Tuesday, February 27, 2018

MIT Technology Review: Genomic Prediction a 2018 Breakthrough Technology

From 10 Breakthrough Technologies 2018:
One day, babies will get DNA report cards at birth. These reports will offer predictions about their chances of suffering a heart attack or cancer, of getting hooked on tobacco, and of being smarter than average.

The science making these report cards possible has suddenly arrived, thanks to huge genetic studies—some involving more than a million people.

It turns out that most common diseases and many behaviors and traits, including intelligence, are a result of not one or a few genes but many acting in concert. Using the data from large ongoing genetic studies, scientists are creating what they call “polygenic risk scores.”

Though the new DNA tests offer probabilities, not diagnoses, they could greatly benefit medicine. For example, if women at high risk for breast cancer got more mammograms and those at low risk got fewer, those exams might catch more real cancers and set off fewer false alarms.

Pharmaceutical companies can also use the scores in clinical trials of preventive drugs for such illnesses as Alzheimer’s or heart disease. By picking volunteers who are more likely to get sick, they can more accurately test how well the drugs work.

The trouble is, the predictions are far from perfect. Who wants to know they might develop Alzheimer’s? What if someone with a low risk score for cancer puts off being screened, and then develops cancer anyway?

Polygenic scores are also controversial because they can predict any trait, not only diseases. For instance, they can now forecast about 10 percent of a person’s performance on IQ tests. As the scores improve, it’s likely that DNA IQ predictions will become routinely available. But how will parents and educators use that information? ...
Also from Technology Review: Forecasts of genetic fate just got a lot more accurate.

Friday, February 23, 2018

Kosen Judo and the origins of MMA

When I was in Japan in the mid-1990s almost no one outside of a small group of MMA fans had ever heard of BJJ or Gracie Jiujitsu. Sometimes when I went to a judo club to practice I would just explain that I was a "newaza specialist" (ground technique specialist) or even that I wanted to do Kosen-style judo.

The Imperial Universities that specialized in Kosen judo did so partially because they were nerds! One could become adept at newaza with less natural athleticism and less practice than was required to become a true tachiwaza (standing technique = dynamic throws) specialist. A relatively small amount of training in ground technique allows a fighter to completely dominate an untrained opponent. The Kosen competitors would simply drag their opponent to the mat without using any flashy throws or takedowns, and then submit or pin them. More video.

I cannot really tell from the video whether these Kosen practitioners have also adopted techniques from modern BJJ. I see some spider guard, but apparently that is an old Kosen style! Don't let the black belts fool you. In Japan you go from white to black belt directly, and 1st dan black belt just means you know the basic moves and are still very much a student. These guys in the video don't look all that advanced to me for the most part. (It's not easy to be admitted to Kyoto University, by the way.)

Here's a top-level Kosen guy. He's destroying those scrubs in Canada ;-)

Wikipedia: Kosen judo (高專柔道 Kōsen jūdō) is a variation of the Kodokan judo competitive ruleset that was developed and flourished at the kōtō senmon gakkō (高等専門学校)(kōsen (高專)) technical colleges in Japan in the first half of the twentieth century. Kosen judo's rules allow for greater emphasis of ne-waza (寝技, ground techniques) than typically takes place in competitive judo and it is sometimes regarded as a distinct style of judo.

Today, the term "kosen judo" is frequently used to refer to the competition ruleset associated with it that allows for extended ne-waza. Such competition rules are still used in the Nanatei Jūdō / Shichitei Jūdō (七帝柔道 Seven Imperials Judo) competitions held annually between the seven former Imperial universities. Similarly, there has been a resurgence in interest in Kosen judo in recent years due to its similarities with Brazilian jiu jitsu.
Brazilian Jiujitsu (BJJ) was introduced to Brazil through the Gracie family by judoka Mitsuyo Maeda. Maeda had significant experience fighting wrestlers and boxers; from this experience he developed a theory of combat that has evolved into modern MMA.
According to Renzo Gracie's book Mastering Jujitsu, Maeda not only taught the art of judo to Carlos Gracie, but also taught a particular philosophy about the nature of combat based on his travels competing and training alongside catch-wrestlers, boxers, savate fighters, and various other martial artists. The book details Maeda's theory that physical combat could be broken down into distinct phases, such as the striking phase, the grappling phase, the ground phase, and so on. Thus, it was a smart fighter's task to keep the fight located in the phase of combat that best suited his own strengths. The book further states that this theory was a fundamental influence on the Gracie approach to combat.

Wednesday, February 21, 2018

Postdoc in Theoretical Physics and Machine Learning

I am searching for a new postdoc. Please refer applicants to this MSU HR posting.
Postdoc in Theoretical Physics and Machine Learning

Stephen Hsu, Vice-President for Research and Professor of Physics at Michigan State University, anticipates filling a Research Associate (postdoctoral) position to start in the summer or fall of 2018. The successful applicant will have broad interests in theoretical physics and good computational skills. In addition to research in particle physics and cosmology, he or she will work on problems in machine learning and computational genomics.

Ongoing MSU theoretical physics research includes QCD theory and phenomenology, electroweak symmetry breaking mechanisms, supersymmetry and other beyond-the-standard-model scenarios, cosmology, and collider phenomenology. Recently, a new group of 3 theorists have been hired in the area of lattice QCD.

The Physics/Astronomy Department at MSU has 60 faculty members; it has strong research programs in Condensed Matter Physics, Nuclear Physics, and Astronomy, in addition to High Energy Physics (http://www.pa.msu.edu/hep/hept.html).


Sunday, February 18, 2018

Giorgio Moroder is Boss

See also The History of Synth Pop.
Wikipedia: In 1977 ... he co-wrote and produced the seminal Donna Summer hit single "I Feel Love",[5][8] the first track in the Hi-NRG genre. The following year he released "Chase", the theme from the film Midnight Express. ... A double album of the Foxes soundtrack was released on the disco label Casablanca Records which includes Donna Summer's hit single "On the Radio", which Moroder both produced and co-wrote. ... The American Gigolo soundtrack featured the Moroder-produced "Call Me" by Blondie, a US and UK number one hit. The combined club play of the album's tracks was number two for five weeks on the disco/dance charts.[9] In 1982 he wrote the soundtrack of the movie Cat People, including the hit single "Cat People (Putting Out Fire)" featuring David Bowie. In 1983, Moroder produced the soundtrack for the film Scarface. ... In 1986, Moroder collaborated with his protégé Harold Faltermeyer (of "Axel F") and lyricist Tom Whitlock to create the score for the film Top Gun (1986) which included Kenny Loggins' hit "Danger Zone" and Berlin's "Take My Breath Away".

0:00 Donna Summer - Hot Stuff 3:49 Donna Summer - I Feel Love 9:28 Giorgio Moroder - Chase 13:10 Donna Summer - Love to Love You Baby 16:35 Giorgio Moroder - From Here to Eternity 22:26 Blondie - Call Me 26:58 Japan - Life in Tokyo 29:29 Paul Engemann - Push it To the Limit 32:32 David Bowie - Cat People (Putting Out the Fire) 36:35 Giorgio Moroder - E=MC² 41:29 Amy Holland - She's On Fire (GTA version) 44:42 Irene Cara - What a Feeling 48:01 Giorgio Moroder - I'm Left, You're Right, She's Gone 53:03 Philip Oakey & Giorgio Moroder - Together in Electric Dreams 56:51 Berlin - Take My Breath Away 1:01:17 Elizabeth Daily - Shake it Up Tonight (GTA version) 1:04:24 Giorgio Moroder - I Wanna Rock You 1:10:52 Michael Sembello - Maniac 1:13:13 Donna Summer & Barbra Straisand - Enough is Enough 1:17:58 Daft Punk - Giorgio by Moroder

This track starts with a Moroder interview -- The sound of the future! :-)

Thursday, February 15, 2018

Genetic testing and embryo selection: current status and ethical issues

This is a conversation with two Stanford students about the current status of genetic testing of embryos in IVF, focusing on related ethical issues. Because there is a lot of interest in this topic I suggested we record the conversation and put it online.

I was at Stanford last fall to give a #nofilter talk on this subject, which is where I met one of the students in the video. When I was at Caltech we used to think of Stanford as kind of a soft place, where people didn't have to work so hard. Well, things are different now! My talk was on Friday evening in the Gates Computer Science Building. As I crossed campus I passed football fans (mostly alumni) clad in cardinal (Stanford) and purple (U Washington) heading toward the stadium. I was shocked to find the CS building full of students working really hard at 5:30pm on Friday! (Just like tech, back in the day, I thought.) I was told that 1000 students are enrolled in the machine learning course...

Frank Herbert interview on the origins of Dune (1969)

The interviewer is Willis E. McNelly, a professor of English (specializing in science fiction). Herbert discusses artistic as well as conceptual decisions made in the writing and background world building for Dune. Highly recommended for any fan of the book.

See also Dune and The Butlerian Jihad and Darwin Among the Machines.
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 ...
"Kwisatz Haderach" is similar to the Hebrew "Kefitzat Haderech", which literally means "contracting the path"; Herbert defines Kwisatz Haderach as "the Shortening of the Way" (Dune: Appendix IV).

Another good recording of Herbert, but much later in his life.

Sunday, February 11, 2018

The History of Synth Pop (video documentary)

I had a vague awareness of synth pop groups like Depeche Mode, Joy Division, New Order, Human League, OMD when I was growing up. I loved the music but knew almost nothing about the bands and the context from which they emerged. This documentary locates them in the post-punk, Kraftwerk-influenced UK of the late 1970s and early 1980s. Highly recommended if songs from these groups give you a jolt of exuberant nostalgia :-)

Now that I'm older I really enjoy this kind of exploration, in which writers, artists, scientists, entrepreneurs reminisce about their youthful moments of creation and discovery. How did it look at the time? And now, in the fullness of life? All those moments, lost in time like tears in rain.

I watched Atomic Blonde on a recent flight and, other than one long fight scene near the end -- "Stoy! Stoy!" (pleading... Bang!), found it mostly forgettable. But the incredible 1980s soundtrack got me thinking about this music again...

AI and Genomics, explained (2 videos)

This video is a nicely done short introduction to AI for non-specialists. It's part of Shift Change, a six part series on automation and the future of work.

I came across the video when creator Joss Fong (Vox) contacted me about her new project on human genomics and genomic prediction. As readers know I think the two most impactful technologies over the next 20-30 years will be AI and genomics. So Fong is on the right track...

This is the best (non-technical) video I've seen on the coming genomic revolution. However, it's from 2016 and does not focus on the machine learning / bioinformatic challenge of figuring out exactly which edits one should make -- i.e., the part of the problem I work on :-)  For the real thing, see here.

From a recent talk I gave at a biomedical research institute:
Your children and grandchildren will not just be competing against other people. They will also compete in the marketplace with machines. The code run on these machines is improving every day, thanks to AI. Will the DNA code run by your descendants also need to improve?


Of course it's not just about competition. How can we put a value on a healthy, long life? The ability to swim effortlessly across a pool or run fast and leap higher? To actually understand what Einstein did, in place of some vague second-hand words?

Friday, February 09, 2018

UFC 221: Rockhold vs Romero

Two superb athletes will meet at UFC 221 for the 185lb championship. I'd say 65% chance Rockhold wins, but I won't be shocked if Yoel explodes and KOs Rockhold with little warning.

Like Chael Sonnen (below) I am really excited to see them grapple -- one of the top MMA BJJ talents (Rockhold) versus a former World Champion in freestyle wrestling. Rockhold's top game is very strong -- he might be the first person ever to control and finish Romero.

See also Yoel Romero, freak athlete. He's 40 years old!

Great analysis of the fight from Firas Zahabi (Georges St. Pierre's coach) and Chael Sonnen:

Wednesday, February 07, 2018

US Needs a National AI Strategy: A Sputnik Moment?

The US needs a national AI strategy. Many academic researchers that could contribute to AI research -- including to fundamental new ideas and algorithms, mathematical frameworks for better understanding why some algorithms and architectures work better than others, etc. -- are not able to get involved at the real frontier because they lack the kind of curated data sets and large compute platforms that researchers at Google Brain or DeepMind have access to. Those resources are expensive, but necessary for rapid progress. We need national infrastructure platforms -- similar to physics user facilities like an accelerator or light source or telescope -- in order to support researchers at our universities and national labs doing work in machine learning, AI, and data science.

In contrast, China has articulated a very ambitious national AI plan which has them taking the lead sometime in the 2020s.

Eric Schmidt discusses these points in the video, declaring this a Sputnik moment:

Sunday, February 04, 2018

Steve Pinker and Joe Rogan

I've just started watching this so I can't give you an evaluation of the whole conversation. Looks promising -- they jump right in on topics like sex differences, political correctness, internet flame wars, the Trump candidacy, social media, ... (I'm skipping the Super Bowl, by the way. I stopped watching the NFL and NBA years ago.)

Pinker: "Virtue Signaling Fanatics are a Thing"  (at about 30min)

In case 2 hours of Steve Pinker is not enough for you, here's a panel he and I were on at the 92nd Street Y.

Thursday, February 01, 2018

Counting branches of the black hole wave function

When I was at Caltech a few weeks ago I had a chance to discuss the recent paper below by Sean Carroll and collaborators. (Authors are at Caltech, Berkeley, and UBC.)

Their paper is very clearly written, but probably suitable only for experts who are already familiar with the black hole information paradox. I discussed related ideas in 2013 papers Macroscopic superpositions and black hole unitarity and Factorization of unitarity and black hole firewalls.
Branches of the Black Hole Wave Function Need Not Contain Firewalls

Abstract: We discuss the branching structure of the quantum-gravitational wave function that describes the evaporation of a black hole. A global wave function which initially describes a classical Schwarzschild geometry is continually decohered into distinct semiclassical branches by the emission of Hawking radiation. The laws of quantum mechanics dictate that the wave function evolves unitarily, but this unitary evolution is only manifest when considering the global description of the wave function: it is not implemented by time evolution on a single semiclassical branch. Conversely, geometric notions like the position or smoothness of a horizon only make sense on the level of individual branches. We consider the implications of this picture for probes of black holes by classical observers in definite geometries, like those involved in the AMPS construction. We argue that individual branches can describe semiclassical geometries free of firewalls, even as the global wave function evolves unitarily. We show that the pointer states of infalling detectors that are robust under Hamiltonian evolution are distinct from, and incompatible with, those of exterior detectors stationary with respect to the black hole horizon, in the sense that the pointer bases are related to each other via nontrivial transformations that mix system, apparatus, and environment. This result describes a Hilbert-space version of black hole complementarity.
At question is a possible loophole in the AMPS argument that black hole (BH) firewalls are a necessary consequence of the assumption of unitary evolution (i.e., that the quantum information associated with things that fall into the hole eventually re-emerges in the Hawking radiation).

I pointed out that as a BH evaporates, fluctuations in the specific pattern of Hawking radiation lead to macroscopically different trajectories of the BH itself. The BH wave function is therefore a superposition of many branches which describe different spacetime geometries. The firewall construction, and many of the older arguments indicating a BH information paradox, assume a fixed semiclassical geometry. I noted that unitarity might be violated on each decoherent branch of the BH wave function, but restored when all the superpositions are added together.

Most of my discussions with AMPS, and their criticism of my papers, focused on counting the number of decoherent branches. They claimed it was obvious that there were not enough decoherent branches to restore unitarity, whereas I claimed that it was obvious that the number of decoherent branches was of the same order as the total number of Hawking radiation states. To construct the BH information paradox one has to assume a universe much larger than the BH, with many more degrees of freedom, so that each Hawking quantum that leaves the BH is decohered via interactions with the environment before reaching future infinity. Thus (I argued***) there are enough branches to (in principle) unitarize the separately non-unitary processes on each branch. Whether and how this actually occurs is still an open question! But it seems possible to me that the complex superposition structure of the "wave function of the universe" containing a BH plays a role in the information paradox.

Sean and his co-authors emphasize that AMPS have the burden of proof to show that summing over branches cannot unitarize the BH amplitude.

For more, see these posts:

Black hole firewalls and all that
Big brains battle black hole firewalls
Fuzzballs, black holes and firewalls

*** The difficult question is whether one should run the AMPS construction over a description that is coarse grained over many decoherent branches, thereby reducing significantly the effective total number.

Blog Archive