This new technique may make it easier to obtain sequences of long dead individuals whose burial sites are known.Science: A High-Coverage Genome Sequence from an Archaic Denisovan Individual We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30X) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity, indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative...
Thursday, 30 August 2012
Sunday, 26 August 2012
Neal Stephenson, in the foreword to David Foster Wallace's Everything and More, wrote about growing up as a faculty kid in a Midwestern American College Town (MACT). The six year old Stephenson, whose father was a professor of Electrical Engineering, moved to Ames, Iowa the year I was born. He attended Ames High School as did I. When I met Stephenson in person, we compared notes and discovered that some of my friends were the younger siblings of...
Wednesday, 22 August 2012
The state of the art in GPU- and statistics-enhanced password cracking. Crackers beating down information entropy just like in the old days at Bletchley Park! (Trivia question: what are "bans" and "cribs"? Answers) Ars technica: ... An even more powerful technique is a hybrid attack. It combines a word list, like the one used by Redman, with rules to greatly expand the number of passwords those lists can crack. Rather than brute-forcing the five letters in Julia1984, hackers simply compile a list of first names for every single Facebook user and...
An interesting Nature paper from deCODE researchers. I find the result stated in the Times coverage of the article a bit shocking. (I haven't read the paper carefully enough to know whether this is an accurate summary.) If these de novo mutations are responsible for a big chunk of the increased autism risk in children of older fathers, then it would be the case that of order 100 additional mutations increases the probability of autism by about 1...
Monday, 20 August 2012
This Atlantic article discusses the application of genomic prediction to cattle breeding. Breeders have recently started switching from pedigree based methods to statistical models incorporating SNP genotypes. We can now make good predictions of phenotypes like milk and meat production using genetic data alone. Cows are easier than people because, as domesticated animals, they have smaller effective breeding population and less genetic diversity. Nevertheless, I expect very similar methods to be applied to humans within the next 5-10 years.The...
Sunday, 19 August 2012
These results were announced last year at a conference talk, now hot off the press at Nature Genetics. As stated in the abstract below, the results are important because they show that selection pressure can work on existing variation in polygenic quantitative traits such as height (no new mutations required! See also here). Group differences in the phenotype are (according to the analysis) not due to drift or founder effects -- it's selection at work. Of course, this has been demonstrated many times in the lab, but certain people refuse to believe...
Friday, 17 August 2012
The excerpts below are from interviews with Benoit Mandelbrot.On the birth of molecular biology under Max Delbruck at Caltech: I would say the more important event was quite outside of my life's work, the arrival of Max Delbruck. Now Max Delbruck was, I think, one of the great personalities of those times. He was a physicist by training, a man belonging to one of the very highest families in Prussia, in many ways a great liberal, in many ways a great authoritarian. Max Delbruck had been told in the '30s, according to rumour, that he was just...
Wednesday, 15 August 2012
Shorter Taleb (much of this was discussed in his first book, Fooled by Randomness): Fat tails + nonlinear feedback means that the majority of successful traders were successful due to luck, not skill. It's painful to live in the shadow of such competitors. What other fields are dominated by noisy feedback loops? See Success vs Ability , Nonlinearity and noisy outcomes , The illusion of skill and Fake alpha.Why It is No Longer a Good Idea to Be in The Investment Industry Nassim N. Taleb Abstract: A spurious...
Tuesday, 14 August 2012
I received this from a practitioner (former physicist) a while ago: The best I have seen on the Knightmare is this: http://www.nanex.net/aqck2/3525.html Also worth noting that the two big shots that made Knight what it is left for Citadel a year ago. Perhaps related, but perhaps not. What a debacle... Earlier post $440M in 45 minut...
Monday, 13 August 2012
Noam Chomsky stirs up some trouble. See also here.A commenter provides another Chomsky quote:"Since no one has succeeded in showing me what I'm missing, we're left with the second option: I'm just incapable of understanding. I'm certainly willing to grant that it may be true, though I'm afraid I'll have to remain suspicious, for what seem good reasons. There are lots of things I don't understand -- say, the latest debates over whether neutrinos have mass or the way that Fermat's last theorem was (apparently) proven recently. But from...
Sunday, 12 August 2012
All dopers? Or just a minority? I had friends in high school who took steroids. At the time, many coaches, doctors and "sports scientists" claimed the drugs didn't work (placebo effect, they said). But it was obvious that they did. I distinctly remember this as the point at which I became very suspicious of statements by medical and "scientific" authorities. If they were wrong about something as simple as this, what else could they be wrong about?Der Spiegel: Angel Heredia, once a doping dealer and now a chief witness for the U.S. Justice Department,...
Thursday, 9 August 2012
This site is a treasure trove of interesting video interviews -- including with Francis Crick, Freeman Dyson, Sydney Brenner, Marvin Minsky, Hans Bethe, Donald Knuth, and others. Many of the interviews have transcripts, which are much faster to read than listening to the interviews themselves.Here's what Murray Gell-Mann has to say about quantum foundations:In '63…'64 I worked on trying to understand quantum mechanics, and I brought in Felix Villars and for a while some comments... there were some comments by Dick Feynman who was nearby. And we...
Bolt becomes the first man to repeat in the 100m and 200m, holding the world and Olympic records in both. As I said in my earlier post, he is a 1 in a billion (or more) talent.“If he wins, that should end the debate about who is the greatest sprinter in history,” Ato Boldon of Trinidad and Tobago, who won bronze medals in the 200 at the 1996 Atlanta Games and the 2000 Sydney Games, said before the race. “Anyone saying it is not Bolt would be doing...
Wednesday, 8 August 2012
Parvez did a PhD in theoretical physics at Oregon and then joined my first startup. Subsequently he worked at Microsoft and then founded his own company, which was recently acquired (I was briefly on the board of advisors). We had a nice breakfast this morning, dwelling on both the past and future. Note the shiny new Porsche :-)See A tale of two geeks, Path integra...
Tuesday, 7 August 2012
I've been corresponding with a German theoretical physicist ("R") recently about quantum mechanics and thought I would share some of it here.[R] Dear Prof.Hsu: I enjoyed reading your recent, very clearly written paper On the origin of probability in quantum mechanics very much. I discussed its subject matter oftentimes with Hans-Dieter Zeh ... We both think that many worlds is an idea that is probably true in some sense.[ME] I have corresponded with Dieter over the years and read most (all?) of his work...
Sunday, 5 August 2012
Friday, 3 August 2012
A new paper from my collaborator James Lee. Ungated copy here, including commentary from other researchers including Judea Pearl.Correlation and Causation in the Study of Personality Abstract: Personality psychology aims to explain the causes and the consequences of variation in behavioural traits. Because of the observational nature of the pertinent data, this endeavour has provoked many controversies. In recent years, the computer scientist Judea Pearl has used a graphical approach to extend the innovations in causal inference developed...
Thursday, 2 August 2012
Does this qualify as the most expensive software bug of all time? Raises concerns about our future as passengers in driverless vehicles ;-)I suppose it's a positive that Knight had to recognize the losses immediately, instead of sweeping them under the rug by adjusting a parameter in a risk model (see, e.g., JP Morgan whale + a million other recent examples). Would Knight have lost even more money if the exchange hadn't shut down trading in the affected names?NYTimes: $10 million a minute. That’s about how much the trading problem that set...
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