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Physicist, Startup Founder, Blogger, Dad

Thursday, November 30, 2017

CMSE (Computational Mathematics, Science and Engineering) at MSU



At Oregon I was part of an interdisciplinary institute that included theoretical physicists and chemists, mathematicians, and computer scientists. We tried to create a program (not even a new department, just an interdisciplinary program) in applied math and computation, but failed due to lack of support from higher administration. When I arrived at MSU as VPR I learned that the faculty here had formulated a similar plan for a new department. Together with the Engineering dean and the Natural Sciences dean we pushed it through and created an entirely new department in just a few years. This new department already has a research ranking among the top 10 in the US (according to Academic Analytics).

Computational Mathematics, Science and Engineering at MSU.


IQ (Institute for Quantitative Health Science and Engineering) at MSU



Chris Contag is the founding director of the Institute for Quantitative Health Science and Engineering and the chairperson of the new Department of Biomedical Engineering in the College of Engineering.

Contag was previously a professor in the Departments of Pediatrics, Radiology, Bioengineering and Microbiology and Immunology at Stanford University. He held the titles of associate chief of Neonatal and Developmental Medicine, director of Stanford’s Center for Innovation in In Vivo Imaging and co-director of the Molecular Imaging Program. Among the new faculty recruited to IQ are researchers previously on the faculties at Stanford, Harvard, and Johns Hopkins University.

Below are some photos from the annual progress report meeting I attended yesterday.






Monday, November 27, 2017

The nuclear physics of neutron star mergers at MSU's FRIB


Science reports on MSU's Facility for Rare Isotope Beams, which will probe the properties of nuclear matter.
Science: Last month, astronomers wowed the world when they announced that they had seen two neutron stars merge, apparently creating heavy elements such as gold and platinum and spewing them into space. Nuclear physicists here at Michigan State University (MSU) also cheered the find. They are building an atom smasher, the $730 million Facility for Rare Isotope Beams (FRIB), that could decipher exactly how those elements were forged in the inferno. “We were hoping to see an event like this someday,” says Witold Nazarewicz, an MSU theorist and FRIB's chief scientist.

First proposed in 1999, the project didn't get the greenlight for construction from the Department of Energy (DOE) until 2014. But since then, progress has been rapid. In what was a grassy patch behind MSU's existing nuclear physics laboratory now stands an imposing 200-meter-long building. In its basement, technicians are installing the first section of FRIB's 500-meter-long linear accelerator, which will shoot beams of nuclei ranging from hydrogen to uranium into a graphite target to blast out short-lived new isotopes. In this context, isotope is just another word for nucleus—one that makes for a better acronym.

The accelerator at the Facility for Rare Isotope Beams will create short-lived nuclei thought to be forged in neutron star mergers.

The project is on budget and ahead of schedule, and most of the major technological puzzles have been solved, says Thomas Glasmacher, FRIB's project director. “We don't have anything that we don't know how to do,” he says. Other physicists are impressed with the progress. “The moment they could, they ran with this project,” says Kate Jones, an experimental nuclear physicist at the University of Tennessee in Knoxville. “It's very impressive when you look down in the basement and see all the kit they've got.”

FRIB's nuclei will be key to understanding how neutron-star mergers make heavy elements. Spotted by gravitational-wave detectors in the United States and Italy and telescopes around the world, the violent collision produced an afterglow that over days faded from bright blue to dimmer red (Science, 20 October, p. 282). The light show jibed with astrophysicists' model of a so-called kilonova, in which the disintegrating neutron stars fling neutron-rich matter into space. The model predicts that in the debris, a chain of nuclear interactions known as the rapid neutron process, or r-process, quickly generates most of the elements heavier than iron. (Other elements emerge from supernova explosions and the deaths of smaller stars, from cosmic ray interactions, and also as leftovers lingering from the big bang.)

For astrophysicists, the observation marked a triumph for the kilonova model. For nuclear physicists, it's just the beginning. In the r-process, a nucleus gains weight by gobbling up one neutron after another. At the same time, the nucleus can change its chemical identity through radioactive beta decay, which turns a neutron into a proton and bumps the nucleus up the periodic table of elements. Exactly how the nucleus evolves depends on the speed of the decay and the probability that it will soak up another neutron.

Those parameters are poorly known. “Honestly, the nuclear physics is not in good shape,” says MSU nuclear astrophysicist Hendrik Schatz. “Most of the nuclei involved have not been identified and the theory has not been developed.” FRIB aims to change that by making as many of the neutron-laden nuclei as possible and measuring their masses and lifetimes. That might seem like a hopeless task, as the r-process involves dozens of intermediate nuclei. However, only a few key nuclei—the slowest decayers and absorbers—should act as bottlenecks to control the process and determine which elements are made in greatest abundance, Schatz explains.

Such data would better constrain models of heavy element production in neutron star mergers. The abundances could then be compared with those observed in the universe to determine whether merging neutron stars are the only astrophysical sites of the r-process, Jones says. Many astrophysicists have suggested as much, but that's a leap, she says. “It's very easy to say, ‘Oh, we've found the site for the r-process—Well done!’ In reality this is just opening a door.”

The 1400 physicists who have signed up to use FRIB will perform many other experiments, ranging from trapping and measuring the properties of a single exotic nucleus, to measuring a hail of novel nuclei scattering off a particular target nucleus. Data from the experiments will feed into a more comprehensive theory of the structure of the nucleus, Nazarewicz says. Physicists already have a fundamental theory of the innards of protons and neutrons, particles called quarks and gluons, and how they interact. But using that theory, known as quantum chromodynamics, to predict nuclear structure is effectively impossible: It is so computationally complex that supercomputers are needed just to simulate the proton and neutron.

To model the behavior of nuclei, theorists now rely on various approximate “effective theories” that work for some nuclei but not others. FRIB's grandest goal, Nazarewicz says, is to develop a deeper understanding that will enable theorists to weave these disparate and sometimes discordant theories together into a coherent whole.

First, researchers have to finish the accelerator. In September, they fired a test beam through its first section, made of copper cavities that work at room temperature. They are now installing the main accelerating modules, which are made of superconducting niobium and must be chilled with liquid helium to 2 K. Researchers hope to send beams through the cold accelerator next year. In 2021, they plan to tear down a wall and connect the finished accelerator to the existing lab so that new experiments can begin. ...
Note this is an old schematic, from 2008 or so.

Remarks on the Decline of American Empire



Some gloomy remarks on the decline of the American Empire.

1. US foreign policy over the last decades has been disastrous -- trillions of dollars and thousands of lives expended on Middle Eastern wars, culminating in utter defeat. This defeat is still not acknowledged among most of the media or what passes for intelligentsia in academia and policy circles, but defeat it is. Iran now exerts significant control over Iraq and a swath of land running from the Persian Gulf to the Mediterranean. None of the goals of our costly intervention have been achieved. We are exhausted morally, financially, and militarily, and still have not fully extricated ourselves from a useless morass. George W. Bush should go down in history as the worst US President of the modern era.

2. We are fortunate that the fracking revolution may lead to US independence from Middle Eastern energy. But policy elites have to fully recognize this possibility and pivot our strategy to reflect the decreased importance of the region. The fracking revolution is a consequence of basic research from decades ago (including investment from the Department of Energy) and the work of private sector innovators and risk-takers.

3. US budget deficits are a ticking time bomb, which cripple investment in basic infrastructure and also in research that creates strategically important new technologies like AI. US research spending has been roughly flat in inflation adjusted dollars over the last 20 years, declining as a fraction of GDP.

4. Divisive identity politics and demographic trends in the US will continue to undermine political cohesion and overall effectiveness of our institutions. ("Civilizational decline," as one leading theoretical physicist observed to me recently, remarking on our current inability to take on big science projects.)

5. The Chinese have almost entirely closed the technology gap with the West, and dominate important areas of manufacturing. It seems very likely that their economy will eventually become significantly larger than the US economy. This is the world that strategists have to prepare for. Wars involving religious fanatics in unimportant regions of the world should not distract us from a possible future conflict with a peer competitor that threatens to match or exceed our economic, technological, and even military capability.

However, I'm not sure that OBOR (One Belt One Road) and a focus on the "world island" of Eurasia will be a winning strategy for China. Mackinder's dream of a unified or even fully economically integrated world island will have to overcome the limitations (in human capital, institutions, culture, etc.) of the under-developed middle...


More McCoy and Mackinder. RAND study on war with China mentioned by McCoy in the video above is linked here.

See also The Stages of Empire:
The empires Glubb studied had a lifespan of about ten human generations, or two hundred and fifty years, despite changing factors such as technology. Glubb describes a pattern of growth and decline, with six stages: the Ages of Pioneers, Conquest, Commerce, Affluence, Intellect and Decadence. He pointedly avoided writing about India or China, focusing rather on middle and western Eurasia, stating that his knowledge was inadequate to the task.

Note that six stages in 10 generations means that significant change can occur over one or two generations -- a nation can pass from one age to the next, as I believe we have in America during my lifetime.

... There does not appear to be any doubt that money is the agent which causes the decline of this strong, brave and self-confident people. The decline in courage, enterprise and a sense of duty is, however, gradual. The first direction in which wealth injures the nation is a moral one. Money replaces honour and adventure as the objective of the best young men. Moreover, men do not normally seek to make money for their country or their community, but for themselves. Gradually, and almost imperceptibly, the Age of Affluence silences the voice of duty. The object of the young and the ambitious is no longer fame, honour or service, but cash. Education undergoes the same gradual transformation. No longer do schools aim at producing brave patriots ready to serve their country. [ Or to discover great things for all mankind! ] Parents and students alike seek the educational qualifications which will command the highest salaries. ...

Duty, Honor, Country:

The unbelievers will say they are but words, but a slogan, but a flamboyant phrase. Every pedant, every demagogue, every cynic, every hypocrite, every troublemaker, and I am sorry to say, some others of an entirely different character, will try to downgrade them even to the extent of mockery and ridicule.

The 21st century American reality (the Age of Decadence):

"Yeah, I calculated the NPV, and, you know, it's just not worth it for me. I really believe in your project, though. And, I share your passion. Good luck."

Tuesday, November 21, 2017

DOJ invokes Title VI against Harvard admissions


“Elections have consequences..." -- Barack Obama

See 20 years @15 percent: does Harvard discriminate against Asian-Americans?
CNN: The Justice Department is actively investigating Harvard University's use of race in its admissions policies and has concluded the school is "out of compliance" with federal law, according to documents obtained by CNN. ...

[Click through for DOJ letter to Harvard. Harvard refused to supply admissions data to DOJ as requested for Title VI investigation of bias against Asian-Americans.]
Wall Street Journal
WSJ: ... The Justice Department, whose Civil Rights Division is conducting the investigation into similar allegations, said in a letter to Harvard’s lawyers, dated Nov. 17 and reviewed by the Journal, that the school was being investigated under Title VI of the Civil Rights Act of 1964, which bars discrimination on the basis of race, color and national origin for organizations that receive federal funding. The letter also said the school had failed to comply with a Nov. 2 deadline to provide documents related to the university’s admissions policies and practices.

The department told Harvard it “may file a lawsuit” to enforce compliance if Harvard doesn’t hand over the documents by Dec. 1, according to a separate letter dated Nov. 17 from John M. Gore, the acting assistant attorney general for the Civil Rights Division.

... if a federal judge finds Harvard has violated Title VI, the court has broad authority to issue a remedy, such as ordering the university to change its admissions policies, the experts say.

Schools in violation of Title VI can also lose access to federal funds.
From DOJ web site:
TITLE VI OF THE CIVIL RIGHTS ACT OF 1964
42 U.S.C. § 2000D ET SEQ.
OVERVIEW OF TITLE VI OF THE CIVIL RIGHTS ACT OF 1964

Title VI, 42 U.S.C. § 2000d et seq., was enacted as part of the landmark Civil Rights Act of 1964. It prohibits discrimination on the basis of race, color, and national origin in programs and activities receiving federal financial assistance. As President John F. Kennedy said in 1963:

Simple justice requires that public funds, to which all taxpayers of all races [colors, and national origins] contribute, not be spent in any fashion which encourages, entrenches, subsidizes or results in racial [color or national origin] discrimination.

Monday, November 20, 2017

Saturday, November 18, 2017

Robot Overlords and the Academy


In a previous post Half of all jobs (> $60k/y) coding related? I wrote
In the future there will be two kinds of jobs. Workers will either

Tell computers what to do    
      or
Be told by computers what to do
I've been pushing Michigan State University to offer a coding bootcamp experience to all undergraduates who want it: e.g., Codecademy.com. The goal isn't to turn non-STEM majors into software developers, but to give all interested students exposure to an increasingly important and central aspect of the modern world.

I even invited the CodeNow CEO to campus to help push the idea. We're still working on it at the university -- painfully SLOWLY, if you ask me. But this fall I learned my kids are taking a class based on Codecademy at their middle school! Go figure.

(Image via 1, 2)

Wednesday, November 15, 2017

Behold, the Super Cow




Hmm... how do they compute the Net Merit and GTPI? (But, but, what about all of that missing heritability?)

See also

Applied genomics: the genetic "super cow"

Genomic prediction: no bull.

Attention climate virtue signalers: more efficient cows produce less methane per liter of milk! Drink milk from genetically engineered cows :-)

Friday, November 10, 2017

23andMe



I'm in Mountain View to give a talk at 23andMe. Their latest funding round was $250M on a (reported) valuation of $1.5B. If I just add up the Crunchbase numbers it looks like almost half a billion invested at this point...

Slides: Genomic Prediction of Complex Traits
Abstract: We apply methods from Compressed Sensing (L1-penalized regression; Donoho-Tanner phase transition with noise) to the UKBB dataset of 500k SNP genotypes. We construct genomic predictors for several complex traits. Our height predictor captures nearly all of the predicted SNP heritability for this trait -- thereby resolving the missing heritability problem. Actual heights of most individuals in validation tests are within a few cm of predicted heights. I also discuss application of these methods to polygenic disease risk: sparsity estimates (of the number of causal loci), combined with phase transition scaling analysis, allow estimates of the amount of case | control data required to construct good predictors.
Here's how people + robots handle your spit sample to produce a SNP genotype:

Wednesday, November 08, 2017

Pocket AI from Beijing and Smartphones

I need to replace my old iPhone 6, and, predictably, this led me down the rabbit hole of learning about mobile phones, the mobile industry, and even mobile technologies. Some quick remarks: from the least to most expensive phones, Chinese companies are now competitive with industry leaders like Samsung and Apple. The Chinese market is hyper-competitive: small innovative startups (Oppo, OnePlus, etc.) compete with medium sized entities (e.g., Xiaomi, only recently a small startup itself) and giants like Huawei and Lenovo (Motorola). To gauge the landscape, watch phone reviews by Indian techies (or this guy in Germany), who tend to be very focused on cost performance and have access to handsets not sold in the US.

Here's a short video about OnePlus which also explains a bit about the Shenzhen hardware ecosystem:




Huawei's Kirin 970 chipset includes a dedicated "Neural Processor Unit" (NPU), optimized for the matrix operations used in machine learning. An NPU allows the phone to execute ML code for tasks such as image and voice recognition, language translation, etc. without relying on cloud connectivity. At the moment it is mostly a marketing gimmick, but one can imagine in a few years (perhaps earlier!) the NPU could be as important to the phone experience as the GPU.

Here's a review of the Mate 10 Pro, Huawei's $1k flagship phone, with a brief demo of some of the AI features:



The NPU appears to be based on technology licensed from a small Beijing startup, Cambricon. The founder is an alumnus of the Special Class for Gifted Young, University of Science and Technology of China. I've reviewed many Physics PhD applications from 19 year old graduates of this program. There is an SV bidding war over chip designers in this area, ever since the advent of Google's proprietary TPU (and software package Tensorflow), which accounts for most of its computation at data centers around the world.

Here's a quick demo of text recognition and machine translation from Chinese to English:




Some marketing video about the AI processor:




From cat recognition to Her or Joi? How long? I was recently offered the opportunity to be a beta tester for a startup that is building a smartphone AI assistant. I was intrigued but didn't want to give them access to all of my information...




PS One of the reasons I am leaving iOS for Android is that Google Assistant is getting very good, whereas in my experience Siri is terrible!

Wednesday, November 01, 2017

The Future is Here: Genomic Prediction in MIT Technology Review


MIT Technology Review reports on our startup Genomic Prediction. Some basic points worth clarifying:

1. GP's first product, announced at the annual ASRM (American Society of Reproductive Medicine) meeting this week, tests chromosomal abnormality. It is a less expensive but more accurate version of existing tests.



2. The polygenic product, to be launched in 2018, checks for hundreds of known single-gene ("Mendelian") disease risks, and will likely have some true polygenic predictive capabilities. This last part is the main emphasis of the story, but it is just one component of the overall product offering. The article elides a lot of challenging laboratory work on DNA amplification, etc.

3. GP will only deliver results requested by an IVF physician. It is not a DTC (Direct to Consumer) company.

4. All medical risk analysis proceeds from statistical data (analyzing groups of people) to produce recommendations concerning a specific individual.

5. I am on the Board of Directors of GP but am not an employee of the company.

MIT Technology Review

Eugenics 2.0: We’re at the Dawn of Choosing Embryos by Health, Height, and More


Will you be among the first to pick your kids’ IQ? As machine learning unlocks predictions from DNA databases, scientists say parents could have choices never before possible.


Nathan Treff was diagnosed with type 1 diabetes at 24. It’s a disease that runs in families, but it has complex causes. More than one gene is involved. And the environment plays a role too.

So you don’t know who will get it. Treff’s grandfather had it, and lost a leg. But Treff’s three young kids are fine, so far. He’s crossing his fingers they won’t develop it later.

Now Treff, an in vitro fertilization specialist, is working on a radical way to change the odds. Using a combination of computer models and DNA tests, the startup company he’s working with, Genomic Prediction, thinks it has a way of predicting which IVF embryos in a laboratory dish would be most likely to develop type 1 diabetes or other complex diseases. Armed with such statistical scorecards, doctors and parents could huddle and choose to avoid embryos with failing grades.

IVF clinics already test the DNA of embryos to spot rare diseases, like cystic fibrosis, caused by defects in a single gene. But these “preimplantation” tests are poised for a dramatic leap forward as it becomes possible to peer more deeply at an embryo’s genome and create broad statistical forecasts about the person it would become.

The advance is occurring, say scientists, thanks to a growing flood of genetic data collected from large population studies. ...

Spotting outliers

The company’s plans rely on a tidal wave of new knowledge showing how small genetic differences can add up to put one person, but not another, at high odds for diabetes, a neurotic personality, or a taller or shorter height. Already, such “polygenic risk scores” are used in direct-to-consumer gene tests, such as reports from 23andMe that tell customers their genetic chance of being overweight.

For adults, risk scores are little more than a novelty or a source of health advice they can ignore. But if the same information is generated about an embryo, it could lead to existential consequences: who will be born, and who stays in a laboratory freezer.

“I remind my partners, ‘You know, if my parents had this test, I wouldn’t be here,’” says Treff, a prize-winning expert on diagnostic technology who is the author of more than 90 scientific papers.

Genomic Prediction was founded this year and has raised funds from venture capitalists in Silicon Valley, though it declines to say who they are. Tellier, whose inspiration is the science fiction film Gattaca, says the company plans to offer reports to IVF doctors and parents identifying “outliers”—those embryos whose genetic scores put them at the wrong end of a statistical curve for disorders such as diabetes, late-life osteoporosis, schizophrenia, and dwarfism, depending on whether models for those problems prove accurate. ...

This week, Genomic Prediction manned a booth at the annual meeting of the American Society for Reproductive Medicine. That organization, which represents fertility doctors and scientists, has previously said it thinks testing embryos for late-life conditions, like Alzheimer’s, would be “ethically justified.” It cited, among other reasons, the “reproductive liberty” of parents.

... Hsu’s prediction is that “billionaires and Silicon Valley types” will be the early adopters of embryo selection technology, becoming among the first “to do IVF even though they don’t need IVF.” As they start producing fewer unhealthy children, and more exceptional ones, the rest of society could follow suit.

“I fully predict it will be possible,” says Hsu of selecting embryos with higher IQ scores. “But we’ve said that we as a company are not going to do it. It’s a difficult issue, like nuclear weapons or gene editing. There will be some future debate over whether this should be legal, or made illegal. Countries will have referendums on it.”

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