Thursday, February 25, 2010

Rainy Day Therapy

If you ask most people around me it is miserable out... cold, rainy, dreary. If it were a bit colder it would be a wonderful snow storm and a good way to end the winter. But, it is raining, raining, raining. The wilderness instructor in me calls this "prime hyperthermia weather". However, I am not in the wilderness, and I do not have to worry about hyperthermia when indoors is always nearby, so I propose a radical notion... it is actually wonderful out. Don't believe me? Follow these steps on your next walk home in the cold rain and enjoy experiencing the elements, the feel of your cold damp skin, and appreciate your warm home when you get there.

1. Walk with a friend
2. Skip until you get warm
3. Stamp in every puddle you pass trying to get your friend wet, make sure they do the same to you
4. Laugh loudly, try to laugh so loudly that people hunched over near you look up and maybe appreciate the experience, just a little bit

Sunday, February 21, 2010

Getting ahead of myself

The pacific ocean.

The view from our "guest office" at MBARI

I have been slacking in blog-land recently, but I have something to report. I want to move to California, at least for a couple of years... like for a post doc. Now all I have to do is finish my PhD. I spent the last week out in the Monteray area working with collaborators at the Monteray Bay Aquarium Research Institute. By "working with" I mean that I was being shown how to use a very complicated instrument that we will eventually get to play with in our lab and bring to sea. I am (mostly) confident that when said instrument arrives I can tinker with it without breaking it. Using this instrument is going to test both my molecular biology skills as well as force me to learn some basic computer programming. As usual, I am looking forward to the challenge.

This was my first school-sponsored trip in this grad program, and it was certainly exciting to learn about this cutting edge technology. I really did try to come up with a less cliche way of saying "cutting edge". My advisor gets serious points for deciding to send my science-partner-in-crime along with me for this training. It cost him some extra money, but the two brains being better than one will certainly hold true when the instrument arrives.

So... back to CA (ah... if only I could go back). The folks at MBARI seemed to really enjoy their work, and why wouldn't you when you got to have the above view from your office each day. I grew up in New England where we like to think that the weather makes us tough, and we are stronger for it. This leads to the mindset that "those Californians can't possibly appreciate all that nice weather, how could they get anything done?". I am certainly willing to go give it a try, and report back!

Sunday, February 7, 2010

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.

Monday, February 1, 2010

a new month and a new semester

One month ago I decided to do monthly goals and self-check-ins rather than make new years resolutions. It is time to see how I did with my January goals.

Overall I would say not too well. Of my 10 goals I partially accomplished 3 of them, partially failed at 2, and totally failed at the rest. As I expected, I did not have nearly as much time for myself as I thought I would. However, this was just month one, and the overall goal was to set more realistic goals. So, now it is time to decide what I will accomplish in February. I have made 7 goals for myself that should be doable. 2 have to do with family. 2 have to do with work. 1 is fitness related (sort of a 3-in-1 goal). 1 is to keep my room clean and organize stacks of papers that have accumulated over the last months, and the last is to write at least 6 blog posts. So far I like the monthly goal setting.

The academic semester has started up and my schedule already seems much busier than last semester. This is primarily because there is lots of lab work to be done before our summer research cruise. I am struggling with the voodoo-like nature of molecular biology, and really hope that things start working out soon! Everyone tells me that this is just the way it goes... you mess up a bunch of times, and then, magically, it works. I am really looking forward to being able to say "it worked!". Some day soon, hopefully...