Information Processing

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Tuesday, July 29, 2014


I have a new candidate for coolest research institute architecture. HKUST's Institute for Advanced Study is housed in an amazing building with a view of Clearwater Bay in HK. The members of the institute will be mostly theoretical physicists and mathematicians :-)

Stiff competition from Benasque's Center and the Perimeter Institute, however. Also Caltech's IQIM!

Click for larger images.

Compare to Dr. No's interrogation chamber :-)

Sunday, July 27, 2014


This paper provides additional support that the GWAS hits found by SSGAC affect cognitive ability. My guess is that UK age 14 SATS scores are pretty g-loaded. Note this is an ethnically homogeneous sample of students.

If the effect size per allele is about 1/30 SD, it would take ~1000 to account for normal population variation. These are the first loci detected, so typical effect size of alleles affecting cognitive ability is probably smaller. This seems consistent with my estimate of ~10k causal variants.

Genetic Variation Associated with Differential Educational Attainment in Adults Has Anticipated Associations with School Performance in Children (PLoS July 17, 2014 DOI: 10.1371/journal.pone.0100248)

Genome-wide association study results have yielded evidence for the association of common genetic variants with crude measures of completed educational attainment in adults. Whilst informative, these results do not inform as to the mechanism of these effects or their presence at earlier ages and where educational performance is more routinely and more precisely assessed. Single nucleotide polymorphisms exhibiting genome-wide significant associations with adult educational attainment were combined to derive an unweighted allele score in 5,979 and 6,145 young participants from the Avon Longitudinal Study of Parents and Children with key stage 3 national curriculum test results (SATS results) available at age 13 to 14 years in English and mathematics respectively. Standardised (z-scored) results for English and mathematics showed an expected relationship with sex, with girls exhibiting an advantage over boys in English (0.433 SD (95%CI 0.395, 0.470), p<10−10) with more similar results (though in the opposite direction) in mathematics (0.042 SD (95%CI 0.004, 0.080), p = 0.030). Each additional adult educational attainment increasing allele was associated with 0.041 SD (95%CI 0.020, 0.063), p = 1.79×10−04 and 0.028 SD (95%CI 0.007, 0.050), p = 0.01 increases in standardised SATS score for English and mathematics respectively. Educational attainment is a complex multifactorial behavioural trait which has not had heritable contributions to it fully characterised. We were able to apply the results from a large study of adult educational attainment to a study of child exam performance marking events in the process of learning rather than realised adult end product. Our results support evidence for common, small genetic contributions to educational attainment, but also emphasise the likely lifecourse nature of this genetic effect. Results here also, by an alternative route, suggest that existing methods for child examination are able to recognise early life variation likely to be related to ultimate educational attainment.

Saturday, July 26, 2014

Success, Ability, and all that

I came across this nice discussion at LessWrong which is similar to my old post Success vs Ability. The illustration below shows why even a strong predictor of outcome is seldom able to pick out the very top performer: e.g., taller people are on average better at basketball, but the best player in the world is not the tallest; smarter people are on average better at making money, but the richest person in the world is not the smartest, etc.

This seems like a trivial point (as are most things, when explained clearly), however, it still eludes the vast majority. For example, in the Atlantic article I linked to in the earlier post Creative Minds, the neuroscientist professor who studies creative genius misunderstands the implications of the Terman study. She repeats the common claim that Terman's study fails to support the importance of high cognitive ability to "genius"-level achievement: none of the Termites won a Nobel prize, whereas Shockley and Alvarez, who narrowly missed the (verbally loaded) Stanford-Binet cut for the study, each won for work in experimental physics. But luck, drive, creativity, and other factors, all at least somewhat independent of intelligence, influence success in science. Combine this with the fact that there are exponentially more people a bit below the Terman cut than above it, and Terman's results do little more than confirm that cognitive ability is positively but not perfectly correlated with creative output.

In the SMPY study probability of having published a literary work or earned a patent was increasing with ability even within the top 1%. The "IQ over 120 doesn't matter" meme falls apart if one measures individual likelihood of success, as opposed to the total number of individuals at, e.g., IQ 120 vs IQ 145 who have achieved some milestone. The base population of the former is 100 times that of the latter!

This topic came up last night in Hong Kong, at dinner with two hedge funders (Caltech/MIT guys with PhDs) who have had long careers in finance. Both observed that 20 years ago it was nearly impossible to predict which of their colleagues and peers would go on to make vast fortunes, as opposed to becoming merely rich.

Tuesday, July 22, 2014

Genome editing excises HIV

See also CRISPR Symposium at MSU and Genetic engineering of monkeys using CRISPR.
The Scientist: ... The researchers, led by Kamel Khalili at Temple University in Philadelphia, Pennsylvania, used the CRISPR/Cas9 genome-editing system to excise HIV from several human cell lines, including microglia and T cells. They targeted both the 5’ and 3’ ends of the virus, called the long terminal repeats (LTRs), so that the entire viral genome was removed.

“We were extremely happy with the outcome,” Khalili told The Scientist. “It was a little bit . . . mind-boggling how this system really can identify a single copy of the virus in a chromosome, which is highly packed DNA, and exactly cleave that region.”

His team showed that not only could Cas9 excise one copy of the HIV genome, but—operating in the same cell—it could also clip out another copy lurking in a different chromosome. Often, Khalili said, a cell can have several copies of latent HIV distributed across various chromosomes. “Most likely the technology is going to clean up the viral DNA” in a cell, he said.

... One limitation of the CRISPR/Cas9 approach is that it can chop up unintended regions of the genome, producing so-called off-target effects. Khalili’s group performed whole-genome sequencing to look for off-target effects, but didn’t find any. T.J. Cradick, the director of the protein engineering core facility at Georgia Tech, said that a more thorough analysis of potential off-target effects is still required to make sure nothing has been overlooked. Nonetheless, “latent HIV provirus is a very exciting target and . . . a very promising way forward,” said Cradick, who did not participate in the study.

W. Hu et al., “RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection,” PNAS, doi:10.1073/pnas.1405186111, 2014

Monday, July 21, 2014

The Creative Mind

 See also Anne Roe's The Making of a Scientist.
The Atlantic: ... One after another, my writer subjects came to my office and spent three or four hours pouring out the stories of their struggles with mood disorder—mostly depression, but occasionally bipolar disorder. A full 80 percent of them had had some kind of mood disturbance at some time in their lives, compared with just 30 percent of the control group—only slightly less than an age-matched group in the general population. (At first I had been surprised that nearly all the writers I approached would so eagerly agree to participate in a study with a young and unknown assistant professor—but I quickly came to understand why they were so interested in talking to a psychiatrist.) 
The Vonneguts turned out to be representative of the writers’ families, in which both mood disorder and creativity were overrepresented—as with the Vonneguts, some of the creative relatives were writers, but others were dancers, visual artists, chemists, architects, or mathematicians. This is consistent with what some other studies have found. When the psychologist Kay Redfield Jamison looked at 47 famous writers and artists in Great Britain, she found that more than 38 percent had been treated for a mood disorder; the highest rates occurred among playwrights, and the second-highest among poets. When Joseph Schildkraut, a psychiatrist at Harvard Medical School, studied a group of 15 abstract-expressionist painters in the mid-20th century, he found that half of them had some form of mental illness, mostly depression or bipolar disorder; nearly half of these artists failed to live past age 60. ... 
This time around, I wanted to examine a more diverse sample of creativity, from the sciences as well as the arts. My motivations were partly selfish—I wanted the chance to discuss the creative process with people who might think and work differently, and I thought I could probably learn a lot by listening to just a few people from specific scientific fields. After all, each would be an individual jewel—a fascinating study on his or her own. Now that I’m about halfway through the study, I can say that this is exactly what has happened. My individual jewels so far include, among others, the filmmaker George Lucas, the mathematician and Fields Medalist William Thurston, the Pulitzer Prize–winning novelist Jane Smiley, and six Nobel laureates from the fields of chemistry, physics, and physiology or medicine. Because winners of major awards are typically older, and because I wanted to include some younger people, I’ve also recruited winners of the National Institutes of Health Pioneer Award and other prizes in the arts. 
Apart from stating their names, I do not have permission to reveal individual information about my subjects. And because the study is ongoing (each subject can take as long as a year to recruit, making for slow progress), we do not yet have any definitive results—though we do have a good sense of the direction that things are taking. By studying the structural and functional characteristics of subjects’ brains in addition to their personal and family histories, we are learning an enormous amount about how creativity occurs in the brain, as well as whether these scientists and artists display the same personal or familial connections to mental illness that the subjects in my Iowa Writers’ Workshop study did. ... 
As I hypothesized, the creative people have shown stronger activations in their association cortices during all four tasks than the controls have. (See the images on page 74.) This pattern has held true for both the artists and the scientists, suggesting that similar brain processes may underlie a broad spectrum of creative expression. Common stereotypes about “right brained” versus “left brained” people notwithstanding, this parallel makes sense. Many creative people are polymaths, people with broad interests in many fields—a common trait among my study subjects.

Saturday, July 19, 2014

Bell Curve @20 @Harvard

The host is Harvard professor Harvey Mansfield. I'm not sure who all of the other panelists are, but they seem to include a professor of government and another of economics. The Asian physics guy is probably Peter Lu.
The Program on Constitutional Government at Harvard University

March 14, 2014: Charles Murray, on “The Bell Curve Revisited.” Charles Murray is a Fellow at the American Enterprise Association, and the author of famous and influential books, among them, Losing Ground (1984), The Bell Curve; Intelligence and Class Structure in American Life (1994, with Richard Herrnstein), and most recently, Coming Apart: the State of White America,1960-2010 (2013). He declares himself a libertarian, has written for many journals, and has received the Irving Kristol award from AEI and the Bradley Prize from the Bradley Foundation. He is Harvard ’65 and received a PhD in political science from M. I. T. in 1974. He is also the author of several “Murray’s laws” of social behavior.

Hail Britannia -- 100k whole genomes

Progress! Genotyping of large, well-phenotyped samples.
TechnologyReview: The British government says that it plans to hire the U.S. gene-sequencing company Illumina to sequence 100,000 human genomes in what is the largest national project to decode the DNA of a populace. ...

Some other countries are also considering large national sequencing projects. The U.K. project will focus on people with cancer, as well as adults and children with rare diseases. Because all Britons are members of the National Health Service, the project expects to be able to compare DNA data with detailed centralized health records (see “Why the U.K. Wants a Genomic National Health Service”).

While the number of genomes to be sequenced is 100,000, the total number of Britons participating in the study is smaller, about 70,000. That is because for cancer patients Genomics England intends to obtain the sequence of both their inherited DNA as well as that of their cancers.
BGI bid for this work but their transition to the upgraded Complete Genomics technology is still in progress. This delay has affected our cognitive genomics project as well.

Big data sets are also being assembled in the US (note in this case only SNP genotyping; cost is less than $100 per person now):
AKESOgen announced today that it has been awarded a $7.5M contract by the U.S. Department of Veterans Affairs (VA) for genotyping samples from U.S. veterans as part of the Million Veteran Program (MVP). This award covers the genotyping of 105,000 veterans in the first year of a five year contract.

"The VA's Million Veteran Program is one of the largest genetic initiatives ever undertaken in the US and its visionary genomics and genetics approach will provide new insights about how genes affect health. The goal is to improve healthcare for veterans by understanding the genetic basis of many common conditions. The data will ultimately be beneficial to the healthcare of all veterans and of the wider community. We are delighted to have been selected by the VA for this unique endeavor and we will provide genetic data of the highest quality to the VA." said Bob Boisjoli, CEO of AKESOgen. To fulfill the VA contract, AKESOgen will utilize a custom designed array based genotyping solution from Affymetrix, Inc. ...
My prediction is that of order a million phenotype:genotype pairs will be enough to deduce the genetic architecture of complex traits such as height or cognitive ability. SNPs will be enough to solve most of the problem, so that cost is now ~ $100M or less -- interested billionaires please contact me :-)

Wednesday, July 16, 2014

Conor Mcgregor

Win or lose, he's entertaining. Definitely the biggest character in the UFC.

Friday, July 11, 2014

Minds and Machines

HLMI = ‘high–level machine intelligence’ = one that can carry out most human professions at least as well as a typical human. I'm more pessimistic than the average researcher in the poll. My 95 percent confidence interval has earliest HLMI about 50 years from now, putting me at ~ 80-90th percentile in this group as far as pessimism. I think human genetic engineering will be around for at least a generation or so before machines pass a "strong" Turing test. Perhaps a genetically enhanced team of researchers will be the ones who finally reach the milestone, ~ 100 years after Turing proposed it :-)
These are the days of miracle and wonder
This is the long-distance call
The way the camera follows us in slo-mo
The way we look to us all
The way we look to a distant constellation
That’s dying in a corner of the sky
These are the days of miracle and wonder
And don’t cry baby don’t cry
Don’t cry -- Paul Simon

Future Progress in Artificial Intelligence: A Poll Among Experts

Vincent C. Müller & Nick Bostrom

Abstract: In some quarters, there is intense concern about high–level machine intelligence and superintelligent AI coming up in a few decades, bringing with it significant risks for humanity; in other quarters, these issues are ignored or considered science fiction. We wanted to clarify what the distribution of opinions actually is, what probability the best experts currently assign to high–level machine intelligence coming up within a particular time–frame, which risks they see with that development and how fast they see these developing. We thus designed a brief questionnaire and distributed it to four groups of experts. Overall, the results show an agreement among experts that AI systems will probably reach overall human ability around 2040-2050, and move on to super-intelligence in less than 30 years thereafter. The experts say the probability is about one in three that this development turns out to be ‘bad’ or ‘extremely bad’ for humanity.

Thursday, July 10, 2014

Chimp intelligence is heritable

A natural place to look for alleles of large effect are the otherwise conserved (from mouse through chimp) variants that are different in humans. See The Genetics of Humanness and The Essential Difference.

My guess (without checking the paper to see if they report it) is that test-retest correlation for chimps is well below the 0.9--0.95 often found for (human) g. Thus the h2 = 0.5 figure reported below could be significantly higher if corrected for reliability.
Nature News: Smart chimpanzees often have smart offspring, researchers suggest in one of the first analyses of the genetic contribution to intelligence in apes. The findings, published online today in Current Biology1, could shed light on how human intelligence evolved, and might even lead to discoveries of genes associated with mental capacity.

A team led by William Hopkins, a psychologist at Georgia State University in Atlanta, tested the intelligence of 99 chimpanzees aged 9 to 54 years old, most of them descended from the same group of animals housed at the Yerkes National Primate Research Center in Atlanta. The chimps faced cognitive challenges such as remembering where food was hidden in a rotating object, following a human’s gaze and using tools to solve problems.

A subsequent statistical analysis revealed a correlation between the animals' performance on these tests and their relatedness to other chimpanzees participating in the study. About half of the difference in performance between individual apes was genetic, the researchers found.

In humans, about 30% of intelligence in children can be explained by genetics; for adults, who are less vulnerable to environmental influences, that figure rises to 70%. Those numbers are comparable to the new estimate of the heritability of intelligence across a wide age range of chimps, says Danielle Posthuma, a behavioural geneticist at VU University in Amsterdam, who was not involved in the research.

“This study is much overdue,” says Rasmus Nielsen, a computational biologist at the University of California, Berkeley. “There has been enormous focus on understanding heritability of intelligence in humans, but very little on our closest relatives.”

Tuesday, July 08, 2014

James Simons: Mathematics, Common Sense, and Good Luck

A great MIT colloquium by Jim Simons (intro by I. Singer). Interesting discussion @28 min about how Simons (after leaving mathematics at 38) became an investor. Initially, he relied both on fundamental / event-driven analysis (reading the newspaper ;-) as well as computer models. But Simons eventually decided on a completely model-driven approach, and the rest is history.

@38 min: on RenTech's secret, We start with first rate scientists ... Great infrastructure ... New ideas shared and discussed as soon as possible in an open environment ... Compensation based on overall firm performance ...

@44 min: Be guided by beauty ... Try to do it RIGHT ... Don't give up and hope for some good luck!

@48 min: a defense of HFT ... the cost of liquidity?

@55 min: world's greatest investor is a Keynesian :-)

@58 min: brief precis of financial crisis ... See also here.

See also Jim Simons is my hero.

Do Standardized Tests Matter?

Thanks to a reader for pointing me to this TEDx talk by Nathan Kuncel. See also SAT and GRE Validity.

Saturday, July 05, 2014

Physics and the Horizons of Truth

I came across a PDF version of this book online. It contains a number of fine essays, including the ones excerpted from below. A recurring question concerning Godel's incompleteness results is whether they impact "interesting" mathematical questions.
CHAPTER 21 The Godel Phenomenon in Mathematics: A Modern View: ... Hilbert believed that all mathematical truths are knowable, and he set the threshold for mathematical knowledge at the ability to devise a “mechanical procedure.” This dream was shattered by Godel and Turing. Godel’s incompleteness theorem exhibited true statements that can never be proved. Turing formalized Hilbert’s notion of computation and of finite algorithms (thereby initiating the computer revolution) and proved that some problems are undecidable – they have no such algorithms.

Though the first examples of such unknowables seemed somewhat unnatural, more and more natural examples of unprovable or undecidable problems were found in different areas of mathematics. The independence of the continuum hypothesis and the undecidability of Diophantine equations are famous early examples. This became known as the Godel phenomenon, and its effect on the practice of mathematics has been debated since. Many argued that though some of the inaccessible truths above are natural, they are far from what is really of interest to most working mathematicians. Indeed, it would seem that in the seventy-five years since the incompleteness theo- rem, mathematics has continued thriving, with remarkable achievements such as the recent settlement of Fermat’s last “theorem” by Wiles and the Poincare conjecture by Perelman. Are there interesting mathematical truths that are unknowable?

The main point of this chapter is that when knowability is interpreted by modern standards, namely, via computational complexity, the Godel phenomenon is very much with us. We argue that to understand a mathematical structure, having a decision pro- cedure is but a first approximation; a real understanding requires an efficient algorithm. Remarkably, Godel was the first to propose this modern view in a letter to von Neumann in 1956, which was discovered only in the 1990s.

Meanwhile, from the mid-1960s on, the field of theoretical computer science has made formal Godel’s challenge and has created a theory that enables quantification of the difficulty of computational problems. In particular, a reasonable way to capture knowable problems (which we can efficiently solve) is the class P, and a reasonable way to capture interesting problems (which we would like to solve) is the class NP. Moreover, assuming the widely believed P ̸= NP conjecture, the class NP -complete captures interesting unknowable problems. ...
This volume also includes Paul Cohen's essay (chapter 19) on his work on the Continuum Hypothesis and his interactions with Godel. See also Horizons of Truth.
Cohen: ... I still had a feeling of skepticism about Godel's work, but skepticism mixed with awe and admiration.

I can say my feeling was roughly this: How can someone thinking about logic in almost philosophical terms discover a result that had implications for Diophantine equations? ... I closed the book and tried to rediscover the proof, which I still feel is the best way to understand things. I totally capitulated. The Incompleteness Theorem was true, and Godel was far superior to me in understanding the nature of mathematics.

Although the proof was basically simple, when stripped to its essentials I felt that its discoverer was above me and other mere mortals in his ability to understand what mathematics -- and even human thought, for that matter -- really was. From that moment on, my regard for Godel was so high that I almost felt it would be beyond my wildest dreams to meet him and discover for myself how he thought about mathematics and the fount from which his deep intuition flowed. I could imagine myself as a clever mathematician solving difficult problems, but how could I emulate a result of the magnitude of the Incompleteness Theorem? There it stood, in splendid isolation and majesty, not allowing any kind of completion or addition because it answered the basic questions with such finality.
My recent interest in this topic parallels a remark by David Deutsch
The reason why we find it possible to construct, say, electronic calculators, and indeed why we can perform mental arithmetic, cannot be found in mathematics or logic. The reason is that the laws of physics "happen" to permit the existence of physical models for the operations of arithmetic such as addition, subtraction and multiplication.
that suggests the primacy of physical reality over mathematics (usually the opposite assumption is made!) -- the parts of mathematics which are simply models or abstractions of "real" physical things are most likely to be free of contradiction or misleading intuition. Aspects of mathematics which have no physical analog (e.g., infinite sets) are prone to problems in formalization or mechanization. Physics (models which can to be compared to experimental observation; actual "effective procedures") does not ever require infinity, although it may be of some conceptual convenience. Hence one suspects, along the lines above, that mathematics without something like the "axiom of infinity" might be well-defined. Is there some sort of finiteness restriction (e.g., upper bound on Godel number) that evades Godel's theorem? If one only asks arithmetical questions about numbers below some upper bound, can't one avoid undecidability?

Tuesday, July 01, 2014

Snowden finale

Anyone care to make predictions?
Alternet: ... According to The Sunday Times of London, Glenn Greenwald will publish the names of Americans targeted by the NSA.

“One of the big questions when it comes to domestic spying is, ‘Who have been the NSA’s specific targets?’” he told the Times. “Are they political critics and dissidents and activists? Are they genuinely people we’d regard as terrorists? What are the metrics and calculations that go into choosing those targets and what is done with the surveillance that is conducted? Those are the kinds of questions that I want to still answer.”

Greenwald has promised that this will be the “biggest” revelation of the nearly two million classified files he received from Edward Snowden, and that “Snowden’s legacy would be ‘shaped in large part’ by this ‘finishing piece’ still to come.” In a May interview with GQ, Greenwald spoke of this “finale:”

"I think we will end the big stories in about three months or so [June or July 2014]. I like to think of it as a fireworks show: You want to save your best for last. There's a story that from the beginning I thought would be our biggest, and I'm saving that. The last one is the one where the sky is all covered in spectacular multicolored hues. This will be the finale, a big missing piece. Snowden knows about it and is excited about it."

Loyalty: Ames High School fight song

My high school fight song. Legend says it was written in the counterculture 60's and that some wag managed to slip "comrades at work and at play" into the lyrics under the noses of the school administrators. It's just the kind of thing clever AHS students might attempt :-)

Thursday, June 26, 2014

Theoreticians as Professional Outsiders

The book also contains essays on Schrodinger, Fisher, Pauling, George Price, and Rashevsky.
Theoreticians as Professional Outsiders: The Modeling Strategies of John von Neumann and Norbert Wiener (Ehud Lamm in Biology Outside the Box: Boundary Crossers and Innovation in Biology, Oren Harman and Michael R. Dietrich (eds.))

Both von Neumann and Wiener were outsiders to biology. Both were inspired by biology and both proposed models and generalizations that proved inspirational for biologists. Around the same time in the 1940s von Neumann developed the notion of self reproducing automata and Wiener suggested an explication of teleology using the notion of negative feedback. These efforts were similar in spirit. Both von Neumann and Wiener used mathematical ideas to attack foundational issues in biology, and the concepts they articulated had lasting effect. But there were significant differences as well. Von Neumann presented a how-possibly model, which sparked interest by mathematicians and computer scientists, while Wiener collaborated more directly with biologists, and his proposal influenced the philosophy of biology. The two cases illustrate different strategies by which mathematicians, the “professional outsiders” of science, can choose to guide their engagement with biological questions and with the biological community, and illustrate different kinds of generalizations that mathematization can contribute to biology. The different strategies employed by von Neumann and Wiener and the types of models they constructed may have affected the fate of von Neumann’s and Wiener’s ideas – as well as the reputation, in biology, of von Neumann and Wiener themselves.
For and Against theory in biology:
... E.B. Wilson articulated the reserved attitude of biologists towards uninvited theoreticians. Wilson’s remarks at the Cold Spring Harbor Symposia on Quantitative Biology in 1934 were ostensibly about the “Mathematics of Growth” but it is impossible to fail to notice their tone and true scope. Wilson suggested orienting the discussion around five axioms or “platitudes” as he called them. The first two are probably enough to get his point across. Axiom 1 states that “science need not be mathematical,” and if that’s not bad enough, axiom 2 solidifies the reserved attitude towards mathematization by stating that “simply because a subject is mathematical it need not therefore be scientific.”

... While the idea of self-reproduction seems incredible, and some might even have thought it to involve a self-contradiction, with objects creating something as complex as they are themselves, von Neumann’s solution to the problem of self-reproduction was remarkably simple. It is based on two operations: (1) constructing an object according to a list of instructions, and (2) copying a list of instructions as is ... This procedure is trivial for anyone computer-literate to understand; it was a remarkable theoretical result in 1948. What, however, does it tell us about biology? It is often observed that von Neumann’s explanation, which involves treating the genetic material both as instructions and as data that is copied as-is, is analogous to the reproduction of cells, since DNA, the analogue of the instruction list, is passively replicated. Von Neumann compared the construction instructions that direct the automaton to genes, noting that genes probably do not constitute instructions fully specifying the construction of the objects their presence stimulates. He warned that genes are probably only general pointers or cues that affect development, a warning that alas did not curtail the “genetic program” metaphor that became dominant in years to come.

Von Neumann noted that his model explained how mutations that do not affect self- replication are possible. If the instruction list specifies not only the self-replicating automaton but also an additional structure, this structure will also be replicated. ...

... As Claude Shannon put it in a 1958 review of von Neumann’s contributions to automata theory, and specifically self-reproducing automata:

If reality is copied too closely in the model we have to deal with all of the complexity of nature, much of which is not particularly relevant to the self-reproducing question. However, by simplifying too much, the structure becomes so abstract and simplified that the problem is almost trivial and the solution is un-impressive with regard to solving the philosophical point that is involved. In one place, after a lengthy discussion of the difficulties of formulating the problem satisfactorily, von Neumann remarks: "I do not want to be seriously bothered with the objection that (a) everybody knows that automata can reproduce themselves (b) everybody knows that they cannot."
See also On Crick and Watson and Reliable Organization of Unreliable Components

Sunday, June 22, 2014

Asia's Cauldron: the South China sea and DF-21D ASBM

I recommend Robert Kaplan's Asia's Cauldron: The South China Sea and the End of a Stable Pacific. A key question: how effective will conventional ballistic missiles (ASBM: e.g., DF-21D, CEP ~ 10m? recent report) and cruise missiles (ASCM) be against US carrier groups?

Over the last decade, the center of world power has been quietly shifting from Europe to Asia. With oil reserves of several billion barrels, an estimated nine hundred trillion cubic feet of natural gas, and several centuries’ worth of competing territorial claims, the South China Sea in particular is a simmering pot of potential conflict. The underreported military buildup in the area where the Western Pacific meets the Indian Ocean means that it will likely be a hinge point for global war and peace for the foreseeable future.

In Asia’s Cauldron, Robert D. Kaplan offers up a vivid snapshot of the nations surrounding the South China Sea, the conflicts brewing in the region at the dawn of the twenty-first century, and their implications for global peace and stability. One of the world’s most perceptive foreign policy experts, Kaplan interprets America’s interests in Asia in the context of an increasingly assertive China. He explains how the region’s unique geography fosters the growth of navies but also impedes aggression. And he draws a striking parallel between China’s quest for hegemony in the South China Sea and the United States’ imperial adventure in the Caribbean more than a century ago.

To understand the future of conflict in East Asia, Kaplan argues, one must understand the goals and motivations of its leaders and its people. Part travelogue, part geopolitical primer, Asia’s Cauldron takes us on a journey through the region’s boom cities and ramshackle slums: from Vietnam, where the superfueled capitalism of the erstwhile colonial capital, Saigon, inspires the geostrategic pretensions of the official seat of government in Hanoi, to Malaysia, where a unique mix of authoritarian Islam and Western-style consumerism creates quite possibly the ultimate postmodern society; and from Singapore, whose “benevolent autocracy” helped foster an economic miracle, to the Philippines, where a different brand of authoritarianism under Ferdinand Marcos led not to economic growth but to decades of corruption and crime.
See also John Mearsheimer: Can China Rise Peacefully?

Wednesday, June 18, 2014

Chicago Conference on Genetics and Behavior (video)

This is video of my talk at the University of Chicago Conference on Genetics and Behavior back in April. Slides -- they are not very readable in the video. Here's another link to the talk on the Chicago page.

Ability, Effort, and Academic Achievement among Asian Americans

What accounts for the academic success of E. Asians? I would have guessed about equal parts cognitive advantage (ability) and hard work (grinding). The paper below tries to quantify this in more detail using data from two nationally representative cohort studies, comparing students of various of ethnicities who attend the same schools. Note the broad conclusion stated in the abstract applies better to Asian Americans (AAs) in aggregate, and less well to the E. Asian subpopulation alone -- see figures below.
Explaining Asian Americans’ academic advantage over whites (PNAS)

The superior academic achievement of Asian Americans is a well-documented phenomenon that lacks a widely accepted explanation. Asian Americans’ advantage in this respect has been attributed to three groups of factors: (i) socio-demographic characteristics, (ii) cognitive ability, and (iii) academic effort as measured by characteristics such as attentiveness and work ethic. We combine data from two nationally representative cohort longitudinal surveys to compare Asian-American and white students in their educational trajectories from kindergarten through high school. We find that the Asian-American educational advantage is attributable mainly to Asian students exerting greater academic effort and not to advantages in tested cognitive abilities or socio-demographics. We test explanations for the Asian–white gap in academic effort and find that the gap can be further attributed to (i) cultural differences in beliefs regarding the connection between effort and achievement and (ii) immigration status. Finally, we highlight the potential psychological and social costs associated with Asian-American achievement success.

While all four AA subpopulations showed positive differences relative to white students in academic achievement and effort, only the E. Asian subgroup had a cognitive advantage.

From the Supplement: for E. Asians, the academic achievement gap appears to be ~ 1/3 due to cognitive ability and ~ 2/3 due to academic effort, with large uncertainties. For the other subpopulations the results are quite different (and actually rather strange). Click for larger version.

Sunday, June 15, 2014

The Age of Ambition and The Fourth Revolution

Evan Osnos (New Yorker China correspondent; successor to Peter Hessler) on his new book Age of Ambition: Chasing Fortune, Truth, and Faith in the New China.

BONUS: Micklethwait and Wooldridge, co-authors of The Fourth Revolution: The Global Race to Reinvent the State, on CELAP (also here).
WSJ: Buried in a Shanghai suburb, close to the city's smoggy Inner Ring Road, the China Executive Leadership Academy Pudong, or Celap, seems to have a military purpose. Razor wire curls along the fences around the huge compound, and guards stand at its gate. But drive into the campus from the curiously named Future Schedule Street, and you enter what looks like Harvard as redesigned by Dr. No.

In the middle of the academy stands a huge, bright-red building in the shape of a desk, with an equally monumental, scarlet inkwell beside it. Surrounding it are lakes and trees, libraries, a sports center and a series of low, brown dormitory buildings, all designed to look like unfolded books. Celap calls this a "campus," but the organization is too disciplined, hierarchical and businesslike to be a university. The locals are closer to the mark: They call it a "Cadre Training School." This is an organization bent on world domination.

Celap's students are China's future leaders. The egalitarian-looking sleeping quarters mask a strict pecking order, with suites for senior visitors from Beijing. The syllabus eschews ideology in favor of technocratic solutions. The two most common questions, says one teacher, are: What works best? And can it be applied here?

Today, Chinese students and officials hurtle around the world, studying successful models from Chile to Sweden. Some 1,300 years ago, Celap's staff remind you, imperial China sought out the brightest young people to become civil servants. For centuries, these mandarins ran the world's most advanced government—until the Europeans and then the Americans forged ahead. Better government has long been one of the West's great advantages. Now the Chinese want that title back.

Western policy makers should look at this effort the same way that Western businessmen looked at Chinese factories in the 1990s: with a mixture of awe and fear. Just as China deliberately set out to remaster the art of capitalism, it is now trying to remaster the art of government. The only difference is a chilling one: Many Chinese think there is far less to be gained from studying Western government than they did from studying Western capitalism. They visit Silicon Valley and Wall Street, not Washington, D.C.

The West pulled ahead of "the rest" because it created a permanent contest to improve its government machinery. In particular, it pioneered four great revolutions. The first was the security revolution of the 16th and 17th centuries, when Europe's princes created modern nation states. As Spain, England and France competed around the globe, they improved statecraft in a way that introverted China never did.

The second great revolution, of the late 18th and 19th centuries, championed liberty and efficiency. Aristocratic patronage systems were replaced with leaner, more meritocratic governments, focused on providing services like schools and police. Under Britain's thrifty Victorians, the world's most powerful country reduced its tax take from £80 million in 1816 to less than £60 million in 1860—even as its population increased by 50%.

This vision of a limited but vigorous state was swept away in the third revolution. In the 20th century, Western government provided people with ever more help: first health care and unemployment pay but eventually college education and what President Lyndon B. Johnson called the Great Society. Despite counterattacks, notably the 1980s half-revolution of Ronald Reagan and Margaret Thatcher, the sprawling welfare state remains the dominant Western model.

In the U.S., government spending increased from 7.5% of GDP in 1913 to 19.7% in 1937, to 27% in 1960, to 34% in 2000 and to 42% in 2011. Voters continue to demand more services, and politicians of all persuasions have indulged them—with the left delivering hospitals and schools, the right building prisons, armies and police forces, and everybody creating regulations like confetti.

In all three of these revolutions, the West led the way. But now, as China's ambitions illustrate, the emerging world is eager to compete again.

And why not? Over the past two years, while the U.S. political system has torn itself apart over Obamacare, China has extended pension coverage to an additional 240 million rural people. Lee Kwan Yew's authoritarian Singapore offers dramatically better education and health care than Uncle Sam, with a state that is a fraction of the U.S.'s size. If you are looking for the future of health care, India's attempt to apply mass-production techniques to hospitals is part of the answer. So too, Brazil's conditional cash transfers are part of the future of welfare. At the very least, the West no longer has a monopoly on ideas. ...

The first is that, while Western voters have overloaded the state with demands, they abhor the result. The U.S. Congress regularly scores an approval rating of 10%. In Britain, membership of the Tory Party slid from 3 million in 1950 to 123,000 today, a performance that would have put a private company into receivership. Voters are frustrated.

Second, government is going broke. The U.S. government has run a surplus only five times since 1960; France hasn't had one since 1974-75. And now the demographic challenge of caring for aging populations will push even left-wing parties toward hard choices about what—and whom—they want to save.

The third reason is more positive. Government can be reformed, but only if Western politicians and electorates decide what they want it to do.

Our own answer is, simply, much less. The overloaded modern state is a threat to democracy: The more responsibilities Leviathan assumes, the worse it performs them, and the angrier citizens get. ...

You may disagree. But this is part of a bigger argument that the West must start having now. A great contest is under way to reinvent the state, and the Chinese have the advantage of knowing what the consequences are if they lose.

Saturday, June 14, 2014

Directional Personality and mate preferences

Some good old evo psych fun -- guaranteed to annoy certain people :-)  Nevertheless, interesting because it raises the point that measurements of Personality (e.g., Big 5 or other constructs) are complicated by the fact that people can behave differently depending on the target of the behavior.

Plenty of sociopaths in large organizations are pleasant to superiors but unpleasant to those below them in the hierarchy.
Kind toward whom? Mate preferences for personality traits are target specific (Evolution and Human Behavior 31 (2010) 29–38)

Previous mate preference studies indicate that people prefer partners whose personalities are extremely kind and trustworthy, but relatively non-dominant. This conclusion, however, is based on research that leaves unclear whether these traits describe the behavior a partner directs toward oneself, toward other classes of people or both. Because the fitness consequences of partners' behaviors likely differed depending on the classes of individuals toward whom behaviors were directed, we predicted that mate preferences for personality traits would change depending on the specific targets of a partner's behavioral acts. Consistent with this, two experiments demonstrated that people prefer partners who are extremely kind and trustworthy when considering behaviors directed toward themselves or their friends/family, but shift their preferences to much lower levels of these traits when considering behaviors directed toward other classes of individuals. In addition, both sexes preferred partners who direct higher levels of dominance toward members of the partner's own sex than toward any other behavioral target category, with women preferring levels of dominance toward other men as high as — or higher than — levels of kindness and trustworthiness. When asked to rate traits for which the behavioral target was left unspecified, furthermore, preferences were very similar to self-directed preferences, suggesting that previous trait-rating studies have not measured preferences for partners' behaviors directed toward people other than oneself. These findings may provide a basic contribution to the mate preference literature via their demonstration that ideal standards for romantic partners are importantly qualified by the targets of behavioral acts.

In the figure below, women (top graph) seem to prefer a larger self--rival asymmetry in their mates than men do. In other words, women like men who are kind to them but who are socially dominant towards other men. (Proponents of Game would argue that even this reflects a bit of false consciousness -- that women actually prefer men who are socially dominant towards them!) Click for larger version.

Thanks to a reader for the reference.

Wednesday, June 11, 2014

Information technology in higher eduction

Slides from a brief talk I gave to a meeting of IT administrators.

Saturday, June 07, 2014

Large-Scale Psychological Differences Within China

The study below discusses a psychological/cognitive/personality gradient between N and S China, possibly driven by a history of wheat vs rice cultivation.
Large-Scale Psychological Differences Within China Explained by Rice Versus Wheat Agriculture (Science)

Cross-cultural psychologists have mostly contrasted East Asia with the West. However, this study shows that there are major psychological differences within China. We propose that a history of farming rice makes cultures more interdependent, whereas farming wheat makes cultures more independent, and these agricultural legacies continue to affect people in the modern world. We tested 1162 Han Chinese participants in six sites and found that rice-growing southern China is more interdependent and holistic-thinking than the wheat-growing north. To control for confounds like climate, we tested people from neighboring counties along the rice-wheat border and found differences that were just as large. We also find that modernization and pathogen prevalence theories do not fit the data.

Editor Summary: On a diverse and large set of cognitive tests, subjects in East Asian countries are more inclined to display collectivist choices, whereas subjects in the United States are more inclined to score as individualists. Talhelm et al. (p. 603; see the Perspective by Henrich) suggest that one historical source of influence was societal patterns of farming rice versus wheat, based on three cognitive measures of individualism and collectivism in 1000 subjects from rice- and wheat-growing regions in China.
The first author of the paper is interviewed below; his comments are quite illuminating. None of the discussants entertain the notion that any of these group differences could be partially genetic in causation.
Sinica: Rice, Wheat and Air Filters

This week on Sinica, we're delighted to be joined by Thomas Talhelm, Ph.D. candidate in psychology at the University of Virginia and author of a recent paper proposing a fascinating connection between rice and wheat-growing communities, and persistent differences in psychological orientations of people from different parts of China. So join us as we talk about divorce, collectivism and violence, and get the dirt on all the various tests psychologists are using to measure it all here in the Middle Kingdom.

And even if psychology isn't your thing, we suspect that breathing is -- which is another reason to listen. In addition to his growing reputation in academic circles, Thomas is also known in China for his production and proselytization of do-it-yourself air filtration kits, which he sells through his company Smart Air Filters. If you are interested in getting a filter without spending a fortune, be sure to check them out.
I corresponded briefly with Talhelm, pointing out that his results are already a part of Chinese folk sociology, and even remarked upon by European visitors to China in the 18th century.

Friday, June 06, 2014

Rare mutations and severe intellectual disability

The paper below describes rare de novo mutations which cause severe intellectual disability. See also Structural genomic variants (CNVs) affect cognition.

By the principle of continuity, I suspect that rare variants of smaller negative effect on cognitive ability also exist. These alleles, although harder to detect, would account for part of the observed population variation in the normal range. As discussed in an earlier post (Common variants vs mutational load), these are likely responsible for additional heritability not included in the h2 ~ 0.5 due to common variants estimated from GCTA.
Genome sequencing identifies major causes of severe intellectual disability (Nature)

Severe intellectual disability (ID) occurs in 0.5% of newborns and is thought to be largely genetic in origin1, 2. The extensive genetic heterogeneity of this disorder requires a genome-wide detection of all types of genetic variation. Microarray studies and, more recently, exome sequencing have demonstrated the importance of de novo copy number variations (CNVs) and single-nucleotide variations (SNVs) in ID, but the majority of cases remain undiagnosed3, 4, 5, 6. Here we applied whole-genome sequencing to 50 patients with severe ID and their unaffected parents. All patients included had not received a molecular diagnosis after extensive genetic prescreening, including microarray-based CNV studies and exome sequencing. Notwithstanding this prescreening, 84 de novo SNVs affecting the coding region were identified, which showed a statistically significant enrichment of loss-of-function mutations as well as an enrichment for genes previously implicated in ID-related disorders. In addition, we identified eight de novo CNVs, including single-exon and intra-exonic deletions, as well as interchromosomal duplications. These CNVs affected known ID genes more frequently than expected. On the basis of diagnostic interpretation of all de novo variants, a conclusive genetic diagnosis was reached in 20 patients. Together with one compound heterozygous CNV causing disease in a recessive mode, this results in a diagnostic yield of 42% in this extensively studied cohort, and 62% as a cumulative estimate in an unselected cohort. These results suggest that de novo SNVs and CNVs affecting the coding region are a major cause of severe ID. Genome sequencing can be applied as a single genetic test to reliably identify and characterize the comprehensive spectrum of genetic variation, providing a genetic diagnosis in the majority of patients with severe ID.

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Wednesday, June 04, 2014

Strategic War (with cards)

War is a simple card game played by children. The most common version does not require decisions, so it's totally deterministic (outcome is determined) once the card order in each deck is fixed. Nevertheless it can be entertaining to watch/play: there are enough fluctuations to engage observers, mainly due to the treatment of ties. The question of how to determine the winner from the two deck orderings (without actually playing the entire game, which can take a long time) was one of the first aspects of computability / predictive modeling / chaotic behavior I thought about as a kid. This direction leads to things like classification of cellular automata and the halting problem.

My children came home with a version designed to teach multiplication -- each "hand" is two cards, rather than the usual single card, and the winner of the "battle" is the one with the higher product value of the two cards (face cards are removed).  I thought this was still too boring: no strategy (my kids understood this right away, along with the meaning of deterministic; this puts them ahead of some philosophers), so I came up with a variant that has been quite fun to play.

Split the deck into red and black halves, removing face cards. Each hand (battle) is played with two cards, but they are chosen by each player. One card is placed faced down simultaneously by each player, and the second cards played are chosen after the first cards have been revealed (flipped over). Winner of most hands is the victor.

This game ("strategic war") is simple to learn, but complex enough that it involves bluffing, calculation, and card counting (keeping track of which cards have been played). A speed version, with, say, 10 seconds allowed per card choice, goes very fast.

Has anyone seen heard of this game before? It's a bit like repeated two card poker (heads up), drawing from a fixed deck. Note the overall strength of hands for each player (combined multiplicative value of all cards) is fixed and equal. Playing strong hands early means weaker hands later in the game. The goal is to win each hand by as small a margin as possible.

Are there strategies which dominate random play (= select first card at random, second card from range not exceeding highest card required to guarantee a win)?

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