30 January 2006

day 2 of cny, it's 7am and i'm delirious

The other night I dreamt that a python bit me on my butt.
Which pissed me off cos that’s a scientifically inaccurate dream.
Because pythons rarely bite.
Which pissed me off cos that was the most geeky thing I could have ever say the moment when I woke up.

Anyway.
It’s been a rough week. I fell victim to the gastric flu bug, same old same old.
Bedridden and nothing but soup for 3 days.
But I’m all better now (thanks to you), ready to devour the box of lovely new year goodies that my wonderful parents send me every year.
Gong xi fa cai everyone!

The year of the dog opened with a whimper.
Essay due, quiz the following day, missed lectures to catch up on...
So how did I spend my first day of CNY?
I pulled my first-ever all-nighter (yay me!), writing about how George Orwell’s 1984 depicts a liberal dystopia against the account of liberalism of Judith Shklar.
Shklar Schmlar…
I don’t like that essay of hers, it’s unstructured and misleading and yet, she’s the prof’s hero.
Bah.
1984 is a good read though, highly recommended!!

Now the question is
Do I go to prop my eyelids up with matches, go to class in 1 hour’s time and snooze through Wainberg?
Or do I snooze at home and screw too-busy-to-offer-me-a-lab-position Wainberg?

18 January 2006

when montreal freezes over

You know how roads are slightly convex so that runoff can drain properly into the sewers? Think that, but completely iced over.
You know how at the traffic lights, the pavement slopes off gently to meet the asphalt? Think that, but completely iced over.
In fact think ANYthing whatsoever, but iced over.

Welcome to the Winter Wonderland from hell!
The Disney on Ice of the Dark Side!!!

Ok I exaggerate. (I can’t help it! It’s the Marseille in me)
Today, freezing rain pummeled down on this wintry city.


Just a quick explanation without getting too geeky on you:
Freezing rain is snow that hits a warm front and melts into water droplets, which then pass through a cold front and is supercooled, such that it freezes on impact.

Every drop that hit was instant ice.
Roads were iced over.
Pavements were iced over.
Highways were iced over.
With all this ice, even the gentlest slope became a treacherous nightmare.


It was hell getting to school. Some roads had to be closed off in the morning; on others, firemen had to string ropes across so that people could tow themselves across. Cars had no traction whatsoever and since the university area is essentially on a hill, this meant that cars were frantically spinning their wheels, not to gain any ground in the process but to simply avoid slipping backwards down the hill and crashing into the other fellow behind him. People were falling left right centre front and back, from the simple ones who catch themselves just in time to the dramatic all-out belly-up cartoon flop! If you didn’t break your neck while going up the hill, no worries you’ll get a chance to break it again when you go down.

Considering that going to school under these circumstances might literally kill you? You’d expect that McGill has been around long enough to realize that students who break their necks in trying to get to classes that they didn’t cancel isn’t such a good idea after all. But no, not a single email from the school or a word on their website. My 9.30 a.m. class was not cancelled at all, never mind the fact that it was in a building on the upper more sloping parts of campus. People actually risked their necks to get there, and well the prof was stuck in traffic on the way there (doh!). So everyone had to slide their way back down to Lower Campus for absolutely nothing. Don’t worry about me – I skipped that class obviously.

Montreal is crazy.
Within a span of 5 days, we went from a toasty 6°C to a deathly -30°C, to snow, to freezing rain.

As one friend put it, the weather here is SO PMS-mood-swingy.

Ennis Del Mar-ism

If you’ve already watched Brokeback Mountain, you’ll know what I mean by Ennis Del Mar-ism.

It's not about cowboys, it’s not about gays, it’s not about whether homosexuality is right or wrong or left or right.
Or top or bottom for that matter.

Now I assure you I’m not one of those desperately-in-love-with-Jake Gyllenhaal types. Sue me but I think he’s ugly. Yet there’s a certain something in his character Jack Twist’s doe-eyed look that enthralled me. His eyes searched the depth of Ennis’ soul, willing him to understand that sometimes you have to take a leap.

Jack Twist is that sliver of optimism waving wildly, trying to cling onto our attention for more than just that fleeting moment.
To say 'somewhere someday somehow things will work out'.
But the voice of realism obscures him, in the way Ennis systematically turns away from hope and towards denial, letting the one good thing he had slip from his grasp.

It’s about that mechanical rationality, which tells us that we’re making the right choice, we ARE, even as we feel our hearts tremble and shrivel in sorrow.
We believe in procedural logic, in the mechanistic evaluation of pros and cons and sweep away the emotions we deem transient and inevitable.

I think we all are Ennis Del Mar in some way.
At each forkroad, we are invariably more tempted to pick the one that is ‘right’, that either yields more apparent benefit or procures less suffering. Instead of reaching for dreams, we’re content to trudge along and play it safe.

Three years ago, I came to such a forkroad, a path leading to Washington University and one leading to Université de la Méditerranée. The former had a greater sense of familiarity and opportunity, the latter a thrill and hesitation of unknown adventure. Frankly speaking, during my first year in France, I did question my decision and sometimes I still do, especially when I worry about becoming irrelevant in today’s society of Harvard and Cambridge graduates. But there are no regrets, only pride, that I took the offbeat path.

Today, there are more decisions to be made, and I risk turning away from an important part of my life because I’m afraid of facing my fear of incapability.

Go away Ennis Del Mar.
When you know you have a good thing, the stupidest you can do is to let it go.

12 January 2006

who said science can't be fun?

BLAST is a bioinformatics tool we use in biology to find regions of similarity between sequences. One function of this tool is that you can enter an unknown sequence, and it returns the best match sequence from its database of organisms. Now we can do it in terms of the nucleotides (the A, C, G, Ts) or we can do it in terms of proteins. Proteins are basically many amino acids strung together, where 20 amino acids are represented 20 letters of the alphabet.

So what happens when you BLAST regular words or names?
A sort of message deeply ingrained in the essence of life perhaps??

Here’s a snippet of the quirky results that someone from Seed Magazine found:

… The query for "BUSH" receives no hits, primarily because it is deemed a "low complexity sequence." This is compounded by the fact that the letters B and U do not exist as specific amino acids

… Finally, in an effort to further demonstrate my impartiality, I begrudgingly entered "PRESIDENTBUSH." In this case, the best non-hypothetical match—one that can actually be assigned a biological function—was from the genome of Entamoeba histolytica. The organism is a single-celled, parasitic protozoan known for infections that sometimes last for years, which may be accompanied by vague gastrointestinal distress or dysentery—complete with blood and mucus in the stool.

A single-celled parasite that infects you for years and might give you bloody diarrhoea. Got that?

Read the full story: Concerning the President of the United States. It’s an amusing read!

So after all the laughing, I decided to be a geek and blasted my own name, to see what DNA has to say about it. I'm such a geek.

The string 'CHARLENETAN' returned 'fumarate reductase, iron-sulfur protein' of the Hildenborough strain of the bacterium Desulfovibrio vulgaris. So yay! I’m a bacterial enzyme!
Not that my name actually appears as part of the bacterial sequence though. I don’t think it's likely that there's an exact match.

For those of you are geeky enough to follow in my geeky footsteps, here’s the link to BLAST.
Simply enter your name and hit the BLAST! button.
On the resulting page that indicates your request ID, click on the Format! button.
Wait a bit for the page to load and then scroll down till you see the heading ‘Sequences producing significant alignments’
Click the top hit and congratulate yourself on your geekiness.


Do post a comment about what you are and if you got an exact match!

Oh yah, in case you didn’t notice… I’m such a geek. :p

09 January 2006

inside and outside

Inside, it’s nice and toasty.
People sipping coffee, reading books, chatting on a pseudo-open air terrace.
Small potted trees carve out a little niche against a brick façade.

You can almost see the people lounging on its broad window ledges, top button undone, cold drink in hand.
You can almost smell the sea in the air, its saltiness and its fishiness.
You can almost hear the people on the streets, that unintelligible background noise that will not fade as one herd replaces the next.
You can almost feel the sun as it washes over gently, a warmth that permeates into the flesh.
You look up and squint, it’s too bright, and you shield your eyes with your hand.

Then you see the yellow spotlights that shine down.
You feel that chilly draft.
The scarves, the gloves, the hats on the tables and the coats over the chairs.
That chilly draft again.

Outside, the snow is falling.
Too fast to be called dainty but with a certain elegance in its rhythm.
It falls wordlessly.
Snowflakes sprinkle fields, roofs and naked trees, like a dose of icing sugar fit for a glutton’s cake.
Cars wheel slowly in the slush, people trudge about their business.
The world plays on in slow-motion, in white and grey.

You look up and feel the drizzle of ice.
You catch the flakes on your tongue.
You close your eyes but you still see.
It falls on you, straight towards you.
It falls wordlessly.
No words can describe it.

05 January 2006

egotistical egoist

Here's an interesting post from a Science-y blog about a parTICularly interesting new virus Gonorrhea Lectim. trust me, you wanna go look at it.

On a geekier note, i won WEBoggle!! nahahahaha here's the proof:







go play and see just how tough it is!
muahahahaha... some people may call me egoTistical. but they ain't #1.
so there.
a

04 January 2006

your genome is patented

Ok. School has started.

One class i’m doing is called Applied Microbiology and Immunology, doesn’t sound like very much but essentially it’s about the business of science. People from academia and industry will be coming in to speak to us about patents, big pharmaceutical companies, small biotech startups, and get this - even a FAILED biotech company. We live in a society where success is blatantly tooted in your face again and again, so much so that we’re averse to failing. I don’t deny that I do NOT like to fail. (Failed a damn communications exam last year. Apparently I can’t communicate.yay.). It’s great that they thought of showing us some of the failures out there.

But anyway, a part of the lecture got me really intrigued and I’d just like to share some thoughts. It may be a little scientific but i tried my best to be less technical.


!!Geek Warning!!
------------------------------

About 20% of all human genes have been patented.*
That makes about 4000 genes with its exclusive rights assigned to someone else for a certain amount of time.
*in the US. Patents are awarded differently in different patent offices around the world.

What does this mean for you and me?
Does it mean that in producing insulin (insulin was patented in 1923) to regulate the metabolism of out carbohydrates, we’ll need to pay some dude royalties?
Are genes even patentable in the first place??

The first criterion for patentability is that the gene in question must be NEW.
It can’t be new if it was already there in your body in the first place, can it? Well, it turns out that a gene as it exists in a chromosome in your cells is obviously not new at all; however, a gene that has been extracted, isolated, cloned and amplified can be (and has been) accepted as an artificial, man-made and therefore, new form. So no, you can go metabolize your carbohydrates in peace. Your genes are not patented as they exist inside you, but you might not wanna take any of them out of your cells.

The second criterion for patentability is that the gene in question must be USEFUL.
Now, utility of a gene is not always obvious. Certain genes have been identified to be implicated in carcinogenesis. One example is the BRCA1 gene, a tumour suppressor gene, which has been found to be defective in breast cancer patients. Using isolated BRCA1, cancer detection tests can be developed and it even evokes the possibility of gene replacement therapy. A gene in a direct relationship with a disease is obviously useful.

However, other genes may not present such possibilities:
In 1995-1996, it was discovered that chemicals called chemokines produced in our body suppressed HIV infections. Subsequently, it was determined that the virus enters cells by latching onto a chemokine receptor called CCR5 on the surface of the cell. People with defective CCR5 genes, and thus do not express the CCR5 protein are less susceptible to HIV!
Imagine, what an incredible achievement for anti-AIDS drug development efforts!

But wait!! Hold your horses. The party pooping has just begun.
Get this: the gene had already been patented by a company named Human Genome Sciences.

If somebody uses this gene in a drug discovery program after the patent has been issued to find drugs [...] and does it for commercial purposes, they have infringed the patent. […] And if a company brings a drug to market after infringing the patent, we'd be entitled not just to damages, but to double and triple damages.
- William A. Haseltine, Chairman, Human Genome Sciences

Oh not just to damages, boys and girls, but to DOUBLE and TRIPLE damages. It sounds like the guy has been playing too much friggin' Mortal Kombat or something man! Power up! Special press-many-button move!! TRIPLE KILL!! OWNING!!!
*ahem*
So now where to draw the line between science and business, between ‘cure the world’ and ‘let’s get a monopoly of this thing we don’t know much of and make shitloads of money of the people who need it’?

Is it correct to reward the person who made the discovery and did no further work on it, at the expense of the scientists and companies who throw themselves head first in working on a drug?

If the patent office awards a patent to someone who clones a gene, even though they have no notion of its function and no real idea of its use, that would be like saying, 'I found a fungus, therefore I should get credit for penicillin.
- Dr. Robert Gallo, co-credited (controversially) with the discovery of HIV

The first-to-invent or first-to-file patent system is in this case debatable, especially when HGS officials acknowledge that they had zero knowledge of the gene’s role in HIV infection at the time when the patent was filed. It sounds frivolous, but that’s the whole point of the patent system in the first place, isn’t it? To protect discoveries and inventions on a first-come-first-served basis, in doing so, handing its inventors a monopoly in exchange for the information, even if it was based on a marginal claim of use. This is the way the system works.

Patenting has to be in place to protect discoveries and to give incentives to the large pharmaceutical companies to invest and develop effective drugs (after all these are multi-million dollar investments, no company would ever back research without a tangible monetary reward expected).

But paying silly companies who jumped in before the crowd just to claim ownership and resulting fees before the guys who really produced something worthwhile with it? That’s just bullshit, 'robber barons of the genetic age'. The patents office has to be more stringent with the definition of usefulness of a proposed genetic sequence before they hand out patents like they were raffle tickets.

What are they gonna say next? I want a patent for this gene so I can use it to produce expensive, overglorified toilet bowl cleaner? It’s useful, as marginal as it may be, so let’s just wait till the next guy comes around and turns it into some anti-cancer drug. Hooray!

01 January 2006

the end is the beginning is the end

Year 2005. aaaahhhhh.

For those of you in the privy, you’ll know that this has been a tumultuous year for me, encompassing probably the insanest/funnest/highest points in my life as well as a really low point.

Now I’m not gonna start chronicling my life story, no memoirs… for now anyway, I’ll do that when I release my greatest hits album yah.
This is more of a platform for me to share some ideas, videos, good reads, issues, games and other blah blah and also quite importantly, to try to regain my ‘cogent’ writing. Believe it or not, I used to be ‘cogent’ in writing my GP papers, or so said my civics tutor in my dolled-up testimonial.

2 years in France, well yeah, I guess my French is more than just not bad but my English? Oh peee-yooooo, it stinks worse than a ______ (insert random rank rubbish). But luckily hor, my Singlish is still quite the powderful. This one will never lose one lah, confirm chop stamp.

Anyway, it’s now 2006.
I’ve been ranting since last year. Sheesh.
Went to Old Montréal to see the fireworks, and man, there were really awesome shimmering sprays of bronze and streaks of every other colour kabooshing and spisshing into the night sky. Bee-OOOO-ti-full~!!
It was really cold though, something like -19°C.
And in the pyrotechnics and frosted breath, I did what most of us do: letting my troubles roll by, shredding the bad memories and framing up the good ones in my mind.
Time to look beyond the what was and the what if to focus on the what IS.
Oh gosh, winter term starts in 2 days. Dang.

A big thank you for all of you who have kept me sane (by surrounding me in your insanity, of course). Tankyew very much hor.

------------------------------

Pour ceux qui était au courant, vous sacheriez que l’an 2005 a été une année pleine de fous rires mais aussi des larmes pour moi, ben oui, les moments les plus dingo-n’importe quoi-fous-furieux de ma vie et le grand point noir.

J’ecrirai pas ici l’histoire de ma vie (si enchantante qu’elle soit pour vous j’imagine), mais plutôt mes opinions, mes conneries et les jeux ou bien les vidéos à partager tout tout tout tout tout. En haut là, j’ai dit que ça servira à améliorer mon anglais écrit mais c’est certainement aussi le cas pour le français. Vous esperez tous quand même que je deviens pas québécoise ?!

J’étais au Vieux-Montréal tout à l’heure pour les feux d’artifice. Il y en avait un en bronze qui scintillait et c’était trooop beau ~ !! Mais il faisait aussi -19°C. Ah oui. C’est la fête.
Et pour cet nouvel an, je vais me débarasser des mauvais souvenirs et garder au cœur les bons, de Marseille à Avignon, de Callelongue à Luminy, des Prophètes à l’Abricotier, du Shamrock au Red Lion, du fondue au chocolat au riz au lait, vous savez que je parle de vous.

Merci à vous qui m’avez gardé normale... euh plus ou moins normale (en m’entourant de vos conneries bien sur !)

Le 2ème semestre commence dans 2 jours. Ils sont cinglés ici, mais au moins c’est pas les partiels après-vacances... courage. Vous me manquez.