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    Rights statement: This is the author’s version of a work that was accepted for publication in Journal of Theoretical Biology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Theoretical Biology, 408, 2016 DOI: 10.1016/j.jtbi.2016.08.007

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Rosen's (M,R) system as an X-machine

Research output: Contribution to journalJournal articlepeer-review

Published
<mark>Journal publication date</mark>7/11/2016
<mark>Journal</mark>Journal of Theoretical Biology
Volume408
Number of pages8
Pages (from-to)97-104
Publication StatusPublished
Early online date9/08/16
<mark>Original language</mark>English

Abstract

Robert Rosen's (M,R) system is an abstract biological network architecture that is allegedly both irreducible to sub-models of its component states and non-computable on a Turing machine. (M,R) stands as an obstacle to both reductionist and mechanistic presentations of systems biology, principally due to its self-referential structure. If (M,R) has the properties claimed for it, computational systems biology will not be possible, or at best will be a science of approximate simulations rather than accurate models. Several attempts have been made, at both empirical and theoretical levels, to disprove this assertion by instantiating (M,R) in software architectures. So far, these efforts have been inconclusive. In this paper, we attempt to demonstrate why - by showing how both finite state machine and stream X-machine formal architectures fail to capture the self-referential requirements of (M,R). We then show that a solution may be found in communicating X-machines, which remove self-reference using parallel computation, and then synthesize such machine architectures with object-orientation to create a formal basis for future software instantiations of (M,R) systems.

Bibliographic note

This is the author’s version of a work that was accepted for publication in Journal of Theoretical Biology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Theoretical Biology, 408, 2016 DOI: 10.1016/j.jtbi.2016.08.007