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Modelling in systems biology: an analysis of the relevance of Rosen's relational viewpoint for current systems biology

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Abstract
Systems Biology aims to take up the challenge of the post-genome era by developing means to handle the data flood in the contemporary ‘omic’ sciences. One of the challenges is to ‘turn data into knowledge’, which gives rise to the question of the functional meaning of the structural data. Systems Biology tries to answer this question by capturing the organisation of a biological system through mathematical and computational modelling. In this regard, however, there is some ambiguity concerning the notions of function, wholeness and system. In this paper, we intend to discuss this ambiguity by analysing the status of modelling in Systems Biology. We do so by articulating the source of the tensions between a relational and a mechanistic approach of living systems, and will inquire upon the potential relevance of a relational account for current Systems Biology. We draw upon Robert Rosen's relational account, in which functionality is an intrinsic and essential part of the organisation of a living system. An organism is complex, e.g. not amenable to a mechanistic, classical or engineering analysis. In this viewpoint, which is quite similar to Kant's, functionality has to be presupposed in order to ‘save’ the organism as a living system. It is the status of this presupposition that qualitatively distinguishes a mechanistic from a relational account, and it is the potentiality of that idea which deserves further investigation in current Systems Biology.
Keywords
complexity, Robert Rosen, modelling, function, Systems Biology

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Chicago
Van Poucke, Joris, and Gertrudis Van de Vijver. 2008. “Modelling in Systems Biology: An Analysis of the Relevance of Rosen’s Relational Viewpoint for Current Systems Biology.” Ed. Daniel M Dubois. Casys : International Journal of Computing Anticipatory Systems 21: 184–198.
APA
Van Poucke, J., & Van de Vijver, G. (2008). Modelling in systems biology: an analysis of the relevance of Rosen’s relational viewpoint for current systems biology. (D. M. Dubois, Ed.)CASYS : INTERNATIONAL JOURNAL OF COMPUTING ANTICIPATORY SYSTEMS, 21, 184–198. Presented at the 8th International conference on Computing Anticipatory Systems (CASYS  ’07).
Vancouver
1.
Van Poucke J, Van de Vijver G. Modelling in systems biology: an analysis of the relevance of Rosen’s relational viewpoint for current systems biology. Dubois DM, editor. CASYS : INTERNATIONAL JOURNAL OF COMPUTING ANTICIPATORY SYSTEMS. 2008;21:184–98.
MLA
Van Poucke, Joris, and Gertrudis Van de Vijver. “Modelling in Systems Biology: An Analysis of the Relevance of Rosen’s Relational Viewpoint for Current Systems Biology.” Ed. Daniel M Dubois. CASYS : INTERNATIONAL JOURNAL OF COMPUTING ANTICIPATORY SYSTEMS 21 (2008): 184–198. Print.
@article{1096714,
  abstract     = {Systems Biology aims to take up the challenge of the post-genome era by developing means to handle the data flood in the contemporary ‘omic’ sciences. One of the challenges is to ‘turn data into knowledge’, which gives rise to the question of the functional meaning of the structural data. Systems Biology tries to answer this question by capturing the organisation of a biological system through mathematical and computational modelling. In this regard, however, there is some ambiguity concerning the notions of function, wholeness and system. In this paper, we intend to discuss this ambiguity by analysing the status of modelling in Systems Biology. We do so by articulating the source of the tensions between a relational and a mechanistic approach of living systems, and will inquire upon the potential relevance of a relational account for current Systems Biology. We draw upon Robert Rosen's relational account, in which functionality is an intrinsic and essential part of the organisation of a living system. An organism is complex, e.g. not amenable to a mechanistic, classical or engineering analysis. In this viewpoint, which is quite similar to Kant's, functionality has to be presupposed in order to ‘save’ the organism as a living system. It is the status of this presupposition that qualitatively distinguishes a mechanistic from a relational account, and it is the potentiality of that idea which deserves further investigation in current Systems Biology.},
  author       = {Van Poucke, Joris and Van de Vijver, Gertrudis},
  editor       = { Dubois, Daniel M},
  isbn         = {2930396083},
  issn         = {1373-5411},
  journal      = {CASYS : INTERNATIONAL JOURNAL OF COMPUTING ANTICIPATORY SYSTEMS},
  keywords     = {complexity,Robert Rosen,modelling,function,Systems Biology},
  language     = {eng},
  location     = {Liège, Belgium},
  pages        = {184--198},
  title        = {Modelling in systems biology: an analysis of the relevance of Rosen's relational viewpoint for current systems biology},
  volume       = {21},
  year         = {2008},
}