Open Thread – 12/26/2021 – Gene Expression

Has anyone read The Dawn of Everything? What are your opinions? What are the best reviews?

My prior is to be skeptical because economic historians and economists tend not be big fans of the coauthors, and I generally agree with the economistic crowd more often than not. But everyone is reading and reviewing it, and I am probably going to be that in that camp.

This Matt Yglesias ($) post Human history in the very long run wouldn’t surprise or seem novel to readers of this blog, but for a lot of Yglesias’ readers, it probably is. Glad he’s pushing this stuff to the fore.

You should subscribe to Cold Takes by the way, it’s good.

Floating the idea that “Basal Eurasian” common migration source is the reason that a lot of tests show that West Eurasians have more affinity to Sub-Saharans Africans than East Eurasians. Thoughts? After nearly a decade we’re still not there will getting a “pure” Basal Eurasian, but it looks like if they existed they’d have diverged 60-80 Kya and perhaps they mixed with other groups soon after?

Open Thread – 12/11/2021 – Gene Expression

Peggy Mohan’s Wanderers, Kings, Merchants is a strange book for a reader of this weblog. The author is really fixated on retroflex consonants, but she’s also aware of the latest archaeogenetic work. It’s a pretty academic work, and if you aren’t interested in questions like how Sanskrit evolved along with early Dravidian languages, it’s not for you, but I think Mohan’s book illustrates a possible future for synthetic interdisciplinary research. I’d like to see more of this.

Defund the Police Meets the Crime Wave. Crime is coming close to my friend’s Leighton Woodhouse’s life (he lives in Oakland). It looks like the Democrats really want the Republicans to win again on “tough on crime.” This shit is not sustainable.

There is now a TV series based on The Wheel of Time. I haven’t read these books since I was a literal teenager, and I do not personally feel the source material is rich enough to really produce anything comparable to Game of Thrones. Obscure fact: this series is set in our far future, in a post-apocalyptic world.

The Man in the Lineup – Alice Sebold’s best-selling account of her own rape was headed for the big screen. Then the film’s unlikely producer started asking questions. The author of The Lovely Bones isn’t going to live this down.

Charles C Mann recently appear ed on the UL podcast. We talked for nearly an hour and a half; there is a lot to talk about. Please rate the podcast on Apple or Stitcher. One thing Charles mentioned to me privately is that it was fun to talk to me because I’d read his books and actually knew his writing. That struck me as funny, but it’s not like I’m Terry Gross, I don’t just talk to anyone. Usually, I am interested in talking to the person for a reason.

Thanksgiving squabbles are a feature, not a bug – How eternally unsettled debates are the lifeblood of the republic. This is on my Substack.

Dark Horse out of the Steppe – Fishing the Sintashta, Scythians and Sarmatians out of obscurity.

Open Thread – 11/29/2021 – Gene Expression

The The Aristocracy of Talent: How Meritocracy Made the Modern World is a fast read. Recommended.

I’ve been too busy to do an “Open Thread” and now that I do stuff similar for my Substack…well, you know the drill. That being said, South & SC Asian neolithic ancestry in Steppe Eneolithic. The big issue here is the space of graphs is big. Is this the best option? Sarazm seems to post-date the emergence of the proto-Yamnaya genetic matrix as outlined by David Anthony in his interview with me.

Also, I’m going to block some people who seem to have started trolling if you don’t stop (you know who you are, you are not a regular).

Finally, anyone have suggestions for people I should have on the podcast? I have a lot recorded already…

Open Thread – 11/07/2021 – Gene Expression

In the mid-2000’s I read a bunch of books on the history of Catholicism in the US. One of the most memorable of those books was Jay P Dolan’s In Search of an American Catholicism: A History of Religion and Culture in Tension.

If you haven’t, please write a positive review of the Unsupervised Learning podcast. The more positive reviews, the better it is for exposure, etc. etc.

Some links on the Substack too. Also, a new paid piece, Heritability of height: the long and the short of it. Using genetics to make historical and cultural inferences are popular, obviously, but the interplay between genetics and evolution are just as interesting to me. Obviously.

I interviewed Eric Berger about SpaceX. Most of the discussion focused on his book, Liftoff: Elon Musk and the Desperate Early Days That Launched SpaceX. I’m generally pro-Musk, so I recommend the book. If you want a negative treatment, just read the rest of the media!

Parent-of-origin effects in the UK Biobank.

Genetic and chemotherapeutic causes of germline hypermutation.

America Needs a New Scientific Revolution.

Replace the Proposed New California Math Curriculum Framework – Open Letter to Governor Gavin Newsom, State Superintendent Tony Thurmond, the State Board of Education, and the Instructional Quality Commission. This is a “whitepill.” Lots of people I respect on this list, even people with a reputation as being very much on the Left.

Horses were domesticated before mammoth went extinct

The origins and spread of domestic horses from the Western Eurasian steppes:

Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture.

And, Late Quaternary dynamics of Arctic biota from ancient environmental genomics:

During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1,2,3,4,5,6,7,8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe–tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe–tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.

Related to the first paper, The horse bit and bridle kicked off ancient empires – a new giant dataset tracks the societal factors that drove military technology:

Starting around 3,000 years ago, a wave of innovation began to sweep through human societies around the globe. For the next millennium the continued emergence of new technologies had a dramatic effect on the course of human history.

This era saw the advancement of the ability to control horses with bit and bridle, the spread of iron-working techniques through Eurasia that led to hardier and cheaper weapons and armor and new ways of killing from a distance, such as with crossbows and catapults. On the whole, warfare became much more deadly.

I still think this is a plausible model:

– Horses were used opportunistically on the Eurasian steppe between 3500 BC and 2000 BC

– The horse was fully domesticated 2000 BC with the emergence of the light war-chariot

– The true power of the horse as a military instrument emerged after 1000 BC due to the emergence of mounted cavalry

I can be convinced that the horse wasn’t used opportunistically but it makes the militaristic expansion of Corded Ware so much more plausible to me. We’ll see what David Anthony comes up with in the near future, as he’s on the horse-beat too…

Open Thread – 10/17/2021 – Gene Expression

Reading Julia Galef’s The Scout Mindset: Why Some People See Things Clearly and Others Don’t. I’ve known Julia for a decade now, and I really respect her. She’s a good-faith actor.

Less time for this blog, but I’ve been posting a lot on the Substack. If you don’t like newsletters (but you should!), I’m still pushing stuff to razib.com, with a total-content-feed RSS.

I’m rebooting the South Asian Genotype Project. Email me at razib.com.

There are 2,438 articles on bioRxiv when you look for China, genetics, and genomics. For India, the figure is 923. Pretty sad.

The Aristocracy of Talent: How Meritocracy Made the Modern World. Another book on my “to-read.”

The promise of disease gene discovery in South Asia.

Untapped opportunities for rare disease gene discovery in India.

Genomic insights into the population history and biological adaptation of Southwestern Chinese Hmong-Mien people.

Admixture dynamics in colonial Mexico and the genetic legacy of the Manila Galleon.

A Genomic Perspective on the Evolutionary Diversification of Turtles.

Open Thread – 10/01/2021 – Gene Expression

Over at my Substack I’ve posted my interview with Steven Pinker on Rationality. You can read my review at UnHerd.

I would appreciate it if readers of this weblog leave positive reviews on my podcast for Apple or Stitcher.

Also, I posted a long piece on the arrival of humans to the New World, and the finds that suggest humans were here before the LGM.

Open Thread – 9/12/2021 – Gene Expression

Adrian Wooldridge has a new book out, The Aristocracy of Talent: How Meritocracy Made the Modern World. The juxtaposition between the terms aristocracy and meritocracy is amusing.

Obviously, I’ve had less time for this weblog due to other things, like my Substack. Please check out Among Afghans: jewel of the dragon if you haven’t. I post correspondence from a reader here there at the end, so it will be familiar.

Also, my mid-month link round-up is up over at Substack. Please check that out!

I don’t know if I mentioned this elsewhere, but I’m a paying subscriber of FdB. Mostly because I want him to be paid to write stuff like this and this. Most Left-liberals outside of genetics aren’t aware of the decreasing cost of sequencing plot from the NIH, or the existence of companies like Genomic Prediction and Orchid. Freddie is woke to all that. He’s an irascible character; I had my run-ins with him when he decided to send me unsolicited emails telling me what he thinks about me (mixed reviews). But I’ve come to the conclusion only the irascible can really speak the truth at this point. So here we are.

Unless you’ve been asleep, you’ve seen Can Progressives Be Convinced That Genetics Matters?, which is a pretty hagiographic profile of Dr. Kathryn Paige Harden in The New Yorker. This is from the same writer who wrote a hit-piece against David Reich. Is it something in journalism that they can only write hit-pieces or hagiographies? Is this demand side?

Two observations:

– The warm-glow of The New Yorker seems to be allowing the left/mainstream press to approach Harden’s ideas fairly instead of dismissing or demonizing

– A lot of scientists really dislike the profile and there’s been a lot of blowback. This, in contrast to the “circle the wagons” reaction around David Reich more or less. I think this is due to the fact that scientists would prefer more neutrality and a mixed portrait. They thought the profile of Reich was one-sided, and they think the profile of Harden is also one-sided. To be frank, I support both Reich and Harden’s projects.

There are some digs at Reich in Harden’s book, The Genetic Lottery. I actually sent the chapter in question to some human population geneticists to make sure my reaction wasn’t too biased (yes, I’m biased, I admire Reich a lot as a scientist and a human), and they told me I wasn’t crazy. So I have some defense of Reich in my full review of the Harden book (this didn’t make the final cut at UnHerd).

As for Harden’s project, I’m on the more pessimistic side because on social media scientists are connecting it to racism. Whether she’s correct or not if that sticks the project is obviously over. It’s a word of power, and will sink the project before it launches.

The Other Afghan Women. This is basically a story that explains how the rural Afghans viewed the American occupation and intervention, and all the horror we generated. This was published in 2021, but really it could have been published as early as 2001. From what I’ve heard American forces caused a lot of “collateral damage.” In the early years, the press was sympathetic, so they never reported on that. And, the US military has clamped down on leaking too much about the atrocities. When I was in grad school I randomly had beers with some construction workers at UC Davis. One of the guys went into a mental fugue and told us that he shot a dozen Iraqi prisoners in the head after one of his buddies got blown up by an IED. He kind of apologized for freaking us out, and explained: “you all don’t know anything about what’s going on, they cover it up when they can.” Others have told me the same, though they haven’t copped to war crimes.

Open Thread – 08/01/2021 – GNXP

Patrick Wyman’s The Verge is out. I quite like it. And that’s pretty clear in my review for National Review, Europe on the Verge of a Revolutionary Breakthrough. I assume the main gripe someone might have is Patrick is too materialist. But if he covered all the bases the book would get out of control.

I talked to Patrick for over an hour for my podcast.

I have a review in UnHerd, Do genes determine intelligence? Both conservatives and liberals are ignoring the realities of biology. I didn’t pick the title. My review is on K. Paige Harden’s book to come out in September, The Genetic Lottery: Why DNA Matters for Social Equality. On the whole, it’s a worthwhile effort. To be frank I had some pointed critiques that ended up on the cutting room floor (the initial draft was 4,500 words).

Finally, also have a review of Charles Murray’s book in Quillette. I ended up reviewing the book because Quillette had a hard time finding anyone who would be willing to review it.

Are Syrian Jews Arabs?.

The omnigenic model and polygenic prediction of complex traits.

Modelling the spatiotemporal spread of beneficial alleles using ancient genomes.

I ask this now and then: can you please review positively my podcast? (I notice someone negatively reviewed it because I “platformed” Charles Murray)

The genetic origin of Daunians and the Pan-Mediterranean southern Italian Iron Age context.

More Covid Mysteries – There’s much to learn about how the virus spreads.

Determining the stability of genome-wide factors in BMI between ages 40 to 69 years.

Precision Autism: Genomic Stratification of Disorders Making Up the Broad Spectrum May Demystify its “Epidemic Rates”.

Beyond Finn-baiting


Over at my Substack, I just closed out a six-part series relating to the genetics and culture of Finland.

  • Part one: Duke Tales: shades of Finnish cultural weirdness in my own backyard (ungated)
  • Part two: Weirdness as a national pastime: culture
  • Part three: Go West Young Siberian: genetics findings
  • Part four: From deepest Siberia to Europe’s edge
  • Part five: Frontier Finns: cabins, rakes & Indians
  • Part sixFinnish brains, baiting and bottlenecks

(also, see my recent podcasts with Patrick Wyman [ungated] and Karl Smith)