Caucasus and Africa. But all of them were swept up in the invasion of the Indian subcontinent driven by Central Asian Turks. This is not exceptional to India, Turkic military elites were often the ruling class of Iran (e.g., the Safavids and Qajars) and many parts of the Arab Near East after 1000 AD. Once in India, the Turks transplanted their Central Asian civilization as best as they could on the very different soil of the subcontinent. A migration of Persians, and even some Arabs such as Ibn Battuta, occurred so as to allow the development of a fully-functioning Islamic civilization co-located within a landscape dominated by diverse Indian traditions that we would today call Hindu (which was at that time was just the generic term for Indian).

Ibn Battuta, in particular, illustrates the fact that within India a whole Muslim world had been transplanted which nevertheless remained not of India, as his own reflections are that of a Muslim moving through Muslim lands, not an Arab in a non-Muslim territory.

The imperialist nature of the conquest dynasties should not be underemphasized. Because of its size and population density, India was attractive to rent-seekers and fortune-hunters. Like the Mongol rule in China, the dominance of a Muslim military elite within India culturally and ideologically distant from the local Brahmin elite opened up an opportunity for West Asians to find favor at court. Ayatollah Khomeini’s paternal grandfather was born in the Indian city of Lucknow. His own ancestors had been invited by the rulers of the region, who were migrants from Nishapur in Iran. Khomeini’s grandfather’s Persian ancestors had left Nishapur and settled in India to receive the patronage and provide service to the rulers who were Shia Muslims of Persian origin such as themselves.

These enclaves of Muslims with recent foreign ancestry have given rise to the ashraf quasi-caste. In White Mughals the author asserts that just as a poor European noble might marry the daughter of a wealthy merchant, so ashraf of pure blood could elevate the lineage of prosperous native stock Indian Muslims.

This digression is to emphasize how the Islamic civilization of South Asia was to some extent a West and Central Asian society intercalated with indigenous elements. The court language of the Mughals, who were in their paternal lineage Timurid arrivistes from Central Asia, was Persian. The camp language was Turki. There were centuries of migration of West and Central Asians into Islamic courts and camps in South Asia that connected India with the Muslim regions to the west and northwest. The non-Indian pretentions of upper-class Muslims from the northwest of the subcontinent are not totally off base. To be sure, the reality is that the vast majority of the ancestry of modern-day South Asian Muslims, even those from the northwest, is indigenous.

Though South Asia remained an overwhelmingly non-Muslim domain, rather early on Islam took on something of the patina of an imperial religion due to the dominance of Muslim military elites. To give an example, in the early 1400s a certain Raja Ganesha, a Hindu, usurped rule in Bengal (which had been under a Turkic dynasty). One concession that mollified Muslim elites toward this usurpation was that he agreed that his son would become a Muslim. And so he did so that Raja Ganesha’s son and grandson ruled Bengal as Muslims. To me, this is reminiscent of the selection of Eugenius as a puppet of the pagan general Arbogast in the West Roman Empire in the late 4th century. Though Eugenius was tolerant toward pagans, he was a Christian. The norm of a Christian ruler of the Roman Empire had already been established by the 390s, even though Christians were only a minority of the population at this time. The Emperor was a Christian ruler of a pagan Empire.

The existence of Islam as an imperial religion resulted in the emergence of an “Islamicate” civilization. Though Rajputs and Pandits remained devout Hindus, they emulated aspects of the elite culture of the Muslims whom they served as vassals or courtiers. Eventually, Muslims of a more native Indian background also came to the fore. Though the powerful ruler of 18th century Mysore, Tipu Sultan, claimed distant West Asian ancestry, the realistic depictions of his features indicate he is clearly an Indian and the descendant of converts to Islam. The Mughal Emperor Akbar exhibits his Turco-Mongol and Persian heritage in his features, while his grandson Shah Jahan looks like the Rajput Indian that three of his four grandparents were. And yet Shah Jahan was a Muslim Mughal prince in culture, and a proud Timurid who wed the daughter of Persian migrants, even if three of his four grandparents were Hindu.

Though any objective analysis shows that the Muslims of South Asia are overwhelming of indigenous ancestry, the cultural and historical imprint of West Asia is indelible upon them, in particular among certain elements of the elite of the northern cities. Their appearance, food, and language, tie them to South Asia. But their religious commitments and romantic attachment to a greater Islamic civilization pull them west.

But of course, there were other people in South Asia. Today we call them Hindus, but that used to be the term for an inhabitant of the Indian subcontinent more generally. Hinduism encompasses a wide range of traditions, from local folk religion to the elite philosophical schools. Perhaps the two things that define Indians, and Hindus, to outsiders are karma and caste. As in Iran the conquest of India did result in some synthesis between the intrusive element, and the native substrate. In the Rise of Islam and the Bengal Frontier the author argues that the rule of the region by Turkic and Afghan Muslims without investment in Sanskrit allowed for the emergence of a native Bengali linguistic tradition. Meanwhile, in Crossing the Threshold: Understanding Religious Identities in South Asia, the author argues that before the assertion of orthodoxy during the Mughal period, many ethno-religious groups in South Asia were liminal to both Islam and Hinduism. The Meo community may be a relic which reflects some of the sub-elite and peasant practices which have vanished.

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The world is more than two categories

A post from Kevin Drum, Once Again, a New Book Debunks Some History I Never Knew In the First Place,* made me wonder a few things. First, Kevin’s confusion:

Am I befuddled by history? Or by historiography? Or do I need a different word altogether?

Until five minutes ago, before I read this book review, it never would have occurred to me that white women were anything less than full partners with men in the white supremacy of the antebellum South. I have never read anything that even remotely suggests such a thing. And yet, apparently this has been a widely held belief—and not just by the masses, but by practicing historians as well.

Additionally, today I listened to the Extremeley Offline podcast where Zaid Jilani moderated a conversation between Liz Bruenig and Jon Chait, and Jilani talks about some of his confusion and discomfort with the racial dichotomies that have recently emerged in the United States (though our politics are very different it seems we have had the same experiences and reactions in relation to this). For example, all nonwhites are now “people of color,” set against whites. The three present a thesis that a dominant form of conceptualization of the world on the modern Left is between the marginalized and those who are not, and so you have dichotomies. People of color vs. whites. Women vs. men. The queer vs. straight. And, of course, the poor vs. the rich.

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The age of prenatal genetic screening is here (let’s call it that!)

In the spring of 2010, I went to the studios of KQED in San Francisco to record an interview with a radio show on the BBC about PGD. Preimplantation genetic diagnosis. I haven’t thought much about the issue in the near ten years since then. Which in a personal sense certainly reflects my luck and circumstance.

But I’m thinking about the issue after reading this story from Emily Mullin, We’re Already Designing Babies: Expanded genetic testing of embryos represents a new era of family planning. But how far should the technology go?:

JJill Pinarowicz’s life has been shaped by a mutation in her mother’s DNA. The genetic error gave her two brothers a rare disease called Wiskott-Aldrich syndrome….

Both of Pinarowicz’s brothers passed away from complications of the disease. One died as a toddler, before she was born, and her other brother died at age 18, when Pinarowicz was a teenager.

Pinarowicz thought it would be too risky to have her own children….

The technique is called preimplantation genetic testing (PGT). By using PGT together with in-vitro fertilization, Pinarowicz and her husband had a healthy son in May 2017.

An incredible “feel-good” outcome so far. And not surprising. I have become more conservative about technology since I first started writing on the internet in the early 2000s, but I will never oppose these sorts of genetic technologies that allow couples whose offspring are at high risk of developing serious debilitating conditions to avoid these scenarios. But the magnitude of how common this now took me aback:

The U.S. Centers for Disease Control and Prevention (CDC) reported in January that PGT was used in 22 percent of IVF cases in 2016, up from just 5 percent in the previous year.

Since the last statistic Mullin could find was from 2016, it’s almost certain that the proportion is greater than 22 percent today. The numbers for 2018 seem difficult to find, but it seems likely that ~75,000 live-births per year in the USA are now due to IVF. Worldwide there are in the range of 10 million humans alive today due to IVF.

How relevant IVF is to fertility varies by social and demographic variables. I know a fair number of people who have done IVF. The average age of a mother at her first birth is 32 in San Francisco and 31 in Manhattan. As many of you probably know many options relating to fertility and genetic testing come “online” for American insurance companies at age 35.

When you transform blue-sky exotic basic science into mass technology they become far less controversial. One of the major themes of Carl Zimmer’s new book, She Has Her Mother’s Laugh, was the vocal and mainstream nature of 20th-century eugenics. A major criticism of Robert Plomin’s Blueprint is that it was resurrecting genetic determinism. Let me quote Mullin:

In Iceland, for instance, the widespread availability of prenatal genetic testing has meant that nearly 100 percent of women choose to abort a fetus with Down syndrome, which has led to a near eradication of babies being born with the condition.

What is in a word? Something in the future is worrisome. Something that professional dual-income-no-kids couples do in their attempt to attain the classic bourgeois lifestyle is not so worthy of comment? Outside of the pro-life movement the discussion of the ubiquity of screening for Down syndrome seems rather muted, even though it is widespread. While we may furrow our brows over decisions made based on polygenic risk scores, the reality is that the age of Mendelian screening is here. It is not speculative science, but applied medicine.

Call it what you want to call it.

Open Thread, 02/24/2019


Probably don’t watch this if you are hungry. It’s on Netflix.

The latest episode of The Insight featured a very long discussion with Jeffrey Rose. If you are curious about the relationship of southern Arabia to the cultures of northeast Africa during the Middle Paleolithic, check it out!

The Freemasons. Not the deepest book. But interesting.

The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data.

Accurate inference of tree topologies from multiple sequence alignments using deep learning.

Human genetic disease is greatly influenced by the underlying fragility of evolutionarily ancient genes.

Unbiased estimation of linkage disequilibrium from unphased data.

China’s CRISPR twins might have had their brains inadvertently enhanced. The title is just plain wrong. Unfortunately the piece “traveled” and now I’m seeing it cited at places like National Review, Eugenics-Engineered Babies’ Brains Changed by CRISPR.

Supreme Court Delivers Unanimous Victory for Asset Forfeiture Challenge.

World’s largest bee, once presumed extinct, filmed alive in the wild.

David Slone Wilson has a book out, This View of Life: Completing the Darwinian Revolution.

‘Austerity, That’s What I Know’: The Making of a U.K. Millennial Socialist.

Ancient whole genome duplications and the evolution of the gene duplication and loss rate.

Recombination and mutational robustness in neutral fitness landscapes.

We Must Defend Free Thought. This is really about Scott Alexander, who is becoming too influential for the tastes of some.

Reihan Salam new President of Manhattan Institute.

Viruses rule over adaptation in conserved human proteins.

Also, if you haven’t, you might check out my RSS, Facebook, or Twitter (or my aggregator page) if something happens to this domain temporarily.

Ancestral proto-Eurasians may have had wavy hair

Australian Aboriginal child photographed in the late 1850s

The above chart is from The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. The basic outlines of this tree were evident as far back as L. L. Cavalli-Sforza. But there were always small details that caused issues. In particular, were East Asians a more natural clade with Australasians or with Europeans? Today with both ancient DNA and whole-genome analyses two things are clear which might have been confounding earlier analyses:

  1. There has been gene flow between many East Asian and European populations. If you look closely at the ancient DNA work it is clear that East Asian gene flow is present in Mesolithic hunter-gatherers. Conversely, many northern Chinese have show low levels of West Eurasian ancestry (I suspect mediated through Mongols and Turks).
  2. The peoples of Australasia have Denisovan ancestry, which is distinct from anything found in East Asians and Europeans (small trace proportions of Denisovan in the former notwithstanding).

With these considerations accounted for, it seems clearer that the peoples of Oceania and East Asia descend from a common group that pushed from the west. And, the most ancient substratum in South Asia is also part of this broad family of peoples, who diversified in the period between 45 to 55 thousand years before the present. This is in contrast to the peoples to the west, who gave rise to Ice Age Europeans, Middle Easterners, and more distantly the “Ancient North Eurasians” who seem to be the first settlers of Siberia.

To understand the context for the emergence of characteristics and traits one has to understand the demographic histories and relationships between people. We are coming close to establishing the latter with good certainty for most groups. Though the sea levels separated New Guinea from Australia only within the last ~10,000 years, genetic work suggests that the differentiation between highland Papuans and Australian Aboriginals long predates this. If I had to hazard a guess I’d suggest that the huge ecological differences were probably critical in reducing gene flow between the wet and warm highlands of Sahul, and the broad deserts that occupied what became Australia.

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“Out of Africa” in 2019

The figure to the left is from Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. It is a graph which captures general features of human population historical relationships as we understand them today. Or at least the model fits the data (remember, many models may fit the data!). The graph is complex…but even within the text of the preprint, the author admits that it is characterized by simplifying assumptions, which nevertheless are informative of some general dynamics and processes (e.g., pulse admixtures).

To some extent, the whole last generation or so has been characterized by the victory of a simplifying assumption that captures general truths about the past, with the accumulation of modifications on the margins as more nuanced results enter the picture. The simplifying assumption I am talking about here is the “out of Africa” 50,000 years ago with a total replacement of all other human lineages framework.

By the last quarter of the 20th century, a combination of archaeological and genetic evidence pointed to the likelihood of a massive bottleneck and expansion of humans outside of Africa in the relatively recent past. In the pre-genomic era, the tools were coarse, from uniparental lineages, classical markers, microsatellites, morphometric analyses, as well as archaeological surveys. But, they strongly pointed to massive expansion and population turnover ~50,000 years ago. This, combined with a line of thinking which suggested that Neanderthals were “evolutionary dead-ends” led to the thesis that there was a total replacement.

To a great extent, this model seems to hold up in the broad sketch. But not to an absolute and total degree. Some paleoanthropologists and geneticists were pointing out for decades that the tools we had could not exclude the possibility of admixture at lower fractions with earlier lineages in Eurasia on purely statistical grounds. These scholars were correct, as it turns out. There is now high confidence that in the range of 1-5% of the ancestry of non-Africans derives from highly diverged “archaic” lineages, Neanderthals and Denisovans. The fraction is low enough that more coarse methods did not definitively pick them up, and without ancient genomes, the “game of inference” was not dispositive in either direction. This, despite the fact that these Eurasian hominins’ ancestors seem to have diverged from those of modern humans ~750,000 years ago. Ultimately, scientists needed a physical ancient genome which they could compare to modern populations to come to this conclusion (before the Denisovan result, scientists had been noticing anomalies in Oceanian data for a decade or so but generally ignored it as beneath comment…a presentation was given an anthropology conference on archaic admixture in Oceania right before the Denisova cave paper).

The second major issue is that the massive expansion and bottleneck that occurred ~50,000 years ago may not explain all of the remaining ancestry that is not “archaic.” That is, there were many modern human lineages present 50,000 years ago. The major lacunae in the current model is a huge one: populations within Sub-Saharan Africa maintained larger population sizes throughout this event. And, anatomically modern humans predate this expansion by hundreds of thousands of years. From an archaeological perspective, a lower limit is 200,000 years ago, and an upper limit probably exceeds 300,000 years ago. Additionally, there are “deep lineages” within Africa which clearly predate the expansion 50,000 years ago. There is a strong consensus that the Khoisan people have at least some substantial ancestry that diverged more than 150,000 years ago from other humans, and tentative suggestions from several different research groups suggest that there are even more “basal” (deep divergence) lineages in parts of West Africa that the component within the Khoisan.

This does not even address the likelihood that some “archaic” ancestry persists within Sub-Saharan Africa just as it does outside of Sub-Saharan Africa.

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