BioBuilder Podcast: Katie Hart Show Notes

Episode Description:

Katie Hart is an assistant professor at Williams College and is on the Board of Directors of the BioBuilder Educational Foundation. Katie spent several years running BioBuilder Professional Development workshops at UC Berkeley for teachers interested in incorporating the BioBuilder curriculum into their classrooms. She is also one of the authors of the “BioBuilder: Synthetic Biology in the Lab” textbook.


BioBuilder workshop, SynBERC, Chemistry, Williams College, Engineering design, Collaboration, Ancestral proteins and evolution, UC Berkeley.


BioBuilder Textbook

Katie Hart’s lab website




Zeeshan Siddiqui (00:00):

Hello, and welcome to the bio builder podcast. I’m your host Zeeshan Siddiqui. And today I talk with Katie Hart, who is an assistant professor at Williams College and a member of the BioBuilder Educational Foundation Board. Katie has spent several years running BioBuilder Professional Development Workshops at UC Berkeley, for teachers interested in incorporating the BioBuilder curriculum into their classroom. She’s also one of the authors of the amazing BioBuilder: Synthetic Biology in the Lab textbook. Let’s dive right in.


Zeeshan Siddiqui (00:34):

Let’s start off with your PhD study at UC Berkeley, which I believe was in chemistry.


Katie Hart (00:41):

Yeah, so, well, yeah, so I was in chemistry. I ended up joining a lab that was in molecular and cell biology and my PI Susan Marqusee is actually a physicist. So it was very, I would say it’s very interdisciplinary, the work we were doing, and it focused on primarily on protein folding. So trying to figure out what it is that allows proteins to achieve their final three-dimensional structure, um, and how that relates to how they work. So very, mostly basic science kind of questions. But my, my advisor, Susan got involved with synthetic biology on the, on the side of kind of tools development. So at the end of the day, when synthetic biologists are kind of tinkering with cells, they’re often trying to manipulate the action of either DNA, RNA or proteins. And so, and so being able to sort of manipulate or change the behavior shape of different proteins can be an attractive target for some synthetic biology goals. So that was sort of on the side that we were working in my project specifically. So it’s, I would say since it’s synthetic biology adjacent. It’s not work, we had been working on with synthetic biology in mind before, but then it became clear that this was a, an application that could be quite powerful.


Zeeshan Siddiqui (01:57):

Which one of your projects, I guess, towards the latter stages of your PhD would be most related to synthetic biology? Chemistry definitely is part of synthetic biology, especially like syn bio is developing a toolkit and making the process of engineering biology easier. So chemistry definitely comes under that umbrella, but what would you say is, is one project that stands out as the most synthetic biology-esc?


Katie Hart (02:23):

Yeah, so the, the first project, as I said, I worked on was on this kind of protein switch, like a general platform where you could turn any enzyme of interest on and off. And that’s really important in designing programs for synthetic biology, because sometimes you’re creating intermediates or products even that are toxic to the host. And so you want to be able to signal to turn something on or off externally to, to maximize yield. And we do that, you know, all the time in the lab when we’re producing proteins, for instance, if it’s toxic, you get a much better yield, if you can control when the production of the protein starts. So it was sort of in that, in that vein, the switch project was not terribly terribly successful. So I did, I did have another project that I worked on that was that I spoke about to the synthetic biology consortium SynBERC, which was using what’s called ancestral sequence resurrection to build and study ancient enzymes.


Katie Hart (03:22):

So, so the idea is that you can look at the sequences of existing proteins in a family and extrapolate what the ancestral sequence must’ve been. So from some extinct organism that no longer exists, but it much in the same way, if you look at all of the different breeds of dogs that exist, and they all have very different features, but if you start to look at the things they share, right, you know, the tail, even if it’s long or short, maybe the shape of the nose or something like that, you can actually extrapolate visually what an ancestor, the wolf, must’ve looked like. So you won’t necessarily get it exactly right, but you can sort of piece together certain things. And so we can do that at the DNA and the protein level now. So I worked with a collaborator, Mike Harms and Joe Thornton at University of Oregon to sort of, to resurrect, I guess, the sequences for some, some extinct enzymes, and then looked at how their biophysics, um, sort of their physical characteristics changed over time.


Katie Hart (04:23):

And the thing that we learned, well, one thing that had been posited before was that these ancient enzymes were much more stable. They were much more robust, particularly to temperature. So typically if you have a protein and you heat it up, it will unfold, sometimes aggregate or stick together. That’s what happens when you cook an egg. And when you’re a synthetic biologist and you’re working potentially under harsh conditions, you want enzymes that are very robust, that are not going to unfold prematurely. So in trying to understand and tease out the determinants of this stability, we were sort of learning things that you could do in synthetic biology to make your proteins in your, in your programs, be more robust. And so you can do this kind of ancestral sequence resurrection, and my project kind of introduced some caveats to that, when it would be useful and when it might not be.


Zeeshan Siddiqui (05:16):

Moving on to BioBuilder, how, and when did the opportunity arise to work with BioBuilder? Was this something during your PhD or was it a bit afterwards?


Katie Hart (05:28):

Yeah, so it was during my PhD. I had been, I was just actually digging up my old, my first correspondence with Natalie Kuldell, who is of course the founder of BioBuilder. And it was in 2011, I reached out to her. So I was several years, I was in the last few years in my PhD. Um, because I knew I was interested in teaching. I had been teaching some summer workshops, lab-intensive workshops for undergraduates who were getting ready to do research, um, in different labs at Berkeley. I heard from my PI Susan Marqusee, who was the director of SynBERC – so SynBERC was kind of this consortium of synthetic biologists. I can’t, it has a new name now that I can’t remember, my apologies, but, um, and, and so Susan was sort of working with Natalie on some of the educational aspects of SynBERC and knew that I had this interest in teaching.


Katie Hart (06:19):

And so said maybe I might be interested in working with Natalie on, on this project BioBuilder, which I didn’t know anything about. And I remember seeing her for the first time at one of these conferences we had within SynBERC. And it was that point in the meeting where, you know, you’ve heard 10 talks, science talks, and your eyes are kind of glazing over. And then, and I don’t even know that I was looking up at the front of the room at the podium, but I heard this voice and Natalie just commands attention. Right? Like she, in the, in the best way possible in the way that the best teacher does, right. So she stood up and all of a sudden it was like, “Whoa, I better pay attention.” And so I, I listened to her talk about this project she was working on with an artist. It was kind of the first, some of the first stages of BioBuilder, where it was really just this ‘zine or magazine. She put together a comic of synthetic biology that kind of launched a lot of things. And I was just so drawn to her, you know, she’s one of the most charismatic people and speakers and I saw her and I just knew she was somebody I wanted to know. And so when Susan had approached me about possibly working with her, I, I jumped at the chance.


Zeeshan Siddiqui (07:34):

Was the first project that you work with Natalie and BioBuilder was that the textbook or was there something else, was there first, like, did you attend a workshop or did you assist in a workshop or was it directly into the textbook?


Katie Hart (07:46):

Yeah, no, the textbook came later. The first thing I did, so Natalie had taught a workshop for teachers at MIT and really that grew very organically, right. She had created this amazing curriculum. She’d worked with an artist to make these supporting materials, videos, comics, and then she kind of released it to the world and was like, yay, we’re done. Here’s this amazing content, use it. Um, and, and the reception was very positive, but also from the teacher side was like, we want, we want more, we want you to show us how to do this. We want to know how to incorporate it. So out of that, she did a workshop at MIT, uh, for them, must’ve been in 2011, that summer. And there were some, I think, I don’t remember how many there were teachers there were, but there were a number. And so she was interested kind of immediately in this model of kind of professional development training for teachers so that they could really use BioBuilder to its fullest. And so my task was thinking about, could we do another workshop on the West coast? Cause I was, of course in California, so have kind of one on the East coast and one of the West coast and draw teachers from all over. So in that next summer in 2012 was the first time I taught a workshop for teachers using the BioBuilder curriculum.


Zeeshan Siddiqui (09:00):

Firstly, it must be like so amazing to see, like, this is, you started these workshops, you know, couple of years ago and now they’re all over the country. What else I wanted to ask was, so how long would the would one workshop last? Was it over a weekend? Over a day.


Katie Hart (09:14):

So now there are many kind of different iterations. We do, you know, one day workshops, two day workshops, three days at the time I was teaching, they were five days. So it was a full week. And I, you know, I don’t know, coming at it from as a graduate student, I think you have a different sort of attitude about, you know, what needs to get done in a certain period of time in graduate school than I think later and realizing where the teachers are. But so it was nine to five, Monday through Friday, very intense, boom, boom, boom, boom, boom…


Zeeshan Siddiqui (09:43):

BioBuilder bootcamp.


Katie Hart (09:45):

It was, it was, it was like, it was chock-full and maybe, um, I don’t necessarily think that was the most effective method [laughing]. So I think, I think we’ve learned a lot from that. And I have grown certainly as a, as an instructor and educator, but at the time it was very much like let’s get in, let’s get your, you know, like your time’s worth here. And the teachers loved it, right? They – teaching teachers is incredibly rewarding. And especially for me at that stage in my development as an educator to, to have such, you know, teachers are the best students really that’s how they’re, that’s why they’re teachers. So this incredible group of teachers who were not only really smart, really dedicated, um, but like they could actually be super, were also super empathetic, right. To me as an instructor because they were in most cases, much older than I was. And so they could give me very good constructive feedback. So it was just an incredible experience for me to be able to do that.


Zeeshan Siddiqui (10:42):

And both the teachers and you were learning from each other and growing from other and growing together.


Katie Hart (10:47):

Yes, yes.


Zeeshan Siddiqui (10:48):

And the content of the, of these workshops, uh, over five days, one would be, I guess, how we implement the BioBuilder curriculum into their teaching style and their schools, as well as I presume also how to approach teaching synthetic biology. So what would be, I guess, the main content of the initial workshops?


Katie Hart (11:09):

Yeah. So I mean, the content was very much rooted in learning and getting to try all of the experiments that are part of the BioBuilder curriculum. So really the hands-on learning aspect. And then, you know, many of the teachers were coming from the biological sciences background, AP Bio or other type things. And so for them, the engineering perspective was really the new part. So thinking about design – build – test cycles, how to explain inputs outputs, you know, and then, and, um, inverters or the kind of, you know, the terminology you use as an engineer. And to be honest, that was all very new to me as well. I was very much biophysical chemist and had never taken an engineering course of any kind. Um, so in, in learning this curriculum and then teaching it, I was also learning what it is an engineering perspective is, and then conveying it to, to the teachers, um, so that they could sort of incorporate that, that line of thinking into, into their curriculum.


Katie Hart (12:14):

And as far as teaching them how to build it into their curriculum, that was actually more of a me asking. We wanted to know, you know, we’re developing this content and we think it has a lot of interesting aspects and it’s certainly tied to current research, but we don’t know what’s new, Natalie and I, and the rest of BioBuilder. We don’t know what’s being taught in high schools, especially at that time, we weren’t as, as plugged in. So really asking like, is this useful? What parts are useful? What would you like to see change or, um, adapted? How could you do this, you know, in the one hour you have with students a day, right. Or maybe it’s one hour every other day. So we learned a ton about what’s possible, and useful for teachers in their setting. And we’re able to incorporate that feedback in iterations of the curriculum.


Zeeshan Siddiqui (13:09):

With the hands-on experiments, what would you say, which part of the BioBuilder curriculum experiment, would is your personal favorite? Like one that made you be like, made you maybe understand what synthetic biology is really about or have had that moment, whoa, I didn’t know that was possible.


Katie Hart (13:30):

Yeah. Oh, that’s a good question. So what captured my imagination? I mean, I think within the, the curriculum, I think the experiments that capture the, the teacher’s imaginations can be well, it’s sort of, it sort of ranges. A lot of them really liked the bacterial photography, which I know you talked about with Karen Ingram. It, it tends to appeal to, I think the more artistic sensibilities that you could develop a photograph or image with, with bacteria using this kind of intricate program. And I actually really liked teaching that lab cause we would do it side by side with a breadboard. So you could really do the analogy of building a circuit and the biological circuit that’s occurring in the cell. And it kind of gives you a tangible, physical way of, of learning that. So I really liked teaching that.


Katie Hart (14:19):

In terms of just what’s possible and kind of captures your imagination. I think one of the first stories I knew and heard about, um, synthetic biology was the kind of the artemisinin story. So Jay Keasling’s group developing a way to produce artemisinin, the anti-malarial drug, in large quantities using yeast. So basically brewing it much like you would brew alcohol and just appreciating, you know, from the science side, the, the feat, but also the impact, right? So like that you could be doing something with your science that could have such a tremendous impact, a global issue, right? The, the access to this drug, which is so much somewhat finicky, because it was from a, derived from the tree, which would, you know, in some years be more productive than others.


Zeeshan Siddiqui (15:11):

When you reflect on your journey so far, what are some of the key lessons in culture, skills, and sensibilities that have served you well in your current position, at Williams College, which I understand is your dream job.


Katie Hart (15:28):

Yeah, yeah. So this is definitely my dream job. I get to do teaching and research and work with really talented undergraduates and an amazing, amazing set of faculty who are really dedicated to education. So this is something I’ve wanted to do for a long time. And so I’m very grateful to be here. And I love this question about the lessons of culture, skills, and sensibilities. I think, especially connecting back to what I learned from BioBuilder. I mean, I told you a little bit about my experience teaching teachers, which I think was huge in how I approached education, but also the experience working with Natalie and everybody else at BioBuilder, it’s always been so collaborative. So one example of that of course, is the textbook. There were, you know, the four, the four authors that were all working together, very collaboratively on writing this and illustrating this, this textbook, which was an incredible experience.


Katie Hart (16:25):

And then also just the way Natalie has always been so generous with sharing resources and materials, and the community that grew around the teachers who were taking the workshops of receiving the BioBuilder curriculum and materials, amending them, sharing them back out, right. We would have these massive Dropbox folders that would get sort of populated and shared between teachers and different regions of the country. So looking not only at the science as truly collaborative and interdisciplinary, which I think is one of the unique aspects of synthetic biology, but that is also infused into the way we think about education around synthetic biology as well. So there’s no kind of central ownership, or there’s not a sense of that. It’s really distributed. And here at Williams, I think, you know, I bring that kind of, have that expectation that that’s how teaching should be.


Katie Hart (17:17):

And that’s very much how this department is, but that’s not true. I think everywhere you go. So the way we really are rooting for each other and sharing all of our materials and insights and not feeling like, you know, you own a particular lesson or a particular resource, but, sharing widely and then best thing about that is that when you get it back, you know, the second time around, I teach this course with two other, two other instructors and we, we pass our materials one to the next, and then it’s like the next time you teach it, you get their materials and it’s yours, but like slightly changed, right? There’s like new lessons or new ways of doing it. And it’s, it’s really fun. It makes, it makes teaching really exciting.


Zeeshan Siddiqui (17:56):

That’s really brilliant because each time is like, each time you teach a workshop or does a BioBuilder curriculum is integrated into a school, or a lesson, there’s like a new perspective to it. Like every time he learns something new that, you know, you may, you may have done it a hundred times before, but each time there’s just something there’s a new element about it, which, which I think is really cool. And especially also the no central ownership idea. Because that’s, that’s the only way how you grow the community as well as grow BioBuilder.


Katie Hart (18:26):

Right? Exactly. It’s great. And I think when you have a design-first sort of approach or an engineering approach, that’s also one of the reasons it’s exciting because no matter who, it depends so much on who’s approaching the problem, how they go about solving it. And then that will lead you down the rabbit hole of, I need to learn XYZ about biology or chemistry or physics to make this happen. And it, and again, everything just feels very organic, which I think is the best way to teach and learn, right? Because you have kind of the motivation, there’s a motivation besides I have to know this material for the test, the motivation is I need to solve this problem that I am somehow invested in, personally or otherwise. And so I’m going to learn what I need to learn to solve the problem.


Zeeshan Siddiqui (19:12):

Do the workshops start like in September, for the teachers?


Katie Hart (19:17):

So, they’ve mostly, the ones I did were all in the summer, because that’s when the teachers had the time.


Zeeshan Siddiqui (19:22):

That makes sense.


Katie Hart (19:22):

So that’s when they do the bulk of their professional, at least external, professional development. I do think we’ve taught some workshops, not myself, that have been during like winter break or other kind of gaps in schedule, but we really try to, you know, especially since we’re pulling teachers from all over and districts can have different times. I think the bulk of them are in the summer when they have the most time to do that. Yeah.


Zeeshan Siddiqui (19:46):

Katie, thank you so much for joining me today. It’s such a pleasure talking to you and really learning about BioBuilder.


Katie Hart (19:54):

One of the best things about BioBuilder, I mean, really the thing, is the community. It’s the people.


Zeeshan Siddiqui (19:59):

Thanks once again, to Katie Hart for joining me today, I thought her comment about not only looking at the science being truly collaborative and interdisciplinary, but how that is also infused into the way we think about education was very insightful because collaboration and no central ownership is truly how education works best. I believe this episode will be very useful to anyone interested in synthetic biology education as well as teachers looking to participate in the BioBuilder professional development workshops. If you’d like to learn more about anything Katie and I discussed today, please refer to the show notes. Join me for the next BioBuilder podcast – we’ll welcome another wonderful guest whose career has been influenced by BioBuilder’s life-changing science. See you next time.