Computational systems biologists create and manipulate computational models of biological systems, but they do not always have straightforward epistemic access to the content and behavioural profile of such models because of their length, coding idiosyncrasies, and formal complexity. This creates difficulties both for modellers in their research groups and for their bioscience collaborators who rely on these models. In this paper we introduce a new kind of visualization that was developed to address just this sort of epistemic opacity. The visualization (...) is unusual in that it depicts the dynamics and structure of a computer model instead of that model’s target system, and because it is generated algorithmically. Using considerations from epistemology and aesthetics, we explore how this new kind of visualization increases scientific understanding of the content and function of computer models in systems biology to reduce epistemic opacity. (shrink)

A cognitive ethnography of how bioengineering scientists create innovative modeling methods. In this first full-scale, long-term cognitive ethnography by a philosopher of science, Nancy J. Nersessian offers an account of how scientists at the interdisciplinary frontiers of bioengineering create novel problem-solving methods. Bioengineering scientists model complex dynamical biological systems using concepts, methods, materials, and other resources drawn primarily from engineering. They aim to understand these systems sufficiently to control or intervene in them. What Nersessian examines here is how cutting-edge bioengineering (...) scientists integrate the cognitive, social, material, and cultural dimensions of practice. Her findings and conclusions have broad implications for researchers in philosophy, science studies, cognitive science, and interdisciplinary studies, as well as scientists, educators, policy makers, and funding agencies. In studying the epistemic practices of scientists, Nersessian pushes the boundaries of the philosophy of science and cognitive science into areas not ventured before. She recounts a decades-long, wide-ranging, and richly detailed investigation of the innovative interdisciplinary modeling practices of bioengineering researchers in four university laboratories. She argues and demonstrates that the methods of cognitive ethnography and qualitative data analysis, placed in the framework of distributed cognition, provide the tools for a philosophical analysis of how scientific discoveries arise from complex systems in which the cognitive, social, material, and cultural dimensions of problem-solving are integrated into the epistemic practices of scientists. Specifically, she looks at how interdisciplinary environments shape problem-solving. Although Nersessian’s case material is drawn from the bioengineering sciences, her analytic framework and methodological approach are directly applicable to scientific research in a broader, more general sense, as well. (shrink)

Scientific research is a highly complex and creative domain of human activity. In addition to its intrinsic value, understanding scientific thinking provides insight into the creative potential of human psychological capacities, as they are imbedded in rich social, material, and cultural environments. I discuss findings from my own investigations using two forms of qualitative research suited to studying scientific thinking as situated in context: cognitive-historical and cognitive-ethnographic.

This chapter focuses on a novel class of models used in frontier research in the bioengineering sciences – in vitro simulation models – that provide the basis for biological experimentation. These bioengineered models are hybrid constructions, composed of living tissues or cells and engineered materials. Specifically, it discusses the processes through which in vitro models were built, experimented with, and justified in a tissue engineering lab. It examines processes of design, construction, experimentation, evaluation, and redesign of in vitro simulation models, (...) in general, as instances of building the source analogy (as distinguished from retrieving an analogy), which figures prominently in creative frontier scientific research. Building the analogical source is a bootstrapping process, which furthers the articulation, as well as the solution of the problem. -/- . (shrink)