# Re: Second law of Thermodynamics

Fri, 21 Nov 1997 15:21:40 -0500 (EST)

At 05:57 PM 11/20/97 -0600, Glenn Morton wrote:
>At 05:26 AM 11/20/97 EST, David Bowman wrote:
>
>>It seems to me that having, on average, one functional cytochrome c molecule
>>for every 10^43 (= 10^(137-94) possible sequences *is* quite limiting, unless
>>most of these excess permutations are forbidden by some dynamical
>>constraints. One in 10^43 is quite a needle in a haystack.
>
>For those who are unfamiliar with sequence space, I need to define the term.
> If you have 4 nucleotides and want to make a 2-unit long DNA there are 4 x
>4 or 16 different possibilities. One can place these 16 possibilities on a
>2d plane which looks like
>
>A....
>T....
>G....
>C....
> ATGC
>
>This is a 2 dimensional sequence space. Each point on that plane represents
>one permutation of the DNA. A 3 unit long DNA has a 3d volume for its
>sequence space. A 4 unit long DNA has a 4 dimensional euclidean space as
>its sequence space. For humans with a 3.5 billion long DNA, we have a 3.5
>billion dimensional sequence space. Scattered throughout the volume are the
>10^93 different permutations of fine and dandy cytochrome c. Surrounding
>each of the points are regions of points in which the functionality is
>harmed but the function still takes place, albeit inefficiently. This can
>be illustrated by the following example. Consider the sequence:
>
>My cat is very stupid
>
>This is a 21 unit long sequence (including spaces) and has a 21 dimensional
>sequence space. Other 21 unit long sequences perform the same function i.e.
>convey information on the intelligence of my cat. These can be statements like
>
>My feline is retarded
>My mouser is retarded
>My tomcat is retarded
>That cat was an idiot
>My cat is awful dense
>She is one stupid cat
>The tomcat is a moron
>
>etc etc.
>
>Now, surrounding each of these reagions in the sequence space are other
>sequences which work but work less effectively. To illustrate these by
>taking one of the above sentence and writing it (or miswriting it):
>
>Thet cat is an idiot
>thet cat is an idyot
>That kat is an idiut
>
>While these don't work as well, if you stumble on to one of these sequences
>and apply a selection which rewards efficient communication, you will end up
>with a sequence that is correctly spelled.
>
>I would direct anyone who wants experimental evidence of this type of
>behavior in biological molecules to
>
>Gerald F. Joyce, "Directed Evolution," Scientific America,Dec. 1992,
>
>Peter Radetsky, "Speeding Through Evolution", Discover, May, 1994, p. 87
>
>Amber A. Beaudry and Gerald F. Joyce, "Directed Evolution of an RNA Enzyme,"
>Science, 257, July 31, 1992, p. 637-638
>
>glenn
>
>Foundation, Fall and Flood
>http://www.isource.net/~grmorton/dmd.htm

Is there a distinction to be made between the characters and the message
conveyed? It is true that given so many monkeys with typewriters they can
eventually type all the works of Shakespeare, but how do they know that the