A few years ago XVIVO and Harvard University released a video of a scientific visualization entitled, “The Inner Life of the Cell.” I wasn’t a big fan. It was a fairy-tale vision of cellular activities.

If you saw a simulation of traffic flow on the highways and every vehicle in each lane was going the same speed, maintaining proper following distance, signalling and changing lanes only when necessary, merging and exiting with decorum—it might be nice, but it would be so fanciful that it would do more harm than good if you were trying to understand highway traffic in the real world. When you look at real-world traffic, you have difficulty believing anyone can travel the highways safely, but the simulation would make it hard to imagine there could ever be such a thing as a freeway collision.

A scientific visualization should induce a mental model that catalyzes an improved understanding of reality, and the 2006 simulation failed.

Of course, a simulation like this is going to be unrealistic. Molecules aren’t distinguished by hues, atoms don’t remain stationary with respect to their neighbors, and there’s no classical music soundtrack in a real cell. But the 2006 simulation was so far removed from reality that (in my opinion, of course) it served more to confuse than clarify perceptions about molecular activities in a living cell. My biggest peeve: all the molecules were shown in stately glides as if a miniature synchronized swimming team was displaying the results of years of practice. On those scales, the “aqueous” environment behaves more like peanut butter. Kinesin molecules grab onto microtubules and pull because they have to to make it through the thick goop through which they travel, and none of that difficulty was shown.

Protein Packing in the Cell

A lot to admire in the new XVIVO/Harvard scientific visualization of molecular activities within a living cell.

Now the same scientific visualization team has created a new video, “Inner Life of a Cell—Protein Packing.” This one is so much better. It’s a much more crowded world, and the actions of proteins are limited by interference from all their neighbors. None of the small molecules are shown (not a criticism—if water, ions, and sugars were visible you wouldn’t be able to visualize anything through the resulting mess), but many of the proteins are shown. Of course it’s not “accurate”—it’s a visualization!—but this one is much more representative of the kind of confused and crowded environment within living cells. The new simulation makes it much clearer that the normal processes of life are challenged with every motion, and the new video makes it easier to be awed by the mere fact that we are alive. Heartily recommended!