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← Drew Berry: Animations of unseeable biology

drew_berry's Avatar Jump to comment 20 by drew_berry

Hi, I am drew berry, the presenter and animator. Thanks for all your feedback and comments. Really appreciated.

I did want to respond (and actually concur with) SteveN's comments about the 'accuracy' of my visualizations. Yes, I should avoid overstating how accurately I have depicted the reality of the molecular world. It is vastly messier, random and crowded, and it's physical nature is unimaginably alien to our normal perception of the world around us. That said, my work is not intended to be a lab-bench-calculated model for research use, it is an impressionistic, artist-generated crude sketch of phenomena and structures science is measuring and discovering at the molecular scale (which is why I begin with Galileo's water colours and Darwin's notebook sketch as reference points). Now that I have put my work in it's place, I would then assert that the animations are firmly founded on real data and are as accurate as I can possibly make them, while making them watchable and interpretable to a human audience. By far the largest portion of my time is spent conducting broad ranging literature reviews of the topic I am working on, gathering the fragments of data scattered throughout the journals, and holistically reconstructing what we currently know and do not know. Wherever data and models are available, I incorporate them directly into the construction of the animation, including molecular structures, dynamics simulations, speed measurements, and so on. My work is most akin to 'review' paper in the literature, presented in visual form.

The goal of my work is to show non-experts – the general public aged 4 to 99, students of biology, journalists and politicians, and so on – what is being discovered in biology, in a format that is accessible, meaningful, and engaging. I hope that my work provides some sense of what biologists and medical researchers are discovering and thinking about, to provide the public with a framework of understanding to discuss these important new discoveries and the impact it will have on us as a society as we head into the future.

In regard to Dynein's walking, it actually is quite directional. They can only walk in one direction along the microtubule (which have a polarity in their physical structure). Dynein can take 8nm, 16nm and 32nm steps, which is where it locks its 'feet' onto the microtubule. The critique I would level at my representation of Dynein is that the legs flail around much more and that the 'steps' are not so regularly timed. It is also much quicker in it's directional movement along the microtubule... I could go on if that is of interest to you. I could also discuss Kinesin (the yellow-orange guys heading the other way) and the kinesin-14 (the long light blue kinesins cross-linking the microtubules). This is all from my vague recollection of the literature review I did mid-2010 for that piece.

The DNA replisome (the replication machine) is one I am particularly proud of as it brought together very fragmentary data and 'accurately' represented our level of understanding mid-2002 when it was created. I deliberately left many out proteins that we knew about and opened-up the whole structure so that students would be able to examine the mechanisms in action.

I know the dozen or so people who are at the top of the game at creating biomedical animations (most have a PhD scientific background) and we all struggle with the problem of having a molecule arrive at a particular location from the thick molecular soup of the cytoplasm and not look directed. Part of the problem is that we strip away most of the surrounding molecules to make this stuff visible. I can make the molecule wander around in a brownian type manner, but for story telling and visual explanations, I need it to get to a certain point and do it's thing at a certain time to move the story along. This can make it look determined and directed. This is a problem I work on and try new approaches to solve with every new piece. I think we will develop/find a resolution or technique that will solve this problem that is acceptable to most at some point. Just one of the many fun challenges of doing this work.

Sun, 15 Jan 2012 01:31:03 UTC | #908389