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Diagrams as Tools for Scientific Reasoning

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Abstract

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.

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Notes

  1. The importance of the visual presentation in a graph can be appreciated by considering the study that first established 37 °C (98.6 °F) as normal mean body temperature. Having collected multiple recordings per day from over 25,000 individuals, Wunderlich (1868) noted oscillations of over 1 ° C between a low in the early morning hours and a peak in the afternoon. But he reported these results using summary tables, in which oscillations could be discerned only via effortful, nonvisual processing; this likely was one reason that most subsequent researchers cited him only for establishing the “normal” human temperature, not its daily oscillations.

  2. Our frequent collaborator, Daniel Burnston, first called our attention to explanatory relations and has led our research group’s initial consideration of how explanatory relations diagrams figure in scientific practice. The specific construals and applications in this section are ours.

  3. At those times of day with the most molecular clock activity, arrowheads are stacked further into the circle as necessary to keep them distinct. The number of arrowheads per plot is not of interest; it simply indicates how many neurons in the slice fluoresced.

  4. Many diagrams of this type, with the addition of a curved line representing the nuclear membrane, incorporate the fact that per mRNA is transported across the membrane into the cytoplasm, where it is translated into PER, which then dimerizes with TIM. To initiate negative feedback, the dimer must be transported back into the nucleus. Together with other time-consuming operations, these achieve a 24-hour cycle.

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Acknowledgments

We gratefully acknowledge the support of National Science Foundation grant 1127640 and the numerous contributions of our collaborators Daniel Burnston and Benjamin Sheredos.

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  1. University of California, San Diego, USA

    Adele Abrahamsen & William Bechtel

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  1. Adele Abrahamsen
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  2. William Bechtel
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Correspondence to William Bechtel.

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Abrahamsen, A., Bechtel, W. Diagrams as Tools for Scientific Reasoning. Rev.Phil.Psych. 6, 117–131 (2015). https://doi.org/10.1007/s13164-014-0215-2

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