Biology

We are primarily interested in the molecular level of life, where the main players are proteins and other organic macromolecules. We recommend the text by Alberts and coauthors [1] as an introduction. Among other things, it explains the central dogma, which holds that DNA, RNA, and proteins are the constituents of life, with DNA acting as the blueprint from which proteins are constructed. A major step in the exploration of that mechanism was the discovery of the double-helix structure of DNA by Crick and Watson. In spite or because of its personal bias, we recommend the booklet by Watson [2] for a recollection of the history that led to this discovery. We group the recommended literature into four categories.

Bio-Chemistry.   About 96.5% of an organism's weight is made up by only four elements, carbon, hydrogen, nitrogen, and oxyen. This fact by itself implies that bio-chemistry is a good deal more specialized than general chemistry. The basics of biochemistry are covered in the comprehensive text by Stryer [3]

Protein Structure.   Each protein is a linear chain or sequence made up of only 20 types of amino acids. A rather surprising finding is that like sequences fold up to form like shapes. We recommend the texts by Dickerson and Geis [4] and Creighton [5] as introductions to these shapes and structures. The next step in understanding life at the molecular level is to figure out the functions different proteins have in this enormous and complicated puzzle. But function follows shape, which is the motivation for the geometric approach to life taken by this project.

X-Ray Crystallography.   Short of being able to simulate the folding process of proteins with the computer, our primary sources of information about protein structures and shapes are indirect experimental measurements. Most common is the use of x-ray crystallography, which generates three-dimensional density maps from diffraction patterns. We recommend the book by Rhodes [6] as an introduction to that technology.

Bio-Informatics.   The complexity of biological systems makes the use of large-scale computation unavoidable. Today it is clear that progress in this field depends on our success in coupling computing with biological research. This leads to the emergence of bio-informatics as a discipline of its own. Its two branches focus on the analysis of sequences and of structures. We recommend the books by Clote and Backofen [7] and by Leach [8], which cover the two aspects of this discipline.


References:
[1] B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, J.D. Watson. Molecular Biology of the Cell. Garland, New York, 1994.
[2] J. D. Watson. The Double Helix. Penguin Putnam, New York, 1968.
[3] L. Stryer. Biochemistry. Freeman, New York, 1988.
[4] R. E. Dickerson and I. Geis. Structure and Action of Proteins. Harper & Row, New York, 1969.
[5] T. E. Creighton. Proteins. Freeman, New York, 1993.
[6] G. Rhodes. Crystallography Made Crystal Clear. Academic Press, San Diego CA, 2000.
[7] P. Clote and R. Backofen. Computational Molecular Biology. Wiley, Chichester, England, 2000.
[8] A. R. Leach. Molecular Modelling. Longman, Harlow, England, 1996.