N/A
2016-02-01–2021-01-04
finished
certainty: log
importance: 0
This is the February 2016 edition of the Gwern.net newsletter; previous, January 2016. This is a summary of the revision-history RSS feed, overlapping with Changelog & /
Writings
Media
Links
Genetics:
Everything Is Heritable:
Politics/
- “Cuban missile crisis: The other, secret one”
- “The Market for Sanctimony, or why we need Yet Another Space Alien Cult (YASAC)”
- “So Far Unfruitful, Fusion Project Faces a Frugal Congress”
- Thomas Jefferson and planning the University of Virginia
Statistics/
- “PlaNet—Photo Geolocation with Convolutional Neural Networks”, Weyand et al 2016
- “When Quality Beats Quantity: Decision Theory, Drug Discovery, and the Reproducibility Crisis”, Scannell & Bosley 2016
- “Deming, data and observational studies: A process out of control and needing fixing”, Young 2011
- “Online Controlled Experiments: Introduction, Learnings, and Humbling Statistics”, Kohavi 2012
- “My published negative result…”
- Gambler’s ruin
- “Bayesian estimation supersedes the t test”, Kruschke 2012
- “Electoral Precedent”
- “A Bayesian view of Amazon Resellers”
Psychology/
- “Aldehyde-stabilized cryopreservation”, McIntyre & Fahy 2015 wins the Small Mammal Brain Preservation Prize by passing their evaluation (commentary)
- “Effects of Initiating Moderate Alcohol Intake on Cardiometabolic Risk in Adults With Type 2 Diabetes: A 2-Year Randomized, Controlled Trial”, Gepner et al 2015
- “My son’s flashcard routine”
- “A Mole of Moles”
- “We Add Near, Average Far”
- “Nothing in Biology Makes Sense Except in the Light of Evolution”
- “The animals that sniff out TB, cancer and landmines”
- “Parenting and Happiness”
- Is sleep to save energy?
Technology:
- “Gravitational Waves Exist: The Inside Story of How Scientists Finally Found Them”
- “How Did Software Get So Reliable Without Proof?”, Hoare 1996 (comments)
- “Stargate Physics 101” (“Testing is sufficient to show the presence of bugs, but not the absence.”)
- Merkle’s Puzzles
- On Ray Kurzweil
- Pokemon: determining the personality settings
- “Can you use a magnifying glass and moonlight to light a fire?”
Economics:
Books
Fiction:
- Thorsby’s Transdimensional Brain Chip (Another Thorsby webcomic has finished. You know what you’re getting: clever high-concept plot which keeps slowly building with occasional comedy of errors, semi-awkward writing, and MS Paint art that never improves. If you liked Accidental Space Spy, you’ll like this. If not, not.)
- Chanson de Geste (Narnia fanfiction: realpolitik-Chthulian romance. Game mechanic reminds me of The Player of Games.)
- Lem’s Memoirs Found in a Bathtub (review)
Nonfiction:
- Hive Mind: how your nation’s IQ matters so much more than your own, Jones 2016 (review)
- Visions of Virtue in Tokugawa Japan (dull history of obscure & obsolete ideologies with no relevance to anything; for Japanese Neo-Confucian specialists only)
Film/TV
Live-action:
- The Black Cat (1934; review)
Anime:
Games
Broforce is a 2D pixel-art scrolling 1-hit-death run-and-gun action-shooter in the vein of Metal Slug with a War on Terror/
‘Murica’/ 1980s-action-movie theme; it adds an almost-fully destructible environment and emphasizes vertical movement, so it’s the campy offspring of Metal Slug & Minecraft. The homages to MS are particularly noticeable in the vehicles you can use to fight in and how the terrorist enemies give way to alien enemies with occasional three-way battles. I loved MS as a kid for its beautiful sprites, touches of humor (like sneaking up on Nazis while they chatted), and perfectly-balanced action gameplay, so when I saw BF come up on Steam during the 2016 Lunar sale for $7.49, I bought it. I figured even as a single-player game, it looked fun. Overall, I enjoyed it a lot. The controls are slick & reactive, with the default mapping of the up d-key to ‘jump’ quickly coming to feel natural; the action is almost instantly addictive, especially as you start to figure out how to work around the limit that you can usually only shoot horizontally and you are often outranged so if you approach enemies the straightforward way, you will typically die immediately. There’s a lot of fun in figuring out how to best dig beneath enemies and attack them from behind, panic or shoot the suicide bombers into exploding amid a group of enemies, shoot out the ground underneath a tricky opponent, or set up chain reactions of explosions; since you do not choose which character & weapons you use, you also must learn how to work with individual characters in different situations (the Man in Black has a powerful shot, but the recoil means it can be tricky to use without knocking yourself into a pit or dropping a boulder onto your head; the Terminator’s minigun is fantastic for tunneling but also has steady recoil and takes a fraction of a second to spin up; MacGyver’s bomb throwing is more useful than it initially seems because you can destroy parts of the environment far from you and create impromptu suicide bombers). It borders on a physics puzzle game at times. While somewhat repetitious, there’s enough variety in level design to keep one interested: many levels are straightforward run-and-gun, but when encountering a mecha, it may be best to tunnel underneath it to kill it instead of hijacking it, and in a level with constant bombardment, tunneling is a necessity. The destructible environment may sound like a recipe for cheap deaths and the possibility of making a level impossible to complete when you’ve destroyed too much ground to progress, but while I had to make some tricky jumps and excavations after some particularly heated firefights, I don’t think I ever totally cut myself off from the end of the level.
All of which made it even more frustrating when I ran into parts of BF which aren’t quite polished yet: either not yet balanced appropriately, or an editor needs to tell the BF developers to kill their darlings. BF is proud of its large assortment of characters, but some of them plain suck and the game punishes you every time you rescue a prisoner and a random character swap is forced onto you and you get one of the sucky characters (random character swaps can be fun when it forces you out of your comfort zone, but not in those cases); I never figured out how to use melee characters like Neo or Blade successfully, and one character with a machine-gun leg (which only fires downwards) is so utterly useless that by the end of the game I was seriously considering just jumping into a pit anytime I got them and sparing myself the frustration of such a gimped character. BF would be much better if the worst 5 or 10 characters were simply deleted. (It would also be good if special attacks transferred. Nothing like saving up for a mecha only to lose it all when you free a prisoner… Fun like a kick in the teeth.) Another intense source of frustration was the lack of even the most vital hints. In the second covert mission, the start has a huge pit which must be jumped across and can only be jumped across if you are ‘sprinting’ by having double-tapped-and-held the directional key; nowhere are you told that ‘sprinting’ even exists and there is no reason you would have tried this double-tap or noticed the sprinting since, as mentioned before, flatout running is a guaranteed way to die. I died 20 or 30 times before I finally gave up and googled “Broforce impossible level”; there were several different levels which were the topic of discussion, and I finally learned about sprinting and beat the level a few deaths later. Another covert mission is still worse: the level begins with an enormous explosion, which you have been trained by dozens of previous enormous explosions to wait out; when you do so, the mission is unbeatable because half the level is gone. It turns out that unknown and unknowable to you, there was an long catwalk at the top of the level, and the solution to the level is to immediately begin running, get a powerup while running, invoke the time-slowing while running, climb a several-screen-high ladder at top speed while the rest of the level is slowed, and then run across the catwalk which is already exploding to the point where you are jumping from falling crate to crate. So just to know that that catwalk exists, much less what you have to do to finish the level you have to have started the level running and time-slow immediately to climb the ladder and get to see that there was a catwalk there! There is no hint whatsoever of any of this by BF. So if anyone was able to figure this level out on their own without checking the Internet & watching YouTube, I doff my chapeau to them. All it would have taken in these two levels is a short hint: ‘double-tap the d-key to sprint’; ‘reach the catwalk before the explosion!’ I am not asking for those levels to be made easier, just that the player has some idea what they’re supposed to do! This lack of hints extends to the characters themselves and their special attacks; what did Neo’s special do? I had no idea—it made a little glowy circle which didn’t seem to do anything. What did Robocop’s special do? I had no idea—it created a green grid on the screen with a targeting reticule you could move, but pressing fire/
special did nothing, and moving the reticule over enemies did nothing. How did Braveheart, the Professional etc? Towards the end I looked them up on the Broforce wikia, but I should not have had to; would it have killed BF to include a one-line summary of the special like “reflects most bullets” or “select each enemy to automatically attack”? A few of the levels trade too heavily on trial-and-error: one alien’s level is unbeatable unless you simply memorize each location it attacks throughout the whole level, because it is invulnerable, and moves too fast to react to. The cave levels feature way too many boulders and rocks so you will constantly die of falling rocks no matter how careful you are. Two levels are so dark that you cannot see where your character is and will die many times from jumping into a wall to avoid an attack. On the giant-helicopter level, you can die and lose even after you’ve won during the animation of the helicopter exploding, which happened to me 3 times in a row because the end of the level is so full of explosives. ‘Fun’. The alien levels are substantially less enjoyable because the various acid explosions extend insta-death across the screen and the fast-moving aggressive melee aliens make certain characters almost useless (good luck using either bomb-thrower when you’re busy being swarmed!). Perhaps partly due to the randomized character selection and total absence of documentation, there seems to be extreme variation in difficulty: I might die 5 times clearing a level, then 30 the next level, then 1 the following level! Certainly some variation in difficulty from level to level is normal and desirable, but that much variation suggests that some levels need some tweaking… Perhaps the developers will fix some of these issues in the future, and meanwhile, to those who play BF, I advise being less proud than myself and to look online for hints.
Link Bibliography
Bibliography of page links in reading order (with annotations when available):
“January 2016 News”, (2016-01-01):
N/A
“Changelog”, (2013-09-15):
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/ 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).Gwern “/r/gwern subreddit”, (2018-10-01):
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.
“Embryo Selection For Intelligence”, (2016-01-22):
With genetic predictors of a phenotypic trait, it is possible to select embryos during an in vitro fertilization process to increase or decrease that trait. Extending the work of Shulman & Bostrom 2014/
Hsu 2014, I consider the case of human intelligence using SNP-based genetic prediction, finding: - a meta-analysis of GCTA results indicates that SNPs can explain >33% of variance in current intelligence scores, and >44% with better-quality phenotype testing
- this sets an upper bound on the effectiveness of SNP-based selection: a gain of 9 IQ points when selecting the top embryo out of 10
- the best 2016 polygenic score could achieve a gain of ~3 IQ points when selecting out of 10
- the marginal cost of embryo selection (assuming IVF is already being done) is modest, at $1500 + $200 per embryo, with the sequencing cost projected to drop rapidly
- a model of the IVF process, incorporating number of extracted eggs, losses to abnormalities & vitrification & failed implantation & miscarriages from 2 real IVF patient populations, estimates feasible gains of 0.39 & 0.68 IQ points
- embryo selection is currently unprofitable (mean: -$358) in the USA under the lowest estimate of the value of an IQ point, but profitable under the highest (mean: $6230). The main constraints on selection profitability is the polygenic score; under the highest value, the NPV EVPI of a perfect SNP predictor is $24b and the EVSI per education/
SNP sample is $71k - under the worst-case estimate, selection can be made profitable with a better polygenic score, which would require n > 237,300 using education phenotype data (and much less using fluid intelligence measures)
- selection can be made more effective by selecting on multiple phenotype traits: considering an example using 7 traits (IQ/
height/ BMI/ diabetes/ ADHD/ bipolar/ schizophrenia), there is a factor gain over IQ alone; the outperformance of multiple selection remains after adjusting for genetic correlations & polygenic scores and using a broader set of 16 traits.
http:/
/ www.sciencedirect.com/ science/ article/ pii/ S016028961630023X http:/
/ www.nature.com/ ncomms/ 2016/ 160202/ ncomms10448/ full/ ncomms10448.html http:/
/ www.nytimes.com/ 2012/ 09/ 30/ science/ fusion-project-faces-a-frugal-congress.html http:/
/ www.johndcook.com/ blog/ 2011/ 03/ 03/ thomas-jefferson-meetings/ “PlaNet - Photo Geolocation with Convolutional Neural Networks”, (2016-02-17):
Is it possible to build a system to determine the location where a photo was taken using just its pixels? In general, the problem seems exceptionally difficult: it is trivial to construct situations where no location can be inferred. Yet images often contain informative cues such as landmarks, weather patterns, vegetation, road markings, and architectural details, which in combination may allow one to determine an approximate location and occasionally an exact location. Websites such as GeoGuessr and View from your Window suggest that humans are relatively good at integrating these cues to geolocate images, especially en-masse. In computer vision, the photo geolocation problem is usually approached using image retrieval methods. In contrast, we pose the problem as one of classification by subdividing the surface of the earth into thousands of multi-scale geographic cells, and train a deep network using millions of geotagged images. While previous approaches only recognize landmarks or perform approximate matching using global image descriptors, our model is able to use and integrate multiple visible cues. We show that the resulting model, called PlaNet, outperforms previous approaches and even attains superhuman levels of accuracy in some cases. Moreover, we extend our model to photo albums by combining it with a long short-term memory (LSTM) architecture. By learning to exploit temporal coherence to geolocate uncertain photos, we demonstrate that this model achieves a 50 over the single-image model.
“When Quality Beats Quantity: Decision Theory, Drug Discovery, and the Reproducibility Crisis”, (2016-02-10):
A striking contrast runs through the last 60 years of biopharmaceutical discovery, research, and development. Huge scientific and technological gains should have increased the quality of academic science and raised industrial R&D efficiency. However, academia faces a “reproducibility crisis”; inflation-adjusted industrial R&D costs per novel drug increased nearly 100× between 1950 and 2010; and drugs are more likely to fail in clinical development today than in the 1970s. The contrast is explicable only if powerful headwinds reversed the gains and/or if many “gains” have proved illusory. However, discussions of reproducibility and R&D productivity rarely address this point explicitly.
The main objectives of the primary research in this paper are: (a) to provide quantitatively and historically plausible explanations of the contrast; and (b) identify factors to which R&D efficiency is sensitive.
We present a quantitative decision-theoretic model of the R&D process [a ‘leaky pipeline’; cf the log-normal]. The model represents therapeutic candidates (e.g., putative drug targets, molecules in a screening library, etc.) within a “measurement space”, with candidates’ positions determined by their performance on a variety of assays (e.g., binding affinity, toxicity, in vivo efficacy, etc.) whose results correlate to a greater or lesser degree. We apply decision rules to segment the space, and assess the probability of correct R&D decisions.
We find that when searching for rare positives (e.g., candidates that will successfully complete clinical development), changes in the predictive validity of screening and disease models that many people working in drug discovery would regard as small and/or unknowable (i.e., an 0.1 absolute change in correlation coefficient between model output and clinical outcomes in man) can offset large (e.g., 10×, even 100×) changes in models’ brute-force efficiency. We also show how validity and reproducibility correlate across a population of simulated screening and disease models.
We hypothesize that screening and disease models with high predictive validity are more likely to yield good answers and good treatments, so tend to render themselves and their diseases academically and commercially redundant. Perhaps there has also been too much enthusiasm for reductionist molecular models which have insufficient predictive validity. Thus we hypothesize that the average predictive validity of the stock of academically and industrially “interesting” screening and disease models has declined over time, with even small falls able to offset large gains in scientific knowledge and brute-force efficiency. The rate of creation of valid screening and disease models may be the major constraint on R&D productivity.
http:/
/ www.exp-platform.com/ Documents/ 2012-09%20ACMRecSysNR.pdf “Gambler's ruin”, (2020-12-22):
The term gambler's ruin is a statistical concept, most commonly expressed as the fact that a gambler playing a negative expected value game will eventually go broke, regardless of their betting system.
“Bayesian estimation supersedes the t test”, (2013-01-01):
Bayesian estimation for 2 groups provides complete distributions of credible values for the effect size, group means and their difference, standard deviations and their difference, and the normality of the data. The method handles outliers. The decision rule can accept the null value (unlike traditional t-tests) when certainty in the estimate is high (unlike Bayesian model comparison using Bayes factors). The method also yields precise estimates of statistical power for various research goals. The software and programs are free and run on Macintosh, Windows, and Linux platforms. [Keywords: Bayesian statistics, effect size, robust estimation, Bayes factor, confidence interval]
http:/
/ www.sciencedirect.com/ science/ article/ pii/ S001122401500245X http:/
/ lesswrong.com/ lw/ na3/ the_brain_preservation_foundations_small/ http:/
/ bentilly.blogspot.com/ 2012/ 10/ my-sons-flashcard-routine.html http:/
/ www.overcomingbias.com/ 2012/ 10/ we-add-near-average-far.html http:/
/ www.pbs.org/ wgbh/ evolution/ library/ 10/ 2/ text_pop/ l_102_01.html http:/
/ mosaicscience.com/ story/ rats-and-dogs-medical-detection-animals-smell-TB-cancer http:/
/ lesswrong.com/ r/ discussion/ lw/ erj/ parenting_and_happiness/ http:/
/ www.overcomingbias.com/ 2012/ 10/ sleep-is-to-save-energy.html “How did software get so reliable without proof?”, (1996-03):
By surveying current software engineering practice, this paper reveals that the techniques employed to achieve reliability are little different from those which have proved effective in all other branches of modern engineering: rigorous management of procedures for design inspection and review; quality assurance based on a wide range of targeted tests; continuous evolution by removal of errors from products already in widespread use; and defensive programming, among other forms of deliberate over-engineering. Formal methods and proof play a small direct role in large scale programming; but they do provide a conceptual framework and basic understanding to promote the best of current practice, and point directions for future improvement.
“Merkle's Puzzles”, (2020-12-22):
In cryptography, Merkle's puzzles is an early construction for a public-key cryptosystem, a protocol devised by Ralph Merkle in 1974 and published in 1978. It allows two parties to agree on a shared secret by exchanging messages, even if they have no secrets in common beforehand.
http:/
/ www.bls.gov/ opub/ mlr/ 2016/ article/ the-life-of-american-workers-in-1915.htm https:/
/ www.aeaweb.org/ aea/ 2016conference/ program/ retrieve.php?pdfid=127 “Memoirs Found in a Bathtub”, (2020-12-28):
Memoirs Found in a Bathtub is a science fiction novel by Polish writer Stanisław Lem, first published in 1961. It was first published in English in 1973; a second edition was published in 1986.
http:/
/ www.amazon.com/ Hive-Mind-Your-Nation%C2%92s-Matters/ dp/ 0804785961 “Garett Jones”, (2020-12-22):
Garett Jones is an American economist and author. His research pertains to the fields of macroeconomics, monetary policy, IQ in relation to productivity, short-term business cycles, and economic development. He is an associate professor at George Mason University and the BB&T Professor for the Study of Capitalism at the Mercatus Center.
http:/
/ www.amazon.com/ Visions-Virtue-Tokugawa-Japan-Kaitokudo/ dp/ 0824819918 “The Black Cat (1934 film)”, (2020-12-28):
The Black Cat is a 1934 American pre-Code horror film directed by Edgar G. Ulmer and starring Boris Karloff and Béla Lugosi. The picture was the first of eight films to feature the two iconic actors. It became Universal Pictures' biggest box office hit of the year, and was among the earlier movies with an almost continuous music score. Lugosi also appeared in the 1941 film with the same title.
“Kaiji (manga)”, (2020-12-28):
Gambling Apocalypse: Kaiji is a Japanese manga series written and illustrated by Nobuyuki Fukumoto. It has been published by Kodansha in Weekly Young Magazine since February 1996. The story centers on Kaiji Itō, a consummate gambler and his misadventures around gambling. The series has currently been divided into six parts. The current part, Tobaku Datenroku Kaiji: 24 Oku Dasshutsu-hen, started in 2017.
“Broforce”, (2020-12-28):
Broforce is a side-scrolling run-and-gun platform video game developed by Free Lives and published by Devolver Digital. Development began in April 2012 as a game jam entry and continued with developer and popular support, existing as an Early Access game. The game was released on 15 October 2015 for Microsoft Windows and OS X, and a Linux port followed two days later. A PlayStation 4 version was released on 1 March 2016 and a Nintendo Switch port was released on 6 September 2018.
“Metal Slug”, (2020-12-28):
Metal Slug is a series of run and gun video games originally created by Nazca Corporation before merging with SNK in 1996 after the completion of the first game in the series. Spin-off games include a third-person shooter to commemorate the 10th anniversary of the series and a tower defense game for the mobile platform. Originally created for Neo-Geo arcade machines hardware (MVS) and the Neo-Geo home game consoles (AES) hardware, the original games have also been ported to other consoles and mobile platforms throughout the years, with several later games created for various other platforms. The games focus on the Peregrine Falcon Squad, a small group of soldiers who fight against a rebel army, aliens, zombies, mummies and various other forces intent on world domination.
“Gwern.net newsletter (Substack subscription page)”, (2013-12-01):
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.
“Gwern.net newsletter archives”, (2013-12-01):
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.)
“On the genetic architecture of intelligence and other quantitative traits”, (2014-08-14):
How do genes affect cognitive ability or other human quantitative traits such as height or disease risk? Progress on this challenging question is likely to be significant in the near future. I begin with a brief review of psychometric measurements of intelligence, introducing the idea of a "general factor" or g score. The main results concern the stability, validity (predictive power), and heritability of adult g. The largest component of genetic variance for both height and intelligence is additive (linear), leading to important simplifications in predictive modeling and statistical estimation. Due mainly to the rapidly decreasing cost of genotyping, it is possible that within the coming decade researchers will identify loci which account for a significant fraction of total g variation. In the case of height analogous efforts are well under way. I describe some unpublished results concerning the genetic architecture of height and cognitive ability, which suggest that roughly 10k moderately rare causal variants of mostly negative effect are responsible for normal population variation. Using results from Compressed Sensing (L1-penalized regression), I estimate the statistical power required to characterize both linear and nonlinear models for quantitative traits. The main unknown parameter s (sparsity) is the number of loci which account for the bulk of the genetic variation. The required sample size is of order 100s, or roughly a million in the case of cognitive ability.
“Genome-wide complex trait analysis”, (2020-12-22):
Genome-wide complex trait analysis (GCTA) Genome-based restricted maximum likelihood (GREML) is a statistical method for variance component estimation in genetics which quantifies the total narrow-sense (additive) contribution to a trait's heritability of a particular subset of genetic variants. This is done by directly quantifying the chance genetic similarity of unrelated individuals and comparing it to their measured similarity on a trait; if two unrelated individuals are relatively similar genetically and also have similar trait measurements, then the measured genetics are likely to causally influence that trait, and the correlation can to some degree tell how much. This can be illustrated by plotting the squared pairwise trait differences between individuals against their estimated degree of relatedness. The GCTA framework can be applied in a variety of settings. For example, it can be used to examine changes in heritability over aging and development. It can also be extended to analyse bivariate genetic correlations between traits. There is an ongoing debate about whether GCTA generates reliable or stable estimates of heritability when used on current SNP data. The method is based on the outdated and false dichotomy of genes versus the environment. It also suffers from serious methodological weaknesses, such as susceptibility to population stratification.