nhaliday + pop-structure   98

Who We Are | West Hunter
I’m going to review David Reich’s new book, Who We Are and How We Got Here. Extensively: in a sense I’ve already been doing this for a long time. Probably there will be a podcast. The GoFundMe link is here. You can also send money via Paypal (Use the donate button), or bitcoins to 1Jv4cu1wETM5Xs9unjKbDbCrRF2mrjWXr5. In-kind donations, such as orichalcum or mithril, are always appreciated.

This is the book about the application of ancient DNA to prehistory and history.

height difference between northern and southern europeans: https://westhunt.wordpress.com/2018/03/29/who-we-are-1/
mixing, genocide of males, etc.: https://westhunt.wordpress.com/2018/03/29/who-we-are-2-purity-of-essence/
rapid change in polygenic traits (appearance by Kevin Mitchell and funny jab at Brad Delong ("regmonkey")): https://westhunt.wordpress.com/2018/03/30/rapid-change-in-polygenic-traits/
schiz, bipolar, and IQ: https://westhunt.wordpress.com/2018/03/30/rapid-change-in-polygenic-traits/#comment-105605
Dan Graur being dumb: https://westhunt.wordpress.com/2018/04/02/the-usual-suspects/
prediction of neanderthal mixture and why: https://westhunt.wordpress.com/2018/04/03/who-we-are-3-neanderthals/
New Guineans tried to use Denisovan admixture to avoid UN sanctions (by "not being human"): https://westhunt.wordpress.com/2018/04/04/who-we-are-4-denisovans/
also some commentary on decline of Out-of-Africa, including:
"Homo Naledi, a small-brained homonin identified from recently discovered fossils in South Africa, appears to have hung around way later that you’d expect (up to 200,000 years ago, maybe later) than would be the case if modern humans had occupied that area back then. To be blunt, we would have eaten them."

Live Not By Lies: https://westhunt.wordpress.com/2018/04/08/live-not-by-lies/
Next he slams people that suspect that upcoming genetic genetic analysis will, in most cases, confirm traditional stereotypes about race – the way the world actually looks.

The people Reich dumps on are saying perfectly reasonable things. He criticizes Henry Harpending for saying that he’d never seen an African with a hobby. Of course, Henry had actually spent time in Africa, and that’s what he’d seen. The implication is that people in Malthusian farming societies – which Africa was not – were selected to want to work, even where there was no immediate necessity to do so. Thus hobbies, something like a gerbil running in an exercise wheel.

He criticized Nicholas Wade, for saying that different races have different dispositions. Wade’s book wasn’t very good, but of course personality varies by race: Darwin certainly thought so. You can see differences at birth. Cover a baby’s nose with a cloth: Chinese and Navajo babies quietly breathe through their mouth, European and African babies fuss and fight.

Then he attacks Watson, for asking when Reich was going to look at Jewish genetics – the kind that has led to greater-than-average intelligence. Watson was undoubtedly trying to get a rise out of Reich, but it’s a perfectly reasonable question. Ashkenazi Jews are smarter than the average bear and everybody knows it. Selection is the only possible explanation, and the conditions in the Middle ages – white-collar job specialization and a high degree of endogamy, were just what the doctor ordered.

Watson’s a prick, but he’s a great prick, and what he said was correct. Henry was a prince among men, and Nick Wade is a decent guy as well. Reich is totally out of line here: he’s being a dick.

Now Reich may be trying to burnish his anti-racist credentials, which surely need some renewal after having pointing out that race as colloquially used is pretty reasonable, there’s no reason pops can’t be different, people that said otherwise ( like Lewontin, Gould, Montagu, etc. ) were lying, Aryans conquered Europe and India, while we’re tied to the train tracks with scary genetic results coming straight at us. I don’t care: he’s being a weasel, slandering the dead and abusing the obnoxious old genius who laid the foundations of his field. Reich will also get old someday: perhaps he too will someday lose track of all the nonsense he’s supposed to say, or just stop caring. Maybe he already has… I’m pretty sure that Reich does not like lying – which is why he wrote this section of the book (not at all logically necessary for his exposition of the ancient DNA work) but the required complex juggling of lies and truth required to get past the demented gatekeepers of our society may not be his forte. It has been said that if it was discovered that someone in the business was secretly an android, David Reich would be the prime suspect. No Talleyrand he.

https://westhunt.wordpress.com/2018/04/12/who-we-are-6-the-americas/
The population that accounts for the vast majority of Native American ancestry, which we will call Amerinds, came into existence somewhere in northern Asia. It was formed from a mix of Ancient North Eurasians and a population related to the Han Chinese – about 40% ANE and 60% proto-Chinese. Is looks as if most of the paternal ancestry was from the ANE, while almost all of the maternal ancestry was from the proto-Han. [Aryan-Transpacific ?!?] This formation story – ANE boys, East-end girls – is similar to the formation story for the Indo-Europeans.

https://westhunt.wordpress.com/2018/04/18/who-we-are-7-africa/
In some ways, on some questions, learning more from genetics has left us less certain. At this point we really don’t know where anatomically humans originated. Greater genetic variety in sub-Saharan African has been traditionally considered a sign that AMH originated there, but it possible that we originated elsewhere, perhaps in North Africa or the Middle East, and gained extra genetic variation when we moved into sub-Saharan Africa and mixed with various archaic groups that already existed. One consideration is that finding recent archaic admixture in a population may well be a sign that modern humans didn’t arise in that region ( like language substrates) – which makes South Africa and West Africa look less likely. The long-continued existence of homo naledi in South Africa suggests that modern humans may not have been there for all that long – if we had co-existed with homo naledi, they probably wouldn’t lasted long. The oldest known skull that is (probably) AMh was recently found in Morocco, while modern humans remains, already known from about 100,000 years ago in Israel, have recently been found in northern Saudi Arabia.

While work by Nick Patterson suggests that modern humans were formed by a fusion between two long-isolated populations, a bit less than half a million years ago.

So: genomics had made recent history Africa pretty clear. Bantu agriculuralists expanded and replaced hunter-gatherers, farmers and herders from the Middle East settled North Africa, Egypt and northeaat Africa, while Nilotic herdsmen expanded south from the Sudan. There are traces of earlier patterns and peoples, but today, only traces. As for questions back further in time, such as the origins of modern humans – we thought we knew, and now we know we don’t. But that’s progress.

https://westhunt.wordpress.com/2018/04/18/reichs-journey/
David Reich’s professional path must have shaped his perspective on the social sciences. Look at the record. He starts his professional career examining the role of genetics in the elevated prostate cancer risk seen in African-American men. Various social-science fruitcakes oppose him even looking at the question of ancestry ( African vs European). But they were wrong: certain African-origin alleles explain the increased risk. Anthropologists (and human geneticists) were sure (based on nothing) that modern humans hadn’t interbred with Neanderthals – but of course that happened. Anthropologists and archaeologists knew that Gustaf Kossina couldn’t have been right when he said that widespread material culture corresponded to widespread ethnic groups, and that migration was the primary explanation for changes in the archaeological record – but he was right. They knew that the Indo-European languages just couldn’t have been imposed by fire and sword – but Reich’s work proved them wrong. Lots of people – the usual suspects plus Hindu nationalists – were sure that the AIT ( Aryan Invasion Theory) was wrong, but it looks pretty good today.

Some sociologists believed that caste in India was somehow imposed or significantly intensified by the British – but it turns out that most jatis have been almost perfectly endogamous for two thousand years or more…

It may be that Reich doesn’t take these guys too seriously anymore. Why should he?

varnas, jatis, aryan invastion theory: https://westhunt.wordpress.com/2018/04/22/who-we-are-8-india/

europe and EEF+WHG+ANE: https://westhunt.wordpress.com/2018/05/01/who-we-are-9-europe/

https://www.nationalreview.com/2018/03/book-review-david-reich-human-genes-reveal-history/
The massive mixture events that occurred in the recent past to give rise to Europeans and South Asians, to name just two groups, were likely “male mediated.” That’s another way of saying that men on the move took local women as brides or concubines. In the New World there are many examples of this, whether it be among African Americans, where most European ancestry seems to come through men, or in Latin America, where conquistadores famously took local women as paramours. Both of these examples are disquieting, and hint at the deep structural roots of patriarchal inequality and social subjugation that form the backdrop for the emergence of many modern peoples.
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march 2018 by nhaliday
Use and Interpretation of LD Score Regression
LD Score regression distinguishes confounding from polygenicity in genome-wide association studies: https://sci-hub.bz/10.1038/ng.3211
- Po-Ru Loh, Nick Patterson, et al.

https://www.biorxiv.org/content/biorxiv/early/2014/02/21/002931.full.pdf

Both polygenicity (i.e. many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield inflated distributions of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from bias and true signal from polygenicity. We have developed an approach that quantifies the contributions of each by examining the relationship between test statistics and linkage disequilibrium (LD). We term this approach LD Score regression. LD Score regression provides an upper bound on the contribution of confounding bias to the observed inflation in test statistics and can be used to estimate a more powerful correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of test statistic inflation in many GWAS of large sample size.

Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n3/extref/ng.3211-S1.pdf

An atlas of genetic correlations across human diseases
and traits: https://sci-hub.bz/10.1038/ng.3406

https://www.biorxiv.org/content/early/2015/01/27/014498.full.pdf

Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n11/extref/ng.3406-S1.pdf

https://github.com/bulik/ldsc
ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
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november 2017 by nhaliday
Ancient Admixture in Human History
- Patterson, Reich et al., 2012
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.”
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november 2017 by nhaliday
The Same Old Story | West Hunter
People often reinterpret past events, recast them in terms of some contemporary ideology. When historians talk about the Monophysites in Byzantine times, they often suggest that those struggle are a mask for a kind of proto-nationalism. Maybe they were: and maybe nobody involved was thinking anything remotely like that. The Communists tried to come up with Marxist interpretations of ancient history, which led them to spend way too much time talking about Mazdakites in Sassanian Persia and the Zealots of Thessalonika . And Spartacus: but at least Spartacus was cool.

Then there are feminist versions of history. Let us never speak of them again.

Generally, this is all crap. But we could at least hope for something new along these lines: bullshit perhaps, but at least fresh bullshit. Obviously the reality underlying both the Punic Wars and the Crusades is the ancient struggle between EEF and ANE.
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november 2017 by nhaliday
Politics with Hidden Bases: Unearthing the Deep Roots of Party Systems
The research presented here uses a novel method to show that contemporary party systems may originate much further back than is usually assumed or might be expected—in reality many centuries. Using data on Ireland, a country with a political system that poses significant challenges to the universality of many political science theories, by identifying the ancestry of current party elites we find ethnic bases for the Irish party system arising from population movements that took place from the 12th century. Extensive Irish genealogical knowledge allows us to use surnames as a proxy for ethnic origin. Recent genetic analyses of Irish surnames corroborate Irish genealogical information. The results are particularly compelling given that Ireland is an extremely homogeneous society and therefore provides a tough case for our approach.
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november 2017 by nhaliday
Scotland’s many subcultures - Demos Quarterly
surname method

Turning to our analysis of the YouGov results, it was much to our surprise that the strongest majority support for independence was not among ‘pure’ historic Scots, but among people of Irish Catholic descent: with the latter being only 6 per cent net against independence, and historic Scots 16 per cent against. On the surface one might suppose this group would take its political lead from the Labour Party, for which it votes more consistently than any other group in Scotland.
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november 2017 by nhaliday
Peter Turchin Catalonia Independence Drive: a Case-Study in Applied Cultural Evolution - Peter Turchin
The theoretically interesting question is what is the optimal size of a politically independent unit (“polity”) in today’s world. Clearly, optimal size changes with time and social environment. We know empirically that the optimal size of a European state took a step up following 1500. As a result, the number of independent polities in Europe decreased from many hundreds in 1500 to just over 30 in 1900. The reason was the introduction of gunpowder that greatly elevated war intensity. The new evolutionary regime eliminated almost all of the small states, apart from a few special cases (like the Papacy or Monaco).

In today’s Europe, however, war has ceased to be an evolutionary force. It may change, but since 1945 the success or failure of European polities has been largely determined by their ability to deliver high levels of living standards to their citizens. Economics is not the only aspect of well-being, but let’s focus on it here because it is clearly the main driver behind Catalonian independence (since culturally and linguistically Catalonia has been given a free rein within Spain).

...

This is applied cultural evolution. We can have lots of theories and models about the optimal polity size, but they are worthless without data.

And it’s much more than a scientific issue. The only way for our societies to become better in all kinds of ways (wealthier, more just, more efficient) is to allow cultural evolution a free rein. More specifically, we need cultural group selection at the level of polities. A major problem for the humanity is finding ways to have such cultural group selection to take place without violence. Which is why I find the current moves by Madrid to suppress the Catalonian independence vote by force criminally reckless. It seems that Madrid still wants to go back to the world as it was in the nineteenth century (or more accurately, Europe between 1500 and 1900).

A World of 1,000 Nations: http://www.unz.com/akarlin/a-world-of-1000-nations/

Brief note on Catalonia: https://nintil.com/brief-note-on-catalonia/
This could be just another footnote in a history book, or an opening passage in the chapter that explains how you got an explosion in the number of states that began around 2017.

Nationalism, Liberalism and the European Paradox: http://quillette.com/2017/10/08/nationalism-liberalism-european-paradox/
Imagine for a moment that an ethnic group declared a referendum of independence in an Asian country and the nation state in question promptly sought to take the act of rebellion down. Imagine that in the ensuing chaos over 800 people were injured in a brutal police crackdown. Imagine the international disgust if this had happened in Asia, or the Middle East, or Latin America, or even in parts of Eastern and Central Europe. There would be calls for interventions, the topic would be urgently raised at the Security Council —and there might even be talks of sanctions or the arming of moderate rebels.

Of course, nothing of that sort happened as the Spanish state declared the Catalonian independence referendum a farce.

...

Remarkably, EU officials have largely remained mute. France’s new great hope, Monsieur Macron has sheepishly supported Spain’s “constitutional unity,” which is weasel-speak for national sovereignty—a concept which is so often dismissed by the very same European nations if it happens immediately outside the geographical region of EU. And this attitude towards nationalism—that it is archaic and obsolete on the one hand, but vitally important on the other—is the core paradox, and, some would say, hypocrisy, that has been laid bare by this sudden outbreak of tension.

It is a hypocrisy because one could argue that since the collapse of the Soviet Union, there has been a consistent and very real attempt to undermine sovereignty in many different parts of the world. To be fair, this has been done with mostly good intentions in the name of institutionalism and global governance, the “responsibility to protect” and universal human rights. With history in the Hegelian sense seemingly over after the collapse of the Berlin Wall, nationalism and great power politics were thought to be a thing of the past—a quaint absurdity—an irrelevance and a barrier to true Enlightenment. But unfortunately history does tend to have a sardonic sense of humour.

The entire European project was built on two fundamentally different ideas. One that promotes economic welfare based on borderless free trade, the free market and social individualism. And the other, promoting a centralized hierarchy, an elite in loco parentis which makes decisions about how many calories one should consume, what plastic one should import, and what gross picture of shredded lungs one should see on the front of a cigarette packet. It endorses sovereignty when it means rule by democracy and the protection of human rights, but not when countries decide to control their borders or their individual monetary and economic policies. Over time, defending these contradictions has become increasingly difficult, with cynical onlookers accusing technocrats of defending an unjustifiable and arbitrary set of principles.

All of this has resulted in three things. Regional ethnic groups in Europe have seen the examples of ethnic groups abroad undermining their own national governments, and they have picked up on these lessons. They also possess the same revolutionary technology—Twitter and the iPhone. Secondly, as Westphalian nation-states have been undermined repeatedly by borderless technocrats, identity movements based on ethnicity have begun to rise up. Humans, tribal at their very core, will always give in to the urge of having a cohesive social group to join, and a flag to wave high. And finally, there really is no logical counterargument to Catalans or Scots wanting to break apart from one union while staying in another. If ultimately, everything is going to be dictated by a handful of liege-lords in Brussels—why even obey the middle-man in Madrid or London?

https://twitter.com/whyvert/status/914521100263890944
https://archive.is/WKfIA
Spain should have either forcibly assimilated Catalonia as France did with its foreign regions, or established a formal federation of states
--
ah those are the premodern and modern methods. The postmodern method is to bring in lots of immigrants (who will vote against separation)
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october 2017 by nhaliday
Caught in the act | West Hunter
The fossil record is sparse. Let me try to explain that. We have at most a few hundred Neanderthal skeletons, most in pretty poor shape. How many Neanderthals ever lived? I think their population varied in size quite a bit – lowest during glacial maxima, probably highest in interglacials. Their degree of genetic diversity suggests an effective population size of ~1000, but that would be dominated by the low points (harmonic average). So let’s say 50,000 on average, over their whole range (Europe, central Asia, the Levant, perhaps more). Say they were around for 300,000 years, with a generation time of 30 years – 10,000 generations, for a total of five hundred million Neanderthals over all time. So one in a million Neanderthals ends up in a museum: one every 20 generations. Low time resolution!

So if anatomically modern humans rapidly wiped out Neanderthals, we probably couldn’t tell. In much the same way, you don’t expect to find the remains of many dinosaurs killed by the Cretaceous meteor impact (at most one millionth of one generation, right?), or of Columbian mammoths killed by a wave of Amerindian hunters. Sometimes invaders leave a bigger footprint: a bunch of cities burning down with no rebuilding tells you something. But even when you know that population A completely replaced population B, it can be hard to prove that just how it happened. After all, population A could have all committed suicide just before B showed up. Stranger things have happened – but not often.
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september 2017 by nhaliday
tcjfs on Twitter: "Yearly legal permanent residencies 1996-2015 with a bit more disaggregated and common-sensical designations than DHS https://t.co/167ms5Xr0s"
https://archive.is/70nNG
https://twitter.com/tcjfs/status/900052649147543552
https://archive.is/5U3Mi
Asian origin according to Department of Homeland Security
not sure tbh. i was just trying to disaggregate "Asian immigration" and I was like holy shit some of these places I would never include

U.S. Lawful Permanent Residents: 2014: https://www.dhs.gov/sites/default/files/publications/Lawful_Permanent_Residents_2014.pdf
Yearbook of Immigration Statistics: https://www.dhs.gov/immigration-statistics/yearbook

https://twitter.com/tcjfs/status/933066198161469440
https://archive.is/pRTqS
Foreign born population by Chinese, Indian, Mexican birth whose residence one year ago was abroad, 2000-2013
The above chart, extended to 2000-2016, with Mexico but also all of Latin/Central/South America:
our latin american immigrants are probably getting less "huwhite"
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september 2017 by nhaliday
Effective population size for advantageous mutations | West Hunter
So, with beneficial mutations, the effective population size is very different. Instead of being dominated by bottlenecks, it is more influenced by eras of large population size – more and more so as the selective advantage of the mutation increases. In the limit, if we imagine  mutations so advantageous that they spread  very rapidly, the effective population size approaches the population mean.
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august 2017 by nhaliday
Polygenic Adaptation has Impacted Multiple Anthropometric Traits | bioRxiv
By comparing these polygenic scores to a null distribution under genetic drift, we identify strong signals of selection for a suite of anthropometric traits including height, infant head circumference (IHC), hip circumference (HIP) and waist-to-hip ratio (WHR), as well as type 2 diabetes (T2D). In addition to the known north-south gradient of polygenic height scores within Europe, we find that natural selection has contributed to a gradient of decreasing polygenic height scores from West to East across Eurasia, and that this gradient is consistent with selection on height in ancient populations who have contributed ancestry broadly across Eurasia. We find that the signal of selection on HIP can largely be explained as a correlated response to selection on height. However, our signals in IHC and WC/WHR cannot, suggesting a response to selection along multiple axes of body shape variation. Our observation that IHC, WC, and WHR polygenic scores follow a strong latitudinal cline in Western Eurasia support the role of natural selection in establishing Bergmann's Rule in humans, and are consistent with thermoregulatory adaptation in response to latitudinal temperature variation.

http://infoproc.blogspot.com/2017/07/natural-selection-and-body-shape-in.html
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july 2017 by nhaliday
Information Processing: Genetic variation in Han Chinese population
Largest component of genetic variation is a N-S cline (phenotypic N-S gradient discussed here). Variance accounted for by second (E-W) PC vector is much smaller and the Han population is fairly homogeneous in genetic terms: ...while we revealed East-to-West structure among the Han Chinese, the signal is relatively weak and very little structure is discernible beyond the second PC (p.24).

Neandertal ancestry does not vary significantly across provinces, consistent with admixture prior to the dispersal of modern Han Chinese.

http://infoproc.blogspot.com/2014/01/china-1793.html
My fellow officers informed me, that while the negotiation was going on, the ships were constantly crowded with all kinds of refreshments, and that when they were first boarded by the Chinese they received every attention from them that could be shown; and that the presents received by the different officers belonging to the embassy, were of immense value. That the natives of this part of China were of different complexions and manners from those in and near Canton; their colour being nearly white; and in their manners were much more free and candid; and that they were of a larger stature, and more athletic than the southern Chinese—they were much more sociable, and not so particular respecting their women being seen by the men. And were even fond of receiving the officers into their houses, when on shore, provided it could be done without the knowledge of the mandarins.

http://infoproc.blogspot.com/2014/06/large-scale-psychological-differences.html
The study below discusses a psychological/cognitive/personality gradient between N and S China, possibly driven by a history of wheat vs rice cultivation.

https://en.wikipedia.org/wiki/Northern_and_southern_China
http://shanghaiist.com/2015/07/01/average-heights-men-women.php
https://www.quora.com/Why-are-Northern-Chinese-people-generally-taller-than-Southern-Chinese

https://gnxp.nofe.me/2017/08/01/the-great-genetic-map-of-china/
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july 2017 by nhaliday
Caste system in India - Wikipedia
A recent series of research papers, by Reich et al. (2009), Metspalu et al. (2011), and Moorjani et al. (2013), make clear that India was peopled by two distinct groups who split genetically ca. 50,000 years ago,[81][82] which they called "Ancestral North Indians" (ANI) and "Ancestral South Indians" (ASI) respectively.[note 1] They found that the ANI genes are close to those of Middle Easterners, Central Asians and Europeans whereas the ASI genes are dissimilar to all other known populations outside India.[note 2][note 3] These two distinct groups, which had split ca. 50,000 years ago, formed the basis for the present population of India.[83]

According to Moorjani et al. these two groups mixed between 4,200 and 1,900 years ago (2200 BCE-100 CE), whereafter a shift to endogamy took place.[84] David Reich stated, "Prior to 4,200 years ago, there were unmixed groups in India. Sometime between 1,900 to 4,200 years ago, profound, pervasive convulsive mixture occurred, affecting every Indo-European and Dravidian group in India without exception.".[85] Following this mixture,

Strong endogamy must have applied since then (average gene flow less than 1 in 30 per generation) to prevent the genetic signatures of founder events from being erased by gene flow. Some historians have argued that "caste" in modern India is an "invention" of colonialism in the sense that it became more rigid under colonial rule. However, our results suggest that many current distinctions among groups are ancient and that strong endogamy must have shaped marriage patterns in India for thousands of years.[81]

Moorjani et al. discerned two waves of admixture in this period, with northern India showing later dates of admixture.[86] GaneshPrasad et al. (2013) studied "12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India." According to this study, southern India was already socially stratified 4,000 to 6,000 years ago, which is best explained by "the emergence of agricultural technology in South Asia." The study concludes that "The social stratification (in Tamil Nadu) was established 4,000 to 6,000 years ago and there was little admixture during the last 3,000 years, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area."[87]

https://en.wikipedia.org/wiki/Wikipedia:Genetic_research_on_the_origins_of_India%27s_population

http://www.nytimes.com/2010/09/11/world/asia/11caste.html
A crucial factor is the collapse of the caste system over the last half century, a factor that undergirds many of the other reasons that the south has prospered — more stable governments, better infrastructure and a geographic position that gives it closer connections to the global economy.

“The breakdown of caste hierarchy has broken the traditional links between caste and profession, and released enormous entrepreneurial energies in the south,” said Ashutosh Varshney, a professor at Brown University who has studied the role of caste in southern India’s development. This breakdown, he said, goes a long way to explaining “why the south has taken such a lead over the north in the last three decades.”

http://www.livemint.com/Opinion/FLn6TiQPArdQZUN9LE2ZsM/The-impact-of-caste-on-economic-mobility-in-India.html
Caste Is Stunting All of India’s Children: http://foreignpolicy.com/2017/09/15/caste-is-stunting-all-of-indias-children/
Fears of impurity continue to steer Indians away from toilets — and towards deadly fecal germs.

https://twitter.com/MWStory/status/895580461879107584
https://archive.is/AsTwB
These Indian govt funded ads to encourage the wealthy but declining Parsi population to reproduce are quite extraordinary

http://marginalrevolution.com/marginalrevolution/2017/12/india-marriage-markets-everything.html
India’s government has expanded a scheme offering payment incentives to Hindus who marry members of the country’s poorest and most oppressed caste, the Dalits.
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june 2017 by nhaliday
Information Processing: Everything Under the Heavens and China's Conceptualization of Power
These guys are not very quantitative, so let me clarify a part of their discussion that was left rather ambiguous. It is true that demographic trends are working against China, which has a rapidly aging population. French and Schell talk about a 10-15 year window during which China has to grow rich before it grows old (a well-traveled meme). From the standpoint of geopolitics this is probably not the correct or relevant analysis. China's population is ~4x that of the US. If, say, demographic trends limit this to only an effective 3x or 3.5x advantage in working age individuals, China still only has to reach ~1/3 of US per capita income in order to have a larger overall economy. It seems unlikely that there is any hard cutoff preventing China from reaching, say, 1/2 the US per capita GDP in a few decades. (Obviously a lot of this growth is still "catch-up" growth.) At that point its economy would be the largest in the world by far, and its scientific-technological workforce and infrastructure would be far larger than that of any other country.

- interesting point: China went from servile toward Japan to callous as soon as it surpassed Japan economically (I would bet this will apply to the US)
- conventional Chinese narrative for WW2: China won the Pacific Theater not the US
http://www.nytimes.com/2004/12/06/world/asia/chinas-textbooks-twist-and-omit-history.html
https://www.theatlantic.com/international/archive/2012/06/a-story-about-world-war-ii-that-china-would-like-you-to-hear/259084/
- serious Chinese superiority complex overall
- "patriotic education", the fucking opposite of our god-awful ideology
- in Chinese history: each dynasty judges the last, unimpeachable
- ceding control of South China Sea would damage relations with neighboring countries (not enforcing their legitimate claims) and damage international norms (rule of law, etc.)
- next 10-15 years dangerous (Thucydides); of course Hsu criticizes
- suggestions: cultivate local alliances, prevent arms races, welcome Chinese international initiatives
I'm highly skeptical of all but the alliances
- ethnic melting in Chinese history, population structure (not actually as much as he thinks AFAIK), "age of nationalism", Tibet, etc.

Gideon Rachman writes for the FT, so it's not surprising that his instincts seem a bit stronger when it comes to economics. He makes a number of incisive observations during this interview.

---

At 16min, he mentions that
I was in Beijing about I guess a month before the vote [US election], in fact when the first debates were going on, and the Chinese, I thought that official Chinese [i.e. Government Officials] in our meeting and the sort of semi-official academics were clearly pulling for Trump.

---

I wonder if the standard of comparison shouldn't be with the West as a whole, not just the United States?

It depends on what happens to the EU, whether western powers other than the US want to play the role of global hegemon, etc.

The situation today is that the US is focused on preserving its primacy, wants to deny Russia and China any local sphere of influence, etc., whereas Europe has little appetite for any of it. They can barely allocate enough resources for their own defense.

Europe and the US have their own demographic problems to deal with in the coming decades. An aging population may turn out to be less challenging than the consequences of mass immigration (note population trends in Africa, so close to Europe).

If China behaved as an aggressive hegemon like the US or former USSR, it would probably elicit a collective back reaction from the West. But I think its first step is simply to consolidate influence over Asia.

---

interesting somewhat contrarian take on China's girth here: https://gnxp.nofe.me/2017/08/03/manufacturing-chinese-history-cheaply/

China Does Not Want Your Rules Based Order: http://scholars-stage.blogspot.com/2016/06/china-does-not-want-your-rules-based.html
There is much that is good in this narrative. McCain proclaims that "no nation has done as much to contribute to what China calls its “peaceful rise” as the United States of America." He is right to do so. No nation has done more to enable China's rise than America has. No country's citizens have done more for the general prosperity of the Chinese people than the Americans have. This is true in ways that are not widely known or immediately obvious. For example, the role American financiers and investment banks played in creating the architecture of modern Chinese financial markets and corporate structures is little realized, despite the size and importance of their interventions. Behind every great titan of Chinese industry--China Mobile, the world's largest mobile phone operator, China State Construction Engineering, whose IPO was valued at $7.3 billion, PetroChina, the most profitable company in Asia (well, before last year), to name a few of hundreds--lies an American investment banker. I do not exaggerate when I say Goldman Sachs created modern China. [2] China has much to thank America for.

...

In simpler terms, the Chinese equate “rising within a rules based order” with “halting China’s rise to power.” To live by Washington’s rules is to live under its power, and the Chinese have been telling themselves for three decades now that—after two centuries of hardship—they will not live by the dictates of outsiders ever again.

The Chinese will never choose our rules based order. That does not necessarily mean they want to dethrone America and throw down all that she has built. The Chinese do not have global ambitions. What they want is a seat at the table—and they want this seat to be recognized, not earned. That’s the gist of it. Beijing is not willing to accept an order it did not have a hand in creating. Thus all that G-2 talk we heard a few years back. The Chinese would love to found a new order balancing their honor and their interests with the Americans. It is a flattering idea. What they do not want is for the Americans to give them a list of hoops to jump through to gain entry into some pre-determined good-boys club. They feel like their power, wealth, and heritage should be more than enough to qualify for automatic entrance to any club.

https://twitter.com/Aelkus/status/928754578794958848
https://archive.is/NpLpR
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june 2017 by nhaliday
The story of modern human origins just got more complicated
https://www.gnxp.com/WordPress/2017/06/06/a-reticulation-pulse-expansion-of-modern-human-genetic-variation/
https://www.gnxp.com/WordPress/2017/06/11/the-search-for-eden-opens-up-new-vistas/
https://www.gnxp.com/WordPress/2017/08/26/northeast-africa/

https://www.gnxp.com/WordPress/2018/01/25/out-of-africa-to-out-of-eden-well-perhaps-not-yet/
https://www.gnxp.com/WordPress/2018/01/28/none-dare-call-it-multiregionalism/

The slow death of Out of Africa: http://dienekes.blogspot.com/2018/04/the-slow-death-of-out-of-africa.html
The significance of the discovery of modern humans in Arabia >85kya is that it provides a second spot (other than Israel) were modern humans existed outside Africa long before the alleged 60kya blitz out of the continent. We now have modern humans outside Africa in roughly two locations (Israel and Arabia), and three time slices (~175-85kya) in Misliya, Shkul/Qafzeh, and Al Wusta-1. It is no longer tenable to claim that these modern humans "died out" to make way for the alleged 60kya OoA event.
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june 2017 by nhaliday
How important was colonial trade for the rise of Europe? | Economic Growth in History
The latter view became the orthodoxy among economists and economic historians after Patrick O’Brien’s 1982 paper, which in one of many of Patrick’s celebrated phrases, claims that “”the periphery vs peripheral” for Europe. He concludes the paper by writing:

“[G]rowth, stagnation, and decay everywhere in Western Europe can be explained mainly by reference to endogenous forces. … for the economic growth of the core, the periphery was peripheral.”

This is the view that remarkable scholars such as N. Crafts, Deirdre McCloskey, or Joel Mokyr repeat today (though Crafts would argue cotton imports would have mattered in a late stage, and my reading of Mokyr is that he has softened his earlier view from the 1980s a little, specifically in the book The Enlightened Economy.) Even recently, Brad deLong has classifyied O’Brien’s 1982 position as “air tight”.

Among economists and economic historians more on the economics side, I would say that O’Brien’s paper was only one of two strong hits against the “Worlds-System” and related schools of thoughts of the 1970s, the other hit being Solow’s earlier conclusion that TFP growth (usually interpreted as technology, though there’s more to it than that) has accounted for economic growth a great deal more than capital accumulation, which is what Hobsbawm and Wallerstein, in their neo-Marxist framework, emphasize.

https://twitter.com/tcjfs/status/890034395456974848
A friend tonight, on the third world and the first world, and our relationships to the past: "They don't forget, and we don't remember."
https://twitter.com/edwest/status/872337163458932736
imo the European Intifada is being fueled by anti-Europeanism & widely taught ideas like this one discussed - Europe stole its riches

https://www.thinkpragati.com/opinion/1863/dont-blame-empire/
The British Empire was cruel, rapacious and racist. But contrary to what Shashi Tharoor writes in An Era Of Darkness, the fault for India’s miseries lies upon itself.

Indeed, the anti-Tharoor argument is arguably closer to the truth, because the British tended to use the landlord system in places where landlords were already in place, and at times when the British were relatively weak and couldn’t afford to upset tradition. Only after they became confident in their power did the British start to bypass the landlord class and tax the cultivators directly. King’s College London historian Jon Wilson (2016) writes in India Conquered, “Wherever it was implemented, raiyatwar began as a form of military rule.” Thus the system that Tharoor implicitly promotes, and which is associated with higher agricultural productivity today, arose from the very same colonialism that he blames for so many of India’s current woes. History does not always tell the parables that we wish to hear.

...

India’s share of the world economy was large in the eighteenth century for one simple reason: when the entire world was poor, India had a large share of the world’s population. India’s share fell because with the coming of the Industrial Revolution, Europe and North America saw increases of income per capita to levels never before seen in all of human history. This unprecedented growth cannot be explained by Britain’s depredations against India. Britain was not importing steam engines from India.

The big story of the Great Divergence is not that India got poorer, but that other countries got much richer. Even at the peak of Mughal wealth in 1600, the best estimates of economic historians suggest that GDP per capita was 61% higher in Great Britain. By 1750–before the battle of Plassey and the British takeover–GDP per capita in Great Britain was more than twice what it was in India (Broadberry, Custodis, and Gupta 2015). The Great Divergence has long roots.

Tharoor seems blinded by the glittering jewels of the Maharajas and the Mughals. He writes with evident satisfaction that when in 1615 the first British ambassador presented himself to the court of Emperor Jehangir in Agra, “the Englishman was a supplicant at the feet of the world’s mightiest and most opulent monarch.” True; but the Emperor’s opulence was produced on the backs of millions of poor subjects. Writing at the same time and place, the Dutch merchant Francisco Pelsaert (1626) contrasted the “great superfluity and absolute power” of the rich with “the utter subjection and poverty of the common people–poverty so great and miserable that the life of the people can be depicted…only as the home of stark want and the dwelling-place of bitter woe.” Indian rulers were rich because the empire was large and inequality was extreme.

In pre-colonial India the rulers, both Mughal and Maratha, extracted _anywhere from one-third to one half of all gross agricultural output_ and most of what was extracted was spent on opulence and the armed forces, not on improving agricultural productivity (Raychaudhuri 1982).

...

The British were awful rulers but the history of India is a long story of awful rulers (just as it is for most countries). Indeed, by Maddison’s (2007) calculations _the British extracted less from the Indian economy than did the Mughal Dynasty_. The Mughals built their palaces in India while the British built most of their palaces in Britain, but that was little comfort to the Indian peasant who paid for both. The Kohinoor diamond that graces the cover of Inglorious Empire is a telling symbol. Yes, it was stolen by the British (who stole it from the Sikhs who stole it from the Afghanis who stole it from the Mughals who stole it from one of the kings of South India). But how many Indians would have been better off if this bauble had stayed in India? Perhaps one reason why more Indians didn’t take up arms against the British was that for most of them, British rule was a case of meet the new boss, same as the old boss.

more for effect on colonies: https://pinboard.in/u:nhaliday/b:4b0128372fe9

INDIA AND THE GREAT DIVERGENCE: AN ANGLO-INDIAN COMPARISON OF GDP PER CAPITA, 1600-1871: http://eh.net/eha/wp-content/uploads/2013/11/Guptaetal.pdf
This paper provides estimates of Indian GDP constructed from the output side for the pre-1871 period, and combines them with population estimates to track changes in living standards. Indian per capita GDP declined steadily during the seventeenth and eighteenth centuries before stabilising during the nineteenth century. As British living standards increased from the mid-seventeenth century, India fell increasingly behind. Whereas in 1600, Indian per capita GDP was over 60 per cent of the British level, by 1871 it had fallen to less than 15 per cent. As well as placing the origins of the Great Divergence firmly in the early modern period, the estimates suggest a relatively prosperous India at the height of the Mughal Empire, with living standards well above bare bones subsistence.

https://twitter.com/pseudoerasmus/status/832288984009207810
but some of the Asian wage data (especialy India) have laughably small samples (see Broadberry & Gupta)

How profitable was colonialism for various European powers?: https://www.reddit.com/r/AskHistorians/comments/p1q1q/how_profitable_was_colonialism_for_various/

How did Britain benefit from colonising India? What did colonial powers gain except for a sense of power?: https://www.quora.com/How-did-Britain-benefit-from-colonising-India-What-did-colonial-powers-gain-except-for-a-sense-of-power
The EIC period was mostly profitable, though it had recurring problems with its finances. The initial voyages from Surat in 1600s were hugely successful and brought profits as high as 200%. However, the competition from the Dutch East India Company started to drive down prices, at least for spices. Investing in EIC wasn’t always a sure shot way to gains - British investors who contributed to the second East India joint stock of 1.6 million pounds between 1617 and 1632 ended up losing money.

...

An alternate view is that the revenues of EIC were very small compared to the GDP of Britain, and hardly made an impact to the overall economy. For instance, the EIC Revenue in 1800 was 7.8m pounds while the British GDP in the same period was 343m pounds, and hence EIC revenue was only 2% of the overall GDP. (I got these figures from an individual blog and haven’t verified them).

...

The British Crown period - The territory of British India Provinces had expanded greatly and therefore the tax revenues had grown in proportion. The efficient taxation system paid its own administrative expenses as well as the cost of the large British Indian Army. British salaries were lucrative - the Viceroy received £25,000 a year, and Governors £10,000 for instance besides the lavish amenities in the form of subsidized housing, utilities, rest houses, etc.

...

Indian eminent intellectual, Dadabhai Naoroji wrote how the British systematically ensured the draining of Indian economy of its wealth and his theory is famously known as ‘Drain of Wealth’ theory. In his book 'Poverty' he estimated a 200–300 million pounds loss of revenue to Britain that is not returned.

At the same time, a fair bit of money did go back into India itself to support further colonial infrastructure. Note the explosion of infrastructure (Railway lines, 100+ Cantonment towns, 60+ Hill stations, Courthouses, Universities, Colleges, Irrigation Canals, Imperial capital of New Delhi) from 1857 onward till 1930s. Of course, these infrastructure projects were not due to any altruistic motive of the British. They were intended to make their India empire more secure, comfortable, efficient, and to display their grandeur. Huge sums of money were spent in the 3 Delhi Durbars conducted in this period.

So how profitable was the British Crown period? Probably not much. Instead bureaucracy, prestige, grandeur, comfort reigned supreme for the 70,000 odd British people in India.

...

There was a realization in Britain that colonies were not particularly economically beneficial to the home economy. … [more]
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june 2017 by nhaliday
Genomic analysis of family data reveals additional genetic effects on intelligence and personality | bioRxiv
methodology:
Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003520
Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005804

Missing Heritability – found?: https://westhunt.wordpress.com/2017/02/09/missing-heritability-found/
There is an interesting new paper out on genetics and IQ. The claim is that they have found the missing heritability – in rare variants, generally different in each family.

Some of the variants, the ones we find with GWAS, are fairly common and fitness-neutral: the variant that slightly increases IQ confers the same fitness (or very close to the same) as the one that slightly decreases IQ – presumably because of other effects it has. If this weren’t the case, it would be impossible for both of the variants to remain common.

The rare variants that affect IQ will generally decrease IQ – and since pleiotropy is the norm, usually they’ll be deleterious in other ways as well. Genetic load.

Happy families are all alike; every unhappy family is unhappy in its own way.: https://westhunt.wordpress.com/2017/06/06/happy-families-are-all-alike-every-unhappy-family-is-unhappy-in-its-own-way/
It now looks as if the majority of the genetic variance in IQ is the product of mutational load, and the same may be true for many psychological traits. To the extent this is the case, a lot of human psychological variation must be non-adaptive. Maybe some personality variation fulfills an evolutionary function, but a lot does not. Being a dumb asshole may be a bug, rather than a feature. More generally, this kind of analysis could show us whether particular low-fitness syndromes, like autism, were ever strategies – I suspect not.

It’s bad new news for medicine and psychiatry, though. It would suggest that what we call a given type of mental illness, like schizophrenia, is really a grab-bag of many different syndromes. The ultimate causes are extremely varied: at best, there may be shared intermediate causal factors. Not good news for drug development: individualized medicine is a threat, not a promise.

see also comment at: https://pinboard.in/u:nhaliday/b:a6ab4034b0d0

https://www.reddit.com/r/slatestarcodex/comments/5sldfa/genomic_analysis_of_family_data_reveals/
So the big implication here is that it's better than I had dared hope - like Yang/Visscher/Hsu have argued, the old GCTA estimate of ~0.3 is indeed a rather loose lower bound on additive genetic variants, and the rest of the missing heritability is just the relatively uncommon additive variants (ie <1% frequency), and so, like Yang demonstrated with height, using much more comprehensive imputation of SNP scores or using whole-genomes will be able to explain almost all of the genetic contribution. In other words, with better imputation panels, we can go back and squeeze out better polygenic scores from old GWASes, new GWASes will be able to reach and break the 0.3 upper bound, and eventually we can feasibly predict 0.5-0.8. Between the expanding sample sizes from biobanks, the still-falling price of whole genomes, the gradual development of better regression methods (informative priors, biological annotation information, networks, genetic correlations), and better imputation, the future of GWAS polygenic scores is bright. Which obviously will be extremely helpful for embryo selection/genome synthesis.

The argument that this supports mutation-selection balance is weaker but plausible. I hope that it's true, because if that's why there is so much genetic variation in intelligence, then that strongly encourages genetic engineering - there is no good reason or Chesterton fence for intelligence variants being non-fixed, it's just that evolution is too slow to purge the constantly-accumulating bad variants. And we can do better.
https://rubenarslan.github.io/generation_scotland_pedigree_gcta/

The surprising implications of familial association in disease risk: https://arxiv.org/abs/1707.00014
https://spottedtoad.wordpress.com/2017/06/09/personalized-medicine-wont-work-but-race-based-medicine-probably-will/
As Greg Cochran has pointed out, this probably isn’t going to work. There are a few genes like BRCA1 (which makes you more likely to get breast and ovarian cancer) that we can detect and might affect treatment, but an awful lot of disease turns out to be just the result of random chance and deleterious mutation. This means that you can’t easily tailor disease treatment to people’s genes, because everybody is fucked up in their own special way. If Johnny is schizophrenic because of 100 random errors in the genes that code for his neurons, and Jack is schizophrenic because of 100 other random errors, there’s very little way to test a drug to work for either of them- they’re the only one in the world, most likely, with that specific pattern of errors. This is, presumably why the incidence of schizophrenia and autism rises in populations when dads get older- more random errors in sperm formation mean more random errors in the baby’s genes, and more things that go wrong down the line.

The looming crisis in human genetics: http://www.economist.com/node/14742737
Some awkward news ahead
- Geoffrey Miller

Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races.

2009!
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june 2017 by nhaliday
Romanticizing the regressive – Brown Pundits
As far back as Herodotus Indian society seems to have been characterized by caste. Genetically the castes, and more precisely jatis, are very distinct. And their persistence on the Indian scene suggest some level of functional utility.

...

The connections between liberal Democratic Indian Americans and right-wing Hindu nationalism in India have been extensively discussed. That is not what I am getting at. Meet the Patels is not a political film, it is a personal one. There is no reason that Ravi should address political topics in the documentary, and much of what I am saying here would be implicit to any South Asian watching Meet the Patels. But to many Americans these darker realities would not be visible or implied in the cultural practices which Ravi admires.

http://www.brownpundits.com/2017/06/05/a-reply-to-a-stupid-ignorant-or-malicious-commenter/
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june 2017 by nhaliday
Genetics allows the dead to speak from the grave - The Unz Review
BOOKMARKIt is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may.

...

At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?
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may 2017 by nhaliday
POPULATION STRUCTURE AND QUANTITATIVE CHARACTERS
The variance of among-group variance is substantial and does not depend on the number of loci contributing to variance in the character. It is just as large for polygenic characters as for single loci with the same additive variance. This implies that one polygenic character contains exactly as much information about population relationships as one single-locus marker.

same is true of expectation apparently (so drift has same impact on polygenic and single-locus traits)
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may 2017 by nhaliday
Lost and Found | West Hunter
I get the distinct impression that someone (probably someone other than Varro) came up with an approximation of germ theory 1500 years before Girolamo Fracastoro. But his work was lost.

Everybody knows, or should know, that the vast majority of Classical literature has not been preserved. Those lost works contained facts and ideas that might have value today – certainly there are topics that we understand much better because of insights from Classical literature. For example, Reich and Patterson find that some of the Indian castes have existed for something like three thousand years: this is easier to believe when you consider that Megasthenes wrote about the caste system as early as 300 BC.

We don’t put much effort into recovering lost Classical literature. But there are ways in which we could push harder – by increased funding for work on the Herculaneum scrolls, or the Oxyrhynchus papyri collection, for example. Some old-fashioned motivated archaeology might get lucky and find another set of Amarna cuneiform letters, or a new Antikythera mechanism.

https://westhunt.wordpress.com/2012/03/06/spontaneous-generation/
Here we have yet another case in which a discovery was possible for a long time before it was actually accepted. Aristotle is the villain here: he clearly endorses spontaneous generation of many plants and animals. On the other hand, I don’t remember him saying that people should accept all of his conclusions uncritically and without further experimentation for the next couple of thousand years, which is what happened. So maybe we’re all guilty.

...

Part of the funny here (not even counting practical experience) is that almost every educated man over these two millennia had read, and indeed studied deeply, a work with a fairly clear statement of the actual fly->egg->maggot->fly process. As I as I can tell, only one person (Redi) seems to have picked up on this.

“But the more Achilles gazed, the greater rose his desire for vengeance, and his eyes flashed terribly, like coals beneath his lids, as he lifted the god’s marvellous gifts and exulted. When he had looked his fill on their splendour, he spoke to Thetis winged words; ‘Mother, the god grants me a gift fit for the immortals, such as no mortal smith could fashion. Now I shall arm myself for war. Yet I fear lest flies infest the wounds the bronze blades made, and maggots breed in the corpse of brave Patroclus, and now his life is fled, rot the flesh, and disfigure all his body.’ ”

You’d think a blind man would have noticed this.

Anyhow, the lesson is clear. Low hanging fruit can persist for a long time if the conventional wisdom is wrong – and sometimes it is.

http://www.bede.org.uk/literature.htm

Transmission of the Greek Classics: https://en.wikipedia.org/wiki/Transmission_of_the_Greek_Classics
https://www.quora.com/How-much-writing-from-ancient-Greece-is-preserved-Is-it-a-finite-amount-that-someone-could-potentially-read

By way of comparison, the complete Loeb Classical Library (which includes all the important classical texts) has 337 volumes for Ancient Greek --- and those aren't 100,000 word-long door-stoppers.
https://www.loebclassics.com/
$65/year for individuals (I wonder if public libraries have subscriptions?)

http://www.roger-pearse.com/weblog/2009/10/26/reference-for-the-claim-that-only-1-of-ancient-literature-survives/
http://www.patheos.com/blogs/geneveith/2015/01/finding-the-lost-texts-of-classical-antiquity/
http://www.historyofinformation.com/narrative/loss-of-information.php
http://www.bede.org.uk/literature.htm

https://twitter.com/futurepundit/status/927344648154112000
https://archive.is/w86uL
1/ Thinking about what Steven Greenblatt described in The Swerve as a mass extinction of ancient books (we have little of what they wrote)
2/ If I could go back in time to, say, 100 AD or 200 AD I would go with simple tech for making books last for a thousand years. Possible?

https://www.gnxp.com/WordPress/2018/01/28/the-rapid-fading-of-information/
I’ve put a lot of content out there over the years. Probably on the order of 5 million words across my blogs. Some publications here and there. Lots of tweets. But very little of it will persist into future generations. Digital is evanescent.

But so is paper. I believe that even good hardcover books probably won’t last more than a few hundred years.

Perhaps we should go back to some form of cuneiform? Stone and metal will last thousands of years.

How long does a paperback book last?: https://www.quora.com/How-long-does-a-paperback-book-last
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may 2017 by nhaliday
Interview: Mostly Sealing Wax | West Hunter
https://soundcloud.com/user-519115521/greg-cochran-part-2
https://medium.com/@houstoneuler/annotating-part-2-of-the-greg-cochran-interview-with-james-miller-678ba33f74fc

- conformity and Google, defense and spying (China knows prob almost all our "secrets")
- in the past you could just find new things faster than people could reverse-engineer. part of the problem is that innovation is slowing down today (part of the reason for convergence by China/developing world).
- introgression from archaics of various kinds
- mutational load and IQ, wrath of khan neanderthal
- trade and antiquity (not that useful besides ideas tbh), Roman empire, disease, smallpox
- spices needed to be grown elsewhere, but besides that...
- analogy: caste system in India (why no Brahmin car repairmen?), slavery in Greco-Roman times, more water mills in medieval times (rivers better in north, but still could have done it), new elite not liking getting hands dirty, low status of engineers, rise of finance
- crookery in finance, hedge fund edge might be substantially insider trading
- long-term wisdom of moving all manufacturing to China...?
- economic myopia: British financialization before WW1 vis-a-vis Germany. North vs. South and cotton/industry, camels in Middle East vs. wagons in Europe
- Western medicine easier to convert to science than Eastern, pseudoscience and wrong theories better than bag of recipes
- Greeks definitely knew some things that were lost (eg, line in Pliny makes reference to combinatorics calculation rediscovered by German dude much later. think he's referring to Catalan numbers?), Lucio Russo book
- Indo-Europeans, Western Europe, Amerindians, India, British Isles, gender, disease, and conquest
- no farming (Dark Age), then why were people still farming on Shetland Islands north of Scotland?
- "symbolic" walls, bodies with arrows
- family stuff, children learning, talking dog, memory and aging
- Chinese/Japanese writing difficulty and children learning to read
- Hatfield-McCoy feud: the McCoy family was actually a case study in a neurological journal. they had anger management issues because of cancers of their adrenal gland (!!).

the Chinese know...: https://macropolo.org/casting-off-real-beijings-cryptic-warnings-finance-taking-economy/
Over the last couple of years, a cryptic idiom has crept into the way China’s top leaders talk about risks in the country’s financial system: tuo shi xiang xu (脱实向虚), which loosely translates as “casting off the real for the empty.” Premier Li Keqiang warned against it at his press conference at the end of the 2016 National People’s Congress (NPC). At this year’s NPC, Li inserted this very expression into his annual work report. And in April, while on an inspection tour of Guangxi, President Xi Jinping used the term, saying that China must “unceasingly promote industrial modernization, raise the level of manufacturing, and not allow the real to be cast off for the empty.”

Such an odd turn of phrase is easy to overlook, but it belies concerns about a significant shift in the way that China’s economy works. What Xi and Li were warning against is typically called financialization in developed economies. It’s when “real” companies—industrial firms, manufacturers, utility companies, property developers, and anyone else that produces a tangible product or service—take their money and, rather than put it back into their businesses, invest it in “empty”, or speculative, assets. It occurs when the returns on financial investments outstrip those in the real economy, leading to a disproportionate amount of money being routed into the financial system.
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may 2017 by nhaliday
Reason is but a slave of passions as it always has been – Gene Expression
http://www.unz.com/gnxp/winning-isnt-everything-winning-your-team-is/
In my short jaunt through Theory writ large I have finally come that conclusion as well. I am a naive realist and a positivist. I work under the assumption that there is a world out there, that that world out there manifests itself in the order we see when we decompose it with analysis and empirical methods. As long as I kept my eyes on prize, the “score,” I felt at peace.

This was dangerously naive. Whereas before I had worked under the hypothesis that my interlocutors were falling prey to cognitive biases when they engaged in ad hominem or logical fallacy, I am now coming to suspect that one some level they are aware that they are engaging in the dialectics of ultimate victory. Every battle they lose is simply another opportunity to shore up their forces in future battles. Just like Rome against Hannibal, their contention that the structure of human society, rather than the world “out there,” is determinative, may very well be true in relation to all that matters.

hmm, women?: https://pinboard.in/u:nhaliday/b:f155b33f986c

https://gnxp.nofe.me/2017/03/26/open-thread-03262017/
Honestly I’ve given up on the future of classical liberalism in the West. Most people are cowards and liars when push comes to shove. I don’t want to speak of this at length, as it’s a bit like a God-is-dead moment for me, but I thought I’d come clean and be frank. The Critical Theorists are right, power trumps truth. I’m not sure they’ll enjoy what’s to come in the future when objectivity is dethroned, but I think I will probably laugh as the liars scramble to lie different lies, because that is almost certain to happen.

https://gnxp.nofe.me/2017/06/12/open-thread-06112017/
Ultimately I think our society is going the way of Dutch Pillarisation (though I think the Dutch have abandoned this). Basically our professional and personal lives are going to be mediated by our socio-political tribes (and it won’t just be Left vs. Right). Too many people are getting fired or pressured over their politics or viewpoints. At some point large corporations and institutions need to just give up on the idea that they serve the whole public, and intellectuals need to concede that public reason is probably not possible.

...

I see referrals to this website now and people make comments about me elsewhere (on reddit, in the comments of Unz, on blogs). Some are wondering about my recent pessimism and darkness of spirit. Because people are stupid or socially unintelligent or something they think they can infer something about my personal or professional circumstances from what I put on this website, no matter how many times I caution them not to do that. I’m pretty clear about separating aspects of my life (I’m not a lifestyle blogger…hot sauce blogging excepted).

What I will say is that I’m very happy at my job and have plenty of friends. My third child and second son is a delight.

The darkness you perceive in my soul is that I suspect that the liberal order, which encompasses politics as well as the intellectual world we’ve cherished since the 19th century, is collapsing around us. Just as the Chinese in 1790 or the Romans in 460 were not aware that their world was coming to an end, we continue to carry on as if all is as it was. I’m sort of at the phase between the death of Optimus Prime in the 1980s cartoon and the emergence of Rodimus. I’m not going to turn into a bald-faced liar or ignoramus like so many of the people in the media around us just yet though (you know who I’m talking about I’m sure). Old ways are hard to give up! God has died but his shadow haunts me.
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may 2017 by nhaliday
When conquered pre-Greece took captive her rude Hellene conqueror – Gene Expression
For various reasons this was always less plausible for Southern Europe. The first reason is that Southern Europeans shared a lot of genetic similarities to Sardinians, who resembled Neolithic farmers. Admixture models generally suggested that in the peninsulas of Southern Europe the steppe-like ancestry was the minority component, not the majority, as was the case in Northern Europe.

different for the Romans: https://www.quora.com/Were-the-Romans-Greek-or-Italians
http://gnxp.nofe.me/2015/03/22/the-etruscan-origins-mystery-and-genetics/

https://gnxp.nofe.me/2017/08/02/when-the-ancestors-were-cyclops/
book recommendations for Ancient Greece: https://gnxp.nofe.me/2017/08/02/when-the-ancestors-were-cyclops/#comment-3356
http://www.nature.com.sci-hub.cc/nature/journal/vaop/ncurrent/full/nature23310.html

Roots of Mediterranean civilisations: http://sci-hub.cc/http://www.sciencedirect.com/science/article/pii/S0960982217311740
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may 2017 by nhaliday
Estimating the number of unseen variants in the human genome
To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small (∼350) and does not differ much among the different populations; our data show that, subject to sequence accuracy, the 1000 Genomes Project is likely to find most of these common variants and a high proportion of the rarer ones (frequency between 0.1 and 1%). The data reveal a rule of diminishing returns: a small number of individuals (∼150) is sufficient to identify 80% of variants with a frequency of at least 0.1%, while a much larger number (> 3,000 individuals) is necessary to find all of those variants.

A map of human genome variation from population-scale sequencing: http://www.internationalgenome.org/sites/1000genomes.org/files/docs/nature09534.pdf

Scientists using data from the 1000 Genomes Project, which sequenced one thousand individuals from 26 human populations, found that "a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence."[11] Nearly all (>99.9%) of these sites are small differences, either single nucleotide polymorphisms or brief insertion-deletions in the genetic sequence, but structural variations account for a greater number of base-pairs than the SNPs and indels.[11]

Human genetic variation: https://en.wikipedia.org/wiki/Human_genetic_variation

Singleton Variants Dominate the Genetic Architecture of Human Gene Expression: https://www.biorxiv.org/content/early/2017/12/15/219238
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may 2017 by nhaliday
Soft sweeps are the dominant mode of adaptation in the human genome | bioRxiv
Detection of 2000 instances of recent human selection, half of which are specific to individual human populations, and many of which affect the central nervous system. Note this doesn’t cover polygenic selection, so it’s a very loose lower bound on how much recent human evolution there has been.

How Sweeps Get Soft: https://westhunt.wordpress.com/2011/09/29/how-sweeps-get-soft/
A puzzling finding from the search for selection in humans is the large number of apparently selected variants versus the apparent absence of high frequency selected regions and regions that have become fixed in our species.

Cochran, John Hawks, and I were involved in some of this work, and we all thought immediately without any discussion that the intermediate frequency sweeps must reflect heterozygote advantage.
study  preprint  bio  sapiens  recent-selection  genetics  selection  stylized-facts  evolution  genomics  GWAS  🌞  population-genetics  gwern  methodology  multi  west-hunter  explanation  gene-flow  scitariat  hetero-advantage  genetic-load  pop-structure  race  europe  africa  migration  gene-drift 
may 2017 by nhaliday
The wheel of history turns to the gods - Gene Expression
The inevitable rise of Amish machines: http://blogs.discovermagazine.com/gnxp/2011/01/the-inevitable-rise-of-amish-machines/
The authors make a nod to the idea that religion may have spread through group selection: but this is also an argument for why very fertile and religious groups such as the Amish and Roma will reach their “limits to growth.” If they persist in their atypical lifestyles their host societies will simply collapse. Or at least restructure in a fashion to make extremely high endogenous growth of minorities impossible.
gnxp  scitariat  books  review  sociology  culture  society  demographics  fertility  religion  demographic-transition  theos  new-religion  israel  MENA  judaism  europe  islam  gallic  britain  nordic  poll  values  morality  gender  sexuality  anthropology  org:sci  rot  the-bones  eric-kaufmann  history  early-modern  usa  elite  flux-stasis  modernity  multi  context  cycles  study  summary  commentary  critique  prediction  trends  pop-structure  free-riding  subculture  hetero-advantage  russia  population  comparison  time-series  :/ 
may 2017 by nhaliday
The Birth of Britain | West Hunter
Recent studies considering modern and ancient DNA show that about 25-40% of British ancestry is Anglo-Saxon, with a high in East Anglia and gradual decreasing as you move north and west. While the Britons of Roman times look like the Welsh.

Winston Churchill wrote about this, in The Birth of Britain, the first installment of his history of the English-speaking peoples. He mentions that place names in Sussex suggested total replacement, while the West Saxon legal code made provision for the rights of Welshmen.. But he didn’t know how much replacement had occurred. Still, he said “.. we may cherish the hope that somewhere a maiden’s cry for pity, the appear of beauty in distress, the lustful needs of an invading force,would create some bond between victor and vanquished. Thus the blood would be preserved, thus the rigours of subjugation would fade as generations passed away. The complete obliteration of an entire race is repulsive to the human mind. There should at least have been, in default of pity, a hearing for practical advantage or the natural temptations of sex.”

However, being repulsive doesn’t stop something from happening. This time, it didn’t. Perhaps Churchill’s ghost, or his ghost’s ghost, is pleased by this result.

Bell beakers – or, the birth of Britain: https://westhunt.wordpress.com/2017/05/17/bell-beakers-or-the-birth-of-britain/
It looks as if people in western Germany picked up these ideas – of course we have a radically imperfect idea of what those ideas were – and then settled Britain. Before all this Britain was populated by a kindof-Sardinian population (with some hunter-gatherer mixed in) that had probably came from Spain. Afterwards they were almost indistinguishable from people of that era living in the Netherlands, who had a lot of steppe ancestry. 93% replacement, minimum. Some Anglo-Saxon ancestry was added about 1400 years ago but A. they’re not very different from the Brits B. most British ancestry today still goes back to the Bell Beaker conquest.

https://gnxp.nofe.me/2003/05/27/british-genes/
https://gnxp.nofe.me/2006/07/18/celts-anglo-saxons-part-n/
https://gnxp.nofe.me/2006/07/19/celts-and-anglo-saxons-part-n-1/
https://gnxp.nofe.me/2006/07/23/celts-and-anglo-saxons-part-n-2/
https://gnxp.nofe.me/2006/09/22/blood-of-the-british/
https://gnxp.nofe.me/2007/02/03/blood-of-the-isles/
https://gnxp.nofe.me/2008/03/04/origins-of-the-british/
https://gnxp.nofe.me/2008/04/23/no-anglo-saxon-apartheid/
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march 2017 by nhaliday
Ancestry inference is precise and accurate(ish) – Gene Expression
“French-German” is a cluster almost certainly because there are no clear and distinct genetic differences between French and Germans. Yes, there is a continuum of allele frequencies between these two groups, but having looked at a fair number of people of French and German background in Family Tree DNA’s database I can tell you that France and Germany have a lot of local structure even among people of indigenous ancestry. Germans from the Rhineland are quite often genetically closer to French from Normandy than they are to Germans from eastern Saxony. Some of this is due to gene flow between neighboring regions, but some of this is due to cultural fluidity as to who exactly is German. It is clear that some Germans from the eastern regions are Germanized Slavs. Some Germans from the north exhibit strong affinities to Scandinavians, while Germans from Bavaria and Austria are classically Central European (whatever that means). The average German is distinct from the average French person, but the genetic clustering of the two groups is not clear and distinct.
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march 2017 by nhaliday
Surnames: a New Source for the History of Social Mobility
This paper explains how surname distributions can be used as a way to
measure rates of social mobility in contemporary and historical societies.
This allows for estimates of social mobility rates for any population for which the distribution of surnames overall is known as well as the distribution of surnames among some elite or underclass. Such information exists, for example, for England back to 1300, and for Sweden back to 1700. However surname distributions reveal a different, more fundamental type of mobility than that conventionally estimated. Thus surname estimates also allow for measuring a different aspect of social mobility, but the aspect that matters for mobility of social groups, and for families in the long run.

The Big Sort: Selective Migration and the Decline of Northern England, 1800-2017: http://migrationcluster.ucdavis.edu/events/seminars_2015-2016/sem_assets/clark/paper_clark_northern-disadvantage.pdf
The north of England in recent years has been poorer, less healthy, less educated and slower growing than the south. Using two sources - surnames that had a different regional distribution in England in the 1840s, and a detailed genealogy of 78,000 people in England giving birth and death locations - we show that the decline of the north is mainly explained by selective outmigration of the educated and talented.

Genetic Consequences of Social Stratification in Great Britain: https://www.biorxiv.org/content/biorxiv/early/2018/10/30/457515
pdf  study  spearhead  gregory-clark  economics  cliometrics  status  class  mobility  language  methodology  metrics  natural-experiment  🎩  tricks  history  early-modern  britain  china  asia  path-dependence  europe  nordic  pro-rata  higher-ed  elite  success  society  legacy  stylized-facts  age-generation  broad-econ  s-factor  measurement  within-group  pop-structure  flux-stasis  microfoundations  multi  shift  mostly-modern  migration  biodet  endo-exo  behavioral-gen  regression-to-mean  human-capital  education  oxbridge  endogenous-exogenous  ideas  bio  preprint  genetics  genomics  GWAS 
march 2017 by nhaliday
Sir Ronald Aylmer Fisher | West Hunter
In 1930 he published The Genetical Theory of Natural Selection, which completed the fusion of Darwinian natural selection with Mendelian inheritance. James Crow said that it was ‘arguably the deepest and most influential book on evolution since Darwin’. In it, Fisher analyzed sexual selection, mimicry, and sex ratios, where he made some of the first arguments using game theory. The book touches on many other topics. As was the case with his other works, The Genetical Theory is a dense book, not easy for most people to understand. Fisher’s tendency to leave out mathematical steps that he deemed obvious (a leftover from his early training in mental mathematics) frustrates many readers.

The Genetical Theory is of particular interest to us because Fisher there lays out his ideas on how population size can speed up evolution. As we explain elsewhere, more individuals mean there will be more mutations, including favorable mutations, and so Fisher expected more rapid evolution in larger populations. This idea was originally suggested, in a nonmathematical way, in Darwin’s Origin of Species.

Although Fisher was fiercely loyal to friends and could be very charming, he had a quick temper and was a fine hater. The same uncompromising spirit that fostered his originality led to constant conflict with authority. He had a long conflict with Karl Pearson, who had also played an important part in the development of mathematical statistics. In this case, Pearson was more at fault, resisting the advent of a more talented competitor, as well as being an eminently hateable person in general. Over time Fisher also became increasing angry at Sewall Wright (another one of the founders of population genetics) due to scientific disagreements – and this was just wrong, because Wright was a sweetheart.

Fisher’s personality decreased his potential influence. He was not a school-builder, and was impatient with administrators. He expected to find some form of war-work in the Second World War, but his characteristics had alienated too many people, and thus his team dispersed to other jobs during the war. He returned to Rothamsted for the duration. This was a difficult time for him: his marriage disintegrated and his oldest son, an RAF pilot, was killed in the war.

...

Fisher’s ideas in genetics have taken an odd path. The Genetical Theory was not widely read, sold few copies, and has never been translated. Only gradually did its ideas find an audience. Of course, that audience included people like Bill Hamilton, the greatest mathematical biologist of the last half of the 20th century, who was strongly influenced by Fisher’s work. Hamilton said “By the time of my ultimate graduation,will I have understood all that is true in this book and will I get a First? I doubt it. In some ways some of us have overtaken Fisher; in many, however, this brilliant, daring man is still far in front.“

In fact, over the past generation, much of Fisher’s work has been neglected – in the sense that interest in population genetics has decreased (particularly interest in selection) and fewer students are exposed to his work in genetics in any way. Ernst Mayr didn’t even mention Fisher in his 1991 book One Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought, while Stephen Jay Gould, in The Structure of Evolutionary Theory, gave Fisher 6 pages out of 1433. Of course Mayr and Gould were both complete chuckleheads.

Fisher’s work affords continuing insight, including important implications concerning human evolution that have emerged more than 50 years after his death. We strongly discourage other professionals from learning anything about his ideas.
west-hunter  history  bio  evolution  genetics  population-genetics  profile  giants  people  mostly-modern  the-trenches  innovation  novelty  britain  fisher  mental-math  narrative  scitariat  old-anglo  world-war  pre-ww2  scale  population  pop-structure  books  classic  speed  correlation  mutation  personality 
january 2017 by nhaliday
The infinitesimal model | bioRxiv
Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. We first review the long history of the infinitesimal model in quantitative genetics. Then we provide a definition of the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, ... We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. In each case, by conditioning on the pedigree relating individuals in the population, we incorporate arbitrary selection and population structure. We suppose that we can observe the pedigree up to the present generation, together with all the ancestral traits, and we show, in particular, that the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order M^{-1/2}. Simulations suggest that in particular cases the convergence may be as fast as 1/M.

published version:
The infinitesimal model: Definition, derivation, and implications: https://sci-hub.tw/10.1016/j.tpb.2017.06.001

Commentary: Fisher’s infinitesimal model: A story for the ages: http://www.sciencedirect.com/science/article/pii/S0040580917301508?via%3Dihub
This commentary distinguishes three nested approximations, referred to as “infinitesimal genetics,” “Gaussian descendants” and “Gaussian population,” each plausibly called “the infinitesimal model.” The first and most basic is Fisher’s “infinitesimal” approximation of the underlying genetics – namely, many loci, each making a small contribution to the total variance. As Barton et al. (2017) show, in the limit as the number of loci increases (with enough additivity), the distribution of genotypic values for descendants approaches a multivariate Gaussian, whose variance–covariance structure depends only on the relatedness, not the phenotypes, of the parents (or whether their population experiences selection or other processes such as mutation and migration). Barton et al. (2017) call this rigorously defensible “Gaussian descendants” approximation “the infinitesimal model.” However, it is widely assumed that Fisher’s genetic assumptions yield another Gaussian approximation, in which the distribution of breeding values in a population follows a Gaussian — even if the population is subject to non-Gaussian selection. This third “Gaussian population” approximation, is also described as the “infinitesimal model.” Unlike the “Gaussian descendants” approximation, this third approximation cannot be rigorously justified, except in a weak-selection limit, even for a purely additive model. Nevertheless, it underlies the two most widely used descriptions of selection-induced changes in trait means and genetic variances, the “breeder’s equation” and the “Bulmer effect.” Future generations may understand why the “infinitesimal model” provides such useful approximations in the face of epistasis, linkage, linkage disequilibrium and strong selection.
study  exposition  bio  evolution  population-genetics  genetics  methodology  QTL  preprint  models  unit  len:long  nibble  linearity  nonlinearity  concentration-of-measure  limits  applications  🌞  biodet  oscillation  fisher  perturbation  stylized-facts  chart  ideas  article  pop-structure  multi  pdf  piracy  intricacy  map-territory  kinship  distribution  simulation  ground-up  linear-models  applicability-prereqs  bioinformatics 
january 2017 by nhaliday
Europeans mutate differently - The Unz Review
But there’s a final element to be explored. Why is there in enrichment in the first place? It turns out that this sort of mutation is very common in melanomas. In particular of interest to me: “Folate deficiency is known to cause DNA damage including uracil misincorporation and double-strand breaks, leading in some cases to birth defects and reduced male fertility.” Folate deficiency can occur when light skinned individuals are exposed to sunlight. It strikes me that the higher mutational load for these particular transitions in Southern Europeans as opposed to Northern Europeans could simply be a function of the fact that they are in sunnier climates.
gnxp  scitariat  study  summary  evolution  sapiens  genetics  hmm  idk  europe  recent-selection  mutation  genomics  pop-structure  pop-diff 
january 2017 by nhaliday
The deleterious mutation load is insensitive to recent population history : Nature Genetics : Nature Research
contrary:
Distance from sub-Saharan Africa predicts mutational load in diverse human genomes: http://www.pnas.org/content/113/4/E440.abstract
“Out Of Africa” Bottleneck Is What Really Matters For Mutations: http://gnxp.nofe.me/2017/04/26/out-of-africa-bottleneck-is-what-really-matters-for-mutations/

Too Much Diversity: https://westhunt.wordpress.com/2012/11/30/too-much-diversity/
There’s a new paper out in Nature, by Wenqing Fu and many other people, about the recent origin of most variants in protein-coding genes. They conclude that most are less than 5-10,000 year old – younger in Europeans than in Africans. This is a natural consequence of the shape of human demographic history – there was a huge population increase with the advent of agriculture, and more people meant more mutations. That agricultural expansion happened somewhat earlier in the Middle East and Europe than in Africa.

...

A very few mutations are beneficial, some are neutral and many are deleterious, although the degree of harm inflicted varies widely. So the population expansion also increased the number of bad mutations – but unless selection also relaxed, it would not have changed the per-capita number of deleterious mutations, or the distribution of their effects (what fraction had large, medium, or small effects on fitness). It increased the diversity of deleterious mutations – they are more motley, not more common. The article never talks about that per-capita number, or, if it did , I was unable to winkle it out. It talks about ages and numbers of mutations – but not the mean number, in either of the two populations studied (European Americans and African Americans) . I think it would been a lot clearer, confused fewer reporters, if it had made that distinction. On the other hand, depending on the facts on the ground, talking about mutational load might be a grant-killer. There was a paper earlier this year (with many of the same authors) that used about half of the same data and did mention per-capita numbers. I’ve discussed it.

...

The paper says that there may be an excess of weakly deleterious mutations in Europeans due to bottlenecks back in the Ice Age. The idea works like this: selection is less efficient in small populations. Deleterious mutations with an effect s < 1/Ne drift freely and are not efficiently removed by selection. This effect takes on the order of Ne generations – so a population reduced to an effective size of of 10,000 for 10,000 generations ( ~250,000 years) would accumulate a large-than-usual number of deleterious mutations of effect size ~10-4. Lohmueller et al wrote about this back in 2008: the scenario they used had a European ancestral bottleneck 200,000 years long, which is A. what you need to make this scenario work and B. impossible, since it’s way before anatomically modern humans left Africa. Back to the drawing board.

disease alleles:
Ascertainment bias can create the illusion of genetic health disparities: https://www.biorxiv.org/content/early/2017/09/28/195768
study  genetics  regularizer  genetic-load  sapiens  europe  africa  comparison  world  recent-selection  org:nat  pop-structure  null-result  pop-diff  multi  evolution  roots  gnxp  scitariat  commentary  summary  migration  gene-drift  long-short-run  bio  preprint  🌞  debate  hmm  idk  disease  genomics  bioinformatics  spreading  west-hunter  antiquity  eden 
january 2017 by nhaliday
Information Processing: Recent human evolution: European height
By studying height, a classic polygenic trait, we demonstrate the first human signature of widespread selection on standing variation. We show that frequencies of alleles associated with increased height, both at known loci and genome wide, are systematically elevated in Northern Europeans compared with Southern Europeans (P < 4.3 × 10^−4). This pattern mirrors intra-European height differences and is not confounded by ancestry or other ascertainment biases. The systematic frequency differences are consistent with the presence of widespread weak selection (selection coefficients ~10^−3–10^−5 per allele) rather than genetic drift alone (P < 10^−15).

good comment (Bates):
The paper doesn't really highlight the fact, but drift looks like a real patsy hypothesis for complex traits: In the "no selection, just drift" neutral world, 1,400+ SNPs all have to have happened to "drift" synchonously from North to South... Hence the p value of 0.0000000000000001 against :-) = No drift ever for complex traits
hsu  scitariat  genetics  embodied  recent-selection  study  summary  europe  mediterranean  street-fighting  GWAS  spearhead  pop-structure  biodet  QTL  mutation  evolution  pop-diff  shift  gene-drift 
december 2016 by nhaliday
Rolling Stones – spottedtoad
I’m not 100% convinced that dads make a huge difference to their kid’s individual development; there are of course reasonable arguments on either side. But I’ve become convinced that the end of married fatherhood is a hugely politically and socially destabilizing force, and that the particular form of the married family was deeply important to both the rise of capitalism and the gradual expansion of liberty where and when it occurred. There are multiple reasons to doubt Deirdre McCloskey’s sanguine conclusion that The Great Enrichment of capitalist wealth and political equality will expand to every corner of the globe, but this seems like one of the important ones.

THERE ARE TWO AMERICAS…: https://spottedtoad.wordpress.com/2017/10/18/there-are-two-americas/
…with almost wholly separate life histories:

Age Women Have Children by Marital Status: First Births 2016

https://twitter.com/WilcoxNMP/status/931365452999249921
https://archive.is/t3juH
Now for some good news (of a sort). Changes in family structure for kids have largely ground to a halt.
ratty  unaffiliated  data  trends  society  murray  visualization  wonkish  sociology  gender  current-events  social-capital  social-norms  capitalism  malaise  chart  coming-apart  dignity  life-history  social-structure  zeitgeist  rot  mokyr-allen-mccloskey  microfoundations  multi  distribution  age-generation  pop-structure  demographics  civilization  douthatish  time-series  optimism  twitter  social  commentary  backup  pro-rata  general-survey 
december 2016 by nhaliday
Standards Drift | West Hunter
We now know that the fraction of Neanderthal ancestry in coding regions has been gradually decreasing with time since the origin admixture, and is now something half as large as it was originally. There were some useful Neanderthal alleles that were favored by selection, and others that deleterious enough to have disappeared completely, but we’re talking about the general trend.

...

I’m thinking of it as standards drift. In a populations, alleles are always being selected for compatibility, for working correctly, conferring high fitness, on a particular average genetic background. Each allele has a spec it needs to meet. That spec doesn’t necessarily stay the same over time: obviously changes in environment will make a difference. Drift should matter too: if a given allele becomes more common, even by chance, the specs will change for other alleles that interact with it. But there’s always a spec.

When two populations split, their specs start to drift apart. There’s no genetic equivalent of that iridium meter bar. Function at the organismal level doesn’t change so much, but there are many slightly different ways of achieving that function.

...

While we’re at it, if there are Pygmies whose genomes are majority ancient Pygmy, their Bantu component is probably slightly incompatible: if left to themselves for a hundred thousand years, they’d probably lose a fair amount of it. Of course they will all be eaten long before that happens.

https://westhunt.wordpress.com/2016/04/08/the-1/
We don’t see people today with Neanderthal Y chromosomes or mtDNA. I keep hearing people argue that this means that mating between Neanderthal males and AMH females must have produced sterile males, or that matings between AMH men and Neanderthal women were all sterile, or whatever.

That is not necessarily the case. A slight disadvantage is all that would be required to totally eliminate Neanderthal Y-chromosomes or mtDNA.

Imagine that a Neanderthal Y-chromosome reduces the bearer’s fitness by 1%, and that the original frequency of Neanderthal Y chromosomes (after admixture) was 2%.

It’s been something like 1500 generations. The expected frequency is 5.67 x 10-9. In real life it would probably have fluctuated to zero, and of course stayed there.

Understand and remember.

https://westhunt.wordpress.com/2017/08/17/mtdna-capers/
The first problem is that there may not have been enough Neanderthals. Selection is not very effective in removing deleterious alleles when their selective disadvantage is < 1/N. For Neanderthals, some analyses indicate the effective population size was around 1000 (others think it was a large but deeply subdivided population), but the effective pop for mtDNA (haploid and only transmitted by females ) was 1/4th that – so, N ~250. Not very big.

The other, general, problem with mtDNA is lack of recombination. In an asexual lineage, mutations accumulate. Muller's ratchet. The only fix is back-mutation, which is very rare, unless the species population size is huge. Sex, on the other hand, reshuffles: a kid can have fewer deleterious mutations than either parent.

So you don’t expect hominid mtDNA to be in great shape, nearly perfectly optimized. That’s closer to true for nuclear genes. Since hominid mtDNA is not too close to optimal, it’s not a huge surprise if population A has noticeably more effective mitochondria than population B.

https://westhunt.wordpress.com/2016/02/18/croatoan/
west-hunter  genetics  evolution  archaics  sapiens  speculation  context  gene-flow  scitariat  gene-drift  multi  aDNA  genomics  archaeology  history  anthropology  critique  explanation  hmm  antiquity  population-genetics  nibble  stylized-facts  methodology  language  selection  ideas  aphorism  rant  africa  lol  population  pop-structure  china  asia  multiplicative  iteration-recursion  magnitude  quantitative-qualitative 
november 2016 by nhaliday
Degenerate Neanderthals | West Hunter
Both papers talk about the likely genetic burden that Eurasians picked up from that Neanderthal admixture. Since East Asians have a somewhat higher level of Neanderthal admixture than people in Europe or the Middle East (~20% more) then they must have even more toxic Neanderthal genes, and Africans the least. This echoes earlier papers that have argued that population history (out-of-Africa bottleneck, Neanderthal admixture, etc) must have increased genetic load in Eurasians.
Evidently extra genetic load has anti-intuitive effects.

interesting: https://westhunt.wordpress.com/2015/11/03/degenerate-neanderthals/#comment-73074
http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2000.tb00693.x/abstract

COMPENSATING FOR OUR LOAD OF MUTATIONS: FREEZING THE MELTDOWN OF SMALL POPULATIONS

The model allows us to investigate compensatory mutations, which restore fitness losses incurred by other mutations, in a context-dependent manner. We have conducted a moment analysis of the model, supplemented by the numerical results of computer simulations. The mean reduction of fitness (i.e., expected load) scaled to one is approximately n/(n + 2Ne), where Ne is the effective population size. The reciprocal relationship between the load and Ne implies that the fixation of deleterious mutations is unlikely to cause extinction when there is a broad scope for compensatory mutations, except in very small populations. Furthermore, the dependence of load on n implies that pleiotropy plays a large role in determining the extinction risk of small populations.
west-hunter  sapiens  genetics  genetic-load  archaics  speculation  methodology  competition  population-genetics  gene-flow  europe  critique  evolution  mutation  pop-structure  multi  study  links  commentary  discussion  context  dimensionality  scitariat  stylized-facts  poast  gene-drift  population  magnitude  street-fighting  nibble  aphorism  pop-diff  africa  antiquity  comparison  troll  lol  stereotypes  alien-character  speaking 
november 2016 by nhaliday
Y-chromosome crash | West Hunter
there probably wasn't vast reproductive inequality ("17 to 1! woah") in the Bronze Age, and there wouldn't have to be to explain observed genetic patterns

https://westhunt.wordpress.com/2014/06/26/kings-of-the-stone-age/
https://westhunt.wordpress.com/2014/08/30/we-three-kings/
https://westhunt.wordpress.com/2014/09/07/the-genghis-khan-effect/

comment on TFR gradients in Malthusian conditions: https://westhunt.wordpress.com/2015/03/21/y-chromosome-crash/#comment-67790
“By contrast, the average number of surviving children for the majority of men was probably somewhere between zero and one – despite that they were having sex and babies.”

Fuck me, that’s obviously ridiculous. In real life, take a peasant village in England: if your model were correct, you’d have surname turnover every couple of generations. But that didn’t happen.

Here’s a model that’s at least in the ballpark: there was some class differential in fitness. The poorest, landless laborers, had a TFR below replacement, but not by a tremendous amount: 1.6? Most peasants were close to break-even, upper farmers did better than break-even, Other groups were mostly too small in number or too urban (population sinks) to matter. Overall TFR was of course break-even over the moderately long haul, in a sloppy way, with occasional epidemics and crop failures.
west-hunter  sapiens  antiquity  regularizer  speculation  gavisti  explanation  thinking  🌞  sex  gender  male-variability  winner-take-all  inequality  pop-structure  science-anxiety  scitariat  nietzschean  sexuality  gender-diff  null-result  deep-materialism  EEA  history  multi  aDNA  archaeology  conquest-empire  china  asia  genetics  genomics  poast  fertility  medieval  britain  demographics  malthus  class  correlation  blowhards 
november 2016 by nhaliday
More than can be imagined in your models - The Unz Review
These results strong indicate that the original Lapita migration did not mix with Melanesians. And, the ancient samples share common ancestry with modern Polynesians, so that their heritage persists down to the present. Looking at the distribution of Melanesian ancestry they concluded this admixture occurred on the order of ~1,500 years before the present (their intervals were wide, but the ancient samples serve as a boundary). Additionally, in line with the Y and mtDNA the X chromosome indicated more of the ancient ancestry than the autosome. The authors conclude that “it is also possible that some of these patterns reflect a scenario in which the later movement of Papuan ancestry into Remote Oceania was largely mediated by males
who then mixed with resident females.”
antiquity  sapiens  asia  world  oceans  gnxp  scitariat  migration  pop-structure  aDNA  archaeology  spreading 
november 2016 by nhaliday
PLOS Genetics: Natural Selection Reduced Diversity on Human Y Chromosomes
The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model.
study  gender  genetics  sapiens  pop-structure  male-variability  genomics 
october 2016 by nhaliday
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