Hughes Mentor:  Carlos Bustamante

Department: Biological Statistics and Computational Biology

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A Day in the Life of an Undergraduate in the Bustamante Lab

After the completion of my freshman year, I was shocked that a year of college had already passed. I had taken introductory courses in biology and biological statistics and completed my mathematics requirements, but could not help asking myself, “Where am I going with this!?” Although I was learning a great deal through my academic studies, I wanted to be able to take my understanding a step further. Being able to apply the knowledge learned in my classes to more practical cases, as in research, could provide me with a deeper understanding of my course material.

Thus, my next step was to find an opportunity to gain practical experience. During my freshman year, the Biometry and Statistics major held brunches on Sunday mornings every several weeks in order for students to ask questions of advisors and faculty, eat Belgian waffles, and get acquainted with others in the major. Here, I learned more about the Statistical Genomics concentration in the major and spoke to Carlos Bustamante about the field. In looking through faculty webpages and their current research projects, I decided that I wanted to eventually become a part of, or at least learn more about, Carlos Bustamante’s lab. In his lab, I would be able to apply statistics to many biological areas such as in the study of the genome or in the evolution of populations.

During the summer before my sophomore year, I emailed Professor Bustamante, expressed my interest in the field, and asked if there were any possible research opportunities in his lab. After meeting with Professor Bustamante, I attended weekly lab meetings to learn more about the wide variety of projects that I personally could be involved in. In order to become more familiar with the field, I met with Professor Bustamante weekly to discuss scientific papers I had read and to implement computer simulations modeling particular phenomena in population genetics.

As the work done in the Bustamante lab by both graduate students and postdoctoral fellows alike is highly independent, a fair amount of background knowledge was necessary before I began my own independent research. First, taking Genetics (BIOGD 281) in the fall of my sophomore year prepared me for many of the biological concepts that I would encounter in my research. Unlike other labs involved with “wet” lab work – counting flies, growing bacteria, examining cells under a microscope – the Bustamante lab is involved with only “dry” lab work. Lab members are typically not involved in obtaining the data, such as DNA sequences, that they analyze. Research instead focuses on developing or implementing computational algorithms and computer programs to perform genetic analyses. Taking core statistics courses was necessary in implementing and understanding the statistical concepts forming the foundation of the analytical methods that I use. Since knowing how to write computer programs is also essential, taking a course in computer programming was extremely helpful.

Once I had the appropriate foundations in statistics, genetics, and computer programming, I was able to begin working on several research projects. One semester, I assisted a graduate student in the analysis of data in the form of a family pedigree to attempt to find a gene for a bleeding disorder in the domestic dog. After working on this project, I began a project of my own where I analyzed DNA sequences from the porbeagle shark to infer the severity of the population decline of the species due to over fishing. Currently, I am working to infer the population history of various breeds of the domestic dog, again examining DNA sequences and using concepts in population genetics to do so.

Since most of my research can be done from any computer, most of my research can theoretically be conducted from home. However, since I am in the process of learning, it is extremely helpful to work in the laboratory. This enables me not only to build relationships with others in my lab but also to interact with them to ask questions and obtain advice on my methods. Typically while in the lab, I write computer programs using various statistical methods, determine if they are functional, fix them when they are not, and implement them on my data to obtain results. Although I may not need to return to the lab at 2 a.m. to count bacterial cells, I must wait for long, computationally intensive programs to complete. Nonetheless, my work can be just as stressful, and has its own unique challenges.

During the summer, I can spend full days at the lab, uninterrupted by homework, classes, and office hours. Throughout the school year, however, these more extensive hours usually are not possible. In past semesters while a part of the Bustamante lab, I was not able to spend a great amount of time in the lab itself. In order to enable myself to spend more time in the lab this coming fall, I plan on taking a slightly lighter courseload. However, for those students without the appropriate level of coursework, this might not be the best option.

As a result of working in the Bustamante lab, I have learned a great deal about myself both as a person and as a researcher. In working on independent research projects, I have come across many stumbling blocks and resolved many problems on my own. It is these stumbling blocks that make even minor accomplishments rewarding and fulfilling. In the process of my research, I have learned a great deal about my field in a manner quite unlike learning from a university course. Conducting research takes a great deal of independent drive and motivation. Throughout my years in the Bustamante lab, I have truly strengthened my drive to learn more about the biological world through my own research.

Working in the field of statistical genomics and computational biology provides a great interaction between the fields of genetics and statistics. Since my interests lie in both of these areas, using statistical approaches to solve biological problems in my field of research is a perfect compromise. Students interested in genetics and computational approaches to analyzing genomic and other data should look into working in the Bustamante lab or one of the other labs in Biological Statistics and Computational Biology. Major developments are being made in my field almost daily, which makes this research very exciting.

Aside from my interests in computational biology, I love coming home from a day at the lab and unwinding while going for a run in the beautiful Ithaca area. Currently, I am training for a half marathon, which I will be running in the beginning of October. I am also involved with the College of Agriculture and Life Sciences (CALS) Ambassadors, where I participate in and plan activities for prospective CALS students. Finally, I love doing art, whether it be painting, drawing with pencils, using oil pastels, or making some form of arts and crafts.

An Interview with Carlos Bustamante

“I have always been interested in evolution, ever since I was a kid”, says Carlos Bustamante, an assistant professor in the Department of Biological Statistics and Computational Biology. In high school, his biology teacher gave him a book, The Genetic Basis of Evolutionary Change by R.C. Lewontin, author of several classic papers in molecular evolution and a man for whom Carlos was later to work. He spent three years as undergraduate in the Lewontin lab learning what was to become his profession: computational statistics in evolutionary genomics.

Prof. Bustamante’s research focuses on developing broad statistical methods to uncover evidence of natural selection from genomic data. “We work on a variety of animals”, he notes. A current project involves comparing the coding regions in the genomes of many members of the mammalian order. When I asked him what excites him most about his research, he replied, “What is it that makes us human? What is it that makes us unique?” His goal is to find the genetic changes that underlie meaningful phenotypic change in the hopes that it will elucidate the factors that makes us human. Of other interest is the genetic differences within humans that produce differences in, for example, disease susceptibility. This is a great time to be occupied in this brand of research for as Prof. Bustamante observes, “It is only in the last year that we have acquired enough data to answer these questions”.

When not doing research, Carlos spends time with his wife and two young children. He enjoys cycling, reading, listing to music, and is a big fan of going to the movies. He also likes visiting family in Venezuela and Miami, especially during winter.

Professor Carlos Bustamante

Professor Carlos Bustamante was born in Caracas, Venezuela. Prof. Bustamante loved to read about history and evolution while he was growing up. In high school, he devoted himself to Richard Lewonton and population genetics. Bustamante began work on a BA and MD in a six year program at the University of Maryland. He began working in a population genetics lab at Maryland, but then transferred to Harvard, the home of his academic hero, Richard Lewonton. At Harvard, Prof. Bustamante chose Lewonton as his undergraduate advisor and research mentor. He also decided to stay at Harvard to earn his PhD in population genetics with Dan Hartl. He began studying X-ray crystallography, working out the structure of alcohol dehydrogenase in Drosophila. Nine months into his work, another lab published the structure of the enzyme.

This defeat allowed Bustamante to ponder what questions he would ask if he had known the enzyme’s structure to begin with. He began to ask questions such as, if a gene differs between species, is that difference significant or is it due to nonselective mutation? Prof. Bustamante’s research now focuses on identifying which genomic differences between humans and chimps are evolutionarily important. He uses data collected during the human genome project to identify rapidly evolving genes in humans, which he compares to homologous chimp genes using computer algorithms.

Prof. Bustamante’s techniques are almost exclusively computational, involving computer science and math skills. Prof Bustamante, however, thinks of himself first as a biologist. “I’m a population geneticist,” he says, “not a mathematician or statistician.” He expects students who work in his lab to have interests in math and computer science, but to be interested in how these techniques can relate to biology. And, although his work does non involve wet lab experimentation, he never forgets how his research affects experiment. “Computational work really is only useful in informing experiments,” Bustamante stated. “The key is to be tied to the experimentalists.” Bustamante may keep an eye on experimental work, but he believes in the importance of computational work. “In human genetics,” he says, “there’s a hell of a lot of data. We need new ways to tackle the questions, not to get new data.” He also pointed out that computational work has its advantages for the undergraduate. “Computational projects are good for undergrads because they yield quick, publishable results.”