This episode features an interview with Dr. Iwasa from University of Utah School of Medicine. She specializes in data visualization using Hollywood and video game techniques to create animations of systems of molecules.
We recorded on location in a restaurant in Salt Lake City. We apologize for the sound quality.
Image Credit: TED
Click Here for Transcript
>> Here we go.
[♪ Blackalicious rapping Chemical Calisthenics ♪]
♪ Neutron, proton, mass defect, lyrical oxidation, yo irrelevant
♪ Mass spectrograph, pure electron volt, atomic energy erupting
♪ As I get all open on betatron, gamma rays thermo cracking
♪ Cyclotron and any and every mic
♪ You’re on trans iridium, if you’re always uranium
♪ Molecules, spontaneous combustion, pow
♪ Law of de-fi-nite pro-por-tion, gain-ing weight
♪ I’m every element around
>> So I’m Janet Iwasa. I am a research assistant professor at the University of Utah in the department of biochemistry.
>> You are known for kind of mixing visuals with your research. So, can you give us like a really quick description of what you do?
>> So I usually say that I’m a molecular animator. So my background is in cell biology. I got a PhD in cell biology from UCSF.
>> What’s UCSF?
>> UCS — oh, UC San Francisco.
>> Oh, OK.
>> But, yeah. So I went to graduate school there and I got interested in animation while I was working on my degree. And so I — I’ve kind of carved out this kind of unique career path where I’m focusing on using animation as a means to visualize process, like molecular processes that, you know, my colleagues and I was studying in graduate school.
And we were right next door to a lab that studied these motor proteins, what are called motor proteins, those proteins that walk along microtubules, which is kind of like the highway of the cell that like spans from like the nucleus to the edge of the cell. And these proteins walk along them and kind of drag along these vesicles or whatever.
>> Or cargo.
>> And is this one of the first animations you kind of like dealt with? I think I remember seeing something that looks like these motor proteins.
>> Yeah. So what happened was that, at the time, I was — we had joint group meetings and so I was going to a lot of like Vale Lab group meetings and they were talking about kinesin, which is this protein. And, you know, they had all this kind of typical scientific figures to show what kinesin looked like and what it did.
And they were like, you know, circles and squares and triangles and lines connecting them. They looked kind of like stick figures. But, anyway, after I saw this kinesin animation, I got really interested in thinking about how to incorporate this into my own research and how to start creating animations by my — on my own.
>> And so I found out that there was a class — you know, UCSF, it’s a medical school. There are no art classes or anything like that.
>> Yeah. Yeah.
>> But, at San Francisco State University, which was like several miles away.
>> Yeah. Where my cousin went.
>> Ah, yeah. Yeah. And so they had art classes there and it turned out that, as a UCSF student, there was like some kind of exchange program where I could take classes at SFSU for free. And the class, you know, it, like most animation classes, it was really, you know, not a scientific class. We were like modeling — I think one of the first projects was modeling a living room. We had like — I modeled a sofa, a lamp, and a table.
>> Yeah. Well, that’s hard, though.
>> It is!
>> And it’s good training.
>> But then, you know, like I would do that and then I’d go back to the lab and I’d — I’d, you know, try to figure out how to get molecules into this software and how to start moving those around. But, yeah. So that was basically the first steps was really taking this class. And one of the things that I think was probably the biggest gift my advisor — you know, he was — I was clearly enjoying it a lot. And he basically said, you know, like if I wanted to keep doing animation, I could take every Friday for as long as I wanted to do animation.
>> And so that’s what I did for like the rest of grad school was like, your Friday, I was doing animation.
>> Wow. So you had taken multiple classes? Like —
>> So I took more classes after this. >> OK. Good.
>> So the class I took at SFSU was a software that’s — it was a software called Light Wave.
>> And, you know, by the time I had finished grad school, I was realizing that it had a lot of limitations.
>> It wasn’t a very commonly used software. Like, so if you went to Hollywood, the software that everyone uses in the studios is called Maya. It’s considered the industry standard like if you wanted to get a job, that’s the software you’d learn.
>> OK. OK.
>> And so I — I ended up doing a course — so, as part of my post-doctoral training, as part of this kind of fellowship that I got. I went to Hollywood for three months to learn this software.
>> What? OK. Wait. Wait. Let’s back up. So you applied to this fellowship and — sorry, listeners, we are at a restaurant. But — so you — do you apply to this fellowship that’s like somehow associated with like science and animation or like where did this fellowship come from?
>> Right. So it wasn’t an animation fellowship.
>> So, you know, by the end of grad school, I was really trying to figure out how I could do animation as a postdoc. Because I think my goal was that I wanted to do this for my career and I wanted to stay in academia because getting outside of academia seems scary. Like I just had no idea what that would entail.
>> You would be making so much more money.
>> Maybe so, but at least I knew what it meant to be in academia. So that was kind of my goal. And also because I felt like this is what academics needed. That, you know, this kind of tool, using — being able to visualize what we do seemed really important. So, anyway.
So I was really focused on this and, you know, I would have thesis committee meetings where, you know, they’d be like, “Well, you’re — you know, you’re going to be graduating in a year or two. Like what are your plans?” and I’d be like, “I want to do animation.”
>> And they would just be like, “Huh. Well, good luck with that.” You know? Like they — they just didn’t have much advice because nobody had ever done that.
>> Yeah. It’s not a common path.
>> It’s not common. Yeah. They just didn’t even — you know, they couldn’t — they couldn’t tell me what to do. But I was also telling my friends and different people about this idea. And one of the — my friends who ended up going into a career development position — and she was already thinking about that direction in graduate school.
>> Like what is career development? What do you mean?
>> Different careers. How to train graduate students and postdocs for — for like kind of the diversity of careers now that people are going into.
>> But she was already thinking about that. So this is Cynthia Fuhrmann.
>> And so she actually — I guess her ear is out for different opportunities as postdocs.
>> Nice to have friends like that.
>> Yeah. So she was the one who told me like, “You know, there’s this — there’s this NSF fellowship. It’s under chemistry, but there’s this NSF fellowship that is interested in creating new postdoctoral models that allow people to integrate kind of what they do in grad school with outreach.” You know, and so it’s called the Discovery Corps.
>> And it was a pilot. So, when I was looking at it, I think only maybe one — one year or two years had been — had started that fellowship.
>> OK. So it was almost brand new.
>> It was brand new.
>> Not many people had been in it. And so I — basically I called the person who was running this and I asked her, you know, like would it be possible for me to do something focused on animation as a postdoc?
>> She was like, “Absolutely!”
>> You know? She was like extremely warm and like very encouraging.
>> So your luck is very good.
>> I guess.
>> You know, like I feel like your story is like, “And then I approached this person and they were like, ‘Great!'” And that’s not, you know — not everyone has that experience. Right?
>> I didn’t expect — but I had a lot of dead ends prior to that.
>> Like where I had looked at traditional postdoctoral fellowships and e-mailed them and asked them like, “Can I do animation? Would that fit?” and I either got no response or just, “No.” You know?
>> So basically — I mean, this story you’re telling me is a very short version of like you’re trying to go all these different avenues.
>> Trying to get money in all these different ways.
>> Just try to figure out how to do this.
>> Because you really want to do animation?
>> And I had no other plans. Like this was all I wanted to do [laughing].
>> Wow. You were like narrow minded. You’re like, “I want to do this.”
>> “This is like — I’m passionate about this.”
>> I had no alternative plan. I — we were years out from graduating and my husband — so he was my boyfriend at the time and I was like, “Well, I think I have to come up with a proposal and write something, but then I need — we need to know where we’re going so I can find an advisor.”
>> And he’s like, “How about Boston because I’ll be able to find something there.”
>> What does he do?
>> So he is a neurobiologist.
>> He was actually in the Vale Lab when I was there.
>> So we were right next door to each other. And so when I was talking to Kathy Covert at the NSF, I said, “Well, so, you know, my background is in biochemistry, cell biology, but, you know, I know this is a chemistry program. So I’d like to meet some chemists who might kind of be interested in working with me on animation. Do you know anybody like that in Boston?”
>> And she —
>> You’re like, “Specifically in Boston.”
>> Yes. And she’s like, “I will send you a list.”
>> Yeah. So she was amazing.
>> Is she still there?
>> Yes. Yes.
>> And so she sent me three people and I e-mail them all. I looked at their research.
>> You just cold e-mailed them?
>> I looked at all — I looked at their research and tried to imagine how animation might be able to help them communicate their research. E-mailed them all. And only one of them responded [laughing].
>> OK. I’m sorry. We’re laughing, listeners, because it is a common scientific outcome.
>> Yeah. And Jack Shaw Sec was the only one who responded, but his response was very favorable.
>> So he was — he’s working on — he’s at Mass General Hospital, also affiliated with Harvard Medical School.
>> And he studies the origins of life, the chemical origins of life. So basically how did — how was biology born, you know, from chemistry basically.
>> How did the — you know, small molecules get together to form what would be like the earliest cells on Earth?
>> And he gets a lot of — there’s a lot of interest in the public about how — how the origins of life — what people think might have happened.
>> But not a lot of very good visuals.
So like, “What did these early cells actually look like?” and there are a lot of people doing experiments to try and think about what’s the most pre-biotically plausible way that these cells may have formed like memories and molecules that had — had a way of encoding information and carrying out enzymatic functions. So that’s kind of what the idea of it is.
>> Yeah. As you’re — as you’re like describing this, I’m trying to like visualize. I’m like, “What would that look like?”
>> So basically the earliest — you know one version, at least, is membrane. Like a vesicle with an RNA inside it that’s capable of both copying itself — well, basically just copying itself, but made out of RNA. So it’s made out of like something that can encode information the same as DNA, but can also catalyze a reaction.
>> So this is the basis of what people call the RNA world. So basically before there were proteins and DNA, there was just a cell with just RNA that could do both.
>> Both the functions of DNA and proteins, but DNA and proteins are better at it. So, you know, that ended up kind of overtaking the RNA world.
>> And there were probably steps before the RNA world.
>> Before these cells. There was something, but, you know, that’s a little hazier.
[♪ Janelle Monae singing Wondaland ♪]
♪ Early late at night
♪ I wander off into a land
♪ You can go, but you mustn’t tell a soul
♪ There’s a world inside
♪ Where dreamers meet each other
>> So you’re helping visualize this primordial cell with just RNA inside and how that would interact with other cells in a community or just by itself? Or like what are you working on at that point?
>> So in the Shaw Sec lab at the time there were a lot of people doing experiments trying to understand the — sort of the characteristics of different aspects of this early cell. One part of the lab studied fatty acids. So these lipids that were thought to be maybe form the membranes of these early cells. So kind of less complicated than the sort of lipids that make up our cells. Anyway, so that — I was — a lot of the animations had to do with trying to just visualize what the lab experiments were doing. So, how do — how does — you know, if you add a bunch of small groups of lipids, called micelles, to a mixture, how do they start forming vesicles, which is like — has a membrane of a different kind of characteristic than the micelle.
>> Like more like a bubble.
>> So things like that. So basically trying to visualize that, but the overall goal was also to do public outreach, to basically create animations that could explain the research to a broader audience. So they would serve a double purpose, a dual purpose. The researchers could use them, say, you know, “This is what we think is going on in our experiment,” basically their model. And then also, you know, to the public, “This is how we think life — one step that life — whereby life may have evolved into having cells.”
>> So yeah. So — and the end goal was to create this sort of — a set of animations that was used in the Museum of Science in Boston. So I worked on an exhibit called Exploring Origins.
>> Yeah. I read that! So how long did this exhibit go and like what was your — I mean, you probably weren’t there like pointing at stuff all the time.
>> But like what was the exhibit? What was it like?
>> So that exhibit, it was a touch screen kiosk. And so I incorporated —
>> So what year was that?
>> It was 2008 when it was released.
>> Oh, OK.
>> So I started — my postdoc was only two years because chemistry postdocs are apparently — are very — I mean, for a biologist, that’s incredibly short. I did a bunch of presentations. They had this kind of a news desk at the museum where a scientist could come in and present things at the museum.
>> I’ve seen that. That’s pretty standard.
>> So I would do these — I think I did it maybe every other week for the summer before I finished my postdoc.
>> I did presentations on the origins of life.
>> So you were there a lot by your exhibit?
>> And I also created this website, which I call like this online exhibit. So it has all the animations. The — that — the narrations on the animations on the website are a little bit more, you know, kind of more complex than the ones that we created for the museum.
>> And kind of digs into the science a little bit more.
>> I mean, because — do you — do you have probably links to things that they can reference and stuff within the website?
>> So it’s like if things are more complex on the website, then they can kind of like figure out what that complexity means. Right?
>> Yeah. So I have like resources to learn more.
>> Yeah. So that was basically the three components of that, but kind of the outreach side of the project.
>> This is 2008. This is when my daughter was born. So, as you’re doing all this, are you also like starting a family and like — that seems very stressful.
>> Yeah. So my husband and I got married in 2008 and we had our first son in 2010.
>> OK. So, yeah.
>> So that was after — yeah. So I didn’t have a kid until I was a faculty member [laughing].
>> For the benefit purposes.
>> Yeah. No. I hear you. I can see how that happens. So I’m reading up about you before I come to interview you. And you’re like known as this person who is really linking, you know, cell biology to animation. Since you started doing that, is there now this like movement towards it? Or are you still like the only person doing it?
>> It’s hard — it’s hard to say. Like I feel like I — I field a lot of questions via e-mail and like I chat with people and I talk — I give a lot of talks about my career at various places. I’ve even written articles about my career path.
>> Yeah. Because this is like almost 10 years ago now. So you would think other people —
>> I’ve been doing this for like 10 years.
>> Yeah. Or more because you — when you were trying to get that postdoc, that was more than 10 years ago.
>> Yeah. Yeah. So it’s been a while.
>> So there’s different paths one can take in this general field of visualizing science. There is — the more established path is one that’s basically a — you can get a master’s degree in medical illustration. There are these programs — I think in this kind of the course that’s run by the AMI, the Association for Medical Illustrators.
>> Thank you.
>> I think they teach you things like — it’s kind of a fine arts sort of degree.
>> So a lot of people going into it are artists. But they teach you the science, but they also teach you kind of like the business side of like if you wanted to run your own freelance studio, like how do you do that.
>> This seems very nice of them to do that.
>> Yeah. Well, I think it’s necessary.
>> Like how do you charge people?
>> Things like that. But, anyway, so I think that kind of trains you to go into illustration studios and kind of a different career path than I ended up taking partially because I come from within the academic sciences.
>> The sciences, yeah.
>> And I think I just, you know, like this is where I prefer to stay.
>> Well, and that’s also — I would say, not knowing very much about fine arts education — but I was say, at least in the sciences, we’re kind of expected to learn things on our own. You know, they’re like, “Well, you’ll figure out.” You know? Like, “There are resources and you’ll figure it out.”
>> So I — I mean, I think that’s how we’re taught to teach too. Right? We’re like, “Oh, you know, you want to be a professor. You’ll figure it out.” Like we’re not giving like teaching courses and we don’t have teaching certificates. And we don’t have to take tests on, you know, methodology — pedagogy or anything like that.
>> Or curriculum creating. My other question was — so who kind of utilizes your skill then? So you have this skill of animation, but are you contacted by people like in Hollywood to like help you with that? Are you contacted by other people — other biologists? Like what do you do now currently? Like what’s your big — what are your big projects now? And like are some of them different from each other? Are they — you know. What’s happening now with that skill?
>> Yeah. Yeah. I have several ongoing projects. So, you know, the goal being a faculty member in a research department is really about becoming, you know, kind of financially stable.
>> And getting fund — which means getting funding.
>> So writing grants and getting funding. So I have several grant funded projects right now. The biggest one — and the biggest one especially, that focuses on animation, is called “The Science of HIV.” And it’s basically — the goal is to create an animation that shows the entire lifecycle of HIV at a molecular scale.
>> And so this is a collaboration with what’s called a P-50 Center. It’s a big NIH funded center that’s based out of the University of Utah chaired by the chair of my department, Wes Sundquist. And so the goal of — there is five P-50 centers around the country. They’re a, I think, like $5 million a year grants. They fund — each center has 10 or 15 — 10 to 15 different PIs. And they’re all studying the structural biology of HIV. So basically what do the molecules that, you know, carry out different functions in the HIV lifecycle, what do they look like? How do they interact with each other?
>> Yeah. Which is very important to understand.
>> Yeah. So like a very mechanistic understanding of what’s happening. And so this has been sort of a collaboration mainly with the P-50 Center I’m associated with, but, well, with a bunch of others too.
>> So that’s one of the main goals that’s been really great to work on. And so the hope is to release this sort of longer animation, kind of a fully fleshed version, in the spring of next year.
>> So that’s be a major one. I have a lot of smaller animation calibrations that have resulted in getting published in various — so kind of the animated model figure has been one of the things that I have been really interested in trying to do, especially now that we’re kind of entering the digital era of publication.
[♪ Janelle Monae singing Wondaland ♪]
♪ Dance in the trees
♪ Paint mysteries
♪ The magnificent droid plays there
♪ Your magic mind
♪ Makes love to mine
♪ I think I’m in love, angel
♪ Take me back to Wondaland
♪ I gotta get back to Wondaland
♪ Take me back to Wondaland
♪ Me thinks she left her underpants
♪ Take me back to Wondaland
♪ I gotta get back to Wondaland
>> I actually was just thinking, I had read something where you have this online free application and free software to — so people can do animation on their own.
>> Yeah. So one of the —
>> So tell me about that real quick, though, before we talk about this now online flip book. I really think it’s amazing what you’re doing because you’re actually helping people understand the science in a way that is very, very much accessible. When you’re reading a textbook, especially in biology, at least you all have the pictures and stuff and that’s really awesome, but, in physics, you know, we have less. But, like you said, if you see an animation, that concept clicks in many, many people’s minds, probably more than I think traditional scientists would think. So with your online flip book, is there also an element of like citizen science or community science — people in the general public that aren’t necessarily biologists can actually contribute to data? Is there a portion of that? Anyway, continue talking about the flip book.
>> So, yeah, the flip book project was born out of two major observations that I had made over the years with — over like dozens of calibrations with researchers who are — actually, you asked this before, but it’s really — most of the people I work with are in the academic biological, like molecular biology. So basically my idea is, you know, if you can see it by a microscope or by eye, I don’t animate it. You can see it. There’s no reason.
>> Got it.
>> So like the reason to do molecular animation is because we can’t see it.
>> This is really about hypothesis exploration and development and being able to basically see something that we would never be able to see otherwise because of the scale at which these things are happening.
>> And the need to kind of take a lot of different types of data to create this — basically this story of what we think is happening.
>> Right. Because you need to have the correct parameters. Like you can’t have this animation and be like, “I have this hypothesis and I put it in,” but if the parameters are wrong, then that’s not what would happen. Right? So you need to have all this data that goes into your animation to verify that that’s happening.
>> Yeah, it’s not so much of a verification so much as — you know, the way I think about it is that a biologist, a molecular biologist, has many lines of different types of research that feed into this idea of what’s happening with a specific — so, for any given protein, a researcher may have been studying this one protein, this one pathway for like decades trying to understand like what it’s doing inside the cell, what it’s main role is, who is it interacting with. And, as a result of many lines of different experiments, they have a movie in their heads of what’s —
>> And some of that might be based on, you know, raw data. And some of it may be conjectural because they haven’t been able to think of an experiment to test something.
>> Oh, OK.
>> Or it hasn’t been tested for whatever reason. And so they have this movie playing in their head, which, you know, the same kind of data, another scientist in the lab would have a different movie playing in their heads.
>> Or they don’t trust some of the data. You know, like whatever — for whatever reason. But it’s what the basis of which — on which they’re forming new experiments. They’re thinking of new experiments, how to test this. But if you can’t even ever see that, you know, like how can you move forward or modify? Or even communicate with other people like what you think is actually happening when you’re sort of limited by this sort of jargon?
And, you know, you’re not really — you’re not showing all the connections you know. So, anyway, the idea is that the understanding of biology, especially now, is very rich. There’s a lot of information that we have that the type of visualizations we can create or have been created are usually very kind of data poor. And so it’s a matter of trying to make those things match a little bit better. But, anyway, so the two things that I had sort of observed over the years is that people want to create their own animations.
And there’s a lot of reasons for that. One is that, I think, you know, in my experience of working with people, the ah-ha moments happen when people are able to really kind of think on their own. They’re exploring things. They’re kind of playing with things and they realize, like, “Something’s missing here. Something must be here that we don’t — we haven’t discovered yet.”
So people can make those kinds of observations, but mostly when they’re kind of sort of hands on. They’re being pretty hands on about that — this process of creating an animation, this visualization. So and the other thing that I noticed — so people want their own animations. They want to be able to do it themselves.
>> And the software that I use — three months in Hollywood it took me to learn it [laughing]. That’s like not a — you know, it’s not something that’s feasible.
>> And I’m going to ask you about those three months after you’re done with this.
>> OK [laughing].
>> And also about cartoons.
>> Yeah. And the second thing is that, you know, I’ve made a lot of animations over the years and people in the same field — like I said, everyone has a different hypothesis in their head of how something works, especially the longer they’ve been in the field, the more different their ideas may be.
>> So, you know, if I make one animation showing a molecular process, it’s almost a guarantee that somebody else will see it and say, “Well, that’s wrong. That doesn’t match my mental model for x, y, and z reasons. Can I just take that animation and change it so it matches my mental model?”
>> And the answer is typically, “no,” because the software is so hard to use.
>> And it’s taken like blood, sweat, and tears over the course of months or years to create this animation.
>> It’s usually just like a little bit of an IP issue just to give away stuff. So my idea for flip book was, “Can we overcome this by creating a software that’s intuitive, that’s easy to use, that lowers this barrier to creating a molecular model, an animated molecular model? And then make people share them online?”
>> So you have this way of like having a database and being able to share that.
>> So it’s almost like, I mean, in astronomy there’s a lot of python — people are using python for plotting and data processing and there’s a lot of online sharing of that. And like, you know, code that you can just put up and share. So it’s kind of like that where you can have the animation code and you’re kind of cutting and pasting somebody else’s work to help your work and all that kind of stuff?
>> Yeah. Sort of. Yeah. So, I mean, with animation —
>> I don’t know anything about animation.
>> Yeah [laughing]. Usually — there’s something called typically a scene file, which is kind of the raw information that you need to open the scene — an animation within a software. And then you can make changes to it. So when you have — when you — you can — once you have a scene file and you have an animation software, you can render it out to like a video. But the video, you can’t change. You can’t edit that. That is like a static thing. It can’t be changed.
So what you need is like the scene file to be able to edit it. So my idea was, you know, like say you’re a biologist, you’re studying some protein pathway, you know, protein A and protein B get together and they do something. You know, I could look at that and I’d be like, “Well, you know, like I just discovered a protein C that is a part of this pathway. Can I just download your animation, your scene file, and add my protein?”
And then you can kind of see how different people’s hypotheses are different visually, like kind of a visual map of how these ideas diverge and kind of like refine over time, getting closer to maybe a consensus model of how something works.
>> That’s awesome. So — and you launched it in March? Right?
>> So this was launched actually in 2014.
>> Oh, OK.
>> The flip book project is actually — is aging a bit.
>> And, you know, so one of the things that I found is that, you know, I’m not a software developer. So this was a grant that was funded by NSF. And I hired software developers to help me with it.
>> Oh, that’s good.
>> But since, you know, the — it was launched, we, you know, haven’t been able to maintain it. So the hope is to really work together with another group to basically create a software that basically other groups may be able to maintain. It was released as an open source software and kind of constitutively beta. More like a test like to figure out, is this something that the research — you know, researchers would be interested in? Is it something that we can make, some software that’s actually intuitive that people can learn over the course of an hour rather than the course of months?
>> Or maybe a week.
>> It is literally! Like so the way flip book, the original version — our test for it was that we had an animation that we created, like protein A binding to protein Be, and we showed it to people, students who had never touched animation software. And then we showed it to like — literally like probably a five or six minute tutorial on flip book and asked them to recreate the animation, you know, the timing, the protein.
>> We told them what proteins they were. And they were all able to do it in 10 minutes.
>> Oh, my God.
>> So it’s pretty easy to use.
>> But I think right now I have to have a caveat that it’s not working in all OSs because of the maintenance issue. But I think it was a good lesson to figure out like what can work. And the fact that people were really interested in having this kind of software.
[♪ Janelle Monae singing Wondaland ♪]
♪ Take me back to Wondaland
♪ Me think she left her underpants
♪ The grass grows inside
♪ The music floats you gently on your toes
♪ Touch the nose, he’ll change your clothes to tuxedos
♪ Don’t freak and hide
♪ I’ll be your secret santa, do you mind?
♪ Don’t resist
♪ The fairygods will have a fit
♪ We should dance
♪ Dance in the trees
♪ Paint mysteries
♪ The magnificent droid plays there
>> Let’s go back to your three year — three years? Three months in Hollywood. Kind of — so you’re in San Francisco. You’re so close to Pixar. Right? And —
>> We visited Pixar as part of SFSU’s — like one of their field trips.
>> OK. Did anyone at Pixar, you know, hear about your work and maybe was like, “Oh, maybe this could help us?” or vice versa where you heard something at Pixar and you were like, “Maybe I could help you?” Did anything happen since you were so close?
>> When I was at UCSF I’d say I was pretty inexperienced with animation.
>> I’d say, no, not really.
>> But you got to go there and it was awesome?
>> It was fun to see. I think, in the end, in animation in general, if you’re in a studio, you end up specializing a lot. So, you know, you’re a modeler or you’re a lighter or you’re a rigger. You know? So you’re really kind of only taking — and, actually, the software — all animation software, you can do all of these things, like all of these different jobs. You know — so what I do, in sort of the industry terms, and called — I’m a generalist. I do everything.
>> I do the lighting. I do the shading. I do the animation.
>> That sounds very stressful.
>> It — well, it’s just one piece of software at the same time.
>> And I kind of like that. Like you’re in control of the entire story. You’re not being told like, “OK. Not you just — you know, you just got to make this mouth move.” Not to say — not to overgeneralize about what animators do, but I like having that amount of kind of artistic control over that. Studios like Pixar seem like it would be really fun to make movies like that, but —
>> It’s like a machine, though, right? Like you were saying, like you have — you have so many people in all these different portions that together create something gigantic.
>> But when you were working in those three months, were you a generalist then too, or were you put into one specific thing?
>> Oh, so I wasn’t working.
>> This was a course.
>> Yeah. So I went to Hollywood for — to take a course in the software that I use now, which is called Maya.
>> Got it.
>> So it was like a 10 week crash course in this one piece of software. Like 9:00 to 5:00 every day for 10 weeks. Yeah. And even then you’re still just kind of scratching the surface of figuring out what the software can do. So that’s basically one of the reasons why I think it’s not reasonable to expect like a scientist who’s working at the bench to be able to just pick up the software and start making models. Like I don’t think that’s reasonable.
>> Yeah. Well, did you get to experience anything in — during that course — because you’re physically in Hollywood. Right? And you’re like in that culture and that environment. Was there anything that was surprising to you that happened or what you learned about that industry that you didn’t expect?
>> I mean, it was a school so I guess, you know, like there was a limited amount of — you know, like a lot of the instructors came from different studios and could speak to having that kind of experience.
>> Were you the only scientist?
>> I was the only scientist and I was the only woman.
>> Yeah. So it was —
>> So they might think that all scientists are women.
>> I think [laughing] — you know, the people there were sort of entertained by what I was doing because it was so sort of out there.
>> Really? Did you get a lot of odd questions?
>> You know, not really, but I think I asked a lot of odd questions. You know, because I’m trying to think of — you know, we’re like modeling robots and like explosions and stuff like that. And I’m thinking, “OK. I’m doing everything that we’re supposed to do for this class, but I’m thinking about, OK, how am I going to use this to animate a virus?” or, you know —
>> A bunch of molecules floating around in a cell?
>> I would be thinking like that would probably not blow up.
>> Yeah [laughing].
>> Like that wouldn’t fall like that.
>> Yeah. Exactly. So I would ask questions like — I think — I was thinking about something about viruses and I would ask questions like, you know, “Say you had a soccer ball and you wanted to remove all of the faces, just kind of blow them up, and then you put them back together piece by piece, pentagons and hexagons, in order from the bottom up. How would you do that?”
>> And they’d be like, “Wow. That’s really — that’s really a strange question. That’s really weird.” but then they’d answer. They’d be like, “OK. So there’s this way or that way you could do that.” So I think a lot of it was just thinking of ways like, OK, this is not really a real-world scenario, but I can at least try to come up with something that sort of describes what I have to be able to do. Yeah. I think there’s a lot of things with molecular animation that people just — you know, like multiples. Like you need thousands of molecules to create like a vesicle or something. And like how do you control all these things at once?
>> I remember I’d seen one of the videos that you had of the PBS video and you talked about this idea of like Lord of the Rings, like the battle scenes had made you think about — like all of these people are in the battle and they’re interacting in some way that looks realistic. How do you do that with molecules?
>> So that’s what we’re working on with the Allen Institute — is agent base modeling. And basically, you know — yeah. So Lord of the Rings — there’s this software called Massive that was used to animate the armies of dwarves and elves and humans and whatever. And so the idea is that [laughing].
>> You’re like, “And whatever..”
>> So [laughing].
>> The molecules.
>> Yeah [laughing]. Ork molecules. But, anyway, like when you think about it as a biologist, like proteins are doing the same thing like based on their surroundings and how close they are to some other protein that they might bind to. They could have a different reaction and a different outcome. And, really, when you’re thinking about multiples, you’re just throwing a lot of these things into one scene and seeing what kind of falls out of that.
>> So, yeah. So that’s the idea for some of the things that we’re working on at the Allen Institute is thinking about how we make proteins into agents to create simulations that are kind of more — more intuitive to think about in biology. So not doing molecular dynamics kind of thing like thinking about where every atom is, but really thinking about proteins as agents being able to make decisions, having different states, and moving between those different states based on what’s around them.
>> Which is very different from how the simulations are done now, is what you’re saying?
>> There are some simulations that are done that way. So I think we’re thinking a little bit more of a zoomed out view than some other researchers are thinking about. So we’re not like thinking about the atomic level. We’re thanking more about how different proteins interact and different — like kinesin walking is one of the things that we’re thinking about in terms of how to create a simulation of that, how it interacts with microtubules and like that kind of thing. Yeah. And so I think that — and then, you know, hopefully we can also build in some animation tools in there too.
>> It all sounds really awesome. When I was a child, I really loved animation and wanted to do that and science. That was always my dream. But I wasn’t very good at art so I just gave up. Plus, I mean, who does that? Who — except for you now! But I just think it’s really, really awesome. I want to like end with two things. One, is there anything I didn’t ask that you want to talk about? You can think about that while I ask the second one. I always ask my guests about some amount of pop culture. So there’s so much of your work that kind of does — like we were just talking about Lord of the Rings. We were just talking about all these things. Are there anything — or any representations of biologists or cell biologists or anything in TV, movie, that is like super inaccurate? Or actually a show or TV/movie that actually did do a good representation of science or how — you know, biology is done? That’s my question. Like, pop culture. How are you —
>> Yeah [laughing]. Cell biologists are not well represented in pop culture as far as I can think of [laughing]. Like I actually can’t think of any — you know, like no Big Bang type equivalent of like — you know [laughing] — for like biologists.
>> There’s that movie Evolution that came out with David Duchovny.
>> I haven’t seen it.
>> In ’94. Yeah, I was a long time ago.
>> That was when Jurassic Park came out. So we’re talking like — I don’t even know how long ago that was. There was some scene where they had a microscope that was made by a specific manufacturer and the scientists in the movie apparently are using it wrong.
>> Yeah. And I think they had — there was some kind of a competition, I remember, to watch the movie and say exactly what they were doing wrong about it or what was kind of wrong. And my dad, who’s a scientist, got really excited about seeing Jurassic Park for this very reason.
>> He was like, “It was an OK movie, but I found that scene.”
>> Yeah. Exactly. “Look at what they’re doing with that microscope.” And, you know, things like X-Files would show things like DNA and they’d be like showing some — some kind of thing that it would be really hard to interpret. And they’d be like, “Look at this!” and, you know, “Look, the sequence is wrong,” or something. And I think that always is good for some laughs because, you know, you can’t — you know, you’re not really looking at just like, you know, an x-ray or something like that and saying something about a sequence.
>> Well, thank you. I want to thank you for taking the time to come to this beautiful restaurant, which just suddenly got quiet here. But thank you for talking to me and hopefully I can talk to you again if this audio turns out to be crazy.
>> OK [laughing]. Sounds like a great plan.
>> Thank you so much.
>> Thank you.
>> Thanks for listening to Spark Science. If you missed any of our show, go to our website, sparksciencenow.com. If there’s a science idea you’re curious about, send us a message on Twitter or Facebook at sparksciencenow. Spark Science is produced in collaboration with KMRE, Spark Radio, and Western Washington University. Our producer is Regina Barber DeGraaff. Our audio engineers are Natalie Moore, Andra Nordin, and Tori Highley. Our theme music is “Chemical Calisthenics” by Blackalicious and “Wondaland” by Janelle Monae.
[♪ Chemical Calisthenics by Blackalicious ♪]
♪ Lead, gold, tin, iron, platinum, zinc, when I rap you think
♪ Iodine nitrate activate
♪ Red geranium, the only difference is I transmit sound
♪ Balance was unbalanced then you add a little talent in
♪ Careful, careful with those ingredients
♪ They could explode and blow up if you drop them
♪ And they hit the ground
[End of podcast.]