When the wheels fall off.

9/08/2009 08:44:00 pm

If someone says to me in the future that they are considering doing an honours year, I will tell them the following story.

Since May I have tried to stay positive. Even though my instincts told me from the beginning that you cannot homogenise tissue samples for RNA extraction without a polytron or you know...something other than scissors. I did what I was told. I should have known better. I should have stuck to my instincts. I should have done so many things differently, but most of all, when I was deciding whether or not I would stick it out for another year and graduate with some more letters behind my name, I should have decided that I did not need those letters. I should have left then with my two degrees and not looked back.

First it began with failed PCR. At first those were my fault, but I figured that out pretty fast. Then the PCR started to look good. Real good. So good that I was getting huge pretty bands, specific for both of my primer sets, in my negative controls.

Two months that took to fix. It took two months because the person I work with decided we should approach the problem in a piecemeal fashion and change one reagent at a time. As in, "it can't be the polymerase, we won't change it...hmmn, it's still there, it must be the polymerase, but I guess the other things should still be ok.

When that was fixed, it reappeared and the piecemeal process was repeated. I started setting up my experiments in a sterile hood. I aliquoted my reagents. I put a sign on them that said, "Ellie's reagents. Do not use." They got used. My special boxes of tips got taken out of the hood.

My supervisor came back from Europe and the conversation went like this:
Me: "The contamination is back."
Him: "WHAT?! I thought that was sorted out two weeks ago."
Me: "Me too."
Him: "It's time to start spending our way out of this. Order new primers. Buy new polymerase. Make fresh dNTPs."
Me: *bangs head on table and thinks WHY FOR FUCK'S SAKE DID WE NOT DO THIS FROM THE BEGINING*

The PCR was fixed. My negatives were clear. I continued. My transformations stopped working. I thought there might be something wrong with the cells because the freezer door was left open. Everyone assured me that the cells were fine and I must be doing something wrong. Something wrong with the ligation. Too rough with the competent cells. Salt contamination. I cleaned up my samples. I tested the ligation. I tested the antibiotic concentration in my plates. I doubted myself. I trusted my instinct and I made new cells. And my transformations started working again.

So I did the plasmid extractions. 192 of them. I set them up for sequencing. 192 of them. And when I was looking at them today and I realised that something was not quite right, the wheels finally fell off. The remaining thread, remnants of motivation I had to haul myself up the hill to our awful lab every day, snapped. It snapped back and it triggered an overflow of the rising tide of panic that I have been managing to keep at bay since May. My supervisor realised this I think, as I started sobbing in the office.

There is only so long one can maintain the veneer of positivity. I don't care anymore. It doesn't matter what I do, it won't work. My sequences are contaminated with samples from Papua New Guinea. I'll have to start at the beginning again. There I was thinking that finally my string of constant bad luck was done. I thought I only had 2 weeks of lab work left. I have no idea how I am going to convince myself to go back. I want to go to bed for a while and see how long it takes for them to notice I've not been to the office in a while.

If someone asks me should they do honours? I have only one word.


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2 comments on this post

  1. James1:27 pm

    I'm sorry that everything has gone pear shaped for you, and I'm sorry about my part in your demise but I did what I could.

  2. Hey Ellie.
    want to write something inspirational, but it will only end up being trite.

    Honours is probably going to be the best year that you ever have at Uni. But you won't realise it until it's long over...

    Hard, of course, excruciatingly painful and psychosis-inducing, yes. But ultimately it's unbelievably rewarding.

    I would recommend lots of caffeine and german electronica to get you through... there is something quite meditative about Kraftwerk for some reason.

    x Huon.


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