Scientists of Stature

The link below is to the published version of the paper we posted on biorxiv in late 2017 (see blog discussion). Our results have since been replicated by several groups in academia and in Silicon Valley. Biorxiv article metrics: abstract views 31k, paper downloads 6k. Not bad! Perhaps that means the community understands now that genomic …

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Institute for Advanced Study: Genomic Prediction of Complex Traits (seminar)

Genomic Prediction of Complex Traits After a brief review (suitable for physicists) of computational genomics and complex traits, I describe recent progress in this area. Using methods from Compressed Sensing (L1-penalized regression; Donoho-Tanner phase transition with noise) and the UK BioBank dataset of 500k SNP genotypes, we construct genomic predictors for several complex traits. Our …

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Low SES does not decrease heritability of cognitive ability (N=300k)

These researchers, from Stanford, Northwestern, and the University of Florida, analyze a large population of twins and siblings (~24k twins and ~300k children in total, born 1994-2002 in Florida). They find no evidence of SES (Socio-Economic Status) moderation of genetic influence on test scores (i.e., cognitive ability). The figure above shows the usual pattern of lower pairwise …

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Survival of the Steepest

Most textbooks tell you that the evolutionary process is really quite simple: three rules are all that’s necessary: inheritance, variation, and selection. It is indeed true that these three rules are all that’s needed for evolution to occur, but that does not mean that the evolutionary process is simple. In fact, quite the opposite. Real systems evolve in …

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Natural Selection and Body Shape in Eurasia

Prior to the modern era of genomics, it was claimed (without good evidence) that divergences between isolated human populations were almost entirely due to founder effects or genetic drift, and not due to differential selection caused by disparate local conditions. There is strong evidence now against this claim. Many of the differences between modern populations …

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Genetic variation in Han Chinese population

Largest component of genetic variation is a N-S cline (phenotypic N-S gradient discussed here). Variance accounted for by second (E-W) PC vector is much smaller and the Han population is fairly homogeneous in genetic terms: …while we revealed East-to-West structure among the Han Chinese, the signal is relatively weak and very little structure is discernible …

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Scientific Consensus on Cognitive Ability?

From the web site of the International Society for Intelligence Research (ISIR): a summary of the recent debate involving Charles Murray, Sam Harris, Richard Nisbett, Eric Turkheimer, Paige Harden, Razib Khan, Bo and Ben Winegard, Brian Boutwell, Todd Shackelford, Richard Haier, and a cast of thousands! ISIR is the main scientific society for researchers of …

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CNGB: China National Gene Bank

Unbeknownst to me I’ve been skyping with a collaborator who has been working from this location. SCMP: China opens first national gene bank, aiming to house hundreds of millions of samples China’s first national gene bank, claimed to be the largest of its kind in the world, officially opened on Thursday to store and carry …

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If

Every day, we propagate the E. coli populations in the long-term evolution experiment (LTEE) by transferring 0.1 ml of the previous day’s culture into 9.9 ml of fresh medium. This 100-fold dilution and regrowth back to stationary phase—when the bacteria have exhausted the resources—allow log2 100 = 6.64 generations (doublings) per day. We round that …

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Everything is Heritable

  The figure above comes from the paper below. A quick glance shows that for pairs of individuals: 1. Increasing genetic similarity implies increasing trait similarity (for traits including height, cognitive ability, years of education) 2. Home environments (raised Together vs Apart; Adoptees) have limited impact on the trait (at least in relatively egalitarian Sweden). …

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The Gulf is Deep (Heinlein)

  The novella Gulf predates almost all of Heinlein’s novels. Online version. The book Friday (1982) is a loose sequel. Wikipedia: Gulf is a novella by Robert A. Heinlein, originally published as a serial in the November and December 1949 issues of Astounding Science Fiction and later collected in Assignment in Eternity. It concerns a secret society …

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Can Life emerge spontaneously?

It would be nice if we knew where we came from. Sure, Darwin’s insight that we are the product of an ongoing process that creates new and meaningful solutions to surviving in complex and unpredictable environments is great and all. But it requires three sine qua non ingredients: inheritance, variation, and differential selection. Three does …

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Genetics, Cognitive Ability, and Education (conversation with Cambridge PhD candidate Daphne Martschenko)

Genetics, Cognitive Ability, and Education (conversation with Cambridge PhD candidate Daphne Martschenko) Further conversation with Cambridge PhD candidate Daphne Martschenko concerning genetics of cognitive ability, implications for education policy, etc. See also earlier conversation: https://www.youtube.com/watch?v=YVqkvHpLfuQ Dunedin paper referenced in the video (polygenic score prediction of adult success for different SES groups): http://infoproc.blogspot.com/2016/09/genomic-prediction-of-adult-life.html Tweet

Machine Learning for Personalized Medicine: Heritability-based models for prediction of complex traits (David Balding)

Highly recommended talk by David Balding on modern approaches to heritability, relatedness, etc. in statistical genetics. (I listened at 1.5x normal speed, which worked for me.) MLPM (Machine Learning for Personalized Medicine) Summer School 2015 Monday 21st of September Heritability-based models for prediction of complex traits by David Balding Complex trait genetics has been revolutionised …

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Cultivated sweet potatoes contain Agrobacterium inserted T-DNA that is absent in wild sweet potato relatives. A natural GMO?

Genetic modification (GM) of food crops is a very hot topic in today’s society. When researchers discovered that certain bacteria had the ability to transfer their own DNA into plant genomes, the applications seemed endless. By taking advantage of this transfer DNA (T-DNA) mechanism, scientists can selectively transfer specific genes into the target plant to …

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This is for PZ Myers

Scott Alexander (Slate Star Codex), Garrett Jones (Hive Mind), and Razib Khan (GNXP) alerted me (via Twitter) of this post by PZ Myers. Myers is both confused and insulting in his blog post, but I’ll refrain from ad hominem attacks, and just focus on the science. Myers seems to think that humans with much better …

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Genetic ancestry and brain morphology

Population structure — i.e., distribution of gene variants by ancestral group — is reflected in brain morphology, as measured using MRI. Brain morphology measurements can be used to predict ancestry. Strictly speaking, the data only show correlation, not genetic causation, but the most plausible interpretation is that genetic differences are causing morphological differences. One could …

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Cognitive Genomics Interview

This is a discussion with Cambridge University PhD candidate Daphne Martschenko. Topics covered include: genetics of cognition, group differences, genetic engineering. The NYC roundtable on genius she mentions is here. Blog readers may also be interested in this event at the 92nd Street Y (Thu, Mar 10, 2016, 8:15 pm, Location: Lexington Avenue at 92nd …

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GCTA, Missing Heritability, and All That

Bioinformaticist E. Stovner asked about a recent PNAS paper which is critical of GCTA. My comments are below. It’s a shame that we don’t have a better online platform (e.g., like Quora or StackOverflow) for discussing scientific papers. This would allow the authors of a paper to communicate directly with interested readers, immediately after the paper …

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The view from here

A mind of von Neumann’s inexorable logic had to understand and accept much that most of us do not want to accept and do not even wish to understand. This fact colored many of von Neumann’s moral judgments. — Eugene Wigner, in John von Neumann (1903 – 1957), Year book of the American Philosophical Society …

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BBC interview with Robert Plomin

I recommend this BBC interview with Robert Plomin. Robert is a consummate gentleman and scholar, working in a field that inevitably attracts controversy. (Via Dominic Cummings.) Professor Robert Plomin talks to Jim Al-Khalili about what makes some people smarter than others and why he’s fed up with the genetics of intelligence being ignored. Born and …

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