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The southern arc papers

Posted on by Razib Khan

Since David has not posted, here they are…

The genetic history of the Southern Arc: A bridge between West Asia and Europe:

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

A genetic probe into the ancient and medieval history of Southern Europe and West Asia:

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom’s northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

And, Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia:

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

I haven’t read the supplements, so no major comment from me, except for one: the Greece-focused paper confirms using phenotypic prediction that West Eurasians have been getting lighter-complected since the late Neolithic/Bronze Age. I have no idea why, but some Nazis are offended by this reality and cherry-pick data, but trust me, I open up all the supplements to look at the HIRIS-plex predictions.

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The re-enchantment of the world

Posted on by Razib Khan

Nature Human Behaviour has a new editorial that has to be read in full to understand what’s going on in academia today, Science must respect the dignity and rights of all humans. But this section jumps out for an intersection of vacuousness combined with expansiveness:

Yet, people can be harmed indirectly. For example, research may — inadvertently — stigmatize individuals or human groups. It may be discriminatory, racist, sexist, ableist or homophobic. It may provide justification for undermining the human rights of specific groups, simply because of their social characteristics.

Along with other Springer Nature colleagues, we led the development of new guidance that addresses these potential harms and is incorporated in our research ethics guidance. This guidance extends consideration of the principles of ‘beneficence’ and ‘non-maleficence’ — key elements of all ethics frameworks for research with human participants — to any academic publication.

…

Editors, authors and reviewers will hopefully find the guidance helpful when considering and discussing potential benefits and harms arising from manuscripts dealing with human population groups categorized on the basis of socially constructed or socially relevant characteristics, such as race, ethnicity, national or social origin, sex, gender identity, sexual orientation, religion, political or other beliefs, age, disease, (dis)ability or socioeconomic status.

In this guidance, we urge authors to be respectful of the dignity and rights of the human groups they study. We encourage researchers to consider the potential implications of research on human groups defined on the basis of social characteristics; to be reflective of their authorial perspective if not part of the group under study; and to contextualise their findings to minimize as much as possible potential misuse or risks of harm to the studied groups in the public sphere. We also highlight the importance of respectful, non-stigmatizing language to avoid perpetuating stereotypes and causing harm to individuals and groups.

Advancing knowledge and understanding is a fundamental public good. In some cases, however, potential harms to the populations studied may outweigh the benefit of publication. Academic content that undermines the dignity or rights of specific groups; assumes that a human group is superior or inferior over another simply because of a social characteristic; includes hate speech or denigrating images; or promotes privileged, exclusionary perspectives raises ethics concerns that may require revisions or supersede the value of publication. For example, the guidance helps in considering whether it is ethically appropriate to question a social group’s right to freedom or cultural rights, above and beyond any considerations of scientific merit.

On the one hand, this is only formalizing the current culture of science. Most young researchers are highly sensitive to these issues, and the older ones who are not will eventually leave the field. But there is some disturbing stuff in there: “may decline publication (or correct, retract, remove or otherwise amend already published content).” You read that right, they reserve the right to expurgate already published literature (it’s mostly online/digital now).

To some extent, there have always been lines in scientific research. The question is where you draw the line. The sorts of people who write up these sorts of editorials live in a monoculture, where everyone agrees on the same values, and what is, and isn’t, licit. They aren’t given to reflecting on the historical precedent for the patterns that self-censorship takes.

Right now the public, and elites, give broad license to academics to publish whatever they want. Despite some political objections to research, the broadly understood idea is that science, and scholarship, by its nature will push the boundaries, even blaspheme, in the quest for truth. This is not always comfortable, but it has paid massive dividends to our civilization. It’s a bargain that the public makes, funding research out of the government budget, even though science is something many of them view ambivalently (but everyone likes nice gadgets!).

Most Americans don’t have strong opinions about physics or geology. But they do have opinions on morality and ethics. If scientists now begin to explicitly admit that they are engaged in a highly moralistic enterprise, expect that the public will also offer up their opinion as a rejoinder.

In the near term, most of the scientists who sign on to these sorts of statements are worried about things like studying group differences in intelligence or sexual orientation. But avoiding this is to some extent a fait accompli. Social norms will prevent this stuff from being explored too much I believe (at least in the West). But that’s not the case in other characteristics, because scientists are not sensitive to everything, because not everyone is part of their ingroup.

Here’s a concrete example. What if researchers find that not only is strong religiosity and social conservatism correlated with lower IQ, but that the same GWAS hits that predict lower IQ also predict religiosity and socially conservative viewpoints? Most scientists don’t know strongly religious people or social conservatives, but I do, and I kow they are a bit offended by these sorts of findings. But, they also understand that science is in the game of truth, not sparing their feelings, sentiments and self-image. Usually, they will concede the research is a legitimate enterprise even if they balk at accepting the specific results.

Now, imagine a future where scientists are quite open that their findings must aim to elevate rather than denigrate. Religious and socially conservative people will feel denigrated, and perhaps they’ll hold scientists to account based on their own avowed values. I doubt most scientists will react positively since they don’t view these groups as legitimate victim categories, but as groups that align with oppressors (honestly, some probably start out thinking “let’s study these evil people and see if we can fix them!”). They will ignore their complaints. Will these groups have any recourse? Of course, once science becomes polarized, then funding will be under consideration. Once scientists give up their moral legitimacy as cold hard practitioners of truth, as opposed to social and political creatures, then it is in the realm of the latter that the game will be played.

This is not to say that scientists were ever objective. They’re human. But in past generations, there was a sense that in some cases, in some instances, they had to put aside their views. To give a concrete example, I know the case of an eminent geneticist who spoke in front of a conservative group, even though his own politics leaned toward socialism.  My understanding is that when queried about this choice he stated that he believes in setting aside politics when it comes to science. Today this would be seen as a regressive viewpoint. Most young geneticists would I’m sure avoid speaking in front of a conservative group.

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American is more secular than it was a generation ago

Posted on by Razib Khan

The Wall Street Journal has an op-ed, Religion Is Dying? Don’t Believe It Many of the ‘Nones’ aren’t secular; they belong to minority faiths. The problem is how to count them, which engages in a lot of sophistry. The co-authors worked with the late Rodney Stark, who died on July 21st of 2022 (seven days before publication). Stark has argued for fifty years that the vibrancy of religion is determined by the offerings that people can choose from. A “religious free market” like the US is optimal for the phenomenon. This is why the secularization of the US over the last thirty years has been disturbing since it goes against their theory.

The authors of the op-ed assert:

Data from five recent U.S. population surveys point to the vibrancy, ubiquity and growth of religion in the U.S. Americans are becoming more religious, and religious institutions are thriving. Consistent with some previous studies but contrary to widely held assumptions, many people who report no religious affiliation—and even many self-identified atheists and agnostics—exhibit substantial levels of religious practice and belief.

The evidence is mostly sophistry. It is probably true that there are more small churches as the big churches collapse, but a lot of small churches may still mean fewer religious people than a few big churches.

Here is belief in God and religious attendance from the GSS (one of their sources), and the trend is obvious:

We’re still mostly a religious nation. But there has been a massive breaking of the uniform religious consensus that was the norm in the 80’s and 90’s, where nominally religious people thought being irreligious was a step too far.

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Indra is absolved: The “caste system” predates the Indo-Aryans

Posted on by Razib Khan


In the near future the ancient DNA group led by David Reich will publish a bunch of stuff, and one paper will note that the variation in steppe ancestry in the Bronze Age Greeks did not have class implications. In other words, the ancient Greeks did not have a caste system as you might find in India, despite the way the Spartans treated the helots or Messinians. Of course, the Indo-Europeans did have a ‘tripartite’ caste system of rulers and warriors, priests and commoners. In the Indian varna system, this was translated into Kshatriyas, Brahmins and Vaishyas. But it is found elsewhere, including among the German Saxons. But to my knowledge nothing like the Indian caste system has been found genetically in these ancient populations; some individuals have more “farmer” ancestry in initial generations, but this is all smoothed away by admixture.

India is different. It has jati-varna, with varna being caste as you would understand, but jati being one of thousands of endogamous “communities” in the subcontinent. At first, like many, I assumed this had something to do with the Indo-Aryan migration into the subcontinent, but I noticed a few things early on. First, there are apparent genetic differences between groups in Non-Aryan South India that are not Brahmin. For example, between Nadars and Dalits. These differences correlated to global biographic fraction differences. Dalits have more AASI (Ancient Ancestral South Indian). Mind you, I believe South Indian “Dravidians” were strongly shaped by the Indo-Aryans, so that’s not dispositive. Nevertheless, Non-Aryan cultural regions have this institution, and, jati is peculiarly India, even if varna is not.

But, what has shifted my view is looking at admixture variation in “Indus Valley Periphery” samples in samples dated from 3000-2000 BC. There’s a wide range of AASI. Why? Well, admixture in structured populations takes time. But there’s something suspicious to me about this variation combined with India’s later endogamy and the mystery of how the Indus Valley Civilization organized itself. There seems to have been very little stratification in a way we would understand it from Egypt or Mesopatamia. Were they anarchists? I doubt it. The early emergence of jati may explain the IVC sociopolitical system. The Indo-Aryans, when they arrived, were simply integrated into the framework.

Ancient DNA will prove me right or wrong. But I’m putting my cards on the table.

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But why is the lactase persistent allele not in HWE?

Posted on by Razib Khan

Dairying, diseases and the evolution of lactase persistence in Europe:

In European and many African, Middle Eastern and southern Asian populations, lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the past 10,000 years1. Although the selection of LP and the consumption of prehistoric milk must be linked, considerable uncertainty remains concerning their spatiotemporal configuration and specific interactions2,3. Here we provide detailed distributions of milk exploitation across Europe over the past 9,000 years using around 7,000 pottery fat residues from more than 550 archaeological sites. European milk use was widespread from the Neolithic period onwards but varied spatially and temporally in intensity. Notably, LP selection varying with levels of prehistoric milk exploitation is no better at explaining LP allele frequency trajectories than uniform selection since the Neolithic period. In the UK Biobank4,5 cohort of 500,000 contemporary Europeans, LP genotype was only weakly associated with milk consumption and did not show consistent associations with improved fitness or health indicators. This suggests that other reasons for the beneficial effects of LP should be considered for its rapid frequency increase. We propose that lactase non-persistent individuals consumed milk when it became available but, under conditions of famine and/or increased pathogen exposure, this was disadvantageous, driving LP selection in prehistoric Europe. Comparison of model likelihoods indicates that population fluctuations, settlement density and wild animal exploitation—proxies for these drivers—provide better explanations of LP selection than the extent of milk exploitation. These findings offer new perspectives on prehistoric milk exploitation and LP evolution.

Two issues

1) Doesn’t seem to explain why LP started becoming common in Britain before the continent

2) Why are the alleles not in HWE? There’s not really any assortative mating.

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On the collaboration with Dry.io

Posted on by Razib Khan

I mentioned this in my latest Time Well Spent (a recurring feature of my newsletter), but I’ve started a collab with a firm called dry.io. On its website they say they want to “Build tools that let your team and your community work how you want.” For over a decade many of you have been reading me via my Total Content Feed, but I now have a new way to interact with all of my content thanks to dry.io, a landing page that pulls from all the various places that I drop content. They also have a nice search engine.

As they say, “watch this space.”

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The replacement of the Neandersovan Y and mtDNA?

Posted on by Razib Khan

Harvard Magazine has a nice piece up on David Reich’s biography and research. The section where Reich addresses the strange issues regarding Neanderthals jumped out at me, as I’ve had the same confused thoughts:

Reich is not resting on his laurels. As the data accumulate, and the tools become more sophisticated and powerful, he has begun revisiting some of his own prior interpretations of human prehistory, and coming to terms with what he describes as “weird signals in the current data.” Mitochondrial DNA shows that modern humans and Neanderthals are much more closely related to each other in the maternal line than either is to Denisovans. The Y chromosomes of modern humans and Neanderthals, passed only in the paternal line, are also much more closely related to each other than to Denisovans. “But then if you look at the whole genome, on average, Neanderthals and Denisovans are more closely related to each other than either one is to modern humans. Having an entirely male line and an entirely female line saying one thing, and then the rest of the genome saying something else, is weird.” The explanation some people give is that there may have been modern human mixture with Neanderthals further back in time than currently understood, somewhere between 250,000 and 400,000 years ago, and that contributed a few percent to the Neanderthal genome. “But it’s very surprising that only a few percent contribution would be the source of both the Y chromosome and mitochondrial DNA for Neanderthals.” Maybe contemporary non-Africans are actually Neanderthals, and later waves of modern human DNA from Africa swamped the rest of non-Africans’ genomes so “non-Africans are best described as Neanderthals, with 98 percent modern human mixture, or something profoundly philosophically unsettling like that,” he says, half seriously.

“There’s going to be a challenging of our understanding of these relationships” in the years ahead, Reich continues, “based on analyzing the data in more sensitive ways and looking at it from new perspectives. We’re taking a couple of steps back and realizing that key events and relationships are different, in a deep way, from the first-pass model we have collectively developed. The model that I’ve had a role in building is teetering. I find that exciting, as well as destabilizing. And I’d like to be part of trying to figure out the truth.”

Neanderthals clearly have a bit of “modern” human-like DNA from paleo-Africans. On the order of a few percent. But strangely, their Y and mtDNA seem to fit into a lade with modern humans, as opposed to the Neanderthal’s Denisovan cousins. This isn’t impossible; over time rare lineages will replace common ones. But what’s the chance that both Y and mtDNA from humans would replace that of Neanderthals? (probability of fixation of a new mutation is 1 over the number of gene copies)

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Open Thread – 7/17/2022 – Gene Expression

Posted on by Razib Khan


The new Rings of Power series debuts on September 2nd, so they have a new trailer out. I’m skeptical, but they pulled all the stops for the effects. My expectation is that this will be to the Tolkien canon what Taco Bell is to Mexican food, but I will be happy to be surprised. It is obvious that they are taking Black Númenóreans a bit too literally, but if they execute well on things unrelated to the identity politics I bet people will be willing to overlook that (it could be that this was just the price they’d have to pay in Hollywood to get this produced).

Tad Williams Into the Narrowdark – Last King of Osten Ard Book 3 is good. Williams, in my opinion, is great at navigating between George R. R. Martin’s somewhat excessively gruesome world-building with Brandon Sanderson’s “boy scout” approach. Like R. Scott Bakker he is excellent at the fashioning of human-like elven analogs that push into the uncanny valley territory of “human nature,” very much like us but different in critical ways as to seem alien and fantastic.

A Late Pleistocene human genome from Southwest China. I haven’t had time to read this closely, but thanks for posting the link.

I don’t have time to write up all the ancient DNA that is coming out, but I do try and read it. Keep the links coming; I do appreciate them.

Most of you know I ungated my Substack podcasts after two weeks. The reviews have trailed off, which means that there will be ‘less discovery’ of them. If you have a moment, I would appreciate a five-star (I may mention this on my podcast at some point, I don’t push this heavily).

I’ve been writing on this blog for 20 years. One sad trend is that a huge swath of academics are becoming incredibly conformist, censorious and ideologically motivated. Yes, this tendency was always there in a field like sociology, for example, but now it’s everywhere. The public doesn’t even know the tenth of it from what the stuff I hear. Just keep your skeptical hat on…