Janet Iwasa (Harvard): Animating Cell Biology

Uploaded by ibiomagazine on 26.09.2011

Hello, my name is Janet Iwasa,
and I am an animator at Harvard Medical School.
I'll be talking to you today
about some of the reasons I first got interested
in animation and the ways I think animation can really give back
to the research community.
So this animation of kinesin was really one of the first
things that I saw that really got me interested
in animation. I remember I was about a first or second
year graduate student in Dyche Mullins' lab,
studying the actin cytoskeleton at the time.
And I remember looking at this animation and thinking, why aren't we all doing this?
Why are we relying on these oversimplified static illustrations
when we can really be doing something like this which shows dynamics
and a lot of things way more accurately
than we currently are.
So within a year I started taking animation courses
at a local university and also started doing animations
of some of the processes that my lab was studying.
So all of my animations are really a close collaboration between myself and the people who are
doing the research, and there's a lot of real
back and forth that goes on
in the process of creating these animations. We go through
many, many iterations and change things like color
and dynamics, and in this case, the number of filaments,
how fast they should be depolymerizing and polymerizing.
And so it really is this great collaborative process.
Animations, it is really a pretty steep learning curve
to learning animations, and it was also...each animation really took me
quite a long time, especially at the beginning,
but I found that I really loved the process.
I loved sitting down with my labmates and trying to figure out what
these kind of processes should look like visually.
And I also found that it could really give back to the research
quite a bit. So, when you are creating an animation,
you are really grappling with a lot of issues that don't necessarily
come up by any other means.
For example, you have to think about not only stoichiometry,
but also dynamics and crowding,
things that may not come up if you are really creating
these very simple illustrations.
So towards the end of graduate school
I became interested in trying to look for opportunities
that I might be able to do animation as a postdoctoral fellow.
And I was really lucky to find an opportunity that was offered by the National Science Foundation
called the Discovery Core.
And so, as a Discovery Core fellow, I worked for two years with Jack Szostak
at Mass General Hospital and the Museum of Science in Boston
to create a multimedia exhibit on the origins of life.
And this used a number of animations that
explored ideas around the RNA World hypothesis
as well as some ideas of what the early Earth might have looked like.
So many of these animations really served a dual purpose.
First they were incorporated into a multimedia exhibit that included
a website as well as a kiosk on the museum floor
that is currently there right now,
as well as a number of live presentations that I gave at the Museum of Science.
And they were also used by researchers in the lab
to talk about their science to other researchers
And what we found was that just by altering the context, as well as
the narration for these animations, you could really
use the same animations for two different audiences.
I also grew quite a lot as an animator during this
time, so I was really lucky to be able to take kind of a
crash course in animation in Hollywood for the summer before my postdoc started.
And this really allowed me to hit the ground running.
And I also found that there are a lot of tricks that you have to use in animation to
create molecular animations. So a lot of the animation packages that we use today
are really more for animating things like Buzz Lightyear
rather than molecules like actin.
So for example for this animation,
I used cloth simulation to try to create a simulation of RNA folding.
So what I also found was that animation could be a
great handle that the public could use to try to grasp
and understand complex molecular ideas.
So animation can really eliminate the need for jargon
in many cases and is also quite approachable.
And so for these kinds of reasons I think animation
can really be a great tool to try to make a positive impact
on science education, as well as the public perception of science
and ultimately, and hopefully, science policy.
After my postdoc, I started working at Harvard Medical School in the Cell Biology department.
One of the things that I am really interested in understanding
is how animation can be used by researchers to better explore and communicate
their kind of molecular hypotheses.
And so this is an example of this kind of project, this is an animation
clathrin mediated endocytosis
that I worked on with Tom Kirchhausen.
And what I found was that animations can really synthesize a
great deal of information, including...you can include molecular structures
from crystal structures and EM sources,
as well as you can include dynamics from light microscopy data,
as well as how protein-protein interactions
that are derived from genetics and biochemical experiments.
And another thing to note is that these kind of animations
are really kind of a visualization of a hypothesis.
So they may not, everything in the animation may not be completely supported by
experimental evidence, while other things may be,
and I think that's the same for any kind of hypothesis.
I also found that animations can really be
quite interesting for researchers, so the process of
creating an animation really makes you, as I mentioned before,
grapple with different issues that may not come up
when you are making other types of illustrations
so it is really kind of putting together a three dimensional
or a four dimensional puzzle. And by manipulating these different pieces you can really come up with
a lot of different ideas that
may not come up otherwise.
And I think for that reason,
these kind of animations and animation tools
may be able to really give back to research
and the research process.
So this final project that I would like to talk to you about
is a project that I am working on with Sam Reck-Peterson
at Harvard Medical School. Her lab is interested in
understanding the motor protein dynein and how
it walks along microtubules.
So as you might imagine this is a really
three dimensional and dynamic process.
And so using a 2D illustration such as this one really can be of limited utility.
when thinking about these kinds of problems.
So what we did together was to create a 3-dimensional
model of dynein that the lab could manipulate and move around
and really kind of use to explore the molecule in ways that they really
weren't able to before.
So really the goal of this project wasn't to create a finished and polished
animation, but really to create a new tool
that the lab could use to better study this process.
And using these kind of models, you can really start to
visualize the walk cycle of dynein, for example.
And each person in the lab, you can imagine, might have a different idea
of how this happens, and you can also start to try to predict
what might happen if, for example, you mutated the protein, or you put it in
to different conditions. And you can compare those things side by side
and potentially start designing experiments around these kinds of ideas.
And finally I wanted to leave you with a list of resources
that I hope might be useful for those of you who are interested
in learning more about animation.
The first is my website at Harvard Medical School
where you can download many of the animations that I showed you today
as well as new animations and new projects as they come up.
The second link here is called molecularmovies.org, which is
a really excellent resource. It has a gallery
of animations that you can download, a number of tutorials specific for molecular animation.
And there's also, in the past few years, been a number of
efforts to try to create new toolkits within
animation programs that can be used by researchers
to more easily upload and manipulate molecules.
And so this includes Molecular Maya, which is available at molecularmovies.org,
And this is for the program Maya.
There's also EPMV, which is available for Cinema4D, Maya, and Blender.
And there's also BioBlender, which is a tool kit for Blender.
So I really encourage you to take a look at some of these websites
if you are interested in learning more, and also feel free to contact me as well.
And also keep in mind that many of the software
that is out there you can download an educational version
and start exploring these animation tools for pretty much no cost.
And so that is something you also might consider doing as well.
Thank you.