Merging big data and marine biology

Junior Ashna Sethi found an opportunity to delve into one of her passions this summer with paleobiologist Lauren Sallan’s lab in the School of Arts & Sciences.

Growing up watching nature programs on the Discovery Channel and BBC during her childhood in Delhi, India, Ashna Sethi, a junior at Penn, fell in love with marine biology. “It’s something I always wanted to get experience doing myself,” she says.

Student Ashna Sethi
Ashna Sethi, a junior from Delhi, scoured various sources to build a fossil-fish databased this summer.

Before the pandemic hit, she had hoped pursue hands-on research at a field station, but closures precluded that possibility, so in the spring she began looking for virtual opportunities. Scanning the list of Penn Undergraduate Research Mentoring (PURM) summer internship project descriptions, Sethi says, “there was just one in marine biology, so I knew I had to apply.”

While the summer didn’t find Sethi in a wetsuit or along a coastline, she did quench her thirst to learn more about the sea and its creatures, even if most of the sea life she encountered this summer lived millions of years ago.

Her internship, conducted under the mentorship of paleobiologist Lauren Sallan in the School of Arts & Sciences, focused on fish that lived during the Cretaceous Period, from 145 million to 65 million years ago. And while most of the work played out in internet search engines and spreadsheets, she says “the possibilities that the work opens up are really fascinating.”

A fossil revolution

Sethi, a biology and psychology double major, had had experience working in labs before, and doing a little statistics work, but this summer was the first time she got a good handle on what it means to create big data. “I didn’t realize how much effort can go into one neat, clean graph,” she says.

As a member of Sallan’s large lab group, she became part of its efforts to employ massive datasets to answer overarching questions in evolution and ecology. Sallan, the Martin Meyerson Assistant Professor in Interdisciplinary Studies, has amassed new collections of fossil-fish data to probe mysteries, from characterizing the triggers of mass extinction events to pinpointing the drivers of spikes in species biodiversity. Such investigations have the power to shed light on modern ecological trends as well.

This summer, Sethi and others in the lab were tasked with growing one such dataset to address the question of whether fish show the same degree of evolutionary turnover, that is, diversification, expansion, and collapse, as other vertebrate groups. The group focused in part on what’s known as the Mesozoic Marine Revolution, a time period starting around 200 million years ago and continuing to the end of the Cretaceous, during which diversity in fishes and reef species expanded exponentially.

Narrowing in on fish diversity in the Cretaceous, Sethi launched countless Google scholar searches to look for fish fossil records that the lab hadn’t yet classified. When she exhausted that resource, she examined other publicly available records, including library books, journal articles, and databases with thousands of entries. She also proactively reached out to museum curators to get access to digital collections that weren’t easily accessible.

Taking her finds, which could include the ancient fish’s taxonomic classification and where it was found, she massively increased the known number of fossil-fish species and appearances beyond those found in a community-wide paleobiologic database updated since 1999.

“The idea was we left almost no stone unturned,” Sethi says. “And when you would get stuck you could reach out to the lab group saying ‘Help, I can’t find any more entries,’ and we would brainstorm together to find new approaches.”

Collaboration online

Help came in the form of frequent interactions with Sallan and the rest of the 18-person lab. On Mondays, group members would present a short slide or two in an informal lab meeting. “The group ranged from rising sophomores all the up to Ph.D. students,” Sethi says. “There was a wide range of comfort with the material, but we were invited to make slides about either our progress, something we came across of interest in the field, or even a little fact about our lives or what we had done the previous weekend.” 

Powerpoint slide with a picture of an ancient fish giving information about it
During weekly lab meetings, Sethi and other lab members shared information about their work or general items of interest related to fish or paleobiology. 

On Fridays, the group would get together once again for a general check-in about any progress or problems students wanted feedback on. Each week Sallan also gave a short presentation on a “dead fish of the week,” a fun way to enhance the group’s familiarity with the vast world of fossil-fish biodiversity.

Sallan takes an interdisciplinary approach to her research and encourages her students to do the same. Some of her trainees come from physics backgrounds, while others have strength in art or photography—skills that aid their reconstructions of ancient fish. Seeing such diversity in interest areas and backgrounds was heartening to Sethi, who hasn’t yet narrowed down which area of science she eventually wants to pursue. “I’m currently leaning toward clinical psychology but also like hardcore biology like genetics and immunology,” she says. “Being in this lab has given me more insight into what biology can be.”

The skills she picked this summer, including knowledge of new statistical analysis and coding methods she gained through free Coursera offerings discovered by other lab members, should serve her well no matter which scientific path she follows.

“No matter what field you work in, if you want to get a Ph.D. you’ll always have lots of data to deal with,” Sethi says. “To not feel daunted by that is a really big thing; that’s now an obstacle I can do away with.”

The Penn Undergraduate Research Mentoring (PURM) program, administered by Penn’s Center for Undergraduate Research & Fellowships, provides students completing their first or second undergraduate year paid opportunities to spend a summer conducting 10-week research projects with Penn faculty. Since its inception in 2007, PURM has funded more than 800 Penn faculty members to provide more than 1,000 undergraduates with cutting-edge research experiences.