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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....


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....


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?....


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.


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.)

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