June 2018 gwern.net newsletter with links on genetics, reinforcement learning, cats, experimentation, with 6 book reviews and 12 music links. newsletter 2018-05-31–2021-01-04finishedcertainty: logimportance: 0
OpenAI progress on 5x5 DoTA: amateur human level (commentary; Human amateur level 5x5 DoTA using nothing but simple PPOLSTMs and a lot of computing power to power self-play over 19 days. No need for anything fancy for ultra-long-range temporal learning, just LSTMs are enough memory to learn strategizing. Deep learning scales. More concerningly: they note that their code can reach human levels even with crashing bugs…)
Pop Team Epic (tremendous visual imagination and dedication married to some of the worst ‘humor’ inflicted on me yet; I was dubious but Poptepipic’s meme game was so stronk I figured it had to be good. But it was not. Except for the “Hellshake Yanno” skit which ranks up with the manga-mation scene in FLCL for mixed-media greatness and is well worth watching on its own.)
Newsletter tag: archive of all issues back to 2013 for the gwern.net newsletter (monthly updates, which will include summaries of projects I’ve worked on that month (the same as the changelog), collations of links or discussions from my subreddit, and book/movie reviews.)
This page is a changelog for Gwern.net: a monthly reverse chronological list of recent major writings/changes/additions.
Following my writing can be a little difficult because it is often so incremental. So every month, in addition to my regular /r/Gwern subreddit submissions, I write up reasonably-interesting changes and send it out to the mailing list in addition to a compilation of links & reviews (archives).
A subreddit for posting links of interest and also for announcing updates to gwern.net (which can be used as a RSS feed). Submissions are categorized similar to the monthly newsletter and typically will be collated there.
Paul Myron Anthony Linebarger, better known by his pen-name Cordwainer Smith, was an American author known for his science fiction works. Linebarger was a US Army officer, a noted East Asia scholar, and an expert in psychological warfare. Although his career as a writer was shortened by his death at the age of 53, he is considered one of the more talented and influential science fiction authors.
Cordwainer Smith’s classic SF short story “Scanners Live in Vain” is remembered in part for its use of the space-madness trope, “the Great Pain of Space”, usually interpreted symbolically/psychologically by critics. I discuss the state of aerospace medicine in 1945 and subsequent research on “the breakaway effect”, “the overview effect”, and other unusual psychological states induced by air & space travel, and suggest Smith’s “the pain of space” is more founded on SF-style speculation & extrapolation of contemporary science/technology and anxieties than is appreciated due to the obscurity of the effects and the relative benignity of the subsequent best documented effects.
We show that genetic endowments linked to educational attainment strongly and robustly predict wealth at retirement. The estimated relationship is not fully explained by flexibly controlling for education and labor income. We therefore investigate a host of additional mechanisms that could help to explain the gene-wealth gradient, including inheritances, mortality, savings, risk preferences, portfolio decisions, beliefs about the probabilities of macroeconomic events, and planning horizons. The associations we report provide preliminary evidence that genetic endowments related to human capital accumulation are associated with wealth not only through educational attainment and labor income, but also through a facility with complex financial decision-making. Our study illustrates how economic research seeking to understand sources of inequality can benefit from recent advances in behavioral genetics linking specific observed genetic endowments to economic outcomes.
We have extensively mapped the genes responsible for hair colour in the UK population. MC1R mutations are well established as the principal genetic cause of red hair colour, but with variable penetrance. We find variation at genes encoding its agonist (POMC), inverse agonist (ASIP) and other loci contribute to red hair and demonstrate epistasis between MC1R and some of these loci. Blonde hair is associated with over 200 loci, and we find a genetic continuum from black through dark and light brown to blonde. Many of the associated genes are involved in hair growth or texture, emphasising the cellular connections between keratinocytes and melanocytes in the determination of hair colour.
Facial attractiveness is a complex human trait of great interest in both academia and industry. Literature on sociological and phenotypic factors associated with facial attractiveness is rich, but its genetic basis is poorly understood. In this paper, we conducted a genome-wide association study to discover genetic variants associated with facial attractiveness using 3,928 samples in the Wisconsin Longitudinal Study. We identified two genome-wide significant loci and highlighted a handful of candidate genes, many of which are specifically expressed in human tissues involved in reproduction and hormone synthesis. Additionally, facial attractiveness showed strong and negative genetic correlations with BMI in females and with blood lipids in males. Our analysis also suggested sex-specific selection pressure on variants associated with lower male attractiveness. These results revealed sex-specific genetic architecture of facial attractiveness and provided fundamental new insights into its genetic basis.
Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases across cohorts. For six additional phenotypes in the UK Biobank data, we find increases in prediction accuracy ranging from 0.7% for height to 47% for type 2 diabetes, when using a multi-trait predictor that combines published summary statistics from multiple traits, as compared to a predictor based only on one trait.
Existing literature connects military service to regional characteristics and family traditions, creating real distinctions between those who serve and those who do not. We engage this discussion by examining military service as a function of personality. In the second portion, we examine military service as predisposed by genetics. Our findings indicate there is a significant heritability component of serving in the military. We find a significant genetic correlation between personality traits associated with progressive political ambition and military service, suggesting that military service represents a different form of political participation to which individuals are genetically predisposed. We discuss the long-term implications of our findings for policy makers and recruiters.
Consumer genomics databases reached the scale of millions of individuals. Recently, law enforcement investigators have started to exploit some of these databases to find distant familial relatives, which can lead to a complete re-identification. Here, we leveraged genomic data of 600,000 individuals tested with consumer genomics to investigate the power of such long-range familial searches. We project that half of the searches with European-descent individuals will result with a third cousin or closer match and will provide a search space small enough to permit re-identification using common demographic identifiers. Moreover, in the near future, virtually any European-descent US person could be implicated by this technique. We propose a potential mitigation strategy based on cryptographic signature that can resolve the issue and discuss policy implications to human subject research.
The role played by natural selection in shaping present-day human populations has received extensive scrutiny [1, 2, 3], especially in the context of local adaptations . However, most studies to date assume, either explicitly or not, that populations have been in their current locations long enough to adapt to local conditions , and that population sizes were large enough to allow for the action of selection . If these conditions were satisfied, not only should selection be effective at promoting local adaptations, but deleterious alleles should also be eliminated over time. To assess this prediction, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to reconstruct how frequencies of risk alleles and their homozygosity changed through space and time in Europe. While the overall deleterious homozygosity consistently decreased through space and time, risk alleles have shown a steady increase in frequency. Even the mutations that are predicted to be most deleterious fail to exhibit any significant decrease in frequency. These conclusions do not deny the existence of local adaptations, but highlight the limitations imposed by drift and range expansions on the strength of selection in purging the mutational load affecting human populations.
Family and twin studies suggest that up to 50% of individual differences in human fertility within a population might be heritable. However, it remains unclear whether the genes associated with fertility outcomes such as number of children ever born (NEB) or age at first birth (AFB) are the same across geographical and historical environments. By not taking this into account, previous genetic studies implicitly assumed that the genetic effects are constant across time and space. We conduct a mega-analysis applying whole genome methods on 31,396 unrelated men and women from six Western countries. Across all individuals and environments, common single-nucleotide polymorphisms (SNPs) explained only ~4% of the variance in NEB and AFB. We then extend these models to test whether genetic effects are shared across different environments or unique to them. For individuals belonging to the same population and demographic cohort (born before or after the 20th century fertility decline), SNP-based heritability was almost five times higher at 22% for NEB and 19% for AFB. We also found no evidence suggesting that genetic effects on fertility are shared across time and space. Our findings imply that the environment strongly modifies genetic effects on the tempo and quantum of fertility, that currently ongoing natural selection is heterogeneous across environments, and that gene-environment interactions may partly account for missing heritability in fertility. Future research needs to combine efforts from genetic research and from the social sciences to better understand human fertility.
Fertility behavior – such as age at first birth and number of children – varies strongly across historical time and geographical space. Yet, family and twin studies, which suggest that up to 50% of individual differences in fertility are heritable, implicitly assume that the genes important for fertility are the same across both time and space. Using molecular genetic data (SNPs) from over 30,000 unrelated individuals from six different countries, we show that different genes influence fertility in different time periods and different countries, and that the genetic effects consistently related to fertility are presumably small. The fact that genetic effects on fertility appear not to be universal could have tremendous implications for research in the area of reproductive medicine, social science and evolutionary biology alike.
The genetic architecture of most human complex traits is highly polygenic, motivating efforts to detect polygenic selection involving a large number of loci. In contrast to previous work relying on top GWAS loci, we developed a method that uses genome-wide association statistics and linkage disequilibrium patterns to estimate the genome-wide genetic component of population differentiation of a complex trait along a continuous gradient, enabling powerful inference of polygenic selection. We analyzed 43 UK Biobank traits and focused on PC1 and North-South and East-West birth coordinates across 337K unrelated British-ancestry samples, for which our method produced close to unbiased estimates of genetic components of population differentiation and high power to detect polygenic selection in simulations across different trait architectures. For PC1, we identified signals of polygenic selection for height (74.5±16.7% of 9.3% total correlation with PC1 attributable to genome-wide genetic effects; p = 8.4×10−6) and red hair pigmentation (95.9±24.7% of total correlation with PC1 attributable to genome-wide genetic effects; p = 1.1×10−4); the bulk of the signal remained when removing genome-wide significant loci, even though red hair pigmentation includes loci of large effect. We also detected polygenic selection for height, systolic blood pressure, BMI and basal metabolic rate along North-South birth coordinate, and height and systolic blood pressure along East-West birth coordinate. Our method detects polygenic selection in modern human populations with very subtle population structure and elucidates the relative contributions of genetic and non-genetic components of trait population differences.
Canine transmissible venereal tumor (CTVT), the oldest known somatic cell line, is a living fossil, originating from cancer cells transmitted from a host to other canids during the mating process7. Clonal origin analyses hints that the original dog infected with CTVT (CTVT founder) came from an ancient sled dog or wolf population. However, the genetic composition of the CTVT founder is still not clear.
In order to explore this issue, we applied whole genome sequencing (WGS) to two CTVT samples, their corresponding hosts, and 24 additional canids (Supplementary Note). Combined with published WGS data of two CTVT samples and high quality canine WGS data, we constructed a data set containing WGS data of four CTVT samples a 169-individual reference panel composed of worldwide gray wolves (Canis lupus), dogs (Canis lupus familiaris), coyotes (Canis latrans) and golden jackals (Canis aureus) (Supplementary Note, Table S1).
…Our results reveal that the CTVT founder was more closely related to present-day arctic sled dogs than to any other populations (Figure S6–8), in accordance with very recent results. However, ADMIXTURE analysis showed that the CTVT founder also possessed an ancestral component found predominantly in non-dog populations, a result that we do not observe for any arctic sled dog (Supplementary Note, Figure 1A). Moreover, the CTVT founder did not cluster tightly with arctic sled dogs in the PCA analysis (Figure S7). These results imply that the CTVT founder belonged to a previously unknown arctic dog population that is not represented in the reference panel…In conclusion, our detailed analyses reveal that the CTVT founder came from an arctic sled dog population that possessed introgression from a population related to coyotes, a result that was not known in previous studies. Considering the habitat of coyotes in North America, we propose two hypotheses: (1) The CTVT founder lived in the arctic region of North America. (2) The CTVT founder lived in the arctic region of the Far East, where arctic dogs possessing the introgressed segments migrated through the Bering Strait in an unknown period. Hence, an ancient story of canine admixture is hidden in the genome of a living fossil, the CTVT. To further test our hypotheses of ancient admixture and to better understand the detailed evolutionary history of dogs from the arctic region and Americas, it is crucial to acquire ancient samples in these regions in future work.
[Review of modern apple breeding techniques: genome sequencing enables selecting on seeds rather than trees by predicting taste & robustness, saving years of delay; this also allows avoiding the ‘GMO’ stigma by crossbreeding (quickly moving genes into new apple trees without direct genetic editing using genomic selection), such as a “fast-flowering gene” to accelerate maturation during evaluation but then select it out for the final tree; the creation of “The Gauntlet”, a greenhouse deliberately stocked with as many pathogens as possible, provides a stress test to weed out weak sapling as quickly as possible; and buds can be cryogenically preserved to cut down storage costs by more than an order of magnitude.]
Until recently, geneticists, their skills honed on Arabidopsis and other quick-breeding flora, avoided fruit-tree research like a blight. Of the 11,000 U.S. field tests on plants with transgenic genes between 1987 and 2004, just 1% focused on fruit trees. That’s partly because of the slow pace. Whereas vegetables like corn might produce two harvests each summer, apple trees need eons—around 5 years—to produce their first fruit, most of which will be disregarded as ugly, bitter, or squishy. But everything in apple breeding is about to change. An Italian team plans to publish the decoded apple genome this summer, and scientists are starting to single out complex genetic markers for taste and heartiness. In some cases the scientists even plan, by inserting genes from other species, to eliminate the barren juvenile stage and push fruit trees to mature rapidly, greatly reducing generation times.
In this paper, we study the problem of learning vision-based dynamic manipulation skills using a scalable reinforcement learning approach. We study this problem in the context of grasping, a longstanding challenge in robotic manipulation. In contrast to static learning behaviors that choose a grasp point and then execute the desired grasp, our method enables closed-loop vision-based control, whereby the robot continuously updates its grasp strategy based on the most recent observations to optimize long-horizon grasp success. To that end, we introduce QT-Opt, a scalable self-supervised vision-based reinforcement learning framework that can leverage over 580k real-world grasp attempts to train a deep neural network Q-function with over 1.2M parameters to perform closed-loop, real-world grasping that generalizes to 96 on unseen objects. Aside from attaining a very high success rate, our method exhibits behaviors that are quite distinct from more standard grasping systems: using only RGB vision-based perception from an over-the-shoulder camera, our method automatically learns regrasping strategies, probes objects to find the most effective grasps, learns to reposition objects and perform other non-prehensile pre-grasp manipulations, and responds dynamically to disturbances and perturbations.
American public attention rarely remains sharply focused upon any one domestic issue for very long—even if it involves a continuing problem of crucial importance to society. Instead, a systematic “issue-attention cycle” seems strongly to influence public attitudes and behavior concerning most key domestic problems. Each of these problems suddenly leaps into prominence, remains there for a short time, and then—though still largely unresolved—gradually fades from the center of public attention. A study of the way this cycle operates provides insights into how long public attention is likely to remain sufficiently focused upon any given issue to generate enough political pressure to cause effective change.
The shaping of American attitudes toward improving the quality of our environment provides both an example and a potential test of this “issue-attention cycle.” In the past few years, there has been a remarkably widespread upsurge of interest in the quality of our environment. This change in public attitudes has been much faster than any changes in the environment itself. What has caused this shift in public attention? Why did this issue suddenly assume so high a priority among our domestic concerns? And how long will the American public sustain high-intensity interest in ecological matters? I believe that answers to these questions analyzing the “issue-attention cycle.”
The dynamics of the “issue-attention cycle”
Public perception of most “crises” in American domestic life does not reflect changes in real conditions as much as it reflects the operation of a systematic cycle of heightening public interest and then increasing boredom with major issues. This “issue-attention cycle” is rooted both in the nature of certain domestic problems and in the way major communications media interact with the public. The cycle itself has five stages, which may vary in duration depending upon the particular issue involved, but which almost always occur in the following sequence:
This chapter comments on Anthony Downs’s 1972 seminal paper “Up and Down with Ecology: The ‘Issue-Attention’ Cycle”, which tackles the concept of “public” or “issue” attention. Focusing on domestic policy, particularly environmental policy in the United States, Downs describes a process called “issue-attention cycle”, by which the public gains and loses interest in a particular issue over time. This chapter summarizes studies that directly put Downs’s propositions to the test, laying emphasis on research that probes the existence of and interrelationships among the public attention cycle, media attention cycle, and government attention cycle. It then reviews the main arguments put forward by Downs before concluding with a discussion of promising avenues for future research as well as important theoretical and methodological questions that need further elucidation.
Female intrasexual competition is competition between women over a potential mate. Such competition might include self-promotion, derogation of other women, and direct and indirect aggression toward other women. Factors that influence female intrasexual competition include the genetic quality of available mates, hormone levels, and interpersonal dynamics.
"Kirk Allen" was the pseudonym given to a patient of Robert M. Lindner's, in his book The Fifty-Minute Hour. Born in Hawaii, "Allen" soon became obsessed with a series of novels, the protagonist of which shared his name. Due to "Allen's" anonymity, it is unclear what the series was, apart from the fact that it was science fiction. Some have theorized that the series was the "Barsoom" books, by Edgar Rice Burroughs, featuring the main character "John Carter".
We have investigated the role of habituation and disinhibition in the control of object (predatory) play by adult domestic cats Felis silvestris catus both with and without prior experience of hunting. We hypothesised that object play is terminated by rapid habituation to the sensory characteristics of the object played with, and therefore should be disinhibited if the sensory characteristics of the object are changed. Three sequential sessions of play with an unchanging object (a toy) caused almost complete habituation of the play response; replacing the toy with one of contrasting colours in a fourth session elicited intense disinhibited play, suggesting that motivation for play itself had not diminished substantially during the first three sessions. The time interval between sessions affected the extent of disinhibition. After a long delay (25–45 min) between each session play was less intense in the fourth session than in the first; if the interval was 5 min, it was more intense, indicative of post-inhibitory rebound, possibly caused by initial positive feedback of play on its own performance. We suggest that object play by adult cats is controlled by two mechanisms derived from predatory behaviour: one responds to prey-like stimulus characteristics, such as texture and small size, which elicit play, while the second detects change in the toy. The behavioural default towards any object is initial interest if it possesses relevant stimulus characteristics, followed by rapid habituation unless these stimulus characteristics change.
Kevin Kelly is the founding executive editor of Wired magazine, and a former editor/publisher of the Whole Earth Review. He has also been a writer, photographer, conservationist, and student of Asian and digital culture.
John Carreyrou is a French-American journalist. He worked for The Wall Street Journal for 20 years between 1999 and 2019 and has been based in Brussels, Paris, and New York City. He has won the Pulitzer Prize twice and is well known for having exposed the fraudulent practices of the multibillion-dollar blood-testing company Theranos in a series of articles published in the Journal.
Between 1983 and 1993, the Defense Advanced Research Projects Agency (DARPA) spent an extra $1 billion on computer research to achieve machine intelligence.1 The Strategic Computing Initiative (SCI) was conceived at the outset as an integrated plan to promote computer chip design and manufacturing, computer architecture, and artificial intelligence software. These technologies seemed ripe in the early 1980s. If only DARPA could connect them, it might achieve what Pamela McCorduck called “machines who think.” What distinguishes Strategic Computing (SC) from other stories of modern, large-scale technological development is that the program self-consciously set about advancing an entire research front. Instead of focusing on one problem after another, or of funding a whole field in hopes that all would prosper, SC treated intelligent machines as a single problem composed of interrelated subsystems. The strategy was to develop each of the subsystems cooperatively and map out the mechanisms by which they would connect. While most research programs entail tactics or strategy, SC boasted grand strategy, a master plan for an entire campaign.
Review of DARPA history book, Strategic Computing: DARPA and the Quest for Machine Intelligence, 1983–1993, Roland & Shiman 2002, which reviews a large-scale DARPA effort to jumpstart real-world uses of AI in the 1980s by a multi-pronged research effort into more efficient computer chip R&D, supercomputing, robotics/self-driving cars, & expert system software. Roland & Shiman 2002 particularly focus on the various 'philosophies' of technological forecasting & development, which guided DARPA's strategy in different periods, ultimately endorsing a weak technological determinism where the bottlenecks are too large for a small (in comparison to the global economy & global R&D) organization best a DARPA can hope for is a largely agnostic & reactive strategy in which granters 'surf' technological changes, rapidly exploiting new technology while investing their limited funds into targeted research patching up any gaps or lags that accidentally open up and block broader applications.
Peter Watts is a Canadian science fiction author. He specializes in hard science fiction. He earned a Ph.D from the University of British Columbia in Vancouver, British Columbia in 1991, from the Department of Zoology and Resource Ecology. He went on to hold several academic research and teaching positions, and worked as a marine-mammal biologist. He began publishing fiction around the time he finished graduate school.
Pop Team Epic, also known as Poptepipic, is a Japanese four-panel surreal comedy webcomic and digital manga series written and illustrated by Bkub Okawa, which started serialization on Takeshobo's Manga Life Win website in August 2014. Takeshobo has released three volumes in Japan. The manga is licensed in North America by Vertical.
Rush was a Canadian rock band formed in Toronto in 1968, consisting of Geddy Lee, Alex Lifeson, and Neil Peart. After its formation in 1968, the band went through several configurations until arriving at its classic lineup with the addition of Peart in 1974, just after the release of their eponymous debut album, which contained their first highly-regarded song, "Working Man".
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