Substack cometh, and lo it is good. (Pricing)

Open Thread – 03/08/2021 – Gene Expression

Reading chapter 9 of Not Born Yesterday: The Science of Who We Trust and What We Believe. Lots of stuff about the Nazis, so juicy. Will put the post up soon.

5,300-word piece up now on Substack: They came, they saw, they left no trace…except for all of Western Civilization. This is focused on Italy from 1000 BC to 1000 AD. I interleave genetics and history. Even if you are not tempted to become a paid subscriber, do consider signing up for free. I’m devoting more and more of my content generation to Substack, and some of it is not paywalled (for example, my recent piece on the Uyghurs).

In Hawaii, Reimagining Tourism for a Post-Pandemic World. I don’t believe it. But who knows?

Human challenge trials with live coronavirus aren’t the answer to a Covid-19 vaccine. From June 2020. I don’t think this ages well.

NASA’s Perseverance Rover Lands on Mars to Renew Search for Extinct Life.

I’m experimenting with a site called Indie Ocean. It’s basically a physical book storefront. You’ll recognize the list. Here is some information on the project. I’ve been talking to them for months, so this isn’t out of the blue.

It looks like the pandemic is finally ending?

26 thoughts on “Open Thread – 03/08/2021 – Gene Expression

  1. Maybe Hawaii could create a decent tech sector, with some affordable housing efforts and policy reforms. Lots of warm weather, lots of potentially cheap geothermal energy for electricity – I can think of worse starting conditions

  2. About a month ago, it seemed obvious to me that Covid deaths would drop sharply in the US because the elderly account for 80% of the death and they were getting vaccinated first. My prediction was that daily deaths go from 3150 at end of January to 2200 by the end of February (actual 1948), 900 by the end of March and 300 by the end of June. My February number was too high but the others seem reasonable.

  3. Even if you are not a paid subscriber, just sign up for free if you haven’t.

    The post is paid subscribers only.

  4. The problem with geothermal is that it’s not really located near any population centers, which makes sense, as it’s an active volcano. The one test power plant nearly got buried under lava a few years back. Add to that valid ecological concerns, contingently valid cultural concerns (if one is of Hawaiian descent, like myself), and the overwhelming power of NIMBYism in this state, and it’s a no-go.

    I’m pretty black-pilled about the future of my home. For scenic places, tourism has the elements of a “resource curse”, and we’ve pretty much boxed ourselves into the “high volume low return” model over the decades. A bunch of boutique farms isn’t going to save the state, especially since those farms directly or indirectly rely on tourism to profit, just like nearly every other business here.

  5. On Perseverance:
    If there was ever life on Mars, I would bet it’s
    still there. The planet probably desiccated slowly
    and life is nothing if not adaptable. There are live organisms
    on Earth a mile deep.

    Of course finding such life on Mars poses quite a challenge.

  6. Razib, question: what do you believe is the standard deviation of Indian IQ? I’m guessing it’s 17 points or thereabouts, but it could be easily higher or lower.

  7. “I don’t believe it.”

    And you are wise to not believe it. Cuba tried it; it failed miserably.

  8. I think the social distancing dam is going to burst soon as the elderly get vaccinated. I think a lot of it is just inertia at this point anyways. It won’t be ‘over’ in the sense that lots of people will continue to get COVID for a few more months but the death toll may be low enough that it’s acceptable.

  9. Z:

    Because Scandis are the exception that proves the rule in regards to group IQ, group social traits and transmitted culture. Also, they do have some resources besides North Sea Oil.

    Stick any other human group in some isolated area and give them one valuable resource and they’ll either misuse it or run it into the ground or both.

  10. Dis you think science was exempt from Wokeness? Think again:

    “Glaciers, gender, and science: A feminist glaciology framework for global environmental change research” Carey M., Jackson M., Antonello A., … January 10, 2016
    https://doi.org/10.1177/0309132515623368
    “Merging feminist postcolonial science studies and feminist political ecology, the feminist glaciology framework generates robust analysis of gender, power, and epistemologies in dynamic social-ecological systems, thereby leading to more just and equitable science and human-ice interactions.”

    +++++++++++++++

    Decolonizing Light follows complementary approaches: We are engaging Indigenous ontologies and epistemologies for knowledge creation, we are studying colonial anchor points in the history of physics in the context of light, we are studying the views of scientists on colonialism, we’re investigating the discourse on contemporary largescale light experiments, we are training Indigenous and racialized students to do research in synchrotrons, and we are encouraging and training Indigenous and racialized students to follow research questions which are not defined by us but by themselves.
    https://decolonizinglight.com/

  11. Was looking at some historic survey/opinion polling on various culture war issues lately. I think it’s been noted before that pro-marijuana and pro-gay marriage sentiment correlate with one another, and according to polling both started to see increases in social acceptance in the early-mid 90s. The 90s also saw greater public acceptance of interracial marriages too. Probably most interestingly of all, the secularization of American society started getting off the ground in the 90s as well. Even self-identified conservatives have moved with the times on all these issues, the only things they’ve really held their ground on are abortion and gun-rights.

    Has anyone ever written any good sociological study on why all these occurred when they did, why the 90s seemed to be a such an under-reported transgressive epoch? An obvious culprit would be the end of the Cold War and the beginning of Pax Americana – the existential threat of communism faded a way, which led to a wave of forward-thinking optimism. Since there was no great external threat we had to constantly be on guard against, a greater emphasis on individualism emerged which privleged personal autonomy and self-actualization over restrictive, old-fashioned social mores. Out with the old and in with the new.

    The above is just my half-baked impressions, but I’m very curious if anyone’s really written about these shifts in a academic manner, tying them all together in a coherent theory. It really does seem like the 90s was the first decade of the 21st century in a fundamental way.

  12. @Walter: Interesting and thought provking Shor. Left parties in UK as well (all FPTP countries?) seem to have tilted to picking up educated liberals at expense of alienating working class and traditional groups (whether “Red Wall” WWC in UK, or it seems “Rust Belt” WWC and now “PoCWC” in the US).

    At first must seem like a “good trade” – these educated liberal people vote at high clip of Working Class mobilisation rate (so it doesn’t matter if you lose 1.3 working class voters for every 1 upper middle you gain?), are being taken from opponents (so diminish their share while rising yours), dominate media sphere and constantly “dunk” on their opponents as ‘The Stupid Party’ in every sphere of society generating 24/7 unpaid propaganda (albeit with quite lame “Daily Show” / “Mash Report” snark), and they also dominate government and business and policy jobs in established civil services and universities to such an extent that makes governing against their preferences challenging (if you can even win elections), because harder to gain talent and ideological clout.

    But eventually problems seem to ensue. If mass mobilisation starts to pick up even modestly among the US and UK’s generally fairly low turnout rates, this erodes advantage in winning elections. Then there are big problems with stacking in particular urban areas in cities and in states, which makes high vote share stacked in a few places less effective at winning power (under either a FPTP Parliamentary System, or for presidency under Electoral College system, in both of which distribution is an advantage).

    (Perhaps shaky analogy; pre-modern states and confederations who relied on natural high mobilisation of pastoral/equestrian elites, who then ended up with problems when high agricultural productivity, improves in state stability and finance, firearms, all came together in allowing competitors states to mass mobilize? Their advantage in “quality” yielded wins for a time, but was vulnerable to reverse in “quantity”, and there wasn’t anywhere they could go to counter.)

    It’s also pretty ideologically unstable in that people who purport to be left wing, yet whose left wingness mostly *seems* to disproportionately passionate about taxing super-rich and corporations to provide services, cheap housing, public utilities and stable, well-paid government jobs to upper-middle class knowledge workers and “Professional Managerial Class” in major cities are… pretty easy to question and denounce as not really that left wing at all in the sense of being the voices of the poor and deprived.

    (Another issue is that of course leaning into the politics of the highly educated left seems to mean policy discussion become dominated by talk of extreme alternatives that are really about one-upmanship to be more-socialist-than-thou and creating excitement in the group. Like this talk of “prison abolition” and “defunding police services” and creating new US states without any political power to do so and so on. “Performative politics”. That eventually will damage credibility as technocrats? It doesn’t look like a bit of impressive technical governance to advocate for dissolving your police force, and then not 9 months later seemingly be recruiting and rebuilding a larger one.)

    Eventually it maybe becomes easy for an electorally successful right to say “Hey, the facts speak for themselves; we win elections, and we have popular working class support. What use is a Left that is rejected by the very people it purports to speak for?” and with even some nominal credibility on science and free-thinking culture (even credibly saying “No, we don’t hate science or public health.”), perhaps you will then start to see defections from high educated share.

  13. Slightly connected to discussion about y-haplogroups on “Indo-Europeans!” comment thread (though not enough to post there), a paper from October 2020 – https://academic.oup.com/mbe/article/38/3/1000/5922624 – “Mutation Rate Variability across Human Y-Chromosome Haplogroups ” (hat tip, an anthrogenica poster who generally posts good links).

    Finds that cell-line mutation accumulation under samples from 1000G and HGDP varies under different y-haplogroups, and the rate positively co-varies with total branch length accumulation of mutations since the common ancestor in the overall phylogeny.

    Suggests that different y-haplo expansion times estimated from a common mutation rate may be somewhat inaccurate. Though seems they of course have less uncertainty around the y-haplo groups which are more well represented in both.

    Where that gets interesting to me is the inference that if there are systematic differences, it could influence the various expansion times for each y-dna haplogroup that are estimated by e.g. Kivisild 2017 (“The study of human Y chromosome variation through ancient DNA”).

    The groups that the paper tends to suggest have lower rates are E1b and R1, while among those for which it is quite high are O1, O2 and G. Haplogroup I is intermediate.

    That is particularly interesting because, while the differences are not large enough to erase the different “star-like” pattern of expansions under R1 and E1b within the last 5k or anything like that, it might smooth out some of the perhaps counter-intuitive thing where O1, O2 and G expansions look like they expand *before* the agricultural era (assuming same rate) rather than *with* agriculture. If O1, O2, G are accumulating mutations at a higher rate, then you need less time since expansion. I’d generally find the idea of an expansion of patrilines *with* agriculture more intuitive than a pre-agricultural expansion of those associated with early agriculturalists, perhaps my bias though.

    This kind of thing also might change estimates of the higher-order branching times (although I’d expect those to me more resilient!), and the split of “Eurasian” y-dna might become a bit flatter (more “rake-like” or “star-like”), and more compatible with rapid diversification after entry into Eurasia. That is plausible as the “more primary” branches under the Out-Of-Africa set (C, D, G, H) seem to be the ones in this paper accumulating more mutations in cell-lines and have higher total branch length. This might also help solve some more of the puzzling geographical patterns in discrepancies between mtdna and y-dna expansion times that some have mentioned.

    (Systematic differences in generation length as per another paper, might also accelerate that, although I’m not totally convinced by some of the evidence in that paper, and the haplogroups with more mutations here are not totally consistent with the geographical pattern from that paper, which was more of a longitude geographical pattern).

    Might be a useful subject for some of the testing under the “Y-chromosome capture enrichment ” method from Rohrlach’s recent preprint (https://www.biorxiv.org/content/10.1101/2021.02.19.431761v1.full), to actually test total derived mutations for different y-chromosomal haplogroup samples at different points in time, and then estimate branch specific mutation rates and expansion times, without as many capture biases as in methodology to date that prevent answering those questions.

  14. I read the “Meritocracy Is Bad” bit by Yglesias – https://www.slowboring.com/p/meritocracy-is-bad

    Although not an obscure piece, thought worth offering a brief comment here as topic of meritocracy discussed much before and worth reading, albeit with a critical eye. I was struck that it has a provocative headline and byline, but really when you get down to it seems to be a much more typical centrist-liberal court-intellectual piece. His main beef expressed with meritocracy seems to be that as currently defined it selects for and provides fewer jobs to orthodox and idealogically conforming Democratic Party supporting intellectual mediocrities from good families. Not actually so much overemphasis on principles of selection for quality and centralisation of decision making (which indeed the piece affirms, if anything).

    (Further thoughts on pastebin because further spamming this Open Thread with my extended thoughts on political stuff people may not care about is legitimately Not A Good Look: https://pastebin.com/7FSXqwaE )

    Perhaps I’m a bit cynical, but I expect such ideas to become more frequent on the centre-left, now that they’ve ascended to social positions and sources of income they want to hand over to their kids and allies. Character or virtue (or “good personalities”) becomes a more useful means to transmit status to kids and allies, since it is easier to fake and redefine.

  15. Interesting preprint by Abdel Abdellaoui (of “Genetic correlates of social stratification”) showing further decline of genetic correlation of educational attainment and various traits (BMI etc) with explicit control for location of birth and/or current address, rather than using genetic PCA: https://www.biorxiv.org/content/10.1101/2021.03.18.435971v1 . SNP heritability of educational attainment has ratio of about 0.5x with full control, intelligence about 0.8x

    A complement to the big siblings preprint from last week which showed even more decline of genetic correlation within sibling groups (https://www.biorxiv.org/content/10.1101/2021.03.05.433935v1), hinting at assortative mating and other effects, not real shared genetic covariation that lives in the genetic architecture. Likely that at least some of the decline is due to geographical structure correlations.

  16. Cheddar Man’s Y-DNA belonged to an ancient sister branch to modern I2-L38 (I2a2). The I2a2 subclade is still extant in males of the modern British Isles and across other parts of Europe (e.g. Serbia). The mitochondrial DNA of Cheddar Man was of haplogroup U5b1.

    >>> He was a SERB – 40% of Serbs have this haplogroup.

  17. @ Matt,

    It’s interesting that you took Yglesias’s post regarding meritocracy as being warmed-over center-left, because it seemed to me that his ultimate conclusion was something a conservative could admire. Essentially he says we should pay less attention to “talent” and more attention to virtue, that brilliance does not equate to good leadership, and the most talented should focus more on doing good than maximizing value.

    There’s of course some discussion of Democratic policy and politicians but…Yglesias is a liberal Democrat, as are most of his audience. Thus it’s no wonder that he uses these cases as examples to make his broader point, which isn’t really about politics at all (or rather, it’s about unspoken priors which are damaging and held across the U.S. political spectrum).

  18. Re: Cheddar Man…
    He reminds me of someone, but I could not recall of whom. So, I did a research. I was searching for his look-alike, of course in his lineage, preferably from the same geographical area and within the same I2a haplogroup.
    And, Eureka, I’ve found him! The same dark complexion, greasy hair and seductive blue eyes. So, here he is:

    https://www.imdb.com/name/nm0000062/mediaviewer/rm242915328/

    He is a descendant of ancient cheese men/women, who much later migrated to US from British Isles. And, surprisingly, along the way, I found some other ex-British Isles specimen from the same I2a category – US president Munro, Davy Crockett, Bill Gates (he is the closest to CM by intellect), Ted Dunston from Cheers and, of course – Chuck Norris. There are also so many relatives in his ‘Indo-European’ Balkan homeland (I said 40% of Serbs), let’s mention one only – Novak Djokovic.

  19. @Karl, interesting counterpoint. To be honest, I do cringe a bit after the fact at about at least a third of my hot-takes on politics, and the tone of that comment probably was a bit heckle-y, so some pushback is fair game.

    I guess the main point I’m trying to get at (without the possibly unnecessary bit) is that it seems like a one of the weaker criticisms of meritocracy that it tests and selects for the wrong sort of highly individualized character traits (intellect or ability, not character), or even not really a criticism of meritocracy at all. It seems the potentially more substantive criticism of meritocracy that a mindset that solving prolems is about selecting people for positions on permanent character traits, and then sort of encouraging them to go off and freely make their own judgments about action, is just not that effective a mindset.

    That we’ll be more likely to get good odds with getting good results on the basis of whether someone offers a coherent program, and then we judge it as feasible, then they have a finite time after, and we’re able to monitor them and discipline them throughout, and there are those social relationships that will enforce them to remain on the path (and even if the have an excess of virtue or intellect that will make them stray from the path, that my not be good). That is really, their character and intellect only comes into it to the extent that we judge they can do it. (And that’s more in spirit of the political ideal.) That is, that a meritocratic ideal in politics focuses too much on traits of office-holders and not really on mechanisms and proposals and the general framework (which are the important bits and may make consideration of personal traits relatively irrelevant).

    Maybe this is getting a bit Quixhotic on my part! In a sense that piece was a mix of being about appointing office-holders, and a wider critical look at what social values are leading towards, so maybe that criticism is not really applicable to what he thought the main thrust of his piece was about.

  20. “Assortative Mating Biases Marker-based Heritability Estimators” – https://www.biorxiv.org/content/10.1101/2021.03.18.436091v1

    Fairly modest changes but, more evidence that assortative mating influences changes (raises) estimtaes of within group heritability.

    One (unfortunate?) implication – genetic differentiation between groups may be higher relative to equilibrium within-population genetic differentiation (net of assortative patterns)?

    E.g. if there is extensive genetic assortative mating for alcohol consumption, then that might raise our expectation of the strength of genetic differentiation on, say, alcohol tolerance between e.g. Han Chinese and Russia, because it’s less credible that a range of genetic phenotypes are maintained within the population by balancing selection (rather than by social structure).

    Or is this line of thinking may be pretty off base?

    I guess another thing on that topic is that existing high assortative mating might also mean that there is a bit less scope to expand the distribution (“high fraction” of some trait) by increasing assortative mating. If you were to go “Oh, mean athletic ability has eroded genetically, so let’s encourage more athletic persons to be assortative and have kids together, in order to realise high elite athletic potential”, then there would be less further scope for that if you’re already starting from an assortative position (of course this kind of thing is not actually feasible, but it is somewhat discussed).

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