I’ve been really busy, so I didn’t post an open thread last week and haven’t been keeping up with the book club. When I come up for some air I’ll try and catch up.
That being said, I should mention that my confederates at Brown Pundits recorded a 2.5-hour podcast with Tim Mackintosh-Smith, author of Arabs: A 3,000-Year History of Peoples, Tribes, and Empires. It’s going to have to be broken into two pieces. Not too much fat to edit out.
One of the things I’ve been busy with is getting my Substack up. A big thanks to all the readers/listeners over the years who have ponied up for a subscription. I’ll be sending out one free newsletter per week probably, but I’ve already started un-gating some podcasts.
Where are we in 2020? The New York Times (to which I still subscribe, but barely now), put up a profile of a new Senator from Wyoming, Cynthia Lummis, a Bull-Coaxing Conservative, Heads to the Senate. Because The New York Times is now so brazenly ideological even in its reporting I’ve started to try and anticipate talking points when I read something about politics (I mostly stick to world news and science now, though even there the little Maoists in charge seem to be interjecting ideological comments!). For example:
Despite her libertarian streak, Ms. Lummis holds some starkly right-wing views.
When I saw “starkly right-wing” I immediately guessed they’d jump to something related to race because no one at The New York Times but Liz Bruenig cares about economic libertarianism except in nominal terms. And here you go:
In a debate during her campaign, Ms. Lummis said she did not believe “racism is actually systemic” in America, saying instead that “pockets of racism” existed.
You can wonder about what the implications of the phrases are, but many of us Americans actually hold “starkly right-wing views” on these race issues. Including many people who are “communities of color.” Basically, the only group which doesn’t hold “starkly right-wing views” on these sorts of issues are white liberals, the core subscriber base of The New York Times.
Get Ready for False Side Effects.
Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.
Anthropogenic extinctions conceal widespread evolution of flightlessness in birds.
Incredible performance by Hugh Grant in HBO’s “The Undoing.” I didn’t think he could act! I got the feeling he was so good because he’s a bit like his character in real life:)
“Time lapse of the Future” https://www.youtube.com/watch?v=uD4izuDMUQA
Sometimes when I’m thinking about something “important” I’m reminded of this video: eventually there will be no evidence that anything has ever existed. A tough pill to swallow.
Razib- excellent piece here from American Affairs, found it through McWhorter’s recommendation:
https://americanaffairsjournal.org/2020/11/liberal-fundamentalism-a-sociology-of-wokeness/
One of the author’s many good points is that in a decentralized moral culture like the West, the market for moral judgments becomes similar to the market for fashion– first the radical types push the boundaries (DiAngelo, Kendi) and then those ideas become chic and adopted by the elites and used as status markers. Eventually those signals get adopted by people lower on the chain.
How many people below the upper middle class have any idea what BiPOC means??? There was just a new study with authors from Harvard, Penn, the Santa Fe Institute, and Microsoft which asserts that Bret Weinstein and Joe Rogan are “far-right.” Of course, this follows the 2018 Data and Society think tank’s study on “far-right radicalization” which was an outstanding performance of Six Degrees From Kevin Bacon.
The terminology (BiPOC, LGBTQetc, Latinx) must keep evolving, because elites always need to be able to showcase their differentiation from the unwashed masses. I bet Kamala Harris uses the word Latinx, unlike actual hispanic americans.
Also, the lack of a centralized moral structure in the West means that there is no easy check on extremism, and given the manner that ideas propagate, the most extreme memes tends to win out (obv also discussed in Taleb’s piece “The Most Intolerant Wins”)
The American Affairs author points to one potential bright spot, which is that Science still has moral cachet among western elites, and that this is a potential weak spot for Woke Ideology, given the obvious incompatibility. The author also points out that potentially unifying meme complexes such as patriotism or formal religion have low status in western society, and therefore are highly unlikely to be successful in moving the elite moral sphere.
Glad you started an open thread! Having seen your post yesterday on Twitter about BDSing China over its treatment of Muslims and the apparent futility of trying to do so (it would be possible, but would require a gigantic geopolitical effort straddling European/North American countries, countries that are majority or plurality Muslim, and probably the whole of South and Southeast Asia as well, and too many of these countries are at cross-purposes), one of the biggest mistakes Western companies took towards China was in treating individual Chinese firms as equal independently-owned and operated firms. It would have been more proper to view such firms as the wholly-owned subsidiaries of the overarching holding company of the CCP. The Chinese government had a long-term strategy for its businesses that has finally started to pay dividends over the past half-decade in terms of geopolitical and economic clout.
Also, why is BDS treated as some magic talisman, the go-to strategy for “outlaw” countries? The paradigmatic case for its effectiveness, South Africa in the 1980s, is dubious; South Africa from the beginning of Apartheid through the early 80s had relied on mining and resource extraction, but throughout the 80s was starting to shift towards a more advanced economy that didn’t revolve around exporting raw materials, so the low-paid black labor that Apartheid created was needed less, and the industries that were targeted by the BDS movement were already in decline.
What’s the best layman-friendly book on cultural evolution to read after The Secret of our Success?
@ Joe – i just read “the ape that understood the universe”…pretty good overview
“Where are we in 2020?”
March 238th as near as I can tell.
“Get Ready for False Side Effects.”
Terrific and very important take.
@Joe
I liked Turchin’s Ultrasociety better than The Secret of our Success. Similar territory.
If you want to read a novel thesis, Richard Wrangham’s The Goodness Paradox: The Strange Relationship Between Virtue and Violence in Human Evolution is insightful and persuasive.
Basically his argument is that homo sapiens has been self-domesticating for many thousands of years by periodically executing its most violent and anti-social males. So it broadly covers similar territory as those other two books, gene-culture co-evolution.
Razib,
Can the DNA of “pure” 6th or 7th generation core Appalachians be distinguished from “pure” 6th or 7th generation New Englanders?
@iffen, obviously you’re not asking me for the answer here but as far as I know the state of art is still “Clustering of 770,000 genomes reveals post-colonial population structure of North America” (https://www.nature.com/articles/ncomms14238)
There is a stable Appalachian subcluster in the USA albeit not very large:
Appalachians = 2048 / 770000 = 0.26% sample (1/400).
(This is one of their identified set of reduced gene-flow groups “Finally, the fourth set of clusters we label as post-migration isolated groups; these groups have historically resided in small or geographically isolated communities within the United States, and are distinguished by stable subsets within the IBD network, suggesting that reduced gene flow with neighbouring groups may have contributed to the identified structure.”)
Could be somewhat undercounted as not necessarily proportionate to population – African-Americans 5.8% of sample though 13% US population.
Reduced gene-flow only though, not necessarily 7th generation isolation.
They don’t detect any “pure New Englander” cluster at all; doesn’t seem to exist. (HP Lovecraft would be disappointed).
There are somewhat large clusters for North-South variation but they are not really separable or isolated (“pure”?) (“The five largest clusters (third set of rows in Table 1), which we describe as assimilated immigrant clusters, account for a large portion (60%) of the IBD network and exhibit a markedly different profile. Lacking distinctive affiliations to non-US populations, they show almost no differentiation in allele frequencies (Fst at most 0.001; Supplementary Table 5) and high levels of IBD to non-cluster members (Supplementary Data 2), suggestive of high gene flow between these clusters. Moreover, few members of these clusters could be assigned to a stable subset, indicating that this clustering is largely driven by continuous variation in IBD. Genealogical data reveal a north-to-south trend (Fig. 5), most consistently east of the Mississippi River (Fig. 3). These findings imply greater east-west than north-south gene flow, which is broadly consistent with recent westward expansion of European settlers in the United States, and possibly somewhat limited north-south migration due to cultural differences. While the precise numbers and boundaries of these clusters are not necessarily meaningful and may be partly driven by the assumption that inter-cluster connectivity follows a random graph model, these findings demonstrate that isolation-by-distance, and specifically geography in the continental United States, can be captured from IBD alone.”).
So in the sense I think you’re asking it (e.g. could you distinguish each of them from each other *and* other Americans with only the genetic data?), not really since there isn’t a detectable cluster in the one case, and possibly neither cluster really exists as a pure population…
Maybe an even more focused study could find more, but I think if you’re sampling close to 0.2% of the entire US population (and probably enriched for White Americans), if you’re not finding it, it’s very loose and weakly bound, if it exists at all.
Thanks very much Matt!
After successfully avoiding it for several years I have tumbled down into the Hillbilly Elegy rabbit hole. I haven’t seen the Red Queen yet, but Kevin Williamson is here. Marist scholars who explain that hillbillies don’t exist and never have are here. You know, social construct and all that. The hyper-woke are here waving their arms and whining that the POC hillbillies are being ignored. I am at the point described by R. Douthat: “a strong epistemological bias toward what you can only find out for yourself, as opposed to what Yale’s experts or Twitter’s warning labels or The New York Times might tell you.”
@iffen i happened to be reading this yesterday. pretty cool piece about “those people,” written in 1899: https://www.theatlantic.com/magazine/archive/1899/03/our-contemporary-ancestors-southern-mountains/581332/
iffen: “Can the DNA of “pure” 6th or 7th generation core Appalachians be distinguished from “pure” 6th or 7th generation New Englanders?”
There is a really nasty marrying your sister joke in there, but I don’t want to make it.
@Robert Ford
Thanks. An interesting read. I was surprised that the writer posits the English as the founding stock with the Scotch-Irish as secondary. I don’t remember seeing that before.
@Walter Sobchak
I used to tell my Yankee friends that kidded me about that subject that they should take a good look at their cousins and then a good look at mine and I think they would understand.
@ Matt
While lurking on Anthrogenica I noticed a recent dust-up regarding the exact relationship of ancient Epipaleolithic North Africans (the Iberomaurusians) to both Africans and West Eurasians, particularly the component of IBM ancestry that’s been dubbed “Ancestral North African,” and whether that component should be regarded as basically a primitive type of “Eurasian” ancestry or if we can appropriately dub it a form of “SSA” ancestry. Previous academic papers using qpGraph and some other methods show IBM being a near half and half blend of this “ANA” component and more conventional West Eurasian ancestry.
Someone brought up that on PCAs IBMs tend to cluster very near Horn Africans, who are essentially a half-and-half mix between SSAs and West Eurasians, give or take. So this would imply the same is true for IBM as well, and that ANA really could be considered more a form of SSA ancestry than anything closely related to Eurasian-proper. Someone even seems to have created a simulated ‘ANA’ component based on G25 coordinates and plotted it on a African vs Eurasian PCA, and it basically clusters with the SSAs but with marked southern shift.
https://anthrogenica.com/showthread.php?22309-The-mixed-genetic-origin-of-the-first-farmers-of-Europe&p=724186&viewfull=1#post724186
Given that you are our resident PCA guru, I was wondering if you had ever really played around much with these guys, and if you have any strong opinions on their ancestry and phylogenetic position one way or the other.
Interesting interview of a Harvard epidemiologist about bringing the pandemic under control while we all await vaccines (largely without having to shut down so far as I can tell):
Rapid Antigen Tests Are Effective, Cheap, and Could Quash the Pandemic Within Weeks (In Theory)
@Mick, thanks, yeah, I’m not sure about that accolade but cheers.
Honestly don’t have a lot of thoughts on it: If IBM overlapping Horn Africans on PC1 Vs PC2 of the normal global PCA, then that *could* be an interpretation… but there could be others? I think it’s not straightforward to interpret intermediate PCA position as admixture. It seems like you’d want to investigate it with formal stats first and foremost.
But there are also challenges with formal stats in Africa (which is kind of both hard mode for population relationships, and also problem everyone wants to unlock to understand origins of Homo Sapiens) as far as I understand it.
Firstly, you have the difficulty of determining a true outgroup, since it’s plausible that the African populations have geneflow with each other and there’s no outgroup today, while Neanderthal, Denisovan and Chimp (and artificial reconstructed ancestral genomes) all have questions.
Secondly, using capture array data and biases is probably more of a significant problem for Africans – take this figure from the HGDP whole genome paper which Iain Mathieson recently mentioned again on twitter (https://mobile.twitter.com/mathiesoniain/status/1334269947422404608). Correlation of “true” whole genome to array is pretty good but particularly for Africans some of the stats on array can be non-sig (sometimes) or reversed (rare but possible) on whole genome (and vice versa). I don’t think the array data in that figure are the Human Origins array used for most capture ancient dna, but there’s a figure in the supplement that shows there’s still some of the same problem on that array.
All that said, if it does appear an admixed cluster I guess you could create a simulated population on PCA that represents an unadmixed cluster…. If the admixture was not remote to the time of the IBM samples and you have a good proxy in sample set and there had been little post-admixture drift in any population (the admixing or admixed). Or it could be done with the population alone which is better, but only if that population had a number of samples with unequal admixture proportions.
I’ll have a look later and see if there’s anything I can work out from Global 25 PCA though anyways.
Some graphs on current state of Covid19 death and case curves, European Union and USA: https://imgur.com/a/oF1gjNT
Seems like the death curve has plateaued for a quite a bit longer than the case curve, after aligning growth. Hungary recently emerged with very high death rates (probably end up close in total deaths as % of population to France and Western Europe in general, along with Czech Republic. Poland will possibly only end up about 75-80% France). Some convergence.
US case fatality rate continues to fall, EU area plateaus. (Case fatality rates should tend to rise logically, but been rare across the pandemic for them to actually do so, because case discovery tends to outpace lagged deaths.)
Some fairly recent new adna Youtube videos:
https://www.youtube.com/watch?v=c_qsR1g6AI0 – “Janet Kelso: Using Ancient DNA to understand modern human history”. Lots of stuff we’ll know about but a good readover, and she mentioned a project to sequence over a hundred Neanderthal genomes which sounded interesting.
https://www.youtube.com/watch?v=_n8CLtPDV8c – “Digging Ancient Haplotypes out of Modern Human Genomes” – 23/11/2020 – Luca Pagani. A lot of reviews of existing papers but there are some interesting bits and its useful to see it all read over. He covers the paper of Marnetto 2020 (“Ancestry deconvolution and partial polygenic score can improve susceptibility predictions in recently admixed individuals”) and Yelmen 2019 (“Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations”).
my interview of david shor https://razib.substack.com/p/david-shor-the-uncancellable
https://twitter.com/jmrphy/status/1336357745889447938 holy crap, I think this guy is seriously doing arranged marriages
murph is a friend. so is “default_friend” (we’re IRL friends)
so it’s a real thing?
Further links:
– https://www.youtube.com/watch?v=xF18mYe5WoA : David Reich ASHG 2020 on possible new adna technology to be used by Reich lab instead of 1240k. Potential for improved coverage, more targeting of phenotype related SNPs of interest.
– https://phys.org/news/2020-12-fatty-residues-ancient-pottery-reveal.html (press coverage) : “Fatty residues on ancient pottery reveal meat-heavy diets of Indus Civilization” / https://www.sciencedirect.com/science/article/pii/S0305440320302120?via%3Dihub (paper).
Further paper on lipid residues on IVC pottery. Headline suggests lots of meat however note the full quote – “Our study of lipid residues in Indus pottery shows a dominance of animal products in vessels, such as the meat of non-ruminant animals like pigs, ruminant animals like cattle or buffalo and sheep or goat, as well as dairy products. However, as one of the first studies in the region there are interpretative challenges. Some of the results were quite unexpected, for example, we found a predominance of non-ruminant animal fats, even though the remains of animals like pigs are not found in large quantities in the Indus settlements. It is possible that plant products or mixtures of plant and animal products were also used in vessels, creating ambiguous results.”
(An earlier one I posted up before in Sept was “Compound specific isotope analysis of lipid residues provides the earliest direct evidence of dairy product processing in South Asia”).
It seems that if any elements of IVC came down in a later synthesis giving rise to later Indian culture, vegetarianism may not have been one of them!
I recently came across a story about the fact there are a few towns in the world where twinning is extremely common, something that in those cases is known to have a hereditary component and is enhanced by Founder effects. https://www.youtube.com/watch?v=vT3N4ukLNLo&fbclid=IwAR2-4S9IGCjvLknopa4c3D1OxHBQXIHTbUhYirTuST9TmiaBIaV1Q7exgmM
This got me to wondering. As you’ve posted many times, lots of jati in South Asia, which while not as geographically isolated as these villages, have extreme levels of endogamy going back 1000 years and extreme founder effects. Given how many jati there are, it wouldn’t be too surprising if one or two of them were known for twinning as well, and it is a hereditary trait whose phenotype is obvious to the untrained eye.
I wonder in particular if there is structure within the Tamil Nadu village mentioned in the link where twinning is common such that the twinning is actually largely confined to one or two jati within that village as a place to start looking.
Connecticut will become the first state to require high schools to offer Black and Latino studies in fall 2022
https://www.cnn.com/2020/12/09/us/connecticut-high-schools-black-latino-studies-trnd/index.html
oh yes. we’re becoming Canada (just the bad parts)
SpaceX landing from a few miles away https://www.youtube.com/watch?v=iauacCNV86s&feature=youtu.be
*cough* Robert, surely you mean Latinx studies, don’t you? DON’T YOU???
BTW, thanks for the Bart Ehrman link you gave (some time or other – I have lost track) – boy did that send me down a rabbit hole.
Glad you enjoyed it! (I had to google his name to remember:)
here’s another i enjoyed if anyone wants a nice summary of the new “Trade Wars are Class Wars” book everyone’s talking about.
https://www.youtube.com/watch?v=QFoJ9j3MFnA
The hungry Brain (good book)
For anyone interested in the international education benchmarking comparisons (PISA by OECD, TIMSS by IEA), saw on Twitter that TIMSS 2019 (https://timss2019.org/reports/achievement/) data was released, so some crossplots against PISA 2018 data that I had to hand: https://imgur.com/a/gOfeCtC
With some similar information for PISA Reading migrant vs non-migrant children (because of some asymmetries there that probably bleed over into Math and Science scores) and TIMSS vs PISA 2015 for comparison (for change over time).
It seems that:
1) TIMSS in 2019 is less “West is Best” than PISA in 2018. TIMSS shows UAE, Southeast Europe and Turkey all overlapping with Western Europe and the “Anglosphere”, unlike PISA where there is a clear rank order in the comparable scores. TIMSS is also kinder to ex Soviet states (Russia, Kazakhstan, Georgia).
2) As a consequence of being less “West Is Best”, TIMSS will of course be less correlated with country income levels (consumption/GDP per capita) than PISA, and instead has more of an East Asian:West Eurasian divide. On PISA, gaps between Japan to Netherlands are smaller than Netherlands to Hungary and gaps from Netherlands to Bulgaria far greater, but this seems not so much the case in TIMSS, where the relative differences within Europe (West Eurasia) are generally smaller in comparison to East Asia and Europe and the best performing European state (Russia/England) seems more compressed towards the most poor performing, relative to the gap with East Asia). It’s the trend for countries who are below regression line in TIMSS than PISA to tend to be richer ones (e.g. Chile, Canada, Netherlands, UAE). TIMSS will also be less associated with complexity of economic production/export complexity.
3) TIMSS 2015 was different than today, with Turkey and UAE large laggards to Europe. It seems in 2019 data, there’s a fair amount of catchup for them both.
For anyone interested in PCA and East Asia, noticed that Davidski’s Eurogenes Blog had added quite a few more East Asian samples to his Global 25 PCA datasheets, so thought I would revisit the now familar method of rerunning these through a sort of PCA-on-PCA to check their affinities on those.
Including North Asians: https://imgur.com/a/nOLbfBx
Excluding North Asians: https://imgur.com/a/0HKCso8
Excluding lots of populations to focus on Chinese provinces: https://imgur.com/a/b47kMe7
(Excluded ancient dna to avoid clutter)
Some of the representation among Han at province level, like Shandong, Shanxi, Henan, Jiangsu (and city level like Sichuan) seems quite interesting as it seems to allow PCA to recapitulate geography in some views. Compared to the Han_NChina from the HGDP, in some views the Jiangsu samples for instance seem quite “North” as well but also more “East” in some ways (forming more of a cline (with gaps) with Korea.
It seems like the province level East->West structure comes out in its most clear form if you include references which don’t have too much deeply divergent East Asian ancestry from Han (e.g. not the more northern Mongolic groups with little West Eurasian ancestry but a lot of North Asian ancestry) but rather groups that are more similar to Han in their East Asian ancestry but who have some West/Central Eurasian ancestry (e.g. Salar, Dongxiang, Dungan, Bonan samples from Western Chinese provinces). It doesn’t seem like there is much West/Central Eurasian related ancestry in Han in provinces at all (just as there’s very little genetic differentiation), but there might be some low close to zero fraction that nevertheless can serve as “tracer dye” for geographical structure?
Some coronavirus and death plots from OurWorldInData:
EU case vs US cases: https://tinyurl.com/y7fsp5v9
EU deaths vs US deaths: https://tinyurl.com/yb584axz
EU cases dropped, but deaths did not drop and plateaued. Now EU deaths look to have started to rise again.
Current top 11 new deaths per day (7 day average): https://tinyurl.com/y83ajgq6 . Pretty regional (centered around SE-Central Europe). Italy and Belgium added for scale against Spring outbreaks: https://tinyurl.com/ya9qhp3u . In cumulative view with Italy and UK for scale: https://tinyurl.com/y7h3mj7d.
I’d add to this that with SE-Central Europe, seems like the worst hit countries within that region are fairly mountainous regions bordering Northern Italy. (Just as the Italian Alps had a hard time in the first European wave. Do mountain regions have difficult environmental characteristics beyond climate? Peru also got hard hit in Latin America…)
Top 11 current new cases (7 day average): https://tinyurl.com/y6wau75u (but this has less relationship with real cases… varying test capacity and detection rate).