Mechanistic Diagrams as Search Organizers

Mechanistic Diagrams as Search Organizers Daniel C. Burnston (dburnsto@ucsd.edu) Department of Philosophy and Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093-0119 USA Abstract Many in cognitive science have noted the importance of external visualizations for reasoning and learning, and have suggested that such visualizations play a role in complex reasoning contexts such as scientific investigation. However, what cognitive role diagrams play in scientific reasoning is unclear. I suggest that mechanistic diagrams function as search organizers in active research projects. Diagrams aid in scientific reasoning by being uniquely positioned to coordinate cognitive search through multiple search spaces, both within an individual and within a field. I examine this role using a number of published diagrams from mammalian chronobiology. Keywords: scientific chronobiology. diagrams; cognitive search; Introduction Diagrams are nearly ubiquitous in biological practice, in which the goal is often to construct an explanation of the mechanisms responsible for complicated phenomena. In journal articles, conference presentations, and whiteboard discussions, research scientists continually engage in the process of constructing, analyzing, and modifying diagrammatic representations. This ubiquity suggests that diagrams play an important role in reasoning about phenomena in biology. However, the specific role that diagrams play in reasoning is not established. Part of the difficulty is the sheer complexity of the reasoning processes involved. Scientists must coordinate a variety of representational resources in constructing mechanistic explanations, and diagrams are often involved in characterizing the phenomena of interest, organizing and presenting obtained data, and conveying the parts, operations, and organization of a proposed mechanism (Gooding, 2010; Sheredos, Burnston, Abrahamsen, & Bechtel, forthcoming). The current literature on diagrams has focused largely on the meaning of diagrammatic elements and how they relate (Tversky, 2011), as well as on how diagrams might encode complete explanations (Perini, 2005), or function as learning tools for novices (Cheng, 2011). While these are important analyses, they leave a gap in understanding how diagrams might play a role, even for experts, in constructing explanations of complex phenomena. Pioneering historical studies of episodes of scientific discovery (Cheng, 1992; Nersessian, 2008) have focused on the use of visualizations in the efforts of individual scientists to explain mathematical or physical phenomena. The use of diagrams in an active field of contemporary science presents new challenges, as diagrams are used, discussed, and appropriated by numerous different researchers, each with different backgrounds, interests, and experimental skills. In this paper I propose an account of how diagrams aid scientific reasoning in an active research field. The proposal draws upon several approaches in cognitive science, which construe reasoning as involving “cognitive search”—a process of selecting the right representations out of a space of possibilities in order to meet a cognitive goal. The search perspective on diagrams contends that diagrams facilitate scientists’ cognitive search through the complex realm of possibilities that are relevant in explaining natural phenomena. Specifically, I contend that diagrams provide an external search space that allows for the coordination of both conceptual and experimental resources, both by individuals and by entire scientific communities. I focus on diagrams of proposed mechanisms in biology. This type of diagram generally consists of proposed entities or events depicted by shapes and/or linguistic labels, organized in visual space, and related via arrows, lines, and enclosures to convey the structural, causal, functional, and/or conceptual (e.g., categorical) relations between them. Often, these diagrams occur at the beginning or end of a research article as a way of organizing the findings into a model of how physical components might interact to produce phenomena of interest. Moreover, these diagrams are often changed and expanded over a series of publications in order to incorporate new results. While receiving relatively little attention in analyses of scientific practice, diagrams of this type can be extremely important, as even minor changes to diagrammatic form can have large effects on how the organization of a mechanism is interpreted. Sheredos et al. (forthcoming) have argued that these differences both constrain thought in particular ways and afford particular inferences that are useful for hypothesis construction. The search perspective expands on this viewpoint to further elucidate the use of mechanistic diagrams in a research field. I will develop this perspective by analyzing the use of mechanistic diagrams in mammalian chronobiology. Chronobiologists study phenomena of circadian rhythms— daily, roughly 24 hour cycles in biological activity—in a variety of different organisms, at each of the behavioral, physiological, and molecular levels. Many biological processes exhibit circadian rhythms, including gene transcription, cell division, metabolism, and overt sleep and feeding behavior. Over the last 25 years, much progress has been made in understanding how these rhythms are