Experimental Modeling in Biology: In Vivo Representation and Stand-Ins as Modeling Strategies

Abstract

Experimental modeling in biology involves the use of living organisms (not necessarily socalled "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand in for a physically different kind of process. I discuss the advantages of this approach in the context of evolutionary biology.

Evolution on the bright side of life: microorganisms and the evolution of mutualism

“…Throughout this review, I have described how microbial mutualisms could be used to address these gaps between theory and empirical research by providing in vivo representations of models . I suggested manipulating the possibilities for cheating or defenses against it in order to learn how each affects adaptation to mutualism.…”

“…Throughout this review, I have described how microbial mutualisms could be used to address these gaps between theory and empirical research by providing in vivo representations of models. 136 I suggested manipulating the possibilities for cheating or defenses against it in order to learn how each affects adaptation to mutualism. In addition, genome sequencing of evolved mutualists may provide an unbiased list of putative adaptations to mutualism, allowing researchers to gain a more comprehensive view of how mutualists adapt.…”

Integrating Philosophy of Science into Research on Ethical, Legal and Social Issues in the Life Sciences

“…Animal models serve a number of epistemic purposes in the life sciences (Weber 2014(Weber , 2018, including exploratory research, developing and testing hypotheses about biological mechanisms, animal-to-human extrapolations and many other things. Recent research in philosophy of science has, however, highlighted a number of purposes or functions of animal models that seem be somewhat different (Ankeny and Leonelli 2016;Hardesty 2018;Levy and Currie 2015).…”

“…If anything, their epistemic flexibility seems to be quite high. First of all, animal models, although standardized organisms, are extremely complex natural systems to be explored; i.e., animal models can in many cases act as generators of surprises in that they yield new and unexpected properties (after scientists have had more time to interact with them and to tinker with the experimental systems of which they are an element) (Rheinberger 1997;Weber 2014). Secondly, the scientific questions that can be investigated using animal experimentation very much depend on the available technologies and tools in the life sciences and, hence, are also not fixed.…”

Microbes, mathematics, and models

“…These analyses have focused primarily on what these experiments say about evolutionary processes and theories (for example, Beatty, 2006;Plutynksi, 2001;Desjardins, 2011;Parke, 2014). However, there are other avenues of philosophical insight afforded by experimental evolutionary research, and one of them is about the nature of modelling itself (Weber, 2014). Analysing the ways in which microbial systems generate knowledge sheds light on how material or concrete models function more generally, and on how they work together with other sorts of models.…”