%0 Journal Article %1 wolkenhauer_abstract_2007 %A Wolkenhauer, Olaf %A Hofmeyr, Jan-Hendrik S %D 2007 %J Journal of Theoretical Biology %K Animals, Autocrine Cell Communication, Phenomena, Physiological Rostock SBI Systems Uncertainty biology, %N 3 %P 461--476 %R 10.1016/j.jtbi.2007.01.005 %T An abstract cell model that describes the self-organization of cell function in living systems %U http://www.ncbi.nlm.nih.gov/pubmed/17328919 %V 246 %X The principal aim of systems biology is to search for general principles that govern living systems. We develop an abstract dynamic model of a cell, rooted in Mesarovi? and Takahara's general systems theory. In this conceptual framework the function of the cell is delineated by the dynamic processes it can realize. We abstract basic cellular processes, i.e., metabolism, signalling, gene expression, into a mapping and consider cell functions, i.e., cell differentiation, proliferation, etc. as processes that determine the basic cellular processes that realize a particular cell function. We then postulate the existence of a 'coordination principle' that determines cell function. These ideas are condensed into a theorem: If basic cellular processes for the control and regulation of cell functions are present, then the coordination of cell functions is realized autonomously from within the system. Inspired by Robert Rosen's notion of closure to efficient causation, introduced as a necessary condition for a natural system to be an organism, we show that for a mathematical model of a self-organizing cell the associated category must be cartesian closed. Although the semantics of our cell model differ from Rosen's (M,R)-systems, the proof of our theorem supports (in parts) Rosen's argument that living cells have non-simulable properties. Whereas models that form cartesian closed categories can capture self-organization (which is a, if not the, fundamental property of living systems), conventional computer simulations of these models (such as virtual cells) cannot. Simulations can mimic living systems, but they are not like living systems.

@article{wolkenhauer_abstract_2007, abstract = {The principal aim of systems biology is to search for general principles that govern living systems. We develop an abstract dynamic model of a cell, rooted in Mesarovi? and Takahara's general systems theory. In this conceptual framework the function of the cell is delineated by the dynamic processes it can realize. We abstract basic cellular processes, i.e., metabolism, signalling, gene expression, into a mapping and consider cell functions, i.e., cell differentiation, proliferation, etc. as processes that determine the basic cellular processes that realize a particular cell function. We then postulate the existence of a 'coordination principle' that determines cell function. These ideas are condensed into a theorem: If basic cellular processes for the control and regulation of cell functions are present, then the coordination of cell functions is realized autonomously from within the system. Inspired by Robert Rosen's notion of closure to efficient causation, introduced as a necessary condition for a natural system to be an organism, we show that for a mathematical model of a self-organizing cell the associated category must be cartesian closed. Although the semantics of our cell model differ from Rosen's {(M,R)-systems,} the proof of our theorem supports (in parts) Rosen's argument that living cells have non-simulable properties. Whereas models that form cartesian closed categories can capture self-organization (which is a, if not the, fundamental property of living systems), conventional computer simulations of these models (such as virtual cells) cannot. Simulations can mimic living systems, but they are not like living systems.}, added-at = {2010-09-17T16:55:15.000+0200}, author = {Wolkenhauer, Olaf and Hofmeyr, {Jan-Hendrik} S}, biburl = {https://www.bibsonomy.org/bibtex/253a2d2501bdd69dc9234d9fe66ab0477/ra1602}, doi = {10.1016/j.jtbi.2007.01.005}, interhash = {1881237c40e024db9e20fc5285232f60}, intrahash = {53a2d2501bdd69dc9234d9fe66ab0477}, issn = {0022-5193}, journal = {Journal of Theoretical Biology}, keywords = {Animals, Autocrine Cell Communication, Phenomena, Physiological Rostock SBI Systems Uncertainty biology,}, month = jun, note = {{PMID:} 17328919}, number = 3, pages = {461--476}, timestamp = {2010-09-17T16:55:21.000+0200}, title = {An abstract cell model that describes the self-organization of cell function in living systems}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17328919}, volume = 246, year = 2007 }