Reject Hero, Farmerbob1 (About; superhero web serial, set in a Worm-like universe; somewhat unusual conservative middle-aged perspective as he negotiates his way into the deeper magical universe, culminating in a fun twist Jurassic Park ending with a sting; good fic but not great, and probably goes on too long)
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.
“Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption”, Cornelis, Marilyn C. Byrne, Enda M. Esko, Tõnu Nalls, Michael A. Ganna, Andrea Paynter, Nina Monda, Keri L. Amin, Najaf Fischer, Krista Renstrom, Frida Ngwa, Julius S. Huikari, Ville Cavadino, Alana Nolte, Ilja M. Teumer, Alexander Yu, Kai Marques-Vidal, Pedro Rawal, Rajesh Manichaikul, Ani Wojczynski, Mary K. Vink, Jacqueline M. Zhao, Jing Hua Burlutsky, George Lahti, Jari Mikkilä, Vera Lemaitre, Rozenn N. Eriksson, Joel Musani, Solomon K. Tanaka, Toshiko Geller, Frank Luan, Jian'an Hui, Jennie Mägi, Reedik Dimitriou, Maria Garcia, Melissa E. Ho, Weang-Kee Wright, Margaret J. Rose, Lynda M. Magnusson, Patrik Ke Pedersen, Nancy L. Couper, David Oostra, Ben A. Hofman, Albert Ikram, Mohammad Arfan Tiemeier, Henning W. Uitterlinden, Andre G. van Rooij, Frank Ja Barroso, Inês Johansson, Ingegerd Xue, Luting Kaakinen, Marika Milani, Lili Power, Chris Snieder, Harold Stolk, Ronald P. Baumeister, Sebastian E. Biffar, Reiner Gu, Fangyi Bastardot, François Kutalik, Zoltán Jacobs, David R. Forouhi, Nita G. Mihailov, Evelin Lind, Lars Lindgren, Cecilia Michaëlsson, Karl Morris, Andrew Jensen, Majken Khaw, Kay-Tee Luben, Robert N. Wang, Jie Jin Männistö, Satu Perälä, Mia-Maria Kähönen, Mika Lehtimäki, Terho Viikari, Jorma Mozaffarian, Dariush Mukamal, Kenneth Psaty, Bruce M. Döring, Angela Heath, Andrew C. Montgomery, Grant W. Dahmen, Norbert Carithers, Teresa Tucker, Katherine L. Ferrucci, Luigi Boyd, Heather A. Melbye, Mads Treur, Jorien L. Mellström, Dan Hottenga, Jouke Jan Prokopenko, Inga Tönjes, Anke Deloukas, Panos Kanoni, Stavroula Lorentzon, Mattias Houston, Denise K. Liu, Yongmei Danesh, John Rasheed, Asif Mason, Marc A. Zonderman, Alan B. Franke, Lude Kristal, Bruce S. Karjalainen, Juha Reed, Danielle R. Westra, Harm-Jan Evans, Michele K. Saleheen, Danish Harris, Tamara B. Dedoussis, George Curhan, Gary Stumvoll, Michael Beilby, John Pasquale, Louis R. Feenstra, Bjarke Bandinelli, Stefania Ordovas, Jose M. Chan, Andrew T. Peters, Ulrike Ohlsson, Claes Gieger, Christian Martin, Nicholas G. Waldenberger, Melanie Siscovick, David S. Raitakari, Olli Eriksson, Johan G. Mitchell, Paul Hunter, David J. Kraft, Peter Rimm, Eric B. Boomsma, Dorret I. Borecki, Ingrid B. Loos, Ruth Jf Wareham, Nicholas J. Vollenweider, Peter Caporaso, Neil Grabe, Hans Jörgen Neuhouser, Marian L. Wolffenbuttel, Bruce Hr Hu, Frank B. Hyppönen, Elina Järvelin, Marjo-Riitta Cupples, L. Adrienne Franks, Paul W. Ridker, Paul M. van Duijn, Cornelia M. Heiss, Gerardo Metspalu, Andres North, Kari E. Ingelsson, Erik Nettleton, Jennifer A. van Dam, Rob M. Chasman, Daniel I (2015):
Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to 91,462 coffee consumers of European ancestry with top single-nucleotide polymorphisms (SNPs) followed-up in ~30 062 and 7964 coffee consumers of European and African-American ancestry, respectively. Studies from both stages were combined in a trans-ethnic meta-analysis. Confirmed loci were examined for putative functional and biological relevance. Eight loci, including six novel loci, met GW significance (log10Bayes factor (BF)>5.64) with per-allele effect sizes of 0.03-0.14 cups per day. Six are located in or near genes potentially involved in pharmacokinetics (ABCG2, AHR, POR and CYP1A2) and pharmacodynamics (BDNF and SLC6A4) of caffeine. Two map to GCKR and MLXIPL genes related to metabolic traits but lacking known roles in coffee consumption. Enhancer and promoter histone marks populate the regions of many confirmed loci and several potential regulatory SNPs are highly correlated with the lead SNP of each. SNP alleles near GCKR, MLXIPL, BDNF and CYP1A2 that were associated with higher coffee consumption have previously been associated with smoking initiation, higher adiposity and fasting insulin and glucose but lower blood pressure and favorable lipid, inflammatory and liver enzyme profiles (p < 5 × 10−8).Our genetic findings among European and African-American adults reinforce the role of caffeine in mediating habitual coffee consumption and may point to molecular mechanisms underlying inter-individual variability in pharmacological and health effects of coffee.
We found that the adverse effect of neighbourhood deprivation on adolescent violent criminality and substance misuse in Sweden was not consistent with a causal inference. Instead, our findings highlight the need to control for familial confounding in multilevel studies of criminality and substance misuse.
Sacculina is a genus of barnacles that is a parasitic castrator of crabs. They belong to a group called Rhizocephala. The adults bear no resemblance to the barnacles that cover ships and piers; they are recognised as barnacles because their larval forms are like other members of the barnacle class Cirripedia. The prevalence of this crustacean parasite in its crab host can be as high as 50%.
Context: Controversy and uncertainty ensue when the results of clinical research on the effectiveness of interventions are subsequently contradicted. Controversies are most prominent when high-impact research is involved.
Objectives: To understand how frequently highly cited studies are contradicted or find effects that are stronger than in other similar studies and to discern whether specific characteristics are associated with such refutation over time.
Design: All original clinical research studies published in 3 major general clinical journals or high-impact-factor specialty journals in 1990–2003 and cited more than 1000 times in the literature were examined.
Main Outcome Measure: The results of highly cited articles were compared against subsequent studies of comparable or larger sample size and similar or better controlled designs. The same analysis was also performed comparatively for matched studies that were not so highly cited.
Results: Of 49 highly cited original clinical research studies, 45 claimed that the intervention was effective. Of these, 7 (16%) were contradicted by subsequent studies, 7 others (16%) had found effects that were stronger than those of subsequent studies, 20 (44%) were replicated, and 11 (24%) remained largely unchallenged. Five of 6 highly-cited nonrandomized studies had been contradicted or had found stronger effects vs 9 of 39 randomized controlled trials (p = 0.008). Among randomized trials, studies with contradicted or stronger effects were smaller (p = 0.009) than replicated or unchallenged studies although there was no statistically significant difference in their early or overall citation impact. Matched control studies did not have a significantly different share of refuted results than highly cited studies, but they included more studies with “negative” results.
Conclusions: Contradiction and initially stronger effects are not unusual in highly cited research of clinical interventions and their outcomes. The extent to which high citations may provoke contradictions and vice versa needs more study. Controversies are most common with highly cited nonrandomized studies, but even the most highly cited randomized trials may be challenged and refuted over time, especially small ones.
The purpose of this paper is to study the responses given to a questionnaire by subjects who received a tap water 'placebo' instead of lysergic acid diethylamide (LSD-25), and to relate the number of responses to other variables. These variables are: body weight, number of responses on a health questionnaire, arithmetic test scores, scores on the Wechsler-Bellevue Intelligence Scale, and Rorschach test responses.
…Figure 4 shows for each question the percentage and number of subjects out of 28 who gave a positive response at least once during the 0.5, 2.5, and 4.5-hour intervals. The questions appear in the figure in the order of decreasing percentages of response to them. The time of the response and the magnitude are disregarded in this tabulation. The question receiving the greatest percentage response was (Subject 24), "Are your palms moist?" As many as 60.7 per cent reported this symptom. Half of the subjects reported headache (Subject 13), fatigue (Subject 44), and drowsiness (Subject 45). About 36 per cent reported anxiety (Subject 47). Illness (Subject 1), and dizziness (Subject 15) were reported by 28.6 per cent of the group and 25 per cent indicated a dream-like feeling (Subject 46), increased appetite (Subject 6), unsteadiness (Subject 16), a hot feeling (Subject 22), heaviness of hands and feet (Subject 30), and weakness (Subject 43). There were 19 questions which received positive responses from between 10 and 22 per cent of the subjects. Less than 10 per cent of the group (or no more than two subjects) responded positively to the remaining questions, but each question received a positive response from at least one subject.
…The findings point out that a substance such as tap water, which is generally considered chemically and pharmacologically inactive, is capable of eliciting certain responses from certain subjects who believe they have received lysergic acid diethylamide. These observations emphasize once more the need for placebo controls in studies investigating the effects of drugs; without them changes which are produced merely by the situation and not by the drug are frequently falsely attributed to the action of the drug…Most subjects who respond to a placebo tend to do so most markedly during the first 0.5 hour after receiving the substance. At this time their anticipation of, and anxiety about, the effects of LSD-25 are probably greatest. Gradually the effects wear off, as the anticipation wears off. Individual differences exist in the time of peak effect, but this is the most common finding. The questions which elicited the greatest percentage response from the group were those related to anxiety (moist palms and feeling anxious) or to phenomena which commonly occur without the presence of any foreign agent (drowsiness, fatigue, and headache). The remaining questions received random responses. The fact that there is a wide range in the number of positive responses made to the questionnaire is of major interest.
Studies initially reported as conference abstracts that have positive results are subsequently published as full-length journal articles more often than studies with negative results.
Less than half of all studies, and about 60% of randomized or controlled clinical trials, initially presented as summaries or abstracts at professional meetings are subsequently published as peer-reviewed journal articles. An important factor appearing to influence whether a study described in an abstract is published in full is the presence of 'positive' results in the abstract. Thus, the efforts of persons trying to collect all of the evidence in a field may be stymied, first by the failure of investigators to take abstract study results to full publication, and second, by the tendency to take to full publication only those studies reporting 'significant' results. The consequence of this is that systematic reviews will tend to over-estimate treatment effects.
Background: Abstracts of presentations at scientific meetings are usually available only in conference proceedings. If subsequent full publication of abstract results is based on the magnitude or direction of study results, publication bias may result. Publication bias, in turn, creates problems for those conducting systematic reviews or relying on the published literature for evidence.
Objectives: To determine the rate at which abstract results are subsequently published in full, and the time between meeting presentation and full publication.
Search methods: We searched MEDLINE, EMBASE, The Cochrane Library, Science Citation Index, reference lists, and author files. Date of most recent search: June 2003. Selection criteria We included all reports that examined the subsequent full publication rate of biomedical results initially presented as abstracts or in summary form. Follow-up of abstracts had to be at least two years.
Data collection and analysis: Two reviewers extracted data. We calculated the weighted mean full publication rate and time to full publication. Dichotomous variables were analyzed using relative risk and random effects models. We assessed time to publication using Kaplan-Meier survival analyses.
Main results: Combining data from 79 reports (29,729 abstracts) resulted in a weighted mean full publication rate of 44.5% (95% confidence interval (CI) 43.9 to 45.1). Survival analyses resulted in an estimated publication rate at 9 years of 52.6% for all studies, 63.1% for randomized or controlled clinical trials, and 49.3% for other types of study designs.
'Positive' results defined as any 'significant' result showed an association with full publication (RR = 1.30; CI 1.14 to 1.47), as did 'positive' results defined as a result favoring the experimental treatment (RR = 1.17; CI 1.02 to 1.35), and 'positive' results emanating from randomized or controlled clinical trials (RR = 1.18, CI 1.07 to 1.30).
Other factors associated with full publication include oral presentation (RR = 1.28; CI 1.09 to 1.49); acceptance for meeting presentation (RR = 1.78; CI 1.50 to 2.12); randomized trial study design (RR = 1.24; CI 1.14 to 1.36); and basic research (RR = 0.79; CI 0.70 to 0.89). Higher quality of abstracts describing randomized or controlled clinical trials was also associated with full publication (RR = 1.30, CI 1.00 to 1.71).
Authors' conclusions: Only 63% of results from abstracts describing randomized or controlled clinical trials are published in full. 'Positive' results were more frequently published than not 'positive' results.
Objective:To determine whether remote, retroactive intercessory prayer, said for a group of patients with a bloodstream infection, has an effect on outcomes.
Design: Double blind, parallel group, randomised controlled trial of a retroactive intervention.
Setting: University hospital.
Subjects:All 3393 adult patients whose bloodstream infection was detected at the hospital in 1990–1996.
Intervention: In July 2000 patients were randomised to a control group and an intervention group. A remote, retroactive intercessory prayer was said for the well being and full recovery of the intervention group.
Main outcome measures: Mortality in hospital, length of stay in hospital, and duration of fever.
Results: Mortality was 28.1% (475⁄1691) in the intervention group and 30.2% (514⁄1702) in the control group (p for difference = 0.4). Length of stay in hospital and duration of fever were significantly shorter in the intervention group than in the control group (p = 0.01 and p = 0.04, respectively).
Conclusions: Remote, retroactive intercessory prayer said for a group is associated with a shorter stay in hospital and shorter duration of fever in patients with a bloodstream infection and should be considered for use in clinical practice.
What is already known on this topic: 2 randomised controlled trials of remote intercessory prayer (praying for persons unknown) showed a beneficial effect in patients in an intensive coronary care unit. A recent systematic review found that 57% of the randomised, placebo controlled trials of distant healing showed a positive treatment effect. What this study adds: Remote intercessory prayer said for a group of patients is associated with a shorter hospital stay and shorter duration of fever in patients with a bloodstream infection, even when the intervention is performed 4–10 years after the infection.
What is the productivity of Science? Can we measure an evolution of the production of mathematicians over history? Can we predict the waiting time till the proof of a challenging conjecture such as the P-versus-NP problem? Motivated by these questions, we revisit a suggestion published recently and debated in the "New Scientist" that the historical distribution of time-to-proof’s, i.e., of waiting times between formulation of a mathematical conjecture and its proof, can be quantified and gives meaningful insights in the future development of still open conjectures. We find however evidence that the mathematical process of creation is too much non-stationary, with too little data and constraints, to allow for a meaningful conclusion. In particular, the approximate unsteady exponential growth of human population, and arguably that of mathematicians, essentially hides the true distribution. Another issue is the incompleteness of the dataset available. In conclusion we cannot really reject the simplest model of an exponential rate of conjecture proof with a rate of 0.01/year for the dataset that we have studied, translating into an average waiting time to proof of 100 years. We hope that the presented methodology, combining the mathematics of recurrent processes, linking proved and still open conjectures, with different empirical constraints, will be useful for other similar investigations probing the productivity associated with mankind growth and creativity.
Background: Chronotype refers to individuals' preference for morning or evening activities. Its two dimensions (morningness and eveningness) are related to a number of academic outcomes.
Aims: The main goal of the study was to investigate the incremental validity of chronotype as a predictor of academic achievement after controlling for a number of traditional predictors. In so doing, a further aim was ongoing validation of a chronotype questionnaire, the Lark-Owl Chronotype Indicator.
Sample: The sample comprised 272 students attending 9th and 10th grades at five German high schools. Data was also obtained from 132 parents of these students.
Method: Students were assessed in class via self-report questionnaires and a standardized cognitive test. Parents filled out a questionnaire at home. The incremental validity of chronotype was investigated using hierarchical linear regression. Validity of the chronotype questionnaire was assessed by correlating student ratings of their chronotype with behavioural data on sleep, food intake, and drug consumption and with parent ratings of chronotype.
Results: Eveningness was a significant (negative) predictor of overall grade point average (GPA), math-science GPA, and language GPA, after cognitive ability, conscientiousness, need for cognition, achievement motivation, and gender were held constant. Validity evidence for the chronotype measure was established by significant correlations with parent-ratings and behavioural data.
Conclusions: Results point to the possible discrimination of adolescents with a proclivity towards eveningness at school. Possible explanations for the relationship between chronotype and academic achievement are presented. Implications for educational practice are also discussed.
Importance: It has been observed that suicidal behavior is influenced by sunshine and follows a seasonal pattern. However, seasons bring about changes in several other meteorological factors and a seasonal rhythm in social behavior may also contribute to fluctuations in suicide rates.
Objective: To investigate the effects of sunshine on suicide incidence that are independent of seasonal variation.
Design, Setting, and Participants: Retrospective analysis of data on all officially confirmed suicides in Austria between January 1, 1970, and May 6, 2010 (n = 69 462). Data on the average duration of sunshine per day (in hours) were calculated from 86 representative meteorological stations. Daily number of suicides and daily duration of sunshine were differentiated to remove variation in sunshine and variation in suicide incidence introduced by season. Thereafter, several models based on Pearson correlation coefficients were calculated.
Main Outcomes and Measures: Correlation of daily number of suicides and daily duration of sunshine after mathematically removing the effects of season.
Results: Sunshine hours and number of suicides on every day from January 1, 1970, to May 6, 2010, were highly correlated (r = 0.4870; p < 10−9). After differencing for the effects of season, a mathematical procedure that removes most of the variance from the data, a positive correlation between number of suicides and hours of daily sunshine remained for the day of suicide and up to 10 days prior to suicide (rmaximum = 0.0370; p < 10−5). There was a negative correlation between the number of suicides and daily hours of sunshine for the 14 to 60 days prior to the suicide event (rminimum = −0.0383; p < 10−5). These effects were found in the entire sample and in violent suicides.
Conclusions and Relevance: Duration of daily sunshine was significantly correlated with suicide frequency independent of season, but effect sizes were low. Our data support the hypothesis that sunshine on the day of suicide and up to 10 days prior to suicide may facilitate suicide. More daily sunshine 14 to 60 days previously is associated with low rates of suicide. Our study also suggests that sunshine during this period may protect against suicide.
We report on a user study that provides evidence that spaced repetition and a specific mnemonic technique enable users to successfully recall multiple strong passwords over time. Remote research participants were asked to memorize 4 Person-Action-Object (PAO) stories where they chose a famous person from a drop-down list and were given machine-generated random action-object pairs. Users were also shown a photo of a scene and asked to imagine the PAO story taking place in the scene (e.g., Bill Gates—swallowing—bike on a beach). Subsequently, they were asked to recall the action-object pairs when prompted with the associated scene-person pairs following a spaced repetition schedule over a period of 127+ days. While we evaluated several spaced repetition schedules, the best results were obtained when users initially returned after 12 hours and then in 1.5× increasing intervals: 77 successfully recalled all 4 stories in 10 tests over a period of 158 days. Much of the forgetting happened in the first test period (12 hours): 89 participants who remembered their stories during the first test period successfully remembered them in every subsequent round. These findings, coupled with recent results on naturally rehearsing password schemes, suggest that 4 PAO stories could be used to create usable and strong passwords for 14 sensitive accounts following this spaced repetition schedule, possibly with a few extra upfront rehearsals. In addition, we find that there is an interference effect across multiple PAO stories: the recall rate of 100 90 stories) is significantly better than the recall rate for participants who were asked to memorize 4 PAO stories. These findings yield concrete advice for improving constructions of password management schemes and future user studies.
Photoacoustic spectroscopy is the measurement of the effect of absorbed electromagnetic energy on matter by means of acoustic detection. The discovery of the photoacoustic effect dates to 1880 when Alexander Graham Bell showed that thin discs emitted sound when exposed to a beam of sunlight that was rapidly interrupted with a rotating slotted disk. The absorbed energy from the light causes local heating, generating a thermal expansion which creates a pressure wave or sound. Later Bell showed that materials exposed to the non-visible portions of the solar spectrum can also produce sounds.
The "kids for cash" scandal centered on judicial kickbacks to two judges at the Luzerne County Court of Common Pleas in Wilkes-Barre, Pennsylvania. In 2008, judges Michael Conahan and Mark Ciavarella were accused of accepting money in return for imposing harsh adjudications on juveniles to increase occupancy at for-profit detention centers.
Every product in the marketplace has substitutes and complements. A substitute is another product you might buy if the first product is too expensive. Chicken is a substitute for beef. If you’re a chicken farmer and the price of beef goes up, the people will want more chicken, and you will sell more. A complement is a product that you usually buy together with another product. Gas and cars are complements. Computer hardware is a classic complement of computer operating systems. And babysitters are a complement of dinner at fine restaurants. In a small town, when the local five star restaurant has a two-for-one Valentine’s day special, the local babysitters double their rates. (Actually, the nine-year-olds get roped into early service.) All else being equal, demand for a product increases when the prices of its complements decrease.
Let me repeat that because you might have dozed off, and it’s important. Demand for a product increases when the prices of its complements decrease. For example, if flights to Miami become cheaper, demand for hotel rooms in Miami goes up—because more people are flying to Miami and need a room. When computers become cheaper, more people buy them, and they all need operating systems, so demand for operating systems goes up, which means the price of operating systems can go up.
…Once again: demand for a product increases when the price of its complements decreases. In general, a company’s strategic interest is going to be to get the price of their complements as low as possible. The lowest theoretically sustainable price would be the “commodity price”—the price that arises when you have a bunch of competitors offering indistinguishable goods. So:
Smart companies try to commoditize their products’ complements.
If you can do this, demand for your product will increase and you will be able to charge more and make more.
Joel Spolsky in 2002 identified a major pattern in technology business & economics: the pattern of “commoditizing your complement”, an alternative to vertical integration, where companies seek to secure a chokepoint or quasi-monopoly in products composed of many necessary & sufficient layers by dominating one layer while fostering so much competition in another layer above or below its layer that no competing monopolist can emerge, prices are driven down to marginal costs elsewhere in the stack, total price drops & increases demand, and the majority of the consumer surplus of the final product can be diverted to the quasi-monopolist. A classic example is the commodification of PC hardware by the Microsoft OS monopoly, to the detriment of IBM & benefit of MS.
This pattern explains many otherwise odd or apparently self-sabotaging ventures by large tech companies into apparently irrelevant fields, such as the high rate of releasing open-source contributions by many Internet companies or the intrusion of advertising companies into smartphone manufacturing & web browser development & statistical software & fiber-optic networks & municipal WiFi & radio spectrum auctions & DNS (Google): they are pre-emptive attempts to commodify another company elsewhere in the stack, or defenses against it being done to them.
Scapa Flow is a body of water in the Orkney Islands, Scotland, sheltered by the islands of Mainland, Graemsay, Burray, South Ronaldsay and Hoy. Its sheltered waters have played an important role in travel, trade and conflict throughout the centuries. Vikings anchored their longships in Scapa Flow more than a thousand years ago. It was the United Kingdom's chief naval base during the First and Second World Wars, but the facility was closed in 1956.
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.)