Sit Down With Dr. Erin Berlew

By: Yastika Singh

I had the wonderful opportunity to interview Dr. Erin Berlew, professor and researcher in the Bioengineering Department at Penn (and my professor last semester!) regarding her unique career trajectory from AmeriCorps to Brian Chow’s lab, her experiences as a female engineer, and her time at Penn. Dr. Berlew teaches Engineering 1050, a Python class centered around data analysis, as well as Senior Design for Bioengineering seniors. Below you can learn about the incredible work she does, as well as her equally incredible advice. 

Key Points:

• Data is for everyone! And everyone should strive to understand the basics of data science because it is everywhere.

• A lot goes into Senior Design: ideation starts Junior year and the process includes developing valuable skills such as needfinding, collaboration, and effective communication

• Dr. Berlew’s current personal mantra: “action is the antidote to anxiety”

We'll start with a little bit of background, educational background, professional background and personal if you want. 

So I grew up in a small town near Scranton, Pennsylvania, so, Northeast PA, about two and a half hours from Philadelphia. I always loved learning and science and education and all of that. And I went to college at Haverford College, outside of Philly, and I've been in the Philly area ever since then, so I never really left. At Haverford, I majored in chemistry. I did research in Biological Chemistry, specifically studying how bacteria are able to make antibiotics, and that became the basis of a lot of what we use in the clinic. And then from there I knew that I liked both research and also teaching, and so I did AmeriCorps for a year. So I did City Year Philadelphia, where I was teaching seventh graders in a middle school in northeast Philly. And it was a really great experience. I learned a ton. I learned that I don't want to be a classroom teacher. When you're managing behavior and doing a lot of the lesson planning and admin stuff, [teaching] kind of gets lost in the shuffle. And so from there, I got a job as a lab tech here in Skirkanich Hall in Brian Chow's lab. And shortly after I started the job, I wanted to do my doctorate there, because I loved the people, I loved the research, and I knew that science was kind of going to be the path for me. And so I started grad school there in 2017 and my research focused on protein engineering, specifically to make optogenetic tools, so things you can use to control the cytoskeleton using light. Coincidentally, I did my PhD when COVID was happening, so I had just proposed my thesis the first week of the shutdown and everything. And so that gave me a few weeks at home where I only had the data that was on my hard drive and nothing else. No new experiments could happen. So I got really into working in Python and building analysis pipelines, and that kind of led me to teach engineering 1050. So my current role is I'm a lecturer in Bioengineering, where I teach Intro to Scientific Computing, and I co teach Senior Design with Mike Siedlik, and full time, I do research in the School of Medicine as a senior scientist. So that's kind of my background.

Can you talk a little bit about why you chose academia versus industry?

I don't think there's a right choice, and everyone has their reasons, and someone's reasons for doing one might be someone else’s reasons for not doing it. In terms of why I really like academia: I love the access to being able to work with students. It's really fun that every year, both through teaching and research, we get to see the new class of students really keep current with what is going on in the cutting edge of science. Because in academia, especially at a place like Penn, people are doing all sorts of really interesting things and inventing new technologies. I also love academia, because while you are kind of charting your own path, you have a lot of flexibility. If you're in a department like Bioengineering, there's a lot of collaboration that can happen. There are courses you can design. You can kind of make what you want with it without having to prioritize shareholders and profit in the way that industry jobs might do. I also love that I live in Philadelphia. I live a 10 minute bike ride from Penn's campus, so that's pretty nice as an additional plus. But yeah, being on an academic campus, there's just kind of nothing like it. And I've technically worked in an academic setting every year since school until now, so I really love it.

Can you talk a little bit about why the skills of scientific computing, but also Python specifically, are important to all engineers, or people in the STEM field? And then also can you talk a little bit about your experience as senior design professor?

So Engineering 1050 is the first college class I ever taught, and I taught it for the first time the first year we were switching to Python. And so that was really exciting and also stressful to try to make a new course. But I think scientific computing is super important for everybody - whether you're interested in STEM or not, it's affecting you. So being able to, I think, in terms of literacy, read a headline in the news about a particular new technology that exists, and have a basic understanding of how that might work, or being able to interface with political polling data and understand things like how sample sizes are calculated and how we understand statistics. And I think knowing Python gives you a lot of flexibility in terms of what you want to do with data. So even if you're someone who has a job where you do a lot of things with spreadsheets and you use a lot of the built in Excel functions, there are ways that Python can make your job easier or make it more robust in terms of the data analysis that you're doing. I think because Python is open source, which I'm really passionate about,  it's amazing that anyone with a computer and an internet connection can use Google Colab for free and be able to run code in the Cloud or download the Python development environment and get started working there. And so the course is really fun because some students come in with some coding experience, but my favorite is having students come in who've never programmed before and seeing them come to office hours and say, like I'm worried, because I think I might be in over my head. I've never done anything like this before. And, you know, we talk about how it's stressful and hard, but they need to stick with it. And then by mid semester and the final project, they are coming up with their own ideas for programs and then making those. So it's really fun to get to see students grow, both in terms of technical skills and in terms of realizing, Oh, when I hear people say machine learning, that's not a big scary thing, that's something that I can actually do myself. And what's even better is when someone claims they did machine learning on something, and therefore it must be the ground truth, and I can kind of poke holes in that. So it's great to see students kind of become their own detectives and inventors of what they want to do and what they want to get out. I think coding is so important. Last summer, I taught a class in my living room for my husband and six of my friends. And it was super fun and really great to see everyone across these different fields and interests was able to do something fun with Python. So that is 1050 and then Senior Design is a whole other adventure. So Senior Design actually starts junior year, so we meet with students in the spring of their junior year and kind of lay out what the year is going to look like. And we do that because our rising seniors do really amazing things over the summer. They're interning in clinics, they are working at companies, they're doing independent research, and they're meeting a lot of people during that time, and so it's really amazing for them to have access to these people that they can run some of their ideas and questions by. So a big question we have students ask potential medical experts or patients or parents of patients, is what are the issues that you see and what are the things that make your day to day life harder? And why is the status quo the way it is? And so they come in in the fall, they form their own teams, and they've done a lot of background research and moved towards identifying a need. So everything we try to do in Senior Design is based on a true biomedical need, rather than this is a gadget I can make, because I know how to do all of these cool things in the lab. And so coming back to the need, the students identify, who are the people who are struggling with this issue, and what is the problem they're facing? And if we were able to solve it what would the positive outcome be? And then from there, they come up with a solution. And it always amazes me, every year that students start from “we've talked to some people, we've done some readings, we are going to make this device, service, app or this system.” I love the class. It's a two semester course. They make what their final product is. They engineer it. They have a prototype. They test it rigorously. A lot of times. They survey potential users, and in the spring, they demo their project in front of the public. And it's exciting to see that in over the course of two semesters plus a summer, they're able to make something that works. And oftentimes, students will patent or will form companies or have collaborators start doing clinical studies with their designs. One of my favorite things about senior design, aside from getting to work with really amazing students, is we are IP neutral, which is unusual for a university. Students own the IP that they create in the class. So I don't own it. Dr. Siedlik, my co instructor, doesn't own it. Penn doesn't own it. The students can actually leave with something that they can take forward. And we have a few companies that have spun out of the course in the few years that I've been teaching it, and we're really proud. And then we get to bring those students back and have them share what they've learned with the next generation.

So I remember in 1050 on the last day, you gave us some advice, and I really resonated with that advice. In general, do you have a mantra or something that you tell yourself to keep a positive attitude, and you know, like set yourself up for success on the daily?

Ooh, a mantra, I would say, one of my favorites that I did not come up with, that I got from a podcast, is action is the antidote to anxiety. And that's not to say that anxiety isn't real and isn't something that I work through. But the idea of, “Oh, I'm nervous about this meeting. I can actually write down the agenda, and then I know exactly what we need to discuss, and I can prepare”. Or, you know, “I'm worried about this experiment that I'm going to be running in a few weeks. Well, let me take some extra time and see what I can set up ahead of time, so that it's less time pressure.” Or I think a big thing with students is, if you're nervous because you don't understand the material, there's no substitute for really getting in and struggling with it and feeling that frustration. So I think that's probably one of my favorites. And then I would also say that you have to enjoy the day to day at least half of the time. And I think you can increase or decrease [that percentage] depending on personality. But I think I worry when I see students kind of delaying their happiness into the future. So when they say things like, “Well, I just need to get through pre med and then I need to get through med school and then residency, and then I'll have a stable job and I'll be happy” like, that's a lot of years in between that you might be miserable! And so thinking about not every day is going to be sunshine and rainbows, and not every task or exam, or course, you're going to find the most thrilling, but there have to be things that you really enjoy about it. And another great place the enjoyment can come from is also the people you're doing it with. So the camaraderie, I think, can be a substitute for a lot of the late nights or hard projects.

Speaking of projects, can you talk a little bit about the coolest project that you worked on and why you were so passionate about it, and how that kind of propelled everything afterward?

In undergrad, in my research, we were studying type two polyketides, which are small molecules made by soil bacteria that can be used as antibiotics, antimycotics, antifungals, all these amazing therapeutics. And so one thing we found, though this would have been like 2013, is that people had done all of this work on them, but there was no central place where all the information was gathered. And that's the kind of thing that my brain really loves, is taking something that's really amorphous and trying to put structure into it. And so what started as a side project ended up kind of taking on a life of its own. I was logging things and tracking down from all of these papers: what molecule was identified, what was the host species it was in? What's the structure of it, and what can we say about the carbon chain length and the chemistry that goes on to make the molecule? What is the first description of it that exists? And what's really neat is that when we first started it, we had like, 66 or something, polyketides, and it's since grown both as we found new references to them in the literature, and as later students in the group have expanded on it. So it became this thing of we're able to both make a resource that's more accessible to people who are studying this that might be useful, and we were able to learn new science from it, because we organized the data in such a way that we could look at the lineages of the species that are making these molecules, and look at the gene clusters and figure out evolutionary relationships there. I love the projects that come out of something where you're thinking, you're just making a tool for yourself, and then in the process of doing that, you learn something totally new. I think a lot of Engineering 1050 Python projects are kind of similar to that, where students will say, Oh, I'm going to compile this data and make this resource and do this analysis on it, and they're thinking about the analysis as a way to satisfy the requirements of the project. And then they learn something new out of that. And it's super fun.

Do you feel you felt any challenges particularly as a woman in a STEM field in your education, or your career? Do you think you face these challenges now? Similarly, do you notice any patterns in female students about challenges they may face in senior design or in your classes?

Great question. I think overall, I remember my first orientation day when I became a grad student in the School of Engineering, we all kind of gathered together and did this orientation thing. And I remember there was like a five minute break. I said, Okay, I'm going to go to the restroom, but there's going to be a really long line. And then there was no line. And I was like, Oh, this is great. And then I was like, Wait a second, what does this mean about the gender breakdown of this group? And I mean Penn in terms of gender breakdown is more even than a lot of places, and my department, Bioengineering, is very evenly split between men and women, which is amazing. And I think a thing that maybe necessarily doesn't always catch up with students, particularly my female students, is coming in with that impression of oh, well, this is going to be a male dominated field, and I'm going to have this experience because this is what I've learned about how engineering and STEM are, and it's great that we have such representation here. And so I think students not selling themselves short is a really important thing, but also being aware that gender dynamics exists, the same as, you know, racial and ethnic biases negatively impact student experiences everywhere as well. So I think for things that I have faced personally, you know, I've been very privileged as a white woman in academia, being able to kind of pursue my research and my teaching career without any serious obstacles. But I think it's important to be aware of the dynamics that exist and the kind of institutional and structural biases that exist in science and just in culture on a larger scale. I think for female students, making sure that they don't necessarily cast themselves or allow themselves to be cast into roles due to stereotypes. So an example is, if we have a group of students and there's one woman in the group, it shouldn't be assumed that she'll be the note taker for the meetings that we have with the group. That's something that we facilitate upfront conversations about when groups form. And in Senior Design there are identities you're all bringing that might lead certain patterns to happen. And how can we prevent those? And so I've seen Bioengineering students be really successful in setting up systems where they say, Oh, we rotate who's the note taker in this group, or, Oh, we, make sure we have time for feedback, ensuring that people can share if things happen, that they can say, hey, it felt like you were really talking over me in that meeting. And I think it's a combination of not selling your ability short due to any particular identity that you have, but also those tendencies and large cultural trends that you can be aware of and work to combat, even in class projects. And I've been really, really impressed with what I've seen students do in this avenue over the years. We have a whole group dynamics workshop that students do, and it covers a lot of things. It's not only based on gender and racial identity, but it also covers, let's say someone disappears right before an assignment is due, and you need their feedback. What are your expectations as a team around that? Teams really have conversations when there's no stress and nothing has happened, so that they have groundwork laid for later on, if issues come up, everyone is on the same page with what the norms are. 

If someone was to consider going into bioengineering or engineering at large, whatever their background is, what would you tell them? 

I think everyone, regardless of what they want to do as a career, should learn and be interested in science and engineering and data fields. Even if you're not interested in data science, data science is interested in you. They're harvesting your data all the time. It's crazy, but I think there's nothing that you can't learn and that you can't catch up on. So it's never really too late to feel like you want to do something in a more technical field. I think every career is hard. I think people say engineering is really hard because there's a lot of math involved, and we're a math phobic society, but I think I look at students in the School of Arts and I'm like, wow, I could never do anything like that. Or I look at people who are doing, you know, political science or English degrees- I think everything's hard. It's just a matter of students, particularly students at Penn, are used to doing hard things, and it's super exciting. They're huge fields. There's a pocket for everyone, and something you'll find really interesting there. And don't let yourself be intimidated by the kind of reputation that engineers sometimes allow engineering to get in terms of how rigorous it is. It is rigorous, but every field is and if you're excited about it or at all interested in it, you know, take a class, go to a seminar. There's not a membership card that really makes you a full fledged, you know, STEM person. And so any level of interest is amazing, even if you are staying in your own field, which is different, it's all really important. And I think bioengineering, particularly at Penn, is a really welcoming field, and we have students from all backgrounds, students with all sorts of interests and goals, and they can all do really amazing things with it. So definitely, if you're interested, you should chase that interest. It's a great time to learn more about engineering and STEM fields in general.