Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have different epistemic characters. (...) Theoretical modelling is grounded in explicit and known analogies between model and target. By contrast, inferences from model organisms are empirical extrapolations. Often such extrapolation is based on shared ancestry, sometimes in conjunction with other empirical information. One implication is that such inferences are unique to biology, whereas theoretical models are common across many disciplines. We close by discussing the diversity of uses to which model organisms are put, suggesting how these relate to our overall account. 1 Introduction2 Volterra and Theoretical Modelling3 Drosophila as a Model Organism4 Generalizing from Work on Model Organisms5 Phylogenetic Inference and Model Organisms6 Further Roles of Model Organisms6.1 Preparative experimentation6.2 Model organisms as paradigms6.3 Model organisms as theoretical models6.4 Inspiration for engineers6.5 Anchoring a research community7 Conclusion. (shrink)

To a large extent, the evidential base of claims in the philosophy of science has switched from thought experiments to case studies. We argue that abandoning thought experiments was a wrong turn, since they can effectively complement case studies. We make our argument via an analogy with the relationship between experiments and observations within science. Just as experiments and ‘natural’ observations can together evidence claims in science, each mitigating the downsides of the other, so too can thought experiments and case (...) studies be mutually supporting. After presenting the main argument, we look at potential concerns about thought experiments, suggesting that a judiciously applied mixed-methods approach can overcome them. (shrink)

Thought experiments play a role in science and in some central parts of contemporary philosophy. They used to play a larger role in philosophy of science, but have been largely abandoned as part of the field’s “practice turn”. This chapter discusses possible roles for thought experimentation within a practice-oriented philosophy of science. Some of these roles are uncontroversial, such as exemplification and aiding discovery. A more controversial role is the reliance on thought experiments to justify philosophical claims. It is proposed (...) that if we adopt an underlying empiricist view of concepts, then thought experiments can be seen as affording us contact with scientific practice, despite their seemingly a priori character. The advantages and drawbacks of thought experiments are discussed via comparison with case studies, on the one, and simulations on the other hand. The chapter closes with some remarks on how to combine thought experiments with other methods. (shrink)