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Oct 22

Video Game predict Protein Structures

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Reported by John Bohannon in Science Now

People playing a simple video game can match, and even surpass, the efforts of a powerful supercomputer to solve a fiendishly difficult biological problem, according to the results of an unusual face-off. The game isn’t Pac-Man or Doom, but one called FoldIt that pushes people to use their intuition to predict the three-dimensional (3D) structure of a protein.

When it comes to solving protein structures, scientists usually turn to x-ray crystallography, in which x-rays shining through a protein crystal reveal the location of atoms. But the technology is expensive and slow and doesn’t work for all proteins. What scientists would love is a method for accurately predicting the structure of any protein, while knowing nothing more than the sequence of its amino acids. That’s no small task, considering that even a moderately sized protein can theoretically fold into more possible shapes than there are particles in the universe.

To get around that problem, computer programs focus on which shapes require the least amount of energy—and thus which ones the protein is most likely to adopt. But these programs must rely on intense computing to make any headway. One of the most powerful, Rosetta@home, was created by David Baker, a molecular biologist at the University of Washington (UW), Seattle. The program distributes its calculations to thousands of home computers around the world, automatically sending the results back to Baker’s lab. (It runs on the same “distributed computing” architecture as the SETI@home search for alien life.) The entire network is capable of nearly 100 trillion calculations per second, dwarfing most supercomputers.

Two years ago, Baker wondered whether humans might help Rosetta@home do better. Although the program is impressively good at solving the first 95% of the folding of a protein, putting the correct finishing touches on a molecule often stumps it. People complained to Baker by e-mail that it was frustrating to watch the program flail around on their computer screens when the necessary final tweaks were sometimes obvious to the human eye.

So Baker teamed up with UW Seattle computer scientist Zoran Popović to turn protein folding into FoldIt, a relatively simple video game where people grab, poke, and stretch a 3D model of a protein, seeking to score more points by minimizing the protein’s total energy. To evaluate this “human computing” strategy, Baker recently challenged FoldIt players to perform the final folding of 10 proteins. The true structure of each had been solved with x-ray crystallography, but the results were not yet released.

It was a close battle: The predicted structures from FoldIt players were closer to reality than those from Rosetta@home for five of the 10 protein structures. They were also significantly more accurate, Baker’s team reports in tomorrow’s issue of Nature.

FoldIt has been a runaway hit, downloaded and played by over 100,000 people since it was released in May 2008. Baker and Popović are now studying the top players in the hopes of teaching computers the humans’ tricks.

When the game debuted, Arthur Olson, a molecular biologist at the Scripps Research Institute in San Diego, California, told Science that he doubted that nonscientist players could get very far. “I’m thrilled to be wrong,” he now says. “What I didn’t know is that this game would actually create experts.” Olson expects that computers will eventually learn enough from the human players to beat them, as IBM’s supercomputer Deep Blue did with chess. But because human spatial reasoning is still so much better, he says, “computers still have a long way to go.”

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Oct 22

Seeing Spots? Must Be a Forest Cat!

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Credit: (Clockwise From Upper Right) Leopard: edg1/Wikipedia; Bengal Tiger: USFWS; Geoffroy’s cat: Charles Barilleaux/Wikipedia; Cheetah: Thinkstock

It seems obvious: Stripes conceal a tiger in the tall grass, whereas spots help a jaguar remain hidden in its shadowy rainforest home. But is this true? Using Internet image searches and wildlife photo archives, researchers classified 35 species of cats according to their markings, including the size, shape, and direction of the pattern. Then the researchers compared those characteristics with factors such as habitat, prey size, and hunting time. As the team reports online today in the Proceedings of the Royal Society B, in each case, the cat’s markings provided camouflage specific to its habitat, confirming the common wisdom. Spotted cats frequent forests, striped tigers lurk in tall grass, and unmarked lions range out in the open. The team also found that the most irregularly marked species, including jaguars and leopards, tend to hunt at night, where their patterns can confuse the night vision of their prey. All of which suggests that protecting big cats means protecting their habitats as well.

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Oct 21

Forget what you know about good study habits!

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Reported by Benedict Carey in The New York Times, September 6, 2010.

Every September, millions of parents try a kind of psychological witchcraft, to transform their summer-glazed campers into fall students, their video-bugs into bookworms. Advice is cheap and all too familiar: Clear a quiet work space. Stick to a homework schedule. Set goals. Set boundaries. Do not bribe (except in emergencies).

And check out the classroom. Does Junior’s learning style match the new teacher’s approach? Or the school’s philosophy? Maybe the child isn’t “a good fit” for the school.

Such theories have developed in part because of sketchy education research that doesn’t offer clear guidance. Student traits and teaching styles surely interact; so do personalities and at-home rules. The trouble is, no one can predict how.

Yet there are effective approaches to learning, at least for those who are motivated. In recent years, cognitive scientists have shown that a few simple techniques can reliably improve what matters most: how much a student learns from studying.

The findings can help anyone, from a fourth grader doing long division to a retiree taking on a new language. But they directly contradict much of the common wisdom about good study habits, and they have not caught on.

For instance, instead of sticking to one study location, simply alternating the room where a person studies improves retention. So does studying distinct but related skills or concepts in one sitting, rather than focusing intensely on a single thing.

“We have known these principles for some time, and it’s intriguing that schools don’t pick them up, or that people don’t learn them by trial and error,” said Dr. Robert A. Bjork, a psychologist at UCLA. “Instead, we walk around with all sorts of unexamined beliefs about what works that are mistaken.”

Take the notion that children have specific learning styles, that some are “visual learners” and others are auditory; some are “left-brain” students, others “right-brain.” In a recent review of the relevant research, published in the journal Psychological Science in the Public Interest, a team of psychologists found almost zero support for such ideas.

“The contrast between the enormous popularity of the learning-styles approach within education and the lack of credible evidence for its utility is, in our opinion, striking and disturbing,” the researchers concluded.

Ditto for teaching styles, researchers say. Some excellent instructors caper in front of the blackboard like summer-theater Falstaffs; others are reserved to the point of shyness.

“We have yet to identify the common threads between teachers who create a constructive learning atmosphere,” said Dr. Daniel T. Willingham, a psychologist at the University of Virginia and author of the book “Why Don’t Students Like School?”

But individual learning is another matter, and psychologists have discovered that some of the most hallowed advice on study habits is flat wrong. For instance, many study skills courses insist that students find a specific place, a study room or a quiet corner of the library, to take their work. The research finds just the opposite. In one classic 1978 experiment, psychologists found that college students who studied a list of 40 vocabulary words in two rooms – one windowless and cluttered, the other modern, with a view on a courtyard – did far better on a test than students who studied the words twice, in the same room. Later studies have confirmed the finding, for a variety of topics.

The brain makes subtle associations between what it is studying and the background sensations it has at the time, the authors say, regardless of whether those perceptions are conscious. It colors the terms of the Versailles Treaty with the wasted fluorescent glow of the dorm study room, say; or the elements of the Marshall Plan with the jade-curtain shade of the willow tree in the backyard. Forcing the brain to make multiple associations with the same material may, in effect, give that information more neural scaffolding.

“What we think is happening here is that, when the outside context is varied, the information is enriched, and this slows down forgetting,” said Bjork, the senior author of the two-room experiment.

Varying the type of material studied in a single sitting seems to leave a deeper impression on the brain than does concentrating on just one skill at a time. Musicians have known this for years, and their practice sessions often include a mix of scales, musical pieces and rhythmic work. Many athletes stick to that line of thinking and routinely combine their workouts with strength, speed and skill drills.

The advantages of this approach to studying can be striking, in some topic areas. In a study recently posted online by the journal Applied Cognitive Psychology, Doug Rohrer and Kelli Taylor of the University of South Florida taught a group of fourth graders four equations, each to calculate a different dimension of a prism. Half of the children learned by studying repeated examples of one equation, say, calculating the number of prism faces when given the number of sides at the base, then moving on to the next type of calculation, studying repeated examples of that. The other half studied mixed problem sets, which included examples all four types of calculations grouped together. Both groups solved sample problems along the way, as they studied.

A day later, the researchers gave all of the students a test on the material, presenting new problems of the same type. The children who had studied mixed sets did twice as well as the others, outscoring them 77 percent to 38 percent. The researchers have found the same in experiments involving adults and younger children.

“When students see a list of problems, all of the same kind, they know the strategy to use before they even read the problem,” said Dr. Rohrer. “That’s like riding a bike with training wheels.”

With mixed practice, he added, “each problem is different from the last one, which means kids must learn how to choose the appropriate procedure – just like they had to do on the test.”

These findings extend well beyond math, even to aesthetic intuitive learning. In an experiment published last month in the journal Psychology and Aging, researchers found that college students and adults of retirement age were better able to distinguish the painting styles of 12 unfamiliar artists after viewing mixed collections (assortments, including works from all 12) than after viewing a dozen works from one artist, all together, then moving on to the next painter.

The finding undermines the common assumption that intensive immersion is the best way to really master a particular genre, or type of creative work, said Dr. Nate Kornell, a psychologist at Williams College and the lead author of the study.

“What seems to be happening in this case is that the brain is picking up deeper patterns when seeing assortments of paintings; it’s picking up what’s similar and what’s different about them,” often subconsciously.

Cognitive scientists do not deny that cramming can lead to a better grade on a given exam. But hurriedly jam-packing a brain is akin to speed-packing a cheap suitcase, as most students quickly learn – it holds its new load for a while, then most everything falls out.

“With many students, it’s not like they can’t remember the material” when they move to a more advanced class, said Dr. Henry L. Roediger III, a psychologist at Washington University in St. Louis. “It’s like they’ve never seen it before.”

When the neural suitcase is packed carefully and gradually, it holds its contents for far, far longer. An hour of study tonight, an hour on the weekend, another session a week from now: such so-called spacing improves later recall, without requiring students to put in more overall study effort or pay more attention, dozens of studies have found.

No one knows for sure why. It may be that the brain, when it revisits material at a later time, has to relearn some of what it has absorbed before adding new stuff – and that that process is itself self-reinforcing.

“The idea is that forgetting is the friend of learning,” said Kornell. “When you forget something, it allows you to relearn, and do so effectively, the next time you see it.”

That’s one reason cognitive scientists see testing itself – or practice tests and quizzes – as a powerful tool of learning, rather than merely assessment. The process of retrieving an idea is not like pulling a book from a shelf; it seems to fundamentally alter the way the information is subsequently stored, making it far more accessible in the future.

Roediger uses the analogy of the Heisenberg uncertainty principle in physics, which holds that the act of measuring a property of a particle alters that property: “Testing not only measures knowledge but changes it,” he says – and, happily, in the direction of more certainty, not less.

In one of his own experiments, Roediger and Jeffrey Karpicke, also of Washington University, had college students study science passages from a reading comprehension test, in short study periods. When students studied the same material twice, in back-to-back sessions, they did very well on a test given immediately afterward, then began to forget the material.

But if they studied the passage just once and did a practice test in the second session, they did very well on one test two days later, and another given a week later.

“Testing has such bad connotation; people think of standardized testing or teaching to the test,” Roediger said. “Maybe we need to call it something else, but this is one of the most powerful learning tools we have.”

Of course, one reason the thought of testing tightens people’s stomachs is that tests are so often hard. Paradoxically, it is just this difficulty that makes them such effective study tools, research suggests. The harder it is to remember something, the harder it is to later forget. This effect, which researchers call “desirable difficulty,” is evident in daily life. The name of the actor who played Linc in “The Mod Squad”? Francie’s brother in “A Tree Grows in Brooklyn”? The name of the co-discoverer, with Newton, of calculus?

The more mental sweat it takes to dig it out, the more securely it will be subsequently anchored.

None of which is to suggest that these techniques – alternating study environments, mixing content, spacing study sessions, self-testing or all the above – will turn a grade-A slacker into a grade-A student. Motivation matters. So do impressing friends, making the hockey team and finding the nerve to text the cute student in social studies.

“In lab experiments, you’re able to control for all factors except the one you’re studying,” said Willingham. “Not true in the classroom, in real life. All of these things are interacting at the same time.”

But at the very least, the cognitive techniques give parents and students, young and old, something many did not have before: a study plan based on evidence, not schoolyard folk wisdom, or empty theorizing.

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Oct 20

Times Higher Education’s list of the world’s top universities for 2010-11.

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World University Rankings 2010-2011

Times Higher Education’s list of the world’s top universities for 2010-11.

Top 200 world universities

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Oct 20

Unconventional Computation 2011 – 10th International Conference on Unconventional Computation

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Call for Papers or Posters

(Download this CFP in text format or in pdf format.)

Important dates

Paper submission deadline: January 31, 2011
– Notification to authors: March 4, 2011
– Final versions due: March 21, 2011
– Poster submission deadline: April 18, 2011
– UC 2011: June 6-10, 2011


Original papers and posters are solicited in all all areas of unconventional computation. Papers/posters dealing with theory as well as with experiments and applications are welcome. Typical, but not exclusive, topics are: natural computing including quantum, cellular, molecular, neural and membrane computing, as well as evolutionary paradigms; chaos and dynamical systems based computing; proposals for computations going beyond the Turing model.


Authors are invited to submit papers (at most 12 pages) or posters electronically, via EasyChair: All submissions are expected to be in the pdf format. Paper submissions should be prepared following the LNCS format of Springer. Poster submissions should contain either a graphical poster or an abstract with sufficient details for the reviewers. Simultaneous submissions to other conferences with published proceedings are not permitted. Each accepted paper/poster must be presented at the conference. The author of the poster is responsible for printing it. The proceedings (only for papers) will be published in the Lecture Notes in Computer Science by Springer, and will be available at the conference.

Conference location

UC 2011 is organized by the FUNDIM laboratory of the mathematics department at the University of Turku, Finland, under the auspices of EATCS. The conference and the satellite workshops will take place in the Calonia and Arcanum buildings of the University of Turku.

Conference History

The first venue of the Unconventional Computation Conference (formerly called Unconventional Models of Computation) was Auckland, New Zealand, in 1998; subsequent sites of the conference were Brussels, Belgium, in 2000; Kobe, Japan, in 2002; Seville, Spain, in 2005; York, UK, in 2006; Kingston, Canada, in 2007; Vienna, Austria, in 2008; Ponta Delgada, Portugal, in 2009; and Tokyo, Japan, in 2010.

Invited speakers

Samson Abramsky (University of Oxford, UK)
Bastien Chopard (University of Geneva, Switzerland)
David Corne (Heriot-Watt University, UK)
Juhani Karhumäki (University of Turku, Finland)
Gheorghe Păun (Institute of Mathematics of the Romanian Academy, Romania)
Grzegorz Rozenberg (Leiden University, The Netherlands)


Quantum Information
Mika Hirvensalo (University of Turku, Finland)
Cellular Automata
Nicolas Ollinger (Aix-Marseille University, France)
Membrane Computing
Mario de J. Pérez Jiménez (University of Sevilla, Spain)

Satellite workshops

Physics and Computation
org. Mike Stannet
org. Mike Stannet
Language Theory in Biocomputing
org. Tero Harju
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Oct 19

Universities in Britain Brace for Cuts in Subsidies

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As reported by Sarah Lyall in The New York Times newspaper in October 15th 2010.

LONDON — For months, Britain’s universities have warned in apocalyptic terms about the devastating cuts they face as part of the government’s grand plan to reduce public-sector costs. Now, with the government poised next week to announce its spending plans, their worst fears seem about to come true.

Prof. Steve Smith, president of Universities U.K., which represents Britain’s higher-learning institutions, said the government was likely to cut about 80 percent of the current $6.2 billion it pays annually for university teaching, and about $1.6 billion from the $6.4 billion it provides for research.

To make up for the shortfall, universities would have to raise tuition to an average of more than $11,000, Professor Smith said, and doing so would require Parliament to lift the cap on such fees, now set at $5,260.

“It’s a savage cut, and it’s unprecedented, and it’s the government moving out of the funding of higher education,” Professor Smith, vice chancellor of the University of Exeter, said in an interview. “We’ve had a big comfort blanket called state funding, and now we’re being thrown out of the nest.”

Education is just one area where the state plans a major retrenchment. With the government aiming to find $130 billion in savings over the next five years, every department has been asked to plan for cuts as high as 40 percent; the government will present the results in its final spending review on Wednesday.

Meanwhile, interest groups representing virtually ever sector — the arts, the military, transportation and the like — have been pleading that they cannot absorb such drastic shocks to their systems.

The pleading, however, has had little effect.

Britain’s universities, heavily subsidized by the state, already feel pared to the bone after a series of cuts in the past year or so. In anticipation of further cuts, many are beginning to lay off instructors, reduce the number of classes and shut down departments. Some instructors and researchers, dismayed by how little money they are being offered and worried about future financing, have abandoned Britain for more lucrative offers at universities abroad.

Adrian Owen, a renowned neuroscientist at the University of Cambridge and an expert on brain injury, announced recently that he and his team of five researchers were moving to the University of Western Ontario in Canada.

“U.K. science is going through a period of uncertainty, and many of my more senior colleagues said this might not be a bad time to be leaving,” The Guardian quoted Dr. Owen as saying. “There’s nobody in the U.K. putting down $20m saying, ‘We think what you’re doing is really cool; come and do it here.’ ”

Middlesex University said last spring that it intended to close its philosophy department. Swansea University in Wales announced proposals to reduce the teaching staff in its modern languages department to 10 people, from 22. King’s College London said it would abolish its chair in paleography, the study of ancient handwriting — the only such post in Britain. (After an international outcry, it proposed creating a new position in “paleography and manuscript studies” that would be “fully funded from philanthropic monies.”)

Saying it would scale back departments not underpinned by “world class” research, the University of Southampton closed its department of sports science and stopped offering undergraduate classes in social work last year.

Britain’s universities currently get about $22.4 billion a year from the government. Until about 10 years ago, they charged no tuition. Tuition since then has been capped by law at $5,260 for students from the European Union. (Students from outside Europe pay much higher tuition that more accurately reflects the actual cost of their schooling.)

A report on higher education financing issued this week by John Browne, the former chairman of British Petroleum, proposed lifting the cap and giving universities the right to set their own tuition. But any institution charging more than $9,500 would have to pay the state a levy on the higher rate.

The proposals in Mr. Browne’s report face a rocky time in Parliament, where many members of the Liberal Democrat party, part of the coalition government, are implacably opposed to higher tuition. But Mr. Smith warned that the increase was the only way universities could fill the gap left by the impending budget cuts.

“If we don’t have them, we’re in a mess,” he said. “There’s no alternative source of funding.”

Mr. Browne’s report also proposes withdrawing government support completely from subjects in the arts and humanities and concentrating it in areas he believes contribute more to the economy, like science and engineering.

“As far as I’m concerned, this is philistinism on a large scale,” said Paul Cottrell, the head of policy at the University and College Union, which represents teachers in higher education. Some universities may have to abolish subjects in the humanities, Mr. Cottrell said. “The alternative is to cut costs,” he said, “but as soon as you do that you get a reputation for poor quality, and you lose your overseas students pretty quickly.”

While institutions like Oxford or Cambridge can easily find students willing to pay, higher tuition would probably create problems for smaller, less respected or less research-intensive universities, or for those with poorer students, Mr. Cottrell said.

“The question is whether all institutions would be able to attract students at that level of tuition,” he said. “We think a lot of students will be put off, so demand will fall. And it’s possible that some of our institutions will fail, if their only source of income is teaching funding and they get very little research funding.”

Professor Smith of Universities U.K. said such drastic cuts in government spending were not necessary. Speaking of Prime Minister David Cameron’s notion of “the big society,” he said, “When they say the big society, they mean the small state.”

He added, “I think they’re cutting the university sector because they can, and I think that’s terribly damaging for the future of the country.”

This article has been revised to reflect the following correction:

Correction: October 19, 2010

An article on Saturday about fears among British universities that the government will severely reduce funding in order to reduce public-sector costs misidentified the university in Wales that has proposed slashing its modern languages teaching staff to 10 instructors from 22 in anticipation of a funding reduction. It is Swansea, not Cardiff.

A version of this article appeared in print on October 16, 2010, on page A4 of the New York edition.
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Oct 19

“He Gave Us Order Out of Chaos” — R.I.P. Benoît Mandelbrot, 1924-2010

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Image via wikipedia commons

It has been confirmed by the mainstream media that Benoît Mandelbrot, the father of fractal geometry and one of the most famous mathematicians of all time, has passed away about a month shy of his 86th birthday. EDIT: The New York Times has confirmed the news.

Matt Blum remembers the rare and amazing privilege of hearing Mandelbrot speak when he came to visit his high school about 20 years ago: “Even at my science-and-technology high school, most of the students didn’t know much about Mandelbrot, but I’d been fascinated by fractals for years and had brought a copy of his seminal work The Fractal Geometry of Nature for him to autograph, and we chatted for a few minutes. I was a bit starstruck — I was 16 or 17 at the time — but I recall that he asked me what kind of fractal-related work I’d done, and showed genuine interest when I told him that I’d played around a lot with the Mandelbrot Set and some variations on the Sierpinski Gasket. In retrospect, I realize this could not possibly have been of much interest to him, but he took a few minutes to make me feel like an intelligent human being because a mathematical genius wanted to hear about what I was working on”.

After the jump, enjoy an awesome video based on Jonathan Coulton’s awesome tribute to Mandelbrot and his most famous subject of study (which was not actually discovered by him, despite its name).
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Oct 18

Hello world!

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Welcome to my site. This is my first post and I hope you will enjoy it!

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