26 June, 2002

6/26/02

Bioinformatics

In the last two days I have been working on two projects at once. The first has been to test different factors in our experimental procedures to ensure that the procedures themselves are not giving some anomalous results. The second task has been to go through a crash course in the field of bioinformatics.

My first task has been an enjoyable one for me. I enjoy employing problem solving skills to a given scenario. In Dr. Duman's lab we have been presented with a problem that at the moment has no answer. Why are the Cucujus larvae showing a bi-modal distribution for their freezing points? As I discussed in earlier entries, some of our larvae freeze at temperatures above -100C, while the remainder of the population freezes at temperatures below -300C. The population with the higher freezing points is of great interest since our temperature data from Alaska shows that these larvae routinely see temperatures well below -100C in the winter. Those temperatures suggest that those Cucujus would have frozen during the winter, yet we have yet to freeze a Cucujus in the lab and have it recover from the freezing process. Our experimental results would suggest that Cucujus are not freeze-tolerant, but if that is the case how are the individuals in the higher population surviving the winter? Dr. Duman believes that the Cucujus are in the process of changing from a freeze-tolerant to a freeze-avoiding survival strategy. If true, this could be the result of the climate change that has been occurring in Alaska over the past 30 or so years.

While the strategy switching is a fascinating possibility, we must first rule out the possibility that the procedures are in some way altering our results. My task over the past few days has been to run a series of procedures to eliminate possible sources of error in our data. So far I have tested for differences in location in the freezing baths, for different placements of the Cucujus inside the freezing tube, for different placements of the thermocouple on the body of the larvae, for different methods of holding the Cucujus in the freezing tubes, and for several other factors. So far all of the tests have been negative. Our experimental procedures do not appear to differentially affect the results. The one procedure I would like to run would test the thought tat we are somehow damaging the larvae as we are preparing them. Unfortunately, I will need a sample of the bi-modal population for this test and that will not be available until at least our fall trip.

While my tests here are not leading to any groundbreaking results, I am hoping they at least give the folks here in the lab some sense of security that the procedures themselves are sound.

My second task over the past few days has been to learn as much as I can about the field of bioinformatics. Bioinformatics is the creation, maintenance and manipulation of enormous databases of biological information. Bioinformatics is a new discipline which blends the fields of biology, computer science and information technology. The field is in large part, the application and use of computers to understand the molecules that make up living organisms. In the future it will include the manipulation of those same molecules through computer technology. The largest undertaking of this new field is the Human Genome Project, in which the entire DNA structure of humans will be cataloged and available in a massive database. While the human genome has the largest database, there are a number of other species with genomic databases as well. Over the past few days I have been becoming more familiar with the use of those databases.

Applying our lab work to the genomic databases has really given me a mixed reaction to entire field of bioinformatics. I am fascinated by the sheer volume of information available at the fingertips of any researcher. The massive nature of these databases will most certainly increase the efficiency of biological research. At the same time however, I am wary of how this field will affect research as a whole. I am a great fan of Aldo Leopold who was often very critical of biologists who study single organisms or parts of single organisms without having an idea of the "big picture". How does that organism relate to its surroundings and how do the parts work together to make a whole? With this new filed of bioinformatics, I can foresee the existence of a large number of scientists working with genetic information without ever really knowing what the organism being studied looks like. I wonder what this dissociation from the actual living organisms will do to biological research.

Still, to know that such a body of information is available and growing daily, is an amazing concept.

Tomorrow, as I post my final entries for this stage of my TEA experience, I'll also post some pictures of the Notre Dame campus.