In 2011 I was having dinner with an old friend who was an engineer at Intel. He also has a Ph.D. from MIT. Smart guy. But when I mentioned casually offhand that we were all a few percent Neanderthal (outside of Africa), he was surprised. I was a bit shocked, as I explained that this was a huge science story. The Neanderthal genome had been published the previous year. How could my friend not have known?

He was totally unembarrassed, and told me I overestimated how closely the public followed genetics and paleontology. I’m sure he was right. But it’s hard to remember sometimes.

We’ve gone further beyond where we were in 2010. We now have a really good grasp of a lot of population dynamics in Eurasia over the past 20,000 years. Probably the best place to start is with this preprint, The genetic structure of the world’s first farmers. But the general outlines were already evident a few years back in Toward a new history and geography of human genes informed by ancient DNA.

Most of the world’s population seems to descend from a mixing of a set of groups which 10,000 years ago were distinct. How distinct? We’re talking about Fst values on the order of 0.10, which means that ~10% of the variation genetically is partitioned across two pairwise populations. That’s about what you see between Europeans and Chinese today. Some of the Fst values were a bit higher, some lower, but the 0.10 seems about right.

To make it easy for some of you, I’ve labeled and placed the approximate locations of ancestral groups to modern Northern Europeans ~10,000 years ago. What I’m trying to represent is a map which shows the modal regions of distribution of ancestors that Northern Europeans today had 10,000 years ago. So, for example, since ~15% of the ancestry of Northern Europeans is “Ancient North Eurasian” (ANE), a lot of ancestors of Northern Europeans alive today would be living somewhere in the broad expanse of Central Eurasia (now, because of various demographic events the number of ANE was probably lower than farmers, perhaps lower than the 15% contribution to the modern genomes).

A substantial proportion of the ancestry of Northern Europeans is “European hunter-gatherer,” dating to the Pleistocene. But here’s the kicker: most of that ancestry dates to after the LGM, to about ~15,000 years ago. The really deep Pleistocene ancestry in Europe is only found at very low levels now.

The final issue is that a lot of the phenotypes that we racially code are recent. This probably explains why groups like the Kalash and Nuristanis can look more like Europeans than South Asians, but they’re genetically more like South Asians.

What does any of this have to do with non-scientific things? I don’t really know. My interest in population structure is intellectual, not personal. But a certain type of person should probably stop talking about how white people have been in Europe for 40,000 years. First, the ancestors of modern Europeans 40,000 years ago were almost all residing outside of Europe. An assertion that holds until 15,000 years ago. And most would still be resident outside of Europe 8,000 years ago as depending on how you count/calculate* And, perhaps more importantly, the typical phenotype of Northern Europeans probably really coalesced only around ~5,000 years ago.

* Definitely true for Southern Europeans, but conditional on Northern Europeans depending on where you draw Europe’s eastern boundary.

Addendum: I stole the title from John McWhorter’s book, Our Magnificent Bastard Tongue.

Also, this is not to say that

1) population structure today is trivial in a phylogenetic sense, it isn’t.

2) it is not to say that population structure functionally irrelevant, it isn’t.

So I don’t really have strong opinions on the whole controversy over women’s sports at the elite level…mostly because I have a really hard time following all the logic. For me the biggest problem seems to be that we have two categories, men’s and women’s, and there are those who are arguing that they’re actually nearly plastic catchalls…which then suggests to me we shouldn’t have two categories in the first place in competition at the highest levels.

With that in mind, D. J. Grothe points me to this prescient interview from a few months back, Hyperandrogenism and women vs women vs men in sport: A Q&A with Joanna Harper. Joanna Harper is a transwoman who is (was?) also a competitive racer and a sports scientist. This portion is where the facts stand:

I would also like to relate a two-part epiphany that I had after my transition. In 2005, nine months after starting HRT, I was running 12% slower than I had run with male T levels; women run 10-12% slower than men over a wide range of distances. In 2006 I met another trans woman runner and the she had the same experience. I later discovered that, if aging is factored in, this 10-12% loss of speed is standard among trans women endurance athletes. The realization that one can take a male distance runner, make that runner hormonally female, and wind up with a female distance runner of the same relative capability was life changing for me.

As they say, “read the whole thing.” It’s long, and detailed, and doesn’t offer easy answers. Ultimately the reality is that no “solution” is going to be fair to world-class athletes. But, it’s probably important to remind ourselves that it is also unfair to those of us without the genetics of world-class athletes, and we seem to be OK with that.

Compare and contrast with this piece from Let Caster Run! We Should Celebrate Semenya’s Extraordinary Talent. The title really captures the reality that it was pretty obvious that the author was going to come down on one side, and would make a lawyerly case. Rather disappointed with Nate Silver’s shop.

Guy Gavriel Kay’s Children of Earth and Sky is set in the same world as the Sarantine Mosaic duology, and the Lions of Al-Rassan, The Last Light of the Sun, and A Song for Arbonne. I’ve enjoyed Kay’s work for more than half my life at this point, so no surprise that I enjoy Children of Earth and Sky. As I’ve noted before, Kay is arguably the world’s greatest historical fantasist, and for someone like me it’s always pleasurable to make connections between our own real history, and his secondary creation. This sort of fantasy is more magical, than characterized by magic.

I know I have readers in India because of IP addresses. Keep an eye out for my byline in India Today, where I’ll make some contributions now and then. The first should drop this Friday in print and online, a short review of Shadi Hamid’s Islamic Exceptionalism. An Indian friend told me that India is one nation where the sales of print are actually increasing, so I’m curious how this will go.

On Twitter most of my blocks come because I’m being tweeted at directly by someone. If I don’t follow you on Twitter in most cases I don’t want to be bothered. The main reason I block isn’t because I’m a coward or I feel unsafe. It’s because the person is probably stupid, and starting to annoy me. Sometimes, it’s because they want me to make a point that they want to make. Needless to say, I don’t take kindly to that. Between all my various adult responsibilities that I have now at this age, I don’t really feel guilty at all muting stupid people (who invariably think they’re genius, because you know, they’re stupid).

So you’ve convinced me that functional programming is the way to go.
Since my genotype is public somehow it got used in an rnsnps tutorial. Pretty funny.

Also, Running Structure-like Population Genetic Analyses with R. Looks like there are some interesting visualizations of admixture components which are feasible with the new program.

People keep emailing me about the HGDP plink data set. I think I removed where it initially was, and it’s linked to my old Admixture tutorials. Well, download this zip, and look at the .fam file. It has clear population labels, so you should be able to do what you want in Plink.

Should We Be Having Kids In The Age Of Climate Change? The arguments really go all the way back to the ZPG movement. Actually, they’ve popped up in philosophical movements from the beginning of time. The world is a “vale of tears”, etc. Myself, I have no guilt about having children. My children are attractive, and seem rather intelligent so far. Would that more children like mine exist in the world!

Stop Tweeting Your #Firstsevenjobs: It’s just a way to disguise your privilege. FUCK YOU. The author of the piece has a degree in French language and literature from Columbia university according to her Linkedin. She gets to write for a living for Slate about food, and was editorial assistant for Mark Bittman. What. The. Fuck. She gets paid to write about food! She was Mark Bittman’s assistant. I guess it takes one to know one. Not that the author tries to mask her privilege: “But this list doesn’t tell you that I went to an Ivy League school and graduated without debt, since my parents were able and willing to pay for my tuition.”

I hate it when people say that gender is a continuum, because that tacitly brings to mind a uniform distribution. It’s not. It’s highly bimodal.

Lou Pearlman is dead. The weirdest thing about his career is that several stories have implied he became a boy-band impresario because he was a closeted gay man, and that was a way for him to have access to young vulnerable teenagers. The fact that he became very prominent in the late 1990s boy-band boom was almost a coincidence.

Sarah Haider has been accused of being a white supremacist.

Let Caster Run! We Should Celebrate Semenya’s Extraordinary Talent. As they would say, “I don’t even.”

The company I work for has a 20% discount on kits right now. So if you want your dog to get genotyped on 200,000 markers, and get ancestry and health, it’s a good time as any.

What are you reading?

The Amazing Atheist youtube channel has some pretty funny videos. E.g.,

Taking a break in my work of the day I stumbled upon the fact that Bernard Cornwell’s series based on King Alfred’s period, which began with The Last Kingdom, is a Netflix series. To be honest I much preferred the three volume Warlord Chronicles, set more than three centuries earlier, in post-Roman and pre-Saxon Britain. A retelling of the Arthurian romance with not too much romance, George R. R. Martin admitted to me in correspondence in the late 1990s that he quite enjoyed it as well. The protagonist of The Last Kingdom is peculiarly similar to the one in Warlord Chronicles.

As a fan of alternate history I’ve occasionally stumbled upon the “what-if” scenario whereby Alfred’s Wessex is conquered, and England becomes Daneland. Would we today be speaking another Scandinavian language? Would Christianity disappear, and the pagan rites of the Norse come to rule the day? It seems broadly likely that that would not be cause at all.

First, the victory of Christianity in Europe was overdetermined by the 9th century. Even in this period there was a Christian presence in Scandinavia. A Scandinavian ruled England would almost certainly be a Christian one. And in fact in the century before the Norman conquest the Scandinavians created a hybrid society with the native English. Harold Godwinson had a Danish mother, and connections to the Danish monarchy.

The second issue is one of language. The English language of Alfred’s time was much more Germanic, so the gap between it and the tongue of the Danes was not that large in any case. And, from what I have seen, it seems that the number of Scandinavians in relation to the native population was much smaller than that of the Saxons in relation to the British, though even in the latter case it must be acknowledged that the Germans who arrived in the 5th to 6th centuries were numerically outnumbered by the native Romano-British (see PoBI results).

Perhaps if the kingdom of Wessex fell England’s identity would be more indubitably aligned with Scandinavia, as it was arguably in the decades before Norman conquest in any case. But cultural identities can be curiously resilient. The Finns endured nearly 600 years of Scandinavian domination, but maintained their language, while the long Irish interaction with the Vikings still left the Irish identity intact.

Joe Pickrell and Yaniv Erlich did an AMA on Reddit yesterday. I recommend you check it out.

They promote their new project, seeq. It looks pretty slick, and I’m excited to be part of the batch of beta testers.

Obviously I’m doing more development right now than I would have expected. But in the long term I want to move beyond hacking to survive for the present, and write some code that’s sustainable. So I think I want to read a design patterns book. The last one I read was 15 years ago and I don’t really have much retention of it. I’m particularly interested in stuff geared toward Python (the language I’m starting to get comfortable in right now).

Readers with recommendations are invited to weigh in. I know I have a fair number of software engineers in the readership, so I’m asking for your thoughts and suggestions. Perhaps the classic from the GoF is still the way to go? Remember, I’m not a software engineering who works on scientific data, I’m a scientists who sometimes needs to do a little engineering and data analysis.

Note: Sean, if you take this as an opportunity to leave a long-winded comment about sexual selection and blond women, again, I’m going to have to finally ban you!

Over at The Genetic Literacy Project Jon Entine has a post up, Usain Bolt’s Olympic gold proves again why no Asian, white–or East African–will ever be crowned world’s fastest human. Fifteen years ago Jon wrote Taboo: Why Black Athletes Dominate Sports And Why We’re Afraid To Talk About It, so he knows something about this topic.

Actually, I think Jon is wrong on this. Better drugs and biological engineering mean that I suspect at some point in the near future the fastest “human” alive is going to be non-African, and, if I had to bet, Chinese. But you know what Jon meant.

There is a lot of detail in Jon’s post because he knows a lot about this topic. But at the end of the day the specific details are less important than the general theoretical framework, which makes it unsurprising that a single group of humans who are genetically related dominate sprinting. Unlike figure skating, sprinting is entirely objective. All that matters are physical inputs. Second, unlike swimming, which is also objective, sprinting seems to have pushed very close to the boundaries of what non-modified or drug-enhanced individuals are capable of. To my knowledge there’s no expectation of a Fosbury Flop in sprinting.

Therefore, sprinting is selecting for raw ability. Training is not irrelevant, but the issue with training is that others can train too. What can’t be mimicked is raw ability due to one’s biological aptitudes and abilities (again, excepting bioengineering). Let’s assume that Olympic caliber sprinters are among the 10,000 fastest humans on the planet, because not all people with the aptitudes become sprinters. Assuming a normal distribution, that’s about five standard deviations above the human norm. I suspect I’m being conservative. Someone like Usain Bolt is probably a six standard deviation unit human. Google tells me that a fit human can run the 100 meter dash in 13.5 seconds. The world record is about 9.5 seconds. The absolute range here is not incredibly large. Small differences in the mean across populations suggest that when you select for extreme individuals those small differences will make all the difference.

If sprinting was less objective, then there would probably be more equality in outcome. I suspect judges would be biased for various reasons, and one set of nations or people of a particular ethnic background dominating a field can get quite embarrassing. But sprinting is rather objective, and the socioeconomic obstacles are low. Given basic nutrition, and the ability to huff it, you have a shot. What matters is the magnitude of your ability.

One peculiar thing population genetics teaches us that non-adaptive traits are more heritable. This is due to the fact that selection tends to remove variation, selecting for fitter individuals. Humans are good runners, there are entire evolutionary theories based around our biomechanical modifications and adaptations. But there’s really no benefit in running in bursts of 10.5 in the 100 meter dash vs. 9.5. We’re not that sort of ambush predator. There’s probably some heritable variation in burst ability, but it’s small, and not visible in any normal set of tasks among large groups of humans.

But modern competitive sports at the Olympic level is not selecting for normality, it’s selecting from outliers. It isn’t that West Africans were guaranteed to be the best sprinters, it’s just that a priori it shouldn’t be surprising that in such a non-adaptively beneficial trait as running a few seconds faster in the 100 meter dash some populations had the genetic die loaded in their direction.

Note that I’m not denying any sort of selective or adaptive argument. There’s a fair amount of evidence that there is some selection in favor of greater height in Northern Europeans vs. Southern Europeans, which probably explains why Lithuanians are more prominent in basketball in relation to their numbers than Italians. But the selection wasn’t for basketball, and the fact that there is heritable variation suggests that selection wasn’t that strong and unidirectional….

Humans vary. Populations vary too. When you select from the tails of the distribution, the differences between populations are going to be very noticeable. If a sport is objective, and pushing its limits, it will select from the tails of the distribution.

Sabine Hossenfelder on her side gig as a physics consult, What I learned as a hired consultant to autodidact physicists:

Sociologists have long tried and failed to draw a line between science and pseudoscience. In physics, though, that ‘demarcation problem’ is a non-problem, solved by the pragmatic observation that we can reliably tell an outsider when we see one. During a decade of education, we physicists learn more than the tools of the trade; we also learn the walk and talk of the community, shared through countless seminars and conferences, meetings, lectures and papers. After exchanging a few sentences, we can tell if you’re one of us. You can’t fake our community slang any more than you can fake a local accent in a foreign country.

…

I haven’t learned any new physics in these conversations, but I have learned a great deal about science communication. My clients almost exclusively get their information from the popular science media. Often, they get something utterly wrong in the process. Once I hear their reading of an article about, say, space-time foam or black hole firewalls, I can see where their misunderstanding stems from. But they come up with interpretations that never would have crossed my mind when writing an article.

I’ve been blogging since 2002. Like Sabine I can often tell if someone has a scientific background after a few sentences, especially if they are biologists of some sort. As for the rest, the chasm is between the intelligent vs. not so intelligent, and it is usually pretty clear too. Mostly the intelligent have liberal arts or social science backgrounds, but have the basic analytic tools to decompose problems at the most general levels. The less intelligent tend to speak in simple formulas when coherent, and devolve into total incomprehensibility when they try and attempt originality.*

The second issue is a somewhat different one from physics. Usually at a given moment there is a topic of particular interest to the media. Evo-devo and epigenetics come to mind. These are real scientific fields of inquiry. But because of disproportionate media attention to these sorts of topics, usually those who rely on their science knowledge from popularizations will assume that evo-devo and epigenetics have “revolutionized” our understanding of evolution and genetics, when in reality these are still developing areas, whose ultimate impact is to be determined.

In fact, I’d take this further: the area of evolutionary genetics has arguably not been “revolutionized” since the 1970s, with the theoretical and empirical debates triggered by allozyme work and the neutralist-selectionist debates. All the rest, including genomics, is just commentary.

* Here is a good example: the stupid reader who was explaining to me patiently how splicing and gene regulation “disprove” heritability estimates. I dismissed them, but the reality is that I’m 99% sure that that reader thinks I’m an idiot as well.

Spencer Wells, along with many others, such as Jared Diamond, argued that agriculture was a disaster in terms of what it wrought for the quality of life for the average human in his book Pandora’s Seed. This is broadly plausible to me. On the other hand, I also think it is highly likely that agriculture and civilization were basically inevitable.

The “great leap forward” in cultural complexity and explosion of symbolic expression ~50,000 years ago, give or take, seems likely to have been only the culmination of a process of encephalization and increased sophistication which had proceeded over millions of years. The precursors to the agricultural life were likely already there before the Holocene.

To a great extent the hypothesis of inevitability has been tested: in the Americas much of the dynamics which characterize the Old World were recapitulated. Agriculture, civilizations with writing and class stratification, and monumental architecture, all with analogs in the Old World, are there. In fact, this National Geographic piece, In Search of the Lost Empire of the Maya, is fascinating to read, because it seems to me that it likely parallels developments in the Old World two thousand years before. The Snake Kings were warlords in a manner which would have been familiar to the “Great Kings” of the ancient Near East.

There are two great schools of history from the pre-modern era. Those which are cyclical, and those which exhibit some intuition that there is an endpoint or progress. The “independent” experiments of human history suggest that both are true, with an arc of history on the macroscale scaffolded by innumerable cycles of rise and fall.

I just bought my friend Sanjeev Sanyal’s book, The Ocean of Churn: How the Indian Ocean Shaped Human History. Sanjeev is a polymath with varied interests, some of which intersect with my own. A few years back I had the pleasure of having dinner with him and Reihan Salam, and the server kept unapologetically offering drinks one of us had ordered to the wrong person. I don’t think we look that much alike!

The top start-up mecca in America is far from Silicon Valley. It’s cheap to live here, and fun for young brogrammers. Also, not too long a flight from elsewhere. As Mark Krikorian observed on Twitter being a blue bubble in a red state means that Austin can take advantage of low-cost and low-tax public policies, while maintaining a culturally liberal social aesthetic.

Bought Python Essential Reference.

Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics.

Sausage Party is a surprising mix of high and lowbrow.

Update: If I don’t post your initial comment, posting five additional times won’t result in your comment being posted.