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Cells 2013, 2(2), 414-431;

Systems Biology — the Broader Perspective

Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, OX1 3QX, UK
Received: 1 April 2013 / Revised: 17 May 2013 / Accepted: 5 June 2013 / Published: 19 June 2013
(This article belongs to the Special Issue Successes of Systems Biology and Future Challenges)
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Systems biology has two general aims: a narrow one, which is to discover how complex networks of proteins work, and a broader one, which is to integrate the molecular and network data with the generation and function of organism phenotypes. Doing all this involves complex methodologies, but underpinning the subject are more general conceptual problems about upwards and downwards causality, complexity and information storage, and their solutions provide the constraints within which these methodologies can be used. This essay considers these general aspects and the particular role of protein networks; their functional outputs are often the processes driving phenotypic change and physiological function—networks are, in a sense, the units of systems biology much as proteins are for molecular biology. It goes on to argue that the natural language for systems-biological descriptions of biological phenomena is the mathematical graph (a set of connected facts of the general form <state 1> [process] <state 2> (e.g., <membrane-bound delta> [activates] <notch pathway>). Such graphs not only integrate events at different levels but emphasize the distributed nature of control as well as displaying a great deal of data. The implications and successes of these ideas for physiology, pharmacology, development and evolution are briefly considered. The paper concludes with some challenges for the future. View Full-Text
Keywords: developmental biology; evolution; graphs; mathematical; networks; phenotypic processes; physiology; systems biology concepts developmental biology; evolution; graphs; mathematical; networks; phenotypic processes; physiology; systems biology concepts
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Bard, J. Systems Biology — the Broader Perspective. Cells 2013, 2, 414-431.

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