nhaliday + org:nat   232

An adaptability limit to climate change due to heat stress
Despite the uncertainty in future climate-change impacts, it is often assumed that humans would be able to adapt to any possible warming. Here we argue that heat stress imposes a robust upper limit to such adaptation. Peak heat stress, quantified by the wet-bulb temperature TW, is surprisingly similar across diverse climates today. TW never exceeds 31 °C. Any exceedence of 35 °C for extended periods should induce hyperthermia in humans and other mammals, as dissipation of metabolic heat becomes impossible. While this never happens now, it would begin to occur with global-mean warming of about 7 °C, calling the habitability of some regions into question. With 11–12 °C warming, such regions would spread to encompass the majority of the human population as currently distributed. Eventual warmings of 12 °C are possible from fossil fuel burning. One implication is that recent estimates of the costs of unmitigated climate change are too low unless the range of possible warming can somehow be narrowed. Heat stress also may help explain trends in the mammalian fossil record.

Trajectories of the Earth System in the Anthropocene: http://www.pnas.org/content/early/2018/07/31/1810141115
We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a “Hothouse Earth” pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be.
study  org:nat  environment  climate-change  humanity  existence  risk  futurism  estimate  physics  thermo  prediction  temperature  nature  walls  civilization  flexibility  rigidity  embodied  multi  manifolds  plots  equilibrium  phase-transition  oscillation  comparison  complex-systems  earth 
august 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
High male sexual investment as a driver of extinction in fossil ostracods | Nature
Sexual selection favours traits that confer advantages in the competition for mates. In many cases, such traits are costly to produce and maintain, because the costs help to enforce the honesty of these signals and cues1. Some evolutionary models predict that sexual selection also produces costs at the population level, which could limit the ability of populations to adapt to changing conditions and thus increase the risk of extinction2,3,4.
study  org:nat  bio  evolution  selection  sex  competition  cost-benefit  unintended-consequences  signaling  existence  gender  gender-diff  empirical  branches  rot  modernity  fertility  intervention  explanans  humility  status  matching  ranking  ratty  hanson 
april 2018 by nhaliday
Prisoner's dilemma - Wikipedia
caveat to result below:
An extension of the IPD is an evolutionary stochastic IPD, in which the relative abundance of particular strategies is allowed to change, with more successful strategies relatively increasing. This process may be accomplished by having less successful players imitate the more successful strategies, or by eliminating less successful players from the game, while multiplying the more successful ones. It has been shown that unfair ZD strategies are not evolutionarily stable. The key intuition is that an evolutionarily stable strategy must not only be able to invade another population (which extortionary ZD strategies can do) but must also perform well against other players of the same type (which extortionary ZD players do poorly, because they reduce each other's surplus).[14]

Theory and simulations confirm that beyond a critical population size, ZD extortion loses out in evolutionary competition against more cooperative strategies, and as a result, the average payoff in the population increases when the population is bigger. In addition, there are some cases in which extortioners may even catalyze cooperation by helping to break out of a face-off between uniform defectors and win–stay, lose–switch agents.[8]

Nature boils down to a few simple concepts.

Haters will point out that I oversimplify. The haters are wrong. I am good at saying a lot with few words. Nature indeed boils down to a few simple concepts.

In life, you can either cooperate or defect.

Used to be that defection was the dominant strategy, say in the time when the Roman empire started to crumble. Everybody complained about everybody and in the end nothing got done. Then came Jesus, who told people to be loving and cooperative, and boom: 1800 years later we get the industrial revolution.

Because of Jesus we now find ourselves in a situation where cooperation is the dominant strategy. A normie engages in a ton of cooperation: with the tax collector who wants more and more of his money, with schools who want more and more of his kid’s time, with media who wants him to repeat more and more party lines, with the Zeitgeist of the Collective Spirit of the People’s Progress Towards a New Utopia. Essentially, our normie is cooperating himself into a crumbling Western empire.

Turns out that if everyone blindly cooperates, parasites sprout up like weeds until defection once again becomes the standard.

The point of a post-Christian religion is to once again create conditions for the kind of cooperation that led to the industrial revolution. This necessitates throwing out undead Christianity: you do not blindly cooperate. You cooperate with people that cooperate with you, you defect on people that defect on you. Christianity mixed with Darwinism. God and Gnon meet.

This also means we re-establish spiritual hierarchy, which, like regular hierarchy, is a prerequisite for cooperation. It is this hierarchical cooperation that turns a household into a force to be reckoned with, that allows a group of men to unite as a front against their enemies, that allows a tribe to conquer the world. Remember: Scientology bullied the Cathedral’s tax department into submission.

With a functioning hierarchy, men still gossip, lie and scheme, but they will do so in whispers behind closed doors. In your face they cooperate and contribute to the group’s wellbeing because incentives are thus that contributing to group wellbeing heightens status.

Without a functioning hierarchy, men gossip, lie and scheme, but they do so in your face, and they tell you that you are positively deluded for accusing them of gossiping, lying and scheming. Seeds will not sprout in such ground.

Spiritual dominance is established in the same way any sort of dominance is established: fought for, taken. But the fight is ritualistic. You can’t force spiritual dominance if no one listens, or if you are silenced the ritual is not allowed to happen.

If one of our priests is forbidden from establishing spiritual dominance, that is a sure sign an enemy priest is in better control and has vested interest in preventing you from establishing spiritual dominance..

They defect on you, you defect on them. Let them suffer the consequences of enemy priesthood, among others characterized by the annoying tendency that very little is said with very many words.

To recap, we started with a secular definition of Logos and noted that its telos is existence. Given human nature, game theory and the power of cooperation, the highest expression of that telos is freely chosen universal love, tempered by constant vigilance against defection while maintaining compassion for the defectors and forgiving those who repent. In addition, we must know the telos in order to fulfill it.

In Christian terms, looks like we got over half of the Ten Commandments (know Logos for the First, don’t defect or tempt yourself to defect for the rest), the importance of free will, the indestructibility of evil (group cooperation vs individual defection), loving the sinner and hating the sin (with defection as the sin), forgiveness (with conditions), and love and compassion toward all, assuming only secular knowledge and that it’s good to exist.

Iterated Prisoner's Dilemma is an Ultimatum Game: http://infoproc.blogspot.com/2012/07/iterated-prisoners-dilemma-is-ultimatum.html
The history of IPD shows that bounded cognition prevented the dominant strategies from being discovered for over over 60 years, despite significant attention from game theorists, computer scientists, economists, evolutionary biologists, etc. Press and Dyson have shown that IPD is effectively an ultimatum game, which is very different from the Tit for Tat stories told by generations of people who worked on IPD (Axelrod, Dawkins, etc., etc.).


For evolutionary biologists: Dyson clearly thinks this result has implications for multilevel (group vs individual selection):
... Cooperation loses and defection wins. The ZD strategies confirm this conclusion and make it sharper. ... The system evolved to give cooperative tribes an advantage over non-cooperative tribes, using punishment to give cooperation an evolutionary advantage within the tribe. This double selection of tribes and individuals goes way beyond the Prisoners' Dilemma model.

implications for fractionalized Europe vis-a-vis unified China?

and more broadly does this just imply we're doomed in the long run RE: cooperation, morality, the "good society", so on...? war and group-selection is the only way to get a non-crab bucket civilization?

Iterated Prisoner’s Dilemma contains strategies that dominate any evolutionary opponent:


analogy for ultimatum game: the state gives the demos a bargain take-it-or-leave-it, and...if the demos refuses...violence?

The nature of human altruism: http://sci-hub.tw/https://www.nature.com/articles/nature02043
- Ernst Fehr & Urs Fischbacher

Some of the most fundamental questions concerning our evolutionary origins, our social relations, and the organization of society are centred around issues of altruism and selfishness. Experimental evidence indicates that human altruism is a powerful force and is unique in the animal world. However, there is much individual heterogeneity and the interaction between altruists and selfish individuals is vital to human cooperation. Depending on the environment, a minority of altruists can force a majority of selfish individuals to cooperate or, conversely, a few egoists can induce a large number of altruists to defect. Current gene-based evolutionary theories cannot explain important patterns of human altruism, pointing towards the importance of both theories of cultural evolution as well as gene–culture co-evolution.


Why are humans so unusual among animals in this respect? We propose that quantitatively, and probably even qualitatively, unique patterns of human altruism provide the answer to this question. Human altruism goes far beyond that which has been observed in the animal world. Among animals, fitness-reducing acts that confer fitness benefits on other individuals are largely restricted to kin groups; despite several decades of research, evidence for reciprocal altruism in pair-wise repeated encounters4,5 remains scarce6–8. Likewise, there is little evidence so far that individual reputation building affects cooperation in animals, which contrasts strongly with what we find in humans. If we randomly pick two human strangers from a modern society and give them the chance to engage in repeated anonymous exchanges in a laboratory experiment, there is a high probability that reciprocally altruistic behaviour will emerge spontaneously9,10.

However, human altruism extends far beyond reciprocal altruism and reputation-based cooperation, taking the form of strong reciprocity11,12. Strong reciprocity is a combination of altruistic rewarding, which is a predisposition to reward others for cooperative, norm-abiding behaviours, and altruistic punishment, which is a propensity to impose sanctions on others for norm violations. Strong reciprocators bear the cost of rewarding or punishing even if they gain no individual economic benefit whatsoever from their acts. In contrast, reciprocal altruists, as they have been defined in the biological literature4,5, reward and punish only if this is in their long-term self-interest. Strong reciprocity thus constitutes a powerful incentive for cooperation even in non-repeated interactions and when reputation gains are absent, because strong reciprocators will reward those who cooperate and punish those who defect.


We will show that the interaction between selfish and strongly reciprocal … [more]
concept  conceptual-vocab  wiki  reference  article  models  GT-101  game-theory  anthropology  cultural-dynamics  trust  cooperate-defect  coordination  iteration-recursion  sequential  axelrod  discrete  smoothness  evolution  evopsych  EGT  economics  behavioral-econ  sociology  new-religion  deep-materialism  volo-avolo  characterization  hsu  scitariat  altruism  justice  group-selection  decision-making  tribalism  organizing  hari-seldon  theory-practice  applicability-prereqs  bio  finiteness  multi  history  science  social-science  decision-theory  commentary  study  summary  giants  the-trenches  zero-positive-sum  🔬  bounded-cognition  info-dynamics  org:edge  explanation  exposition  org:nat  eden  retention  long-short-run  darwinian  markov  equilibrium  linear-algebra  nitty-gritty  competition  war  explanans  n-factor  europe  the-great-west-whale  occident  china  asia  sinosphere  orient  decentralized  markets  market-failure  cohesion  metabuch  stylized-facts  interdisciplinary  physics  pdf  pessimism  time  insight  the-basilisk  noblesse-oblige  the-watchers  ideas  l 
march 2018 by nhaliday
Altruism in a volatile world | Nature
The evolution of altruism—costly self-sacrifice in the service of others—has puzzled biologists1 since The Origin of Species. For half a century, attempts to understand altruism have developed around the concept that altruists may help relatives to have extra offspring in order to spread shared genes2. This theory—known as inclusive fitness—is founded on a simple inequality termed Hamilton’s rule2. However, explanations of altruism have typically not considered the stochasticity of natural environments, which will not necessarily favour genotypes that produce the greatest average reproductive success3,4. Moreover, empirical data across many taxa reveal associations between altruism and environmental stochasticity5,6,7,8, a pattern not predicted by standard interpretations of Hamilton’s rule. Here we derive Hamilton’s rule with explicit stochasticity, leading to new predictions about the evolution of altruism. We show that altruists can increase the long-term success of their genotype by reducing the temporal variability in the number of offspring produced by their relatives. Consequently, costly altruism can evolve even if it has a net negative effect on the average reproductive success of related recipients. The selective pressure on volatility-suppressing altruism is proportional to the coefficient of variation in population fitness, and is therefore diminished by its own success. Our results formalize the hitherto elusive link between bet-hedging and altruism4,9,10,11, and reveal missing fitness effects in the evolution of animal societies.
study  bio  evolution  altruism  kinship  stylized-facts  models  intricacy  random  signal-noise  time  order-disorder  org:nat  EGT  cooperate-defect  population-genetics  moments  expectancy  multiplicative  additive 
march 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]
biodet  deep-materialism  new-religion  evolution  eden  gender  gender-diff  concept  jargon  wiki  reference  bio  roots  explanans  🌞  ideas  EGT  sex  analysis  things  phalanges  matching  parenting  water  competition  egalitarianism-hierarchy  ranking  multi  study  org:nat  nature  meta-analysis  survey  solid-study  male-variability  darwinian  empirical  realness  sapiens  models  evopsych  legacy  investing  uncertainty  outcome-risk  decision-theory  pdf  life-history  chart  accelerationism  horror  capital  capitalism  similarity  analogy  land  gnon  🐸  europe  the-great-west-whale  industrial-revolution  science  kinship  n-factor  speculation  personality  creative  pop-diff  curiosity  altruism  cooperate-defect  anthropology  cultural-dynamics  civil-liberty  recent-selection  technocracy  frontier  futurism  prediction  quotes  aphorism  religion  theos  enhancement  biotech  revolution  insight  history  early-modern  gallic  philosophy  enlightenment-renaissance-restoration-reformation  ci 
january 2018 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.


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
What Does a “Normal” Human Genome Look Like? | Science
So, what have our first glimpses of variation in the genomes of generally healthy people taught us? First, balancing selection, the evolutionary process that favors genetic diversification rather than the fixation of a single “best” variant, appears to play a minor role outside the immune system. Local adaptation, which accounts for variation in traits such as pigmentation, dietary specialization, and susceptibility to particular pathogens is also a second-tier player. What is on the top tier? Increasingly, the answer appears to be mutations that are “deleterious” by biochemical or standard evolutionary criteria. These mutations, as has long been appreciated, overwhelmingly make up the most abundant form of nonneutral variation in all genomes. A model for human genetic individuality is emerging in which there actually is a “wild-type” human genome—one in which most genes exist in an evolutionarily optimized form. There just are no “wild-type” humans: We each fall short of this Platonic ideal in our own distinctive ways.
article  essay  org:nat  🌞  bio  biodet  genetics  genomics  mutation  genetic-load  QTL  evolution  sapiens  survey  summary  coding-theory  enhancement  signal-noise  egalitarianism-hierarchy  selection  tradeoffs  immune  recent-selection  perturbation  nibble  ideas  forms-instances 
november 2017 by nhaliday
Measles and immunological amnesia | West Hunter
A new paper in Science , by Michael Mina et al,  strongly suggests that measles messes up your immunological defenses for two or three years. This is the likely explanation for the fact that measles inoculation causes much greater decreases in child morbidity and mortality than you’d expect from preventing the deaths directly due to measles infection. The thought is that measles whacks the cells that carry immunological memory, leaving the kid ripe for reinfections.  I think there can be a similar effect with anti-cancer chemotherapy.

If correct, this means that measles is much nastier than previously thought. It must have played a significant role in the demographic collapse of long-isolated peoples (such as the Amerindians). Its advent may have played a role in the population decrease associated with the decline of the Classical world.  Even though it is relatively new (having split off from rinderpest a couple of thousand years ago) strong selection for resistance may have  favored some fairly expensive genetic defenses (something like sickle-cell) in Eurasian populations.

We already know of quite a few complex side effects of infectious disease, such the different kind of immunosuppression we see with AIDs, Burkitt’s lymphoma hitting kids with severe Epstein-Barr infections followed by malaria, acute dengue fever that requires a previous infection by a different strain of dengue, etc: there may well be other important interactions and side effects, news of which has not yet come to Harvard.
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october 2017 by nhaliday
Genome Editing
This collection of articles from the Nature Research journals provides an overview of current progress in developing targeted genome editing technologies. A selection of protocols for using and adapting these tools in your own lab is also included.
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october 2017 by nhaliday
Of mice and men: why animal trial results don’t always translate to humans
It showed that of the most-cited animal studies in prestigious scientific journals, such as Nature and Cell, only 37% were replicated in subsequent human randomised trials and 18% were contradicted in human trials. It is safe to assume that less-cited animal studies in lesser journals would have an even lower strike rate.
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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
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september 2017 by nhaliday
Mechanisms of microbial traversal of the blood–brain barrier
A journey into the brain: insight into how bacterial pathogens cross blood–brain barriers: http://sci-hub.tw/10.1038/nrmicro.2016.178
How do extracellular pathogens cross the blood-brain barrier?: https://www.ncbi.nlm.nih.gov/pubmed/11973156
Defense at the border: the blood–brain barrier versus bacterial foreigners: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589978/
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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.

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.
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august 2017 by nhaliday
Predicting the outcomes of organic reactions via machine learning: are current descriptors sufficient? | Scientific Reports
As machine learning/artificial intelligence algorithms are defeating chess masters and, most recently, GO champions, there is interest – and hope – that they will prove equally useful in assisting chemists in predicting outcomes of organic reactions. This paper demonstrates, however, that the applicability of machine learning to the problems of chemical reactivity over diverse types of chemistries remains limited – in particular, with the currently available chemical descriptors, fundamental mathematical theorems impose upper bounds on the accuracy with which raction yields and times can be predicted. Improving the performance of machine-learning methods calls for the development of fundamentally new chemical descriptors.
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july 2017 by nhaliday
National hiring experiments reveal 2:1 faculty preference for women on STEM tenure track
Here we report five hiring experiments in which faculty evaluated hypothetical female and male applicants, using systematically varied profiles disguising identical scholarship, for assistant professorships in biology, engineering, economics, and psychology. Contrary to prevailing assumptions, men and women faculty members from all four fields preferred female applicants 2:1 over identically qualified males with matching lifestyles (single, married, divorced), with the exception of male economists, who showed no gender preference. Comparing different lifestyles revealed that women preferred divorced mothers to married fathers and that men preferred mothers who took parental leaves to mothers who did not.

Double-blind review favours increased representation of female authors: http://www.sciencedirect.com/science/article/pii/S0169534707002704
Double-blind peer review, in which neither author nor reviewer identity are revealed, is rarely practised in ecology or evolution journals. However, in 2001, double-blind review was introduced by the journal Behavioral Ecology. Following this policy change, there was a significant increase in female first-authored papers, a pattern not observed in a very similar journal that provides reviewers with author information. No negative effects could be identified, suggesting that double-blind review should be considered by other journals.

Teaching accreditation exams reveal grading biases favor women in male-dominated disciplines in France: http://science.sciencemag.org/content/353/6298/474
This bias turns from 3 to 5 percentile ranks for men in literature and foreign languages to about 10 percentile ranks for women in math, physics, or philosophy.
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july 2017 by nhaliday
Corrupting cooperation and how anti-corruption strategies may backfire | Nature Human Behaviour
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


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/

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.
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july 2017 by nhaliday
Economics empiricism - Wikipedia
Economics empiricism[1] (sometimes economic imperialism) in contemporary economics refers to economic analysis of seemingly non-economic aspects of life,[2] such as crime,[3] law,[4] the family,[5] prejudice,[6] tastes,[7] irrational behavior,[8] politics,[9] sociology,[10] culture,[11] religion,[12] war,[13] science,[14] and research.[14] Related usage of the term predates recent decades.[15]

The emergence of such analysis has been attributed to a method that, like that of the physical sciences, permits refutable implications[16] testable by standard statistical techniques.[17] Central to that approach are "[t]he combined postulates of maximizing behavior, stable preferences and market equilibrium, applied relentlessly and unflinchingly."[18] It has been asserted that these and a focus on economic efficiency have been ignored in other social sciences and "allowed economics to invade intellectual territory that was previously deemed to be outside the discipline’s realm."[17][19]

The Fluidity of Race: https://westhunt.wordpress.com/2015/01/26/the-fluidity-of-race/
So: what can we conclude about this paper? It’s a classic case of economic imperialism, informed by what ‘intellectuals’ [ those that have never been introduced to Punnet squares, Old Blue Light, the Dirac equation, or Melungeons] would like to hear.

It is wrong, not close to right.

Breadth-first search: https://westhunt.wordpress.com/2015/05/24/breadth-first-search/
When I complain about some egregious piece of research, particularly those that are in some sense cross-disciplinary, I often feel that that just knowing more would solve the problem. If Roland Fryer or Oded Galor understood genetics, they wouldn’t make these silly mistakes. If Qian and Nix understood genetics or American post-Civil War history, they would never have written that awful paper about massive passing. Or if paleoanthropologists and population geneticists had learned about mammalian hybrids, they would have been open to the idea of Neanderthal introgression.

But that really amounts to a demand that people learn about five times as much in college and grad school as they actually do. It’s not going to happen. Or, perhaps, find a systematic and effective way of collaborating with people outside their discipline without having their heads shaved. That doesn’t sound too likely either.

Hot enough for you?: https://westhunt.wordpress.com/2015/10/22/hot-enough-for-you/
There’s a new study out in Nature, claiming that economic productivity peaks at 13 degrees Centigrade and that global warming will therefore drastically decrease world GDP.

Singapore. Phoenix. Queensland. Air-conditioners!

Now that I’ve made my point, just how stupid are these people? Do they actually believe this shit? I keep seeing papers by economists – in prominent places – that rely heavily on not knowing jack shit about anything on Earth, papers that could only have been written by someone that didn’t know a damn thing about the subject they were addressing, from the influence of genetic diversity on civilization achievement (zilch) to the massive race-switching that happened after the Civil War (not). Let me tell you, there’s a difference between ‘economic imperialism’ and old-fashioned real imperialism: people like Clive of India or Raffles bothered to learn something about the territory they were conquering. They knew enough to run divide et impera in their sleep: while economists never say peccavi, no matter how badly they screw up.
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july 2017 by nhaliday
Alzheimers | West Hunter
Some disease syndromes almost have to be caused by pathogens – for example, any with a fitness impact (prevalence x fitness reduction) > 2% or so, too big to be caused by mutational pressure. I don’t think that this is the case for AD: it hits so late in life that the fitness impact is minimal. However, that hardly means that it can’t be caused by a pathogen or pathogens – a big fraction of all disease syndromes are, including many that strike in old age. That possibility is always worth checking out, not least because infectious diseases are generally easier to prevent and/or treat.

There is new work that strongly suggests that pathogens are the root cause. It appears that the amyloid is an antimicrobial peptide. amyloid-beta binds to invading microbes and then surrounds and entraps them. ‘When researchers injected Salmonella into mice’s hippocampi, a brain area damaged in Alzheimer’s, A-beta quickly sprang into action. It swarmed the bugs and formed aggregates called fibrils and plaques. “Overnight you see the plaques throughout the hippocampus where the bugs were, and then in each single plaque is a single bacterium,” Tanzi says. ‘

obesity and pathogens: https://westhunt.wordpress.com/2016/05/29/alzheimers/#comment-79757
not sure about this guy, but interesting: https://westhunt.wordpress.com/2016/05/29/alzheimers/#comment-79748

All too often we see large, long-lasting research efforts that never produce, never achieve their goal.

For example, the amyloid hypothesis [accumulation of amyloid-beta oligomers is the cause of Alzheimers] has been dominant for more than 20 years, and has driven development of something like 15 drugs. None of them have worked. At the same time the well-known increased risk from APOe4 has been almost entirely ignored, even though it ought to be a clue to the cause.

In general, when a research effort has been spinning its wheels for a generation or more, shouldn’t we try something different? We could at least try putting a fraction of those research dollars into alternative approaches that have not yet failed repeatedly.

Mostly this applies to research efforts that at least wish they were science. ‘educational research’ is in a special class, and I hardly know what to recommend. Most of the remedial actions that occur to me violate one or more of the Geneva conventions.

APOe4 related to lymphatic system: https://en.wikipedia.org/wiki/Apolipoprotein_E

Look,if I could find out the sort of places that I usually misplace my keys – if I did, which I don’t – I could find the keys more easily the next time I lose them. If you find out that practitioners of a given field are not very competent, it marks that field as a likely place to look for relatively easy discovery. Thus medicine is a promising field, because on the whole doctors are not terribly good investigators. For example, none of the drugs developed for Alzheimers have worked at all, which suggests that our ideas on the causation of Alzheimers are likely wrong. Which suggests that it may (repeat may) be possible to make good progress on Alzheimers, either by an entirely empirical approach, which is way underrated nowadays, or by dumping the current explanation, finding a better one, and applying it.

You could start by looking at basic notions of field X and asking yourself: How do we really know that? Is there serious statistical evidence? Does that notion even accord with basic theory? This sort of checking is entirely possible. In most of the social sciences, we don’t, there isn’t, and it doesn’t.

Hygiene and the world distribution of Alzheimer’s disease: Epidemiological evidence for a relationship between microbial environment and age-adjusted disease burden: https://academic.oup.com/emph/article/2013/1/173/1861845/Hygiene-and-the-world-distribution-of-Alzheimer-s

Amyloid-β peptide protects against microbial infection in mouse and worm models of Alzheimer’s disease: http://stm.sciencemag.org/content/8/340/340ra72

Fungus, the bogeyman: http://www.economist.com/news/science-and-technology/21676754-curious-result-hints-possibility-dementia-caused-fungal
Fungus and dementia
paper: http://www.nature.com/articles/srep15015
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july 2017 by nhaliday
Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders : Nature Genetics : Nature Research
Autism spectrum disorder (ASD) risk is influenced by common polygenic and de novo variation. We aimed to clarify the influence of polygenic risk for ASD and to identify subgroups of ASD cases, including those with strongly acting de novo variants, in which polygenic risk is relevant. Using a novel approach called the polygenic transmission disequilibrium test and data from 6,454 families with a child with ASD, we show that polygenic risk for ASD, schizophrenia, and greater educational attainment is over-transmitted to children with ASD. These findings hold independent of proband IQ. We find that polygenic variation contributes additively to risk in ASD cases who carry a strongly acting de novo variant. Lastly, we show that elements of polygenic risk are independent and differ in their relationship with phenotype. These results confirm that the genetic influences on ASD are additive and suggest that they create risk through at least partially distinct etiologic pathways.

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july 2017 by nhaliday
On the effects of inequality on economic growth | Nintil
After the discussion above, what should one think about the relationship between inequality and growth?

For starters, that the consensus of the literature points to our lack of knowledge, and the need to be very careful when studying these phenomena. As of today there is no solid consensus on the effects of inequality on growth. Tentatively, on the grounds of Neves et al.’s meta-analysis, we can conclude that the impact of inequality on developed countries is economically insignificant. This means that one can claim that inequality is good, bad, or neutral for growth as long as the effects claimed are small and one talks about developed countries. For developing countries, the relationships are more negative.

I recently finished The Spirit Level, subtitled "Why More Equal Societies Almost Almost Do Better", although "Five Million Different Scatter Plot Graphs Plus Associated Commentary" would also have worked. It was a pretty thorough manifesto for the best kind of leftism: the type that foregoes ideology and a priori arguments in exchange for a truckload of statistics showing that their proposed social remedies really work.

Inequality: some people know what they want to find: https://www.adamsmith.org/blog/economics/inequality-some-people-know-what-they-want-to-find

Inequality doesn’t matter: a primer: https://www.adamsmith.org/blog/inequality-doesnt-matter-a-primer

Inequality and visibility of wealth in experimental social networks: https://www.nature.com/articles/nature15392
- Akihiro Nishi, Hirokazu Shirado, David G. Rand & Nicholas A. Christakis

We show that wealth visibility facilitates the downstream consequences of initial inequality—in initially more unequal situations, wealth visibility leads to greater inequality than when wealth is invisible. This result reflects a heterogeneous response to visibility in richer versus poorer subjects. We also find that making wealth visible has adverse welfare consequences, yielding lower levels of overall cooperation, inter-connectedness, and wealth. High initial levels of economic inequality alone, however, have relatively few deleterious welfare effects.

Our own work has shown that the *visibility* of inequality, more then the inequality per se, may be especially corrosive to the social fabric. https://www.nature.com/articles/nature15392 … I wonder if @WalterScheidel historical data sheds light on this idea? end 5/
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june 2017 by nhaliday
Kinship Systems, Cooperation and the Evolution of Culture
In the data, societies with loose ancestral kinship ties cooperate and trust broadly, which is apparently sustained through a belief in moralizing gods, universally applicable moral principles, feelings of guilt, and large-scale institutions. Societies with a historically tightly knit kinship structure, on the other hand, exhibit strong in-group favoritism: they cheat on and are distrusting of out-group members, but readily support in-group members in need. This cooperation scheme is enforced by moral values of in-group loyalty, conformity to tight social norms, emotions of shame, and strong local institutions.

Henrich, Joseph, The Secret of Our Success: How Culture is Driving Human Evolution,
Domesticating Our Species, and Making Us Smarter, Princeton University Press, 2015.
—, W.E.I.R.D People: How Westerners became Individualistic, Self-Obsessed, Guilt-Ridden,
Analytic, Patient, Principled and Prosperous, Princeton University Press, n.d.
—, Jean Ensminger, Richard McElreath, Abigail Barr, Clark Barrett, Alexander Bolyanatz, Juan Camilo Cardenas, Michael Gurven, Edwins Gwako, Natalie Hen- rich et al., “Markets, Religion, Community Size, and the Evolution of Fairness and Punishment,” Science, 2010, 327 (5972), 1480–1484.


—, —, Will M. Gervais, Aiyana K. Willard, Rita A. McNamara, Edward Slingerland, and Joseph Henrich, “The Cultural Evolution of Prosocial Religions,” Behavioral and Brain Sciences, 2016, 39, e1.


Purzycki, Benjamin Grant, Coren Apicella, Quentin D. Atkinson, Emma Cohen, Rita Anne McNamara, Aiyana K. Willard, Dimitris Xygalatas, Ara Norenzayan, and Joseph Henrich, “Moralistic Gods, Supernatural Punishment and the Expansion of Human Sociality,” Nature, 2016.

Table 1 summarizes
Figure 1 has map of kinship tightness
Figure 2 has cheating and in-group vs. out-group
Table 2 has regression
Figure 3 has univeralism and shame-guilt
Figure 4 has individualism-collectivism/conformity
Table 4 has radius of trust, Table 5 same for within-country variation (ethnic)
Tables 7 and 8 do universalism

Haidt moral foundations:
In line with the research hypothesis discussed in Section 3, the analysis employs two dependent variables, i.e., (i) the measure of in-group loyalty, and (ii) an index of the importance of communal values relative to the more universal (individualizing) ones. That is, the hypothesis is explicitly not about some societies being more or less moral than others, but merely about heterogeneity in the relative importance that people attach to structurally different types of values. To construct the index, I compute the first principal component of fairness / reciprocity, harm / care, in-group / loyalty, and respect /authority. The resulting score endogenously has the appealing property that – in line with the research hypothesis – it loads positively on the first two values and negatively on the latter two, with roughly equal weights, see Appendix F for details.²⁴I compute country-level scores by averaging responses by country of residence of respondents. Importantly, in Enke (2017) I document that – in a nationally representative sample of Americans – this same index of moral communalism is strongly correlated with individuals’ propensity to favor their local community over society as a whole in issues ranging from taxation and redistribution to donations and volunteering. Thus, there is evidence that the index of communal moral values captures economically meaningful behavioral heterogeneity.

The coevolution of kinship systems, cooperation, and culture: http://voxeu.org/article/kinship-cooperation-and-culture
- Benjamin Enke

pretty short

good linguistics reference cited in this paper:
On the biological and cultural evolution of shame: Using internet search tools to weight values in many cultures: https://arxiv.org/abs/1401.1100v2
Here we explore the relative importance between shame and guilt by using Google Translate [>_>...] to produce translation for the words "shame", "guilt", "pain", "embarrassment" and "fear" to the 64 languages covered. We also explore the meanings of these concepts among the Yanomami, a horticulturist hunter-gatherer tribe in the Orinoquia. Results show that societies previously described as “guilt societies” have more words for guilt than for shame, but *the large majority*, including the societies previously described as “shame societies”, *have more words for shame than for guilt*. Results are consistent with evolutionary models of shame which predict a wide scatter in the relative importance between guilt and shame, suggesting that cultural evolution of shame has continued the work of biological evolution, and that neither provides a strong adaptive advantage to either shame or guilt [? did they not just say that most languages favor shame?].


The roots of the word "shame" are thought to derive from an older word meaning "to cover". The emotion of shame has clear physiological consequences. Its facial and corporal expression is a human universal, as was recognized already by Darwin (5). Looking away, reddening of the face, sinking the head, obstructing direct view, hiding the face and downing the eyelids, are the unequivocal expressions signaling shame. Shame might be an emotion specific to humans, as no clear description of it is known for animals.
Classical Greek philosophers, such as Aristotle, explicitly mention shame as a key element in building society.

Guilt is the emotion of being responsible for the commission of an offense, however, it seems to be distinct from shame. Guilt says “what I did was not good”, whereas shame says “I am no good"(2). For Benedict (1), shame is a violation of cultural or social values, while guilt feelings arise from violations of one's internal values.


Unobservable emotions such as guilt may be of value to the receiver but constitutes in economy “private information”. Thus, in economic and biological terms, adaptive pressures acting upon the evolution of shame differ from those acting on that of guilt.

Shame has evolutionary advantages to both individual and society, but the lack ofshame also has evolutionary advantages as it allows cheating and thus benefiting from public goods without paying the costs of its build up.


Dodds (7) coined the distinction between guilt and shame cultures and postulated that in Greek cultural history, shame as a social value was displaced, at least in part, by guilt in guiding moral behavior.
"[...]True guilt cultures rely on an internalized conviction of sin as the enforcer of good behavior, not, as shame cultures do, on external sanctions. Guilt cultures emphasize punishment and forgiveness as ways of restoring the moral order; shame cultures stress self-denial and humility as ways of restoring the social order”.


For example, Wikipedia is less error prone than Encyclopedia Britannica (12, 17); and Google Translate is as accurate as more traditional methods (35).

Table 1, Figure 1


This regression is close to a proportional line of two words for shame for each word for guilt.


For example, in the case of Chinese, no overlap between the five concepts is reported using Google Translate in Figure 1. Yet, linguistic-conceptual studies of guilt and shame revealed an important overlap between several of these concepts in Chinese (29).


Our results using Google Translate show no overlap between Guilt and Shame in any of the languages studied.
[lol:] Examples of the context when they feel “kili” are: a tiger appears in the forest; you kill somebody from another community; your daughter is going to die; everybody looks at your underwear; you are caught stealing; you soil your pants while among others; a doctor gives you an injection; you hit your wife and others find out; you are unfaithful to your husband and others find out; you are going to be hit with a machete.


Linguistic families do not aggregate according to the relationship of the number of synonyms for shame and guilt (Figure 3).


The ratios are 0.89 and 2.5 respectively, meaning a historical transition from guilt-culture in Latin to shame-culture in Italian, suggesting a historical development that is inverse to that suggested byDodds for ancient to classical Greek. [I hope their Latin corpus doesn't include stuff from Catholics...]

Joe Henrich presentation: https://www.youtube.com/watch?v=f-unD4ZzWB4

relevant video:
Johnny Cash - God's Gonna Cut You Down: https://www.youtube.com/watch?v=eJlN9jdQFSc

this says Dems more guilt-driven but Peter Frost says opposite here (and matches my perception of the contemporary breakdown both including minorities and focusing only on whites): https://pinboard.in/u:nhaliday/b:9b75881f6861

this is an amazing paper:
The Origins of WEIRD Psychology: https://psyarxiv.com/d6qhu/
Recent research not only confirms the existence of substantial psychological variation around the globe but also highlights the peculiarity of populations that are Western, Educated, Industrialized, Rich and Democratic (WEIRD). We propose that much of this variation arose as people psychologically adapted to differing kin-based institutions—the set of social norms governing descent, marriage, residence and related domains. We further propose that part of the variation in these institutions arose historically from the Catholic Church’s marriage and family policies, which contributed to the dissolution of Europe’s traditional kin-based institutions, leading eventually to the predominance of nuclear families and impersonal institutions. By combining data on 20 psychological outcomes with historical measures of both kinship and Church exposure, we find support for these ideas in a comprehensive array of analyses across countries, among European regions and between individuals with … [more]
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june 2017 by nhaliday
Dogs and Men | West Hunter
Razib Khan talks about a new article that suggests that dogs were domesticated quite a long time ago, perhaps more than 35,000 years ago, well before the last glacial maximum.

We know that dogs have adapted to life with people, have changed in many ways.

I wonder how humans adapted to dogs.  If they were like modern pariah dogs, hanging around the village and eating garbage, doesn’t seem that they would have been that influential. But if used in hunting, they could have been very important, especially back in the Ice Age – and if they were that important, the partnership might have generated significant selective pressures in humans.
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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.
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june 2017 by nhaliday
World Without Stars | West Hunter
Seems to me that forming in a galaxy might give a solar system enough heavy elements, while being flung into the intergalactic deeps would protect you from cosmic catastrophes like gamma-ray bursts.   Such stars might be good homes for complex life, especially a few billion years ago.

Interstellar travel is hard enough for us, but for these guys, it would be a bitch. That first step is a doozy.
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june 2017 by nhaliday
Secular rise in economically valuable personality traits
small decline starting at YOB~1980:
Growing evidence suggests that the Flynn effect has ended and may have reversed in Western Europe (32, 33, 44–46). The last three birth cohorts in our data coincide with the peak in cognitive test scores in Finland (31). There is no clear trend for personality scores between these cohorts, which suggests that the end of the Flynn effect could also be reflected in personality traits. However, the data on these three birth cohorts are not fully comparable with our main data, and thus, it is not possible to make strong conclusions from them.
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june 2017 by nhaliday
Cultural group selection plays an essential role in explaining human cooperation: A sketch of the evidence
Pursuing Darwin’s curious parallel: Prospects for a science of cultural evolution: http://www.pnas.org/content/early/2017/07/18/1620741114.full

Axelrod model: http://ncase.me/trust/

Peer punishment promotes enforcement of bad social norms: https://www.nature.com/articles/s41467-017-00731-0
Social norms are an important element in explaining how humans achieve very high levels of cooperative activity. It is widely observed that, when norms can be enforced by peer punishment, groups are able to resolve social dilemmas in prosocial, cooperative ways. Here we show that punishment can also encourage participation in destructive behaviours that are harmful to group welfare, and that this phenomenon is mediated by a social norm. In a variation of a public goods game, in which the return to investment is negative for both group and individual, we find that the opportunity to punish led to higher levels of contribution, thereby harming collective payoffs. A second experiment confirmed that, independently of whether punishment is available, a majority of subjects regard the efficient behaviour of non-contribution as socially inappropriate. The results show that simply providing a punishment opportunity does not guarantee that punishment will be used for socially beneficial ends, because the social norms that influence punishment behaviour may themselves be destructive.

Peer punishment can stabilize anything, both good and bad norms. This is why you need group selection to select good social norms.
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june 2017 by nhaliday
An Economic Analysis of the Protestant Reformation
- Ekelund, Hébert, Tollison

This paper seeks to explain the initial successes and failures of Protestantism on economic grounds. It argues that the medieval Roman Catholic Church, through doctrinal manipulation, the exclusion of rivals, and various forms of price discrimination, ultimately placed members seeking the Z good "spiritual services" on the margin of defection. These monopolistic practices encouraged entry by rival firms, some of which were aligned with civil governments. The paper hypothesizes that Protestant entry was facilitated in emergent entrepreneurial societies characterized by the decline of feudalism and relatively unstable distribution of wealth and repressed in more homogeneous, rent-seeking societies that were mostly dissipating rather than creating wealth. In these societies the Roman Church was more able to continue the practice of price discrimination. Informal tests of this proposition are conducted by considering primogeniture and urban growth as proxies for wealth stability.

Causes and Consequences of the Protestant Reformation: https://pseudoerasmus.files.wordpress.com/2017/01/becker-pfaff-rubin-2016.pdf
- Sascha O. Becker, Steven Pfaff, Jared Rubin

The Protestant Reformation is one of the defining events of the last millennium. Nearly 500 years after the Reformation, its causes and consequences have seen a renewed interest in the social sciences. Research in economics, sociology, and political science increasingly uses detailed individual-level, city-level, and regional-level data to identify drivers of the adoption of the Reformation, its diffusion pattern, and its socioeconomic consequences. We take stock of this research, pointing out what we know and what we do not know and suggesting the most promising areas for future research.

Table 1: Studies of the Supply and Demand-Side Factors of the Reformation
Table 2: Studies on the Consequences of the Reformation: Human Capital
Table 3: Studies on the Consequences of the Reformation: Work and Work Ethic
Table 4: Studies on the Consequences of the Reformation: Economic Development
Table 5: Studies on the Consequences of the Reformation: Governance
Table 6: Studies on the “Dark” Consequences of the Reformation

LUTHER AND SULEYMAN: http://www.jstor.org.sci-hub.tw/stable/40506214
- Murat Iyigun

Various historical accounts have suggested that the Ottomans' rise helped the Protestant Reformation as well as its offshoots, such as Zwinglianism, Anabaptism, and Calvinism, survive their infancy and mature. Utilizing a comprehensive data set on violent confrontations for the interval between 1401 and 1700 CE, I show that the incidence of military engagements between the Protestant Reformers and the Counter-Reformation forces between the 1520s and 1650s depended negatively on the Ottomans' military activities in Europe. Furthermore, I document that the impact of the Ottomans on Europe went beyond suppressing ecclesiastical conflicts only: at the turn of the sixteenth century, Ottoman conquests lowered the number of all newly initiated conflicts among the Europeans roughly by 25 percent, while they dampened all longer-running feuds by more than 15 percent. The Ottomans' military activities influenced the length of intra-European feuds too, with each Ottoman-European military engagement shortening the duration of intra-European conflicts by more than 50 percent. Thus, while the Protestant Reformation might have benefited from - and perhaps even capitalized on - the Ottoman advances in Europe, the latter seems to have played some role in reducing conflicts within Europe more generally.

Religious Competition and Reallocation: The Political Economy of Secularization in the Protestant Reformation: http://www.jeremiahdittmar.com/files/RRR_20170919.pdf
- Davide Cantoni, Jeremiah Dittmar, Noam Yuchtman*

Using novel microdata, we document an unintended, first-order consequence of the Protestant Reformation: a massive reallocation of resources from religious to secular purposes. To understand this process, we propose a conceptual framework in which the introduction of religious competition shifts political markets where religious authorities provide legitimacy to rulers in exchange for control over resources. Consistent with our framework, religious competition changed the balance of power between secular and religious elites: secular authorities acquired enormous amounts of wealth from monasteries closed during the Reformation, particularly in Protestant regions. This transfer of resources had important consequences. First, it shifted the allocation of upper-tail human capital. Graduates of Protestant universities increasingly took secular, especially administrative, occupations. Protestant university students increasingly studied secular subjects, especially degrees that prepared students for public sector jobs, rather than church sector-specific theology. Second, it affected the sectoral composition of fixed investment. Particularly in Protestant regions, new construction from religious toward secular purposes, especially the building of palaces and administrative buildings, which reflected the increased wealth and power of secular lords. Reallocation was not driven by pre-existing economic or cultural differences. Our findings indicate that the Reformation played an important causal role in the secularization of the West.

look at Figure 4, holy shit

History: Science and the Reformation: http://www.nature.com/nature/journal/v550/n7677/full/550454a.html?WT.mc_id=TWT_NatureNews&sf126429621=1
The scientific and religious revolutions that began 500 years ago were not causally related, but were both stimulated by printing, argues David Wootton.
No, the Reformation did not cause the scientific revolution. Nice brief article. 👍

No RCT = No causal claims, for or against ;)
Though I'm open to a regression discontinuity design! cc: @pseudoerasmus
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may 2017 by nhaliday
Proportionality: the fairness of inequality - The Unz Review
At this stage it should be made clear that all the “equality in the lab” researchers have not been telling lies. They are aware that inequality and unfairness are being confounded, but that message has been downplayed in the telling. From a research strategy perspective, I think it shows how a particular approach (strangers in a lab) fails to produce results which map onto real world observations. When participants come together without any back history, the ideal of equality rules. When the fuller context is given a chance to be considered, then subjects in an experiment have no hesitation in rewarding those people who rise early to go to work over those who rise late to do nothing.

Drawing upon laboratory studies, cross-cultural research, and experiments with babies and young children, we argue that humans naturally favour fair distributions, not equal ones, and that when fairness and equality clash, people prefer fair inequality over unfair equality. Both psychological research and decisions by policymakers would benefit from more clearly distinguishing inequality from unfairness.

We measured two key aspects of fairness decisions: disadvantageous inequity aversion (peer receives more than self) and advantageous inequity aversion (self receives more than a peer). We show that disadvantageous inequity aversion emerged across all populations by middle childhood. By contrast, advantageous inequity aversion was more variable, emerging in three populations and only later in development. We discuss these findings in relation to questions about the universality and cultural specificity of human fairness.

Three countries that exhibited AI aversion were USA, Canada (only WEIRD countries studied), and Uganda (interesting). Senegal was different.

The Mexican (think they were Mayan) children didn't have much of a reaction in any case.
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may 2017 by nhaliday
Genetically engineered humans will arrive sooner than you think. And we're not ready. - Vox
lol "epigenetics" makes an appearance ofc


For now, that’s prohibitively expensive, but it won’t always be that way. In 2003, it cost 4 dollars to press one of the keys on Endy’s hypothetical synthesizer. This month, it costs just two cents—a 200-fold decrease in price in just 14 years. In the same time frame, the cost of tuition at Stanford has doubled, and is now around $50,000. Given all of that, the first question that Stanford’s budding bioengineers get is this:

At what point will the cost of printing DNA to create a human equal the cost of teaching a student in Stanford?
And the answer is: 19 years from today.

But the follow-up question is a little more complicated:

If you and your future partner are planning to have kids, would you start saving money for college tuition, or for printing the genome of your offspring?
The question tends to split students down the line, says Endy. About 60 percent say that printing a genome is wrong, and flies against what it means to be a parent. They prize the special nature of education and would opt to save for the tuition. But around 40 percent of the class will say that the value of education may change in the future, and if genetic technology becomes mature, and allows them to secure advantages for them and their lineage, they might as well do that.


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may 2017 by nhaliday
When conquered pre-Greece took captive her rude Hellene conqueror – Gene Expression
For various reasons this was always less plausible for Southern Europe. The first reason is that Southern Europeans shared a lot of genetic similarities to Sardinians, who resembled Neolithic farmers. Admixture models generally suggested that in the peninsulas of Southern Europe the steppe-like ancestry was the minority component, not the majority, as was the case in Northern Europe.

different for the Romans: https://www.quora.com/Were-the-Romans-Greek-or-Italians

book recommendations for Ancient Greece: https://gnxp.nofe.me/2017/08/02/when-the-ancestors-were-cyclops/#comment-3356

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

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

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

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

Singleton Variants Dominate the Genetic Architecture of Human Gene Expression: https://www.biorxiv.org/content/early/2017/12/15/219238
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may 2017 by nhaliday
China Overtakes US in Scientific Articles, Robots, Supercomputers - The Unz Review
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may 2017 by nhaliday
Syphilis in Renaissance Europe: rapid evolution of an introduced sexually transmitted disease?
When syphilis first appeared in Europe in 1495, it was an acute and extremely unpleasant disease. After only a few years it was less severe than it once was, and it changed over the next 50 years into a milder, chronic disease. The severe early symptoms may have been the result of the disease being introduced into a new host population without any resistance mechanisms, but the change in virulence is most likely to have happened because of selection favouring milder strains of the pathogen.
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may 2017 by nhaliday
Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network
Towards explaining non-shared-environment effects on intelligence, psychiatric disorders, and other cognitive traits - developmental noise such as post-conception mutations in individual cells or groups of cells
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may 2017 by nhaliday
Backwardness | West Hunter
Back around the time I was born, anthropologists sometimes talked about some cultures being more advanced than others. This was before they decided that all cultures are equal, except that some are more equal than others.


I’ve been trying to estimate the gap between Eurasian and Amerindian civilization. The Conquistadors were, in a sense, invaders from the future: but just how far in the future? What point in the history of the Middle East is most similar to the state of the Amerindian civilizations of 1500 AD ?

I would argue that the Amerindian civilizations were less advanced than the Akkadian Empire, circa 2300 BC. The Mayans had writing, but were latecomers in metallurgy. The Inca had tin and arsenical bronze, but didn’t have written records. The Akkadians had both – as well as draft animals and the wheel. You can maybe push the time as far back as 2600 BC, since Sumerian cuneiform was in pretty full swing by then. So the Amerindians were around four thousand years behind.

Excepting the use of iron, sub-Saharan Africa, excepting Ethiopia, was well behind the most advanced Amerindian civilizations circa 1492. I am right now resisting the temptation to get into a hammer-and-tongs discussion of Isandlwana, Rorke’s Drift, Blood River, etc. – and we would all be better off if I continued to do so.

The Battle of Blood River (Afrikaans: Slag van Bloedrivier; Zulu: iMpi yaseNcome) is the name given for the battle fought between _470 Voortrekkers_ ("Pioneers"), led by Andries Pretorius, and _an estimated 80,000 Zulu attackers_ on the bank of the Ncome River on 16 December 1838, in what is today KwaZulu-Natal, South Africa. Casualties amounted to over 3,000 of king Dingane's soldiers dead, including two Zulu princes competing with Prince Mpande for the Zulu throne. _Three Pioneers commando members were lightly wounded_, including Pretorius himself.


In the morning of Tuesday, June 15, while we sat at Dr. Adams's, we talked of a printed letter from the Reverend Herbert Croft, to a young gentleman who had been his pupil, in which he advised him to read to the end of whatever books he should begin to read. JOHNSON. 'This is surely a strange advice; you may as well resolve that whatever men you happen to get acquainted with, you are to keep to them for life. A book may be good for nothing; or there may be only one thing in it worth knowing; are we to read it all through? These Voyages, (pointing to the three large volumes of Voyages to the South Sea, which were just come out) WHO will read them through? A man had better work his way before the mast, than read them through; they will be eaten by rats and mice, before they are read through. There can be little entertainment in such books; one set of Savages is like another.' BOSWELL. 'I do not think the people of Otaheite can be reckoned Savages.' JOHNSON. 'Don't cant in defence of Savages.' BOSWELL. 'They have the art of navigation.' JOHNSON. 'A dog or a cat can swim.' BOSWELL. 'They carve very ingeniously.' JOHNSON. 'A cat can scratch, and a child with a nail can scratch.' I perceived this was none of the mollia tempora fandi; so desisted.

Déjà Vu all over again: America and Europe: https://westhunt.wordpress.com/2014/11/12/deja-vu-all-over-again-america-and-europe/
In terms of social organization and technology, it seems to me that Mesolithic Europeans (around 10,000 years ago) were like archaic Amerindians before agriculture. Many Amerindians on the west coast were still like that when Europeans arrived – foragers with bows and dugout canoes.

On the other hand, the farmers of Old Europe were in important ways a lot like English settlers: the pioneers planted wheat, raised pigs and cows and sheep, hunted deer, expanded and pushed aside the previous peoples, without much intermarriage. Sure, Anglo pioneers were literate, had guns and iron, were part of a state, all of which gave them a much bigger edge over the Amerindians than Old Europe ever had over the Mesolithic hunter-gatherers and made the replacement about ten times faster – but in some ways it was similar. Some of this similarity was the product of historical accidents: the local Amerindians were thin on the ground, like Europe’s Mesolithic hunters – but not so much because farming hadn’t arrived (it had in most of the United States), more because of an ongoing population crash from European diseases.

On the gripping hand, the Indo-Europeans seem to have been something like the Plains Indians: sure, they raised cattle rather than living off abundant wild buffalo, but they too were transformed into troublemakers by the advent of the horse. Both still did a bit of farming. They were also alike in that neither of them really knew what they were doing: neither were the perfected product of thousands of years of horse nomadry. The Indo-Europeans were the first raiders on horseback, and the Plains Indians had only been at it for a century, without any opportunity to learn state-of-the-art tricks from Eurasian horse nomads.

The biggest difference is that the Indo-Europeans won, while the Plains Indians were corralled into crappy reservations.

Quantitative historical analysis uncovers a single dimension of complexity that structures global variation in human social organization: http://www.pnas.org/content/early/2017/12/20/1708800115.full
Do human societies from around the world exhibit similarities in the way that they are structured, and show commonalities in the ways that they have evolved? These are long-standing questions that have proven difficult to answer. To test between competing hypotheses, we constructed a massive repository of historical and archaeological information known as “Seshat: Global History Databank.” We systematically coded data on 414 societies from 30 regions around the world spanning the last 10,000 years. We were able to capture information on 51 variables reflecting nine characteristics of human societies, such as social scale, economy, features of governance, and information systems. Our analyses revealed that these different characteristics show strong relationships with each other and that a single principal component captures around three-quarters of the observed variation. Furthermore, we found that different characteristics of social complexity are highly predictable across different world regions. These results suggest that key aspects of social organization are functionally related and do indeed coevolve in predictable ways. Our findings highlight the power of the sciences and humanities working together to rigorously test hypotheses about general rules that may have shaped human history.

Fig. 2.

The General Social Complexity Factor Is A Thing: https://www.gnxp.com/WordPress/2017/12/21/the-general-social-complexity-factor-is-a-thing/
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may 2017 by nhaliday
Secular decline in testosterone levels - Rogue Health and Fitness
A Population-Level Decline in Serum Testosterone Levels in American Men: http://sci-hub.tw/10.1210/jc.2006-1375
Secular trends in sex hormones and fractures in men and women: http://www.eje-online.org/content/166/5/887.full.pdf
Small n and older sample, but interesting that while testosterone decreases have been large for men they’ve been even larger (in % terms) for women; wonder if this contributes to declining pregnancy and sexual frequency, rising depression.

Strangelove: https://youtu.be/N1KvgtEnABY?t=67

People offering human-centric explanations like cell phones: Note also that the sperm quality of dogs has decreased 30% since 1988.

mendelian rand.:
1 SD genetically instrumented increase in BMI was associated with a 0.25 SD decrease in serum testosterone

Ibuprofen linked to male infertility: study: https://nypost.com/2018/01/08/ibuprofen-linked-to-male-infertility-study/

Tucker Carlson: "Men Seem To Be Becoming Less Male": https://www.realclearpolitics.com/video/2018/03/08/tucker_carlson_men_seem_to_be_becoming_less_male.html
Carlson interviewed Dr. Jordan Peterson who blamed the "insidious" movement being driven by the "radical left" that teaches there a problem of "toxic masculinity." He said ideological policies focus on "de-emphasizing masculinity may be part of the problem."


Those are the numbers. They paint a very clear picture: American men are failing, in body, mind and spirit. This is a crisis. Yet our leaders pretend it’s not happening. They tell us the opposite is true: Women are victims, men are oppressors. To question that assumption is to risk punishment. Even as women far outpace men in higher education, virtually every college campus supports a women’s studies department, whose core goal is to attack male power. Our politicians and business leaders internalize and amplify that message. Men are privileged. Women are oppressed. Hire and promote and reward accordingly.

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.
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may 2017 by nhaliday
Environmental Cancer? | In the Pipeline
And while I take the point that endocrine disruptors and the like need to be watched (and that we really do need to study these things more), I don’t see why the alarm bells need to be rung quite this loudly.
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may 2017 by nhaliday
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