Comments on: The Cell is Like Tron! http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/ Random samplings from a universe of ideas. Fri, 05 Dec 2008 04:09:32 +0000 http://wordpress.org/?v=2.3.1 By: David http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20804 David Sat, 23 Dec 2006 04:05:01 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20804 Praise God. Praise God.

]]> By: Amor http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20795 Amor Tue, 05 Dec 2006 05:09:32 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20795 Beautiful in every way. Does anyone know where this music came from? Beautiful in every way. Does anyone know where this music came from?

]]> By: The Inner Life of the Cell « Perfectly Reasonable Deviations http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20794 The Inner Life of the Cell « Perfectly Reasonable Deviations Wed, 15 Nov 2006 15:36:24 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20794 [...] Here’s a rather spectacular computer animation: The Inner Life of a Cell (via Cosmic Variance). [...] […] Here’s a rather spectacular computer animation: The Inner Life of a Cell (via Cosmic Variance). […]

]]> By: Mira http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20796 Mira Thu, 09 Nov 2006 20:56:09 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20796 Does anybody know where I can find a copy of the full version? Does anybody know where I can find a copy of the full version?

]]> By: George http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20801 George Thu, 19 Oct 2006 18:51:37 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20801 Does anyone have a copy of the full version or know where I can find it? Does anyone have a copy of the full version or know where I can find it?

]]> By: Andreas http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20799 Andreas Wed, 11 Oct 2006 22:46:09 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20799 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. 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.

]]> By: TXyankee http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20798 TXyankee Sat, 07 Oct 2006 12:23:55 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20798 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. 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.

]]> By: Thinking Aloud: The Pulpmovies Weblog » Fascinatingly beautiful http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20797 Thinking Aloud: The Pulpmovies Weblog » Fascinatingly beautiful Thu, 05 Oct 2006 20:40:38 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20797 [...] You’ll need to head over to Cosmic Variance if you want to find out more, but before you do stop and be amazed at the sheer gorgeousness of The Inner Life of The Cell. [...] […] You’ll need to head over to Cosmic Variance if you want to find out more, but before you do stop and be amazed at the sheer gorgeousness of The Inner Life of The Cell. […]

]]> By: Andre http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20783 Andre Mon, 02 Oct 2006 22:55:15 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20783 farrold, I had a similar <a href="http://biocurious.com/cell-visualizations" rel="nofollow">reaction</a> 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: http://www.tacitus.com/ farrold,

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:

http://www.tacitus.com/

]]> By: farrold http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20802 farrold Mon, 02 Oct 2006 07:00:48 +0000 http://blogs.discovermagazine.com/cosmicvariance/2006/09/29/the-cell-is-like-tron/#comment-20802 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.) 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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