In today's podcast, Ilona talks to Gael McGill, Director of Molecular Visualization at Harvard Medical School and CEO of Digizyme. While earning a PhD in Cell and Molecular Biology at Harvard Medical School, Gael recognized a need for scientifically-informed design that would support both the communication and analysis of scientific ideas. To meet this need, he began Digizyme, a scientific animation and design studio that supports scientists in biotech, pharma, and academia to help them create animations of molecules. These animations incorporate actual measurements of molecular structure and movement, and therefore depict their authentic function and process. Together with his team at Harvard, Gael creates molecular animations and does research on how to best design visual media for science and education. Gael is currently applying his talents and research results as Digital Media Director for the Life on Earth Project, spearheaded by E. O. Wilson, which aims to develop an interactive digital biology textbook that will be free and available to all. Until then, we can enjoy his ongoing effort to select and disseminate molecular animations with a high teaching value in the ever-growing collection of animations at MolecularMovies.org. [15:27]

Full transcript

ILONA MIKO: Welcome to the latest edition of NatureEdCast. I'm Ilona Miko, and today we're talking to Gael McGill, Director of Molecular Visualization at Harvard Medical School and CEO of Digizyme. While earning a PhD in Cell and Molecular Biology at Harvard Medical School, Gael recognized a need for scientifically-informed design that would support both the communication and analysis of scientific ideas. To meet this need, he began Digizyme, a scientific animation and design studio that supports scientists in biotech, pharma, and academia alike to help them create animations of molecules. These animations incorporate actual measurements of molecular structure and movement, and therefore depict their authentic function and process. Together with his team at Harvard, Gael creates molecular animations and does research on how to best design visual media for science and education. As part of a full-fledged effort to apply the fruits of this kind of work to the greater good, Gael is also Digital Media Director for the Life on Earth Project, spearheaded by E. O. Wilson, which aims to develop an interactive digital biology textbook that will be free and available to all. Welcome, Gael.

GAEL MCGILL: Well, thanks for having me.

MIKO: So, can you tell us a little bit, what is data visualization, and what can we learn from it?

MCGILL: Sure. So, I think broadly speaking, I would reduce that to bio-visualization, which is the specific area that my activities are focused on. And I think of it as a way to understand nature by creating images or movies of it. So there are many ways in which the processes of nature remain hidden from us, either because the structures are so infinitely small or because the processes happen on timescales that are beyond the reach of the human senses, whether it's the incredibly rapid conformational changes of a protein or whether it's changes that happen on ecological or evolutional timescales — to me bio-visualization is an opportunity to make those changes visible and to reveal those structures and processes to the audience in an intuitive and visual way. And so I think the other thing about visualization that I like think about is that it's actually — there's quite a variety of projects. I think of it as a continuum of activities. On the one end of the spectrum, you have the use of animation and multimedia to communicate and for educational purposes. These are usually very narrative-driven movies and you're telling a specific story. And so I think that's the traditional way we think of science animation. But at the other end of the spectrum, you also have the use (often using the very same software tools) of visualization to look for answers or patterns in raw data. And here you're using it more as a discovery tool, and really just to formulate new hypotheses. So my groups actually create projects at either end of the spectrum, whether it's an outreach movie for the Boston Museum of Science or WGBH, all the way to the other end, such as creating accurate visualizations for colleagues at Harvard Medical School. So anyway, it's an exciting field. It's more than pretty pictures. We try to be as accurate as we can, and it's an opportunity for knowledge synthesis, I think, in biology as well.

MIKO: So how do you make these animations? And specifically, what is the form of the information you use to create such detailed and authentic animations?

MCGILL: Well, so you might expect that specialized software coming out of the research community would be really what's used in this case. But actually, there's a recent trend where people have been looking to the entertainment and gaming industries and to borrow from essentially what has been billions of dollars of investment in software development. So this is the Hollywood-type software that they've used to create any of the Pixar movies or Star Wars or Avatar. Those are incredibly powerful software animation and simulation suites, and in particular the one that we use, and one of the more established packages is called Maya, which is made by Autodesk. The thing is, those packages were never meant, really, to animate biological data or even to import it. So we wanted to build upon the power of that software and give it the ability to directly import scientific data, and thereby increase the accuracy. So a few years back, we created a new software called Molecular Maya that sits on top of Maya and lets you animate and import molecular — and it's not just molecular, also cellular data — there's really no limit, in a sense, to where we can gather the data for these movies. We do start a lot of times from the PDB, the Protein Databank, or the EM databank for electronic microscopy. So those are the, those are the tools and the sources, but I would just add that I think even more important is to start with an interest for developing accurate animations, which has not always been, I think, the priority in science movies, at least ones driven by marketing dollars. So, you know—

MIKO: Yes, well, making beautiful pictures is often, goes a long way, yeah — whether they're accurate or not.

MCGILL: Right. Yeah, and actually, knowing how to find the right data, as well. I think those are challenging things. It's one of the reasons why everyone on my team is a scientist by training. I think it's important to be passionate about the science that you depict, and the aesthetics of the movies serve the content, rather than being kind of eye candy for its own sake.

MIKO: And apparently using them, you can use these in ways to find out about how students learn. So I'm curious here, your team recently completed a research project that tracked students' understanding of the biological processes they observed in animations, and they also used — you also used eye tracker recordings to follow what components of an animation an eye dwelled on and spent the most time with. Can you tell us a little bit about that project and the results you found?

MCGILL: Sure. So in addition to our visualization and software development efforts, we're very interested in how the design of an animation has an impact on how students learn the science, and there's a lot of talk about the potential for multimedia engaging students, and in certain cases, I think of it almost as buying attention credits. But actually we're interested in pushing that further. We would really like to know how the design of a scientific animation can directly be connected to knowledge transfer. What is the best way to use these tools for maximal pedagogical impact? So the experiment itself is to take a very simple, in this case a very simple molecular binding event, a ligand is binding a receptor. But what we did is, we created that short theme in four different versions. And I can briefly describe those versions. Version one is where the ligand and the receptor meet in a very predictable way, let's say. The ligand flies in, lands very smoothly on the receptor as if it new exactly where it was going, there are no additional proteins in the environment, there's no particular internal motion (in other words, the proteins are dealt with as rigid bodies), and it overall looks like a very controlled process. Version two has the same actors, let's say, in the movie, but we have random motions on both so that you don't really have a sense that the ligand knows where it's going. Version three is identical to version two, except that we add molecular crowding in the environment, so a lot of other proteins bumping around. And version four is the same as version three, but we add even more visual complexity, where now we're showing actual molecular water and it's actually a complete mess, visually, but one in which the student can still follow the ligand and the receptor binding event.

So we have 200 students. We break them into four groups. Each group sees a different animation. They get a test before they see it; they get a test right afterwards. And they also have a test two weeks later for long-term memory. And then for some of the students, as you mentioned, we also have eye tracking data, so we know exactly what the students were looking at as they viewed the animation. And in a nutshell, what we found is that perhaps surprisingly, the students who were exposed to the more complex versions, visually-complex versions, tend to do quite a bit better than students who were exposed to the simplified versions. And I think the reason why I'd find that quite interesting is that it tells us that if the animation is cleanly designed, if you still can pull out the main event of the ligand binding, you can add all kinds of additional motion (and in this case crowding, let's say, of the environment) that gives students an intuition for how molecular environments may behave. And that type of information carries across the entire curriculum. It's no longer about, does A bind B. It's about having an intuition for Brownian motion or diffusion or things that we need to start thinking about embedding in the design of our animations. So we're very excited by this preliminary data, and I think quickly some obvious next steps to us relate to research that's been done, where we know that sometimes a movie, even a beautiful and accurate movie, that plays at you is not enough. You need to engage students. You need to trigger their ability to ask questions and even make mistakes. It's a, learning is an iterative process, and a lot of this comes out of kind of the inquiry-based learning field. So we've been looking at ways to give students control over dialing in and out the visual complexity of the animations interactively. So that it gives them the ability to essentially scaffold their understanding of the process — if they can dial in some of these additional, more complex visual layers. And even better, and I'll end on that for this question, is the idea that they might able to control a simulation of the binding event in real time, and actually we've started to create those tools as well. So it's not just about dialing in the visual complexity, but about changing the temperature, the concentration, so that they find conditions where the binding event may never even occur or they discover on their own what are the best parameters to allow the binding event to happen. And I think that would be an exciting thing to test.

MIKO: So this is like a very complex dimensional interactive, as opposed to a very 2D interactive, which is the popular form these days, where the student can remove action in the animation and see how that action actually affects the focus of the animation, which is really interesting. And I think that does really blend well with the inquiry based strategies that many people advocate now in science ed. What I'm curious about is, do you see this kind of — obviously this is a very labor intensive work — do you see this kind of science instruction becoming more popular? And do you see it as a trend increasing in science education in general?

MCGILL: I think that it's definitely a field in full expansion right now. I think scientific animation itself has been around for a little while. So that in itself is not really what's new. What may be new and improving is the care and accuracy with which these are created. And I think that comes not only from better tools, but also there's kind of a new generation, I think, of scientist animators, of people who have not only a command of the content but also the technical capabilities to pull off these high-end animations. So in that sense, I think, there's a new trend. And I'm involved in the creation of a new digital biology textbook, E. O. Wilson's Life on Earth. And I mention that, because it's been a great platform to test and develop our visualization skills and to be more proactive, basically, about putting some of these design principles into practice. So the focus, again, is not just to engage the students, but with the existing team that we have, and with this project, it gives us the ability to ask for every nugget of information: What is the best approach to teaching that one concept? It's no longer the idea that you write 1,000 pages of a textbook, and almost as an afterthought, you think of an art program. You think of developing figures for it. This is a bit of a new process where we can ask ourselves for every concept that we're teaching: What's the most efficient way to teach that? It may still be just a paragraph of text in certain cases. But in other cases, it may be a static diagram or an interactive diagram or an animation or even just a video interview with a charismatic scientist. So I think because we have all of these techniques in our toolbox, we're really excited to be embarking on this new project. And you know, in general, it's just a very exciting field to be in. Bio-visualization gives you an opportunity to combine not only your passion for science and your love of biology, but also it's quite technical in the way that you would implement these. So that combined with any artistic tendencies you might have, it's really an exciting field to be in at the moment.

MIKO: Well, thanks, Gael, for telling us about that today, and thanks for joining us.

MCGILL: Thank you.

MIKO: Thank you for listening to this edition of NatureEdCast. You can find this podcast and others at nature.com/scitable. That's nature.com/s-c-i-t-a-b-l-e. Please join us again next time.

In today's podcast, Ilona talks with Natalie Kuldell, a scientist and instructor in MIT's Department of Biological Engineering. Natalie began her career as a microbiologist, and her interest in education led her to apply her scientific knowledge to what she calls "authentic" curriculum development. With funding from the NSF, Natalie created BioBuilder, an online resource for both teachers and students about synthetic biology. BioBuilder features short, animated primers that explain the basics of gene expression alongside some foundational tools for engineering biology. This information is combined into teachable activities that explore how scientists can control the genes of microorganisms to enable new discoveries, or to construct useful new biological systems. As a part of the NSF-funded Engineering Research Center known as SynBERC, BioBuilder makes an important contribution by offering accessible, easy to use, and easy to learn from material that is appropriate for both high school and college classrooms. Listen to this podcast to learn how you can use BioBuilder. [10:51 ]

Full transcript

ILONA MIKO: Welcome to the latest edition of NatureEdCast. I'm Ilona Miko and today we're talking to Natalie Kuldell, professor of biological engineering at MIT, and creator of BioBuilder.org, an online learning resource about synthetic biology. Natalie began her science career as a microbiologist and her interest in education led her to MIT where she currently develops curriculum and teaches. With funding from the NSF, Natalie created BioBuilder, an online resource for both teachers and students to provide them with reliable instructional material about the fairly new science of synthetic biology. BioBuilder features short animated primers that explain the basics of gene expression as well as some basic technical bioengineering tools. This information is combined into teachable activities that explore how scientists can control the genes of microorganisms to either enable new discoveries or to construct useful new biological systems. As part of the NSF-funded engineering research center known as SynBERC, BioBuilder offers accessible, easy-to-use, and easy-to-learn-from material that is appropriate for both high school and college classrooms. Welcome, Natalie.

NATALIE KULDELL: It's great to be talking to you.

MIKO: Thank you for joining us. So tell us why did you create BioBuilder?

KULDELL: Well, let's see, I had been using synthetic biology in my classes at MIT to teach my students both the scientific ideas that they needed for bioengineering as well as some of the engineering principles, and I really liked the way that worked. So my students, as they were trying to design new systems or redesign existing ones, had to understand both the basic biology — things like enzymes and genetic control — but also had to work through the design and construction plans of their systems and synthetic biology really seemed to lend itself to those kinds of learning. So now, BioBuilder started when it was folks outside my classroom who heard about my teaching and grew really interested in this topic and wanted to learn about it. So it's interesting that synthetic biology does draw a lot of people into the field. They're interested, I think, because it's interdisciplinary, but also because there are some concerns and misunderstandings around it. So BioBuilder was my solution to trying to help people who might be expert in one thing learn the basics about something else. So for example, the policymakers who would come to me wanting to know about biology or maybe the biologist wanting to learn some engineering. So my initial idea was that BioBuilder could be an open website where anyone who was interested in synthetic biology could learn from.

MIKO: How did you create it? You already have a full-time job. So what resources were you able to assemble and how did you actually make it happen?

KULDELL: Yeah, my teaching at MIT keeps me busy for sure. But the National Science Foundation funded an engineering research center for synthetic biology, and with that funding, it really felt like I had an opportunity to work on something that was a little beyond the norm, something that could reach a broader community. So at that time, BioBuilder was leveraging the success of a comic strip that had appeared in Nature. It was in 2005 and that comic strip was called Adventures in Synthetic Biology. It drew a lot of attention to this new field and it was also trying to teach—

MIKO: Who made the comic? I'm just curious, who made the comic?

KULDELL: My colleagues Drew Endy, Isadora Deese here at MIT, and the Synthetic Biology Working Group that we have here at MIT. The comic was really successful in many ways, but we also found that it was hard for real newcomers to the field to understand all of it. And so, our next thought was that we could scaffold the material a little bit more, maybe break it down into smaller single-page comic strips and activities that people could do, and that would keep the content both interesting and entertaining but could also educate a broader community. So as you mentioned, I had wonderful colleagues working on this with me, including Drew Endy, who's now at Stanford University, but also had some wonderful high school teacher working with me. He's from Sharon, Massachusetts, named Jim Dixon and a great animation company in New York.

MIKO: So tell us more about how BioBuilder is organized. How can someone, once they get there, how can they use it?

KULDELL: So the site is fully open access and will always be that way. It's built for both teachers and students. Right now if you go to the site, you would find some hands-on laboratory activities that connect the science and engineering standards that most high schools have to meet or maybe could be suitable for biotechnology lab class or some early college-level laboratory class. There are also some classroom activities that don't require laboratory space. Those are focused on bioethics or biodesign. But the site is really modular, so there's no order, prescribed order, to the content that's there and no set number that needed to be, would need to be complete. So if you were a student, you could go, you could watch the animations and learn from them. You could engage in the activities, answer some of the questions. There's also a place to submit your data. If you were a teacher coming to the site, you could find some resources for preparing the reagents, grading rubrics, some sample data if you wanted to compare your class data to other data that's available, and see, there's also a forum, a discussion forum so teachers can share information with one another about how things are going.

MIKO: I took a look at some of the animations and I was impressed with the personalities that you ascribe to certain people, like the teacher, the lab person, and the student in the lab. Can you tell me a little bit about how you came to those kind of characterizations and what the creative process was for that?

KULDELL: Yeah, that's a collaborative process that we've come to over a time. I've really enjoyed how the characters have evolved. We've tried to sort of draw in a curious student and somebody who's a little expert in science and another person who's more expert in engineering, and I think the interactions really speak to the community and the necessary collaboration that has to occur in this field.

MIKO: I liked particularly the personality traits that you ascribe to some of the folks in the lab. I think a lot of scientists will see it a very familiar set of people in those interactions, and you make it kind of fun. You make it interesting and familiar, but you also make it fun. This seems like a new way to approach teaching, and I'm curious. It starts from an application-based sensibility and it sort of addresses why we should care or how can we use aspects of science. And it's a natural question for a graduate engineering student, but not really so natural for high schoolers or intro biology students. So how does BioBuilder fit into the current and future landscape of science learning do you think, as far as making science more accessible to broader audiences?

KULDELL: Yeah. For me, the real heart and fun of doing science is the investigation and the actual practice of it. So I would love in the future to see more teaching being done through the investigation of some good existing examples and through asking students to become participants and engage with the content directly. A lot of teaching and certainly some of what I had when I was coming through the ranks was teaching around technical aspects of what you can do. But really, techniques change so much over time, it really doesn't feel like there's a lot of usefulness in teaching just techniques. And then, in terms of just knowledge and direct content, that's so discoverable through Wikipedia and through any Internet search. So the message I would love to have students take away from this and other parts of their learning is that what they think really matters, that they need to engage with the content, not just as technicians about it but actual thinking members of a community. So if they do that, they could approach the material with a lot of enthusiasm and we'd expect them to approach it with thoughtfulness. People, maybe given how they've learned science or thought about it, don't really have a good feeling. Many people don't have a good feeling about what it is to be a scientist and don't really get engineering. But people can be just brilliant at it if they're given the room to make some discoveries and make some mistakes and maybe just make some choices about what it is they want to study. I mean, who wouldn't want to do that, right?

MIKO: Yeah. Do you think that BioBuilder and synthetic biology in particular, these kinds of approaches, do you think they serve a larger purpose of informing maybe not just students but the public about things like synthetic biology? Can you talk a little bit about some of the concerns that the public might have about synthetic biology and what a site like this can do to help rectify some of those negative images that the field sometimes has?

KULDELL: Right. So I'm actually in New York teaching at a community lab space some of the BioBuilder content and yesterday I got to teach an artist who was interested in working with biology and a physics undergraduate student and somebody who hadn't been in a lab for thirty years, but was a biology major in college. I think there are a lot of people who find interest and sort of a tantalizing aspect to biology, sort of see it as the future direction for solving many problems. But there is a fear that it inspires as well, that we don't really know what we're doing, that we're overreaching and not considering the impact of what we do. So I think that by actually trying some of the content and making it open and accessible, not only does it convey the notion that this is a community working hard at this, but also it really drives home the limitations of what we are able to do at this point, that much of the hype around synthetic biology talks about a future that is far off and hard to imagine and that what we have in hand right now is far more humble.

MIKO: Thanks for telling us about all of this today, BioBuilder and the way it actually is crafted to help us understand synthetic biology in a new way, and hopefully, attract lots of different audiences to the field. Thanks, Natalie.

KULDELL: Thanks for giving me the chance.

MIKO: Thank you for listening to this edition of NatureEdCast. You can find this podcast and others at nature.com/scitable. That's Nature.com/s-c-i-t-a-b-l-e. Please join us again next time.