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It is not often that you read familiar names in local news reports. Even less so if the locale itself is one you haven’t lived in for over 6 years.

This is why, when I first came upon a mention, in the SF Chronicle, of a slain college teacher living in Oakland, CA, it did not register much: random acts of violence and the senseless killing of innocent, beloved community members is unfortunately too common an occurrence in Oakland these days, to raise one’s attention…

And then today, while parsing Californian news again, I glanced upon the name of that teacher and realized that, against all odds, I knew him.

Not only did I know Dr. Dennis, but I also personally kept a very fond memory of these two semesters I studied with him. In fact, it was he who gave me a taste for Political Science, to the point of making it my college major the following semester, when I had originally just thought of it as a quick requirement to cross off my list before transferring with a science major.

Out of the very few classes I took at CCSF, “Dr. D” was easily the most striking professor: both as an incredibly smart, witty and engaging teacher and at the same time, obviously dedicated toward helping all students and making sure everybody got their fair chance in the end. I remember his fits of calculated zaniness in the middle of the most serious dissections of US Federal Institution and Constitutional Law. I remember that one time where, upon learning of my odd place of birth, he surprised us all by giving a quick but thorough geo-political recap of that tiny Indian Ocean island most wouldn’t even know where to put on a map, all in impeccable French. More so, I remember how astounded I was, when he concluded by throwing in a couple cheerful comments in perfect Seychellois Creole… I even remember that house of his in Oakland, where he traditionally invited his students for a semester-capping potluck dinner…

I still can’t believe now that his name, of all people, would add itself onto that seemingly unending list of tiresome injustices that is Oakland’s violent crimes reports.

He truly was a good man, in deeds and in inspiration for others. I know he will be missed by a lot.

Good bye Dr. D: may you rest in peace, Oh Zany One…

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Further reason why reading up reference material for your own neuroscience paper is a total bummer:

[…] After neuronal recording was completed, monkey RO was anesthetized with an overdose of Nembutal (90 mg/kg, i.m.) and transcardially perfused with 10 % formaldehyde in 0.9 % NaCl. The brain was removed and consecutive, 50 µm-thick, frozen sections were cut parallel to the recording electrode penetrations in the frontal plane.

“Ooh, my, that’s interesting… and what fascinating data did we get from those frozen sections of the frontal pl… Hey! Wait a minute… You did what to monkey RO?! I was just getting to know monkey RO! Damn you people. He was just an innocent Japanese monkey (Macaca fuscata, male, 8.9 kg): young and promising, with still so much to give!”

[…]

“Oh well, I guess on the upside, we now know that corticostriatal neurons show distinct action-value-related firing patterns when you let monkeys play Pong… You shall not have died in vain (and your brain frozen and sliced to pieces while your heart was being pumped full of embalming fluid), little monkey RO!”

PS: For those wondering: as is commonly the case in such research papers, “anesthetized” is the mother of all euphemisms for “killed the death out of it”.

PPS: I guess this shall simultaneously address a question on everybody’sthree people’s (family and cat included) mind: “What is Dave up to and why don’t we see much of him here lately”.

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Protein Alignment

Protein 1: Cytochrome P450-Terp (412 residues)
Protein 2: Cytochrome P450 (Bm-3) (E.C. 1.14.14.1) (457 residues)
Iteration #4: RMSDc=3.36383

My first α-carbon-based protein alignment!

I’ve got a lump in my throat…

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Having the opportunity to pick a class slightly outside of my main curriculum, I signed-up for an eight-week pluridisciplinary session on bioinformatics in genetics. I had my first lecture on Friday.

What I’ve learned so far:

  1. This particular area of bioinfo (applying advanced AI algorithms to genetic research) is absolutely fascinating. With its mixing of cutting-edge results in biology, mathematics, physics and AI, it’s tough not being sucked in by the way they all combine into truly sci-fiesque results.
  2. About 3 month away from graduating into a field I have planned to pursue my researches in, I am suddenly starting to wonder about a switch in research paths. Yes: yet another existential academic crisis. Just what I needed now.
  3. During the introductory part on gene decoding patterns, when asked about information entropy in gene sequences, the lecturer: “Oh, it varies a lot between life forms. Viruses, for instance, have an extremely high entropy: lots of genes are coded using both directions of the helix”.
  4. What this means in layman’s term: viruses’ use compression in their genetic code… Yes, your flu virus may come in its own zip archive, just like your e-mail viruses!
  5. “Viruses are amazing things”, she concluded with an earnest look of admiration on her face (maniacal laughter did not follow, however).
  6. Yes, there is something ever so slightly chilling about hearing a respected biotech researcher uttering such phrases.
  7. I think I want to go into bioinformatics.
  8. Viruses are, like, totally cool.

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You know those “time-capsules” you buried in your backyard as a kid? The ones you unearthed the following week, upon realizing it was your favourite GI Joe’s action figure you put in that box (and cynical, anti-imperialist, you-of-twenty-years-from-then would probably discard it with a sneer, anyway)…

Well, I got my time-capsule back two weeks ago. Seventy kilos of it, to be exact. It wasn’t buried in my parents garden (I’m pretty sure my mum wouldn’t had let me dig a hole that size), but sitting in a storage facility for the past 15 years, whence I was kindly asked to come pick it up for good, last month.

Half is stuff that I should have binned, long before I even embarked on my current regime of bi-yearly intercontinental moves. The other half, I probably cared for, but decided wouldn’t fit in with the furniture of a decrepit London warehouse. At any rate, I have already started working my way through, slimming it down to a box and half, which, according to current life principles, will also have to go before next Spring (OK, maybe I’ll keep some of the books).

But before I complete my last round of recycling/discarding, I felt I could document some of those memorabilia, if not for their historical value, at least for the sake of providing a few laughs at the expense of the hopelessly dorky 11-year old I was. Yes, I know this might come as a bit of a shock to you, dear reader, but I wasn’t always this shiny beacon of elegance and hipster good-taste that I have matured into over the years. To tell the truth, only one thing comes to mind when contemplating some of the evidence: how the hell didn’t I get beaten up more often as a kid?

Sure, I could just play it cute and show you all those wacky serious adult books I read back then and marvel with mock-disapproval at little young prodigy Dave’s precocious readings (yes, I read all those Nietzsche’s books when I was 12, no I didn’t understand half of it, but it sure pissed the hell out of my grandmother and that was good enough for me)…

But when I say dorky, trust me I mean it. And it is with no secret pride whatsoever that I present you with:

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My friend Scott (he of the once-a-year updated blog), once coined a term to describe that all-too-common affliction of the garden-variety blogger: the way one single little item will clog your entire production line and delay infinitely the publication of your next post. He called it weblocked, which is as good a term as any other. And guess what: it happens a lot around these parts. It goes a long way toward those long stretches of blog silence, where the more I wait, the harder it seems to find an angle to break back in.

So in the spirit of clearing my current bloggage (and also because I really don’t have the time), allow me yet another life update potpourri entry, hopefully the last one in a while.

Paris hasn’t changed over the Summer. Still mostly cold and grey on an average day. Still offering a wide variety of options to liquor oneself up. Which sorta makes up for the previous part. Also has free bikes, which is way cool.

Vélib’ is easily the best thing to happen to Paris in a long while. Dirt cheap, ubiquitous, self-service, bike stations now cover every inch of Parisian sidewalk. Which means I rarely, if ever, step into the subway or bus anymore (rainy days aside). Biking amidst Parisian notoriously psychotic car drivers is not as fear-inducing as I thought it woud be, although it requires staying alert and attentive to your surroundings at all times. Unless, that is, you are drunk, riding full speed at two on a bike, down the Montagne Sainte Geneviève (that hill atop of which sits the Pantheon) on to the next bar. But we know of no people who would do such a mindblowingly stupid thing.

Of course, this being France and perfection being neither human nor French, this wonderful system has its downsides, one of which is the many bureaucratic hoops and near-month-long wait, one has to go through in order to receive their one-year subscription card. Still waiting for mine (and living off weekly passes in the meantime).

Winterish temperatures have also finally arrived. Which had for first consequence to keep me in bed the best of last week, waiting for my usual seasonal bout of flu to pass. But now that my tissue consumption has gotten back under the metric-tonne-a-day, I have finally come to give some limited appreciation to the cold albeit rather sunny outdoors. I don’t know if it’s me growing soft or cough syrup acting up, but I swear: breathing in the fresh crisp air on a cold Parisian night nearly makes me feel all mushy inside these days. I have turned on the heater at home nonetheless.

Shortly before I started hacking my lungs out, I did manage to attend a couple miscellaneous social affairs and cool art-related thingies. In particular, I had a really good time during the yearly Nuit Blanche celebration, spent in the north of Paris where a friend was showing her paintings. I do suspect spending the night outside discussing contemporary artists’ sexuality in relation to their art, with only a light jacket and some whisky to fight off the cold, might not be completely unrelated to aforementioned health problems.

Somewhere amidst the 20-points list of excuses for my being remiss from this blog all this time, is my official decision to sign up for JLPT 2-kyuu this year. What can I say: I like pain. The test takes place at the beginning of December. By even the most optimistic estimates, I will fail by a long shot, but I figured paying the 60 euros signup fee was the best way to kick my ass into some hardcore Japanese studying for the next two months.

Of course, being a geek first and foremost, I immediately concluded that 10% of my precious 50 days of revision would be much better spent on coding a nifty Japanese drill application. Also, because I am a geek 2.0, this application is on Facebook. But I swear it doesn’t suck (at least not as much as all those vampire/pirate/ninja bollocks). Trust me, if you are studying for JLPT, or even if you are just learning Japanese for fun (mind-boggling as the concept might be), this app is all you’ve ever dreamt off.

And now that I’m done selling it, I guess it is time for me to go back to using it.

I promise I’ll try to post more frequent, if succinct, updates for the near future.

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… for me at least.

These are times of project wrap-ups, end-of-stay work presentations, last drinks with friends and last cozy nights with more-than-friends. I have practically shaved my head and started packing my luggage. Next weekend I fly off to Bangkok for a couple days: not so much for relaxation as for a very necessary transitional break before resuming six months of intensive studying in Paris. Vacation time is over. Not that it was exactly vacation to begin with, but what’s ahead is sure to make this ending Summer feel like a slice of paradise in comparison.

Actually, I am not dreading return as much as I thought I would. I know those six months aren’t gonna be much fun, but the mere fact that they have a specific timeframe and the knowledge that I’ll be done at the end of March, helps make it all feel like a sort of extended vacation to Paris. And Paris is much more enjoyable if you feel you are visiting than if you actually live there. Parisian life is a different form of fun that only appeals to me, given the certainty that it won’t last: fancy dinners out, cozy wine-sipping evenings at home, opera season, art exhibits, cocktail party crashing, overwhelmingly beautiful architecture on every corner, drunken bar-counter philosophical debates… All so typically Parisian, overly sophisticated fun… that after a while makes you yearn for simpler, more natural ways of having a good time. Which is when I will be about done with my current academic pursuits and will gladly move onto another period of my life, presumably far from Paris, without regret or bitterness. So, timing is perfect, it appears.

Plans for next year are still deliberately very vague. Much less definite as they were at the beginning of this Summer. I no longer know whether a Ph.D. is the necessary path to what I later want to achieve, in fact, maybe university research altogether, isn’t. Or perhaps it is my field of research that needs revising. Throw in a couple very tempting offers, brought over to me lately, that I would be a fool not to at least consider…

Part of my Summer here was coloured by the fact that college friends I hadn’t seen much in ages, now work and live in Tokyo. Hanging out with them coincidentally reminded me of an essential conclusion of those years, that I might have lost sight of otherwise: The fact you have the abilities to do something doesn’t mean you should, and definitely doesn’t mean it will make you happier. Back then, I once did the mistake of picking what most people seemed to hold as a universally enviable life/career path, only to quickly realize that most people’s idea of happiness in life probably didn’t match mine and therefore neither did their conception of how to achieve it.

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Friday night’s Birthday Party was brilliant indeed.

Even though I am still here for another couple weeks, it had a certain feeling of grand season finale: what with the improbable juxtaposition of characters plucked from miscellaneous episodes of my life: past, current and hopefully future.

The mood and settings weren’t unlike the last time we had a party at Cozmo’s, in a good way. This time around: no drunken ex-girlfriend discussing the size of my manhood with friends, but lots of friends and friends-of-friends having a good time and mingling across groups, much drunken DJing with Atsushi and Ian (escaped from Sapporo for the weekend), unexpected gifts and free drinks pouring on me ceaselessly and, most of all, Hako clad in her geisha kimono bouncing around to the music, being her usual upliftingly cute self…

A very drunk subgroup essentially made of Ian, Deny, Rie and myself then headed out for Shibuya’s very own no-name bar (aka the Chandeliers Bar, aka the Red Room etc) whence the merriness kept on going until (very) late, although we shall keep the late remainders of that evening under an opaque veil of virginal mystery.

Expectedly, the following Saturday was a bit more low-key. Movies huddled on a bed most of [what was left of] the day. Hawaiian burger lunch/dinner in Shibuya. Fruity cocktails in Harajuku. Early sleep at home.

Sunday afternoon was both Saeko’s and Etsuko’s birthday party, as well as the day of my own actual birthday. All duly celebrated in much fancy wine-drinking and buffet-eating at a gorgeous floating restaurant in Shinagawa. Some of us then went for tea and dessert nearby and I finally left to attend my own birthday dinner in a more intimate settings.

I had purposely kept my evening very mellow and was just planning to meet Rie at Araku for a couple drinks around 9pm. Noticing how unusually busy the place was for a Sunday evening, we realized that day was Golden Gai Festa: 5,000 yens would get you a pass that’d let you get into most of the tiny Golden Gai hole-in-the-wall bars with no seating charge and one drink free. Additionally, you could ask for your card to be stamped at each place and get some sort of reward upon collecting all 30-some stamps (presumably a very fresh wet towel to alleviate next day’s massive hangover). The festa had officially begun at 1pm and by evening, a lot of people were actually already on their way home. With only three hours left to go, we still decided to give it a go, figuring it was as good a way to cap the day as any other…

We didn’t regret. It was the best bar fun we’d had in a long time. Everybody was friendly and having a good time: a great mix of ages, styles and interests… We got to see a dozen such tiny bars with their peculiar themes and strange decoration before finishing the night at Albatross‘ Golden Gai branch: same cool people and cozy atmosphere, marginally more seating space (say, 10 people instead of 6)…

The rest of the week was predictably spent recovering and catching up with work. Still managed a couple drinks with Sandy in the middle of Thursday’s wild thunderstorms, discussing relationships, God and viruses… Also met up with the lovely M. yesterday, just long enough to learn that her favourite way of procrastinating at the office involves talking dirty to her coworkers, all the while pondering what “only 60% of what he wanted” could mean exactly, in the context of an overeager Italian suitor’s love nest…

Unfortunately gotta do some work-related stuff all day tomorrow, so no big plans this weekend. As of now.