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. Focusing on circadian rhythm research in biology to explore these roles, we examine diagrammatic formats that have been devised to identify and illuminate circadian phenomena and to develop and modify mechanistic explanations of these phenomena.

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2012.

Truth diagrams are introduced as a novel graphical representation for propositional logic. To demonstrate their epistemic efficacy a set of 28 concepts are proposed that any comprehensive representation for PL should encompass. TDs address all the criteria whereas seven other existing representations for PL only provide partial coverage. These existing representations are: the linear formula notation, truth tables, a PL specific interpretation of Venn Diagrams, Frege’s conceptual notation, diagrams from Wittgenstein’s Tractatus, Pierce’s alpha graphs and Gardner’s shuttle diagrams. The comparison (...) of the representations succeeds in distinguishing ideas that are fundamental to PL from features of common PL representations that are somewhat arbitrary. (shrink)

We contend that diagrams are tools not only for communication but also for supporting the reasoning of biologists. In the mechanistic research that is characteristic of biology, diagrams delineate the phenomenon to be explained, display explanatory relations, and show the organized parts and operations of the mechanism proposed as responsible for the phenomenon. Both phenomenon diagrams and explanatory relations diagrams, employing graphs or other formats, facilitate applying visual processing to the detection of relevant patterns. Mechanism diagrams guide reasoning about how (...) the parts and operations work together to produce the phenomenon and what experiments need to be done to improve on the existing account. We examine how these functions are served by diagrams in circadian rhythm research. (shrink)

The possibility of ideography is an empirical question. Prior examples of graphic codes do not provide compelling evidence for the infeasibility of ideography, because they fail to satisfy essential cognitive requirements that have only recently been revealed by studies of representational systems in cognitive science. Design criteria derived from cognitive principles suggest how effective graphic codes may be engineered.