Biology and Informatics - Essays in Bioinformatics - page 6

Earlier philosophical systems analysed economics and society as equilibrium
systems, in many cases fixed by the unchanging dogmas of sacred texts. Change can now
also be handled explicitly. Newton and Leibnitz, with the differential calculus, provided the
tools for physics and Hegel introduced the idea of dialectics into philosophy 24 . In science
there are many new ways of handling change, for example, the epigenetic landscape of C.
H. Waddington for biology, all kinds of computer simulations of systems ranging from the
Solar system (found to be weakly chaotic) to the British economy. Arthur Winfree, a
pioneer in dealing with non-linear systems, gave his topic the intriguing title “The geometry
of biological time” indicating that changes in time and space were intimately mixed (as also
in relativity) although Joseph Needham had much earlier written: "form is simply a short
time-slice of a single spatio-temporal entity''. The sudden changes in such systems have
been illustrated in the 'catastrophe theory' of René Thom which has been expounded by
Christopher Zeeman for social as well as for physical systems. They find that there are only
seven types of geometrical singularities in the configuration space. These are by way of
being mathematisations of the “double bind” kind of situation which philosophers describe
where one can get out of a knot only by jumping to some other position.
9. Experimental techniques
Of course the whole progress of bioinformatics has depended on the development of
experimental methods and their implementation, both facilitated by the advent of computer
hardware and of appropriate algorithms. Structural studies stand on X-ray crystal structure
analysis, electron microscopy, atomic force microscopy and nuclear magnetic resonance
and all their variants.
Fred Sanger in Cambridge quietly provided the methods for sequencing both
proteins (1949-55) and DNA, which are the absolute fundamentals for bioinformatics, but
the flood of sequence data is a result of the industrial-scale implementation of sequencing
methods on a huge scale 33 .
Numerous automated biochemical techniques for identification and, for example,
for combinatorial chemistry, have become essential.
Computer handling of gigantic data-banks and computer modelling of the
conformations of proteins and the expected chemical properties of molecules are now
central to bioinformatics.
10. Genomics
The key problems 25 include:
x The structure of proteins, protein folding, the operation of proteins.
x DNA, its sequence, replication, transcription, its interaction with proteins,
the switching of genes.
x The ribosome.
x The structure and operation of chromosomes, meosis, mitosis, replication,
mutation, variation. Extra-chromosomal nuclei acid.
x Phylogenetics, evolution, speciation.
The nematode worm, Caenorhabditis elegans, with 302 nerve cells , was the
essential link, chosen by Sydney Brenner, between behaviour, molecules and genetics.