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.