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

Open Thread, 05/04/2020

Imperial Twilight: The Opium War and the End of China’s Last Golden Age is pretty good. It gives a blow-by-blow of the lead up to the Opium Wars. One gets a more visceral sense of why Chinese nationalists hate the West so much.

Influenza: The Hundred-Year Hunt to Cure the 1918 Spanish Flu Pandemic and Salt: A World History are both Amazon Kindle deals. Recommended, especially the second.

Understanding the Eneolithic steppe. If you are curious about ancient DNA and you aren’t reading David what’s wrong with you?

The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics.

Fast and accurate approximation of the joint site frequency spectrum of multiple populations.

SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?

Multiethnic catalog of structural variants and their translational impact for disease phenotypes across 19,652 genomes.

In a City Frozen in Fear, Time Freezes, Too. Great images of Delhi during lockdown.

Can Genetic Engineering Bring Back the American Chestnut?

Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. Low-coverage sequencing is getting competitive with arrays.

China’s Factories Are Back. Its Consumers Aren’t. “Demand shock!”

De novo mutation in ancestral generations evolves haplotypes contributing to disease.

Cuomo’s N.Y. Reopening Plan: 10 Regions, 4 Phases, Many Caveats.

Got Muhammad and the Empires of Faith.

On this weblog, I’ve expressed optimism about COVID-19. 45,000 deaths in the USA? Perhaps 85,000? Seems like I was too optimistic. It looks like we’ll go well over 100,000 thousand, and we don’t have a good roadmap for the future. Hopefully, something helps us.

15 thoughts on “Open Thread, 05/04/2020

  1. So, this is kinda random, but it’s been on my mind lately:

    I’ve been re-reading the Old Testament for the first time in like two decades. I’ve also been reading off and on some different modern interpretations of it, in large part because without the historic context under which it was written, you really miss a lot of the nuance of the stories.

    Regardless, as I had been aware for some time, the archaeological consensus is that the narrative which is given in the Torah and Deuteronomistic history is almost completely false, save for perhaps the period immediately prior to Babylonian captivity.

    One particular element however is niggling to me: the now-accepted consensus seems to be that there was no invasion of Canaan, with the Israelite identity developing organically – and peacefully – within the region as some sort of a cultural movement. Under this understanding the virulent hatred of the Canaanites was seen as essentially a way to distinguish between those native to the area who remained polytheist, and those who became henotheists who worshiped Yahweh, and eventually outright monotheists.

    The problem I have with this analysis is it’s the exact same “no evidence for migration, pots not people” crap that proved utterly false regarding Europe and South Asia. It makes me wonder if there might be a little bit more truth to the historical narrative within the Old Testament than it is commonly given credit for.

    This probably isn’t something we can disentangle with ancient DNA – as we had for Europe and South Asia – given even if they weren’t identical the Israelites and the Canaanites were very closely related peoples. Still, I’m left wondering if maybe we’re missing some important archaeological clues suggesting that maybe that the formation of the Israelite identity was indeed as bloody as was written.

  2. Sorry for my sieve-like memory. If I could trouble you to explain to me again why gene drive won’t work to kill off the newly U.S. invasive Asian ‘murder hornet’: https://www.nytimes.com/2020/05/02/us/asian-giant-hornet-washington.html , and other such pests, e.g. ticks (although their absence might prove ecologically disastrous as I have heard that ticks are a large part of the diet of some bird species). Oh yeah now I remember I asked you this same question regarding the anthropocenic shit-show loam-destroying ‘jumping worms’, which, as of yesterday’s garden tilling, still haven’t overtaken my patch of ground.

  3. @Karl, I’m not sure it is an analogous case. In the instance of Europe and the Corded Ware we had:

    – Physical anthropology that suggested a new people or element had arrived…

    – … But detailed analysis of material culture suggested that much of it was made in situ in Central Europe, leading to theories that dismissed phys anth evidence.

    – Ancient dna then validated the phys anth evidence, and showed that was originally correct.

    At no point did we actually prove that either “Pots = Peoples” (material cultures change with and dramatically only with migration waves and peoples) and indeed the archaeology seems to generally reject that, still.

    The crucial point is, really, this is a case of an older phys anth based theory winning out over objections, once dna could validate it. A victory for “Skulls = Peoples”. (Also true in the case of the Beakers. Other instances of adna such as in Britain have given a mixed picture, with Anglo-Saxon dna suggesting a great deal of assimilationism, probably driven by a change in emphasis of trade and defense orienting towards North Sea.)

    It’s definitely not, in my view, validation for every old hoary myth that suggests people are either ever autocthonous or are from elsewhere; indeed the dna evidence, if anything, encourages more skepticism about these stories as generally false (Greece, India).

    The crucial thing that adna shows us is not that IMO, that we should be more or less skeptical of every migration story that has ever been told through history (many of which are probably completely fabricated), but that we should lean towards careful phys anth (generally craniometric) evidence for migrations being more likely to have been correct, and not to dismiss it.

  4. @Karl

    Is there any chance that the enmity goes much deeper than what is normally taken to be the time depth of Canaanites (bronze to iron age)? Like even they don’t remember the exact stories, only the figments of what might have happened in the distant past and reconstructed new stories based on that. And by that I mean first the movement of Anatolians in the Levant during the PPNB period. I know it sounds far fetched but it doesn’t require remembering all of the details of the past. Just the notion that there was a vague movement of people and from the mixture, some clung to the old local (Natufian) ways while others took to the ways of the migrants (Anatolian farmers).

    Alternatively could it be a memory of more recent yet still older than bronze age movements like the copper age Seh Gabi-like movement or the early bronze age Kura Araxes migrations?

  5. The author of the Influenza book also has a very interesting blog about the portrayal of the natural world / medicine etc. in the Talmud (talmudology.com).

  6. The U Washington group revised its model yesterday and came up with 134,475 COVID-19 deaths projected by August 4, 2020.
    https://covid19.healthdata.org/united-states-of-america

    They are estimating 72 thousand Covid-19 deaths as of yesterday.

    The model revision was based on new data and considerations.
    “COVID-19: What’s New for May 4, 2020: Main updates on IHME COVID-19 predictions since April 29, 2020
    http://www.healthdata.org/covid/updates

    CDC says that National Vital Statistics system had received 39,910 death certificates with a COVID-19 code as yesterday. That number is lagged by a week or two because it only counts received paper work.

  7. “Can Genetic Engineering Bring Back the American Chestnut?”

    Let us hope so.

    And after they do that, they can bring back the American Elm.

  8. @Karl, It’s probably dated in many respects now, but I’ve always liked Asimov’s Guide to the Bible, for considering the Bible from an historic p.o.v. He describes the Levant as under competing control/influence btw/ Egypt and whichever civilization is dominant in the Tigris-Euphrates during this period. The Canaanites are described as descending from Ham, indicating the view that they were seen as related to Egyptians, and it was only when the Egyptians withdrew from the Levant in response to attacks from the Sea Peoples (Philistines?) that the Israelite were able to subjugate the Canaanites.

    He emphasizes the tribal conflicts referenced in the Bible and assumes that if a tribe is described as close in relationship to the Israelites, it has allied or cooperated from time to time.

  9. Re; Opium Wars and Chinese nats, I get the second hand impression Chinese nationalist education gives them a pretty cold, clear eyed view of them; a terrible consequence of national weakness, but not fundamentally a cause of later decline.

    I get the impression that in some contrast there are a lot of myths that float around about them in the West though:

    – British govt planned / encouraged turned to opium because worried about ‘Drain of Silver’; actually probably because supply of Spanish silver dollars cut off so private merchants turned to alternate trade good they could produce cheaply in their Indian holdings.

    – Britain could not compete on trade (because Chinese workers were “too productive” to compete with) so “turned to selling drugs”; actually China heavily regulated possible imports and had relatively poor consumer base with strong demand for foreign currency. Silver currency, then opium was all British merchants could get into country (first through satisfying Chinese mercantilism, second through smuggling), and one which could be produced competitively in tropical holdings, not all that Britain was potentially competitive in exports at.

    – Opium ruined China; but well before opium imports, China on the path to declining rural incomes and subsistence farming poverty due to policies of Qing that favoured skyrocketing rural population eking more out of marginal land, and did not really favour business, trade and more productive manufacturing. This led to a weak state scrounging around for money from a weak tax base as well. Neither outflows of silver or immediate harms from opium (probably fairly modest; fairly weak drug) probably had much to do with this trend.

    Chinese nats look at it fairly clearly (if perhaps angry about Chinese loss of face); Qing China was “weak and backwards” unable to enforce its laws and defend its territory.

    In the West it’s often crammed into more of a story about how the colonialism destroyed an advanced and peaceful, less militaristic non-Western world. Even though that is quite deficient in understanding what really happened and why it was able to happen.

  10. @Karl Zimmerman:

    The “Old Testament”, a Christian conception (The Hebrew Term is Tanakh but it is structured differently than Christian Bibles), is a very difficult document to read and understand without a great deal of aid. The document was assembled by a number of writers and redactors over a very long time. The linguistic difficulties of the vorlage are immense. There are different text types that are adhered to by different faith traditions. E.g, Jews rely on the Masoretic text and Orthodox traditions rely on the ancient Greek translation known as the Septuagint.

    Biblical texts contain a great deal of material that is obscure or contradictory. Much of our understanding depends upon the faith traditions from which we read it. And those faith traditions affect the the choice of text and translation.

    For my own -part as a non-orthodox Jew, I have enjoyed the essays at TheTorah.com. The following is a link to an index page:

    Exodus, Historicity
    https://www.thetorah.com/topic/exodus-historicity

    Here is a good essay on the historicity issue:

    “The Torah’s Exodus: Weighing the historicity of the exodus story entails more than addressing the lack of archaeological evidence.” by Dr. Rabbi Zev Farber
    https://www.thetorah.com/article/the-torahs-exodus

    I found the following intriguing: “The Historical Exodus: The Evidence for the Levites Leaving Egypt and the Introduction of YHWH into Israel” by Prof. Richard Elliott Friedman
    https://www.thetorah.com/article/the-historical-exodus

    The author argues that it was only the Levites who took part in the Exodus.

  11. I second the recommendation of TheTorah.com, but there is a lot of material there, and it presupposes a fair deal of background knowledge.

    “How to Read the Bible” by James Kugel is a good text for a layman’s intro to the scholarly-academic approach to understanding the context of the Hebrew Bible. After that, a dive into TheTorah.com would likely be easier.

  12. @Walter

    I would welcome English elms too. I still have a chopping board in my kitchen that my mother gave me 40 years ago, made from one of the last surviving mature trees

  13. “Why is it that Indo-Aryans contribute at least ~15% of the ancestry on the Gangetic plain, while the later Turco-Muslims contribute almost none?”

    The absense of Turco-muslim ancestry in Indian muslim population is really a mystery for which there is no satisfactory answers. The world over the trend is that a conquering people ruling a subject population for centuries will inevitably leave its genetic trace over subjugate population. Look at the african american or indigenous latin american populations where the european genes are present in significant proportion.

    Even if the subjugate people are a docile rent paying population, nothing prevents the ruling foreign elites to seek women from native population as consorts steadily in limited numbers.

    Unless we assume that the Turco muslim armies were accompanied by foreign women as well, and in ratios like 1:3 for male:female, it is hard to believe that these foreign soldiers did not take local women as wives. In fact the large harems of muslim nawabs containing hundreds and even thousands of women are well attested by colonial writers. And because of the fact that the children of the union of foreign male rulers and local women will unquestionably be brought up as muslims, we have a smaller population in which to look for foreign ancestries.

    I have no alternate theories. I am just seeking answers.

  14. Razib this question is kind of random but when are we going to get a follow up to the Abusir mummy study from years ago? Have you heard any inside information about another extensive DNA study (whether it be y-DNA, mtDNA, or autosomal) on the Ancient Egyptians?

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