Open Thread – 09/06/2020 – Gene Expression

India in the Persianate Age: 1000–1765 is a decent read. Recommended if you have the time.

I have a Wikipedia page. Don’t believe everything you read on the internet.

Inferring Causal Direction Between Two Traits in the Presence of Horizontal Pleiotropy with GWAS Summary Data.

The Age Of The Mega-City Is Over. Probably wrong. But who knows?

Evolution is in the details: Regulatory differences in modern human and Neandertal.

Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years. David has some comments.

‘Be smart’: New Yorkers get good news on virus numbers, but also a warning.

This Fish Should Not Exist.

Brandon Sanderson has book 4 of The Stormlight Archive. This is out of 10 projected books. He began the series in 2010. Different than some authors.

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20 thoughts on “Open Thread – 09/06/2020 – Gene Expression

  1. ordered Deboer, Zimmer, Damasio, Yglesias, Richie, david graeber, Kurt Anderson’s books. Got “Japan’s Infamous Unit 731” and “Breaking the Two party doom loop.” “The Short Life and Curious Death of Free Speech in America”

    Finished “To Start a War” and am listening to “reaganland.” Surprising how similar Trump is to Reagan. He’s basically stealing his act but performing it differently. Still waiting for “Who gets in and Why” to come out…looks like a good one!

  2. Interesting tweet by Balloux – https://twitter.com/BallouxFrancois/status/1302859330006458368 . Seralogical study of Maranhao, Brazil. 40.4% Infected, IFR 0.17%.

    To get an idea of what that might look like on Western demographics: Back in the relatively early stages of this thing Bommer and Vollmer published a study estimating country IFRs using the Chinese Wuhan returnee IFR of 0.66% (best quality at the time) using age structure, and I adjusted that by a simple multiplier to see how it would translate under high and low IFR estimates, one US = 11.9% (ridiculously high) and Gangelt Germany study of 0.37% (assuming representative for Germany).

    See here – https://imgur.com/a/YIUmImQ

    Since that Maranaho IFR was the same as “Brazil age demographics on Gangelt” estimate, that also shows that under a simple multiplier Maranaho IFR would translate to about 0.27% in the USA.

    Now, to walk back a bit, again, this is another outlier IFR! So I wouldn’t take home that it’s accurate.

    (Perhaps the seralogical samples are skewed toward infected, which is often the case in low IFR results, and I believe this was a problem with the Gangelt study for example? Perhaps Maranhao is younger than Brazil as a whole? Though say they’re off by a factor of 2, then the IFR is still *only* 0.34%, so they would have to pretty badly off on serology to get a much higher IFR. Being off by a factor of two and that would also indicate *yet another* dense urban area topping out at 20% infected…).

    However, that aside, it does seem to suggest one clear thing. Back in the early days of the pandemic, there was a contention that poor but young countries still needed to lockdown, as poor age adjusted health among citizens and low healthcare resources would mean that they’d quickly get overwhelmed by the disease and have *very* high excess mortality comparable or higher than older, richer countries.

    This was a reasonable argument. Though a lot of the same people making the argument seem to have been the ones arguing for some other stuff which was clearly wrong, like definite evidence for extensive sequalae, compulsory population wide “lockdowns” as 9x as effective than mere social distancing advice and limited closures, WHO estimates of IFR at 3.8%, identified cases = true number of infections, and a gaggle of similar things which seem to have proved by time extremely wrong.

    But the evidence of Maranhao seems to suggest this is wrong, at least for countries as “rich” as Brazil (though in a world context, let’s remember Brazil is pretty middle of the pack, albeit with very high income and wealth inequalities!).

    The evidence from South Africa also seems to indicate that despite very high HIV, etc. laying a health burden, and low healthcare resources, this hasn’t really led to particularly high age adjusted IFR. Even Africa outside SA seems to have had very little outbreaks or excess mortality.

    I of course argued against this “Poor countries will be overwhelmed due to poor healthcare and high population morbidity, so lockdown is necessary for them, despite the high additional economic cost” idea, so I am perhaps somewhat biased to “I informed you thusly, oh, I informed you thusly”.

  3. Wow, reading the comments at Eurogenes Re: the lactase persistence piece, Davidski certainly doesn’t have a high opinion of the study’s authors.

  4. @Matt,

    What’s your take on this whole “immunological dark matter” leading to previously unaccounted for levels of population-level immunity? Antibody tests in NYC in June showed around 20-25% of people had been exposed to the virus, much less than the conventional 70% needed for herd immunity. Yet newly reported cases had already fallen off a cliff by June from the March/April levels, and there’s been no real uptick in cases at all in NYC this summer, even though there have been plenty of potential super-spreader events due to mass protests, looting/riots, etc.

    There were some studies a few weeks ago showing cross-reactivity between common cold coronaviruses and Covid-19, potentially resulting in an unaccounted for immunity to the latter in 10-30% of the population. If you take the high end of that estimate and add it to the % of confirmed antibody cases in NYC, you get around 50-60% herd immunity levels, which would explain the massive decline in cases there?

    Looking at other states that exploded this summer – Florida, Texas, Arizona, California – again after severeal weeks of massive increases in reported cases, we’ve started to see huge declines now, despite the fact there’s no way any these places have reached herd immunity and their lockdowns seem to have been marginal at best.

  5. he did? ouch. that’s bullshit. nothing personal, but i still have to say he’s a dang good writer. “Fantasyland” was quite good.

    about to start “A Rebel’s Recollections.” 7 part essay by a southern rebel published in the Atlantic in 1874. looks promising

    One man’s battle shows why covid-19 and obesity are a toxic mix
    https://www.msn.com/en-us/news/us/one-man-s-battle-shows-why-covid-19-and-obesity-are-a-toxic-mix/ar-BB18IMXH

    Watched Charlie Kaufman’s new film last night. i really liked it but it was very tough to figure out what was going on. i think i’d have liked it better if i’d read spoilers first, actually. he is a genius script writer, for sure.

  6. Mick: Honestly I just don’t know enough about the low HIT and IDM topics really to add anything useful. Like you say, if there is some significant IDM obviously it will reduce the HIT, if that’s the case. Just as a completely banal observation it seems like it’s possible to say there’s “dark matter” in the models (things we can’t explain) and what could be suspicious patterns and consistencies in total peak estimated infections, but harder to prove it’s definitely due to preexisting cross immunity and things like this.

    The obvious problem with low HIT from IDM idea though is that there seem to be clear *local* breaches of that in Bronx etc. So if there is this, it seems has to be kind of acting as a soft limit – something like “This acts as a limit, but only if the total infectious dose from environment is not too high”, or it doesn’t stop the virus if people are constantly moving through a larger area where infection can survive and getting infected or something.

    Only thing I would add is I am personally a bit suspicious of some of the claims that cross immunity from naturally spreading viruses is significant in some *between* country differences – it still doesn’t feel right to be feasible that Germany would have high cross immunity through a virus that had no spread significantly in rest of Western Europe, or even more so that Africans in Africa could have high cross immunity when African migrants to UK and France etc have really been hit hard…

    These are both just the sort of basic obvious observations though.

    Another thing on Balloux’s Twitter (don’t worry, not gonna repost the whole thing) suggesting shift in age distribution of covid cases may *not* be main reason for decline in fatalities:case ratio in recent later infection spurts in Europe and US (possibly helping to explain Brazil result above too) … https://mobile.twitter.com/BallouxFrancois/status/1302717560388046848

    Though caution this is purely age; within age groups, risks v different for people who are infected in hospital / care home vs general community, so different patterns there could matter. OTOH, that said, seems care home infections should *raise* ratio of detected fatalities:infections, within old age bracket, while that doesn’t seem to happen in this data and in fact the opposite happens.

    One possible reason may be that seasonality matters to fatalities:infection… Maybe IFRs were and are higher in cooler climates? Relatively high infections in summer (e.g. sunbelt) may be less bad alternative to winter infections.

  7. I have a Wikipedia page. Don’t believe everything you read on the internet.

    Razib, do you have a doctorate?

  8. https://www.nature.com/articles/s41562-020-0930-x – “Physical topography is associated with human personality”. 3 million samples. Big 5. Measures “mountainness” as associated with personality, rather than elevation.

    Finds fairly strong effects of “mountainness” on personality, fairly strong for “openess to experience” (O) and weaker effects on C, A, E and N. Mountain dwellers more open, less conscientious, agreeable, extraverted and neurotic.

    However, big east-west split in these. After controlling for east-west location, small positive effect of mountainness on openness-to-experience remains, and also small increase effect of neuroticism in mountainess, while agreeableness, conscientious and extraversion become neutral.

    Eastern Mountains (“Appalachians” sometimes equated with “Scotch-Irish”, sometimes not?) both more open to experience and neurotic, but otherwise fairly similar to others. Western Mountains (“Rockies”) folk more different. Quite a signal of a Western Mountains personality found, but not really an Eastern Mountains one.

    Of course, all these effects are weak compared to lifecycle effects, sex and education effects. (Pop density significant for Openess too) And they partial out these effects before considering mountainess I think.

    So the actual profile of people living in the mountain regions may be larger, but this could probably be attributed to education, age, etc. (For instance, people living in Appalachia might have different Big 5 traits, but primarily due to being a region of lower general education, and not too different from an education matched sample from, Midwest of equal rurality or something like this, other than slightly more open to experience, less conscientious and slightly more negative emotionality.)

    Main result figures: https://imgur.com/a/NjTkda5

  9. An Open Letter to Our Fellow American Citizens
    https://www.realclearfoundation.org/liberty-and-justice-for-all/index.html#mc_embed_signup

    Over the next several years, the noble sentiments and ideas that gave birth to the United States will either be repudiated or reaffirmed.

    * * *

    In the face of this threat, the American institutions we must now reaffirm are these:

    Free speech.
    Representative government.
    Federalism.
    Market commerce.
    Education.
    Family.
    Religion.
    We invite all citizens of good will to join us so that together we can strive for liberty and justice for all.

    ============================

    Razib. I know you have emphasized family so here is the rest of that graf:

    An affirmation of the traditional family—the belief that men and women should be encouraged to marry and have sons and daughters—cannot be thought a crime. Civilization perishes unless such unions are encouraged. The noble longing for a plural society, in which not all are cast in the same mold, must not be realized by belittling the family. Strong families headed by married couples have been the key to success in black America ever since slavery was abolished a century and a half ago, and this remains the key today for all Americans.

  10. There is a new abstract about dna from Satsurblia 25,000 years ago. I wonder when the preprint will be available. Who knows, maybe the Dzudzuana delay have had something to do with this. If it doesn’t then that potentially means even more samples from the LGM. The more the merrier.

  11. Might as well be as exciting as a good thriller if the amount of delay is proportional to the surprises in store.

  12. Interview with David Reich on South Asian ancestry and ancient DNA:
    “They mixed with people, more to the south, more similar to the Andamanese and population in South-East Asia, and to some of the ancestry in Austro-Asiatic speakers, like Khasi. And, on the other hand, they also mixed with people to the north, who have ancestry related to the south. The mixture of these people associated with this gradient of ancestry that we have now documented through ancient DNA, both people to the north, that forms one of the ancestral populations of India, and people from the south, that forms the later ancestral populations. But most of the ancestry of both of the groups comes from the Harappan gradient. So the Harappan-related ancestry is actually the single largest source population for almost all people in India today. It mixed with other groups, probably in peninsular India or the south-east as well as groups from the north. These contributed important components, but the single largest component both of northern ancestral groups and other ancestral groups is the Harappan ancestral type.”

    https://frontline.thehindu.com/arts-and-culture/heritage/harappan-ancestryis-the-single-largest-source-population-for-almost-all-people-in-india-today/article32514104.ece

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