Open Thread – 08/27/2020 – Gene Expression

17 thoughts on “Open Thread – 08/27/2020 – Gene Expression”

1. First Wayne LaPierre and his self-dealing and corruption at the NRA and now the Falwells.

   Eric Hoffer’s line – “Every great cause begins as a movement, becomes a business, and eventually degenerates into a racket – aptly describes “the conservative movement” in America. Is it any wonder that Trumpism has vanquished “conservatism” in the GOP?

   I am not surprised. LaPierre was never a “true-believer” in gun rights (he purged from the NRA all the gun rights “absolutists,” you know, people who care about principles and such, and packed its board with loyalists and lackeys). And Falwell, Jr. was never a spiritual person (he was a “real estate developer”) and, with his imperious wife*, pushed out his minister of a brother who was supposed to be the spiritual guardian of their much-respected father’s legacy.

   Both were very adept at empire-building, but completely corroded the soul and the mission of the respective institutions they came to dominate (I gave up my NRA membership years ago when I found out that most of the money was going to self-perpetuation of the NRA and its upper management, not gun rights, the real legislative work for which was done by a separate legal entity, the NRA-ILA).

   *Becki Falwell was apparently very mousey and didn’t even squeak loudly when Falwell, Sr. was alive, but then turned into a complete diva once her husband took over (supposedly she got upset when people didn’t make way for her like she was the empress).

2. Can you give a summary of what’s in the cinnamon tail (depending on a person’s interests, is it still worth going to the paywall and to be bombarded by the ads for South Asia-related stories from the magazine?)

   I understand that the two cinnamons are closely related species with distinct cultivars of differing flavor subtypes (the uninitiated can read a short review here:
   https://www.bonappetit.com/story/types-of-cinnamon )
   and that in South Asia, cinnamon may be more associated with savory rather than sweet dishes. But I am not into recipe sites or tales of ethnic food richness, not at all. Now if there is a lawyer of human migrations or unknown explorations, some unappreciated mankind history dimension…

3. When I read about how religion was conceived in the decades around the turn of the 18th Century in the Anglo world by a large number of philosophers and theologians who were troubled by the boundless intolerance of the time (people like Roger Williams, John Locke), specifically amongst Protestants and all their various sects, it becomes apparent that they viewed religion to be as immutable, and thus inviolable, as the way we today view things like race or sexual orientation. The idea was that every person has an internal conscience, and that conscience leads them to the religion that they follow. Thus, a Quaker could have been none other than a Quaker, a Methodist none other than a Methodist, a Presbyterian none other than a Presbyterian. That said, Catholics specifically rejected this framing, as their approach emphasized education and upbringing (not to mention governing). There obviously remained some intolerant Protestant sects as well.

4. On matters WEIRD… this came into my feed – http://nautil.us/issue/81/maps/the-cultural-distances-between-us . One of Henrich’s students talking about a paper to create cultural fst, which I think we’ve discussed before.

   That pointed me to this website http://www.culturaldistance.com/.

   I got curious as to whether the “cultural fst” (just taking “All” measures and “All” countries) could be converted into a set of dimensions using Principal Coordinates Analysis, like Fst scores can.
   Predictably, when I do, I get one big dimension separating developed countries (33% of variance) and then a bunch of smaller dimensions (varying from 8% downwards) for the remaining variance. E.g. https://imgur.com/a/inI9fIP . The WEIRD dimension…

   The “cultural dendrogram” is also pretty predictable – https://imgur.com/a/3j51u03

   When you then correlate the “Cultural Dimensions” produced by their “Cultural Fst” output with most recent PISA (converting in the World Bank equivalent for countries outside PISA) and consumption levels (as an index of living standards), it seems like both of those correlate heavily with the first dimension, but not much with the subsequent ones… https://imgur.com/a/ZcYOAHx

   That’s kind of interesting – it tells you at least that most of the cultural variance in their set correlates with education. The correlation is R=0.8 with test scores, so pretty strong.

   One of the interesting things you can do is then residualize the effect of test scores on dimension 1, and then recalculate the cultural distances and dendrogram for an “Education adjusted” cultural dendrogram of the world: https://imgur.com/a/eza0K0R

   To contrast with the original “education unadjusted” dendrogram, there’s a lot less of a “West vs the Rest” flavour, and you get more of a pattern where there are some subclusters that are recognisably regional (East Asia, Latin, Nordic, English speaking offshoots, core Soviet, Anglo-French) but a lot of the European countries are a lot more distanced to each other on the dendrogram and don’t cluster together.

   Suggests that in the WEIRD formulation, the *E* is doing a lot of the work and there’s not *so* much shared W once adjusting out for that, and European countries are otherwise rather culturally diversified, shared high education levels notwithstanding. (Escape From Rome….?). Or put alternatively, the shared Western values are robustly linked to education improvements across the world…

   Considering the size of the first dimension, adjusting out for test scores can have quite a bit effect… cultural distance from Japan and Great Britain, for instance, is quite correlated when test scores are not adjusted for (r= 0.68) but mildly negatively correlated when the shared effect of education on the main cultural dimension is removed (r= -0.35) – https://imgur.com/a/kd52xwJ (e.g. what is in common between Japan and GB is overwhelmingly mediated by same factors with shared education outputs). On the other hand, cultural distance from Germany and Japan are still pretty highly correlated after education adjustment (r=0.63).

   (Above is not necessarily a perfect way to do this, and you might get more out of a less dumb approach than just taking all their data in one go, and is getting a bit almost “blog post in the comments”-y, but thought might be of interest to some. Ultimately it seems like this could be useful for working out which cultures have “unexplained” similarity once education and living standards are resolved ).

5. So there was this new Tagliente sample fromm almost 17,000 BP showing the oldest known Villabruna cluster individual so far, but there is Villabruna ancestry in El Miron in 19,000 BP already from a paper a few years ago and thus it isn’t big news. Though the recent Tagliente paper makes connections between change in material culture and the appearance of Villabruna ancestry in the region, idk if the older (2016 was it?) paper made that comment specifically regarding Villabruna.

   https://www.biorxiv.org/content/10.1101/2020.08.10.241430v1

   Something interesting from the preprint is that the Tagliente2 individual’s mtDNA haplogroup is a fairly old U4’9!

6. The Smearing of Nikki Haley: Liberal Indian-Americans accuse her of denying her heritage. | By Tunku Varadarajan | Aug. 27, 2020 | https://www.wsj.com/articles/the-smearing-of-nikki-haley-11598549001

   … Ms. Haley—née Nimrata Randhawa—is the daughter of Sikh immigrants from India. She was born in South Carolina in 1972, and as a child she worked at her mom’s clothing store. She graduated from Clemson University with a bachelor’s degree in accounting and returned to work in the family business….

   At 24, she marries a white man. A year later she converts to Christianity, taking on her husband’s faith. Her biggest ethnic sin, however, was to join the Republican Party. …

   At the Republican National Convention this week, she steered clear of the strident tone of many other speakers. America’s “is a story that’s a work in progress,” Ms. Haley said, stressing the need to make the country “even freer, fairer, and better for everyone.” She was “the proud daughter of Indian immigrants.” In an echo of Kamala Harris’s much-lauded shout-out to her own Indian mother at the Democratic National Convention, Ms. Haley said, “My father wore a turban. My mother wore a sari.”…

   Responding to a line in Ms. Haley’s speech—“America is not a racist country”—a group called South Asians for Biden tweeted: “If America isn’t racist, why did Nimrata Haley feel compelled to change her name to ‘Nikki.’” …

   Liberal Indian-American ethnocrats have long alleged that Ms. Haley’s preference for a name that many Americans would find easier to say is a form of self-loathing, proof of her desire to erase her Indianness. This reflects a belief that while it’s fitting for America to accommodate immigrants, it’s somehow wrong for immigrants to have to accommodate America. I also suggest they brush up on their languages. “Nikki” is a Punjabi word that means “little one,” often used as a term of endearment for the youngest girl in a Sikh family. …

   Far from changing her name to fit in—which, surely, would be her own rightful decision and no one else’s—Ms. Haley has used a name her parents bestowed on her at birth. “Nikki is my name on my birth certificate,” she tweeted in May 2018. “I was born Nimarata Nikki Randhawa.” She married a man called Michael Haley, becoming Nikki Haley. … To suggest that Ms. Haley is trying to pass for white—and to bury her own identity in the process—is not only desperately overheated. It is racist.

7. Twinkie: The LaPierre story is not interesting. OTOH, the Falwell story needs to be a straight to PornHub movie. I don’t think a lesser outlet like Netflix could do it justice.

8. “I really want Thermidor.”

   Who is Robespierre in this sequel?

   And when and where should the whiff of grapeshot be delivered?

   I don’t necessarily disagree with you, but I remind you of Marx’s dictum that history repeats itself, the first as tragedy, then as farce.

9. “The Trap The Democrats Walked Right Into: If law and order are what this election is about, they will lose it.”
   Andrew Sullivan | Aug 28 | https://andrewsullivan.substack.com/p/the-trap-the-democrats-walked-right

   * * *

   But here’s one thing I have absolutely no conflict about. Rioting and lawlessness is evil. And any civil authority that permits, condones or dismisses violence, looting and mayhem in the streets disqualifies itself from any legitimacy. This comes first. If one party supports everything I believe in but doesn’t believe in maintaining law and order all the time and everywhere, I’ll back a party that does. In that sense, I’m a one-issue voter, because without order, there is no room for any other issue. Disorder always and everywhere begets more disorder; the minute the authorities appear to permit such violence, it is destined to grow. And if liberals do not defend order, fascists will.

   … This is how violence metastasizes. And as I’ve watched protests devolve over the summer into a series of riots, arson expeditions, and lawless occupations of city blocks, … And when I watched the Democratic Convention and heard close to nothing about ending this lawlessness, I noted the silence.

   * * *

   Remember the pivotal moment earlier this summer when the New York Times caved to its activist staff and fired James Bennet? It’s no accident this was over an op-ed that argued that if New York City would not stop the rioting in the streets, the feds should step in to restore order. For the far left activists who now control that paper, the imposition of order was seen not as an indispensable baseline for restoring democratic debate, but as a potential physical attack on black staffers. They saw restoring order within the prism of their own critical race ideology, which stipulates that the police are enforcers of white supremacy, and not enforcers of the rule of law in a liberal society. It was a sign that the establishment left were willing to tolerate disorder and chaos if they were directed toward the ideologically correct ends — which is how Democratic establishments in Minneapolis and Seattle and Portland responded. The NYT, CNN and the rest tried to ignore the inexcusable, and find increasingly pathetic ways to dismiss it. This week, their staggering bias was exposed as absurd.

   * * *

10. Slight continuation of the above comment on “Cultural Distances” website, and the Principal Coordinates dimensions generated.

    Kind of just amusing myself really but thought it would be interesting to see if any of the “dimensions of culture” generated from their distance matrix correlated with TFR (total fertilty rate), given all the talk about Western cultural trends and WEIRDness and demographic consequences and shift.

    Predictably, the only one that does correlate is the big Dimension 1 that maps to a kind of “High test scores developed country vs Low test scores undeveloped country” axis (or WEIRDism, put another way). (The other axes splitting apart countries have no real association). See – https://imgur.com/a/rBJ4zEx

    Then you can go on from there and ask whether, after accounting for the relationship between Dimension 1 and Test Scores (or other highly correlated education variables like EduYears), there is any residual relationship between Dimension 1 (“WEIRDism”). It turns out that there is not, and the relationship between “Residual WEIRDism relative to education” and TFR is almost zero, and mildly positive. See – https://imgur.com/a/0TllrNo

    (There could be a few phenomena behind that very mild level of positivity; factors might be that residual WEIRDism is associated with higher immigration, or self expression values, or welfare states that improve TFRs slightly.)

    That’s interesting to me because you see in the world today these proposals by some countries to go “Well, we’ll embrace high levels of education, but by avoiding other cultural Westernization, we can maintain higher TFRs”. But it seems that after education is accounted for, at least as this measures it, residual cultural Westernization has no national level relationship with TFR at all. A political regime might be possible that sort of managed to combine high educational standards with high TFRs, but there’s no national culture in this dataset that could actually provide a model for that (nor even any cultural group of nations that point in that direction).

    You also see the same thing if you use the World Bank’s Learning Adjusted Years of Education (rather than the mix of PISA test scores and World Bank Estimated Test scores normalized to PISA): https://imgur.com/a/RaZcWN6.

    And the same if you use take both measures for education, adjusted the “Cultural Distance” for that, and then look at remaining distance from the United States: https://imgur.com/a/40QGbdE (Some fairly substantial positive correlation on TFR for cultural distance from United States in raw… but once accounted for effects of education on cultural distance, slight negative correlation).

    From what I can tell, to explain leftover effects after Test Scores / Education you probably would have still have effects of male:female education inequality and child mortality, as independent correlates of TFR (child mortality+female education ratio probably explains Sub-saharan Africa, which World Bank rate as not too far in test scores to the Greater Middle East).

11. “Again, there is a certain tendency in college life, a tendency encouraged by some of the very papers referred to, to make educated men shrink from contact with the rough people who do the world’s work, and associate only with one another and with those who think as they do.”

    https://www.theatlantic.com/magazine/archive/1894/08/the-college-graduate-and-public-life/304483/

    From good ol’ TR

12. did a podcast with joe henrich. he said that the ‘big societies cause big gods’ paper (as opposed to big gods => big societies) was almost retracted. some authors agreed, some resisted, re: missing data.

    the podcast will be live next week, but i’m going to post a rough cut for patrons in the next hour https://www.patreon.com/razibkhan

13. Given you’re talking to Stuart Ritchie, unless that happened, I kind of have one point on that topic.

    I think he’s published some papers indicating that longer experience in education relates to real IQ gains (at least crystallized IQ gains?), so long as education happened before 20? E.g. if you have an extra year of education, you’re smarter.

    On a similar note, there also seems to be a lot of enthusiasm about lately for mandatory pre-schooling again (it seems like one of those Proggish flowers that bloom every time there’s an unswelling of faith in the power of government to spend money and transform humanity, among youngish demographics, usually when they don’t control a high % of the wealth).

    I was thinking that if either of these were true we’d probably see higher performance among people who begun education earlier, and finished it post 20. Fortunately, there’s naturally a lot of variation in the population to test this.

    Children who are born in the Autumn (Fall) start education later relative to their biological age, so by the time they get to 20, assuming they’ve been in education the whole time, they should have spent more of their life before 20 in education. Likewise they would have started less young. That being the case, if there are benefits to spending more of your life in education before 20, or starting earlier, we should see them show up in IQ here.

    Someone who started school earlier and stayed their until 20 has had effectively an “extra year” of education up to age 20.

    The advantage of this is that births are otherwise random, and there’s no plausible preexisting IQ related structure there. (It should be “The fault in their star(signs)” or nothing, with no other structure to hide in).

    As far as I can tell from the GSS, which has a zodiac variable allowing us to roughly divide up the samples into births early and late in the academic year, there is absolutely no difference in Wordsum for cohorts that should have started educaton earlier in their life, and absolutely no difference within levels of educational achievement.

    (Funnily enough, there’s also no difference in overall years of education by zodiac, which also puts the kibosh on notions that biologically younger children who compete with biologically older in the same year of school end up achieving lower education!).

    (Few graphics to show the generally zero relationship between star sign – and hence being an early or late starter in school, relative to your biological age – and Wordsum, on the GSS: https://imgur.com/a/Z47hY0u).

    (This is not really a question for you to put to Ritchie, as far too long and awkward to do so, but wondering if he was reading this thread…)

14. On “A geometrical framework for f –statistics”, seems like the sort of paper I should try and understand as interested as a hobby, but probably beyond me.

    I did notice though it referenced a result from Cavalli-Sforza on page 20 where an admixture fraction can be determined by the formula; admixture = 0.5+((FstTargetA-FstTargetB)/(2*FstAB)).

    Hadn’t seen this before so thought I’d see what it gave with the Fst data from ancient populations, and to test Nganasan fraction in present-day Europeans.

    Results: https://imgur.com/a/ygr4x69

    It seems generally pretty accurate actually, returning the expected values for Steppe admix in European late CWC Germany, and for WHG in Neolithic farmers, as well as for the fractions expected of Nganasan like admixture in Saami, Finnish and Northern Russians.

    (Even if you have a strong drift specific to Target, the admixture ratio here is unaffected, because FstTargetA-FstTargetB is unchanged, e.g. https://imgur.com/a/EHZHLLr . That’s useful you suspect Fst is inflated but equally so from Target to A and B for example.).

    Where there is some problem is where there is strong and specific drift of Target or Target’s ancestor as a clade from either of A and B. Hence why these methods based on outgroups become necessary, I guess, as well as to deal with more complex admixture models.

    But it might be useful to have a quick reckoning that can be worked out just from Fsts, so long as you’re fairly confident all populations involved really are on an admixture cline.

15. https://www.theatlantic.com/ideas/archive/2020/08/an-immigrants-plea-dont-turn-our-america-white/615646/

    “Please Don’t Convert to Whiteness”

16. https://www.biorxiv.org/content/10.1101/2020.09.03.281261v1 – “Bioarchaeological analysis of one of the earliest Islamic burials in the Levant” – “Here, we present for the first time, a multidisciplinary bioarchaeological analysis of two individuals dated to late 7th and early 8th centuries from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates, religious and cultural burial evidence indicate that this site represents one of the earliest Islamic Arab burials in the Levant during the Late Antiquity period. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This is highlighted through substantial Neolithic Levant ancestry in our samples, inviting an alternative scenario of long-term continuity in this region. This raises questions about the influence of ancient populations and historical migrations to genetic structure in the Middle East.”

17. “Interrogate the writings of the wise,” he advised, “Asking them to tell you how you can / Get through your life in a peaceable tranquil way.” – Horace
    https://www.theatlantic.com/ideas/archive/2020/09/hate-sinner-not-book/616066/

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