Teaser
“A neglected topic, of particular interest to me, refers to the benefits that different representation formats, and especially visual formats in contrast to sentential/linguistic ones, provide for epistemically oriented cognitive activities such as hypothesis generation and discovery, data aggregation and organization, model construction and simulation, and explanation of various kinds. Visual representations are so prominent and relevant for biology – and especially, I think, for systems biology approaches – that they are often objects of special interest… Our understanding of the role of visuals in biological practice, from both philosophy and cognitive science, has not kept pace with these developments. This is, I think, an underappreciated area for philosophical inquiry – and an attractive area too, if you enjoy putting visuals into papers and presentations.”
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References
Abrahamsen, A., & Bechtel, W. (2015). Diagrams as tools for scientific reasoning. Review of Philosophy and Psychology, 6, 117–131.
Bachmaier, C., Brandes, U., & Schreiber, F. (2013). Biological networks. In R. Tamassia (Ed.), Handbook of graph drawing and visualization (pp. 621–651). Hoboken: CRC Press.
Bertolaso, M. (2011). Hierarchies and causal relationships in interpretive models of the neoplastic process. History and Philosophy of the Life Sciences, 33, 515–536.
Brigandt, I. (2013). Systems biology and the integration of mechanistic explanation and mathematical explanation. Studies in History and Philosophy of Biological and Biomedical Sciences, 44, 477–492.
Carusi, A. (2014). Validation and variability: Dual challenges on the path from systems biology to systems medicine. Studies in History and Philosophy of Biological and Biomedical Sciences, 48, 28–37.
Fortunato, S. (2010). Community detection in graphs. Physics Reports, 486, 75–174.
Giuliani, A., Filippi, S., & Bertolaso, M. (2014). Why network approach can promote a new way of thinking in biology. Frontiers in Genetics, 5, 1–5.
Green, S., Fagan, M., & Jaeger, J. (2015). Explanatory integration challenges in evolutionary systems biology. Biological Theory, 10, 18–35.
Green, S., & Jones, N. (2016). Constraint-based reasoning for search and explanation: Strategies for understanding variation and patterns in biology. Dialectica, 70, 343–374.
Huneman, P. (2010). Topological explanations and robustness in biological sciences. Synthese, 177, 213–245.
Jones, N. (2014). Bowtie structures, pathway diagrams, and topological explanation. Erkenntnis, 79, 1135–1155.
Jones, N. (2016). Inference to the more robust explanation. British Journal for the Philosophy of Science. Published online doi:10.1093/bjps/axw009.
Jones, N., & Wolkenhauer, O. (2012). Diagrams as locality aids for explanation and model construction in cell biology. Biology and Philosophy, 27, 705–721.
Leonelli, S. (2014). What difference does quantity make? On the epistemology of Big Data in biology. Big Data & Society, 1, 1–11.
Malaterre, C. (2007). Organicism and reductionism in cancer research: Towards a systemic approach. International Studies in the Philosophy of Science, 21, 57–73.
Novere, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalarante, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villeger, A., Boyd, S. E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K., & Kitano, H. (2009). The systems biology graphical notation. Nature Biotechnology, 27, 735–741.
Rives, A. W., & Galitski, T. (2003). Modular organization of cellular networks. Proceedings of the National Academy of Sciences, 100, 1128–1133.
Saraiya, P., North, C., & Duca, K. (2005). An insight-based methodology for evaluating bioinformatics visualizations. Visualization and Computer Graphics, 11, 443–456.
Sheredos, B., Burnston, D., Abrahamsen, A., & Bechtel, W. (2014). Why do biologists use so many diagrams? Philosophy of Science, 80, 931–944.
Soto, A. M., & Sonnenschein, C. (2006). Emergentism by default: A view from the bench. Synthese, 151, 361–376.
Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of ‘small-world’ networks. Nature, 393, 440–442.
Wilkinson, L., & Friendly, M. (2009). The history of the cluster heat map. The American Statistician, 63, 179–184.
Wouters, A. (2007). Design explanation: Determining the constraints on what can be alive. Erkenntnis, 67, 65–80.
Suggested Readings by Nicholaos Jones
Jones, N. (2014). Bowtie structures, pathway diagrams, and topological explanation. Erkenntnis, 79, 1135–1155.
Jones, N. (2016). Inference to the more robust explanation. British Journal for the Philosophy of Science. Published online doi:10.1093/bjps/axw009.
Jones, N., & Wolkenhauer, O. (2012). Diagrams as locality aids for explanation and model construction in cell biology. Biology and Philosophy, 27, 705–721.
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Jones, N. (2017). Extracting Phenomena, Integrating Explanations, and Styling Representations: Some Frontiers for Philosophizing About Biology. In: Green, S. (eds) Philosophy of Systems Biology. History, Philosophy and Theory of the Life Sciences, vol 20. Springer, Cham. https://doi.org/10.1007/978-3-319-47000-9_14
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