Two Weeks!

Random Picture: Wellsville Mountains 2006

I have, thus far, been in class for two weeks. I am taking three seminars and two lecture/discussion type classes. We do a lot of reading! We read articles out of scientific journals and then have group discussions. There are no tests. Interesting; but why?

The idea behind this is that we are being trained as scientist, research scientists to be specific. As undergraduates we were taught principles of various aspects of science and then were tested to see if we had learned the principles. This approach does not allow too much wiggle room to seriously question what is being taught. Sure, as undergraduates we can ask, ‘how do they know that?’ If known, the professor can explain an experiment that was used (or may have been used) to ascertain the information. In undergraduate courses this system works great because the courses, for the most part, teach established data. However, as “PhD’s in training” we are now focusing on how scientific knowledge is gained. Also, if we are given a lecture, the material will most likely be penetrating the current boundaries of knowledge. It does no good to read an article and then say, ‘That’s it; we’ve figured it out.’ We need to seriously analyze the data and see if it makes sense. As scientists we have the responsibility to question the publication and, if we have the same research emphasis of the article’s authors, perhaps perform experiments to confirm or discredit the publication. Enough on the processes of scientific discovery.

This last week I started my first rotation. Again, a rotation is an eight week projects in a research lab that allows the student to essentially ‘test drive’ the lab. We do rotations in three different labs and then we can choose the lab that fits us the best. There is a story about how I got into my first rotation. I was looking at three different labs for possible rotations. There was a fourth lab that actually really wanted me. They had a computational project and I was an obvious fit as computation is all I do. However, working at McDonald’s was slightly more appealing than working in that lab.

Anyway, I had three labs that I was seriously considering for a first rotation but none of them could really take a student for the first rotation. Two were going to be gone for most of the first rotation and one was moving to a new lab. So I had a choice; see if I could rotate with the lab that was going to move or I could go to the fourth lab that really wanted me. I took the former course of action. When I explained the situation the PI, he said that I could do a rotation despite the eminent move. Now they have another set of hands to help move!

If you care to know what I do in my rotation, by all means keep reading. If not, that’s perfectly fine; I’ll say good bye and thanks for reading.

In my rotation I am working with a husband and wife team; the Richardson’s. They are very significant figures in the field of computational structural biology. In the lab I am trying to find patterns of errors in low resolution models. Now what does that mean?

(Disclaimer: The following may not be scientifically correct but gets the correct ‘concepts’ across nonetheless.) Protein structures (models) are made from shooting a crystal of the protein with x-rays. For the current discussion suffice it to say that we take very crude ‘pictures’ of the protein (scientists: please read disclaimer). Imagine a picture of a clock. At high resolution we can see the hands, the numbers, the screw holding the hands on, flaws on the face, every little detail. With this ‘picture’ we can then make a fairly accurate model of the clock. But you very well could have a low resolution ‘picture’ too. You can imagine that it is going to be difficult to make a model from this ‘picture.’ However, when low resolution is all you have you do your best. My goal is to find patterns of errors in models derived from low resolution ‘pictures.’ I hope that made sense.

I hope you all are doing well. Feel free to drop me a line. Have a wonderful week!