Protein Alignment

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

My first α-carbon-based protein alignment!

I’ve got a lump in my throat…

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.

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.

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.

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

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.

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