Eco-informatics
Yale student uses ecological modeling in UD research experience program
12:08 p.m., July 31, 2015--Zach Miller spent last summer catching lizards. The rising junior at Yale University worked with a Yale doctoral candidate, kayaking between Greek islands and studying the effects of human development on the reptiles.
“It was a fun experience,” Miller said, “but this summer, I wanted to be more than a pair of hands. I wanted to be involved in developing research, and to dig deeper into asking the questions that shape a [research] study.”
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Miller, an ecology and evolutionary biology major, is one of 10 students participating in the University of Delaware College of Earth, Ocean, and Environment’s (CEOE) summer Research Experiences for Undergraduates (REU) program in marine sciences, sponsored by the National Science Foundation.
Each year, an estimated 300 students from across the country compete for the opportunity to work with CEOE faculty on rigorous independent research projects through the 10-week REU program, hosted at UD’s Hugh R. Sharp Campus in Lewes.
Since it began in 1987, the college’s REU program has hosted 268 students from 144 institutions across the United States, Puerto Rico and Guam.
Eco-informatics research
Working under advisor Adam Marsh, associate professor in CEOE’s School of Marine Science and Policy, Miller is using bioinformatics — a combination of mathematical models, biology and computer science — to study the ways organisms interact and evolve together.
Researchers use bioinformatics to manage large, complex sets of biological information. Miller was fascinated by Marsh’s work using bioinformatics to examine the human genome, research that could lead to personalized treatment for patients with terminal diseases.
Like the human genome, ecosystems are comprised of many varied parts that interact with each other in complex ways. Miller is using bioinformatics to develop a computer program that simulates organisms in real-world ecosystems.
“Essentially, I’m creating a virtual ecosystem and seeding it with virtual, individual organisms. Then I program them to interact with each other according to rules that model the way they act in real life,” Miller explained.
By changing variables in the virtual ecosystem, researchers can study how changes in real organisms’ behaviors pan out in the long term.
Colony Collapse Disorder (CCD), for example, is the sudden disappearance or fatality of populations of bees — essential pollinators — which threatens important crops from strawberries and peaches to avocados and cucumbers. With bioinformatics, researchers can simulate bee population drops or behavior changes associated with CCD to better predict the effects on vulnerable crops.
Specifically, Miller is building a general model of two species that work together — like flowers and bees, or clownfish and anemones. He aims to examine how partnering organisms in the marine environment evolve together and affect each other in the long term.
A history of excellence
Miller said he was attracted to the marine sciences REU program at UD because of its long-standing reputation and exceptional resources. The UD program will celebrate its 30th anniversary in 2017.
Interns live on campus in Lewes, where they have direct access to the shore, research facilities, faculty expertise and, at times, the University’s premier research vessels, the R/V Hugh R. Sharp and the R/V Joanne Daiber.
The program involves an independent research project, comprehensive lectures and field excursions that all prepare interns for a future in research.
UD marine sciences REU graduates have achieved substantial academic and professional success. Since 2001, some 80 percent of CEOE REU interns have gone on to graduate studies, and others to careers in education, research and development, the medical field and government agencies, including the National Park Service and the United States Department of Agriculture.
“Every year, we send at least one or two students to a national or international scientific conference, and many of our interns publish their results jointly with their advisers, or carry their research on to senior thesis programs or graduate school,” said Joanna York, REU program coordinator and research assistant professor in CEOE.
York continued, “CEOE faculty members are dedicated to helping interns accomplish these things, because we get excited about science and research, and we want students to know that this is something they can do for life.”
Miller aims to build on his summer experience at UD by pursuing a research career and delving deeper into the complexities of bioinformatics.
Article by Caren Fitzgerald
Video by Leah Dodd and Richie Raspa