Rosen's (M,R) system in process algebra

BMC Systems Biology
Derek Gatherer, Vashti Galpin

Abstract

Robert Rosen's Metabolism-Replacement, or (M,R), system can be represented as a compact network structure with a single source and three products derived from that source in three consecutive reactions. (M,R) has been claimed to be non-reducible to its components and algorithmically non-computable, in the sense of not being evaluable as a function by a Turing machine. If (M,R)-like structures are present in real biological networks, this suggests that many biological networks will be non-computable, with implications for those branches of systems biology that rely on in silico modelling for predictive purposes. We instantiate (M,R) using the process algebra Bio-PEPA, and discuss the extent to which our model represents a true realization of (M,R). We observe that under some starting conditions and parameter values, stable states can be achieved. Although formal demonstration of algorithmic computability remains elusive for (M,R), we discuss the extent to which our Bio-PEPA representation of (M,R) allows us to sidestep Rosen's fundamental objections to computational systems biology. We argue that the behaviour of (M,R) in Bio-PEPA shows life-like properties.

References

May 1, 1974·Currents in Modern Biology·F G VarelaR Uribe
May 3, 2003·Journal of Theoretical Biology·Juan Carlos LetelierJorge Mpodozis
Jun 1, 1964·The Bulletin of Mathematical Biophysics·R ROSEN
Jul 13, 2004·Artificial Life·Barry McMullin
Apr 19, 2005·Genome Biology·Athel Cornish-Bowden
May 13, 2005·Bio Systems·Kwang-Hyun ChoOlaf Wolkenhauer
Aug 27, 2005·Journal of Theoretical Biology·Juan-Carlos LetelierMaría Luz Cárdenas
Dec 31, 2005·Journal of Integrative Neuroscience·A H Louie
Mar 21, 2007·Proteomics·Athel Cornish-BowdenJorge Soto-Andrade
Jun 15, 2007·Artificial Life·A H Louie
Oct 24, 2007·Chemistry & Biodiversity·Arno L Goudsmit
Jul 1, 2008·Bioinformatics·Noga AlonS Cenk Sahinalp
Oct 16, 2008·Artificial Life·Keisuke Suzuki, Takashi Ikegami
Jan 27, 2009·Journal of Theoretical Biology·Matteo MossioJohn Stewart
Dec 8, 2009·Journal of Theoretical Biology·María Luz CárdenasJorge Soto-Andrade
Mar 17, 2010·BMC Systems Biology·Derek Gatherer
Aug 12, 2010·PLoS Computational Biology·Gabriel PiedrafitaAthel Cornish-Bowden
Jan 24, 2012·Journal of Theoretical Biology·Gabriel PiedrafitaFrancisco Montero
Jul 5, 2012·Nature Communications·Joshua A LermanBernhard O Palsson

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Citations

Jan 3, 2016·Bio Systems·Ling ZhangDerek Gatherer
Jul 21, 2015·Progress in Biophysics and Molecular Biology·Andrée C Ehresmann, Jaime Gomez-Ramirez
Aug 16, 2016·Journal of Theoretical Biology·Michael L PalmerDerek Gatherer
Jun 23, 2018·Circulation Research·Andrew A Gibb, Bradford G Hill
Dec 29, 2020·Journal of Molecular and Cellular Cardiology·Lindsey A McNallyBradford G Hill
May 7, 2021·Theory in Biosciences = Theorie in Den Biowissenschaften·Athel Cornish-Bowden, María Luz Cárdenas

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Software Mentioned

- Eclipse Plug - in
COPASI
PEPA Java Eclipse tool
PEPA Eclipse Plug - in
Bio
PEPA
MatLab
MetaTool
SPICE
PEPA Eclipse Plug - in tool

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