Dr. Jonathan Eisen is a professor at the Genome Center at the University of California, Davis, where he holds appointments in the Department of Evolution and Ecology and the Department of Medical Microbiology and Immunology.
A grantee through the Moore Foundation’s Science Program, Eisen’s research involves investigating communities of microbes, and he is widely known as a leading authority on studies of microbes based on DNA sequencing with more than 300 papers on this topic. He is also a vocal advocate for open-access scientific publication and scholarly communication.
What inspired you to become a scientist?
My parents were both scientists, so it’s not random that I ended up being a scientist. They both worked at the National Institutes for Health. My grandfather was a physicist and was the real inspiration—he bought my brother and me our first home computer, with four kilobytes of memory from Radio Shack, and we were so excited when we upgraded to 16K. We were very scientific in our family discussion. That shelf there (Eisen points to his office bookshelf)—that was key. I was a birder. And my grandmother and mom and I used to go out, even when I was eight or nine, just to go bird watching. I think I got really into natural history from that, and that’s basically what I do now with microbes.
I just had this amazing appreciation of the natural world, but when I went to college at Harvard, I was an East Asian studies major for 1.5 years. I somehow got it into my head, I guess this was all the rage in the 80s, that Japan was the place to go, not sure why—I don’t really plan much of anything. I took an evolution course from Stephen Jay Gould, for non-science majors. I had read all of his books, and was into evolution, and that class basically tilted me toward science. I dropped all my Japanese classes and switched to a biology major.
And then I was like, what am I going to do? I’m not going to take classes, who cares about classes? I got a job in the summer at this field biology station in Colorado called RMBL, the Rocky Mountain Biology Laboratory, which was unbelievable—some of the top ecologists on the planet go there. I worked on hummingbird physiology and that was my first taste of field biology research. I’ve done lots of other things since—it was almost a random walk to get into microbes, but I loved doing research in ecology and evolution. I worked with Colleen Cavanaugh, who studied organisms living in symbiosis with tubeworms and clams living in hydrothermal vents, and I was captivated by microbes ever since.
What areas/topics in science are you most interested in addressing?
From a research point of view, most of what I work on is the natural history and function of microbes and communities/ecosystems of microbes that live on a host (microbiome). I like this area because it’s really unknown and it’s ecology in a captive environment which is very unusual compared to the ecology I was used to. There’s a lot of interesting interplay between evolution and ecology and function: how do these organisms interact with each other, how do they interact with the host; do they provide something for the host or are they just going along for the ride?
Between the beginning of my research and now, most of what I worked on was single symbionts, single microbes that lived in or on a host. The reason I like microbiomes is that it’s so much more complicated—it’s what do they do, not what does it do. My foundation-funded project perfectly covers those interests—we’re studying these marine flowering plants called seagrass that are very weird organisms/microbes. We’re looking at the evolution, ecology and function of their microbes. Seagrass is a perfect system because at heart I’m a marine biologist: I worked on J. Craig Venter’s Sargasso Sea data, the Moore Foundation’s CAMERA database and the global ocean sampling mission, so most of my projects have been on marine host/microbe interactions. When we moved into microbes, we moved to terrestrial systems, like corn, flies, cats and humans.
I’m also very interested in scholarly communication, in particular, open scholarly communication and the practice of communicating scholarship and science: how can we leverage social media to communicate about science, encourage people to be more open by changing the reward system or the stick system in science, and encourage more sharing of data and tools and samples? So I have multiple funded projects on scholarly communication and I see where there are some things we’ve done really well in the scientific community, and some things we’ve done poorly.
I’m really interested in microbes. Most people hate germs--they want to kill them all--and when you tell them there are some beneficial microbes out there for people or their pets or their plants, the lightbulb goes on for some of them. Some of them go overboard and think all microbes are good and want to lick their toilet seat, so it’s an interesting arena for scholarly and public communication. I’m also interested in citizen science, and blending together my interests in research, communication and public engagement.
How do your colleagues, students and others help you achieve your goals?
How do they help me? I don’t do anything! On top of all the other things we talked about, I’m a generalist. The science I do is what you basically could call comparative biology, so I don’t spend a lot of time digging into one system deeply, I’m much more interested in comparing across many systems. For example, for the single symbionts that live in a host, what are the rules that govern how a single microbe can go from a free-living microbe to one that interacts with a host, to one that depends on a host? What is that trajectory or evolutionary path, why does it happen and what are the effects on the partners? And the same questions hold for microbes.
The reason we’ve done Drosophila and corn and cats and dogs and humans and seagrass and walnut is that I’m interested in comparison across these systems. For most of my research projects, I would not say we are the experts in the biology of a system, so we need people who understand this part. What we bring is the ability to open up the microbial world in this system.
I didn’t know anything about seagrass, or Drosophila, or rice when I started, but we worked with experts at UC Davis and said, “you gotta look at their microbes.” For example, I’m working with a colleague in geology on studying microbes in Antarctic lakes, and her students work in my lab and attend my group meetings—I don’t know squat about the geology of Antarctic subsurface lake ecosystems, so all of my work is highly networked and highly dependent on other colleagues who work on a given system.
It’s hard sometimes, but that’s why I’m interested in scholarly communication. If you look at the people in my lab, what I want to encourage them to think about is the same type of thing: what are the broader rules? Whether it’s the microbiome of a frog, a koala, or a domestic cat, I view my lab as the home of microbiome studies, and what I hope for in people is passion for a topic, and some interest in microbes and microbiomes, and I try to provide the ecosystem so they can do that work.
What motivates you and keeps you engaged in the work?
When I was looking to move from the Institute of Genomic Research ten years ago, one of the things that appealed to me about UC Davis was the direct connection to applied work—we have a medical school and now a nursing school, the strong agriculture and field ecology programs, and the vet school. I still consider myself a basic scientist, I don’t actually do clinical studies or agricultural studies, but it’s nice to have that driver. Much of what has kept me interested in model systems for agriculture. Seagrass is an excellent example: it’s this incredible ecological system with almost no work on its microbiome when we started.
And the other piece is the communication issues, how can we make science work better? How can we communicate this science better to the public? There are so many issues there that there’s always something to do. I’ve also done a lot to support women in science, which is how I originally got involved in the policy and practice of scholarship. Scholarly practice and openness and fairness are the two parts that I really care about. I fundamentally believe that scientific papers, especially those funded by the government should be open at every stage. So that would include the final paper should be in a fully open-access journal.
If people can’t make their published paper open, I’d like to convince them to make a version of it open. I view it as a massive, 70-front battle, and if we can get the whole community to post more of their material openly and early, the better off we are going to be.
Another area I care about is improving the hiring, retention, promotion and life of women and underrepresented minorities in STEM (science, technology, engineering and math) disciplines as part of a NSF ADVANCE grant at UC Davis. Some of the outcomes: judging people by the quality of the work, not the journal in which they publish—related to the open-access and “plague” of impact factor and how that has convinced people to submit stuff to closed journals just because they have a famous name. Realizing there are biases and trying to develop systems to correct for these biases, whether that’s between different fields or otherwise. Women in science are more likely to be in applied fields, statistically, and applied science is less likely to be published in the high impact factor journals than basic science, so if you judge people by the impact factor of where they publish you just damaged women by 25 percent, without any intent to do so.
There are all these things that relate to the communication of science and how if we want people to be more open, we need to make sure they get rewarded—or at least recognized—for their openness, and make sure we make changes in the system. Peer review is generally closed in most places, and it doesn’t mean there aren’t individual cases that aren’t done really well. But the fact that it’s closed prevents people from publishing competitive stuff, prevents young people from entering into a field, and it’s totally abused. And it would be less abused if it were completely open, but if it’s completely open, then junior people are really afraid of publishing reviews of senior colleagues for fear of retribution. There are so many areas where this overlaps with the fairness and practice of science and gender issues. I wasn’t expecting this overlap. That’s what keeps me going: even if you don’t make a big discovery, you are contributing to something really important.
What are your greatest challenges/limitations as a scientist/researcher?
Unquestionably, my biggest challenge is just time. The world of academia is so overwhelming and one of the reasons I like open science is my dream is the more I share the less I have to actually answer any questions. One of the reasons I’ve started doing a lot of social media relates to the time issue—when my kids were born, I really got into social media and it’s because I didn’t want to travel and leave my kids. And now everybody knows what I do and I don’t have to go anywhere, give talks at departments and meetings. Does it take some time, yes, but I think it saves me time in the long run. If people want to know what I’m working on, they don’t have to send me email, they can look on our blog.
Also, I am completely committed to work-life balance. I go home at 5 PM, and I don’t go to evening or weekend events, which is hard—I get invited to a million things and say no to 90 percent of these things. I’m connected 24 hours if you need to reach me, of course.
Sometimes I wish we’d only studied one thing deeply. It’s fun to go around to different things and we learn a lot, but there’s a learning curve for each one. If I could figure out a way, we would focus on seagrass and the seagrass microbiome as our system for a long time, because it covers all these areas that we’re interested in—the climate change component, the human impact, interface of terrestrial and marine component, the most interesting part is there are three separate lineages of freshwater plants that moved into the marine environment and converged upon looking like seagrasses. And that’s the perfect evolutionary biology scenario: convergent evolution is the thing to learn what the rules are for a system. And it occurs on the coastal environment of the entire planet—the field work is just horrible!
Learn more about Jonathan Eisen’s work on seagrass, read his blog, and follow him on Twitter here.
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