Sarah (Sally) Elgin remembers being drawn to science as a child because it offered a concrete way to understand the world around her. "I liked poking and prodding things," she says. "I wanted to figure how they worked." It's that joy in learning new things that has pushed Elgin to create a program that provides the same opportunity for her students at Washington University in St. Louis, Missouri.
Elgin does research on genomes, a field of study focused on the DNA sequence of individuals and organisms. In the past 15 years, high-throughput machines that can quickly determine an organism's DNA sequence have revolutionized the field, turning it from a lab-based field that looked at the genome one gene at a time to a computationally based field focused on large-scale data collection and analysis, a field now referred to as "genomics."
As the field became increasingly complex and data oriented in recent years, Elgin realized that her students no longer had the same sort of easy access to the science that she loved as a kid. Biologists often spend their days studying numbers on computer screens, not microscope slides or fruit flies wriggling with life.
Elgin thought she could motivate students by having them play a real role in the scientific process—not just sitting in a classroom jotting down notes—so she decided to develop a curriculum to do just that. "The goal is twofold. One is to bring more genomics into the undergraduate curriculum, most of which was written before we knew how to sequence genomes. The other goal is to do it in such a way that students are actually involved in the research project," she explains.
The result is a research-based course; students learn to work with large data sets and interact with the university's Genome Sequencing Center in transforming a genome's raw sequence data into a more polished, finished sequence and then analyze the information in that sequence. The task of sifting through mountains of data to find relevant information requires both brute force and brainpower. "Think of a genome like a copy of Moby Dick—but instead of being its usual thick volume, it's 20 times longer because someone has inserted gibberish at random places," Elgin says. "Our job is to find the sentences." Computers have become good at finding the "words" within a genome, but they often fail to construct good sentences. The students analyze the computer output and learn to use several lines of evidence to construct testable models of genes and chromosomes.
As she was developing and testing the curriculum, Elgin quickly realized there was so much interesting work to do that the class could become a nationwide effort that provided a research experience for students across the country. With the help of her colleagues at Washington University, that vision became the Genomics Education Partnership (GEP), which Elgin began in 2006 with her second HHMI professor grant. The partnership now includes more than 60 colleges and universities across the country that provide students the opportunity to work on large-scale DNA sequencing projects.
The work is challenging in its own right, but it also offers students an opportunity to move the science forward. The results of the students' work serve as a foundation for papers that Elgin and others submit for publication in research journals; two journal articles based on the scientific research have been published since 2006. The information also goes into a national database that scientists use for their own research. In addition, GEP faculty have published two papers in the science education literature to help others adopt this style of teaching.
For students, the chance to do something that matters is an incentive to do top-notch work. Currently, the project focuses on the fruit fly's dot chromosome, which may hold important information about genome organization and gene expression. "Students are so excited to do something that doesn't end up in the wastebasket at the end of the semester," says Elgin, who also serves as an advisor for HHMI's Science Education Alliance. "They've been apprentices for so long, and they're just dying for the chance to do something real."