nhaliday + biodet   549

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
Links 3/19: Linkguini | Slate Star Codex
How did the descendants of the Mayan Indians end up in the Eastern Orthodox Church?

Does Parental Quality Matter? Study using three sources of parental variation that are mostly immune to genetic confounding find that “the strong parent-child correlation in education is largely causal”. For example, “the parent-child correlation in education is stronger with the parent that spends more time with the child”.

Before and after pictures of tech leaders like Jeff Bezos, Elon Musk, and Sergey Brin suggest they’re taking supplemental testosterone. And though it may help them keep looking young, Palladium points out that there might be other effects from having some of our most powerful businessmen on a hormone that increases risk-taking and ambition. They ask whether the new availability of testosterone supplements is prolonging Silicon Valley businessmen’s “brash entrepreneur” phase well past the point where they would normally become mature respectable elders. But it also hints at an almost opposite take: average testosterone levels have been falling for decades, so at this point these businessmen would be the only “normal” (by 1950s standards) men out there, and everyone else would be unprecedently risk-averse and boring. Paging Peter Thiel and everyone else who takes about how things “just worked better” in Eisenhower’s day.

China’s SesameCredit social monitoring system, widely portrayed as dystopian, has an 80% approval rate in China (vs. 19% neutral and 1% disapproval). The researchers admit that although all data is confidential and they are not affiliated with the Chinese government, their participants might not believe that confidently enough to answer honestly.

I know how much you guys love attacking EAs for “pathological altruism” or whatever terms you’re using nowadays, so here’s an article where rationalist community member John Beshir describes his experience getting malaria on purpose to help researchers test a vaccine.

Some evidence against the theory that missing fathers cause earlier menarche.

John Nerst of EverythingStudies’ political compass.
ratty  yvain  ssc  links  multi  biodet  behavioral-gen  regularizer  causation  contrarianism  education  correlation  parenting  developmental  direct-indirect  time  religion  christianity  eastern-europe  russia  latin-america  other-xtian  endocrine  trends  malaise  stagnation  thiel  barons  tech  sv  business  rot  zeitgeist  outcome-risk  critique  environmental-effects  poll  china  asia  authoritarianism  alt-inst  sentiment  policy  n-factor  individualism-collectivism  pro-rata  technocracy  managerial-state  civil-liberty  effective-altruism  subculture  wtf  disease  parasites-microbiome  patho-altruism  self-interest  lol  africa  experiment  medicine  expression-survival  things  dimensionality  degrees-of-freedom  sex  composition-decomposition  analytical-holistic  systematic-ad-hoc  coordination  alignment  cooperate-defect  politics  coalitions  ideology  left-wing  right-wing  summary  exit-voice  redistribution  randy-ayndy  welfare-state 
6 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
Cultural variation in cultural evolution | Proceedings of the Royal Society of London B: Biological Sciences
Cultural evolutionary models have identified a range of conditions under which social learning (copying others) is predicted to be adaptive relative to asocial learning (learning on one's own), particularly in humans where socially learned information can accumulate over successive generations. However, cultural evolution and behavioural economics experiments have consistently shown apparently maladaptive under-utilization of social information in Western populations. Here we provide experimental evidence of cultural variation in people's use of social learning, potentially explaining this mismatch. People in mainland China showed significantly more social learning than British people in an artefact-design task designed to assess the adaptiveness of social information use. People in Hong Kong, and Chinese immigrants in the UK, resembled British people in their social information use, suggesting a recent shift in these groups from social to asocial learning due to exposure to Western culture. Finally, Chinese mainland participants responded less than other participants to increased environmental change within the task. Our results suggest that learning strategies in humans are culturally variable and not genetically fixed, necessitating the study of the ‘social learning of social learning strategies' whereby the dynamics of cultural evolution are responsive to social processes, such as migration, education and globalization.

...

Western education emphasizes individual discovery and creativity, whereas East Asian education emphasizes rote learning from authority [25]. The adoption of consumer products shows less social influence in Western than East Asian countries [26]. Westerners are described as more individualistic/independent, while East Asians are described as more collectivistic/interdependent [27], dimensions which intuitively map on to asocial and social learning, respectively.

Societal background influences social learning in cooperative decision making: https://www.sciencedirect.com/science/article/pii/S1090513817303501
We demonstrate that Chinese participants base their cooperation decisions on information about their peers much more frequently than their British counterparts. Moreover, our results reveal remarkable societal differences in the type of peer information people consider. In contrast to the consensus view, Chinese participants tend to be substantially less majority-oriented than the British. While Chinese participants are inclined to adopt peer behavior that leads to higher payoffs, British participants tend to cooperate only if sufficiently many peers do so too. These results indicate that the basic processes underlying social transmission are not universal; rather, they vary with cultural conditions. As success-based learning is associated with selfish behavior and majority-based learning can help foster cooperation, our study suggests that in different societies social learning can play diverging roles in the emergence and maintenance of cooperation.
study  org:nat  anthropology  cultural-dynamics  sapiens  pop-diff  comparison  sociality  learning  duplication  individualism-collectivism  n-factor  europe  the-great-west-whale  china  asia  sinosphere  britain  anglosphere  strategy  environmental-effects  biodet  within-without  auto-learning  tribalism  things  broad-econ  psychology  cog-psych  social-psych  🎩  🌞  microfoundations  egalitarianism-hierarchy  innovation  creative  explanans  education  culture  curiosity  multi  occident  cooperate-defect  coordination  organizing  self-interest  altruism  patho-altruism  orient  ecology  axelrod 
may 2018 by nhaliday
Harnessing Evolution - with Bret Weinstein | Virtual Futures Salon - YouTube
- ways to get out of Malthusian conditions: expansion to new frontiers, new technology, redistribution/theft
- some discussion of existential risk
- wants to change humanity's "purpose" to one that would be safe in the long run; important thing is it has to be ESS (maybe he wants a singleton?)
- not too impressed by transhumanism (wouldn't identify with a brain emulation)
video  interview  thiel  expert-experience  evolution  deep-materialism  new-religion  sapiens  cultural-dynamics  anthropology  evopsych  sociality  ecology  flexibility  biodet  behavioral-gen  self-interest  interests  moloch  arms  competition  coordination  cooperate-defect  frontier  expansionism  technology  efficiency  thinking  redistribution  open-closed  zero-positive-sum  peace-violence  war  dominant-minority  hypocrisy  dignity  sanctity-degradation  futurism  environment  climate-change  time-preference  long-short-run  population  scale  earth  hidden-motives  game-theory  GT-101  free-riding  innovation  leviathan  malthus  network-structure  risk  existence  civil-liberty  authoritarianism  tribalism  us-them  identity-politics  externalities  unintended-consequences  internet  social  media  pessimism  universalism-particularism  energy-resources  biophysical-econ  politics  coalitions  incentives  attention  epistemic  biases  blowhards  teaching  education  emotion  impetus  comedy  expression-survival  economics  farmers-and-foragers  ca 
april 2018 by nhaliday
Effects of Education on Political Opinions: An International Study | International Journal of Public Opinion Research | Oxford Academic
Education and Political Party: The Effects of College or Social Class?: https://www.jstor.org/stable/2778029
The impact of education on political ideology: Evidence from European compulsory education reforms: https://www.sciencedirect.com/science/article/pii/S0272775716301704
correlation is with leftism, causal effect is shift to right

Greg thinks there are some effects: https://pinboard.in/u:nhaliday/b:5adca8f16265

https://twitter.com/GarettJones/status/964209775419457536
https://archive.is/oFELz
https://archive.is/f1DBF
https://archive.is/5iiqn

http://econlog.econlib.org/archives/2008/12/education_ideol.html

https://twitter.com/pseudoerasmus/status/963451867912130561
https://archive.is/sHI7g
https://archive.is/B5Gdv
https://archive.is/hFERC
https://archive.is/8IUDm
Bryan Caplan has written a very persuasive book suggesting that retention/transfer of learning is very low. how do we know it’s not the same with the “PoMo ethos”
study  polisci  sociology  education  higher-ed  intervention  branches  politics  ideology  world  general-survey  correlation  causation  left-wing  right-wing  phalanges  multi  coalitions  history  mostly-modern  usa  cold-war  europe  EU  natural-experiment  endogenous-exogenous  direction  west-hunter  scitariat  twitter  social  discussion  backup  econotariat  garett-jones  cracker-econ  data  analysis  regression  org:econlib  biodet  behavioral-gen  variance-components  environmental-effects  counter-revolution  strategy  tactics  pseudoE  demographics  race  gender  markets  impetus  roots  explanans  migration  social-norms 
february 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
Anisogamy - Wikipedia
Anisogamy is a fundamental concept of sexual dimorphism that helps explain phenotypic differences between sexes.[3] In most species a male and female sex exist, both of which are optimized for reproductive potential. Due to their differently sized and shaped gametes, both males and females have developed physiological and behavioral differences that optimize the individual’s fecundity.[3] Since most egg laying females typically must bear the offspring and have a more limited reproductive cycle, this typically makes females a limiting factor in the reproductive success rate of males in a species. This process is also true for females selecting males, and assuming that males and females are selecting for different traits in partners, would result in phenotypic differences between the sexes over many generations. This hypothesis, known as the Bateman’s Principle, is used to understand the evolutionary pressures put on males and females due to anisogamy.[4] Although this assumption has criticism, it is a generally accepted model for sexual selection within anisogamous species. The selection for different traits depending on sex within the same species is known as sex-specific selection, and accounts for the differing phenotypes found between the sexes of the same species. This sex-specific selection between sexes over time also lead to the development of secondary sex characteristics, which assist males and females in reproductive success.

...

Since this process is very energy-demanding and time consuming for the female, mate choice is often integrated into the female’s behavior.[3] Females will often be very selective of the males they choose to reproduce with, for the phenotype of the male can be indicative of the male’s physical health and heritable traits. Females employ mate choice to pressure males into displaying their desirable traits to females through courtship, and if successful, the male gets to reproduce. This encourages males and females of specific species to invest in courtship behaviors as well as traits that can display physical health to a potential mate. This process, known as sexual selection,[3] results in the development of traits to ease reproductive success rather than individual survival, such as the inflated size of a termite queen. It is also important for females to select against potential mates that may have a sexually transmitted infection, for the disease could not only hurt the female’s reproductive ability, but also damage the resulting offspring.[7]

Although not uncommon in males, females are more associated with parental care.[8] Since females are on a more limited reproductive schedule than males, a female often invests more in protecting the offspring to sexual maturity than the male. Like mate choice, the level of parental care varies greatly between species, and is often dependent on the number of offspring produced per sexual encounter.[8]

...

Since females are often the limiting factor in a species reproductive success, males are often expected by the females to search and compete for the female, known as intraspecific competition.[4] This can be seen in organisms such as bean beetles, as the male that searches for females more frequently is often more successful at finding mates and reproducing. In species undergoing this form of selection, a fit male would be one that is fast, has more refined sensory organs, and spatial awareness.[4]

Darwinian sex roles confirmed across the animal kingdom: http://advances.sciencemag.org/content/2/2/e1500983.full
Since Darwin’s conception of sexual selection theory, scientists have struggled to identify the evolutionary forces underlying the pervasive differences between male and female behavior, morphology, and physiology. The Darwin-Bateman paradigm predicts that anisogamy imposes stronger sexual selection on males, which, in turn, drives the evolution of conventional sex roles in terms of female-biased parental care and male-biased sexual dimorphism. Although this paradigm forms the cornerstone of modern sexual selection theory, it still remains untested across the animal tree of life. This lack of evidence has promoted the rise of alternative hypotheses arguing that sex differences are entirely driven by environmental factors or chance. We demonstrate that, across the animal kingdom, sexual selection, as captured by standard Bateman metrics, is indeed stronger in males than in females and that it is evolutionarily tied to sex biases in parental care and sexual dimorphism. Our findings provide the first comprehensive evidence that Darwin’s concept of conventional sex roles is accurate and refute recent criticism of sexual selection theory.

Coevolution of parental investment and sexually selected traits drives sex-role divergence: https://www.nature.com/articles/ncomms12517
Sex-role evolution theory attempts to explain the origin and direction of male–female differences. A fundamental question is why anisogamy, the difference in gamete size that defines the sexes, has repeatedly led to large differences in subsequent parental care. Here we construct models to confirm predictions that individuals benefit less from caring when they face stronger sexual selection and/or lower certainty of parentage. However, we overturn the widely cited claim that a negative feedback between the operational sex ratio and the opportunity cost of care selects for egalitarian sex roles. We further argue that our model does not predict any effect of the adult sex ratio (ASR) that is independent of the source of ASR variation. Finally, to increase realism and unify earlier models, we allow for coevolution between parental investment and investment in sexually selected traits. Our model confirms that small initial differences in parental investment tend to increase due to positive evolutionary feedback, formally supporting long-standing, but unsubstantiated, verbal arguments.

Parental investment, sexual selection and sex ratios: http://www.kokkonuts.org/wp-content/uploads/Parental_investment_review.pdf
The second argument takes the reasonable premise that anisogamy produces a male-biased operational sex ratio (OSR) leading to males competing for mates. Male care is then predicted to be less likely to evolve as it consumes resources that could otherwise be used to increase competitiveness. However, given each offspring has precisely two genetic parents (the Fisher condition), a biased OSR generates frequency-dependent selection, analogous to Fisherian sex ratio selection, that favours increased parental investment by whichever sex faces more intense competition. Sex role divergence is therefore still an evolutionary conundrum. Here we review some possible solutions. Factors that promote conventional sex roles are sexual selection on males (but non-random variance in male mating success must be high to override the Fisher condition), loss of paternity because of female multiple mating or group spawning and patterns of mortality that generate female-biased adult sex ratios (ASR). We present an integrative model that shows how these factors interact to generate sex roles. We emphasize the need to distinguish between the ASR and the operational sex ratio (OSR). If mortality is higher when caring than competing this diminishes the likelihood of sex role divergence because this strongly limits the mating success of the earlier deserting sex. We illustrate this in a model where a change in relative mortality rates while caring and competing generates a shift from a mammalian type breeding system (female-only care, male-biased OSR and female-biased ASR) to an avian type system (biparental care and a male-biased OSR and ASR).

LATE FEMINISM: https://jacobitemag.com/2017/08/01/late-feminism/
Woman has had a good run. For 200,000 years humankind’s anisogamous better (and bigger) half has enjoyed a position of desirability and safety befitting a scarce commodity. She has also piloted the evolutionary destiny of our species, both as a sexual selector and an agitator during man’s Promethean journey. In terms of comfort and agency, the human female is uniquely privileged within the annals of terrestrial biology.

But the era of female privilege is ending, in a steady decline that began around 1572. Woman’s biological niche is being crowded out by capital.

...

Strictly speaking, the breadth of the coming changes extend beyond even civilizational dynamics. They will affect things that are prior. One of the oldest and most practical definitions for a biological species defines its boundary as the largest group of organisms where two individuals, via sexual reproduction, can produce fertile offspring together. The imminent arrival of new reproductive technologies will render the sexual reproduction criteria either irrelevant or massively expanded, depending upon one’s perspective. Fertility of the offspring is similarly of limited relevance, since the modification of gametes will be de rigueur in any case. What this looming technology heralds is less a social revolution than it is a full sympatric speciation event.

Accepting the inevitability of the coming bespoke reproductive revolution, consider a few questions & probable answers regarding our external-womb-grown ubermenschen:

Q: What traits will be selected for?

A: Ability to thrive in a global market economy (i.e. ability to generate value for capital.)

Q: What material substrate will generate the new genomes?

A: Capital equipment.

Q: Who will be making the selection?

A: People, at least initially, (and who coincidentally will be making decisions that map 1-to-1 to the interests of capital.)

_Replace any of the above instances of the word capital with women, and you would have accurate answers for most of our species’ history._

...

In terms of pure informational content, the supernova seen from earth can be represented in a singularly compressed way: a flash of light on a black field where there previously was none. A single photon in the cone of the eye, at the limit. Whether … [more]
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january 2018 by nhaliday
Frontiers | Can We Validate the Results of Twin Studies? A Census-Based Study on the Heritability of Educational Achievement | Genetics
As for most phenotypes, the amount of variance in educational achievement explained by SNPs is lower than the amount of additive genetic variance estimated in twin studies. Twin-based estimates may however be biased because of self-selection and differences in cognitive ability between twins and the rest of the population. Here we compare twin registry based estimates with a census-based heritability estimate, sampling from the same Dutch birth cohort population and using the same standardized measure for educational achievement. Including important covariates (i.e., sex, migration status, school denomination, SES, and group size), we analyzed 893,127 scores from primary school children from the years 2008–2014. For genetic inference, we used pedigree information to construct an additive genetic relationship matrix. Corrected for the covariates, this resulted in an estimate of 85%, which is even higher than based on twin studies using the same cohort and same measure. We therefore conclude that the genetic variance not tagged by SNPs is not an artifact of the twin method itself.
study  biodet  behavioral-gen  iq  psychometrics  psychology  cog-psych  twin-study  methodology  variance-components  state-of-art  🌞  developmental  age-generation  missing-heritability  biases  measurement  sampling-bias  sib-study 
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
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
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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.
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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
The weirdest people in the world?
Abstract: Behavioral scientists routinely publish broad claims about human psychology and behavior in the world’s top journals based on samples drawn entirely from Western, Educated, Industrialized, Rich, and Democratic (WEIRD) societies. Researchers – often implicitly – assume that either there is little variation across human populations, or that these “standard subjects” are as representative of the species as any other population. Are these assumptions justified? Here, our review of the comparative database from across the behavioral sciences suggests both that there is substantial variability in experimental results across populations and that WEIRD subjects are particularly unusual compared with the rest of the species – frequent outliers. The domains reviewed include visual perception, fairness, cooperation, spatial reasoning, categorization and inferential induction, moral reasoning, reasoning styles, self-concepts and related motivations, and the heritability of IQ. The findings suggest that members of WEIRD societies, including young children, are among the least representative populations one could find for generalizing about humans. Many of these findings involve domains that are associated with fundamental aspects of psychology, motivation, and behavior – hence, there are no obvious a priori grounds for claiming that a particular behavioral phenomenon is universal based on sampling from a single subpopulation. Overall, these empirical patterns suggests that we need to be less cavalier in addressing questions of human nature on the basis of data drawn from this particularly thin, and rather unusual, slice of humanity. We close by proposing ways to structurally re-organize the behavioral sciences to best tackle these challenges.
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november 2017 by nhaliday
The Wilson Effect: the increase in heritability of IQ with age. - PubMed - NCBI
FIGURE 2 Estimates of genetic and shared environmental influence on g by age. The age scale is not linear (see text for details).
study  biodet  behavioral-gen  iq  psychology  cog-psych  metabuch  stylized-facts  variance-components  developmental  data  visualization  twin-study  correlation  🌞  pdf  piracy  age-generation  plots  psychometrics 
november 2017 by nhaliday
Darwinian medicine - Randolph Nesse
The Dawn of Darwinian Medicine: https://sci-hub.tw/https://www.jstor.org/stable/2830330
TABLE 1 Examples of the use of the theory of natural selection to predict the existence of phenomena otherwise unsuspected
TABLE 2 A classification of phenomena associated with infectious disease
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november 2017 by nhaliday
Reconsidering the Heritability of Intelligence in Adulthood: Taking Assortative Mating and Cultural Transmission into Account
Heritability estimates of general intelligence in adulthood generally range from 75 to 85%, with all heritability due to additive genetic influences, while genetic dominance and shared environmental factors are absent, or too small to be detected. These estimates are derived from studies based on the classical twin design and are based on the assumption of random mating. Yet, considerable positive assortative mating has been reported for general intelligence. Unmodeled assortative mating may lead to biased estimates of the relative magnitude of genetic and environmental factors.

...

Under the preferred phenotypic assortment model, the variance of intelligence in adulthood was not only due to non-shared environmental (18%) and additive genetic factors (44%) but also to non-additive genetic factors (27%) and phenotypic assortment (11%).This non-additive nature of genetic influences on intelligence needs to be accommodated in future GWAS studies for intelligence.
study  biodet  behavioral-gen  psychology  cog-psych  iq  twin-study  sib-study  biases  gotchas  models  map-territory  assortative-mating  variance-components  🌞  nonlinearity  regularizer  intricacy 
november 2017 by nhaliday
Fish on Friday | West Hunter
There are parts of Europe, Switzerland and Bavaria for example, that are seriously iodine deficient. This used to be a problem. I wonder if fish on Friday ameliorated it: A three-ounce serving size of cod provides your body with 99 micrograms of iodine, or 66% of the recommended amount per day.

Thinking further, it wasn’t just Fridays: there were ~130 days a years when the Catholic Church banned flesh.

Gwern on modern iodine-deficiency: https://westhunt.wordpress.com/2017/10/28/fish-on-friday/#comment-97137
population surveys indicate lots of people are iodine-insufficient even in the US or UK where the problem should’ve been permanently solved a century ago
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october 2017 by nhaliday
Alcohol consumption and lifetime change in cognitive ability: a gene × environment interaction study | SpringerLink
We found a significant gene × alcohol consumption interaction on lifetime cognitive change (p = 0.007). Individuals with higher genetic ability to process alcohol showed relative improvements in cognitive ability with more consumption, whereas those with low processing capacity showed a negative relationship between cognitive change and alcohol consumption with more consumption.
study  psychology  cog-psych  psychometrics  iq  metabolic  ethanol  mendel-randomization  endo-exo  GxE  homo-hetero  biodet  behavioral-gen  environmental-effects  endogenous-exogenous 
october 2017 by nhaliday
The First Men in the Moon | West Hunter
But what about the future? One generally assumes that space colonists, assuming that there ever are any, will be picked individuals, somewhat like existing astronauts – the best out of hordes of applicants. They’ll be smarter than average, healthier than average, saner than average – and not by just a little.

Since all these traits are significantly heritable, some highly so, we have to expect that their descendants will be different – different above the neck. They’d likely be, on average, smarter than any existing ethnic group. If a Lunar colony really took off, early colonists might account for a disproportionate fraction of the population (just as Puritans do in the US), and the Loonies might continue to have inordinate amounts of the right stuff indefinitely. They’d notice: we’d notice. We’d worry about the Lunar Peril. They’d sneer at deluded groundlings, and talk about the menace from Earth.

https://westhunt.wordpress.com/2014/09/29/the-first-men-in-the-moon/#comment-58473
Depends on your level of technical expertise. 2 million years ago, settlement of the Eurasian temperate zone was bleeding-edge technology – but it got easier. We can certainly settle the Solar system with near-term technology, if we choose to. And you’re forgetting one of the big payoffs: gafia.
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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.
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october 2017 by nhaliday
Biopolitics | West Hunter
I have said before that no currently popular ideology acknowledges well-established results of behavioral genetics, quantitative genetics, or psychometrics. Or evolutionary psychology.

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

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

...

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

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

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

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

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

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

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

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

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

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

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

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

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

Turned out that no one had ever asked. The Colonial Office had no idea.
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october 2017 by nhaliday
Taboo Issues in Social Science: Questioning Conventional Wisdom
sample of book

1 Postmodernism, Political Correctness and the Tyranny of the Academy 17
2 Feminism: The Good, the Bad, and the Ugly 39
3 Whiteness Studies and Racist Amerikkka 59
4 Ideological Battles over Human Nature 79
5 Social Constructionism and Gender 99
6 Race: A Dangerous Concept? 119
7 Politics and Personality: Callous Conservatives and Loving Liberals? 139
8 Capitalism and Socialism: The Devil’s Dung versus Satan’s Spore 161
9 Socioeconomic Success: Talent Plus Effort or White Privilege? 181
10 Cultural Relativism, Multiculturalism, Violence, and Human Rights 201
11 “Lies, Damn Lies, and Statistics:” Crime and Justice 223
12 Culture, Constitution, and Government 243
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october 2017 by nhaliday
Why are children in the same family so different from one another? - PubMed - NCBI
- Plomin et al

The article has three goals: (1) To describe quantitative genetic methods and research that lead to the conclusion that nonshared environment is responsible for most environmental variation relevant to psychological development, (2) to discuss specific nonshared environmental influences that have been studied to date, and (3) to consider relationships between nonshared environmental influences and behavioral differences between children in the same family. The reason for presenting this article in BBS is to draw attention to the far-reaching implications of finding that psychologically relevant environmental influences make children in a family different from, not similar to, one another.
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october 2017 by nhaliday
Does Learning to Read Improve Intelligence? A Longitudinal Multivariate Analysis in Identical Twins From Age 7 to 16
Stuart Richie, Bates, Plomin

SEM: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4354297/figure/fig03/

The variance explained by each path in the diagrams included here can be calculated by squaring its path weight. To take one example, reading differences at age 12 in the model shown in Figure​Figure33 explain 7% of intelligence differences at age 16 (.262). However, since our measures are of differences, they are likely to include substantial amounts of noise: Measurement error may produce spurious differences. To remove this error variance, we can take an estimate of the reliability of the measures (generally high, since our measures are normed, standardized tests), which indicates the variance expected purely by the reliability of the measure, and subtract it from the observed variance between twins in our sample. Correcting for reliability in this way, the effect size estimates are somewhat larger; to take the above example, the reliability-corrected effect size of age 12 reading differences on age 16 intelligence differences is around 13% of the “signal” variance. It should be noted that the age 12 reading differences themselves are influenced by many previous paths from both reading and intelligence, as illustrated in Figure​Figure33.

...

The present study provided compelling evidence that improvements in reading ability, themselves caused purely by the nonshared environment, may result in improvements in both verbal and nonverbal cognitive ability, and may thus be a factor increasing cognitive diversity within families (Plomin, 2011). These associations are present at least as early as age 7, and are not—to the extent we were able to test this possibility—driven by differences in reading exposure. Since reading is a potentially remediable ability, these findings have implications for reading instruction: Early remediation of reading problems might not only aid in the growth of literacy, but may also improve more general cognitive abilities that are of critical importance across the life span.

Does Reading Cause Later Intelligence? Accounting for Stability in Models of Change: http://sci-hub.tw/10.1111/cdev.12669
Results from a state–trait model suggest that reported effects of reading ability on later intelligence may be artifacts of previously uncontrolled factors, both environmental in origin and stable during this developmental period, influencing both constructs throughout development.
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september 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
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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
House O’Rats | West Hunter
Not content with our simple selection experiment, we also install complicated mazes with flaming hoops that the rats have to jump through in order to get extra food and mates: we want rats with different brains, and eventually we get them. They’re maze-bright and flaming-hoop-bright. We install treadmills and feed the rats according to their work output, and eventually they produce more work per amount of food eaten. They’ve maximized efficiency rather than surge power, which was more useful back when they were wild and free. Not only that, they eventually come to like being on the treadmill, almost as if it’s some sort of race.

There are other silos – one full of rice and another full of maize. They have different mazes and flaming hoops, built at different times: and there are still wild rats, too, although not as many as in the silos.

But no matter how much they change, they’re still just a bunch of rats.
west-hunter  scitariat  discussion  ideas  gedanken  analogy  comparison  parable  sapiens  pop-diff  recent-selection  agriculture  farmers-and-foragers  population  metabolic  nutrition  diet  immune  disease  parasites-microbiome  egalitarianism-hierarchy  ethanol  iq  intelligence  eden  embodied  fitness  efficiency  race  conceptual-vocab  🌞  biodet  behavioral-gen  agri-mindset  realness 
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
Scanners Live in Vain | West Hunter
Of course, finding that the pattern already exists at the age of one month seriously weakens any idea that being poor shrinks the brain: most of the environmental effects you would consider haven’t even come into play in the first four weeks, when babies drink milk, sleep, and poop. Genetics affecting both parents and their children would make more sense, if the pattern shows up so early (and I’ll bet money that, if real,  it shows up well before one month);  but Martha Farah, and the reporter from Nature, Sara Reardon, ARE TOO FUCKING DUMB to realize this.

https://westhunt.wordpress.com/2015/03/31/scanners-live-in-vain/#comment-93791
Correlation between brain volume and IQ is about 0.4 . Shows up clearly in studies with sufficient power.

“poverty affects prenatal environment a lot.” No it does not. “poverty” in this country means having plenty to eat.

The Great IQ Depression: https://westhunt.wordpress.com/2014/03/07/the-great-iq-depression/
We hear that poverty can sap brainpower, reduce frontal lobe function, induce the fantods, etc. But exactly what do we mean by ‘poverty’? If we’re talking about an absolute, rather than relative, standard of living, most of the world today must be in poverty, as well as almost everyone who lived much before the present. Most Chinese are poorer than the official US poverty level, right? The US had fairly rapid economic growth until the last generation or so, so if you go very far back in time, almost everyone was poor, by modern standards. Even those who were considered rich at the time suffered from zero prenatal care, largely useless medicine, tabletless high schools, and slow Internet connections. They had to ride horses that had lousy acceleration and pooped all over the place.

In particular, if all this poverty-gives-you-emerods stuff is true, scholastic achievement should have collapsed in the Great Depression – and with the miracle of epigenetics, most of us should still be suffering those bad effects.

But somehow none of this seems to have gone through the formality of actually happening.
west-hunter  scitariat  commentary  study  org:nat  summary  rant  critique  neuro  neuro-nitgrit  brain-scan  iq  class  correlation  compensation  pop-diff  biodet  behavioral-gen  westminster  experiment  attaq  measure  multi  discussion  ideas  history  early-modern  pre-ww2  usa  gedanken  analogy  comparison  time  china  asia  world  developing-world  economics  growth-econ  medicine  healthcare  epigenetics  troll  aphorism  cycles  obesity  poast  nutrition  hypochondria  explanans 
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
Corrupting cooperation and how anti-corruption strategies may backfire | Nature Human Behaviour
https://images.nature.com/original/nature-assets/nathumbehav/2017/s41562-017-0138/extref/s41562-017-0138-s1.pdf
Exposure to Norms: https://images.nature.com/original/nature-assets/nathumbehav/2017/s41562-017-0138/extref/s41562-017-0138-s1.pdf#page=114
Here we test how exposure to corruption norms affect behavior in our game. We do so by using our exposure score (a mean of the corruption perceptions of the countries the participant has lived in) and the heritage corruption score (a mean of the corruption perceptions of the countries the participant has an ethnic heritage). Since there is no incentive to offer bribes or contribute, except when compelled to do so by punishment, we predict that exposure to norms should primarily affect Leader decisions. Nonetheless, internalized norms may also affect the behavior of players in contributing and bribing.

...

The correlation between the direct exposure and heritage measures of corruption is r = 0.67, p < .001.

...

Then we see that direct exposure to corruption norms results in increased corrupt behavior—i.e. in our Canadian sample, those who have lived in corrupt countries from which they do not derive their heritage behave in more corrupt ways.

hard to interpret

https://twitter.com/Evolving_Moloch/status/884477414100697092
http://psych.ubc.ca/when-less-is-best/

I don't think the solution is to just do nothing. Should look to history for ideas; process of "getting to Denmark" took centuries in NW Euro. Try to replicate and don't expect fast results.

Trust and Bribery: The Role of the Quid Pro Quo and the Link with Crime: http://www.nber.org/papers/w10510
I study data on bribes actually paid by individuals to public officials, viewing the results through a theoretical lens that considers the implications of trust networks. A bond of trust may permit an implicit quid pro quo to substitute for a bribe, which reduces corruption. Appropriate networks are more easily established in small towns, by long-term residents of areas with many other long-term residents, and by individuals in regions with many residents their own age. I confirm that the prevalence of bribery is lower under these circumstances, using the International Crime Victim Surveys. I also find that older people, who have had time to develop a network, bribe less. These results highlight the uphill nature of the battle against corruption faced by policy-makers in rapidly urbanizing countries with high fertility. I show that victims of (other) crimes bribe all types of public officials more than non-victims, and argue that both their victimization and bribery stem from a distrustful environment.

Kinship, Fractionalization and Corruption: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=2847222
The theory of kin selection provides a straightforward justification for norms of nepotism and favoritism among relatives; more subtly, it also implies that the returns to such norms may be influenced by mating practices. Specifically, in societies with high levels of sub-ethnic fractionalization, where endogamous (and consanguineous) mating within kin-group, clan and tribe increases the local relatedness of individuals, the relative returns to norms of nepotism and favoritism are high. In societies with exogamous marriage practices, the relative returns to norms of impartial cooperation with non-relatives and strangers are increased. Using cross-country and within-country regression analyses and a cross-country lab experiment, we provide evidence for this account.

Ethnic favouritism: Not just an African phenomenon: http://voxeu.org/article/ethnic-favouritism-not-just-african-phenomenon
Ethnic favouritism is a global phenomenon
We find robust evidence for ethnic favouritism – ethnographic regions that are the current political leader’s ethnic homeland enjoy 7%-10% more intense night-time light, corresponding to 2%-3% higher regional GDP. Furthermore, we show that ethnic favouritism extends to ethnic groups that are linguistically close to the political leader.

Most significantly, these effects are as strong outside of Africa as they are within, challenging the preconception that ethnic favouritism is mainly or even entirely a sub-Saharan African phenomenon. For example, Bolivian presidents tended to favour areas populated by European descendants and Criollos, largely at the expense of the indigenous population. After the election of Evo Morales, a member of the indigenous Ayamara ethnic group, luminosity in indigenous areas grew substantially. Notably, critics suggest Morales gave special attention to the interests and values of the Ayamara at the expense of other indigenous peoples (e.g. Albro 2010, Postero 2010).

Democratisation is not a panacea
Our results further suggest that, while democratic institutions have a weak tendency to reduce ethnic favouritism, their effect is limited. In particular, a change from autocratic regimes to weak democracies does not seem to reduce ethnic favouritism (and may even increase it).

This result could in part be explained by political leaders’ motivations for engaging in ethnic favouritism. We find that the practice intensifies around election years in which the political leader's office is contested, suggesting that leaders may target policies towards their ethnic homelands to improve their re-election prospects, and not solely out of co-ethnic altruism. To the extent that political leaders engage in ethnic favouritism for electoral purposes, democratisation is not likely to be effective in curbing the practice.

Facebook’s war on free will: https://www.theguardian.com/technology/2017/sep/19/facebooks-war-on-free-will
Though Facebook will occasionally talk about the transparency of governments and corporations, what it really wants to advance is the transparency of individuals – or what it has called, at various moments, “radical transparency” or “ultimate transparency”. The theory holds that the sunshine of sharing our intimate details will disinfect the moral mess of our lives. With the looming threat that our embarrassing information will be broadcast, we’ll behave better. And perhaps the ubiquity of incriminating photos and damning revelations will prod us to become more tolerant of one another’s sins. “The days of you having a different image for your work friends or co-workers and for the other people you know are probably coming to an end pretty quickly,” Zuckerberg has said. “Having two identities for yourself is an example of a lack of integrity.”

The point is that Facebook has a strong, paternalistic view on what’s best for you, and it’s trying to transport you there. “To get people to this point where there’s more openness – that’s a big challenge. But I think we’ll do it,” Zuckerberg has said. He has reason to believe that he will achieve that goal. With its size, Facebook has amassed outsized powers. “In a lot of ways Facebook is more like a government than a traditional company,” Zuckerberg has said. “We have this large community of people, and more than other technology companies we’re really setting policies.”

Facebook and the Destruction of Private Life: http://www.socialmatter.net/2014/12/30/facebook-and-the-destruction-of-private-life/
- HENRY DAMPIER

The key value of privacy, which tends to be lost amid all the technological babble about the concept, is that it makes social cooperation more feasible among people who disagree, share different tastes, or fundamental points of view.

...

This is especially an issue with democracy. The reason why the United States has anonymous voting laws is because without them, people are persecuted for their party affiliations by people with rival party loyalties. This being forgotten, the age of Facebook and similar technologies has opened up ordinary people to this sort of ordinary political persecution. Moderating influences like that of the respect for privacy put a brake on some of the more rapacious, violent aspects of party politics.

...

The impulse for this comes less from the availability of the technology, and more because of the preexisting social trends. When there is a family life, there is communication and closeness within the family.

With more people living without a family life, they go to the public square to get their needs for social validation met. This doesn’t work so well, because strangers have no skin in the life of the atomized individual that only exists as an image on their screens.
study  org:nat  polisci  sociology  government  corruption  law  leviathan  crooked  world  developing-world  policy  cooperate-defect  free-riding  cultural-dynamics  anthropology  multi  twitter  social  commentary  scitariat  public-goodish  institutions  behavioral-econ  org:sci  summary  n-factor  trust  media  social-norms  spreading  equilibrium  🎩  🌞  broad-econ  GT-101  economics  growth-econ  org:edu  microfoundations  open-closed  leaks  canada  anglo  migration  pdf  polarization  longitudinal  social-capital  network-structure  cohesion  social-structure  axelrod  anomie  tribalism  group-level  kinship  econometrics  field-study  sapiens  stylized-facts  divergence  cliometrics  anglosphere  incentives  biodet  the-great-west-whale  populism  roots  putnam-like  behavioral-gen  sex  chart  wealth-of-nations  political-econ  polanyi-marx  eden  path-dependence  variance-components  correlation  assimilation  ethics  org:ngo  econotariat  africa  ethnocentrism  race  democracy  latin-america  asia  news  org:lite 
july 2017 by nhaliday
Genetic and Environmental Contributions to Variance in Age at First Sexual IntercoursePsychological Science - M.P. Dunne, N.G. Martin, D.J. Statham, W.S. Slutske, S.H. Dinwiddie, K.K. Bucholz, P.A.F. Madden, A.C Heath, 1997
Structural equation model fitting found that the genetic contribution to variance was considerably greater among twins aged 40 years or less (72% for males and 49% for females) than for those aged from 41 to 70 years (0%for males and 32% for females) Among the older cohort, there was evidence that somewhat different aspects of the shared social environment influenced age at onset in males and females In a more laissez-faire social climate in recent decades, it is likely that biological and psychological characteristics that are partly under genetic control significantly influence the age at which a person commences sexual activity
study  psychology  social-psych  evopsych  biodet  behavioral-gen  variance-components  gender  gender-diff  sex  sexuality  history  mostly-modern  cold-war  modernity  pdf  piracy  social-norms  life-history  age-generation  shift  correlation  tradition 
july 2017 by nhaliday
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