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Physicist, Startup Founder, Blogger, Dad

Sunday, March 31, 2013

The talented 1 in 10,000

David Lubinski sent me a copy of his latest paper from a longitudinal study of individuals who scored at the 1 in 10k level (normalized by age) on SAT-M or SAT-V before 13. This population is similar to the one whose DNA we are using in our intelligence GWAS.

How can a brief test administered to a 12 year old be so good at picking out individuals who are likely to be exceptionally successful at age 38? If I hadn't been repeatedly told otherwise by "experts" I might conclude it had some validity ;-)
Who Rises to the Top? Early Indicators

Youth identified before age 13 (N = 320) as having profound mathematical or verbal reasoning abilities (top 1 in 10,000) were tracked for nearly three decades. Their awards and creative accomplishments by age 38, in combination with specific details about their occupational responsibilities, illuminate the magnitude of their contribution and professional stature. Many have been entrusted with obligations and resources for making critical decisions about individual and organizational well-being. Their leadership positions in business, health care, law, the professoriate, and STEM (science, technology, engineering, and mathematics) suggest that many are outstanding creators of modern culture, constituting a precious human-capital resource. Identifying truly profound human potential, and forecasting differential development within such populations, requires assessing multiple cognitive abilities and using atypical measurement procedures. This study illustrates how ultimate criteria may be aggregated and longitudinally sequenced to validate such measures.
The authors note that about 2% of the US general population earn doctoral degrees (JD, MD, PhD), whereas about 22% of gifted students who test at the top 1% level do so, and 44% percent of this population (in the 1 in 10k population there were many times more PhDs than MDs and JDs). From the paper:
... Other investigators have observed the importance of ability patterning for differential accomplishments in education and the world of work among talented students (Gottfredson, 2003; Wai, Lubinski, & Benbow, 2009), and even students in the top 1% of ability (Gohm, Humphreys, & Yao, 1998; Park, Lubinski, & Benbow, 2007). However, the current investigation studied participants who were profoundly gifted (top 1 in 10,000), as indicated by at least one SAT score. Moreover, for 94% of these participants their less impressive SAT score placed them in the top 1% of ability—and the lower score for 78% was in the top 0.5% (see Fig. S1 in the Supplemental Material); almost all members of this sample had both mathematical and verbal reasoning abilities higher than those of the vast majority of Ph.D.s in any discipline (Wai et al., 2009, Figs. 6 and B1).

... More than 7% of participants held tenure at research intensive universities (including many considered the best in the world) by the time they were age 38. The 14 attorneys were predominantly working in positions of significant responsibility for major firms or organizations. The 19 physicians were also highly accomplished: Seven were assistant professors, 2 were directors of major private practices, and 1 codirected a hospital organ-transplant center serving more than 3 million people. Rather than working for established organizations, 14 individuals founded companies of their own. Two individuals were vice presidents at Fortune 500 companies; 2 others were Fortune 500 senior hardware or software engineers. Several participants were active in government agencies at local and federal levels—one advised the president of the United States on national policy issues.

Thursday, March 28, 2013

Machine translation

In a 2010 post, I wrote:
Machines and bilingualism: I had a terrifying thought the other day. I would guess that at 90 percent confidence level machine translation and voice recognition will be good enough in 20 years that people will be able to communicate pretty well across most language barriers using cheap and unobtrusive devices. If so, is it worth all this effort to make sure my kids are bilingual?

I say it's terrifying because of the significant effort we're expending on our Bilingual Kids Project -- including relocating to Taiwan for this sabbatical. Another point of clarification: I'm not saying in 20 years we'll have AI (far from it). But something that translates basic phrases and simple content (surely we'll have that: Moore's law, massive corpora of translated text, statistical machine learning, yada yada) would reduce significantly the value of all but the most sophisticated language skills.
This video shows the current state of the art from Microsoft Research. See the realtime speech to speech (English to Chinese) demo starting at just before 6 minutes in. The demo could have been faked a bit -- Rashid might be sticking to a prepared script -- but let's hope it was legitimate.


Wednesday, March 27, 2013

On the radio: NPR's On Point

I'll be on live (I think) for an hour starting at 11 AM eastern. If you dial in, you might be able to ask me a question on the air :-)

WBUR On Point. (More on the show and its host here.)

"To join the conversation on the air, call us at 1-800-423-8255 during a live broadcast."

Genius Babies

The internet headline was “engineering genius babies” out of China. Not true. But the reality is very interesting. We’ll check it out.

Guests

Nita Farahany, Professor of Law, Philosophy, Genome Sciences & Policy at Duke University School of Law, and a member of the Presidential Commission for the Study of Bioethical Issues.

Lee Silver, Professor of Molecular Biology and Public Affairs at Princeton University, Co-editor of the journal of the International Mammalian Genome Society, Fellow at the American Association for the Advancement of Science, and author of “Remaking Eden: Cloning and Beyond in a Brave New World” (1997).

Dr. Steve Hsu, member of the core team at BGI’s Cognitive Genomics Lab, Vice President for Research and Graduate Studies and Professor of Theoretical Physics at Michigan State University.

Here's the audio:

Monday, March 25, 2013

Koxinga



I haven't read this yet but it looks quite interesting. Koxinga is pretty well known in Taiwan and China, of course (see picture at bottom).
Princeton University Press: During the seventeenth century, Holland created the world's most dynamic colonial empire, outcompeting the British and capturing Spanish and Portuguese colonies. Yet, in the Sino-Dutch War--Europe's first war with China--the Dutch met their match in a colorful Chinese warlord named Koxinga. Part samurai, part pirate, he led his generals to victory over the Dutch and captured one of their largest and richest colonies--Taiwan. How did he do it? Examining the strengths and weaknesses of European and Chinese military techniques during the period, Lost Colony provides a balanced new perspective on long-held assumptions about Western power, Chinese might, and the nature of war.

It has traditionally been asserted that Europeans of the era possessed more advanced science, technology, and political structures than their Eastern counterparts, but historians have recently contested this view, arguing that many parts of Asia developed on pace with Europe until 1800. While Lost Colony shows that the Dutch did indeed possess a technological edge thanks to the Renaissance fort and the broadside sailing ship, that edge was neutralized by the formidable Chinese military leadership. Thanks to a rich heritage of ancient war wisdom, Koxinga and his generals outfoxed the Dutch at every turn.

Exploring a period when the military balance between Europe and China was closer than at any other point in modern history, Lost Colony reassesses an important chapter in world history and offers valuable and surprising lessons for contemporary times.

Tonio Andrade is associate professor of history at Emory University. He is the author of How Taiwan Became Chinese: Dutch, Spanish, and Han Colonization in the Seventeenth Century.
More from the author:
... Most westerners even believe that the Chinese invented gunpowder but never used it in weapons, reserving it for fireworks.

In fact, the first guns were developed in China, as were the first cannons, rockets, grenades, and land mines. The Chinese eagerly studied foreigners’ weapons, such as Japanese muskets and English cannons. So it’s no surprise that on Taiwan, the Dutch found themselves hard pressed by Chinese firepower. The Dutch were no laggards. Dutch cannons and handguns were famous throughout Europe, and the Dutch arms industry was a major part of its booming early-capitalist economy. Yet the guns aimed against them by their Chinese foes were strikingly effective, and the Chinese gunners were so fast and so accurate that, as one Dutch commander wrote in chagrin, “they put our own men to shame.”

Yet an even greater Chinese advantage in this Sino-Dutch War was in the area of leadership. The Dutch were known throughout Europe as the inventors of modern military drill, and, indeed, Dutch innovations revolutionized warfare in Europe. Dutch drilling regimes — in which musketmen were trained to march in lockstep, carry out intricate maneuvers, and act as one coordinated unit — spread throughout the West, prompting military historians to argue that Europeans possessed a special “Western Way of War,” making them the most effective fighting troops in the world.

But, in a striking coincidence of world history, at the same time as Europeans were developing their new drilling regimens, China was undergoing a military revolution of its own. Perhaps one should instead say “revival” of its own, because ancient Chinese armies were incredibly well drilled and disciplined. Still, the revival of the 1500s and 1600s went well beyond ancient models, and Chinese commanders experimented with training regimens that sound strikingly modern – the simulation of combat stress, the assumption of prone positions for firefights (Westerners were trained to stand up, exposing their bodies to more bullets), advanced strength and endurance training regimens.

The Chinese forces the Dutch faced on Taiwan were extremely well-trained, and the Dutch, for all their Western Way of War, were routed on the battlefields like novices.

But the most important Chinese advantage was in strategic and tactical culture. Chinese military commanders were able to draw on two millennia of careful thinking on warfare. Most Westerners know about Sun Tzu’s Art of War, which is read by CEO’s from Germany to California, but most westerners have no idea how many brilliant strategists, tacticians, and logistics experts succeeded Sun Tzu, building the world’s richest corpus of military thought.

Zheng Chenggong and his generals referenced complex scenarios and stratagems by means of a few words, much as westerners use the term “Trojan Horse.” This store of knowledge helped the Chinese to outwit the Dutch at nearly every turn, luring them into traps, making careful use of terrain, combining naval and land power in unexpected and effective ways.

The Dutch, concluding that they had no hope to prevail against the superior Chinese forces, ultimately gave up and handed Taiwan over to the Chinese. The next war between Chinese and Western forces wasn’t fought for another two centuries, and by that time the global balance of power had shifted. Europe was industrializing. China was in decline.

Thursday, March 21, 2013

He is a second Dirac, only this time human

Another historical letter sent by a reader. My understanding is that Feynman was not appointed at Berkeley because of Birge's anti-semitism: "One Jew (Oppenheimer) is enough," he is reported to have said.

CONFIDENTIAL

November 4, 1943

Professor R. T. Birge
Chairman, Department of Physics
University of California
Berkeley, California

Dear Professor Birge:

In these war times it is not always easy to think constructively about the peace that is to follow, even in such relatively small things as the welfare of our department. I would like to make one suggestion to you which concerns that, and about which I have myself a very sure and strong conviction.

As you know, we have quite a number of physicists here, and I have run into a few who are young and whose qualities I had not known before. Of these there is one who is in every way so outstanding and so clearly recognized as such, that I think it appropriate to call his name to your attention, with the urgent request that you consider him for a position in the department at the earliest time that that is possible. You may remember the name because he once applied for a fellowship in Berkeley: it is Richard Feynman. He is by all odds the most brilliant young physicist here, and everyone knows this. He is a man of thoroughly engaging character and personality, extremely clear, extremely normal in all respects, and an excellent teacher with a warm feeling for physics in all its aspects. He has the best possible relations both with the theoretical people of whom he is one, and with the experimental people with whom he works in very close harmony.

The reason for telling you about him now is that his excellence is so well known, both at Princeton where he worked before he came here, and to a not inconsiderable number of "big shots" on this project, that he has already been offered a position for the post war period, and will most certainly be offered others. I feel that he would be a great strength for our department, tending to tie together its teaching, its research and its experimental and theoretical aspects. I may give you two quotations from men with whom he has worked. Bethe has said that he would rather lose any two other men than Feyman from this present job, and Wigner said, "He is a second Dirac, only this time human."

Of course, there are several people here whose recommendation you might want; in the first instance Professors Brode and McMillan. I hope you will not mind my calling this matter to your attention, but I feel that if we can follow the suggestion I have made, all of us will be very happy and proud about it in the future. I cannot too strongly emphasize Feynman's remarkable personal qualities which have been generally recognized by officers, scientists and laity in this community.

With every good wish,

Robert Oppenheimer

"Stupid fools"

A friend sent me this letter from Feynman to Wolfram. Wolfram received a Caltech PhD in theoretical physics at the age of 20, before turning to other topics such as complexity and software development. Wolfram did not heed Feynman's advice: the next year he founded UIUC's Center for Complex Systems Research; then, in 1987, he formed Wolfram Research, the company responsible for Mathematica and, more recently, Wolfram Alpha.

I wish I had read this letter before taking my new job ;-)

CALIFORNIA INSTITUTE OF TECHNOLOGY
CHARLES C. LAURITSEN LABORATORY OF HIGH ENERGY PHYSICS

October 14, 1985

Dr. Stephen Wolfram
School of Natural Sciences
The Institute for Advanced Study
Princeton, NJ 08540

Dear Wolfram:

1. It is not my opinion that the present organizational structure of science inhibits "complexity research" - I do not believe such an institution is necessary.

2. You say you want to create your own environment - but you will not be doing that: you will create (perhaps!) an environment that you might like to work in - but you will not be working in this environment - you will be administering it - and the administration environment is not what you seek - is it? You won't enjoy administrating people because you won’t succeed in it.

You don’t understand "ordinary people." To you they are "stupid fools" - so you will not tolerate them or treat their foibles with tolerance or patience - but will drive yourself wild (or they will drive you wild) trying to deal with them in an effective way.

Find a way to do your research with as little contact with non-technical people as possible, with one exception, fall madly in love! That is my advice, my friend.

Sincerely,

(Signed, 'Richard P. Feynman')

Richard P. Feynman

Wednesday, March 20, 2013

Roe's scientists

Some years ago I posted on Harvard psychologist Anne Roe's study of eminent scientists. Roe's 64 scientists -- selected in their 40's and 50's for outstanding research contributions -- scored much higher on a set of high ceiling psychometric tests than the general population of scientists or PhDs.

A reader directed me to an archive of Roe's papers, maintained by the American Philosophical Society. An inventory reveals the identities of Roe's subjects. Physicists will recognize names such as Luis Alvarez, Julian Schwinger, Wendell Furry, J.H. Van Vleck and others. Also in the group were Carleton Coon, B.F. Skinner, Linus Pauling and Sewall Wright.

Allport, Gordon W.(Gordon Willard), 1897-1967
Alvarez 1911-1988, Luis Walter
Anderson, Edgar, 1897-1969
Babcock, Horace W., 1912-2003
Beach, Frank A., (Frank Ambrose), 1911-1988
Beadle, George Wells, 1903-1989
Beams, Jesse W., (Jesse Wakefield), 1898-1977
Bearden, J.A. (Joyce Alvin), 1903-1987
Bonner, James Frederick, 1910-1996
Bruner, Jerome S. (Jerome Seymour), 1915-
Cleland, Ralph E., (Ralph Erskine), 1892-1971
Coon, Carleton S., (Carleton Stevens), 1904-1981
Corner, George Washington, 1889-1981
Doisy, Edward Adelbert, 1893-1986
Epling, Carl, 1894-1968
Ewing, W. Maurice, (William Maurice), 1906-1974
Furry, W.H. (Wendell Hinkle) , 1907-1984
Guilford, J. P. , (Joy Paul), 1897-1987
Hallowell, A. Irving , (Alfred Irving), 1892-1974
Hansen, William Webster, 1909-1949
Harlow, Harry Freerick, 1905-1981
Hilgard, Ernest R., (Ernest Ropiequet), 1904-2001
Joseph Edward, Mayer, 1904-1983
Kirkwood, John Gamble, 1907-1959
Kluckhohn, Clyde, 1905-1960
Knudsen, Vern Oliver, 1893-1974
Lashley, Karl Spencer, 1890-1958
Lindsey, Donald B.
Linton, Ralph, 1893-1953
Mayer, Joseph Edward, 1904-1983
McMillan, Edwin M. (Edwin Mattison), 1907-1991
Morse, Philip M., (Philip McCord), 1903-1985
Mueller, J. Howard, (John Howard), 1891-1954
Muller, H. J., (Hermann Joseph), 1890-1967
Mulliken, Robert Sanderson, 1896-1986
Muskat , M. (Morris) , 1906-1998
Northrop, John Howard, 1891-1987
Pauling, Linus, 1901-1994
Rhoades, Marcus M., (Marcus Morton), 1903-1991
Ritcher, Curt Paul, 1894-1994
Robbins, William Jacob, 1890-1978
Robertson, H. P., (Howard Percy), 1903-1961
Roe, Anne, 1904-1991
Rogers, Carl R., (Carl Ransom), 1902-1987
Romer, Alfred Sherwood, 1894-1973
Schwinger, Julian Seymour, 1918-1994
Sears, Robert R., (Robert Richardson)
Shapiro, Harry L., (Harry Lionel), 1902-1990
Skinner, B. F. (Burrhus Fredric), 1904-1990
Smith, Homer William, 1895-1962
Sonneborn, T.M., (Tracy Morton), 1905-1981
Stanley, Wendell M., (Wendell Meredith), 1904-
Stebbins, G. Ledyard, (George Ledyard), 1906-2000
Stevens, S. S., (Stanley Smith), 1906-1973
Stewart, Homer Joseph, 1915-2007
Stratton, Julius Adams, 1901-1994
Strong, William Duncan, 1899-1962.
Sturtevant, A.H. (Alfred Henry), 1891-1970
Tuve, Merle Antony, 1901-1982
Van Vleck, J. H., (John Hasbrouck), 1899-1980
Willey, Gordon R., (Gordon Randolph), 1913-2002
Wright, Sewall, 1889-1988

Sunday, March 17, 2013

Genetic Architecture of Intelligence

Video from a talk I gave recently at the Cognitive Science Forum at MSU. This is a more reliable source of information about the BGI intelligence study than coverage in the popular media  :-(


Saturday, March 16, 2013

Dreams from my children

My kids made these posters in art class. I didn't know my son aspired to be a mathematician  :-)



In the backyard.


Sunday, March 10, 2013

Inside the 1%

The figures below are from a recently released IRS study using 2007 data (the most recent available; note this is pre-2008 credit crisis). The study focuses on the top 1% of adults by wealth (net worth of at least $2M or so). Medians and means differ by a lot, which is explained by the distribution in the bottom figure. Click for larger images.




About 50% of the top 1% in wealth are over 60. Having $2M saved up for retirement is not nearly as unusual as, e.g., having accumulated $2M before age 50.



Net worth distribution within the population of top wealth holders (assets > $2M; about top 1% of adult population): having $10M puts you in the 90th percentile (so, top 0.1% of total population) and $50M puts you in the 99th percentile (top 0.01% of total population).




See also Real Wealth: "Most of those in the bottom half of the top 1% lack power and global flexibility and are essentially well-compensated workhorses for the top 0.5%, just like the bottom 99%. In my view, the American dream of striking it rich is merely a well-marketed fantasy that keeps the bottom 99.5% hoping for better and prevents social and political instability."

Friday, March 08, 2013

It's all in the gene: myostatin and racehorses

"Horses ain't like people, man, they can't make themselves better than they're born. See, with a horse, it's all in the gene. It's the f#cking gene that does the running. The horse has got absolutely nothing to do with it." --- Paulie (Eric Roberts) in The Pope of Greenwich Village.

For more on myostatin mutations in people and dogs, see here.

The genetic origin and history of speed in the Thoroughbred racehorse

Nature Communications 2012 Jan 24;3:643. doi: 10.1038/ncomms1644

Abstract
Selective breeding for speed in the racehorse has resulted in an unusually high frequency of the C-variant (g.66493737C/T) at the myostatin gene (MSTN) in cohorts of the Thoroughbred horse population that are best suited to sprint racing. Here we show using a combination of molecular- and pedigree-based approaches in 593 horses from 22 Eurasian and North-American horse populations, museum specimens from 12 historically important Thoroughbred stallions (b.1764-1930), 330 elite-performing modern Thoroughbreds and 42 samples from three other equid species that the T-allele was ancestral and there was a single introduction of the C-allele at the foundation stages of the Thoroughbred from a British-native mare. Furthermore, we show that although the C-allele was rare among the celebrated racehorses of the 18th and 19th centuries, it has proliferated recently in the population via the stallion Nearctic (b.1954), the sire of the most influential stallion of modern time, Northern Dancer (b.1961).
From the paper:
Athletic phenotypes are influenced markedly by environment, management and training; however, it has long been accepted that there are underlying genetic factors that influence a horse’s athletic performance capabilities. Indeed, selection and breeding of racehorses is predicated on the belief that racing performance is inherited. Although the physiological adaptations to elite athleticism and exercise are well described for the Thoroughbred, few genes have been identified to explain these traits. In humans more than 200 genes have been reported to be associated with fitness-related health and exercise traits17, and it is likely that racing performance in the Thoroughbred is also polygenic and is influenced by genes that contribute to the wide range of anatomical, metabolic and physiological adaptations that enable elite-racing performance. The athletic potential of a racehorse will therefore depend on a favourable environment as well as inheriting the optimal combination of DNA variants at loci that significantly affect exercise.

Recently, variation at the MSTN locus has been found to be highly predictive of genetic potential for race distance aptitude in Thoroughbred racehorses18–21 and contributes to morphological type in other horse breeds22. The MSTN locus is associated with muscle hypertrophy phenotypes in a range of mammalian species23–27 and a single nucleotide polymorphism (SNP, g.66493737C/T) located in the first intron of the MSTN gene influences speed in the Thoroughbred19. Thoroughbred homozygous C/C horses are best suited to fast, shortdistance, sprint races (1,000–1,600m); heterozygous C/T horses compete favourably in middle-distance races (1,400–2,400m); and homozygous T/T horses have greater stamina (>2,000m). Evaluation of retrospective racecourse performance, physical growth and stallion progeny performance has demonstrated that C/C and C/T horses are more likely to be physically precocious and enjoy greater racecourse success as 2-year-old racehorses than T/T horses19,28.

These findings have been subsequently validated in three independent genome-wide association (GWA) studies18,20,21 in populations of Thoroughbreds originating in Ireland, Great Britain, New Zealand20, USA18 and Japan21. The singular, genomic influence on optimum race distance at the MSTN locus in the Thoroughbred is supported by a high heritability for race distance (h2=0.94)29. Further evidence for the role of chromosomes containing the C-allele in influencing speed comes from association tests with field-measured speed indices30 and from previous analysis of g.66493737C/T genotypes in the Quarter Horse, for which a high frequency of C/C homozygotes (0.83) has been reported19. The Quarter Horse is a North-American breed that excels at sprinting over distances of a quarter of a mile (400m) or less. Because of the specificity of its role in short-distance racing, this breed has undergone intense selection for speed since its foundation in the mid-1800s.

Innocent abroad? Frampton alive



Theoretical physicist Paul Frampton was recently convicted by an Argentine court of smuggling cocaine, and sentenced to 4 years in prison. Frampton maintains he was duped into transporting the cocaine by a bikini model he had met online. I am unsure as to the facts in the case but I can say that the portrait of Paul in the article is fairly accurate. He remains, for the moment, a professor at UNC-Chapel Hill.

Here is a 2008 paper I wrote with Frampton: What is the entropy of the universe? See also Supermassive black holes and the entropy of the universe.
NYTimes: ... As Frampton tells it, his life is one unbroken line of impressive grades, advanced degrees and innumerable citations of his work in cosmology and physics. There is certainly much truth to this. “He has always been very inventive in thinking of new ideas extending and going beyond the standard model of particle physics,” says Prof. Edward Witten of the Institute for Advanced Study at Princeton. But then there is Frampton’s tendency to transfer his professional accomplishments to his personal life. In what a fellow physicist described as a “very vain, very inappropriate” talk delivered on the 80th birthday of Murray Gell-Mann, a Nobel laureate in physics, Frampton veered into autobiography, recounting how his ability to multiply numbers in his head at 4 led him to see himself as “cleverer than Newton.” This line became a refrain throughout the talk. Interspersed with the calculations and hypotheses were his Oxford grades, which, he said, showed that he, like Newton, was in the top 1 percentile for intelligence. Frampton insists that he was merely joking and that his sense of humor was misinterpreted as self-regard. Yet in many of my conversations with him, he seemed to cling to the idea of his own exceptionalism. During our first meeting, when I asked him what attracted him to Milani, he said, “Not to offend present company,” referring to me and the representative from the penitentiary service, “but, to start with, she’s in the top 1 percentile of how women look.” And in an e-mail to Milani — or, rather, the fake Milani — Frampton wrote, “As these days tick by, and I think about it a lot, the more I realize that we are the perfect couple in all respects.”

The strategy of Frampton’s defense team was to present Frampton as a brilliant man out of touch with day-to-day life. They called in a psychologist, who pronounced him unusually gullible without, however, diagnosing a mental illness. The judges sent their own doctor, who declared Frampton normal. A total of three psychological evaluations were presented at the trial, and two agreed that he had the traits of a narcissistic personality — an overblown and unrealistic image of himself. One concluded that it did not constitute a pathology, while the other suggested that there were pathological aspects to his narcissism that led to gaps in his understanding of reality.

Fidel Schaposnik, a physics professor at the National University of La Plata, which, along with the University of Buenos Aires, had offered Frampton a visiting professorship to help get him released from Devoto while he awaited trial, said of Frampton: “He’s a typical person trained at Oxford. He knows he’s part of an elite and can’t imagine such things would happen to him.” Indeed, Frampton sees academia’s denizens as creative misfits who deserve special protection. “People who are socially inept can nevertheless be the most creative people,” he told me one afternoon on the telephone. “It’s very important that they can’t be fired. This is the genius of tenure.”

Synthetic biology and the hype cycle



Hype cycle (Wikipedia). Let's hope synthetic biology can someday reach the plateau ...
Chronicle: ... The cost of genetic sequencing and synthesis continues to plunge, but the functions of many genes in even the simplest forms of life, like bacteria and yeast, stubbornly hold on to their secrets. Genetic networks interact in complex, mysterious ways. Engineered parts take wild, unexpected turns when inserted into genomes. And then evolution, a system that would drive any electrical engineer mad, tiptoes in.

As synthetic biology passes from precocious youth toward maturity, it is returning home to academe. Collins sees an upside to that retrenchment: The science, once a domain of biological amateurs and outsiders, can now inform basic research into life's unending complexity.

Trim and tall, Collins, 47, has had a remarkable rise. A former physicist who, until the late 1990s, knew little about molecular biology, he wears his laurels—MacArthur "genius," Rhodes scholar, Howard Hughes investigator—lightly. If you're outside the field, you'd have little idea he's considered a founder of synthetic biology.

But what is the field, exactly? As one engineer once quipped, ask five people the definition of synthetic biology, you'll get six different answers, because one person is bound to be conflicted. It's a field where most of its practitioners consider its most visible success—Craig Venter and company's wiring together of a microbial genome in 2010—to be an impressive technical feat, but not synthetic biology. The phrase has subsumed whole disciplines. Many scientists who once practiced genetic engineering, methods relatively unchanged, now operate under the grant-friendly halo of synthetic biology. ...

"The hype is a thing that's hurt the field," Collins said. "Some in the community are hyping our capabilities well beyond where we're at. I think it's better to be a bit sober. I think it's fine to speak to emerging applications and emerging capabilities, but to really qualify where we are at and what we can do now, versus what might this field bring decades down the line."
Don't miss the comments at the Chronicle, if you can stomach a view into modern hype-driven science. Contrast to the painstaking accumulation of statistical significance leading up to a Higgs announcement!
The problem with synthetic biology is characterization. This takes time and isn't sexy. I did it for 3 years, trying to properly characterize different promoter, reporter combinations. I painstakingly ground out a bit of data, but not enough for publication, and a career over before it ever began. In the era of publish or perish you quickly ligate genetic elements together, take a few quick measurements, and bang it out to the journals with a few headline grabbing keywords in the abstract. When the rubber hits the road with biotech or medical applications, the wheels fall off the wagon. Much of it could be attributed to "show boating", but in the fight for funding, the hype machine has to go into over-drive. I saw the same wave of hysteria in systems biology, and it carried on into synthetic biology, and it will move into the "big thing". But what do you do? Play down your work in the media frenzy world we live in, or go for broke?
I was very suspicious of the synthetic biology hucksters I first encountered five years or so ago, and it turns out my instincts were correct.

Glial cells for Algernon



See also Flowers for Algernon.
Forebrain Engraftment by Human Glial Progenitor Cells Enhances Synaptic Plasticity and Learning in Adult Mice

Human astrocytes are larger and more complex than those of infraprimate mammals, suggesting that their role in neural processing has expanded with evolution. To assess the cell-autonomous and species-selective properties of human glia, we engrafted human glial progenitor cells (GPCs) into neonatal immunodeficient mice. Upon maturation, the recipient brains exhibited large numbers and high proportions of both human glial progenitors and astrocytes. The engrafted human glia were gap-junction-coupled to host astroglia, yet retained the size and pleomorphism of hominid astroglia, and propagated Ca2+ signals 3-fold faster than their hosts. Long-term potentiation (LTP) was sharply enhanced in the human glial chimeric mice, as was their learning, as assessed by Barnes maze navigation, object-location memory, and both contextual and tone fear conditioning. Mice allografted with murine GPCs showed no enhancement of either LTP or learning. These findings indicate that human glia differentially enhance both activity-dependent plasticity and learning in mice.

Thursday, March 07, 2013

US wealth inequality

This is a great example of the visual presentation of quantitative information.



One quibble: I suspect that the top 1% individual discussed near the end has wealth equal to the average among the top 1%, which is strongly distorted by individuals at, e.g., the top 0.1% level. If they used threshold 1% wealth the result would not be as dramatic.

It's also important to note that there is a 30+ year lever arm influencing average wealth -- relatively modest disparities in annual income can, when combined with differentials in investment,  consumption, etc., result in substantial differences in accumulated average wealth.

See also Real wealth.

Wednesday, March 06, 2013

Gell-Mann, Feynman, Hawking

Murray Gell-Mann on his relationship with Feynman.



See also Gell-Mann, Feynman, Everett.

I had only one memorable encounter with Murray while I was a student at Caltech. On the other hand I have quite a few memories of Feynman, who enjoyed interacting with students. I don't really blame Murray for not being particularly interested in students. The gap between him and us must have been (and still is) quite vast :-)

Hawking was on campus and was giving a kind of "secret" (not advertised) seminar in the medium sized lecture room on the second floor of Lauritsen. In those days Hawking could sort of talk, although only people who had worked closely with him could understand what he was saying. Nick Warner, at that time a postdoc at Caltech, was Hawking's interpreter. Hawking would gurgle briefly, and Nick would translate (decompress?) the message as Consider a 4-manifold endowed with a metric ...  drawing a blob on the blackboard and even writing equations. I could never figure out how this communication worked because what Nick said was so much more elaborate than the brief gurgle from Hawking. Perhaps the gurgle messages were something like Give the setup for the no-boundary wavefunction on a Euclidean 4-manifold!

They were filming the lecture for a documentary. A statuesque blonde woman in a tank top and jeans was holding a boom mike (microphone attached to long white plastic tube), standing in the aisle next to my seat. To keep the mike off camera she had both arms extended above her head with her chest thrust forward in a dramatic posture. Murray was seated directly ahead of me, and he couldn't keep his eyes on the lecture. He spent the first 15 minutes craning his neck to look at the chest display of boom mike girl. But he must have been half listening because at some point he got agitated about what Nick was saying and jumped up to disagree. He ran to the blackboard and hijacked the lecture from the postdoc and the guy in a wheelchair to explain his ideas about the wavefunction of the universe. After holding the speaker, interpreter and audience hostage for about 10 minutes, he relinquished the chalk and sat back down to resume peeking over his shoulder. That's my most vivid memory of Murray.

Friday, March 01, 2013

A Greek bearing gifts

Another great Econtalk podcast.
Yanis Varoufakis of the University of Athens, the University of Texas, and the economist-in-residence at Valve Software talks with EconTalk host Russ Roberts about the unusual structure of the workplace at Valve. Valve, a software company that creates online video games, has no hierarchy or bosses. Teams of software designers join spontaneously to create and ship video games without any top-down supervision. Varoufakis discusses the economics of this Hayekian workplace and how it actually functions alongside Steam--an open gaming platform created by Valve. The conversation concludes with a discussion of the economic crisis in Europe.
Varoufakis is a lot of fun. Listen for his opinions on academic economics, the euro crisis, the meaning of life, happiness, and other topics.
Russ: Well, yeah. I think calculation is over-rated generally. But that puts me in a minority in the profession. The profession is going in the other direction don't you think?

Guest: Of course. Catastrophically so. And there is a fundamental difference between the social sciences and the real sciences. In the real sciences, if you tell me that Person X has published 30 articles in Nature or Science, I am prepared to take it for granted that they are very good physicists. But in our neck of the woods ... that's not necessarily the case. [ Actually physicists tend not to publish in Nature or Science, rather Physical Review or similar ... ]

Russ: I agree with you. But we are in the minority. Why do you think that has happened?

Guest: Oh, it goes back a long way. It goes back to the 1879s and 1880s, when economists entered the universities. Because they needed to prove that they are the scientists of society. And they had, they created a false science whereby classical mechanics of the 19th century were copied into mathematical models of exceptional complexity--and aesthetic beauty--and the only way of closing them, of solving the mathematics that was created, was by making assumptions which ensure that these models have nothing to do with real capitalism. So the more successful you were in creating these models which gave you discursive power and academic power in the corridors of economics departments, the more irrelevant you were in explaining the real world. It is a very peculiar failure. [ See also Brad DeLong Confessions of an economist. ]

Russ: Yeah. I have a little bit of mixed feelings about it. I think we've gone down the wrong path. And my preference would be to go back to Adam Smith. I think he had the right path, which is descriptive, narrative. I think we're more like historians than physicists and we should admit it.

Guest: Indeed. We should go back to the classical economics tradition. Whatever your political or ideological or methodological take is, I think it is exceptionally worrying to all intellectuals, who think things through, that today, Adam Smith, David Ricardo, John Stuart Mill, Karl Marx, Friedrich Hayek, even John Maynard Keynes, would never get a job at Harvard University's Economics Department. Never. Under no circumstances.

Russ: It's true.

... [Great discussion of the euro crisis] ...

... a Great Depression, in the periphery of Europe. Which already is happening in places like Greece and Spain. [?] unemployment can reach 30% soon. It's unbelievable in this day and age that we should have such unemployment rates. And this is a self-reinforcing depression in places like Greece and Spain. Either the Euro is going to break up, or you can have a large part of Europe being turned into Kosovo-like protectorates. ... But I think that the Eurozone is not going to survive that because the political pressure in places like proud nations like Italy and Spain are going to be such that the whole thing is simply going to go belly up. But the reason why we are having all this, just to cut to the chase, is because in 2010 when a country like Greece, like the Greek state went bankrupt, was that Europe refused to allow it to default within the Eurozone. This was just a crime ...

Greece had a debt that was unsustainable; and so as to make sure that Deutschebank ... wouldn't suffer more than they would have to, even though they were themselves insolvent, and relied on the generosity of the German and the French taxpayers, the largest loan in history was piled upon the shoulders of the weak and bankrupt Greek state. This was effectively a con job. The German electorate was being told that this was an act of solidarity towards the Greeks. When in reality all that was happening was that the losses of Deutschebank were being piled on the shoulders of the German taxpayers. ... Guest: The German taxpayers realized that. And when the German taxpayers realized that, they hated the Greeks; and the Greeks hated the Germans. And we've lost the plot completely. The only beneficiaries of that are the Nazis.

While we fight over $9 or $10 minimum wage, high g game designers and coders enjoy the work environment described below.
[Russ Roberts:] I'm going to read another excerpt here from the [Valve] Employee Handbook. It's subtitled "The Office." It says:

Sometimes things around the office can seem a little too good to be true. If you find yourself walking down the hall one morning with a bowl of fresh fruit and Stump-town-roasted espresso, dropping off your laundry to be washed, and heading into one of the massage rooms, don't freak out. All these things are here for you to actually use. And don't worry that somebody's going to judge you for taking advantage of it--relax! And if you stop on the way back from your massage to play darts or work out in the Valve gym or whatever, it's not a sign that this place is going to come crumbling down like some 1999-era dot-com start-up. ...

I wonder why I wonder why

Chris Adami joins the blogosphere! Let's hope the long post linked to below is a harbinger of more to come. Chris started in theoretical physics but has since migrated into areas like artificial life, evolution and neuroscience. See also Brain, Mind, Evolution.
Your conscious you: ... After all this mathematics is done, we are left with a number that Tononi calls "Phi" (also the title of his most recent book), which characterize the capacity of any computing machinery to integrate information. What does this construction do for you? Right now, nothing of course. But imagine Tononi could record the activity patterns of your brain as you read this... shall we call it a blog? Phi could tell you if you are dreaming or in dreamless sleep, because your brain integrates information only during dreaming sleep. In the dreamless sort, you are unconscious, you have no experience at all. And as it so happens, Tononi is in a position to make precisely these types of measurements, as the director of a sleep laboratory. But this is not where the usefulness of Phi ends. If Phi can measure whether or not you are conscious, then shouldn't it be able to determine whether people in a comatose state are in a vegetative state without any consciousness at all, or else in a so-called locked-in state, fully conscious but unable to communicate this state to the outside world (think "The Diving Bell and the Butterfly")? There is now some evidence that Phi can distinguish between vegetative and conscious states but definitive proof will only be available when we can record from brains in more sophisticated ways than we can do today.

"Fine" you say, "I grant you that there may be a way to measure whether a computing machine integrates, or just reproduces, information". "Unless I'm caught in a coma, why should I care?"

And I tell you in return: "You have forgotten the first half of this blog post haven't you, where I insisted that evolution--the process that knows not what it designs--can do things that people can't do." Yes, that's right: evolution can create computational systems that integrate information at high levels, because evolution is not concerned with beautiful, predictable design. Evolution is messy, opportunistic, and unpredictable. Evolution takes what works and runs with it, whether it is neat or not, whether it adheres to design standard ISO9000 or not. More importantly, evolution creates designs that wastes as little as possible, reusing the same components over and over, and doing all these things at the same time. As a result, evolved computing systems integrate information. At a massive scale.

So, what makes natural computing machines such as brains interesting is information integration, and from what we know today, this level of integration cannot be achieved by design. What should we learn from this? Well, I think you beat me to it, this time. We should use evolution as the process that leads us toward the undesignable, toward the computer that integrates (for reasons of expediency only) to such an extent that the objects it perceives don't just evoke a reaction, they evoke an experience. There is a good reason we should expect experiences to be selected for: they allow the recipient of the experience to make better predictions about the future, and further the survival of the species that has these experiences.

I wonder why I wonder why. I wonder why I wonder. I wonder why I wonder why I wonder why I wonder! —Richard Feynman

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