Science out of the big box
March 21, 2016
The story of life on Earth is a story that spans some four billion years. It's written in every desert and jungle, mountain and ocean; carried by wind and water, sunlight and molten rock. From basic chemical reactions to the 100 trillion neural connections within the human brain, it is as overwhelmingly complex as it is important.
And it's a story being told at the University of Chicago by researchers within the Darwinian Sciences Cluster. Drawing from the Departments of Ecology & Evolution and Organismal Biology & Anatomy, as well as the unique interdisciplinary and multi-institutional Committee on Evolutionary Biology, this community represents every graduate division of the university and beyond, including Argonne National Laboratory, the Field Museum, Lincoln Park and Brookfield Zoos, the Chicago Botanic Garden and Morton Arboretum.
Evolutionary scientists at UChicago are MacArthur Geniuses and Emmy Award winners, National Academy medalists and Popular Science luminaries. They are even world leaders in sustainable architecture. For good reason, US News & World Report ranked UChicago's graduate programs in Paleontology first in the country, and Ecology & Evolution fourth.
UChicago faculty and students have scoured deserts to reveal the largest carnivorous dinosaur to ever live, and dug into frigid tundra to unearth the first fish to walk on land; delved deep into geological formations in China for shrew-sized forerunners to modern mammals, and fossil beds in the U.S. for 300 million-year-old shark nurseries; explored lush, vibrant bacterial environments on plants and in our own homes; analyzed ancient flora and fauna to theorize how to survive mass extinctions; spent long hours in laboratories in Hyde Park, resurrecting billion-year-old proteins and illuminating the genetic secrets of butterflies, octopuses, woolly mammoths and of course humans. That's just the start.
It might be surprising then, that despite all these achievements and accolades, sometimes the science that gets done requires some... improvisation. In a story published in the recent issue of Medicine on the Midway, science writer Kevin Jiang explores how two current and one recently graduated student from the Committee on Evolutionary Biology are making their own contributions to the study of the story of life using tools they designed and built by hand (or purchased from Walmart).
CEB graduate student Courtney Stepien in her office in the Zoology building (Photo by Joel Wintermantle)
Every summer, the remote community of Sekiu, Washington swells with transient visitors drawn by the natural beauty of the Pacific Northwest and easy access to ocean waters. Tourism, however, is the last thing occupying the mind of Courtney Stepien, sixth-year graduate student in the Committee on Evolutionary Biology, as she carefully makes her way through the few remaining bare patches of concrete floor in her summer landlord's two-car garage. Strewn across the ground is an assortment of plastic buckets, chest coolers and dozens of small jars. Most are filled with water. A hodgepodge of equipment - wires, cans, boxes, tubes - occupies every shelf, table and chair. The room hums with the sound of electric motors and pumps.
Stepien carries with her several different species of seaweeds, a glistening dark green and brown bounty gathered from nearby waters of the Strait of Juan de Fuca, the channel that separates Olympic Peninsula from Canada. She places them into labeled plastic jars and transfers them onto a rack slowly tilting back and forth inside the largest chest cooler. There, the seaweeds bask under a network of powerful lights while bathed in seawater kept at a constant, frigid temperature by aquarium cooling pumps.
To gather data for her study on how changing climate affects the composition of ocean communities, Stepien will check each of the 36 jars every few hours for the next 24 hours. She'll measure what form of carbon the seaweeds consume and how fast they do so, and repeat this process with freshly harvested seaweeds, again and again, over several weeks - almost entirely through the use of equipment she designed and built by hand.
"Usually you would use a commercial environmental chamber with very specific light and temperature controls to do this kind of experiment," Stepien said. "But we don't have those kinds of facilities in the field. I had to build something to mimic it as best I could. So I went to Walmart and got the biggest tailgating beer cooler I could find and went from there. The garage was my lab for the summer."
The University of Chicago has a long, storied history of world-leading research, much of it built on some of the most state-of-the-art technologies ever developed. But sophisticated research doesn't always require expensive technology. Graduate students in the Committee on Evolutionary Biology (CEB), a unique interdepartmental and inter-institutional training program dedicated to the study of life on earth, know this better than most. For them, constructing their own tools and experimental rigs - from materials purchased in big box stores or local markets, improvised for uses that manufacturers could never have possibly imagined - is simply how science gets done.
Without a healthy dose of ingenuity, Stepien's field experiments in the Pacific Northwest, guided by her advisor Cathy Pfister, PhD, professor in the Department of Ecology and Evolution, could not be conducted. Commercial environmental chambers come with a steep price tag, and finding ones that fit her scientific needs - the ability to handle seawater, to hold and agitate large samples, to set up in a remote location - was unfeasible. Building her own chamber, to the exact specifications she needed, was the only option that made sense.
"If we had unlimited funds I would just buy a whole lab setup right near the field site; we don't, so we have to be creative," Stepien said. "I think it's fairly typical for anyone who does field work in ecology. We've all made something with duct tape and a painter's bucket for our experiments."
Lab or laundry room? Why not both?
Often, however, just finding the right materials to begin construction can be its own adventure. This past spring, on the other side of the world, third-year CEB graduate student Shane DuBay faced a problem: there is no Home Depot in Chengdu, China. And to do what he had traveled thousands of miles to do, he needed large-diameter PVC pipe. A large construction market on the outskirts of the city, where PVC could be special ordered and cut, turned out to be the solution. With the right materials in hand, DuBay set about his ambitious project - constructing hypobaric chambers to house mountain birds.
Migration is typically thought of as a long distance phenomenon, but many bird species native to mountain ranges undergo altitudinal migration, breeding at upper elevations in the summer and wintering downslope. As such, individual birds must adapt to dramatic changes in temperature and atmospheric pressure every year. However, adaptations to high elevations, such as hemoglobin that binds tightly to oxygen, can be detrimental traits at low elevations.
"How species mitigate the stress of this switch and whether there is a cost to being physiologically flexible are not well understood," DuBay said. "These are important evolutionary questions, and birds that inhabit the eastern Himalayas are an exceptional model to explore them."
Shane DuBay, with his hyperbaric chamber (Photo by Andrew Nelles)
With the help of his advisors Trevor Price, PhD, professor in the Department of Ecology and Evolution, who has spent his career studying Himalayan birds, and John Bates, PhD, associate curator at the Field Museum, DuBay connected with collaborators at Sichuan University in southwestern China. There, in a small room in the Natural History Museum, they constructed a bespoke laboratory.
Newly acquired PVC sections served as the frame for chambers that mimicked the pressure and temperature at altitude or at sea level. DuBay drilled holes into the sections, attached pressure relief valves, and hooked them up to medical-grade vacuum pumps purchased from another Chinese market. Suction kept plexiglass sheets firmly attached to top and bottom of the pipe sections, and voila - hypobaric chambers with flowing fresh air that simulated the low air pressure at 13,000 feet. For temperature control, DuBay and his collaborators purchased a drink refrigerator, the kind found at convenience stores, large enough to hold nine chambers. The rest of the chambers sat on the floor, with a space heater nearby to keep them warm.
Setup complete, the team spent the next month and a half at a meteorological station on the lower slopes of Mt. Gongga, a 23,000-foot peak a few hours drive from Chengdu. While performing a variety of other experiments, they captured specimens of two closely related species of the Tarsiger bush robin - one that undergoes altitudinal migration, and one that does not.
The birds were brought back to the makeshift lab and each housed for two weeks under one of four conditions (low or normal pressure paired with cold or warm temperature). DuBay then performed a suite of physiological measurements to characterize gene expression, blood chemistry, metabolic capacity and more. By controlling both temperature and pressure, and studying two closely related species with different migration patterns, he hopes to tease apart the relative and combined effects of the two conditions.
"We think that these birds must have some ability to fine-tune their biochemistry and inner physiology in response to their local environment, and constructing these chambers was the best way to shed light on what those adaptations are, at least with the budget I had," DuBay said. "I'm going back next spring to finish data collection. If had more money? I'd buy a climate-controlled room. That fridge is a huge pain to work with."
DuBay and a colleague on the lower slopes of Mt. Gongga.
All that glitters
It's not always remote or exotic field work that forces the exercise of creative resourcefulness, however. To Lincoln Park Zoo from Hyde Park is a 20-minute drive, or an hour or so via CTA. Recent CEB graduate Christopher Schell, PhD'15, knows the trip well. Every year, millions visit the zoo to view sea lions and zebras and other exotic animals, but few are aware of its less prominent inhabitants, such as research-designated coyotes from the USDA (yes, that USDA).
Coyotes are remarkable survivors. They inhabit almost the entirety of North and Central America, from Alaska to Panama - a range that covers many major cities, including Chicago. Recent efforts, such as by the Urban Wildlife Institute at Lincoln Park Zoo, are beginning to show that cities represent a unique ecological system, with barriers to survival that can drive the evolutionary divergence of species - including the coyote. "My main interest is in how urbanization influences behavioral, hormonal, and even to a certain extent genetic patterns of urban versus rural populations of coyote," Schell said. "But to build a base of knowledge and develop the necessary techniques to study these traits, I had to start with captive animals."
Christopher J. Schell, PhD, at the Lincoln Park Zoo (Photo by Robert Kozloff)
To accomplish this, he had to improvise. Under the guidance of advisors Jill Mateo, PhD, associate professor of comparative human development, and Rachel Santymire, PhD, director of the Davee Center for Epidemiology and Endocrinology at Lincoln Park Zoo, Schell spent hundreds of hours observing coyote behaviors - particularly, the trait of boldness, which has been hypothesized to be important for success in urban environments. Among his experiments were novel object tests, which involved exposing the animals to completely new things. Colorful dog toys purchased from a local Petsmart turned out to be the perfect tool for this test. To develop an objective, repeatable paradigm to evaluate coyote behaviors, he created his own version of the Volhard Puppy Aptitude Test, a checklist of actions normally used to assess the suitability of dogs for service or police work.
"I got very good at looking for things that normally go unnoticed: their gaze, their posture, their breathing, what they do with novel objects, and more," Schell said. "Our data are starting to show that instead of calling it boldness, we should probably be calling it tolerance or avoidance for novel objects."
Of particular interest to Schell and his advisors are stress hormones, which drive the "fight-or-flight" response in all animals. Parental stress has been shown to have lasting effects on offspring - a possible route that shapes differences between urban and rural animals. They tested this by exposing a breeding pair to a minor stressor (foreign scent lures) during pregnancy, and then measuring hormone levels in both parents and their pups over time.
To avoid additional stress caused by drawing blood, they used hair and fecal samples. Shaved hair was easy enough to track, but figuring out which animal left which fecal sample wasn't quite as simple - they couldn't be watched at all times, after all. The solution? Glitter. By spiking treats with common, non-toxic glitter, determining which animal deposited which sample could be achieved by just looking at the color of the sparkling flakes contained within.
Detailed in his recently defended dissertation, Schell found that parental reproductive and stress hormones, particularly when they spike late in pregnancy, correlate with differences in traits such as personality and hormone levels among pups - correlations that endure as the pups become adults.
With the support of an NSF postdoctoral fellowship, he is now taking the techniques, insights and finely honed improvisational skills generated through his captive studies and applying them to study urban coyote populations in Denver and Los Angeles.
"It's amazing what you can learn with some dog toys and glitter," Schell laughs. "And it's really cost effective too."
Photo courtesy USDA