This is a summary of the revision-history RSS feed, overlapping with Changelog & including material from /r/gwern/. This broadcast has been brought to you by Royal Kooparillo and my donors on Gratipay.
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.
I compile a table and discussion of all known arrests and prosecutions related to English-language Tor-Bitcoin darknet markets (DNMs) such as Silk Road 1, primarily 2011–2015, along with discussion of how they came to be arrested.
“Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N = 53,949)”, G. Davies, N. Armstrong, J. C. Bis, J. Bressler, V. Chouraki, S. Giddaluru, E. Hofer, C. A Ibrahim-Verbaas, M. Kirin, J. Lahti, S. J. van der Lee, S. Le Hellard, T. Liu, R. E. Marioni, C. Oldmeadow, I. Postmus, A. V. Smith, J. A Smith, A. Thalamuthu, R. Thomson, V. Vitart, J. Wang, L. Yu, L. Zgaga, W. Zhao, R. Boxall, S. E. Harris, W. D. Hill, D. C. Liewald, M. Luciano, H. Adams, D. Ames, N. Amin, P. Amouyel, A. A Assareh, R. Au, J. T. Becker, A. Beiser, C. Berr, L. Bertram, E. Boerwinkle, B. M. Buckley, H. Campbell, J. Corley, P. L. De Jager, C. Dufouil, J. G. Eriksson, T. Espeseth, J. D. Faul, I. Ford, Generation Scotland, R. F. Gottesman, M. E. Griswold, V. Gudnason, T. B. Harris, G. Heiss, A. Hofman, E. G. Holliday, J. Huffman, S. L. R. Kardia, N. Kochan, D. S. Knopman, J. B. Kwok, J-C Lambert, T. Lee, G. Li, S-C Li, M. Loitfelder, O. L. Lopez, A. J. Lundervold, A. Lundqvist, K. A Mather, S. S. Mirza, L. Nyberg, B. A Oostra, A. Palotie, G. Papenberg, A. Pattie, K. Petrovic, O. Polasek, B. M. Psaty, P. Redmond, S. Reppermund, J. I Rotter, H. Schmidt, M. Schuur, P. W. Schofield, R. J. Scott, V. M. Steen, D. J. Stott, J. C. van Swieten, K. D. Taylor, J. Trollor, S. Trompet, A. G. Uitterlinden, G. Weinstein, E. Widen, B. G. Windham, J. W. Jukema, A. F. Wright, M. J. Wright, Q. Yang, H. Amieva, J. R. Attia, D. A Bennett, H. Brodaty, A. J. M. de Craen, C. Hayward, M. A Ikram, U. Lindenberger, L-G Nilsson, D. J. Porteous, K. Räikkönen, I. Reinvang, I. Rudan, P. S. Sachdev, R. Schmidt, P. R. Schofield, V. Srikanth, J. M. Starr, S. T. Turner, D. R. Weir, J. F. Wilson, C. van Duijn, L. Launer, A. L. Fitzpatrick, S. Seshadri, T. H. Mosley Jr, I. J. Deary (2015-02-03):
General cognitive function is substantially heritable across the human life course from adolescence to old age. We investigated the genetic contribution to variation in this important, health-related and well-being-related trait in middle-aged and older adults. We conducted a meta-analysis of genome-wide association studies of 31 cohorts (N = 53 949) in which the participants had undertaken multiple, diverse cognitive tests. A general cognitive function phenotype was tested for, and created in each cohort by principal component analysis. We report 13 genome-wide significant single-nucleotide polymorphism (SNP) associations in three genomic regions, 6q16.1, 14q12 and 19q13.32 (best SNP and closest gene, respectively: rs10457441, p =3.93 × 10−9, MIR2113; rs17522122, p = 2.55 × 10−8, AKAP6; rs10119, p =5.67 × 10−9, APOE/TOMM40). We report one gene-based significant association with the HMGN1 gene located on chromosome 21 (p = 1 × 10−6). These genes have previously been associated with neuropsychiatric phenotypes. Meta-analysis results are consistent with a polygenic model of inheritance. To estimate SNP-based heritability, the genome-wide complex trait analysis procedure was applied to two large cohorts, the Atherosclerosis Risk in Communities Study (N = 6617) and the Health and Retirement Study (N = 5976). The proportion of phenotypic variation accounted for by all genotyped common SNPs was 29% (s.e.=5%) and 28% (s.e.=7%), respectively. Using polygenic prediction analysis, ~1.2% of the variance in general cognitive function was predicted in the Generation Scotland cohort (N = 5487; p = 1.5 × 10−17). In hypothesis-driven tests, there was significant association between general cognitive function and four genes previously associated with Alzheimer’s disease: TOMM40, APOE, ABCG1 and MEF2C.
Environmental measures used widely in the behavioral sciences show nearly as much genetic influence as behavioral measures, a critical finding for interpreting associations between environmental factors and children's development. This research depends on the twin method that compares monozygotic and dizygotic twins, but key aspects of children's environment such as socioeconomic status (SES) cannot be investigated in twin studies because they are the same for children growing up together in a family. Here, using a new technique applied to DNA from 3000 unrelated children, we show significant genetic influence on family SES, and on its association with children's IQ at ages 7 and 12. In addition to demonstrating the ability to investigate genetic influence on between-family environmental measures, our results emphasize the need to consider genetics in research and policy on family SES and its association with children's IQ.
“Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication”, Michael J. Montague, Gang Li, Barbara Gandolfi, Razib Khan, Bronwen L. Aken, Steven M. J. Searle, Patrick Minx, LaDeana W. Hillier, Daniel C. Koboldt, Brian W. Davis, Carlos A. Driscoll, Christina S. Barr, Kevin Blackistone, Javier Quilez, Belen Lorente-Galdos, Tomas Marques-Bonet, Can Alkan, Gregg W. C. Thomas, Matthew W. Hahn, Marilyn Menotti-Raymond, Stephen J. O’Brien, Richard K. Wilson, Leslie A. Lyons, William J. Murphy, and Wesley C. Warren (2014-10-03):
Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.
Paroxetine is a selective serotonin reuptake inhibitor (SSRI) that is currently available on the market and is suspected of causing congenital malformations in babies born to mothers who take the drug during the first trimester of pregnancy. We utilized organismal performance assays (OPAs), a novel toxicity assessment method, to assess the safety of paroxetine during pregnancy in a rodent model. OPAs utilize genetically diverse wild mice (Mus musculus) to evaluate competitive performance between experimental and control animals as they compete amongst each other for limited resources in semi-natural enclosures. Performance measures included reproductive success, male competitive ability and survivorship. Paroxetine-exposed males weighed 13% less, had 44% fewer offspring, dominated 53% fewer territories and experienced a 2.5-fold increased trend in mortality, when compared with controls. Paroxetine-exposed females had 65% fewer offspring early in the study, but rebounded at later time points. In cages, paroxetine-exposed breeders took 2.3 times longer to produce their first litter and pups of both sexes experienced reduced weight when compared with controls. Low-dose paroxetine-induced health declines detected in this study were undetected in preclinical trials with dose 2.5-8 times higher than human therapeutic doses. These data indicate that OPAs detect phenotypic adversity and provide unique information that could useful towards safety testing during pharmaceutical development. [Keywords: intraspecific competition, pharmacodynamics, reproductive success, semi-natural enclosures, SSRI, toxicity assessment.]
Earlier work described a mutation in DEC2 also known as BHLHE41 (basic helix-loophelix family member e41) as causal in a family of short sleepers, who needed just 6 h sleep per night. We evaluated whether there were other variants of this gene in two well-phenotyped cohorts. Sequencing of the BHLHE41 gene, electroencephalographic data, and delta power analysis and functional studies using cell-based luciferase. We identified new variants of the BHLHE41 gene in two cohorts who had either acute sleep deprivation (n = 200) or chronic partial sleep deprivation (n = 217). One variant, Y362H, at another location in the same exon occurred in one twin in a dizygotic twin pair and was associated with reduced sleep duration, less recovery sleep following sleep deprivation, and fewer performance lapses during sleep deprivation than the homozygous twin. Both twins had almost identical amounts of non rapid eye movement (NREM) sleep. This variant reduced the ability of BHLHE41 to suppress CLOCK/BMAL1 and NPAS2/BMAL1 transactivation in vitro. Another variant in the same exome had no effect on sleep or response to sleep deprivation and no effect on CLOCK/BMAL1 transactivation. Random mutagenesis identified a number of other variants of BHLHE41 that affect its function. There are a number of mutations of BHLHE41. Mutations reduce total sleep while maintaining NREM sleep and provide resistance to the effects of sleep loss. Mutations that affect sleep also modify the normal inhibition of BHLHE41 of CLOCK/BMAL1 transactivation. Thus, clock mechanisms are likely involved in setting sleep length and the magnitude of sleep homeostasis. Pellegrino R, Kavakli IH, Goel N, Cardinale CJ, Dinges DF, Kuna ST, Maislin G, Van Dongen HP, Tufik S, Hogenesch JB, Hakonarson H, Pack AI. A novel BHLHE41 variant is associated with short sleep and resistance to sleep deprivation in humans. SLEEP 2014;37(8):1327-1336.
To determine the speed at which the Grim Reaper (or Death) walks. Population based prospective study. Older community dwelling men living in Sydney, Australia. 1705 men aged 70 or more participating in CHAMP (Concord Health and Ageing in Men Project). Walking speed (m/s) and mortality. Receiver operating characteristics curve analysis was used to calculate the area under the curve for walking speed and determine the walking speed of the Grim Reaper. The optimal walking speed was estimated using the Youden index (sensitivity + specificity-1), a common summary measure of the receiver operating characteristics curve, and represents the maximum potential effectiveness of a marker. The mean walking speed was 0.88 (range 0.15-1.60) m/s. The highest Youden index (0.293) was observed at a walking speed of 0.82 m/s (2 miles (about 3 km) per hour), corresponding to a sensitivity of 63% and a specificity of 70% for mortality. Survival analysis showed that older men who walked faster than 0.82 m/s were 1.23 times less likely to die (95% confidence interval 1.10 to 1.37) than those who walked slower (P = 0.0003). A sensitivity of 1.0 was obtained when a walking speed of 1.36 m/s (3 miles (about 5 km) per hour) or greater was used, indicating that no men with walking speeds of 1.36 m/s or greater had contact with Death. The Grim Reaper's preferred walking speed is 0.82 m/s (2 miles (about 3 km) per hour) under working conditions. As none of the men in the study with walking speeds of 1.36 m/s (3 miles (about 5 km) per hour) or greater had contact with Death, this seems to be the Grim Reaper's most likely maximum speed; for those wishing to avoid their allotted fate, this would be the advised walking speed.
Project Iceworm was a top secret United States Army program of the Cold War, which aimed to build a network of mobile nuclear missile launch sites under the Greenland ice sheet. The ultimate objective of placing medium-range missiles under the ice — close enough to strike targets within the Soviet Union — was kept secret from the Government of Denmark. To study the feasibility of working under the ice, a highly publicized "cover" project, known as Camp Century, was launched in 1960. Unstable ice conditions within the ice sheet caused the project to be canceled in 1966.
[Fierce but witty critique by David Stove of philosophy throughout the ages and defense of Logical Positivism, with Christian theology, Neoplatonism, and German Idealism as examples. Logical Positivists took the easy way out: the problem with these philosophies is not that they are gibberish or meaningless, because at least then they would all be wrong in the same way and could perhaps be refuted in the same way, but that they each are wrong in a myriad of different ways, ways for which we have no existing “fallacy” defined, entire universes of new errors—undermining the hope of using reason or philosophy to make any kind of progress. What is wrong with philosophy, and ourselves, if we cannot even explain why these are so badly wrong after millennia of thought and debate?]
Peopleware: Productive Projects and Teams is a 1987 book on the social side of software development, specifically managing project teams. It was written by software consultants Tom DeMarco and Tim Lister, from their experience in the world of software development. This book was revised in 2013.
Dead Birds is a 1963 American documentary film by Robert Gardner (1925-2014) about the ritual warfare cycle of the Dugum Dani people who live in the Baliem Valley in present-day Irian Jaya province on the western half of the island of New Guinea that is part of present-day Indonesia. The film presents footage of battles between the Willihiman-Wallalua clan and the Wittaia clan with scenes of the funeral of a small boy killed by a raiding party, the women's work that goes on while battles continue, and the wait for enemy to appear. In 1964 the film received the Grand Prize "Marzocco d'Oro" at the 5th Festival dei Populi rassegna internazionale del film etnografico e sociologico in Florence, Italy, the Robert J. Flaherty Award given by the City College of New York, and was a featured film at the Melbourne Film Festival. In 1998, Dead Birds was included in the annual selection of 25 motion pictures added to the National Film Registry of the Library of Congress. being deemed "culturally, historically, or aesthetically significant" and recommended for preservation. Dead Birds has come to hold canonical status among ethnographic films.
A State of Mind is a 2004 documentary film directed by Daniel Gordon and produced by Nicholas Bonner. It follows two North Korean child gymnasts and their families for over eight months during training for the 2003 Pyongyang mass games. The film won two awards at the North Korean Pyongyang International Film Festival in 2004 and was shown at 11 other film festivals worldwide before being released in a theatrical run in 2005.
Cowboy Bebop is a Japanese science-fiction anime television series animated by Sunrise featuring a production team led by director Shinichirō Watanabe, screenwriter Keiko Nobumoto, character designer Toshihiro Kawamoto, mechanical designer Kimitoshi Yamane, and composer Yoko Kanno. The twenty-six episodes ("sessions") of the series are set in the year 2071, and follow the lives of a bounty hunter crew traveling in their spaceship called the Bebop. Although it covers a wide range of genres throughout its run, Cowboy Bebop draws most heavily from science fiction, western and noir films, and its most recurring thematic focal points include adult existential ennui, loneliness and the difficulties of trying to escape one's past.
Subscription page for the monthly gwern.net newsletter. There are 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. You can also browse the archives since December 2013.
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.)