Experimental modeling in biology involves the use of living organisms (not necessarily so-called "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. (shrink)

This contribution provides an assessment of the epistemological role of scientific models. The prevalent view that all scientific models are representations of the world is rejected. This view points to a unified way of resolving epistemic issues for scientific models. The emerging consensus in philosophy of science that models have many different epistemic roles in science is presented and defended.

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the (...) use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

Researchers often pursue proof of concept research, but criteria for evaluating such research remain poorly specified. This article proposes a general framework for proof of concept research that k...

Confirmation in evolutionary biology depends on what biologists take to be the genuine rivals. Investigating what constrains the scope of biological possibility provides part of the story: explaining how possible helps determine what counts as a genuine rival and thus informs confirmation. To clarify the criteria for genuine rivalry I distinguish between global and local constraints on biological possibility, and offer an account of how-possibly explanation. To sharpen the connection between confirmation and explaining how possible I discuss the view that (...) formal inquiry can provide a kind of confirmation-theoretic support for evolutionary models, and offer an example of how-possibly explanation interacting with testing practice. (shrink)

Recent philosophy of science has witnessed a shift in focus, in that significantly more consideration is given to how scientists employ models. Attending to the role of models in scientific practice leads to new questions about the representational roles of models, the purpose of idealizations, why multiple models are used for the same phenomenon, and many more besides. In this paper, I suggest that these themes resonate with central topics in feminist epistemology, in particular prominent versions of feminist empiricism, and (...) that model-based science and feminist epistemology each has crucial resources to offer the other's project. (shrink)

Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and (...) equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry. (shrink)

It is undeniable that much scientific work is model-based. Despite this, the justification for this reliance on models is still controversial. A particular difficulty here is the fact that many scientific models are based on assumptions that do not describe the exact details of many or even any empirical situations very well. This raises the question of why it is that, despite their frequent lack of descriptive accuracy, employing models is scientifically useful.One..