Briefings in Bioinformatics Advance Access originally published online on March 10, 2009
Briefings in Bioinformatics 2009 10(4):462-474; doi:10.1093/bib/bbp003
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This article appears in the following Briefings in Bioinformatics issue: Special Issue: Challenges in Bioinformatics and Computational Biology [View the issue table of contents]
Exploring autonomy through computational biomodelling*
Corresponding author. Niall Palfreyman, Department of Biotechnology and Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany. Tel: +49 8161 714814; Fax: +49 8161 715116; E-mail: niall.palfreyman{at}fh-weihenstephan.de
The question of whether living organisms possess autonomy of action is tied up with the nature of causal efficacy. Yet the nature of organisms is such that they frequently defy conventional causal language. Did the fig wasp select the fig, or vice versa? Is this an epithelial cell because of its genetic structure, or because it develops within the epithelium? The intimate coupling of biological levels of organisation leads developmental systems theory to deconstruct the biological organism into a life-cycle process which constitutes itself from the resources available within a complete developmental system. This radical proposal necessarily raises questions regarding the ontological status of organisms: Does an organism possess existence distinguishable from its molecular composition and social environment? The ambiguity of biological causality makes such questions difficult to answer or even formulate, and computational biology has an important role to play in operationalising the language in which they are framed. In this article we review the role played by computational biomodels in shedding light on the ontological status of organisms. These models are drawn from backgrounds ranging from molecular kinetics to niche construction, and all attempt to trace biological processes to a causal, and therefore existent, source. We conclude that computational biomodelling plays a fertile role in furnishing a proof of concept for conjectures in the philosophy of biology, and suggests the need for a process-based ontology of biological systems.
Keywords: autonomy, computational biomodelling, emergence, enactive evolution, niche construction
Submitted: December 3, 2008. Received (in revised form): January 14, 2009.