Mechanistic Explanations and Models in Molecular Systems Biology

Foundations of Science 18 (4):725-744 (2013)
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Abstract

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon.

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Author Profiles

Fred C. Boogerd
VU University Amsterdam
Robert Richardson
University of Cincinnati

Citations of this work

Toward Mechanism 2.1: A Dynamic Causal Approach.Wei Fang - 2021 - Philosophy of Science 88 (5):796-809.
Design principles and mechanistic explanation.Wei Fang - 2022 - History and Philosophy of the Life Sciences 44 (4):1-23.

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