DNA data deluge

NYTimes reports: DNA Sequencing Caught in Deluge of Data. Spooks and other scientists have similar problems. See also here.

NYTimes: BGI, based in China, is the world’s largest genomics research institute, with 167 DNA sequencers producing the equivalent of 2,000 human genomes a day.

BGI churns out so much data that it often cannot transmit its results to clients or collaborators over the Internet or other communications lines because that would take weeks. Instead, it sends computer disks containing the data, via FedEx.

“It sounds like an analog solution in a digital age,” conceded Sifei He, the head of cloud computing for BGI, formerly known as the Beijing Genomics Institute. But for now, he said, there is no better way.

The field of genomics is caught in a data deluge. DNA sequencing is becoming faster and cheaper at a pace far outstripping Moore’s law, which describes the rate at which computing gets faster and cheaper.

The result is that the ability to determine DNA sequences is starting to outrun the ability of researchers to store, transmit and especially to analyze the data.

... The cost of sequencing a human genome — all three billion bases of DNA in a set of human chromosomes — plunged to $10,500 last July from $8.9 million in July 2007, according to the National Human Genome Research Institute.

That is a decline by a factor of more than 800 over four years. By contrast, computing costs would have dropped by perhaps a factor of four in that time span.

The lower cost, along with increasing speed, has led to a huge increase in how much sequencing data is being produced. World capacity is now 13 quadrillion DNA bases a year, an amount that would fill a stack of DVDs two miles high, according to Michael Schatz, assistant professor of quantitative biology at the Cold Spring Harbor Laboratory on Long Island.

There will probably be 30,000 human genomes sequenced by the end of this year, up from a handful a few years ago, according to the journal Nature. And that number will rise to millions in a few years.

In a few cases, human genomes are being sequenced to help diagnose mysterious rare diseases and treat patients. But most are being sequenced as part of studies. The federally financed Cancer Genome Atlas, for instance, is sequencing the genomes of thousands of tumors and of healthy tissue from the same people, looking for genetic causes of cancer. ...

Here's a slide I sometimes use in talks.

Higher education: signaling vs learning

This paper presents evidence in favor of the signaling (as opposed to human capital building) model of elite higher education. Of course, the data is quite crude and different fields may tilt more in one direction or the other. For example, I think most science and engineering students who attend MIT or Caltech are doing it because they feel it will develop their human capital (i.e., they will learn more and receive a perhaps painfully rigorous education) than because of the signaling value, although the latter is non-negligible.

See earlier posts here.

Worker Signals Among New College Graduates: The Role of Selectivity and GPA

Brad Hershbein - The University of Michigan
October, 2011

Abstract
Recent studies have found a large earnings premium to attending a more selective college, but the mechanisms underlying this premium have received little attention and remain unclear. In order to shed light on this question, I develop a multi-dimensional signaling model relying on college grades and selectivity that rationalizes students' choices of effort and firms' wage-setting behavior. The model is then used to produce predictions of how the interaction of the signals should be related to wages. Using five data sets that span the early 1960s through the late 2000s, I show that the data support the predictions of the signaling model, with support growing stronger over time. I also discuss alternative explanations, including di fferent types of human capital models; provide robustness checks; and relate the findings to both the returns-to-college-quality and employer learning literatures.

From the introduction:

Recently, there has been a sizable interest in the return to attending a more selective or prestigious college. Students who attend more prestigious schools earn more over their lifetime, on average, than those who attend less selective schools, but the mechanism underlying this premium is not well understood. In particular, there is disagreement over whether the earnings di fference is primarily due to the college itself or whether it is driven by unobserved student characteristics. The first of these channels is consistent with human capital theory -- attending the more selective school actually makes the worker more productive -- and the second more closely accords with models of signaling -- more innately productive workers are more likely to attend more selective schools.

[It's also possible that attending the right school gives access to networks and valuable information about career paths; see here.]

Given that annual U.S. higher education expenditures are over $460 billion, but per-student expenditures increase dramatically with college selectivity, understanding why students who attend selective colleges earn more over their lifetimes has dramatic implications for how those dollars are optimally allocated. Recent theoretical work seeking to explain why students increasingly sort by ability across college selectivities suggests a positive complementarity in human capital acquisition between students' ability and the greater resources available at selective colleges, but these models have received little empirical attention. On the other hand, the relatively few studies that have attempted to measure student learning in college have found little di fference across di fferent types of colleges once pre-college characteristics are controlled for (Pascarella and Terenzini 2005; Arum and Roksa 2011). While it is not clear whether the "learning" measured in these studies is of the type that fi rms would care about, this evidence suggests that the return to selectivity is unlikely to be due to human capital alone and that the signaling mechanism is worth a more careful investigation.

Success in legal careers: status, credentials and grades

This detailed study concludes that law school grades, not prestige, have the strongest correlation with career success. I'd be interested in reactions from attorneys to these results. See earlier post credentialistm and elite performance, and links therein. Compare to success of graduate programs in physics in placing theoreticians.

The Secret of My Success: How Status, Eliteness and School Performance Shape Legal Careers

Richard Sander and Jane Yakowitz

Abstract
If we study the forty thousand law graduates who join the legal profes- sion each year, how well can we predict their future careers? How much of their future is predicted by their social class? The law school they attend? Their law school grades? This paper undertakes the first in-depth examination of these questions. Drawing on several large and recently-released datasets, we examine the role of class, school prestige and law school grades on the career earnings of lawyers and the success of big firm associates in becoming partners. We find that social class strongly conditions who goes to law school, but no longer predicts much about post-graduate outcomes. Law school prestige is important, but it is generally trumped by law school performance (as measured by law school grades). Law school grades reflect both personal characteristics not well captured by pre-law credentials, and one’s relative position in a law school class as measured by pre-law credentials. Our findings suggest that there is little empirical basis for the overwhelming importance students assign to “eliteness” in choosing a law school. [italics mine]

Here is part of Table 10, which displays the deduced impacts of law school eliteness and grade performance in law school on long term career success (earnings) from a large database of Chicago lawyers. In the 1994 survey grades had much larger impact than school prestige. (Click for larger version.)



The authors' comments on this table:

Of course, since there is significant error in the measurement of law school grades, these models almost certainly understate their full impor- tance.38 Moreover, since we are here considering long-term career outcomes – not short-term recruitment – the effect of law school performance is not simply a credentialing effect of high grades leading to attractive job offers. Something about doing well in law school is strongly associated with lasting career success, and proves to have more efficacy than law school eliteness.

The eliteness of one’s law school is, compared with grades, a relatively weak explanatory factor in the 1994 equation. 39 And while the grade coef- ficients are biased in a way that understates their actual influence, the law school coefficients are almost surely overstated. The Chicago Lawyers equations do not include measures of pre-law credentials, such as LSAT scores and undergraduate grades. Since these factors do predict income for broad cross-sections of lawyers, and since the tight hierarchy of law school admissions makes law school eliteness a close proxy for student credentials, an unknown but probably large part of what seems to be explained by school eliteness is actually just a measure of pre-law credentials.

Is it possible that there are two paths to high income legal careers: BigLaw (BL) and RegionalLaw (RL)? Perhaps LS prestige is a big factor for the former and less so for the latter, which draws from regional schools (i.e. state flagship campus). Top partners in RL might make almost as much as those in BL, so that grades (which predict both BL and RL success) have a higher income correlation than LS reputation alone, which only manifests in BL.

The utility of grades or class rank as predictors does not surprise me, as they measure a combination of ability, willingness to work hard, and motivation. See here for results on high school GPA and SAT as predictors of college GPA. However, some fields seem to have ability thresholds that can't be surmounted through hard work.

Godel's proof, compressed

I found this here, but it is originally due to Raymond Smullyan. I first learned about Godel's theorem when I read Douglas Hofstader's book Godel, Escher, Bach in high school. I still remember lugging the thick volume around in my backpack, and working through the early chapters on predicate logic. This treatment is much more compact! :^)

We have some sort of machine that prints out statements in some sort of language. It needn't be a statement-printing machine exactly; it could be some sort of technique for taking statements and deciding if they are true. But let's think of it as a machine that prints out statements.

In particular, some of the statements that the machine might (or might not) print look like these:

P*x (which means that the machine will print x)
NP*x (which means that the machine will never print x)
PR*x (which means that the machine will print xx)
NPR*x (which means that the machine will never print xx)

For example, NPR*FOO means that the machine will never print FOOFOO. NP*FOOFOO means the same thing. So far, so good.

Now, let's consider the statement NPR*NPR*. This statement asserts that the machine will never print NPR*NPR*.

Either the machine prints NPR*NPR*, or it never prints NPR*NPR*.

If the machine prints NPR*NPR*, it has printed a false statement. But if the machine never prints NPR*NPR*, then NPR*NPR* is a true statement that the machine never prints.

So either the machine sometimes prints false statements, or there are true statements that it never prints.

So any machine that prints only true statements must fail to print some true statements.

Or conversely, any machine that prints every possible true statement must print some false statements too.

Talk cancelled

This talk has been cancelled, for complex reasons that I will not discuss.

Podcast roundup: November 2011

Gary Taubes discusses fat, sugar, cholesterol and nutrition on Econtalk. See also medical science?

Progress in the age of Obama -- Nation editor Katrina vanden Heuvel.

Strongly Coupled Components -- interviews with mathematicians.

The Continental-Analytic Split in philosophy.

Is the wavefunction real?

This is a nice result.

I haven't checked the calculations, but I like the logic very much. I'm kicking myself for not having tried harder to precisely formalize what the authors refer to as the "statistical interpretation" (note: this is quite a confusing terminology for most people -- see Further comments below) of the quantum state. Apparently, once you formalize this interpretation, it is easy to prove that it has to disagree with the predictions of ordinary quantum theory.

This "statistical interpretation" (e.g., that the wavefunction, or quantum formalism, only describes the knowledge state of the observer and does not correspond to physical reality) is the last shaky dodge of those who are against the reality (or correspondence to reality) of the wavefunction. The latter has always seemed to me the natural first interpretation of the formalism, subject, of course, to further analysis.

The quantum state cannot be interpreted statistically

Matthew F. Pusey, Jonathan Barrett, Terry Rudolph

http://arxiv.org/abs/1111.3328

Quantum states are the key mathematical objects in quantum theory. It is therefore surprising that physicists have been unable to agree on what a quantum state represents. There are at least two opposing schools of thought, each almost as old as quantum theory itself. One is that a pure state is a physical property of system, much like position and momentum in classical mechanics. Another is that even a pure state has only a statistical significance, akin to a probability distribution in statistical mechanics. Here we show that, given only very mild assumptions, the statistical interpretation of the quantum state is inconsistent with the predictions of quantum theory. This result holds even in the presence of small amounts of experimental noise, and is therefore amenable to experimental test using present or near-future technology. If the predictions of quantum theory are confirmed, such a test would show that distinct quantum states must correspond to physically distinct states of reality.

Here's what Nature News had to say:

Quantum theorem shakes foundations: The wavefunction is a real physical object after all, say researchers.

Further comments:

There seems to be widespread misunderstanding of what the authors are trying to do in this paper.

They are not trying to refute qm or the standard rules of calculation (e.g., Born rule). Perhaps their use of the term "statistical interpretation" is unfortunate because some people seem to have jumped to the conclusion that they claim to prove qm is deterministic or non-probabilistic. That is not the case.

They are addressing a particular interpretation of qm. This interpretation says: there is an underlying physical reality, but the state Psi only describes an observer's knowledge about that underlying reality. Psi is not itself a direct representation of that reality. ("Psi is not real".) I would classify this as a variant of Copenhagen; its proponents sometimes refer to it as a "Bayesian" or "Epistemic" interpretation. I prefer to call it the "Mysterian" interpretation: reality is some vast mysterious thing (never specified!), Psi only characterizes the observer's mental state; collapse of the wavefunction is simply a Bayesian update of the mental state.

Mysterian/Bayesian: "The reduction of the wavefunction takes place in the consciousness of the observer ... because the state is a construct of the observer's mind and not an objective property of the physical system."

Many Worlder: "The wavefunction is real (i.e., a direct representation of physical reality), but it does not collapse."

Note, both groups try to avoid the possibility that Psi is real and collapses. But see Weinberg's recent preprint for an attempt to understand that possibility: http://arxiv.org/abs/1109.6462

A modern proponent of the Mysterian point of view is Chris Fuchs. I would be very interested to hear his reaction to this paper. But Rob Spekkens (quoted in the Nature article) also thinks along these lines, and he seems to believe that the (lambda, q) formalization of Mysterianism captures something useful. I am still pondering it myself.

Technically, the (lambda, q) formalization describes a model in which (i) there is an underlying reality (some Mysterians apparently do not actually believe this) and (ii) the state vector Psi does not describe the underlying reality but rather an observer's knowledge about it.

The fact that a given underlying reality lambda has probability q of being consistent with two different preparations of a state, which each yield different pure states phi_0 and phi_1 (their notation), is meant to capture (i) and (ii) above. Remember that to a Mysterian the pure state is a description of a state of knowledge, not of reality. So nonzero q means that two different states of knowledge (preparations) are consistent with the same underlying state of reality.

These Fuchs slides might be of use in understanding the mysterious Mysterians: Being Bayesian in a Quantum World (I am a Bayesian, who lives in a quantum world, but not a Mysterian :-)

This blog post by Matt Leifer is very clear and gives the context for the paper in the qm foundations subfield.

Predictive power of early childhood IQ, part 2

I came across this table in Intelligence by N. Brody. Berkeley Growth Study (61 participants).


See earlier post predictive power of early childhood iq.

Baumeister on Gender Differences and Culture

Nice discussion on Econtalk. I suspect Baumeister has slightly stronger opinions than he expressed to Russ.

Roy Baumeister of Florida State University and the author of Is There Anything Good About Men talks with EconTalk host Russ Roberts about the differences between men and women in cultural and economic areas. Baumeister argues that men aren't superior to women nor are women superior to men. Rather there are some things men are better at while women excel at a different set of tasks and that these tradeoffs are a product of evolution and cultural pressure. He argues that evolutionary pressure has created different distributions of talent for men and women in a wide variety of areas. He argues that other differences in outcomes are not due to innate ability differences but rather come from different tastes or preferences.

The podcast got me through 30 pullups, 100 pushups, situps, kettlebells and cycling :-)

Sonmi 451

My vote for best recent dystopian fiction featuring genetic engineering goes to the An Orison Of Sonmi 451 chapters of David Mitchell's Cloud Atlas. Can't wait to see the big budget movie. Will they retain the Korean peninsula setting?

Honorable mention: Margaret Atwood's Oryx and Crake.

Popular wisdom has it that fabricants don’t have personalities. This fallacy is propagated for the comfort of purebloods.

“Comfort”? How do you mean? To enslave an individual troubles your consciences, Archivist, but to enslave a clone is no more troubling than owning the latest six-wheeler ford, ethically. Because you cannot discern our differences, you believe we have none. But make no mistake: even same-stem fabricants cultured in the same wombtank are as singular as snowflakes. ...

Did your second day outside provide any answers? Some: but yet more surprises. The first stood across the anteroom from my cot as I awoke. A pylonic man, over three meters tall and dressed in an orange zipsuit, was studying the bookshelves. His face, neck, and hands were scalded red, burnt black, and patched pale, but he did not seem to suffer pain. His collar confirmed he was a fabricant, but I could not guess his stemtype: lips genomed out, ears protected by hornvalves, and a voice deeper than any I heard before or since. “No stimulin here. You wake when you wake. Especially if your postgrad is as lazy as Boom-Sook Kim. Xec postgrads are the worst. They have their asses wiped for them. From kindergarten to euthanasium.” With a giant, two-thumbed hand, he indicated a blue zipsuit half the size of his. “For you, little sister.” As I changed from my Papa Song’s uniform into my new garment, I asked if he had been sent by a seer. “No seers, either,” said the burnt giant. “Your postgrad and mine are friends. Boom-Sook called yesterday. Complained about your unxpected delivery. I wished to visit you pre-curfew. But Genome Surgery postgrads work late. Unlike slackers here in Psychogenomics. I’m Wing027. Let’s find out why you’re here.” ...

What sort of fabricant was Wing-027? A militiaman? No, a disasterman. He boasted he could operate in deadlands so infected or radioactive that purebloods perish there like bacteria in bleach; that his brain had only minor genomic refinements; and that disastermen’s basic orientation provides a more thoro education than most pureblood universities. Finally, he bared his hideously burnt forearm: “Show me a pureblood who could stand this! My postgrad’s Ph.D. is tissue flameproofing.”

Wing027’s xplanation of deadlands appalled me, but the disasterman anticipated their approach with relish. The day when all Nea So Copros is deadlanded, he told me, will be the day fabricants become the new purebloods. ...


Huamdonggil is a noxious maze of low, crooked ramshacks, flophouses, pawnshops, drug bars, and comfort hives, covering perhaps five square miles southeast of Old Seoul Transit Station. Its streets are too narrow for fords to enter; its alleys reek of waste and sewage. ShitCorp goes nowhere near that quarter. Hae-Joo left the ford in a lockup and warned me to keep my head hooded: fabricants stolen here end up in brothels, made serviceable after clumsy surgery. Purebloods slumped in doorways, skin enflamed by prolonged xposure to the city’s scalding rain. One boy lapped water from a puddle on his hands and knees. “Migrants with enceph or leadlung,” Hae-Joo told me. “Hospitals drain their Souls until they’ve got only enough dollars for a euthanasia jab—or a ride to Huamdonggil. These poor bastards made the wrong choice.”

I could not understand why migrants fled Production Zones for such a squalid fate. Hae-Joo listed malaria, flooding, drought, rogue crop genomes, parasites, encroaching deadlands, and a natural desire to better the lives of their children. Papa Song Corp, he assured me, seems humane if compared to factories these migrants ran away from. Traffickers promise it rains dollars in the Twelve Cities, and migrants yearn to believe it; the truth never filters back, for traffickers operate only one way. Hae-Joo steered me away from a meowing two-headed rat. “They bite.”

I asked why the Juche tolerates this in its second capital.

Every conurb, my guide answered, has a chemical toilet where the city’s unwanted human waste disintegrates quietly, but not quite invisibly. It motivates the downstrata: “Work, spend, work,” say slums like Huamdonggil, “or you, too, will end your life here.” Moreover, entrepreneurs take advantage of the legal vaccuum to erect ghoulish pleasurezones for upstrata bored with more respectable quarters. Huamdonggil can thus pay its way in taxes and bribes. MediCorp opens a weekly clinic for dying untermensch to xchange any healthy body parts they may have for a sac of euthanaze. OrganiCorp has a lucrative contract with the city to send in a daily platoon of immune-genomed fabricants, similar to disastermen, to mop up the dead before the flies hatch. Hae-Joo then told me to stay silent; we had reached our destination.

More excerpts here. See also this.

Paris Review interview with David Mitchell.

Veritas

Perhaps we will meet the ghosts of Stephen J. Gould.

Good riddance, JoePa

I've always hated Joe Paterno and Penn State's holier than thou sham. Careful scrutiny suggests it's mostly sociopaths at the top.

NYTimes: ... I have a hard time understanding why a 28 year old man, the grad student, did not go straight into that shower and rescue the kid. He is a coward. Law, lawsuits and all the oversight in the world is valueless unless people step up. This creep Sandusky was “caught” several times, in each case the so called men who witnessed it, quietly back away. Shame on them all. Shame on Mr. Paterno whose god status created the environment.

Paterno admits he was told by the assistant mentioned above that he saw former defensive coordinator Sandusky having anal sex with a naked 10 year old boy in the showers. Paterno reports it to superiors but doesn't follow up further and Sandusky retains an office in the athletic complex. The graduate assistant, a former Penn State QB, is now an assistant coach, so Paterno can hardly claim he didn't find the charge credible. This was definitely a coverup that extended over a decade, and JoePa was involved.

I wonder how the Penn State players feel about using the shower facilities in the Lasch Building (football complex).

Sandusky Grand Jury Presentment.


"When we stood at childhood's gate, Shapeless in the hands of fate, .... May no act of ours bring shame"

The Penn State Alma Mater

For the glory of old State,
For her founders strong and great,
For the future that we wait,
Raise the song, raise the song.

Sing our love and loyalty,
Sing our hopes that, bright and free,
Rest, O Mother dear, with thee,
All with thee, all with thee.

(Softly)

When we stood at childhood's gate,
Shapeless in the hands of fate,
Thou didst mold us, dear old State,
Dear old State, dear old State.

(Louder)

May no act of ours bring shame
To one heart that loves thy name,
May our lives but swell thy fame,
Dear old State, dear old State.

Generation gap

Look for intergenerational conflict to get worse as more boomers retire. Figure via Atlantic Monthly. 2001 net worth by age group.

OW! Learning can hurt

Two good articles on the state of higher education. The first dares broach the "higher education bubble" question.

NY Review of Books: ... In Academically Adrift, Arum and Roksa paint a chilling portrait of what the university curriculum has become. The central evidence that the authors deploy comes from the performance of 2,322 students on the Collegiate Learning Assessment, a standardized test administered to students in their first semester at university and again at the end of their second year: not a multiple-choice exam, but an ingenious exercise that requires students to read a set of documents on a fictional problem in business or politics and write a memo advising an official on how to respond to it. Data from the National Survey of Student Engagement, a self-assessment of student learning filled out by millions each year, and recent ethnographies of student life provide a rich background.

Their results are sobering. The Collegiate Learning Assessment reveals that some 45 percent of students in the sample had made effectively no progress in critical thinking, complex reasoning, and writing in their first two years. And a look at their academic experience helps to explain why. Students reported spending twelve hours a week, on average, studying—down from twenty-five hours per week in 1961 and twenty in 1981. Half the students in the sample had not taken a course that required more than twenty pages of writing in the previous semester, while a third had not even taken a course that required as much as forty pages a week of reading.

Results varied to some extent. At every institution studied, from research universities to small colleges, some students performed at high levels, and some programs fostered more learning than others. In general, though, two points come through with striking clarity. First, traditional subjects and methods seem to retain their educational value. Nowadays the liberal arts attract a far smaller proportion of students than they did two generations ago. Still, those majoring in liberal arts fields—humanities and social sciences, natural sciences and mathematics—outperformed those studying business, communications, and other new, practical majors on the CLA. And at a time when libraries and classrooms across the country are being reconfigured to promote trendy forms of collaborative learning, students who spent the most time studying on their own outperformed those who worked mostly with others.

Second, and more depressing: vast numbers of students come to university with no particular interest in their courses and no sense of how these might prepare them for future careers. The desire they cherish, Arum and Roksa write, is to act out “cultural scripts of college life depicted in popular movies such as Animal House (1978) and National Lampoon’s Van Wilder (2002).” Academic studies don’t loom large on their mental maps of the university. Even at the elite University of California, students report that on average they spend “twelve hours [a week] socializing with friends, eleven hours using computers for fun, six hours watching television, six hours exercising, five hours on hobbies”—and thirteen hours a week studying.

For most of them, in the end, what the university offers is not skills or knowledge but credentials: a diploma that signals employability and basic work discipline. Those who manage to learn a lot often—though happily not always—come from highly educated families and attend highly selective colleges and universities. They are already members of an economic and cultural elite. Our great, democratic university system has become a pillar of social stability—a broken community many of whose members drift through, learning little, only to return to the economic and social box that they were born into.

... Is this a crisis? Arum and Roksa say no, since students and their parents continue to seek and pay for places at colleges and universities, and government and graduate schools continue to accept their products, and corporations continue to hire them (and to spend more than $50 billion a year to train their employees in the skills they need). But those already born into the wealthy and professional classes benefit disproportionately from the best educations. Acquire any sort of college education, and you’ll make more money than you would have if you didn’t. But don’t expect you’ll make what you would have if you had studied applied math at Stanford. And no one knows how long families will be able and willing to pay for four years of largely symbolic training that steadily becomes more expensive and loses impact. [italics mine]

This NYTimes article notes that, gee, STEM majors are hard and have high attrition rates. Readers immediately point out that the incentives for slogging through a difficult science or engineering curriculum aren't great. Better to work on your "soft skills" and leave the hard stuff for the suckers.

It's also about career path. Why bust your hump in engineering, when a degree in finance will land you a 6-figures job on Wall St., and a shot at 7 or 8 figures, for about the same effort? Especially knowing that corporate America considers engineers to be discardable, and does not hesitate to offshore engineering jobs to India or the Philippines. Some of the CEOs who whine the loudest about shortage of STEM graduates are the biggest culprits in making engineering an undesirable profession.



I am a foreigner. I have gone to undergrad back home for a Computer Science major. I have then come here to the US to get my MBA - at what is considered a top level institution.

What I saw among my fellow students who were American- those purported to be the best and the brightest, the cream of the crop - shocked me.

Grown men and women who are incapable of doing simple fractions, or understand the concept of percentage increase; let alone integrate a function, or indeed, understand what an integral is.

"Science is hard"? Well, Tough Luck, kids. Life ain't easy. The reason that people drop out of science classes is because they're spoiled brats, who, at the age of 18, lack the willpower to actually pursue something that pays off later. I endured 400 person Linear Algebra lessons in which I understood not a thing, calculus classes that made my eyes bleed, and final exams in which I got the grade of 13 out of 100.

Did I drop out and go study English Lit, or Poli Sci? Did I go and complain that "math is too hard"? No. Like the Indian or Slovenian kid that's busy kicking your American tush in the "Getting stuff done" department I grit my teeth and persevered.

The problem is not so much that kids drop out of math, it is [where they] drop out TO. American children are coddled, and told that it's confidence and people skills that matter, and that's what gets you through in life, and it's OK if you can't tell me what a common denominator is in fractions, because someone else is going to do all the "hard stuff".

Don't get me wrong: Soft skills and people skills matter a lot. They do. They really do, that's why American business culture is still among the top in the world: But make no mistake, the pendulum has swung so far towards the "soft skills" side of the equation that "hard skills" are simply impossible to come by.

See also psychometric thresholds for physics and mathematics and data mining the university.

The burden of students

I always enjoyed interacting with Sidney Coleman (sadly, now deceased) when I was a postdoc. I was quite pleased to find this interview, part of the AIP Oral History project.

His views about working with students are not surprising to me, despite the high quality of Harvard PhD students. The gap in brainpower between Sidney and even an exceptional graduate student might be vast. It's worth noting that Sidney had a large number of PhD students who became prominent theorists.

I often make the analogy between teaching (or training PhD students) and pushups or running. Perhaps unpleasant while you are doing it, but (hopefully) it makes you stronger. Certainly I learn a lot from teaching, if only from reviewing the material in preparation for lectures. If the students are exceptionally good, I might even learn things from questions asked in class.

But you do enjoy working with students, or do you?

Coleman: No. I hate it. You do it as part of the job. Well, that's of course false...or maybe more true than false when I say I hate it. Occasionally there's a student who is a joy to work with. But I certainly would be just as happy if I had no graduate students. There are plenty of colleagues around here whom I can work with. There are plenty of research fellows; junior faculty. This is true all through the Cambridge area. There's not only Harvard, there are people to work with at MIT, at Brandeis, and there are some good people at places like Northeastern... places loaded with physicists to collaborate with, to talk about physics ideas with, who are ready and KNOW basically how to do research. You know who's good and who's bad. It's not a question of their being embryonically possibly good or possibly rotten. So certainly if I want physicists to collaborate with I don't have to have graduate students. Occasionally there is a graduate student who is a joy to collaborate with. Both David (Politzer) and Eric (Weinberg) were of this kind, but they were essentially almost mature physicists. They were very bright by the time they came to me. In general, working with a graduate student is like teaching a course. It's tedious, unpleasant work. A pain in the neck. You do it because you're paid to do it. If I weren't paid to do it I certainly would never do it.

Interview with Dr. Sidney Coleman by Katherine Sopka at Harvard Physics Department, Cambridge, Massachusetts January 18, 1977.

My Beautiful Genome

A nice interview with science writer Lone Frank about her book My Beautiful Genome.




Click below for audio.

Festival della Scienza Genova and Italy: final thoughts

Here are the "official" video links from the Festival della Scienza in Genova: my public lecture , interview.

I had a wonderful time in Genova. My visit wasn't very long, because I had to come back to teach.

On the trip I spoke to quite a few young Italians (young here is probably, err, 35 and below), who all expressed pessimism about the future of the country and the economy. On the other hand, at the fancy dinners with Genovese families, I met a number of wealthy business types who reassured me that Italy would be fine and would have no trouble servicing its debt.

On Friday equity markets rallied in relief after the announcement of the latest plan to deal with the Euro debt crisis. However, ominously, bond investors demanded higher rates for Italian 10 year debt.

WSJ: ... Those sorts of concerns played out in Italy's €7.935 billion debt sale on Friday. On each of the four bond issues it sold, Italy was forced to pay higher yields than in the recent past. Most significantly, 10-year debt—a market benchmark—was sold at a yield 6.06%, up from 5.86% only a month ago.

"With a 120% debt-to-GDP ratio and 10-year Italian bonds yielding roughly 6%, they can't do that forever or the borrowing costs will get to an unsustainable level," said Eric Stein, portfolio manager at the Eaton Vance Global Macro Absolute Return Fund. "As your rates go up, it means you're paying more and more to service your debt, and your whole debt dynamics become harder and harder and harder.

As often noted by professionals, equity markets are driven by emotion, whereas bond markets are driven by quantitative analysis.

Steve Jobs, intuition, and genius

Walter Isaacson, biographer of both Einstein and Steve Jobs, on smarts, intuition and innovation.

NYTimes: ONE of the questions I wrestled with when writing about Steve Jobs was how smart he was. On the surface, this should not have been much of an issue. You’d assume the obvious answer was: he was really, really smart. Maybe even worth three or four reallys. After all, he was the most innovative and successful business leader of our era and embodied the Silicon Valley dream writ large: he created a start-up in his parents’ garage and built it into the world’s most valuable company.

But I remember having dinner with him a few months ago around his kitchen table, as he did almost every evening with his wife and kids. Someone brought up one of those brainteasers involving a monkey’s having to carry a load of bananas across a desert, with a set of restrictions about how far and how many he could carry at one time, and you were supposed to figure out how long it would take. Mr. Jobs tossed out a few intuitive guesses but showed no interest in grappling with the problem rigorously. I thought about how Bill Gates would have gone click-click-click and logically nailed the answer in 15 seconds, and also how Mr. Gates devoured science books as a vacation pleasure. But then something else occurred to me: Mr. Gates never made the iPod. Instead, he made the Zune.

So was Mr. Jobs smart? Not conventionally. Instead, he was a genius. That may seem like a silly word game, but in fact his success dramatizes an interesting distinction between intelligence and genius. His imaginative leaps were instinctive, unexpected, and at times magical. They were sparked by intuition, not analytic rigor. Trained in Zen Buddhism, Mr. Jobs came to value experiential wisdom over empirical analysis. He didn’t study data or crunch numbers but like a pathfinder, he could sniff the winds and sense what lay ahead.

He told me he began to appreciate the power of intuition, in contrast to what he called “Western rational thought,” when he wandered around India after dropping out of college. “The people in the Indian countryside don’t use their intellect like we do,” he said. “They use their intuition instead ... Intuition is a very powerful thing, more powerful than intellect, in my opinion. That’s had a big impact on my work.”

Mr. Jobs’s intuition was based not on conventional learning but on experiential wisdom. He also had a lot of imagination and knew how to apply it. As Einstein said, “Imagination is more important than knowledge.”

Einstein is, of course, the true exemplar of genius. He had contemporaries who could probably match him in pure intellectual firepower when it came to mathematical and analytic processing. Henri Poincaré, for example, first came up with some of the components of special relativity, and David Hilbert was able to grind out equations for general relativity around the same time Einstein did. But neither had the imaginative genius to make the full creative leap at the core of their theories, namely that there is no such thing as absolute time and that gravity is a warping of the fabric of space-time. (O.K., it’s not that simple, but that’s why he was Einstein and we’re not.)

... Both Einstein and Mr. Jobs were very visual thinkers. The road to relativity began when the teenage Einstein kept trying to picture what it would be like to ride alongside a light beam. Mr. Jobs spent time almost every afternoon walking around the studio of his brilliant design chief Jony Ive and fingering foam models of the products they were developing.

Mr. Jobs’s genius wasn’t, as even his fanboys admit, in the same quantum orbit as Einstein’s. So it’s probably best to ratchet the rhetoric down a notch and call it ingenuity. Bill Gates is super-smart, but Steve Jobs was super-ingenious. The primary distinction, I think, is the ability to apply creativity and aesthetic sensibilities to a challenge.

In the world of invention and innovation, that means combining an appreciation of the humanities with an understanding of science — connecting artistry to technology, poetry to processors. This was Mr. Jobs’s specialty. “I always thought of myself as a humanities person as a kid, but I liked electronics,” he said. “Then I read something that one of my heroes, Edwin Land of Polaroid, said about the importance of people who could stand at the intersection of humanities and sciences, and I decided that’s what I wanted to do.”

The ability to merge creativity with technology depends on one’s ability to be emotionally attuned to others. Mr. Jobs could be petulant and unkind in dealing with other people, which caused some to think he lacked basic emotional awareness. In fact, it was the opposite. He could size people up, understand their inner thoughts, cajole them, intimidate them, target their deepest vulnerabilities, and delight them at will. He knew, intuitively, how to create products that pleased, interfaces that were friendly, and marketing messages that were enticing.

... China and India are likely to produce many rigorous analytical thinkers and knowledgeable technologists. But smart and educated people don’t always spawn innovation. America’s advantage, if it continues to have one, will be that it can produce people who are also more creative and imaginative, those who know how to stand at the intersection of the humanities and the sciences. That is the formula for true innovation, as Steve Jobs’s career showed.

The top 1 percent by profession

Notice anything funny about the trends? Source: tax data (complete tables at the link; what I display below is truncated). Click for larger versions.



Here is the share of national income by profession.




More interesting would be the top .1 percent, because secular growth in financier representation would be even more apparent.


Here are two more just for fun.

The illusion of skill

Daniel Kahneman claims that differences in the performance of professional investors are mostly due to luck, whereas compensation is awarded as if differences are due to skill. Most alpha is fake alpha.

This of course raises all sorts of questions about why such people are allowed to become so extravagantly wealthy. The usual argument is that their investment decisions lead to more efficient resource allocation in the economy. (They are a "necessary evil" of a capitalist market system that benefits all of us :-) But if the decisions of the highest paid professionals are no better than those of average professionals, we could replace the services of the highest earners at much lower cost (or cap their salaries or impose high marginal tax rates) without negatively impacting the overall quality of decisions or the efficiency of the economy.








The article is worth reading in its entirety.

NYTimes: ... No one in the firm seemed to be aware of the nature of the game that its stock pickers were playing. The advisers themselves felt they were competent professionals performing a task that was difficult but not impossible, and their superiors agreed. On the evening before the seminar, Richard Thaler and I had dinner with some of the top executives of the firm, the people who decide on the size of bonuses. We asked them to guess the year-to-year correlation in the rankings of individual advisers. They thought they knew what was coming and smiled as they said, “not very high” or “performance certainly fluctuates.” It quickly became clear, however, that no one expected the average correlation to be zero.

What we told the directors of the firm was that, at least when it came to building portfolios, the firm was rewarding luck as if it were skill. This should have been shocking news to them, but it was not. There was no sign that they disbelieved us. How could they? After all, we had analyzed their own results, and they were certainly sophisticated enough to appreciate their implications, which we politely refrained from spelling out. We all went on calmly with our dinner, and I am quite sure that both our findings and their implications were quickly swept under the rug and that life in the firm went on just as before. The illusion of skill is not only an individual aberration; it is deeply ingrained in the culture of the industry. Facts that challenge such basic assumptions — and thereby threaten people’s livelihood and self-esteem — are simply not absorbed. The mind does not digest them. This is particularly true of statistical studies of performance, which provide general facts that people will ignore if they conflict with their personal experience.

The next morning, we reported the findings to the advisers, and their response was equally bland. Their personal experience of exercising careful professional judgment on complex problems was far more compelling to them than an obscure statistical result. When we were done, one executive I dined with the previous evening drove me to the airport. He told me, with a trace of defensiveness, “I have done very well for the firm, and no one can take that away from me.” I smiled and said nothing. But I thought, privately: Well, I took it away from you this morning. If your success was due mostly to chance, how much credit are you entitled to take for it?

From the comments.

If you read the whole article, you see that Kahneman does believe in skill. For example, his studies show that some doctors are better at diagnosis than others. I am also sure that some entrepreneurs or some physicists or some athletes are better than others. (Although in the case of entrepreneurs it would be very hard to demonstrate statistically since outcomes are noisy and the number of attempts per entrepreneur is relatively small.)

But there may be areas where *the differences between high level professionals* (e.g., people who have been hired to run money, have top MBAs or graduate degrees, etc.) are statistically seen to be mostly due to luck. This has already been convincingly demonstrated for pundits or analysts of complex world events by Tetlock's studies of expertise. (You can find several posts on this blog on the topic.) Whether it's true of money managers (or even big company CEOs) is controversial. If you argue the skill side, I'd like to see *your* statistical evidence, not just repetition of your priors (again and again).

Expert predictions

In all areas of human activity, even the skill dominated ones, luck plays a big factor. This is a good argument for redistribution -- almost every successful person owes some of their success to luck.

and

It seems to me that the 20th century trend in democracies is toward greater redistribution: social safety nets, guaranteed minimum income, etc. People have been conditioned to believe these are aspects of a just society.

The question is: what is the optimum level of redistribution? (Given a particular utility function for society.)

One argument is that we have to let the rich get rich in order to have strong economic growth. Too much redistribution means a smaller pie to split. But the Illusion of Skill argument (if correct) suggests that for some activities like finance a high marginal tax rate (say, which kicks in above the income of the *average* finance professional; this would then only affect the top earning financiers who, according to the argument are not adding any real value that the average guys can't also provide) would not negatively affect economic efficiency.

If people irrationally and incorrectly believe that only Harvard MDs are capable of treating pneumonia, and bid up their compensation to exorbitant levels (levels so high that the Harvard MDs begin exerting financial and political control over society as a whole), wouldn't it be better for society to impose a high tax rate on Harvard MDs, which kicks in above the income of other doctors with similar credentials (but who are not beneficiaries of the irrational belief)?

Festival della Scienza Genova: videos and photos

Video of my public lecture and an interview, both available in English or Italian translation. The slides for my talk are here.

Some more photos below.

An interview with Rai (Italian version of BBC). Matt Ridley (author and science writer) was also interviewed (the woman sitting between us is the translator).





More views of Genova.

Foto di Genova 2

The lecture hall. See here for video and a short interview. (Not up at the moment but should appear later today.)






Translator booth. Most people listened via headset.




The interview studio.






Plaza outside the Palazzo Ducale.




At the pier.




View from the hills. Each night the speakers have been invited to dinners hosted by local Genovese families "of repute" :-) Last night's dinner was one of the best meals I can remember!

Foto di Genova

Views from my hotel in central Genova:






Cattedrale di San Lorenzo and Via San Lorenzo:






Palazzo Ducale, where I will give my lecture later today:

IQ malleability

This paper got a lot of attention in the press. I don't have time to discuss it in detail, but it is worth emphasizing that the correlation between scores on WISC and WAIS for the n=33 subjects was around .8 -- typical for two different IQ tests administered years apart. (Note, the same test -- e.g., the SAT -- administered twice with a gap of 1 year might have correlation of .9 or even .95.) In other words, knowing an individual's WISC score gives you good power to predict their eventual WAIS score, but with a big chunk of variance (say, 30-40% of total variance) still unaccounted for. In light of this, a 1 SD shift in score is to be expected for a reasonable fraction of participants, as found in the study. What is a bit more novel is that they correlated the score shifts to actual MRI observations of the brain.

(One might also interpret this as saying that the residual uncertainty in "true g score" is a good chunk of an SD even after an individual is carefully tested using WAIS or WISC; personally I don't think "g" is much better defined than at this level of accuracy.)

I am very jet-lagged right now, so I hope what I wrote makes sense :-)

Verbal and non-verbal intelligence changes in the teenage brain (Nature):

... Our participants were 33 healthy and neurologically normal adolescents with a deliberately wide and heterogeneous mix of abilities (see Supplementary Information for details and the implications of our sampling for the generalizability of our conclusions). They were first tested in 2004 (‘time 1’) when they were 12–16 yr old (mean, 14.1 yr). Testing was repeated in 2007/2008 (‘time 2’) when the same indivi- duals were 15–20 yr old (mean, 17.7 yr). See Table 1 for further details of the participants. During the intervening years, there were no testing sessions, and participants and their parents had no knowledge that they would be invited back for further testing. On both test occasions, each participant had a structural brain scan using magnetic resonance imaging (MRI) and had their IQ measured using the Wechsler Intelligence Scale for Children (WISC-III) at time 1 and the Wechsler Adult Intelligence Scale (WAIS-III) at time 2 (see Supplementary Information for details). These two widely used, age-appropriate assess- ments5 produce strongly correlated results at a given time point, con- sistent with them measuring highly similar constructs6. Scores on individual subtests are standardized against age-specific norms and then grouped to produce separate measures of verbal IQ (VIQ) and performance IQ (PIQ), with VIQ encompassing those tests most related to verbal skills and PIQ being more independent of verbal skills. Nevertheless, VIQ and PIQ scores are very significantly correlated with each other across participants: in our sample, the correlations between VIQ and PIQ were r50.51 at time 1 and r50.55 at time 2 (in both cases, n 5 33; P , 0.01). Full-scale IQ (FSIQ) is the composite of VIQ and PIQ and is regarded as the best measure of general intellectual capacity (the g factor) that has previously been shown to correlate with brain size and cortical thickness in a wide variety of frontal, parietal and temporal brain regions7,8.

The wide range of abilities in our sample was confirmed as follows: FSIQ ranged from 77 to 135 at time 1 and from 87 to 143 at time 2, with averages of 112 and 113 at times 1 and 2, respectively, and a tight correlation across testing points (r 5 0.79; P , 0.001). Our interest was in the considerable variation observed between testing points at the individual level, which ranged from 220 to 123 for VIQ, 218 to 117 for PIQ and 218 to 121 for FSIQ. Even if the extreme values of the published 90% confidence intervals are used on both occasions, 39% of the sample showed a clear change in VIQ, 21% in PIQ and 33% in FSIQ. In terms of the overall distribution, 21% of our sample showed a shift of at least one population standard deviation (15) in the VIQ measure, and 18% in the PIQ measure. However, only one participant had a shift of this magnitude in both measures, and, for that particip- ant, one measure showed an increase and the other a decrease. This pattern is reflected in the absence of a significant correlation between the change in VIQ and the change in PIQ. The independence of changes in these two measures allows us to investigate the effect of each without confounding influences from the other.

... Using regression analysis, we studied the brain changes associated with a change in VIQ, PIQ or FSIQ (see Methods Summary for details). The results (Fig. 1) showed that changes in VIQ were positively corre- lated with changes in grey matter density (and volume) in a region of the left motor cortex that is activated by the articulation of speech10. Conversely, changes in PIQ were positively correlated with grey matter density in the anterior cerebellum (lobule IV), which is associated with motor movements of the hand

Tall and good looking

There's an interesting discussion of height and selection at Razib's blog Gene Expression. I can think of lots of plausible tradeoffs related to greater height -- increased calorie requirements, perhaps not so adaptive for females, effects on metabolism or other body systems, etc. But what about facial attractiveness or symmetry? Every so often I see a really good looking face and the effect is very striking. Surely there are lots of benefits from this, but are there any plausible genetic costs? I would guess that evolution can tweak facial bone structure without affecting the brain or other bodily systems... If so, why aren't we all much better looking? :-)

See earlier post female faces.



[Posted from CDG in Paris; see you in Genova soon!]