Links

Genetics:

• Engineering:

  • Andrew Hessel interview (on progress in genome synthesis, origin of HGP-Write, current goals of synthesizing ultra-safe cells, and human applications)

  • Overview of various approaches to improving genome synthesis

  • “Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs”, Gonen et al 2017 (Fun idea to use gene drive as a part of normal genetic engineering, but probably too baroque and complicated for realistic use before genome synthesis.)

  • “Gene Editing for Good: How CRISPR Could Transform Global Development” (Bill Gates)

  • “6 cloned horses help rider win prestigious polo match”; “The Clones of Polo—Adolfo Cambiaso interview” (I had no idea horse cloning had developed to this extent. Cambiaso, polo champion, has cloned his best horse 14 times now, 10 more due ~2018, and is winning polo championships on all-clone teams. He says they perform well, similar to the original, despite how “‘Every scientist that deals with epigenetics told me this would never work’, says Meeker, referring to the fact that the environment modifies gene activity and helps explain why identical twins aren’t truly identical.” Quite a case study of the benefits of cloning elite individuals.)

  • “Science is Getting Us Closer to the End of Infertility” (Towards massive embryo selection & IES: “Hayashi…guesses it will take 5 years to produce egg-like cells from other human cells…Adashi is less sure of the timing than he is of the outcome. ‘I don’t think any of us can say how long’, he says. ‘But the progress in rodents was remarkable: In 6 years, we went from nothing to everything. To suggest that this won’t be possible in humans is naive.’”)

  • “Phenomic selection: a low-cost and high-throughput alternative to genomic selection”, Rincent et al 2018 (commentary; another unusual use of GCTA-style variance-components for phenotypes?)

• Everything Is Heritable:

  • “Based on current rates, the number of [DTC genetic testing] customers is predicted to be close to 100 million by end of 2020.”

  • “Broad Institute to sequence its 100,000th whole human genome…as the worldwide estimate for whole human genomes sequenced approaches one million”

  • “GSEM: Genomic SEM Provides Insights into the Multivariate Genetic Architecture of Complex Traits”, Grotzinger et al 2018 (Aside from the scientific value, this will increase GWAS power considerably and importantly, can match the factor structure of traits like IQ—instead of dumb regression on a single crude number…)

  • “Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability”, Hysi et al 2018 (for those who care about that—PGSes: 9.4% blonde, 7.4% red, & 5.6% black. AUCs ~ 80%.)

  • “Genome-wide association study of social genetic effects on 170 phenotypes in laboratory mice”, Baud et al 2018 (The environment is genetic.)

  • “GWAS in 446,118 European adults identifies 78 genetic loci for self-reported habitual sleep duration supported by accelerometer-derived estimates”, Dashti et al 2018; “Genome-wide association analyses of chronotype in 697,828 individuals provides new insights into circadian rhythms in humans and links to disease”, Jones et al 2018

  • “The IQ trap: how the study of genetics could transform education” (The limited hangout continues.)

• Recent Evolution:

  • “Polygenic adaptation and convergent evolution across both growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers”, Bergey et al 2018 (African & Indian pygmies have evolved similar height/heart-growth genetic adaptations to their niche)

  • “Physiological and Genetic Adaptations to Diving in Sea Nomads”, Ilardo et al 2018 (Razib Khan; Indonesian Bajau divers have evolved 50% larger spleens for storing reserve of oxygenated blood needed in long dives.)

  • “Evidence of a nonadaptive buildup of mutational load in human populations over the past 40,000 years”, Aris-Brosou2018

AI:

• “SPIRAL: Synthesizing Programs for Images using Reinforced Adversarial Learning”, Ganin et al 2018 (blog; another fun RL-GAN/GAIL mashup, this time, for teaching a robot to paint simple images given a dataset of images)

• “Planning chemical syntheses with deep neural networks and symbolic AI”, Segler et al 2018

• “Learning to Navigate in Cities Without a Map”, Mirowski et al 2018 (blog; kind of an RL extension to Weyand et al 2016)

• “The Mathematics of 2048: Optimal Play with Markov Decision Processes” (up to 4x4 boards by careful optimization)

• “Lessons Learned Reproducing a Deep Reinforcement Learning Paper” (wisdom earned over 8 months: DRL is hard; sweat the small stuff; keep records of changes; measure everything; use cloud to iterate faster; and replicate repeatedly due to instability.)

Statistics/Meta-Science:

• “Agreement of treatment effects for mortality from routinely collected data and subsequent randomized trials: meta-epidemiological survey”, Hemkens et al 2016 (How often does correlation=causation?)

• “Teacher Expectations and Self-Fulfilling Prophecies: Knowns and Unknowns, Resolved and Unresolved Controversies”, Jussim & Harber2005; “We’ve Been Here Before: The Replication Crisis over the ‘Pygmalion Effect’”

• “Evaluation of Evidence of Statistical Support and Corroboration of Subgroup Claims in Randomized Clinical Trials”, Wallach et al 2017 (Lies, damn lies, and subgroups.)

• “Inventing the randomized double-blind trial: the Nuremberg salt test of 1835”, Stolberg2006 (The first double-blind randomized pre-registered clinical trial in history was a 1835 German test of homeopathic salt remedies.)

• “Framed for Murder By His Own DNA: We leave traces of our genetic material everywhere, even on things we’ve never touched. That got Lukis Anderson charged with a brutal crime he didn’t commit.” (Meehl’s ‘crud factor’: everything is correlated with everything; in this case, physically, because ultra-sensitive DNA forensic testing means you can pick up DNA from just about anybody not just perpetrators.)

Politics/religion:

• “Company Eight: The true story of one man’s quest to reform corrupt firefighting in Boston”

Psychology/biology:

• “Azithromycin to Reduce Childhood Mortality in Sub-Saharan Africa”, Keenan et al 2018 (media; Surprisingly large mortality reduction from prophylactic antibiotics in children—do we continue to underestimate how pervasive infections are in mortality & morbidity?)

• “The importance of eating local: slaughter and scurvy in Antarctic cuisine”, Anthony2011

• “Phytochemical mimicry of reproductive hormones and modulation of herbivore fertility by phytoestrogens”, Hughes1988 (Reminder: plants aren’t your friends. Also an interesting comment on reproduction—it’s somehow never phytoandrogens you hear about…)

• “Why dumb recruits cost the Army, big-time”; “Determinants of Productivity for Military Personnel: A Review of Findings on the Contribution of Experience, Training, and Aptitude to Military Performance”, Kavanagh2005

• “Androgens and the Evolution of Male-Gender Identity among Male Pseudohermaphrodites with 5-α-reductase Deficiency”, Imperato-McGinley et al 1979 (A remarkable natural experiment)

• “LSD and Quantum Measurements: Can you see Schrödinger’s cat both dead and alive on acid?” (Does LSD let you perceive alternate quantum branches of the MWI? Preliminary experimental results indicate, no.)

• Frankie Muniz can’t remember acting on Malcolm in the Middle due to TBIs/head injuries: 1, 2

Technology:

• “Revisiting ‘The Rise and Decline’ in a Population of Peer Production Projects [769 wikis]”, TeBlunthuis et al 2018 (discussion)

• “One Week of Bugs, or, Everything is Broken” / “Operant Conditioning by Software Bugs” (why do some people seem to trigger computer bugs all the time?)

• “The dizzying story of Symphony of the Seas, the largest and most ambitious cruise ship ever built”

• “Google workloads for consumer devices: mitigating data movement bottlenecks” (“For example, when scrolling through a Google Docs web page, simply [physically] moving data accounts for 77% of the system energy consumption.”)

Economics:

• “Questioning the evidence on hookworm eradication in the American South”, Roodman2017

• “How bike-sharing conquered the world: A two-wheeled journey from anarchist provocation to high-stakes capitalism”

• “Dog Fight: Dog rescuers, flush with donations, buy animals from the breeders they scorn”

Philosophy:

• SSC is offering a $1000 prize for best adversarial collaboration

Fiction:

• Lu Chi’s The Art of Writing

• “Pangur Bán” (A poem written in the 800s AD by an Irish monk about his cat; 4 parallel versions.)

Film/TV

Live-action:

• A Quiet Place (review)