Fun time sat the ISIR 2019 meeting in Minneapolis. Lots of deviltry, but that’s for the open thread.
I will tell readers that James Lee has more to come after 2018’s Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. And Greg Clark has something in the works on the heels of A Farewell to Alms: A Brief Economic History of the World and The Son Also Rises: Surnames and the History of Social Mobility.
Probably the most interesting and but unsurprising empirical result at the conference is that recommendations add pretty much zero toward evaluation possible admittees to graduate school.
Again I’d recommend John Barton’s A History of the Bible: The Story of the World’s Most Influential Book. There’s an interesting section on why the early Christians tended to distribute what became the New Testament in the codex as opposed to scroll form. It’s not totally clear or coherent, but highly informative.
As I noted in my other weblog, India After Gandhi has a Kindle sale right now. This is not a book without controversy or dispute, but it is probably worth reading nonetheless.
India Launches Mission to Land a Rover on Moon’s South Pole. There’s a link within the story with the text “an increasingly competitive space race”, that describes the race between China and India. Welcome to the 21st-century.
Lessons in genome engineering: opportunities, tools and pitfalls. We’re not even 10 years into the CRISPR-Cas9 engineering era.
Selection against archaic DNA in human regulatory regions.
The Lessons of a Hideous Forest. No surprise.
Localization of a feline autosomal dominant dwarfism locus: a novel model of chondrodysplasia.
Cross-border agonies: Dhaka’s middle-class Hindus lead a dual life straddling two countries. Basically in Bangladesh educated Hindus experience a “glass ceiling.” For professional or social advancement they have to leave for India, so of course, they do.
Genome diversity and species richness in mammals.
Pervasive introgression of MHC genes in newt hybrid zones.
Cultural evolution by capital accumulation.
DNA Testing Creates Wrenching Dilemmas for the Family Historian.
Microsoft’s Cloud Business Drives Record Sales. I feel like the 2000s for Microsoft was a bit like the 1990s for Apple, where there was a period where the brand was in sharp decline before its bounce back. While the Silicon Valley firms have been dealing with PR nightmares, Microsoft seems to have stayed under the radar.
Genetic architecture influences when and how hybridization contributes to colonization.
Barton is confusing about a lot of stuff. But one thing a codex forces is standardization of the canonical books. Everything between the covers is canonical. Everything outside isn’t. When your Bible is a collection of scrolls kept on shelves or in jars, the canon is debatable.
Anyway, the Jews standardized the Tanakh around 100 AD, and Christians standardized the New Testament in the 4th Century or so. In both cases, the actual texts have been faithfully reproduced with hardly any errors for about 2,500 and 1,900 years, respectfully.
Another interesting book is Christopher De Hamel’s “The Book: A History of the Bible,” Phaidon Press, Ltd., 2001.
The Vedas have a long history, too. When were they standardized, and how good has the copying been?
Dear Mr. Razib Khan,
Re: Khazars not related to Ashkenazi Jews
Kevin Brook as posted a link to Mrs. Tatiana Tatarinova work (published in Russian) about ancient DNA from Khazar burials (kurgans).
Mr. Brook summary IN English is a faithful renditions of the main points in the original:
In this bulletin:
1. Tatiana Tatarinova’s Interview with PCR News on Khazar DNA
2. The Remains of the Khazar Fortress Sarkel Rediscovered Underwater
=====================================================================
1. Tatiana Tatarinova’s Interview with PCR News on Khazar DNA
The June 22, 2019 issue of Khazaria News presented a summary of the
genetic research of Tatiana Tatarinova’s team.
Further details were revealed in the interview Tatarinova gave to Aleksey
Torgashev for the Russian-language science website PCR News. Torgashev’s
article “Tatarinova i khazary” was published there on June 9, 2019 at
http://pcr.news/stati/tatarinova-i-khazary/
Tatarinova, who specializes in bioinformatics, indicated there that her
team studied the DNA of 9 ruling-class ethnic Khazars whose bones were
provided for the research in 2014 by the archaeologist Vladimir
Klyutchnikov and his colleague, the historian and anthropologist Elena
Batieva. She approached Klyutchnikov after reading the 2013 book he
co-authored titled “Khazary”. They had been buried near the Don River
during the 8th-10th centuries. Some of them were buried next to horses
and one was buried with a camel. Tatarinova views the camel as having
been a status symbol in that place and time.
She also mentioned that all but one of the Khazar DNA samples show large
amounts of Mongoloid ancestry from the original Turkic homeland of
southern Siberia and Central Asia, and that ancestry is described by her
as approximately what is found in modern Yakuts, Buryats, Kyrgyz, and
Kazakhs. One of those people shows indications of being substantially
mixed with Europeans. The only un-Turkic-like sample appears to have an
Arabian origin.
The female Khazar samples were found to typically carry higher amounts of
Mongoloid autosomal DNA than the male Khazar samples had.
The uniparental haplogroups of the Khazar samples were also identified.
In this interview, Tatarinova reiterates that the Khazar samples aren’t
genetically close to Ashkenazic samples, and Ashkenazim don’t carry any
DNA from the Turkic homeland. She also states “There was an article a few
years ago in which researchers presented specific Ashkenazi Jewish
[genetic] markers. The Khazars do not have them.”
The interview also contains technical details on how they extracted and
analyzed the DNA from the Khazars, discussing such issues as varying
degrees of preservation of ancient DNA (some of the approximately 300
other Khazar skeletons that were available to the team had no surviving
DNA left to test) and how to identify genetic contamination. She also
discusses the high cost of testing each sample’s genome.
Altogether there are 10 people working on this Khazar DNA project.
Tatarinova explained that team member Alexander “Sasha” Mikheyev came up
with an efficient method of sequencing ancient DNA and that he works in
two laboratories: one at the Australian National University in Canberra,
Australia and the other at the Okinawa Institute of Science and Technology
Graduate University in Okinawa, Japan.
Another of the team members credited by Tatarinova in this interview is
Igor Kornienko, a geneticist from Rostov, Russia who did such tasks as DNA
extraction, determination of the sex of each sample, analysis of STR
markers on the males’ Y chromosomes, and determination of the haplogroup
assignments.
The team’s full paper will be forthcoming in print. It was previously
announced that at least the abstract of the paper will appear in Russian
Journal of Genetics but I imagine that the full paper will also go in
there.
Tatarinova also expresses the hope that their next project will test the
bones of the ethnically-diverse residents of Khazarian cities. These
cities’ residents included multi-ethnic and multi-religious traders like
Arabs, Jews, and Slavs, so their DNA would be expected to have differences
from the typical elite ethnic Khazar nomad of the steppes.
=====================================================================
2. The Remains of the Khazar Fortress Sarkel Rediscovered Underwater
Sarkel was flooded in 1952 when the Soviet Union constructed and began to
operate a hydraulic structure for the new, artificial Tsimlyansk
Reservoir. It was pretty well excavated during the 1930s-1950s by a team
assembled by the Russian archaeologist Mikhail Artamonov, who subsequently
published the findings.
Nikolay Grishchenko’s Russian-language article “Video: khazarskiy gorod
Sarkel pokazali na dnie Tsimlyanskogo morya” was published in Rossiyskaya
Gazeta on June 14, 2019 at
https://rg.ru/2019/06/14/reg-ufo/video-hazarskij-gorod-sarkel-pokazali-na-dne-cimlianskogo-moria.html
and the related article “Zatoplenniy khazarskiy gorod nashli uchenye v
Rostovskoy oblasti” was released by Argumenty i fakty (AIF) of Rostov on
June 19, 2019 at
http://www.rostov.aif.ru/society/details/zatoplennyy_hazarskiy_gorod_nashli_uchenye_v_rostovskoy_oblasti
The articles state that the film crew of the OCEAN-TV television channel
probably rediscovered the ruins of Sarkel at the bottom of the reservoir
while they were working on their “Great Rivers” project. The crew shot
photos and videos of this assemblage of square-shaped bricks. On June 14,
2019, OCEAN-TV released Yurii Tkachenko’s 1 minute 16 second dive video
“Video podvodnogo Sarkela” at https://www.youtube.com/watch?v=kAwhlZZHNzo
Researchers from the Russian Academy of Sciences (RAS) believe this is
Sarkel “with a high degree of confidence”, according to Andrei Podkolzin,
editor-in-chief of OCEAN-TV, who also serves as chairman of the
supervisory board of the Russian Oceanographic Community. Grishchenko
added that the bottom relief of this area under the reservoir is said to
match reports of what was seen above land during the 19th and 20th
centuries.
The researchers from RAS planned to conduct an underwater archaeological
expedition of Sarkel beginning on July 1, 2019.
=====================================================================
kbrook@khazaria.com
Ancient origins of low lean mass among South Asians and implications for modern type 2 diabetes susceptibility:
https://www.nature.com/articles/s41598-019-46960-9#Tab1
Very interesting paper. Low lean body mass in South Asia seems to date all the way back to at least the beginning of the Holocene, and is not a product of the Neolithic transition or more recent historical episodes (famines, etc.) A couple of thoughts:
1. I didn’t realize there was apparently a good amount of Mesolithic skeletal material available from India – why hasn’t any of it been sequenced yet? We should finally have a proper example of a genuine AASI people, instead of having to use Onge as a proxy.
2. The authors don’t take a strong stand on the underlying genetic basis for low lean body mass, positing either long-term climatic adaption to a hot, arid environmemt or neutral selection. They cite the low lean mass of Australian Aborigines and Nilo-Saharan East Africans as examples of other peoples with similar body types who also come from arid biomes. I’m not sure I really buy climate-adaption as being the biggest driver of human physiology – it assumes that these groups A.) Have been living more or less in the same region for tens of thousands (though I admit in the case of Australian Aborigines this is more than likely true) B.) Those same regions have had more or less the same climactic conditions during that length time as they do now. Just because most of India, Australia, and East Africa are really hot and dry today doesn’t mean the climate wasn’t more temperate going back 10, 20, 50, 100,000 years, etc.
3. In this paragraph the authors seemingly give a nod to possible epigenetic factors influencing low lean body mass:
“Alternatively, the heritability of low lean mass may originate from an intense cycle of inter-generational plasticity that is hard to break: low maternal lean mass may be the strongest predictor of low offspring lean mass at birth46, and low birth weight (associated with lower lean mass) predicts low adult lean mass47. Fifty generations of undernutrition in a rat model led to the development of a similar phenotype (including low birth weight, central adiposity, insulin resistance, and vitamin B12 and folate deficiency) in the absence of genetic change48. The phenotype largely persisted for 2 generations after returning the offspring to a standard diet (although birth weight and fat mass did show partial recovery), indicating that the South Asian phenotype might plausibly result from multigenerational undernutrition.”
Razib, I think you’ve been critical in the past on some of the purported effects of epigenetic influences, so I’d be curious if you have anything to add one way or the other to this point.
Good Afternoon Sir!
Just got done reading the supplemental data for the Margaryan Viking paper and was wondering about the LCT analysis… or lack therefore of. I would have thought with the data from figure 5 that the authors would have estimated the selection coefficient required for the observed rate of change. Is that something you could take a stab at with the provided data?
Cheers,
Guy
@Stefan F.:
I don’t know what Razib makes of your report. The links you gave were to Cyrillic writing.
The result confirms the Behar 2013 paper which used Turkic populations from the Caucasus and Volga areas as the comparison set.
The Khazar theory of Jewish origins is limited to a small bunch of cranks with a very definite political agenda.
i thought kevin brook disavowed his earlier work? he used to comment on this blog.
Years and years ago, Kevin Brook believed that most or all Ashkenazi Jews descend from Khazars. As autosomal DNA studies of Ashkenazi Jews started to be published, he faithfully posted them on khazaria.com, even if they contradicted his views. He continued to do this and as more evidence kept accumulating he modified his opinions in agreement with the current state of science.
sf
Dear Mr. Walter Sobchak,
I reposted Mr. Kevin Brooks news letter. On 6/22/2019 he wrote:
” On May 30, 2019 Tatiana V. Tatarinova, Associate Professor of Biology at
the University of La Verne in La Verne, California, presented her team’s
paper “Population history of Russian medieval nomads” at the “Centenary of
Human Population Genetics” conference in Moscow, Russia during the session
called “North Eurasia: where West meets East”. ….”
This explains why the links go to Russian Text. Perhaps eventually we’ll get English abstracts.
You write:
“The Khazar theory is limited to a small bunch of cranks with a very definite political agenda.”
Definitely true.
But it was not so in 1976 when “The Thirteenth Tribe” (Arthur Koestler) was published. My dad was very much interested. Being a Khazar sounded much better than being the “Ost-Juden” that we were.
For me today, being a “Yehudi Galuti” (Ghetto Jew) does not sound so bad.
Genomic Medicine: Is it becoming a reality?
“How Drug Companies Are Using Your DNA To Make New Medicine: Partnership between Glaxo and 23andMe has produced six potential drug targets but raises ethical questions” By Denise Roland on July 22, 2019
https://www.wsj.com/articles/23andme-glaxo-mine-dna-data-in-hunt-for-new-drugs-11563879881
For the past year, 23andMe has been sharing its huge trove of genetic data with drug giant GlaxoSmithKline PLC, which took a $300 million stake last summer. That collaboration has so far produced six potential drug targets, and the companies expect to start human trials on at least one candidate drug next year. …
The company says it has sold around 10 million test kits and analyzed more than eight million people’s DNA, making it the largest repository of human genetic information in the world. That information is especially valuable to drugmakers because the majority of 23andMe’s customers also choose to answer questionnaires on their health.
For Glaxo, the 23andMe deal is part of a wider effort to use genomic data to hunt for new drugs. The company also is involved in research projects with government-funded genome collections in the U.K. and Finland. It hopes that genomics could help solve a problem that plagues the pharmaceutical industry: a high failure rate in turning promising leads into drugs that work. …
Glaxo expects the collaboration to accelerate the costly and arduous process of finding patients to join clinical trials. … One of Glaxo and 23andMe’s targets is a rare mutation in a gene called LRRK2 that raises the risk of developing Parkinson’s. Around one in a thousand people are carriers, which would make them very difficult to find using traditional trial-recruitment tactics. 23andMe has contact details for 7,500 carriers it can invite to participate.
23andMe asks customers to consent to their genetic information being used for research purposes, and the firm says 80% say yes. … “You get this gigantic valuable treasure chest, and people are going to wind up paying for it twice,” said Arthur Caplan, a professor of bioethics at NYU School of Medicine. “All the people who sent in DNA will be paying the same price for any drugs that are developed as anybody else.”
… The company says it only shares high-level summaries of its data with Glaxo, but the partnership highlights a broader privacy concern: that 23andMe’s customers may not have realized their data would be used by the pharmaceutical industry. … A 23andMe spokesman said customers are sent letters informing them about for-profit collaborations, and that they have the option of withdrawing consent for that research.
I thought the above article was interesting, except that the so called ethics experts, especially the odious Arthur Caplan, had absolutely nothing interesting to say.
It does strike me that the gains from Genomic medicine will come slowly and incrementally, like the ability to identify trial candidates. I hope that when we look back in 10 or 20 years we will be able to say that it has been a very worthwhile effort.
23andMe asks customers to consent to their genetic information being used for research purposes, and the firm says 80% say yes. … “You get this gigantic valuable treasure chest, and people are going to wind up paying for it twice,” said Arthur Caplan, a professor of bioethics at NYU School of Medicine. “All the people who sent in DNA will be paying the same price for any drugs that are developed as anybody else.”
“I am not going to do this cost-free yet worthwhile thing for mankind, because big pharma isn’t going to give me a discount!”
amir sirialasan has a blog http://amirsariaslan.com/archives/1010
Boris Johnson’s two top deputies are South Asian:
“First up is Sajid Javid, who moves from the Home Secretary’s office to Chancellor of the Exchequer. The second-most powerful position in the British government, the chancellor sets the government budget and acts as a high-level representative for the prime minister. … Javid is a self-made millionaire the son of Pakistani immigrants. But Javid’s fervent capitalism fits well with Johnson’s evolving pro-capitalist message. Javid has earned positive coverage for his Home Office management. …”
“Then, there’s Priti Patel. A former Cabinet minister known for her conservative credentials, Patel replaces Javid at the Home Office. That puts her in charge of Britain’s domestic security management, especially in relation to counterterrorism operations. It’s a challenging job known for making and breaking careers. Notably, her Twitter background features Ronald Reagan and Margaret Thatcher.”
https://www.washingtonexaminer.com/opinion/boris-johnson-just-cleaned-house-in-the-uk-and-his-new-cabinet-is-far-more-conservative
Razib – I thought you would find this interesting. Nothing too surprising..
https://fivethirtyeight.com/features/what-americans-know-about-religion-and-what-they-dont/