Biologists Weep for Joy

This inside-the-cell animation really does make biologists weep for joy:

Niches :: We Interrupt this Program: [I]t’s magnificent. It made me cry to watch it. My only regret is that it’s only 3 minutes long....

UPDATE: After some viewing I think that this isn’t just a series of pretty pictures. This is a real story. What we’re watching is the innards of helper T-cell activation. The lymphocyte crawling along the arteriole wall at the beginning has picked up a foreign signal, and has latched onto a macrophage through the T-cell receptors and major histocompatibility receptors. Then we dive into the cell, and the majority of the video shows the synthesis, sorting, and delivery of T-cell receptors, cytokines, and other proteins, and we finish with the now-alerted and activated lymphocyte slipping in-between the capillary wall cells on its way to trouble....

robin andrea: That’s a stunning animation. I understand the emotional response to watching all that amazing work going on inside every cell in our body. I still remember the first time I saw graphics of mitosis. I thought it was the most beautiful dance I’d ever seen, and anaphase just knocked me out. This animation is like that only a hundred times better! Great link, Wayne.

Wayne: Robin - it was about 12 years ago that I first made the acquaintance of kinesin, that burly fellow who’s stepping along the microtubule carrying this enormous mass. It enraptured me then to think of “motor proteins”, and the visualization is perfect. I sent the link to the biology professor who teaches about a thousand students every semester. I imagine she hasn’t seen it, but I suspect she’s going to weep like I did....

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More comments:

The Cell is Like Tron! | Cosmic Variance: Samantha on Sep 30th, 2006 at 1:51 pm:

Hi! This movie is fantastic!

I also think we are seeing a lymphocyte rolling along inside a blood vessel. We first see the exterior of the cell and then we zoom in to see the proteins in the membrane that are mediating the rolling, by contacting other proteins in the surface of the substrate. We then go inside the cell and first have a tour of the various cellular components - mostly the elements of the cytoskeleton and proteins being moved around in the membrane on lipid rafts. We then, in just a beautiful sequence, see the assembly and disassembly of actin and then microtubules before watching a motor protein (kinesin, I would say) staggering along a microtubule bearing its enormous cargo (a vesicle). In a further extended sequence we watch mRNA being processed into protein. It is ejected from the nucleus, processed and translated by ribosomes into the endoplasmic reticulum, the protein is transported to the Golgi apparatus, where it is further processed and then finally ejected into the cytosol where it carried (lipid raft again?) to the membrane where its function will be to mediate the rolling of the lymphocyte. Thus, we come back full circle....

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bob on Sep 30th, 2006 at 10:26 pm: The video posted here is condensed from an eight minute piece. The longer piece has a voiceover and labels and is actually intended as a teaching tool, whereas this edit is more about just showing off the visuals. (from: http://www.spinquad.com/forums/showpost.php?p=141933&postcount=15) Does anybody know where the full version can be found?....

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TFox on Oct 1st, 2006 at 6:33 pm: With respect to crowding, see just about anything by David Goodsell for static pictures with accurate representations of cytosolic space. This is a beautiful video though, and I think it'd be hard to see what was going on if it was realistically busy.

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farrold on Oct 2nd, 2006 at 2:00 am: This is a beautiful piece of work, and accurate in many dimensions -- the animators worked closely with Harvard faculty. I'd like to see more of this work, but I'd also like to see a version that makes clear which aspects are utterly false (and why the animators were forced to do it this way).

The main cheat is in the motion trajectories. What looks like action-at-a-distance is, in most instances, a consequence of this cheat. The animations shows smooth motions at the molecular scale that are in reality random walks by twisting, tumbling objects. Brownian motion and thermal fluctuations rule dynamics in the biological world of soft molecular structures moving in water. (By contrast, stiff, anchored structures could indeed move smoothly while merely vibrating.)

To give a sense of the magnitudes, the rotational relaxation time for an ordinary, mid-size protein is less than a microsecond: that is, it will typically rotate through a large angle in that time. In a time of the same order, it will typically travel a large fraction of its diameter. Many of the scenes portray protein mechanisms on a millisecond time-scale, however, so the smooth motions shown represent what are actually random walks following paths perhaps 100 times as long. If shown realistically, the molecular parts would thrash, rattle, and wander, sometimes blundering away to nowhere, but sometimes passing close enough to a target location to respond to short-range forces that align and bind them.

However, this realism would obscure the functional behaviors, making it hard to see the net result of all the jiggling. The actual animation instead obscures the fundamental physical nature of the processes, producing a false impression of mysterious vital forces at work. I'd like to see a version that shows a few mechanisms both ways, giving an explanation of their relationship and the reason for the cheat in the rest of the scenes.

(Also note that the among the objects shown, the ratio of actual size to screen size varies by a thousand or more, and the time scaling varies by a similar factor. Making this clear would be a great help.)

Comments

[Platypus]

I laughed, I cried. Five stars. Could use subtitles though.

I spend a lot of time in the lab so I could identify most of the images on the first go round. However, you have to realize what an impact this has on those of us who study these processes and have never seen them visualized so well. Awesome!

Hands down beats my own QuickTime movies of how human cells respond when you break their chromosomes. (Although my movies are constructed from actual microscopic images of living cells.)

A moving picture is worth so much more than 1000 words. Just like the rest of humanity, we scientists are total suckers for a good visual image.

[Wayne]

It was a great idea, I think, to bring in posts and comments about this piece. My emotional response was more rooted in delight at seeing a level of description that is so hard to attain otherwise.

The other posts have merit though. There are obvious artistic shortcuts. I think the small scale movements could be depicted by changes in coloration or reflectance, to fool the mind in thinking there was motion without blotting out the main intent.

The movements toward a goal as opposed to a long rapid random walk occasionally and fortuitously encountering the target were, I suspect tossed aside as needlessly distracting. So too were the immense concentration of activities going on at the same time in near the same place, again for reasons of clarity. Perhaps a piece could be developed that showed the ideal images, along with the one that we see stripped of the distracting realities. Now *there* would be a fascinating view.

I saw elsewhere that this was derived from the 8-minute piece, although I didn't know about the voiceovers. Hmmmm, no, I don't know about voiceovers. This one exercised my attention for a full two days to try to get everything down, and that was because after the first dozen watchings I realized it really wasn't *just* pretty pictures, but what I came to trust was a coherent tight story.

And that was a delight too. When I realized how this coherent tight story was so small, such a tiny example of the myriads of possibilities and not just a one-time treatment of all processes, well. I can now see all kinds of possible new stories.

I don't know how they're going to beat the Kinesin Kid though, but they're going to have to try.

[shah8]

Permutation City, by Greg Egan touches on works like the video...

[Roger Bigod]

The pleasure is like seeing a dramatization of a novel or piece of history that the viewer already knows. It's a mixture of confirmation and discovery. I haven't opened a biochemistry text in many years and stopped following the cell biology a while back, but I knew immediately I was following a day in the life of Joe Leukocyte. For me, it worked much better without captions.

The only surprise was the ribosomes. I learned about them as a part of biochemistry so my mental picture is big and detailed, with subunits and active sites. The animation showed them as part of the cell biology of protein processing so the perspective was more distant and they came off looking like cute little kitchen pasta machine extruding spaghetti.