Biology Reference
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measure the amount of everything there is to be measured inside a cell under
different conditions (DNA, RNA, proteins, metabolites), and then 'data-mining'
will do the rest. The other approach has as its aim the 'silicon cell' (Snoep et al.,
2005), a computer simulation of the complete cellular network of reactions and
interactions based on the experimentally measured properties of the 'agents' of
the cell (enzymes, pumps, receptors, etc.). What is not always so clear is exactly
how the results of these two approaches - exhaustive cell-wide data-sets and
complete cell models - necessarily lead to deeper understanding. In the rest of
this introduction, I would like to propose that what needs to be added first is a
clear view of what the 'systemic approach' entails.
The geneticist Theodosius Dobzhansky summed up the dominant explanatory
modality for biology of the last century in the mantra 'Nothing in biology makes
sense except in the light of evolution' (Dobzhansky, 1973). Ernst Mayr, however,
pointed out that there are two types of explanation in biology, ultimate and
proximate, which would respectively follow from evolutionary and functional
considerations (Mayr, 1988). I suggest that systems biology seeks to expose
general principles that underlie proximate explanations of what governs life.
My mantra for systems biology would therefore be 'Nothing in an organism
makes sense except in the light of context'. There are three words here that
need elaboration. First, 'sense' emphasises that what is sought is explanation
and understanding, not just description. As an example, an indispensable part of
the system-wide study of the cell is to make a complete map of all reactions and
interactions that comprise the intracellular network. However, in the words of
Count Alfred Korzybski (1994) 'a map is not the territory'; making the map does
not in itself afford understanding; neither does measuring the concentrations of
all the nodes on the cellular map. Second, 'organism' emphasises that systems
biology studies a particular cell or organism as a material system that is to
be explained in terms of itself and its interactions with its environment; in
contrast, an evolutionary explanation would be in terms of its history. Third,
and most important, 'context' captures the essence of the systems approach.
Always taking context into account amounts to using a 'macroscope' (de Rosnay,
1979), a tool for studying the very complex (in contrast to using a microscope
for the very small and a telescope for the very large).
1
The macroscope is a
'symbolic instrument' that collects a number of techniques and methods into
what De Rosnay calls the 'systemic approach', which, in contrast to the analytical
approach, takes into account not only all the elements in the system under study
but also all their interactions. A 'system' itself is, in de Rosnay's words 'a set of
interacting elements that form an integrated whole'. The living cell is prototypic
of such systems.
1
A web-edition of this topic is freely available from Principia Cybernetica (http://pespmc1.vub.ac.be/
LIBRARY.html). It is recommended reading for all systems biologists.
