•  82
    Inter-level relations in computer science, biology, and psychology
    with Frank Bruggeman, Catholijn Jonker, Huib Looren de Jong, Allard Tamminga, Jan Treur, Hans Westerhoff, and Wouter Wijngaards
    Philosophical Psychology 15 (4). 2002.
    Investigations into inter-level relations in computer science, biology and psychology call for an *empirical* turn in the philosophy of mind. Rather than concentrate on *a priori* discussions of inter-level relations between 'completed' sciences, a case is made for the actual study of the way inter-level relations grow out of the developing sciences. Thus, philosophical inquiries will be made more relevant to the sciences, and, more importantly, philosophical accounts of inter-level relations wi…Read more
  •  67
    Mechanistic Explanations and Models in Molecular Systems Biology
    with Frank J. Bruggeman and Robert C. Richardson
    Foundations of Science 18 (4): 725-744. 2013.
    Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart …Read more
  •  59
    Biocomplexity: A pluralist research strategy is necessary for a mechanistic explanation of the "live" state
    with F. J. Bruggeman and H. V. Westerhoff
    Philosophical Psychology 15 (4). 2002.
    The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.