Friday, May 30, 2014

Reader survey

Every now and then I look at the statistics for this blog. My rough estimate is that there is a core group of at least several thousand who read it regularly (i.e., a few times per week or more), and typical posts are eventually read by ~ 10 thousand people or more.

I know very little about my readers, hence this survey. Answer whichever parts you like and paste into the comments. Many thanks!
1. Age, gender, ethnicity, nationality?

2. What's your background (education, profession, hobbies)?

3. What do you like best about this blog?

4. What do you like least about this blog?

5. How often do you find posts hard to understand?

6. Have we met in real life? Should we?

7. What should I do with my life?   :-)
I can guess that there are several overlapping subgroups of readers: physicists, genomicists, financiers, tech / startup types, professors, ... But I'd really like to know more!

Internet trends 2014


Verita$

Harvard senior survey conducted by the Crimson.


Tuesday, May 27, 2014

Brainy but Weak


Figure shows metabolic difference in various tissue types for 4 species; PFC = Prefrontal Cortex. Human brain function accounts for about 20% of total calorie consumption. See also Cognition über alles and The genetics of humanness.

We're the geeks of the animal kingdom ;-)

Exceptional Evolutionary Divergence of Human Muscle and Brain Metabolomes Parallels Human Cognitive and Physical Uniqueness (PLOS)

Abstract

Metabolite concentrations reflect the physiological states of tissues and cells. However, the role of metabolic changes in species evolution is currently unknown. Here, we present a study of metabolome evolution conducted in three brain regions and two non-neural tissues from humans, chimpanzees, macaque monkeys, and mice based on over 10,000 hydrophilic compounds. While chimpanzee, macaque, and mouse metabolomes diverge following the genetic distances among species, we detect remarkable acceleration of metabolome evolution in human prefrontal cortex and skeletal muscle affecting neural and energy metabolism pathways. These metabolic changes could not be attributed to environmental conditions and were confirmed against the expression of their corresponding enzymes. We further conducted muscle strength tests in humans, chimpanzees, and macaques. The results suggest that, while humans are characterized by superior cognition, their muscular performance might be markedly inferior to that of chimpanzees and macaque monkeys.

Author Summary

Physiological processes that maintain our tissues' functionality involve the generation of multiple products and intermediates known as metabolites—small molecules with a weight of less than 1,500 Daltons. Changes in concentrations of these metabolites are thought to be closely related to changes in phenotype. Here, we assessed concentrations of more than 10,000 metabolites in three brain regions and two non-neural tissues (skeletal muscle and kidney) of humans, chimpanzees, macaque monkeys, and mice using mass spectrometry-based approaches. We found that the evolution of the metabolome largely reflects genetic divergence between species and is not greatly affected by environmental factors. In the human lineage, however, we observed an exceptional acceleration of metabolome evolution in the prefrontal cortical region of the brain and in skeletal muscle. Based on additional behavioral tests, we further show that metabolic changes in human muscle seem to be paralleled by a drastic reduction in muscle strength. The observed rapid metabolic changes in brain and muscle, together with the unique human cognitive skills and low muscle performance, might reflect parallel mechanisms in human evolution.

Monday, May 26, 2014

The Mystery of Go

Nice article on the progress of computer Go.

See also The Laskers and the Go master: "While the baroque rules of Chess could only have been created by humans, the rules of Go are so elegant, organic, and rigorously logical that if intelligent life forms exist elsewhere in the universe, they almost certainly play Go." (Edward Lasker, International Master and US Chess champion)



WIRED: ... Even in the West, Go has long been a favorite game of mathematicians, physicists, and computer scientists. Einstein played Go during his time at Princeton, as did mathematician John Nash. Seminal computer scientist Alan Turing was a Go aficionado, and while working as a World War II code-breaker, he introduced the game to fellow cryptologist I.J. Good. ... Good gave the game a huge boost in Europe with a 1965 article for New Scientist entitled “The Mystery of Go.”

... Good opens the article by suggesting that Go is inherently superior to all other strategy games, an opinion shared by pretty much every Go player I’ve met. “There is chess in the western world, but Go is incomparably more subtle and intellectual,” says South Korean Lee Sedol, perhaps the greatest living Go player and one of a handful who make over seven figures a year in prize money. Subtlety, of course, is subjective. But the fact is that of all the world’s deterministic perfect information games — tic-tac-toe, chess, checkers, Othello, xiangqi, shogi — Go is the only one in which computers don’t stand a chance against humans.

...

After the match, I ask Coulom when a machine will win without a handicap. “I think maybe ten years,” he says. “But I do not like to make predictions.” His caveat is a wise one. In 2007, Deep Blue’s chief engineer, Feng-Hsiung Hsu, said much the same thing. Hsu also favored alpha-beta search over Monte Carlo techniques in Go programs, speculating that the latter “won’t play a significant role in creating a machine that can top the best human players.”

Even with Monte Carlo, another ten years may prove too optimistic. And while programmers are virtually unanimous in saying computers will eventually top the humans, many in the Go community are skeptical. “The question of whether they’ll get there is an open one,” says Will Lockhart, director of the Go documentary The Surrounding Game. “Those who are familiar with just how strong professionals really are, they’re not so sure.”

According to University of Sydney cognitive scientist and complex systems theorist Michael Harré, professional Go players behave in ways that are incredibly hard to predict. In a recent study, Harré analyzed Go players of various strengths, focusing on the predictability of their moves given a specific local configuration of stones. “The result was totally unexpected,” he says. “Moves became steadily more predictable until players reached near-professional level. But at that point, moves started getting less predictable, and we don’t know why. Our best guess is that information from the rest of the board started influencing decision-making in a unique way.” ...
The current handicap accorded a computer against a professional player is 4 stones. In the story below the world chess champion and his brother are given 9 stones by the Japanese mathematician (shodan = lowest non-beginner or black belt).
Mr. Kitabatake one day told us that a Japanese mathematician was going to pass through Berlin on his way to London, and if we wanted to we could play a game with him at the Japanese Club. Dr. Lasker asked him whether he and I could perhaps play a game with him in consultation, and was wondering whether the master – he was a shodan – would give us a handicap.

“Well, of course,” said Mr. Kitabatake.
“How many stones do you think he would give us?" asked Lasker.
“Nine stones, naturally,” replied Mr. Kitabatake.
“Impossible!” said Lasker. “There isn’t a man in the world who can give me nine stones. I have studied the game for a year, and I know I understood what they were doing.”
Mr. Kitabatake only smiled.
“You will see,” he said.

The great day came when we were invited to the Japanese Club and met the master – I remember to this day how impressed I was by his technique – he actually spotted us nine stones, and we consulted on every move, playing very carefully. We were a little disconcerted by the speed with which the master responded to our deepest combinations. He never took more than a fraction of second. We were beaten so badly at the end, that Emanuel Lasker was quite heartbroken. On the way home he told me we must go to Japan and play with the masters there, then we would quickly improve and be able to play them on even terms. I doubted that very strongly, but I agreed that I was going to try to find a way to make the trip.

Sunday, May 25, 2014

Isabel and the dwarf king

This is an old story I told the kids.



One day Max and Isabel were hiking in the mountains and came upon a cave.

Exploring in the gloom, they found a giant cavern, filled by a pile of gold and jewels. Atop the pile was a huge throne. On that throne sat the dwarf king.

Who dares enter my throne room? asked the dwarf king.

My name is Isabel and this is my brother Max.

You sure have a lot of gold, said Max.

Yes, said the dwarf king with a gleam in his eye. I am the richest in the world!

What use are riches in this dark cave? asked Max.

What?!? I am the richest in the world!!

Oh dwarf king, said Isabel, no hoard of gold is worth even a single flower, growing in the summer sun.



Years later, after the dragon came and burned all the king's kinsmen, Isabel wondered what had become of him ...


Bring on Jon Jones




Great interview with former Olympian (freestyle) Dan Cormier after he submitted another Olympian (greco) Dan Henderson at UFC 173 last night. I believe Cormier can beat Jon Jones. Cormier is only about 5"10 whereas Jones is 6"4 (both fighting at 205). Previous fighters have been forced by Jones to play his striking / top control game. But Cormier is smart -- he didn't get into striking exchanges with Henderson, who has a dangerous right hand. He kept the fight on the ground and dominated from the top. He can do the same to Jones. Using this strategy, he can use Jones's length against him -- we'll see Jon Jones fighting off his back for the first time. What I like about Cormier is that he is really developing his jiujitsu. Many wrestlers are unable to capitalize on top position due to lack of high level submission skills.

Saturday, May 24, 2014

Hollywood Hills

I'm not a materialistic guy, but I do like modern architecture. My eyes nearly popped out when I saw this photo in Dwell. The house is in the Hollywood Hills and the view is of downtown LA.


Saturday, May 17, 2014

Intervention and Replication


This article describes surprisingly effective interventions that improve college success rates for low SES/SAT students. Let's hope they can be broadly replicated.
NYTimes: ... Laude was hopeful that the small classes would make a difference, but he recognized that small classes alone wouldn’t overcome that 200-point SAT gap. “We weren’t naïve enough to think they were just going to show up and start getting A’s, unless we overwhelmed them with the kind of support that would make it possible for them to be successful,” he said. So he supplemented his lectures with a variety of strategies: He offered TIP students two hours each week of extra instruction; he assigned them advisers who kept in close contact with them and intervened if the students ran into trouble or fell behind; he found upperclassmen to work with the TIP students one on one, as peer mentors. And he did everything he could, both in his lectures and outside the classroom, to convey to the TIP students a new sense of identity: They weren’t subpar students who needed help; they were part of a community of high-achieving scholars.

Even Laude was surprised by how effectively TIP worked. “When I started giving them the tests, they got the same grades as the larger section,” he said. “And when the course was over, this group of students who were 200 points lower on the SAT had exactly the same grades as the students in the larger section.” The impact went beyond Chemistry 301. This cohort of students who, statistically, were on track to fail returned for their sophomore year at rates above average for the university as a whole, and three years later they had graduation rates that were also above the U.T. average.

... Laude wanted something that would help him predict, for any given incoming freshman, how likely he or she would be to graduate in four years. The Institutional Research team analyzed the performance of tens of thousands of recent U.T. students, and from that analysis they produced a tool they called the Dashboard — an algorithm, in spreadsheet form, that would consider 14 variables, from an incoming student’s family income to his SAT score to his class rank to his parents’ educational background, and then immediately spit out a probability, to the second decimal place, of how likely he was to graduate in four years.

In the spring of 2013, Laude and his staff sat down with the Dashboard to analyze the 7,200 high-school seniors who had just been admitted to the class of 2017. When they ran the students’ data, the Dashboard indicated that 1,200 of them — including Vanessa Brewer — had less than a 40 percent chance of graduation on time. Those were the kids Laude decided to target. He assigned them each to one or more newly created or expanded interventions. The heart of the project is a portfolio of “student success programs,” each one tailored, to a certain extent, for a different college at U.T. — natural sciences, liberal arts, engineering — but all of them following the basic TIP model Laude dreamed up 15 years ago: small classes, peer mentoring, extra tutoring help, engaged faculty advisers and community-building exercises.

... Students were randomly sorted into four categories. A “belonging” treatment group read messages from current students explaining that they felt alone and excluded when they arrived on campus, but then realized that everyone felt that way and eventually began to feel at home. A “mind-set” treatment group read an article about the malleability of the brain and how practice makes it grow new connections, and then read messages from current students stating that when they arrived at U.T., they worried about not being smart enough, but then learned that when they studied they grew smarter. A combination treatment group received a hybrid of the belonging and mind-set presentations. And finally, a control group read fairly banal reflections from current students stating that they were surprised by Austin’s culture and weather when they first arrived, but eventually they got used to them. Students in each group were asked, after clicking through a series of a dozen or so web pages, to write their own reflections on what they’d read in order to help future students. The whole intervention took between 25 and 45 minutes for students to complete, and more than 90 percent of the incoming class completed it.

... In January 2013, when Yeager analyzed the first-semester data, he saw the advantaged students’ results were exactly the same as they were every year. No matter which message they saw in the pre-orientation presentation, 90 percent of that group was on track. Similarly, the disadvantaged students in the control group, who saw the bland message about adjusting to Austin’s culture and weather, did the same as disadvantaged students usually did: 82 percent were on track. But the disadvantaged students who had experienced the belonging and mind-set messages did significantly better: 86 percent of them had completed 12 credits or more by Christmas. They had cut the gap between themselves and the advantaged students in half.
One problem with this type of treatment or intervention is that the selected group should not be stigmatized, or even aware of why they were selected for the special treatment. As awareness grows (e.g., through this high profile article in the NYTimes magazine), it becomes harder and harder to camouflage the criteria used to select students for programs like TIP. Note, in the last intervention described above it appears the entire freshman class (~ 7k students) at UT Austin was used, so sample size was fairly large.

Wednesday, May 14, 2014

What's New Since Montagu?

I wrote this to help a journalist who is trying to understand the current controversy over A Troubled Inheritance, the new book by NYTimes genetics correspondent Nicholas Wade. (Link above goes to earlier discussion on this blog, with additional useful links and figures.)

The anthropologist Ashley Montagu advanced the idea that race is a social construct rather than a biological reality. For Wade, Montagu is a foil against which to benchmark recent advances in human genomics.
Wade: ... So I decided that I would write a book that explained what we know about race and what the consequences might be, and I think Montagu made a terrible mistake, though I share his motives.
Note the discussion below avoids using the term "race" and focuses instead on groups of humans that share ancestry. The degree of sharing can now be directly measured through genotypes.
What's New Since Montagu?

Two modern humans differ at about 1 in 1000 loci (out of ~ 3 billion in the human genome). There are a few million differences between any two individuals across their entire genome.

A common argument is that 99.9 percent genetic similarity cannot leave room for "consequential" differences. But modern humans and Neanderthals are almost as similar (~ 99.8 percent; we have high accuracy sequences now for Neanderthals), and there are significant differences between us and them: both physical and cognitive. However, because humans and Neanderthals are known to have interbred, we are still part of the same species. (Would it be fair to refer to them as a separate "race"? Is the modern-Neanderthal difference merely a social construct?) Furthermore, this 0.1 percent genetic variation accounts for human diversity encompassing Confucious, Einstein, Shaq and Shakespeare.

Genetic variation is patterned -- two individuals who trace their ancestry to the same geographical region (e.g., two Japanese) will have about 15 percent fewer total differences between them than if we were to compare individuals from widely separated ancestries (e.g., a Nigerian and a Japanese). This means hundreds of thousands of fewer differences between individuals from the same group than for two randomly selected people from different groups. 
Gene variants (alleles) which are common in one population (e.g., 90 percent of Japanese have version A) can be rare in another (e.g., only 20 percent of Nigerians have version A). Differences in allele frequencies are correlated across populations. From these correlations one can easily identify a genome (or even a small chunk of DNA as long as it includes many alleles) as belonging to a particular ancestral group. To oversimplify: just ask whether the DNA chunk in question has mostly the variants that are common in one group as opposed to another. Even if the differences in allele frequency are small -- e.g., allele X is 62 percent likely in Japanese, versus 57 percent likely in Nigerians -- once we consider thousands of such alleles the statistical signal becomes apparent. Each individual (or chunk of DNA) can be associated with a particular ancestral group.

Is this genetic difference consequential? Does it make two Nigerians more similar, on average, to each other than to a random European? Obviously, on some superficial phenotypes such as skin color or nose shape, the answer is yes.

But what about more complicated traits, such as height or cognitive ability or personality? All of these are known to be significantly heritable, through twin and adoption studies, as well as more modern methods.

We can't answer the question without understanding the specific genetic architecture of the trait. For example, are alleles that slightly increase height more common in one group than another? We need to know exactly which alleles affect height... But this is challenging as the traits I listed are almost certainly controlled by hundreds or thousands of genes. Could population averages on these traits differ between groups, due to differences in allele frequencies? I know of no argument, taking into account the information above, showing that they could not.

In fact, in the case of height we are close to answering the question. We have identified hundreds of loci correlated to height. Detailed analysis suggests that the difference in average height between N and S Europeans (about one population SD, or a couple of inches) is partially genetic (N Europeans, on average, have a larger number of height increasing alleles than S Europeans), due to different selection pressures that the populations experienced in the recent past (i.e., past 10k years).

Many who argue on Montagu's side hold the prior belief that the ~ 50k years of isolation between continental populations is not enough time for differential selection to produce group differences, particularly in complex traits governed by many loci. This is of course a quantitative question depending on strength of selection in different environments. The new results on height should cause them to reconsider their priors.

It is fair to say that results on height, as well as on simpler traits such as lactose or altitude tolerance, are consistent with Wade's theme that evolution has been recent, copious, and regional.

Further extrapolation to behavioral and cognitive traits will require more data, but:

1) The question is scientific -- it can be answered with known methods. (I estimate of order millions of genotype-phenotype pairs will allow us to extract the genetic architecture of complex traits like cognitive ability -- perhaps sometime in the coming decade.)

2) There is no a priori argument, given what we currently know, that such differences cannot exist. (Cf. Neanderthals!) Note this is NOT an argument that differences exist -- merely that they might, and that we cannot exclude the possibility.

An honest Ashley Montagu would have to concede points 1 and 2 above.

The second part of A Troublesome Inheritance covers controversial topics such as genetic group differences in behavioral and cognitive predispositions, and their societal implications. Wade is mostly careful to present these as speculative hypotheses, but nevertheless his advocacy leaves him vulnerable to easy attack. What I have summarized above are the incontestable (albeit, in some circles, perhaps still controversial and poorly understood) new results that have accumulated through the last decade of genomic research.
See also Recent human evolution: European height and The Neanderthal Problem.

Note Added: Distinguished evolutionary biologist H. Allen Orr has written a review in The New York Review of Books which I find quite similar to mine.

There was some back and forth between Razib Khan, Orr and Jerry Coyne. I added the comment below.
My take on the book is similar to that of Orr/Coyne: does a decent job of explaining population structure; too much speculation in the second part.

However, I think Orr/Coyne/Wade all miss the most interesting piece of science regarding strength of recent selection: evidence that the N-S height gradient (about 1 SD of difference between the two regions) in Europeans is due to selection pressure. That would constitute an example of fairly strong (in the context of the debate over group differences in humans) selection pressure acting over relatively short periods of time (~ 10 kya or less). I would think this result, if it holds up, might require significant updating of priors for certain people. It also provides a good example of how science in this area should be done: observed phenotype group difference, large data sets (GIANT) teasing out the genetic architecture, tests for selection on associated genetic variants.

http://infoproc.blogspot.com/2014/05/whats-new-since-montagu.html
http://infoproc.blogspot.com/2012/08/recent-human-evolution-european-height.html

Another point, for the cognoscenti: Wade does a good job explaining the difference between soft and hard sweeps. Orr notes that small adjustments of allele frequencies is one of the primary mechanisms for evolutionary change (so nothing new in Wade’s discussion; goes all the way back to Fisher), but many many readers, even biologists who aren’t in population genetics, don’t understand this point very well. So reading that section in the book would increase understanding for a large number of people.

Sunday, May 11, 2014

Life impacts of personality and intelligence

Here are two nice figures I came across recently.

The first, based on SMPY data, displays odds ratios for various accomplishments (doctorate degree, STEM publication, patent, high income, tenure) as a function of SAT-M score at age 13. The quartiles correspond roughly to 1 in 200 ability (Q1) to 1 in 10k ability (Q4). This data soundly refutes the "IQ above 120 doesn't matter" Malcolm Gladwell nonsense. See earlier post Horsepower matters; Psychometrics works.

In (imprecise) words: "Profoundly gifted children are 10+ times more likely than merely gifted children to, e.g., earn a patent or gain tenure at a top research university. They are at least several times more likely to earn exceptionally high incomes." (Note "merely gifted" is somewhat below the Q1 SMPY cut -- most school systems use top few percent vs top 0.5 percent.)



The second figure shows regression coefficients of income (at various ages) vs IQ and personality traits (standardized, so returns for each SD of trait). This was originally discussed in Earnings effects of personality, education and IQ for the gifted; see also this paper (Miriam Gensowski, Copenhagen). Note the IQ returns may be underestimated for average individuals since the data source is Terman and there is significant restriction of range (everyone tested at better than 1 in 200 or so on the Stanford-Binet). Nevertheless there are still positive returns to above average IQ within the Terman group (analogous to SMPY results above).

It pays to be Smart, Disciplined/Focused, Extraverted, and Mean! 8-(


Saturday, May 10, 2014

Height, Flynn Effect, and shared environment


Some interesting examples of shared environmental effects on height.
Atlantic: ... a database of 2,236 British soldiers who served in World War I, and then they looked up their birth records. The soldiers were relatively representative of the male population as a whole—about two-thirds of the 1890 British male birth cohort enlisted. It turns out that subtle differences in their heights hinted at their origins:

Those from white-collar backgrounds were taller: This follows the theory that wealth buys better food and living conditions, and thus greater height in adulthood. The men who hailed from the top two social classes stood a half-inch taller, on average.

The more kids there were in a household, the shorter they were: Not only because there was less food to go around, but also because it made it more likely that there were more people in each bedroom. “Crowding can help spread respiratory and gastrointestinal infections,” Hatton said. “People sneezing on each other, that sort of thing.” Each additional sibling cost the men an eighth of an inch, and having more than one person per bedroom shaved off a quarter-inch.

Children of literate mothers were taller: When mothers couldn’t read, they were less likely to know about the importance of a balanced diet or clean cutlery. The researchers measured the percentage of women by region who were only able to sign their marriage certificates with an X, rather than their name. People from areas with a high percentage of illiterate mothers were a quarter-inch shorter.

People from industrial districts were shorter than those from agricultural areas: Regardless of income, the Dickensian living conditions of 19th century British cities suppressed height by about nine-tenths of an inch.
Average European male height increased 11 centimeters between 1870 and 1970, about a centimeter per decade, or 1.5 SD in a century. Seems suspiciously similar to the Flynn Effect! In addition, over the same period of time average years of schooling went up significantly: e.g., UK 1870 4 years to 1930 7 years (see Appendix A of this paper). Most individuals born 100 years ago experienced significant deprivation by modern standards.

My own view is that there is nothing particularly mysterious about the Flynn Effect: living conditions, nutrition, and availability of education have all improved drastically in the last 150 years. So g scores should have as well. The Flynn Effect can be consistent with high heritability for non-deprived individuals in modern environments.

See also Swedish height in the 20th century and Flynn on the Flynn Effect.

The north-south gradient in average height found in Europe (see figure) may be a consequence of differential selection pressures that vary by region.

Michael Lewis, Longform, and HFT

I recommend this podcast interview with Michael Lewis (Longform.org). As with other Longform interviews, it focuses on his work/career as a writer and journalist. Flash Boys is only mentioned in passing.

Re: Flash Boys and high frequency trading (HFT): some years ago, post-financial crisis, I was in touch with some people at the SEC (Securities Exchange Commission, not the football conference) who were trying to build a quant group. Traditionally the SEC hires mostly lawyers, but the financial crisis and the Madoff scandal convinced them they needed to improve their analytical horsepower. I posted this job ad on the blog for them (no idea whether it was useful). At the time I also suggested that the SEC investigate HFT practices, but they didn't seem to know what I was talking about! 8-(

Thursday, May 08, 2014

Nicholas Wade interview: A Troublesome Inheritance

Leonard Lopate interviews Nicholas Wade (veteran genetics correspondent for the NYTimes) about his new book A Troublesome Inheritance: Genes, Race and Human History. The interview is slow at first but the second half is good.



Update: Another interview (May 9), with CBC, that gets right to the point regarding "social construction" -- the convenient but incorrect legacy of anthropologist Ashley Montagu (Israel Ehrenberg). The second guest, Stanford anthropologist Duana Fullwiley, foreshadows the counterattack on Wade.

See also this well-written essay in Time, adapted from the book.


I received a copy of A Troublesome Inheritance from the publisher. My initial impressions:

(1) The first part of the book covers well-established science concerning the genetic clustering of human populations. Some of the results will be surprising to those who have not followed the last 10 years of progress in genomics. See, e.g., here and here for my thoughts on this subject.

(2) The second part of the book covers controversial topics such as genetic group differences in behavioral and cognitive predispositions. Wade is mostly careful to present these as speculative hypotheses, but nevertheless his advocacy leaves him vulnerable to easy attack.

It will be interesting to see how this book, by a prominent science writer (indeed, the chief genetics correspondent for the paper of record), is received by the intelligentsia, the punditocracy, and actual scientists.

Additional remarks:


Below I have excerpted from the first link in (1) above, a post I originally wrote in 2007. I think these remarks are quite relevant to Wade's new book; note specific comments in brackets [ ... ].
... Two groups that form distinct [ genetic ] clusters are likely to exhibit different frequency distributions over various genes, leading to group differences. [ One does not require a more precise definition of "races" to get immediately to the thorny questions: two groups that differ in allele frequencies may differ statistically in phenotype! ]

This leads us to two very different possibilities in human genetic variation:

Hypothesis 1: (the PC mantra) The only group differences that exist between the clusters (races) are innocuous and superficial, for example related to skin color, hair color, body type, etc.

Hypothesis 2: (the dangerous one) Group differences exist which might affect important (let us say, deep rather than superficial) and measurable characteristics, such as cognitive abilities, personality, athletic prowess, etc.

... As scientists, we don't know whether H1 or H2 is correct, but given the revolution in biotechnology, we will eventually. Let me reiterate, before someone labels me a racist: we don't know with high confidence whether H1 or H2 is correct.

... it is important to note that group differences are statistical in nature and do not imply anything definitive about a particular individual. Rather than rely on the scientifically unsupported claim that we are all equal, it would be better to emphasize that we all have inalienable human rights regardless of our abilities or genetic makeup. [ Consider individuals, who are clearly unequal in their gifts: greater abilities should not confer greater rights! ]

... Clustering makes it possible that H2 is correct, because the alleles (genetic variants) affecting a particular phenotype will tend to have different frequencies in different groups. The average value of the trait might or might not be the same in different groups. In the case of height, enough is known to suggest that variants which lead to increased height are more frequent in northern Europe than in the south, and there is evidence that this is due to selection, not drift. [ i.e., this is evidence of recent selection driving group differences in a complex trait, controlled by thousands of loci. Wade: “Human evolution has been recent, copious, and regional.” ]

... I think it's especially important to be epistemologically careful in thinking about these matters, because of our difficult history with race. [ By articulating so many speculative theories in the second part of his book, Wade risks being perceived as not careful. ]

... I would much rather live in a world where H1 is true and H2 false. But my preference alone does not make it so. (I would also much rather live in a universe created by a loving God, and in which I and my children have eternal souls; not a cruel Darwinian universe in which our species arose merely by chance. But my preference does not make it so.)

Monday, May 05, 2014

Soylent is for people





New Yorker: ... I was relieved when factory-made Soylent arrived in the mail. It was basically Rhinehart’s formula, which I’d tasted in L.A.: a thick, tan liquid that is yeasty, grainy, and faintly sweet. Compared with the taste of my chocolate version, regular Soylent was pleasant. (Office taste-test results: “Naked protein shakes that are made of husks”; “One step better than what you drink before getting a colonoscopy.”)

I lived on the mixture, more or less, for a three-day weekend. Many of the tips I’d heard proved true. Soylent tastes better when it’s been in the fridge overnight. (A D.I.Y. user told me that this is “because the ingredients have been able to congeal.”) It’s more appealing after physical activity—when you’re hungry, you find that you actually crave it. The smell is a downside. On Friday, after a few hours, the doughy fragrance seemed to be everywhere—in my mouth, on my breath, my fingers, and my face. And the stomach takes a while to adjust to liquid food: by the afternoon, I felt like a walking water balloon.

Living on Soylent has its benefits, though. As Rhinehart puts it, you “cruise” through the day. If you’re in a groove at your computer, and feel a hunger pang, you don’t have to stop for lunch. Your energy levels stay consistent: “There’s no afternoon crash, no post-burrito coma.” Afternoons can be just as productive as mornings.

But that is Soylent’s downside, too. You begin to realize how much of your day revolves around food. Meals provide punctuation to our lives: we’re constantly recovering from them, anticipating them, riding the emotional ups and downs of a good or a bad sandwich. With a bottle of Soylent on your desk, time stretches before you, featureless and a little sad. On Saturday, I woke up and sipped a glass of Soylent. What to do? Breakfast wasn’t an issue. Neither was lunch. I had work to do, but I didn’t want to do it, so I went out for coffee. On the way there, I passed my neighborhood bagel place, where I saw someone ordering my usual breakfast: a bagel with butter. I watched with envy. I wasn’t hungry, and I knew that I was better off than the bagel eater: the Soylent was cheaper, and it had provided me with fewer empty calories and much better nutrition. Buttered bagels aren’t even that great; I shouldn’t be eating them. But Soylent makes you realize how many daily indulgences we allow ourselves in the name of sustenance.

Rinehart spends a lot of time in Soylent discussion forums, discovering how people have tweaked his formula. He told me that he relishes criticism, as long as it’s evidence-based, rather than “emotional”: “Putting a lot of eyeballs on the problem is only going to help.” In L.A., after our stop at the taco truck, I accompanied him to meet some D.I.Y.ers: a group of students in Ricketts House, a dorm at Caltech, who he’d heard were subsisting on Soylent. ...

... At Ricketts, Rhinehart asked the students if there were any more questions. Nick asked, “How do you feel about the fact that, after a lot of people eat Soylent, Soylent becomes people?”

Rhinehart smiled. “It’s pretty awesome,” he said. “I think about this a lot, actually.” He held out his arms, displaying his healthy torso. “I’ve been on it for a year now, and pretty much everything you see is built out of Soylent.”

Thursday, May 01, 2014

Seth Roberts


I was saddened to learn a few days ago that Seth Roberts (Wikipedia) had passed away. Andrew Gelman posts some recollections of their friendship here.

Seth and I came into contact first via the internet, although we later met in Beijing, where he had a second career as a professor at Tsinghua University. You can find some references to Seth on my blog here.
Beijing Photos 2: ... Last night I had Beijing duck with Seth Roberts. Seth has an interesting history. He started college at Caltech but transferred to Reed to study psychology. He was on the Berkeley faculty for many years but has moved to China and is now a professor at Tsinghua university. He knew Feynman and Jane Jacobs. We talked so long they closed down the restaurant around us!

PPP Apocalypse Now

Because the Chinese population is about 4 times larger than the US population, GDP parity (PPP adjusted) still implies a large disparity in per capita income.
Bloomberg: China is poised to overtake the U.S. as the world’s biggest economy earlier than expected, possibly as soon as this year, using calculations that take purchasing power into account.

China’s economy was 87 percent of the size of the U.S. in 2011, based on so-called purchasing power parity, the International Comparison Program said in a statement yesterday in Washington. The program, which involves organizations including the World Bank and United Nations, had put the figure at 43 percent in 2005.

The latest tally adds to the debate on how the world’s top two economic powers are progressing. Projecting growth rates from 2011 onwards suggests China’s size when measured in PPP may surpass the U.S. in 2014, which would be years earlier than many economists had previously estimated, according to Arvind Subramanian of the Peterson Institute for International Economics.

“There’s a symbolic element to this, to China overtaking the U.S., and that seems to be happening,” said Subramanian, a senior fellow at the Washington-based Peterson Institute. The latest data “plays to the idea that China is very big and getting bigger. It’s not to be underestimated.” ...
Perhaps more interesting:
The Needham Question

What do these things have in common? Fireworks, wood-block printing, canal lock-gates, kites, the wheelbarrow, chain suspension bridges and the magnetic compass. The answer is that they were all invented in China, a country that, right through the Middle Ages, maintained a cultural and technological sophistication that made foreign dignitaries flock to its imperial courts for trade and favour. But then, around 1700, the flow of ingenuity began to dry up and even reverse as Europe bore the fruits of the scientific revolution back across the globe.

Why did Modern Science develop in Europe when China seemed so much better placed to achieve it? This is called the Needham Question, after Joseph Needham, the 20th century British Sinologist who did more, perhaps, than anyone else to try and explain it.

But did Joseph Needham give a satisfactory answer to the question that bears his name? Why did China’s early technological brilliance not lead to the development of modern science and how did momentous inventions like gunpowder and printing enter Chinese society with barely a ripple and yet revolutionise the warring states of Europe?

With Chris Cullen, Director of the Needham Research Institute in Cambridge; Tim Barrett, Professor of East Asian History at SOAS; Frances Wood, Head of Chinese Collections at the British Library.
If current trends continue the Needham Question might be replaced by the more mundane Why did China have a bad 200 years starting in ~ 1800 AD? (See China 1793.)

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