THE ROLE OF MODELING IN SYSTEMS BIOLOGY 3 1 . 1 Philosophical overview

The use of models in biology is at once both familiar and arcane. It is familiar because, as we shall argue, biologists presently and regularly use models as abstractions of reality: diagrams, laws, graphs, plots, relationships, chemical formulae and so on are all essentially models of some external reality that we are trying to describe and understand (Fig. 1.1). In the same way we use and speak of ‘model organisms’ such as baker’s yeast or Arabidopsis thaliana, whose role lies in being similar to many organisms without being the same as any other one. Indeed, our theories and hypotheses about biological objects and systems are in one sense also just models. Yet the use of models is for most biologists arcane because familiarity with a subset of model types, especially quantitative mathematical models, has lain outside the mainstream during the last 50 years of the purposely reductionist and qualitative era of molecular biology. It is largely these types of model that are an integral part of the ‘new’ (and not-so-new) Systems Biology and on which much of the rest of this book concentrates. Since all such models are developed for some kind of a purpose, our role in part is to explain why this type of mathematical model is both useful and important, and will likely become part of the standard armory of successful biologists.

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