Free Thought

Back at my old digs last week, I put up a post about programming languages and types. It produced an interesting discussion, which ended up shifting topics a bit, and leading to a very interesting question from one of the posters, and since the answer actually really does involve math, I'm going to pop it up to the front page here. In the discussion, I argued that programmers should know and use many different programming languages; and that that's not just a statement about todays programming languages, but something that I think will always be true: that there will always be good reasons…
My Quantum Optics class this term is a junior/ senior level elective, one of a set of four or five such classes that we rotate through, offering one or two a year. We require physics majors to take one of these classes in order to graduate, and encourage grad-school-bound students to take as many as they can fit in their schedule. Students in all majors are also required to take five "Writing Across the Curriculum" classes, which are intended to be courses with a strong writing component that should build their writing skills both in their discipline and out. As you might imagine, the bulk of…
Hansen's 1988 paper that Pat Michaels misrepresented in testimony is not available online. I've put some extracts here. Hansen, J., I. Fung, A. Lacis, D. Rind, Lebedeff, R. Ruedy, G. Russell, and P. Stone 1988. Global climate changes as forecast by Goddard Institute for Space Studies three-dimensional model. J. Geophys. Res. 93, 9341-9364. Abstract We use a three-dimensional climate model, the Goddard Institute for Space Studies (GISS) model II with 8° by 10° horizontal resolution, to simulate the global climate effects of time-dependent variations of atmospheric trace gases and aerosols.…
Dave Bacon asks, I answer. Well, OK, Dave was asking how one would go about teaching quantum computing to CS undergrads, while what I provide here is a set of lectures on presenting quantum computing ideas to undergrad physics majors in my Quantum Optics class. But, really, isn't that almost the same thing (don't answer that). The notes: Lecture 17: Computing theory, logic gates, quantum gates, entangling operations. Lecture 18: Quantum algorithms, the Deutsch-Josza algorithm. Lecture 19: Physical implementations of quantum computing, the DiVincenzo Criteria. This more or less concludes the…
When I were a lad (a long time ago) I went to the science museum (with my mother? father? both? I forget...) and remember the wonderful gallery of models of steam engine valve gear, models of old engines (some original models by the actual engineers made as demos before the full-sized ones were built), many of which you could turn and watch the bits move. A few years back I started taking my son there, and to my surprise and delight I found that the same old models were still there, the same as ever (or at least much the same as my fading memories). But yesterday we went to the science museum…
Woke up, got out of bed Ran a comb across my head... 8:40: Leave home, bike to work. 8:50: Arrive at work, stow bike in lab 8:55: Download electronically submitted papers to be graded. Determine which students haven't handed papers in yet. 9:15: Change into teaching clothes, review lecture notes. (Continued...) 9:35-10:40: Teach class on basics of quantum computing, logic gates, supeerpositions and entanglement. 10:45: Let class go five minutes late. Run to bathroom. 10:50-11:55: Second class, review for Tuesday's exam. Answer questions about right-hand rules, magnetic fields, and Faraday's…
Over at my old site, I lamented the apparent death of distance based tree building algorithms. Just as all of life on earth can be divided into three domains, phylogenetic methods can be split into three groups: distance based, maximum parsimony, and maximum likelihood. Distance and parsimony based approaches have been around for a while (and were used prior to the availability of molecular data). The combination of molecular data and more powerful computers allowed large molecular datasets to be analyzed using parsimony methods. Our great computing power has also allowed for the advent…
Last week, we asked our readers a few questions about procrastination: how long it takes them to wake up on a typical morning, how close to the deadline they finish computing their taxes, and so on. The basic question was, are there different types of procrastinators, or if you put off one type of activity, are you more likely to put off another? The results suggest there is some truth to both notions. Let's first look at the evidence that procrastination in one realm is associated procrastination in another. This chart compares sleep habits with tax preparation habits: It does indeed…
The Coalition Against Biopiracy has announced their winners for the 2006 Captain Hook Awards for Biopiracy, and they're a hoot. We already knew that Darwin was a pirate, but now we learn that so are Craig Venter and Google. What are their crimes? Venter is accused of being the "Greediest Biopirate", and Google is accused of being the "Biggest Threat to Genetic Privacy". I have some more details on these charges below the fold, in addition to showing why the Coalition Against Biopiracy needs to walk the plank. Venter is accused of: "undertaking, with flagrant disregard for national…
If you've ever read and been confused by computing theory books, you might appreciate the discussion of Turing machines at Good Math, Bad Math. Or, if you're already happy with the whole Turing machine thing, you might just like that post for the link to a Turing machine simulator applet. Either way, it's all good.
OK after making fun of System Biologists out comes Peter Sorger's latest paper in Cell. In this paper, Sorger's team collected almost 8000 intracellular measurements (they collected some of the data directly and got the rest from the literature - I'll have to check on that) plugged it into an algorithm or a ... ... compact representation of the entire compendium by using discriminant partial least squares regression (DPLSR; Janes et al., 2004). A DPLSR map was created such that the signaling proteins and cytokines were projected onto a set of "principal components" that maximized covariation…
You have two 50g containers of cream. One is 10% fat, and the other 20% fat. You combine them. What is the percentage of fat in the mixture? A. 10% of 50 is 5, 20% of 50 is 10. (10+5)/(50+50) is 15%. The answer is 15%, the arithmetic mean of 10% and 20%. B. 14.1%, the geometric mean of 10% and 20%. C. 15.8%, the root mean square of 10% and 20%. D. It could be either A, B, or C. There is nothing to stop you using any of these means as the answer. And anyway, the Navier-Stokes equations are hard to solve, so how can we figure out what happens when we combine two fluids? If…
This is too cool. One of the world's most powerful supercomputers has conjured a fleeting moment in the life of a virus. The researchers say the simulation is the first to capture a whole biological organism in such intricate molecular detail. The simulation pushes today's computing power to the limit. But it is only a first step. In future researchers hope that bigger, longer simulations will reveal details about how viruses invade cells and cause disease. (Continued below) The fleeting simulation, published in this month's Structure, reveals that although the virus looks symmetrical it…
{NOTE: Here is the post that was delayed last week due to my announcement of arson at the Holocaust History Project.} It occurs to me that I haven't done much straight science blogging lately. Yes, debunking pseudoscience and quackery is fun, useful, and has the potential to educate people about how science is misused, but this is ScienceBlogs. Since arriving here four weeks ago, I haven't fulfilled my quota of science blogging, and it's time to remedy that. Fortunately, while perusing a recent issue of Cancer Research, I found just the ticket, something that would let me discuss science and…
Buried beneath some unseemly but justified squee-ing, Scalzi links to an article about "counterfactal computation", an experiment in which the group of Paul Kwiat group at Illinois managed to find the results of a quantum computation without running the computer at all. Really, there's not much to say to that other than "Whoa." The article describing the experiment is slated to be published in Nature, so I don't have access to it yet, but I'll try to put together an explanation when I get a copy. The experiment involves a phenomenon know as the "Quantum Zeno Effect," though, which deserves a…
Last week's Casual Friday study was all about illusion. For example, you may have thought our goal was to see how well you could recognize an illusion. However, we really just wanted to know what kind of computers our readers use: Amazingly, Cognitive Daily readers use Macs at a rate (22.8 percent) about seven times higher than the U.S. market share of Apple Computers (roughly 3 percent). We did also want to know something about how you see illusions, so we designed a simple experiment based on a brilliant illusion by Akiyoshi Kitaoka. If you haven't visited his web site full of astonishing…
The final and most recent of the Top Eleven is an experiment that goes right to the heart of the weirdness inherent in quantum mechanics. Who: Alain Aspect (1947-present), a French physicist. (Again, Wikipedia is a let-down, but CNRS has useful information.) When: Around 1982 (there are several experiments involved, but the 1982 one is cited by most people). What: His group performed the first experimental tests of Bell's Inequality, which shows that the predictions of quantum mechanics cannot be explained by a "local hidden variable" theory. Explaining that will take some space, so I'll…
Sure enough, Bush did the "science" thing last night. I've already preemptively explained why he's not a credible messenger on this topic; so has DarkSyde (and I'm sure many others on the blogs). Still, let's parse the president's message a bit more: First, I propose to double the federal commitment to the most critical basic research programs in the physical sciences over the next 10 years. This funding will support the work of America's most creative minds as they explore promising areas such as nanotechnology and supercomputing and alternative energy sources. Second, I propose to make…
Over at Gene Expression, Razib spins an interesting question off my call for blog posts: why are there so many biology bloggers? As I said in comments over there, I think there are two main reasons why you find more bio-bloggers than physics bloggers. The first is that there are simply more biologists than physicists-- we're expecting an unprecedented 13 senior physics majors next year, which is forcing some frantic re-organization to handle the load, but a class that small would be a major crisis for the Biology department. The second reason is that biology is really the main front of the "…
Chris Mooney has a well-written review of Michael Crichton's State of Fear. I picked up a copy at the book store and read a couple of pages from the middle. It was like a Tech Central Station column, except that it was a speech by one of the characters, with occasional lame objections by another character. Oh, and it had footnotes. I don't know if you were supposed to imagine Crichton's character speaking the footnotes or what. I didn't buy the speech or the book. John Quiggin also has a book review. His is of Lomberg's new book. Over at RealClimate Michael…