Scientific practices have been changed by the increasing use of computer simulations. A central question for philosophers is how to characterize computer simulations. In this paper, we address this question by analyzing simulations in biochemistry. We propose that simulations have been used in biochemistry long before computers arrived. Simulation can be described as a surrogate relationship between models. Moreover, a simulative aspect is implicit in the classical dichotomy between in vivo–in vitro conditions. Based on a discussion about how to characterize (...) a simulative aspect in this dichotomy, we will argue that an adequate understanding of computer simulations in biochemistry requires a previous understanding of simulations in experimental contexts. (shrink)

The Epistemology Of Computer Simulation has developed as an epistemological and methodological analysis of simulative sciences using quantitative computational models to represent and predict empirical phenomena of interest. In this paper, Executable Cell Biology and Agent-Based Modelling are examined to show how one may take advantage of qualitative computational models to evaluate reachability properties of reactive systems. In contrast to the thesis, advanced by EOCS, that computational models are not adequate representations of the simulated empirical systems, it is shown how (...) the representational adequacy of qualitative models is essential to evaluate reachability properties. Justification theory, if not playing an essential role in EOCS, is exhibited to be involved in the process of advancing and corroborating model-based hypotheses about empirical systems in ECB and ABM. Finally, the practice of evaluating model-based hypothesis by testing the simulated systems is shown to constitute an argument in favour of the thesis that computer simulations in ECB and ABM can be put on a par with scientific experiments. (shrink)