Representing Time in Scientific Diagrams

Representing Time in Scientific Diagrams William Bechtel (bechtel@ucsd.edu) Daniel Burnston (dburnston@ucsd.edu) Benjamin Sheredos (bsheredos@ucsd.edu) Department of Philosophy and Center for Circadian Biology, University of California, San Diego La Jolla, CA, 92093-0119 USA Adele Abrahamsen (aabrahamsen@ucsd.edu) Center for Research in Language and Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093 USA Abstract tively for graphical representations of the parts and opera- tions of a mechanism. We refer to these as mechanism dia- grams, and they are of particular interest as they play crucial roles in developing, evaluating, and presenting mechanistic explanations. Biologists often begin by identifying a system that in relevant conditions generates a phenomenon of inter- est and then seek a mechanistic account of how it does so. This involves identifying its parts, determining the opera- tions they perform, and showing how, when organized ap- propriately, the parts and operations generate the phenome- non of interest (Bechtel & Abrahamsen, 2005; Bechtel & Richardson, 1993/2010; Machamer, Darden, & Craver, 2000). This practice is often supported by mechanism dia- grams in which icons or glyphs (Tversky, 2011) specify parts of the mechanism and arrows indicate the operations by which parts affect other parts or are transformed into other types of parts. However, these mechanism diagrams do not stand alone. To relate parts and operations represent- ed in the diagram to a phenomenon, researchers need to represent both how the phenomenon is realized in time and how the mechanism operates in time. We will examine both. Circadian rhythms are approximately 24-hour oscillations generated endogenously within organisms that regulate a host of physiological, behavioral, and cognitive functions. They are found in organisms ranging from bacteria and fun- gi to plants and animals. Much early research focused on the phenomenon of circadian rhythmicity as observed in ani- mals’ fluctuating levels of activity. During the last few dec- ades of the 20 th century, circadian researchers began tracing these rhythms to intracellular molecular mechanisms involv- ing feedback relations between proteins and the genes from which they are transcribed and translated. Challenged to understand how individual cells maintain an approximately 24-hour oscillation and how populations of cells synchronize their activity, circadian rhythm re- searchers have developed a variety of diagram formats. Most straightforward is to map time to one of the two spa- tial dimensions (or hours to one dimension and days to the other), but this comes at the cost of pre-empting a resource and hence limiting what else can be included. If, a circle is used instead to represent a 24-hour duration, that opens up several ways to incorporate other kinds of information. We will display and discuss examples of how these formats dis- play timing either of a phenomenon or of an operation with- Cognitive scientists have shown increased interest in dia- grams in recent years, but most of the focus has been on spa- tial representation, not conventions for representing time. We explore a variety of ways in which time is represented in dia- grams by one research community: scientists investigating circadian rhythms at the behavioral and molecular levels. Di- agrams that relate other variables to time or indicate a mecha- nism’s states across time use one or two spatial dimensions or circles to represent time and sometimes include explicit time markers (e.g., the hours on a clockface). Keywords: Circadian rhythms; diagrams; mechanistic expla- nation; time Introduction A number of cognitive scientists have become interested in the interaction between human reasoning and external visu- alizations. Projects in such areas as knowledge representa- tion, human-computer interaction, and situated cognition have all focused on how information can be represented in a range of distinct formats and used as reasoning tools. Exper- imental and theoretical work on diagrams in particular has made great strides in recent years (Cheng, 2002, 2011; Gooding, 2010; Hegarty, 2004, 2011; Nersessian, 2008; Tversky, 2011). Still, significant challenges remain in un- derstanding visualization. Our focus is on how diagrams support reasoning in complex empirical domains (Sheredos, Burnston, Abrahamsen, & Bechtel, 2013). A critical chal- lenge researchers face in developing diagrams is how to represent multiple aspects of a problem space. For instance, while two-dimensional diagrams readily support spatial rea- soning tasks, many tasks require reasoning about time, and representing time and integrating both spatial and temporal information pose special challenges. Our strategy in this paper is to examine published dia- grams from a field in empirical science that has dedicated significant attention to ways of representing events in time: chronobiology, the study of circadian and other biological rhythms. What is learned here has broader implications. The term diagram is used in both inclusive and restricted senses. In its inclusive sense, indicated by the etymology of the word, diagrams are visuospatial representations. All the figures in a scientific paper, including line graphs, typically count as diagrams. Sometimes the term is used more restric-