rapid rambling reflections

It is hard to believe that my first year back in school is almost at its end. 3 days of classes, 2 exams, and 1 paper stand between me and the relative relaxation of simply being a scientist rather than juggling doing science alongside taking science classes. I am looking forward to being able to focus on my research and getting ready for summer field work. I have really felt like classes were slowing down the research this semester. I also have a good feeling for what material I need to read up on to increase my background knowledge directly relevant to my research, and I haven't been able to make much progress in that while focusing on my classwork. I have 3 textbooks that I would like to read this summer. I am hoping I can get other students to read them with me. It is funny how much more likely I am to stick to something (be it reading a textbook or going to the climbing gym regularly) when I set a schedule with a friend. Somehow it is easier to come up short on promises to myself than to others (I wonder what a psychologist would say about that). I think I am finally getting over my inferiority complex and beginning to feel like I actually belong in this program, and have (or will eventually have) something meaningful (albeit probably small) to contribute to the general body of knowledge that is science.

a (not so) productive day

Things have been hectic lately. The lab work is ramping up, and finals and papers are rapidly approaching. I decided to be extra productive today. I got to lab early and got one reaction going and did some sampling for someone in the lab who is out all before my morning class. I came back from class and looked at my samples and did the next round of lab work before lunch. After lunch I set up another reaction and finished sampling for the person who is out before the whole lab went over to a nearby school for a particularly relevant talk. I came back looked at my reaction, and did the final bit of lab work in time to go meet with my cohort to discuss Darwin's Origin of Species that we have been reading in monthly installments. I was busy all day, and was all ready to feel like I had accomplished something... except that the reactions I was trying were not working. The DNA refuses to amplify, and I keep returning to square one. I will keep trying, but it kind of feels like all my efforts to be super-productive today were a waste. Sigh.

Molecular Biology Actually Works

Up until this past Friday I was semi-convinced that molecular biology doesn't really work. Or, at least, that it was never going to work for me. Since I transitioned into biology from the world of Geology and Environmental Science I have been playing catch up in terms of learning lab techniques, some of which are very finicky. I can now say that it is very exciting when these processes actually work.

We have been attempting to increase the volume of our extracted DNA using a Whole Genome Amplification (WGA) kit. In contrast to the more common PCR which amplifies a specific region of the DNA, the WGA process amplifies all of the DNA in a sample. This is great if you have very small amounts of DNA, but the downside is that if there is any non-sample DNA present that will amplify along with your sample.

My science partner and I spend about 2 weeks trying to work with our WGA kit. In order to make sure we were really amplifying our sample DNA and not a contaminant that we inadvertently introduced we used water as a negative control along side our sample. If we did things correctly we should have seen amplified DNA in our sample and no DNA in the water control when we were done. However, time after time we had more DNA in our water control than we did in the actual sample. This was very frustrating. We tried everything we could think of to be more sterile, and kept getting the same result. Finally we contacted the company and they sent us a new kit to work with. The first time we used it we got good results! There was no DNA in our water control, and plenty of DNA in the sample. It is really good to know the process works, and now we might actually be able to send some DNA out for sequencing. I am beginning to believe all the people who have told me that in molecular biology you do something over and over and over and over again... and then, finally, it works.