TY - JOUR

T1 - Rosen's (M,R) system as an X-machine

AU - Palmer, Michael L.

AU - Williams, Richard A

AU - Gatherer, Derek

N1 - 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

PY - 2016/11/7

Y1 - 2016/11/7

N2 - 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.

AB - 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.

KW - Systems biology

KW - Computability

KW - Reductionism

KW - Mechanism

KW - Self-reference

KW - Turing machine

KW - UML

KW - Unified Modelling Language

KW - Finite state machine

KW - Stream X-machine

KW - Communicating X-machine

U2 - 10.1016/j.jtbi.2016.08.007

DO - 10.1016/j.jtbi.2016.08.007

M3 - Journal article

C2 - 27519952

VL - 408

SP - 97

EP - 104

JO - Journal of Theoretical Biology

JF - Journal of Theoretical Biology

SN - 0022-5193

ER -