Trapped in the USA

This Be The Verse

2007-01-27T15:35:00.000-08:00

Philip Larkin

They fuck you up, your mum and dad.
They may not mean to, but they do.
They fill you with the faults they had
And add some extra, just for you.

But they were fucked up in their turn
By fools in old-style hats and coats,
Who half the time were soppy-stern
And half at one another's throats.

Man hands on misery to man.
It deepens like a coastal shelf.
Get out as early as you can,
And don't have any kids yourself.

7min Masterpiece Documentary of Race

2007-01-25T23:36:00.000-08:00

This short-film made by a 17-year old film-maker Kiri Davis (NYC) is winning awards and stirring up a storm of controversy across the United States.

Simulating a very small peptide: enkephalin

2007-01-25T13:23:00.000-08:00

At parties, people often ask me what I do. Normally I answer that I simulate molecules on a computer. Most people seem satisfied with that answer, after all, it's only an ice-breaking question (people are secretly hoping you answer something along the lines of "sex-worker" or "published novelist").

But once in a while, I'll actually get someone who really wants to know. Then, I'll give an impromptu explanation, complete with flying arms and sound effects.

But really, the best way to understand what I do, is to look at the results of a simulation. And here is one of the simplest simulations using the techniques of molecular dynamics, the neuro-peptide enkephalin in a box of water molecules:

Rolling Stones on why and how Al Gore should run

2007-01-24T17:29:00.000-08:00

A stiff Vice President campaigns on his administration's legacy of unprecedented prosperity. Looks terrible on TV. Bows out, following a disputed vote count. Then, two terms later, with no incumbent in the race, he re-enters the fray. Promises to change the course of a disastrous war founded on lies. And charges to victory. I'm referring, of course, to the 1968 campaign of Richard Milhous Nixon. But four decades later, history has a chance to repeat itself for Albert Arnold Gore. .... [more]

Listen

2007-01-24T11:29:00.000-08:00

My intentions are pure
But my gaze begins to wander
As the voice drones on and on

It is the nature of the Speaker
to Speak
And his words pour forth like raindrops
But try as I might I can only
Focus on the space between the words
The voice drones on and on

He pulls out a handkerchief
Dabbing one round silvery bead of sweat
That has appeared on his high shiny Brow
All the meanwhile
The voice drones on and on

My concentration is my friend
But my friend is weak
I wish it were made of steel
Instead of one-ply toilet paper
My mind is easily scattered into the eight corners of the room
The voice drones on and on

My mind drops my body
But not in a good way
The voice drones on and on

Looking up at the scorching white of the overhead
An errant pointer scurries across my eyes
The screen flickers
The power is cut
A universe dies
But the voice drones on and on

Tea-time #341

2007-01-24T11:28:00.000-08:00

I look into my cup of tea
And see some people swimming
I swirl my cup
Making waves and minor storms
I look carefully and see
That they are mostly accountants
Treading tea in pin-striped suits
Some are frightened, others just smile
And wave
I wave back
If they could they would advise me
Of fantastic opportunities
I could invest in the toaster
For example
After a time my thirst takes hold
I raise the cup to my lips
Surprised, I see that some
Are hanging onto the rim
But undeterred I take a sip
The liquid swirls around the accountants
As they wash down my throat and
I barely notice them
Like the 37th decimal place of π
I feel the tea slide
Some of the accountants no doubt will try to
Abseil back up my windpipes
But that would be as futile
As filling in a tax return

Comic art meets Freud

2007-01-11T11:38:00.000-08:00

Maddox's page of Unintentionally Sexual Comic Book Covers. Here's one example to the left (can you see anything vaguely sexual?).

And while we're at it, here's Pop Culture Addict's Top Ten Lamest Superheroes of All Time, including Matter Eater Lad, with his power of (you guessed it) "super eating":

Books read 2006

2007-01-10T12:12:00.000-08:00

I read 49 books, 3 short of a book a week, which in my books, is close enough. This year, I got to read some contemporary poetry. I also revisited some old friends. I also spent an ungodly amount of time wiping Proust and Pynchon off my classics reading-list.

*the canonical essayist* Montaigne "Essais I". This is the original book of essays, the book in which the term "essay" is coined. Unlike most people's experience of the average essays, these essays are as fun as they are profound, as Montaigne takes any topic and pursues it to its bitter, and witty end. Unfortunately my French is weak and I couldn't appreciate the full flavour of Montaigne's incandescent prose. One to re-read.

Günter Grass "My Century". Itty bitty stories about Germans.

Orhan Pamuk "My Name is Red". I managed to get this in before all the Nobel Prize winning brouhaha. I was surprisingly not so entertained. Is it the translation? I found that Pamuk tried to do much in this novel, without really hitting pay-dirt with any of it - historical fiction, thriller, shifting perspective, meditations about the nature of art. Still, a bunch of Swedes in a secret committee can't be that wrong. In many ways, "My Name is Red", reminded me of Umberto Eco's "The Name of the Rose", where a bunch of Medieval monks hunt for missing illuminated book. In "My Name is Red", a bunch of medieval Muslim clerics hunt for a missing illuminated book. .

John Perkins "Confessions of an Economic Hitman". I have sympathy with the theme of the book, World Bank super-spy lives a life of excitement, then gets guilty conscience, loses family, quits and becomes sage-like enviromental entrepeneur. I expected Perkins to get down-and-dirty with the expose, instead we get this barely believeable James Bond rip-off with the most simplistic explanation of global economics. The prose is perfunctory to say the least.

Henry James "Turn of the Screw". Billed as the scariest story ever written, I was mildy disturbed.

*the biography of the original philosopher-king* Margeurite Yourcenar "Memoires d'Hadrien". This decade-long labour-of-love re-imagines the life of Hadrien, one of the most fascinating of Emperors. Schooled under greek philosophy, he took on the administration of the Roman empire as a spiritual journey. This impressive biography plumbs the depth of a singular mind.

*poetry for alchoholics anonymous* Kim Addonizio "What is This Thing Called Love". Addonizio is a poet's poet, a san francisco woman that writes about love entangled in booze and cigarettes, the way it should be written. No metaphysical flights of fancy, but carving luminosity out of the bottom of an empty beer-glass.

Robert Hughes "The Fatal Shore". This is a fabulous book but suffocating in the sheer bulk of the story-telling. In the end I found that there was just too much, as Hughes takes a masochistic delight in detailing the brutality of life in the early years of the white Australian colony. It would not be too far from the truth to say that I learnt more about the history of Australia between these pages than 13 years of public Australian education.

*The living master of the short story form* Kelly Link "Magic For Beginners". Kelly Link is notoriously difficult to categorize. Is it sci-fi? Fantasy? Literature? Magical-realism? Post-modern? Meta-narrative? She is a true American original (I do not use this word lightly). Her take of the short story form is innovative in the way Calvino's writing is, but she always has an unshakeable grasp of the emotional core of her stories.

Michael Frayn "Copenhagen". If I were ever to direct a play, I think it would be this one. Apart from the fact that it's a three hander, the play tackles science in the way it should be done, not as a pop-sci proselytizer, but as drama, feeling its way through betrayal, love and the meaning of truth.

Albert Camus "La peste"

Margeurite Duras "La plui d'été"

*Allegra Goodman "Intuition"

Charles Mann "1491"

Kim Addonizio "Tell Me"

*Li-Yong Lee "The City in Which I Love You"

E. D. Hirsch Jr. "The Knowledge Deficit"

Jonathan Lethem "The Dissappointment Artist"

*F. Scott Fitzgerald "The Great Gatsby"

*Martha Stout "The Sociopath Next Door"

Bruno Latour "Nous n'avons pas été moderne"

Susan Sontag "On Photograph"

Dom Delilio "White Noise"

Jeffrey Paine "Reenchantment"

Saul Bellows "Ravelstein"

Li-Young Lee "Book of My Nights"

David Duncan "Masterminds of DNA"

*Patricia McMillan "Ruin of Robert Oppenheimer"

Shan Sa "La Jouese de Go"

*J. Armstrong & Markos Zuniga "Crashing the Gate"

Daniel Gilert "Stumbling on Happiness"

John Beebe "Integrity in Depth"

Thomas Pynchon "Gravity's Rainbow"

Gustav Flaubert "Trois Comtes"

*Marcel Proust "À la recherce du temp perdu"

Octavia Butler "Parable of the Talents"

Victor Mchleny "Watson & DNA"

Nelly Arcan "Putain"

Sylvia Plath "The Bell Jar"

*Michael Bérubé "What's Liberal About the Liberal Arts"

*Adam Gopnik "Through the Children's Gate"

*Ken Wilber "Integral Spirituality"

Mikaly Csikszentmihaly "Flow: Psychology of Optimal Experience"

Marcel Proust "À l'ombre des jeunes filles en fleur"

Iegor Gran "Ipso Facto"

Lee Smolin "The Trouble with Physics"

*Michael Bérubé "Rhetorical Occasions"

*Philip K. Dick "Do Androids Dream of Electric Sheep"

*Shan Sa "Impératrice"

Amateur psychoanalysis in the Mission

2007-01-09T23:09:00.000-08:00

On people who like Joanna Newsom:

"It's like people who say they love nature but you can't imagine them camping because their haircuts are too complicated."

~Brianna Toth (new flatmate)

You don't want this guy on the other team

2007-01-09T19:40:00.000-08:00

I live in California, ergo, I must do some kind of exercise. My chosen sport (or anti-death activity) is football, or as they call it here, soccer. For convenience, I play it indoors. Some people I play indoor soccer with are very good, some are average. And then, there's Zinedine Zidane:

DecapiCones®: "The economical mouse and rodent restrainer"

2007-01-03T22:01:00.000-08:00

"Make injections and decapitations quicker and easier with Braintree's DecapiCones®.

...injections can be made directly through the film!

...DecapiCones® restrain post-decapitation kicking and prevent personal contact with feces and urine.

...Animals enter readily, heading for the breathing hole at the small end. Then you simply roll and squeeze the large end closed.

...For decapitation, hold at the rear and insert the small end into the decapitator."

The Thoren 308 Caging System

2007-01-03T21:40:00.000-08:00

Get it quick before it goes, for mice (or gerbil) fetishists:

Comes with everything you see: Complete small-mouse, double-section, fixed Racks with Hepa Filter/Blower Module; Cages; Wire Screens; Water Bottles; Cage Filters; and Identification Tags. 11 cages high, 7 cages on each side of shelf.

Feelings Swarming Your Browser

2007-01-03T21:21:00.000-08:00

wefeelfine.org is one of the most unusual websites I've come across. It's a trippy animation. It's a social network. It's a place to tell the world how you feel.

Camille: singing "le sac des filles" like an mental patient, so good

2007-01-02T00:26:00.000-08:00

Why do I love les chantueses françaises so much? See following, this girl sings from her id:

Camille live : Le sac des filles

Come together, electrostatically, as one

2006-12-31T01:50:00.001-08:00

How do 2 proteins come together to form a complex? Although we can sometimes determine the crystal structure of a complex, this only gives us a static picture, the end product of a dynamic process.

To provide a glimpse into how two proteins come together, Tang and co-workers, in the paper "Visualization of transient encounter complexes in protein–protein association" Nature (2006) 444:383, devised a brilliant scheme to capture the alternative ways that two proteins bind together in solution.

They studied the binding of the N-terminal domain of enzyme I (EIN) to the phosphocarrier protein (HPr). The figure on the left shows EIN on the left (mostly blue). HPr is the protein on the right (green). In the experiment, they attached Mn2+ ions (3 red balls on the far right) onto the surface of HPr.

The key idea is that these Mn2+ ions induce a magnetic response in EIN where the magnetic response (ΔΓ2) of the backbone H atoms in EIN depends on the distance of the H atoms from the Mn2+ ions. The magnetic response ΔΓ2 (red dots) for each backbone H atom in EIN is plotted below:

The black line in the figure above is the ΔΓ2 calculated from the crystal structure of the complex of EIN bound to HPr. The measured ΔΓ2 (red dots) show a number of peaks that deviate from the black line. These peaks correspond to transient binding sites of HPr to other parts of the EIN surface.

From the results of a series of similar experiments, Tang and co-workers reconstructed the most likely transient binding sites of HPr to EIN. The alternate conformations of HPr are shown as a density map (green) in the following image. The actual binding site of HPr in the crystal structure is shown in blue, and EIN is shown as an eletrostatic surface map (red is positive, white neutral, blue is negative):

The alternative conformations of HPr bind to positively charged parts of the surface of EIN. However, near the actual binding site, there are few alternate conformations, even though the surface around the actual binding site is also strongly charged.

Tang and co-workers conclude that it is very easy for two proteins to stick together, drawn by simple electrostatic attraction. But this binding is weak. To explain the absence of alternative conformations around the actual binding sites, they argue that once the HPr binds close to the actual binding site, there is a large energy funnel that forces the HPr into the actual binding site.

This is the first study to show, experimentally, that two proteins can transiently bind anywhere through electrostatic interaction, a truly significant result.

Looking at the surface of a membrane

2006-12-30T15:55:00.000-08:00

What does the the membrane that wraps around our cells look like? We know that the membrane is choc-a-bloc full of proteins, but we can't see them directly because the level of detail is too small for our electron microscopes to look at, without destroying the cell.

Is there a way to re-construct the mosaic of proteins that normally stud a membrane? In "Molecular Anatomy of a Trafficking Organelle" Cell (2006) 127:831, Takamori and co-workers studied the synaptic vesicle - a little bubble wrapped up in membrane that carries neuro-transmitters from one synapse in the brain to another.

This is a synaptic vesicle as seen with electron microscopy. You can't go into any more detail. Instead, Takamori and co-workers determined the precise composition of all the proteins that float in the membrane of the synaptic vesicle. With this information, they built this delightful model of a synaptic vesicle:

This image is somewhat reminiscent of the vibrant watercolors painted by David Goodsell, which were created using some deep intuitions about protein density and oodles of artistic license:

How to tell if a relationship is over

2006-12-30T14:04:00.000-08:00

Short film (90s) at depict.org. I learnt heaps.

The Outsider Chronicles

2006-12-27T13:33:00.001-08:00

If I were to tell you that recently, I went to an experimental modern dance piece , you might raise your eyebrows. If I were to tell you that the piece explored trans-gender issues in a social activism festival, you might even start to smirk. And if I were tell you that it was brilliant, you would roll your eyes around and around until I could only see the whites of your eyes. Well, I went to, saw, and vastly enjoyed Sean Dorsey's "The Outsider Chronicles", as part of the ManiFestival (Dance Brigade's Festival for Social Change) in San Francisco.

"The Outsider Chronicles" is a loosely biographical collection of consists of 6 short pieces. The stories revolve around the theme of sexual identity. Before the show, I was a little afraid that this was going to be a niche piece. The audience was not your typical theater crowd, mainly lesbian couples and trans-gender folks. Would the piece speak in a secret code of the trans-gender community, impenetrable to the ears of an outsider? Fortunately this was not the case. "The Outsider Chronicles" spoke in a universal language. It spoke in the form of story.

The most significant artistic choice that Dorsey made, was to perform the dance pieces over a spoken word performance. I had never seen this fusion of spoken word and dance before. By engaging the audience through a series of beautifully written story, Dorsey had highlighted a fundamental problem with most forms of dance that I have seen - although kinetically enthralling, most dance is intellectually dis-engaging. To fully engage in a scene, I think it is imperative that we get under the skin of the characters on stage. Dance alone cannot tell such stories. With spoken word, character and dialog are refracted onto the movements on the stage.

The miracle of the "The Outsider Chronicles" is that Sean Dorsey is every bit as good a spoken-word performer as he is a dancer. There were six beautifully written stories, full of vigor, life and humor. There was a piece about the first time he kissed a girl. Another was a poignant piece about the drive of a couple to have an emergency meeting with his father. These spoken word pieces could easily stand on their own. Here, they formed the platform on which the dance unfolded.

The stories and the dance dove-tailed as we see flying bodies act out the conflicts and confusions of the relationships embedded in the stories. The spoken dialogue gave flesh to the movements. Movement and intention become one. I could felt the stories wash over me, kinetically, bodily. Reflecting on this, I realized that the vacuity of much of traditional ballet was due to the inherent limit of dance to convey rich emotional experience. Whereas seasoned ballet enthusiasts already know the story of the ballet that they will see, and hence can interpret the actions on the stage, there is no such recourse for a novice. In "The Outsider Chronicles", Dorsey cuts through that incomprehensibility by merging voice with dance.

I was also enthralled by the lighting and staging. The staging was spare, allowing the rather imaginative use of light to cut through the space. Slabs of light were used to conjure up a conjugal bed, another to project the interior of a car free-wheeling on a road-trip. In another scene, a wash of vertical light conjured up a bath-room on the front of the stage.

Dorsey examines the line from desire to the fulfillment of a fully-realized self-identity. His stories document his struggle to engage with the world, though specific to trans-gender issues, there is a universal dimension to his story. The strength and compassion in the way he recounts his past, makes his struggle heroic. In the last piece "Creativity", Dorsey laments a moment in his youth where he missed a chance to seize the moment and declare himself, and pit himself against everyone around him. But if he failed in that moment in the past, he has more than made-up for it in sublimating his story into a muscular work of art.

The Penguin who Goes Shopping

2006-12-17T23:55:00.000-08:00

I know the cute factor to this video will drip through your computer screen and onto the carpet. But I really, I couldn't resist posting the daily adventures of penguin shopper, Lala-chan:

Credentials to run a South American country

2006-12-11T11:50:00.000-08:00

I was just reading about Verónica Michelle Bachelet Jeria, the current president of Chile. Her biography is phenomenal (from wikipedia):

Bachelet—a surgeon, pediatrician and epidemiologist with studies in military strategy—served as Health Minister and Defense Minister under President Ricardo Lagos. She is a separated mother of three and a self-described agnostic, which sets her apart in a predominantly conservative and Catholic country. A polyglot, she speaks Spanish, English, German, Portuguese and French.

How could anyone so talented become the head of state of any nation?

Stop motion animation genius

2006-11-29T10:46:00.000-08:00

Iraqi voice

2006-11-27T23:45:00.000-08:00

When you are inside the political circus of the United States, it's easy to forget that the victims of the spasmodic American war machine in the Iraqi war are actually living, thinking human beings, some even brilliant bloggers: http://riverbendblog.blogspot.com/

Movable comment system

2006-11-24T11:56:00.000-08:00

I love the comment system invented by those guys at reddit.com. It's a genuine innovation by bringing together a couple of simply ideas, resulting in an elegant way of visually structuring a conversation.

Reddit started with the idea of ranking comments, form sites such as slashdot and amazon. Each comment in a thread is scored, whereby comments in a thread can be rated with an unobtrusive up-or-down arrow. The innovation is that the comments in a thread flow up or down a page in terms of the comment rating. Those that are popular float to the top of the page, and those that are unhelpful sink to the bottom.

It's a remarkably intuitive system that rewards good contribution to the conversation, without resorting to draconian censoring measures. Bad comments are not hidden; they just sink to the bottom of the page. If you feel inclined, you simply scroll down to the bottom-feeders and see the shit. Good comments are not just rewarded just by brownie points, but they get to be read first simply in lieu of being at the top of the page. This provides a genuinely useful service for other readers.

Having threaded comments is also important. Replies to specific comments get attached to the parent comment, and they move up or down with them. However brilliant rejoinders to a shitty comment deserve their day in the sun, and whole threads get moved up if the replies are rated higher than the parent comment.

On reddit.com, the cream does float to the top. But if you really want to, you can still lick the scum at the bottom.

A real australian christmas

2006-11-24T11:27:00.001-08:00

This was seen in a display window of the Myers department store in Melbourne, Australia. As an Australian expat, I believe it demonstrates the true meaning of Australian mate-ship, marsupial-style:

Party-poopers claim the hydraulics was "broken", in a brokeback mountain kind of way

Talking in (another) tongue

2006-11-23T13:13:00.000-08:00

I'm of the opinion that more people should know at least one other language. I'm not talking about some kind of cheesy tourist phrase-book or a I'm-trying-to-pick-up-girls-at-a-summer-course kind of thing.

I'm talking about honest-to-god bilingualism. I'm talking about being in a place where you have to use the language just to survive. I'm talking getting the power cut-off if you can't explain to the guy on the phone that your papers are in actual order. I'm talking about being able to order the food that you actually wanted. It's hard, it's difficult, and it'll turn your world upside down.

Being able to talk in another language means that you'll end up thinking differently. It's a strange thing to slip in and out of one language. Strange associations jump out at you from different angles, as you begin to understand different idioms. Each language has its favorite phrases and pronouns. By choosing that slightly different alternative to say the same thing - you start seeing the world in slightly different ways, with profound effects on what you easily see, or don't see. Speaking in another language, textures your world much more than a character mod in a DOOM extension pack.

There's also nothing quite like the loneliness and frustration in being stuck in a land where no one can communicate with you. People who are generally smart will feel the pain of being slow and retarded. Your tongue will feel thick and unwieldy. Whereas once you were always quick with a witty rejoinder, you are suddenly reduced to monosyllabic responses. Yet there are subtle joys. As you feel your language skills click up a gear, you will feel the pleasure of rediscovering latent social skills.

But more importantly, once you realize that, what was once your monolithic world, is but one of many worlds bound by your native vocabulary, you will realize that it is just that - only one world in a vast universe of possible worlds.

What is a molecule?

2006-11-13T20:40:00.000-08:00

I am a computational biologist. I compute molecules. I sit in the darkness of the computer lab and sculpt molecules by wielding the sharp scalpel of my mouse. Inside the computer I manipulate the coordinates of a molecule (currently the PDZ domain) and surrounding bath of water molecules. I apply force-fields, mathematical descriptions of the interactions between atoms, to my molecule, and hopefully, I coax the molecule into doing something remarkable: a flip, a rotation, a clamping of the active site - an action that might explain a chemical reaction in precise atomic detail.

This kind of precision is beguiling, and it engenders a kind of arrogance. That's why I often have to pinch myself hard to remember that, even though I might know the behaviour of these molecules down to the sub-Angstrom (0.00000001 m) level, I barely know anything about the molecule.

Chemicals start off as something in the ground, or in the ground up substances of animals. I rarely know whether the molecules that I study inside my computer comes from an animal, a plant or a bacterium. And what if I did? I still have to know how to squeeze that particular chemical out of the carcass of, say, a dead cow. This requires expertise in the manifold arts of physical chemistry, whereby you separate, from the rough and guts of a ground-up cow, the millions of different chemicals that make up the once living cow. Understanding a chemical requires not just in knowing how to find it in nature, but also how to purify it till it's purer than the driven snow. But to truly understand a chemical, you have to know what it does, how it reacts with other chemicals, and under what conditions.

In biochemistry, the problem of knowing what a chemical has taken a rather strange turn. We actually possess a rich source of important biological chemicals, but no way of knowing what these chemicals actually do. This source is the human genome, which exists as a publicly available database. As we know quite a lot about the grammar and syntax of DNA, a computer scientist can trawl the database for sequences of DNA that code for a completely novel biological molecules. It's then a simple matter of sending in an order for a biotech company to make the molecule from scratch.

But how to figure out what the molecule does in our bodies? We don't believe in mysterious life forces any more. We believe that all of life's processes, from digestion to respiration to the way old people lose their memories must rest on some kind of chemical process. Every chemical extracted from living things could potentially have an important function in the living process. But given a molecule picked out at random from the human genome, we have no way of knowing where the molecule should be found in the body, what biological processes that it takes part in, and what other processes it depends on. The human genome remains silent on such issues.

The precise knowledge of the 3-dimensional coordinates of a molecule is probably the last thing that scientists get to know about a chemical. 3-dimensional coordinates are finicky things, and knowledge of them normally comes at the end of a long investigative process. By then, much of the chemical properties of the chemical are already known.

Sculptor in Conversation

2006-11-12T18:41:00.000-08:00

The other day, we had the world's greatest sculptor, Richard Serra, visit the UCSF campus where I work, in Mission Bay, a former industrial area south of downtown San Francisco, which was a dead zone that the local council was in the process of converting into a biotechnology park.

A solemn man, Richard Serra's face is permanently set into a metaphysical scowl, yet he dressed in casual gear - jeans, comfortable dark-blue shirt, and sneakers. He had been commissioned by UCSF to build a sculpture, and thereby, was obliged to come to UCSF and talk about his piece. The piece, "Ballast", consists of two huge flat metal plates, 50 feet high and 14 feet wide, that lent in slightly off-horizontal off-vertical directions. If you stand at the base and look up, you will see a disorientating curve in the metal.

The meeting was held in an auditorium in our new community center, a striking building designed by Mexican architects Ricardo and Victor Legorreta, which was bathed in a bold earthy red, which balanced the lego-like austerity of the form. The community center building stood out from the surrounding beige-ness of the other buildings.

I was keen to see how they would set up the talk. In the auditorium, two comfortable sofa chairs were set up on the stage with a black curtain backdrop. The talk was going to be conducted as an interview in a PBS special. I didn't know who the interviewer was, but a friend later informed that the interviewer was a local construction magnate. I had always known about the symbiotic relationship between obscene wealth and high-end art, but I had never seen it in the flesh like here in the auditorium, where a very rich man doubled as the probing interviewer of an artist of very expensive modern art.

The entanglements of moneyed interests and art was more intricate in this case, as the piece was commissioned by UCSF, which was investing in a very large construction project at the Mission Bay campus, which necessarily involved complex construction and real estate interests. So it made sense that a construction magnate would interview the artist, who was patronized by a scientific institute that was rapidly expanding its building infrastructure.

Serra was a brilliant interviewee, crisp, articulate, and was an inexhaustible source of anecdotes, which involved the suitable name-dropping of everyone from Phillip Glass to Jasper Johns to Charlie Mingus. Because Serra was born and raised in San Francisco, he recounted many childhood reminiscences - baseball games in the local park a couple of blocks from the campus, climbing through old warehouses - typical experiences of a nascent internationally acclaimed sculptor.

Later, he moved on to more familiar territory - a standard narrative of how he became the sculptor that he is today - from English lit major, to embryonic painter/drawer, to studying art history at Yale with abunch of soon-to-be-very-famous artists, and then onto a fellowship in Italy, and finally to New York as struggling artist. It was an absorbing story, which illustrated how the contingent factors of his biography inevitably coalesced into the choice of large-scale fabricated steel as his media of choice, and "weight" as the leit-motif of his artistic vision. This was as deft a piece of self-invention if I ever heard one.

The sculpture was described as the "centerpiece" of the new UCSF campus at Mission Bay by the UCSF chancellor, Michael Bishop, the 1989 winner of the Nobel Prize in medicine. Such was the occasion that Michael Bishop himself gave the opening address to the interview, thus completing the on-stage triumvirate of the interaction of science (Bishop), art (Serra) and money (construction magnate/interviewer).

Still, what surprised me was how the interaction between the work of art and the science at UCSF was virtually non-existent. Michael Bishop did not interact with Serra at all, on-stage, but more to the point, the purpose of UCSF - medical research - played no part in the design of the sculpture. Serra described his process: when during a visit to the site, he realized that the campus was an immensely flat landscape. Wouldn't it be interesting to put up something completely vertical? Serra had already done a vertical metal plate piece in Germany(?), so he decided that for this piece, he would explore the interaction of two such vertical standing pieces.

Science played no part in the design of the piece. And as I looked around the auditorium, which was very well attended, I realized that there were very few grad-students or faculty from the medical research facility next door. Instead, the audience was made up of architects, art patrons (including the former owner of the Bank of America), and students from the nearby College of Creative Arts. Though fetching that female art-students often are, as an art-loving scientist, I felt very lonely indeed.

Madame Speaker of the House

2006-11-08T00:52:00.000-08:00

So Nancy Pelosi of San Francisco (the seventh circle of hell for bible-belt americans) will be the Speaker of the House, the third highest political position in the USA. Maybe one day the USA will join much of the Islamic world in electing a woman head-of-state.

To the Founding Fathers of the USA

2006-11-08T00:43:00.000-08:00

All praise to those brilliant men who conceived of the Constitution of the United States of America. They foresaw the inevitable tides of fascism that roll back and forth every few decades and constructed a system of government that keeps it at bay. The system of checks and balances works, slowly, but it works. The Democrats have taken back the House, the Senate is tied. The Executive is next. The world can take a deep deep breath.

words for a friday

2006-10-20T12:51:00.001-07:00

xenolalia - speaking in a language that you don't know the meaning of

The future of work

2006-10-18T10:06:00.000-07:00

This article ostensibly talks about a Walmart first, the whole staff of a Wal-mart store walking out. Given Wal-mart's aggressive anti-union, anti-labour policies, what drove these, mainly hispanic workers, to take such a drastic step. It was the implentation of a new company policy, that is a sign of indentured work in the future to come:

moves to cut the hours of full-time employees from 40 hours a week to 32 hours, along with a corresponding cut in wages, and to compel workers to be available for shifts around the clock.

In addition, the shifts would be decided not by managers, but by a computer at company headquarters. Employees could find themselves working 7 a.m. to 4 p.m. one week and noon to 9 p.m. the next. "So workers cannot pick up their children after school everyday, and part-timers cannot keep another job because they can be called to work anytime," says Vasquez.

In addition to scheduling changes and reduction in hours, workers are now required to call an 800 number when they are sick. "If we are at an emergency room and spend the night in a hospital and cannot call the number, they won't respect that," says Larosa, who has worked at the store for six years. "It will be counted as an unexcused absence."

Nostalgia in Hindi

2006-10-10T03:09:00.001-07:00

I went to India 7 years ago, and it was one of the most mind-blowing experiences of my life. Music and vibrant primary colors saturate every pore of your skin.

The songs of a blockbluster movie are released months before the movie is released. These songs are broadcasted over every little tin-pot battery radio receiver held by every grizzled shopkeeper in every roadside stall in every dusty streets in the state of Utter Pradesh.

And so the songs of the hit of 1999, "Taal" has sedimented somewhere in the deep dark recesses of my travelling memories. The movie stars the scrumptuous Aishraya Rai, former Miss World (who only lipsynchs). It was the only film I saw in a cinema, somewhere in Delhi. Although I didn't understand a word of Hindi (namaste), I got the gist of the 3 1/2 hour story, and a kindly doctor explained the story to me a week later. Well i had though those memories lost, that is, until I found on Youtube, a music video of "Ishq Bina", the hit-song from the movie, a gorgeous fusion of Indian lyricism with some western flourishes. Enjoy.:

Note the product placement and displaced sexual metaphor in the last frenzied minute of the film clip.

In the prophet's own words

2006-10-09T22:54:00.000-07:00

Why do earnest spiritual seekers often find it necessary to learn to read spiritual texts in the original language? We have middle-class white buddhists contorting their hands around sanskrit letters, young black muslims coughing out arabic glutturals, biblical scholars struggling with declensions of aramaic and ancient greek, and of course, young american jews struggling with the hebrew of the Torah in downtown Manhattan.

Learning languages is hard. I lived in a foreign country and it took me over a year and a half to learn the basics. That's only to have a non-idiotic conversation at a party, talking about where I come from. It takes at least double that time to achieve the proficiency to read complex spiritual texts. So why the bother?

Most religion wrap themselves around a holy book. There's something majestic and authoritative about marks on papyrus. And ultimately, theology in written form is just more transportable. In the days before the printing press, books were much more precious commodities - laborious to make, expensive to finance, and difficult to make accurate copies of - books were expensive treasures for the rich and indolent, and the scholars that they would patronize. Even today, with the technologies of the printing press and the word processor, a beautifully produced book still possesses the qualities of a magical object.

Religious books in America are less exotic treasures and more of a marketable commodity. There is a whole cottage industry of translating religious books. All you have to do is march down to your nearest esoteric book store, and you will find a gazillion different translations of the Bhagavad Gita, all printed on cheap india paper in dirt cheap ink-type, that is thick and heavy, and hard to read. Differences between translations are enormous. Some translations translate difficult terms literally, keeping the phoneticisms of the original language. In other translations, english words are appropriated in awkward sounding ways, like the use of that clunker, lovingkindness, in South-east asian buddhist texts.

However, in many different traditions, it is taught that the earnest seeker must learn the original language that a holy book is written in, before they can truly understand the meaning behind the books. Why watch a grainy video shot by a handicam inside a noisy cinema when you can experience glorious 75 mm film in dolby surround sound?

If you've ever met earnest beginning spiritual seekers, you will find that they generally tend to be insufferable puritanical party-poopers, full of pointless trivia, and prescriptive to the hilt. Like the cool kids, they'll wear the right gear, say the right things, and rain down a stream of do's-and-dont's. To join a new religion is to deny one's original culture. It is an act of identity recreation. Speaking a new language, is the final erection of the new self.

But what is to be gained in reading the original book in the original language? The simple reason is that the great holy books are often, also great works of poetry. Spiritual power is poetic power married with spiritual insight. And poetry transmits meaning not just in the simple meaning of the words, but through shades of meaning and technical effects of rhyme, rhythm and meter. The Koran contains a myriad of puns and in-jokes, in arabic.

And because spiritual writing is poetry, it suffers the same difficulty in translation. Poetry is notoriously virtually impossible to translate. Most religious translations are made by earnest religious scholars, not linguistically adept poets. That is why teachers of religions find translations tinny and stilted. When religious teachers complain that a translation misses the spiritual essense, they are really saying that it lacks poetic fluency. So when a spiritual seeker takes the long and arduous journey in learning the original language of a spiritual text, they are really taking the world's most painful poetry class.

Guest blog from Warren Longmire

2006-10-03T20:40:00.000-07:00

Live and direct from the marsh cafe, this is warren longmire bouncing light across the keys of one BASCO HO's macbook. Lovely keyboard indeed I must say. There is something sexy about a nice keyboard. But I digress...

Check out my search for the san fran god scene at www.ascatteredlight.blogspot.com. It's the hotness. Be well. Be merry. I'm out.

bic runga does jacques brel

2006-10-01T23:00:00.000-07:00

Trawling on youtube, I find an extreme example of pan-national cross-cultural fertilization. Bic Runga, new zealand singer of malaysian chinese descent sings in french - "ne me quitte pas" the signature song by belgium's greatest export, jacques brel. It's the torch-burning song, and Bic gets to shows off her singing chops, on-stage emotional histrionics, and command of the french language:

Art Schools versus Science Schools

2006-09-30T19:52:00.001-07:00

Today, I had a conversation with two friends, an architect and a painter, and we started talking about psychologically disturbed people to be found in art school. (They both went to the former CCAC, now known as the CCA).

At the end of an anecdote, my painter friend concluded that there must be a lot of people with border-line personality disorder amongst art-school students. My architect friend added that, when she went to the CCAC, the psychological distresses of art-school was so severe that the CCAC had round-the-clock counselors to service troubled art-school students.

That got me thinking, whilst studying physics, I didn't meet many border-line psychotics, but I did know a lot of socially dysfunctional people. Boys who couldn't interact with normal people, who couldn't emphasize with other people's emotion, let alone recognize emotions, or make eye contact. In short, in science schools, there was a surfeit of borderline autistics.

In conclusion, one can say that art-schools breed border-line psychosis, whilst science schools breed autism.

A Poetic Form: The Pantoum

2006-09-28T15:24:00.000-07:00

I was introduced to a new poetic form the other day. It's called the Pantoum, and it's one of the most brilliant forms I've encountered. It originates from Malaysian, often used in song form, and it goes something like this:

First line
Second Line
Third Line
Fourth Line

Last Second Line
New Second Line
Last Fourth Line
New Fourth Line

.
.
.
.

Last Second Line
Original Second Line
Last Fourth Line
Original First Line

The structured repetitions produce a hypnotic trance state. I will try to find examples of them.

What no American man has

2006-09-25T09:48:00.000-07:00

"He could almost have been an American, but I could tell straight away that he wasn't. He had what no American man I've ever met has had, and that's intuition."

~ Sylvia Plath, "The Bell Jar"

Self-referential promotion letter

2006-09-20T00:25:00.001-07:00

Recently (as in the last two years) I published papers in the journals, BMC Structural Biology and Protein Science. It appears that BMC Structural Biology trawls through the authors of Protein Science, and spams these authors to get them interested in their journal, BMC Structural Biology. I got one of those emails:

Dear Dr Ho,

We noticed that you recently published an article in Protein Science. As an active researcher publishing in the field of structural biology, have you considered publishing in BMC Structural Biology?...

Who is BMC Structural Biology?

BMC Structural Biology boasts a wide, international readership. More than 4,900 users have signed up to receive email alerts, and last month alone articles in BMC Structural Biology were accessed over 3,500 times from our website, and many times via the PubMed Central website.

Seems a reputable journal. But it's open-source. It's too new. To assuage my worries and fears, BMC Structural Biology sent me a worthy example of one of their popular recent articles:

For example, this article by Ho and Brasseur has been accessed 205 times in the past 30 days:

Research article
The Ramachandran plots of glycine and pre-proline
Bosco K Ho, Robert Brasseur
BMC Structural Biology 2005, 5:14 (16 August 2005)

This article looked vaguely familiar. That author Bosco K Ho, he looks like ...

Why, that's me!

They were trying to entice me into submitting an article to them by showing me an article that I had already written, for them.

...Why not submit your next research article to BMC Structural Biology?...

Why not indeed.. oh, I already have.

hipsterotica

2006-09-19T23:46:00.000-07:00

The latest blog that has captured my rapt attention is hipsterotica. I see hipsters all around in the Mission, here in San Francisco. They're like pigeons, pecking crumbs off the ground and swarming away when little kids try to catch them. Imagine if they had sex.

U2: With or Without You

2006-09-17T23:20:00.000-07:00

U2's "with or without you" is one of the greatest song ever written - it's a song that tears at your heart and then shreds it into a thousand pieces. I've seen various versions of them performing it, but never quite like this. If rock-stars are the gods of the secular era then the girl that was pulled-up unto the stage, got to make love with a fallen god, in front of 50,000 people. Cry girl. Cry.

Les livres françaises

2006-09-17T11:46:00.000-07:00

Je suis recemment allé à Montreal où j'ai pu achêté des livres françaises. C'etait vraiment un longtemp que je peux le faire. Après une grande peine de reflechir, j'ai choisi:

Marcel Proust, À l'ombre des jeunes filles en fleurs
Iegor Gran, Ipso facto
Jean-Pierre Changeux, L'homme neuronal
Jacques Derrida, L'écriture et la différence
Shan Sa, Impératrice
Marguerite yourcenar, L'Œuvre au Noir
Nelly Arcan, Putain

Best title in a Science magazine article, ever

2006-09-16T21:58:00.000-07:00

Washing Away Your Sins: Threatened Morality and Physical Cleansing
Chen-Bo Zhong and Katie Liljenquist
Science 8 September 2006: 1451-1452

Physical cleansing has been a focal element in religious ceremonies for thousands of years. The prevalence of this practice suggests a psychological association between bodily purity and moral purity. In three studies, we explored what we call the "Macbeth effect"—that is, a threat to one's moral purity induces the need to cleanse oneself. This effect revealed itself through an increased mental accessibility of cleansing-related concepts, a greater desire for cleansing products, and a greater likelihood of taking antiseptic wipes. Furthermore, we showed that physical cleansing alleviates the upsetting consequences of unethical behavior and reduces threats to one's moral self-image. Daily hygiene routines such as washing hands, as simple and benign as they might seem, can deliver a powerful antidote to threatened morality, enabling people to truly wash away

Only in San Francisco

2006-09-16T01:50:00.000-07:00

A while ago, a friend dragged me off on a Friday night, out to the burbs, to see a show that had San Francisco plastered all over it. It was the Peaches Christ "Midnight Mass", an alternative religious festival to coincide (fortuitously) with the Christian festival of Easter.

Who is Peaches Christ? She is a transvestite cabaret performer, a consummate entertainer. She is her own institution, a dynamo of sneering attitude and arch campness. She is a large woman, with, obviously, the frame of a man, and with a huge hairdo, and thick garish makeup, she was more god than human. She owned the stage. In the show that I saw, she entered the stage but bursting out of volcano, complete with flames and crumbling plaster.

Every year, Peaches Christ puts on a number of movies that score through the roof on the camp scale. As the movies are shown at midnight and involve a pre-movie cabaret show, the cinema which hosts the event is waaay out in the outer Richmond, and we had to get there by taxi (taxis in San Francisco are not all like taxis in nyc, they are expensive and infrequent).

That night's show was based on scenes from Showgirls and also involved a free lap-dance at the end of the cabaret act (more on the lap-dance). The cabaret show took crucial scenes from the movie - in this case, it was the masterful dialogue from screen-wright Joe "My adolescent sex-fantasy" Ezterzas - and took the scenes to their logical conclusion. The one that stuck in my mind was where the feuding show-girls were reminiscing about their childhoods where one of the girls admitted that she was once so poor that she had to eat dog-food. "You too," squealed the other show-girl, as they shared their stories about their favourite dog-food. Peaches Christ and friend then replayed the scene which ended up with the two of them eating dog-food on stage and then fisting each other under strobe lights. You get the idea.

At the end of the cabaret set, we were treated to the real draw-card of the show, the free lap-dance for everyone who had a box of pop-corn. Shamefully, I have to admit that I had to hide my box of pop-corn, because the thought of getting a lap-dance from a heavy set bearded transvestite was somewhat unsettling. Call me a prude if you must. Except it was much much worse. We were first asked to raise our box of pop-corn. About a hundred people raised their pop-corn, there was going to be a lot of lap-dances a coming. Then the lap-dancers were brought up. The first one was what you might imagine, a femmy looking transvestite, that thin sleek androgynous looking tranny in tight tight clothing.

After that, my mind was blown. The other lap-dancers included: an abraham lincoln look-alike in suspenders and pants, a large person in a suit and wearing a bunny head, large bearded men, someone in a green martian suit, some very drunk people in stripped stockings... and so the list went on. And just when you'd seen it all, the very last lap-dancer was introduced, who made everybody in the audience gasp. This lap-dancer was a short stocky woman in a full burkha.

Glimpse into the glorious past (1665) of science

2006-09-15T10:56:00.000-07:00

The Royal Society of England, the most venerable scientific institution in the world, has just release online, the archive of their journal, Philosophical Transactions, which dates back from the year of our lord, 1665.

They will allow free access for non-sciencey peoples for the next two months. So check out those musty pdf's. Guardian blogs have provided links to some classic papers that can be found in the Royal Society archive.

Culinary desire

2006-09-14T07:33:00.000-07:00

This is a writing exercise that I didn't know what to with, except to post it here:

If I don't eat at the French Laundry my life would not be complete. But how to get there. I don't have a car. It's not near public transport. Nor do I have filthy lucre, I don't have a sugar daddy. The mechanics of the deal is simple. Ring up exactly 6-months to the day that you want to go, and book a table. Keep ringing and ringing until they pick up the phone. But it seems so far away, some undetermined time in the future, like some kind of spy-thriller novel, "Igor, I will meet you on the Steps of Rome, in 6 months time". It's a restaurant for god's sake, not state secrets of inner Siberia. Perhaps I can with Igor. I've got to go with someone. Someone, preferably, no necessarily, with a car. For that drive up to that place up in the middle of the country-side. People with cars, who like to eat. You know, maybe I should just advertise on Craigslist, and offer something in return.

Time-lapsed video of 160 hot-air balloons

2006-09-13T23:53:00.000-07:00

This is beautiful and wonderfully ridiculous at the same time

A Smear of Blood

2006-09-01T17:13:00.000-07:00

Whining, you wriggle in my nose
You loop in my ear canal
Striking always in the moments before sleep

I can't take it

I want to snatch you up
Smash your face
Just like that
Then crumple you with my fingers
into a mixture of pus and blood leaving a tiny little stain of red
I rub that smear of insect paste into my cheeks Like rouge
I feel the cool of new death on my skin

It is not unpleasant

It calms
It feels like sacrament
Like the fist time I touched a dead body, I have violated the living
The breathing and the dead are separated by a film so thin but impenetrable
I run my fingertips along its surface
before long, I can longer tell
where my warm body begins from where the dead insect ends
My blood coagulates
The tracery of my veins harden into marble

New York

2006-08-31T17:18:00.000-07:00

Standing hunched over keyboard in this apple store
Tap tap tapping away before they catch me
Spinning words on the fly, stolen
From the crackled energy of this city

I look up to see buildings whoosh up from the ground
The trees here are not kings but servants
They serve but to green the
Feet of the true masters of this city
Those glorious scrapers of the sky
Shaving off the majesty of high flying birds
And flinging it back down onto the masses below

I see potent mixes of blacks and whites, olive and brown
All packed in the ovens of the underground
The subway so hot that everybody perspires
Their sweat melts, merges and pools in
The hidden arteries from Harlem to Soho
To Wiliamsburg from the hispanic busboys
To the dolled-up girls of fashion school
To the grizzled Italian bar-man serving
As much attitude as alcohol

And the beating thudding heart in that
Neon black-hole of times square
A bear-trap for the epileptic
It ripples and flirts and entertains
I see dancers and singers and poets
And tourists looking for that elusive something.

Godless Sight

2006-08-28T17:16:00.000-07:00

The eye that I see God with
Is the eye that God sees me with

~ Meister Eckhart

I am the eye
The all-seeing eye
Worlds fall in my ken

Who then sees through that
Shiny plastic screen
Screwed inside the cone of the cramped cockpit
Diving screaming
From the vacuumed air above
Into the thickened smog below
A vertical prayer
From eye to screen to cross hair
To the phosphorescent green trace below
A trace with legs scrambling
A headless chicken
Your daughter's head
Scrambled at the sight of you
You squint harder into the screen
And with greater resolution it might even show
The creasing of the skin
As their face contorts at the moment of sweet impact

I see with pure electricity
The wires that fall away
It is an action as easy
As banging a cartridge into the hole
Joining hardware
to software
to joystick
To hand
To eye
You see through the eyes of another
Carrying some oversized triple-barrelled double-loaded shot-gun
Spraying pixelated bullets in technicolor death and fury
It is a pure expression of the soul
It is a divine handshake
It is an armored tank on threaded tracks
The hand that slaps the ground
And leaves plutonium dust in its wake
That corrodes the lining of the lungs of all who pass by

I see with eyes bloodshot from desire
Just as he, our god, desires
Not from on high
But from below
Like a trick in a peep-show
He shoves another coin into the greasy slot
The window opens
He watches
It is the dance of the seven veils
As each piece of fabric falls to the ground
Another patch of skin is exposed
Luminous and white
That burns into his far-gone eyes
And then the glass rises up again
The circle is complete
The cycle ended
Until the next coin drops

I see the stars through a telescope
A slivered tube of metal
That cups a piece of frosted glass
Calibrated crystalline
It scatters my vision amongst the stars
Grains of light
Balls of fire
Touching off a finger of corona
A strange filigree of light stretching
From star to telescope
Filling my head with starlight
Bursting my skull, a throbbing migraine
The pain
Reminds me that I
Are here but also there
The same point but far apart
The lord giveth the lord taketh away

To see is to perceive the naked
Peel off the eyelid
With a rusty potato peeler
Expose the viscous fluid to the corrosion of the air
Do you see better?
Unending sight
Blinkless
Without interruption your
Inner eye reflects off
The surface of the outer eye
The two converge
The light becomes the dark
You must realise
It is darkly
As it was in the beginning,
and ever shall be.

The Soul of the Box

2006-08-01T17:14:00.000-07:00

Sometimes the body just sits there, floppy
Cupped around that second-hand sofa
The bones jutting into rusted springs
The eyes dangling on
The face twisted to face the television set

There is a relationship, symbiotic in nature
Between man and cathode-ray tube
The two joined in communion
Through physicality and intent
The electromagnetic waves fizzes and spurts
through the air from miles away

But we would otherwise be so much colder
Than now, transfixed by another episode of friends

Blood Theater

2006-08-01T00:07:00.000-07:00

The Chainsaw Massacres - The Stage Show.

Yes. It can be done. You can depict chainsaw weilding flesh-flaying, gore-inducing action in a stage show, and look good in the process.

Recently I went to Cell-space, a kind of community-based theater/performance/gallery space, where everything from new-age hippie conferences to pyro-technic gore theater is put on. It 's a bare-bones kind of space with exposed girders and cement.

Whilst I had a little inkling of what was to take place there, the plastic-sheets covering every square inch onf the floor and walls should have given me conisderable fore-taste of what was to come.

The idea is redicuously simple. Construct a simple genre pliece that enables plenty of opportunities to dismember body parts in front of a live evidence, and use that as an excuse to spray the audience with as much fake blood as possible. The blood, really some kind of watermelon kool-aid had a sticky sweet consistency. And considerable ingenuity must have taken place to design the squirting equipment, because there was definitely method in the madness of gushing blood. No part of the audience was spared, as the blood was squirted to all corners of the room.

Of course, I had bought a plastic bag to be safe, but even then the bag couldn't keep the blood out. I walked out of the theater with streaks of red all down my eyes and splotches that looked like chicken pox covering my face.

Asian-americans breaking through the entertainment barrier

2006-07-26T10:47:00.000-07:00

America is a white-bread nation, at least culturally, and on television. Sure, cultural others are shown on television, but they are often parded out as cultural stereotypes - Indian grocer, Chinese over-achieving academic automatons, Japanese ninjas, black gang-members, gay-queens.

But over the years, certain groups have managed to detach themselves from being token stock characters, to becoming normalized - acceptable as real characters on television, where their experiences as people trumps their experience as a minority group. Think Bill Cosby and Will & Grace.

The next break-out group is the Asians. My question is then, where are the mainstream Asian-american acts?

Well, I think I found them - on NBC's show "American's Got Talent.", a variety talent show, a kind of uber-vaudeville where the judges include Brandy and David Hasselhoff (think Baywatch for you younger readers).

They are At Last, an asian boy band from LA. They sing great, have great charisma, and are poised to win a major American talent show. They are on the brink of stardom, and if they do, my bet is that they will finally normalize Asian americans on TV.

But best of all, they innovate: they sing accapella harmonies, barber-shop quartet style, fused with human beatbox, and crazy rythmic vocallings.

Can Americans finally embrace Asian-americans culturally?

From the June 26th semi-final (Aint No Sunshine):

Pay attention to the interview that captures their rupture from the old asian stereo-type, and embracing the american entertainment big-time:

"Our family and friends were really suportive of us, in the beginning they were a little hesitant because they wanted us to pursue profession careers ..in law, in medicine, and stuff like that.. but now they're our biggest fan club."

Bonus: watch Brandy's reaction when the boys start singing. Priceless.

The semifinal on July 20 (Let's Stay Together):

The Peace that Passeth Understanding

2006-07-19T17:14:00.000-07:00

I swallow it
Without hesitation
It is a squat sausage
Mottled pink and brown so thick and juicy
You would want to suck it down In one desperate gulp

But it is not easy to swallow
It gets stuck somewhere between the stomach and the gut
Caught in the windings of the intestines
The body knows too well
To welcome such pleasure so easily

It has a sharp metallic aftertaste
Like the blood of the body of a child
Crumpled up beside a road made of asphalt
Melting in the noonday sun
The tarry sludge covers your tongue
Licking the staleness of a spent bullet

Though temptuous its tough fibres
Can only be digested strand by strand
Infiltrating the marrow the bone until
The body cannot be said to be a body anymore
But a frame to hold an idea

Mix n' match music

2006-07-19T10:01:00.002-07:00

Here's two of music's most ~~uncomprising~~ uncomprimising female performers covering one of the great testosterone tracks of rock n' roll, the Stones' "Satisfaction" - a jarring meld of the avant-garde squeals of Bjork to the rumbling menace of PJ Harvey. Truly brilliant.

Infogami, hosting served just right

2006-07-14T18:55:00.000-07:00

I've slowly been transferring my web-site from my academic research group's server (with the rather unweildy url of http://www.dillgroup.ucsf.edu/~bosco , which is now defunct) to my new infogami web-site (http://bosco.infogami.com).

And I've really enjoyed the transition. For what I want to do, infogami fits the bill. Perfectly.

I don't really want to build my own server, I just need somewhere free to store it.

I don't want to write fancy html/ajax/flash widgets, I just want to write text in an attractive template.

I don't want to register a domain name, I want someone to give me a sensible one for free.

Infogami fits all these requirements.

Yes it is a wiki, but you don't have to host it. Yes it is a wiki, but you don't have to register a domain name. Yes it is a wiki, but you won't have to write one single linux shell script. Yes it is a wiki, but you don't have figure out how to install it.

But unlike a wiki, infogami makes it very easy for you to change the template. To make it look good. It's really hard to change the look of some wikis - and boy are they sometimes ugly. This is because Aaron Swartz is a damn fine programmer who keeps it simple, who knows how to keep the templates in infogami simple and flexible.

To all those people who say infogami is just a glorified wiki, you've missed the point about infogami. Infogami aims to cut-out all the headaches involved in setting up the wiki on some computer.

But what I like most of all is the text editor in infogami - it's bare-bores functionality is precisely it's strength. The text editor always sizes to the window size. i like that. I never have that window within a window scrolling rat-race. I love the mark-down format - it's power wrapped in simplicity - it can handle clean text and embed complex html.

I use to be a total coding monkey - I'd spend hours writing code for recreation. Now I am more interested in writing prose - which is, contrary to popular geek wisdom, a much harder thing to do than programming. Very few writers can write to the level of a typical New Yorker article.

Now I just want a web-site where I can put essays and articles up with a minimum of fuss, and which allows me edit easily. The wiki format makes it so easy to edit a file. No more save and ftp on some random computer, requiring multiple clickety-click steps.

Like a good English butler, Infogami serves me when I need something and dissappears into the background when I don't.

Why AMBER sticks a finger in its users eyes.

2006-07-14T17:57:00.000-07:00

I use molecular dynamics packages - complex computer software that simulate the action of very large molecules. There are many such packages, but the big ones are amber, charmm, xplor, gromacs and namd.

I have now used namd and amber, and based on that example, I have to say that amber's input files are a piece of shit.

My complaints are:

1. In the input files for AMBER, why do they use crappy variable names for the pre-historic days of FORTRAN naming conventions. No, I really don't what the variable ntxb. It's the 21st century, variables can be longer than 8 characters. They can even be meaningful. They shouldn't give you eye-sore and send you running to the manual everytime you read the input files 1 week later.

2. If you use input files to start a simulation, why do you also have to add up to 10 command line gcc style options? Why can't you have keywords in the input file to convey the same information to the program??? Everything is in one place, and stored? How friggin' hard is that?

3. Putting positional constraints on different atoms is a great idea. In NAMD, you submit a pdb file, and NAMD will read the constraints from the B-factor column. Great idea - simple to use, complete flexibility for the user. And AMBER? You must enter the positional constraints in the input file via a very special "restraintmask" string, and it's not even defined in the right place in the manual - because you have to run to the appendix where they give you an anemic language to describe what atoms you want constrain, using the very special amber numbering convention. Except that you really have to go back to the beginning of the manual to find that you only have 80 characters to describe constraints.

Poke my eyes out please.

Dance around the world

2006-07-13T15:24:00.000-07:00

There's something transcendentally beautiful about this video. It's a little like the first time a cosmonaut looked upon the earth and saw that it was a beautiful globe with no boundaries.

more info: wherethehellismatt.com

migrations

2006-07-05T22:17:00.000-07:00

Last weekend, I went to the ODC theater with Kim and friends to see some dance. Although there were only three pieces on offer, I saw one of the best, and one of the worst dance performances of my life.

First the good, Paco Gomes Dancers produced one absolutely breathtaking piece. Five dancers and four frames, of differing heights, this was a beautifully flowing piece where dancers would move frames, and frames would move dancers, in order to produce a walkway on stage for the dancer in the black flowing dress. This was a kinetic piece where points of movement would flow back and forh between dancers and across the stage. The choreography struck that perfect balance between the chaos of the dancers manipulating the frame, and the focus of the walker along the imaginary walkway.

The bad was a horribly stilted mixed media piece called the Red Shoes, which used projected video, pillows, and pebbles, lots of pebbles. There was surprisingly little dancing for a dance piece and lots of poetry. Bad poetry. It was this continuous babble of colourless words delivered in a monotonic drawl. Sometimes the movement on the stage seemed to almost connect with the dialogue. Almost. Not that the words made any sense. The beginning was promising, a pile of pillows, from which a dancer emerged. But throwing piles and piles of pebbles on stage, and then sweeping them around in vaguely geometric waves does not a conceptual art piece make. And random images of huts and rocks and beach become wearing after the 10 minute mark.

Forutunately for us, the evening ende dwith Paco Gomes, and we left the theater in high spirits.

butoh in the dark

2006-07-05T16:34:00.000-07:00

The other night, I bumped into Paul who was going to Adobe Books to find a travel book for his road trip. Having nothing better to do, I joined him in the hope of passing some time browsing books. Instead, I was to stumble onto one of the most riveting performances I had ever seen in the Mission.

So we putter inside and I noticed a musician playing a clarinet at the counter. We struck up a conversation. "Oh," said Paul, "I used to play soprano sax, but I've always wanted to play the clarinet." The musician replied that he too, used to play the sax, but switched because the clarinet was a much more versatile and flexible instrument. "After all," the muscician said, "you can make a clarinet sound like a sax but you can't make a sax sound like a clarinet. But guys, you should stay hear to watch the butoh show coming up."

So Paul and I sat down and waited for the show to start, not that I had any idea what "butoh" was, except that it sounded vaguely Japanese. The musicien started playing the clarinet, a vaguely oriental sounding melody with any manner of shuffling changes in tempo. As the music trailed off into silence, the room was doused into darkeness.

From the platform that was raised above the entrance of the building, a figure crept out from behind a board, holding the candle in her hands. In the candle light, the face was hideous lit in an overdone chiaroscuro (full body makeup is one of the characteristics of butoh, which made the figure look ever so creepy). Her movements slow and ponderous. She first explored the top of the platform, using slow in careful movements, where every scrape of the floor, every rustle of clothing could be heard.

Very slowly she made her way down the ladder, with a reptilian grace. At one point, one of her headdresses caught on fire. She quickly pulled the piece of flaming clothing off and smacked it onto the ladder until it went out. Once she got to the ground, she made her way slowly down the shape of the bookshore. Adobe books is a small and disorganised space. It had a long narrow shape with pot-plants, sculptures and sofas scattered throughout the length of the shop.

It took a glacial age for her to make it to the end of the room. She would take slow, deliberate steps, sometimes pausing to explore all the objects in the room. She brushed past us, the audience sitting on the sofas as if we were ghosts. She would roll her frenzied eyes over objects in the room as if seeing for the first time.

Finally, she got towards the end of the room, and the clarinet came back to life. She disappeared behind a bookshelf, and I lost track of her. She then ran around the room, her quiet steps making her a moving target that was difficult to pinpoint. This was accompanied by improvised clarinet and some low-level lights. She ran through the room with a primal energy, like a coiled banshee, at times collapsing in the middle of the room, and the springing back up as if a puppet master pulled on a hidden spring. Screaming, crying, staring, I felt I had made contact with an elemental being.

Finally, after a round of traumatic collapsing and rising, the show ended. With barely a flourish, she snapped back into normalcy. The lights go back up.

What had I seen? I recall the chapter on Masks by Keith Johnstone and it seemed that "butoh" is a form Mask work, which encompases commedia dell'arte, voodoo possession, and classic clown work. In mask work, the wearing of the mask shocks the mind into more primitive states of being.

Heart work

2006-07-01T17:15:00.000-07:00

My heart is ready to explode
Pumping hard against my ribcage
A rugby player kicking his way out of a sack
With every kick my sternum rattles
Wind rushes into my overworked lungs
Hungrily sucking in oxygen
Softly absorbed by the tendrils lining the surface of the lung
I feel collapse creeping over my limbs
Crimson-scented flow of blood flush my face
I must look like a tomato
I stop
Breathe
Breathe again

"Say It's Possible", copies

2006-06-28T18:05:00.000-07:00

I've been watching a spate of youtube, and one of the most wondrous discoveries, apart from some amazing lip-synching, are videos of every boy/girl and his/her guitar rocking out to cover their favourite songs, and dumping them onto youtube for all the world to see.

Now I know this phenomena because I play guitar, and I've had my dreams of being a guitar rock god. However, I've disabused myself of this notion, now facing the third decade of my life, as I now possess a more measured appreciation of skills that I have not. I know that I do not have a good voice. Yet that never stopped me from belting out my songs as if I did.

I'm sure there are thousands of covers on youtube, but I'm interested in this one song, because the song is so new, it's not even been released. The original could even be classed as a homegrown amateur song. The song, "Say It's Possible" was written by one of my favourite californian songmeister, the effervescent Terra Naomi, a singer from Los Angeles, who I discovered from browsing the jungle of music known as cdbaby. I'd even had the pleasure of seeing Terra play live in San Francisco, admittedly not a difficult feat since she is still not so widely known, so much so that all 10 of us showed up to her gig at the Red Devil Lounge in San Francisco. So if you go to her website, you will find that she is unable to tour the States this summer, and instead, she's exploited the technology available now, in our it wonderland, with youtube, and dls, and digital cameras, and she's put together a virutal tour.

It's a seductively simple idea, Naomi records a song every few days for the whole of summer and putting it on the web. It sounds so simple, but it is probably one of the most fiendlishly ambitious projects an artist can think of: recording in the bedroom, using workable but by no means fancy equipment: this is exposing the singer in all her nakedness - no mixing, no processing, just her voice, her guitar and a digital camera.

One of her songs "Say It's Possible" (and at this moment of counting, she's recorded 14) has managed to make it viral, hitting the front page of youtube at one point, and has received 300000+ page views.

So listening to it, I was surprised to find that within days, had attracted the cover efforts of a bunch of people.

Here's PJsurfs, June 24:

Here's Mac1302, June 26:

Here's briennalauryn June 24:

Here's kol28, on June 27:

Added on June 27, 2006, 11:45 PM
by tlee0129 (3 videos)

Indeed, the youtube flowering of the song has even encouraged the indefatigable Naomi to record a "How to Play" video for the song, and as she says, "It's a really simple song, and some of you have been kind enough to point out..."

Expect to see more attempts in the future. Hmmm, I need a digital camera so I can try my version ... I'm thinking a reggae version, which, it must be said, requires a big hit of the ganga ...

Update: I've created a page to store all the videos, and I'm going to keep it current...

A Rose by any other Name

2006-06-05T14:08:00.000-07:00

I was at a bbq yesterday in SF with a bunch of musicians. Asking one of them what band he was in, he said he was in the "Poontang Wranglers."

"The Poo.. what?" I ask.

"The Poontang Wranglers."

"The KooKang Bunglers?" I ask.

"No. The Poontang Wranglers."

"I still didn't get it?" I ask.

"The Poontang Wranglers."

"Oh. The Poontang Wranglers." I finally said.

Then he added, "I think our band name recently got voted onto the AV list of worst band-names."

Colbert's Advice for the Young (tm)

2006-06-04T21:53:00.000-07:00

"Remember, you cannot be both young and wise. Young people who pretend to be wise to the ways of the world are mostly cynics. Cynicism masquerades as wisdom, but it is the farthest thing from it. Because cynics don’t learn anything. Because cynicism is a self-imposed blinder, a rejection of the world because we are afraid it will hurt us or disappoint us."

"Cynics always say no. But saying yes begins things. Saying yes is how things grow. Saying yes leads to knowledge. Yes is for young people. So for as long as you have the strength to, say yes."

~ Stephen Colbert, 2006 Commencement Speech at Knox College in Galesburg, Ill.

notes on filming tv

2006-05-19T09:01:00.000-07:00

I recently stumbled onto the filming of a TV pilot, and saw some behind-the-scenes stuff that perhaps you might be interested in.

I found out that the opening credits, where the audience are screaming the host into existence, are actually filmed in the middle of the show. This is because the audience is not actually warmed up at the beginning of the show but will be by the half-way mark (at least you'd hope so).

On TV, when you see the host rush out in front of the audience at the top of show, it's actually the second time that the host has rushed out. We were told this, at the half-time interval by some bearded guy, who was not the MC but popped out onto the stage, who proceeded to explain the filming of the opening sequence to us.

We were told to scream like a bunch of rabid monkies, and, of course, being a bunch of celebrity-starved attention tools, we cheered on the host back on stage to welcome us once again.

The icing on the bike

2006-05-14T09:12:00.000-07:00

What is the most important thing on a bike? Well I was recently talking Lizzie, an avid bike-rider, about bike accessories. We were at a party at my place, and she and I and a couple of other people were gathered around the bikes parked in our apartment, where she pointed out the features of her bike. Being a bike-enthousiast, Lizzie's bike was a labour of love, a hand-crafted, custom-made work of art, built around a bright blue Bridgestone frame.

But then she said that it wasn't quite perfect. Not perfect? She pointed me towards her handle-bars. "There," she said, "Can you see that I've only get one set of brake handles". It had one of those curvy handles that look like ram horns. The brake handles flared over the edge of the horns.

"What I really need is to have another brake handles set over the top," as she pointed to the top part of the handles near the fulcrum joining the handle to the frame.

"Why is that?" I asked.

"It's much easier to smoke a cigarette with when you can hold the top of the handlebar with your other hand."

Great 10 min Short Film

2006-04-25T00:19:00.001-07:00

Watch this short film - brilliant concept with a unpredictable twist at the end. So good, I watched it again immediately as soon as it finished. A super-super tight script, which may not be apparent on first viewing.

The Preview Bait-And-Switch

2006-04-23T12:47:00.000-07:00

Have you ever gone to see a movie, and after watching it, felt utterly cheated because the movie looked nothing like the preview. How was it possible that the only funny thing in the movie were the 3 jokes in the prevew? How was it possible that the preview seemed so much more funny, exciting, scary than the actual movie itself?

Here's how. Devious editors, armed with a magician's sense of misdirection, can make dog-turd seem like a steamingly hot delicious meat-loaf.

The proof? Here's two previews that have been floating around the net, showing how one can cut a classic into a completely different genre, using some brilliant moves on the cutting floor. Watch how music, pacing timing, and montage, can make light into dark, and dark into light.

1. The first is "The Shining" [redux] as redemptive family comedy:

2. And the second, reversing the genre-switch, is "Sleepless in Seattle" as horror:

He Got Game

2006-04-05T23:59:00.000-07:00

So I was out on the town with Kim and Petrice, our beloved 6" 11 (I exaggerate somewhat) Nubian Princess. As we were just about to walk into the AMC Van Ness cinema complex, a sultry voice called out behind us, "Hey you, wait, wait a second."

Not knowing who the voice was addressing, we all turned around to see a tall fresh-faced young man, flashing a thousand-dollar smile in the direction of Petrice.

"I justed wanted to say that you are a beautiful woman," he said as he moved towards Petrice, looking straight into her eyes.

A royal flush appeared on Petrice's face.

"Anyway, that's all I wanted to say," he said as he made the most casual of gestures, brushing her elbow with the tips of his fingers. He paused for a fraction of a second, before turning around to leave.

Squealing like a teen-age girl, Petrice cried, "No! No! Wait. Hold on." as she grabbed for his hand, desperate to prevent him leaving.

At this point, I and Kim decide to prudently enter the building, leaving Petrice to tete-a-tete with the stranger. As soon as we got inside to a safe enough distance away, we turned around and tried to make out what was going through the glass doors.

We see the two of them in animated conversation, at one point, he kicks his legs out sideways, eyes a fluttering, whilst she is lost in the glow of male attention.

Then he ups the ante - he kisses her, first on one cheek, then slowly, the other.

They swap numbers and he leaves.

Petrice joins us inside the theater with a self-satisfied smile painted on her face.

"Well what happened?" we asked. "What did he say?"

"Hurrumph," answered Petrice, composing herself, "he said that I was the most beautiful spoken word artist that he'd ever seen. That's interesting becaused I haven't performed in *quite* a while."

"No no no. Tell us what line did he use to make you let him kiss you?"

"Oh," giggled Petrice, "he said my dimples were so cute that he asked if he could kiss them."

Asking to kiss the dimples, oh my, did he have game.

museum of freaks

2006-04-05T23:53:00.000-07:00

I while ago, I visited the American Museum of Natural History in New York - this was a disturbing place, where all sorts of under-handed racially offesnsive displays were mounted. Anyway, it's taken me a while to gather my thoughts and photographs, but I think I've polished the piece enough to tell the peoples about it. In this museum, you will find pornographic displays in the name of science:

and displays that play a little bit hard and fast with fantasy:

I, web-designer

2006-02-17T10:10:00.000-08:00

This is San Francisco, where cyber-savvy geek-girls sip lattes with the shiny-new-ibooks in seattle-style cafes located in the hispanic neighbourhood. So I guess it was inevitable that I would put together a web-site for somebody. In this case, it was for the lovely Jennifer Hale, girlfriend of roommate Dan. I had to get down-and-dirty with html so that the world can get to see the photographs of Miss Jen Hale. I say: go look at her portrait series, and you might get a sense of what low-down-sf-hipsters look like.

And if somehow you are some big-wig looking for a photographer with style-and-panache, then don't hesitate and contact Miss Jen Hale.

At one to the World Cup

2005-11-25T01:39:00.000-08:00

I have been traipsing around my homeland, the land known as Australia. I thought that I had come back for a friend's wedding and to visit friends and family. But I realise now that I had come back for something much more important. I came back to to witness Australia qualify for the World Cup with my fellow Australians.

So on the second night that I came back, still slightly knocked out by jet-lag, I groped for something to do. Nick and Ben, the two guys I was staying with told me that they were going down to the pub to watch the second leg of the final qualifier for the World Cup. This was epic stuff. Australia, being the winner of the Oceania group in FIFA, were obliged to play a knock-off return-leg with Urguary, the fifth placed South American team.

Now four years ago, it was the same situation. Then, the first leg was won 1-0 by Australia courtesy of a penalty. The second leg, in Montevedo, Urguary, involved people spitting on the Australian team at the airport, and coins thrown on the players. Uruaguay thrashed Australia 3-0.

This time it was different, better players, a team of millionaires. The newly appointed coach, Guus Hiddink, had world class pedagory. It was a mature and measured approach compared to the hurly-whirly bluster of yesteryear. So the second leg was played at Olympic park in Sydney, the geographic center of Sydney, way out west in the burbs.

We, Nick and Ben and I, watched the first half at home, eating a Thai takeaway. And when the goal was scored, a beautiful flowing movement involving 6 players, 3 flicks, a cuffed shot, and a predatory rocket finish - we three jumped for joy, and immediately headed down to the pub. The scores at this point was locked 1-0 from the previous game to Uruaguay, and now 0-1 in our favor.

At the pub, we watched a nail biting hour and a half including extra time. And the deadlock was not broken. However, it was with pride watching the Australian team dominate the Uruguays, as the Australian talsiman, Harry Kewell, wove his spells all over the Urguayan defence.

And then we got to the penalty shootout - perhaps the most nailbiting thing ever invented in modern sport. A team game is suddenly reduced to a series of one-v-ones. The Australian keeper produced two remarkable saves. And the moment that John Aloisi scored the goal, Australians all were united through the television erupted in joy as we were accepted into the holy pantheon of 32 nations who had clawed their way into the last 32 of the nations. We jumped and screamed and hugged. It was cathartic and realised there and then that, even though I am now a citizen of the world, I will always be 'straylin.

The Tide has turned...

2005-11-10T00:55:00.000-08:00

in the last spate of elections, Democrats all across the United States have swept into the local councils of traditionally Republican strongholds. The Democratic party under Howard Dean has been hard at work rebuilding the base

Dean spends two days a week max at the DNC office here, preferring instead to visit state parties. Recently he had lunch with, as he described them, some "very old influential heavy-hitter lobbyists." They gently suggested that he ought to do more time in Washington.

"I can't," he said. "No votes in Washington."

The America of Martin Luther King and Franklin Delano Roosevelt is starting to wake up from a very deep sleep.

Cutting someone down with a smile

2005-11-02T09:32:00.000-08:00

Another assistant professor at M.I.T. has been fired for falsifying data. Whilst scientific fraud happens everywhere, it seems that M.I.T. has had more than it's fair share with the spectacular example of the case involving David Baltimore who was the president at the time.

One of the things that we postdocs pay attention to is the tenure rate of universities. When universities hire young faculty, there is a probation period of 3 to 5 years, at the end of which, tenure is either awarded or the professor is fired. This can be a heart-breaking moment but tenure is a serious committment for a university. But the exact rate of tenure gives an indication of how ruthlessly a university culls the young faculty.

Where I work, the tenure rate is around the 80% mark, a pleasingly high rate for new young faculty. It's likely that a new hire will get tenure, but not so absurdly high that jeckyl-and-hyde personality types automatcially become faculty members. But this is an anomaly amongst top universities. Harvard, Berekeley and MIT have ridiculously low tenure rates, of the order of ~15%. This means that most new-hire faculty will not get tenure. Often these universities will hire young professors with similar qualifications and watch them compete viciously so that they will get tenure.

Whilst at Harvard, this is recognized, and the professors there are known for their cold-blooded competitiveness, MIT seems a little bit schizophrenic. A colleague of mine who had just done the job rounds was really weirded out by the professors at MIT when he gave a job interview there. All the professors at MIT tried really hard to pretend to be nice and jovial and not ruthlessly competitive. But it came across as a charade, as some kind of cognitive dissonance.

The low tenure-rate clearly says otherwise for MIT professors. Because how a university is run structurally flows through into how the staff sees each other. What makes MIT odd is the need for the professors to feel the need to pretend to be collegial when clearly they are not. This schism I think may be one of the reasons why fraud has manifested itself once again at that place.

Asian Pop Soul

2005-10-31T19:30:00.000-08:00

I grew up amongst Australian whiteness, and as a result I've developed a weird prejudice against asians. Maybe it's because the contact I had with my asian brothers were usually middle-class conformist honkies but i associate asian with souless exam-taking-automatons. But I think I may have to change mind after seeing this beautiful example of amateur Asian passion [google video]. Notice the figure in the background throughout the video - so zen.

Falling from a Height, Holding Hands

2005-10-13T08:05:00.000-07:00

What was that?
storms of flying glass
& billowing flames

a clear day to the far sky -

better than burning,
hold hands.

We will be
two peregrines diving

all the way down

~ Gary Snyder, Sep 2001.

Lewontin speaks...

2005-10-12T22:53:00.000-07:00

Richard Lewontin, the greatest living prose-stylist of science writing, has handed-down another missive on the intelligent-design wars. Read and weep.

Democrat Goals for the next Ten Years

2005-10-06T12:21:00.000-07:00

On slate.com, Bruce Reed wrote:

On Sunday, Tim Russert was gobsmacked to discover that when he asked his usual showstopper, "But what are the Democratic ideas?", Illinois congressman and ex-has-been Rahm Emanuel actually had an answer.

Rahm could have said, "Three things: Convict DeLay. Filibuster Miers. Stick pins in our voodoo dolls of George Bush and Karl Rove." Instead, he spelled out five real ideas:
making college universal,
demanding a budget summit,
cutting energy dependence in half with a hybrid economy,
creating a science and technology institute to rival NIH, and
making health care universal over the next 10 years.

Of proteins, clusters and musical chairs

2005-10-05T08:43:00.000-07:00

Recently, I've been reading about how computationally-intense problems in science, such as protein folding, has been driving the adoption of cutting-edge computer technologies, such as Beowolf clusters. But it works the other way as well. The adoption of Beowolf clusters has, in turn, chipped away at the foundations of protein folding so much so that theory in protein science has had to evolve in ways that accomodate the use Beowolf clusters.

I work in the area of protein folding, one of the hairy workhorses of scientific computing. One of course, would like to simulate a protein molecule in as much detail as possible. In most approaches, the lowest level of detail is the covalent bond: every covalent bond is modeled but not allowed to break. This approach is known as molecular dynamics. Modeling the covalent bonds imposes a limit to the simulation: the biggest step you can take must be smaller than a typical vibration of a covalent bond - you must use baby-steps no bigger than a femto-second, or 0.0000000001 s.

A typical protein has tens of thousands of atoms and one normally bathes a protein in another few thousand water molecules. A realistic system might contain hundreds of thousands of atoms. Given the need to model the covalent bonds, the number of time-steps needed to simulate large motions in a protein, typically a microsecond 0.0000001 s, pushes the envelope of even the largest computing systems.

In the past, only well-endowed labs, with access to restricted Pentagon number-crushers, could dream of simulating a protein using molecular dynamics. Even ten years ago, Peter Kollman got a paper in the prestigous journal Science simply for simulating a small protein (the Villin headpiece) for what seemed like an eternity, a single micro-second (0.000001s). He didn't find out anything new but the study was hailed as a tour de force computation (read: my computer is bigger than yours).

But over the last 5 years, a sea-change has swept the field of protein modeling. What has happened is that linux has now commoditized hardware, processors have reached a critical performance hump, and communication protocols between individual computers have matured (MPI - message passing). For a rather modest investment, one can buy 10 or 20 cheap PC clones (Xeon motherboards), and hook them together into a tightly coupled network, known as a beowolf cluster. In theory, a beowolf cluster provides computation that rivals even outrageously expensive super-computers.

As forward-thinking (and penny-pinching) scientists have jumped onto the beowolf-cluster bandwangon, they've collectively run into a methodological brick wall. How do you slice up a molecular dynamics computer program that was written to run on one computer? The probelm is that running a computer simulation is a little like following a recipe for baking a cake. You have to mix the eggs and flour in a batter before you put the batter in the oven. Putting the flour and eggs in the oven whilst mixing the dough will not result in a cake. However, various strategies have been devised to bake a protein in parallel.

The first is the shot-gun approach. This approach used mainly by Vijay Pande at Standford in the feel-good folding@home program. Folding@home is unique in that it farms out the computation to tens of thousands of desktop computers scattered around the world. The essence of the shot-gun approach is that running a very long molecular-dynamics of a single protein should be just like running thousands of short simulations of the same protein. In order to make sure that each simulation is different, the protein is scrambled at the begining of each simulation. This makes it easy to farm out a short simulation to one of the many desktop computers in the folding@home project. At the end of all the simulations, the results are averaged out to find the consensus solution. The prevailing philosophy is that with enough shots in the catridge, you will hit the bird, no matter what.

Another approach is the divide-and-conquer approach. Machiavelli famously advocated that, when facing a coalition of enemy forces, instead of hurtling into an full-frontal assault, one should learn to play each enemy against another. By using subterfuge and dipolacy to foster internal strife, victory is brought closer to fruition. Similarly, in a simulation of a protein and its vassal water molecules, the simulation is broken-up into little spatial grids where all the atoms in each grid-cell is simulated by a single computer in a beowolf cluster. Just as a successful divide-and-conquer approach depends on subterfuge and diplomancy, the success of the simulation will depend on the quality of the cross-talk between the grid-cells. This is a rather new technique and time will tell if it can be successfully applied to protein folding.

But by far the most popular technique is replica-exchange, or the musical-chairs approach to molecular-dynamics simulation. In replica-exchange, a modest number of copies of the protein are run on the processors of a beowolf cluster. But unlike the shotgun approach, each copy of the protein, called a replica, is run for a very long time. The replicas running on the beowolf clusters play a game of musical chairs. The replicas are mixed around so that each processor gets a chance to simulate each of the replicas. Of course, there's no point in mixing the replicas around unless each chair is different. When the music stops, each replica sits down on a chair with a different temperature - some are tepidly warmed at room-temperature, whilst others are hot enough to deep-fry a turkey. The idea is mixing-and-matching replicas at different temperatures supposedly speeds-up the simulation where only proteins that are in a good shape can sit down onto a cooler chair. This method of speeding up the simulation is wildly speculative but seems to be tailor-made for beowolf clusters - only a few number of processors are used with swaps between processors happening at regular intervals. It calls to mind afternoon cable television commericals - you really do get more for less.

But during a recent conference, my boss heard a speaker quip that replica-exchange was a hack technique that doesn't improve molecualar-dynamics simulations. The room erupted. It turned out that pretty much everyone in the room was using replica-exchange. The speaker then pointed out that, anecodotal evidence withstanding, nobody had yet shown quantitatively that replica-exchange was more efficient. But what was left unspoken was that the guys in the room had to believe in replica-exchange, if only for the luxury of using their affordably cheap beowolf-clusters.

Perl is...

2005-09-30T15:51:00.000-07:00

...the duct tape of the internet.

~Hassan Schroeder, first web-master of Sun.

Transcription as Compilation

2005-09-24T13:52:00.000-07:00

It occurred to me the other day that a useful metaphor for making proteins is, not a factory as current thinkiing goes, but rather, that of compiling a computer program from its source code. Treating transcription, the making of protein from its DNA sequence, as a parser seems to be a more natural end-point to the idea that is a computer code.

Like any science, molecular biology is driven by metaphors. The most popular method has been the factory metaphor. DNA is understood to be a DNA serves as a blue-print of the cell. A rough-n-ready copy of the blue-print is made in the form of RNA, which is read by machinery of the ribosome to make a protein. This forms the infamous central dogma of molecular biology: DNA -> RNA -> Protein

blueprint-factory metaphor has reigned supreme. In this method, we think of proteins as little machines, and we marvel at the Rube Goldberg machines that seem to inhabit the cell no matter where we look.

Traditionally, transcription inside the cell is seen as a manufacturing process. The

But recently, cracks have started to appear in this edifice. Now that researchers are beginning to glean the intricate machinery that regulates the DNA, the language of networks have started filter down into the literature. Filaments of interactions, where proteins that are made from the DNA blueprint, then itself binds back onto the DNA, producing a convulted linkages of cause-and-effect that is impossible to separate back into the clean stark lines of the central dogma.
What is a compiler? A compiler is a computer program that turns text written in one language (C++) into machine code that can be read by a computer. But reading a Joel Spolsky article, I came across the idea that translation from one language into another is also compilation. The example given was the first C++ compiler. Bjorne Stroustroup originally wrote the object-oriented extension to C as a pre-processor command. But the idea was that you would write the C++ program, as designed by Bjorne, and then the pre-compiler would turn that into C, then a C compiler would turn that into machine code, ready to run on your machine's microchip. Joel pointed out that this pre-compilation step is actually compilation. There was just as much work in translating C++ to C as there was in translating C to machine code.

And then I saw the analogy. What if DNA was C++, RNA was C and proteins was machine code? Yes, the hard and dirty work inside the cell was done by the protein code, representing the deep dark actions of the biochemistry, and of course, DNA was the C++. The analogy stretches even further when you think about compiler macros that are often embedded in C++ source files that depend on important information about the enviroment that the program is compiled in. This would make the compiler the ribosome.

So what does this analogy gain us? Well for starters, we can steal some ideas from compilers and apply it transcription. For instance, one common goal in language designers is boot-strapping. A computer language is essentially embedded in the compiler, a binary program that translates a computer program, as expressed in the text C++ file, into machine language. Boot-strapping means that a particular computer language is sophisticated enough to encode everything needed to write the compiler in that language. In C, we write the C compiler in C itself. With an existing C compiler, we should be able to compile the source code the compiler and output a functional binary of the compiler (this need not be identical to the existing compiler). In designing new versions of a C compiler, one must first use an older version of the compiler, to generate the binary of the new version of the compiler. But the moment of truth is when we use the new version of the compiler to generate itself in itself using its own source code.

So a test of a DNA, RNA, ribosome, protein is the ability to bootstrap. We use the ribosome to read the RNA that includes the ribosome component proteins, to make the new proteins, which are assembled into a new ribosome. There even examples of the old versions running around. For instance, mutant experiments often fold RNA from a latter eukaryotic orgnaism into the cell of a prokaryote. And the prokaryote will happily make (or compile) the visitor RNA, if the RNA makes it all the way through the cellular protective layer.

A strategy for all political stripes...

2005-09-14T21:42:00.001-07:00

An apt summary of Republican political strategy:

....voice or no voice, the people can always be brought to the bidding of the leaders. That is easy. All you have to do is tell them that they are being attacked and denounce the pacifists for lack of patriotism and exposing the country to danger. It works the same way in any country.

~Hermann Goering, 1946.

source: made in a statement to G. M. Gilbert, a pyschologist who intervied Goering in prison during the Nuremberg war-crimes tribunal (Nuremberg Diary, Gilbert, 1961, Signet NY).

Diving into the ocean shore for the very first time...

2005-09-12T23:36:00.000-07:00

Most of the stories about the Israeli pull-out of the Gaza strip seem to be derogatory of the Palestinians, except for this poignant story [need subscription] in the San Jose Mercury Times:

Palestinian teenagers Mahmoud Barbakh and Mohammed Jaroun grew up just a few minutes from the Mediterranean, but had never been to the beach.

On Monday, they waded into the waves with their jeans rolled up, then abandoned all caution and threw themselves into the surf.

"It was the sweetest thing in the whole world," said 15-year-old Mahmoud.

Candide on Katrina

2005-09-11T15:35:00.000-07:00

Jon Stewart is the Voltaire of the early 21st century. He and his talented band of writers/editors/directors sum up, in a brilliantly edited montage, everything that is sickening about the Bush Administration's response to Katrina. And they are never less than absolutely funny about it. (source: onegoodmove.org/1gm/1gmarchive/002364.html).

[click on picture to play video]

Mini-sex

2005-09-08T13:31:00.000-07:00

I was at this dinner-party, and as the topic of conversation wandered to sex, one women blurted out, "I lost my virginity to mini-sex."

Mini-sex? What the hell was that? Was it sex amongst midgets? I had to find out.

So I asked, "What, ah, is mini-sex?"

"Oh you don't know? Well, mini-sex is when it's five thrusts or less." Apparently, not very satisfying for a woman.

So boys, just try to hold it out for the sixth, and you won't be shamed and laughed-about behind your back.

Runaway email

2005-09-08T11:14:00.000-07:00

Two secretaries in a Sydney law firm got sacked, after a flamewar started over a missing ham sandwich.

Ms Nugent writes a group email, "Yesterday I put my lunch in the fridge on level 19 which included a packet of ham, some cheese slices and two slices of bread which was going to be for my lunch today. Overnight it has gone missing and as I have no spare money to buy another lunch today, I would appreciate being reimbursed for it."

Melinda Bird replies that Ms Nugent had probably left her lunch on a different floor.

Ms Nugent taunts Ms Bird for being blonde.

Ms Bird responds, "Being a brunette doesn't mean you're smart, though."

Ms Nugent e-mails co-worker: "Let's not get personal, Miss Can't-Keep-A-Boyfriend."

Flame-war escalates.

Email exchange is forwarded to other colleagues at the firm (Allens Arthur Robinson).

Email is then forwarded to other offices in Sydney, including Westpac, Deloitte, Macquarie Bank, and JP Morgan. As one on-looker remarks, "This is magic. You can't script this sort of thing."

Ms. Bird and Ms. Nugent are fired.

Update: Groin's Grab has the complete exchange, with pictures.

Racist AP captions

2005-08-31T07:25:00.000-07:00

From metafilter,

black people loot , white people find. Racist photo captions by Yahoo News/AP illuminate more than Katrina's aftermath. If these pictures are taken down, there are mirrors here (loot, loot, find).

The Punctuated Equilibrium of Bush's Popularity

2005-08-10T09:18:00.000-07:00

Via Slate, I was directed to this graph of popularity of President Bush, created by Professor Pollkatz. It's fascinating - there has been no sudden decline due to the effects of the war. Rather, it's the return to the natural popularity of Bush before the perturbation due to 9/11.

You can't handle the truth

2005-08-02T23:31:00.000-07:00

I am a scientist and supposedly, I deal with truth. You can always read about the miraculous powers of science in ferreting the secret knowledge of the universe in nepotistically self-congratulatory editorials of journals like Nature, Science or PNAS (pronounced Pee-Nas). But when I try to compare the mystical experience of finding the (scientific) truth to my daily ritual of coming in to lab every day, writing code, running computer programs and formatting tidy little tables in Microsoft Word, I have great difficulty in seeing where the truth actually blossoms.

At what point does one discover the truth? Is it when I have the idea, when the program has calculated the numbers and written to the hard-disk? When I see the data for the first time? But then, one is never sure that the run is good, so you run it again. Then you type up a breezy little paper, situating your idea in the forest of competing claims and counter-claims. That delicate process of positioning your data so that it never strays too far from the main-stream, yet says something of some originality. And so, you might publish a paper. But, like the tree that falls in the forest and no one hears it, what good is a paper if no one cites it? Yes, the process of submitting a paper to a professional journal is full of heart-ache and pain. Waiting for an editor and his cohort of reviwers to pass judgement on your article seems more like being in middle school again, waiting to be admitted into the circle of popular kids. Is your science hot or not?

I got to thinking about this especially after following yet another round of Creationism vs. Evolution debate that has wracked the United States for decades. Of course, the Defenders of Rationality have all come out of the wood-work to defend the legacy of Charles Darwin from the Heathens of the Gate. Whereas the Fathers of the Christian Faith is bravely trying to scale the walls of the godless traitors of this great Christian land (after all Jesus Christ was voted as the 13th greatest American). Whilst we can all laugh heartily in the ivory towers of academia at the shoddy arguments produced by the Creationism, and in particular the Intelligent Designers, I can't help wondering if the argument of the Evolutionists is all that airtight.

Don't get me wrong, I love evolution, I buy it, I'm a card-carrying (phd) scientist. But I've rarely heard any scientist explain how ideas change into experiment into data into theory, fact and truth. Every step of this evolution seems to me, fraught with logical holes. Most scientists don't realize this because they've spent their who careers learning science and not the history of science. Few have grappled with Hume's challenge to empiricism, Kant's rebuttal of Hume, Hegel's theoretical rejoinder to Kant, and the whole ecology of sociologists of science. Not that I blame my fellow scientists for their ignorance. There's only so many hours in a day, and it's tough enough to absorb a few branches of the many scientific disciplines. I call myself a biophysicist but definitely less biology than physics. I'd have trouble telling you what fungi is.

This confusion I think is at the heart why most of my fellow post-docs and grad students dread that most onerous of tasks - writing an article. The fact is, they don't know why, or how the process of justifying their scientific claims really entails. Now of course, any post-doc who makes it up the next rung of the academic ladder must learn this, but it's by osmosis. Like at the moment, our lab is hard at work on the next "big" paper from the lab. My boss is keenly trying to position the paper in such a way that it will seem important. It's not so much bending the results but it's like rotating a sculpture of woman around at the right angle so that the shaft of light from the sky-light will catch the lips just so.

Pop-sci tripe

2005-07-29T00:36:00.000-07:00

I've just finished yet another popular sience (pop-sci) and I feel nauseauted by how bad it is. As a practising scientist but also an avid reader, I feel obliged to read my fair share of pop-sci. Apart from D'Arcy Thompson's sublime "On Growth And Form", recently, I've read a slew of terribly-written pop-sci books. There was: Robert Laughlin "A Different Universe", Steve Rose "Lifelines", Andrew Parker "In the Blink of an Eye", Martin Brooks "Fly". All horrible. None of these writers can write concisely, stay on topic, structure an argument, or even tell a godamn story. The prose is graceless, studded with prickly pieces of jargon, drier than the Gobi desert, and smeared with a holier-than-thou attitude. But most of all, these writers can't write a decent metaphor even if someone stuck a gun to their head and threatened them with a game of russian roulette. They use half-baked metaphors and wax lyrical without a trace of poetry. Poke my eye out with a stick. Please.

What do readers want?

2005-07-28T21:04:00.000-07:00

So I am writing Jonathen Franzen's essay "Why Bother" again. It's a briliant essay on why we, readers of fiction, even bother to read. He gives a pithy answer.

Franzen's answer channels the sociologist Shirley Heath, who has spent much of her career studying people who read, the one thing that pops up over-and-over in her study is that readers are drawn to unpredictability. The difficulty in "difficult" novels is the unpredictability of how a life turns out.

Shirley Heath found that the type of person who is a serious reader is not limited to white over-educated college graduates, but is rather diverse. The one thing that unites them is that readers are people who have faced serious up-heavels in their lives. Is it then a surprise that the bulk of book buyers, according to national book-seller statistics, are middle-aged white women? The sexual revolution created a fundamental schism in the expectations of women that separated their dreams of their own mother's simple future, to that of their own, vastly more complicated and more-fulfilling one.

Unpredictability is also about the contradictions that life throws up. Great fiction doesn't avoid the comforting fictions that we often tell ourselves about life. It doesn't hide the sudden heart-attack, the betrayal of a 50 year marriage, the back-stab in the time of war. Dilemnas are dilemnas precisely because conventional wisdoms cannot tell us which way we should go. Moral contradictions and ethical dilemnas are the deep well-springs of unpredictability.

However, great fiction, according to Franzen, is predictable in a certain way. It is predictable in the sense that the great mysteries of life have always been there. They have never been solved and they will never be solved. Ever since the first ape asked, "why me?", such questions have been asked over-and-over again. The question has not changed but the form of the question has. And they form it takes, has manifested in every age, in every decade, in every life-time in every possible, surprising and unpredictable way.

Transcendent Moments in Film

2005-07-23T19:24:00.000-07:00

I stumbled onto this list of 100 greatest moments in film that was put together by the Guardian. As someone who believes that specificity is key in good artistic criticism, I find that reading about single moments in a film sure beats reading prose expounding on entire films, such prose is usually so waffly that a severe case of critical indigestion normally follows. Anyway, I've started you on 91-100, as voted by the Guardian readers. And just in case you're wondering, moment number 1 is one of my all-time favourites as well.

I Can See Clearly Now, the Pain is Gone

2005-07-23T18:58:00.000-07:00

So I bumped into H the other day, and asked a casual, "What's up?"

"Not much", she anwsered. "Well, actually, I got laser surgery on my eyes yesterday."

"Does it hurt?" I asked.

"Well no. It's remarkable, there was hardly any recovery time. I can see clearly right now."

"Wow, you must have had general anesthetic", I said.

"No. I had local."

"You were conscious through the operation?", I asked.

"Yes. Although there was no physical pain, it was gross. It's amazing, millions of years of evolution has wired us to flinch at objects that come near the eye. In the operation, I had to hold my head still, conscious, and watch someone clamp something over my iris to hold it still."

"Then the doctor brought up an electric knife up to carve open the lens. It was an electric knife but, even though I couldn't feel anything, the sound of the electric knife, which resembled a dentist's drill, was horrible. After he cut open the lens, I could feel the lid flapping in the air." [helpful image from Luis Bunuel's Le chien d'Andalou]

"What was worst was that I had been wearing my old contacts incorrectly. I would often leave them on whilst sleeping. Having the contacts in the eye for so long prevents oxygen from entering the eye. As a result my eye had grown more than its fair share of blood vessels inside the eye. My eye was engorged with blood. So when the laser started cutting open my eye, the blood vessels burst. My vision started to color red, and I could feel the blood pouring out of my eye-balls."

"You can still see the bruising," she said as she pulled away her eye-lid to show me the large splotches of bruise over the top of her eyeball.

"The operation lasted maybe 15 minutes and I felt no pain but it was one of the worst experiences of my life."

The Ressurection of Angie Hart

2005-07-17T23:38:00.000-07:00

I still remember many years ago in Australia when I first heard the voice of Angie Hart. I can't remember exactly what I was doing, but I do remember that I stopped what I was doing. The song was "Ordinary Angels", 2 minutes and 26 seconds of perfect acoustic pop. The ethereal voice of Angie Hart floated over a shuffling slightly-left-of-center chordal progression. The voice had a vulnerable, breathy quality but there was something else. Now, many years later, I realise that part of the charm of the voice is a Australian cadence, a slight flattening of the vowels and roundening of the consonants.

The song was from the band, Frente, and the song was written by the guitarist Simon Austin, still one of my favourite acoustic guitarists. They released two fantastic e.p.'s, which contained a bevy of great songs, including t"Labour of Love" (20 MB avi). The future boded well for the band, as they started to make headway into the Australian music scence. They even played at the university where I studied.

The first album, Marvin the Album, included most of the good songs from the ep's with a few new ones. Unfortunately, the first single from the album was the garish "Accidentally Kelly Street", a song with a very catchy melody but terrible lyrics (Here's the door / And here's the window / Here's the ceiling / and here's the floor), contrasting painfully with the other songs. And to pile misery onto misfortune, they made a terribly gauche music-video for the song, where Angie is dressed up in a house-wife costume cleaning a card-board cut-out house with oversized brooms and dustpans. It was a frightening possibly inspired by a session with Lucy in the Sky with Diamonds. The second album, "Shape", was where I lost interest. The problem was that Simon Austin, whilst a brilliant acoustic guitarist, couldn't really handle the electric guitar. Frente mutated from a lively acoustic band to a languid electic prog-rock guitar band. Of course, there was a relationship within the band and not long after Austin and Hart broke up, the band ended.

I lost track of them for a while but a few years later, Angie Hart popped up again with her new band, Splendid. Well it was not so much a band, but a love child. Touring with Frente, Angie met former Chilli-peppers guitarist, Jesse Tobias, and they got married, formed the band Splendid, and released an album, "Have you got a name for this."

After Frente ended, Angie moved to L.A. and Simon moved to New York. Apparently, Splendid got jerked around by the record company where they didn't even bother releasing their first album in the States. And if you crawl through the splendid web-site, you'll find that Angie spent several years trying to write music, live in l.a., maintain a relationship, whilst working a 9-to-5 job in retail. But it seems that phase is over. Although Splendid has released their second album, Angie is now back in Australia. And Frente, well, recognizing the spark that made them great, Angie and Simon recently started playing again, and recognizing the error of their ways (mp3) , they have now reformed Frente. Long live Frente.

The Nature of Rock and Roll

2005-07-14T23:27:00.000-07:00

Stephen Metcalf, in his review of Nick Hornby's new book, penned this remarkable insight:

Nick Hornby has built his admirable career, as comedian of manners for the album rock era, out of a single, hedgehoglike insight: The majority of people touched by rock music weren't makers of rock music. In fact, they weren't even remotely like the makers of rock music. They were consumers of rock music, or dorky suburban boys in poster-filled bedrooms.

People who love rock music are people who see refracted in the rock idols, the sublimation of their desires, which for the briefest of moments, lifts them out of their (typically) middle-class homogenity. Or, as Stephen Metcalf puts it:

Sublime banality and self-centered mediocrity and a pitiful moonlit pining: Hornby captured perfectly the voice of the Baby Boomer more or less permanently fixed to the emotional vocabulary of his own pubescence.

The Power of Wikipedia

2005-07-07T10:17:00.000-07:00

It is 10:17am Western Pacific US time, Wednesday, July 7th. Already, there is a detailed entry on wikipedia on the London Bombings that happened yesterday. Reading some of the forum responses, it seems that people are inching to undestand what it may be like to have a brutal occupying power run by soldiers with frighteningly powerful guns and bombs who speak another language, and who have slaughtered over 100,000 of your countrymen.

Guitar Etiquette

2005-05-30T12:54:00.000-07:00

When at a party, chances are, someone will bring out a guitar. A guitar in a party is a magnet that sucks out guitar players from the mass of party-goers.

Typically, the owner of guitar will play a few songs, songs that he (or she) has practised for many hours in the privacy of his own room and is therefore comfortable playing in public. Like moths to the flame, guitar players in room will be drawn to the guitar, motivated by a combination of fascination with live music, but more importantly, positioning themselves for a crack of the guitar after the song is finished.

Guitar etiquette says the person who owns the guitar (Owner) must share the guitar with the other players (Guest).

"Wanna play?" asks Owner to Guest. Guest can accept or decline. Here are the rules.

If Guest is significantly inferior to Owner, Guest must decline the invitation.

If Guest feels on a par with the Owner, then Guest can accept the invitation and play one song. Then what follows will be an alternation between Guest and Owner, as they "trade" favourite songs, licks, and tricks, wowing the audience (hopefully) in the process.

If Guest is better than Owner then Guest is allowed to play several songs in a row, demonstrating Guest's superiority. Owner will then say, "Can you show me a few tricks," to which Guest is obliged to show at least one trick that Owner can learn. Then Guest owns the guitar for the rest of the night.

But if Guest is many times better than Owner, Guest will generally decline invitation to play.

Because, after all, when Owner asks "wanna play?", Owner is really asking "are you better than me?"

Farewell HuaFeng Xu

2005-05-27T15:33:00.000-07:00

One of my colleagues in the lab is leaving and I am sad. Huafeng Xu (HFX) a.k.a. Chinese Blade a.k.a. Eye of the Blade a.k.a. the Jewish-Asian magician David McKowski has decided to bid farewell to academic science on the West Coast for the pulsating glories of commerical research on the East Coast.

Oh, and his future-wife-to-be is also waiting for him there as well.

HFX, I am afraid to say, is a die-hard romantic. This was not evident at first, but he left clues. I stumbled on the first clue in, of all places, his PhD thesis. Normally, a thesis is a grindingly boring piece of prose that budding scientists are required to do. It is no joy to write. The only real emotion in a thesis is normally found in the preface/acknowledgements - I vented a few of my frustations in a page long diatribe. Not HFX. His preface was a five-page effusive outpouring of scientific romance,

"...my mental image of a theoretical chemist was a solitary figure walking down the Long Island Beach with his advisor. They would exchange a few words now and then, or squat to write some esoteric mathematical equations on the sand with their fingers. Theoretical chemistry seemed too romantic to be for me..."

Reminds me of the story about the Christian walking along the beach. Looking back, he sees that for most of the journey, there are two sets of footprints faintly impressed upon the sand - his and the Lord's. But then the Christian notices that occasionally there was only one set of prints. "Why," he asked the Lord, "did you abandon me?" "No, my son," replied the Lord, "when there was only one set of footprints, it was I who was carrying you." Think of that story as an allegory for the many conversations that I had with HFX in our journey to the truth. Sometimes only one of us would be right, then there would only be one set of footprints in the sand, as one of us would carry the weight of the error of the other. Man, does HFX like to talk. We talked about everything, the meaning of life, love under communism, the future of business in a melt-down world, chinese poetry, ethical dilemnas involving members of one's own family, the meaning of the second order pertubation expansion in the Schrodinger equation, the symbolic order behind a glass of wine in Sideways. But his is always a generous and expansive conversation, and more-often-than-not, funny as hell.

HFX has the face of an innocent child but the heart of a prankster. One of our favourite activites would be to draw cartoons in the middle of a seminar with a visiting professor and try to make the other crack up. We would write pseudo officious pronoucements that would be irresistibly funny to us but (apparently) not to anyone else. But over the last year, I saw HFX flex his writing muscles, transmorgifying his writing into something substantial. HFX reinvented himself as the blogger chineseblade, a trenchant social critic and a witty commentator of the world around him.

Talk about flexing muscles, I cannot fail to mention the time that a bunch of us, staying late at night on a Friday, decided to do a fashion parade down the catwalk of our work cubicles. One by one, we would play a song on Banu's laptop, and slither down our imaginary catwalk, strutting our stuff. When it was HFX's turn, he disappeared for a good 5 minutes before appearing in King's oversized leather jacket. He glided down the catwalk like a panther, and when he reached the end, with a well-practised motion, he whipped off the jacket to reveal his naked torso.

Many a dull afternoon at work was enlivened by an impromptu card trick from HFX. The tricks got better and better such that one night, we organized a private show. Of course, a magician cannot use his everyday persona, he must draw something from the world of fanatasy, and so the persona of David McKowski, a chinese-jew was born - son of a hasidic master of magic, refugee from Nazi Germany, who forms an illicit relationship with a simple chinese peasant girl. Growing up, Mckowski discovers his mystical roots, and learns to manipulate cards, eventually fulfiling his destiny as a Magician.

And so, I end this post, my farewell gift to you, HFX. Adieu.

First glimpse of another planet

2005-04-30T13:12:00.000-07:00

Sure astronomers believe other planets exist. But finally, someone has managed to photograph one. A bunch of international astronomers, working at the Very Large Telescope (it's a real name) at the European Southern Observatory in the Atacama Desert in Chile, thinks they've photographed the very first planet outside our solar system:

The red spot is the planet, a giant that is four times bigger than Jupiter. As they say an image is worth a thousand words, an optical photograph is worth a thousand spectroscopic radiation analyses. The sun, dubbed 2MASSWJ1207334-393254 or "2M1207" to his friends, is a small brown-dwarf, a sun that failed to light up properly. According to spectroscopic analysis, water is found on the planet, a sure sign that it is cool and planet-like.

I'll borrow that for a dollar

2005-04-15T19:41:00.000-07:00

Open source software is free, right?

Public libraries are also free, right?

Then how hard would it be to give out open-source software in public libraries?

Well it turns out to be much harder than expected. Librarians deal with all sorts of issues in accepting things for a library. Being free is only one of many complex considerations that librarians consider. In this article, Bob Kerr shows how to mediate the interests of the open-source advocate and the public librarian.