Open Thread – 11/08/2020 – Gene Expression

20 thoughts on “Open Thread – 11/08/2020 – Gene Expression”

1. Or else basic science will transmute further into its role as a moralising priesthood while its institutions keep political support, now as a branch of the state religion.

   A sufficiently self-aware woke-scientist will see this as a desirable end goal.

2. Sir, this all sounds fictionally fraught and functionally racist.

3. “I’m seeing a lot of chatter by young scientists that one should question whether one should engage in certain types of basic science due to their ethical/moral implications.”

   Can you share some links please?

4. Razib, what books would you recommend on the sociology of religion? Along the lines of this SSC post: https://slatestarcodex.com/2016/04/04/the-ideology-is-not-the-movement/

5. If they are garden variety Progressives (and that seems the dominant faith), then I wonder if it matters if they knew the history of that line of thought.

   Thinking on the Progressive-to-Woke end of the spectrum tends not to be a way of thinking that has a lot of time for dialectic – beyond the interchange of variations of party-line thought – or for the idea of perverse consequences generally.

6. Decades? Ok, but it’s been many decades since Galileo’s trial.

7. Basic science indeed. How does a 47-story steel structure fall completely within its own footprint at freefall speed? Oh, “fires fueled from office furnishings.” We’re all in building 7 now.

8. This happened in public health decades ago, which is kind of science-y and can at least hold itself as STEM-adjacent, and it’s happening very fast in medicine now, which is even more STEM-adjacent (medicine being clinical rather than laboratory). Pretty soon all the STEM dominoes will fall, and every hypothesis that could lead to a “repugnant conclusion” will be treated the way we have treated eugenics post-WWII: “Why would you even want to investigate that? Do you know what could happen?”

9. @Mekal, I could see stasis as one evolution. Another may be that science in those areas can still happen, but a “social justice” case has to be made before and concurrently, and the risks of a misstep are significant.. That is, should something discovered in “good faith” with “social justice”, turn out to lead to wrongthink, it’ll retroactively be cause for problems or not depending on favoured/unfavoured social dynamics, and so scientists somewhat selected more for social ingroup fluency rather than other qualities.

   In practical terms that might be indistinguishable from stasis tho (if risk is too much greater than reward, why do science rather than simply surficially science-y things?). It’s “all to play for”… (Or perhaps this is all paranoid worry over nothing… I hope.)

   …

   New modelling paper on East Asia (https://www.biorxiv.org/content/10.1101/2020.11.08.373225v1) is interesting. Presents rather complex model in which East Eurasian populations are mixtures in varying proportions between a core East Asian lineage and lineages that form a *very* weak clade with Andaman_HG and a stronger clade with main ancestry of Jomon and a minority contributor to Tibetans (the y-dna D people?). Split depth about the same as between ANE ancestor of Native American and WHG. Within this model Native Americans East Asian lineage thereafter first to split off from core East Asian, and they have no Jomon/Tibetan-related lineage. Today only some Amur Basin people 100% Core East Asian.

   Unusual as usual model is Core East Asian splits from SE East Asian *then* split of NE East Asian and East Asian ancestor of Native Americans (usually proposed to be supported by EDAR adaptation, but maybe this is just selection creating a pattern different from main phylogeny).

   Also based on whole-genome sequences and site-frequency spectrum of rare alleles they propose split times of Ami/Atayal and Ulchi about 50% of split time of both from Europeans. Plus Native American and Ulchi/Ami about 66% of split time from Europeans. Which seems relatively deeper than I’d have thought.

   Figures: https://imgur.com/a/7YstBHM

   Other stuff in that paper too of course.

10. I’d say that if one wants a regime that the ‘rules of the discourse’ are that if it’s true one can say it, and if it’s false one shouldn’t say it, rather than if it’s thought ‘offensive’, or more exactly ‘unpleasant’ one cannot say it with the contra to that being ‘useful’ I guess, one really cannot work with or at an american university without where you work being a major headache. Or at least what it looks like from the outside looking in.

    Any ‘intellectual’ life that cares about ‘is this actually right’ is much better done outside of universities. I don’t think that was true in the past, but it’s certainly the case now.

    I am not sure that if one thinks the at best indifference to true/false that universities presently have is a bad thing, that it’s a problem that can be fixed in a direct way. At least I don’t know how.

11. Razib,

    I’ve been seeing this Twitter thread being passed around my Facebook circles yesterday:

    https://twitter.com/Ayjchan/status/1326291377999785987

    You’ve been tracking the pandemic deeply for quite some time. How plausible do you regard the theory from Alina Chan that COVID19 originated as a accidental/criminally incompetent lab leak from the Wuhan Institute of Virology?

12. Here’s a good example of the kind of phenomenon I referenced above:

    https://link.springer.com/article/10.1007/s10459-020-10006-x

    We have long been raised to think of “science” as based around building on what came before; instead, those holding themselves out as gatekeepers of “science” now say it is very self-consciously about dismantling what came before it. What makes science different from a fashion trend then?

13. Finished “the cult of smart” by deBoer. I’d give it a 3/5. Decent book but nothing new for most readers here. Talks a lot about the genetics of IQ.

14. Found the Shor article on the “partisanization”(?) of poll response bias somewhat amusing – https://www.vox.com/platform/amp/policy-and-politics/2020/11/10/21551766/election-polls-results-wrong-david-shor

    He indicates that he believes part of the phenomenon as applied to 2020 relates to very strong “liberal” poll participation in 2020. He attributes this to a Covid19 effect, but I wonder if he’s without saying so explicitly explaining that the “Social Justice Warriors”, who have an opinion and boy do they want you to know it*, started being overrepresented in polling without pollsters realising (since only showed up to some noisy extent in shifting demographics of respondents!). Fits with responses that find that demo each produce on average 5x each the amount of social media content of the rest of the population (who are represented online reasonably proportionately) and so end up dominant voice in conversation – see https://unherd.com/thepost/who-are-the-real-tribes-of-britain/ (where termed “Progressive Activists”). Overrepresentation in self publishing bleeding into polls? “Twitter is not real” lesson n.

    Maybe fits with how Pew found plateauing response bias in 2012 (as the “Awokening” began to be felt as a generational change in these late Millennials), possibly because of the uptake of these folks offsetting the general trend? – https://www.pewresearch.org/methods/2017/05/15/what-low-response-rates-mean-for-telephone-surveys/. (Note on civic trust, describes on survey in 2016 leaning to higher Repub civics “A similar analysis conducted with 2016 data found that the overrepresentation of civically engaged adults in phone surveys, if anything, increases support for both the Republican Party and Donald Trump. Among non-Hispanic whites, the share identifying as Republican or leaning to the Republican Party was 55% among those volunteering in the past year, as compared to 45% identifying as Republican or leaning Republican among non-volunteers.” But maybe in an adjustable way.

    After all the “Where is this so-called ‘Silent Majority’ stuff? Seeing no such thing in my survey data.” that was banded around in earnest early in the year, in response to Republican claims that a Silent Majority would reject the violent protests. Well, it’s certainly no majority (lost the popular vote!), but it may be a fair number that were “silent” (as far as polling concerned).

15. https://www.theatlantic.com/magazine/archive/2020/12/can-history-predict-future/616993/ Peter Turchin interviewed by Graeme Wood. Still not clear to me what the actual process of elite overproduction leading to violence is…

16. Would love to hear The Insight cover the genetic history of the Roma and Sinti. Any plans for such an episode?

17. So, Covid-19 and Africa news from this week:

    https://science.sciencemag.org/content/early/2020/11/11/science.abe1916 – Kenya, Seroprevalence about 5.6%, identified deaths about 341… Compared to: “At the end of the epidemic wave in Spain, seropositivity was 5.0% in a random population sample of 60,897.”. Similar population size between two countries, 28,000 in Spain, so naively assuming identified deaths at similar rates (massive assumption) IFR in Spain 76x Kenya.

    Naively, Kenya has the lowest average age of any country… but demographic adjust by Bommer and Vollmer suggested that a country with Spanish vs Kenyan age structure should still only have 6x IFR difference, not 76x! Again, note the massive assumption in identifed deaths (maybe only 1/10 identified?).

    https://www.ijidonline.com/article/S1201-9712(20)32310-9/fulltext – “High prevalence of serological cross-reactivity against SARS-CoV-2 in pre-COVID-19 pandemic plasma samples from sub-Sahara Africa.”

    Compared to samples from the USA (2.4%), the prevalence of serological cross-reactivity against SARS-CoV-2 was significantly higher in Tanzania (19%) (P = 0.0002) and Zambia (14.1%) (P = 0.0069) (Fig. 2A). A breakdown of the anti-SARS-CoV-2 cross-reactivity indicates that most of the Tanzanian and Zambian cross-reactive responses targeted the SARS-CoV-2 nucleocapsid protein, 17.1% (P = 0.0001) and 13.1% (P = 0.0018), respectively, levels significantly higher than in samples from the USA 1.2% (Fig. 2B).

    Maybe cross-reactivity does actually matter…? For spread and IFR…. Might be a youth effect – children supposedly more cross-reactive I think I read.

    It would be good news if we didn’t actually need to worry as much about vaccine in Africa. Vaccine strategies can be optimized more for protection of older adults in the wider Western sphere (Europe, and the Americas).

    Of course questions – if this is the case, why not in African migrant populations in Europe/US? (Apparently).

18. “India Has The Longest Running Fascist Movement in the World”

    https://thewire.in/politics/benjamin-zachariah-fascism-sangh-parivar

19. https://twitter.com/NYTmag/status/1325435163262771201

    “How do you know when a society is about to fall apart”

20. Matt – “why not in African migrant populations in Europe/US?”

    The facile answer to that is Vitmin D. But maybe that really is the answer?

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