Tufts Biologists Find Virtual Ways to Study the Outdoors

Faculty have transformed Experiments in Ecology amid COVID-19 but continue to provide students with a window into the natural world
When an ecology course had to shift to remote labs, faculty got creative. Botanist George Ellmore sent students kits with seeds. "We’re saying: This is the system you will observe in nature. You tell us what questions you want to ask." Photo: Ingimage
When an ecology course had to shift to remote labs, faculty got creative. Botanist George Ellmore sent students kits with seeds. "We’re saying: This is the system you will observe in nature. You tell us what questions you want to ask." Photo: Ingimage
October 5, 2020

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Part of an occasional series of stories on how faculty in the School of Arts and Sciences and the School of Engineering are adapting to virtual and hybrid formats in the time of COVID-19. Read an earlier story about the School of Arts and Sciences here.

Biologists Philip Starks, George Ellmore, and Elizabeth Crone have worked together in recent years to make sure Experiments in Ecology, a longstanding course that draws on a rotating collection of engaged researchers, gets students outdoors.

The lab course gives students a window onto the natural world, specifically onto amazing strategies for animal and plant survival and abundance—from honey bee hives to old growth forests. Most importantly, the course, divided into three units, give students first-hand experience with the rigors of methodology—including thoughtful analysis—that underpin all scientific research.

“Our course has always been a heavy research and a heavy science communication course,” said Starks, associate professor, and who currently directs Experiments in Ecology. “We want students generating hypotheses, collecting and interpreting data, making group presentations publicly, and then, finally, individually writing a complete report. They should come away with a clear understanding of what it means to be a scientist.”

This fall, faculty are trying new paths to achieve that understanding as they adapt to academic constrictions brought by the COVID-19 health crisis. Tufts has put strict safety protocols in place, and labs and field trips are on hold.

That presented a conundrum, said Ellmore, botanist and associate professor. “We always made sure that we were in close contact with nature. At first, we thought, what are we going to do if we can’t do that? Then I said, why don't we reverse it? Instead of us telling the students what to do, why not let the students decide what experiments they want to run once we got them started? It took about a month of focusing to figure it out, but in the end we were all confident it would work.”

The faculty’s creative responses, as described below, are threaded together by a cerebral pursuit of knowledge that is highly self-motivated, and Starks hopes that focus continues to make Experiments in Ecology eye-opening and memorable.

“We really want the students to feel some creative influence in the choices they make,” he said, “and feel the joy of discovering something and sharing that information with others. That is a uniquely human experience.” 

“Flipping” the Study of Heat-Shielding Honey Bees

Starks, a behavioral ecologist, traditionally takes his students to observation hives in a small enclosure on the Medford/Somerville campus to show them the bees in action. Specifically relevant to research in the Starks Lab is how honey bees thermoregulate the comb; elevating or decreasing temperature when conditions differ from optimal brood-rearing conditions. 

“Our course has always been a heavy research and science communication course,” said Philip Starks, associate professor. "Students should come away with a clear understanding of what it means to be a scientist.” Photo: Jodi Hilton for Tufts UniversityThis year, given physical distancing requirements, the enclosed space is off limits, so he has flipped the classroom. Instead, students working in their dorm rooms or apartments near campus—or from home—will devise their own experiments that Starks and his teaching assistants will conduct for them.

Their questions will pivot around thermoregulation and involve selectively heating the hives with electric pads or theater lights. Teaching assistant and PhD candidate Isaac Weinberg in the Starks Lab will capture bee behavior on a GoPro HERO7 camera and then share photos and video files with students. Students are then responsible for extracting and interpreting their data, writing up their findings, and then presenting their conclusions to the class in Zoom presentations. 

While the flipped classroom requires more coordinated logistics, it introduces an important shift in how students approach the work, said Starks. Students are now essentially, “the lab PI,” or principal investigator, said Starks. “They aren’t following instructions we’ve already set out for them—they generate the ideas themselves, just as a professional scientist would do,” he said. “I think that will only make the experiment that much more meaningful.”

Sprouting Seeds—and Questions

Ellmore, whose research and teaching interests take deep dives into plant anatomy and morphology, would typically launch his unit with a three-mile walk through the old growth forest of the Charles W. Ward Reservation in Andover. That is followed by using taxonomic keys to identify the variety of trees found on the Medford-Somerville campus. Then students circle back to ecology of old growth woods, this time measuring the chemical compounds that accumulate in tree species that compete for survival in the dense understory, like witch hazel, spicebush, and sassafras.

George Ellmore included kale and radish seeds, two types of beans, potting soil, and a ruler in kits he sent to students for the class. Photo: Alonso Nichols/Tufts UniversityCOVID-19, he said, has inspired him to modify the unit by looking at forest ecology in the very earliest stages of tree growth: germination of the seed. He’s asking students to look at the first leaves produced by plants—known as cotyledons. These “seed leaves” are critical to plant survival because they can access the stored nutrients in the seed and thus feed the plant until the true leaves sprout and begin to generate nutrients via photosynthesis.

In individual kits he developed this summer, he included kale and radish seeds, as well as two types of beans, potting soil, and a ruler. The vegetable seeds will send up photosynthetic cotyledons—they require sunlight to make food essential to continued growth. Legume cotyledons, thick and plump with food reserves, are already packed and ready to go. 

What students will do is, in essence, mimic the harsh reality of nature. In nature, cotyledons are vulnerable to attack by insects, herbivores, and soil microbes, putting the survival of the plant at risk. Students will imitate that impact by removing cotyledons from three-day old seedlings to measure how those seedlings, once deprived of their energy source, grow compared to the growth of intact seedlings.

What’s most important, he stressed, is that the students learn the value of testing an idea. Pandemic or not, it’s critical that Tufts guide young scientists through opportunities that encourage them to be independent, creative, and critical thinkers.

“We’re saying: This is the system you will observe in nature,” he said. “Now, you tell us what kind of questions you want to ask and how you want to ask them. We never know what the answers to these experiments are—it’s all about discovery.”

Computer Modeling for Cause and Effect

In a normal academic year, biology professor Elizabeth Crone, and head of the Crone Lab (focused on population biology) would be asking undergraduates to take a close look at the green hill known as the Presidents’ Lawn, which was essentially their lab for observing how squirrels respond to red and white acorns.

Squirrels, it turns out, are choosy. They find the red oak acorns bitter—they are richer in tannins—and tend to discard them. White acorns, lower in tannins, are more likely to be eaten.

Elizabeth Crone's students will use software that allows them to simulate disease ecology and epidemiology. “Biology is increasingly becoming a quantitative science where you have to understand applied math and statistics, and in that sense, it’s a cool addition to the course." Photo: Alonso Nichols/Tufts UniversityThis fall, Crone shows students a different way of studying population dynamics through epidemiology mathematical modeling. “Biology is increasingly becoming a quantitative science where you have to understand applied math and statistics, and in that sense, it’s a cool addition to the course,” she said.

Her students, with support from teaching assistant and PhD candidate Brendan Carson, will learn and use software that allows them to simulate disease ecology and epidemiology. Students will design scenarios connected to two studies. One looks at how badger social networks correlate with tuberculosis infection. Another focused on African buffalo infected with parasitic worms and also exposed to bovine tuberculosis, evaluating the intersection of TB treatment with animal death and pathogen resistance and persistence. The lead author of the African buffalo study, Vanessa Ezenwa, a professor at University of Georgia, was a colleague-friend from their days together at the University of Montana.

“I enjoy using Experiments in Ecology as a way to step back from my main research and channel some of my friends' most exciting research systems,” said Crone, whose own research is on butterflies, which are mostly active when classes are not in session.

These case studies will be springboards for understanding cause an effect. “What happens if we change just one parameter? What happens if you intervene early or later?” she said. “What happens if susceptible animals interact with each other—will that change the transmission rate? Will it lead to a bad outcome? Modeling helps us understand all the possible ways that diseases may spread, recede, or be eradicated.”

Given that students themselves are living through a global pandemic, she agreed she’s teaching a topic with implications well beyond these two studies. Epidemics impact humans too, and she’s capitalizing on that relevance by assigning additional reading: a special report published in Nature about simulations driving the world’s response to COVID-19.

“I’m sad to give up the squirrels this fall, but I think we’ll be digging into a really interesting and timely topic,” she said. “We have been given an unexpected opportunity to think about the pandemic as ecologists and understand the critical role modeling can play. Ultimately, I hope we instill in our students a love of scientific inquiry that will serve them well, no matter what they decide to do.” 

Laura Ferguson can be reached at laura.ferguson@tufts.edu.