Biology Reference
In-Depth Information
8.3.
'Realistic' representation and systems biological
'models of everything'
The reliance of top-down systems biology on genomic data is often associated
with the promise that this allows for a 'realistic' representation of biological
processes in mathematical terms (e.g., Kitano, 2002b, 2006). The most realistic
model, Kitano believes, is a model of all genomic and proteomic interactions and
dynamics of an organism. The project to build such a model runs under the title
of 'systeome', though what is envisaged is also a simulation model, not only an
'omic' data set. Kitano proposes to include research on the systeome from five
different organisms as the grand challenge for systems biology. He regards the
human systeome project (which, if funded, would certainly become the grand
cornucopia of the field) as most important. The promise is to have realized the
systeome of the human cell by the year 2020, with 20% error margin, and to
have included all genetic variations, drug responses, and environmental stimuli
ten years later (Kitano, 2002b, p. 25). We are not in a position to assess the
feasibility of this project, nor can we judge its scientific and medical value in
the long run; but we do want to ask what kind of a model such an envisaged
'realistic' systeomic model is, how it relates to the kinds of models we have
discussed in this chapter, and, most importantly from our point of view, what
explanatory power it might have.
Calling an envisaged systeomic model, 'realistic' suggests that it can give a
reliable, undistorted picture of biological processes. This would seem to require
that the picture ought to be as detailed as the processes going on in nature,
and that the structure of the model, i.e., the components and their relations,
is isomorphic to the structure found in nature. (Given that we have no direct
access to nature, it is far from obvious how such a comparison between nature
and our models of it could ever be made.) It does
not
mean that the model
has to consist of material components like an organism, as it does not represent
the material nature - the embodiment - of the system. The model is 'realistic'
in the sense that it does not simplify by neglecting parameters. A realistic
model, then, is maximally detailed and unbiased. It is not obvious that any
model can be realistic in this sense, and certainly no model referred to in
this chapter meets this requirement. Most, if not all, bottom-up models are not
realistic in this sense. Even detailed models usually neglect, e.g., that organismic
cells are spatially inhomogeneous, i.e., that chemical gradients are present and
consequently transport phenomena occur. Ordinary differential equations that
are used in most models describe homogeneous ('well-stirred') systems only.
Using partial differential equations may lead to increased realism, but quickly
results in intractable systems.
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Top-down models are not realistic either. As we
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Prokaryotes, at least, may be described in a phenomenologically adequate way as homogeneous systems.
