Razib Khan One-stop-shopping for all of my content

October 29, 2018

Muslims have always known how weird Saudi Arabia is

Filed under: Islam,Saudi Arabia — Razib Khan @ 9:40 am

I’m not a big fan of Hasan Minhaj’s “Millennial smug” style of comedy. What it really reminds me is Brad Stine’s “Christian comedy.” It’s aimed toward ingroups and comes off as tone-deaf and stupid to outgroups. So you know what you’re getting into.

That being said, as someone who is Muslim Minhaj has always “gotten” the issue with Saudi Arabia. Most Muslims I have known, from very conservative Salafi types to irreligious cultural varieties, have strange and strong attitudes toward Saudi Arabia. Even the most conservative often have mixed attitudes, because Saudi Arabia may sponsor Salafism worldwide, but no one can deny that the ruling family are hypocrites in their private practice.

Believing Muslims though have to admit that the Saudis are currently the guardians of Islam’s holy sites, and, the kingdom provides a great deal of money for various Muslim causes as well as Muslims more generally. And of course, Saudi Arabia has been a source of employment for many Muslims from outside the kingdom for many decades.

The fact that we are “having a discussion” about Saudi Arabia as if there is a discussion to have is a testament to the power of money in public discourse, and how one can buy elite complicity.

October 28, 2018

Open Thread, 10/28/2018

Filed under: Open Thread — Razib Khan @ 1:35 pm

An old friend from college has a new book out, Augmented Mind: AI, Superhumans, and the Next Economic Revolution. This looks to be in Jim Miller territory.

Sex in humans may not be binary, but it’s surely bimodal. Jerry Coyne is a well known evolutionary biologist who is also a vocal atheist. He’s now emeritus from the University of Chicago, and so I feel he’s kind of “out of step” with the culture. For example, within this post, which I generally agree with, he uses the term “transsexual” when most academics would use “transgender” to mean what he means. A lot of biologists don’t comment on this issue for two reasons. First, it’s politically fraught and you can’t really win. Second, the terms, norms, and frameworks are changing fast and constantly, so that people don’t even know what they’re addressing.

Speaking of fraught, the first robust SNP hits for male nonheterosexual behavior were reported at ASHG. The preprint should be out in less than four months. Antonio Regalado has already reported on it, Genes linked to being gay may help straight people get more sex. We plan to interview one of the authors on our podcast.

Recently talked to some people from Andy Kern’s lab about implications of Wright-Fisher vs. non-Wright-Fisher models in terms of spatial heterogeneity. It really makes me excited for the “forward simulation revolution.” Talking to people in evolutionary genomics that isn’t focused on getting NIH grants for human research, and it is clear why Matt Hahn has stated that there’s already enough data produced for many years to come.

A Tentative OUT OF INDIA Model To Explain The Origin & Spread Of INDO-EUROPEAN LANGUAGES. I’m skeptical of the conclusion, but this post has a lot of interesting information. Additionally, I think that AASI ancestry is going to be found in the Indus Valley between 3000 and 2000 BC…but I’m not totally sure. Johanna Nichols’ work is recommended though.

The Fifth Column podcast talks to Sarah Haider. In general, I’m a fan of the podcast.

Recently I’ve been thinking about China and Saudi Arabia. Recently we’re looking skeptically at our elite’s ties with Saudi Arabia. But what about China? Many researchers and businesspeople “have” to work with China, and unlike Saudi Arabia, it seems implausible that we can “avoid” interactions. But there are plenty of human rights issues with the Chinese state. The only conclusion I draw is that people need to be careful about getting on their high horses. Researchers who criticize working with the Saudis or in Israel should also consider them working with Chinese colleagues who are under the purview of a problematic state…but that penalize their Chinese colleagues, and would be harder and harder to maintain over the years.

Fast Hierarchical Bayesian Analysis of Population Structure.

The truth behind America’s most famous gay-hate murder. The media and the mainstream institutions basically colluded to create a narrative more politically convenient. Are we surprised?

15,000 Year Old Spearpoints Reveal Details About The Peopling Of The Americas.

When It Comes to Sleep, One Size Fits All.

Rare genetic sequences illuminate early humans’ history in Africa

The shadow of culture persists

Filed under: Albion's Seed,American historical "dark matter",American History — Razib Khan @ 12:40 pm

A new working paper, Ancestry of the American Dream, presents some unsurprising results:

Income inequality and intergenerational mobility—the degree to which (dis)advantage is passed on from parents to children—are among the defining political challenges of our time. While some scholars claim that more unequal countries exhibit a stronger persistence of income across generations, others argue that mobility rates are unaffected by social equality and are equally low in most societies. We compare economic opportunity across U.S. areas populated by different European ancestral groups, and find a substantial variation that mirrors current differences across descendants’ countries of origin: mobility is highest in areas dominated by descendants to Scandinavian immigrants, lower in places where the Italian, French, or Germans settled, and lower still in areas with British ancestral origins. A similar pattern is observed for income equality, which gives rise to a gradient closely resembling the “Great Gatsby Curve” across European countries. We provide suggestive evidence that these differences arise mainly at the community level and that similar mobility patterns apply to the black minority population, so they are not simply a function of ancestral groups themselves being more or less mobile. A more plausible explanation is that cultural differences among immigrant groups gave rise to local economic and social institutions that are more or less conducive to mobility. Our findings suggest that present cross-country differences in inequality and intergenerational mobility are real and may have deeper historical origins than has hitherto been recognized.

Looking at county-level ethnicity data from the 1980 census as well as the income tax data that Raj Chetty uses, the authors found some interesting patterns in the “synthetic countries” within the USA:
 

The overall thesis that the culture immigrants brings persists for generations seems plausible.  In Not By Genes Alone Robert Boyd and Peter Richerson report data from Illinois where farmers of German-American background behave very differently from their neighbors of Anglo-American background when given the same conditions. Anglo-Americans behaved much more like homo economicus . They sold their farms when the market price was right. In contrast, the German-Americans would attempt to keep the farms within the family even through periods when it was not economically rational.

My point is that there are non-economic aspects of culture that may not be picked up by these analyses which have economic consequences.

1856 Republican vote as a proxy for Yankee dominance

The second issue is that not all Americans of “British” origin are the same culturally. Long-time readers know where I’m going with this. The argument in Albion’s Seed: Four British Folkways in America is that English American New England Yankees are culturally very distinct from British Americans from the South, whose origins often range from southwest England to the borders with Scotland, as well as Ulster-Scots who arrived in the middle of the 18th century.

If you look at at the map within the preprint you see that Utah has a high fraction of British Americans, but its socio-demographic profile is more like the Upper Midwest, dominated by Scandinavians and Germans. The British Americans of Utah, of course, descend to a great extent from New England Yankees, as well as various Northern European immigrant groups converted to Mormonism by 19th-century missions. Though similarly socially and politically conservative, Utah Mormons are culturally very different from white Southerners. One way to describe it is that Utah Mormons have a lot of social cohesion and an orientation toward communalism. This is in line with their Yankee origins. Yankee migrants to the West organized their towns very differently from those from the South (to be frank, Southerners didn’t much organize their towns at all in comparison to Yankee rationalism and collectivism).

Going back to the Upper Midwest, it is important to recall that this was once termed  the “Yankee Empire”. Before 1850 the whites of New England were the most fecund subculture in the United States, and they overflowed to upstate New York, and then the northern swath of Ohio, Illinois, as well as dominated Michigan and the Upper Midwest.

Today the Upper Midwest states of Minnesota and Wisconsin are among the least “Anglo-American” predominantly white states because of the high fraction of Northern Europeans. The rise of socialist politics and the persistence of German-speaking communities deep into the 20th century attest to this density of immigrant ethnicities. But, there were cultural affinities between the natives and the immigrant groups, in particular, Protestant Germans and Scandinavians and Yankees. Unlike in old New England, the developers of the Yankee Empire welcomed migration to settle the farms of the Midwest. Though a plain economistic reading works (there was a deficit of labor and surplus of land), I suspect that conflicts between Irish Catholics and Yankees in New England, as opposed to Scandinavians and Germans (many of whom were Catholics) and older Yankees in the Midwest, were functions of contrasts in complementarity and cultural affinity.

An opposing case to Northern European complementary with the ethos of the Yankee Midwest is that of Germans (and Swedes and Czechs) in Texas. These immigrant groups were settled in the uplands of central Texas because these were the least fertile lands. In short, the white Anglo-Texans often cheated the European ethnics because they could. These Northern European Texan groups were much of the source for the progressive and Left-wing populist tradition in the politics of this state in the 20th century. But over time they have by and large assimilated to white Anglo-Texan norms and folkways. That is, they are not much different than the descendants of white British Texans.

This goes to show you that numbers matter. Where in the Midwest the original Yankees were overwhelmed demographically, that did not happen in Texas. Where in the Midwest the Northern Europeans amplified the collective populist moralism of the Yankees, making it more institutional robust with explicit socialism, in the South the Northern Europeans were eventually absorbed into the region’s customary hierarchal individualism.

Addendum: The authors of the above paper showed that the mobility impacted blacks as well as whites, indicating that the dominant ethos had policy implications which shaped society on the macroscale.

October 27, 2018

Laws of engineering are meant to be broken

Filed under: Genomics — Razib Khan @ 8:54 pm

A reader pointed out a very interesting passage in Richard Dawkins’ The Greatest Show on Earth: The Evidence for Evolution on the future possibilities of genome sequencing. Since the book was published in the middle of 2009, it is quite possible the passage was written in 2008, or even earlier.

Unfortunately for Dawkins’ prognostication track-record, but fortunately for science, he was writing at the worst time to make a prediction:

…the doubling time [data produced for a given fixed input] is a bit more than two years, where the Moore’s Law doubling time is a bit less than two years. DNA technology is intensely dependent on computers, so it’s a good guess that Hodgkin’s Law is at least partly dependent on Moore’s Law. The arrows on the right indicate the genome sizes of various creatures. If you follow the arrow towards the left until it hits the sloping line of Hodgkin’s Law, you can read off an estimate of when it will be possible to sequence a gnome the same size as the creature concerned for only £1,000 (of today’s money). For the genome the size of yeast’s, we need to wait only till about 2020. For a new mammal genome…the estimated date is just this side of 2040

Obsolete plot from The Greatest Show on Earth

The cost for a sequence here is somewhat fuzzy. The first assembly of a genome sequence of an organism is much more difficult than subsequent alignments of later organisms (though more in computation than in the sequencing). But, the upshot is that Dawkins was writing when “Hodgkin’s Law” was collapsing. From 2008 to 2011 Moore’s Law was destroyed by the sequencing revolution pushed forward by Illumina.

Though you can get a $1,000 consumer human sequence today, the reality is that this is for 30× coverage. For lower coverage, which means you aren’t as sure of the validity of any given variant, the price drops rapidly. And for the type of evolutionary questions Dawkins is interested in, the coverage needed is far lower than 30× (you probably want to get a larger number of samples than a single high-quality sample).

October 24, 2018

The Insight Show Notes — Season 2, Episode 5: Reflections on ASHG 2018

Filed under: ASHG,Genetics — Razib Khan @ 3:46 pm

The Insight Show Notes — Season 2, Episode 5: Reflections on ASHG 2018

This week on The Insight (Apple Podcasts, Stitcher and Google Play) Razib Khan and Gareth Highnam discuss our impression of the most recent meeting of the American Society of Human Genetics.

The ASHG meetings have been putting technology front and center. That is because human genetics, that is, human genomics, have been very technology-driven fields of science. Many of the commercial vendors focus on information technology and data storage, due to the copious production of DNA sequence in high-throughput genomics.

There was also extensive discussion about the need to diversify genomics from an ethnic perspective for more accurate medical inference. Here’s an article on this topic: Genetics has learned a ton — mostly about white people. That’s a problem.

Massive sample sizes and whole-genome analyses have been transforming our understanding of human variation and disease. One area where we saw new results was in the domain of “missing heritability.” See this: Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits.

Many people at the meeting were talking about the intersection of race and genetics, triggered by an article in The New York Times: Why White Supremacists Are Chugging Milk (and Why Geneticists Are Alarmed). Here is the ASHG response: ASHG Denounces Attempts to Link Genetics and Racial Supremacy.

We discussed two important results that were novel presented at the conference. Further refinement of the human mutation rate from the sequencing of a well-known pedigree. And, the first GWAS hits that are likely to be replicated for homosexuality.

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 5: Reflections on ASHG 2018 was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The crash of the cost of genome sequencing

Filed under: Genomics — Razib Khan @ 10:24 am

It’s been a wild 10 years. There’s a reason that data compression companies are a big thing in genomics now.

October 23, 2018

The state origins of “modern humans” in 2018 (it’s a flux)

Filed under: Human Evolution — Razib Khan @ 10:33 pm

After reading the supplements to the new Siberian paper I have a few general thoughts that I want to lay out.

First, the clines vs. clusters considerations seem to be one we need to revisit. Like the expansion of Native American peoples ~15,000 years ago, it seems that the “Out of Africa” migration pulse happened so quick that a lot of different groups emerged at the same time. In the new paper the earliest proto-“Ancient North Eurasians” can be modeled as most similar to the West Eurasian branch of humanity (sans Basal Eurasian), but with some minor component affinity to East Eurasians. It could but that this is a function of admixture between the distinct lineages. Or, it could be that there was a fair amount of substructure within the post-Basal Eurasian “Out of Africa” meta-population.

The problem with the idea of lots of structure within this population that I see is that it might depend on the plausible effective population sizes. I’d need to know more ethnography than I do, but it seems not impossible for ~10,000 humans to be highly structured in Paleolithic social contexts. But, this would entail a great deal of xenophobia and likely inter-group conflict.

Second, I am convinced that there were earlier “Out of Africa” migrations. Many of them. As John Hawks pointed out at ASHG the Neanderthals and Denisovans seem to be descended from a migration of African hominins that dates to somewhere after 1 million years ago. This means they replaced hominins that were present in Eurasia for ~1 million years already. Geneticists and paleontologists have both also discovered suggestive clues to likely “proto-modern” human populations that were present and admixing before the rapid expansion of Eurasians and Australasians ~40-50,000 years ago. With more ancient DNA and subtle analysis, I think we’ll find that modern human absorbed some layers between that of Denisovans and Neanderthals and the most recent expansion.

Finally, I think multi-regionalism within Africa is between plausible and likely, and that major back-to-Africa migrations that modify/challenge “Out of Africa” are possible. We are learning a lot. But that means simple elegant models are falling by the wayside.

Reflections on ASHG Meeting 2018

Filed under: ASHG,Genetics,Genomics,Illumina — Razib Khan @ 10:17 pm

Another meeting of the American Society of Human Genetics has come and gone. I’ve been going since 2012, and so want to post some observations of how things have changed. This is a big conference. From less than 1,000 people in the late 1970s to nearly 10,000 today.

First, more genomics, less genetics.

The meeting dates to the late 1940s, and originally focused on the classical genetic analysis of human characteristics. Consider the pedigree one might find in a medical text.

Over the past generation more and more of the presentations and posters focus on genomics, surveys of the whole totality of our DNA sequence. This is where medicine and human genetics more generally is moving in any case.

Vendors such as Illumina loom large, but the firehose of data is so powerful that compression companies also arrive at ASHG. In other words, ASHG is a combination of a science, medical, and tech, conference.

Second, a major shift in focus outside of traditional European study populations.

ASHG foregrounded the focus on Africa and other non-European regions to highlight the importance of the capturing of global genetic variation. A fair number of presentations and posters were on this topic, as well as a series of plenary talks.

One thing I’ve noticed is that many talks and posters now present data and results which have been posted as preprints. In past years a lot of novel and new results were first presented at the conference, but now the meetings seem to be more like a halfway point between posting the preprint and the publication of the final paper. This means that networking and career development have become as important as the science itself.

Probably the most notable result that hasn’t been posted as a preprint was the first robust signals of association between genetic variations and homosexual orientation in men. Though there is a history of these reports, this one is clearly a case where the authors went through all the statistical checks to make sure these are true hits. Some in the audience reacted negatively, but the research group was really careful.

Exciting times in the world of genetics and genomics. Very excited for what 2019 brings.

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


Reflections on ASHG Meeting 2018 was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

October 22, 2018

The phylogenetic trees falling on the tundra

Filed under: Historical Population Genetics,Population genetics,Siberia — Razib Khan @ 9:59 pm


A massive new ancient DNA preprint just dropped, The population history of northeastern Siberia since the Pleistocene:

…Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of “Ancient North Siberians” (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and “Ancient Paleosiberians” (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the “Neosiberians” from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

The preprint is very interesting and thorough, and the supplements are well over 100 pages. I read the genetics and linguistics portions. They make for some deep reading, and I really regret making fun of Iosif Lazaridis’ fondness for acronyms now.

I will make some cursory and general observations. First, the authors got really high coverage (so high quality) genomes from the Yana RS site. Notice that they’re doing more data-intense analytic methods. Second, they did not find any population with the affinities to Australo-Melanesian that several research groups have found among some Amazonians. Likely they are hiding somewhere…but the ancient DNA sampling is getting pretty good. We’re missing something. Third, I am not sure what to think about the very rapid bifurcation of lineages we’re seeing around ~40,000 years ago.

The ANS population, ancestral by and large to ANE, seems to be about ~75% West Eurasian (without much Basal Eurasian) and ~25% East Eurasian. Or at least that’s one model. Did they then absorb other peoples? Or, was there an ancient population structure in the primal ur-human horde pushing out of the Near East? That is, are the “West Eurasians” and “East Eurasians” simply the descendants of original human tribes venturing out of Africa ~50,000 years ago? Also, rather than discrete West Eurasian and East Eurasian components, perhaps there was a genetic cline where the proto-ANS occupied a position closer to the former, as opposed to some later pulse admixture?

Without more ancient DNA we probably won’t be able to resolve the various alternative models.

Open Thread – Brown Pundits

Filed under: Uncategorized — Razib Khan @ 9:25 pm

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

October 21, 2018

Open Thread, 10/21/2018

Filed under: Open Thread — Razib Khan @ 11:20 pm

You may have noticed I haven’t been posting much. Busy with other things, like ASHG, work, family, etc. I don’t normally post “won’t be posting often” notices, as no one really cares much about blogs…but when I go into lower production mode people sometimes worry. No reason to worry.

Tim Blanning’s Frederick the Great: King of Prussia is an excellent book. So is The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815. Finally, Iron Kingdom: The Rise and Downfall of Prussia, 1600–1947. One of the most interesting things about Frederick the Great: King of Prussia is how Blanning recounts the importance of personally playing and repeatedly listening to music in the life of the German monarch. He was apparently a very competent flutist.

There was talk about ASHG about the Amy Harmon article, Why White Supremacists Are Chugging Milk (and Why Geneticists Are Alarmed). It seems most of the geneticists I know personally were contacted by Harmon at some point over the last two years. A lot of work went into this. Many of our quotes were obviously not used. That’s called journalism.

There was a period when many frog-Nazis were on Twitter brandishing a particular STRUCTURE bar plot (since frog-Nazism has been severely purged by Twitter I see this far less often). I understand that many journalists and people of the “chattering-thinking” classes are strongly influenced by what they see on Twitter in terms of their perception of what’s going on in the world.

Additionally, to be honest for many white people racism is somewhat an abstraction. They need to make recourse to instrumental variables. The SNL election night sketch which shows white liberals talking about how it’s never been so bad, and black comedians nodding along, illustrates a real trend, and that is that many white liberals feel like there has been a massive upsurge of racism over the past few years.* But as a nonwhite person who has lived in this country since the early 1980s, it is clear that America is far less racist than it was back then, and our society has been defined by a gradual decrease in racial prejudice. White support for laws banning interracial marriage went from about 25% in the 1980s to 10% in 2002, when the question stopped being asked because it was such a marginal viewpoint.

A story about the social and political of implications evolutionary population genetics is a reasonable one. And, it might make a somewhat interesting academic paper as well. But the prominence of this piece to me cuts to a deep disagreement about the nature of racial conflict and difference within human societies. Immanuel Kant’s abstract and intellectual reflections on race may be alarmingly white supremacist to many moderns, but the profitable character of exploitation of sugar and the utility of slavery in the West Indies, and the rise of the West in a much more robust manner as signified by the McCartney Mission in the 1790s, was far more important in shaping the emergence of a very vigorous white supremacist ideology in the late 19th century which culminated in Madison Grant and Lothrop Stoddard.

I enjoy discourses on the intersection of race and genetics as much as the next person. I write them myself. But the most concrete thing I can do for the “racial question” is what I’m doing already: participating in the amalgamation of very distinct pedigrees and producing Americans related to a much larger fraction of the world’s population. White Americans who believe in the cause of racial social justice and anti-racism can do something very easily if they so choose: select a non-white partner and produce mixed children. If you are already partnered up, encourage your children to do so. This will make a bigger difference than retweeting how great diversity is, while not living it in your own life. For white progressives, do understand that your nonwhite allies notice the overwhelming pallor of the types of people who become and remain your intimates. You spend an afternoon on a racially diverse panel. Why not spend life in a racially diverse manner? Because I am a political outsider to these issues nonwhites probably feel more comfortable telling me how they perceive you don’t have much skin in the game. An ounce of action is worth a pound of talk (also, you can proactively give money to nonwhite people from your own disposable income).

The above is not a troll at all. I’m not the sort of person who thinks that the type of person another human being becomes friends with, or partners with, is my business. Do as you wish. But if you accept the premises of most forms of anti-racist talk, then Norman Podhoretz’s 1963 essay which enjoins action still applies.

The Uralic podcast is up. Brown Pundits now have a podcast.

This Elizabeth Warren fact-check by the Daily Caller Foundation’s Emily Larsen is pretty good. Having to listen to political pundits talk about ancestry testing all week has been painful. More need for education….

ASHG photo that I find most amusing.

As most of you probably know, the human genome still has gaps. I felt this year more people talked about those gaps, and how to fill them in. Also, lots of African genetics (this was by plan).

May write some more tutorials soon. Depends on the time.

The Slow Burn podcast ended with talking about Juanita Broderick. The Broderick allegations really have shot into prominence over the last few years. But if the Republicans knew about them in detail, that does make their determination to impeach Bill Clinton far more comprehensible.

I don’t have much to say about the Khashoggi thing you haven’t heard elsewhere.

A new analysis of CEU mutation rates is there is an age effect, most mutations are paternal, and, there might be variation in increases in mutations with older individuals by family.

* Most of my white friends tend to point to particular media anecdotes. As a nonwhite person I have not perceived any difference, and I travel in various parts of the country. Your experience may vary.

October 17, 2018

The Insight Show Notes — Season 2, Episode 4: Finnish Genetics

Filed under: science — Razib Khan @ 11:02 am

The Insight Show Notes — Season 2, Episode 4: Finnish Genetics

Midsummer in Finland

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we discussed the prehistory and genetics of the Uralic peoples, with a particular focus on the people of Finland, who are among their most numerous exemplars.

We mentioned that the Uralic languages have a northern distribution, extending from north-central Siberia to northern Europe.

See for yourself:

We mention two recent papers of interest:

We discussed the past 20 years of debate on the origin of the TAT-C/N1c Y chromosomal haplogroup. This male lineage is found at high frequencies all across the northern fringe of Eurasia, and in particular among Uralic populations.

Here is an early paper on the topic: Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. If you want to know the origin of the name “TAT-C”, listen to the podcast! Spencer tells you.

There was a lot of discussion about Uralic culture. For example Kalevala and blood sausage. The eastern Baltic was also one region where farmers from Anatolia never migrated. See The genetic prehistory of the Baltic Sea region.

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 4: Finnish Genetics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The expansion of the polar people

Filed under: Finland,History,science — Razib Khan @ 10:58 am

The expansion of the polar people

Sami in the far north of Europe

Since the development of agriculture 12,000 years ago, the cultural and genetic landscape of our world has been transformed by the emergence of peasants as the dominant demographic. For most of the recorded history, the average human was a peasant; a laboring tiller of the soil.

There were of course exceptions. Some peoples took up pastoralism. Others specialized in extracting resources from the sea — such as fisherman. And of course, there were hunter-gatherers who continued to practice a lifestyle as old as the human race itself.

Muskox in the Taimyr Peninsula

Though we often think of hunter-gatherers in a tropical context, the reality is that some of the most successful practitioners of this lifestyle have flourished in and around the Arctic. Not only have they flourished, but they have vastly expanded! For instance, the Thule culture of North America famously replaced the Norse agriculturalists of Greenland in the 15th century.

But perhaps the most speculator expansion of a non-agriculturalists in the north has been that of the Uralic peoples. A paper titled “Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations” has an excellent map which illustrates the geographic span of this language family:

Citation: Tambets, Kristiina, et al. “Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations.” Genome biology 19.1 (2018): 139.

Over twenty years ago researchers noted that one particular Y haplogroup lineage, N1c, was very common among Uralic peoples. Notice the overlap in distribution between this lineage and the Uralic populations below.

Distribution of N1c

The question then emerges: did the Uralic peoples come from the east, into northern Europe, or were they indigenous to northern Europe and expanded eastward? Examining patterns of genetic diversity indicate that this Y chromosomal lineage emerged in Siberia and later spread to northern Europe. Why? Because diversity accumulates in regions where the lineage has been present the longest.

Citation: Lamnidis, Thiseas Christos, et al. “Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.” bioRxiv (2018): 285437.

New research from ancient DNA has clarified the timing of the arrival of these Siberians, Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.

What we do know from modern genetic variation is that the Uralic people, including the Finns, seem to have recent Siberian affinities. In contrast, most other Northern Europeans do not have this — making it even more distinct. This Siberian affinity is strongest in the Sami hunter-gatherers of the far north.

Samples from a population in the Kola Peninsula of northern Russia from to 3,500 years ago yielded individuals who were even more Siberian than the Sami — as you can see in the admixture plot to the left. In particular, the Siberian ancestry of the Finnic people seems to be similar to that of the Ngananasn people of the Taymyr peninsula in Russia.

Looking at patterns within the genome of these ancient people, researchers have concluded that these people are the product of mixing between Siberians and indigenous European hunter-gatherers, which began to occur ~4,000 years ago. This aligns with other work that suggests that the Ceramic Comb Culture, the dominant Mesolithic hunter-gatherer society of northeast Europe before the expansion of agriculture, lacked Siberian ancestry.

Nenet Samoyed people

Where does this leave us? If we use genetics as a guide, it seems that around ~4,000 years ago a migration of Arctic hunter-gatherers swept out of the northern fringe of Siberia to the west. These people were likely related to the easternmost of modern Uralic peoples: the Samoyed tribes. The Y chromosomes of western Uralic peoples, such as the Sami and Finn, carry the hallmarks of ancestry similar to the Samoyeds. But the mitochondrial lineage is almost wholly similar to their European neighbors. Therefore, it seems that the spread of Uralic languages westward was due to the migration of males.

One of the implications of these conclusions is that the Uralic languages may have arrived in the Baltic after the Indo-European languages! In much of Estonia and southern Finland, the Corded Ware culture, presumed to be associated with Indo-Europeans, predates 2000 BC by centuries.

Though we often imagine that history and culture move in a singular direction, toward agriculture, the Uralic people may be an instance of an exception. If it is correct that hunter-gatherer Siberian men moved into large areas of northeastern Europe, and culturally assimilated more numerous peoples, some of whom were agriculturalists, it may indicate that the trajectory of history is more winding and complex than we may imagine.

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


The expansion of the polar people was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

October 16, 2018

Open Thread – Brown Pundits

Filed under: Open Thead,Open Thread — Razib Khan @ 12:24 pm

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

October 15, 2018

Elizabeth Warren carries Native American DNA – she’s running!

Filed under: Uncategorized — Razib Khan @ 3:19 am

Since I’ve talked about this issue before, Warren releases results of DNA test:

There were five parts of Warren’s DNA that signaled she had a Native American ancestor, according to the report. The largest piece of Native American DNA was found on her 10th chromosome, according to the report. Each human has 23 pairs of chromosomes.

“It really stood out,” said Bustamante in an interview. “We found five segments, and that long segment was pretty significant. It tells us about one ancestor, and we can’t rule out more ancestors.”

He added: “We are confident it is not an error.”

The proportion of ancestry is not large. But it is clearly there. They compared to the Utah white and British European 1000 Genomes populations, which is a good standard for Old Stock Anglo-Americans. She’s clealry an outlier, with about an order of magnitude more “Native American” ancestry. So it’s unlikely to be some artifact.

There is some talk in the article about lack of reference populations. But remember, the key is to identify Native American ancestry, so all of this should coalesce back 10-15,000 years ago. Compared to the divergence from Northern Europeans, this is going to jump out against the genetic background.

So does Elizabeth Warren have Native American ancestry? 99% sure that that is a yes. Is she going to run? Well, I wouldn’t say 99%, but that seems likely too….

(I doubt she’ll do it, but it would be neat if she released her raw results)

Open Thread, 10/15/2018

Filed under: Open Thread — Razib Khan @ 1:16 am


I pinned the above chart to my Twitter profile because I’m “trying to make it happen.” It was David Mittelman’s idea, and the data was courtesy of ISOGG, but putting it together as a graph has really brought home to people how the consumer genomic landscape has changed over the last half a decade.

The plot to the right, which shows a smoothed chart of the total number of kits over time, is also important.

I recorded a podcast for the Urbane Cowboys last week. It should go up today, so watch for it. I talked about a variety of topics, so I don’t know how it will drop in regards to editing.

Was talking to a friend about the importance of emotion in reasoning, or at least how emotion allows us to reason better. He asked about books, and Descartes’ Error came to mind. But I’ve read about critiques of its interpretation of the history of science and philosophy, though I think the big picture conclusion is probably still valid.

Will be at ASHG this week. Mostly I’m going to learn more about African genomics. Not as much on pop-gen as in previous years. If I approach your poster, don’t worry that I’m going to tweet or write about. Just be cool.

Noticed Tim Blanning’s massive survey of Frederick the Great is now less than $10 on Kindle. Because of the World Wars, I think we learn a lot less about Prussia from 1700 on than we otherwise would. Blanning’s The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815 is also excellent.

I’m listening to John Keegan’s A History of Warfare on Audible. To be honest I think I’m much better at reading than listening. This should be surprising. In courses, I generally prefer to learn from the textbook as opposed to listening to lectures. And I have a lot of experience reading over my lifetime. Less so listening.

Xuzi: The Complete Text has been a difficult read for me. I’ve gone back and reread passages several times. It is definitely on the discursive side. That being said, I have come to a strange observation: Xunzi’s view of religion is strangely similar to Ludwig Wittgenstein’s. Here from the Stanford Encylopedia of Religion:

He opposed interpretations of religion that emphasize doctrine or philosophical arguments intended to prove God’s existence, but was greatly drawn to religious rituals and symbols, and considered becoming a priest. He likened the ritual of religion to a great gesture, as when one kisses a photograph. This is not based on the false belief that the person in the photograph will feel the kiss or return it, nor is it based on any other belief. Neither is the kiss just a substitute for a particular phrase, like “I love you.” Like the kiss, religious activity does express an attitude, but it is not just the expression of an attitude in the sense that several other forms of expression might do just as well….

This seems similar to Xunzi’s belief that religious rituals were an important part of life, even if supernatural beings did not exist. Though Wittgenstein seems to have had some sort of fundamental mystical religious beliefs, whereas Xunzi was more of a naturalist.

The whale shark genome reveals how genomic and physiological properties scale with body size. Dim on comparative genomics. But I do like sharks.

Harvard and the Brigham call for more than 30 retractions of cardiac stem cell research. The medical science literature is going to yield a lot of problems sooner than later.

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease.

The Democrats Have a Latino Problem Hispanic voters were supposed to be the party’s future. It’s not working out that way.

Jason Collin’s on global fertility projections.

Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters.

Hidden ‘risk’ in polygenic scores: clinical use today could exacerbate health disparities.

Identity inference of genomic data using long-range familial searches. If they solve the Zodiac killer, forget about the worries.

Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.

Adaptive walks on high-dimensional fitness landscapes and seascapes with distance-dependent statistics.

Existence and implications of population variance structure.

Megalakes in the Sahara? A Review.

On this week’s episode of The Insight we’re talking about the genetics of the Uralic peoples, and Finns in particular.

Have you been noticing more intrusive and stranger advertisements in the media? That’s because it’s in trouble. The whole sector. But you knew that.

Nikki Haley shows she’s a good politician in regards to religion too

Filed under: Nikki Haley,Politics — Razib Khan @ 12:29 am


This week on The Remnant podcast, Jonah Goldberg, whose wife works for Nikki Haley, expounded at length about her skill as a politician. His point, which is legitimate, is that Haley is well liked by the broad mass of Trump-supporting Republicans (if not elite pro-Trump idealogues), as well as Trump-skeptical conservatives.

I’ve known of Nikki Haley since 2004, a few years after Bobby Jindal came onto to the national scene. Both are conservative Indian American Republicans elected as governors in the South. But there are differences between the two. While Haley can arguably “pass” as white, Jindal cannot (both are of Punjabi ethnicity). But a bigger difference has been their attitude toward religion: Jindal has worn his Christian conversion and faith on his sleeve, while Haley has been much more low-key. Throughout her career, Haley has admitted that the Sikh gurdwara remains a part of her life, despite her conversion to Methodist Christianity. Could you imagine Jindal saying such a thing about a Hindu temple?

The above is a video clip of Haley during a 2014 visit to India, where she visited the Golden Temple with her husband. When asked about her conversion to Christianity, she avers the sincerity of her belief. But Haley also speaks in an ecumenical language and seems to express the view that her choice of religion was in keeping with her culture as an American. Her turn to Christianity was not a denial of Sikhism, which she seems to see as grounded in India.

I can’t look into Haley’s heart, and to be frank her religious faith is not my business. But, I think I can say many people of subcontinental background tend to view converts to American Christianity as opportunists or somehow lacking in cultural pride and internal strength. American evangelical Protestant acquaintances would often mock Hinduism in front of me, despite the fact that I have a Muslim name and have been an atheist since I was a small child. To convert to Christianity is perceived by some to be conceding the point of that mockery.

And yet above Haley seems to be interpreting her conversion to Christianity as an expression of her alignment with the Dharma of the land in which she grew up, the United States. You may agree or disagree with her, but her emotional expression above certainly does make it seem that she retains a deep fondness for her Sikh upbringing.

October 13, 2018

Brown Pundits podcast, the Browncast episode 1

Filed under: Podcast — Razib Khan @ 11:02 pm

I’ve already submitted to iTunes and Stitcher. So I’ll post those links for those of you who want to subscribe that way….

The leisure class of the ancient world

Filed under: History,trade — Razib Khan @ 8:06 pm

The years before 1914 and the First World War are often termed the “first age of globalization” (with our current era the second). But that’s a little short-right, even though arguably correct in some sense.

Books such as The Fate of Rome and The Fall of Rome: And the End of Civilization make it quite clear that Classical Antiquity achieved some level of globalization in its corner of Eurasia. At the other end of Eurasia, the Grand Canal also illustrates the importance of trade and economic interdependence in complex pre-modern societies.

But what has been made can be unmade. One of the major arguments in Framing the Early Middle Ages is that the decline in the social complexity of the early medieval period in Europe was due in part to the collapse of the whole fiscal apparatus of the Roman bureaucratic state. Some of these weak post-Roman states were really chiefdoms bound together with personalized rule. A process which advanced the furthest in Britain and the Balkans.

And yet during the first grat maximum of human civilization in the years after 0 international trade extended even beyond the bounds of specific imperium, from one end of Eurasia to the other.

The Roman Empire and the Indian Ocean: The Ancient World Economy and the Kingdoms of Africa, Arabia and India focus mostly on the international aspect of the trade. Much of it is concerned with the role of conspicuous consumption among elites in the Roman Empire in driving this trade, and so the bullion drain to the east. Silk, incense, ivory, and medicines were all imported in large quantities from the east. The state benefited in some sense through taxation, but the drain on specie was a constant consideration. It is well known that Roman coinage, sometimes modified, became the standard in the southern half of India in the first centuries AD.

In a stepwise fashion, East Roman traders pushed across the Indian ocean until in 166 we know that they reached the imperial court in China. This connection seems to have been made by following the trade routes which were already established by Indians into Southeast Asia. Roman geographers were familiar with the general shape of Peninsular Malaysia, as well as Java.

Because our records from China and the Roman Empire are very good, is easy to ignore the reality that a whole network of cities existed along the shores of the Indian ocean. These cities grew up around trade and acted as intermediaries for the demand for particular luxury goods which also pumped specie out of Roman mines. But the decades after the Antonine plague seems to have been defined by multiple regressions across Eurasia, as societies dependent and expecting trade faltered when local nodes collapsed and interrupted the flow.

October 12, 2018

A historical slice of evolutionary genetics

Filed under: Evolutionary Genetics — Razib Khan @ 1:10 am

A few friends pointed out that I likely garbled my attribution of who were the guiding forces between the “classical” and “balance” in the post below (Muller & Dobzhansky as opposed to Fisher & Wright as I said). I’ll probably do some reading and update the post shortly…but it did make me reflect that in the hurry to keep up on the current literature it is easy to lose historical perspective and muddle what one had learned.

Of course on some level science is not as dependent on history as many other disciplines. The history is “baked-into-the-cake.” This is clear when you read The Origin of Species. But if you are interested in a historical and sociological perspective on science, with a heavy dose of narrative biography, I highly recommend Ullica Segerstrale’s Defenders of the Truth: The Battle for Science in the Sociobiology Debate and Beyond and Nature’s Oracle: The Life and Work of W.D. Hamilton.

Defenders of the Truth in particular paints a broad and vivid picture of a period in the 1960s and later into the 1970s when evolutionary thinkers began to grapple with ideas such as inclusive fitness. E. O. Wilson’s Sociobiology famously triggered a counter-reaction by some intellectuals (Wilson was also physically assaulted in the 1978 AAAS meeting). Characters such as Noam Chomsky make cameo appearances.

Segerstrale’s Nature’s Oracle focuses particularly on the life and times of W. D. Hamilton, though if you want that at high speed and max density, read Narrow Roads of Gene Land, Volume 2. Because Hamilton died before the editing phase, the biographical text is relatively unexpurgated. Hamilton also makes an appearance in The Price of Altruism: George Price and the Search for the Origins of Kindness.

The death of L. L. Cavalli-Sforza reminds us that the last of the students of the first generation of population geneticists are now passing on. With that, a great of history is going to be inaccessible. The same is not yet true of the acolytes of W. D. Hamilton, John Maynard Smith, or Robert Trivers.

« Newer PostsOlder Posts »

Powered by WordPress