Benjamin Sheredos

Why Do Biologists Use So Many Diagrams

Diagrams have distinctive characteristics that make them an effective medium for communicating research findings, but they are even more impressive as tools for scientific reasoning. To explore this role, we examine diagrammatic formats that have been devised by biologists to (a) identify and illuminate phenomena involving circadian rhythms and (b) develop and modify mechanistic explanations of these phenomena.

HIT on the Psychometric Approach

Traditionally, identity and supervenience have been proposed in philosophy of mind as metaphysical accounts of how mental activities (fully understood, as they might be at the end of science) relate to brain processes. Kievet et al. (this issue) suggest that to be relevant to cognitive neuroscience, these philosophical positions must make empirically testable claims and be evaluated accordingly—they cannot sit on the sidelines, awaiting the hypothetical completion of cognitive neuroscience. We agree with the authors on the importance of rendering these positions relevant to ongoing science. We disagree, however, with their proposal that a metaphysical relationship (identity or supervenience) should “serve as a means to conceptually organize and guide the analysis of neurological and behavioral data” (p. 69). Instead, we advance a different view of the goals of cognitive neuroscience and of the proper means of relating metaphysics and explanation. Our central objection to the psychometric approach deployed by Kievet et al. is that the formal models only account for correlations between variables (measurements) and do not aid in explaining phenomena. Cognitive neuroscience is concerned with the latter. We develop this point in the next section, in which we present what we find to be problematic in their proposed models. In the Identity Claims and Mechanistic Explanations in Cognitive Neuroscience section, we advance an account of what is required to explain phenomena: (a) providing an adequate description of a phenomenon, and (b) characterizing the mechanism responsible for it. In doing so we characterize a version of the identity theory—heuristic identity theory (HIT), which figures centrally in developing such explanations—and illustrate its role in what we take to be a prototypical example of research in cognitive neuroscience. Finally, in the Levels, Mechanisms and Identity Claims section, we turn to how levels and interlevel relations should be construed in a metaphysical account that fits the mission of cognitive neuroscience.

Using Diagrams to Reason About Biological Mechanisms

In developing mechanistic explanations for biological phenomena, researchers have their choice of several different types of diagrams. First, a mechanism diagram spatially represents a proposed mechanism, typically using simple shapes for its parts and arrows for their operations. Beyond this representational role, such diagrams can provide a platform for further reasoning. Published diagrams in circadian biology show how question marks support reasoning about the proposed molecular mechanisms by flagging where there are knowledge gaps or uncertainties. Second, an annotated mechanism diagram can support computational modeling of the dynamics of a proposed mechanism. Each variable and parameter needed for the model is added to the diagram adjacent to the appropriate part or operation. Anchoring the model in this way helps with its construction, revision, and interpretation. Third, a network diagram fosters a different approach to mechanistic reasoning. Layout algorithms are applied to data generated by high-throughput experiments to reveal modules that correspond to mechanisms. We present examples in which network diagrams enable viewers to advance hypotheses about previously unknown mechanisms or unknown parts and operations of known mechanisms as well as to develop new understanding about how a given mechanism is situated in a larger environment.