Distributed Computing, Marshalling Volunteers for Science and Mathematics

Years ago, I participated in SETI@home, a massively distributed computing project by the Search for Extraterrestrial Intelligence program. Millions of ordinary people contributed their idle computing power to process the vast amounts of data that SETI collects. Distributed computing has expanded since then.

This site tracks many distributed computing projects–past, current, and upcoming.

Some examples:

Evolution@home “is the first public global distributed computing project targeting evolutionary questions by distributing the work to many PCs like the SETI@home and other similar projects . A central server distributes the work to those computers who want to participate in their idle time. So, while you are sleeping at night, your computer will simulate the effects of various evolutionary factors. . .on the survival of populations of endangered species and. . .on the evolution of novel functional adaptations.” (For the more technically minded, see the paper here.)

The Virtual Laboratory project is engaged in research, design, and development of Grid technologies that help in solving large-scale compute and data intensive science applications in the area of molecular biology. . . This helps in examining/screening millions of chemical compounds (molecules) in the Chemical Data Bank (CDB) to identify those having potential use in drug design. “

ZetaGrid aims to verify Riemann’s hypothesis which states that “all non-trivial zeros of the Riemann zeta function are on the critical line (1/2+it where tis a real number).” (This is for those who don’t care if they really understand what they’re trying to help.)

Similarly but easier to understand, this project takes a stab at the Goldbach conjecture, which states that ever even number larger than 2 can be expressed as the sum of two primes.

Here’s a good two part article on distributed computing and the technical issues involved with implementing it.

Julia Child, 1912-2004

Continuing with obituaries, here’s one death that’s had extensive news coverage: Julia Child’s. But having been a fan for so long, I thought that I’d add my voice to the choir, or to the auidience pointing to the choir, by linking to the New York Times‘ extensive coverage of Julia Child. My fondness for Child comes from something best expressed by Sara Dickerman in Slate.

“In many ways, Julia’s greatest contribution to cooking was not bringing French food to America. . .but in freeing Americans from the necessity of cooking for a purpose other than pleasure.”

Food became more thoughtful, in the sense that that adjective can apply to the senses, with Julia Child.

And while it’s old news, the blog of the Julie/Julia project, in which Julie Powell . . . well in her own word:

Mastering the Art of French Cooking. First edition, 1961. Louisette Berthole. Simone Beck. And, of course, Julia Child. The book that launched a thousand celebrity chefs. Julia Child taught America to cook, and to eat. It’s forty years later. Today we think we live in the world Alice Waters made, but beneath it all is Julia, 90 if she’s a day, and no one can touch her.

The Contender [Julie Powell]:

Government drone by day, renegade foodie by night. Too old for theatre, too young for children, and too bitter for anything else, Julie Powell was looking for a challenge. And in the Julie/Julia project she found it. Risking her marriage, her job, and her cats’ well-being, she has signed on for a deranged assignment.

365 days. 536 recipes. One girl and a crappy outer borough kitchen.”

Monday, August 16, 2004

The Future Dictionary of America. McSweeney’s, 208 pp., $28.

The Future Dictionary of America enters the pantheon of satirical dictionaries like Flaubert’s and Bierce’s with a notable distinction: It is jam-packed with winningly offbeat suggestions for making the world a better place. Its jaundiced eye is interconnected to both a brain and a heart, not to mention a first aid kit, a hammer and a tiny vial of fingernail polish in a color called Burnt Icicle… In a world in which everyone has an opinion but no one has any advice, this book is manna.” More of Henry Alford’s review here in Newsday.

Critic with a Cause

In his new incarnation as defender of the realm, Christopher Hitchens predictably cannot help vilifying Edward Said toward the end of his review of Said’s posthumous book, From Oslo to Iraq. This, despite the fact the he and Said were longtime friends (Hitchens even offended Saul Bellow at a dinner party once with his vigorous defense of Said and his views), and despite his still-obvious admiration for Said, both as an intellectual polymath, as well as a man of rare moral character. The review is here in yesterday’s Washington Post. (More worth reading as part of our continuing effort to comprehend what happened to Christopher Hitchens, than for any insight into Said or his work. See my earlier posts about the Hitch here and here.)

Evolvability is a selectable trait

“Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, because of the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object of Darwinian selection, emphasizing the collective nature of the process. We quantify our theory with computer simulations of protein evolution. These simulations demonstrate that rapid or dramatic environmental change leads to selection for greater evolvability. The selective pressure for large-scale genetic moves such as DNA exchange becomes increasingly strong as the environmental conditions become more uncertain. Our results demonstrate that evolvability is a selectable trait and allow for the explanation of a large body of experimental results.” Paper by David J. Earl and Michael W. Deem here in the Proceedings of the National Academy of Sciences.

Pollutants cause huge rise in brain diseases

“The numbers of sufferers of brain diseases, including Alzheimer’s, Parkinson’s and motor neurone disease, have soared across the West in less than 20 years, scientists have discovered. The alarming rise, which includes figures showing rates of dementia have trebled in men, has been linked to rises in levels of pesticides, industrial effluents, domestic waste, car exhausts and other pollutants, says a report in the journal Public Health.” There is more here in The Observer.

Some more on Milosz, Herbert and the Experience of Art and Conscience in the East Bloc

Thinking about Milosz’s death, I remembered a poem written by Zbigniew Herbert and translated by Milosz, allegedly dedicated to Czeslaw Milosz, with Herbert in the role of Fortinbras to Milosz’s Hamlet, and also on the problem of surviving–a trope worth considering now, 15 years after the collapse of the experiment, folly, nightmare, tragedy, what have you, in Eastern Europe.

Elegy of Fortinbras

for C.M.

Now that we’re alone we can talk prince man to man
though you lie on the stairs and see no more than a dead ant
nothing but black sun with broken rays
I could never think of your hands without smiling
and now that they lie on the stone like fallen nests
they are as defenceless as before The end is exactly this
The hands lie apart The sword lies apart The head apart
and the knight’s feet in soft slippers

You will have a soldier’s funeral without having been a soldier
the only ritual I am acquainted with a little
there will be no candles no singing only cannon-fuses and bursts
crepe dragged on the pavement helmets boots artillery horses drums drums I know nothing exquisite those will be my manoeuvres before I start to rule
one has to take the city by the neck and shake it a bit

Anyhow you had to perish Hamlet you were not for life
you believed in crystal notions not in human clay
always twitching as if asleep you hunted chimeras
wolfishly you crunched the air only to vomit
you knew no human thing you did not know even how to breathe

Now you have peace Hamlet you accomplished what you had to
and you have peace The rest is not silence but belongs to me
you chose the easier part an elegant thrust
but what is heroic death compared with eternal watching
with a cold apple in one’s hand on a narrow chair
with a view of the ant-hill and the clock’s dial

Adieu prince I have tasks a sewer project
and a decree on prostitutes and beggars
I must also elaborate a better system of prisons
since as you justly said Denmark is a prison
I go to my affairs This night is born
a star named Hamlet We shall never meet
what I shall leave will not be worth a tragedy

It is not for us to greet each other or bid farewell we live on archipelagos
and that water these words what can they do what can they do prince

(translated from the Polish by Czeslaw Milosz)

Czeslaw Milosz, 1911-2004

Czeslaw Milosz died Saturday in Krakow, Poland. Milosz, a Polish exile, was the recipient of the 1980 Nobel Prize in Literature. His words captured the effort to survive and salvage decency in a world ruined by war and totalitarianism. His fellow East bloc-exiled poet and Nobel Laureate Joseph Brodsky once said of him, “I have no hesitation whatsoever in stating that Czeslaw Milosz is one of the greatest poets of our time, perhaps the greatest.”

I’ve been a fan of his work for a long time, especially of this one, which captures so much . . .

To Raja Rao

Raja, I wish I knew
the cause of that malady.

For years I could not accept
the place I was in.
I felt I should be somewhere else.

A city, trees, human voices
lacked the quality of presence.
I would live by the hope of moving on.

Somewhere else there was a city of real presence,
of real trees and voices and friendship and love.

Link, if you wish, my peculiar case
(on the border of schizophrenia)
to the messianic hope
of my civilization.

Ill at ease in the tyranny, ill at ease in the republic,
in the one I longed for freedom, in the other for the end of corruption.
Building in my mind a permanent polis
forever deprived of aimless bustle.

I learned at last to say: this is my home,
here, before the glowing coal of ocean sunsets,
on the shore which faces the shores of your Asia,
in a great republic, moderately corrupt.

Raja, this did not cure me
of my guilt and shame.
A shame of failing to be
what I should have been.

The image of myself
grows gigantic on the wall
and against it
my miserable shadow.

That’s how I came to believe
in Original Sin
which is nothing but the first
victory of the ego.

Tormented by my ego, deluded by it
I give you, as you see, a ready argument.

I hear you saying that liberation is possible
and that Socratic wisdom
is identical with your guru’s.

No, Raja, I must start from what I am.
I am those monsters which visit my dreams
and reveal to me my hidden essence.

If I am sick, there is no proof whatsoever
that man is a healthy creature.

Greece had to lose, her pure consciousness
had to make our agony only more acute.

We needed God loving us in our weakness
and not in the glory of beatitude.

No help, Raja, my part is agony,
struggle, abjection, self-love, and self-hate,
prayer for the Kingdom
and reading Pascal.

(Berkeley, 1969)

Sunday, August 15, 2004

Visualizing the Blogosphere

Recently, I mentioned to Abbas that a topology of the blogosphere would be useful. I had in mind a visual representation that would show the traffic between blogs. This kind of visualization would, for example, help us to see whether and to what extent the blogosphere is segmented according to like-mindedness. I haven’t found one which has that information, but I have come across some other representations of the blogosphere.

My favorite: “a map of the city that shows where the bloggers are, organized by subway stop. Find out who’s blogging in your neighborhood!” A similar site, the location of bloggers in DC, can be found here. The one here shows bloggers in the UK.

I personally like this one, “3D Artists Around the World. . . a geo-coded database of 3D artists, dynamically displayed on world map. Individual points are overlaid on the map every few seconds. Mouse over a point to obtain the artist’s name and location. Click on the point to visit their site.”

A brief article in e-zine InfoVis.net about visualization of the blogosphere has more links.

Be Afraid, Be Very Afraid

This news is terrifying for aspiring slacker, yours truly.

“Just in time for back-to-school season, researchers have turned procrastinating monkeys into workaholics by suppressing a gene that encodes a receptor for a key brain chemical. The receptor, for the neurotransmitter dopamine, is important for reward learning. By suppressing it, researchers at the US National Institute of Mental Health (NIMH) in Bethesda, Maryland caused monkeys to lose their sense of balance between reward and the work required to get it. . .”

Woolf’s Lost London Essay

“The truth was she did not want intimacy; she wanted conversation. Intimacy has a way of breeding silence, and silence she abhorred. There must be talk, and it must be general, and it must be about everything. It must not go too deep, and it must not be too clever, for if it went too far in either of these directions somebody was sure to feel out of it, and to sit balancing his tea cup, saying nothing.”

This lovely passage comes from a lost Virginia Woolf essay originally written for Good Housekeeping in 1931. Woolf originally wrote a series of six lyrical essays on London for the magazine, but when they were published as the book The London Scene in 1975, only five appeared, “The Docks of London,” “Oxford Street Tide,” “Great Men’s Houses,” “Abbeys and Cathedrals,” and “‘This is The House of Commons’.” In “‘This is The House of Commons’,” Woolf remarks: “The mind, it seems, like to perch, in its flight through empty space, upon some remarkable nose, some trembling hand; it loves the flashing eye, the arched brow, the abnormal, the particular, the splendid human being.” This is as good as it gets; a nice encapsulation of Woolf’s entire philosophy; writing as a great house of commons. London, of course, was the Dublin of Woolf’s Ulysses, Mrs. Dalloway.

The London Scene is set to be republished in September by Snowbooks in the UK with the sixth essay finally added. The Guardian has republished the essay for the first time in over 70 years.

A Debate on Whether Psychoanalysis is a Science or Just a Historical Curiosity

Few issues inflame heated discussion in the scientific community as the scientific standing of psychoanalysis. (One editor cannot but help add “that Viennese quack” after any mention of Freud. I began thinking about the issue of what kind of knowledge is critical theory after coming upon Raymond Geuss’ concise and brilliant The Idea of a Critical Theory.)

Now Butterflies and Wheels, one of more intelligent on-line journals/debate fora, has an exchange on Psychoanalysis as Science with Norman Holland insisting:

“Current objections to psychoanalysis as untestable and unscientific ignore two facts. First, a large body of experimental evidence has tested psychoanlaytic ideas, confirming some and not others. Second, psychoanalysis itself, while it does not usually use experimentation, does use holistic method. This is a procedure in wide use in the social sciences and even in the “hard” sciences.” (Read the full article here.)

And Frederick Crews rejoins:

“[Norman] Holland maintains that important parts of psychoanalytic theory have been experimentally confirmed . . . As he recognizes, this judgment stands at odds with the tacit, all but unanimous verdict of North American psychology faculties. Where psychoanalysis appears at all in the catalogs of well-regarded university departments of psychology, it usually figures as a prescientific historical curiosity, not as a viable body of theory. . . Holland asserts that this snub bespeaks not a considered scientific assessment but rather “a deep-seated prejudice against psychoanalysis” on the part of psychology professors and textbook authors. The academic establishment, he holds, has turned its back on a mountain of studies validating key portions of psychoanalytic doctrine . . .”

Three hours, one ficus, and eleven dimensions…

In “The Universe According to Brian Greene,” Jonah Lehrer profiles the already-high-profile Greene, physics wunderkind at Columbia University, author of the book The Elegant Universe, and host of the PBS television series of the same name. The article can be found here in the interesting magazine Seed. (Thanks to Steven Pinker for drawing my attention to this publication.)

The Internet as Research Laboratory

Back in the good ole days of grad school, my nerdier colleagues and I would joke (sort of) about having a panel at the American Political Science Association on things like “Trembling-hand Perfect Equilibria in Alpha-Quadrant Negotiations between the Federation and the Dominion” or “Klingon Martial Cultures, Federation Citizen-Militias, Romulan Political Officers and Genetically Engineered Janissaries: Towards a non-Teleological Hermeneutic of Security Studies.” That was very geeky, yes.

But with the advent of the Internet and large virtual communities, scholars (and not just computer scientists) have found new laboratories among the fetishes of geeks.

Edward Castranova’s research was among the first to bring new scholarly uses of Internet communities to the attention of social scientists. (His story is fascinating.) For a long time, the dilemma of social science, in the words of the economist Edward Chamberlain, was that scholars “cannot observe the actual operation of a real model under controlled circumstances. Economics [and for that matter social science in general] is limited by the fact that resort cannot be had to the laboratory techniques of the natural sciences.”

Castranova realized that massive multiplayer online role playing games offer a way around this dilemma. For example, in the on-line world of Everquest, Star Wars Galaxies and Ultima-Online, everyone begins with the same endowments. What happens when equals interact in a dynamic environment?

And since your character can be either male or female, these virtual worlds are labs for examing how gender is valued. “The average avatar [character] price is 333 dollars; the price discount for females is 40 to 55 dollars, depending on methods.” This despite the fact that there are no differences in talent among these virtual charater-types.

Moreover, these communities could be measured in real world terms in interesting ways, usually through eBay, as in Castronova’s estimation of the economy of “‘Norrath’, populated by an exotic but industrious people. The nominal hourly wage is about USD 3.42 per hour, and the labors of the people produce a GNP per capita somewhere between that of Russia and Bulgaria.”

(Read the interview with him, here.)

Now a linguist has found an interesting use for “Hot or Not.” “Amy Perfors of the Massachusetts Institute of Technology in Boston, US, placed photos with fake names on a website called “Hot or Not”, which allows viewers to rank strangers’ photos for attractiveness. She found that men labelled with names including “front vowels,” such as the “aaa” sound in Matt were rated as more attractive by website viewers than photos labelled with “back vowel” names, such as the “aw” sound in Paul. The opposite was true for women’s names.” Check out the study, here, or just the synopsis, here.

I’m waiting for an internet as laboratory research methodology graduate class.

Co-operation has brought the human race a long way in a staggeringly short time

From The Economist:

“Our everyday life is much stranger than we imagine, and rests on fragile foundations.” This is the intriguing first sentence of a very unusual new book about economics, and much else besides: “The Company of Strangers”, by Paul Seabright, a professor of economics at the University of Toulouse. (The book is published by Princeton University Press.) Why is everyday life so strange? Because, explains Mr Seabright, it is so much at odds with what would have seemed, as recently as 10,000 years ago, our evolutionary destiny. It was only then that “one of the most aggressive and elusive bandit species in the entire animal kingdom” decided to settle down. In no more than the blink of an eye, in evolutionary time, these suspicious and untrusting creatures, these “shy, murderous apes”, developed co-operative networks of staggering scope and complexity—networks that rely on trust among strangers. When you come to think about it, it was an extraordinarily improbable outcome.

More here.

Two score and seventeen years ago…

“Long years ago we made a tryst with destiny, and now the time comes when we shall redeem our pledge, not wholly or in full measure, but very substantially. At the stroke of the midnight hour, when the world sleeps, India will awake to life and freedom. A moment comes, which comes but rarely in history, when we step out from the old to the new, when an age ends, and when the soul of a nation, long suppressed, finds utterance.”

Unless one is a block, a stone, a worse than senseless thing, it is impossible to remain unmoved by Jawaharlal Nehru’s stirring words on the occasion of India’s hard-won independence from British rule. Listen to a recording of the speech here, or read the text here.

John Maynard Smith, (1920—2004)

JMSEarlier this year, one of the greatest evolutionary biologists of our time, John Maynard Smith, died. Lamentably, his name remains largely unknown outside his field. His prodigious oevre includes contributions to aeronautical engineering and game theory, in addition to biology. He was trained in biology by the legendary J.B.S. Haldane.

“He had the trained eye of a field biologist and an inspiring knowledge of natural history to draw on, and also made major contributions to our understanding of bacteria, genetics, and the evolution of animal signaling. The complete biologist, with expertise and bold hypotheses to offer on every topic from the origins of life to the evolution of human language and culture, he was also one of biology’s best explainers. He was, in fact, what every philosopher should try to be and few succeed in becoming: a connoisseur of beautiful ideas. To him, a puzzle about the twofold cost of sex, or hypercycles, or the evolution of honest signalling, or any other problem of evolutionary theory, was like a new species of butterfly to a lepidopterist–something to be examined with rigorous attention to detail, so it can be understood from the ground up, its life cycle and prospects and kin all framed and mapped with loving care and brilliant insight. Even his most technical articles can be grasped in their essentials (with effort!) by non-experts thanks to his lucid style and abhorrence of jargon, but he also lavished attention on more accessible versions of the best specimens for a wider reading public. I suspect that almost as many professors as students have gratefully clung to these beacons of authority and clarity in the storm-tossed seas of theoretical controversy.”

That is from an obituary by Daniel Dennett here; there is an obituary by Richard Dawkins here; one by David Harper here.

Here is an interview with JMS in The Evolutionist. More obituaries and other information can be found here.

Saturday, August 14, 2004

Reinventing Pakistan

QuaidOn this, the 57th anniversary of my homeland, Pakistan’s, birth, could we for a few moments not think about military government, nuclear proliferation, or terrorism, but about Pakistan’s beautiful and rich cultural variety?

“Pakistan is witnessing an explosion of music, part of a revolution in art and media with potentially far greater appeal to its young people than the sermons of religious conservatives urging them to abandon modernity and confront perceived threats to Islam. Over the past three years, a dozen independent television channels have sprung up, from general networks to specialized news, fashion and music stations. Combined with a boom in advertising, increasing economic growth and rapid cable and satellite penetration, these outlets are fueling not only a new industry, but also a new culture—one not limited to a narrow Westernized elite.”

pak_studentsThat quote is from novelist Mohsin Hamid’s lovingly written article in Smithsonian Magazine.

Our younger twin, India (which turns 57 tomorrow), has sent a message of congratulation.