Gumballs and Molecular Machines

The wonderful clarity of long distance telephone conversations and compact disks (CD) traces back to work in the 1940's by Claude Shannon (Shannon1993, Pierce1980). Surprisingly, if you scratch a CD from the center to the outside it will often still play without interruption of any kind. (If you try this, use a CD you don't like! Keep scratching until it does get destroyed.) This resistance to noise was predicted by Shannon's channel capacity theorem, and it depends on the coding of the information on the disk. (The code runs in concentric circles around the disk, so scratches made when cleaning the disk can be corrected. This is why instructions say to wipe CD's from the center to the outside.)

In the 1980's it was clear to Tom Schneider that since Shannon's other work on information theory could be fruitfully applied to molecular biology, his work on channel capacity should also apply. It took Tom about 10 years (roughly 1980 to 1990) to reconstruct Shannon's theory solidly in molecular biology terms.

In Shannon's communication theory, each gumball represents a distinct message while in molecular machine theory each gumball represents a distinct state of a biological molecule. Because the geometry is the same, Shannon's famous channel capacity theorem also applies to the molecular case.

Programs used to generate figures that describe Shannon spheres are: sphere, ring and riden. The program which was used to generate figure 9 in the paper "Channel Capacity of Molecular Machines" is cisq.

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Schneider Lab

origin:    before 1995 June 23
updated: 1998 Jan 24

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