Friday, September 03, 2010

How language shapes our thinking

Just after drafting Monday's post  on how cultural setting shapes our visual cognition,  I read an excellent article by Guy Deutscher in the Sunday NYTimes Magazine, on how language shapes our thinking.  He starts by reviewing the story of the rise and fall of "the Whorfian hypothesis,"  which maintained that if a language had no term for a concept (such as the future), then the speaker of that language would not be able to grasp the concept in the sense that we can.  Hard data crashed the hypothesis, and the counter reaction was so severe that for many years no limits of language on basic cognition have been admitted.  How it turns out that the baby may have been thrown out with the bathwater. Some clips from the article, starting with some fact about differences between languages pointed out 50 years ago by linguist Roman Jakobson:
Languages differ essentially in what they must convey and not in what they may convey...if different languages influence our minds in different ways, this is not because of what our language allows us to think but rather because of what it habitually obliges us to think about.

In recent years, various experiments have shown that grammatical genders can shape the feelings and associations of speakers toward objects around them. In the 1990s, for example, psychologists compared associations between speakers of German and Spanish. There are many inanimate nouns whose genders in the two languages are reversed. A German bridge is feminine (die Brücke), for instance, but el puente is masculine in Spanish; and the same goes for clocks, apartments, forks, newspapers, pockets, shoulders, stamps, tickets, violins, the sun, the world and love...When speakers were asked to grade various objects on a range of characteristics, Spanish speakers deemed bridges, clocks and violins to have more “manly properties” like strength, but Germans tended to think of them as more slender or elegant.

Of course, all this does not mean that speakers of Spanish or French or German fail to understand that inanimate objects do not really have biological sex — a German woman rarely mistakes her husband for a hat, and Spanish men are not known to confuse a bed with what might be lying in it...Did the opposite genders of “bridge” in German and Spanish, for example, have an effect on the design of bridges in Spain and Germany? Do the emotional maps imposed by a gender system have higher-level behavioral consequences for our everyday life?

The area where the most striking evidence for the influence of language on thought has come to light is the language of space — how we describe the orientation of the world around us...egocentric coordinates...depend on our own bodies: a left-right axis and a front-back axis orthogonal to it. The second system uses fixed geographic directions, which do not rotate with us wherever we turn... a remote Australian aboriginal tongue, Guugu Yimithirr, doesn’t make any use of egocentric coordinates at all...Guugu Yimithirr does not use words like “left” or “right,” “in front of” or “behind,” to describe the position of objects. Whenever we would use the egocentric system, the Guugu Yimithirr rely on cardinal directions. If they want you to move over on the car seat to make room, they’ll say “move a bit to the east.” To tell you where exactly they left something in your house, they’ll say, “I left it on the southern edge of the western table.”...languages that rely primarily on geographical coordinates are scattered around the world, from Polynesia to Mexico, from Namibia to Bali.

How does this work? The convention of communicating with geographic coordinates compels speakers from the youngest age to pay attention to the clues from the physical environment (the position of the sun, wind and so on) every second of their lives..This habit of constant awareness to the geographic direction is inculcated almost from infancy...When Guugu Yimithirr speakers were asked how they knew where north is, they couldn’t explain it any more than you can explain how you know where “behind” is.

Recently, it has been demonstrated in a series of ingenious experiments that we even perceive colors through the lens of our mother tongue. There are radical variations in the way languages carve up the spectrum of visible light; for example, green and blue are distinct colors in English but are considered shades of the same color in many languages. And it turns out that the colors that our language routinely obliges us to treat as distinct can refine our purely visual sensitivity to certain color differences in reality, so that our brains are trained to exaggerate the distance between shades of color if these have different names in our language. As strange as it may sound, our experience of a Chagall painting actually depends to some extent on whether our language has a word for blue.

Thursday, September 02, 2010

Sealing the emotions genie

Need to put out of mind an unpleasant memory or unfulfilled desire? By offering yet another example of embodied cognition and metaphorical thinking Li et al. may have just the trick for you:
This research investigated whether the physical act of enclosing an emotionally laden stimulus can help alleviate the associated negative emotions. Four experiments found support for this claim. In the first two experiments, emotional negativity was reduced for participants who placed a written recollection of a regretted past decision or unsatisfied strong desire inside an envelope. A further experiment showed that enclosing a stimulus unrelated to the emotional experience did not have the same effect. Finally, we showed that the effect was not driven by participants simply doing something extra with the materials, and that the effect of physical enclosure was mediated by the psychological closure that participants felt toward the event.

Robbed of lasting pleasures by drugs

Friedman does a nice summary of the course of drug addiction and withdrawal,  noting work on brain correlates of the craving that persists after drug highs have ceased and drug usage has stopped. 

Wednesday, September 01, 2010

Money looms larger to the powerless.

DuBois et al. make observations on an accentuation bias. They explore:
...how people’s place in a power hierarchy alters their representations of valued objects. The authors hypothesized that powerlessness produces an accentuation bias by altering the physical representation of monetary objects in a manner consistent with the size-to-value relationship. In the first three experiments, powerless participants, induced through episodic priming or role manipulations, systematically overestimated the size of objects associated with monetary value (i.e., quarters, poker chips) compared to powerful and baseline participants. However, when value was inversely associated with size (i.e., smaller objects were more valuable), the powerless drew these valued objects smaller, not larger. In addition, the accentuation bias by the powerless was more pronounced when the monetary value associated with the object was greater, increased when the object was physically present, and was mediated by differences in subjective value. These findings suggest that powerlessness fosters compensatory processes that guide representations of valued objects.

Social learning - The importance of copying others

In the August 24 issue of Current Biology Grüter et al. offer a description of experiments on social learning carried out by Rendell et al. that enhance the description given in the abstract of the original paper:
In humans, learning by observing or asking others can save time and effort. For example, a traveler can bypass the need to check out the numerous available restaurants in an unknown city by asking the residents where there is a good place to eat. However, relying on others can be a risky strategy. The person you rely on might have a different taste, a bad memory, or not have visited a restaurant for years. An inability to avoid out-of-date or unreliable information is considered a major pitfall of social learning. As a consequence, theory has predicted that both individuals and populations should usually employ a mixture of both social and individual learning. A new study by Rendell et al. challenges this view and argues that social learning is usually superior.... Inspired by a classic evolutionary tournament that investigated the evolution of cooperation, Rendell et al. organised a computer tournament in which social learning strategies, submitted by entrants, competed in a game of natural selection for a 10,000 Euro prize. Each strategy specified when an individual should copy another, when it should gather its own information, and when it should simply use the information it had already acquired. They found that the strategies that performed best relied almost exclusively on social learning. Because ‘demonstrators’ have information about the expected pay-off of different behaviours, they selectively perform those that are most beneficial for themselves. By doing so, they inadvertently filter information for all other individuals in the population. As a result, individuals relying mostly on copying acquire high-payoff behaviours as well.
Here is the Rendell et al abstract:
Social learning (learning through observation or interaction with other individuals) is widespread in nature and is central to the remarkable success of humanity, yet it remains unclear why copying is profitable and how to copy most effectively. To address these questions, we organized a computer tournament in which entrants submitted strategies specifying how to use social learning and its asocial alternative (for example, trial-and-error learning) to acquire adaptive behavior in a complex environment. Most current theory predicts the emergence of mixed strategies that rely on some combination of the two types of learning. In the tournament, however, strategies that relied heavily on social learning were found to be remarkably successful, even when asocial information was no more costly than social information. Social learning proved advantageous because individuals frequently demonstrated the highest-payoff behavior in their repertoire, inadvertently filtering information for copiers. The winning strategy (discountmachine) relied nearly exclusively on social learning and weighted information according to the time since acquisition.

Tuesday, August 31, 2010

Doing good (or evil) increases physical strength

Kurt Gray offers some interesting observations on the embodyment of moral typecasting:
Moral transformation is the hypothesis that doing good or evil increases agency—the capacity for self-control, tenacity, and personal strength. Three experiments provide support for this hypothesis, finding that those who do good or evil become physically more powerful. In Experiment 1, people hold a 5 lb. weight longer after donating to charity. In Experiment 2, people hold a weight longer when writing about themselves helping or harming another. In Experiment 3, people hold a hand grip longer after donating to charity. The transformative power of good and evil is not accounted for by affect. Moral transformation is explained as the embodiment of moral typecasting, the tendency to “typecast” good- and evildoers as more capable of agency and less sensitive to experience. This has implications for power, aging, self-control, and recovery.

Making decisions: Optimally interacting minds

Bahrami et al. find conditions under which two heads are - and are not - better than one. Science Magazine gives a nice summary:
When two people peer into the distance and try to figure out if a faint number is a three or an eight, classical signal detection theory states that the joint decision can only be as good as that of the person with higher visual acuity. Bahrami et al. propose that a discussion not only of what each person perceives but also of the degree of confidence in those assignments can improve the overall sensitivity of the decision. Using a traditional contrast-detection task, they showed that, when the individuals did not differ too much in their powers of visual discrimination, collective decision-making significantly improved sensitivity. The model offered here formalizes debates held since the Enlightenment about whether collective thinking can outperform that of elite individuals.
The Bahrami et al. abstract:
In everyday life, many people believe that two heads are better than one. Our ability to solve problems together appears to be fundamental to the current dominance and future survival of the human species. But are two heads really better than one? We addressed this question in the context of a collective low-level perceptual decision-making task. For two observers of nearly equal visual sensitivity, two heads were definitely better than one, provided they were given the opportunity to communicate freely, even in the absence of any feedback about decision outcomes. But for observers with very different visual sensitivities, two heads were actually worse than the better one. These seemingly discrepant patterns of group behavior can be explained by a model in which two heads are Bayes optimal under the assumption that individuals accurately communicate their level of confidence on every trial.

Monday, August 30, 2010

Religion and spatial cognition

The latest Science Magazine 'Editor's choice' points to an interesting bit of work. It is well known that East Asians see visual scenes via a holistic mindset in contrast to the Western style of focusing on salient objects. Variation within these cultural categories (between Chinese and Japanese, for example) can be shown. Colzato et al. have looked at the linkage between religious upbringing and visual perception in three somewhat less heterogeneous populations—neo-Calvinists in the Netherlands, Roman Catholics in Italy, and Orthodox Jews in Israel—and found that adherents of each of these religions differed from atheists of the same cultural background. The Calvinists, whose tradition emphasizes the role of the individual, showed greater visual attentiveness to local features, whereas the big picture perspective was favored by Catholics and Jews, whose traditions stress social togetherness. The abstract:
Religion is commonly defined as a set of rules, developed as part of a culture. Here we provide evidence that practice in following these rules systematically changes the way people attend to visual stimuli, as indicated by the individual sizes of the global precedence effect (better performance to global than to local features). We show that this effect is significantly reduced in Calvinism, a religion emphasizing individual responsibility, and increased in Catholicism and Judaism, religions emphasizing social solidarity. We also show that this effect is long-lasting (still affecting baptized atheists) and that its size systematically varies as a function of the amount and strictness of religious practices. These findings suggest that religious practice induces particular cognitive-control styles that induce chronic, directional biases in the control of visual attention.

More trusting people are better lie detectors

Carter and Weber make the interesting counter-intuitive observation that being a pollyanna does not make one more gullible (cf. with my Aug. 24 post). Their research:
...used a job interview context to investigate the relationship between peoples’ degrees of generalized trust—their default assessments of the likely trustworthiness of others—and their ability to detect lies. Participants watched videos of eight simulated job interviews: Half of the interviewees were completely truthful; half told a variety of lies to make themselves more attractive job candidates. Contrary to lay wisdom, high trusters were significantly better than low trusters were at detecting lies. This finding extends a growing body of theoretical and empirical work suggesting that high trusters are far from foolish Pollyannas and that low trusters’ defensiveness incurs significant costs.

Friday, August 27, 2010

Upstairs-Downstairs pathways regulating our cravings.

Kober et al. provide yet another "upstairs/downstairs" story of how it takes increased activity in our frontal cortex to override addictions and cravings fueled by the deeper structures in our old mammalian brain:
The ability to control craving for substances that offer immediate rewards but whose long-term consumption may pose serious risks lies at the root of substance use disorders and is critical for mental and physical health. Despite its importance, the neural systems supporting this ability remain unclear. Here, we investigated this issue using functional imaging to examine neural activity in cigarette smokers, the most prevalent substance-dependent population in the United States, as they used cognitive strategies to regulate craving for cigarettes and food. We found that the cognitive down-regulation of craving was associated with (i) activity in regions previously associated with regulating emotion in particular and cognitive control in general, including dorsomedial, dorsolateral, and ventrolateral prefrontal cortices, and (ii) decreased activity in regions previously associated with craving, including the ventral striatum, subgenual cingulate, amygdala, and ventral tegmental area. Decreases in craving correlated with decreases in ventral striatum activity and increases in dorsolateral prefrontal cortex activity, with ventral striatal activity fully mediating the relationship between lateral prefrontal cortex and reported craving. These results provide insight into the mechanisms that enable cognitive strategies to effectively regulate craving, suggesting that it involves neural dynamics parallel to those involved in regulating other emotions. In so doing, this study provides a methodological tool and conceptual foundation for studying this ability across substance using populations and developing more effective treatments for substance use disorders.


Figure - Regions active during or modulated by the cognitive regulation of craving. (A) Medial (Left) and lateral (Right) views of brain regions that showed greater activation when participants used a cognitive strategy to reduce their craving. Highlighted activations are shown in regions previously implicated in regulation of aversive emotion. (B) Medial (Left) and coronal (Right) views of brain regions that showed reduced activation. Highlighted reductions are shown in regions previously reported in studies of cue-induced craving or emotion. corr, Corrected for multiple comparisons; uncorr, uncorrected for multiple comparisons.

Delusions of Gender.

Katherine Bouton reviews what looks like a very interesting book by cognitive neuroscientist Cordelia Fine which has the title of this post. The book:
takes on that tricky question, Why exactly are men from Mars and women from Venus?, and eviscerates both the neuroscientists who claim to have found the answers and the popularizers who take their findings and run with them...Summarizing the research, she writes, “Nonexistent sex differences in language lateralization, mediated by nonexistent sex differences in corpus callosum structure, are widely believed to explain nonexistent sex differences in language skills.”...What all this adds up to, she says, is neurosexism. It’s all in the brain....But Dr. Fine persuasively argues that it is, in fact, all in the mind. Jan Morris, the historian, travel writer and male-to-female transsexual, saw this implicit stereotyping firsthand: “The more I was treated as a woman, the more woman I became. ”

Thursday, August 26, 2010

Metacognitive deficits in public political discourse

Some interesting chunks from a recent David Brooks column in the NYTimes, on what he takes to be the underlying problem facing this country. He starts by describing the decay in the 19th and early 20th century emphasis on moral character,
...when people were more conscious of the fallen nature of men and women. People were held to be inherently sinful, and to be a decent person one had to struggle against one’s weakness...This emphasis on mental character lasted for a time, but it has abated. There’s less talk of sin and frailty these days...In the media competition for eyeballs, everyone is rewarded for producing enjoyable and affirming content. Output is measured by ratings and page views, so much of the media, and even the academy, is more geared toward pleasuring consumers, not putting them on some arduous character-building regime.

...we’re all less conscious of our severe mental shortcomings and less inclined to be skeptical of our own opinions...We have confirmation bias; we pick out evidence that supports our views. We are cognitive misers; we try to think as little as possible. We are herd thinkers and conform our perceptions to fit in with the group...The ensuing mental flabbiness is most evident in politics. Many conservatives declare that Barack Obama is a Muslim because it feels so good to say so...a seller’s market in ideologies...gives people a chance to feel victimized. There’s a rigidity to political debate. Issues like tax cuts and the size of government, which should be shaped by circumstances (often it’s good to cut taxes; sometimes it’s necessary to raise them), are now treated as inflexible tests of tribal purity.

To use a fancy word, there’s a metacognition deficit. Very few in public life habitually step back and think about the weakness in their own thinking and what they should do to compensate.

Inflammatory and neural responses to social rejection.

Slavich et al. measure changes in both brain activity and inflammatory chemical activity in response to social rejection:
Although stress-induced increases in inflammation have been implicated in several major disorders, including cardiovascular disease and depression, the neurocognitive pathways that underlie inflammatory responses to stress remain largely unknown. To examine these processes, we recruited 124 healthy young adult participants to complete a laboratory-based social stressor while markers of inflammatory activity were obtained from oral fluids. A subset of participants (n = 31) later completed an fMRI session in which their neural responses to social rejection were assessed. As predicted, exposure to the laboratory-based social stressor was associated with significant increases in two markers of inflammatory activity, namely a soluble receptor for tumor necrosis factor-α (sTNFαRII) and interleukin-6 (IL-6). In the neuroimaging subsample, greater increases in sTNFαRII (but not IL-6) were associated with greater activity in the dorsal anterior cingulate cortex and anterior insula, brain regions that have previously been associated with processing rejection-related distress and negative affect. These data thus elucidate a neurocognitive pathway that may be involved in potentiated inflammatory responses to acute social stress. As such, they have implications for understanding how social stressors may promote susceptibility to diseases with an inflammatory component.

Wednesday, August 25, 2010

The psychology of possibility.

An interesting article in the Harvard Magazine describes the life work of Ellen Langer, her demonstrations that our social self image (old versus young, for example) strongly patterns our actual vitality and physiology, her work on Mindfulness, unconscious processing, etc. I recommend that you read the article. Here are some clips from its beginning that hooked me (I actually did my own mini-repeat of the experiment described, a simple self-experiment of pretending that I had been transported back in time to 40 years ago, and convinced myself I was experiencing some of the effects described)...
In 1981, early in her career at Harvard, Ellen Langer and her colleagues piled two groups of men in their seventies and eighties into vans, drove them two hours north to a sprawling old monastery in New Hampshire, and dropped them off 22 years earlier, in 1959. The group who went first stayed for one week and were asked to pretend they were young men, once again living in the 1950s. The second group, who arrived the week afterward, were told to stay in the present and simply reminisce about that era. Both groups were surrounded by mid-century mementos—1950s issues of Life magazine and the Saturday Evening Post, a black-and-white television, a vintage radio—and they discussed the events of the time: the launch of the first U.S. satellite, Castro’s victory ride into Havana, Nikita Khrushchev and the need for bomb shelters.

...Before and after the experiment, both groups of men took a battery of cognitive and physical tests, and after just one week, there were dramatic positive changes across the board. Both groups were stronger and more flexible. Height, weight, gait, posture, hearing, vision—even their performance on intelligence tests had improved. Their joints were more flexible, their shoulders wider, their fingers not only more agile, but longer and less gnarled by arthritis. But the men who had acted as if they were actually back in 1959 showed significantly more improvement. Those who had impersonated younger men seemed to have bodies that actually were younger.

Delaying age-related damange to nerves and muscle

Both exercise and drastic dieting have been shown to have anti-ageing effects in the brain. Studies on mice now suggest that such lifestyle changes preserve communication between nerves and muscles:
The cellular basis of age-related behavioral decline remains obscure but alterations in synapses are likely candidates. Accordingly, the beneficial effects on neural function of caloric restriction and exercise, which are among the most effective anti-aging treatments known, might also be mediated by synapses. As a starting point in testing these ideas, we studied the skeletal neuromuscular junction (NMJ), a large, accessible peripheral synapse. Comparison of NMJs in young adult and aged mice revealed a variety of age-related structural alterations, including axonal swellings, sprouting, synaptic detachment, partial or complete withdrawal of axons from some postsynaptic sites, and fragmentation of the postsynaptic specialization. Alterations were significant by 18 mo of age and severe by 24 mo. A life-long calorie-restricted diet significantly decreased the incidence of pre- and postsynaptic abnormalities in 24-mo-old mice and attenuated age-related loss of motor neurons and turnover of muscle fibers. One month of exercise (wheel running) in 22-mo-old mice also reduced age-related synaptic changes but had no effect on motor neuron number or muscle fiber turnover. Time-lapse imaging in vivo revealed that exercise partially reversed synaptic alterations that had already occurred. These results demonstrate a critical effect of aging on synaptic structure and provide evidence that interventions capable of extending health span and lifespan can partially reverse these age-related synaptic changes.

Tuesday, August 24, 2010

Predicting inherited risk for anxiety

Ned Kalin and his colleagues here at the University of Wisconsin have made the interesting observation that increased brain activity in the amygdala (not inheritable) and anterior hippocampus (inheritable) of young monkeys can predict anxious temperament in young monkeys, leading Kalin to suggest that "that young children who have higher activity in these brain regions are more likely to develop anxiety and depression as adolescents and adults, and are also more likely to develop drug and alcohol problems in an attempt to treat their distress." The study looked at 238 young rhesus monkeys from a family of more than 1500 lab-raised monkeys with well-documented pedigrees. By analyzing the family connections among the young monkeys, which ranged from siblings to distant cousins, the finding was that an anxious temperament was partly heritable, accounting for about 36% of the variability in individual monkeys' responses on a human intruder test (as measured by the reduction in movement and vocalization and increase in stress hormone levels). Elevated responses in the hippocampus were heritable (accounting for about half of individual variability), whereas the elevated responses in the amygdala were not.



Figure from paper - Anxious monkeys show elevated activity in the amygdala (left) and anterior hippocampus (right), but the effects of heredity seem to act more on the hippocampus.

Oxytocin makes people trusting, but not gullible.

Mikolajczak et al. demonstrate that oxytocin (OT) is not the magical “trust elixir” described in the news, on the Internet, or even by some influential researchers. They design experiments to show that it does not make people indiscriminately prosocial (trusting to a fault). They used a customized version of the trust game that manipulated partners’ trustworthiness and measured participants’ investment in each partner. They found higher investment by participants who received a nasal OT spray than by control participants, unless there were cues that a partner might not be trustworthy. They also observed a significant effect of OT when the partner was a computer suggesting that OT’s effect may be primarily moderated not by the human versus nonhuman nature of the partner, but rather by the perceived risk inherent to the interaction. In case you are interested, here is their description of the setup:
Each participant assumed the role of investor and could transfer money to a “trustee,” in whose hands the funds would triple. The trustee would then transfer all the money, part of it, or none of it back to the investor. If the investor entrusted the trustee with all of his money, he could maximize his profits if the trustee was reliable and fair. Conversely, he could lose everything if the trustee was not fair. The trust game is perfectly suited to establish the investor’s level of trust (i.e., the higher the trust, the higher the transfer). Each participant played with three different types of trustees: seemingly reliable humans, seemingly unreliable humans, and the computer (i.e., a fully neutral device). By manipulating the partners’ trustworthiness, we sought to determine the extent to which OT impairs sensitivity to potential signs of dishonesty.

In one part of the game, participants were told that they would play 10 rounds with the computer, which would randomly determine the back transfers; in another part, participants were told that they would play online with real people. We gave participants a brief description of their partner before each round. Based on a pretest, these descriptions were manipulated to induce high or low trust: We combined trustworthy academic fields (e.g., philosophy) and activities (e.g., practicing first aid) to make some partners seem reliable, and untrustworthy academic fields (e.g., marketing) and activities (e.g., playing violent sports) to make other partners seem unreliable. The main effect of partner type  confirms that these descriptions were effective in inducing trust or mistrust in this study. Each participant played 10 rounds with 10 different partners (5 trustworthy, 5 untrustworthy). No back-transfers feedback was provided during the experiment, and presentation order was randomized. Before leaving the laboratory, participants were asked to guess the group (OT or control) to which they had been assigned.

Monday, August 23, 2010

Coping with stress stimulates new brain cell growth.

Interesting stuff from Lyons et al., experiments on monkeys which look like they would extrapolate to us humans:
Coping with intermittent social stress is an essential aspect of living in complex social environments. Coping tends to counteract the deleterious effects of stress and is thought to induce neuroadaptations in corticolimbic brain systems. Here we test this hypothesis in adult squirrel monkey males exposed to intermittent social separations and new pair formations. These manipulations simulate conditions that typically occur in male social associations because of competition for limited access to residency in mixed-sex groups. As evidence of coping, we previously confirmed that cortisol levels initially increase and then are restored to prestress levels within several days of each separation and new pair formation. Follow-up studies with exogenous cortisol further established that feedback regulation of the hypothalamic-pituitary-adrenal axis is not impaired. Now we report that exposure to intermittent social separations and new pair formations increased hippocampal neurogenesis in squirrel monkey males. Hippocampal neurogenesis in rodents contributes to spatial learning performance, and in monkeys we found that spatial learning was enhanced in conditions that increased hippocampal neurogenesis. Corresponding changes were discerned in the expression of genes involved in survival and integration of adult-born granule cells into hippocampal neural circuits. These findings support recent indications that stress coping stimulates hippocampal neurogenesis in adult rodents. Psychotherapies designed to promote stress coping potentially have similar effects in humans with major depression.

Solving protein folding - humans outperform computers

I remember from my graduate student days in the 1960's attending biochemistry lectures in which the professors expressed confidence that we would soon know the algorithms for predicting from the linear sequence of amino acids in a protein the three dimensional shape into which it would fold. That goal has seemed to recede from view despite increasing effort with sophisticated supercomputers. (The problem is that even a moderately sized protein can theoretically fold into more possible shapes than there are particles in the universe.) It turns out that Foldit, a multiplayer online game that engages non-scientists, is now yielding more accurate predictions of correct protein folding than one of the best known computer folding programs, Rosetta@home, which was created by molecular biologist David Baker at Univ. Washington, Seattle. (The program distributes its calculations to thousands of home computers around the world, automatically sending the results back to Baker's lab.) From the abstract of the Cooper et al. paper on their Foldit game:
...top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.
Two useful reviews summarize this work, one in the NYTimes, the other in Science Now.

Friday, August 20, 2010

A Brahms Capriccio as a TGIF offering...

I've been lazy about playing and recording lately, and so have decided to spend a bit more time with my piano. This Brahms Capriccio has one randomly occurring error, which happens with any piece I play regardless of how well I know the notes. (I don't do the cut and paste editing of the good parts. Whatever happens on one complete play through is what you get.) See if you can find the stumble.