Archive for the 'Academic Adventures' Category

My Ambitions

Tuesday, May 6th, 2008

Currently, they still oscillate between Nobel Prize and two Advils.

Seriously: who goes out until morning on a Monday night? More to the point: who goes to work the day after, on a national holiday?

A sucker, that’s who.

Roadmap

Monday, April 14th, 2008
  • Vita
  • Academia
    • Finish all unfinished uni projects
    • Get seriously started on my research.
    • Make up my mind on the whole PhD thing.
    • Pick a subject.
    • Pick a country.
    • Pick an advisor (not necessarily in the above order).
  • Technica
  • Et caetera
    • Sushi.
    • Beer.
    • Music.
    • Art.
    • Et alia caetera.

“By eschewing obfuscatory verbosity of locutional rendering, the circumscriptional appelations are excised.” [sic, emphasis mine]

End of an Era

Thursday, March 27th, 2008

This morning, I sat through the last written test of my life.(*)

(*) Don’t get all excited now: I am far from done… Still got a couple reports and projects to hand in, not to mention thesis defense(s) in the coming months/years. Not to mention JLPT in December and any other such certification test I may ever be foolish enough to apply for… Still:

The last written test of my entire existence!

Good Byes to Dr. D…

Tuesday, February 12th, 2008

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…

Downsides of neuroscience papers, pt. 2

Tuesday, February 5th, 2008

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”.

Emotion…

Sunday, December 16th, 2007

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…

Bioinformatics

Saturday, December 1st, 2007

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 lowhigh 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.

When your name sounds anything like “Vladimir Vapnik” or “Alexey Chervonenkis“, you just should not be allowed a career in mathematics by the cliché police.

No offense meant to our Russian mathematician friends.

Running out of procrastination material…

Tuesday, August 21st, 2007

You know there are serious problems with your motivation levels when you’d rather spend the day reading up Agrawal’s [sublimely elegant but entirely irrelevant] PRIMES is in P paper than do actual work.

Names and situations have been changed to protect the not-so-innocent (me). For clarity purposes, some bits that may have been merely thought at the time, are fully spelt out here.

A bit over a year ago, last class of the semester:

Prof. Travoltus: And I wish you all a successful career and might see you again one day, shall you decide to go for a post-grad in AI.

Dave: Does that mean you are involved in that curriculum too? Oh god, no.

Prof. Travoltus: Indeed I am. And don’t worry, I hate your guts too.

Dave: Why, thanks. You are quite a tool yourself.

Prof. Travoltus: You little arrogant piece of self-sufficient shit. Don’t you think I didn’t notice your constant sneering at every other one of my [very unfunny] jokes and comments, all semester long.

Dave: Same to you sir. By the way, 1970 called and it wants its corduroy bellbottoms back. ’said you could keep the pungent cologne, though.

(more…)

What I do these days…

Thursday, February 1st, 2007

Wherein the author unabashedly stares at his navel while describing in painfully boring details his past and current academic endeavours under the guise of introducing some of the topics bound to become a fixture of this blog.

As morbidly obsessed faithful readers of this blog may remember, I made a decision 18 months ago to go back to school and try for one of these fancy post-graduate degree in Compooter Thingies.

As it happen, my original bachelor was mostly centered around Mathematics and Physics, two sciences that turned out to make for infinitely more entertaining conversation topics than university majors (also, it was sorta interspersed with half a dozen other totally unrelated course of studies). Having come to develop uncontrollable rash-like allergic reactions to the mere mention of either topic, it sounded wise to shift the focus of my academic pursuits over to a slightly different major. Hence Computer Science, or to be exact: Artificial Intelligence (which is, to paraphrase some guy, as much about computers as astronomy is about telescopes). As for the “going-back-to-university” thing altogether, it was mostly motivated by the pointed realization that, of the entire spectrum of available jobs, university student was the one I was most happily fitted for: After being a corporate droid for many years, a beach bum for another couple, I figured being paid a [rather mediocre] salary to work on cool research projects while learning semi-interesting things, sounded like a very fun way to pass time before retiring to a desert island in the Indian Ocean. That and the possibility that I may one day be responsible for the enslavement of humanity under the cold, merciless dominion of superiorly intelligent thinking machines.

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Last days before reset…

Thursday, January 4th, 2007

Saturday, December 23rd, 2006

Woke up naked, curled up in the middle of my living room. Calendar on the wall says it’s been about two months. Paper everywhere. Found a couple dead rats impaled with sharpened pencils into stacks of graph theory and bayesian statistics papers… Decide to burn it all in the building’s courtyard and forego any attempts at piecing back together whatever hazy memories remain of that painful episode.

Tuesday, December 26th, 2006

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Scotty, we need more productivity…

Sunday, December 17th, 2006

This just in from our stating-the-obvious department: this blog will undergo a severe slow-down for the month (that is, the month already nearing its end and the slow-down now ongoing for a good three weeks already).

Computer failures, livelihood-earning work, research projects, assignments, sleep deprivation, final exams and overall the sad realities of the M.Sc.’s student life crashing into my own, theretofore much happier, shiny rosy reality… are all to blame for this sudden interruption. Expect some improvement at the end of next week, if I make it this far.

PS: and sorry for leaving last month’s quizz out to dry. I swear I’ll post the results as soon as I’m back among the living.

You think your Tuesday mornings suck?

Tuesday, November 7th, 2006

Picture amphi_mog.jpg Just so you don’t think for a moment that I am out there having fun when I leave this blog unattended for weeks on end…

Note that this snapshot entirely fails to convey the real Soviet-era ambiance of my 8am-1pm weekly Tuesday lecture: attended by twelve hardcore students huddled in a 300-seat auditorium, fighting sleep and hypothermia, with the dreary droning of a disinterested lecturer as background lullaby.

Can I get a Hell Yeah for advanced graph theory?!?

Hell… zzz