"Say It's Possible", copies

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

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

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

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

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



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

Here's PJsurfs, June 24:



Here's Mac1302, June 26:



Here's briennalauryn June 24:



Here's kol28, on June 27:



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




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



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

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

A Rose by any other Name

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

"The Poo.. what?" I ask.

"The Poontang Wranglers."

"The KooKang Bunglers?" I ask.

"No. The Poontang Wranglers."

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

"The Poontang Wranglers."

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

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

Colbert's Advice for the Young (tm)

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

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

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

notes on filming tv

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

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

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

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

The icing on the bike

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

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

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

"Why is that?" I asked.

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

Great 10 min Short Film

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

The Preview Bait-And-Switch

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

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

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

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


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

He Got Game

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

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

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

A royal flush appeared on Petrice's face.

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

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

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

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

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

They swap numbers and he leaves.

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

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

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

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

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

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

museum of freaks

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



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

I, web-designer

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

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

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.