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

BMC Systems Biology
Derek Gatherer, Vashti Galpin


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.


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

❮ Previous
Next ❯


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

❮ Previous
Next ❯

Software Mentioned

- Eclipse Plug - in
PEPA Java Eclipse tool
PEPA Eclipse Plug - in
PEPA Eclipse Plug - in tool

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.