David Hendrix shows his drawing of an idealized RNA secondary structure that illustrates the structural features identified by bpRNA, a tool that his lab wrote. The figure has cool colors to represent weak-pairing nucleotides, and warm colors for strong-pairing nucleotides. Photo by Gale Sumida.
For as long as he can remember, David Hendrix loved to draw, particularly cartoons and comic strips. This passion has helped his career as an associate professor at Oregon State University. But as a child, his enthusiasm sometimes got him in trouble. During the second grade, while the teacher read stories to his class, Hendrix illustrated the highlights, directly onto his desk. Fortunately, he used a pencil. One morning soon after, the teacher was waiting for him with paper towels and a bottle of surface cleaner.
Physics also captivated his imagination, especially popular representations of quantum mechanics, relativity, space-time, chaos theory, and other arcana. And he noticed how well-known scientists used illustrations to clarify the complex concepts and mathematics that explain the universe.
“Drawings are a great way to represent mathematical ideas, and there’s a parallel between the spatial reasoning that goes into both drawing and math,” Hendrix said. “The two definitely feed into one another.”
Even as his interest in science grew, Hendrix still imagined a future as an artist. Around the eighth grade, though, the realization struck him that science is not circumscribed by strict rules and rote formulas. To the contrary: A creative mind is essential for doing good science.
“It came to me that science and creativity go together. Discovering new things takes hard work, but it also requires imagination,” he said. “That’s the part that’s really exciting.”
Though Hendrix earned undergraduate degrees in math and physics and a doctorate in physics, in his postdoctoral work he explored connections between computational physics and genomics. Then he gravitated toward the emerging field of computational biology.
“My career has followed an unusual trajectory for sure,” he said. Even his position at Oregon State is unusual — it is split between computer science in the College of Engineering and biochemistry and biophysics in the College of Science.
Hendrix’s research combines multiple academic disciplines. He approaches biological sequences, structures, and systems from a computational data-science perspective. He applies a range of computational tools — including machine learning, bioinformatics, and data mining — to reveal new patterns within biological systems and DNA sequence elements that drive gene regulation and to validate known biology.
“More and more, the field is moving toward systems biology, where we try to model the organism or the tissue as a whole and sort out how genes regulate one another and work collectively to determine function,” he said.
Of particular interest to Hendrix is the use of computational mathematics to comb through vast amounts of genomic data and identify core molecular functions regulated by the circadian clock. This biological timekeeper regulates important processes like metabolism, sleep/wake cycles, memory consolidation, and neuronal health. Disruptions to the circadian rhythm, which occur with aging, can lead to age-onset diseases, including neurodegeneration.
But the genetic mechanisms of how those perturbations negatively influence health — and lifespan — are not well understood. Hendrix wants to change that by determining the role the circadian clock plays in regulating the genes that influence aging and related illnesses. He’s also looking into genetic components of how and why circadian rhythms change with age. Down the road, that understanding could lead to molecular interventions to improve circadian function and possibly defeat age-related diseases.
“First, though,” he emphasized, “we need to understand how the biology of it all works.”
To model the effects of circadian rhythm, Hendrix uses genetic material from common fruit flies, because the core molecular functions of the genes involved in circadian clocks are remarkably similar in flies and in humans. His research led to a startling finding: The 24-hour cyclical expression of specific genes that protect against age-related biological stressors either intensifies or becomes more rhythmic in older fruit flies. Conventional wisdom held that circadian rhythms weaken with age. Hendrix and his research collaborators dubbed the phenomenon late-life cycling.
“Our data support a model in which the circadian system enlists late-life cycling to mitigate the damage that results from diverse sources of cellular stress and its destructive effects on a cell’s genetic material,” Hendrix said.
For an article in The Scientist that summarizes his discovery, Hendrix was not just the source of the groundbreaking research, but of the artwork as well. He also uses illustrations to convey concepts at Oregon State’s annual STEM Academy computational biology summer camp for middle school students, where he and his students help out.
Science also touches his home life — in a way. A few years ago, Hendrix adopted Bunsen, a rescued Havanese dog, from a local shelter. The Havanese is the national dog of Cuba, from where Hendrix’s mother fled when she was 13, along with his grandmother and grandfather. The dog’s shelter name, Rubidium, didn’t seem right. (All of the dogs in the rescued group were named after elements.)
“I looked up the element and found that it had been discovered by Robert Bunsen, the guy that invented the Bunsen burner,” he said. “It was a much better name and very fitting for my dog, whose long bushy hair sometimes makes him look like a mad scientist.”