Junior Faculty Awardee Profile: Allie Obermeyer, PhD
So tell me about yourself and your background. Where are you from?
I'm from Texas and Michigan. I went to college at Rice where I was a chemistry major. That's where I first got involved in research. I went to Berkeley for my PhD, where I was in an NIH-funded chemical biology training program, which allowed me to do rotations in several different labs to explore greater research opportunities. Ultimately, I did my PhD developing protein materials with Matt Francis in the chemistry department. From there, I moved to MIT to postdoctoral work with Brad Olsen, an outstanding engineer in the chemical engineering department. While there, my research focused more on how to incorporate proteins into practical, useful materials.
When you were young, what sparked your interest in studying science—specifically chemistry?
I think I had some inherent curiosity as a kid. I had a grandfather who was a mechanical engineer and a great uncle who was a geologist. I was really interested in the natural world around me–including things like rocks. But also, I think there are a lot of female-centric activities that are often not considered scientific that I always enjoyed as a kid–things like cooking and baking. There's a lot of amazing chemistry in cooking and that is basically what a synthetic chemist does: you mix things together at appropriate ratios and heat them for the appropriate amount of time. And you have a final product at the end. But if you're baking, you also get to eat it. Also, as a kid, I "formulated" cosmetics and personal care products, so I think I had some inherent interest in testing things out to see what would happen. I would now call this experimentation. Later, it came down to having excellent teachers, both in high school and college, that really got me excited about science and math and made me want to stay on that path.
"I've been interested in the interface between chemistry, biology and engineering: how can we use our understanding of chemical matter to change or alter or understand biological systems? I think there's a lot of power in that."
Can you tell me a little bit about your current research and how it evolved?
Since I started doing research as an undergraduate, I've been interested in the interface between chemistry, biology and engineering: how can we use our understanding of chemical matter to change or alter or understand biological systems? I think there's a lot of power in that. Biology has developed over time to function better than any system that exists, but is best evolved to function within an organism. As humans, we're trying to replicate that in a much faster timescale and larger magnitude, rather than on the individual scale that an organism uses. So there's a lot of power in understanding how biology works and then manipulating it and using it for our purposes. My research interests have generally been in this area.
My group now engineers proteins and polymers to combine the best properties of both. For example, we're working with some polymers or plastics that are ubiquitous everywhere in our lives these days, but that are frequently made from petroleum feedstocks. They're not necessarily sustainable and they don't have of the amazing functionality that you would have in a biopolymer like a protein. We're trying to combine those two things. The protein is a more sustainable source and has broader—and a lot more exotic—functionality. And then the polymer has things like stability and processability. We try to combine those two things together to make new materials for protein formulation, protein stabilization, or for protein delivery. These are mostly in vitro applications of proteins and polymers, but we are also trying to control these processes, of how proteins interact with polymers inside of living cells.
Interesting. To what extent are you working with anyone, say, in biomedical engineering or at CUIMC?
We do a lot of the protein work ourselves, but we do have an ongoing collaboration with Professor Henry Hess in the BME department looking at studying enzymes in these environments. This relies on the catalytic properties of proteins rather than their biomedical function. Right now, we make chemicals using a lot of synthetic chemistry. And this is usually, again, not very sustainable, but it's pretty cheap. This includes things like pharmaceuticals, things that you buy from Duane Reade—like Advil, Tylenol, or Lipitor—are made using chemical reactions. But enzymes can do a lot of the same chemistry that chemists have developed over the past century, and they have the ability to be more sustainable in that they all operate in water. But there are some limitations of enzymes that we have to overcome: stability and cost. These are things that we’re hoping to address by interfacing the enzymes with polymers.
Are there other broad problems that you hope to solve with your work?
I would say that's directly related to the Provost’s award. It’s a seed to start pursuing some of these bigger, grander challenges. In the materials community and in the biomaterials community, someone will make a new material and then have to make enough of it so that they can test it and understand its properties. And then they go back and make another material and test its properties in this iterative cycle. But they're usually limited by how many things they can test because the measurement requires a certain amount of material and this testing is the hard part and the slow part. There's a big national initiative to use data science and computation to develop what's called a materials genome. And that is one approach: to be able to test thousands to millions of different materials using a computer. It's really hard to model biomaterials computationally when we don't know much about them. We're trying to develop a new way to test biomaterials using biology itself. We use evolution techniques. All of these cells have evolved to survive; if we can link that cell survival to the materials property that we're interested in, then we can screen thousands to billions of materials all at once.
This broad idea of using evolution to improve enzymes and binding interactions is what won the Nobel Prize two years ago. These are two functions of proteins: to function as enzymes or to function in a binding recognition event. But proteins have thousands of different functions. There are millions of known proteins on earth and these are two main functions that were originally discovered. Proteins are also really important in things like the elasticity of your skin, and a lot of other structural properties of organisms that are really hard to screen and evolve. What we're trying to do is to develop methods to use evolution artificially to screen for these mechanical properties of proteins.
Switching from the lab to the classroom, what are you teaching this semester?
This semester I am teaching a biochemical engineering course. As chemical engineers, a lot of what the students learn is how to design a chemical plant and how to think about setting up chemical reactions on a very large scale. We look at the kinetics and thermodynamics of those processes, and how to transport in those large systems and chemical reactors. In the biochemical engineering course, we generally touch what they should have learned in their chemical engineering curriculum. But what happens when instead of optimizing a chemical reaction on a large scale, now, in your reactor, you have cells that you need to keep alive? And how does that change different assumptions that you made, and what additional considerations do you need to take into account when designing a new bio-based process?
How do you test this? Do you use case studies or simulations with the students?
It's all in the classroom. It's a really interesting group of students that I usually get, some of whom have no background in biology. There are also some students who come in without a background in chemical engineering—they might be biomedical engineers or earth and environmental engineers or even chemists or biochemists. They may get the biology part, but now they need to get the chemical engineering part. It involves putting those pieces together and making sure everybody can communicate. We do some case studies, like penicillin, which was the first major pharmaceutical that was produced using organisms. It's one of the big victories for bioprocess engineering, but it happened in the 1940s. We also talk about modern examples.
What do you enjoy most about your job?
My favorite part of the job is interacting with students, both in research and in teaching. I really love seeing the moment when students become independent and are able to do things for themselves. That includes research and being able to ask open-ended, important questions and figure out how to solve those. Or similarly, in the classroom. I love when students really get what I've been trying to communicate; students are also enthusiastic and ask interesting questions that I wouldn't have thought of, and that is fun.
Can you speak about your experience as a woman in STEM, either as a student or as a professor?
When you are no longer a student, you realize that there aren't that many women still in STEM. But I feel that along the path here, I was fortunate enough to work for several men who always made sure that their labs were representative with at least 50 percent women. I think that was really important—and also kind of rare. And I was conscientious about selecting advisers who were supporters of women. You have to find mentors where you can, even if there aren't ones who look like you.
Another thing that was valuable for me was being around other women; Berkeley was a great place for this. I had a network of peers that was hugely supportive. For example, I was in a couple of all-female book clubs both in graduate school and as a postdoc; those were all scientists and engineers who liked to read and cook and get together. Those friendships and connections are wonderful and super helpful.
What's most challenging for you in your work?
Time management and balance. I’m at this point where there are more things to do than I have time in the day. And there are a lot of great opportunities that I would like to take advantage of, but I am learning to say no to some. And I try not to let the seemingly urgent take over what is important. Finding that right balance has been the hard part. For example, I am expecting my first child this winter and I will be working and going to conferences in the spring. At this career stage, it feels like you want to take all of the opportunities that you can get. Fortunately, my network of female friends from graduate school and my postdoc have been really helpful in this respect. But my friends say, “No, it's OK. You don't need to give three talks when you have a newborn.” They have reminded me that saying no to this allows me to say yes to something else. I recognize that when I’m saying no, I’m opening the door for another opportunity.
Speaking of opening doors to other things, how do you spend your free time?
I am working to make sure that I have balance. I think it is important for students to know we're all human. I'm not going to be the most effective scientist, engineer, or teacher if I am burned out. What do I do? I like to work out. I spend lots of time in Riverside Park and Central Park and I also cook and knit—blankets, scarves, and baby hats. And then I watch a lot of basketball – mostly the Warriors. I spent a lot of time in the Bay Area, before the Warriors were good. They got really good when I left. It has been fun to watch them be successful from afar.
Do you have any books that you’d recommend?
I’m reading a lot of parenting books, so I can recommend two of those written by an economist, Emily Oster. The titles are Expecting Better and Crib Sheet. They are great for scientists. Everybody gives you advice about these things, but what does the research actually show? As a scientist, what does the research say? And fortunately, the research says coffee is OK. I recently read Just Mercy, a fantastic book by Bryan Stevenson; it’s an eye-opening look into the criminal justice system. Other books that I would recommend would be The Immortal Life of Henrietta Lacks, a nonfiction book about science that is accessible for non-scientists. And then The Emperor of all Maladies by Siddhartha Mukherjee.
Finally, are there any sorts of collaborations that you either see on the horizon or that you would be open to?
That's a great question. We’re hoping that the technology we are developing will be valuable to bring to a collaboration. We are really trying to generate that promising preliminary data to show that these proposals to merge polymers and proteins together have the ability to provide all these advantages that we think they do. Right now, we're right at that cusp. We would love to work with people who are interested in having proteins formulated and incorporated into materials for biomedical applications. I'm always open to working to show that our technology and our techniques work more broadly for anybody’s protein of interest.