Stop motion animation genius

Iraqi voice

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

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

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

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?

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

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

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

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.