Links

Genetics:

• everything is heritable:

  • Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations, Khera et al 2018 (PGSes for coronary artery disease, atrial fibrillation, type 2 diabetes, inflammatory bowel disease, and breast cancer are now clinically useful: figure 2/3 - more extremizing for visualizing PGS power)
  • Genome-wide statistically-significant regions in 43 Utah high-risk families implicate multiple genes involved in risk for completed suicide, Coon et al 2018 (Suicide is hard to study, but some more progress.)
  • Consumer genomics will change your life, whether you get tested or not, Khan & Mittelman 2018; There could be 100 million genotyping kits sold by 1 January 2020 (Figure 1)

• recent evolution:

  • Enrichment of genetic markers of recent human evolution in educational and cognitive traits, Srinivasan et al 2018 (Net selection for human intelligence from 400kya-present)
  • Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours, Kukekova et al 2018 (media)

• engineering:

  • Correction of the Marfan Syndrome pathogenic FBN1 mutation by CRISPR base editing in human cells and heterozygous embryos, Zeng et al 2018 (media)
  • Inside the Very Big, Very Controversial Business of Dog Cloning (update on Hwang Woo-suk’s Sooam Biotech - bigger than ever)
  • Heredity before genetics: a history, Cobb 2006 (a look into why heritability and selective breeding, so apparently easy to see, were difficult & had to be invented; I was particularly fascinated by the description of Robert Bakewell inventing economically-efficient selective breeding using sheep & influencing Charles Darwin/Gregor Mendel, among other things like using blocking to show benefits of irrigation - for more, see Wykes 2004, Robert Bakewell (1725-1795) of Dishley: farmer and livestock improver/Housman 1894/Lawrence 1805)
  • Chromosome transplantation as a novel approach for correcting complex genomic disorders, Paulis et al 2015 (possibly useful for implementing an optimal chromosome selection)
  • Crunch: Building a Better Apple (on apple selective breeding & the development of the Honeycrisp & SweeTango varieties; I took the opportunity buy 6 kinds of apples from my local grocery stores, and the Honeycrisp & SweeTangos were the best apples. I feel disappointed I let my bad experiences as a kid with Red Delicious stop me from trying better apples. Current apple ranking: SweeTango > Honeycrisp > Granny Smith > Golden Delicious > Braeburn > Smitten > Kanzi > Jazz > Fuji > Kiku > Ambrosia > Cripps Pink > Envy > McIntosh > Paula Red > Ginger Gold > Red Delicious. Red Delicious is often told as a cautionary tale of how breeding inevitably destroys what we value about something, because dumb consumers bought with their eyes and ruined everything; but if that was the case, why do I have 16 better apples to choose from, most of which look like they sell better both in the aggregate & individually judging by displayed volumes, and why did the Red Delicious applegrowing industry implode starting in the 1990s under competition from better apples? A more likely story is that, like so many foodstuffs, the priority during industrialization and especially around WWII was to reduce the large fraction of individual incomes spent sheerly on subsistence by feeding the world as cheaply as possible with large-scale factory farming, with quality a lower priority, and culinary knowledge/sophistication further taking a big hit during the simultaneous urbanization, and, in a sort of a culinary Kuznets curve or Durkheim effect, have been gradually recovering ever since as consumers can now spend a trivial fraction of income on food for survival & instead treat food as a hobby in learning about & buying luxuries like fast food & meat & better apples & cheese & beer - and everything, really.)

AI:

• OpenAI/DoTA2:

  • OpenAI Five Benchmark: Results (OpenAI 5x5 DoTA agent crushes audience & ex-pro teams; link roundup & commentary)
  • The International 2018: Results (0/2) (round & commentary: game 1, game 2 - losses, but pure PPO self-play went further than it had any right to. If PPO can go so far in a large-scale fog-of-war team game, one wonders what DM has achieved on SC2 with its access to even more compute and high-throughput DRL architectures like Ape-X & Impala… OA continues to run OA5 and has increased the model size substantially. I would give good odds for a victory at the next TI.)
• Safety-first AI for autonomous data center cooling and industrial control, Kasparik/Gamble/Gao (Finally, DeepMind provides some details: +12% efficiency, increasing to 30%. The July patent provides more details on the RL implementation, implying it uses standard LSTM RNNs w/Osband’s bootstrap ensemble for exploration etc)
• Large-Scale Study of Curiosity-Driven Learning, Burda et al 2018
• Dijkstra’s Algorithm in Disguise, Eric Jang (optimizing graph traversals in currency arbitrage, Q-learning, & ray-tracing/light-transport)
• Fast.ai: training ImageNet in 18m for $40 (progressive resizing + rectangular convolutions + weight decay + dynamic batch sizes + warmup)
• OpenAI files proposal for new larger campus near Golden Gate Bridge in SF, by developing Fort Winfield Scott (OA has big plans.)
• John von Neumann on the Singularity

• Improving Shape Deformation in Unsupervised Image-to-Image Translation, Gokaslan et al 2018 (Some new work using my Danbooru2017 anime dataset for anime⟺face CycleGAN. It’s far from perfect but recognizable.)

Statistics/meta-science/mathematics:

• Don’t believe the mice: Experiments using mice are often heavily publicized - but very, very few of them translate into humans. Anthony King reports on why animal models are of questionable value
• Plan to replicate 50 high-impact cancer papers shrinks to just 18 (being unable to even try to replicate critical papers seems worse to me than a simple non-replication)
• What Do Workplace Wellness Programs Do? Evidence from the Illinois Workplace Wellness Study, Jones et al 2018 (media; How often does correlation=causation? In this demonstration of the Stainless & Brass Laws of evaluation, a workplace wellness program randomized experiment finds half its measures don’t even have overlapping CIs; comparing to the (correlational) research literature on workplace wellness effects, they reject equality for 20/22, 23/33, 43/55, 43/60, and 96/115 of previous reported effects. Graphs: figure 8, Jones vs prior correlational literature/table 5, Jones, randomized vs correlational results/table 5, NYT visualization)
• Researcher at the center of an epic fraud remains an enigma to those who exposed him

Politics/religion:

• The American Voter in 1932: Evidence from a Confidential Survey, Norporth 2018 (FDR voters cared more about his promise to end Prohibition than the Great Depression? This is a surprising result, but there’s nothing clearly wrong with the survey…)

Psychology/biology:

• Personality, IQ, and lifetime earnings, Gensowski 2018
• Are bigger brains smarter? Evidence from a large-scale pre-registered study, Nave et al 2018 (yes)
• Searching for the bottom of the ego well: failure to uncover ego depletion in Many Labs 3, Vadillo et al 2018
• Pre-sleep treatment with galantamine stimulates lucid dreaming: A double-blind, placebo-controlled, crossover study, LaBerge et al 2018 (media; my initial experience with galantamine is that it wrecks my sleep when I take either 4 or 8mg at bedtime; this is presumably why LaBerge et al 2018 instead wakes subjects up in the middle of the night to take the galantamine; I could do this by taking it if I find myself waking up at 4AM to use the bathroom or something, but I’m worried about ruining half a night of sleep…)
• This Parasite Drugs Its Hosts With the Psychedelic Chemical in Shrooms: It Also Makes Their Butts Fall Off (see also Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms, Awan et al 2018; Discovery of psychoactive plant and mushroom alkaloids in behavior-modifying fungal cicada pathogens, Boyce et al 2018 - given the psychoactive precedents of caffeine/nicotine, makes one think…)
• Exploring the effect of microdosing psychedelics [psilocybin] on creativity in an open-label natural setting, Prochazkova et al 2018 (disappointingly, unlike my microdosing self-experiment, this was not blinded)

Technology:

• The Untold Story of NotPetya, the Most Devastating Cyberattack in History (Few firms have paid more dearly for dragging their feet on security…)
• Capturing the Unicorn: How two mathematicians came to the aid of the Met
• Chaff Bugs: Deterring Attackers by Making Software Buggier, Hu et al 2018 (Our programs are insecure because they have so many bugs, which is why we need to add more bugs)

Economics:

• The Shape of Human Progress: 40 Ways the World Is Getting Better
• Pricing the Future in the Seventeenth Century: Calculating Technologies in Competition, Deringer 2017 (interestingly, 99-year English leases were badly underpriced compared to full ownership/perpetuities, despite near-identical economic value)
• Private Ordering at the World’s First Futures Exchange, West 2000 (Edo-period Japan developed a remarkably complete rice futures market centuries before you would expect such a thing, roughly contemporaneous with the more famous Dutch stock exchange which had futures for the Dutch East India Company)

Fiction:

• Slow Tuesday Night (R. A. Lafferty’s classic 1965 (SF?) short story; see also Robin Hanson’s ems & The Hyperbolic Time Chamber)

Books

Nonfiction:

• The Vaccinators: Smallpox, Medical Knowledge, and the Opening of Japan, Jannetta 2007:

  Before convenient smallpox vaccines, transmitting cowpox required a human chain of donors, who were infectious for short periods before recovering; Jannetta covers the difficult logistics of this global feat of philanthropy, orchestrated by Jenner, such as the extraordinary Balmis Expedition, which required 22 orphans to carry the pox safely across the Atlantic Ocean to the New World. Eventually the narrative reaches Japan where it runs up against the shogunate’s policy of exclusion and minimal Dutch trade. The Dutch governors in Batavia made dutiful efforts, once a year, to ship a serum sample to the Nagasaki outpost where it could be used to infect a volunteer and seed Japanese vaccination, but the pox repeatedly died en route. After a great while, they succeeded and the problem became how to build a critical mass: the shogunate refused to endorse vaccination, but benignly neglected it; in the end, the successful strategy was for the Dutch-educated Japanese doctors to vaccinate their families and the families of their sponsoring daimyo, and by this display of elite confidence in the vaccination, the ordinary people would gradually be willing to send their children for a stay in the pox clinics and vaccinate other children in turn. Many didn’t, but the effect size of vaccination was so large that it could be observed with the naked eye during subsequent smallpox outbreaks. Western medicine was already one of the best arguments for opening Japan to foreigners, and the smallpox vaccination surely helped; ironically, the eventual opening of Japan would lead to even more epidemics (as the isolation had been so successful at blocking importation of infectious diseases as well) and the need for formal government public health bureaucracies and official vaccination campaigns.

  Perhaps the most striking aspect of Jannetta’s whole history is the sheer casualness and unconcern manifested by almost everyone but Jennerites: despite smallpox being a global threat killing >10% of all people, nearly guaranteed and of regular occurrence, preferentially killing children & the aged, and the vaccination indisputably and dramatically effective - one of the greatest silver bullets in the history of medicine - most people… just. didn’t. care. The earlier method of variolation killed around or less than 1%, dramatically less than the usual smallpox mortality of >10%, but was still highly unpopular. Even the people who did something, like the Dutch governors & station-chiefs, often did so in a bizarrely lackadaisical manner: the death toll of smallpox was so well known, and the population of Japan sufficiently numerous, that if they had thought about it for even a few seconds, it would be clear that the cost of each year of delay was on the order of 360,000 lives; but their reaction to the failure of sending one package of cowpox samples to the Nagasaki station was to try the same thing again, the next year, instead of, I don’t know, trying 5 or 10 packagings simultaneously - or anything resembling a genuine effort. In a similar vein, Jannetta spends a peculiar amount of space defending Jenner against charges that his cowpox research was unethical and immorally conducted and could not have been approved by an IRB; I don’t know whether to laugh or cry at the existence of such criticism, other than to note that if Jenner’s cowpox research would not have been approved by an IRB, that is a sufficient refutation of IRBs, and I seriously wonder whether humanity would still be capable of curing a future equivalent of smallpox. In general, I’m reminded of a tweet about self-driving cars:

  so what did you do before self-driving cars?
  we just drove ’em ourselves!
  wow, no one died that way?
  oh no, millions of people died

  Sometimes people read about a concept like nuclear war, or strong AI, or Effective Altruism, or astronomical waste, and they seem to be unable to deal with it: surely, they think, if it was really that bad or serious, someone would have said so; there would be enormous ongoing efforts to deal with it; surely there isn’t any real risk that nuclear war could kill hundreds of millions or billions of people, or that so many lives are wasted in Africa, or that there could be silver bullets sitting around unfired. Humans aren’t like that, we’d fix it. And it’s good to not be reckless or move fast, and be Very Serious People and carefully check that there are no rare malaria-mosquito-eating frogs before we gene drive malaria out of existence and save millions of lives a year. It’s not like delays are really killing millions of people, that’s just alarmist and not serious or respectable! The history of smallpox shows that none of these comforting assumptions are true; when you fail to do enough, reality doesn’t care and people just die:

  In the real world things are very different. You just need to look around you. Nobody wants to die that way. People die of disease and accident. Death comes suddenly and there is no notion of good or bad. It leaves, not a dramatic feeling but great emptiness. When you lose someone you loved very much you feel this big empty space and think, If I had known this was coming I would have done things differently. These are the feelings I wanted to arouse in the players with Aerith’s death relatively early in the game. Feelings of reality and not Hollywood.

• Low Aptitude Men in the Military: Who Profits, Who Pays?, Laurence & Ramsberger 1991 (on Project 100,000 and the ASVAB Misnorming)

• Confusion of Confusions, Joseph de la Vega 1688 (First long description of the Dutch stock exchange & market manipulation/trading strategies. Amusing.)

Fiction:

• Memories of the Space Age, J.G. Ballard (some striking images let down by short stories padding them out; reading them in one sitting, I thought that only 6 stories seemed like a rather short anthology - but it was actually 8 and I had completely confused some of them so much did they overlap, especially the time compression theme, which I struggled to see how it related to the Space Age at all and is overwrought. I thought it might provide some examples for my Scanners Live in Vain essay but it all comes off as more of a sublimated reaction to psychedelics than the Space Age. To invert The Martian Chronicles effectively, Ballard would have had to vary the topics much more, gone less into his inexplicable metaphysics of time, and made the stories leaner.)

Film/TV

Live-action:

• Ant-Man and the Wasp (2018; while featuring some of the typically unnecessarily convoluted plotting of the Marvel movies and idiot-ball-holding, Ant-Man pleasantly surprised me with a steady fare of humor and action scenes showing that someone involved once thought for a few seconds about how to effectively use shrink-rays, and didn’t feel like it was 2 hours long)

Animated:

• Miss Kobayashi’s Dragon Maid (one of the most popular anime that season, it drew interest for its low-key lesbian romance/slice-of-life/fantasy mashup; I found it considerably overrated. The same-sex aspect is almost entirely irrelevant and, forgetting that admitting a fault is not fixing that fault, lampshaded numerous times; the pacing was badly timed and early on highly demanding of emotional engagement which it had not remotely earned; the grim-dark fantasy counterpoint to the slice-of-life was too cursory to provide a real contrast or motivation for the eponymous dragon maid; the side characters were one-note and unimaginative caricatures (although the Genshiken-esque pair of side characters might have worked if the series had tried a lot harder), indeed, eventually thoroughly obnoxious. The animation, aside from the care lavished on Tohru’s striking dragon eyes, was serviceable. There are a few nice touches: I was amused to note that the protagonist programs in Python - of course! although Ruby would’ve been almost as appropriate. Overall, boring.)