Biology and Informatics - Essays in Bioinformatics - page 3

proteins and Astbury the fibrous. There are several excellent studies of the development of
molecular biology 11 . Schroedinger's well-known topic “What is life” (1945) 12 appeared
rather late in the day.
C. H. Waddington (1905-1975), a biologist, one of the Cambridge Club, after the
war organised a series of influential seminars under the title of "Towards a Theoretical
Biology" (1968, 1969, 1971) which brought together varied people who digested the
revolution in computing, information, the structure of molecules, genetics and the origin of
life. He himself promoted the concept of the “epigenetic landscape” as a way of visualising
the development of an organism as genes were switched on and off to make choices
between various paths. Almost all the people concerned with protein structure had
exceptionally well-developed abilities for spatial visualisation (now shown by PET
scanning to correspond to physical development of structures in the brain. Information and
thought really have a material basis as Lucretius had suspected).
3. Hierarchy
The great success of X-ray crystal structure analysis in providing the shapes of molecules,
has obscured the fact that most materials are not crystalline, although almost everything
gives useful X-ray diffraction patterns. Crystallisation is a test for purity, but crystals are
exceptional in that one rule takes one from the atomic level of 1 Angstrom (0.1nm) right up
to 10 cm. The span of operation of this rule is unusually great. The recent discovery of
quasi-crystals has led to a profound re-assessment, leading in the direction of hierarchy, of
the laws of crystallography.
Biological structures are distinctively hierarchic with perhaps six levels of
organisation with much smaller spans, each with its characteristic rules of ordering. These
levels overlap to a greater or lesser extent. Properties at one scale are determined by
structure at that scale, but may be critically influenced by certain detailed configurations in
the level below for which the level above forms an average climate.
Levels of organisation or integration were clearly recognised by, for example,
Joseph Needham 13 , representing the thought of the Club for Theoretical Biology.
4. Information theory and the computer. Information and material structure
The concept of information began to appear in the 1920s. Not surprisingly, information
theory began with the question: "How much should you pay for your telegraph message and
how fast would it go?" At first it was so much a word but then newspaper correspondents
began to make up pseudo-words like "Pariswise urgentmost". Theory began to be
developed for questions of military cryptography, as the story of the Enigma machine has
revealed. The Colossus computer 14 was built for cryptography at Bletchley Park. Questions
of bandwidth arose. How much information could be transmitted over a land-line? The first
Atlantic cable could only carry a few bits per second. Nyquist (1924), Kolmogorov and
Hartley (1928), Claude Shannon, Louis Brillouin, Warren Weaver, Leo Szilard, Norbert
Wiener were all concerned with the foundation of information theory 15 .
John Tukey invented the word "bit" for a binary digit and Shannon used the word
"entropy" for information content. as 6 p i log p i. (where p i is the fractional probability of
the i-th kind of character. There is still great confusion as to the entropy content of
meaningless and meaningful information. Shannon's example was of printed English text
and he showed that about half the information is arbitrary, that is, is "meaning", and half is