Sunday, July 31, 2016

Trump, Putin, Stephen Cohen, Brawndo, and Electrolytes

Every now and then something jars me into thinking that Idiocracy has already arrived, a bit ahead of schedule. The CNN guy on the left is obviously from the "Brawndo's got electrolytes" school of reasoning that somehow passes for journalism these days. Stephen Cohen, a distinguished emeritus professor of Russian History, is a holdover from the previous era (sadly missed, at least by me) when logic and facts actually mattered.

See also Obama: "Don't do stupid sh*t" and Bear Baiting is Dangerous.

Saturday, July 30, 2016

Perestroika and the discovery of price signals

I read The Oligarchs: Wealth And Power In The New Russia many years ago. A passage which I found fascinating, and still remember today, describes the explorations of reformist Soviet economists toward market economics and price signals. Imagine groping dimly most of your adult life for subtle but monumental concepts that lie far down a forbidden path of reasoning.

Some leftists in the West are still groping for (or perhaps not even seeking) these ideas. Just as the Soviet economists failed to appreciate for most of their lives the monstrous nature of state control of the economy, many on the left take for granted the miraculous fruits of the market economy.
[Chapter 4: Anatoly Chubais] ... As perestroika dawned with the arrival of Gorbachev in 1985, the topics at the Leningrad seminars grew more ambitious. The participants began to broach an altogether bold idea: introducing some aspects of the market to Soviet socialism. For a long time, they intensely debated whether the economy could be saved by such reform concepts as self-financing or by decentralization, which meant allowing factory directors to make more of their own decisions. Later, as the years went on, they concluded that the existing machine was probably doomed and would have to be massively restructured. Still later, they spent many days contemplating the prospect of a “transition” to some new kind of a system. Even the notion of a “transition” was a thrilling idea.

... They had ample access to more radical texts in samizdat, the dog-eared, self-typed, or mimeographed manuscripts that were officially prohibited but widely distributed from hand to hand. ...

Then came a sudden bolt of inspiration. They were profoundly inspired by a two-volume, 630-page book published in 1980 by a Hungarian economics professor, János Kornai. The Economics of Shortage, more than any other text, offered an insight into the failings of Soviet socialism. Hungary had been at the forefront of more market-oriented economic reform in the Eastern Bloc since 1968, and Kornai’s groundbreaking work was almost entirely based on his observations about Hungary. But for the young scholars around Chubais, the work opened a window as no other Soviet or Western study had done on why the economy of shortage existed and how it functioned. Kornai examined the behavior of buyers, sellers, and producers in an absence of free prices, as well as the relationship between firms and the state under socialism and central planning. [ See János Kornai’s Contributions to Economic Analysis. ]

The book first arrived in Leningrad as smuggled photocopies and instantly “became a Bible,” Vasiliev recalled. “We had some ideas initially, but the book was kind of a catharsis. It pushed our thinking forward. You met a person and you said, ‘Have you read Kornai? Yes?’ And then it was a starting point for discussion. ...

But Kornai alone did not lead the Chubais team out of socialism; he just helped them see it much more clearly. The other great inspiration of those years came from the Austrian economist Friedrich von Hayek, one of the most trenchant early critics of socialism, who was especially acute in his searing denunciation of central planning. Although Hayek’s best-known work was The Road to Serfdom, a 1944 treatise about the dangers to individual liberty of socialism and central planning, Chubais took to heart a lesser-known economics text.11 It was an article that Hayek had published in 1945, “The Use of Knowledge in Society.”12 The article articulated clearly what the Leningrad scholars had been groping toward since the debate at the collective farm: that free prices were the single most powerful “indicator” to measure all the millions of decisions in a large, complex economy. ...

Hayek declared that the price system was a “marvel” which could free people from the “conscious control” of the central planners. At the time Chubais read this essay in Leningrad, the Soviet Union was the world’s largest example of “conscious control,” with rigid, fixed state prices set throughout the economy. Hayek, who won the 1974 Nobel Prize in economics for his work, had taken a battering ram to the underpinnings of Soviet socialism. Amazingly, his wisdom was smuggled past the KGB on those dog-eared photocopies, and it landed in the hands of an eager young generation of knowledge-hungry Leningrad academics.

Many years later, Chubais recalled the thrill of reading Hayek and instantly gave his own example of how Hayek’s theory worked in practice in the United States. “One person is selling hamburgers somewhere in New York,” he told me, “while another person is grazing cows somewhere in Arkansas to produce meat that will be used to make those hamburgers. But in order for that person in Arkansas to graze cows, there needs to be a price for meat, which tells him that he should graze cows.” ...

... “We started trying to think about real things, instead of all that bullshit we were engaged in during our formal jobs,” Glazkov said. The Gaidar-Chubais group produced a 120-page report, adapting some of the Hungarian and Yugoslav reforms to the Soviet system. They called for abandoning planning dictates and permitting some free market mechanisms. When Gaidar’s boss came back one day, he brought bad news: the plan had been rejected. “Which meant we were to give up our fruitless daydreaming” and come up with something “on a more mundane level,” Gaidar recalled. But when Gaidar went home that day and turned on the television, he heard Gorbachev deliver a speech using some of the same terms they had put in the rejected report. It was a strange time ...
My samizdat.

Friday, July 29, 2016

Michael Moore: Trump Will Win

Michael Moore received an honorary degree from Michigan State University in December 2014. Said I to the packed Breslin Center: "President Simon, it is my honor to present Michael Moore for the degree Doctor of Humanities." :-) ... I am sorry to be the bearer of bad news, but I gave it to you straight last summer when I told you that Donald Trump would be the Republican nominee for president. And now I have even more awful, depressing news for you: Donald J. Trump is going to win in November. This wretched, ignorant, dangerous part-time clown and full time sociopath is going to be our next president. President Trump. Go ahead and say the words, ‘cause you’ll be saying them for the next four years: “PRESIDENT TRUMP.”

Never in my life have I wanted to be proven wrong more than I do right now.

I can see what you’re doing right now. You’re shaking your head wildly – “No, Mike, this won’t happen!” Unfortunately, you are living in a bubble that comes with an adjoining echo chamber where you and your friends are convinced the American people are not going to elect an idiot for president. You alternate between being appalled at him and laughing at him because of his latest crazy comment or his embarrassingly narcissistic stance on everything because everything is about him. And then you listen to Hillary and you behold our very first female president, someone the world respects, someone who is whip-smart and cares about kids, who will continue the Obama legacy because that is what the American people clearly want! Yes! Four more years of this!

You need to exit that bubble right now. You need to stop living in denial and face the truth which you know deep down is very, very real. Trying to soothe yourself with the facts – “77% of the electorate are women, people of color, young adults under 35 and Trump cant win a majority of any of them!” – or logic – “people aren’t going to vote for a buffoon or against their own best interests!” – is your brain’s way of trying to protect you from trauma. Like when you hear a loud noise on the street and you think, “oh, a tire just blew out,” or, “wow, who’s playing with firecrackers?” because you don’t want to think you just heard someone being shot with a gun. It’s the same reason why all the initial news and eyewitness reports on 9/11 said “a small plane accidentally flew into the World Trade Center.” We want to – we need to – hope for the best because, frankly, life is already a shit show and it’s hard enough struggling to get by from paycheck to paycheck. We can’t handle much more bad news. So our mental state goes to default when something scary is actually, truly happening. The first people plowed down by the truck in Nice spent their final moments on earth waving at the driver whom they thought had simply lost control of his truck, trying to tell him that he jumped the curb: “Watch out!,” they shouted. “There are people on the sidewalk!”

Well, folks, this isn’t an accident. It is happening. And if you believe Hillary Clinton is going to beat Trump with facts and smarts and logic, then you obviously missed the past year of 56 primaries and caucuses where 16 Republican candidates tried that and every kitchen sink they could throw at Trump and nothing could stop his juggernaut. As of today, as things stand now, I believe this is going to happen – and in order to deal with it, I need you first to acknowledge it ...

And therein lies the problem for November – who is going to have the most motivated, most inspired voters show up to vote? You know the answer to this question. Who’s the candidate with the most rabid supporters? Whose crazed fans are going to be up at 5 AM on Election Day, kicking ass all day long, all the way until the last polling place has closed, making sure every Tom, Dick and Harry (and Bob and Joe and Billy Bob and Billy Joe and Billy Bob Joe) has cast his ballot? That’s right. That’s the high level of danger we’re in. And don’t fool yourself — no amount of compelling Hillary TV ads, or outfacting him in the debates or Libertarians siphoning votes away from Trump is going to stop his mojo. 
Here are the 5 reasons Trump is going to win:

1. Midwest Math, or Welcome to Our Rust Belt Brexit. I believe Trump is going to focus much of his attention on the four blue states in the rustbelt of the upper Great Lakes – Michigan, Ohio, Pennsylvania and Wisconsin. Four traditionally Democratic states – but each of them have elected a Republican governor since 2010 (only Pennsylvania has now finally elected a Democrat). In the Michigan primary in March, more Michiganders came out to vote for the Republicans (1.32 million) that the Democrats (1.19 million). Trump is ahead of Hillary in the latest polls in Pennsylvania and tied with her in Ohio. Tied? How can the race be this close after everything Trump has said and done? Well maybe it’s because he’s said (correctly) that the Clintons’ support of NAFTA helped to destroy the industrial states of the Upper Midwest. Trump is going to hammer Clinton on this and her support of TPP and other trade policies that have royally screwed the people of these four states. When Trump stood in the shadow of a Ford Motor factory during the Michigan primary, he threatened the corporation that if they did indeed go ahead with their planned closure of that factory and move it to Mexico, he would slap a 35% tariff on any Mexican-built cars shipped back to the United States. It was sweet, sweet music to the ears of the working class of Michigan, and when he tossed in his threat to Apple that he would force them to stop making their iPhones in China and build them here in America, well, hearts swooned and Trump walked away with a big victory that should have gone to the governor next-door, John Kasich.

From Green Bay to Pittsburgh, this, my friends, is the middle of England – broken, depressed, struggling, the smokestacks strewn across the countryside with the carcass of what we use to call the Middle Class. Angry, embittered working (and nonworking) people who were lied to by the trickle-down of Reagan and abandoned by Democrats who still try to talk a good line but are really just looking forward to rub one out with a lobbyist from Goldman Sachs who’ll write them nice big check before leaving the room. What happened in the UK with Brexit is going to happen here. ...

2. The Last Stand of the Angry White Man ... a small peek into the mind of the Endangered White Male. There is a sense that the power has slipped out of their hands, that their way of doing things is no longer how things are done. This monster, the “Feminazi,”the thing that as Trump says, “bleeds through her eyes or wherever she bleeds,” has conquered us — and now, after having had to endure eight years of a black man telling us what to do, we’re supposed to just sit back and take eight years of a woman bossing us around? After that it’ll be eight years of the gays in the White House! Then the transgenders! You can see where this is going. By then animals will have been granted human rights and a fuckin’ hamster is going to be running the country. This has to stop!

3. The Hillary Problem ... her vote for the Iraq War made me promise her that I would never vote for her again. ... Let’s face it: Our biggest problem here isn’t Trump – it’s Hillary. She is hugely unpopular — nearly 70% of all voters think she is untrustworthy and dishonest. She represents the old way of politics, not really believing in anything other than what can get you elected. That’s why she fights against gays getting married one moment, and the next she’s officiating a gay marriage. Young women are among her biggest detractors, which has to hurt ...

4. The Depressed Sanders Vote. ... The fire alarm that should be going off is that while the average Bernie backer will drag him/herself to the polls that day to somewhat reluctantly vote for Hillary, it will be what’s called a “depressed vote” – meaning the voter doesn’t bring five people to vote with her. He doesn’t volunteer 10 hours in the month leading up to the election. She never talks in an excited voice when asked why she’s voting for Hillary. A depressed voter. Because, when you’re young, you have zero tolerance for phonies and BS. Returning to the Clinton/Bush era for them is like suddenly having to pay for music, or using MySpace or carrying around one of those big-ass portable phones. They’re not going to vote for Trump; some will vote third party, but many will just stay home.

5. The Jesse Ventura Effect. ... the voting booth. It’s one of the few places left in society where there are no security cameras, no listening devices, no spouses, no kids, no boss, no cops, there’s not even a friggin’ time limit. You can take as long as you need in there and no one can make you do anything. ... There are no rules. And because of that, and the anger that so many have toward a broken political system, millions are going to vote for Trump not because they agree with him, not because they like his bigotry or ego, but just because they can. ...

Thursday, July 28, 2016

Bear baiting is dangerous

What do we have to gain by placing interceptor missiles in Romania? Putin's concerns are legitimate, and security through Mutually Assured Destruction has always been an unstable equilibrium. Watch the video closely. ... “At the moment the interceptor missiles installed have a range of 500 kilometers, soon this will go up to 1000 kilometers, and worse than that, they can be rearmed with 2400km-range offensive missiles even today, and it can be done by simply switching the software, so that even the Romanians themselves won’t know,” said Putin, who is in Greece for a two-day tour.

“We have the capability to respond. The whole world saw what our medium-range sea-based missiles are capable of [in Syria]. But we violate no agreements. And our ground-based Iskander missiles have also proven themselves as superb,” continued Putin.

Russia’s political and military leadership has repeatedly spoken out against the missile defense shield since it was proposed during the George W. Bush administration, and Putin reiterated that Moscow does not believe the European part of it is targeted against a potential threat from Iran.

“NATO fend us off with vague statements that this is no threat to Russia… That the whole project began as a preventive measure against Iran’s nuclear program. Where is that program now? It doesn’t exist,” said Putin, referring to the nuclear treaty that was concluded between the world’s major powers and Tehran last year. “We have been saying since the early 2000s that we will have to react somehow to your moves to undermine international security. No one is listening to us.”
Link to full interview and better translation.
They have built this system and are now delivering missiles there. You probably know that the launch systems of the Tomahawk sea-launched intermediate-range missiles will be used to launch anti-missiles with an effective range of 500 kilometres. However, technology does not stand still, and we know more or less precisely when the Americans will create a new missile that will have a range of 1,000 kilometres or more. From that time on, they will be a threat to our nuclear arsenals.

We know what will happen and in which year, and they know we know it. They are just throwing dust in our eyes, as the saying goes, and you in turn are throwing dust in the eyes of your people. What bothers me is that people are not aware of the danger. We fail to understand that we are dragging the world into a completely new dimension. This is what this is all about. They are pretending as if nothing is going on. I do not even know how to put my message across.

We are being told that this is part of a defensive, not offensive, capability, that these systems are intended to ensure defence against aggression. This is not true. This is not the way things are. A strategic missile defence system is part of an offensive strategic capability, and is tightly linked to offensive missile strike systems. Some high-precision weapons are used to carry out a pre-emptive strike, while others serve as a shield against a retaliatory strike, and still others carry out nuclear strikes. All these objectives are related, and go hand in hand with the use of high-precision conventional weapons.

All right, even if we put aside the interceptor missiles that will be developed in the future, increasingly threatening Russia, but the launch tubes where these missiles are stored, as I said, are the same that are used on navy ships to carry Tomahawk missiles. You can replace interceptor missiles with Tomahawks in a matter of hours and these tubes will no longer be used to intercept missiles. How do we know what is inside them? All they need is to change the software. This can be done seamlessly; even the Romanians would not know what is going on, since they cannot access these facilities, right? No one will know, neither the Romanians, nor the Poles. I know how this is done. In my opinion, this is a major threat.

When we discussed this with our US partners, they had the idea of creating nonnuclear ballistic missiles. We said, “Listen, do you understand what this would be? Imagine that you fire a submarine-launch or land-based missile. A ballistic missile is launched. How do we know whether it is carrying a nuclear warhead or not? Do you understand the kind of threat this would create?” As far as we know, this programme is currently suspended. They have stopped it for now. However, they are still working on it.

I do not know where this will take us. However, Russia will definitely have to retaliate. I know already that we will be accused of acting aggressively, even though all we do is respond. It is clear that we will have to ensure security, and not just in Russia, since ensuring the strategic balance of power globally is a matter of great importance for us.

Tuesday, July 26, 2016

Genomics of complex traits and evolutionary selection pressure on DNA regions linked to cognitive ability

Two recent papers relevant to the genetics of complex traits. The second paper is specifically about the genetic architecture of cognition. Thanks to blog readers for pointing them out to me.

See also The tipping point.
Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

DOI: 10.1098/rspb.2016.0569
Proceedings of the Royal Society 27 July 2016 Volume 283, issue 1835

Complex or quantitative traits are important in medicine, agriculture and evolution, yet, until recently, few of the polymorphisms that cause variation in these traits were known. Genome-wide association studies (GWAS), based on the ability to assay thousands of single nucleotide polymorphisms (SNPs), have revolutionized our understanding of the genetics of complex traits. We advocate the analysis of GWAS data by a statistical method that fits all SNP effects simultaneously, assuming that these effects are drawn from a prior distribution. We illustrate how this method can be used to predict future phenotypes, to map and identify the causal mutations, and to study the genetic architecture of complex traits. The genetic architecture of complex traits is even more complex than previously thought: in almost every trait studied there are thousands of polymorphisms that explain genetic variation. Methods of predicting future phenotypes, collectively known as genomic selection or genomic prediction, have been widely adopted in livestock and crop breeding, leading to increased rates of genetic improvement.

Molecular genetic aetiology of general cognitive function is enriched in evolutionarily conserved regions

Differences in general cognitive function have been shown to be partly heritable and to show genetic correlations with a several psychiatric and physical disease states. However, to date few single nucleotide polymorphisms (SNPs) have demonstrated genome-wide significance, hampering efforts aimed at determining which genetic variants are most important for cognitive function and which regions drive the genetic associations between cognitive function and disease states. Here, we combine multiple large genome-wide association study (GWAS) data sets, from the CHARGE cognitive consortium and UK Biobank, to partition the genome into 52 functional annotations and an additional 10 annotations describing tissue-specific histone marks. Using stratified linkage disequilibrium score regression we show that, in two measures of cognitive function, SNPs associated with cognitive function cluster in regions of the genome that are under evolutionary negative selective pressure. These conserved regions contained ~2.6% of the SNPs from each GWAS but accounted for ~ 40% of the SNP-based heritability. The results suggest that the search for causal variants associated with cognitive function, and those variants that exert a pleiotropic effect between cognitive function and health, will be facilitated by examining these enriched regions.

Monday, July 25, 2016

The Mendel of Cancer Genetics

See also earlier post Where Men are Men and Giants Walk the Earth.
NYTimes: Dr. Alfred G. Knudson, the ‘Mendel of Cancer Genetics,’ Dies at 93

Dr. Alfred G. Knudson, who deduced how certain cancers strike a family generation after generation, died on Sunday at his home in Philadelphia. He was 93.

... “Funny as it may sound, heritable cancer was hardly discussed in the 1960s and 1970s,” Dr. Albert de la Chapelle, a professor in the human genetics program at Ohio State University, said in an email.

Dr. Knudson, trained as a pediatrician, tackled the issue by looking at retinoblastoma, a cancer of the eye that strikes children, even newborns. Childhood cancers would be easier to understand, he reasoned, because there would be fewer confounding factors, like the random mutations that accumulate over a lifetime.

“It had been known for a long time that there were inherited forms of retinoblastoma, that it would run in families,” said Dr. Jonathan Chernoff, the chief scientific officer at Fox Chase. “And then there were, on the other hand, sporadic cases that didn’t run in families. Some child would randomly get retinoblastoma.”

Dr. Knudson analyzed the records of retinoblastoma patients and found that the inherited form struck children at a younger age and often in both eyes, while the sporadic cases usually involved older children and just one eye.

That led him to his “two-hit” hypothesis, and his insight that cancer sometimes results not from a particular cause, but rather from the disabling of something known today as the tumor suppressor gene.

... Dr. Chernoff said Dr. Knudson was in some ways “the Mendel of cancer genetics,” referring to Gregor Mendel, the 19th-century monk who demonstrated, through the crossbreeding of pea plants, how traits are passed from one generation to the next.

“He provided the conceptual framework for how we think about cancer now,” Dr. Chernoff said.

Dr. Knudson published his hypothesis in 1971. “Knudson’s hypothesis was conceived before we had a clue about the underlying molecular genetic events,” Dr. de la Chapelle said. “I believe Knudson’s work stimulated retinoblastoma researchers so strongly that this led to an early breakthrough.”

Dr. Knudson’s theory was proved in 1986, when researchers figured out the gene and the mutations that led to the disease.

... Alfred George Knudson Jr. was born on Aug. 9, 1922, in Los Angeles. He went to the California Institute of Technology thinking he would major in physics.

“I had never had any biology in high school,” he recalled in a 2013 interview. “Then, after two years of physics at Caltech, I thought: ‘Oh, they know everything in physics. Why do I want to go into physics?’”

The quantitative aspects of genetics appealed to him, he said: “It has some of the features I admire about physics, so I’ll study that.”

He finished his bachelor of science degree at Caltech in 1944 and went on to receive a medical degree from Columbia in 1947. He returned to Caltech to earn a doctorate in biochemistry and genetics in 1956. He served in the Navy during World War II and the Army during the Korean War.

Sunday, July 24, 2016

Scifoo 2016

Photos from Palo Alto and Scifoo 2016. We weren't allowed to take photos inside the Googleplex.

Wednesday, July 20, 2016

Farewell Asia, Hello Scifoo

Apologies for the lack of blog posts. I've been on the road in Asia and quite busy for the past week. I head back to the bay area for Scifoo this weekend. See you there!

The Tipping Point

This is only the beginning. To serious people who read this blog, but may have been confused over the past 5+ years about things like missing heritability, genomic prediction, complex genetic architecture, gloomy prospects: isn't it about time to consider updating your priors? Read all about it here. Genetic scoring predicts how children do at school

Professor Robert Plomin, senior author, called the study “a tipping point for predicting individuals’ educational strengths and weaknesses from their DNA”. It is published in the journal Molecular Psychiatry.

An individual’s “polygenic score” is based on the presence or absence of 20,000 common DNA variants across many different genes. Each has a tiny effect on its own but together they explain 10 per cent of the variation in children’s educational attainment at the age of 16.
It's important to note that 9 percent of variance accounted for implies that the resulting polygenic score predictor would correlate about 0.3 with actual educational achievement. This is similar to the correlation between high school and college grades at a typical flagship state university (note there is some restriction of range) -- not a weak predictor by the standards of social science.
Predicting educational achievement from DNA

Nature Molecular Psychiatry 19 July 2016; doi: 10.1038/mp.2016.107

A genome-wide polygenic score (GPS), derived from a 2013 genome-wide association study (N=127,000), explained 2% of the variance in total years of education (EduYears). In a follow-up study (N=329,000), a new EduYears GPS explains up to 4%. Here, we tested the association between this latest EduYears GPS and educational achievement scores at ages 7, 12 and 16 in an independent sample of 5825 UK individuals. We found that EduYears GPS explained greater amounts of variance in educational achievement over time, up to 9% at age 16, accounting for 15% of the heritable variance. This is the strongest GPS prediction to date for quantitative behavioral traits. Individuals in the highest and lowest GPS septiles differed by a whole school grade at age 16. Furthermore, EduYears GPS was associated with general cognitive ability (~3.5%) and family socioeconomic status (~7%). There was no evidence of an interaction between EduYears GPS and family socioeconomic status on educational achievement or on general cognitive ability. These results are a harbinger of future widespread use of GPS to predict genetic risk and resilience in the social and behavioral sciences.

Saturday, July 16, 2016

Monday, July 11, 2016

My neighbor's kid is a designer baby (or not)

I happened to see Knoepfler's book at the HKUST bookstore yesterday. He's a stem cell researcher at UC Davis.
GMO Sapiens: the Life-Changing Science of Designer Babies is an exciting new book which takes a look at the cutting edge biotechnology trends that are making human genetic modification and cloning a more practical potential reality in the coming years. The convergence of advances in bioengineering, genetics, genomics, assisted reproduction and stem cells have brought us to the astonishing point where literally making new forms of human beings is possible. Surprisingly, some people and organizations are strong advocates for allowing genetic modification of humans while others feel equally passionately opposed. Meanwhile, the general public is largely unaware that we have reached this remarkable turning point in human history when we can literally change what it means to be human.

As much as the public is engaged in the topic of genetically modified organism (GMO) foods, this book will capture their imaginations and fire their passions by educating them on the potential coming of GMO people while, at the same time, educating them.

Sunday, July 10, 2016


By coincidence, they're hosting the International Math Olympiad here. There are teams of kids from all over the world, but less geeky looking than I expected.

This deck of cards was created by the HKUST math chair, formerly of MSU.

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