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# New Approaches in Mathematical Biology:

Information Theory and Molecular Machines

**Thomas D. Schneider
Frederick Cancer Research and Development Center, **

P. O. Box B,

Frederick, MD 21702-1201.

fax: (301) 846-5598,

email:
toms@alum.mit.edu
http://www.lecb.ncifcrf.gov//

### Abstract:

My research uses classical information theory to study genetic
systems. Information theory, founded by Claude Shannon in the 1940's,
has had an enormous impact on communications engineering and computer
sciences. Shannon found a way to measure information. We use this measure
to precisely characterize the sequence conservation at nucleic-acid
binding sites. The resulting methods completely replace the use of
``consensus sequences'', and therefore
provide better models for molecular biologists. An
excess of sequence conservation at bacteriophage T7
promoters and at F plasmid IncD repeats led us to predict the existence
of proteins that bind the DNA.
In another application of information theory,
the wonderful fidelity of telephone
communications and compact disk (CD) music can be traced directly to Shannon's
channel capacity theorem. When rederived for molecular biology, this theorem
explains the surprising precision of many molecular events. Through
connections with the Second Law of Thermodynamics and Maxwell's Demon, this
approach also has implications for the development of technology at the
molecular level.
^{1}

The theory of molecular machines describes molecular interactions
by using the mathematics of information theory [2,3].
For convenience, I have divided the theory into three levels, which are
characterized by these topics:

- Level 0. Sequence Logos: patterns in genetic sequences.
- Level 1. Machine Capacity: energetics of macromolecules.
- Level 2. The Second Law: Maxwell's Demon and the limits of computers.

This paper is a brief guide to papers presented elsewhere.
See
https://alum.mit.edu/www/toms/ftp/cover.ps
for a list of references
and
http://www.lecb.ncifcrf.gov//paper/nano2
[4]
for a review.
Other information is available
on the world wide web at
http://www.lecb.ncifcrf.gov//.
Discussions of these topics are held on the internet newsgroup
bionet.info-theory.

** Next:** Level 0. Sequence Logos:
*Tom Schneider*

*2000-10-13*