nhaliday + genetics   587

Comparing within- and between-family polygenic score prediction | bioRxiv
https://twitter.com/StuartJRitchie/status/1116074740475736066
https://archive.is/bQnjM
See this thread for our new study on polygenic scores within fraternal twin pairs! Main point: take extra care with polygenic scores for traits like IQ & education, because they're confounded by (what seem to be) socioeconomic status effects. Not so for traits like height & BMI.
The idea is that the parenting is caused by the parental genotype, so it gets (mis)classified as a genetic effect on the children. It's really another way of looking at "genetic nurture" - see the papers from last year.
study  bio  preprint  biodet  behavioral-gen  genetics  sib-study  GWAS  class  s-factor  iq  education  attention  disease  psychiatry  embodied  health  environmental-effects  parenting  regularizer  spearhead  multi  twitter  social  commentary  backup 
13 days ago by nhaliday
Sci-Hub | The genetics of human fertility. Current Opinion in Psychology, 27, 41–45 | 10.1016/j.copsyc.2018.07.011
very short

Overall, there is a suggestion of two different reproductive strategies proving to be successful in modern Western societies: (1) a strategy associated with socially conservative values, including a high commitment to the bearing of children within marriage; and(2) a strategy associated with antisocial behavior, early sexual experimentation, a variety of sexual partners, low educational attainment, low commitment to marriage, haphazard pregnancies, and indifference to politics. This notion of distinct lifestyles characterized in common by relatively high fertility deserves further empirical and theoretical study.
pdf  piracy  study  fertility  biodet  behavioral-gen  genetics  genetic-correlation  iq  education  class  right-wing  politics  ideology  long-short-run  time-preference  strategy  planning  correlation  life-history  dysgenics  rot  personality  psychology  gender  gender-diff  fisher  giants  old-anglo  tradition  religion  psychiatry  disease  autism  👽  stress  variance-components 
5 weeks ago by nhaliday
Manifold – man·i·fold /ˈmanəˌfōld/ many and various.
https://infoproc.blogspot.com/2019/01/a-grand-experiment.html
Silicon Valley (Big Tech and startups and VC)
Financial Markets
Academia (Good, Bad, and Ugly)
The View from Europe
The View from Asia (Life in PRC? Fear and Loathing of PRC?)
Frontiers of Science (AI, Genomics, Physics, ...)
Frontiers of Rationality
The Billionaire Life
MMA / UFC
What Millennials think us old folks don't understand
True things that you are not allowed to say
Bubbles that are ready to pop?
Under-appreciated Genius?
Overrated Crap and Frauds?
podcast  audio  stream  hsu  scitariat  science  frontier  interview  physics  genetics  biotech  technology  bio  interdisciplinary  spearhead  multi  genomics  sv  tech  finance  academia  europe  EU  china  asia  wealth  class  fighting  age-generation  westminster  censorship  truth  cycles  economics  people  realness  arbitrage  subculture  ratty  rationality 
7 weeks ago by nhaliday
Heritability of life span in the Old Order Amish | Request PDF
Offspring longevity was correlated with longevity of both parents, and in more or less additive fashion.

...

We estimated heritability of life span to be 25% +/- 5%, suggesting that the additive effects of genes account for one quarter of the total variability in life span in the OOA. We conclude that longevity is moderately heritable in the OOA, that the genetic effects are additive, and that genetic influences on longevity are likely to be expressed across a broad range of ages.
study  biodet  variance-components  genetics  longevity  time  medicine  health  data  usa  northeast 
september 2018 by nhaliday
The first ethical revolution – Gene Expression
Fifty years ago Julian Jaynes published The Origin of Consciousness in the Breakdown of the Bicameral Mind. Seventy years ago Karl Jaspers introduced the concept of the Axial Age. Both point to the same dynamic historically.

Something happened in the centuries around 500 BCE all around the world. Great religions and philosophies arose. The Indian religious traditions, the Chinese philosophical-political ones, and the roots of what we can recognize as Judaism. In Greece, the precursors of many modern philosophical streams emerged formally, along with a variety of political systems.

The next few centuries saw some more innovation. Rabbinical Judaism transformed a ritualistic tribal religion into an ethical one, and Christianity universalized Jewish religious thought, as well as infusing it with Greek systematic concepts. Meanwhile, Indian and Chinese thought continued to evolve, often due to interactions each other (it is hard to imagine certain later developments in Confucianism without the Buddhist stimulus). Finally, in the 7th century, Islam emerges as the last great world religion.

...

Living in large complex societies with social stratification posed challenges. A religion such as Christianity was not a coincidence, something of its broad outlines may have been inevitable. Universal, portable, ethical, and infused with transcendence and coherency. Similarly, god-kings seem to have universally transformed themselves into the human who binds heaven to earth in some fashion.

The second wave of social-ethical transformation occurred in the early modern period, starting in Europe. My own opinion is that economic growth triggered by innovation and gains in productivity unleashed constraints which had dampened further transformations in the domain of ethics. But the new developments ultimately were simply extensions and modifications on the earlier “source code” (e.g., whereas for nearly two thousand years Christianity had had to make peace with the existence of slavery, in the 19th century anti-slavery activists began marshaling Christian language against the institution).
gnxp  scitariat  discussion  reflection  religion  christianity  theos  judaism  china  asia  sinosphere  orient  india  the-great-west-whale  occident  history  antiquity  iron-age  mediterranean  the-classics  canon  philosophy  morality  ethics  universalism-particularism  systematic-ad-hoc  analytical-holistic  confucian  big-peeps  innovation  stagnation  technology  economics  biotech  enhancement  genetics  bio  flux-stasis  automation  ai  low-hanging  speedometer  time  distribution  smoothness  shift  dennett  simler  volo-avolo  👽  mystic  marginal  farmers-and-foragers  wealth  egalitarianism-hierarchy  values  formal-values  ideology  good-evil 
april 2018 by nhaliday
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.
west-hunter  scitariat  books  review  sapiens  anthropology  genetics  genomics  history  antiquity  iron-age  world  europe  gavisti  aDNA  multi  politics  culture-war  kumbaya-kult  social-science  academia  truth  westminster  environmental-effects  embodied  pop-diff  nordic  mediterranean  the-great-west-whale  germanic  the-classics  shift  gene-flow  homo-hetero  conquest-empire  morality  diversity  aphorism  migration  migrant-crisis  EU  africa  MENA  gender  selection  speed  time  population-genetics  error  concrete  econotariat  economics  regression  troll  lol  twitter  social  media  street-fighting  methodology  robust  disease  psychiatry  iq  correlation  usa  obesity  dysgenics  education  track-record  people  counterexample  reason  thinking  fisher  giants  old-anglo  scifi-fantasy  higher-ed  being-right  stories  reflection  critique  multiplicative  iteration-recursion  archaics  asia  developing-world  civil-liberty  anglo  oceans  food  death  horror  archaeology  gnxp  news  org:mag  right-wing  age-of-discovery  latin-america  ea 
march 2018 by nhaliday
Existential Risks: Analyzing Human Extinction Scenarios
https://twitter.com/robinhanson/status/981291048965087232
https://archive.is/dUTD5
Would you endorse choosing policy to max the expected duration of civilization, at least as a good first approximation?
Can anyone suggest a different first approximation that would get more votes?

https://twitter.com/robinhanson/status/981335898502545408
https://archive.is/RpygO
How useful would it be to agree on a relatively-simple first-approximation observable-after-the-fact metric for what we want from the future universe, such as total life years experienced, or civilization duration?

We're Underestimating the Risk of Human Extinction: https://www.theatlantic.com/technology/archive/2012/03/were-underestimating-the-risk-of-human-extinction/253821/
An Oxford philosopher argues that we are not adequately accounting for technology's risks—but his solution to the problem is not for Luddites.

Anderson: You have argued that we underrate existential risks because of a particular kind of bias called observation selection effect. Can you explain a bit more about that?

Bostrom: The idea of an observation selection effect is maybe best explained by first considering the simpler concept of a selection effect. Let's say you're trying to estimate how large the largest fish in a given pond is, and you use a net to catch a hundred fish and the biggest fish you find is three inches long. You might be tempted to infer that the biggest fish in this pond is not much bigger than three inches, because you've caught a hundred of them and none of them are bigger than three inches. But if it turns out that your net could only catch fish up to a certain length, then the measuring instrument that you used would introduce a selection effect: it would only select from a subset of the domain you were trying to sample.

Now that's a kind of standard fact of statistics, and there are methods for trying to correct for it and you obviously have to take that into account when considering the fish distribution in your pond. An observation selection effect is a selection effect introduced not by limitations in our measurement instrument, but rather by the fact that all observations require the existence of an observer. This becomes important, for instance, in evolutionary biology. For instance, we know that intelligent life evolved on Earth. Naively, one might think that this piece of evidence suggests that life is likely to evolve on most Earth-like planets. But that would be to overlook an observation selection effect. For no matter how small the proportion of all Earth-like planets that evolve intelligent life, we will find ourselves on a planet that did. Our data point-that intelligent life arose on our planet-is predicted equally well by the hypothesis that intelligent life is very improbable even on Earth-like planets as by the hypothesis that intelligent life is highly probable on Earth-like planets. When it comes to human extinction and existential risk, there are certain controversial ways that observation selection effects might be relevant.
bostrom  ratty  miri-cfar  skunkworks  philosophy  org:junk  list  top-n  frontier  speedometer  risk  futurism  local-global  scale  death  nihil  technology  simulation  anthropic  nuclear  deterrence  environment  climate-change  arms  competition  ai  ai-control  genetics  genomics  biotech  parasites-microbiome  disease  offense-defense  physics  tails  network-structure  epidemiology  space  geoengineering  dysgenics  ems  authoritarianism  government  values  formal-values  moloch  enhancement  property-rights  coordination  cooperate-defect  flux-stasis  ideas  prediction  speculation  humanity  singularity  existence  cybernetics  study  article  letters  eden-heaven  gedanken  multi  twitter  social  discussion  backup  hanson  metrics  optimization  time  long-short-run  janus  telos-atelos  poll  forms-instances  threat-modeling  selection  interview  expert-experience  malthus  volo-avolo  intel  leviathan  drugs  pharma  data  estimate  nature  longevity  expansionism  homo-hetero  utopia-dystopia 
march 2018 by nhaliday
Why Sex? And why only in Pairs? - Marginal REVOLUTION
The core conclusion is that mutations continue to rise with the number of sex-participating partners, but in simple Red Queen models the limiting features of the genotypes is the same whether there are two, three, or more partners.

Men Are Animals: http://www.overcomingbias.com/2018/06/men-are-animals.html
I agree with all the comments citing motility/sessility.
econotariat  marginal-rev  commentary  study  summary  economics  broad-econ  interdisciplinary  bio  biodet  deep-materialism  new-religion  eden  gender  sex  EGT  explanans  red-queen  parasites-microbiome  mutation  comparison  evolution  roots  🌞  population-genetics  genetics  marginal  equilibrium  number  ecology  whole-partial-many  uniqueness  parsimony  multi  cost-benefit  outcome-risk  uncertainty  moments  spatial  travel  explore-exploit  ratty  hanson 
january 2018 by nhaliday
The Space Trilogy - Wikipedia
Out of the Silent Planet:

Weston makes a long speech justifying his proposed invasion of Malacandra on "progressive" and evolutionary grounds, which Ransom attempts to translate into Malacandrian, thus laying bare the brutality and crudity of Weston's ambitions.

Oyarsa listens carefully to Weston's speech and acknowledges that the scientist is acting out of a sense of duty to his species, and not mere greed. This renders him more mercifully disposed towards the scientist, who accepts that he may die while giving Man the means to continue. However, on closer examination Oyarsa points out that Weston's loyalty is not to Man's mind – or he would equally value the intelligent alien minds already inhabiting Malacandra, instead of seeking to displace them in favour of humanity; nor to Man's body – since, as Weston is well aware of and at ease with, Man's physical form will alter over time, and indeed would have to in order to adapt to Weston's programme of space exploration and colonisation. It seems then that Weston is loyal only to "the seed" – Man's genome – which he seeks to propagate. When Oyarsa questions why this is an intelligible motivation for action, Weston's eloquence fails him and he can only articulate that if Oyarsa does not understand Man's basic loyalty to Man then he, Weston, cannot possibly instruct him.

...

Perelandra:

The rafts or floating islands are indeed Paradise, not only in the sense that they provide a pleasant and care-free life (until the arrival of Weston) but also in the sense that Ransom is for weeks and months naked in the presence of a beautiful naked woman without once lusting after her or being tempted to seduce her. This is because of the perfection in that world.

The plot thickens when Professor Weston arrives in a spaceship and lands in a part of the ocean quite close to the Fixed Land. He at first announces to Ransom that he is a reformed man, but appears to still be in search of power. Instead of the strictly materialist attitude he displayed when first meeting Ransom, he asserts he had become aware of the existence of spiritual beings and pledges allegiance to what he calls the "Life-Force." Ransom, however, disagrees with Weston's position that the spiritual is inherently good, and indeed Weston soon shows signs of demonic possession.

In this state, the possessed Weston finds the Queen and tries to tempt her into defying Maleldil's orders by spending a night on the Fixed Land. Ransom, perceiving this, believes that he must act as a counter-tempter. Well versed in the Bible and Christian theology, Ransom realises that if the pristine Queen, who has never heard of Evil, succumbs to the tempter's arguments, the Fall of Man will be re-enacted on Perelandra. He struggles through day after day of lengthy arguments illustrating various approaches to temptation, but the demonic Weston shows super-human brilliance in debate (though when "off-duty" he displays moronic, asinine behaviour and small-minded viciousness) and moreover appears never to need sleep.

With the demonic Weston on the verge of winning, the desperate Ransom hears in the night what he gradually realises is a Divine voice, commanding him to physically attack the Tempter. Ransom is reluctant, and debates with the divine (inner) voice for the entire duration of the night. A curious twist is introduced here; whereas the name "Ransom" is said to be derived from the title "Ranolf's Son", it can also refer to a reward given in exchange for a treasured life. Recalling this, and recalling that his God would (and has) sacrificed Himself in a similar situation, Ransom decides to confront the Tempter outright.

Ransom attacks his opponent bare-handed, using only physical force. Weston's body is unable to withstand this despite the Tempter's superior abilities of rhetoric, and so the Tempter flees. Ultimately Ransom chases him over the ocean, Weston fleeing and Ransom chasing on the backs of giant and friendly fish. During a fleeting truce, the "real" Weston appears to momentarily re-inhabit his body, and recount his experience of Hell, wherein the damned soul is not consigned to pain or fire, as supposed by popular eschatology, but is absorbed into the Devil, losing all independent existence.
fiction  scifi-fantasy  tip-of-tongue  literature  big-peeps  religion  christianity  theos  space  xenobio  analogy  myth  eden  deep-materialism  new-religion  sanctity-degradation  civil-liberty  exit-voice  speaking  truth  realness  embodied  fighting  old-anglo  group-selection  war  paying-rent  counter-revolution  morality  parable  competition  the-basilisk  gnosis-logos  individualism-collectivism  language  physics  science  evolution  conquest-empire  self-interest  hmm  intricacy  analytical-holistic  tradeoffs  paradox  heterodox  narrative  philosophy  expansionism  genetics  duty  us-them  interests  nietzschean  parallax  the-devil  the-self 
january 2018 by nhaliday
Sacred text as cultural genome: an inheritance mechanism and method for studying cultural evolution: Religion, Brain & Behavior: Vol 7, No 3
Yasha M. Hartberg & David Sloan Wilson

Any process of evolution requires a mechanism of inheritance for the transmission of information across generations and the expression of phenotypes during each generation. Genetic inheritance mechanisms have been studied for over a century but mechanisms of inheritance for human cultural evolution are far less well understood. Sacred religious texts have the properties required for an inheritance system. They are replicated across generations with high fidelity and are transcribed into action every generation by the invocation and interpretation of selected passages. In this article we borrow concepts and methods from genetics and epigenetics to study the “expressed phenotypes” of six Christian churches that differ along a conservative–progressive axis. Their phenotypic differences, despite drawing upon the same sacred text, can be explained in part by differential expression of the sacred text. Since the invocation and interpretation of sacred texts are often well preserved, our methods allow the expressed phenotypes of religious groups to be studied at any time and place in history.
study  interdisciplinary  bio  sociology  cultural-dynamics  anthropology  religion  christianity  theos  protestant-catholic  politics  ideology  correlation  organizing  institutions  analogy  genetics  genomics  epigenetics  comparison  culture  pdf  piracy  density  flexibility  noble-lie  deep-materialism  new-religion  universalism-particularism  homo-hetero  hypocrisy  group-selection  models  coordination  info-dynamics  evolution  impact  left-wing  right-wing  time  tradition  spreading  sanctity-degradation  coalitions  trees  usa  social-capital  hari-seldon  wisdom  the-basilisk  frequency  sociality  ecology  analytical-holistic 
january 2018 by nhaliday
A genetic map of the world – Gene Expression
The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow.  It is no great surprise that so many of the barriers correlate with rivers, mountains, and deserts. But the aim of this sort of work seems to be to make precise and quantitative intuitions which are normally expressed verbally.
gnxp  scitariat  commentary  bio  preprint  study  summary  genetics  genomics  pic  data  maps  visualization  stock-flow  gene-flow  walls  world  africa  europe  MENA  india  asia  china  japan  korea  anglo  developing-world  russia  sapiens  gavisti  population-genetics  geography  🌞  mediterranean  britain  oceans  race  tribalism 
december 2017 by nhaliday
Estimation of effect size distribution from genome-wide association studies and implications for future discoveries
We report a set of tools to estimate the number of susceptibility loci and the distribution of their effect sizes for a trait on the basis of discoveries from existing genome-wide association studies (GWASs). We propose statistical power calculations for future GWASs using estimated distributions of effect sizes. Using reported GWAS findings for height, Crohn’s disease and breast, prostate and colorectal (BPC) cancers, we determine that each of these traits is likely to harbor additional loci within the spectrum of low-penetrance common variants. These loci, which can be identified from sufficiently powerful GWASs, together could explain at least 15–20% of the known heritability of these traits. However, for BPC cancers, which have modest familial aggregation, our analysis suggests that risk models based on common variants alone will have modest discriminatory power (63.5% area under curve), even with new discoveries.

later paper:
Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variants: http://www.pnas.org/content/108/44/18026.full

Recent discoveries of hundreds of common susceptibility SNPs from genome-wide association studies provide a unique opportunity to examine population genetic models for complex traits. In this report, we investigate distributions of various population genetic parameters and their interrelationships using estimates of allele frequencies and effect-size parameters for about 400 susceptibility SNPs across a spectrum of qualitative and quantitative traits. We calibrate our analysis by statistical power for detection of SNPs to account for overrepresentation of variants with larger effect sizes in currently known SNPs that are expected due to statistical power for discovery. Across all qualitative disease traits, minor alleles conferred “risk” more often than “protection.” Across all traits, an inverse relationship existed between “regression effects” and allele frequencies. Both of these trends were remarkably strong for type I diabetes, a trait that is most likely to be influenced by selection, but were modest for other traits such as human height or late-onset diseases such as type II diabetes and cancers. Across all traits, the estimated effect-size distribution suggested the existence of increasingly large numbers of susceptibility SNPs with decreasingly small effects. For most traits, the set of SNPs with intermediate minor allele frequencies (5–20%) contained an unusually small number of susceptibility loci and explained a relatively small fraction of heritability compared with what would be expected from the distribution of SNPs in the general population. These trends could have several implications for future studies of common and uncommon variants.

...

Relationship Between Allele Frequency and Effect Size. We explored the relationship between allele frequency and effect size in different scales. An inverse relationship between the squared regression coefficient and f(1 − f) was observed consistently across different traits (Fig. 3). For a number of these traits, however, the strengths of these relationships become less pronounced after adjustment for ascertainment due to study power. The strength of the trend, as captured by the slope of the fitted line (Table 2), markedly varies between traits, with an almost 10-fold change between the two extremes of distinct types of traits. After adjustment, the most pronounced trend was seen for type I diabetes and Crohn’s disease among qualitative traits and LDL level among quantitative traits. In exploring the relationship between the frequency of the risk allele and the magnitude of the associated risk coefficient (Fig. S4), we observed a quadratic pattern that indicates increasing risk coefficients as the risk-allele frequency diverges away from 0.50 either toward 0 or toward 1. Thus, it appears that regression coefficients for common susceptibility SNPs increase in magnitude monotonically with decreasing minor-allele frequency, irrespective of whether the minor allele confers risk or protection. However, for some traits, such as type I diabetes, risk alleles were predominantly minor alleles, that is, they had frequencies of less than 0.50.
pdf  nibble  study  article  org:nat  🌞  biodet  genetics  population-genetics  GWAS  QTL  distribution  disease  cancer  stat-power  bioinformatics  magnitude  embodied  prediction  scale  scaling-up  variance-components  multi  missing-heritability  effect-size  regression  correlation  data 
november 2017 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.
nibble  pdf  slides  talks  bio  biodet  genetics  genomics  GWAS  genetic-correlation  correlation  methodology  bioinformatics  concept  levers  🌞  tutorial  explanation  pop-structure  gene-drift  ideas  multi  study  org:nat  article  repo  software  tools  libraries  stats  hypothesis-testing  biases  confounding  gotchas  QTL  simulation  survey  preprint  population-genetics 
november 2017 by nhaliday
Open Thread, 11/26/2017 – Gene Expression
A few days ago there was a Twitter thing about top five books that have influenced you. It’s hard for me to name five, but I put three books down for three different reasons:

- Principles of Population Genetics, because it gives you a model for how to analyze and understand evolutionary processes. There are other books out there besides Principles of Population Genetics. But if you buy this book you don’t need to buy another (at SMBE this year I confused Andy Clark with Mike Lynch for a second when introducing myself. #awkward)
- The Fall of Rome. A lot of historical writing can be tendentious. I’ve also noticed an unfortunate tendency of historians dropping into contemporary arguments and pretty much lying through omission or elision to support their political side (it usually goes “actually, I’m a specialist in this topic and my side is 100% correct because of obscure-stuff where I’m shading the facts”). The Fall of Rome illustrates the solidity that an archaeological and materialist take can give the field. This sort of materialism isn’t the final word, but it needs to be the start of the conversation.
- From Dawn to Decadence: 1500 to the Present: 500 Years of Western Cultural Life. To know things is important in and of itself. My own personal experience is that the returns to knowing things in a particular domain or area do not exhibit a linear return. Rather, it exhibits a logistic curve. Initially, it’s hard to make sense of anything from the facts, but at some point comprehension and insight increase rapidly, until you reach the plateau of diminishing marginal returns.

If you haven’t, I recommend you subscribe to Patrick Wyman’s Tides of History podcast. I pretty much wait now for every new episode.
gnxp  scitariat  open-things  links  commentary  books  recommendations  list  top-n  confluence  bio  genetics  population-genetics  history  iron-age  the-classics  mediterranean  gibbon  letters  academia  social-science  truth  westminster  meta:rhetoric  debate  politics  nonlinearity  convexity-curvature  knowledge  learning  cost-benefit  aphorism  metabuch  podcast  psychology  evopsych  replication  social-psych  ego-depletion  stereotypes 
november 2017 by nhaliday
Amish Mutation Protects Against Diabetes and May Extend Life - The New York Times
What Dr. Vaughan and his colleagues discovered was striking. Amish carriers of the mutation live on average to age 85, about 10 years longer than their peers. Among the Amish who did not have the mutation, the rate of Type 2 diabetes was 7 percent. But for carriers of the mutation, the rate was zero, despite leading the same lifestyle and consuming similar diets. Tests showed that carriers of the mutation had 28 percent lower levels of insulin, a hormone whose chronic elevation can lead to Type 2 diabetes.
news  org:rec  genetics  genomics  pop-diff  recent-selection  usa  midwest  longevity  health  hetero-advantage  cardio  metabolic 
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.”
nibble  pdf  study  article  methodology  bio  sapiens  genetics  genomics  population-genetics  migration  gene-flow  software  trees  concept  history  antiquity  europe  roots  gavisti  🌞  bioinformatics  metrics  hypothesis-testing  levers  ideas  libraries  tools  pop-structure 
november 2017 by nhaliday
SEXUAL DIMORPHISM, SEXUAL SELECTION, AND ADAPTATION IN POLYGENIC CHARACTERS - Lande - 1980 - Evolution - Wiley Online Library
https://twitter.com/gcochran99/status/970758341990367232
https://archive.is/mcKvr
Lol, that's nothing, my biology teacher in high school told me sex differences couldn't evolve since all of us inherit 50% of genes from parents of both sexes. Being a raucous hispanic kid I burst out laughing, she was not pleased
--
Sex differences actually evolve more slowly because of that: something like 80 times more slowly.
...
Doesn't have that number, but in the same ballpark.

Sexual Dimorphism, Sexual Selection, And Adaptation In Polygenic Characters

Russell Lande

https://twitter.com/gcochran99/status/999189778867208193
https://archive.is/AR8FY
I believe it, because sex differences [ in cases where the trait is not sex-limited ] evolve far more slowly than other things, on the order of 100 times more slowly. Lande 1980: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1980.tb04817.x

The deep past has a big vote in such cases.
...
as for the extent that women were voluntarily choosing mates 20k years ago, or 100k years ago - I surely don't know.

other time mentioned: https://pinboard.in/u:nhaliday/b:3a7c5b42dd50
study  article  bio  biodet  gender  gender-diff  evolution  genetics  population-genetics  methodology  nibble  sex  🌞  todo  pdf  piracy  marginal  comparison  pro-rata  data  multi  twitter  social  discussion  backup  west-hunter  scitariat  farmers-and-foragers  sexuality  evopsych  EEA 
november 2017 by nhaliday
What Does a “Normal” Human Genome Look Like? | Science
So, what have our first glimpses of variation in the genomes of generally healthy people taught us? First, balancing selection, the evolutionary process that favors genetic diversification rather than the fixation of a single “best” variant, appears to play a minor role outside the immune system. Local adaptation, which accounts for variation in traits such as pigmentation, dietary specialization, and susceptibility to particular pathogens is also a second-tier player. What is on the top tier? Increasingly, the answer appears to be mutations that are “deleterious” by biochemical or standard evolutionary criteria. These mutations, as has long been appreciated, overwhelmingly make up the most abundant form of nonneutral variation in all genomes. A model for human genetic individuality is emerging in which there actually is a “wild-type” human genome—one in which most genes exist in an evolutionarily optimized form. There just are no “wild-type” humans: We each fall short of this Platonic ideal in our own distinctive ways.
article  essay  org:nat  🌞  bio  biodet  genetics  genomics  mutation  genetic-load  QTL  evolution  sapiens  survey  summary  coding-theory  enhancement  signal-noise  egalitarianism-hierarchy  selection  tradeoffs  immune  recent-selection  perturbation  nibble  ideas  forms-instances 
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.
west-hunter  scitariat  discussion  rant  troll  letters  academia  politics  ideology  biases  is-ought  history  iron-age  medieval  mediterranean  the-classics  MENA  class  class-warfare  polanyi-marx  communism  gender  europe  war  genetics  genomics  sapiens  pop-structure 
november 2017 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
Genome-wide association analysis identifies 30 new susceptibility loci for schizophrenia | Nature Genetics
We conducted a genome-wide association study (GWAS) with replication in 36,180 Chinese individuals and performed further transancestry meta-analyses with data from the Psychiatry Genomics Consortium (PGC2). Approximately 95% of the genome-wide significant (GWS) index alleles (or their proxies) from the PGC2 study were overrepresented in Chinese schizophrenia cases, including ∼50% that achieved nominal significance and ∼75% that continued to be GWS in the transancestry analysis. The Chinese-only analysis identified seven GWS loci; three of these also were GWS in the transancestry analyses, which identified 109 GWS loci, thus yielding a total of 113 GWS loci (30 novel) in at least one of these analyses. We observed improvements in the fine-mapping resolution at many susceptibility loci. Our results provide several lines of evidence supporting candidate genes at many loci and highlight some pathways for further research. Together, our findings provide novel insight into the genetic architecture and biological etiology of schizophrenia.
study  biodet  behavioral-gen  psychiatry  disease  GWAS  china  asia  race  generalization  genetics  replication 
november 2017 by nhaliday
Genetics: CHROMOSOMAL MAPS AND MAPPING FUNCTIONS
Any particular gene has a specific location (its "locus") on a particular chromosome. For any two genes (or loci) alpha and beta, we can ask "What is the recombination frequency between them?" If the genes are on different chromosomes, the answer is 50% (independent assortment). If the two genes are on the same chromosome, the recombination frequency will be somewhere in the range from 0 to 50%. The "map unit" (1 cM) is the genetic map distance that corresponds to a recombination frequency of 1%. In large chromosomes, the cumulative map distance may be much greater than 50cM, but the maximum recombination frequency is 50%. Why? In large chromosomes, there is enough length to allow for multiple cross-overs, so we have to ask what result we expect for random multiple cross-overs.

1. How is it that random multiple cross-overs give the same result as independent assortment?

Figure 5.12 shows how the various double cross-over possibilities add up, resulting in gamete genotype percentages that are indistinguisable from independent assortment (50% parental type, 50% non-parental type). This is a very important figure. It provides the explanation for why genes that are far apart on a very large chromosome sort out in crosses just as if they were on separate chromosomes.

2. Is there a way to measure how close together two crossovers can occur involving the same two chromatids? That is, how could we measure whether there is spacial "interference"?

Figure 5.13 shows how a measurement of the gamete frequencies resulting from a "three point cross" can answer this question. If we would get a "lower than expected" occurrence of recombinant genotypes aCb and AcB, it would suggest that there is some hindrance to the two cross-overs occurring this close together. Crosses of this type in Drosophila have shown that, in this organism, double cross-overs do not occur at distances of less than about 10 cM between the two cross-over sites. ( Textbook, page 196. )

3. How does all of this lead to the "mapping function", the mathematical (graphical) relation between the observed recombination frequency (percent non-parental gametes) and the cumulative genetic distance in map units?

Figure 5.14 shows the result for the two extremes of "complete interference" and "no interference". The situation for real chromosomes in real organisms is somewhere between these extremes, such as the curve labelled "interference decreasing with distance".
org:junk  org:edu  explanation  faq  nibble  genetics  genomics  bio  ground-up  magnitude  data  flux-stasis  homo-hetero  measure  orders  metric-space  limits  measurement 
october 2017 by nhaliday
Genome Editing
This collection of articles from the Nature Research journals provides an overview of current progress in developing targeted genome editing technologies. A selection of protocols for using and adapting these tools in your own lab is also included.
news  org:sci  org:nat  list  links  aggregator  chart  info-foraging  frontier  technology  CRISPR  biotech  🌞  survey  state-of-art  article  study  genetics  genomics  speedometer 
october 2017 by nhaliday
Genetic influences on measures of the environment: a systematic review | Psychological Medicine | Cambridge Core
Background. Traditional models of psychiatric epidemiology often assume that the relationship between individuals and their environment is unidirectional, from environment to person. Accumulating evidence from developmental and genetic studies has made this perspective increasingly untenable.

Results. We identified 55 independent studies organized into seven categories: general and specific stressful life events (SLEs), parenting as reported by child, parenting reported by parent, family environment, social support, peer interactions, and marital quality. Thirty-five environmental measures in these categories were examined by at least two studies and produced weighted heritability estimates ranging from 7% to 39%, with most falling between 15% and 35%. The weighted heritability for all environmental measures in all studies was 27%. The weighted heritability for environmental measures by rating method was: self-report 29%, informant report 26%, and direct rater or videotape observation (typically examining 10 min of behavior) 14%.
study  meta-analysis  biodet  behavioral-gen  genetics  population-genetics  🌞  regularizer  environmental-effects  GxE  psychiatry  epidemiology  composition-decomposition 
october 2017 by nhaliday
1 Genetics and Crime
The broader construct of antisocial behavior – which includes criminal offending, as well as aggression – also shows substantial genetic influence. In a meta-analysis combining effect sizes in 51 twin and adoption studies, Rhee and Waldman (2002) reported a heritability estimate of 41 per cent, with the remaining 59 per cent of variance being due to environmental factors. Interestingly, when comparing results for various definitions of antisocial behavior, only criminal offending appeared to be influenced by both additive genetic effects and non-additive genetic effects – possibly due to genetic dominance and epistatic interactions between genes – based on a pattern of results whereby, on average, identical (monozygotic) twin correlations are more than twice the value of fraternal (dizygotic) twin correlations, and also that biological parent–offspring correlations are less than fraternal twin correlations. Such non-additive genetic effects could arise if one or more high risk alleles act in a recessive fashion, or if certain alleles at one locus affect gene expression at other loci (epistasis).

One intriguing aspect of the literature on genetics and crime is that the strong and consistent genetic influence seen for property offending does not hold true for violent criminal convictions. None of the major adoption studies in Scandinavia or the United States found any elevated risk for violent convictions as a function of either biological or adoptive parent criminal offending, although one early twin study did find greater identical (monozygotic) than fraternal (dizygotic) concordance for violent convictions (see Cloninger and Gottesman, 1987). This pattern of twin, but not parent-offspring, similarity for violent criminal behavior suggests the possibility of non-additive genetic effects due to dominance or epistasis, which would result in increased resemblance for siblings (and twins), but not for parents and offspring. Thus, there may be genetic risk for violent crimes such as murder and rape, which may stem from rare recessive genes, or specific combinations of alleles that do not appear in studies of vertical transmission across generations.

A Swedish national twin study of criminal behavior and its violent, white-collar and property subtypes: https://www.cambridge.org/core/journals/psychological-medicine/article/a-swedish-national-twin-study-of-criminal-behavior-and-its-violent-white-collar-and-property-subtypes/0D9A88185ED0FD5525A5EBD5D2EBA117
For all criminal convictions, heritability was estimated at around 45% in both sexes, with the shared environment accounting for 18% of the variance in liability in females and 27% in males. The correlation of these risk factors across sexes was estimated at +0.63. In men, the magnitudes of genetic and environmental influence were similar in the three criminal conviction subtypes. However, for violent and white-collar convictions, nearly half and one-third of the genetic effects were respectively unique to that criminal subtype. About half of the familial environmental effects were unique to property convictions.

Heritability, Assortative Mating and Gender Differences in Violent Crime: Results from a Total Population Sample Using Twin, Adoption, and Sibling Models: https://link.springer.com/article/10.1007/s10519-011-9483-0
Using 36k twins, violent crime was moderately heritable (~ 55%) w/ 13% shared environment influence. Using 1.5 mil siblings, heritability was higher for males, & family environment higher for females. Moderate assortative mating for violent crime (r = .4).

The impact of neighbourhood deprivation on adolescent violent criminality and substance misuse: A longitudinal, quasi-experimental study of the total Swedish population: https://academic.oup.com/ije/article/42/4/1057/656274/The-impact-of-neighbourhood-deprivation-on
In the crude model, an increase of 1 SD in neighbourhood deprivation was associated with a 57% increase in the odds of being convicted of a violent crime (95% CI 52%–63%). The effect was greatly attenuated when adjustment was made for a number of observed confounders (OR 1.09, 95% CI 1.06–1.11). When we additionally adjusted for unobserved familial confounders, the effect was no longer present (OR 0.96, 95% CI 0.84–1.10). Similar results were observed for substance misuse. The results were not due to poor variability either between neighbourhoods or within families.

Childhood family income, adolescent violent criminality and substance misuse: quasi-experimental total population study: http://bjp.rcpsych.org/content/early/2014/08/14/bjp.bp.113.136200
https://www.economist.com/news/science-and-technology/21613303-disturbing-study-link-between-incomes-and-criminal-behaviour-have-and
What did surprise him was that when he looked at families which had started poor and got richer, the younger children—those born into relative affluence—were just as likely to misbehave when they were teenagers as their elder siblings had been. Family income was not, per se, the determining factor.

Indicators of domestic/intimate partner violence are structured by genetic and nonshared environmental influences: https://www.researchgate.net/publication/233737219_Indicators_of_domesticintimate_partner_violence_are_structured_by_genetic_and_nonshared_environmental_influences
Three indicators of IPV were measured and genetic factors accounted for 24% of the variance in hitting one's partner, 54% of the variance in injuring one's partner, and 51% of the variance in forcing sexual activity on one's partner. The shared environment explained none of the variance across all three indicators and the nonshared environment explained the remainder of the variance.
pdf  essay  article  biodet  behavioral-gen  genetics  crime  criminology  variance-components  GxE  gender  gender-diff  twin-study  summary  survey  social-science  data  class  correlation  environmental-effects  candidate-gene  attention  self-control  discipline  🌞  usa  europe  nordic  meta-analysis  nonlinearity  comparison  homo-hetero  attaq  developmental  QTL  peace-violence  multi  study  psychology  social-psych  psych-architecture  large-factor  genetic-correlation  regularizer  assortative-mating  sib-study  spearhead  scitariat  epidemiology  sociology  chart  longitudinal  confounding  endo-exo  wealth  news  org:rec  org:anglo  org:biz  effect-size  null-result  endogenous-exogenous 
october 2017 by nhaliday
Testing the moderation of quantitative gene by environment interactions in unrelated individuals | bioRxiv
We use simulation to estimate the accuracy, power, and type I error rates of our method and to gauge its computational performance, and then apply this method to IQ data measured on 40,172 individuals with whole-genome SNP data from the UK Biobank. We found that the additive genetic variation of IQ tagged by SNPs increases as socioeconomic status (SES) decreases, opposite the direction found by several twin studies conducted in the U.S. on adolescents, but consistent with several studies from Europe and Australia on adults.
study  bio  preprint  biodet  behavioral-gen  genetics  GxE  class  iq  britain  environmental-effects  regularizer  variance-components  correlation  s-factor 
september 2017 by nhaliday
Accurate Genomic Prediction Of Human Height | bioRxiv
Stephen Hsu's compressed sensing application paper

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ~40, 20, and 9 percent of total variance for the three traits. For example, predicted heights correlate ~0.65 with actual height; actual heights of most individuals in validation samples are within a few cm of the prediction.

https://infoproc.blogspot.com/2017/09/accurate-genomic-prediction-of-human.html

http://infoproc.blogspot.com/2017/11/23andme.html
I'm in Mountain View to give a talk at 23andMe. Their latest funding round was $250M on a (reported) valuation of $1.5B. If I just add up the Crunchbase numbers it looks like almost half a billion invested at this point...

Slides: Genomic Prediction of Complex Traits

Here's how people + robots handle your spit sample to produce a SNP genotype:

https://drive.google.com/file/d/1e_zuIPJr1hgQupYAxkcbgEVxmrDHAYRj/view
study  bio  preprint  GWAS  state-of-art  embodied  genetics  genomics  compressed-sensing  high-dimension  machine-learning  missing-heritability  hsu  scitariat  education  🌞  frontier  britain  regression  data  visualization  correlation  phase-transition  multi  commentary  summary  pdf  slides  brands  skunkworks  hard-tech  presentation  talks  methodology  intricacy  bioinformatics  scaling-up  stat-power  sparsity  norms  nibble  speedometer  stats  linear-models  2017  biodet 
september 2017 by nhaliday
Second Bananas | West Hunter
Still thinking about domestication. Mostly,  the wild ancestors of domesticate animals were social: presumably, such behavioral tendencies were preadaptations that helped the domesticates come to bond with or at least tolerate people.   Social animals can have adaptive personality variation – difference behavioral strategies.  Sometimes those strategies are facultative, sometimes genetic, sometimes a mix.

I would guess that those wild individuals that account for most of the ancestry of f a domesticated species didn’t have a representative mix of personality types. Probably they were more likely to be followers rather than leaders – not the alphas of the pack, not the most aggressive stallions.  Sidekicks.  With dogs, we can probably check this hypothesis fairly easily, since wolves are still around.

https://westhunt.wordpress.com/2013/04/03/wyld-stallyns/
A few years ago, I was thinking about genetic male morphs. Turns out that you find qualitatively different forms of males in many species: Barry Sinervos’s lizards, Shuster’s isopods, Lank’s ruffs, jack salmon, etc. Logically, the Y chromosome would be the best place for a such a genetic switch, since that would avoid negative side effects in females. The problem is that the Y carries very few genes.

Alternate strategies don’t have to to be as complicated as they are in ruffs or Uta stansburiana. Different levels of aggressiveness, or different points on the cad/dad axis, would have different selective payoffs in different environments. If a new environment favored lower (or higher) aggressiveness in males , a Y-chromosome that induced lower (or higher) aggressiveness would take off. And since different Y chromosomes do indeed affect the level of aggressiveness in mice [which I just found out], possibly by affecting testosterone production – this mechanism is plausible.

This could explain a funny genetic pattern in the domestication of horses. There’s a fair amount of diversity in horse mtDNA: it looks as if many different mares were domesticated. On the other hand, it looks as if only one stallion was ever domesticated. All living stallions today are his descendants.

Stallions are pretty aggressive, and must have been hard to tame. Maybe one was genetically unusual – wimpier. Tameable.

Fortunately for all concerned, the selective value of aggressiveness, etc. has been the same for all human populations forever and ever, before and after the development of agriculture. Otherwise you might see weirdly rapid expansions of particular Y-chromosome haplogroups – common, yet only a few thousand years old.

https://westhunt.wordpress.com/2018/04/18/wyld-stallyns-part-deux/
A while ago, I wondered if modern stallions are a male morph adapted to domestication, one in which the strategy is mediated via the Y chromosome.

Looks as if I was right*. Check out “Decline of genetic diversity in ancient domestic stallions in Europe”.

Selection favored one particular kind of Y-chromosome. This had to be based on phenotype, not genealogy. Most likely it was favored under the new environment of domestication. Somehow, these stallions performed better, or were easier to get along with (my bet).

We already knew that Y-chromosomes could do things: Haplogroup I increases the risk of heart disease by about 50%, while the particular variant of Y chromosome influences aggression in mice.

Which means you have to re-examine the starburst phylogeny of R1b and R1a: it’s probably biology, rather than history, that drove those expansions. Some kind of selective advantage. Possibly one reason that those particular Y chromosomes far outraced steppe autosomal contributions. Most likely, R1a and R1b induce specific morphs – their carriers are somehow different. Maybe they’re born to be mild, or born to be princes of the universe. Maybe an R1b guy just finds it easier to cooperate with other R1b guys… Or maybe they’re resistant to typhoid.

* correct predictions mean nothing in biology. Ask any biologist.
west-hunter  scitariat  discussion  ideas  speculation  domestication  nature  egalitarianism-hierarchy  multi  genomics  recent-selection  genetics  biodet  behavioral-gen  ecology  EGT  strategy  gavisti  theory-practice  bio  paying-rent  being-right  elite  europe  antiquity  migration  conquest-empire  consilience  explanans 
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"
gnon  unaffiliated  right-wing  twitter  social  discussion  data  analysis  visualization  migration  usa  history  mostly-modern  time-series  scale  distribution  world  developing-world  latin-america  india  asia  china  backup  government  intricacy  gotchas  demographics  population  multi  race  stock-flow  org:gov  white-paper  pdf  the-west  california  northeast  nyc  list  top-n  database  age-generation  gender  pop-structure  genetics  genomics  maps  pro-rata 
september 2017 by nhaliday
The Genetics of Alzheimer Disease
Twin and family studies indicate that genetic factors are estimated to play a role in at least 80% of AD cases. The inheritance of AD exhibits a dichotomous pattern. On one hand, rare mutations in APP, PSEN1, and PSEN2 virtually guarantee early-onset (<60 years) familial AD, which represents ∼5% of AD. On the other hand, common gene polymorphisms, such as the ε4 and ε2 variants of the APOE gene, can influence susceptibility for ∼50% of the common late-onset AD. These four genes account for 30%–50% of the inheritability of AD. Genome-wide association studies have recently led to the identification of 11 additional AD candidate genes.

Role of Genes and Environments for Explaining Alzheimer Disease: http://jamanetwork.com/journals/jamapsychiatry/fullarticle/209307
study  biodet  twin-study  sib-study  variance-components  candidate-gene  GWAS  medicine  neuro  neuro-nitgrit  dementia  disease  🌞  aging  multi  org:nat  genetics  genomics  immune  health 
september 2017 by nhaliday
Medicine as a pseudoscience | West Hunter
The idea that venesection was a good thing, or at least not so bad, on the grounds that one in a few hundred people have hemochromatosis (in Northern Europe) reminds me of the people who don’t wear a seatbelt, since it would keep them from being thrown out of their convertible into a waiting haystack, complete with nubile farmer’s daughter. Daughters. It could happen. But it’s not the way to bet.

Back in the good old days, Charles II, age 53, had a fit one Sunday evening, while fondling two of his mistresses.

Monday they bled him (cupping and scarifying) of eight ounces of blood. Followed by an antimony emetic, vitriol in peony water, purgative pills, and a clyster. Followed by another clyster after two hours. Then syrup of blackthorn, more antimony, and rock salt. Next, more laxatives, white hellebore root up the nostrils. Powdered cowslip flowers. More purgatives. Then Spanish Fly. They shaved his head and stuck blistering plasters all over it, plastered the soles of his feet with tar and pigeon-dung, then said good-night.

...

Friday. The king was worse. He tells them not to let poor Nelly starve. They try the Oriental Bezoar Stone, and more bleeding. Dies at noon.

Most people didn’t suffer this kind of problem with doctors, since they never saw one. Charles had six. Now Bach and Handel saw the same eye surgeon, John Taylor – who blinded both of them. Not everyone can put that on his resume!

You may wonder how medicine continued to exist, if it had a negative effect, on the whole. There’s always the placebo effect – at least there would be, if it existed. Any real placebo effect is very small: I’d guess exactly zero. But there is regression to the mean. You see the doctor when you’re feeling worse than average – and afterwards, if he doesn’t kill you outright, you’re likely to feel better. Which would have happened whether you’d seen him or not, but they didn’t often do RCTs back in the day – I think James Lind was the first (1747).

Back in the late 19th century, Christian Scientists did better than others when sick, because they didn’t believe in medicine. For reasons I think mistaken, because Mary Baker Eddy rejected the reality of the entire material world, but hey, it worked. Parenthetically, what triggered all that New Age nonsense in 19th century New England? Hash?

This did not change until fairly recently. Sometime in the early 20th medicine, clinical medicine, what doctors do, hit break-even. Now we can’t do without it. I wonder if there are, or will be, other examples of such a pile of crap turning (mostly) into a real science.

good tweet: https://twitter.com/bowmanthebard/status/897146294191390720
The brilliant GP I've had for 35+ years has retired. How can I find another one who meets my requirements?

1 is overweight
2 drinks more than officially recommended amounts
3 has an amused, tolerant atitude to human failings
4 is well aware that we're all going to die anyway, & there are better or worse ways to die
5 has a healthy skeptical attitude to mainstream medical science
6 is wholly dismissive of "a|ternative” medicine
7 believes in evolution
8 thinks most diseases get better without intervention, & knows the dangers of false positives
9 understands the base rate fallacy

EconPapers: Was Civil War Surgery Effective?: http://econpapers.repec.org/paper/htrhcecon/444.htm
contra Greg Cochran:
To shed light on the subject, I analyze a data set created by Dr. Edmund Andrews, a Civil war surgeon with the 1st Illinois Light Artillery. Dr. Andrews’s data can be rendered into an observational data set on surgical intervention and recovery, with controls for wound location and severity. The data also admits instruments for the surgical decision. My analysis suggests that Civil War surgery was effective, and increased the probability of survival of the typical wounded soldier, with average treatment effect of 0.25-0.28.

Medical Prehistory: https://westhunt.wordpress.com/2016/03/14/medical-prehistory/
What ancient medical treatments worked?

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76878
In some very, very limited conditions, bleeding?
--
Bad for you 99% of the time.

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76947
Colchicine – used to treat gout – discovered by the Ancient Greeks.

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76973
Dracunculiasis (Guinea worm)
Wrap the emerging end of the worm around a stick and slowly pull it out.
(3,500 years later, this remains the standard treatment.)
https://en.wikipedia.org/wiki/Ebers_Papyrus

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76971
Some of the progress is from formal medicine, most is from civil engineering, better nutrition ( ag science and physical chemistry), less crowded housing.

Nurses vs doctors: https://westhunt.wordpress.com/2014/10/01/nurses-vs-doctors/
Medicine, the things that doctors do, was an ineffective pseudoscience until fairly recently. Until 1800 or so, they were wrong about almost everything. Bleeding, cupping, purging, the four humors – useless. In the 1800s, some began to realize that they were wrong, and became medical nihilists that improved outcomes by doing less. Some patients themselves came to this realization, as when Civil War casualties hid from the surgeons and had better outcomes. Sometime in the early 20th century, MDs reached break-even, and became an increasingly positive influence on human health. As Lewis Thomas said, medicine is the youngest science.

Nursing, on the other hand, has always been useful. Just making sure that a patient is warm and nourished when too sick to take care of himself has helped many survive. In fact, some of the truly crushing epidemics have been greatly exacerbated when there were too few healthy people to take care of the sick.

Nursing must be old, but it can’t have existed forever. Whenever it came into existence, it must have changed the selective forces acting on the human immune system. Before nursing, being sufficiently incapacitated would have been uniformly fatal – afterwards, immune responses that involved a period of incapacitation (with eventual recovery) could have been selectively favored.

when MDs broke even: https://westhunt.wordpress.com/2014/10/01/nurses-vs-doctors/#comment-58981
I’d guess the 1930s. Lewis Thomas thought that he was living through big changes. They had a working serum therapy for lobar pneumonia ( antibody-based). They had many new vaccines ( diphtheria in 1923, whopping cough in 1926, BCG and tetanus in 1927, yellow fever in 1935, typhus in 1937.) Vitamins had been mostly worked out. Insulin was discovered in 1929. Blood transfusions. The sulfa drugs, first broad-spectrum antibiotics, showed up in 1935.

DALYs per doctor: https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/
The disability-adjusted life year (DALY) is a measure of overall disease burden – the number of years lost. I’m wondering just much harm premodern medicine did, per doctor. How many healthy years of life did a typical doctor destroy (net) in past times?

...

It looks as if the average doctor (in Western medicine) killed a bunch of people over his career ( when contrasted with doing nothing). In the Charles Manson class.

Eventually the market saw through this illusion. Only took a couple of thousand years.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100741
That a very large part of healthcare spending is done for non-health reasons. He has a chapter on this in his new book, also check out his paper “Showing That You Care: The Evolution of Health Altruism” http://mason.gmu.edu/~rhanson/showcare.pdf
--
I ran into too much stupidity to finish the article. Hanson’s a loon. For example when he talks about the paradox of blacks being more sentenced on drug offenses than whites although they use drugs at similar rate. No paradox: guys go to the big house for dealing, not for using. Where does he live – Mars?

I had the same reaction when Hanson parroted some dipshit anthropologist arguing that the stupid things people do while drunk are due to social expectations, not really the alcohol.
Horseshit.

I don’t think that being totally unable to understand everybody around you necessarily leads to deep insights.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100744
What I’ve wondered is if there was anything that doctors did that actually was helpful and if perhaps that little bit of success helped them fool people into thinking the rest of it helped.
--
Setting bones. extracting arrows: spoon of Diocles. Colchicine for gout. Extracting the Guinea worm. Sometimes they got away with removing the stone. There must be others.
--
Quinine is relatively recent: post-1500. Obstetrical forceps also. Caesarean deliveries were almost always fatal to the mother until fairly recently.

Opium has been around for a long while : it works.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100839
If pre-modern medicine was indeed worse than useless – how do you explain no one noticing that patients who get expensive treatments are worse off than those who didn’t?
--
were worse off. People are kinda dumb – you’ve noticed?
--
My impression is that while people may be “kinda dumb”, ancient customs typically aren’t.
Even if we assume that all people who lived prior to the 19th century were too dumb to make the rational observation, wouldn’t you expect this ancient practice to be subject to selective pressure?
--
Your impression is wrong. Do you think that there some slick reason for Carthaginians incinerating their first-born?

Theodoric of York, bloodletting: https://www.youtube.com/watch?v=yvff3TViXmY

details on blood-letting and hemochromatosis: https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100746

Starting Over: https://westhunt.wordpress.com/2018/01/23/starting-over/
Looking back on it, human health would have … [more]
west-hunter  scitariat  discussion  ideas  medicine  meta:medicine  science  realness  cost-benefit  the-trenches  info-dynamics  europe  the-great-west-whale  history  iron-age  the-classics  mediterranean  medieval  early-modern  mostly-modern  🌞  harvard  aphorism  rant  healthcare  regression-to-mean  illusion  public-health  multi  usa  northeast  pre-ww2  checklists  twitter  social  albion  ability-competence  study  cliometrics  war  trivia  evidence-based  data  intervention  effect-size  revolution  speculation  sapiens  drugs  antiquity  lived-experience  list  survey  questions  housing  population  density  nutrition  wiki  embodied  immune  evolution  poast  chart  markets  civil-liberty  randy-ayndy  market-failure  impact  scale  pro-rata  estimate  street-fighting  fermi  marginal  truth  recruiting  alt-inst  academia  social-science  space  physics  interdisciplinary  ratty  lesswrong  autism  👽  subculture  hanson  people  track-record  crime  criminal-justice  criminology  race  ethanol  error  video  lol  comedy  tradition  institutions  iq  intelligence  MENA  impetus  legacy 
august 2017 by nhaliday
Genetic Architectures | West Hunter
Dairy cattle eventually graduate to McDonalds, so there is some interest in the genetics of beef production in dairy breeds. There is course more interest in the genetics of beef production in beef breeds of cattle.

Usually you don’t find a single allele that makes a lot of difference, but in some beef breeds, there are myostatin mutations that result in a ridiculous-looking, ‘double-muscled’ beast. Homozygosity for myostatin mutations causes difficulties in birth, so it takes really strong selection for beef production to make a myostatin null common. I don’t think you ever see this in dairy breeds.

But, as it turns out, there is a deletion that is pretty common in some dairy breeds that significantly increases milk production while killing homozygotes before birth.

Breeds under weaker selection for single traits, your typical cow of the past, probably have neither.

The point is that the genetic architecture of a quantitative trait does not have to be the same in different populations of the same species. For example, I have the impression that height is not as highly polygenic in Pygmies as it is most other human populations. There’s a particular region on chromosome 3 that seems to influence height- you don’t see such a concentration in Europeans.
west-hunter  scitariat  discussion  ideas  speculation  sapiens  pop-diff  genetics  population-genetics  QTL  homo-hetero  analogy  agriculture  nature  food  comparison  embodied  archaics  africa  genomics 
august 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
Demography of the Roman Empire - Wikipedia
There are few recorded population numbers for the whole of antiquity, and those that exist are often rhetorical or symbolic. Unlike the contemporaneous Han Dynasty, no general census survives for the Roman Empire. The late period of the Roman Republic provides a small exception to this general rule: serial statistics for Roman citizen numbers, taken from census returns, survive for the early Republic through the 1st century CE.[41] Only the figures for periods after the mid-3rd century BCE are reliable, however. Fourteen figures are available for the 2nd century BCE (from 258,318 to 394,736). Only four figures are available for the 1st century BCE, and are feature a large break between 70/69 BCE (910,000) and 28 BCE (4,063,000). The interpretation of the later figures—the Augustan censuses of 28 BCE, 8 BCE, and 14 CE—is therefore controversial.[42] Alternate interpretations of the Augustan censuses (such as those of E. Lo Cascio[43]) produce divergent population histories across the whole imperial period.[44]

Roman population size: the logic of the debate: https://www.princeton.edu/~pswpc/pdfs/scheidel/070706.pdf
- Walter Scheidel (cited in book by Vaclav Smil, "Why America is Not a New Rome")

Our ignorance of ancient population numbers is one of the biggest obstacles to our understanding of Roman history. After generations of prolific scholarship, we still do not know how many people inhabited Roman Italy and the Mediterranean at any given point in time. When I say ‘we do not know’ I do not simply mean that we lack numbers that are both precise and safely known to be accurate: that would surely be an unreasonably high standard to apply to any pre-modern society. What I mean is that even the appropriate order of magnitude remains a matter of intense dispute.

Historical urban community sizes: https://en.wikipedia.org/wiki/Historical_urban_community_sizes

World population estimates: https://en.wikipedia.org/wiki/World_population_estimates
As a general rule, the confidence of estimates on historical world population decreases for the more distant past. Robust population data only exists for the last two or three centuries. Until the late 18th century, few governments had ever performed an accurate census. In many early attempts, such as in Ancient Egypt and the Persian Empire, the focus was on counting merely a subset of the population for purposes of taxation or military service.[3] Published estimates for the 1st century ("AD 1") suggest an uncertainty of the order of 50% (estimates range between 150 and 330 million). Some estimates extend their timeline into deep prehistory, to "10,000 BC", i.e. the early Holocene, when world population estimates range roughly between one and ten million (with an uncertainty of up to an order of magnitude).[4][5]

Estimates for yet deeper prehistory, into the Paleolithic, are of a different nature. At this time human populations consisted entirely of non-sedentary hunter-gatherer populations, with anatomically modern humans existing alongside archaic human varieties, some of which are still ancestral to the modern human population due to interbreeding with modern humans during the Upper Paleolithic. Estimates of the size of these populations are a topic of paleoanthropology. A late human population bottleneck is postulated by some scholars at approximately 70,000 years ago, during the Toba catastrophe, when Homo sapiens population may have dropped to as low as between 1,000 and 10,000 individuals.[6][7] For the time of speciation of Homo sapiens, some 200,000 years ago, an effective population size of the order of 10,000 to 30,000 individuals has been estimated, with an actual "census population" of early Homo sapiens of roughly 100,000 to 300,000 individuals.[8]
history  iron-age  mediterranean  the-classics  demographics  fertility  data  europe  population  measurement  volo-avolo  estimate  wiki  reference  article  conquest-empire  migration  canon  scale  archaeology  multi  broad-econ  pdf  study  survey  debate  uncertainty  walter-scheidel  vaclav-smil  urban  military  economics  labor  time-series  embodied  health  density  malthus  letters  urban-rural  database  list  antiquity  medieval  early-modern  mostly-modern  time  sequential  MENA  the-great-west-whale  china  asia  sinosphere  occident  orient  japan  britain  germanic  gallic  summary  big-picture  objektbuch  confidence  sapiens  anthropology  methodology  farmers-and-foragers  genetics  genomics  chart 
august 2017 by nhaliday
And your little dog, too! | West Hunter
It sure looks as if we’re talking near-complete replacement – which means that the historical process involved does not look much like a peaceful, diffusion-style range expansion.  Perhaps more like the Death Song of Ragnar Lodbrok, which abounds in phrases like this: “Where the swords were whining while they sundered helmets”

Interestingly, there is a very similar  pattern in canine mtDNA.  Today Europeans dogs fall into four haplotypes: A (70%), B(16%), C (6%), and D(8%).  But back in the day, it seems that the overwhelming majority of dogs (88%)  were type C,  12% were in group A, while B and D have not been detected at all.

The ancestors of today’s Europeans didn’t fool around.
west-hunter  scitariat  discussion  ideas  speculation  history  antiquity  europe  sapiens  gavisti  farmers-and-foragers  genetics  genomics  gene-flow  migration  conquest-empire  peace-violence  kumbaya-kult  nature  nihil  death  archaeology  nietzschean  traces 
august 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.
west-hunter  scitariat  discussion  ideas  speculation  bio  evolution  sapiens  genetics  population-genetics  pop-structure  population  gene-drift  magnitude  street-fighting  methodology  stylized-facts  nibble  🌞 
august 2017 by nhaliday
trees are harlequins, words are harlequins — bayes: a kinda-sorta masterpost
lol, gwern: https://www.reddit.com/r/slatestarcodex/comments/6ghsxf/biweekly_rational_feed/diqr0rq/
> What sort of person thinks “oh yeah, my beliefs about these coefficients correspond to a Gaussian with variance 2.5″? And what if I do cross-validation, like I always do, and find that variance 200 works better for the problem? Was the other person wrong? But how could they have known?
> ...Even ignoring the mode vs. mean issue, I have never met anyone who could tell whether their beliefs were normally distributed vs. Laplace distributed. Have you?
I must have spent too much time in Bayesland because both those strike me as very easy and I often think them! My beliefs usually are Laplace distributed when it comes to things like genetics (it makes me very sad to see GWASes with flat priors), and my Gaussian coefficients are actually a variance of 0.70 (assuming standardized variables w.l.o.g.) as is consistent with field-wide meta-analyses indicating that d>1 is pretty rare.
ratty  ssc  core-rats  tumblr  social  explanation  init  philosophy  bayesian  thinking  probability  stats  frequentist  big-yud  lesswrong  synchrony  similarity  critique  intricacy  shalizi  scitariat  selection  mutation  evolution  priors-posteriors  regularization  bias-variance  gwern  reddit  commentary  GWAS  genetics  regression  spock  nitty-gritty  generalization  epistemic  🤖  rationality  poast  multi  best-practices  methodology  data-science 
august 2017 by nhaliday
Born that way | West Hunter
In the Atlantic Monthly , which no longer has any reason for existence, since there’s really no point in placing a computer screen on the bottom of a birdcage, Jason Silverstein  – a doctoral candidate in anthropology at Harvard –  has a piece explaining that genes don’t cause racial health disparities – society does! Moreover,  it’s immoral to even look for such genetic explanations.

I guess he should have gotten this published earlier, since we’ve already found some of those naughty genes – pretty important ones. So it’s too late.

...

Which means that Silverstein is a jackass. Nothing stopped him from digging into biomedical research to see if his thesis was substantially true: he didn’t bother. But why is he a jackass? Born that way, probably.
west-hunter  scitariat  discussion  ideas  rant  critique  race  medicine  pop-diff  health  genetics  embodied  attaq  prudence  straussian 
august 2017 by nhaliday
Genes, Evolution and Intelligence
I argue that the g factor meets the fundamental criteria of a scientific construct more fully than any other conception of intelligence. I briefly discuss the evidence regarding the relationship of brain size to intelligence. A review of a large body of evidence demonstrates that there is a g factor in a wide range of species and that, in the species studied, it relates to brain size and is heritable. These findings suggest that many species have evolved a general-purpose mechanism (a general biological intelligence) for dealing with the environments in which they evolved. In spite of numerous studies with considerable statistical power, we know of very few genes that influence g and the effects are very small. Nevertheless, g appears to be highly polygenic. Given the complexity of the human brain, it is not surprising that that one of its primary faculties—intelligence—is best explained by the near infinitesimal model of quantitative genetics.
pdf  study  survey  psychology  cog-psych  iq  intelligence  psychometrics  large-factor  biodet  behavioral-gen  genetics  neuro  neuro-nitgrit  brain-scan  🌞  psych-architecture 
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
study  bio  preprint  biodet  genetics  evolution  sapiens  pop-diff  embodied  recent-selection  survey  🌞  europe  asia  shift  GWAS  population-genetics  pop-structure  spearhead  environment  temperature  correlation  multi  hsu  scitariat  commentary 
july 2017 by nhaliday
« earlier      
per page:    204080120160

bundles : frame

related tags

-_-  2016-election  :/  aaronson  ability-competence  abortion-contraception-embryo  absolute-relative  abstraction  academia  accelerationism  accretion  accuracy  acm  additive  aDNA  advertising  advice  africa  age-generation  age-of-discovery  aggregator  aging  agri-mindset  agriculture  ai  ai-control  akrasia  albion  algorithms  alien-character  alignment  allodium  alt-inst  altruism  ama  amazon  american-nations  AMT  analogy  analysis  analytical-holistic  anarcho-tyranny  anglo  anglosphere  announcement  anomie  anonymity  anthropic  anthropology  antidemos  antiquity  aphorism  apollonian-dionysian  apple  applicability-prereqs  applications  arbitrage  archaeology  archaics  aristos  arms  art  article  asia  assimilation  assortative-mating  atmosphere  attaq  attention  audio  authoritarianism  autism  automation  aversion  axelrod  axioms  backup  baez  bare-hands  barons  bayesian  behavioral-econ  behavioral-gen  being-becoming  being-right  benevolence  best-practices  bias-variance  biases  big-peeps  big-picture  big-yud  bio  biodet  biohacking  bioinformatics  biomechanics  biophysical-econ  biotech  bitcoin  bits  blog  blowhards  books  bootstraps  bostrom  bounded-cognition  brain-scan  branches  brands  brexit  britain  broad-econ  buddhism  business  business-models  c:*  c:**  c:***  calculation  california  canada  cancer  candidate-gene  canon  capital  capitalism  cardio  cartoons  causation  censorship  chan  chapman  charity  chart  cheatsheet  checklists  chicago  china  christianity  civic  civil-liberty  civilization  clarity  class  class-warfare  classic  climate-change  clinton  cliometrics  clown-world  coalitions  coarse-fine  cochrane  cocktail  coding-theory  cog-psych  cohesion  cold-war  collaboration  columbia  comedy  comics  coming-apart  commentary  communication  communism  community  comparison  compensation  competition  complement-substitute  complex-systems  composition-decomposition  compressed-sensing  computation  computer-vision  concentration-of-measure  concept  conceptual-vocab  concrete  conference  confidence  confluence  confounding  confucian  confusion  conquest-empire  consilience  constraint-satisfaction  consumerism  context  contradiction  contrarianism  control  convergence  convexity-curvature  cool  cooperate-defect  coordination  core-rats  corporation  correlation  corruption  cost-benefit  counter-revolution  counterexample  counterfactual  courage  course  cracker-econ  creative  crime  criminal-justice  criminology  CRISPR  critique  crooked  crosstab  crux  crypto  cryptocurrency  cs  cultural-dynamics  culture  culture-war  curiosity  current-events  curvature  cybernetics  cycles  cynicism-idealism  dark-arts  darwinian  data  data-science  database  dataset  death  debate  debt  decentralized  decision-making  deep-learning  deep-materialism  deepgoog  defense  definite-planning  definition  degrees-of-freedom  dementia  democracy  demographic-transition  demographics  dennett  density  dependence-independence  descriptive  detail-architecture  deterrence  developing-world  developmental  diet  differential-privacy  dignity  dimensionality  direct-indirect  direction  dirty-hands  discipline  discovery  discrimination  discussion  disease  distribution  divergence  diversity  diy  documentary  domestication  dominant-minority  douthatish  DP  draft  drama  dropbox  drugs  duplication  duty  dynamic  dynamical  dysgenics  early-modern  earth  eastern-europe  ecology  econ-metrics  econ-productivity  econometrics  economics  econotariat  ed-yong  eden  eden-heaven  education  EEA  effect-size  effective-altruism  efficiency  egalitarianism-hierarchy  ego-depletion  EGT  einstein  elections  electromag  elite  embedded-cognition  embodied  embodied-cognition  embodied-pack  emergent  emotion  empirical  ems  endo-exo  endocrine  endogenous-exogenous  energy-resources  engineering  enhancement  enlightenment-renaissance-restoration-reformation  entertainment  entrepreneurialism  entropy-like  environment  environmental-effects  envy  epidemiology  epigenetics  epistemic  equilibrium  ergodic  error  essay  essence-existence  estimate  ethanol  ethical-algorithms  ethics  ethnocentrism  ethnography  EU  europe  events  evidence  evidence-based  evolution  evopsych  examples  existence  exit-voice  expansionism  experiment  expert  expert-experience  explanans  explanation  exploration-exploitation  exploratory  explore-exploit  exposition  expression-survival  externalities  extra-introversion  extrema  facebook  faq  farmers-and-foragers  fashun  FDA  fermi  fertility  feudal  feynman  fiction  field-study  fighting  film  finance  fire  fisher  fitness  fitsci  flexibility  fluid  flux-stasis  flynn  focus  food  foreign-lang  foreign-policy  formal-values  forms-instances  free-riding  frequency  frequentist  frontier  fungibility-liquidity  futurism  gallic  galor-like  galton  game-theory  games  garett-jones  gavisti  gbooks  GCTA  gedanken  gelman  gender  gender-diff  gene-drift  gene-flow  general-survey  generalization  genetic-correlation  genetic-load  genetics  genomics  geoengineering  geography  geopolitics  germanic  giants  gibbon  gnon  gnosis-logos  gnxp  god-man-beast-victim  good-evil  google  gotchas  government  grad-school  graphical-models  graphs  gray-econ  great-powers  gregory-clark  ground-up  group-level  group-selection  growth-econ  GT-101  guide  guilt-shame  GWAS  gwern  GxE  haidt  hanson  hanushek  happy-sad  hard-tech  hari-seldon  harvard  hashing  hate  health  healthcare  heavy-industry  henrich  hetero-advantage  heterodox  heuristic  hi-order-bits  hidden-motives  hierarchy  high-dimension  high-variance  higher-ed  history  hive-mind  hmm  hn  homo-hetero  honor  horror  housing  howto  hsu  huge-data-the-biggest  human-capital  human-ml  human-study  humanity  humility  hypochondria  hypocrisy  hypothesis-testing  ideas  identity  identity-politics  ideology  idk  iidness  illusion  immune  impact  impetus  incentives  increase-decrease  india  individualism-collectivism  industrial-org  industrial-revolution  inequality  inference  info-dynamics  info-econ  info-foraging  infographic  information-theory  infrastructure  inhibition  init  innovation  input-output  insight  instinct  institutions  integral  integrity  intel  intelligence  interdisciplinary  interests  internet  interpretation  intersection  intersection-connectedness  intervention  interview  intricacy  investing  ioannidis  iq  iraq-syria  iron-age  is-ought  islam  israel  isteveish  iteration-recursion  janus  japan  jargon  jobs  journos-pundits  judaism  justice  kinship  knowledge  korea  kumbaya-kult  labor  land  language  large-factor  latent-variables  latin-america  lattice  law  leadership  learning  lecture-notes  lectures  left-wing  legacy  legibility  len:long  len:short  lens  lesswrong  let-me-see  letters  levers  leviathan  lexical  libraries  life-history  limits  linear-models  linearity  liner-notes  linguistics  links  list  literature  lived-experience  lmao  local-global  lol  long-short-run  long-term  longevity  longform  longitudinal  love-hate  low-hanging  machiavelli  machine-learning  macro  madisonian  magnitude  malaise  male-variability  malthus  management  managerial-state  map-territory  maps  marginal  marginal-rev  market-failure  market-power  markets  markov  martial  matching  math  math.CA  math.CO  math.DS  mathtariat  matrix-factorization  maxim-gun  meaningness  measure  measurement  media  medicine  medieval  mediterranean  memes(ew)  MENA  mena4  mendel-randomization  mental-math  meta-analysis  meta:medicine  meta:prediction  meta:rhetoric  meta:science  meta:war  metabolic  metabuch  metameta  methodology  metric-space  metrics  micro  microfoundations  microsoft  midwest  migrant-crisis  migration  military  minimum-viable  miri-cfar  missing-heritability  mit  ML-MAP-E  mobile  mobility  model-class  model-organism  models  modernity  moloch  moments  monetary-fiscal  money  morality  mostly-modern  multi  multiplicative  murray  music  musk  mutation  mystic  myth  n-factor  narrative  nascent-state  nationalism-globalism  natural-experiment  nature  near-far  network-structure  neuro  neuro-nitgrit  neurons  new-religion  news  nibble  nietzschean  nihil  nitty-gritty  nl-and-so-can-you  nlp  no-go  noble-lie  noblesse-oblige  noise-structure  nonlinearity  nootropics  nordic  norms  north-weingast-like  northeast  nostalgia  novelty  nuclear  null-result  number  nutrition  nyc  obama  obesity  objective-measure  objektbuch  occam  occident  oceans  ocw  offense-defense  old-anglo  open-closed  open-things  operational  opioids  optimate  optimism  optimization  order-disorder  orders  org:anglo  org:biz  org:bleg  org:data  org:davos  org:econlib  org:edge  org:edu  org:foreign  org:gov  org:health  org:inst  org:junk  org:lite  org:local  org:mag  org:mat  org:med  org:nat  org:ngo  org:popup  org:rec  org:sci  organization  organizing  orient  orwellian  oscillation  other-xtian  outcome-risk  outliers  overflow  oxbridge  PAC  paganism  paleocon  papers  parable  paradox  parallax  parasites-microbiome  parenting  parsimony  paternal-age  path-dependence  patho-altruism  patience  paul-romer  paulg  paying-rent  pdf  peace-violence  pennsylvania  people  personality  persuasion  perturbation  pessimism  peter-singer  phalanges  pharma  phase-transition  philosophy  phys-energy  physics  pic  pigeonhole-markov  pinker  piracy  planning  plots  poast  podcast  poetry  polanyi-marx  polarization  policy  polisci  political-econ  politics  poll  pop-diff  pop-structure  popsci  population  population-genetics  populism  postmortem  postrat  power  power-law  pragmatic  pre-2013  pre-ww2  prediction  prediction-markets  preference-falsification  prejudice  prepping  preprint  presentation  primitivism  princeton  priors-posteriors  privacy  pro-rata  probability  problem-solving  procrastination  prof  profile  programming  project  proofs  propaganda  properties  property-rights  proposal  protestant-catholic  protocol  prudence  pseudoE  psych-architecture  psychiatry  psychology  psychometrics  public-goodish  public-health  publishing  putnam-like  q-n-a  qra  QTL  quantitative-qualitative  quantum  questions  quixotic  quiz  quotes  race  random  random-matrices  randy-ayndy  ranking  rant  rationality  ratty  realness  realpolitik  reason  recent-selection  recommendations  recruiting  red-queen  reddit  redistribution  reduction  reference  reflection  regional-scatter-plots  regression  regression-to-mean  regularization  regularizer  regulation  reinforcement  religion  rent-seeking  replication  repo  reputation  research  responsibility  retention  revealed-preference  review  revolution  rhetoric  rhythm  right-wing  rigidity  rigor  rindermann-thompson  risk  ritual  robotics  robust  rock  roots  rot  russia  s-factor  s:*  s:**  s:***  saas  safety  sanctity-degradation  sapiens  scale  scaling-tech  scaling-up  schelling  scholar  science  science-anxiety  scifi-fantasy  scitariat  search  securities  security  selection  self-control  self-interest  self-report  selfish-gene  sensitivity  sequential  sex  sexuality  shakespeare  shalizi  shift  sib-study  signal-noise  signaling  similarity  simler  simulation  singularity  sinosphere  skeleton  skunkworks  sky  sleep  sleuthin  slides  slippery-slope  smoothness  social  social-capital  social-choice  social-norms  social-psych  social-science  social-structure  sociality  society  sociology  socs-and-mops  software  solid-study  solzhenitsyn  space  sparsity  spatial  speaking  spearhead  speculation  speed  speedometer  spock  sports  spreading  ssc  stackex  stagnation  stanford  startups  stat-mech  stat-power  state  state-of-art  statesmen  stats  status  stereotypes  stochastic-processes  stock-flow  stories  strategy  straussian  stream  street-fighting  stress  structure  study  studying  stylized-facts  subculture  sublinear  success  sulla  summary  supply-demand  survey  sv  symmetry  synchrony  synthesis  systematic-ad-hoc  tactics  tails  talks  tapes  taubes-guyenet  taxes  tcstariat  tech  technocracy  technology  techtariat  telos-atelos  temperance  temperature  terrorism  tetlock  the-basilisk  the-bones  the-classics  the-devil  the-founding  the-great-west-whale  the-monster  the-self  the-south  the-trenches  the-watchers  the-west  the-world-is-just-atoms  theory-of-mind  theory-practice  theos  thermo  thick-thin  thiel  things  thinking  threat-modeling  tidbits  time  time-preference  time-series  tip-of-tongue  todo  toolkit  tools  top-n  toxo-gondii  toxoplasmosis  toys  traces  track-record  trade  tradeoffs  tradition  transportation  travel  trees  trends  tribalism  tricks  trivia  troll  trump  trust  truth  tumblr  turchin  tutorial  tv  twin-study  twitter  unaffiliated  uncertainty  unintended-consequences  uniqueness  unit  universalism-particularism  urban  urban-rural  us-them  usa  utopia-dystopia  vaclav-smil  values  vampire-squid  variance-components  venture  video  virginia-DC  virtu  visual-understanding  visualization  visuo  vitality  volo-avolo  von-neumann  walls  walter-scheidel  war  water  waves  wealth  wealth-of-nations  web  weightlifting  weird  welfare-state  west-hunter  westminster  whiggish-hegelian  white-paper  whole-partial-many  wiki  wild-ideas  winner-take-all  wire-guided  wisdom  within-group  within-without  woah  wonkish  workflow  world  world-war  X-not-about-Y  xenobio  yak-shaving  yc  yvain  zeitgeist  zero-positive-sum  zooming  🌞  🎓  🎩  🐝  🐸  👽  🔬  🖥  🤖  🦀 

Copy this bookmark:



description:


tags: