BGI cleared to acquire Complete Genomics

Sequencing is a fast moving field with many competing technologies. The claim that the acquisition of Complete Genomics has national security implications is highly implausible. Earlier posts here and here.

NYTimes: ... BGI-Shenzhen, said in a statement this weekend that its acquisition of Complete Genomics, based in Mountain View, Calif., had been cleared by the federal Committee on Foreign Investment in the United States, which reviews the national security implications of foreign takeovers of American companies. The deal still requires antitrust clearance by the Federal Trade Commission.

Some scientists, politicians and industry executives had said the takeover represented a threat to American competitiveness in DNA sequencing, a technology that is becoming crucial for the development of drugs, diagnostics and improved crops.

The fact that the $117.6 million deal was controversial at all reflects a change in the genomics community.

A decade ago, the Human Genome Project, in which scientists from many nations helped unravel the genetic blueprint of mankind, was celebrated for its spirit of international cooperation. One of the participants in the project was BGI, which was then known as the Beijing Genomics Institute.

... Some other executives at American sequencer manufacturers said they saw no cause for concern. “I can’t believe they can come up with a rational explanation of why this is a national security issue,” said Michael W. Hunkapiller, the chief executive of Pacific Biosystems.

Jonathan M. Rothberg, who runs the Ion Torrent sequencer division of Life Technologies, also said the acquisition “does not appear to raise national security issues.”

That which is not

"Whatever you see in this world, it is an illusion." (Maya)

Happy New Year!



Varanasi, India: "Beyond" from Cale Glendening on Vimeo.

The Universal Mind of Bill Evans

My Xmas present to you: The Universal Mind of Bill Evans

... Here is Evans, his hair slicked back, his terrible teeth uncapped, a cigarette waving in the air, in intense conversation with his composer brother Harry Evans (a professor of music at Louisiana State University) on the nature of creativity in jazz.

This documentary features in-depth discussion of Evans' internal process of song interpretation, improvisation, and repertoire. Through demonstration on the piano, Bill uses the song 'Star Eyes' to illustrate his own conception of solo piano and how to interpret and expand upon the melody and underlying chord structure.

Onstage, Evans was famously reticent about speaking, but here he's surprisingly, stirringly provocative.

Best introspective bits about his development, improvisational ability, intellectual / analytical approach versus raw talent @30 min and thereafter.

Not bad for a heroin junkie (like Chet Baker: see earlier post Time After Time).

All About Jazz: ... He played an equal role with Miles Davis in composing Kind Of Blue, the top-selling jazz album ever, yet the association proved disastrous as Evans' shyness and pressures of the stage fed a drug addiction that led to his death in 1980. His intelligence allowed him to surpass other players with more raw talent and he inspired a rare cult-like following, but also endured critics who saw him as a fraudulent lightweight.

Evans is generally acknowledged as the most influential pianist since Bud Powell, and a primary influence on players such as Keith Jarrett and Chick Corea. Many consider his Sunday At The Village Vanguard the best piano trio album ever and compositions such as "Waltz For Debby" are all-time standards. He is also credited with advancing harmonic and voicing structures. and pioneering modern trio format elements such as giving sidemen equal interplay during improvisations.

His career peaked early during the late 1950s and early 1960s, then went through a series of peaks and valleys for the rest of his life. The best of those latter periods were probably during the early 1970s and right before his death, although neither reached the pinnacle of his early days.

The Bill Evans Web Pages: ... Throughout his entire professional career, Evans was also hopelessly addicted to drugs, a fact that was no secret while he was alive, but one that remains difficult to absorb even today. Obviously drugs are not foreign objects in the jazz ambient, but it is too easy to simply throw Evans onto jazz’s steep junkie pile. He was too intelligent, too administrative over his physical and emotional capacities to allow himself to succumb to an addiction which he did not really want. Why then was the man whose shimmering touch and blush-hued harmonies were responsible for transforming the piano into a jazz instrument as expressive and beautiful as any sighing horn such an afflicted soul? For those who have truly fallen under his spell, this lingering question weighs on his entire legacy.

DNA Dreams -- documentary

DNA Dreams -- a Dutch documentary about the BGI Cognitive Genomics Lab -- is now online. This version only has Dutch subtitles, although I've also seen an English version. Most of the dialog is in English, some in Mandarin.

DNA Dreams (Translated from Dutch.) 

What would happen if the gene was found that IQ determines us? And when people and animals could be easily cloned? Wait there a new world full of perfect people? And we want that world be? In China's Pearl River Delta is that world in the making. On the outskirts of Shenzhen is BGI, recently the largest genetic research world. Working day and night here 4000 young scientists at mapping the DNA of plants, animals and humans. Knowledge of this code of life opens up many new possibilities. For instance, the eighteen year old high school dropout Zhao Bowen an international research team that wants to find the genes for intelligence. He works with the young, brilliant psychologist Yang Rui, that IQ tests decreases with gifted children and their blood samples to collect DNA. In a later lab work forty young people led by the 24-year-old Lin Lin a clone project, which includes fluorescent mini-pigs produces and clone factory will grow. Between the cloning of humans and animals exist ethical, but hardly practical differences. Which applications are in the offing as this knowledge will soon become common property? China has few legal obstacles to the life sciences and also to capital is not a defect. The young scientists can fully indulge their fascination. They are optimistic and want to progress. But reality is stubborn and it exists for them not only in bits, bytes and algorithms.

Some reactions to the documentary:

1. As you might expect, it emphasizes sensational aspects of our research -- genetic engineering, drugs for cognitive enhancement, etc. These are all possibilities, obviously topics we discussed at the behest of the film makers, but of course for now our work is basic research with no near term applications. (Basic research tends to be less interesting to viewers than science fiction extrapolations.)

2. I find the video visually interesting, but at times it emphasizes the alien or sinister. Even the musical background seems chosen for this purpose.

3. Several important members of our team have little or no role in the documentary, despite being interviewed extensively during its making. I suppose the director was limited in what she could include, given the 60 minute format. The young woman who leads the cloning team is not actually part of our group.


Below are some photos of the documenters at work. (Scroll down here for more.)

Film crew takes in a technical discussion. Rare mutations, pseudogenes and rs numbers.

Shooting at a hipster pad in Dameisha. Barbeque and a showing of Gattaca :-)

 

Shooting in the BGI cafeteria.

 

Sheraton Dameisha. (The dinner discussion was shot here.)

 

EMH vs Macro, Fischer Black

Arnold Kling on the tension between macroeconomics and the Efficient Markets Hypothesis (EMH). I'm surprised this isn't more often noticed by economists. But I suppose macro types don't tend to think deeply about finance (at least, not before the recent crisis; how many macro types actually understand Black-Scholes-Merton?) and vice versa. I was shocked at the beginning of the credit crisis to meet famous macroeconomists who didn't know what a credit default swap was, and I still often meet finance types who laugh at macro models.

askblog: Consider financial variables, such as the long-term interest rate or the price-earnings ratio of the overall stock market. According to the efficient markets hypothesis, these are not predictable on the basis of known information. To put this another way, you cannot beat the market forecast for these variables.

On the other hand, in conventional macroeconomics these variables can be predicted using models and controlled using policy levers. Reconciling this with the EMH has challenged economists for decades. ...

I prefer a third way of looking at things, which might be expressed in the work by Frydman and Goldberg. That is, there is no reason for all participants in markets to be using the same model. They have different information sets. The EMH is a useful guide to everyone, because it serves as a reminder that it is unwise to assume that your information set is somehow superior. However, it is not correct to impose “rational expectations,” in which everyone uses the same model.

... Incidentally, I recently re-read Perry Mehrling’s biography of Fischer Black. Black was perhaps the first economist to think about the contrast between modern finance theory and conventional macro, and Black was the first and perhaps the only one to attempt to recast macro entirely in terms of modern finance.

More thoughts on EMH here. My comments on Mehrling's bio and Fischer Black are here.

... on the topic of finance books, I highly recommend this biography of Fischer Black, which I should have reviewed here long ago. Fischer was yet another outsider (his background was in theoretical physics) to finance who made an important contribution. Unlike Kelly, he was accorded mainstream recognition (professorship at Chicago and partnership at Goldman) during his career. The most impressive thing about Black was his ability to think deeply and independently -- beyond the conventional wisdom. There are some very intriguing passages in the book about his views on money and banking which are, I think, quite unconventional to mainstream economics.

... Black was both an undergrad and grad student at Harvard in physics. He didn't really complete his PhD in physics, but sort of drifted into AI-related stuff(!) at MIT, under cover of math or applied math.

The bio says the only course he ever had trouble with was Schwinger's course on advanced quantum. The biographer suggests Black did poorly due to lack of interest, but I find that hard to believe given the subject matter, the lecturer and the times ;-)

Black's point of view was clearly that of a physicist or applied mathematician. He really was a fascinating guy, and the biographer, being an academic economist, can appreciate a lot of Black's thinking -- it's not an entirely superficial book despite being non-technical.

After reading the book, I don't feel so bad about questioning some of the fundamental assumptions made by academic economists. Black was asking some of the very same questions during his career.

Peace on Earth, Good Will to Men 2012

For years, when asked what I wanted for Christmas, I've been replying: peace on earth, good will toward men :-)

No one ever seems to recognize that this comes from the bible, Luke 2.14 to be precise!

Linus said it best in A Charlie Brown Christmas:

And there were in the same country shepherds abiding in the field, keeping watch over their flock by night.

And, lo, the angel of the Lord came upon them, and the glory of the Lord shone round about them: and they were sore afraid.

And the angel said unto them, Fear not: for, behold, I bring you good tidings of great joy, which shall be to all people.

For unto you is born this day in the city of David a Saviour, which is Christ the Lord.

And this shall be a sign unto you; Ye shall find the babe wrapped in swaddling clothes, lying in a manger.

And suddenly there was with the angel a multitude of the heavenly host praising God, and saying,

Glory to God in the highest, and on earth peace, good will toward men.

Merry Christmas!



Here's a longer excerpt from A Charlie Brown Christmas.

Brainwash

The video below is the second in the series Brainwash, a Norwegian documentary on the science of nature and nurture. This episode concerns parental influence, and features a very clear explanation by Robert Plomin of heritability as determined by adoption studies (a bit after 15:45). (Note to experts: Plomin refers to his Colorado adoption study, but even larger studies have replicated the results, across multiple countries. He found that the effect of shared environment on cognitive ability was consistent with zero, but the actual value could be somewhat higher due to statistical uncertainties. See The mystery of non-shared environment for more discussion.)

Brainwash caused a big controversy in Norway, but I think the narrator does a great job of making the presentation fair, accurate and entertaining. His background is standup comedy :-)

Thanks to a reader for the link.

Fears of an Asian Quota in the Ivy League

NYTimes Room for Debate.

Fears of an Asian Quota in the Ivy League

Determined to use educational opportunities as a road to advancement, Asian-Americans have won a disproportionate number of spots at top high schools and colleges that base admission on objective standards. But some have questioned how affirmative action programs might hurt their chances for admission, or say that the most competitive schools do not want to have too many Asian students.

Are top colleges deliberately limiting the number of Asian-Americans they admit?

Only one side in this debate uses numbers and statistics. You can guess which that is.

Debate rule #1: always pay close attention to what the physicist says. There are two in this debate, Ron Unz and S.B. Woo.

S.B. Woo, a physicist and former lieutenant governor of Delaware, was the founding president of the 80-20 National Asian American Educational Foundation, which filed an amicus brief, supporting race-neutral admissions, in the Supreme Court case Fisher v. University of Texas.

Top colleges are clearly limiting the number of Asians they admit, and what’s at stake for America is of more importance than just the number of Asians going to Harvard.

The Princeton sociologist Thomas Espenshade wrote in his 2009 book, "No Longer Separate, Not Yet Equal: Race and Class in Elite College Admission and Campus Life,'' that “to receive equal consideration by elite colleges, Asian Americans must outperform Whites by 140 points, Hispanics by 280 points, Blacks by 450 points in SAT (Total 1600)." As Ron Unz demonstrates, the percentage of Asians among the student bodies of Ivy League schools has been a steady 17 percent, give or take a couple of points, for about 20 years.

The value of equal opportunity is being trampled. The creditability of elite colleges suffers. Meritocracy is compromised. This clearly shows that these colleges set a quota for Asian students.

The percentage of Asian students at the California Institute of Technology, which uses a "race-neutral" admission policy, has roughly followed the proportion of college-age Asians in the general population.

And it’s not just a matter of Asian-Americans doing well on tests. In 2006, they were 27 percent of Presidential Scholars, who were chosen based on scholarship, service, leadership and creativity.

This all demonstrates that top colleges have a "merits-be-damned" approach to limit the number of Asian students. They did that once before -- against Jewish students about a century ago.

America's core value of equal opportunity is being trampled. The 14th Amendment on equal protection is trampled upon. America and Asian American students suffer.

The creditability of elite colleges suffers. The administrators of these colleges may be steadfast in their righteous posturing. But as the truth emerges, fewer people are with them; more are shaking their heads and chuckling at their facade. The meritocracy of the American culture is compromised. America's future is too important to allow race-conscious admission to continue hurting all of us. It's time for the game to stop.

Lion in winter: James Salter

See earlier post James Salter.

INTERVIEWER

But why a memoir?

SALTER

To restore those years when one says, All this is mine—these cities, women, houses, days.

INTERVIEWER

What do you think is the ultimate impulse to write?

SALTER

To write? Because all this is going to vanish. The only thing left will be the prose and poems, the books, what is written down. Man was very fortunate to have invented the book. Without it the past would completely vanish, and we would be left with nothing, we would be naked on earth.

Risk, Moneyball, Leadership

Some slides for an MSU leadership meeting. Click for larger version.

See also Moneyball in Academia.

Brain, Mind and Evolution

Some slides for opening remarks at an MSU workshop tomorrow. Click for larger version.

Manhattan winter wonderland

Actually, it was pretty warm.

President Simon and I did a nice Q&A with the alumni guests in an auditorium at the JP Morgan building on Madison. Some of my buddies were probably upstairs working when the event started at 5:30 pm.

Sequencing around the world

omicsmaps.com shows the locations of next-gen sequencing devices around the world. The map below is of Illumina HiSeqs -- note the 137 at BGI. As far as I can tell the other big concentration is 50 at the Broad Institute. The Wellcome Trust Sanger Institute (Cambridge, UK) has 23. Click for larger version.

Two more nice figures from MIT Technology Review. Click for larger version.

Harvard as giant hedge fund

Ron Unz seems to be getting some traction on Twitter with his observation that Harvard looks like a giant hedge fund ($30B AUM) attached to a smaller educational institution (annual budget about $1B?) for tax purposes ;-)

Paying Tuition to a Giant Hedge Fund: ... Harvard’s Division of Arts and Sciences—the central core of academic activity—contains approximately 450 full professors, whose annual salaries tend to average the highest at any university in America. Each year, these hundreds of great scholars and teachers receive aggregate total pay of around $85 million. But in fiscal 2004, just the five top managers of the Harvard endowment fund shared total compensation of $78 million, an amount which was also roughly 100 times the salary of Harvard’s own president.

... The typical private foundation is legally required to spend 5 percent of its assets on charitable activities, and with Harvard’s endowment now back over $30 billion, that sum would come to around $1.5 billion annually. This is many times the total amount of undergraduate tuition ...

However, there has been very little media attention to his analysis of meritocracy in elite higher education. The humorous hedge fund observation is merely a sidebar to the meritocracy article.

More human capital mongering

See also Elite universities and human capital mongering. The numbers below suggest that the top 30 schools enroll half or more of all students who are in the top, say, half percent of ability as measured by SAT/ACT.

Chronicle: ... In past decades, many of our best students attended state universities close to home, where they often received an excellent education at reasonable cost. Today, such students are likely to be vying for admission to the nation's most elite colleges and universities. Does this widening of the "prestige gap" between elite and lower-tier institutions, this "tracking" of students into educational institutions by their ability, raise matters of public concern? Or are these shifts simply of interest to institutions at or near the top? We think they raise issues of general social importance.

The increased interest of top students in attending the most- prestigious institutions is easily documented. During the 1980s, for example, 59 per cent of the finalists in the Westinghouse Science Talent Search (one of the nation's premier academic contests for high-school students) chose to enroll at one of just seven institutions -- Cornell, Harvard, Princeton, Stanford, and Yale Universities, the California Institute of Technology, and the Massachusetts Institute of Technology. The same seven institutions led the list in the 1970s, but enrolled only 48 per cent of the Westinghouse finalists.

Further, by 1990, about 43 per cent of students scoring above 700 on the verbal section of the Scholastic Assessment Test chose one of the 30 "most competitive" colleges listed in Peterson's Guide to Four-Year Colleges, up from 32 per cent in 1979. And Richard Spies, vice-president for finance at Princeton, has estimated that from 1976 to 1987, the probability increased by about half that a student with a combined S.A.T. score above 1,200 would apply to one of the 33 elite private institutions belonging to the Consortium on Financing Higher Education. This trend in applications has continued into the 1990s. ...

The Chronicle also has a related article about the field of Political Science (see comment thread!):

Chronicle: ... Departments at 11 elite universities provide half of the field's tenured and tenure-track professors, according to an analysis of more than 3,000 professors.

Placement numbers for theoretical physics: Survivor: theoretical physics.

John Von Neumann Documentary

Thanks to a reader for these links. YouTube is amazing!






Teller on von Neumann's enjoyment of thinking, and his horror at the breakdown of this ability due to his terminal cancer. (Also mention's that vN's relation to "the rest of us" was similar to talking to a 3 year old :-)  "Only he was fully awake"

Dig deep

I love this video.




This one is also good :-)  Check out the guy who won't tap and is choked completely out. I've done this to other people but I'm a quick tapper so it's never happened to me.




I think in my mid to late 20's prime I could have beaten up any other theoretical physicist in the world in a fight ;-)  But those days are gone!

The Myth of American Meritocracy

Ron Unz has performed an exhaustive analysis of elite university admissions in The Myth of American Meritocracy (December issue of the American Conservative). He finds strong evidence for de facto quotas on Asian-Americans at Ivy League universities. See below for a brief summary. I suggest reading his entire article, which is filled with additional insights, including one rather shocking surprise. Don't miss the statistical supplement.

Asian-American Quotas at Ivy League Universities?

November 28, 2012 - America’s elite Ivy League universities appear to follow a de facto Asian-American admissions quota policy according to “The Myth of American Meritocracy,”a 30,000-word cover story in the December issue of The American Conservative by publisher Ron Unz.

Unz provides detailed statistical evidence that the pattern of Asian-American enrollment over the last two decades is remarkably similar to what followed the establishment of Ivy League Jewish quotas in the mid-1920s. Soon after the U.S. Department of Justice closed its early 1990s investigation into allegations of anti-Asian admissions bias at the Ivy League:

• Asian-American numbers at Harvard, Yale, and Columbia began large declines. 

• Asian-American enrollments throughout the Ivy League strangely converged to very similar levels. 

• The college-age population of Asian-Americans doubled during 1993-2011 as did their top academic awards, but none of this was reflected in their Ivy League enrollments. 

• As one example, the percentage of college-age Asian-Americans at Harvard dropped by more than 50% during 1993-2011, a larger decline than that suffered by Jews following the 1925 establishment of ethnic quotas. 

• Meanwhile, race-neutral Caltech saw its Asian-American enrollment increase closely in line with the growth of the college-age Asian-American population. 

• Comparing the Ivy League enrollments of Asian-Americans with those of high-performing white subpopulations rules out general “diversity” factors as an explanation for these patterns.

See also Defining Merit. Guess which university produces the most Nobel prizes per student?


Some additional figures from the article (click for larger versions). Note that not only did the number of college age Asian-Americans increase in recent decades, so did (overwhelmingly) their performance at the high end of academic achievement. If admissions were race neutral (meritocratic) at Harvard, why did the percentage of Asians decrease?

The Caltech student population is demographically similar to the most intellectually talented portion of the US population (see below); the Ivy League student population is not -- there are curious distortions.

Persistence, motivation and reliability

GED holders are roughly comparable to high school graduates in terms of cognitive ability, but weaker in terms of personality factors such as conscientiousness. Labor market outcomes for GED holders are closer to those of high school dropouts than to graduates.

Heckman talk (mp3) at Yale Law School (also available on iTunes). For related results on personality and earnings for cognitively gifted individuals, see Earnings effects of personality, education and IQ for the gifted.

The GED

James J. Heckman, John Eric Humphries, Nicholas S. Mader

NBER Working Paper No. 16064

The General Educational Development (GED) credential is issued on the basis of an eight hour subject-based test. The test claims to establish equivalence between dropouts and traditional high school graduates, opening the door to college and positions in the labor market. In 2008 alone, almost 500,000 dropouts passed the test, amounting to 12% of all high school credentials issued in that year. This chapter reviews the academic literature on the GED, which finds minimal value of the certificate in terms of labor market outcomes and that only a few individuals successfully use it as a path to obtain post-secondary credentials. Although the GED establishes cognitive equivalence on one measure of scholastic aptitude, recipients still face limited opportunity due to deficits in noncognitive skills such as persistence, motivation and reliability. The literature finds that the GED testing program distorts social statistics on high school completion rates, minority graduation gaps, and sources of wage growth. Recent work demonstrates that, through its availability and low cost, the GED also induces some students to drop out of school. The GED program is unique to the United States and Canada, but provides policy insight relevant to any nation's educational context.

This figure shows that high school completion probability varies mainly according to cognitive ability, whereas GED completion is positively correlated with low non-cognitive ability (i.e., low conscientiousness). (Numerical score 1 = low, 10 = high; click for larger version.)

The related question we will be facing in the near future: what are relative job success probabilities for students with degrees from a traditional college versus those with credentials obtained via online education? For example, consider a smart kid who obtains high grades in linear algebra and C++ from MIT/Harvard/Berkeley edX, but chooses not to attend university, versus a graduate from a traditional engineering program. Exactly what is being signaled or predicted by these two life paths? Who would you hire?

Schwinger on quantum foundations

The excerpt below is from the excellent biography Climbing the Mountain by Mehra and Milton. Milton was one of Schwinger's last Harvard grad students, eventually a professor at the University of Oklahoma. Schwinger's view is the one shared by all reasonable physicists: quantum mechanics must apply to the measuring device as well as that which is measured. Once this assumption is made (as Hawking and others have noted): many worlds follows trivially.

(p.369) Schwinger: "To me, the formalism of quantum mechanics is not just mathematics; rather it is a symbolic account of the realities of atomic measurements. That being so, no independent quantum theory of measurement is required -- it is part and parcel of the formalism.

[ ... recapitulates usual von Neumann formulation: unitary evolution of wavefunction under "normal" circumstances; non-unitary collapse due to measurement ... discusses paper hypothesizing stochastic (dynamical) wavefunction collapse ... ]

In my opinion, this is a desperate attempt to solve a non-existent problem, one that flows from a false premise, namely the vN dichotomization of quantum mechanics. Surely physicists can agree that a microscopic measurement is a physical process, to be described as would any physical process, that is distinguished only by the effective irreversibility produced by amplification to the macroscopic level. ..."

Similar views have been expressed by Feynman and Gell-Mann and by Steve Weinberg. Interestingly, this chapter in the biography seems to describe (in slightly odd language) some Schwinger work on decoherence, analyzing a collaborator's claim that Stern-Gerlach beams could be recombined coherently.

See also my paper On the origin of probability in quantum mechanics.

Schwinger's precocity, explored in the biography in far greater detail than I had seen before, is overwhelming. At age 17 or so he had read everything there was to read about quantum mechanics, early field theory, nuclear and atomic physics. For example, he had read and understood Dirac's papers, had invented the interaction picture basis, had already read the Einstein, Podolsky, Rosen paper and explained it to Rabi when they first met. He met Bethe and they discussed a problem in quantum scattering (Schwinger had improved Bethe's well-known result and noticed an error that no other theorist had). Bethe later wrote that the 17 year old Schwinger's grasp of quantum electrodynamics was at least as good as his own.

Feyerabend on the giants: "... The younger generation of physicists, the Feynmans, the Schwingers, etc., may be very bright; they may be more intelligent than their predecessors, than Bohr, Einstein, Schrodinger, Boltzmann, Mach and so on. ..."

Schwinger survived both Feynman and Tomonaga, with whom he shared the Nobel prize for quantum electrodynamics. He began his eulogy for Feynman: "I am the last of the triumvirate ..."

DC photos

National Museum of the American Indian.

Hirshhorn Museum. Next four images are of the Ai Wei Wei exhibition.

Fed town

Council on Competitiveness meeting in Washington. Fed town is weird. It's jarring to see people using ancient Blackberries ...

State Department dinner.