We explore the crucial role of diagrams in scientific reasoning, especially reasoning directed at developing mechanistic explanations of biological phenomena. We offer a case study focusing on one research project that resulted in a published paper advancing a new understanding of the mechanism by which the central circadian oscillator in Synechococcus elongatus controls gene expression. By examining how the diagrams prepared for the paper developed over the course of multiple drafts, we show how the process of generating a new explanation vitally involved the development and integration of multiple versions of different types of diagrams, and how reasoning about the mechanism proceeded in tandem with the development of the diagrams used to represent it.
(2011) The cognitive science of visual-spatial displays: Implications for design. Topics in Cognitive Science, 31, 446–474.
Iwasaki, H., Williams, S.M., Kitayama, Y., Ishiura, M., Golden, S.S., & Kondo, T.
(2000) A kaiC-interacting sensory histidine kinase, SasA, necessary to sustain robust circadian oscillation in cyanobacteria. Cell, 1011, 223–233.
Machamer, P., Darden, L., & Craver, C.F.
(2000) Thinking about mechanisms. Philosophy of Science, 671, 1–25.
Mackey, S.R., Golden, S.S., & Ditty, J.L.
(2011) The itty-bitty time machine: Genetics of the cyanobacterial circadian clock. Advances in genetics, 741, 13–53.
MacLeod, M., & Nersessian, N.J.
(2013) Coupling simulation and experiment: The bimodal strategy in integrative systems biology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 441, 572–584.
(2013) Active output state of the Synechococcus Kai circadian oscillator. Proceedings of the National Academy of Sciences, 1101, E3849–E3857.
(2005) Explanation in two dimensions: Diagrams and biological explanation. Biology and Philosophy, 201, 257–269.
(2013) Scientific diagrams as traces of group-dependent cognition: A brief cognitive-historical analysis. Proceedings of the 35th Annual Meeting of the Cognitive Science Society (pp. 2396–2401). Austin, TX: Cognitive Science Society.
Sheredos, B., Burnston, D., Abrahamsen, A., & Bechtel, W.
(2013) Why do biologists use so many diagrams?Philosophy of Science, 801, 931–944.
Stieff, M., Hegarty, M., & Deslongchamps, G.
(2011) Identifying representational competence with multi-representational displays. Cognition and Instruction, 291, 123–145.
Takai, N., Nakajima, M., Oyama, T., Kit, R., Sugita, C., Sugita, M., Kondo, T., & Iwasaki, H.
(2006) A KaiC-ssociating SasA–RpaA two-component regulatory system as a major circadian timing mediator in cyanobacteria. Proceedings of the National Academy of Sciences, 103(32), 12109–12114.
(2011) Visualizing thought. Topics in Cognitive Science, 31, 499–535.
(2000) Putting quantum mechanics to work in chemistry: The power of diagrammatic representation. Philosophy of Science, 671, S612–S627.
Cited by 12 other publications
Abrahamsen, Adele & William Bechtel
2015. Diagrams as Tools for Scientific Reasoning. Review of Philosophy and Psychology 6:1 ► pp. 117 ff.
Ariga, Kana & Manabu Tashiro
2022. Change in the graphics of journal articles in the life sciences field: analysis of figures and tables in the journal “Cell”. History and Philosophy of the Life Sciences 44:3
2021. Explaining features of fine-grained phenomena using abstract analyses of phenomena and mechanisms: two examples from chronobiology. Synthese 198:S24 ► pp. 1 ff.
Bechtel, William, Adele Abrahamsen & Benjamin Sheredos
2018. Using Diagrams to Reason About Biological Mechanisms. In Diagrammatic Representation and Inference [Lecture Notes in Computer Science, 10871], ► pp. 264 ff.
Burnston, Daniel C.
2016. Data graphs and mechanistic explanation. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 57 ► pp. 1 ff.
2016. Spot the difference: Causal contrasts in scientific diagrams. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 60 ► pp. 77 ff.
2017. Communicating with scientific graphics: A descriptive inquiry into non-ideal normativity. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 63 ► pp. 32 ff.
Sheredos, Benjamin & William Bechtel
2017. Sketching Biological Phenomena and Mechanisms. Topics in Cognitive Science 9:4 ► pp. 970 ff.
2018. Mechanism diagrams and abstraction-by-aggregation. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 71 ► pp. 17 ff.
2018. Fictional Models and Fictional Representations. Axiomathes 28:4 ► pp. 375 ff.
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