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Tiny and beautiful worlds: Talking molecular animation with TED2014 Fellow Janet Iwasa

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At the TED2014 Fellows talks, Janet Iwasa’s astonishing video — which showed the process of molecular self-assembly — went by very quickly, a flurry of green strands and fragments fluttering, before flying into the shape of a soccer ball. If you missed it, or if you’d like a more in-depth explanation of what is actually going on here, watch a longer version of the video, above.

Iwasa spent years learning the 3D software that allows her to model these processes. This week at TED2014, she is launching Molecular Flipbook — free, open source animation software that will make it easy for scientists to create their own molecular animations, allowing them to visualize, modify, and share their own hypotheses. Here, Iwasa tells us about the importance of molecular animation to the research process.

What are we seeing in this video?

This is a process that’s called clathrin-mediated endocytosis. Basically, it shows how a bubble (or vesicle) is formed from the membrane that surrounds the cell, allowing molecules that were once outside the cell to get trapped and taken in.  This process is important for a number of things, like how cells communicate with other cells and how they interact with their environments. It’s a process that can also get hijacked, for example, by viruses that want to gain access to a cell.

How did you begin animating molecular processes? 

When I was in graduate school, I realized that the way we visualize hypotheses — typically using simple stick-figure like drawings, didn’t capture all of the information we had about how processes occur. We use a lot of different kinds of techniques to understand what molecules look like, how they move around in a cell, what interactions they have with other molecules, and what reactions they carry out, and a lot of these things aren’t conveyed in these simple drawings we make. I started learning 3D animation in order to better visualize the processes that my lab studied, mainly as a way to better communicate our ideas with other researchers.

Why is it important to do so?

Historically, physical models have played an important role in scientific discovery. Paper models were critical in the discovery of the structure of DNA and of proteins. Nowadays, many of our hypotheses in cell biology involve lots of molecules, moving dynamically over time and space.  It’s hard to make physical models that show these ideas, but we can use animation software to visualize what we’re thinking about. These models are important not only for communicating our ideas, but also for exploring our data, and understanding complex hypotheses. Having models that truly reflect our hypotheses will allow researchers to ask better questions and design better experiments. Animations are also a great way to share our research and ideas with broad audiences, including students and the interested public.

You’ve launched animation software for molecular biologists called Molecular Flipbook. What is it for, and why do scientists need this when they can rely on animators like you?

I’ve been using a commercial 3D animation software from the entertainment industry to create animations. I’ve held workshops to teach this software to biologists, and have found that it’s really time-consuming and unintuitive for most researchers. They almost immediately forget how to do simple tasks, like rotating the screen or object, if they haven’t used the software in a day or so, and they get frustrated by that. For animation to become one of the tools that researchers use regularly, it needs to be more intuitive.

So, through a grant funded by the National Science Foundation, I brought together a team to create new animation software that’s free and open source, and designed it specifically with molecular biologists in mind. We’ve done some testing, and found that biologists are able to start creating their own animations after watching a really short 5-minute tutorial. This is amazing, especially considering the months it took me to learn the commercial animation software that I use! We’re hoping that biologists will use Molecular Flipbook to animate their own hypotheses to better wrap their heads around the complex processes they study, and to use these animations in their presentations and publications. We’re also launching an online database in April that will allow biologists to share the models they create, allowing other researchers to tweak these animations to really reflect their own hypotheses.