nhaliday + adna   46

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
The Science of Roman History: Biology, Climate, and the Future of the Past (Hardcover and eBook) | Princeton University Press
Forthcoming April 2018

How the latest cutting-edge science offers a fuller picture of life in Rome and antiquity
This groundbreaking book provides the first comprehensive look at how the latest advances in the sciences are transforming our understanding of ancient Roman history. Walter Scheidel brings together leading historians, anthropologists, and geneticists at the cutting edge of their fields, who explore novel types of evidence that enable us to reconstruct the realities of life in the Roman world.

Contributors discuss climate change and its impact on Roman history, and then cover botanical and animal remains, which cast new light on agricultural and dietary practices. They exploit the rich record of human skeletal material--both bones and teeth—which forms a bio-archive that has preserved vital information about health, nutritional status, diet, disease, working conditions, and migration. Complementing this discussion is an in-depth analysis of trends in human body height, a marker of general well-being. This book also assesses the contribution of genetics to our understanding of the past, demonstrating how ancient DNA is used to track infectious diseases, migration, and the spread of livestock and crops, while the DNA of modern populations helps us reconstruct ancient migrations, especially colonization.

Opening a path toward a genuine biohistory of Rome and the wider ancient world, The Science of RomanHistory offers an accessible introduction to the scientific methods being used in this exciting new area of research, as well as an up-to-date survey of recent findings and a tantalizing glimpse of what the future holds.

Walter Scheidel is the Dickason Professor in the Humanities, Professor of Classics and History, and a Kennedy-Grossman Fellow in Human Biology at Stanford University. He is the author or editor of seventeen previous books, including The Great Leveler: Violence and the History of Inequality from the Stone Age to the Twenty-First Century (Princeton).
books  draft  todo  broad-econ  economics  anthropology  genetics  genomics  aDNA  measurement  volo-avolo  environment  climate-change  archaeology  history  iron-age  mediterranean  the-classics  demographics  health  embodied  labor  migration  walter-scheidel  agriculture  frontier  malthus  letters  gibbon  traces 
november 2017 by nhaliday
Biopolitics | West Hunter
I have said before that no currently popular ideology acknowledges well-established results of behavioral genetics, quantitative genetics, or psychometrics. Or evolutionary psychology.

What if some ideology or political tradition did? what could they do? What problems could they solve, what capabilities would they have?

Various past societies knew a few things along these lines. They knew that there were significant physical and behavioral differences between the sexes, which is forbidden knowledge in modern academia. Some knew that close inbreeding had negative consequences, which knowledge is on its way to the forbidden zone as I speak. Some cultures with wide enough geographical experience had realistic notions of average cognitive differences between populations. Some people had a rough idea about regression to the mean [ in dynasties], and the Ottomans came up with a highly unpleasant solution – the law of fratricide. The Romans, during the Principate, dealt with the same problem through imperial adoption. The Chinese exam system is in part aimed at the same problem.

...

At least some past societies avoided the social patterns leading to the nasty dysgenic trends we are experiencing today, but for the most part that is due to the anthropic principle: if they’d done something else you wouldn’t be reading this. Also to between-group competition: if you fuck your self up when others don’t, you may be well be replaced. Which is still the case.

If you were designing an ideology from scratch you could make use of all of these facts – not that thinking about genetics and selection hands you the solution to every problem, but you’d have more strings to your bow. And, off the top of your head, you’d understand certain trends that are behind the mountains of Estcarp, for our current ruling classes : invisible and unthinkable, That Which Must Not Be Named. .

https://westhunt.wordpress.com/2017/10/08/biopolitics/#comment-96613
“The closest…s the sort of libertarianism promulgated by Charles Murray”
Not very close..
A government that was fully aware of the implications and possibilities of human genetics, one that had the usual kind of state goals [ like persistence and increased power] , would not necessarily be particularly libertarian.

https://westhunt.wordpress.com/2017/10/08/biopolitics/#comment-96797
And giving tax breaks to college-educated liberals to have babies wouldn’t appeal much to Trump voters, methinks.

It might be worth making a reasonably comprehensive of the facts and preferences that a good liberal is supposed to embrace and seem to believe. You would have to be fairly quick about it, before it changes. Then you could evaluate about the social impact of having more of them.

Rise and Fall: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/
Every society selects for something: generally it looks as if the direction of selection pressue is more or less an accident. Although nations and empires in the past could have decided to select men for bravery or intelligence, there’s not much sign that anyone actually did this. I mean, they would have known how, if they’d wanted to, just as they knew how to select for destriers, coursers, and palfreys. It was still possible to know such things in the Middle Ages, because Harvard did not yet exist.

A rising empire needs quality human capital, which implies that at minimum that budding imperial society must not have been strongly dysgenic. At least not in the beginning. But winning changes many things, possibly including selective pressures. Imagine an empire with substantial urbanization, one in which talented guys routinely end up living in cities – cities that were demographic sinks. That might change things. Or try to imagine an empire in which survival challenges are greatly reduced, at least for elites, so that people have nothing to keep their minds off their minds and up worshiping Magna Mater. Imagine that an empire that conquers a rival with interesting local pathogens and brings some of them home. Or one that uses up a lot of its manpower conquering less-talented subjects and importing masses of those losers into the imperial heartland.

If any of those scenarios happened valid, they might eventually result in imperial decline – decline due to decreased biological capital.

Right now this is speculation. If we knew enough about the GWAS hits for intelligence, and had enough ancient DNA, we might be able to observe that rise and fall, just as we see dysgenic trends in contemporary populations. But that won’t happen for a long time. Say, a year.

hmm: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/#comment-100350
“Although nations and empires in the past could have decided to select men for bravery or intelligence, there’s not much sign that anyone actually did this.”

Maybe the Chinese imperial examination could effectively have been a selection for intelligence.
--
Nope. I’ve modelled it: the fraction of winners is far too small to have much effect, while there were likely fitness costs from the arduous preparation. Moreover, there’s a recent
paper [Detecting polygenic adaptation in admixture graphs] that looks for indications of when selection for IQ hit northeast Asia: quite a while ago. Obvious though, since Japan has similar scores without ever having had that kind of examination system.

decline of British Empire and utility of different components: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/#comment-100390
Once upon a time, India was a money maker for the British, mainly because they appropriate Bengali tax revenue, rather than trade. The rest of the Empire was not worth much: it didn’t materially boost British per-capita income or military potential. Silesia was worth more to Germany, conferred more war-making power, than Africa was to Britain.
--
If you get even a little local opposition, a colony won’t pay for itself. I seem to remember that there was some, in Palestine.
--
Angels from on high paid for the Boer War.

You know, someone in the 50’s asked for the numbers – how much various colonies cost and how much they paid.

Turned out that no one had ever asked. The Colonial Office had no idea.
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october 2017 by nhaliday
It made their brown eyes blue.. | West Hunter
Assuming population continuity, the selective advantage of the alleles they examined must have been very high. In order to see if there had been population continuity, they looked at the mtDNA frequencies of the ancient populations and compared them with mtDNA frequencies of modern populations in the same areas. Since they’re different, but not wildly different, they conclude that there has been population continuity, which was their null assumption.

That null assumption might have been reasonable, if someone had burned every history book ever written, while at the same time suppressing all the ancient DNA evidence.

Since that has not yet happened, I think their assumption is downright embarrassing. People have been moving in and out of this area for all of recorded history (as Razib Khan has also pointed out) : Cimmerians, Scythians, Goths, Khazars, Kievian Rus, the Golden Horde, eventually Russians.

There is no logical reason for geneticists to ignore information outside their field. Ignorance is no excuse. I could say the same for every other discipline. Cross the streams – it would be good.
west-hunter  scitariat  commentary  study  summary  critique  rant  sapiens  genetics  genomics  aDNA  migration  gene-flow  europe  eastern-europe  gavisti  conquest-empire  recent-selection  science  interdisciplinary  knowledge  gnxp 
august 2017 by nhaliday
The Genomic Health Of Ancient Hominins | bioRxiv
On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past.

Gwern has interesting take (abstract is misleading): https://twitter.com/gwern/status/871061144152178688

here it is in conclusion (and cf Figure 3A):
The genomic health of ancient individuals appears to have improved over time (Figure 3B). This calls into question the idea that genetic load has been increasing in human populations (Lynch 2016). However, there exists a perplexing pattern: ancient individuals who lived within the last few thousand years have healthier genomes, on average, than present day humans.

http://www.pnas.org/content/early/2017/08/08/1703856114
After controlling for age, BMI, and other variables, knee OA prevalence was 2.1-fold higher (95% confidence interval, 1.5–3.1) in the postindustrial sample than in the early industrial sample. Our results indicate that increases in longevity and BMI are insufficient to explain the approximate doubling of knee OA prevalence that has occurred in the United States since the mid-20th century. Knee OA is thus more preventable than is commonly assumed, but prevention will require research on additional independent risk factors that either arose or have become amplified in the postindustrial era.
study  bio  preprint  sapiens  genetics  biodet  disease  health  history  antiquity  aDNA  farmers-and-foragers  agriculture  anthropology  GWAS  genetic-load  multi  twitter  social  commentary  gwern  dysgenics  trends  mutation  embodied  org:nat  obesity  public-health  epidemiology  🌞  science-anxiety 
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
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?
gnxp  scitariat  books  review  reflection  sapiens  genetics  genomics  pop-structure  recommendations  history  antiquity  iron-age  the-classics  mediterranean  medieval  MENA  archaeology  gene-flow  migration  big-picture  deep-materialism  world  aDNA  methodology  🌞  europe  roots  gavisti  the-great-west-whale  culture  cultural-dynamics  smoothness  asia  india  summary  archaics  discussion  conquest-empire  canon  shift  eden  traces 
may 2017 by nhaliday
War Before Civilization | West Hunter
When you think of war, you usually think of organized states, or at minimum peoples with moderately sophisticated modes of production, agriculturalists or pastoralists. But hunter-gatherers manage as well. Not just war, but decisive war, the kind that that obliterates the enemy and results in a major geographic expansion. Before the Eskimos, there was a different population living in arctic North America and Greenland, the Dorset culture. Over a fairly short period, between 1000 AD and 1500 AD, the Thule (ancestors of modern Inuit) moved east, replacing the Dorset. It looks as if the Thule didn’t mix much with the previous occupants either: we have an early Dorset genome that looks very Na-dene-like, while the Eskimos are not. The conflict was recent enough to leave legends among the Eskimo: they say the first inhabitants were giants, taller and stronger but easily scared off.

https://westhunt.wordpress.com/2014/08/28/deguello/
There’s a new paper out on the genetic prehistory of the Canadian Arctic. Basically, it says that existing Eskimos replaced a genetically different population less than 700 years ago, and that those earlier Paleo-Eskimos (Dorset culture) represent yet another separate migration from Asia (in addition to the PaleoIndians, the Na-Dene, and the Eskimo). They put this in such a nice way: “the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population.”

Which likely means that the neo-Eskimos killed off the Dorset people. Obviously they weren’t farmers, the usual suspects in replacement, but the new guys had a more sophisticated technology ( and probably greater numbers) , with bows, large skin boats, dog sleds, whale-hunting gear, etc. The neo-Eskimos have certainly done their share of fighting in recent historical times – they went at it hammer-and-tongs with various Amerindian tribes.

This is fairly obvious, so much so that even the New York Times and the Washington Post mentioned extermination by the newcomers as a possible explanation. There is no mention of that possibility in the original research article, but I’m sure that some of the authors were quite aware of it. What they said is probably influenced by the fear that saying anything negative, no matter how true, might cause the Eskimos to refuse cooperation in the future.

This pre-agricultural genocide makes you wonder just how often similar wipeouts may happened in the past. Maybe the Gravettians and Aurignacians weren’t the same people.
west-hunter  scitariat  discussion  sapiens  genetics  gene-flow  migration  history  antiquity  farmers-and-foragers  canada  usa  multi  archaeology  peace-violence  conquest-empire  war  kumbaya-kult  aDNA  traces 
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
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://www.unz.com/gnxp/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.tw/nature/journal/vaop/ncurrent/full/nature23310.html

Roots of Mediterranean civilisations: http://sci-hub.tw/http://www.sciencedirect.com/science/article/pii/S0960982217311740
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may 2017 by nhaliday
Reconstruction | West Hunter
Since power descended through the male line, you don’t expect to see the same thing happen with autosomal genes. Genghis accounts for about 25% of Mongolia’s Y-chromosomes, but the general ancestry fraction attributable to him must be a lot lower. Still, what if the average Mongol today is 0.5% Genghis? Upon sequencing lots of typical contemporary Mongols, you would notice certain chromosomal segments showing up again and again: not just in one family but in the whole country, and in other parts of inner Asia as well. If you started keeping track of those segments, you would eventually be able to make a partial reconstruction of Genghis’s genome. It would be incomplete, since any given region of the genome might have missed being transmitted to any of his four legitimate sons (Jochi, Chagatai, Ogedei, and Tolui). They certainly didn’t carry his X-chromosome. You might be able to distinguish the autosomal genes of Genghis and his wife Borte by looking at descendants of his by-blows, if you could find them. Still, even if you managed to retrieve 75% of his genome, that’s not enough to make a clone. It would however, allow sure identification if we found his tomb.

And since he’s likely buried in permafrost, his DNA could be in good shape. Then we could clone him (assuming reasonable continuing progress in genetics) and of course some damn fool would. Will.
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april 2017 by nhaliday
The Ionian Mission | West Hunter
I have have had famous people ask me how the Ionian Greeks became so smart (in Classical times, natch). In Classical times, the Greeks – particularly the Ionian Greeks – gave everybody this impression – in everyday experience, and certainly in terms of production of outstanding intellects. Everybody thought so. Nobody said this about the Persians – and nobody said it about the Jews, who never said it about themselves.

It’s an interesting question: perhaps there was some process analogous to that which we have proposed as an explanation for the high intelligence of the Ashkenazi Jews. Or maybe something else happened – a different selective process, or maybe it was all cultural. It’s hard to know – the Greek Dark Ages, the long period of illiteracy after the fall of Mycenaean civilization, is poorly understood, certainly by me.

Suppose that your biological IQ capacity (in favorable conditions) is set by a few hundred or thousand SNPS, and that we have identified those SNPS. With luck, we might find enough skeletons with intact DNA to see if the Ionian Greeks really were smarter than the average bear, and how that changed over time.

More generally, we could see if civilization boosted or decreased IQ, in various situations. This could be a big part of the historical process – civilizations falling because average competence has dropped, science being born because the population is now ready for it…

I think we’ll be ready to try this in a year or two. The biggest problems will be political, since this approach would also predict results in existing populations – although that would probably not be very interesting, since we already know all those results.

The Ancient Greeks Weren’t All Geniuses: http://www.unz.com/akarlin/ancient-greeks-not-geniuses/
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april 2017 by nhaliday
The Vasconic Program | West Hunter
https://westhunt.wordpress.com/2013/10/09/the-old-breed-2/
My question is what local circumstances give the best chance for a substantial dollop of the formerly-common genotypes persisting for a long time – ideally, to the present day. Where do we find the blood of the Old Ones?

https://westhunt.wordpress.com/2014/07/24/washukanni/
Mitanni, controlling northern Syria and southeastern Anatolia, was a major player in the Bronze Age Near East from 1500 BC-1300 BC. They contended and negotiated with the Hittites and the Egyptian New Kingdom.

Most of the population seems to have spoken Hurrian, but there are traces of something very different in their ruling class. We have preserved diplomatic correspondence (cuneiform tablets last!) showing that the rulers of Mitanni swore by Mitra, Varuna, Indra, and Nasatya. There are other hints: names of the ruling class often make sense in Sanskrit. Kikkuli of Mitanni’s horse conditioning manual has some Indo-Aryan words (aika, tera, panza, satta). Etc. The semi-educated guess is that Indo-Aryans, as early charioteers, were hired by Mitanni as mercenaries and eventually grabbed the reins of power. After, of course, making a wrong turn at Albuquerque: North Syria is quite a ways from the known stomping grounds of the Indo-Aryans.

There’s likely an interesting story here, but we are missing almost all of it, because we have never found Washukanni, the Mitanni capital. If we did, we’d probably find lots of cuneiform tablets – as we have other capital cities of that era, such as Boğazköy.

Washukanni was probably somewhere in the Khabur triangle. Which brings me to the present, and possible near future: if we end up occupying that area, it’d be nice if we could manage a little digging on the side. We just need to start embedding archaeologists into the infantry.
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april 2017 by nhaliday
Bloggingheads.tv: Gregory Cochran (The 10,000 Year Explosion) and Razib Khan (Unz Foundation, Gene Expression)
http://bloggingheads.tv/videos/1999
one interesting tidbit: doesn't think Homo sapiens smart enough for agriculture during previous interglacial period
https://westhunt.wordpress.com/2014/06/04/the-time-before/
Although we’re still in an ice age, we are currently in an interglacial period. That’s a good thing, since glacial periods are truly unpleasant – dry, cold, low biological productivity, high variability. Low CO2 concentrations made plants more susceptible to drought. Peter Richerson and Robert Boyd have suggested that the development of agriculture was impossible in glacial periods, due to these factors.

There was an earlier interglacial period that began about 130,000 years ago and ended about 114,000 years ago. It was a bit warmer than the current interglacial (the Holocene).

The most interesting events in the Eemian are those that didn’t happen. In the Holocene, humans developed agriculture, which led to all kinds of interesting trouble. They did it more than once, possibly as many as seven times independently. Back in the Eeemian, nichevo. Neanderthals moved father north as the glaciers melted, AMH moved up into the Middle East, but nobody did much of anything new. Populations likely increased, as habitable area expanded and biological productivity went up, but without any obvious consequences. Anatomically modern humans weren’t yet up to displacing archaic groups like the Neanderthals.

So, it is fair to say that everybody back then, including AMH, lacked capabilities that some later humans had. We could, if we wished, call these new abilities ‘behavioral modernity’.

The Bushmen are the most divergent of all human populations, and probably split off earliest. They are farther from the Bantu (in genetic distance) than the French or Chinese are.

According to some models, this split (between the Bushmen and other populations of sub-Saharan Africa) occurred more than 100,000 years ago. Recent direct measurements of mutations show much lower rates than previously thought, which tends to place such splits even farther back in time.

The question is whether they split off before the development of practical behavioral modernity.

https://westhunt.wordpress.com/2016/04/08/the-long-count/
They are anatomically modern: they have chins, etc. Behaviorally modern? There have been only a few attempts to measure their intelligence: what has been done indicates that they have very low IQs. They definitely talk, tell stories, sing songs: does that imply that they could, given the right environment, have developed the Antikythera mechanism or a clipper ship?

This means that language is older than some had thought, a good deal older. It also means that people with language are quite capable of going a quarter of a million years without generating much technological advance – without developing the ability to push aside archaic humans, for example. Of course, people with Williams syndrome have language, and you can’t send them into the kitchen and rely on them to bring back a fork. Is the sophistication of Bushman language – this means the concepts they can and do convey, not the complexity of the grammar – comparable with that of other populations? I don’t know. As far as I can see, one of the major goals of modern anthropology is to make sure that nobody knows. Or that they know things that aren’t so.

...

Some have suggested that the key to technological development is higher population: that produces more intellects past a high threshold, sure. I don’t think that’s the main factor. Eskimos have a pretty advanced technology, but there were never very many of them. On the other hand, they have the highest IQ of any existing hunter-gatherer population: that’s got to help. Populations must have gone up the Eemian, the previous interglacial period, but nothing much got invented back then. It would seem that agriculture would have been possible in the Eemian, but as far as we know it didn’t happen. Except for Valusia of course. With AMH going back at least 300,000 years, we have to start thinking about even earlier interglacial peiods, like Mindel-Riss (424-374 k years ago)

https://en.wikipedia.org/wiki/Interglacial

https://westhunt.wordpress.com/2017/08/28/same-old/
We now know ( from ancient DNA) that Bushmen split off from the rest of humanity (or we from them) at least a quarter of a million years ago. Generally, when you see a complex trait in sister groups, you can conclude that it existed in the common ancestor. Since both Bushmen and (everybody else) have complex language, one can conclude that complex language existed at least a quarter million years ago, in our common ancestor. You should also suspect that unique features of Bushmen language, namely those clicks, are not necessarily superficial: there has been time enough for real, baked-in, biologically rooted language differences to evolve. It also shows that having complex language isn’t enough, in itself, to generate anything very interesting. Cf Williams syndrome. Certainly technological change was very slow back then. Interglacial periods came and went without AMH displacing archaics in Eurasia or developing agriculture.

Next, the ability to generate rapid cultural change, invent lots of stuff, improvise effective bullshit didn’t exist in the common ancestor of extant humanity, since change was very slow back then.

Therefore it is not necessarily the case that every group has it today, or has it to the same extent. Psychic unity of mankind is unlikely. It’s also denied by every measurement ever made, but I guess invoking data, or your lying eyes, would be cheating.

https://westhunt.wordpress.com/2017/08/28/bushmen-palate/
“it has been observed by several researchers that the Khoisan palate ends to lack a prominent alveolar ridge.”

https://westhunt.wordpress.com/2013/02/17/unchanging-essence/
John Shea is a professor of anthropology at Stony Brook, specializing in ancient archaeology. He’s been making the argument that ‘behavioral modernity’ is a flawed concept, which it is. Naturally, he wants to replace it with something even worse. Not only are all existing human populations intellectually equal, as most anthropologists affirm – all are ‘behaviorally modern’ – all past populations of anatomically modern humans were too! The idea that our ancestors circa 150,000 B.C. might not be quite as sharp as people today is just like the now-discredited concept of race. And you know, he’s right. They’re both perfectly natural consequences of neodarwinism.

Behavioral modernity is a silly concept. As he says, it’s a typological concept: hominids are either behaviorally modern or they’re not. Now why would this make sense? Surely people vary in smarts, for example: it’s silly to say that they are either smart or not smart. We can usefully make much finer distinctions. We could think in terms of distributions – we might say that you score in the top quarter of intelligence for your population. We could analyze smarts in terms of thresholds: what is the most complex task that a given individual can perform? What fraction of the population can perform tasks of that complexity or greater? Etc. That would be a more reasonable way of looking at smarts, and this is of course what psychometrics does.

It’s also a group property. If even a few members of a population do something that anthropologists consider a sign of behavioral modernity – like making beads – everyone in that population must be behaviorally modern. By the the same argument, if anyone can reach the top shelf, we are all tall.

The notion of behavioral modernity has two roots. The first is that if you go back far enough, it’s obvious that our distant ancestors were pretty dim. Look at Oldowan tools – they’re not much more than broken rocks. And they stayed that way for a million years – change was inhumanly slow back then. That’s evidence. The second is not. Anthropologists want to say that all living populations are intellectually equal – which is not what the psychometric evidence shows. Or what population differences in brain size suggest. So they conjured up a quality – behavioral modernity – that all living people possess, but that homo erectus did not, rather than talk about quantitative differences.
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april 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/
west-hunter  books  big-peeps  britain  anglo  anglosphere  sapiens  genetics  roots  history  iron-age  migration  gene-flow  unaffiliated  ratty  scitariat  optimate  aristos  old-anglo  statesmen  conquest-empire  canon  alien-character  multi  gnxp  archaeology  aDNA  genomics  discussion  social-science  error  being-right  realness  europe  gavisti  antiquity  pop-structure  kumbaya-kult  elite  traces 
march 2017 by nhaliday
Interview Greg Cochran by Future Strategist
https://westhunt.wordpress.com/2016/08/10/interview/

- IQ enhancement (somewhat apprehensive, wonder why?)
- ~20 years to CRISPR enhancement (very ballpark)
- cloning as an alternative strategy
- environmental effects on IQ, what matters (iodine, getting hit in the head), what doesn't (schools, etc.), and toss-ups (childhood/embryonic near-starvation, disease besides direct CNS-affecting ones [!])
- malnutrition did cause more schizophrenia in Netherlands (WW2) and China (Great Leap Forward) though
- story about New Mexico schools and his children (mostly grad students in physics now)
- clever sillies, weird geniuses, and clueless elites
- life-extension and accidents, half-life ~ a few hundred years for a typical American
- Pinker on Harvard faculty adoptions (always Chinese girls)
- parabiosis, organ harvesting
- Chicago economics talk
- Catholic Church, cousin marriage, and the rise of the West
- Gregory Clark and Farewell to Alms
- retinoblastoma cancer, mutational load, and how to deal w/ it ("something will turn up")
- Tularemia and Stalingrad (ex-Soviet scientist literally mentioned his father doing it)
- germ warfare, nuclear weapons, and testing each
- poison gas, Haber, nerve gas, terrorists, Japan, Syria, and Turkey
- nukes at https://en.wikipedia.org/wiki/Incirlik_Air_Base
- IQ of ancient Greeks
- history of China and the Mongols, cloning Genghis Khan
- Alexander the Great vs. Napoleon, Russian army being late for meetup w/ Austrians
- the reason why to go into Iraq: to find and clone Genghis Khan!
- efficacy of torture
- monogamy, polygamy, and infidelity, the Aboriginal system (reverse aging wives)
- education and twin studies
- errors: passing white, female infanticide, interdisciplinary social science/economic imperialism, the slavery and salt story
- Jewish optimism about environmental interventions, Rabbi didn't want people to know, Israelis don't want people to know about group differences between Ashkenazim and other groups in Israel
- NASA spewing crap on extraterrestrial life (eg, thermodynamic gradient too weak for life in oceans of ice moons)
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march 2017 by nhaliday
Adaptation of the FADS gene family in Europe: Variation across time, geography and subsistence | bioRxiv
The FADS gene family encodes rate-limiting enzymes for the biosynthesis of omega-6 and omega-3 long chain polyunsaturated fatty acids (LCPUFAs), which is essential for individuals subsisting on LCPUFAs-poor diets (e.g. plant-based).
...
Here, with analyses of ancient and modern DNA, we demonstrated positive selection acted on variants centered on FADS1 and FADS2 both before and after the advent of farming in Europe, but adaptive alleles in these two periods are opposite.
study  preprint  bio  sapiens  genetics  genomics  history  antiquity  agriculture  farmers-and-foragers  biodet  tradeoffs  metabolic  recent-selection  aDNA 
february 2017 by nhaliday
Amish Paradise | West Hunter
French Canadian researchers have shown that natural selection has noticeably sped up reproduction among the inhabitants of Île aux Coudres, an island in the St. Lawrence River – in less than 150 years. Between 1799 and 1940, the age at which women had their first child dropped from 26 to 22, and analysis shows this is due to genetic change.
west-hunter  fertility  history  early-modern  antiquity  sapiens  age-of-discovery  northeast  usa  anglo  canada  genetics  aDNA  scitariat  recent-selection  natural-experiment  pre-ww2  life-history  malthus  other-xtian 
february 2017 by nhaliday
Holocene selection for variants associated with cognitive ability: Comparing ancient and modern genomes. | bioRxiv
- Michael Woodley

https://news.ycombinator.com/item?id=13759949

Human populations living in Eurasia during the Holocene experienced significant evolutionary change. It has been predicted that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favoured via directional selection genetic variants associated with higher general cognitive ability (GCA).
...
These observations are consistent with the expectation that GCA rose during the Holocene.
study  preprint  bio  sapiens  genetics  genomics  GWAS  antiquity  trends  iq  dysgenics  recent-selection  aDNA  multi  hn  commentary  gwern  enhancement  evolution  blowhards  behavioral-gen 
february 2017 by nhaliday
Timing the Wave | West Hunter
A recent paper in PNAS talks about ancient DNA results in Ireland. The story is getting to be a familiar one: 5000 years ago Ireland was inhabited by a Sardinian-like population, 4000 years ago by people pretty similar to the Irish today. Looks like near-total replacement. Since the Corded Ware culture was in place by 4900 years ago, we know that the replacement process in northern Europe took less than 900 years, maybe a lot less. Ongoing ancient DNA investigations should give us a pretty good chronology in the next few years.

Some questions are going to be harder to answer. Why near-replacement in northern Europe, but not in southern Europe? Obviously Indo-Europeans imposed their languages, lots of Y-chromosomes, and made an autosomal contribution to southern Europe, but it doesn’t look like replacement. Sometimes these things boil down to choices, as when the Mongols started taxing the southern Chinese rather pursuing extermination. Maybe a prehistoric Yelü Chucai convinced the invaders that the EEF population was good for something (pizza?), or on the other hand, maybe some of those southern populations put up stronger resistance. Yet the G2a Y chromosomes, once dominant, are very much reduced in number.
west-hunter  study  summary  sapiens  europe  gavisti  britain  mediterranean  commentary  migration  antiquity  org:nat  anglo  aDNA  gene-flow  scitariat  archaeology  conquest-empire  genetics  genomics  spreading  traces 
november 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
What’s the catch? | West Hunter
Neanderthals and the Wrath of Khan

if someone were to try to create a Neanderthal a few years from now, starting with ancient DNA, they’d have to have worry a lot about data errors, because such errors would translate into mutations, which might be harmful or even lethal. Assume that we have figured out how to get the gene expression right, have all the proper methylation etc: we have modern humans as a template and you know there isn’t that much difference.

They might try consensus averaging – take three high-quality Neanderthal genomes and make your synthetic genome by majority rule: we ignore a nucleotide change in one genome if it’s not there in the other two. ‘tell me three times’, a simple form of error-correcting code.

But doing this would cause a problem. Can you see what the problem is?
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november 2016 by nhaliday
First-Mover Advantage | West Hunter
Increasingly, it looks as if the hunter-gatherers who lived in Europe at the end of the ice age have been largely replaced. Judging from all those U5 mtdna results from ancient skeletons, I’d say that the hunters don’t account for more than 10% of the ancestry of modern Europeans. It looks as if something similar happened in the Bantu expansion: modern Africans are mostly not descended from the hunter-gatherers who lived in those same places a few thousand years ago. The same could be said for south-east Asia, Indonesia, and the Philippines. Farmers spread, more than knowledge of farming.

In part, this may be explained by a kind of first-mover advantage. If a population has already farmed for a couple of thousand years, they should already be more adapted to that ecological niche: in terms of metabolism, immune system, and psychology. So if a few boatloads of Anatolian farmers land in a hunter-gatherer Italy, they will be better at farming than the locals _can_ be. They will be less prone to alcoholism, will have more resistance to crowd diseases, will be better at living a relatively boring way of life. Their population will grow faster than that of the local hunters, even if the hunters are trying agriculture. Extrapolate that trend for a few centuries and they dominate.
west-hunter  sapiens  speculation  agriculture  farmers-and-foragers  technology  antiquity  evolution  recent-selection  EEA  immune  competition  aDNA  scitariat  pop-diff  spreading  cultural-dynamics  roots  eden  agri-mindset  population  density  scale 
november 2016 by nhaliday
The Hyborian Age | West Hunter
I was contemplating Conan the Barbarian, and remembered the essay that Robert E. Howard wrote about the background of those stories – The Hyborian Age. I think that the flavor of Howard’s pseudo-history is a lot more realistic than the picture of the human past academics preferred over the past few decades.

In Conan’s world, it’s never surprising to find a people that once mixed with some ancient prehuman race. Happens all the time. Until very recently, the vast majority of workers in human genetics and paleontology were sure that this never occurred – and only changed their minds when presented with evidence that was both strong (ancient DNA) and too mathematically sophisticated for them to understand or challenge (D-statistics).

Conan’s history was shaped by the occasional catastrophe. Most academics (particularly geologists) don’t like catastrophes, but they have grudgingly come to admit their importance – things like the Thera and Toba eruptions, or the K/T asteroid strike and the Permo-Triassic crisis.

Between the time when the oceans drank Atlantis, and the rise of the sons of Aryas, evolution seems to have run pretty briskly, but without any pronounced direction. Men devolved into ape-men when the environment pushed in that direction (Flores ?) and shifted right back when the environment favored speech and tools. Culture shaped evolution, and evolution shaped culture. An endogamous caste of snake-worshiping priests evolved in a strange direction. Although their IQs were considerably higher than average, they remained surprisingly vulnerable to sword-bearing barbarians.

...

Most important, Conan, unlike the typical professor, knew what was best in life.
west-hunter  sapiens  antiquity  aphorism  gavisti  martial  scitariat  nietzschean  archaeology  kumbaya-kult  peace-violence  conquest-empire  nihil  death  gene-flow  archaics  aDNA  flux-stasis  smoothness  shift  history  age-of-discovery  latin-america  farmers-and-foragers  migration  anthropology  embodied  straussian  scifi-fantasy  gnosis-logos  god-man-beast-victim 
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  traces 
november 2016 by nhaliday
Faster than Fisher | West Hunter
There’s a simple model of the spread of an advantageous allele:  You take σ, the typical  distance people move in one generation, and s,  the selective advantage: the advantageous allele spreads as a nonlinear wave at speed  σ * √(2s).  The problem is, that’s slow.   Suppose that s = 0.10 (a large advantage), σ = 10 kilometers, and a generation time of 30 years: the allele would take almost 7,000 years to expand out 1000 kilometers.

...

This big expansion didn’t just happen from peasants marrying the girl next door: it required migrations and conquests. This one looks as if it rode with the Indo-European expansion: I’ll bet it started out in a group that had domesticated only horses.

The same processes, migration and conquest, must explain the wide distribution of many geographically widespread selective sweeps and partial sweeps. They were adaptive, all right, but expanded much faster than possible from purely local diffusion. We already have reason to think that SLC24A5 was carried to Europe by Middle Eastern farmers; the same is probably true for the haplotype that carries the high-activity ergothioniene transporter and the 35delG connexin-26/GJB2 deafness mutation. The Indo-Europeans probably introduced the T-13910 LCT mutation and the delta-F508 cystic fibrosis mutation, so we should see delta-F508 in northwest India and Pakistan – and we do !

https://westhunt.wordpress.com/2014/11/22/faster-than-fisher/#comment-63067
To entertain a (possibly mistaken) physical analogy, it sounds like you’re suggested a sort genetic convection through space, as opposed to conduction. I.e. Entire masses of folks, carrying a new selected variant, are displacing others – as opposed to the slow gene flow process of “girl-next-door.” Is that about right? (Hopefully I haven’t revealed my ignorance of basic thermodynamics here…)

Has there been any attempt to estimate sigma from these time periods?

Genetic Convection: https://westhunt.wordpress.com/2015/02/22/genetic-convection/
People are sometimes interested in estimating the point of origin of a sweeping allele: this is probably effectively impossible even if diffusion were the only spread mechanism, since the selective advantage might well vary in both time and space. But that’s ok, since population movements – genetic convection – are real and very important. This means that the difficulties in estimating the origin of a Fisher wave are totally insignificant, compared to the difficulties of estimating the effects of past colonizations, conquests and Völkerwanderungs. So when Yuval Itan and Mark Thomas estimated that 13,910 T LCT allele originated in central Europe, in the early Neolithic, they didn’t just go wrong because of failing to notice that the same allele is fairly common in northern India: no, their whole notion was unsound in the first place. We’re talking turbulence on steroids. Hari Seldon couldn’t figure this one out from the existing geographic distribution.
west-hunter  genetics  population-genetics  street-fighting  levers  evolution  gavisti  🌞  selection  giants  nibble  fisher  speed  gene-flow  scitariat  stylized-facts  methodology  archaeology  waves  frontier  agri-mindset  analogy  visual-understanding  physics  thermo  interdisciplinary  spreading  spatial  geography  poast  multi  volo-avolo  accuracy  estimate  order-disorder  time  homo-hetero  branches  trees  distribution  data  hari-seldon  aphorism  cliometrics  aDNA  mutation  lexical 
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
DNA in London Grave May Help Solve Mysteries of the Great Plague
The strain of bacteria that caused the Great Plague of London in 1665 has been identified for the first time. Scientists recovered DNA of Yersinia pestis—known to have been responsible for the Black Death in the 14th century—from skeletons discovered last year during the construction of the new Crossrail underground rail link beneath London.
news  popsci  disease  history  europe  bio  sapiens  medieval  org:mag  org:sci  parasites-microbiome  early-modern  events  aDNA  archaeology 
september 2016 by nhaliday
Information Processing: Evidence for (very) recent natural selection in humans
height (+), infant head circumference (+), some biomolecular stuff, female hip size (+), male BMI (-), age of menarche (+, !!), and birth weight (+)

Strong selection in the recent past can cause allele frequencies to change significantly. Consider two different SNPs, which today have equal minor allele frequency (for simplicity, let this be equal to one half). Assume that one SNP was subject to strong recent selection, and another (neutral) has had approximately zero effect on fitness. The advantageous version of the first SNP was less common in the far past, and rose in frequency recently (e.g., over the last 2k years). In contrast, the two versions of the neutral SNP have been present in roughly the same proportion (up to fluctuations) for a long time. Consequently, in the total past breeding population (i.e., going back tens of thousands of years) there have been many more copies of the neutral alleles (and the chunks of DNA surrounding them) than of the positively selected allele. Each of the chunks of DNA around the SNPs we are considering is subject to a roughly constant rate of mutation.

Looking at the current population, one would then expect a larger variety of mutations in the DNA region surrounding the neutral allele (both versions) than near the favored selected allele (which was rarer in the population until very recently, and whose surrounding region had fewer chances to accumulate mutations). By comparing the difference in local mutational diversity between the two versions of the neutral allele (should be zero modulo fluctuations, for the case MAF = 0.5), and between the (+) and (-) versions of the selected allele (nonzero, due to relative change in frequency), one obtains a sensitive signal for recent selection. See figure at bottom for more detail. In the paper what I call mutational diversity is measured by looking at distance distribution of singletons, which are rare variants found in only one individual in the sample under study.

The 2,000 year selection of the British: http://www.unz.com/gnxp/the-2000-year-selection-of-the-british/

Detection of human adaptation during the past 2,000 years: http://www.biorxiv.org/content/early/2016/05/07/052084

The key idea is that recent selection distorts the ancestral genealogy of sampled haplotypes at a selected site. In particular, the terminal (tip) branches of the genealogy tend to be shorter for the favored allele than for the disfavored allele, and hence, haplotypes carrying the favored allele will tend to carry fewer singleton mutations (Fig. 1A-C and SOM).

To capture this effect, we use the sum of distances to the nearest singleton in each direction from a test SNP as a summary statistic (Fig. 1D).

Figure 1. Illustration of the SDS method.

Figure 2. Properties of SDS.

Based on a recent model of European demography [25], we estimate that the mean tip length for a neutral sample of 3,000 individuals is 75 generations, or roughly 2,000 years (Fig. 2A). Since SDS aims to measure changes in tip lengths of the genealogy, we conjectured that it would be most likely to detect selection approximately within this timeframe.

Indeed, in simulated sweep models with samples of 3,000 individuals (Fig. 2B,C and fig. S2), we find that SDS focuses specifically on very recent time scales, and has equal power for hard and soft sweeps within this timeframe. At individual loci, SDS is powered to detect ~2% selection over 100 generations. Moreover, SDS has essentially no power to detect older selection events that stopped >100 generations before the present. In contrast, a commonly-used test for hard sweeps, iHS [12], integrates signal over much longer timescales (>1,000 generations), has no specificity to the more recent history, and has essentially no power for the soft sweep scenarios.

Catching evolution in the act with the Singleton Density Score: http://www.molecularecologist.com/2016/05/catching-evolution-in-the-act-with-the-singleton-density-score/
The Singleton Density Score (SDS) is a measure based on the idea that changes in allele frequencies induced by recent selection can be observed in a sample’s genealogy as differences in the branch length distribution.

You don’t need a weatherman: https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/
You can do a million cool things with this method. Since the effective time scale goes inversely with sample size, you could look at evolution in England over the past 1000 years or the past 500. Differencing, over the period 1-1000 AD. Since you can look at polygenic traits, you can see whether the alleles favoring higher IQs have increased or decreased in frequency over various stretches of time. You can see if Greg Clark’s proposed mechanism really happened. You can (soon) tell if creeping Pinkerization is genetic, or partly genetic.

You could probably find out if the Middle Easterners really have gotten slower, and when it happened.

Looking at IQ alleles, you could not only show whether the Ashkenazi Jews really are biologically smarter but if so, when it happened, which would give you strong hints as to how it happened.

We know that IQ-favoring alleles are going down (slowly) right now (not counting immigration, which of course drastically speeds it up). Soon we will know if this was true while Russia was under the Mongol yoke – we’ll know how smart Periclean Athenians were and when that boost occurred. And so on. And on!

...

“The pace has been so rapid that humans have changed significantly in body and mind over recorded history."

bicameral mind: https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/#comment-78934

https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/#comment-78939
Chinese, Koreans, Japanese and Ashkenazi Jews all have high levels of myopia. Australian Aborigines have almost none, I think.

https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/#comment-79094
I expect that the fall of all great empires is based on long term dysgenic trends. There is no logical reason why so many empires and civilizations throughout history could grow so big and then not simply keep growing, except for dysgenics.
--
I can think of about twenty other possible explanations off the top of my head, but dysgenics is a possible cause.
--
I agree with DataExplorer. The largest factor in the decay of civilizations is dysgenics. The discussion by R. A. Fisher 1930 p. 193 is very cogent on this matter. Soon we will know for sure.
--
Sometimes it can be rapid. Assume that the upper classes are mostly urban, and somewhat sharper than average. Then the Mongols arrive.
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august 2016 by nhaliday
First Farmers | West Hunter
By the Bronze age Natufians and Zagros mountaineers and Anatolian farmers were mixing a lot – but before agriculture, such mixing must have been very rare for a long time, in order to generate that big Fst. There was probably more trade with the advent of agriculture ( more mixing) , and later, technical developments like ships and wheeled vehicles probably favored mixing. Farmers can have specialists, who may make use of exotic materials ( like tin or lapis lazuli) than are imported over long trade routes. Eventually there were empires, some of which seem to have shuffled ethnic groups around the chess board simply because they could. Probably the horrible Ice Age climate played a role in keeping populations isolated before the Holocene.

But back before the Holocene, it seems that, more often than not hunter-gatherers either didn’t mix or exterminated each other. It looks as if there were two waves of replacement ( with little admixture) in Europe after modern humans replaced Neanderthals and before Anatolian farmers largely replaced the last population of European hunter-gatherers!

We see a couple of cases in which new populations are found almost entirely with males from one population and females from another: early Indo-Europeans and Amerindians.
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june 2016 by nhaliday

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