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December 9, 2018

A genetic history of the human race is not controversial science nor is it fraught

Filed under: Elizabeth Warren,Personal genomics — Razib Khan @ 2:06 pm

Recently I was talking to a journalist about genetic genealogy, and we both agreed that soon Christine Kenneally’s The Invisible History of the Human Race: How DNA and History Shape Our Identities and Our Futures will need an update. Though published in 2015, much of the research in The Invisible History of the Human Race dates to much earlier.  In the last few years, personal genomics has gone from a sector of millions to tens of millions. In years after 2020 it will go to hundreds of millions.

And yet I’m not sure the educated public is ready to understand what a genomic future is going to look like.

This is why I think that the Elizabeth Warren DNA story is important to get right. The reality is that this isn’t really about Elizabeth Warren’s ancestry, it’s a story at the intersection of high politics and culture wars, and genetics is getting caught in the undertow. Recently I heard Ben Shapiro comment that Warren likely had “maybe 1/1024th Native American.” Actually, I think it’s very likely she has 0.5 to 1% Native American ancestry (read this Elizabeth Warren DNA story“>post why) Not to be trite, but facts don’t care about Ben Shapiro’s feelings. I know he’s not a fan of Warren, but he shouldn’t be laundering misrepresentations.

Even in the comments of this website motivated reasoning cropped up when the original Warren story became a national sensation. Many on the Right side of the spectrum laughed at the results and interpreted them in the least generous terms. The falsehoods and misunderstandings promoted by the media, often inadvertently because most journalists don’t have the skills to navigate the science, were injected into the conservative memesphere.  Shapiro has admitted, to his own chagrin, his lack of science background, and I suspect if I explained it to him he wouldn’t use “maybe 1/1024th Native American” line. He doesn’t need to. If you are a conservative there are many reasons to be critical of Elizabeth Warren.

But I can’t blame Shapiro too much. He was reacting to this story in The New York Times, Elizabeth Warren Stands by DNA Test. But Around Her, Worries Abound. In this piece, the attacks on Warren are coming from the Left and Native American activists. There is a real story here. The Boston Globe has published an editorial warning her not to run. The air has changed around her.

From the piece in The Times:

Warren’s presidential ambitions, she has yet to allay criticism from grass-roots progressive groups, liberal political operatives and other potential 2020 allies who complain that she put too much emphasis on the controversial field of racial science — and, in doing so, played into Mr. Trump’s hands.

Ms. Warren’s allies also say she unintentionally made a bigger mistake in treading too far into the fraught area of racial science — a field that has, at times, been used to justify the subjugation of racial minorities and Native Americans.

There is “racial science” like there is “evolution science” or “Creation science.” The term is not used by any scientist that I know of, but comes up by critics and polemicists. The New York Times, whether consciously or not, is going to convince a lot of scientifically illiterate people who don’t read their science pages that there is a field of “racial science” (using the term “race science” liberally is a thing on the Left…reminds me of social conservatives who used to call everyone who was not an evangelical Protestant a “non-Christian”)

Here’s what went on in the Warren case is:

  1. Not scientifically controversial
  2. But scientifically new

Here is a review, A comprehensive survey of models for dissecting local ancestry deconvolution in human genome which looks at “20 methods or tools to deconvolve local ancestry.” There may be disagreement on the best method for various reasons, but there is no disagreement that local ancestry deconvolution is possible. It is not controversial. In fact, it is rather important in areas such as admixture mapping for diseases.

The science isn’t that hard to explain at a high level. The figure to the left is from a new paper that recently came on the genetics of the New World (using ancient DNA). What you see is that some human populations are isolated from other human populations. For example, the last common substantial ancestry of Native American populations before 1492 and Northern Europeans dates to the period between 20,000 to 40,000 years ago.

Tens of thousands of years of genetic separation result in genetic distinctiveness. This is a standard old population genetic model. When populations come back together and mix, that daughter population is clearly going to be genetically a mix between the two parent populations. But the human genome is a sequence of three billion distinct base pairs, and the mixing exhibits discrete patterns within the genome.

Humans are diploid, which means we have two copies of each gene. These genes are aligned along homologous chromosomes. One homolog you inherit from the father and one homolog you inherit from the mother. These two homologs are the basis for Mendel’s Law of Segregation.

When sex cells, sperm and eggs, are formed they carry only one of the homologs. They are haploid, with single gene copies. If they weren’t, you’d end up tetraploid instead of diploid. You get one gene copy from the mother and one gene copy from the father.

But, before the formation of sex cells, during meoisis, the homologs undergo recombination. In humans that means that there is swapping between stretches of homologous chromosomes. The average human has between 20 and 40 recombination events across the genome. A concrete way to think about it is that the individual who is producing sperm or egg is taking the chromosomes they inherited from their parents, and mixing them together, so the final set of chromosomes are a synthetic combination of the chromosomes of grandparents.

Purple segments half-identical to paternal grandfather

To make this concrete, to the left is a partial depiction of one of my children’s chromosomes, and the relatedness to my father. The purple regions are genomic stretches where the child is half-identical to the paternal grandfather. The light gray sections have no genetic descent from my father. The reason is that one of the homologs is from the maternal side. The other homolog is from me, and could be from either my father or my mother. Where the purple alternates with light gray, you see clearly where recombination events happened, as maternal and paternal homologs broke and paired together to produce sperm with novel chromosomes (e.g., my contributed chromosome 11 is 90% my father, 10% my mother…while chromosome 19 is more balanced.

But that’s not the only way to look at recombinations. To the right is an ancestry painting for 23andMe from a friend of mine who is ~25% East Asian and ~75% Northern European. On their chromosome you see two homologs. The blue segments are Northern European. The dark brown segments are East Asian. Notice the alternation between European and East Asian on one of the homologs: this chromosome is almost certainly from the parent who is 50% East Asian and 50% European. There was a recombination event where an “East Asian” homolog, inherited from the parent of East Asian origin, recombined with the “European” homolog, inherited from the parent of European origin.

The resultant chromosome is something new in a physical sequence, with alternating segments of East Asian and European ancestry. Just as the whole genome has an imprint of the genetic history of a population, so sequences of the genome also exhibit distinctiveness due to their origins. Because each generation introduces recombination events, the lengths of these distinct ancestry blocks can tell you how many generations in the past the admixture may have happened.

That’s the theory. The new aspect is that genomic technology have allowed science to assess patterns of local ancestry to a much greater extent than was possible even 15 years ago. With hundreds of thousands of genomic positions, variants, scientists are now able to map regions of the genome to an incredible level of granularity, deploying theoretical understanding of Mendelian and population genetics that dates back to the 20th century.

To look at Elizabeth Warren’s genome, and discover that a small segment of a particular length derives from a Native American population, is not a “controversial field of racial science.” This sort of analysis is now becoming de rigueur in much of medical genetics in larger part because population history has a major impact on disease risk susceptibility. To be fair, doing a local ancestry deconvolution on populations which are much, much, closer genetically due to recent shared history is difficult. But Warren’s is not one of those cases!

Honestly, I don’t know what the outcome of The New York Times calling this “racial science” is going to be, seeing as how it seems likely in the next few years >100 million Americans will have likely done ancestry tests. Many scientists, fairly, do criticize of the interpretations of these tests, and how the public perceives them. But the underlying models and methods are workaday.

It is the interpretation, and how they interact with social and political values, is fraught. The link in the phrase “controversial field of racial scienceactually goes to an article where social and political commentators and activists react to Warren’s decision to take the DNA test. There is no discussion of the science at all. It’s controversial because of what they believe the implications are, not because the science is faulty or unsound.

For example, many (though not all) Native Americans object to the idea of using genetic science to shed light on the status of particular individuals as Native American or not. The decision to take this DNA test, in an environment where many already privately grumbled about Warren’s claims, was obviously clearly a political and public relations misstep. But that does not speak to whether the science itself is sound or unsound.

Conservatives will be highly skeptical of Warren because of her policy positions. And, if the above article is correct, it seems that some of the Left is now against her on the grounds of her impolitic foray into Native American identity. That is all fine, and not much of a concern of mine. But when non-science journalists get their hands on a science story, they tend to mess it up, and that is a problem in the long-term. The sands of politics and society are protean, and always shifting. Science is something more solid, and we should not try to muddy the waters.

December 6, 2018

Of Plagues and Prehistory

Filed under: Disease,Plague,The Fate of Rome — Razib Khan @ 11:02 pm

The Fate of Rome: Climate, Disease, and the End of an Empire is an excellent book. I highly recommend it! But one of its assertions, which I accepted at face value at the time I read it, now seems to be less certain (likely wrong). The author contends that the network of trade and interaction facilitated by the emergence of the Pax Romana was instrumental in the rise of periodic pandemics. There was the Antonine Plague, the Plague of Cyprian, and the Plague of Justinian. In contrast, Neolithic Europe, and earlier civilizations may have been subject to endemic diseases. But not pandemics.

A new paper in Cell seems to falsify this view. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline:

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

The plot to the right shows that Yersinia pestis in Swedish Neolithic farmers, who are genetically similar to modern Sardinians, is basal to the Yersinia pestis in Bronze Age steppe pastoralists, which is basal to later outbreak strains. The point here is that Yersinia pestis seems to a dynamic part of the broader Eurasian pathogenic landscape. The Plague of Justinian was not something new, but the latest manifestation of a reoccurring phenomena. The conditions for its flourishing existed before the rise of Rome.

What was probably different in the case of the Roman Empire was a matter of frequency and rapidity. As the paper, and David of the Eurogenes blog note, there was a massive demographic and social regression in late Neolithic Europe. It is hard to disentangle the variables though because they are all connected. When you read the impact that plague had in the New World on native societies, one of the key elements is that societies on the Malthusian margin often collapse when mortalities go above expectation. Crops go unharvested, and people have to tie up their labor in taking care of the ill. This leads to malnutrition and further susceptibility to the plague.

Or, you can imagine a system where a warm and rainy climatic regime increases primary productivity (e.g., medieval climatic optimum), which leads to greater population density and therefore specialization and economic activity and trade. Then, you might be subject to a climatic shift, in which case productivity drops, and famine ensues. This famine results in increased susceptibility to disease, and plague spreads through the preexistent trade networks established during times of plenty.

The decline is partially endogenous to the system of human societies. External climatic shocks are going to happen now and then. But there are internal dynamics, such as population density, which are going to impact how resilient a society is to an external shock.

It seems likely that the first dense agglomerations of humans were likely going to run up against the limits scale no matter what. Disease serves as a natural Malthusian check, and it was likely inevitable due to the vicissitudes of the circumstances that there would be spikes in mortality so that the population was reduced back to its carrying capacity.

This is a general point. Early societies were subject to random shocks, and those shocks knocked them down a peg for quite some time. But eventually social systems became less fragile, and total collapse and cultural amnesia was generally avoided. The socio-economic complexity of the Roman Empire declined precipitously in the 5th century, with the post-Roman world having to slowly wind itself back up during the “High Middle Ages” (in Western Europe at least). But the ideological superstructure of the Roman world, Christianity and such, maintained an intellectual and cultural continuity, so that Roman institutions and forms could be resurrected when social and economic complexity necessitated it (e.g., Roman civil law). The post-Roman Europeans were primitive in many ways compared to Rome, but their society had not be totally obliterated, so they did not have to reinvent the wheel, so to speak.

More specifically in this instance, it seems that the arrival of the Eurasian agro-pastoralists in the third millennium BC into Northern Europe was not due to their inadvertent biological weaponry. The diseases they brought. The Neolithic societies descended from those who introduced farming were already in collapse, and likely very vulnerable to the predations of agro-pastoralists. This is almost certainly a common event in prehistory, which we will become much more aware of in the near future due to science. For example, I predict pestilence will be associated with the end of the Uruk Period in the Near East.

December 5, 2018

Criticizing Islam is turned into “hate speech” on Facebook

Filed under: Islam,Religion — David Hume @ 11:49 pm

Obviously, this isn’t happening to everyone who criticizes Islam. But someone like Abdullah Sameer is getting popular, and he’s a pretty attractive face for apostasy from Islam. He was until recently a rather conservative Muslim himself. He’s the person you need to shut up if you want to retain Muslims.

As he notes manipulating Facebook isn’t that hard for motivated individuals. And the platform has billions of people on it. Hundreds of millions at least are Muslim. For Muslims traditionally apostasy has been a serious crime, analogous to treason. Which is why the customary punishment (albeit often not enforced) is death.

Sameer speaking in a way that makes it obvious he’s not crazy is really the problem from this perspective. So they shut him down by any means necessary. From a Muslim perspective, he’s dragging people down to hell. And Facebook isn’t the public square, they’re a massive corporation that needs to make governments and diverse cultures happy. Though obviously, Facebook doesn’t necessarily support blasphemy laws, it’s probably not a high priority to clamp down on this sort of coordinated behavior. After all, who is going to complain?

People who are passionate ex-Muslims are a small and marginal group. Muslims are a huge group. As for progressives, it’s much more important to throw a shit-fit over something Richard Dawkins says (without any knowledge of what the call to prayer is actually saying), than put the spotlight on this sort of illiberal behavior and the culture from which it emerges. Such are the wages of “allyship.”

The Insight Show Notes — Season 2, Episode 10: the genetics of Game of Thrones

Filed under: Game of Thrones,Genetics — Razib Khan @ 12:11 pm

The Insight Show Notes — Season 2, Episode 10: the genetics of Game of Thrones

This week on The Insight (Apple Podcasts and Stitcher) we discuss the genetics and history of the world of Game of Thrones, from the mountains to the olive grove, the First Men, Andals, and Rhoynar.

We mention the various peoples of the world of Game of Thrones:

There was extensive discussion of the geography of the world of Game of Thrones. In particular the two major continents:

Westeros and western Essos:

There was extensive discussion about the noble Houses in the quasi-medieval world of Game of Thrones. In particular, the genetics and pedigree of the Targaryen ruling House, that of Daenerys. The Targaryens are phenotypically and genetically unique. They have the ability to tame dragons, are resistant to plague, and also seem to suffer fewer ill effects from inbreeding.

Pedigree of Daenerys and John

Like the ancient Valyrians the Targaryens practice incestuous marriage within the family, most notably but not exclusively between siblings. This increases their inbreeding coefficient. The offspring of the mating of siblings has an inbreeding coefficient of 25%, which means that there is a 25% probability that two alleles at a particular genetic position come from the same ancestor. Daenerys Targaryen has an inbreeding coefficient of 37.5% because she is the product of two generations of sibling marriage.

One the issues that emerge out of Targaryen inbreeding is that Daenerys and Jon are more closely related than their simple relationship would imply. Jon’s father was Daenerys’ brother. But since they are products of two generations of sibling mating, they are nearly 90% genetically identical! That means that Jon Snow and Daenerys Targaryen are nearly siblings genetically (about 45% related, as Jon’s mother was unrelated to Daenerys).

Finally, have you ever wondered how it is that the Valyrian characteristics that the Targaryans have are passed down through the generations? It turns out that Daenerys’ and her siblings are only around 12.5% Valyrian in ancestry at most. How is it that the physical features of the Valyrians, as well as dragon taming, are passed down across all these generations?

The answer that presents itself is meiotic drive.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

The Insight Show Notes — Season 2, Episode 10: the genetics of Game of Thrones was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

December 4, 2018

How paternity testing is like international trade

Filed under: Cuckoldry,Human Population Genetics,paternity — Razib Khan @ 9:44 pm
Nonpaternity rate % N
Switzerland 0.83 1607
USA, Michigan, white 1.49 1417
USA, California, white 2.1 6960
USA, Hawaii 2.3 2839
UK, West London 3.7 2596
Paternity Testing Laboratories
UK 16.6 1702
USA, Los Angeles, white 24.9 1393
Sweden 38.7 5018
South Africa, Cape Coloured 40 1156

The results above are from Kermyt Anderson’s How Well Does Paternity Confidence Match Actual Paternity? This is still one of the best surveys of the field, despite being 12 years ago. A more recent paper, Cuckolded Fathers Rare in Human Populations, uses more powerful genetic genealogy methods to come to the same conclusion as Anderson’s survey: extrapair paternity, or nonpaternity events, are rare in Western societies. I don’t think it is limited to Western societies. I suspect that when high throughput sequencing is applied to Chinese clan lineages and Hindu gotras, you will found that nonpaternity events are similar to those in the West.*

On the other hand, in some small-scale societies, the rates are much higher.

I won’t delve into the evolutionary anthropology here. Rather, I want to point to a new paper, Growth of ancestry DNA testing risks huge increase in paternity issues. Ancestry testing is huge. Within the next year, it is almost certain that 10% of the American population when having some sort of high-density genomic testing done.

As the author of the paper pointed out to me on Twitter, 1% of 16 million people is still a lot. Yes, in absolute terms. But we need to look at the other side of the equation.

In Anderson’s original data one of the interesting results is that in most datasets drawn from paternity testing laboratories, where there is a very high suspicion of nonpaternity events, most of the fathers nevertheless were biological fathers! In a nonpaternity testing context, nonpaternity events will be much closer to ~1%. But, I think it is reasonable to suppose that some of the 99% of the fathers who turn out to be biological fathers also have suspicions…which are unfounded.

Like free trade, you tend to see one side of the equation much more than the other. In free trade scenarios, a minority of workers may lose their jobs or have to work under reduced wages, but the vast majority of consumers will get cheaper or better products. The former is much more salient than the latter.

Similarly, the small minority of fathers and families who are going to be “surprised” in a negative way, is balanced out by the likely larger number who have low-grade suspicions, but in fact, are confirmed in their biological relatedness.

Addendum: Needless to say, if you are part of the “cuckold community”, you should probably not getting this sort of testing.

* The necessity of good quality whole-genome sequencing is due to the fact that male relatives are excellent candidates for nonpaternity events. To get a certain estimate one would want to count unique mutations across the pedigree.

Game of Thrones, a journey of three peoples

Filed under: Cultural Anthropology,Fantasy,Game of Thrones — Razib Khan @ 12:00 pm
Westeros and western Essos

The HBO television series, Games of Thrones, has captured the imagination of modern American culture. It has been used as a metaphor and example for many things, from national politics to international relations, and of course a reimagining of the medieval period in a grittier and more realistic fashion.

Characters from Game of Thrones have even inspired baby-names!

The television series is rich, complex, and multifaceted, but it draws from the novels of George R. R. Martin, a cycle which is called A Song of Ice and Fire. These works are much more deeply textured in their lore and backstory. Martin’s world-building has taken on a life of his own, with several books published related to the geographies, peoples, and histories, which serve as the backdrop for the plot and character.

One of the peculiar aspects of what we know about the historical background of the world that Martin has imagined, with its continents of Westeros, Essos, and Sothoryos, is at once very precise, and somewhat inaccurate. In the novels and accompanying books which elaborate on the ‘world-building’, the voice of the explanatory narrators are the ‘maesters’, a scholarly priesthood in Westeros.

Maesters give the reader a sense of what informed people in Westeros believe to have been their past, or the nature of distant lands, but they do not speak in an omniscient voice. That is, they may, in fact, be inaccurate their beliefs, though it seems likely that their interpretations usually contain a grain of truth. Martin has explicitly stated that one should not take assertions that the something happened “10,000 years ago” literally. Rather, if you are told that something happened 10,000 years ago, perhaps it is best to just understand it happened long, long, ago.

The history of Westeros in terms of its demographic past seems straightforward. The first humans who crossed over from the eastern continent, Essos, were the First Men. They rode on horses and used bronze weapons. House Royce of the Vale of Arryn have a family heirloom of bronze armor, that reputedly dates to this period.

When the First Men arrived in Westeros, the lands were empty of humans, but there were various other peoples, such as the diminutive Children of the Forest, who seem to have been hunter-gatherers. The conflict between the First Men and the Children of the Forest ended in a stalemate and a truce. The First Men brought their own gods, some of which may persist in the Iron Islands, but eventually, they adopted the religion of the Children of the Forest, which focused on nameless gods whose powers were located within groves with forbidding trees, the weirdwoods.

To a great extent, many of the things we know about the First Men are legends and folk memories. Though the First Men utilized simple runic scripts, the art of copious writing and recording was to come later, with the second great migration to Westeros, that the of the Andals

Where the First Men arrived in the mists of prehistory, the Andals came to prominence on the edge of the imaginary history of A Song of Ice and Fire. The Andal migration seems to have been triggered by the rise of the Vaylrian Freehold, whose emergence resulted in the crushing of the ancient empires to the east, west, and north. In the hinterlands of northwest Essos, around the “Hills of Andalos”, the Andal tribes came together. United by a belief in a monistic pantheon of gods, the Faith of the Seven. Each of the gods of the Andals was actually a manifestation of an underlying divinity.

The Andals escaped the expanding reach of the Valyrian Freehold by migrating west, across the Narrow Sea.

While the First Men are reputed to have crossed a land bridge that connected Dorne, the southeastern realm of Westeros, to Essos, the Andals landed in the Kingdom of Mountain and Vale. They brought their language, the ancestor of modern Westerosi, their religion, which became dominant in the far more populous southern half of the continent, as well as institutions such as knighthood.

The dominance of Andal culture is such that when people from Westeros travel to Essos they are often termed “Andals,” even if they are from the North, and so First Men in identity. And yet the Andals did not replace the lineages of the First Men. This is easiest to see for the elite houses.

In the North, the First Men remained preeminent. A region geographically protected from Andal invasions, the First Men in this vast lightly populated domain did not fuse with the Andals, for they turned them back. While the North eventually adopted the language of the Andals, they retained their own indigenous religion, the “old gods,” in contrast to the “new gods” of the Andals, the Faith of the Seven.

But in the South, a new aristocracy arose, Andal in religion and language, but often First Men in lineage. Some powerful families in the South, such as the Blackwoods and Royce claim First Men heritage. But, more importantly, when Aegon I Targaryen began to conquer Westeros 300 years before the events in Game of Thrones, only one of the Seven Kingdoms was ruled by an exclusively Andal ruling dynasty, the Kings of Mountain and Vale. The Storm Kings, the Gardener Kings of the Reach, the Lannisters of the Kingdom of the Rock, the Starks of the North, and the ruler of the Riverlands and Iron Islands, could all trace their ancestry to the First Men (though the Lannisters only through the maternal line).

If such prominent families were of at least partial First Men stock, it is reasonable that the Andal impact was significant culturally, but most of the common population retains ancestry from the original Bronze Age migration. Though there are subtle distinctive physical characteristics of Houses such as the Starks, it does not seem that there is anything particular to Andals or First Men by the time that Game of Thrones is occurring.

The final kingdom that is not listed above is the Principality of Dorne. And this hot southern domain is home to the last major group to arrive in Westeros: the Rhoynar. The full title of the individual who sits on the Iron Throne is the King or Queen of the Andals, the Rhoynar, and the First Men.

Long after the Andals arrived and settled in Westeros, the Rhoynar too fled the expanding might of the Valyrian Freehold. A vast armada led by their princess, Nymeria, sailed westward until they reached the shores of Dorne. There the Rhoyne mixed with the local Andal and First Men populations and produced a fused culture with its own distinctive elements. While the Andals and First Men are fair-skinned people, the Rhoyne, who migrated out of the warm lands of southwest Essos, are darker in complexion. But the Dornish exhibit a range, from sandy and salty Dornish people who live in the deserts and coasts, who have more Rhoynish blood and culture, to the stony Dornish of the mountains, who are more akin to the Andals and First Men.

Though there are other peoples who have inflected the cultural landscape of Westeros, the First Men, Andals, and the Rhoynar, together contribute to the vast majority of threads that create the tapestry of Westeros. The First Men cleared the ancient forest and brought settled life to the land. Most of the ancestors of the people of Westeros were these Bronze Age tribes. Their adopted religion persists in the North, and in parts of the South, but the language that they spoke has mostly disappeared, only found north of the Wall, and perhaps among the barbarian tribes of the Mountains of the Moon.

History and iron came to Westeros with the Andals, warlike followers of a new religion who were fleeing an ancient enemy. Andal warlords fused with the ruling class of the First Men, and brought their institutions and language, and made them dominant across the land. Though only a minority of the ancestry of the people of Westeros derives from the Hills of Andalos, in the main the language they speak and the gods they worship are those of the Andals.

Finally, there are the Rhoynar. Unlike the First Men and the Andals, their influence is not suffused through Westeros but preoccupies a particular corner. They stand as a contrast and rebuke to the cold and harsh First Men of the North and the stuffy Andals of the South. Dorne is a hybrid land of its own, exotic and yet of Westeros. The Dornish bring together the three distinct human strands of Westeros into one, and out of it comes a rich and unique melange which adds a spice to A Song of Ice and Fire.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

Game of Thrones, a journey of three peoples was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

December 3, 2018

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:45 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

Notes the emergence of “Indic civilization”

Filed under: History — Razib Khan @ 12:04 am

Note: This post is a supplement to the podcast below.

People get hung up on particular words a lot. This post is to clarify some terminology from my own perspective. It needs to make clear here that I am a semantic instrumentalist. Words don’t have power or meaning in and of themselves but point to particular concepts and patterns. If we disagree on words while agreeing on the concepts and patterns, the disagreement is semantic.

To give an illustration about the “power of words,” I have read works on “Western history” which begin the narrative in Egypt and Sumeria. As the centuries proceed, the focus moves north and west, and eventually, the Near East is excluded from the West. Clearly, most people can agree that the Near East is, and became, very distinct from what we term “the West,” but if our history is to deal with Northwestern Europe, it will start with the Roman period, and its roots clearly owe something to the earlier Near East. The reality is that the West that the histories outline developed much later (arguably after the fall of the Western Roman Empire), but its roots are diverse and broad, inclusive of Near East antiquity.

When I use the world “Indic,” please keep in mind that I am focused in particular on the civilization which had crystallized by the Gupta period across South Asia. The civilization which gave rise to concepts which form the basis of the Dharmic family of religions. Moving forward, and moving backward, this is the reference cluster of characteristics.

In the podcast below I made the assertion that the precursors to Indian, Indic, civilization from the north to the south are rooted in prehistory. That the adoption of a set of religious ideas and identities promoted by Brahmins across much of South India several thousand years ago was not a coincidence, because South India was connected in some deep ways to North India in the prehistory period after the fall of the Indus Valley Civilization (IVC) 4,000 years ago.

Shortly I will have a book review in India Today on a work by Tony Joseph which tries to synthesize archaeology, linguistics, mythology, and genetics. Though I knew many of the details in the book, Joseph brings the strands together which clarified and solidified some general intuitions I have developed.

First, I do think that the most likely point when the Indo-Aryan eruption into South Asia occurred is around 1500 BC. Earlier I had been very vague about the timing because there had not been any ancient DNA. But the presence of people with a “steppe” genetic profile, which is ubiquitous in much of Northern India today, seems to date to the period after 2000 BC. Additionally, 1500 BC is when Indo-Aryan rulers (albeit, culturally assimilated) seem to become dominant in the Upper Euphrates are of Syria.

One can push the date a few centuries earlier (there is a possible Indo-Aryan text in Syria dated to 1750 BC), but not too much earlier. And, Joseph claims that the dominant metal in the earliest Vedas was copper, not iron. Since the Iron Age in India starts around 1200 BC that definitely puts a lower limit on when the Aryans arrived (though the earliest genetic samples in the Swat Valley with “steppe” ancestry shows up around 1200 BC, so we already knew this).

So we can put the ethnogenesis of the Indo-Aryan Indic component in Northwest India in the centuries around 1500 BC.

But they did not come into an empty subcontinent. The Harappan society, the IVC began to go into decline around 1900 BC. There are various debates as the regional continuity of this civilization down to 1300 BC, and as to why it declined. Though more archaeology needs to be done, here is my own personal position as of now:

– The IVC was likely fragile and in decline before the arrival of large numbers of agro-pastoralists

– A good model for the arrival and cultural domination of the Indo-Aryans may be the situation of post-Roman Britan or the post-Roman Balkans, where large numbers of barbarians arrived and assimilated peasant cultures whose elites had disappeared

– In the Near East the Indo-Aryans, and later the Iranians, show no overwhelming ideological reason to destroy civilizations that were existent prior to their arrival. On the contrary, agro-pastoralist elites aim often to take over elite positions in those societies so that they can extract rents and become wealthy. The problem is that sometimes the arrival of these people destabilize weak or declining societies, and the social order rearranges and regresses.

We don’t know the details of how the IVC was organized, but its relative uniformity of architectural design and layout indicate large-scale elite coordination of some sort. The societies and subsequent to the IVC seem simpler and less indicative of large-scale coordination. This sort of “unwinding” was common to earlier societies.

But we also need to move beyond the focus on the Indus Basin the Doab.

The Neolithic, indicative of a transition from hunting and gathering to pastoralism and farming, began in South India after ~2500-3000 BC (depending on the source). While the IVC was flourishing, a zone of agro-pastoralists seems to have pushed south along the western edge of the Deccan. Joseph (and others) reports that placenames of Dravidian origin seem to be common in both Maharashtra and Gujarat. Curiously, he notes that Dravidian placenames do not seem to exist in Bihar or Bengal.

Recent phylogenetic work on the extant Dravidian languages indicates diversification beginning 4,500 years ago. This is 2500 BC. A possible beginning date for the South Indian Neolithic.

When the IVC was a mature civilization it seems that some farmers pushed the frontier further. While the IVC was unwinding in the northwest of the Indian subcontinent, I believe that their “country cousins” in South India continued with their small-scale society.

The “Ancestral South Indians” (ASI) have now been shown by the Reich group to be about ~25% “West Eurasian” in ancestry. This is almost all “Iranian Farmer.” That is, the ancestry derived from western Iran before there was much mixing between Iranian farmers and Anatolian farmers (which occurred before the rise of civilization). Today there are tribal and low-caste groups in South India whose ancestry is nearly all ASI.

I believe that this ASI population formed during the South Indian Neolithic when ash mounds were common through the fusion of people out of the IVC with indigenous people, Ancient Ancestral North Indians (AASI).

But South India is not all ASI. There is in fact caste genetic stratification between Dalits and Adivasis on the one hand, and local non-Brahmin peasant and elite groups (e.g., Reddy). The latter has more “Ancestral North Indian” (ANI), specifically, Iranian farmer.

I believe this is a function of the second wave of continuous migration out of northwest India, likely via the lower Sindh and Gujarat. These people assimilate and conquered the earlier agro-pastoralists and likely absorbed the remaining hunter-gatherers. The relatively deprived position of the original  ASI populations is indicative to me of their long-term marginalization by the new arrivals.

But these people were not simply “Dravidian traditionalists” who were fleeing their homelands. A quick survey of Y haplogroups shows that R1a, associated with the Northwest, and upper-castes, is found through India. Though in far lower frequencies, it is found among Dravidian peoples, even Dalits, and Adivasis in the South.

To me, this is suggestive that the Dravidian-speaking populations that moved south along the western coast of India were, in fact, a synthetic people who were expanding out of a hybrid cultural zone. Some of the populations, tribes, in this hybrid zone, were Indo-Aryan. Likely the dominant element was. But some of them retained their Dravidian language, though they assimilated some Indo-Aryan groups in their mix. The linguistic diversity may have been greater than this, as indicated by the presence of Burusho, a linguistic isolate.

The later expansion of polities such as that of the Maurya to the south on the edge of history then is not an expansion into alien territory, but a conquest of a related set of peoples, distinct, but nevertheless connected.

Obviously, the push east out of the Doab, and down the Ganges, would have resulted in an encounter with Munda people. The people who were moving eastward were Indo-Aryans, who had possibly assimilated Dravidian peoples in the region of Harappa (most of the ancestry even of Brahmins from the Gangetic plain remains non-Indo-Aryan, as is the case for the Kalash of Pakistan). The Munda seem to have arrived after 2000 BC, and admixed with another AASI population. This suggests that Northeast South Asia was not touched by the movement of Dravidian peoples that affected the Deccan. Additionally, the extant Munda tribes lack Indo-Aryan ancestry.

The final point I’d like to make then is that the prehistoric roots of what we term perceive to mature into Indic civilization by the period of the Gupta as its Classical form has its roots in the synthesis between 2000 BC and 1000 BC. First, as the IVC as a civilization defined by widespread coordination and uniformity unwound, and Indo-Aryans enter into the matrix as a hegemonic agro-pastoralist group who introduced a way of life accessible to many local non-Aryan elites, who were assimilated into their culture. Meanwhile, other groups remained Dravidian speaking, while assimilating into themselves some groups of Indo-Aryans, and following a southward trajectory that had been pathbroken by cultural relatives centuries earlier during the IVC.

December 2, 2018

Open Thread, 10/2/2018

Filed under: Open Thread — Razib Khan @ 2:44 pm

I’m reading Ramesh Menon’s The Mahabharata: A Modern Reading before I go to sleep. If you are ignorant, the Mahabharata is about an epic poem that’s an order of magnitude longer than the Iliad or The Odyssey combined. Menon’s prose rendering seems to get some good marks, so I that’s not why I chose it. It’s not the most artful writing, but that’s not what I was looking for, nor would I appreciate it in any case.

My rationale for reading this two-fold. First, as someone who was raised on Bulfinch’s Mythology and has read Genesis in dozens of translations, I thought it was behoove me to become a bit more culturally fluent about brown stuff. Especially in light of the fact that I’m “tagged” on a “Hindu Twitter” thread every few weeks now (12+ hard science disciplines apparently prove the Mahabharata happened 25,000 years ago!).

Second, the age of Indian historical population genetics is coming to an end. Perhaps ten years from now people will be doing temporal transects of eastern Maharashtra, but the bigger framework will be nailed down soon enough. And real intellectual understanding is going to have to synthesize archaeology and mythology with the demographic inferences.

The Urbane Cowboys podcast now has had three Bengali American conservatives on. #representation You should subscribe (I might be on again to talk about CRISPR soon).

Browncast #3. I talk about Indian genetics.

Does DNA Make Us Who We Are? Review of Blueprint: How DNA Makes Us Who We Are. A reader of this weblog shouldn’t find anything new in this book. There are some technical issues in this book you might pick up, as well as airbrushing out of Eric Turkheimer citation. But I left that stuff out of the review since regular people won’t care or understand.

Plomin is definitely an enthusiast on some counts. But most of the book covers his career and views on behavior genetics.

Why There Will Not Be a Beige Future: Skin Color, Genetics, Race and Racism. Written for an audience less familiar with genetics. You shouldn’t need to read this. But some of you still don’t know what the breeder’s equation is.

The New Evolution Deniers. I haven’t read this piece, but people keep asking me about it. Plenty of biologists have these sorts of views from what I can tell, but they’re never going to say a word.

So that’s why this battle is lost in my opinion. I don’t really care. American culture is now a battle between different groups of propagandists who manipulate the levers of power. The rest is commentary, and positivism and critical-rationalism are dead in the broader culture. They only persist in the “inner party” of the elect. Truth is the real conspiracy….

The Harlot by the Side of the Road: Forbidden Tales of the Bible. Good book.

I’ve been defending Marc Lamont Hill’s right to speak and express his views, and retain his professional positions. Mostly because “free speech” really doesn’t matter unless you kind of detest the views you are defending…. So I guess I’ m still delusional and not a realist. I contain multitudes.

Inside the chaos and corruption of Tripoli, where militias rule the streets. We violated the “Pottery Barn rule.”

Mountain lion genomes provide insights into genetic rescue of inbred populations.

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). Last author “Krause.” You’ll be seeing that a lot related to historical genomics from this group in the near future. Ancient DNA is cheap enough that it can be used to resolve historical questions as opposed to shedding light on prehistory.

Simulation of Karyotype Evolution and Biodiversity in Asexual and Sexual Reproduction.

Sex differences in gene expression in the human fetal brain.

December 1, 2018

Brown Pundits – Episode 3, the genetics edition

Filed under: Uncategorized — Razib Khan @ 6:55 pm

The latest BP Podcast is up. You can listen on Libsyn, iTunes and Stitcher. Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe at one of the links above.

Would be really nice if more people reviewed the podcast.

Does DNA Make Us Who We Are?

Filed under: Books, Arts & Manners — Razib Khan @ 3:30 am
A new book from a prominent scientist makes the case.

November 28, 2018

The battle for the soul of the Heart of Asia

Filed under: Indian Genetics,international relations,Tarim Basin,Xinjiang — Razib Khan @ 11:33 pm

Kumārajīva was one of the early translators of the Buddhist canon into Chinese. His father’s lineage was reputedly Indian, while his mother was from the elite of the city of Kucha, on the northern edge of the Tarim basin. It was one of the cities where a form of Tocharian was spoken. This enigmatic Indo-European language family is extinct and known from only a few examples in this region of the world (the different forms of Tocharian seem to have been mutually unintelligible, suggesting a long history in this region of the world for these languages). But Tocharian was not the only Indo-European language group that was represented in the Tarmin. Along the southern and western edge of the Taklamakan Iranian dialects were more common, such as in the city of Khotan.

Over the last 1,000 years, the Tarim Basin has undergone major changes. First, the collapse of the ancient Uyghur Turk Empire resulted in their retrenchment to the Tarim Basin. A previously pastoralist people, they became settled city-dwellers. By the time Genghis Khan rose to power, the Uyghurs had become a predominantly Buddhist people, with a focus around Turpan. They seem to have absorbed the predominantly Tocharian city-states of the eastern portion of the Tarim Basin.

But after 1000 AD a second change began to occur. A group of Turks, who spoke a Karluk dialect, converted to Islam and conquered Kashgar in the west of the Tarim Basin, and began to push eastward, conquering and converting the Buddhist city-states in turn. By 1400 the cultural expansion and military conquest reached the eastern fringe of the Tarim Basin, as Turpan and Hami were absorbed into the Islamic cultural sphere. With this, a new identity unified the city-states of the Tarim Basin. In language they spoke Karluk dialects, and in religion they were Muslim. In the 20th century the Uyghur ethnonym was resurrected in what was known as East Turkestan, but the cultural descendents of the ancient Uyghurs are actually the Yugurs (whose traditional language descends from that of Old Uyghur).

Click to Enlarge

This narrative will be familiar to anyone who reads a book such as Valerie Hansen’s excellent Silk Road. Hansen in particular focuses on the period when the Tarim Basin was at some equipoise between the west, east, and the south, with Sogdians, Turks, Chinese and some Indians, all being part of the dramatis personae of the cities of the Silk Road during the heyday of the Tang dynasty. And none of this should be surprising. Though this region of the world is divided by the highest mountains on earth, the geographic distance between Northern India, Transoxiana, and the Tarim Basin is quite minimal. As the crow flies, New Delhi is less than half the distance from Hotan as Lanzhou, in the far western province of China proper, Gansu.

9th century cave painting from Turpan

The past doesn’t always map easily onto our contemporary topographies. Some of the earliest Chinese contacts with Buddhism was through the devotions of an often blue-eyed people whose physical type was European if anything, who had no doubt learned of the religion ultimately through a chain of transmitters that went back to brown-skinned South Asians. This world did not match the demarcations which we take for granted today. It was a thing different.

Normally when I’m enjoining people to think outside of the boxes that they’re used to thinking in, I’m talking to people of white European descent, around whom the world has revolved for several centuries, and around whom they assume the world will revolve until the last day of universe. But today I’ll point to another group, and that is Indians.

A friend forwarded me this erudite post on Medium, The Rāma Story and Sanskrit in Ancient Xinjiang. It received 324 claps, which in my experience means that tens of thousands of people at minimum have read this piece.

Here is the first paragraph:

Most people do not know that until about a thousand years ago, the Tarim Basin (northwest of Tibet, which is the part of Xinjiang below the Tian Shin Mountains) was Indic in culture and it was a thriving part of the Sanskritic world; its people spoke the Gāndhārī language which many see as descended from Vedic Sanskrit, and Khotanese Saka, which is also closely related to Sanskrit. Perhaps the region to compare it most is Kashmir, to whose north it lay. There was also much interaction between the two regions with many scholars traveling from Kashmir to Khotan, and silk culture is believed to have passed from Khotan to Kashmir and then into India.

The bolded sections are misleading. The italicized section is correct. There was a great deal of Indian-Tarim Basin interaction. Sometimes directly. Sometimes through intermediaries (Sogdians). But it is simply wrong to imply that this is “Indic culture” in a way that communicates to the audience reading it the proper state of the facts.

First, the author makes some statements about the genetic connections of modern people in the Tarim Basin and Indians which are false. He does link to some papers, but they are old, and lack the power to really get at the questions that would allow us to accept or reject the hypothesis of affinity.

Since the HGDP has some Uyghurs in the dataset it’s easy to pull them, and compare them to various South Asians, Iranians, and Han Chinese.

Let’s look at the PCA:

You see a bit of an admixture cline here from the Han Chinese samples, to something more West and South Eurasian. If you run the cline outward toward the West and South Eurasians, it lands somewhere between Pathans and Iranians.

Let’s run Treemix with 4 migration edges. You see the results….

I believe most of the Iranians in this data are sampled from the west of the country. This explains the contrast, where Pathans are more South Asian, and more like Europeans, than the Iranians (at least when not taking into account the migration edge). The steppe genetic impact seems to have stronger in Turan and Khorasan, than the classical heart of Persian civilization in the Fars. The gene flow from the base of the Lithuanian-Pathan clade to the Uyghurs is indicative to me of the steppe genetic influence in this region, perhaps starting with the Afanasievo culture, and later the expansion of the Andronovo complex.

Finally, the requisite admixture analysis:

Menander I, Indo-Greek Buddhist king

These data don’t reject the thesis that the Tarim Basin in the years before 1000 AD were dominated by “Indic culture.” That is because Indic culture is separate from the predominant element that characterizes Indic genes. There was almost certainly some gene flow from northwest India into the Tarim Basin. But it was likely relatively modest. Nevertheless, it is quite possible to characterize someone as having been substantially Indic in their cultural orientation no matter their genetic provenance. The great Greco-Bactrian king, Menander, seems to have been a patron of Buddhism, which was then still perceived as a fundamentally Indian religion.

In the centuries around 400 AD the Chinese still described Buddhism as a foreign “Western religion,” in particular, from India. Indian translators of Buddhist texts are a common presence in China and elsewhere in East Asia during this period, because the original works were in Indian languages. Meanwhile, Chinese Buddhists made pilgrimage to India, in part to retrieve texts from the great ancient monasteries.

But by the end of the Tang dynasty Buddhism was no longer thought of as simply an Indian religion. Though Confucian and Daoist critics never failed to point out its foreign origins, it was clearly indigenized. By the Song dynasty no more Indian translators are mentioned. And, by this period Buddhism in South Asia itself was in serious decline, first in the face of a newly vigorous set of religious practices which we call Hinduism, but also due to the predations of Turkic Muslim invaders, who destroyed many of the great monasteries.

The primary takeaway here though is that the semantic pointers we provide to the audience often give them implications which are not warranted. For example, when scholars describe Classical Greeks as ethnocentric Europeans, that misleads many modern people into thinking that the concept of European as we understand it today entailed the same things then that it does today. The Classical Greeks were part of a broader Mediterranean civilization, and culturally at least as distinct from the peoples of Northern Europe as they were those of the Levant. Their ethnocentrism was of a very different kind than that that developed in Europe in the 19th century, after the Congress of Vienna with the synthesis between resurgent Christian chauvinism and biological essentialism.

A similar issue crops up in discussion of ancient India and Indians. In Sanjeev Sanyal’s The Ocean of Churn he assumes that the Indo-Aryans who clearly were part of the military elite of the Bronze Age Syria state of Mitanni were Indian. First, the reality is that in the Bronze Age “Indians” as we understand them today did not exist. While Mitanni flourished in the Upper Euphrates region, the great cultural complex that was the Indus Valley Civilization was unwinding, to be succeeded by a simpler society. The biological and cultural synthesis that we think of as Indian today had not come into being in the totality. Second, the Indo-Aryan elite of the Mitanni (who had quickly switched their language to the Hurrian of their subjects) likely never had any experience of India. Rather, in the coalitions of steppe agro-pastoralists the Indo-Aryans were distinct from the Iranians, and one branch of the former seems to have pushed westward into the Near East, and another gone eastward to India.

Warriors from Bronze Age Pylos

Ultimately, what is in a label? The Greeks of the Mycenaean period spoke Greek. They worshipped some Greek gods that persisted down to the Classical period. But their descendants had only the vaguest of ideas about these people. When archaeologists of the 19th and 20th century excavated Bronze Age sites in Greece they assumed that people were not Greek. The assumption was that the Greeks of the Classical period descended from people who had come down from the Balkans during the Dark Age (the Dorians). The decipherment of Linear B shocked the world. These people spoke Greek. But culturally they were very different from the Classical Greeks.

To understand the world we must reassemble and filter it in categories what are comprehensible to us, that give us meaning. But we should never confuse the categories and concepts that are our tools for the reality that is out there. Our words always collapse distinctions, and erase subtleties. The further we go back into the past, the greater the disjunction between our categories and the details that they propose to bracket.

In the specific context of Indian history and the controversies and co-options I see bubbling to the surface due to the disruptive impact of genetics, is the fact that for many of the most motivated protagonists history began with Mahmud of Ghazni. For some, the Indo-Aryans are seen as precursors to the Turkic Muslims. And so the alien becomes the indigene, and the indigene becomes the alien. For others, the Indo-Aryans are the root and basis of the Hindu Rashtra. Due to this they must by necessity be grounded in Bharat Matā everlasting. The truth from where I stand does not suggest that either narrative is correct. The Indians of today, whether from the southern tip of the subcontinent, or the high fastness of Kashmir, are not comprehensible without the Aryans of the Vedas. But the Aryans are of the Vedas are not comprehensible without the the Punjab, without their residence and immersion in the Indian subcontinent. They came from elsewhere, but they became who they were because of their emulsification in the matrix of South Asian people and environments.

Similarly, Central Asia, from Xinjiang to the Caspian, from the fringe of Siberia to the edge of India, occupies a central pivot on the World Island. Both receiving and transmitting, over the past 2,000 years it has transformed itself many times, and yet retained some elements of continuity. There is no reason that India, China, or Russia should claim it as a natural extension of their own civilizational development. It was, and is, part of them all and yet not all of any.

Welcome to our brave new 21st century

Filed under: Crispr,Genetic Engineering,Genetics,science — Razib Khan @ 4:44 pm

Sometimes you know something is going to happen. But you don’t know when it’s going to happen. It’s inevitable, but you don’t know when that inevitability is going to realize itself. In a way, death is like that for most of us.

And so it is with genetic engineering in the 21st century. This week MIT Technology Review broke the story that a researcher in China, He Jankui, used the CRISPR/Cas9 system to modify the genes of twin girls. His goal was to have them be were born with a deletion in the CCR5 gene, which would confer resistance to infection with HIV (about ~10% of Northern Europeans carry the deletion). These are the two first human beings born with genetic modifications that were directed by human beings.

Additionally, these are the first genetically modified human beings who will pass that modification to their children (unlike adults who might be targeted by genetic engineering, where their sex cells would not transmit the modification).

Humans have begun to direct their own evolution!

The science, or perhaps more precisely, the engineering, behind CRISPR/Cas9 is well outlined by this video:

There are many scientific and ethical details that go into the unpacking of the story of the gene edited children. But it is important to take a step back, evaluate the present, and consider prospects for the future. The CRISPR/Cas9 system for gene editing has been in use since 2012. In contrast, genetic engineering more broadly has been part of the scientific toolkit for nearly 50 years.

Asilomar, CA

In 1975 140 individuals from a range of disciplines came together in Asilomar, California, and agreed on rough guidelines for the use of the then-nascent technology of recombinant DNA.

This was the technology which brought the idea of genetic engineering to the public, with its first big success being the development of synthetic insulin, which has transformed the lives of millions of people who suffer from diabetes. The private sector biotechnology industry was birthed by the revolution triggered by recombinant DNA techniques in the second half of the 20th century.

For decades after 1975 genetic engineering occupied a prominent spot in science and popular culture. From genetically modified corn to transgenic mice, genetic engineering had widespread uses in both industrial and academic science.

So why is CRISPR/Cas9 such a big deal? In 2012 researchers realized that it was an efficient, cheap, and simple way to do genetic engineering (it had been known earlier as a peculiarity of bacterial defenses against viruses). In less than a decade, it has become even more effective as an editing tool.

In short, CRISPR/Cas9 democratized genetic engineering, so that small labs with few resources could perform experiments and trials. Previously, only laboratories with extensive experience and funding, or industrial scale corporations, could enter into genetic engineering projects. Within a few months, innumerable laboratories switched from other techniques of genetic engineering, which they had spent decades honing, to CRISPR/Cas9.

The nature of the transformation is obvious when you think about what has surfaced in the media in previous decades. One reason that you have heard about genetic engineering in the context of maize, “corn”, is that this is a crop with enormous economic implications. With older and more expensive technologies, genetic engineering could only be justified by a huge economic upside. Because of its cheapness and effectiveness, CRISPR/Cas9 methods have been applied to stem cells, plant and animal breeding, as well as public health. It may help in curing the most common form of muscular dystrophy, ushering in the era of curing of most Mendelian diseases.

Within the last six years, CRISPR/Cas9 has transformed whole sciences, opening up avenues of basic research which were previously not practical. Experimentation has taken over in the realm of experimentation! The plain truth of it is is that what happened in China may appeal to the love of the sensational, but it absolutely marginal to what CRISPR/Cas9 means to most scientists in their working life today. But, it reflects the fact that genetics is now an international discipline with hundreds of thousands of practitioners.

The times when 140 individuals could come together and agree on rules which industry and academia should follow, will follow, are likely long behind us. When scientists would talk about an “international consensus” in 1975, they meant North America, Western Europe, and Japan. Today that consensus has to extend to China, which is now the home to a great deal of cutting-edge biological science. But the cultural and social chasm between China and the developed world is large. And CRISPR/Cas9 is so simple and cheap that its use will likely spread to less developed countries, even less integrated into the community of science than China.

Though He, the researcher behind the “CRISPR babies”, may get the entry in Wikipedia he mentioned offhand to the media, the reality is that the scientific impact of his work is murky at best. Rather, his brazen contravention of the norms of international science presages the new era of the genetic engineering democracy, as the tools to modify the very stuff of life are now accessible to the many, rather than restricted to the few.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

Welcome to our brave new 21st century was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Why There Will Not Be a Beige Future: Skin Color, Genetics, Race and Racism

Filed under: Evolutionary Biology,Genetics,race,Science & Tech — Razib Khan @ 2:05 pm
There is more in heaven and earth than can be dreamt of in any human philosophy. This is why science is not philosophy. Those who map the skies, observe the…
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November 27, 2018

Going being WEIRD dichotomies-cultural anthropology with a genetical lens

Filed under: Cultural Evolution — Razib Khan @ 8:35 pm

From my 10 questions for Luigi Luca Cavalli-Sforza I asked him about the reaction of anthropologists to Cultural Evolution and Transmission, a book written in the late 1970s with Marcus Feldman:

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

He judged that Cultural Evolution and Transmission had little influence. But Peter Richerson and Robert Boyd learned the application of population and quantitative genetic modeling to cultural dynamics from Feldman in the 1980s. In their own turn, they trained researchers such as Joe Henrich.

Henrich in his turn helped train scholars such as Michael Muthukrishna. Here’s a preprint that has me really excited, Beyond WEIRD Psychology – Measuring and Mapping Scales of Cultural and Psychological Distance:

We present a new tool that provides a means to measure the psychological and cultural distance between two societies and create a distance scale with any population as the point of comparison. Since psychological data is dominated by samples drawn from the United States or other WEIRD nations, this tool provides a “WEIRD scale” to assist researchers in systematically extending the existing database of psychological phenomena to more diverse and globally representative samples. As the extreme WEIRDness of the literature begins to dissolve, the tool will become more useful for designing, planning, and justifying a wide range of comparative psychological projects. We have made our code available and developed an online application for creating other scales (including the “Sino scale” also presented in this paper). We discuss regional diversity within nations showing the relative homogeneity of the United States. Finally, we use these scales to predict various psychological outcomes.

For the people who know genetics, they have created a cultural analogy of Fst!!!. From the preprint:

Cultural FST (CFST) is calculated in the same manner as Genetic FST, but instead of a genome, we use a large survey of cultural values as a “culturome”, with questions treated as loci and answers treated as alleles.

I’m going to just present two figures without comment:

u mean english. the scottish are british as . are the welsh

Filed under: Uncategorized — Razib Khan @ 5:02 pm

u mean english. the scottish are british as . are the welsh

November 26, 2018

Open Thread, 11/26/2018

Filed under: Open Thread — Razib Khan @ 9:35 pm

So Spencer and I talked to Antonio Regalado today for the podcast (Apple and Stitcher, should be live soon as I just pushed it). We talked way more about Brave New World than I was expecting. The engineering is moved further than I had realized.

Here are the show notes for the episode.

NASA Probe Lands Safely On Martian Surface.

The Siberian unicorn lived at the same time as modern humans.

Robust estimation of recent effective population size from number of independent origins in soft sweeps.

Fire and Fire & Blood: 300 Years Before A Game of Thrones is a quick read.

Historical contingency shapes adaptive radiation in Antarctic fishes.

The Trouble With White Women: An Interview With Kyla Schuller.

Meet Denny, the ancient mixed-heritage mystery girl.

A vast 4,000-year-old spatial pattern of termite mounds.

On the Nature of Patriarchy.

Alice Dreger’s Middle Finger: Sex, Gender and Unhelpful Hair-Splitting.

What the Cult of Ruth Bader Ginsburg Got Wrong. The Right loves Ginsburg.

Woman who inherited fatal illness to sue doctors in groundbreaking case.

I was raised as a Native American. Then a DNA test rocked my identity. Dad “passed” as Native American. He was black American and Chinese American.

Regular Exercise May Keep Your Body 30 Years ‘Younger’.

Worldwide phylogeography and history of wheat genetic diversity.

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 5:43 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

November 25, 2018

When myth becomes reality

Filed under: History — Razib Khan @ 9:40 pm

Netflix now has Arjun: The Warrior Prince on its stream. I watched most of it to get a feel for some of the details of the story. I know the general outline of the Mahabharata, but I know the Bible or the Iliad far better (in case you can’t be bothered to follow the link, it’s only a small part of Arjun’s early life).

Depending on the sources you trust, the events of the Mahabharata date to around ~1000 BC. They were probably refined at a later date, perhaps around 500 years later.

I watched a fair amount of Arjun: The Warrior Prince. In some ways, it reminded me a lot of the Iliad and the Odyssey. These two works are a melange of influences and time periods, synthesizing true recollections of the large polities with highly stratified social systems and literacy of the Bronze Age, with the simple chiefdoms of the Dark Age Greece. The issue is disentangling the different periods.

One assumes the same is true of the Mahabharata and Ramayana.

The “wild card” here is that the most recent work has now likely confirmed the arrival of agro-pastoralists from the steppe in the period between 1500 and 1000 BC. By the time the historical analogs of the Pandavas were settled in the Gangetic plain, they’d likely been there for many centuries.

The human CRISPR revolution will probably be written in Chinese

Filed under: Crispr — Razib Khan @ 5:32 pm

I am probably biased because of my professional focus, but this may be the biggest story of 2018, Chinese scientists are creating CRISPR babies:

According to Chinese medical documents posted online this month (here and here), a team at the Southern University of Science and Technology, in Shenzhen, has been recruiting couples in an effort to create the first gene-edited babies. They planned to eliminate a gene called CCR5 in order to render the offspring resistant to HIV, smallpox, and cholera.

We knew this was coming. Soon. But now we can confirm it. It confirms my assumption that gene editing in the human context is going to mostly focus on preventing disease in the near future. In a world of low fertility, every expectant parent prays (literally or metaphorically) for a healthy child. After the child is born they can think about other things like how tall they are going to be or how smart they are. But health, that is always the number one concern.

From what I know the United States still has the largest number of top-flight researchers in the basic and applied sciences. American scientific culture, for all its faults, is second to none. But for various reasons, I can’t see America trying to keep up with the Chinese when it comes to gene editing of humans. CRISPR technology will probably be applied to other things, such as in applied plant and animal sciences.

The future is here. We’re just along for the ride….

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