Friday, April 29, 2016

Gell-Mann on quantum foundations

Google knows enough about me that my YouTube feed now routinely suggests content of real interest. A creepy but positive development ;-)

Today YouTube suggested this video of Murray Gell-Mann talking about Everett, decoherence, and quantum mechanics. I had seen this video on another web site years ago and blogged about it (post reproduced below), but now someone has uploaded it to YouTube.

More on Murray here and here:
After the talk I had a long conversation with John Preskill about many worlds, and he pointed out to me that both Feynman and Gell-Mann were strong advocates: they would go so far as to browbeat visitors on the topic. In fact, both claimed to have invented the idea independently of Everett.
See also my recent paper The measure problem in many worlds quantum mechanics.

Gell-Mann, Feynman, Everett

This site is a treasure trove of interesting video interviews -- including with Francis Crick, Freeman Dyson, Sydney Brenner, Marvin Minsky, Hans Bethe, Donald Knuth, and others. Many of the interviews have transcripts, which are much faster to read than listening to the interviews themselves.

Here's what Murray Gell-Mann has to say about quantum foundations:
In '63…'64 I worked on trying to understand quantum mechanics, and I brought in Felix Villars and for a while some comments... there were some comments by Dick Feynman who was nearby. And we all agreed on a rough understanding of quantum mechanics and the second law of thermodynamics and so on and so on, that was not really very different from what I'd been working on in the last ten or fifteen years.

I was not aware, and I don't think Felix was aware either, of the work of Everett when he was a graduate student at Princeton and worked on this, what some people have called 'many worlds' idea, suggested more or less by Wheeler. Apparently Everett was, as we learned at the Massagon [sic] meeting, Everett was an interesting person. He… it wasn't that he was passionately interested in quantum mechanics; he just liked to solve problems, and trying to improve the understanding of quantum mechanics was just one problem that he happened to look at. He spent most of the rest of his life working for the Weapon System Evaluation Group in Washington, WSEG, on military problems. Apparently he didn't care much as long as he could solve some interesting problems! [Some of these points, concerning Everett's life and motivations, and Wheeler's role in MW, are historically incorrect.]

Anyway, I didn't know about Everett's work so we discovered our interpretation independent of Everett. Now maybe Feynman knew about… about Everett's work and when he was commenting maybe he was drawing upon his knowledge of Everett, I have no idea, but… but certainly Felix and I didn't know about it, so we recreated something related to it.

Now, as interpreted by some people, Everett's work has two peculiar features: one is that this talk about many worlds and equally… many worlds equally real, which has confused a lot of people, including some very scholarly students of quantum mechanics. What does it mean, 'equally real'? It doesn't really have any useful meaning. What the people mean is that there are many histories of the… many alternative histories of the universe, many alternative course-grained, decoherent histories of the universe, and the theory treats them all on an equal footing, except for their probabilities. Now if that's what you mean by equally real, okay, but that's all it means; that the theory treats them on an equal footing apart from their probabilities. Which one actually happens in our experience, is a different matter and it's determined only probabilistically. Anyway, there's considerable continuity between the thoughts of '63-'64 and the thoughts that, and… and maybe earlier in the ‘60s, and the thoughts that Jim Hartle and I have had more recently, starting around '84-'85.
Indeed, Feynman was familiar with Everett's work -- see here and here.

Where Murray says "it's determined only probabilistically" I would say there is a subjective probability which describes how surprised one is to find oneself on a particular decoherent branch or history of the overall wavefunction -- i.e., how likely or unlikely we regard the outcomes we have observed to have been. For more see here.

Murray against Copenhagen:
... although the so-called Copenhagen interpretation is perfectly correct for all laboratory physics, laboratory experiments and so on, it's too special otherwise to be fundamental and it sort of strains credulity. It's… it’s not a convincing fundamental presentation, correct though… though it is, and as far as quantum cosmology is concerned it's hopeless. We were just saying, we were just quoting that old saw: describe the universe and give three examples. Well, to apply the… the Copenhagen interpretation to quantum cosmology,  you'd need a physicist outside the universe making repeated experiments, preferably on multiple copies of the universe and so on and so on. It's absurd. Clearly there is a definition to things happening independent of human observers. So I think that as this point of view is perfected it should be included in… in teaching fairly early, so that students aren't convinced that in order to understand quantum mechanics deeply they have to swallow some of this…very… some of these things that are very difficult to believe. But in the end of course, one can use the Copenhagen interpretations perfectly okay for experiments.

Thursday, April 28, 2016

Can't we all just get along? Albion's Seed reviewed on Slate Star Codex

Highly recommended! Scott Alexander reviews and summarizes Albion's Seed. The copy I read years ago belonged to the university library. Scott mentions so many interesting topics I had forgotten that I just now got a personal copy of the book.
Slate Star Codex: Albion’s Seed by David Fischer is a history professor’s nine-hundred-page treatise on patterns of early immigration to the Eastern United States. It’s not light reading and not the sort of thing I would normally pick up. I read it anyway on the advice of people who kept telling me it explains everything about America. And it sort of does.

In school, we tend to think of the original American colonists as “Englishmen”, a maximally non-diverse group who form the background for all of the diversity and ethnic conflict to come later. Fischer’s thesis is the opposite. Different parts of the country were settled by very different groups of Englishmen with different regional backgrounds, religions, social classes, and philosophies. The colonization process essentially extracted a single stratum of English society, isolated it from all the others, and then plunked it down on its own somewhere in the Eastern US. ...

... If America is best explained as a Puritan-Quaker culture locked in a death-match with a Cavalier-Borderer culture, with all of the appeals to freedom and equality and order and justice being just so many epiphenomena – well, I’m not sure what to do with that information. Push it under the rug? Say “Well, my culture is better, so I intend to do as good a job dominating yours as possible?” Agree that We Are Very Different Yet In The End All The Same And So Must Seek Common Ground? Start researching genetic engineering? Maybe secede? I’m not a Trump fan much more than I’m an Osama bin Laden fan; if somehow Osama ended up being elected President, should I start thinking “Maybe that time we made a country that was 49% people like me and 51% members of the Taliban – maybe that was a bad idea“.

I don’t know. But I highly recommend Albion’s Seed as an entertaining and enlightening work of historical scholarship which will be absolutely delightful if you don’t fret too much over all of the existential questions it raises.

Tuesday, April 26, 2016

New Yorker on epigenetics

This is a fairly balanced account of recent progress in epigenetics (at least the part I excerpt below). But see here for negative reactions.
New Yorker: ... But, if epigenetic information can be transmitted through sperm and eggs, an organism would seem to have a direct conduit to the heritable features of its progeny. Such a system would act as a wormhole for evolution—a shortcut through the glum cycles of mutation and natural selection.

My visit with Allis had ended on a cautionary note. “Much about the transmission of epigenetic information across generations is unknown, and we should be careful before making up theories about the kind of information or memory that is transmitted,” he told me. By bypassing the traditional logic of genetics and evolution, epigenetics can arouse fantasies about warp-speeding heredity: you can make your children taller by straining your neck harder. Such myths abound and proliferate, often dangerously. A child’s autism, the result of genetic mutation, gets attributed to the emotional trauma of his great-grandparents. Mothers are being asked to minimize anxiety during their pregnancy, lest they taint their descendants with anxiety-ridden genes. Lamarck is being rehabilitated into the new Darwin.

These fantasies should invite skepticism. Environmental information can certainly be etched on the genome. But such epigenetic scratch marks are rarely, if ever, carried forward across generations. A man who loses a leg in an accident bears the imprint of that accident in his cells, wounds, and scars, but he does not bear children with shortened legs. A hundred and forty generations of circumcision have not made the procedure any shorter. ...

Monday, April 25, 2016

Prince Rogers Nelson

If you're a true fan, and like guitar, you'll enjoy this 20 minute live version of Purple Rain. The whole concert.

Prince was at his peak in 1985. I saw him on the Purple Rain tour in Los Angeles, with Sheila E. opening. We camped out at a Tower Records in Pasadena to get the tickets.

When the movie opened in 1984 I was home for the summer in Iowa after my freshman year. I think all of my high school friends were big fans. Eventually I had it on VHS and watched it many times with my girlfriend.

Here's Sheila E. doing The Glamorous Life. 80's forever! :-)

Thursday, April 21, 2016

Deep Learning tutorial: Yoshua Bengio, Yann Lecun NIPS 2015

I think these are the slides.

One of the topics which I've remarked on before is the absence of local minima in the high dimensional optimization required to tune these DNNs. In the limit of high dimensionality a critical point is overwhelmingly likely to be a saddlepoint (have at least one negative eigenvalue). This means that even though the surface is not strictly convex the optimization is tractable.

Wednesday, April 20, 2016

Free Harvard, Fair Harvard

Desert scale model of the solar system

Magnetic brain stimulation and autism

If this account is true, it's simply amazing.
NY Magazine: What It’s Like to ‘Wake Up’ From Autism After Magnetic Stimulation

... Though he wasn’t diagnosed with autism until he was 40, John Elder Robison felt isolated and disconnected throughout his entire youth and early adulthood. But in 2008, at 50, he took part in what became a three-year research project looking at brain function in individuals with autism spectrum disorders and exploring the use of transcranial magnetic stimulation (TMS) to help them.

TMS is a noninvasive procedure that uses magnetic pulses to stimulate nerve cells in the brain. During treatment, a coil is placed against the patient’s scalp and the TMS energy passes through the skull into the outermost layer of the brain. ...

The treatment left Robison momentarily crippled by the weight of other people’s feelings, and he spoke with Science of Us about his experience, which he also discusses in his recently released book, Switched On: A Memoir of Brain Change and Emotional Awakening. ...

Do you understand now what was happening?
TMS modified my emotional response to what you might call ordinary situations. I often put it this way: You might be crossing the street and you fall and you skin your knee. I’d say, “Come on, get up!” The very best advice I could give is come on, get going, this car could run you over. People would see my practical response as cold and emotionless. After TMS, I’d look at you and wince at your skinned knee. I never did that before. And I now realize that wincing at your skinned knee is the response most people have. I still have the autistic response, but I’m also aware of what you might now call the “empathetic response from personal experience.” People can tell you about something a million times, and it won’t mean anything to you until you experience it. That said, it’s important to understand that I always had the ability to feel your pain. Like, if you were my girlfriend and you got sick I’d be more worried about you than your own mother. I was always that way. But no matter how much I cared about you, if we were crossing the street, you fell down and skinned your knee, I would see your skinned knee and I would say “Come on, we gotta get going,” or I would say, “Here, I’ll get you a Band-Aid.” I would have a practical response. The way I responded is no reflection on how much I cared for you. I could care for you with all the love in the world and still I’d respond practically.

So you don’t feel you’d really lacked empathy before?
No. In fact, studies have shown that autistic people feel things more deeply, not less at all. It’s true that autism is described as a condition with communication impairment. And so, to be diagnosed with autism, you must have an impaired ability to speak, to understand speech, or to understand or convey unspoken cues.

So what exactly happened when you first stated noticing emotional cues?
It hit me all at once with an intensity that was absolutely scary. As I lay in bed, trying to fall asleep, the world started revolving. I became afraid I was having a stroke. I’d close my eyes and the world would spin like I was drunk, about to throw up. I don’t drink or do drugs. So for me to have the world spinning like that made me think there was something terribly wrong. And not only was the world spinning, I would close my eyes and I would have these really vivid, half-awake, half-asleep dreams that were a collage of things from the past and things that had just happened that day and they were just so real. The experience was so unsettling that I woke up and wrote a 1,500-word missive to the scientists describing what had happened. Then, finally, I was able to fall asleep.

The next day at work I looked at one of my colleagues and I thought to myself: He has the most beautiful brown eyes. That’s the type of thought I simply do not have. I don’t usually have any comment on your eyes because I don’t look in anyone’s eyes. For me to look in your eyes and say that they are beautiful is totally out of character. When I got to work I walked into the waiting room, as I usually do, and I looked at everyone and there was this flood of emotion. I could see it all: They were scared and anxious and eager, and never in my life had I seen something like that. I had to step out of the room because I didn’t know how to cope. It felt like ESP. Maybe in the past I used the logical part of my brain to look at people around me and carefully analyze. I figured out situations using logic. So I had that powerful ability but now the screen of emotion was turned on, too. ...

Tuesday, April 19, 2016

Julian Assange, Eric Schmidt, and real-time psychometry

In this excerpt from his 2014 book, Julian Assange analyzes Google CEO Eric Schmidt and his sidekick Jared Cohen. See also Chief Executives: brainpower, personality, and height.
Google is not what it seems: ... The stated reason for the visit was a book. Schmidt was penning a treatise with Jared Cohen, the director of Google Ideas, an outfit that describes itself as Google’s in-house “think/do tank.” I knew little else about Cohen at the time. In fact, Cohen had moved to Google from the US State Department in 2010. He had been a fast-talking “Generation Y” ideas man at State under two US administrations, a courtier from the world of policy think tanks and institutes, poached in his early twenties. He became a senior advisor for Secretaries of State Rice and Clinton. At State, on the Policy Planning Staff, Cohen was soon christened “Condi’s party-starter,” channeling buzzwords from Silicon Valley into US policy circles and producing delightful rhetorical concoctions such as “Public Diplomacy 2.0.”

... Schmidt was a good foil. A late-fiftysomething, squint-eyed behind owlish spectacles, managerially dressed—Schmidt’s dour appearance concealed a machinelike analyticity. His questions often skipped to the heart of the matter, betraying a powerful nonverbal structural intelligence. It was the same intellect that had abstracted software-engineering principles to scale Google into a megacorp, ensuring that the corporate infrastructure always met the rate of growth. This was a person who understood how to build and maintain systems: systems of information and systems of people. My world was new to him, but it was also a world of unfolding human processes, scale, and information flows.

For a man of systematic intelligence, Schmidt’s politics—such as I could hear from our discussion—were surprisingly conventional, even banal. He grasped structural relationships quickly, but struggled to verbalize many of them, often shoehorning geopolitical subtleties into Silicon Valley marketese or the ossified State Department microlanguage of his companions.9 He was at his best when he was speaking (perhaps without realizing it) as an engineer, breaking down complexities into their orthogonal components.

I found Cohen a good listener, but a less interesting thinker, possessed of that relentless conviviality that routinely afflicts career generalists and Rhodes scholars. As you would expect from his foreign-policy background, Cohen had a knowledge of international flash points and conflicts and moved rapidly between them, detailing different scenarios to test my assertions. But it sometimes felt as if he was riffing on orthodoxies in a way that was designed to impress his former colleagues in official Washington. ...
See Creators and Rulers and this earlier Assange post, specifically reference to his early pursuit of theoretical physics and thoughts on high cognitive ability. He registered the domain for his (now defunct) blog, and cites psychologist Leta Hollingworth in his 23 Sept 2006 post: ... Observation shows that there is a direct ratio between the intelligence of the leader and that of the led. To be a leader of his contemporaries a child must be more intelligent but not too much more intelligent than those to be led... But generally speaking, a leadership pattern will not form--or it will break up--when a discrepancy of more than about 30 points of IQ comes to exist between leader and led ...

See also Human capital mongering: M-V-S profiles. Note deviation scores (SDs) below are relative to the average among the gifted kids in the sample, not relative to the general population. The people in this sample are probably above average in the general population on each of M-V-S.

The figure below displays the math, verbal and spatial scores of gifted children tested at age 12, and their eventual college majors and career choices. This group is cohort 2 of the SMPY/SVPY study: each child scored better than 99.5 percentile on at least one of the M-V sections of the SAT.

Scores are normalized in units of SDs. The vertical axis is V, the horizontal axis is M, and the length of the arrow reflects spatial ability: pointing to the right means above the group average, to the left means below average; note the arrow for business majors should be twice as long as indicated but there was not enough space on the diagram. The spatial score is obviously correlated with the M score.

Upper right = high V, high M (e.g., physical science)
Upper left = high V, lower M (e.g., humanities, social science)
Lower left = lower V, lower M (e.g., business, law)
Lower right = lower V, high M (e.g., math, engineering, CS)

Thursday, April 14, 2016

The story of the Monte Carlo Algorithm

George Dyson is Freeman's son. I believe this talk was given at SciFoo or Foo Camp.

More Ulam (neither he nor von Neumann were really logicians, at least not primarily).

Wikipedia on Monte Carlo Methods. I first learned these in Caltech's Physics 129: Mathematical Methods, which used the textbook by Mathews and Walker. This book was based on lectures taught by Feynman, emphasizing practical techniques developed at Los Alamos during the war. The students in the class were about half undergraduates and half graduate students. For example, Martin Savage was a first year graduate student that year. Martin is now a heavy user of Monte Carlo in lattice gauge theory :-)

Tuesday, April 12, 2016

Applied genomics: the genetic "super cow"

This figure and the excerpt below come from the genomics column of The Bullvine, a publication aimed at dairy breeders (via Carl Shulman). In the highly-developed world of genomic cattle breeding, it has been speculated that the theoretical "maximal type" bull could have ten times the merit (defined in terms of increased earnings of its progeny, see below) of the top breeding bulls that exist today. Sound familiar? See This is for PZ Myers for related discussion concerning human cognition.

While the "maximal type" may never be achieved, it is interesting that each new top sire surpasses the previous record holder, and previous generations, by a substantial margin. In the human context, this would correspond to a steady stream of individuals, each of greater ability, all of whom surpass the greatest historical geniuses.

By Andrew Hunt

During the recent “Advancing Dairy Cattle Genetics: Genomics and Beyond”, Paul VanRaden with USDA’s Animal Improvement Programs Laboratory pointed out that “If we took the best haplotypes (genes) from all the cows genomic tested to date, we would have a cow at $7515 Net Merit”. That’s pretty spectacular considering the current top Sire on the $NM list is DE VOLMER DG SUPERSHOT at 1000 $NM.

Now to put that into perspective the current rate of gain is $80 per year. So in order to breed that $7515 animal it would take us 81 years to actually breed that animal. Therefore it raises the question whether such an animal is actually achievable and is there technology out there that could accelerate the process of getting that Super Cow.

The interesting fact here is the greatly accelerated rate of genetic gain since the introduction of genomics. This results for the most part from the greatly shortened generation interval. Females are now being used as bull mothers 18 months sooner than in the past (as yearlings vs mid 1st lactation), and sires of sons are now being used 24 and sometime 36 months sooner than they were in the past. (Genomic indexes vs waiting for proven sires). The almost 40% increase in reliability of estimated transmitting ability has breeders and AI companies contracting and working with these elite animals at a significantly younger age. ...
See also this post from 2012: Genomic prediction: no bull
The Atlantic: ... Data-driven predictions are responsible for a massive transformation of America's dairy cows. While other industries are just catching on to this whole "big data" thing, the animal sciences -- and dairy breeding in particular -- have been using large amounts of data since long before VanRaden was calculating the outsized genetic impact of the most sought-after bulls with a pencil and paper in the 1980s. Dairy breeding is perfect for quantitative analysis. Pedigree records have been assiduously kept; relatively easy artificial insemination has helped centralized genetic information in a small number of key bulls since the 1960s; there are a relatively small and easily measurable number of traits -- milk production, fat in the milk, protein in the milk, longevity, udder quality -- that breeders want to optimize; each cow works for three or four years, which means that farmers invest thousands of dollars into each animal, so it's worth it to get the best semen money can buy. The economics push breeders to use the genetics.

The bull market (heh) can be reduced to one key statistic, lifetime net merit, though there are many nuances that the single number cannot capture. Net merit denotes the likely additive value of a bull's genetics. The number is actually denominated in dollars because it is an estimate of how much a bull's genetic material will likely improve the revenue from a given cow. A very complicated equation weights all of the factors that go into dairy breeding and -- voila -- you come out with this single number. For example, a bull that could help a cow make an extra 1000 pounds of milk over her lifetime only gets an increase of $1 in net merit while a bull who will help that same cow produce a pound more protein will get $3.41 more in net merit. An increase of a single month of predicted productive life yields $35 more. When you add it all up, Badger-Fluff Fanny Freddie has a net merit of $792. No other proven sire ranks above $750 and only seven bulls in the country rank above $700.
... theoretical calculations suggest that even outliers with net merit of $700-800 will be eclipsed by specimens with 10x higher merit that can be produced by further selection on existing genetic variation. Similar results apply to humans. ...

Ralph Nader and Ron Unz on the Free Harvard, Fair Harvard Overseer Campaign

Ralph Nader and Ron Unz discuss the Free Harvard, Fair Harvard Overseer campaign. The discussion starts about 4 minutes in.

Previous posts on Free Harvard, Fair Harvard.

Friday, April 08, 2016

Harvard Overseer Election

Harvard Overseer ballots have been mailed. Please vote for the Free Harvard, Fair Harvard ticket!

Earlier posts here.

Below is my candidate statement.
Stephen Hsu is Vice President for Research and Graduate Studies and Professor of Theoretical Physics at Michigan State University. He oversees roughly $600 million in annual research expenditures on a campus of 50,000 students and over 5,000 faculty and academic staff.

Previously, he was Founder and CEO of SafeWeb, a Silicon Valley information security startup acquired by Symantec, and held faculty positions at Yale and the University of Oregon. Hsu was a Junior Fellow of the Harvard Society of Fellows, 1991–1994. His research areas include quantum field theory, cosmology, and computational genomics.

"As a scientist, university administrator, and technology entrepreneur, I believe I have unique insight into the challenges facing modern research universities.

"My father immigrated here in 1948 to pursue graduate studies, and I was blessed to have a wonderful midwestern upbringing in a small college town. Many teachers, professors, and mentors contributed to my growth and development. Therefore, I am obliged to contribute to the continued vitality of the U.S. educational and scientific enterprise. Toward this goal, it would be my great honor to serve as a Harvard Overseer. Two of my objectives, which I hope you share: 1. let us make Harvard more accessible to talented students of limited means, 2. let us ensure that Harvard admits the students who are most able to benefit from its gifts, and in return benefit the world."

Thursday, April 07, 2016

GWAS of cognitive function using UK Biobank data

This paper is based on analysis of UK Biobank data. The phenotypes (cognitive scores) were obtained via brief on-screen tests. Although there is significant noise in the scores obtained (see test-retest correlations in the table at bottom), there was enough signal to obtain a number of genome-wide significant SNP hits.
Genome-wide association study of cognitive functions and educational attainment in UK Biobank (N=112,151)

Nature Molecular Psychiatry 5 April 2016 doi: 10.1038/mp.2016.45

People’s differences in cognitive functions are partly heritable and are associated with important life outcomes. Previous genome-wide association (GWA) studies of cognitive functions have found evidence for polygenic effects yet, to date, there are few replicated genetic associations. Here we use data from the UK Biobank sample to investigate the genetic contributions to variation in tests of three cognitive functions and in educational attainment. GWA analyses were performed for verbal–numerical reasoning (N=36 035), memory (N=112 067), reaction time (N=111 483) and for the attainment of a college or a university degree (N=111 114). We report genome-wide significant single-nucleotide polymorphism (SNP)-based associations in 20 genomic regions, and significant gene-based findings in 46 regions. These include findings in the ATXN2, CYP2DG, APBA1 and CADM2 genes. We report replication of these hits in published GWA studies of cognitive function, educational attainment and childhood intelligence. There is also replication, in UK Biobank, of SNP hits reported previously in GWA studies of educational attainment and cognitive function. GCTA-GREML analyses, using common SNPs (minor allele frequency>0.01), indicated significant SNP-based heritabilities of 31% (s.e.m.=1.8%) for verbal–numerical reasoning, 5% (s.e.m.=0.6%) for memory, 11% (s.e.m.=0.6%) for reaction time and 21% (s.e.m.=0.6%) for educational attainment. Polygenic score analyses indicate that up to 5% of the variance in cognitive test scores can be predicted in an independent cohort. The genomic regions identified include several novel loci, some of which have been associated with intracranial volume, neurodegeneration, Alzheimer’s disease and schizophrenia.


The results of the present study make novel contributions to three scientific aims of GWAS: helping towards identifying specific mechanisms of genomic variation; describing the genetic architecture of complex traits; and predicting phenotypic variation in independent samples. The most important novel contribution of the present study is the discovery of many new genome-wide significant genetic variants associated with reasoning ability, cognitive processing speed and the attainment of a college or university degree. The study provided robust estimates of the SNP-based heritability of the four cognitive variables and their genetic correlations. The study makes important steps toward genetic consilience, because several of the genomic regions identified by the present analyses have previously been associated in GWASs of general cognitive function, executive function, educational attainment, intracranial volume, neurodegenerative disorders and Alzheimer’s disease. The study was successful in using the GWAS results from UK Biobank to predict cognitive variation in new samples. ...

Unnatural Selection

Starting @15:20 you can watch the 2016 Vice documentary Unnatural Selection. Among the topics covered: CRISPR, PGD (Preimplantation Genetic Diagnosis), biobanks, etc. If you've never seen individual sperm and eggs manipulated by a lab tech, this is your chance :-)

Tuesday, April 05, 2016

This is for PZ Myers

[ See here for added detailed discussion of this topic. ]

Scott Alexander (Slate Star Codex), Garett Jones (Hive Mind), and Razib Khan (GNXP) alerted me (via Twitter) of this post by PZ Myers.

Myers is both confused and insulting in his blog post, but I'll refrain from ad hominem attacks, and just focus on the science.

Myers seems to think that humans with much better cognitive abilities than our own can't exist. Sort of like a farmer in 1957 claiming that chickens that are bigger and faster maturing than his own could not exist (see figure below). I urge Myers to read some books on quantitative / population genetics before returning to this discussion.

The argument for why there are probably genomes not very different from our own, but which lead to much better cognitive ability, is very simple, and I went through it in a post called Explain it to me like I'm five years old, excerpted below:
1. Cognitive ability is highly heritable. At least half the variance is genetic in origin.

2. It is influenced by many (probably thousands) of common variants (see GCTA estimates of heritability due to common SNPs). We know there are many because the fewer there are the larger the (average) individual effect size of each variant would have to be. But then the SNPs would be easy to detect with small sample size.

Recent studies with large sample sizes detected ~70 SNP hits, but would have detected many more if effect sizes were consistent with, e.g., only hundreds of causal variants in total.

[ Myers seems to be confused about the difference between specific (protein coding) genes, of which there may be only ~20k in the human genome, and the set of all variations in the DNA code, of which there are many, many more. Thousands of variants (or 10k) out of this much larger number is a tiny fraction much less than one. ]

3. Since these are common variants the probability of having the negative variant, with (-) effect on g score, is not small (e.g., like 10% or more).

4. So each individual is carrying around many hundreds (if not thousands) of (-) variants.

5. As long as effects are roughly additive, we know that changing ALL or MOST of these (-) variants into (+) variants would push an individual many standard deviations (SDs) above the population mean. Such an individual would be far beyond any historical figure in cognitive ability. [ This is exactly what has been accomplished via selection in the chickens below. ]
Given more details we can estimate the average number of (-) variants carried by individuals, and how many SDs are up for grabs from flipping (-) to (+). As is the case with most domesticated plants and animals, we expect that the existing variation in the population allows for many SDs of improvement (see figure below).
For references and more detailed explanation, see On the Genetic Architecture of Cognitive Ability and Other Complex Traits.

Attention PZ: The basic quantitative / population genetics used above is recapitulated by famous geneticist James Crow (Wisconsin-Madison) here and here. You can take his word over mine, since I'm only a physicist. But note that Crow cites Feynman PhD student (i.e., theoretical physicist) Thomas Nagylaki (later a famous geneticist at Chicago) for proving a tour de force result in evolutionary genetics of additive traits. Do your HW next time.

Note Added: See this August 2016 post for more discussion, in response to some comments by Greg Cochran.

References: There are some requests for references in the discussion thread below. The place to start is On the Genetic Architecture of Cognitive Ability and Other Complex Traits, but see below.

In this paper Crow discusses the prevalence of additive genetic effects, and the consequent (in the case of highly polygenic traits) large pool of variance upon which selection can act. I have merely pointed out that cognitive ability is an example of the kind of complex polygenic trait that Crow described.

Nagylaki's paper The Evolution of Multilocus Systems under Weak Selection extends Fisher's Fundamental Theorem of Natural Selection (fundamental to our theoretical understanding of evolution, but unknown to most biologists; note the role of additive variance). Evidence for additive genetic architecture in, e.g., mice, yeast, cows, etc. Additive models are used extensively in agricultural breeding.

Nagylaki's textbook on population genetics is free.

Physicists can master these results quickly via Statistical Genetics and Evolution of Quantitative Traits (Neher and Shraiman).

Monday, April 04, 2016

EPR and Bell for pedestrians

My old friend Mark Alford (WUSTL) was on campus last week for the inaugural meeting of the FRIB-TA (Facility for Rare Ion Beams Theory Alliance). Over beers he told me he had come up with a pedagogical way to explain Bell's inequality in a single picture. Here it is.
Ghostly action at a distance: a non-technical explanation of the Bell inequality

Mark G. Alford

We give a simple non-mathematical explanation of Bell's inequality. Using the inequality, we show how the results of Einstein-Podolsky-Rosen (EPR) experiments violate the principle of strong locality, also known as local causality. This indicates, given some reasonable-sounding assumptions, that some sort of faster-than-light influence is present in nature. We discuss the implications, emphasizing the relationship between EPR and the Principle of Relativity, the distinction between causal influences and signals, and the tension between EPR and determinism.

FIG. 4: One trial in the EPRB measurement of polarization for two photons. The final result in this trial is that photon 1 encountered a filter of type B and reflected off it, while photon 2 encountered a filter of type C and passed through it. According to the Bell inequality (Eq. (3)) this sort of result, where the two photons do different things when encountering different filters, should happen no more than 2/3 of the time.

... When polarizations of pairs of spin-singlet photons are measured in real-world experiments, it is found that they do show agreement in same-axis measurements, but when we perform different-axis measurements the two photons only show the same behavior 1/4 of the time; 3/4 of the time they show different behavior: one bounces off its filter and the other passes through. This violates the Bell inequality. Such violation has now been seen in many experiments ...

The global jiujitsu phenomenon

This is promo footage for Polaris, a professional BJJ competition. The four competitors profiled train in Toulouse (France), Florida, San Diego, and NYC. Gezary Matuda reminds me of an old girlfriend who also trained.

One of the fights at Polaris 3 features 37 year old Jake Shields against 25 year old A.J. Agazarm. Both were college wrestlers before taking up BJJ. Shields has been a top MMA competitor for a decade now. It's funny that Agazarm wants to act tough because if this were a real fight he'd have been sent to the hospital. Warning, this footage may get taken down at some point.

Although I enjoy watching sport BJJ, a lot of the modern innovations are only suited to sport and would get you killed if strikes were allowed. If a match starts with competitors sitting on their butt and pulling guard (e.g., Miyao brothers) I usually turn it off.

See also Jiujitsu renaissance.

Sunday, April 03, 2016


Rutgers Historian Jochen Hellbeck, author of Stalingrad: The City that Defeated the Third Reich.
LA Review of Books: ... The archive was compiled by a historical commission headed by a Moscow professor, Isaak Mints. Members of the commission were allowed into Stalingrad in late December 1942 — this was more than a month before the battle would end, and there was bitter fighting going on in the city. Over the next weeks they conducted more than 200 interviews with soldiers and other eyewitnesses. These first-person accounts were so frank and multifaceted that they couldn’t be published at the time. They were locked away, but not destroyed.

I found them quite by chance. Several Russian colleagues who knew about my interest in first-person accounts told me about entire boxes filled with memoirs, somewhere in the basement of a Moscow archive. When I finally received permission to study these documents, my jaw dropped. I first assumed they were recollections of the war written in the 1960s or 1970s — but the archive was full of first-person statements delivered during the war. It shows the interviewed soldiers steeped in the events that they describe. In 1942 nobody knew when or how the Second World War would end, and the interviews show you the horizons of people at war, they bring you closer to their thoughts and emotions than any other source.

... When I began my project I initially wanted to compare the voices and emotions of German and Soviet soldiers. There are many diaries available on the German side, but hardly any from the Soviet perspective. The Red Army forbade personal diaries, and Soviet censors ensured that soldiers wrote only bland letters along the lines of, “Hello, I’m well and alive,” so that the letters couldn’t be used for intelligence or propaganda if they fell into German hands. Consequently there are few sources that present us with a full record of unmediated wartime voices.

... In the account I mentioned earlier, the otherwise unexceptional Lieutenant Averbukh fell back from his command post after it was overrun and, shot, retreated while carrying his dying unit commander:
Captain Lizunov was showing little sign of life, but I could hear him whispering, saying that I should leave him and save myself. Obviously I didn’t leave him. We crawled to Verkhnyaya Elshanka, in the area of the radio station. I sat up to get my bearings and got hit again. Submachinegun fire to the left side of my chest and my left arm. I lost consciousness. I don’t know how long I was out. I woke up because it got really cold. It was late, around four in the morning. It was already starting to get light. I could hear people speaking German all around me. I couldn’t see Lizunov anywhere. I decided to shoot myself because I didn’t have any strength left, and I didn’t want them to take me alive. I figured there was no way out. I pulled the trigger, but the Mauser was clogged with sand and wouldn’t fire. My right arm was still okay. With my right arm I crawled away and by some miracle made it to the division command post. It was already midday.
See also Hellbeck's project Facing Stalingrad.
Portraits of German and Soviet Survivors

The Battle of Stalingrad was one of the most ferocious military campaigns of all time. Ending with the rout of an entire German army, it marked a turning point in World War II. “Facing Stalingrad” features portraits of German and Soviet veterans who were interviewed in their homes in 2009. The project illuminates the battle’s human dimension and juxtaposes perspectives from both sides.
Johan Scheins, 16th Panzer Division, captured January 29, 1943. Released from captivity in late 1949.
... The general said nothing; they said nothing. They were afraid. They were officers. I then said: “What should we do now?” And then a staff sergeant, who could speak perfect Polish, entered at a trot. He was Polish, but a German Pole. He announced that four tanks, Russian T-34, had run over and cut the cables, that there was no longer any connection. There was nothing that could be done. One could no longer make telephone calls. They had run over the cable. We should surrender. The general then stood up. He adjusted his collar to make it neater. He was tall. He put on his cap. I stood here; he stood there. He just stood there, then he took his revolver – Long live Germany! Long live my country! – and he shot himself here and then fell forwards. I thought he would fall off the table. I stood right there. I had never seen such a thing: some white stuff came out at the top. The stuff that comes out of a herring when you cut it up. Not the bones. The white stuff. ...

Does Stalingrad appear in your dreams?

I’ve only been speaking to you for a couple of days. I can say that I sit every day in my bed – for hours. All the memories surface. Always before Christmas. Terrible. Christmas was the worst time when I was a prisoner. On Christmas Eve the Russians would come in at 10 PM. They would count us. We then had to go outside – quickly, quickly. Nearly barefoot, only wearing socks. 20, 30 degrees cold. We stood outside half-naked. Just padded jackets on. And we had to form groups of five men each. Raz, dva – always five men.

Then the Russians started counting. The commander. And then they went back to the headquarters, in the house, to booze. Then they returned after an hour. Nichevo [Russian: “no problem”]. “Have you counted?” I said: “Nope.” “Count!” Then there was a new count. We counted from 10 PM, 11 PM till 2, 3 AM. The sentries stood outside with carbines. Then one man fell over due to the cold. Another man fell over… 10, 12 men, 16 men, the number varied, fell over. They had to be placed in front. So that they could also be counted. Oh, zavtra [Russian: “tomorrow”] it’s all over. Tomorrow morning he’ll be dead. We went indoors and they remained lying on the ground. They weren’t allowed to be brought indoors. In the morning they were frozen stiff – broken. Zavtra utrom – tomorrow morning it’ll be all over with them. Posmotri! [Russian:“Look!”] Look up, that’s where God is, He’s seen that and you bandits will go to hell.

I was invited several times to Stalingrad. It’s definitive – I’ll never go there again. I’d rather walk with a dead man.

Saturday, April 02, 2016

Jonathan Haidt and Tyler Cowen

Highly recommended: a great conversation (transcript) between Tyler Cowen and NYU psychology professor Johnathan Haidt. More Haidt.

The transformation of the Academy and the two universities:
COWEN: But is it at least possibly the case that we’re seeing the greatest threat to intellectual diversity in some of the areas which matter least, and when the stakes are high we overcome it. Physics looks pretty good, computer science looks pretty good.

HAIDT: No, it’s not — there are two universities now, but it’s not which ones matter more and which ones matter less. It’s what is the sacred value. The sacred value of universities from sometime in the 19th century through maybe the 1980s was truth. Now it was not perfect, but we all talked that way. Look at the mottos of Harvard and Yale — Veritas, Lux et Veritas, it’s right there on the motto, veritas, truth.

We made a big show — it was largely true — of saying this is what we’re here for, we’re here to find truth. But in the 1970s and ’80s as we had a big influx of baby boomers who were involved in social protest, who were fighting for very good causes, civil rights, women’s rights — they flood into the academy in ’70s and ’80s, they get tenure in the ’80s and ’90s, but also in the 1990s, the Greatest Generation begins to retire. There were a lot of Republicans who became professors after World War II.

But the ’90s is the decade where everything flips. At the start of the 1990s, the overall left‑right ratio of the academy, taking all departments, was two to one, just twice as many people on the left as right. That’s fine, that’s not a problem. But by 2005, it had gone to five to one, five people on the left for every one on the right. Those people on the right are mostly engineering, nursing, things like that. If you look at the core — the humanities and the social sciences, other than economics, it’s closer to 10 to 1 or 20 to 1.

In other words, right‑wing, or libertarian, or social conservative voices have basically vanished between 1995 and 2005. This has made us unfunctional, but it’s in the social sciences and humanities where the sacred value has become social justice and the protection of victims. That’s the division. One university of the sciences still pursues truth, the other university in the social sciences and humanities pursues social justice.
The Replication Crisis (see also One funeral at a time?):
HAIDT: ... I think Brian Nosek, who’s been leading the charge on the problems in psychology, is largely right. That our methods have been sloppy, which has allowed us to engage in practices where we’re just more likely than we should be to get a significant result. And then of course, that’s more likely to get published.

Given that we find the same problem in cancer research and biomedical research — in almost every field where it’s been looked at — I think that the replication crisis is very real. It should be a top priority for science.

A lot of my work is on how we are not fully rational creatures. We are deeply emotional and tribal creatures. If you have this idealized view of researchers and our null hypothesis significant testing is based on idealized view of researchers who are basically testing samples honestly.

“Well, this could only happen 1 in 20 times by chance,” but we’re not those creatures. We want certain outcomes to happen. We make certain choices unconsciously. We all have to up our game. I don’t think there’s anything special about social psychology. It’s no worse than other fields. But we have been the leaders at actually addressing it, and saying, “Why are we not able to replicate each other’s work so much?”

I actually am impressed that the young generation has really embraced this and simply committing to making your data available — if you know that other people are going to get access to your SPSS file, or whatever, your data file, and they’re going to be looking it over, boy, you’re going to be a lot more careful.

I think just by raising the crisis, raising the alarm last year, the quality of our work is going to go substantially up. I’m really excited by this.
Social Psychology IS worse than some other fields, when it comes to reproducibility. First, it is in the wrong (SJW) part of the two universities Haidt describes in the earlier excerpt. Secondly, along with biomedical research, it is in the part of the university where most researchers lack a deep understanding of statistics and quantitative inference. See What is medicine's 5 sigma?

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