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Stanford Report, October 22, 2008

Jasper Ridge: Research in the field at Stanford’s biological preserve

After the United Nations' Intergovernmental Panel on Climate Change (IPCC) was the co-recipient of the 2007 Nobel Peace Prize, Christopher Field, faculty director of Jasper Ridge Biological Preserve, director of the Carnegie Institution's Department of Global Ecology and one of the lead authors of the IPCC reports, remarked that the collective nature of the honor was significant. One person alone cannot advance the field of climate change, he said; it requires teamwork and many discoveries in many fields.

So, it is no accident that Field works at Jasper Ridge. There, natural scientists, archaeologists, computer scientists and even a few historians can be found hiking trails and sometimes tramping through the brush, setting cameras, scribbling in notebooks, squinting at computers. It's a place where scholars and scientists can wander in every sense of the word, where students from many schools and departments (and not just from Stanford) take classes, do fieldwork, complete theses and dissertations and make a difference.

"With researchers from seven departments at Stanford conducting studies at Jasper Ridge, the possibilities for new discoveries through collaboration are remarkable," said Jasper Ridge research coordinator Nona Chiariello. Conversations with undergraduate interns and honors-laden graduates confirm that Stanford students are learning that science that matters must reach broadly as it digs deep—often literally.

Through the woods

But starting up above, rather than digging down below, one of the roughly 60 ongoing projects at Jasper Ridge seeks to estimate ecosystem biomass. This involves cross-mapping data gleaned from the air using light detection and ranging (LiDAR) technology with data from hyperspectral imaging by NASA's Advanced Visible Infrared Imaging Spectrometer (AVIRIS). Using geographic information systems (GIS) software to combine these datasets, scientists and students can learn infinitely more about biomass than they could before because the data reveal precise details about the plant canopy and the foliage's biochemical composition.

But it's not all technology. One morning in summer, biology graduate student Kyla Dahlin and undergraduates Sara Maatta and Chris Fedor, majoring in civil engineering and Earth systems, respectively, set out for a wooded area of the preserve to count and measure trees and shrubs. They were appropriately dressed to discourage the omnipresent poison oak and always dangerous ticks. The previous afternoon, when the satellites of the global positioning system (GPS) are most easily accessed, Dahlin, who is supervising the other two, had used GIS and a stratified random sampling method to pick out what would be the southwest corner of a 20-by-20-meter plot. Within that plot, they would record all trees with a diameter of more than 5 centimeters, noting foliage, the percentage of the tree that is alive, presence of disease and type of canopy. In honor of a visitor, they chose a nice, clean plot, not too poison-oaky, not too steep: "the most perfect plot we've laid," Maatta said happily. She held the clipboard, jotting down the numbers that Dahlin and Fedor shouted as they measured the circumference of the trees with very cool tapes that automatically divide by pi to give the diameter.

Maatta's summer project concerns bay laurel trees that host sudden oak death; researchers are not sure the disease is present at Jasper Ridge, though they consider it likely. Fedor is interested in fire prevention and prediction in a chaparral ecosystem, a subject of concern at the preserve.

They found oak, bay, madrone and coffeeberry trees that day. One bay tree in particular would be useful for Maatta, Dahlin said, as it had five strong stems. A specimen that big for sure would show up in the aerial data in the computer. Once she locates it on the computer, reading the chemical and physical information thanks to the LiDAR, she could create a map of bay trees and then go back into the field to check that they're actually where the computer said they would be.

"That's the basics of remote sensing," Dahlin said.

After they were done with the trees, the group recorded all the shrubs of a certain size, and then the teensy understory vegetation in a 1-by-1-foot sample plot—even the poison oak.

The flight of the butterflies

GIS technology has become the instrument of choice for an array of scientific research. It can map and analyze the presence (or absence) of vegetation, as well as its composition, and help interpret the impact of human beings. It can help track invasive plant species or project backward the presence of faunal populations long gone.

One of the most famous studies to emerge from Jasper Ridge was performed in the 1960s by biologist and ecologist Paul Ehrlich. For decades, he studied the Bay checkerspot butterfly population until the creature's disappearance from the preserve in 1997. What history graduate student Jon Christensen calls the "dominant historical narrative" of the butterfly's local extinction posits that the checkerspot could not survive development. That may be true in many places around the Bay Area, but here, Christensen suggests, the butterfly may have vanished because grazing vanished. In fact, the butterfly's host and nectar plants benefit from disturbances such as grass fires or munching cows, though not from bulldozers. Christensen is now assembling a comparative history of more than 50 checkerspot populations to test the hypothesis that disturbance is a key to survival for the butterfly.

His study is part of the Spatial History Project, a larger set of digital history investigations funded by the Andrew W. Mellon Foundation and taking place at Stanford's Bill Lane Center for the West. The project, led by historian Richard White, uses GIS and other technology to analyze disparate spatial and temporal datasets.

The question arises: How did a former environmental journalist working on a doctorate in history end up studying plants and butterflies? Christensen first came to Stanford as a Knight Fellow interested in studying how conservation is measured. Conversations with White led him to realize that the best way of thinking about that subject would be to work in a historical archive. That led him to Ehrlich's papers, which led him to grazing records, Jane Stanford's letters, leases, government documents and plant databases.

"I was asking, how can thinking historically deepen our understanding of what happened to the butterflies? How would that affect how we think about reintroduction?

"It was very troubling to watch the butterfly go extinct," he said. "Now there's a real possibility that their grassland habitat could disappear. There are fewer wildflowers than before, more invasive species. Without fire and without grazing, grasslands will change. What do we value? What do we want? What will it take to have the kinds of habitats we want?"

The research group working on the butterfly project at Jasper Ridge includes two historians, several biologists, a lawyer (Barton H. "Buzz" Thompson, co-director of the Woods Institute for the Environment) and a soil scientist, who all came together through a Stanford Environmental Venture grant.

"The intersection between science and the humanities can be richly productive," Christensen said. "We make them rethink their questions, and vice versa. You can have a general-level conversation between sciences and the humanities, but it gets really meaningful here on the particular level. When we talk about particular places and species, that's when it gets really interesting."

White's Mellon grant, along with funding from the Office of the Vice Provost for Undergraduate Education, allows the group to hire undergraduate research assistants. The students spent their summer entering data, creating maps and coming up with hypotheses and conclusions regarding the butterflies.

"Decades ago, people didn't collect the sort of data we would have wanted them to," Christensen said. "People asked their own questions, not our questions. So we have to figure out how to use their data."

Among the research assistants was Carrie Denning, a 2008 graduate in history pursuing a co-terminal degree in sociology, and Gabriel Shields-Estrada, a pre-med who loves both biology and statistics. Their respective maps literally illustrate the breadth and audacity of combining the new and the old.

Denning constructed a map of the history of development and conserved areas in towns, cities and counties throughout the Bay Area since 1940. Using city records and plant databases, she hoped to reach conclusions about the reciprocal relationship between conservation and development, which will be relevant to the butterflies in testing hypotheses about their disappearance. Shields-Estrada, meanwhile, created maps depicting the butterflies' probable historical habitat, which will then be overlain with building and grazing maps.

Only a sophomore, he nonetheless zeroed in on one of the key challenges when you put humanists and scientists in the same room.

"I've challenged some assertions, saying there's not enough data," he said. "We have different ideas about exactitude."

His realization that humanists and scientists have different ways of doing things, and that they must work together, is one of the most valuable aspects of collaboration at Jasper Ridge, Christensen said.

"The staff there has been incredibly interested and supportive of our historical research," he said. "While they are managing dozens of research sites on the preserve, producing results that regularly end up in top science journals, they have given just as much care and attention and thought to our research. That is truly remarkable."

Vanishing birds

The checkerspot butterflies are not the only species to go missing.

Bill Love Anderegg, '08, did his honors thesis on wetland bird populations at Jasper Ridge. He repeated a survey conducted in 1971 that showed that Jasper Ridge was home to the highest known breeding density of land birds in the United States. Thirty-five years later, Anderegg tested the effects of development and climate change.

He found "significant" declines in avian diversity. Some species were below Anderegg's detection threshold, and one has nearly disappeared. Other species that don't seem to mind humans have increased. His honors thesis, which earned him a Firestone Medal for Excellence in Undergraduate Research, concluded that more habitat protection and better development planning along streams is imperative.

Anderegg, who is now in Stanford's biology doctoral program, never intended to be a scientist. He started off as an English major, one who particularly loved creative writing. A semester abroad made him rethink his priorities, and he returned from Spain a human biology major.

"My interest in multidisciplinarity grew out of the thesis," he said last spring, a few days before graduation and then a summer trip to Africa. "I expected to just be doing birds. But more and more I was looking into human interactions. I found myself talking to old birders, looking at their data. I asked them, how did you get your data, how did you count the birds? One old guy—he did his dissertation with Ehrlich in the sixties, I think—sent me his old field notes."

As with the longitudinal study of butterflies, the ornithology work extended far beyond the birds. Anderegg's adviser was Terry Root, a biologist, expert on global warming and another IPCC author. "So that led me to climate change," Anderegg said. "And Trevor Hebert," the GIS manager for Jasper Ridge, "gave me aerial photos and GIS data, so I could track changes in land use and map it against bird habitation."

Soil carbon dynamics

Along with Anderegg, Darcy McRose also won a Firestone award last year for her honors thesis at Jasper Ridge. She investigated the amount of carbon stored in the soil in the well-known Jasper Ridge global change experiment, which has been running for 10 years. It keeps track of how different levels of carbon dioxide, nitrogen, heat and precipitation affect photosynthesis and other ecosystem properties.

McRose used six years' worth of data and found there was no observable carbon content change under a higher CO2 environment.

An Earth systems major, McRose did her thesis in the Goldman Honors Program, run by the Woods Institute.

"So almost by definition it was multidisciplinary," she said. Rosamond Naylor and Walter Falcon, directors of the program, "forced me to go from the science to a more global perspective."

Her undergraduate journey was as unexpected as that of her colleagues.

"I started off being interested in community organizing. Then I took an anthropology class that tied together all my interests and showed me I could do the social things through science. It was kind of scary to make that switch."

The class in question was Conservation and Evolutionary Ecology, taught by Doug Bird. It addresses the interaction between people and their environment, which involves many human decisions, all with material consequences. Studying those decisions thus illuminates environmental problems.

"I hope the kind of work I do provides strategies for thinking and acting: What will it actually take to solve perpetual problems of collective action when individuals face very real consequences of their decisions about survival and reproduction?" Bird said, reflecting on McRose's journey from community organizing to anthropology to science. "We need to understand why human resource use varies under particular circumstances. This just can't be done along a unidisciplinary front. And, I'd argue, that's what makes the problems and approach so interesting to students like Darcy, who are interested in both action and the environment."

McRose first was a human biology major (her adviser was Carol Boggs, a butterfly colleague of Christensen's) and ended up in Earth systems, where she is now pursuing a co-terminal degree.

Another Earth systems student working at Jasper Ridge is Briana Swette. She, too, is conducting her project at the site of the climate change experiment. The experiment comprises more than 100 plots in which tests are demonstrating how a typical grassland ecosystem responds to environmental changes. Her objective is to quantify the growth of new roots in the plots, using a tiny rotating scanner inserted into tubes beneath the soil.

And she, too, never expected to be where she is.

"I don't think of myself as a scientist," she said. "Originally I wanted to be a journalist. But instead, I'll study what I wanted to write about," which is agriculture, food and the environment. She is studying life sciences in Norway this fall, a country where, she said, farmers are "very educated."

Computers and cognition

Eric Abelson has always been tracking animals: when he was a kid, when he worked as an audio engineer in Hollywood and when he was in community college. Life took an unexpected professional turn when he went to the University of California-Berkeley and began studying animal cognition (tracking all the while). Now he's a biology doctoral student at Stanford. Still tracking, of course, much of it at Jasper Ridge.

Abelson uses camera traps, along with tracks, to better understand what wild animals are doing when no one is watching.

"Looking at tracks you can collect many types of information," he said. "What kind of animal left them? How long ago were they made? In which direction was the animal moving? Then there are what we call gait patterns, which are more difficult to read; they include things like how the animal is moving and why he stopped. Gait patterns create something like a video reconstruction in the mind of the tracker of exactly what the animal did, even though hours or even days may have passed. When I look at tracks I see patterns and stories unfolding, and sometimes they are amazing."

But, he said, it is essential to double-check by using cameras. "Trackers say a tracker alone is always right," he pointed out.

When Abelson arrived at Stanford, biologist Rodolfo Dirzo told him he was puzzled at the apparent scarcity of gray foxes at Jasper Ridge. Dirzo had cameras installed, but the foxes weren't showing up as often as one might expect. So in addition to using TrailMaster monitors, which make a noise and emit a flash as they snap photographs when animals cross an infrared beam, Abelson set up Reconyx cameras, which are invisible, silent and scentless to the animal. These cameras respond to both heat and motion, taking a speedy five frames per second. Comparing images from the two devices should yield information about how the TrailMaster is affecting animals' behavior and visitation patterns.

While scientists sleep, the cameras keep working. As a result, Abelson had half a million images and was in dire need of technological assistance. He had a tech background himself, but his data was getting out of hand. It turned out that the Computer Science Department had grant money available and asked the Biology Department if it might need some gadgetry. The result was the development of PhotoSpread, a sort of advanced spreadsheet software program that will allow Abelson and his undergraduate assistants to grab bunches of images and tag them with metadata regarding fauna, temperature, activity, etc. The tagging time should be reduced to manageable levels, and the researchers will be able to test their hypotheses about animal behavior.

PhotoSpread is the most recent example of how computer scientists can assist natural scientists without venturing near the poison oak. Another tool Abelson and others use is CyberTracker, an image-based system on handheld computers that was developed to harness the traditional tracking knowledge of Bushmen without a written language. Along the same lines is ButterflyNet, software developed by Ron Yeh, who earned his PhD in computer science at Stanford this year. The software enables researchers in the field to use a pen, marketed under various names, whose script is linked to computing capabilities.

As with PhotoSpread, the genesis of the project was money in search of a useful project. The Human Computer Interaction group, led by Scott Klemmer, contacted Dirzo, who was enthusiastic. Lots of brainstorming (and lots of dumb ideas, Yeh said) and prototyping ensued, resulting in a pen that was tested at Jasper Ridge.

"I loved working at Jasper Ridge," Yeh said. "The students there were very receptive. They thought it was cool. And we learned a lot."

The experiences, Abelson said, point to the different ways in which computer and field scientists work, and how each approach benefits the other. In computer science, you come up with an idea and test it to see if it works. In biology, you identify a need and then seek out a tool.

Abelson is hoping to work with Stanford's neurobiologists in the coming years.

"I want to understand better how animals move through anthropogenic landscapes. Can we better predict what they will do as they come under increasing human-created pressures?" he asked.

He pointed to a case in which scientists figured out why sea turtles emerged from their eggs, walked from the beach into town and there died rather than head to the ocean. It turned out the town lights were drawing them; once the frequency was shifted to longer wavelengths, the turtles went back to their old habits. But scientists can't yet stop deer from crossing busy roads without building fences. If dolphins create permeable barriers with bubbles to drive their prey, why couldn't we also exploit animals' innate predispositions to make them go in directions that would protect them and humans?

"What I want to do has really never been done before, and maybe it's impossible," Abelson said. But just in case it's not, he's spending lots of time at Jasper Ridge tracking animals, taking pictures and avoiding the poison oak.

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