Science in the City

After hitting a bit of a down note on Tuesday, I spent most of Wednesday and Thursday tidying up affairs in and around the lab.  Unlike my work at the Chang lab in NYC, the space and materials at JCU were shared, and so a careful cost-accounting of my activities had to be undertaken, from the first cell extraction kit to the last  pipette tip.  I also had to leave behind detailed notes of all of the lab protocols I used, and go through various fridges to chuck out what was no longer needed, and preserve those things that would perpetuate my efforts after I’m gone.

But after coming to such a full stop, we found a bit of time to try one last time a couple of the tricky reactions I’d been having trouble with earlier in the week.  Equipment had been serviced and new reagents mixed up, so if there was to be a last chance, it would happen now.  I prepared the master mix, added the DNA from each of my samples, and with hands now trained to the purpose, mixed and spun down the plates on the centrifuge.  We popped them into the thermal cycler, and I programmed in the sequence of steps to yield fresh DNA.  Like a master chef, Kor suggested a bit more magnesium chloride in the starting mix (to help the DNA unravel for copying) and adjusted the temperatures of the stages.  Essentially, add a pinch of salt and let it bake a bit longer.

After running my last load of laundry, I headed back to the lab to pour a gel to be set for our product.  After it was ready, I used a multichannel pipette with twelve tips to load the samples.  It’s like adding a fancy border to many little cakes at once.  I took pride in hearing Paolo, a lab hand famous for his speed and dexterity with the gear say “ooh, fancy pipette work….very nice.”  Coming from him, it was a fine punctuation mark for the evolution of my own skill set.

After 30 minutes, we checked the samples, with the results you see above.  We have results from two distinct sets of DNA collected from the same plants.  One is blurry and unclear, and the other nice and sharp.  This means that one gene managed to copy nicely, while the other, for no lack of effort on my part, simply won’t work according to the recipe in place for it.  It was vindication on two fronts.  On the first, the clean bands can now be processed directly, saving a step in the project after I leave.  These genes should be sequenced by the end of the coming week, and will serve as the third independent barcode experiment I worked on.  The other yet failed, but provided clear enough documentation that the process itself is not working for this gene.  No matter how many times I did it, it simply wasn’t going to work…..so it wasn’t something I was doing to muck it up!

To start anew, different starting strand ingredients will be tried, a simplified thermal cycle will be attempted.  But for the smudge-y gene, we managed to learn something useful in the failure.  So in spite of that it had already been called a successful summer, we managed to wring just a bit more out of my time here.  

The last day reinforced a couple things.  One is the value of persistence and the importance of meticulous documentation.  Especially in lab work, small differences yield important results, and being able to refer back to one’s own trials is essential.  The other is a sense of efficacy.  After seeing what happened, I believe that I know what is needed next, if there was another week or month in the can here.  I know enough to be able to steer the car a little bit, even if someone else is keeping an eye on the map.  Notwithstanding my aching home-sickness for family, I felt a twinge of ‘if only’ before I realized something else:  That whatever work one does in science is purpose-built not to have a neat conclusion.  Every question can and should lead to other, interesting questions.  Although I know where we will go next, I know that the path is a journey with no fixed destination….only mile markers to show the distance traveled from one day to the next, from one discovery to failure to breakthrough, stretching away into the unseen, off in the horizon just beyond.