Ola! After 5 years, I've abandoned this blog. If you want more, go to boscoh.com

10.09.2006

In the prophet's own words

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.

10.03.2006

Guest blog from Warren Longmire

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.

10.01.2006

bic runga does jacques brel

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:

9.30.2006

Art Schools versus Science Schools

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.

9.28.2006

A Poetic Form: The Pantoum

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.

9.25.2006

What no American man has

"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"

9.20.2006

Self-referential promotion letter

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.

9.19.2006

hipsterotica

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.

9.17.2006

U2: With or Without You

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

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

9.16.2006

Best title in a Science magazine article, ever

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

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.

9.15.2006

Glimpse into the glorious past (1665) of science

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.

9.14.2006

Culinary desire

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.

9.13.2006

Time-lapsed video of 160 hot-air balloons

This is beautiful and wonderfully ridiculous at the same time

9.01.2006

A Smear of Blood

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

8.31.2006

New York

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.

8.28.2006

Godless Sight

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.

8.01.2006

The Soul of the Box

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

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.

7.26.2006

Asian-americans breaking through the entertainment barrier

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):

7.19.2006

The Peace that Passeth Understanding

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

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.

7.14.2006

Infogami, hosting served just right

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.

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.

7.13.2006

Dance around the world

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

7.05.2006

migrations

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

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.

7.01.2006

Heart work

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

6.28.2006

"Say It's Possible", copies

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...

6.05.2006

A Rose by any other Name

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."

6.04.2006

Colbert's Advice for the Young (tm)

"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.

5.19.2006

notes on filming tv

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.

5.14.2006

The icing on the bike

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."

4.25.2006

Great 10 min Short Film

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.

4.23.2006

The Preview Bait-And-Switch

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:

4.05.2006

He Got Game

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

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:

2.17.2006

I, web-designer

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.

11.25.2005

At one to the World Cup

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.

11.10.2005

The Tide has turned...

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.

11.02.2005

Cutting someone down with a smile

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.

10.31.2005

Asian Pop Soul

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.

10.13.2005

Falling from a Height, Holding Hands

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.

10.12.2005

Lewontin speaks...

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

10.06.2005

Democrat Goals for the next Ten Years

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:
  1. making college universal,
  2. demanding a budget summit,
  3. cutting energy dependence in half with a hybrid economy,
  4. creating a science and technology institute to rival NIH, and
  5. making health care universal over the next 10 years.

10.05.2005

Of proteins, clusters and musical chairs

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.

9.30.2005

Perl is...

...the duct tape of the internet.
~Hassan Schroeder, first web-master of Sun.

9.24.2005

Transcription as Compilation

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.

9.14.2005

A strategy for all political stripes...

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).