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.

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.

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.

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.

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.

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.

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.

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.

Perl is...

...the duct tape of the internet.

~Hassan Schroeder, first web-master of Sun.

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.

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).

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

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

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

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

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

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

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

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

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?

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

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

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

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

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

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

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

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

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

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.

I am now closer to understanding the American Mind

America, "we are one (warning:audio)" !

The Wolf is really the friend of Tree

Ecology is a rather young science, being more the province of the leisurely hiker than the hard-nosed sceptic. Often ecological writings are wishy-washy and vague. In contrast, this Scientific American article recounts a very specific and surprising example of the impact of a single species on a particular ecology. William J. Ripple, professor of botany at Oregon State University, has been studying the reintroduction of wolves into Yellowstone National Park.

In Yellowstone, the last wolf died out in the 1920's, which lead to the overpopulation of the elk population in Yellowstone. The engorged elk population exerted a severe pressure on the ecosystem. In 1995, to control the elk population, wolves from Canada were reintroduced back into Yellowstone.

As expected, the wolves quickly reduced the elk population. What was not expected was that the trees would come back just as quickly.

Elks, when they do not have to worry about wolves, are indiscriminate eaters, happy to munch on any vegetation they can find. Scared elks graze differently. Instead of dining lazily on delicate river-side vegatation in the Lamar Valley, scared elks must dine on higher ground where they can keep a look-out for wolves - wolves that smack their lusty lips at the thought of elk-meat.

During the 1920's, when the elks could eat indisriminately, magnificent trees, such as aspens and cottonwoods, stopped regenerating. Without the wolves running around in the park, when the elks got the pick of young juicy treelings. But now that the wolves back in town, the elks can't eat just anywhere, they have to watch their back like mafia gangsters dining on pasta in their favourite diner in Little Italy. The elks have to avoid exposed areas, the areas that treelings like to spread their leaves to grow.

Thanks to the wolves, young aspens and cottonwoods trees are sprouting all over the Lamar Valley again. And so, the moral of the story is: discriminate meat-eating is the best possible thing you could do to save the trees.

Offices that squeeze your Creative Juice

Joel Spolsky has his list of desiderata for programming office-space. And so does IBM (pdf).

Publishing Contract Land Mines

Dave Taylor provides a fascinating interpretation of clauses in publishing contracts.

Tourniqueting the financial bleeding at the NIH

After much gnashing of teeth, the mighty National Institute of Health has seen the light, and made open access an official requirement of NIH-funded research.

"Beginning May 2, 2005, NIH-funded investigators are requested to submit to PubMed Central (PMC) an electronic version of the author’s final manuscript upon acceptance for publication, resulting from research supported in whole or in part, with direct costs from NIH. The author’s final manuscript is defined as the final version accepted for journal publication, and includes all modifications from the publishing peer review process."

Not one minute too soon. For too long, scientific publishers, like Elsevier CEO Crispin Davis, have been leeching their 30% net profit from the scientific comuunity (compare that to the 5-10% in the rest of the publishing industry). Crispin Davis paid his dues in companies such as Proctor & Gamble, Guinness and Aegis, a midsize European buyer of ad space, where he, no doubt, learnt the values of publicly-funded research. The financial value that is.

They walk amongst us

They walk amongst us, deadly but silent.
They are frightening.
They are Zogg!!

More Classic Science Done on Rats

Will they ever stop? Andersen et. co. were not satisfied with tormenting young rats with cocaine and sleep-deprivation in order to see how that affects their ability to get-it-up, now they want to find out the same in old rats...

Does paradoxical sleep deprivation and cocaine induce penile erection and ejaculation in old rats? [link]
Andersen ML, Bignotto M, Machado RB, Tufik S
Addict Biol. 2002 Jul ; 7(3): 285-90

"To discover whether the same effects occurred in old animals ..."

"...we administered cocaine (15 mg/kg) to young (3-month) and old (22-month) male rats after a 4-day period of PSD [paradoxical sleep deprivation] ..."

"...we then evaluated erections and ejaculations."

"...in conclusion, our results suggest that although genital reflexes usually decrease with age, testosterone levels alone cannot account for these changes..."

Stitch n'Bitch: The Many Ways of Joining Strings in Python

Oliver Crow has written an interesting analysis of the many different ways of stitching strings together in Python. The benchmark results are rather surprising.

How many letters can fit on the head of a pin?

Everything and more on topics like: the optimal size of fonts for reading; or how many letters should fit on the width of a line.

Wolfowitz removes the fig leaf

George Monbiot, one of the most insightful writers of the left has argued that the appointment of the neocon hawk Wolfowitz to the head of the World Bank, is, in fact, the best thing to happen for progressive causes. Monbiot argues that the World Bank, has never in its history, promoted human development in the third world.

The World Bank has always been a tool of US economic unilaterism, where the US power of veto makes a gimp out of the World Bank, a fact that is "clevely packaged to grant other nations just enough slack to prevent them from fighting it." This is something that the neocons are too stupid to understand, and thus, by appointing Wolfitz, the neocons are replacing "a hegemonic system that is enduring and effective with one that is untested and (because other nations must fight it) unstable." Great read.

Hispanic high-school kids kicks MIT's ass

This is a true story of how 4 hispanic high-school kids from Phoenix kicked the ass of M.I.T. in the recent Navy underwater bot competition. If there is any PG-13 story begging to be made into a film, this is it. Hey, you could bring back James Olmos and make Stand and Deliver II. But the story doesn't end yet: as the kids are undocumented, they're not eligible for state scholarship subsidies. Any one of these kids would be worth 100 trust-fund kiddies in the american university system. But hey, we all know that equal "opportunities" is a convenient fiction.

Iranian policewomen action

Puts a whole new meaning to caped crusader fights crime. Move over spiderman. Follow the advice of the Iranian newsreader, "the policewomen are very serious. Take a look"

Testestorene in Sport can make you Blind

In this week's game in the English football Premiership between Newcastle and Aston Villa, Newcastle got three players sent off. Now you might think Aston Villa were being provacatively aggressive, but no, as you can see:



Look how an Aston Villa player is bravely trying to pry apart the two feuding Newcastle players.

the chinglish files

I, for one am all in favor of cross-cultural pollination, but not at the expense of the purity of the english language, as in these superb examples of chinglish.

It's official, Australia is Asian

Well, not exactly, but the big news in the world of Australian soccer is that the Asian Football Federation has formally invited Australia to wean themselves away from the puny Oceania Football Federation to join the much larger Asian Football Federation.

Normally the province of painters and poets, in this case, it's soccer players who are the harbringers of change. And the future is Asian.

Of course, Australia joining Asia is only the latest episode in the entertaining sideshow Australia gets jerked around by FIFA. But it's precisely because geographically, Australia is located awkardly between the America and Asia, that Australian sport can be jerked around. It's not that FIFA is blind to geo-politics: Israel plays in the European Federation, whereas the rest of the Middle East play in the Asian Football Federation.

In previous years, for Australia to make it into the World Cup tournament, it would have to win the Oceania Federation - in which the only decent opponent is New Zealand - and then Austalia would have to beat the fifth placed South American team. Beating a South American team is always a daunting prospect as South America has produced some of the greatest players ever, Pele, Ronaldo, Romario, Maradona. North America and Asia players do not inspire nearly as much fear.

Over the last few years, the qualification to the World Cup has been a roller-coaster of capricious changes. For the 98 World Cup in France, FIFA changed the rules to help Australia where Australia had to beat the fifth-based Asian team on a wild-card to get in. Australia got so close, leading 2-0 in the penultimate match, only for the plucky Iranians to squeak in 2 goals in the last 20 minutes. But then for the 2002 World Cup in South Korea and Japan, Australia got put back into South America, as FIFA had to make room for both South Korea and Japan, thereby reducing the number of places for Asian teams. Australian officials then tried to get an automatic qualification for Oceania. This was accepted by Fifa but then immediately rejected, and rightly so, because the entire population of Oceania barely fits into a province in Brazil.

It's not that Australia lacks talent, players like Harry Kewell, Mark Viduka, and Tim Cahill ply their trade in the upper-echelons of European club soccer. But it's hard to imagine these Premiership millionares getting worked up to swat past the amateur players that some of the Oceania nations offer. Now with the tough new Asian teams (South Korea and Asia), Australian super-stars can look forward to qualifying games that will truly test their steel. If they do qualify, it would be due to a steady accumulation of points and not to a sudden-death Russian roulette with the fifth-placed South American team.

So Australian soccer officials finally saw the light that Australia's future is with Asia, an Asia that welcomes us with open arms. Unfortunately, it is a light that our current Prime Mininster John Howard, in his racist myopia, cannot see - that Australia is the gateway, the door, the doorman for the West to the East. This is something that the previous prime minister, the reviled but neverthteless visionary Paul Keating, clearly understood. Under Paul Keating, the Australian government had started to tilt its cultural axis towards Asia - promoting business and cultural exchanges, bringing in the high-flying Asian tourists, and more imporatantly, implementing educational policies such as requiring all high-school students to learn one asian language.

All this has been reversed under the Howard government. Australians are now pasty yes-men to Americans, immigration policies are used to create fear of anyone non-anglo-american. If Australian soccer followed this strategy, they would be playing stodgy defensive football, with the only attacking option being a hopeful long ball lobbed over the midfield. To its credit, Australian soccer can now play entertaining football, passing its way through the midfield, and finishing with aplomb. Such confidence has allowed Australia Soccer to stake its claim in Asia. And if this is a sign to come, the rest of Australia will surely follow.

Evolution of a Wiki-Article

This is really quite a fascinating analysis (includes audio track) by Jon Udell on collabrative writing as applied to the wikipedia entry on the Heavy Metal Umlat. It covers a diverse range of topics including letter encoding in html, article vandalism, and cultural mores. It is also a neat mix of slides, audio commentary, and timely mouse pointing - a rather useful blueprint for online seminars.

Rearranging Tori Amos

I have the power! The power to erase filler from albums. Thanks to the power of iTunes, I can trim the fat from a cheap-cut album and get a muscular collection of songs - slicing away until I end up with the album that I would have wanted to listen to.

Why, you might ask, would I even buy albums that I don't want to listen from beginning to the bitter end? Loyalty.

There is a period in your life, around early adolescence, where your mind is plastic and your tastes embryonic. Whatever happens to lodge itself into the little space between your eyes will quickly ossify and exert an undue influence on the listening habits of the rest of your life. (Of course, a few exceptional individuals have fresh ears their whole lives and include many music critics and sycohpahnts).

One of my idols is the tremendously talented tiny bundle of vocal histrionics, the one and only Tori Amos. All the way back in 1992, I stumbled onto her album, "Little Earthquakes" and quickly fell in luurvee. Heartbreak, poetry, gorgeous melodies, ethereal harmonies, and a very wry sense of humour packaged in, what is for me, an almost perfect album. Alas, it's been downhill ever since. It's not that she lost her ability to write great music, or her facility for language. It's just that somewhere along the way, Tori decided to produce her own material. You can definitely hear the learning-pains in "Boys for Pele" where the production veers from the harshly underproduced to songs that were bewilderingly over-layered. Compare that to the almost perfect production in "Little Earthquakes", which were produced by some real old-hands. But sonic-wise, she has always had a firm grasp of the sublime - evidence her experiments with the harpsicord and electronica.

Her main problem is that without someone else as producer, there isn't anyone else who is in a position to say, "huh! what the f*#uck are you yakking on about????" Maybe her writing is simply dense poetry. Yes, great poetry is similar in many respects to great lyrics, but there is one important difference. Poetry is written, and the speed of comprehension can be slowed right down to a single crawling word. Lyrics, on the other hand, must flow to the music. You cannot afford Joycean levels of overreading in lyrics. Besides, the words just plain don't make sense. So without some other control freak in the mixing room, what you get is stream-of-consciousness pomo ramblings that lack emotional omph.

Evidence? "The Beekeeper", the latest offering from Tori, is a case in point. According to Tori, a hexagonal garden theme is the underlying structure to the latest album "The Beekeeper". Knowing this adds absolutely no insight to the songs, it even detracts from my joy from finding my own interpretative line through the album. Standing at a good 80 minutes, it is a chore to listen-to straight through. Listening to music is meant to be joy-ride, not a punishing pilgrimmage. And so, after a few listens, I gleefully deleted all the songs that made my eyelids droop. No, I do not want to hear about Tori's Saab roaring through Ireland. No I don't have to suffer through the cringe-worthy pun "Original Sin-sinuality".

So I merrily zapped away, and I cut the album down to a very listenable 30 minutes of music. And listening to the revised album, I am reminded that when all-is-said-and-done, Tori is still an amazing musician. Buried in the middle of "The Beekeeper" is the heart-breaking "Ribbons Undone", surely one of the most beautiful paens written by a mother for her daughter. It is a slow balland, effortlessly, capturing a fleeting moment of motherhood.

Listening to "Ribbons Undone", I couldn't help but think of "Winter", a song on "Little Earthquakes". "Winter" is still one of her most poignant songs, a song about the emotional bond between a girl on her father. And I couldn't help but notice how the two songs bookend the 15 year transformation from the wide-eyed girl of "Winter" to the wordly mother of "Ribbons Undone". It is for moments such as these that rewards the musical devotion of all these years.

Boltzmann in JavaLand

I found this rather impressive java applet that simulates a box of bouncing balls. This java applet makes it easy to picture how the Second Law of Thermodynamics works.

The Second Law of Thermodynamics was the master-work of the great 19th centur physicist, Ludwig Boltzmann. Boltzmann gazed into the heart of the Second Law of Thermodynamics and found statistics. Then he rephrased the Second Law of Thermodynamics in terms of statistics: the probability of the system increases until it reaches the maximum probability.

What does that mean for our box of balls? Since thermodynamics deal with energies, it turns out that the speed of a ball is a great proxy for its' energy. So for a slice of time, you can count how often any of the balls has a certain speed. And so the probability of a box of balls can be understood as the distribution of speeds of the balls. This distribution is the probability that Boltzmann is getting at.

So the Second Law of Thermodynamics for a box of balls means that (1) there is an ultimate distribution of speeds, which we call the "equilibrium distribution" (the formula for this was derived by James Clerk Maxwell), and (2) any collection of balls will collide and mix-up their speeds until the distribution of speeds reaches this equilibrium distribution, after which no matter how the balls collide further, the distribution will not really change any more.

In this java applet, you can see how distribution of speeds change over time, as the balls do their thing and collide. Be sure you play around with the "parameters" - reduce the number of balls and bump up the radius of the balls. See how the Second Law works as the distribution of speeds changes inexorably towards the equilibrium distribution, even for a few balls.

Open access is spreading

The sprawling publications of the American Chemical Society, which encompasses 33 peer-reviewd journals, will now be submited to public-accessible archives after 1 year of publication. It seems only fair that all not-for-profit organizations to do the same. We will see.

Jazz Flash Animation

Micheal Levy animates: vector block graphics meets John Coltrane.

Classic Science Papers

Boldy advancing rat science, where no rat has gone before...

Hormone treatment facilitates penile erection in castrated rats after sleep deprivation and cocaine.
Andersen ML, Bignotto M, Tufik S.
Universidade Federal de Sao Paulo, Sao Paulo, Brazil.
J Neuroendocrinol (2004) Feb;16(2):154-9.[link]

"...we conducted two experiments to determine whether sleep deprivation and cocaine administration could also induce spontaneous penile erection in castrated rats ...

"...these data show that progesterone treatment facilitates penile erection in sleep deprived-cocaine castrated rats."

Classic Science Papers

I was told about this fantastic paper by a fellow grad student many years ago. I thought I'd lost the reference, but I found it again:

Lysergic acid diethylamide: its effects on a male Asiatic elephant
by West, L. J., Pierce, C. M. & Thomas, W. D.
Science (1962) 138:1100-1104.

In this article, they found that a single, intramuscular dose of 297 mg of LSD caused sudden death in an elephant tested in Lincoln Park Zoo, Oklahoma City.

Scientific Self-abnegation

This story has recently been doing the rounds in my postdoc circle.

"Don't become a scientist," advises physics professor Jonathan Katz from Washington University, St. Louis, in a polemic op-ed piece for brash-young would-be scientists. It was written in 1999 but if anything, is even more relevant with the diminishing science budget of the United States. He's voicing a lot of things that we postdocs have been muttering amongst ourselves.

Essentially, "American universities train roughly twice as many Ph.D.s as there are jobs for them." And using elementary economics, Katz shows how the labor "glut of scientists" has completely changed the career path of scientists, from what it was 30 years ago when Katz started. Now the postdoc stage is greatly prolonged, frequently up to 10 years, as opposed to the 2 years that Katz did. And how did this happen? The glut was due to "funding policies (almost all graduate education is paid for by federal grants)... [where] ...for many years the NSF propagated a dishonest prediction of a coming shortage of scientists".

I recently brought up this article with a colleague of mine, a visiting professor. He was much annoyed by the article. "A scientist," he said, "A true scientist is not swayed by external factors. Science is a calling." Although I liked his idealism, I feel a human being cannot be shovelled into one definition, whether it be scientist, or doctor, or builder. It's important to keep the rest of your life in view.

Like family, for instance. Katz points out that it's normal for a would-be scientist to be a post-doc for up to 10 years. And as a post-doc in your thirties, Katz asks if you "can support a family on that [postdoc] income?" One postdoc in my lab is leaving science because he wants to start a family.

Regardless, the article should make any postdoc wake-up and smell the (probably instant) coffee.

Art Lesson

Punk'd refers to the MTV show where a bunch of skaters go around performing practical jokes on celebrities. The pranksters reveal their hoax by yelling out "Punk'd" to the victim.

The painting depicts the scene where the Lord sends an angel to tell Abraham that he'd been punk'd. Background: the Lord had ordered Abraham, the Lord's humble and most valued servant, to kill Isaac, Abraham's only beloved son. The very son that Abraham had to wait till his 60's before the Lord gave him strong fertile sperm to impregnate his wife Sarah.

This scene was painted by Caravagio, and is one of the most powerfully composed pieces of drama of the late renaissance. The unity of movement from left to right, as we see the angel staying the hand of Abraham that is holding the knife, moves the eye towards the writhing face of Isaac. As per usual, Caravagio models all three bodies perfectly, and the light unifies the scene. Although the light seems to be of an interior quality.

The Homeless

When I walk the streets and a homeless-looking person approaches me, I normally try to politely avoid them. Sometimes I am walking with someone else, and that someone else might make a comment about the homeless. But the more I think about it the more I realise that I don't anything about them and so, this extract from Alexander Masters book was very revealing.

I Could've Been a Contender

The Times Higher Education Supplement (THES) has published a list of the world's best universities . It is gratifying that I did ugrad+grad at #36 and now I postdoc at #20.

This is how THES ranked the universities:

"Universities were placed in the table with the help of findings from a survey for the THES of 1,300 academics in 88 countries. They were asked to name the best institutions in the fields that they felt knowledgeable about."

"The table also included data on the amount of cited research produced by faculty members as an indicator of intellectual vitality, the ratio of faculty to student numbers and a university's success in attracting foreign students and internationally renowned academics in the global market for education. The five factors were weighted and transformed against a scale that gave the top university 1,000 points and ranked everyone else as a proportion of that score."

If you haven't guessed, Harvard, with an annual operating budget of over 2 billion dollars and more than most third-world nations, is at position #1.

Science Pays, For Journal Publishers

The enormous Wellcome Trust has finally knuckled down and produced a report on the viability of scientific publishing as we know it. They should know, since they pay for much of it.

What does the Wellcome Trust conclude? They conclude that "the current market structure does not operate in the long-term interests of the research community" Ouch. And that "the ‘public good’ element of scientific work means market solutions are inefficient." Double Ouch.

Now you might think this is a question of sour grapes because allegedly, the origin of the report occured when the Director of the Wellcome Trust was told about a breakthrough article written by one of the Wellcome investigators scientists working in Africa. But when he went to look the article up on-line, he was greeted instead with a "you are not subscribed to our journal". This is the director of one of the biggest medical funding bodies in the world, and he funded the research.

Nevertheless, this report is a solid piece of investigation into the scientific publishing industry. There is some excellent muckracking. For instance,on describing the business tactics of the largest science publisher Elsevier, the report attributed the Elsevier business strategy to the CEO Crispin Davis, who, the report quotes "was recently described in Forbes magazine as 'an unlikely choice [for Elsevier CEO]. Davis had previously worked for Proctor & Gamble, mostly in Cincinnati, Ohio, before messing up at Guinness, then resurrecting his reputation at Aegis, a midsize European buyer of ad space.' " That's really solid publishing credentials.

The report gives a sobering analysis of the supply-demand economics of science-publishing and shows how there is no feed-back loop, because the buyers of the journals (mostly libraries) are not the readers of the journals (the scientists). This makes it ripe for monopolistic manipulation. Yearly increases in journal prices (30% in 1999) exceed the rate of inflation. And the profit margins, sometimes up to 30% is sweet-as. Science is a public endeavour, a social good paid for federal funds. And as scuh, the largesse of the huge conglomerated publishing houses flows directly from the pocket of the american tax-payer.

Battlestar Galactica

Let me say that I hate Sci-Fi on TV. I never used to, but I do. There. I've said it. It seems wrong to do science and not luurve sci-fi, but dramatic conflict, rich characterizations and layered dialogue are rarely found in space ships zooming around in space on TV. Until now.

The new Battlestar Galactica has somehow slipped through the cracks, giving us a superbly written sci-fi series. It is a 'reimagining' of the original series, or in this case, throwing out all the camp. Of course, this is anaethema to the fans of the original series. They see high camp as nobility, the lack of real dark human emotions as up-lifting, speechifying dialogue as lofty classical theatre. Oh how wrong!

I have this theory that sci-fi is bad because it used to mainly appeal to adolescent teen-age boy and so the writing has to reflect their level of consciousness. It is the age where fine ideals are imagined, with a tinge of mythological self-importance. Complexity on the individual is non-existent and everything is seen in terms of epic battles between the forces of good and evil. Great for blockbuster movies, bad for TV.

But in the new Battlestar Galactica, people die. Characters betray other characters, and they die. There is real gut-wrenching fear and damnit if the directors don't milk the end-of-the-world for every compulsive moment. Pretty adolesent aesthetics be damned. People have sex, want it, get it, fail to get it, and do very bad things to get it. These are issues that used to be too painful to show as your typical sci-fi fan was emotionally underdeveloped to see it.

The sets in Battlestar Galactica do not look like toys that you can buy at Toys R Us. It is not an extended advertisement for new plastic spaceships you can buy. The ships in Battlestar Galactica look every bit as dirty and tired and old as the captain played by the superlative Edward James Olmos. He's no pretty boy William Shatner that all young adolescent boys used to want to be but Olmos' understated gravitas and weariness is a masterclass in acting compared to the smirking William Shatner as Captain Kirk of the USS Starship Enterprise. Besides William Shatner now plays campy characters such as the host of the Miss America pageant in movies such as Miss Cogeniality.

I've heard it said that whilst the quality of American movies have been debased, the quality of American tv has risen, driven in large, by the wildly succesful HBO. As such, american TV is now confident it can write complex characters in ambiguous situations, and give first-rate actors the room to strut their stuff. Not only is the writing improved but the general production borrows much from shows such as Law Order. In particular, the use of the documentary-style camera work, the floating camera with their human eye-ball angles. The lavish attention on character details and even the Scorsesean camera movements. The producers have even stated that with CGI graphics, the cost of special effects are now miniscule and the larger part of the cost is to pay for class actors.

Much has been said of the battle scenes, and they are groundbreaking. There's no music, only the sounds of the pilots and the sounds of gunfire. This adds layers and layers of authenticity. There are no deux ex machinas and the battle scenes are well thought out action sequences that unfold like a falling sunset. It's as if sci-fi is taking back the depth and seriousness of films like 2001: A Space Odyessey from the giddy simple-minded fun of Star Wars.

Eloquent Defense of Open Source Software

Open-source software is the future - it will commodify computer software. Commodification, in economics, occurs in an industry, when a product becomes generic and completely replaceable. This only occurs in industry where there are enormous competitive market pressures. For instance, it doesn't matter what brand of batteries you buy, they will all work in your sony mp3 player (they're sooo popular). Other things, like aircraft bodies, are not commodifiable. You cannot easily exchange a Boeing 747 body for an Airbus body.

I am stretching the point here, but essentially, some open-source software may commodify certain software markets. When I say open-source software, I mean software that is licensed in such a way that the seller of software is legally obliged to also provide the source-code and the right to change and use the source code for whatever purposes. Certain open-source software might one day achieve parity with or exceed commerical products in terms quality and hence, blow the bottom right out of the market. It may have already happened with Firefox, and OpenOffice.org is on its way.

Is open-source a good thing? Recently, the Peruvian Government contemplated legislation for mandating open-source software in the Peruvian Government. This scared the bejesus out of Microsoft Peru as can be seen in this letter from Microsoft General Manager Señor Juan Alberto González. Microsoft, as you can see, only sees it from a profit point of view. But even more weirdly, Microsoft considers open-source software dangerous, "from the point of view of security, guarantee, and possible violation of the intellectual property rights of third parties." This is a particular interesting conflation of ideas - security is elided into intellectual property rights of third parties.

But open-source is much more than monetary saving. It guarantees transparency. This is a social good. But I am explaining it poorly. Perhaps there is no one better to explain this than Peruvian Congressmen Edgar Villanueva Nuñez, who wrote this eloquent defense of the Peruvian software bill. As Nuñez points out, what is valuable about open-source is that it ensures "free access to public information by the citizen, permanence of public data, security of the state and citizens [from intefering foreign software companies such as, oh, you-know-who]".

The bill, incidentally, was passed.

Romancing the Grad Student

Here we go again. Another wave of Recruitments will arive at UCSF in a few days. Like a bunch of matrons preparing for a debutante ball, anticipation and excitement rush through the faculty. Here at UCSF, a purely grad university, graduate recruitment is taken very very seriously.

A cadre of carefully handpicked candidates, from the hundreds that apply, will be flown into the city of San Francisco. They will be put in luxurious comfortable hotels, probably the first time some of them have experienced such luxury. Once ensconced in their comfortable hotels, and after sight-seeing the city, a couple of intensive days are scheduled.

These kids, with their freshly-scrubbed faces and newly-minted bachelor degrees, now partake in an elaborate ritual. Each of them will undergo a long series of interviews with a series different professors. In the interviews, the professors will try to delve behind those sparkling cv's, stratospheric sat scores and gushing personal essays, to see if, indeed, they have the right stuff. The right stuff, that is, to slave away for the next five years. For the kids who are accepted, they are the clay for these masters of science to mold into the next generation of scientists. What are they looking for? A sharp mind, passion, acuity, but most of all, the ability to submit.

Submission? These kids might think they've been treated like royalty, but little do they realise that, for the calculating professors tenured at ucsf, those who end up here, will provide el cheapo research-per-dollar. Research can be counted in real dollar terms. An top research school like UCSF is judged on its research. This can be measured in terms of papers published in big journals, and on the number of citations. High-quality incoming students will provide the best shock-troops in the battle for the research dollar.

For the next five years, the kids who choose grad-school will watch their friends from college who did law or engineering, one by one, begin to find jobs and earn vastly more money than they. They will suffer the iniquities of being a shit-kicker, but do research that may grace the most prestigous science journals, whilst working hours that might even make a lawyer blush. Of course, this will not dawn on them until far into the future.

Meanwhile, the magic is to make all these worries dissappear. The trick is alcohol. High class catering companies are called in and liberal amounts of alcohol will be served. During the next few days, there will be reception after reception. Waiters in tuxedos and white gloves will pour glass after glass of medium quality wines (after all, what does a 21 year old really know about wine?). Roasted meats, sweetmeats, hors d'oeuvres, cakes will be provided in obscene mountainous piles. This is obscene mainly because the grad students who are already at UCSF, will eye the available food and alcohol with ravenous envy, such is the disparity between life-before-recruitment and life-after-recruitment. Some will manage to sneak into the reception and gorge themselves, despite the best efforts of the Recruitment officers to quarantine them. Others will only look on longingly, unable to break etiquette.

Yet there is something a little stiff about a reception at the university. No, the piece-de-resistance, will be the "after-party". A spontaneous expression of camaderie and scientific togetherness? No, it's planned. Before every recruitment, a "socially-active" grad student or post-doc is tapped. "Don't you just want to hold a party for the recruits?" asks the Recruiting Officer. The tapped student equivocates. "You know, it will be funded by the school," the officer reassures. "Generously." The student begins to cave; just one more push should do it. "But don't worry, we won't need to know what happens. Just show the kids a good time. A very good time." The last Recruitment party ended up in the nether regions of the Castro.

So after a heady weekend of interviews, receptions and parties, most of these kids pack their bags and head-off to their next recruitment.

A Very San Francisco Moment

San-Francisco Moments are highlighted with (*)

I had recently promised myself to *see more dance, and so it came to pass that I had a Saturday night with nothing to do but to *leaf through the San Francsico Guardian, where I find that, just down the street, a *Women of the Way Festival is taking place, a small festival running over a few weeks with an emphasis on *contempary dance.

It wasn't going to start until 8pm, so *I go to La Taquiera, a rather famous Tex-Mex eatery, which had got itself listed in the San Francisco Chronicle* top 100 restaurants, and is arguably the cheapest restaurant on the list. This is a subjective thing, but I like the burritos at La Taquiera as they leave out the rice, which amplifies the flavours of the other ingredients in the burrito. Fed and satiated, I stumble over to the Mission Dance Theater, and get one of the last tickets. I sit in the front, the lights dim, the dancers ghost onto the stage in silhouette. I watch a couple of okay performances, a little bland in execution and completely devoid of narrative.

Then came a wonderful piece called 'Two Kisses', from Fresh Meat Productions, which was performed under a spoken story about the coming-of-age of a *trans-gender boy/girl and his/her first experience in school. It was beautifully acted , where the dance both supported and expanded the story. No matter what art form - I have now come to believe that characterization and story are essential. This 10 minute dance masterpiece had both in abundance. It was so well-executed that I ended-up discussing with my neighbour in the theater, the exact meaning of the order of the lifts at the end of the piece.

Of course, some of the pieces had an overt *leftist political overtone.The last piece Rennaisance, by Rococo Risque: Red Gate Performance Collective Project, was a smart, satiric, self-consciously camp, fast-paced romp of burlesque comedy. It's all about cultural stereotypes, and the homo-erotic German envoy to the United Nations Security Council had me in stitches.

But I neglect to tell you the piece that had me laughing so hard that I thought my kidneys were going rupture out of their moorings. It's called War n' Worms. In the beginning, we have on-stage an electric-violin, a bass, a wooden box-like tone-drum, and a african drum. All the musicians are wearing *hippy clothes. The bass starts up, with some some fluttering ornamentation from the electric-violin.

Then, the woman who is playing the violin, looks the audience in the eye, and says "I am hummingbird", and proceeds to play some hummingbird-like sounds. Next, the tall thin bespectacled nerdy looking guy at the tone-drum, wearing a large green sarong, starts rubbing his stick on the tone box producing a moaning sound "oooooooohhhhhh", "ooooooooooohhh". He, too, looks at the audience in the eye, and declares, "I am whale". I am trying very hard not to laugh at this point, which is not helped by sounds of muffled laughter behind me.

This followed by the bassist. Which of God's earthly creatures can the bass guitar represent, we, the collective audience, were wondering? Why, isn't it obvious, "I am dolphin, holder of the rhythm." And the african drum declared that, "I am squirrel". It was at this point, that the star of the show, stepped out from behind the curtain, a white woman wearing a flowing white robe. She sings with an awkard mix of operatic/blues mix. After running up and down the scales a few times, she sang on high, "I am Worm, from the Kingdom of Worm". I guess the slithering worm-loke warbling of her soprano voice was the Worm. But wait, there's one more character not introduced for there was still one more mircophone on stage. Out from the other side of the stage steps a tall black dude wearing, not hippy clothes, but a dapper suit with a matching red beret and long red scarf. He ambles over to the microphone, and in a rich chocalaty voice, declares that, no, wait, that, "I am Dragon.".

There is then vocal combat between the Dragon and the Worm, the Dragon rapping against the operatic gymnastics of the Worm. This goes on and on and on, in an incoherent improvistory kind of way. Something about pestilence and evil and or so.

Then the show stops. In song, the squirrel informs us that we are to find a piece of paper and a pencil under seat. We, the audience are then instructed to write our greatest fear on one side of the paper. On the other side, we write the quality we most desire to surve the War N' Worm.

I search desperately but cannot find my piece of paper, so I ask for a piece. I cannot help myself. I write down "Laughter" on one side. On the other I write "Decorum". I show the woman next to me, who has been stiffling her laughter for the last ten minutes. She finally breaks down and runs away.

What You'all think about the second person plural in English?

So I spent me some time in Texas, home on the range, dry desert heart-land. It's a rather pretty place, in a dry-scrub wide-blue-sky kind-of-way. The Texans are nice and friendly. Only one of the three Texan homes I visited had a gun display case next to their doorway. A beautiful mahogany case containing five beautiful shotguns. People who say Texan are gun-crazy are just pussies.

More than one Texan remarked to me how similar Australians are to them. They have a point. The dry desert feel of the land is similar - I can see the same squint of eyes under the harsh Texan sun. Texans and Australians are laconic in demeanour, and fond of loud straight-talking (not like those slippery city-slickers of the Eastern Seaboard). They are both connected to the land, though more in affect than in substance. Cowboy hats and spurs in Texas, Drizabone coats and bull-whips in Australia.

I rather like the slow-shuffle of the Texan drawl. And perhaps the most distinctive of the Texan dialect is the proliferation use of You'all. What a wonderful word. In English, there is no second person plural, and it's much the poorer for it. Elaborate constructions are needed to indicate the plural from the singular. In Australian, we use the rather clumsy Yous, which kind of slides around the mouth like treacle. Compare that that to the rounded cadence of You'all, with the crisp clean 'l' that embraces all the people you are addressing.

I, for one, would support the official adoption of You'all as the English second person plural.