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Wednesday, November 29, 2006

Whole Pictures and Python

  Yes, this is an unusual combination of topics, but it's not worth writing two separate posts for them. First, On the subject of seeing the 'whole picture', as I ranted on about the other day, I'd like to point out that - despite my criticism - I really don't know how to do this in my own respective field, let alone in other people's. Thus, my comments on Dr. Black's lecture are more a reflection of my own interest in breaking out of the "one gene - one thesis" picture, than a comment on Dr. Black's Research.

  I really believe there's a need for scientists, and particularly those dealing with biology, to look on from outside objectively and ask what it is they're contributing to the general pool of knowledge. However, that doesn't mean we should stop working on the focused projects that abound and that make up the vast majority of tractable projects in the field.

  Anyhow, with that said, I also wanted to jump over and mention Python. A couple of recent classes on the subject have been given here at the GSC, which have given me a very light feel for the language. At first, I figured it was just as wonky as perl, but after writing my very first Python script, I can see the beauty, elegance and flexibility of the language. With no further ado, let me unveil my first script for processing a large data flat file:

import os, sys, re

readfile = file('/home/afejes/Desktop/SNPanalysis.TUandREADS', "r")

Mutation= re.compile(r"[1-9]+[A-Z]+>>>[A-Z]\s\(\w+\)", re.VERBOSE)
Genename = re.compile (r"------>\sENSG", re.VERBOSE)

writefile = file('/home/afejes/Desktop/SNPanalysis.SNPS', "w")

for line in readfile:
if Genename.match(line):
Gene = line[8:23]
elif Mutation.match(line):
writefile.write(Gene + '\t' + line)


Monday, November 27, 2006

Snowy Pictures of Vancouver

  I promised a couple of pictures of Vancouver under some snow... so here are a couple for you.

  Yes, my ulterior motive is to test out my blog formatting with images, but are you really complaining?

On Science Seminars...

   Going back to the Article I mentioned in my first post, I thought I'd comment on a seminar I saw today By Dr. Doug Black. To begin with, by all accounts, it was a good talk. All his data were clearly supported, all his hypotheses were consistent with the case he presented, and all of his slides were clear.

  Unfortunately, I found myself putting it into the context of the Biologists working on the radio, in which case, this reduced down to a 1 hour talk on a single capacitor. Yes, when the radio is in one state, the capacitor holds it's charge, and in another, it discharges - followed by 45 minutes of supporting evidence.

  Somewhere near the end, Dr. Black put up a fantastic slide - using Mass Spectrometry, they were able to investigate ALL of the components of the fancy structure (called a Spliceosome) all at once. Now, in theory, this is suddenly getting a snapshot of the big picture. If you could do this for 5 different cell types, we could start looking at what are the variable parts, what are the consistent parts - and what parts are worthy of more attention.

  Unfortunately, this fantastic snapshot of what makes up the Spliceosome was only a sideline in the talk. Although, I have to admit, the one component in this talk did have a fancy name. (-;

A quick update...

  I spent a good part of the weekend updating my gallery, so for anyone who hasn't been there lately, there are about 120 new pictures up. That's what I get for falling behind in processing my pictures.

  On the other hand, I've taken a whole bunch more over the last day or two, now that Vancouver has a good 10-20cm of snow covering everything. Hopefully, I'll have a chance to post those tonight - and I might even get around to cross-posting with my blog.

  Oh, and of course, we're now on day 11 of the "Boil Water Advisory" for Vancouver... and counting.

Friday, November 24, 2006

First Post - How many biologists does it take to fix a radio?

  I think it's time to relaunch my blog. No fanfare, no emails.. just a quiet "one more blog added to the web" un-event. Sort of like in Alice in Wonderland, where the Mad Hatter et al celebrate their un-birthdays, which I'm sure get tedious somewhere near the 360th of each year.

  In any case, I've been thinking of way too many rants to keep quiet about, and a chance discovery at the printer this morning had me grinning like a fool, so I figured it would be a good time to start sharing with the world, again.

  What's the discovery, you ask?

  I came across an article titled Can a Biologist Fix a Radio? - or, What I Learned while Studying Apoptosis. With a title like that, who could resist reading the intro... or the whole article.

  In essence, it's a call to arms for the biological community to develop useful terminology, and to re-assess how we look at our subjects. In his example, Dr. Lazebnik asks how would biologists fix a radio. A wonderful quote from the article goes as follows:

How would we begin? First, we would secure funds to obtain a large supply of identical functioning radios in order to dissect and compare them to the one that is broken. We would eventually find how to open the radios and will find objects of various shape, color and size. We would describe and classify them into families according to their appearance.

  He then goes on to describe various methods where biologists start pulling objects out of the radio, one by one, and naming the components by their effect on the radio, and making nice acronyms for each one.

  And that's what I really found striking. Biologists, Biochemists and anyone dissecting cells is guilty of that crime - not seeing the big picture. In many cases, there is no way to see the big picture, but if we try to understand a radio in terms of resistor #58, versus understanding why we have resistors, we end up with two very different world views.

  So, where's this all going? I've just spent the last week looking for "nails that stick up" on cancer cells (very successfully, I'd like to think), with the aim of beating them down. Maybe it's time I start looking at what these nails are holding together.