nhaliday + preprint   178

Comparing within- and between-family polygenic score prediction | bioRxiv
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
OSF | Near and Far Transfer in Cognitive Training: A Second-Order Meta- Analysis
In Models 1 (k = 99) and 2 (k = 119), we investigated the impact of working-memory training on near-transfer (i.e., memory) and far-transfer (e.g., reasoning, speed, and language) measures, respectively, and whether it is mediated by the type of population. Model 3 (k = 233) extended Model 2 by adding six meta-analyses assessing the far-transfer effects of other cognitive-training programs (video-games, music, chess, and exergames). Model 1 showed that working-memory training does induce near transfer, and that the size of this effect is moderated by the type of population. By contrast, Models 2 and 3 highlighted that far-transfer effects are small or null.
study  preprint  psychology  cog-psych  intelligence  generalization  dimensionality  psych-architecture  intervention  enhancement  practice 
8 weeks ago by nhaliday
[1804.04268] Incomplete Contracting and AI Alignment
We suggest that the analysis of incomplete contracting developed by law and economics researchers can provide a useful framework for understanding the AI alignment problem and help to generate a systematic approach to finding solutions. We first provide an overview of the incomplete contracting literature and explore parallels between this work and the problem of AI alignment. As we emphasize, misalignment between principal and agent is a core focus of economic analysis. We highlight some technical results from the economics literature on incomplete contracts that may provide insights for AI alignment researchers. Our core contribution, however, is to bring to bear an insight that economists have been urged to absorb from legal scholars and other behavioral scientists: the fact that human contracting is supported by substantial amounts of external structure, such as generally available institutions (culture, law) that can supply implied terms to fill the gaps in incomplete contracts. We propose a research agenda for AI alignment work that focuses on the problem of how to build AI that can replicate the human cognitive processes that connect individual incomplete contracts with this supporting external structure.
nibble  preprint  org:mat  papers  ai  ai-control  alignment  coordination  contracts  law  economics  interests  culture  institutions  number  context  behavioral-econ  composition-decomposition  rent-seeking  whole-partial-many 
april 2018 by nhaliday
SocArXiv Papers | Gender, Religion, and Values: A Cross-National Examination of Moral Justification and Partisanship
Using data from a diverse set of 56 countries in the World Values Survey (N=85,181), I find that religiousness suppresses what would otherwise be larger and more consistent gender differences in values among Christians. Among most other groups, including Jews, Hindus, Buddhists, Taoists, and Muslims in non-Muslim contexts, religiousness does not greatly alter gender differences in values. However, among Muslims in Muslim-majority contexts—where men tend to be more religious than women—religiousness amplifies what would otherwise be smaller gender differences in values. Accordingly, gender differences in values tend to be larger among Muslims than Christians. I conclude that religions are complex and powerful social structures that can complicate group differences in values
study  sociology  preprint  general-survey  poll  values  correlation  gender  gender-diff  politics  ideology  religion  christianity  islam  trade  world  developing-world  egalitarianism-hierarchy  inequality  prejudice  westminster  identity-politics  theos  usa  europe  expression-survival  the-great-west-whale  rot 
april 2018 by nhaliday
[1410.0369] The Universe of Minds
kinda dumb, don't think this guy is anywhere close to legit (e.g., he claims set of mind designs is countable, but gives no actual reason to believe that)
papers  preprint  org:mat  ratty  miri-cfar  ai  intelligence  philosophy  logic  software  cs  computation  the-self 
march 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
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.


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


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

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
[1509.02504] Electric charge in hyperbolic motion: The early history and other geometrical aspects
We revisit the early work of Minkowski and Sommerfeld concerning hyperbolic motion, and we describe some geometrical aspects of the electrodynamic interaction. We discuss the advantages of a time symmetric formulation in which the material points are replaced by infinitesimal length elements.

SPACE AND TIME: An annotated, illustrated edition of Hermann Minkowski's revolutionary essay: http://web.mit.edu/redingtn/www/netadv/SP20130311.html
nibble  preprint  papers  org:mat  physics  electromag  relativity  exposition  history  mostly-modern  pre-ww2  science  the-trenches  discovery  intricacy  classic  explanation  einstein  giants  plots  manifolds  article  multi  liner-notes  org:junk  org:edu  absolute-relative 
november 2017 by nhaliday
We find that supporters of the major parties (Labour, the Conservatives and the Liberal Democrats) have substantively different personality traits. Moreover, we show that those not identifying with any party, who are close to holding the majority, are similar to those identifying with the Conservatives. We show that these results are robust to controlling for cognitive skills and parental party preferences, and to estimation on a subsample of siblings. The relationship between personality traits and party identification is stable across birth cohorts.

Table 2: Big Five Personality Traits: Predictions.
Figure 3: Relationship between personality traits and stable party identification

Conservative core supporters are antagonistic towards others (low Agreeableness), they are closed to new experiences (low Openness), they are energetic and enthusiastic (high Extraversion), they are goal-orientated (high Conscientiousness), and they are even-tempered (low Neuroticism).

In contrast, the core supporters of the Labour Party have a pro-social and communal attitude (high Agreeableness), they are open to new experiences and ideas (high Openness), but they are more anxious, tense and discontented (high Neuroticism) and less prone to goal-directed behavior (low Conscientiousness). The core supporters of the Liberal Democrats have similar traits to the typical Labour supporters with two exceptions. First, they do not show any particular tendency towards pro-social and communal attitudes (insignificant Agreeableness). Second, they are more reserved and introverted than the more extraverted supporters of either the Conservatives or Labour (low Extraversion).

Psychological and Personality Profiles of Political Extremists: https://arxiv.org/pdf/1704.00119.pdf
We revisit the debate over the appeal of extremism in the U.S. context by comparing publicly available Twitter messages written by over 355,000 political extremist followers with messages written by non-extremist U.S. users. Analysis of text-based psychological indicators supports the moral foundation theory which identifies emotion as a critical factor in determining political orientation of individuals. Extremist followers also differ from others in four of the Big Five personality traits.

Fig. 2. Comparing psychological profiles of the followers of moderate and extremist single-issue groups, compared to random users.

Overall, the differences in psychological profile between followers of extremist and moderate groups is much larger for left-wing extremists (environmentalists) than right-wing (anti-abortion and anti-immigrant).

Fig. 3. Big Five Personality Profiles.

Results show that extremist followers (whether left or right) are less agreeable, less neurotic, and more open than nonextremists.

Ideology as Motivated Cultural Cognition: How Culture Translates Personality into Policy Preferences: https://www.psa.ac.uk/sites/default/files/conference/papers/2017/Ideology%20as%20Motivated%20Cultural%20Cognition.pdf
This paper summarises the results of a quantitative analysis testing the theory that culture acts as an intermediary in the relationship between individual perceptual tendencies and political orientation. Political psychologists have long observed that more “left-wing” individuals tend to be more comfortable than “right-wing” individuals with ambiguity, disorder, and uncertainty, to equivocate more readily between conflicting viewpoints, and to be more willing to change their opinions. These traits are often summarised under the blanket term of “open-mindedness”. A recent increase in cross-cultural studies, however, has indicated that these relationships are far less robust, and even reversed, in social contexts outside of North America and Western Europe. The sociological concept of culture may provide an answer to this inconsistency: emergent idea-networks, irreducible to individuals, which nonetheless condition psychological motivations, so that perceptual factors resulting in left-wing preferences in one culture may result in opposing preferences in another. The key is that open-mindedness leads individuals to attack the dominant ideas which they encounter: if prevailing orthodoxies happen to be left-wing, then open minded individuals may become right-wing in protest. Using conditional process analysis of the British Election Study, I find evidence for three specific mechanisms whereby culture interferes with perceptual influences on politics. Conformity to the locally dominant culture mediates these influences, in the sense that open-minded people in Britain are only more left-wing because they are less culturally conformal. This relationship is itself moderated both by cultural group membership and by Philip Converse’s notion of “constraint”, individual-level connectivity between ideas, such that the strength of perceptual influence differs significantly between cultural groups and between levels of constraint to the idea of the political spectrum. Overall, I find compelling evidence for the importance of culture in shaping perceptions of policy choices.
pdf  study  polisci  sociology  politics  ideology  personality  psych-architecture  correlation  britain  coalitions  phalanges  data  things  multi  preprint  psychology  social-psych  cog-psych  culture-war  gnon  🐸  subculture  objective-measure  demographics  org:mat  creative  culture  society  cultural-dynamics  anthropology  hari-seldon  discipline  extra-introversion  stress  individualism-collectivism  expression-survival  values  poll  chart  curiosity 
november 2017 by nhaliday
Stability of the Solar System - Wikipedia
The stability of the Solar System is a subject of much inquiry in astronomy. Though the planets have been stable when historically observed, and will be in the short term, their weak gravitational effects on one another can add up in unpredictable ways. For this reason (among others) the Solar System is chaotic,[1] and even the most precise long-term models for the orbital motion of the Solar System are not valid over more than a few tens of millions of years.[2]

The Solar System is stable in human terms, and far beyond, given that it is unlikely any of the planets will collide with each other or be ejected from the system in the next few billion years,[3] and the Earth's orbit will be relatively stable.[4]

Since Newton's law of gravitation (1687), mathematicians and astronomers (such as Laplace, Lagrange, Gauss, Poincaré, Kolmogorov, Vladimir Arnold and Jürgen Moser) have searched for evidence for the stability of the planetary motions, and this quest led to many mathematical developments, and several successive 'proofs' of stability of the Solar System.[5]


The planets' orbits are chaotic over longer timescales, such that the whole Solar System possesses a Lyapunov time in the range of 2–230 million years.[3] In all cases this means that the position of a planet along its orbit ultimately becomes impossible to predict with any certainty (so, for example, the timing of winter and summer become uncertain), but in some cases the orbits themselves may change dramatically. Such chaos manifests most strongly as changes in eccentricity, with some planets' orbits becoming significantly more—or less—elliptical.[7]

Is the Solar System Stable?: https://www.ias.edu/ideas/2011/tremaine-solar-system

Is the Solar System Stable?: https://arxiv.org/abs/1209.5996
nibble  wiki  reference  article  physics  mechanics  space  gravity  flux-stasis  uncertainty  robust  perturbation  math  dynamical  math.DS  volo-avolo  multi  org:edu  org:inst  papers  preprint  time  data  org:mat 
november 2017 by nhaliday
[1709.01149] Biotechnology and the lifetime of technical civilizations
The number of people able to end Earth's technical civilization has heretofore been small. Emerging dual-use technologies, such as biotechnology, may give similar power to thousands or millions of individuals. To quantitatively investigate the ramifications of such a marked shift on the survival of both terrestrial and extraterrestrial technical civilizations, this paper presents a two-parameter model for civilizational lifespans, i.e. the quantity L in Drake's equation for the number of communicating extraterrestrial civilizations. One parameter characterizes the population lethality of a civilization's biotechnology and the other characterizes the civilization's psychosociology. L is demonstrated to be less than the inverse of the product of these two parameters. Using empiric data from Pubmed to inform the biotechnology parameter, the model predicts human civilization's median survival time as decades to centuries, even with optimistic psychosociological parameter values, thereby positioning biotechnology as a proximate threat to human civilization. For an ensemble of civilizations having some median calculated survival time, the model predicts that, after 80 times that duration, only one in 1024 civilizations will survive -- a tempo and degree of winnowing compatible with Hanson's "Great Filter." Thus, assuming that civilizations universally develop advanced biotechnology, before they become vigorous interstellar colonizers, the model provides a resolution to the Fermi paradox.
preprint  article  gedanken  threat-modeling  risk  biotech  anthropic  fermi  ratty  hanson  models  xenobio  space  civilization  frontier  hmm  speedometer  society  psychology  social-psych  anthropology  cultural-dynamics  disease  parasites-microbiome  maxim-gun  prepping  science-anxiety  technology  magnitude  scale  data  prediction  speculation  ideas  🌞  org:mat  study  offense-defense  arms  unintended-consequences  spreading  explanans  sociality  cybernetics 
october 2017 by nhaliday
[1709.06560] Deep Reinforcement Learning that Matters
I’ve been experimenting w/ various kinds of value function approaches to RL lately, and its striking how primitive and bad things seem to be
At first I thought it was just that my code sucks, but then I played with the OpenAI baselines and nope, it’s the children that are wrong.
And now, what comes across my desk but this fantastic paper: (link: https://arxiv.org/abs/1709.06560) arxiv.org/abs/1709.06560 How long until the replication crisis hits AI?

Seriously I’m not blown away by the PhDs’ records over the last 30 years. I bet you’d get better payoff funding eccentrics and amateurs.
There are essentially zero fundamentally new ideas in AI, the papers are all grotesquely hyperparameter tuned, nobody knows why it works.

Deep Reinforcement Learning Doesn't Work Yet: https://www.alexirpan.com/2018/02/14/rl-hard.html
Once, on Facebook, I made the following claim.

Whenever someone asks me if reinforcement learning can solve their problem, I tell them it can’t. I think this is right at least 70% of the time.
papers  preprint  machine-learning  acm  frontier  speedometer  deep-learning  realness  replication  state-of-art  survey  reinforcement  multi  twitter  social  discussion  techtariat  ai  nibble  org:mat  unaffiliated  ratty  acmtariat  liner-notes  critique  sample-complexity  cost-benefit  todo 
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.


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:

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
Global determinants of navigation ability | bioRxiv
Using a mobile-based virtual reality navigation task, we measured spatial navigation ability in more than 2.5 million people globally. Using a clustering approach, we find that navigation ability is not smoothly distributed globally but clustered into five distinct yet geographically related groups of countries. Furthermore, the economic wealth of a nation (Gross Domestic Product per capita) was predictive of the average navigation ability of its inhabitants and gender inequality (Gender Gap Index) was predictive of the size of performance difference between males and females.

- Figure 1 has the meat
- gender gap larger in richer/better-performing countries
- Anglo and Nordic countries do best (Finnish supremacy wins the day again)
- surprised China doesn't do better, probably a matter of development
- Singapore is close behind the Anglo-Nords tho
- speculation that practice of orienteering (originally Swedish) may be related to Nords doing well
- somewhat weird pattern wrt age
study  bio  preprint  psychology  cog-psych  iq  psychometrics  spatial  navigation  pop-diff  gender  gender-diff  egalitarianism-hierarchy  correlation  wealth  wealth-of-nations  econ-metrics  data  visualization  maps  world  developing-world  marginal  europe  the-great-west-whale  nordic  britain  anglo  usa  anglosphere  china  asia  sinosphere  polis  demographics  age-generation  aging  EU  group-level  regional-scatter-plots  games  simulation 
september 2017 by nhaliday
PRRI: America’s Changing Religious Identity
America, that is, the United States of America, has long been a huge exception for the secularization model. Basically as a society develops and modernizes it becomes more secular. At least that’s the model.


Today everyone is talking about the Pew survey which shows the marginalization of the Anglo-Protestant America which I grew up in. This marginalization is due to secularization broadly, and non-Hispanic whites in particular. You don’t need Pew to tell you this.


Note: Robert Putnam’s American Grace is probably the best book which highlights the complex cultural forces which ushered in the second wave of secularization. The short answer is that the culture wars diminished Christianity in the eyes of liberals.

Explaining Why More Americans Have No Religious Preference: Political Backlash and Generational Succession, 1987-2012: https://www.sociologicalscience.com/articles-vol1-24-423/
the causal direction in the rise of the “Nones” likely runs from political identity as a liberal or conservative to religious identity

The Persistent and Exceptional Intensity of American Religion: A Response to Recent Research: https://osf.io/preprints/socarxiv/xd37b
But we show that rather than religion fading into irrelevance as the secularization thesis would suggest, intense religion—strong affiliation, very frequent practice, literalism, and evangelicalism—is persistent and, in fact, only moderate religion is on the decline in the United States.

As in the U.K., so now too in America: the left establishment is moving towards an open view that orthodox Christians are unfit for office.

i've had the thought that it's a plausible future where traditional notions of theism become implicitly non-white


Some writers and Christian observers deny the flight of young people altogether, but the growing statistics should alarm us enough as Church leaders to do something about the dilemma. My hope in this post is to simply consolidate some of the research (many of the summaries are directly quoted) so you can decide for yourself. I’m going to organize the recent findings in a way that illuminates the problem:

'Christianity as default is gone': the rise of a non-Christian Europe: https://www.theguardian.com/world/2018/mar/21/christianity-non-christian-europe-young-people-survey-religion
In the UK, only 7% of young adults identify as Anglican, fewer than the 10% who categorise themselves as Catholic. Young Muslims, at 6%, are on the brink of overtaking those who consider themselves part of the country’s established church.

Other scholars have disputed the global decline of Christianity, and instead hypothesized of an evolution of Christianity which allows it to not only survive, but actively expand its influence in contemporary societies.

Philip Jenkins hypothesized a "Christian Revolution" in the Southern nations, such as Africa, Asia and Latin America, where instead of facing decline, Christianity is actively expanding. The relevance of Christian teachings in the global South will allow the Christian population in these areas to continually increase, and together with the shrinking of the Western Christian population, will form a "new Christendom" in which the majority of the world's Christian population can be found in the South.[9]
news  org:ngo  data  analysis  database  white-paper  usa  religion  christianity  theos  politics  polisci  coalitions  trends  zeitgeist  demographics  race  latin-america  within-group  northeast  the-south  the-west  asia  migration  gender  sex  sexuality  distribution  visualization  age-generation  diversity  maps  judaism  time-series  protestant-catholic  other-xtian  gender-diff  education  compensation  india  islam  multi  org:rec  pro-rata  gnxp  scitariat  huntington  prediction  track-record  error  big-peeps  statesmen  general-survey  poll  putnam-like  study  sociology  roots  impetus  history  mostly-modern  books  recommendations  summary  stylized-facts  values  twitter  social  discussion  journos-pundits  backup  tradition  gnon  unaffiliated  right-wing  identity-politics  eric-kaufmann  preprint  uniqueness  comparison  similarity  org:lite  video  links  list  survey  internet  life-history  fertility  social-capital  wiki  reference  org:anglo  world  developing-world  europe  EU  britain  rot 
september 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.

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
A combined analysis of genetically correlated traits identifies 107 loci associated with intelligence | bioRxiv
We apply MTAG to three large GWAS: Sniekers et al (2017) on intelligence, Okbay et al. (2016) on Educational attainment, and Hill et al. (2016) on household income. By combining these three samples our functional sample size increased from 78 308 participants to 147 194. We found 107 independent loci associated with intelligence, implicating 233 genes, using both SNP-based and gene-based GWAS. We find evidence that neurogenesis may explain some of the biological differences in intelligence as well as genes expressed in the synapse and those involved in the regulation of the nervous system.


Finally, using an independent sample of 6 844 individuals we were able to predict 7% of intelligence using SNP data alone.
study  bio  preprint  biodet  behavioral-gen  GWAS  genetics  iq  education  compensation  composition-decomposition  🌞  gwern  meta-analysis  genetic-correlation  scaling-up  methodology  correlation  state-of-art  neuro  neuro-nitgrit  dimensionality 
july 2017 by nhaliday
A genome-wide polygenic approach to HIV uncovers link to inflammatory bowel disease and identifies potential novel genetic variants | bioRxiv
We further showed that the genetic overlap between HIV acquisition and schizophrenia is likely driven in part by their shared overlap with cannabis use and sexual behavior.
study  bio  preprint  biodet  behavioral-gen  GWAS  genetic-correlation  correlation  trivia  cocktail  disease  sex  sexuality  drugs  psychiatry  genetics 
june 2017 by nhaliday
Young Men Are Playing Video Games Instead of Getting Jobs. That's OK. (For Now.) - Reason.com
This is like a reversal of the industrious revolution studied in my JEBO paper: new consumption technologies are money cheap but time pricey

participation has changed along an understudied margin of labor supply. I find that “in-and-outs”—men who temporarily leave the labor force—represent a growing fraction of prime age men across multiple data sources and are responsible for roughly one third of the decline in the participation rate since 1977. In-and-outs take short, infrequent breaks out of the labor force in between jobs, but they are otherwise continuously attached to the labor force. Leading explanations for the growing share of permanent labor force dropouts, such as disability, do not apply to in-and-outs. Instead, reduced-form evidence and a structural model of household labor supply both indicate that the rise of in-and-outs reflects a shift in labor supply, largely due to the increasing earnings of men’s partners and the growth of men living with their parents.

Pointer from Tyler Cowen. My thoughts:

1. When we think of labor force participation declining, we think of, say, John Smith, deciding to never work again. What this paper is saying is that the statistics reflect something different. One month Smith takes a break, then next month he gets a job and Tom Jones takes a break.

2. I think we have always had a large number of workers who are not fully employed year round. That is, there have always been a lot of workers who take breaks between jobs. This is common in construction work, for example.

3. I don’t know if this matters for the phenomenon at hand, but we used to have inventory recessions. In those cases, workers would be out of a job for a while, but they would still be in the labor force, because they were waiting to be recalled by the firm that had laid them off.

4. It seems to me that this is an important paper. Re-read the last sentence in the quoted excerpt.

Job outlook growing worse for young American men: https://www.courier-journal.com/story/opinion/contributors/2018/01/02/job-outlook-growing-worse-young-american-men-opinion/996922001/
As one might imagine, the absence of a job, quality education, or spouse has not bred otherwise productive citizens. Multiple studies have found that young men have replaced what would otherwise be working hours with leisure time at a near 1-1 ratio. Erik Hurst, an economist at the University of Chicago, found that young men spent a startling 75 percent of this leisure time playing video games, with many spending more than 30 hours a week gaming and over 5 million Americans spending more than 45 hours per week.

Higher suicide rates, violent crime, and drug addiction among young men have followed. Suicide rates in the United States are at a 30-year high, with men more than three and a half times more likely to take their own lives than women. Around the United States, violent crimes, homicide in particular, has increased in two-thirds of American cities, with overwhelming young male perpetrators driving the increase. A 2015 Brookings Institute study estimated that nearly half of working-age American men who are out of the labor force are using painkillers, daily.

These problems have been “invisible” for too long.

As video games get better, young men work less and play more: http://review.chicagobooth.edu/economics/2017/article/video-games-get-better-young-men-work-less-and-play-more

Why Are Prime-Age Men Vanishing from the Labor Force?: https://www.kansascityfed.org/~/media/files/publicat/econrev/econrevarchive/2018/1q18tuzemen.pdf

Prime-Age Men May Never Return to U.S. Workforce, Fed Paper Says: https://www.bloomberg.com/news/articles/2018-02-23/prime-age-men-may-never-return-to-u-s-workforce-fed-paper-says
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june 2017 by nhaliday
The Genomic Health Of Ancient Hominins | bioRxiv
On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past.

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

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

After controlling for age, BMI, and other variables, knee OA prevalence was 2.1-fold higher (95% confidence interval, 1.5–3.1) in the postindustrial sample than in the early industrial sample. Our results indicate that increases in longevity and BMI are insufficient to explain the approximate doubling of knee OA prevalence that has occurred in the United States since the mid-20th century. Knee OA is thus more preventable than is commonly assumed, but prevention will require research on additional independent risk factors that either arose or have become amplified in the postindustrial era.
study  bio  preprint  sapiens  genetics  biodet  disease  health  history  antiquity  aDNA  farmers-and-foragers  agriculture  anthropology  GWAS  genetic-load  multi  twitter  social  commentary  gwern  dysgenics  trends  mutation  embodied  org:nat  obesity  public-health  epidemiology  🌞  science-anxiety 
june 2017 by nhaliday
Genomic analysis of family data reveals additional genetic effects on intelligence and personality | bioRxiv
Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003520
Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005804

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

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

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

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

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

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

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

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

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

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

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

study  preprint  bio  biodet  behavioral-gen  GWAS  missing-heritability  QTL  🌞  scaling-up  replication  iq  education  spearhead  sib-study  multi  west-hunter  scitariat  genetic-load  mutation  medicine  meta:medicine  stylized-facts  ratty  unaffiliated  commentary  rhetoric  wonkish  genetics  genomics  race  pop-structure  poast  population-genetics  psychiatry  aphorism  homo-hetero  generalization  scale  state-of-art  ssc  reddit  social  summary  gwern  methodology  personality  britain  anglo  enhancement  roots  s:*  2017  data  visualization  database  let-me-see  bioinformatics  news  org:rec  org:anglo  org:biz  track-record  prediction  identity-politics  pop-diff  recent-selection  westminster  inequality  egalitarianism-hierarchy  high-dimension  applications  dimensionality  ideas  no-go  volo-avolo  magnitude  variance-components  GCTA  tradeoffs  counter-revolution  org:mat  dysgenics  paternal-age  distribution  chart  abortion-contraception-embryo 
june 2017 by nhaliday
[1705.08807] When Will AI Exceed Human Performance? Evidence from AI Experts
Researchers predict AI will outperform humans in many activities in the next ten years, such as translating languages (by 2024), writing high-school essays (by 2026), driving a truck (by 2027), working in retail (by 2031), writing a bestselling book (by 2049), and working as a surgeon (by 2053). Researchers believe there is a 50% chance of AI outperforming humans in all tasks in 45 years and of automating all human jobs in 120 years, with Asian respondents expecting these dates much sooner than North Americans.

study  preprint  science  meta:science  technology  ai  automation  labor  ai-control  risk  futurism  poll  expert  usa  asia  trends  hmm  idk  definite-planning  frontier  ideas  prediction  innovation  china  sinosphere  multi  reddit  social  commentary  ssc  speedometer  flux-stasis  ratty  expert-experience  org:mat  singularity  optimism  pessimism 
may 2017 by nhaliday
[1705.03394] That is not dead which can eternal lie: the aestivation hypothesis for resolving Fermi's paradox
If a civilization wants to maximize computation it appears rational to aestivate until the far future in order to exploit the low temperature environment: this can produce a 10^30 multiplier of achievable computation. We hence suggest the "aestivation hypothesis": the reason we are not observing manifestations of alien civilizations is that they are currently (mostly) inactive, patiently waiting for future cosmic eras. This paper analyzes the assumptions going into the hypothesis and how physical law and observational evidence constrain the motivations of aliens compatible with the hypothesis.


simpler explanation (just different math for Drake equation):
Dissolving the Fermi Paradox: http://www.jodrellbank.manchester.ac.uk/media/eps/jodrell-bank-centre-for-astrophysics/news-and-events/2017/uksrn-slides/Anders-Sandberg---Dissolving-Fermi-Paradox-UKSRN.pdf
Overall the argument is that point estimates should not be shoved into a Drake equation and then multiplied by each, as that requires excess certainty and masks much of the ambiguity of our knowledge about the distributions. Instead, a Bayesian approach should be used, after which the fate of humanity looks much better. Here is one part of the presentation:

Life Versus Dark Energy: How An Advanced Civilization Could Resist the Accelerating Expansion of the Universe: https://arxiv.org/abs/1806.05203
The presence of dark energy in our universe is causing space to expand at an accelerating rate. As a result, over the next approximately 100 billion years, all stars residing beyond the Local Group will fall beyond the cosmic horizon and become not only unobservable, but entirely inaccessible, thus limiting how much energy could one day be extracted from them. Here, we consider the likely response of a highly advanced civilization to this situation. In particular, we argue that in order to maximize its access to useable energy, a sufficiently advanced civilization would chose to expand rapidly outward, build Dyson Spheres or similar structures around encountered stars, and use the energy that is harnessed to accelerate those stars away from the approaching horizon and toward the center of the civilization. We find that such efforts will be most effective for stars with masses in the range of M∼(0.2−1)M⊙, and could lead to the harvesting of stars within a region extending out to several tens of Mpc in radius, potentially increasing the total amount of energy that is available to a future civilization by a factor of several thousand. We also discuss the observable signatures of a civilization elsewhere in the universe that is currently in this state of stellar harvesting.
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may 2017 by nhaliday
Estimating the number of unseen variants in the human genome
To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small (∼350) and does not differ much among the different populations; our data show that, subject to sequence accuracy, the 1000 Genomes Project is likely to find most of these common variants and a high proportion of the rarer ones (frequency between 0.1 and 1%). The data reveal a rule of diminishing returns: a small number of individuals (∼150) is sufficient to identify 80% of variants with a frequency of at least 0.1%, while a much larger number (> 3,000 individuals) is necessary to find all of those variants.

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

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

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

Singleton Variants Dominate the Genetic Architecture of Human Gene Expression: https://www.biorxiv.org/content/early/2017/12/15/219238
study  sapiens  genetics  genomics  population-genetics  bioinformatics  data  prediction  cost-benefit  scale  scaling-up  org:nat  QTL  methodology  multi  pdf  curvature  convexity-curvature  nonlinearity  measurement  magnitude  🌞  distribution  missing-heritability  pop-structure  genetic-load  mutation  wiki  reference  article  structure  bio  preprint  biodet  variance-components  nibble  chart 
may 2017 by nhaliday
Soft sweeps are the dominant mode of adaptation in the human genome | bioRxiv
Detection of 2000 instances of recent human selection, half of which are specific to individual human populations, and many of which affect the central nervous system. Note this doesn’t cover polygenic selection, so it’s a very loose lower bound on how much recent human evolution there has been.

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

Cochran, John Hawks, and I were involved in some of this work, and we all thought immediately without any discussion that the intermediate frequency sweeps must reflect heterozygote advantage.
study  preprint  bio  sapiens  recent-selection  genetics  selection  stylized-facts  evolution  genomics  GWAS  🌞  population-genetics  gwern  methodology  multi  west-hunter  explanation  gene-flow  scitariat  hetero-advantage  genetic-load  pop-structure  race  europe  africa  migration  gene-drift 
may 2017 by nhaliday
Places and Preferences: A Longitudinal Analysis of Self-Selection and Contextual Effects | British Journal of Political Science | Cambridge Core
preferences -> place, not place -> preferences (mostly)
Cosmopolitan immigration attitudes in Europe's large cities: Adaptation or selection: https://www.dropbox.com/s/lb3yrsdlhpxprfs/RahsaanMaxwellAPSACosmopolitanImmigrationCities.pdf?dl=0
The myth of London exceptionalism: https://quarterly.demos.co.uk/article/issue-5/ukip-in-london/
London is not as invulnerable to the appeal of UKIP as commonly reported, finds new research from Eric Kaufmann.

Are White British Londoners more accepting of immigration than White British elsewhere? The British Election Study (BES)’s 2015 panel survey asks whether immigration enriches or undermines cultural life. 34.7 per cent of White British outside London say immigration strongly undermines cultural life. But so do 34.4 per cent of White British Londoners. Not much difference there. 44 per cent of White Brits outside London want to leave the EU, but so do 42.3 per cent of White British Londoners. Again, not much in it.


Finally, when we control for a fuller range of demographic and attitudinal characteristics, as in figure 4, London and the South East emerge as significantly more likely than the rest of England and Wales to have voted UKIP in 2014, according to the BES.

Cosmopolitan cities and their country cousins – UK in a changing Europe: http://ukandeu.ac.uk/london-voted-leave-or-why-local-differences-in-populist-right-voting-are-overstated/
study  sociology  politics  polisci  ideology  elections  data  correlation  null-result  confounding  endo-exo  migration  causation  stylized-facts  selection  britain  urban  polarization  longitudinal  context  intervention  roots  piracy  pdf  class-warfare  multi  eric-kaufmann  brexit  trust  social-capital  race  demographics  org:ngo  summary  values  poll  dropbox  phalanges  geography  wonkish  analysis  variance-components  chart  populism  nationalism-globalism  org:edu  org:anglo  psychology  social-psych  org:mag  news  endogenous-exogenous  preprint  urban-rural  hari-seldon  sentiment 
may 2017 by nhaliday
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