Systems Biology (Methods in Molecular Biology)

Chapter 1

Conceptual Challenges in the Theoretical Foundations

of Systems Biology

Marta Bertolaso and Emanuele Ratti

Abstract

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-
based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed
out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the
conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are
prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined
primarily by the context they are embedded within—and hence by the web of relations they are part of.

Key wordsSystems biology, Relational ontology, Relational properties, Ontological dependence

1 Introduction

Systems Biology is an approach to the understanding and concep-

tualization of the biological realm that emphasizes systemic and

holistic aspects rather than reductionist and mereological features.

However, the conceptualization of the aspects system biologists

emphasize has been elusive. Here, we want to introduce some

general notions that can account for the scope of Systems Biology.

In particular, we will ground our understanding of Systems Biology

within arelational ontology. A relational ontology is not simply an

ontology of relations. Systems thinking, well before the rise of

Systems Biology, had proposed an ontology of systems that was

aimed at displacing and replacing an ontology of things and objects;

these were seen as making sense only in their interconnections as

parts of larger systems. Relational ontology, in our acceptation,

does not consist in a further replacement of systems with relations.

A relational ontology holds that relations are what maintains and

dynamically transforms all we can observe; as such, relations are the

way to access our observables. In this way, relational ontology

involves epistemology; indeed, it is a way to combine ontology

and epistemology in the same view of the world and of living

Mariano Bizzarri (ed.),Systems Biology, Methods in Molecular Biology, vol. 1702,
https://doi.org/10.1007/978-1-4939-7456-6_1,©Springer Science+Business Media LLC 2018

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