Crowd-sourcing for scientific research

Computers are much better than most humans at some tasks (eg, remembering large amounts of information, tedious and routine processing of large amounts of data), but worse than many humans at others (eg, generating new ideas, spatial pattern matching, strategic thinking). Progress may come from combining both types of machine (humans, computers) in ways which make use of their specific skills.  The journal Nature yesterday carried a report of a good example of this:  video-game players are able to assist computer programs tasked with predicting protein structures.  The abstract:

People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully ‘crowd-sourced’ through games, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. We show that 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.”

Seth Cooper et al. [2010]: Predicting protein structures with a multiplayer online gameNature, 466:  756–760.  Published:  2010-08-05.
Eric Hand [2010]:  Citizen science:  people powerNature 466, 685-687. Published 2010-08-04.
The Foldit game is here.

Berger on drawing

Following Bridget Riley on drawing-as-thinking, I have been reading Jim Savage’s fascinating collection of writings by John Berger on the topic of drawing.  Although Berger does not say so, he is talking primarily about representational drawing – the drawing of things in the world (whether seen or remembered) or things in some imagined world – not abstract drawing.  Some excerpts:

  • “For the artist drawing is discovery.  And that is not just a slick phrase, it is quite literally true.  It is the actual act of drawing that forces the artist to look at the object in front of him, to dissect it in his mind’s eye and put it together again; or, if he is drawing from memory, that forces him to dredge his own mind, to discover the content of his own store of past observations.” (page 3)
  • “It is a platitude in the teaching of drawing that the heart of the matter lies in the specific process of looking.  A line, an area of tone, is not really important because it records what you have seen, but because of what it will lead you on to see.  Following up its logic in order to check its accuracy, you find confirmation or denial in the object itself or in your memory of it.  Each confirmation or denial brings you closer to the object, until finally you are, as it were, inside it:  the contours you have drawn no longer marking the edge of what you have seen, but the edge of what you have become.  Perhaps that sounds needlessly metaphysical.  Another way of putting it would be to say that each mark you make on the paper is a stepping-stone from which you proceed to the next, until you have crossed your subject as though it were a river, have put it behind you.” (page 3)
  • “A drawing is an autobiographical record of one’s discovery of an event – seen, remembered or imagined.” (page 3)
  • “A drawing of a tree shows, not a tree, but a tree-being-looked-at.  . . .  Within the instant of the sight of a tree is established a life-experience.” (page 71)
  • “All genuine art approaches something which is eloquent but which we cannot altogether understand.  Eloquent because it touches something fundamental.  How do we know?  We do not know.  We simply recognize.”   (page 80)
  • “Art cannot be used to explain the mysterious.  What art does is to make it easier to notice. Art uncovers the mysterious. And when noticed and uncovered, it becomes more mysterious.”  (page 80)
  • “The pen with which I’m writing is the one with which I draw.  And there are times, like tonight, when it won’t flow and when it demands a bath or a hand moving differently.  All drawings are a collaboration, like most circus-acts.” (page 110)
  • “where are we, during the act of drawing, in spirit?  Where are you at such moments – moments which add up to so many, one might think of them as another life-time?    Each pictorial tradition offers a different answer to this query.  For instance, the European tradition, since the Renaissance, places the model over there, the draughtsman here, and the paper somewhere in between, within arms reach of the draughtsman, who observes the model and notes down what he has observed on the paper in front of him.   The Chinese tradition arranges things differently.  Calligraphy, the trace of things, is behind the model and the draughtsman has to search for it, looking through the model.   On his paper he then repeats the gestures he has seen calligraphically.  For the Paleolithic shaman, drawing inside a cave, it was different again.  The model and the drawing surface were in the same place, calling to the draughtsman to come and meet them, and then trace, with his hand on the rock, their presence.” (page 123)

John Berger [2005]:  Berger on Drawing.  Edited by Jim Savage.  Aghabullogue, Co. Cork, Eire:  Occasional Press.  Second Edition, 2007.
I have written more on the relationships between hand and mind and eye and object here.

Dream on

Over at Normblog, Norm is thinking about anxiety dreams, and seeks to answer the question:  Who is the author of these dreams of ours?  Some think it seems not to be us, since the events in the dream come as a surprise to us and trouble us.  He concludes that it is the dreamer who is the author. If we think of dreams as being like films that we view in our sleep, then I assume Norm means that the author is the film-director, or perhaps the projectionist.
But there is another explanation of  all our dreams, not only those which cause us angst.  That explanation is that our dreams are just random images flashed before us by some mechanical process in our brain.  Here there is no continuous film, no coherent plot, no themes, no actors, no film-director, and the projectionist is outside having a cigarette while images are being loaded automatically by a random reel selector that management installed to save on staff.   We, however, are not outside.  We are sitting down in the front-row of the stalls of the cinema, being the audience for the film. So its no wonder we are surprised by what we see.   We try our best, both then and after waking, to make sense of the images that flash past us, looking for some narrative coherence.  If we have anxieties, this is when they appear, in our attempts at reconstruction of  a plot or a theme or some identifiable characters.   We are indeed the authors of our dreams, but only in the way that texts are written by their readers, and not their writers.

Macho mathematicians

Pianist and writer Susan Tomes has just published a new book, Out of Silence, which the Guardian has excerpted here.  This story drew my attention:

Afterwards, my husband and I reminisced about our attempts to learn tennis when we were young. I told him that my sisters and I used to go down to the public tennis courts in Portobello. We had probably never seen a professional tennis match; we just knew that tennis was about hitting the ball to and fro across the net. We had a few lessons and became quite good at leisurely rallies, hitting the ball back and forth without any attempt at speed. Sometimes we could keep our rallies going for quite a long time, and I found this enjoyable.
Then our tennis teacher explained that we should now learn to play “properly”. It was only then that I realised we were meant to hit the ball in such a way that the other person could not hit it back. This came as an unpleasant surprise. As soon as we started “playing properly”, our points became extremely short. One person served, the other could not hit it back, and that was the end of the point. It seemed to me that there was skill in hitting the ball so that the other person could hit it back. If they could, the ball would flow, one got to move about and there was not much interruption to the rhythm of play. It struck me that hitting the ball deliberately out of the other person’s reach was unsportsmanlike. When I tell my husband all this, he laughs and says: “There speaks a true chamber musician.”

This story resonated strongly with me.  Earlier this year, I had a brief correspondence with mathematician Alexandre Borovik, who has been collecting accounts of childhood experiences of learning mathematics, both from mathematicians and from non-mathematicians.  After seeing a discussion on his blog about the roles of puzzles and games in teaching mathematics to children, I had written to him:

Part of my anger & frustration at school was that so much of this subject that I loved, mathematics, was wasted on what I thought was frivolous or immoral applications:   frivolous because of all those unrealistic puzzles, and immoral because of the emphasis on competition (Olympiads, chess, card games, gambling, etc).   I had (and retain) a profound dislike of competition, and I don’t see why one always had to demonstrate one’s abilities by beating other people, rather than by collaborating with them.  I believed that “playing music together”, rather than “playing sport against one another”, was a better metaphor for what I wanted to do in life, and as a mathematician.
Indeed, the macho competitiveness of much of pure mathematics struck me very strongly when I was an undergraduate student:  I switched then to mathematical statistics because the teachers and students in that discipline were much less competitive towards one another.  For a long time, I thought I was alone in this view, but I have since heard the same story from other people, including some prominent mathematicians.  I know one famous category theorist who switched from analysis as a graduate student because the people there were too competitive, while the category theory people were more co-operative.
Perhaps the emphasis on puzzles & tricks is fine for some mathematicians – eg, Paul Erdos seems to have been motivated by puzzles and eager to solve particular problems.  However, it is not fine for others — Alexander Grothendieck comes to mind as someone interested in abstract frameworks rather than puzzle-solving.  Perhaps the research discipline of pure mathematics needs people of both types.  If so, this is even more reason not to eliminate all the top-down thinkers by teaching only using puzzles at school.”

More on the two cultures of mathematics here.

Learning jazz improvisation

A few days ago, writing about bank bonuses, I talked about the skills needed to get-things-done, a form of intelligence I believe is distinct (and rarer than) other, better-known forms — mathematical, linguistic, emotional, etc. There are in fact many skill sets and forms of intelligence which don’t feature prominently in our text-biased culture. One of these is musical intelligence, and I have come across a fascinating description of taking jazz improvisation and composition lessons from pianist and composer Hall Overton (1920-1972), written by Jack Reilly (1932-2018):

The cigarette dangled out the right side of his mouth, the smoke rising causing his left eye to squint, the ashes from the burning bush got longer and longer, poised precipitously to fall at any moment on the keyboard. Hall always sat at the upright piano smoking, all the while playing, correcting, and making comments on my new assighment, exercises in two-part modern counterpoint. I was perched on a rickety chair to his left, listening intensely to his brilliant exegesis, waiting in vain for the inch-long+ cigarette ash to fall. The ashes never fell! Hall instinctively knew the precise moment to stop playing , take the butt out of his mouth and flick the ashes in the tray on the upright piano to his left. He would then throw the butt in the ash tray and immediately light another cigarette. His concentration and attention to every detail of my assighment made him unaware that he never took a serious puff on the bloody cigarette. I think the cigarette was his “prop” so to speak, his way of creating obstacles that tested my concentration on what he was saying. In other words, Hall was indirectly teaching me to block out any external distractions when doing my music, even when faced with a comedic situation like wondering when the cigarette ashhes would fall on the upright keyboard or even on his tie. Yes, Hall wore a tie, and a shirt and a jacket. All memories of Hall Overton by his former students 9 times out ot 10 begin with the Ashes to Ashes situation. A champion chain smoker and indeed, a master ash flickerer, never once dirtying the floor, piano or his professorial attire.

Hall Overton, composer, jazz pianist, advocate/activist for the New Music of his time and a lover of Theolonius Monk’s music, was my teacher for one year beginning in 1957. I first heard about him from a fellow classmate at the Manhattan School of Music, which at that time was located on East 103rd street, between 2nd and 3rd avenue, an area then known as Spanish Harlem. This chap was playing in one of the basement practice rooms where I heard him playing Duke Jordan’s “Jordu”. I liked what I heard so much so I asked him where he learned to play that way. Hall Overton, was his reply. I took down Hall’s number, called him and said I wanted to take jazz piano lessons. He sounded warm and gracious over the phone which made me feel relaxed because I was nervous about playing for him. I had been playing jazz gigs and casuals since my teens but still felt light years away from my vision of myself as a complete jazz pianist. Hall was going to push the envelope. We set up weekly lessons.
Continue reading ‘Learning jazz improvisation’

Language and thought

A very interesting essay by Lera Boroditsky on the relationship between language and thought.  Comparing languages and cognitive styles in different cultures, she concludes that the structure of a language may influence what we most attend to, and thus our modes of thinking.  (HT: AS)

Follow me to Pormpuraaw, a small Aboriginal community on the western edge of Cape York, in northern Australia. I came here because of the way the locals, the Kuuk Thaayorre, talk about space. Instead of words like “right,” “left,” “forward,” and “back,” which, as commonly used in English, define space relative to an observer, the Kuuk Thaayorre, like many other Aboriginal groups, use cardinal-direction terms — north, south, east, and west — to define space. This is done at all scales, which means you have to say things like “There’s an ant on your southeast leg” or “Move the cup to the north northwest a little bit.” One obvious consequence of speaking such a language is that you have to stay oriented at all times, or else you cannot speak properly. The normal greeting in Kuuk Thaayorre is “Where are you going?” and the answer should be something like ” Southsoutheast, in the middle distance.” If you don’t know which way you’re facing, you can’t even get past “Hello.”
The result is a profound difference in navigational ability and spatial knowledge between speakers of languages that rely primarily on absolute reference frames (like Kuuk Thaayorre) and languages that rely on relative reference frames (like English). Simply put, speakers of languages like Kuuk Thaayorre are much better than English speakers at staying oriented and keeping track of where they are, even in unfamiliar landscapes or inside unfamiliar buildings. What enables them — in fact, forces them — to do this is their language. Having their attention trained in this way equips them to perform navigational feats once thought beyond human capabilities. Because space is such a fundamental domain of thought, differences in how people think about space don’t end there. People rely on their spatial knowledge to build other, more complex, more abstract representations. Representations of such things as time, number, musical pitch, kinship relations, morality, and emotions have been shown to depend on how we think about space. So if the Kuuk Thaayorre think differently about space, do they also think differently about other things, like time? This is what my collaborator Alice Gaby and I came to Pormpuraaw to find out.
To test this idea, we gave people sets of pictures that showed some kind of temporal progression (e.g., pictures of a man aging, or a crocodile growing, or a banana being eaten). Their job was to arrange the shuffled photos on the ground to show the correct temporal order. We tested each person in two separate sittings, each time facing in a different cardinal direction. If you ask English speakers to do this, they’ll arrange the cards so that time proceeds from left to right. Hebrew speakers will tend to lay out the cards from right to left, showing that writing direction in a language plays a role. So what about folks like the Kuuk Thaayorre, who don’t use words like “left” and “right”? What will they do?
The Kuuk Thaayorre did not arrange the cards more often from left to right than from right to left, nor more toward or away from the body. But their arrangements were not random: there was a pattern, just a different one from that of English speakers. Instead of arranging time from left to right, they arranged it from east to west. That is, when they were seated facing south, the cards went left to right. When they faced north, the cards went from right to left. When they faced east, the cards came toward the body and so on. This was true even though we never told any of our subjects which direction they faced. The Kuuk Thaayorre not only knew that already (usually much better than I did), but they also spontaneously used this spatial orientation to construct their representations of time.
People’s ideas of time differ across languages in other ways. For example, English speakers tend to talk about time using horizontal spatial metaphors (e.g., “The best is ahead of us,” “The worst is behind us”), whereas Mandarin speakers have a vertical metaphor for time (e.g., the next month is the “down month” and the last month is the “up month”). Mandarin speakers talk about time vertically more often than English speakers do, so do Mandarin speakers think about time vertically more often than English speakers do? Imagine this simple experiment. I stand next to you, point to a spot in space directly in front of you, and tell you, “This spot, here, is today. Where would you put yesterday? And where would you put tomorrow?” When English speakers are asked to do this, they nearly always point horizontally. But Mandarin speakers often point vertically, about seven or eight times more often than do English speakers.

POSTSCRIPT (ADDED 2010-08-29):  An article by Guy Desutscher in the NYT covering similar ground is here.

Demystifying genius

One of the benefits of training in philosophy is an ability to demystify human ideas, and human language.  A good example is given by Tony Grayling’s article in The Guardian today, which makes the case that human intelligence is more than whatever is measured by IQ tests.  Although Grayling is sometimes prone to unbehooving belligerence (especially when he argues against religious belief), his argument here is clear and calm.  It is not, however, original.  My first investigations into the literature on IQ tests were conducted almost 30 years ago, and even then empirical evidence existed that the test scores of US children were significantly impacted by the race of the persons handing out the test papers; black children do significantly better if the test invigilators are black rather than white.  In the light of such evidence it requires a special kind of either stupidity or malfeasance to believe that only something innate is being tested in an IQ test.  IQ tests test one’s ability to do IQ tests, under the circumstances in which the test is conducted, and nothing more.
However, despite his admirable efforts in demystifying IQ testing, Grayling continues to leave mystified part of the story.  He says:

Some mental aptitudes are hard-wired: gifts for maths and music (which often go together) require no knowledge, and manifest themselves early in life. So does artistic ability.

Professor Grayling appears to know nothing about mathematics, music or art.   While certainly benefiting from natural abilities (and perhaps lucky wirings of the brain or other physical quirks), no one gets very far without acquiring a great deal of knowledge, and undertaking many hours of training, in each of these fields.  Even Srinivasa Ramanujan, every non-mathematician’s favourite example of a “natural-born genius mathematician” was taught, first by himself (from text-books he found), and then by G. H. Hardy.  Ramanujan was famous for his ability to intuit mathematical relationships between numbers which were completely non-obvious, even to other mathematicians working in the same field.  Some of these intuitions were sublime and very profound.  But even at the height of his powers as a mathematician, these intuitions were just as likely to be wrong as correct.  As John Forbes Nash once remarked of his own madness, there was no difference inside his head between his great mathematical ideas and his paranoid lunacies; only the outside world treated these ideas differently.
The situation in music is the same as in mathematics,   Perhaps the greatest musical prodigy of all time in western culture was Felix Mendelssohn-Bartholdy, more advanced even than the young Mozart.   And some of Mendelssohn’s greatest music, and some of the greatest in the western canon, was composed in his teens — for example, the string Octet, written when he was 16. But listen to his 12 string symphonies, composed between the ages of 12 and 14.    There is a discernible increase in sophistication and musicality across the 12, with the last 3 being considerably more sophisticated musically than the preceding 9, and the 3 before that likewise clearly more sophisticated than the first 6.   These are not the works of someone relying on hard-wired gifts or natural ability, with the music arriving fully formed from some untrained, black-box genius-brain, as Grayling would have us believe.  Rather they are the contingent and constructed works of someone struggling with the material – learning, improving, experimenting and visibly maturing as he practiced and trained himself to be a composer.  One can’t compose music without having lots of very specific knowledge — knowledge of the capabilities and constraints of different instruments; knowledge of the rules (as were then believed) of melody and harmony; knowledge of the patterns and styles used for organizing musical materials across long time durations (eg, Sonata form; key relationships across movements).  None of this knowledge (which is both know-what and know-how) is hard-wired in anyone, and all of it has to be learnt, no matter how good one’s musical ear is.   Most of it is socially constructed (ie, it differs from one society to another, and from one time to another), and thus cannot possibly be innate.
No doubt Mendelssohn had some natural abilities, perhaps congenital (since both his father’s and his mother’s families had musicians across several previous generations), but he also had some very strong sociological advantages:  a nurturing and loving home life, the best teachers in the Prussian empire, the best instruments, original manuscript copies of the works of the great composers, and weekly musical salons organized by his mother in the family living room, where Berlin’s best musicians would play the western canon (as it then was) and also play his new compositions.   Who could but prosper in such an environment. If I had to bet on the ratio of nurture (including training and hard-work) to nature in the case of Mendelssohn, I would put it at 95% to 5%.
Coincidentally or otherwise, the demystified view of genius was presented (with references to the literature) by David Brooks in the NY Times yesterday.

Of quacking ducks and homeostasis

After reading a very interesting essay (PDF) by biologist J. Scott Turner discussing Intelligent Design (ID) and Evolution which presents an anti-anti-ID case, I was led to read Turner’s recent book, The Tinkerer’s Accomplice: How Design Emerges from Life Itself. Turner argues that Darwinian Evolution requires, but lacks, a notion of intentionality. Despite the use of an apparently teleological concept, he is no creationist: he argues that both Evolutionary theorists (who refuse to consider any such notions) and Creationists/IDers (who have such a notion, but refuse to examine it scientifically) are missing something important and necessary.

Turner’s key notion is that biological and ecological systems contain entities who create environments and seek to regulate them. Typically, such entities seek to maintain their environment in a particular state, i.e., they aim for environmental homeostasis.  The concept of homeostasis is due to the French pioneer of physiology, Claude Bernard (1813-1878), who observed that the human body and its various organs seek to maintain various homeostatic states internally, for example, the chemical composition of the blood stream. That indefatigable complex systems theorist and statistician Cosma Shalizi has thus proposed calling entities which create and regulate environments, Bernard Machines, and Turner also uses this name. (Turner credits Shalizi for the name but provides no citation to anything written by Shalizi, not even a URL — I think this very unprofessional of Turner.)
For Turner, these entities have some form of intentionality, and thus provide the missing component of Darwinian evolution. For a computer scientist, at least for those who have kept up with research since 1990, a Bernard Machine is just an intelligent agent:  they are reactive (they respond to changes in their environment), they are pro-active (ie, goal-directed), and they are autonomous (in that they may decide within some parameters, how, when, and whether to act). Some Bernard Machines may also have a sense of sociality, i.e., awareness of the existence of other agents in their environment, to complete the superfecta of the now-standard definition of agenthood due to Wooldridge and Jennings (1995).
I understand that the more materialist biologists become agitated at any suggestion of non-human entities possibly having anything like intentionality (a concept with teleological or spiritual connotations, apparently), and thus they question whether goal-directedness can in fact be said to be the same as intentionality. But this argument is exactly like the one we witnessed over the last two decades in computer science over the concept of autonomy of software systems: If it looks like a duck, walks like a duck, and quacks like a duck, there is nothing to be gained, either in practice or in theory, by insisting that it isn’t really a duck. Indeed, as software agent people know very well (see Wooldridge 2000), one cannot ever finally verify the internal states of agents (or Bernard machines, or indeed ducks, for that matter), since any sufficiently clever software developer can design an agent with any required internal state. Indeed, the cleverest software developers can even design agents themselves sufficiently clever to be able to emulate insincerely, and wittingly insincerely, any required internal states.
POSTSCRIPT: Of course, with man-made systems such as economies and societies, we cannot assume all agents are homeostatic; some may simply seek to disrupt the system. For computational systems, we cannot even assume all agents always act in their own self-interest (however they perceive that), since they may simply have buggy code.
J. Scott Turner [2007]: Signs of design. The Christian Century, June 12, 2007, 124: 18-22. Reprinted in: Jimmy Carter and Philip Zaleski (Editors): Best American Spiritual Writing 2008. Houghton Mifflin.
J. Scott Turner [2007]: The Tinkerer’s Accomplice: How Design Emerges from Life Itself. Cambridge, MA, USA: Harvard University Press.
Michael J. Wooldridge [2000]: Semantic issues in the verification of agent communication languages. Journal of Autonomous Agents and Multi-Agent Systems, 3 (1): 9-31.
Michael J. Wooldridge and Nicholas R. Jennings [1995]: Intelligent agents: theory and practice. The Knowledge Engineering Review, 10 (2): 115-152.