Thoughts of a Computational Biologist
Well, before I start I should say that I have not read the book whose title I paraphrased. So, to the purists out there: no need to point this out. But I do know it is about career choices and changes, and that is enough for me to play the metaphor.
Just yesterday I was among a group of people with diverse research interests. As usual for not-so-big groups, we introduced ourselves, and described each our research. Well, often, in such situations I say that I don’t know what I am. Then go on to say that I am interested in almost anything genomics, any organisms, et cetera, as long as I can use a computer to do my part. But why would it be hard for me to self-describe?
I started my career as a fresh-out-of-undergrad-school, as a biologist-who-wants-to-be-a-molecular-biologist within a lab that was said to be a lab of biotechnology. There I learned to take care of a microbial collection, grew all kinds of inoffensive microbes, watched all kinds of shapes and colors of microbial colonies, isolated colonies, made sure of phenotypes, grew in some broth, added glycerol, and put the little bugs in a -70 C freezer. Oh, almost forgot. I also learned to lyophilize.
That was not all. I was required to work on a thesis if I were to have my undergrad diploma. So, I did work on using the Microbial Ames Mutagenicity Test. A beauty of a test designed to detect a substance’s capacity to cause mutations by counting colonies. These colonies grow in a medium lacking an important nutrient. Without this nutrient, these Bacteria cannot grow unless they get a mutation enabling them to produce the nutrient themselves. Thus, a substance that causes mutations will be detected because some cells will get a mutation and grow (Hum, I never thought of it, but talk about beneficial mutations–There you have it creationists! All in less than 48 hours!)
Anyway, there goes some experience in mutagenesis, and testing, and taking extra care to keep the phenotype of these delicate Ames Salmonella strains too.
Then, I went to Xalapa, to another institution where I was to learn about underexploited wild or semi-wild plants. Measured starch, weighted tubers, you name it. Then an offer to come back to the first institution to continue now with the idea of mutating strains of Escherichia coli so that they would overproduce aromatic amino acids. Important for one reason or another, such as to give us precursors for aspartame, you know how it gets when it is all about low calorie but ultra-sweet pleasures. This by exposing the E. coli poor things to mutagenic substances, and selecting media for insensitiveness to aromatic amino acid mimics that would be mortal unless these Bacteria lost regulation of the mimicked amino acid. Yes, the mimic would fool the normal bacterium into “thinking” that the amino acid is present, thus the bacterium would not produce this amino acid and would fail to grow. Mutants would continue to produce the amino acid of interest despite its abundance because of loss of regulation. Oh, we did get some mutants, and they did overproduce amino acids. But I left for the Ph.D.
I had been taken by the idea of protein engineering. There was an article in a magazine called “Food Technology” titled “Want an enzyme? Make your own!” or something to the effect. I was dazzled. So, I pursued this area for my thesis. Long story short, I learned about site-directed mutagenesis, PCR, sequencing–Sanger method, which is a beauty of elegance in the way it translates the microscopic events of DNA replication into a signal we can detect by eye. I also ran enzyme kinetics in reverse micelles. I ran many kinetic reactions, and had to format, reformat, exchange, and modify files to go from one program to another, from one operative system to another, and finally get the reaction fit into the Michaelis-Menten equation, and so on. Thus, I decided to learn a programming language to save time with the reformatting and calculation of reaction speeds. I had learned to play with the csh shell, which is also programming, but, well, let us skip that.
Lo and behold, the genomics revolution was under way. I knew about it. The environment at the Institute of Biotechnology is communicative, collegial, and inspiring. You get to know about all things science, and mostly all things molecular biology and biotechnology. I was still a protein engineer in the making, I guess, but I was finishing my thesis, and needed a job. I accepted a job at a lab dedicated to computational genomics, focused on E. coli. It was, I thought, just for a while, then I would go back to proteins. But, I fell for genomics and have not looked back ever since.
So, what color is my parachute? It has all kinds of hues, all kinds of colors, blacks, reds, yellows, blues, oranges, violets, whites, all with no well-defined boundaries, all mixing and playing with each other. I cannot define myself. Now I am also into microbiome diversity, adding colors to my parachute as life goes on.
I was reminded of all that yesterday. I heard some pretty interesting talks that reminded me that my jumps have colored my academic life. The talks illuminated my new interests in ways I had not thought about before, and added to my passion. As if I needed that!