Where It All Began

Caltech's pioneering geobiology program, which began in the '90s, is uncovering knowledge about the forces that created our world and continue to shape it.

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Although Caltech’s focus on the once unheard-of field of geobiology—a combination of geology, geochemistry, and biology—may have given other universities and scientists pause, now the Institute is in a leading position to help explain why life exists on Earth. 

"Geobiology is really asking very systematic questions about the coevolution of Earth and life," says John Grotzinger, the Ted and Ginger Jenkins Leadership Chair for the Division of Geological and Planetary Sciences (GPS) and the Fletcher Jones Professor of Geology. "We're merging our understanding of geologic processes in the past with modern approaches in molecular microbiology and using state-of-the-art geochemistry to explore the links between these disciplines."

Already, the research the division has done has led to insights about the origin of molecular oxygen in the atmosphere and oceans, work that shows promise in the treatment of cystic fibrosis, and the naming of two Caltech geobiologists as MacArthur Fellows.

Even with 38 tenured faculty members, the division knows it cannot do everything—and so does not attempt to do so. Instead, the division leadership has cultivated a tradition of reinvention aimed at predicting and preparing for the future. In the '50s, after the death of division chair Chester Stock, a major figure in vertebrate paleontology, the GPS division sold its world-class collection of fossils (primarily composed of hundreds of thousands of specimens from the La Brea Tar Pits) to the Natural History Museum of Los Angeles County and invested the proceeds in a new program in isotope geochemistry. At the time, the move was viewed as an odd one by the American geological community, but it paid huge dividends. Within 10 years, Caltech's geochemists were positioned to take the lead in analyzing moon rocks brought back from the Apollo missions.

From left: Edward Stolper, Mel Simon, and John Abelson on a field trip in Western Australia to look for evidence of the earliest history of life on Earth. Photo courtesy Jon Grotzinger

From left: Edward Stolper, Mel Simon, and John Abelson on a field trip in Western Australia to look for evidence of the earliest history of life on Earth. Photo courtesy Jon Grotzinger

It was in this spirit of reinvention that GPS put together a faculty committee in 1994 to try to peer into the future of geosciences and determine where the division should go next. The committee was led by Peter Goldreich, now the Lee A. DuBridge Professor of Astrophysics and Planetary Physics, Emeritus. In what came to be known as the Goldreich Report, the faculty specifically identified geobiology as a field to build on for the future. (The report also identified global environmental science and solar-system astronomy as exciting opportunities for GPS, both of which the division invested in as well.)

"We use an internal review process to look hard at fields that may be emerging and which would make sense for us," Grotzinger says about the report, performed periodically. "We try to see where new science opportunities lie and how Caltech’s small size and quantitative approach to problem-solving would tease out novel approaches to solve difficult problems that require cross-disciplinary integration."

Joseph Kirschvink, at the time Caltech's only geobiology professor, recognized the potential to think of DNA not as a finished product but as an evolutionary record. And though the gene-sequencing revolution that made DNA analysis cheap and easy was still a decade away at the time of the Goldreich Report, Kirschvink became a leading voice in the push toward geobiology.

"My colleagues [at other institutions] scratched their heads and said, 'What are you doing?'" says Kirschvink, the Nico and Marilyn Van Wingen Professor of Geobiology. "But a few years later, they were scrambling to catch up."

Caltech Provost and William E. Leonhard Professor of Geology Edward Stolper, who was division chair at the time, took the Goldreich Report and committed the division to hiring several new faculty members in the broad area of geobiology—but without increasing the size of the department. Starting with Dianne Newman in 2000, Caltech has hired five faculty members who are now part of the geobiology program. In that time, the GPS division has also established geobiology options for both undergraduates and graduate students, and has attracted dozens of geobiology students.  

Right time, right place

When Stolper committed the division to building a geobiology program at Caltech, the allocation of such substantial resources was not without risk. "It takes a lot to say that five people are going to retire, let's replace them all with geobiologists," says Grotzinger. "That just doesn't happen as readily in other academic institutions." 

As a field of scientific inquiry, geobiology had existed for over a century—at least since the late 1800s, when Russian microbiologist Sergei Winogradsky first began looking at how organisms metabolize minerals. But for years, it was something of an academic fringe area.

Shortly after Caltech began investing in the field, technological advances gave geobiology a jump start—including the new genomic-sequencing methods. Completed in 2000, the first human-genome-sequencing cost about $2.7 billion and took 15 years. Today, that same analysis costs just over $1,000 and can be completed in a matter of days—and for microorganisms, the cost is far lower and can be completed in a matter of hours.

Research scientist Patricia Tavormina removes a small amount of Aliso Canyon soil from frozen samples for DNA extraction as part of a collaboration with Victoria Orphan.

Research scientist Patricia Tavormina removes a small amount of Aliso Canyon soil from frozen samples for DNA extraction as part of a collaboration with Victoria Orphan.

In broad terms, geobiology gives scientists a framework for asking questions about how life on Earth evolves, as well as how its evolution influences and is influenced by its environment. One of the first big geobiology questions tackled by Caltech researchers—the origin of oxygen in Earth's atmosphere—is an example of that, says Stolper. The geological record indicates that sometime around 2.5 billion years ago, oxygen abruptly became prevalent in the atmosphere. This event, known as the Great Oxygenation Event, fundamentally changed the planet, making complex, multicellular life possible. Geobiologists at Caltech connected this event to the evolution of photosynthetic cyanobacteria.

"Only because of life do we have significant molecular oxygen, so that influences the evolution of the planet. But also, life evolves and develops in a geological environment," Stolper says. Most of the genetic sequence encoded in our DNA evolved billions of years ago when the earth was a very different place, and the sequence itself and the biological processes it encodes can tell us something about what that place was like, he says.

Building on this approach, Caltech's Woody Fischer studied the evolution of cyanobacteria in 2016, discovering that the planet-shaping evolution of oxygenic photosynthesis evolved just this once, around 2.5 billion years ago. No other known organism duplicated the process—instead, plants, algae, and other organisms that perform oxygenic photosynthesis simply "borrowed" the technique by subsuming cyanobacteria as organelles (chloroplasts) in their cells at some point during their evolution, according to endosymbiotic theory.

Geobiology's insights are not limited to the ancient past. Molecular biologist Dianne Newman, the Gordon M. Binder/Amgen Professor of Biology and Geobiology, focuses her work on microbial stress responses, with an emphasis on how microbes generate energy and survive when oxygen is scarce. Last year, she and her colleagues used soil samples collected in the courtyard of Beckman Institute on the Caltech campus, isolating a bacterium that produces a small protein called pyocyanin demethylase (PodA). That protein inhibits the development of the glue-like biofilms that protect Pseudomonas aeruginosa, a major opportunistic pathogen found in a variety of infections, like cystic fibrosis.

Kyle Costa, a postdoctoral scholar, collecting soil in the courtyard of Beckman Institute from which Dianne Newman’s lab isolated a bacterium that disrupts biofilms.

Kyle Costa, a postdoctoral scholar, collecting soil in the courtyard of Beckman Institute from which Dianne Newman’s lab isolated a bacterium that disrupts biofilms.

Grotzinger, who was recruited into the geobiology program from MIT in 2005, has applied the principles of geobiology to his work as project scientist for the NASA/JPL Mars Science Laboratory mission’s Curiosity rover, searching for evidence of ancient environments that could have been habitable for microbes. In pursuing this theoretical question, scientists ask more sophisticated questions than whether or not water existed on the ancient martian surface. By understanding how geobiology is applied to the study of early environments on Earth, the Curiosity science team was able to ascertain the salinity, redox state, and duration of ancient martian water bodies, and whether they contained dissolved nutrients and even organic compounds.  This of course does not mean that Mars was inhabited, but in asking questions of habitability the conversation becomes more sophisticated regarding past environments, providing the basis for comparing the early environmental evolution of both planets.

Beyond gene sequencing, several techniques and technologies that are fundamental to geobiology also blossomed during the early 2000s, including the ability to take in-situ samples of microbes and analyze their genomes without having to culture them in a lab as well as the use of stable-isotope labeling that can reveal the composition of cells. Victoria Orphan, the James Irvine Professor of Environmental Science and Geobiology, has used these techniques to study microorganisms that live in deep-ocean sediment beds and consume large quantities of methane released from seeps in the ocean floor. She and her colleagues have also studied soil samples from the 2015 methane leak at Southern California Edison's Aliso Canyon storage facility to learn more about the methanotrophs—microbes that consume methane—which could one day be used to mitigate such leaks.

Research by the geobiology program has not only helped to attract outstanding students, postdoctoral scholars, and faculty members to this new field, but the work has also led to recognition from the scientific academy as a whole, including the naming of Newman and Orphan as MacArthur Fellows last fall. "Their MacArthur awards celebrate their roles in pioneering geobiology," says Grotzinger.

A little help from our friends

It is impossible to tell the story of geobiology without recognizing the instrumental contributions of the Agouron Institute, which gave the field support and helped launch geobiology at Caltech.

The Agouron Institute is a nonprofit organization formed in 1978 that owned part of a successful company, Agouron Pharmaceuticals, which saw great success through the creation of a widely used HIV protease inhibitor, Viracept. In turn, the Agouron Institute has used that success to help fund research. The institute has strong ties to Caltech: Its president and executive director is John Abelson, the George W. Beadle Professor of Biology, Emeritus; and its chairman of the board of directors is Melvin Simon, the Anne P. and Benjamin F. Biaggini Professor of Biological Sciences, Emeritus. Grotzinger and Stolper also sit on the board of directors.

Abelson served as chair of the biology division from 1989–95, succeeded by Simon, who held the position from 1995–2000. As chairs, they were members of the Institute Academic Council around the time that geobiology was gaining traction at Caltech. Also around that same time, Caltech participated in the Biological Sciences Initiative, which raised $111 million by 2001 to strengthen biological-sciences research across the Institute.

Against this backdrop, Abelson and Simon took an early interest in geobiology, starting with an assessment of the field in 2001—led by Newman. Though both Abelson and Simon made their fortunes as biologists, they viewed geology as a field in which they could make a bigger impact with their funding.

GPS graduate student Nathan Stein (at right) conducting summer research fieldwork on Turks and Caicos’s Little Ambergris Cay, along with Maya Gomes from Johns Hopkins. Photo courtesy Jon Grotzinger

GPS graduate student Nathan Stein (at right) conducting summer research fieldwork on Turks and Caicos’s Little Ambergris Cay, along with Maya Gomes from Johns Hopkins. Photo courtesy Jon Grotzinger

"There didn't seem to us to be any chance to make an impact in any of the biomedicine fields because the National Institutes of Health is so huge. It has a budget of $20 billion. It didn't seem to us that we could do anything significant there," Abelson says. "For the most part, geologists are applying to the National Science Foundation ... which is just far too small. It's hard to pay the expenses for a field trip, and so the rate at which geology could grow is confined by that. We really put money into that."

Simon says he saw a field with enormous potential to tackle big questions, such as how does carbon get sequestered? How is the atmosphere maintained? What controls the nitrogen cycle?

"It has to do with climate change, the stability of the earth, and just trying to understand where we come from," says Simon. "It's very fundamental. There's a lot we don't know, and there's a lot we can learn from this interaction between disciplines. And Caltech, for its small size, has a very powerful group of young people now."

One of the most visible contributions to the field of geobiology by the Agouron Institute has been the support of annual fieldwork. The institute established the International Geobiology Course, which unites students and faculty from biology, geology, and chemistry to learn from one another beginning with all-important course work in the field.

"GPS has always had a strong tradition of going to the field," says Grotzinger. "Every faculty member really believes in the experiential education that occurs in the field. Collecting data, and analyzing data back in the lab is essential, but it all begins in the field where you deduce the environmental context of important samples."

Originally managed by the University of Southern California, the hands-on, multidisciplinary summer course for graduate students and postdocs explores the coevolution of Earth and its biosphere, with an emphasis on how microbial processes affect the environment and leave imprints on the rock record. This year Professor of Geobiology Alex Sessions, Woody Fischer, and Victoria Orphan took over as the course directors, and so for the first time the course was taught at Caltech.

"I was actually a student in the course during its second year while I was a graduate student at Harvard," says Fischer. "It unites students from geology, biology, and chemistry, forging relationships across disciplines and allowing [students] to share tools and techniques."

Participants in the course learn from a broad team of scientists and get hands-on experience in the latest geobiological techniques in the Eastern Sierras, the USC Wrigley Marine Institute on Catalina Island, and, now, at Caltech. "It's become a legendary class," says Newman, "and many of the people now in prominent faculty positions throughout the U.S. went through that course at one point." The Agouron Institute followed up on its support of the geobiology course with a postdoctoral fellowship program that they continue to support.

From the deep past to the stars

Oxphotobacteria in microbial mats in Yellowstone. Photo courtesy Fischer Laboratory/Caltech

Oxphotobacteria in microbial mats in Yellowstone. Photo courtesy Fischer Laboratory/Caltech

Looking to the future, Grotzinger expects geobiology to become increasingly important in the study of exoplanets. He and Fischer are currently studying Mars as an analog for an Earth-like planet that might have once had oxygen in its atmosphere as a result of inorganic processes. Studying Mars and Earth simultaneously—such similar planets but with such different outcomes—has the potential to give researchers a "null hypothesis" for the evolution of life. That is, given how generally similar Earth and Mars are, studying the specific differences in the geological history of the two can help pin down why life exists on Earth today but has not been observed on Mars.  "We have this intensive culture of collaboration in geology, geochemistry, and planetary science [at Caltech]. Really what unites a large group of us is trying to figure out the early evolution of planetary systems, including our biosphere," Grotzinger says.

For her part, Newman is encouraged by the number of people around the country who are now engaged in geobiology and the number of new programs that have sprung up. Her very first doctoral student, Lora Croll, launched the Southern California Geobiology Symposium, now in its 14th year, which rotates between Caltech, USC, and UC Riverside and has generated sister conferences in the Southeast and Midwest.

In a competitive world, Stolper sees the geobiology program as another way that Caltech is distinctive. "This focus gives you an advantage—graduate students will come, postdocs will come, people on sabbatical will want to come, people who want to become faculty members in that area will come."

Geobiology is the latest success story, he says, but it's simply an example of a mind-set the Institute has always had, of letting the people do what they do best. "These programs always started with hiring somebody about whom everybody thinks, 'This person's never going to fit in because they're a chemist, they're a physicist, they're not going to be comfortable here.' And then they just take off. In the end, those people are the pioneers."

Fall 2017, FeaturesJon Nalick