Friday, September 30, 2011

Market solution for PhD advising

I knew the author of this article when she was an assistant professor at UO. Since then, she moved to UIUC (Illinois), received tenure, became a department head, left academia and moved back to Eugene. Her web site.

Karen, stop by and see us some time! :-)

Chronicle of Higher Education:

Dear faculty members:

I sell Ph.D. advising services on the open market. And your Ph.D. students are buying. Why? Because you're not doing your job.

Lest you think that by advising, I mean editing research papers and dissertations, let me disabuse you. I offer those services, but rarely am I asked for them.

A former tenured professor at a major research university, I am now running an academic-career consulting business. That's right: I am doing graduate advising for pay. I am teaching your Ph.D. students to do things like plan a publishing trajectory, tailor their dissertations for grant agencies, strategize recommendation letters, evaluate a journal's status, judge the relative merits of postdoctoral options, interpret a rejection, follow up on an acceptance, and—above all—get jobs. And business is so good I'm booked ahead for months. ...

See Advice to a new graduate student.

Soros: nationalize European banks

Soros outlines his proposal for solving the eurozone crisis. It seems to me that the best informed people are the most alarmed by the current situation. I notice Pimco just went into "risk-off" mode.

Financial Times: Financial markets are driving the world towards another Great Depression. The authorities, particularly in Europe, have lost control of the situation. They need to regain control and they need to do so now.

Three bold steps are needed. First, the governments of the eurozone must agree in principle on a new treaty creating a common Treasury for the eurozone. In the meantime, the main banks must be put under European Central Bank direction in return for a temporary guarantee and permanent recapitalisation. The ECB would direct banks to maintain credit lines and outstanding loans, while closely monitoring risks taken for their own accounts. Third, the ECB would enable countries such as Italy and Spain to temporarily refinance themselves within limits at a very low cost. These steps would calm markets and give Europe time to develop a growth strategy, without which the debt problem cannot be solved.

[ More privatizing gains and socializing losses? ]

... This course of action does not require leveraging or increasing the size of the EFSF but it is more radical because it puts the banks under European control. That is liable to arouse the opposition of both the banks and the national authorities. Only public pressure can make it happen.

I'm not sure what the "growth strategy" would be. Despite what Keynes wrote, it's not easy for governments to simply order up (healthy, real) growth, even with checkbook in hand. I'm with Hayek that this kind of growth is something you might pay for dearly in the long run. In addition, governments are running out of ammunition.

*** I realize that what Soros proposes isn't exactly nationalization of at-risk banks. But ultimately the ECB and European taxpayers will assume responsibility for their prior investment decisions.

Wednesday, September 28, 2011

The next lost decade?

Satyajit Das on what's ahead in the eurozone: video

Possible chain of events: More pain ahead for Greece, culminating in a big write down for its creditors. ECB solvency challenges. Sovereign debt crises for Italy and Spain. Global recession followed by debt deflation. A lost decade worse than what Japan experienced in the 1990s.

Larry Summers interview with Martin Wolf: video

Amazon Silk

I wonder what Apple's response will be to this. Perhaps we'll see a "split-browser" update of (mobile) Safari soon. On the desktop I switched over to Chrome 1-2 years ago because it feels faster and it runs Google apps flawlessly. If Silk tries to do things too aggressively it might break a few applications or web pages (very tough to QA stuff like that). But probably there are speedups (e.g., smart pre-caching of popular content) that can be achieved without risk of breaking functionality and which can be exploited within a more conservative approach. Users will probably be forgiving because it's running on a $199 device with a 7" screen (Amazon Fire). The Silk team blog is here.

Sunday, September 25, 2011

Papa's life

A fine essay on Hemingway by James Salter, a review of the new book by Paul Hendrickson.

NY Review of Books: ... From his father, who loved the natural world, Hemingway learned in childhood to fish and shoot, and a love of these things shaped his life along with a third thing, writing. Almost from the first there is his distinct voice. In his journal of a camping trip he took with a friend when he was sixteen years old, he wrote of trout fishing, “Great fun fighting them in the dark in the deep swift river.” His style was later said to have been influenced by Sherwood Anderson, Gertrude Stein, Ezra Pound, journalism, and the forced economy of transatlantic cables, but he had his own poetic gift and also the intense desire to give to the reader the full and true feeling of what happened, to make the reader feel it had happened to him. He pared things down. He left out all that could be readily understood or taken for granted and the rest he delivered with savage exactness. There is a nervy tension in his writing. The words seem to stand almost in defiance of one another. The powerful early stories that were made of simple declaratives seemed somehow to break through into a new language, a genuine American language that had so far been undiscovered, and with it was a distinct view of the world.

... the sea, Key West, Cuba, all the places, the life he had and gloried in. His commanding personality comes to life again in these pages, his great charm and warmth as well as his egotism and aggression.

“Forgive him anything,” as George Seldes’s wife said in the early days, “he writes like an angel.”

Friday, September 23, 2011

Luttwak interview

Excerpts from an interview with Edward Luttwak.

... Kissinger at 88 is writing brochures for Kissinger Associates. His last book on China is one such work written by the staff at Kissinger Associates. It is designed to curry favor with the Chinese authorities and nothing else.

I know him personally very well, but he is such a deceptive person; he’s a habitual liar and dissembler. Although I’ve spent a lot of time talking to him, I have no insight on him at all. His book ends with a paean to U.S.-Chinese friendship and how every other country has to fit in. I have to review it for the TLS, but I’ve been delaying it by weeks because I don’t know whether it is a case of senility or utter corruption.

... Personally, from an emotional point of view, myself, as me, I prefer the Z.O.G. explanation above all others. I love the idea that the Zionists have sufficient power to actually occupy America, and through America to basically run the world. I love the idea of being a member of a secretive and powerful cabal. If you put my name Luttwak together with Perle and Wolfowitz and you search the Internet, you will get this little list of people who run the American government and the world, and I’m on it. I love that.

Are strategic minds nurtured through upbringing and education, or is the ability to think strategically an inborn gift, like mathematics? It’s a gift like mathematics. The paradoxical logic of strategy contradicts the logic of everyday life, it goes against all normal definitions of intelligence we have. It only makes sense if you understand the dialectic. If you want peace, prepare for war. If you actively want war, disarm yourself, and then you’ll get war. Virile and martial elites understand that kind of thinking instinctively.

[Putin] ... Obviously such a person is much more wily and cunning and able to handle conflict than his American counterpart. But when such a person is the head of a department, the whole department is actually paralyzed and they are all reduced to serfs and valets. Therefore, what gets applied to a problem is only the wisdom of the aforementioned wily head of the department. All the other talent is wasted, all the other knowledge is wasted.

Now you have a choice: You can have a non-wily head of a department and the collective knowledge and wisdom of the whole department, or else you can have a wily head and zero functioning. And that is how the Russian government is currently working. Putin and Medvedev have very little control of the Russian bureaucracy. When you want to deal with them, and I dealt with them this morning, they act in very uncooperative, cagey, and deceptive ways because they are first of all trying to protect their security and stability and benefits from their boss. They have to deceive you because they are deceiving their boss before he even shows up to work. And they are all running little games. So, that’s the alternative. You can have a wily Putin and a stupid government. Or an intelligent government and an innocent head. There’s always is a trade-off. A Putin cannot be an inspiring leader.

FTL neutrinos and stat arb


Thursday, September 22, 2011

Australian Aborigine genome

I was wondering when they would get around to this. Australian Aborigines are one of the most unique human populations. Many people have been curious about their genetics and deep history.

Although I was just recently at BGI (where this sequencing was done), no one told me anything about a hair sample!

See also Razib's discussion.

Science: We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

Confidence Men

A good interview with Ron Suskind about his new book Confidence Men. I believe what Suskind wrote about the Bush administration has been largely vindicated. Suskind comes across as very careful with his sourcing. (So does Joe McInnis in this interview about his Palin bio The Rogue.)

Careful scrutiny suggests it's mostly sociopaths at the top ;-)

Fresh Air: ... Suskind says Summers' style of leadership at the White House was to "control the show" and "lead by fiat."

"A young economist ... [once told me that Larry once said] 'Here's the way it works. ... I can win either side of the argument. That's my genius. That's what I do. And then I win both sides and I think about which side I won more fairly when deciding which is right. Sometimes I decide otherwise,' " says Suskind. "The young economist who recounts the story says, 'Jeez, Larry, that gives you an awful lot of power to shape everything,' and Larry sort of says, 'Yeah, that's the point.' And that's kind of how Larry sees it — the economic policy will be what Larry decides in consultation with a president who has very, very little in the way of training in economic theory or practice." In his book, Suskind quotes Summers as saying, on record, that "Clinton would never have made these mistakes" that the Obama administration made. Summers has denied making those comments. He told The Washington Post last week that "the hearsay attributed to me is a combination of fiction, distortion and words taken out of context. I can't speak to what others have told Mr. Suskind but I have always believed that the president has always led this country with determined, steady and practical leadership."

... Suskind tells Terry Gross that he talked to Summers as the book was going to press about his statements in the book, including the one where he said "Clinton would never have made these mistakes."

"At first Larry blurted out, 'I deny it,' and then I said, 'Look, Larry, lots of people heard you talk about this and say this. This is not something you uttered once to one person. Lots of people remember where they were when they heard it.' ... Then after a few minutes, he came back with his response. He said, 'Look, we had five times as many problems, we didn't have five times as many people. It was an overwhelming time, very difficult for everyone involved.' He lays it on the door of circumstances. ... The Washington walk back has a long history, as anyone who works in this town knows."

Monday, September 19, 2011

Passing the torch

From Fermi Remembered. The insightful biographical sketch at the beginning of the book, by Emelio Segre, includes details of Fermi's early (self) education and entry into Scuola Normale Superiore.
Murray Gell-Mann: When Fermi lay dying in Billings Hospital, I realized how much I cared for this brilliant, funny, difficult man. I was on leave in the East, and I invited Frank (C.N.) Yang to come with me to Chicago to see him. When we got to the bedside, Enrico kept telling us not to be downcast. "It is not so bad," he said. He told of a Catholic priest who had visited him and whom he had had to comfort. And Frank reminded me a few years ago of what Enrico said when we left, never to see him again. "Now, it is up to you."

Saturday, September 17, 2011

Talpiot and Israeli psychometrics

The other day I was discussing the Israeli Talpiot program with another Caltecher. I thought it would be great if we had a similar program in the US. He said it sounded like Ender's Game :-)

If anyone out there is an expert on the Israeli Psychometric Entrance Test (their SAT-equivalent), please contact me. We're trying to determine the +3 SD cutoff (relative to the US population) for our GWAS.

See earlier post on Talpiot and Israeli startups.

USAToday: ... The "Talpiot" program is perhaps the best reflection of the army's technological drive.

The unit, one of the most selective in the military, was formed in the wake of the 1973 war, when Israel was caught off guard and lost some 2,500 men.

"One of the lessons was that we need a technological edge over our enemies and we need to develop this edge from within," said Talpiot's commander, Maj. Amir Schlachet.

In Israel, where military service is mandatory, more than 5,000 young people apply to Talpiot each year, hoping to be among the 50 or so accepted. They must pass a grueling battery of tests in math, physics, group dynamics, leadership skills and intelligence.

The reward: a nine-year commitment, beginning with a 3½-year dual bachelor's degree program in mathematics and physics at Hebrew University in Jerusalem. Vacations are spent jumping out of airplanes and participating in other military exercises. Along the way, roughly one out of five soldiers leave the program, Schlachet said.

Those who survive go on to careers as officers in some of the military's most prestigious operations, mostly in research and development projects, Schlachet said. From there, the 500-odd Talpiot grads have tended to find their way to the upper echelons of business and academia, he said.

"You learn self-confidence, not to be afraid of anything. No subject is too complex to go after, and no answer should be taken for granted," said Talpiot grad Gilad Almogy, 38, Applied Materials' top executive in Israel.

The Nasdaq-traded biotech company Compugen was formed by three of Almogy's Talpiot comrades. A fourth, Mor Amitai, now runs the company.

Amitai says some of the most complicated work he ever did was during his time in Talpiot. "The experience of sometimes succeeding, almost always as part of a team, involving something that really seemed impossible, I think this is something we took with us," he said.

Wednesday, September 14, 2011

True grit

The next project with my colleague Jim Schombert is to see whether student personality inventories increase our ability to predict college GPA. In previous work we found a .4 or so correlation between SAT score and upper division in-major GPA. (Other studies, which focus on freshman GPA, typically find lower correlations but this is partly because academically stronger freshmen usually take harder courses. At the upper division level, majors typically have to take certain core courses, so there is more uniformity.) The correlation is somewhat higher (.5 to .6) if we use a z score derived from high school GPA and SAT. We think GPA is a proxy for conscientiousness, or what is referred to below as grit. But there is too much grade inflation in high school these days, and GPA depends both on work ethic and cognitive ability. So we'd like to see how well personality variables work. Optimistically, I think we can do better than correlations of .6, which is pretty impressive for social science.

NYTimes: ... People who accomplished great things, she noticed, often combined a passion for a single mission with an unswerving dedication to achieve that mission, whatever the obstacles and however long it might take. She decided she needed to name this quality, and she chose the word “grit.”

She developed a test to measure grit, which she called the Grit Scale. It is a deceptively simple test, in that it requires you to rate yourself on just 12 questions, from “I finish whatever I begin” to “I often set a goal but later choose to pursue a different one.” It takes about three minutes to complete, and it relies entirely on self-report — and yet when Duckworth took it out into the field, she found it was remarkably predictive of success. At Penn, high grit ratings allowed students with relatively low college-board scores to nonetheless achieve high G.P.A.’s. Duckworth and her collaborators gave their grit test to more than 1,200 freshman cadets as they entered West Point and embarked on the grueling summer training course known as Beast Barracks. The military has developed its own complex evaluation, called the Whole Candidate Score, to judge incoming cadets and predict which of them will survive the demands of West Point; it includes academic grades, a gauge of physical fitness and a Leadership Potential Score. But at the end of Beast Barracks, the more accurate predictor of which cadets persisted and which ones dropped out turned out to be Duckworth’s 12-item grit questionnaire.

[Of course, the grit score can't be used for admissions -- too easy to game, unlike an IQ test! Instead we use proxies for grit, like extracurriculars.]

... The first question Duckworth addressed, again, was the relative importance of I.Q. and self-control. She and her team of researchers gave middle-school students at Riverdale and KIPP a variety of psychological and I.Q. tests. They found that at both schools, I.Q. was the better predictor of scores on statewide achievement tests, but measures of self-control were more reliable indicators of report-card grades.

Duckworth’s research convinced Levin and Randolph that they should try to foster self-control and grit in their students. Yet those didn’t seem like the only character strengths that mattered. ... After a few small adjustments (Levin and Randolph opted to drop love in favor of curiosity), they settled on a final list: zest, grit, self-control, social intelligence, gratitude, optimism and curiosity.

Here's a figure from our paper Data Mining the University, which shows how SAT predicts GPA. The stars are over- and under-achievers (blue = male, red = female). Do the people in the upper left (over-achievers) have grit?

MMA and paleo

"From cave to cage: Mixed martial arts in ancestral health" by Tucker Max from Ancestry on Vimeo.

Via Seth Roberts. Beyond the technical coolness of MMA, I just like the idea that if you and I mix it up, you'll end up unconscious or with a broken limb.

Tuesday, September 13, 2011

US oligarchy net worth

Is this true? Let's say the top 400 families average a few billion each. Then the average net worth for the bottom 50 million families would have to be about $20-30k. Seems possible.

Guardian: ... In fact, so staggeringly unbalanced has America become that the richest 400 American families have the same net worth as the bottom 50% of the nation.

If this outrages or saddens you, I recommend Who rules America?

If you believe this is a just, pareto optimal outcome, I suggest graduate school in economics, perhaps in Chicago ;-)

Better beta?

It's rough at the top! But, better to reign in hell than serve in heaven.

I guess I'm an alpha trying to adapt to living beta. Nothing like a steep drop in testosterone level to help with this ...
WSJ: One evening a week, a group of CEOs meets in a Manhattan psychiatrist's office and engages in an ancient ritual. Ostensibly, it is a support group.

Inevitably, it becomes a battle for dominance."Whenever you put alpha males together, the most aggressive will overpower the others," says T. Byram Karasu, the veteran psychiatrist who has run the sessions for the past 23 years. The fighting is subtle, but it's vicious. "Even giving advice is geared toward lowering the others' self-esteem. Those at the lower end of the group come away doubting themselves, and their testosterone falls. They tell me they can't have sex for three or four days afterward."

Alpha males get the girls, but beta males have fewer stress-related health problems, at least among baboons, according to a recent Princeton study. As Melinda Beck explains on Lunch Break, that appears to have health consequences for humans, too.

It isn't easy being an alpha male. Getting to the top and staying there takes a physical toll.

The latest evidence comes from wild baboons in Kenya's Amboseli basin. Researchers from Princeton and Duke universities studied 125 males in five groups over nine years and found that while the alpha males got the best food and the most mates, they experienced far more stress than the beta males just beneath them in the hierarchy, based on the levels of cortisol, a stress hormone, in fecal samples.

The beta males had almost as many mates and got just as much grooming from others, but they didn't have to spend as much time fighting or following females around to keep other males away.

"Being an alpha is exhausting. I'd rather be a beta," says Laurence Gesquiere, lead author of the study that appeared in the journal Science in July.

In the human savannah, where smarts matter more than brute strength, alphas run companies, amass fortunes and dominate any meeting they're in. They are ambitious, assertive, confident and competitive. "You can smell it in about 30 seconds," says Dr. Karasu, who is psychiatrist-in-chief of Montefiore Medical Center in New York.

... Beta males, by contrast, are nice guys, peacemakers and team players. They make good husbands, fathers and friends. Some experts say they tend to be happier than alphas, since they aren't driven by the need to be on top. Betas can come in many forms—from competent wingmen to extreme introverts who are so determined to avoid conflict they suffer anxiety of their own.

Many observational studies of people and primates have shown that, in general, it's more stressful at the bottom of the social hierarchy than the top. Two long-running studies of British civil-service workers found that people in the lowest ranks had many more health problems and were three times as likely to die as the highest-grade administrators in a 10-year period—even though they all had access to health-care services.

To date, there have been few studies assessing whether human alphas or betas are healthier. ...

Alpha quiz:

Masters of the Universe

In the work world, alpha males are ambitious, assertive, confident and competitive. Here's a quiz that helps define who's an alpha male:

Alpha Strengths

1. No matter what, I don't give up until I reach my end goal.
2. I always say exactly what I think.
3. I have no problem challenging people.
4. I make the decision I believe is correct, even when I know other people don't agree.
5. I seldom have any doubts about my ability to deliver.

Alpha Risks

1. I believe that my value is defined by the results I achieve.
2. I don't care if my actions hurt people's feelings, if that's what's required to produce results.
3. When people disagree with me, I often treat it as a challenge or an affront.
4. If I have a good idea and I'm asked to hold off and listen to inferior ideas, I can quickly become visibly annoyed.
5. People say I become curt, brusque, or frustrated when I have to repeat myself.


If all or nearly all of your responses to statements 1 to 5 were "yes," you are probably an alpha with many of the strengths that make alphas such dynamic and influential leaders.

Monday, September 12, 2011

Fatherhood suppresses testosterone

No wonder I feel so wimpy :-(

NYTimes: ... Testosterone was measured when the men were 21 and single, and again nearly five years later. Although testosterone naturally decreases with age, men who became fathers showed much greater declines, more than double the childless men.

And men who spent more than three hours a day caring for children — playing, feeding, bathing, toileting, reading or dressing them — had the lowest testosterone.

Below is the abstract from the original paper (PNAS).

In species in which males care for young, testosterone (T) is often high during mating periods but then declines to allow for caregiving of resulting offspring. This model may apply to human males, but past human studies of T and fatherhood have been cross-sectional, making it unclear whether fatherhood suppresses T or if men with lower T are more likely to become fathers. Here, we use a large representative study in the Philippines (n = 624) to show that among single nonfathers at baseline (2005) (21.5 ± 0.3 y), men with high waking T were more likely to become partnered fathers by the time of follow-up 4.5 y later (P < 0.05). Men who became partnered fathers then experienced large declines in waking (median: −26%) and evening (median: −34%) T, which were significantly greater than declines in single nonfathers (P < 0.001). Consistent with the hypothesis that child interaction suppresses T, fathers reporting 3 h or more of daily childcare had lower T at follow-up compared with fathers not involved in care (P < 0.05). Using longitudinal data, these findings show that T and reproductive strategy have bidirectional relationships in human males, with high T predicting subsequent mating success but then declining rapidly after men become fathers. Our findings suggest that T mediates tradeoffs between mating and parenting in humans, as seen in other species in which fathers care for young. They also highlight one likely explanation for previously observed health disparities between partnered fathers and single men.

Saturday, September 10, 2011

Labor and Capital in 21st century America

Bill Gross of PIMCO writes:

During this country’s recent economic “recovery,” real corporate profits increased by four times the amount of working wages in dollar terms, and, as the chart below shows, are 50% higher than at the turn of the century while wages remain relatively unchanged, something that has not occurred since this country’s nuptials were concluded over three centuries ago. Is it any wonder that preliminary battlefield skirmishes in Wisconsin and Ohio between labor and capital promise to spread across every state of this land? (Not Texas!) Is it any wonder that Republican orthodoxies favoring tax cuts for the rich and Democratic orthodoxies promoting entitlements for the poor threaten to hamstring any constructive efforts to reduce unemployment over the foreseeable future?

[See comments, where it is suggested Gross might be wrong on the facts.]

Thursday, September 08, 2011

In transit: HK

Sunrise over China.

Red Carpet Club, HK airport.

I've never liked HK, but the infrastructure here is first rate.

Wednesday, September 07, 2011

BGI photos

I've now lost track of how many times I've been here.

$10 million in sequencing machines in this room ($500k Illumina HiSeqs). But I think they're just for training. There are a hundred more at the HK lab.

An old poster. Monitor Group report whose cover is depicted.

Amusing signage (if you can read Chinese). Note the Gattaca background.

Shooting interviews for the documentary on our research project.

The dreaded baijiu. This brand is called "Red Star"!

Monday, September 05, 2011

Advice to a new graduate student

A friend who is starting graduate school asked for some advice.

1. There is often a tradeoff between the advisor from whom you will learn the most vs the one who will help your career the most. Letters of recommendation are the most important factor in obtaining a postdoc/faculty job, and some professors are 10x as influential as others. However, the influential prof might be a jerk and not good at training students. The kind mentor with deep knowledge or the approachable junior faculty member might not be a mover and shaker.

2. Most grad students fail to grasp the big picture in their field and get too caught up in their narrowly defined dissertation project.

3. Benchmark yourself against senior scholars at a similar stage in their (earlier) careers. What should you have accomplished / mastered as a grad student or postdoc in order to keep pace with your benchmark?

4. Take the opportunity to interact with visitors and speakers. Don't assume that because you are a student they'll be uninterested in intellectual exchange with you. Even established scholars are pleased to be asked interesting questions by intelligent grad students. If you get to the stage where the local professors think you are really good, i.e., they sort of think of you as a peer intellect or colleague, you might get invited along to dinner with the speaker!

5. Understand the trends and bandwagons in your field. Most people cannot survive on the job market without chasing trends at least a little bit. But always save some brainpower for thinking about the big questions that most interest you.

6. Work your ass off. If you outwork the other guy by 10%, the compound effect over time could accumulate into a qualitative difference in capability or depth of knowledge.

7. Don't be afraid to seek out professors with questions. Occasionally you will get a gem of an explanation. Most things, even the most conceptually challenging, can be explained in a very clear and concise way after enough thought. A real expert in the field will have accumulated many such explanations, which are priceless.

Please feel free to contribute your own advice!

Sunday, September 04, 2011


Dune is my favorite science fiction novel. But I never finished any of the sequels, which I found tedious. I more or less stopped reading science fiction when I was a kid, so perhaps my opinion about the sequels is unreliable.

The appendix below hints at a larger framework (see last sentence) that is not revealed in the first book. (Nor in the Wikipedia entries on Dune, as far as I can tell.) What is this larger plan, in which the Bene Gesserit are only pawns? Is it revealed in later books or in interviews with Frank Herbert?

Appendix III: Report on Bene Gesserit Motives and Purposes

Here follows an excerpt from the Summa prepared by her own agents at the request of the Lady Jessica immediately after the Arrakis Affair. The candor of this report amplifies its value far beyond the ordinary. Because the Bene Gesserit operated for centuries behind the blind of a semimystic school while carrying on their selective breeding program among humans, we tend to award them with more status than they appear to deserve. Analysis of their "trial of fact" on the Arrakis Affair betrays the school's profound ignorance of its own role.

It may be argued that the Bene Gesserit could examine only such facts as were available to them and had no direct access to the person of the Prophet Muad'Dib. But the school had surmounted greater obstacles and its error here goes deeper. The Bene Gesserit program had as its target the breeding of a person they labeled "Kwisatz Haderach," a term signifying "one who can be many places at once." In simpler terms, what they sought was a human with mental powers permitting him to understand and use higher order dimensions.

They were breeding for a super-Mentat, a human computer with some of the prescient abilities found in Guild navigators. Now, attend these facts carefully:

Muad'Dib, born Paul Atreides, was the son of the Duke Leto, a man whose bloodline had been watched carefully for more than a thousand years. The Prophet's mother, Lady Jessica, was a natural daughter of the Baron Vladimir Harkonnen and carried gene-markers whose supreme importance to the breeding program was known for almost two thousand years. She was a Bene Gesserit bred and trained, and should have been a willing tool of the project.

The Lady Jessica was ordered to produce an Atreides daughter. The plan was to inbreed this daughter with Feyd-Rautha Harkonnen, a nephew of the Baron Vladimir, with the high probability of a Kwisatz Haderach from that union. Instead, for reasons she confesses have never been completely clear to her, the concubine Lady Jessica defied her orders and bore a son. This alone should have alerted the Bene Gesserit to the possibility that a wild variable had entered their scheme. But there were other far more important indications that they virtually ignored:

1. As a youth, Paul Atreides showed ability to predict the future. He was known to have had prescient visions that were accurate, penetrating, and defied four-dimensional explanation.

2. The Reverend Mother Gaius Helen Mohiam, Bene Gesserit Proctor who tested Paul's humanity when he was fifteen, deposes that he surmounted more agony in the test than any other human of record. Yet she failed to make special note of this in her report!

3. When Family Atreides moved to the planet Arrakis, the Fremen population there hailed the young Paul as a prophet, "the voice from the outer world." The Bene Gesserit were well aware that the rigors of such a planet as Arrakis with its totality of desert landscape, its absolute lack of open water, its emphasis on the most primitive necessities for survival, inevitably produces a high proportion of sensitives. Yet this Fremen reaction and the obvious element of the Arrakeen diet high in spice were glossed over by Bene Gesserit observers.

4. When the Harkonnens and the soldier-fanatics of the Padishah Emperor reoccupied Arrakis, killing Paul's father and most of the Atreides troops, Paul and his mother disappeared. But almost immediately there were reports of a new religious leader among the Fremen, a man called Muad'Dib, who again was hailed as "the voice from the outer world." The reports stated clearly that he was accompanied by a new Reverend Mother of the Sayyadina Rite "who is the woman who bore him." Records available to the Bene Gesserit stated in plain terms that the Fremen legends of the Prophet contained these words: "He shall be born of a Bene Gesserit witch."

(It may be argued here that the Bene Gesserit sent their Missionaria Protectiva onto Arrakis centuries earlier to implant something like this legend as safeguard should any members of the school be trapped there and require sanctuary, and that this legend of "the voice from the outer world" was properly to be ignored because it appeared to be the standard Bene Gesserit ruse. But this would be true only if you granted that the Bene Gesserit were correct in ignoring the other clues about Paul-Muad'Dib.)

5. When the Arrakis Affair boiled up, the Spacing Guild made overtures to the Bene Gesserit. The Guild hinted that its navigators, who use the spice drug of Arrakis to produce the limited prescience necessary for guiding spaceships through the void, were "bothered about the future" or saw "problems on the horizon." This could only mean they saw a nexus, a meeting place of countless delicate decisions, beyond which the path was hidden from the prescient eye. This was a clear indication that some agency was interfering with higher order dimensions!

(A few of the Bene Gesserit had long been aware that the Guild could not interfere directly with the vital spice source because Guild navigators already were dealing in their own inept way with higher order dimensions, at least to the point where they recognized that the slightest misstep they made on Arrakis could be catastrophic. It was a known fact that Guild navigators could predict no way to take control of the spice without producing just such a nexus. The obvious conclusion was that someone of higher order powers was taking control of the spice source, yet the Bene Gesserit missed this point entirely!)

In the face of these facts, one is led to the inescapable conclusion that the inefficient Bene Gesserit behavior in this affair was a product of an even higher plan of which they were completely unaware!

Keynes v Hayek

At the beginning of the debate you get to hear a bunch of Brits at the LSE shouting "Yo Keynes!" and "Yo Hayek!" in support of their respective sides. No one seems capable of convincing the other side of anything, but the discussion is entertaining.

Keynes v Hayek

Speaker(s): Professor George Selgin, Professor Lord Skidelsky, Duncan Weldon, Dr Jamie Whyte

Recorded on 26 July 2011.

How do we get out of the financial mess we're in? Two of the great economic thinkers of the 20th century had sharply contrasting views: John Maynard Keynes believed that governments could create sustainable employment and growth. His contemporary and rival Friedrich Hayek believed that investments have to be based on real savings rather than fiscal stimulus or artificially low interest rates.

See also round 2 of the Keynes Hayek rap video:

Saturday, September 03, 2011

Shenzhen key lab

Shenzhen municipality key laboratory -- cognitive genomics research.

Supposedly this means I'll get a special visa and won't have to keep applying for a new one every 12 months.

Note this distinction doesn't mean our group is part of the Chinese government, as some paranoids have claimed. BGI is a private institution with both for-profit and non-profit arms.

Thursday, September 01, 2011

Epistasis vs additivity

Continuing the discussion from my previous post: strong interactions at the level of individual genes do not preclude a linear (additive) analysis of population variation and natural selection.

On epistasis: why it is unimportant in polygenic directional selection

[Phil. Trans. R. Soc. B (2010) 365, 1241–1244 doi:10.1098/rstb.2009.0275]

James F. Crow*
Genetics Laboratory, University of Wisconsin, Madison, WI 53706, USA

There is a difference in viewpoint of developmental and evo-devo geneticists versus breeders and students of quantitative evolution. The former are interested in understanding the developmental process; the emphasis is on identifying genes and studying their action and interaction. Typically, the genes have individually large effects and usually show substantial dominance and epistasis. The latter group are interested in quantitative phenotypes rather than individual genes. Quantitative traits are typically determined by many genes, usually with little dominance or epistasis. Furthermore, epistatic variance has minimum effect, since the selected population soon arrives at a state in which the rate of change is given by the additive variance or covariance. Thus, the breeder’s custom of ignoring epistasis usually gives a more accurate prediction than if epistatic variance were included in the formulae.

Why did Crow have to write this 2010 paper? Don't evo-devo folks understand population genetics? Why do they find the dominance of additive heritability to be so counter-intuitive? Which of the two groups of scientists has a better understanding of how evolution works? Evo-devo folks seem to be from the traditional "revel in complexity" branch of biology: perfectly happy to find that living creatures are too complicated to be modeled by equations. (But are they?)

Some excerpts from the paper:

... Recent years have seen an increased emphasis on epistasis (e.g. Wolf et al. 2000; Carlborg & Haley 2004). Students of development and evo-devo, as well as some human geneticists, have paid particular interest to interactions. For those in these fields, epistasis is an interesting phenomenon on its own and studying it gives deeper insights into developmental and evolutionary processes. Ultimately one wants to know which individual genes are involved, and if one is studying the effects of such genes, it is natural to con- sider the ways in which they interact. Historically, among many other uses, epistasis has provided a means for identifying steps in biochemical and developmental sequences. More generally, including epistasis is part of the description of gene effects. So epistasis, despite methodological challenges, is usually welcomed as providing further insights. Students of development or evo-devo typically study genes of major effect. Of course, genes with major effects are more easily discovered, so they may be providing a biased sample. But we can say that at least some of the genes involved have large effects. And such genes typically show considerable dominance and epistasis.

In contrast, animal and plant breeders have traditionally regarded epistasis as a nuisance, akin to noise in impeding or obscuring the progress of selection. It may seem surprising that the traditional practice of ignoring epistasis has not led to errors in prediction equations. Why? It is this seeming paradox that I wish to discuss.

Continuously distributed quantitative traits typically depend on a large number of factors, each making a small contribution to the quantitative measurement. In general, the smaller the effects, the more nearly additive they are. Experimental evidence for this is abundant. This is expected for reasons analogous to those for which taking only the first term of a Taylor series provides a good estimate. ...

The most extensive selection experiment, at least the one that has continued for the longest time, is the selection for oil and protein content in maize (Dudley 2007). These experiments began near the end of the nineteenth century and still continue; there are now more than 100 generations of selection. Remarkably, selection for high oil content and similarly, but less strikingly, selection for high protein, continue to make progress. There seems to be no diminishing of selectable variance in the population. The effect of selection is enormous: the difference in oil content between the high and low selected strains is some 32 times the original standard deviation.

... Students of development, evo-devo and human genetics often place great emphasis on epistasis. Usually they are identifying individual genes, and naturally the interactions among these are of the very essence of understanding. The individual gene effects are usually large enough for considerable epistasis to be expected.

Quantitative genetics has a contrasting view. The foregoing analysis shows that, under typical conditions, the rate of change under selection is given by the additive genetic variance or covariance. Any attempt to include epistatic terms in prediction formulae is likely to do more harm than good. Animal and plant breeders who ignored epistasis, for whatever reasons, good or bad, were nevertheless on the right track. And prediction formulae based on simple heritability measurements are appropriate.

The power of using microscopic knowledge (genes) to develop macroscopic theory (phenotypes), whereby phenotypic measurements are used to develop prediction formulae, is beautifully illustrated by quantitative genetics theory.

Can we understand evolution without mathematics? Two more useful references:

Statistical Mechanics and the Evolution of Polygenic Quantitative Traits

The Evolution of Multilocus Systems Under Weak Selection

Note I am at BGI right now so there may be some latency in communication.

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