title: Organizing principles as tools for bridging the gap between system theory and biological experimentation.
abstract: Twentieth-century theoretical efforts towards the articulation of general system properties came short of having the significant impact on biological practice that their proponents envisioned. Although the latter did arrive at preliminary mathematical formulations of such properties, they had little success in showing how these could be productively incorporated into the research agenda of biologists. Consequently, the gap that kept system-theoretic principles cut-off from biological experimentation persisted. More recently, however, simple theoretical tools have proved readily applicable within the context of systems biology. In particular, examples reviewed in this paper suggest that rigorous mathematical expressions of design principles, imported primarily from engineering, could produce experimentally confirmable predictions of the regulatory properties of small biological networks. But this is not enough for contemporary systems biologists who adopt the holistic aspirations of early systemologists, seeking high-level organizing principles that could provide insights into problems of biological complexity at the whole-system level. While the presented evidence is not conclusive about whether this strategy could lead to the realization of the lofty goal of a comprehensive explanatory integration, it suggests that the ongoing quest for organizing principles is pragmatically advantageous for systems biologists. The formalisms postulated in the course of this process can serve as bridges between system-theoretic concepts and the results of molecular experimentation: they constitute theoretical tools for generalizing molecular data, thus producing increasingly accurate explanations of system-wide phenomena.
authors.affiliation: Department of Philosophy, Stonehill College, 320 Washington Street, Easton, MA, 02357, USA. cmekios@stonehill.edu.
authors.forename: Constantinos
authors.initials: C
authors.lastname: Mekios
mesh_terms: D008954:Models, Biological; D012107:Research Design; D049490:Systems Biology / Q000379:methods*
keywords: Complexity; Explanation; General system theory; Network motifs; Organizing principles