The Cell is Like Tron!

By Sean Carroll | September 29, 2006 8:43 pm

At least that’s the impression I got from this quite spectacular animation. (Via Shtetl-Optimized.)

Admittedly, real biological molecules would be quite a bit more densely packed. Either that, or there’s an awful lot of spooky-action-at-a-distance going on inside cells.

After you’re done being amazed, you could do worse than check out the lecture notes for Scott Aaronson’s class, Quantum Computing Since Democritus. And when you’re done with those, here are some videos of Feynman lecturing on QED in New Zealand. (Thanks to Ed Copeland for reminding me of these.)

  • jepe

    Wow! That’s beautiful. It’s this kind of thing that gets molecular biological physicists, like, totally high. Transcription , translation, and even kinesin moving around…we want to know how does this all come from Cl/Q Mechanics and Stat Mech? This little flick would be a great recruiting tool to get physics students interested in ‘alive and squishy state physics’.

  • Brad DeLong

    Can I get a translation or interpretation of what is going on?

  • Richard

    Wow! Incredible! I’m not sure what I was looking at most of the time, but I believe the last sequence was showing a lymphocyte leaving a blood vessel through a flap into surrounding tissue.

  • Robert

    Wow! It took @ 2 billion years for evolution to get this far — and from the eukaryotic cell to us is a mere @ 1.2 billion.

  • Sean

    Brad, I haven’t found one. PZ mentioned the video a couple of weeks ago, but for some reason I didn’t click on it then.

  • schnitzi

    That’s pretty awesome. I agree with your “spooky action-at-a-distance” assessment — that’s something that has always bothered me about biologicaly chemistry. It seems that some molecules are like little homonculi with volition of their own. I would love to know how accurate the animation is, and what the actual processes we’re witnessing are.

  • Quasar9

    Great video-tron-ics Sean. Beautiful!

    Particles in molecular biology dance with such seemingly effortless and melodious grace (note background music) creating spectacular designs in nature, bar exceptions when they are subject to extreme temperatures or forces, or other disturbances (mutations, cancers)

    Particles and events in particle physics appear so much more faster and violent (heavy rock music).
    Simply different Energy Scales and tempo, Time(?) Scales

  • Doug

    This is a great mathematical pictorial representation of bio-physical-chemistry!

    Could this biological energy exchange mathematical game have anything in common with a possible QM energy exchange mathematical game?

    Perhaps a change in scale or gauge may prevent identical but not similar games?

  • Samantha

    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

    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.


    Does anybody know where the full version can be found?

  • Neil

    If you enjoyed that, do a web or PubMed search for “cryoelectron tomography” or “Wolfgang Baumeister”, one of its main practitioners. This is a revolutionary imaging technique that allows 3D visualisation of large protein complexes such as ribosomes and the cytoskeleton in situ in cells.

  • TFox

    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

    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.)

  • Andre


    I had a similar reaction to you. Have you heard of a company called Tacitus? They make what they call “data gaming” software using techniques from video game developers to make interactive presentations of complex data sets. I haven’t seen anything from them yet but they talk about biological applications on their website:

  • Pingback: Thinking Aloud: The Pulpmovies Weblog » Fascinatingly beautiful()

  • TXyankee

    I’ve always had a bit of trouble reconciling the the astounding differences between two halves of planet Earth: the terrestrial and the submarine.

    Now I have to think that just below the skin, we’re
    every bit as strange as the sea.

  • Andreas

    nice, but a scientifically misleading cartoon. cells are so packed, there is no “looking around” without having another protein right in front of your “eyes”. that this dense chaos inside a cell is so accurate and reliable is a true mystery.

  • George

    Does anyone have a copy of the full version or know where I can find it?

  • Mira

    Does anybody know where I can find a copy of the full version?

  • Pingback: The Inner Life of the Cell « Perfectly Reasonable Deviations()

  • Amor

    Beautiful in every way. Does anyone know where this music came from?

  • David

    Praise God.


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Cosmic Variance

Random samplings from a universe of ideas.

About Sean Carroll

Sean Carroll is a Senior Research Associate in the Department of Physics at the California Institute of Technology. His research interests include theoretical aspects of cosmology, field theory, and gravitation. His most recent book is The Particle at the End of the Universe, about the Large Hadron Collider and the search for the Higgs boson. Here are some of his favorite blog posts, home page, and email: carroll [at] .


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