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1

Introduction

morphing into “governor”. A governor such as Watts’ for the steam engine uses a

relatively simple feedback mechanism in its operation, and feedback has remained

an important concept within cybernetics. It appears to have already been used by

Plato as a metaphor for governance in society (which was the interest of Ampère in

the topic). According to Aristotle, kappa upsilon beta epsilon rho nu eta tau iota kappa etaκυβeρνητικη tau eta chi nu epsilonτηχνe, the art of the steersman,

implied teleological (goal-oriented) activity as well as knowledge, which is, as Som-

merhoff (1950) has pointed out, perhaps the most characteristic apparent feature

of living organisms. Information is, of course, central to considering how control

and communication are enacted and, hence, bioinformatics and cybernetics greatly

overlap, with communication and control in complex adaptive biological systems

constituting the common ground.

We see thus two great areas where information is required for understanding living

organisms. One is the set of instructions for specifying an organism (the genome),

notwithstanding the fact that these instructions are not sufficient for creating an

organism. The other is the web of regulatory interactions that allows cells to survive

in the organism of which they are a part, and allows an organism to survive in its

environment. The first area encompasses the analysis and comparison of sequences,

the search for “differences that make a difference” in the words of Gregory Bateson,

which is greatly advancing the study of phylogeny and disease. The second area

follows from Descartes’ insight that the physical part of an organism is machine-

like, and it should allow us, inter alia, to better understand the many diseases caused

by metabolic disorders.

1.2

What Can Bioinformatics Do?

Although it began with sequence comparison (which is a subbranch of the study of the

nonrandomness of DNA sequences), bioinformatics has become an extremely active

research field encompassing a far wider spread of activity, which truly epitomizes

modern scientific research. It is highly interdisciplinary, requiring at least mathe-

matical, biological, physical, and chemical knowledge, and its implementation may

furthermore require knowledge of computer science, chemical engineering, biotech-

nology, medicine, pharmacology, etc. There is, moreover, little distinction between

work carried out in the public domain, either in academic institutions (universities)

or state research laboratories, or privately by commercial firms.

The handling and analysis of DNA sequences remains one of the prime tasks of

bioinformatics. This topic is usually divided into two parts: (1) functional genomics,

which seeks to determine the rôle of the sequence in the living cell, either as a

transcribed and translated unit (i.e., a protein, the description of the function of

which might involve knowledge of its structure and potential interactions) or as

a regulatory motif, whether as a promoter site or as a short sequence transcribed

as a piece of small interfering RNA; and (2) comparative genomics, in which the

sequences from different organisms, or even different individuals, are compared in

order to determine ancestries and correlations with disease. Clearly, the comparison