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Experimental Modeling in Biology: In Vivo Representation and Stand-Ins as Modeling Strategies

Published online by Cambridge University Press:  01 January 2022

Marcel Weber
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Abstract

Experimental modeling in biology involves the use of living organisms (not necessarily so-called model organisms) in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call “in vivo representations,” where one kind of causal process is used to stand in for a physically different kind of process. I discuss the advantages of this approach in the context of evolutionary biology.

Type
Signaling Theory in Biological and Cognitive Sciences
Information
Philosophy of Science , Volume 81 , Issue 5 , December 2014 , pp. 756 - 769
Copyright
Copyright © The Philosophy of Science Association

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Footnotes

†

I wish to thank Kristina Hillesland, Mike Travisano, Ken Waters, and the San Diego audience for an exciting PSA 2012 Symposium on experimental modeling. This paper also benefited from discussion with audiences at the Ludwig Maximilian University of Munich, the Sorbonne, and the Second European Advanced Seminar in the Philosophy of the Life Sciences (Hermance).

References

Balagaddé, Frederick K., Song, H., Ozaki, J., Collins, C. H., Barnet, M., Arnold, F. H., Quake, S. R., and You, L.. 2008. “A Synthetic Escherichia Coli Predator-Prey Ecosystem.” Molecular Systems Biology 4:187.10.1038/msb.2008.24CrossRefGoogle ScholarPubMed
Burian, Richard M. 1997. “Exploratory Experimentation and the Role of Histochemical Techniques in the Work of Jean Brachet, 1938–1952.” History and Philosophy of the Life Sciences 19:27–45.Google ScholarPubMed
Clarke, Ellen. 2012. “Plant Individuality: A Solution to the Demographer’s Dilemma.” Biology and Philosophy 27:321–61.10.1007/s10539-012-9309-3CrossRefGoogle Scholar
Elliott, Kevin. 2007. “Varieties of Exploratory Experimentation in Nanotoxicology.” History and Philosophy of the Life Sciences 29:311–34.Google ScholarPubMed
Frigg, Roman. 2010. “Models and Fiction.” Synthese 172:251–68.10.1007/s11229-009-9505-0CrossRefGoogle Scholar
Frigg, Roman, and Hartmann, Stephan. 2012. “Models in Science.” In Stanford Encyclopedia of Philosophy, ed. Zalta, Edward N.. Stanford, CA: Stanford University. http://plato.stanford.edu/archives/fall2012/entries/models-science/.Google Scholar
Giere, Ronald N. 2004. “How Models Are Used to Represent Reality.” Philosophy of Science 71:742–52.10.1086/425063CrossRefGoogle Scholar
Griesemer, James R. 1990. “Material Models in Biology.” In PSA 1990: Proceedings of the 1990 Biennial Meeting of the Philosophy of Science Association, Vol. 2, ed. Arthur Fine, Michael Forbes, and Linda Wessels, 79–93. East Lansing, MI: Philosophy of Science Association.Google Scholar
Guala, Francesco. 2002. “Models, Simulations, and Experiments.” In Model-Based Reasoning: Science, Technology, Values, ed. Magnani, Lorenzo and Nersessian, Nancy, 59–74. Dordrecht: Kluwer.10.1007/978-1-4615-0605-8_4CrossRefGoogle Scholar
Hillesland, Kristina L., and Stahl, David A.. 2010. “Rapid Evolution of Stability and Productivity at the Origin of a Microbial Mutualism.” Proceedings of the National Academy of Sciences 107:2124–29.10.1073/pnas.0908456107CrossRefGoogle Scholar
Lenski, Richard E., and Travisano, Michael. 1994. “Dynamics of Adaptation and Diversification: A 10,000-Generation Experiment with Bacterial Populations.” Proceedings of the National Academy of Sciences 91:6808–14.10.1073/pnas.91.15.6808CrossRefGoogle ScholarPubMed
Leonelli, Sabina, and Ankeny, Rachel. 2011. “What’s So Special about Model Organisms?” Studies in History and Philosophy of Science 42:313–23.Google Scholar
Levy, Arnon, and Currie, Adrian. Forthcoming. “Model Organisms Aren’t (Theoretical) Models.” British Journal for the Philosophy of Science.Google Scholar
Lotka, Alfred. 1925. Elements of Physical Biology. Baltimore: Williams & Wilkins.Google Scholar
Love, Alan C., and Travisano, Michael. 2013. “Microbes Modeling Ontogeny.” Biology and Philosophy 28:161–88.10.1007/s10539-013-9363-5CrossRefGoogle Scholar
Mäki, Uskali. 2005. “Models Are Experiments, Experiments Are Models.” Journal of Economic Methodology 12:303–15.10.1080/13501780500086255CrossRefGoogle Scholar
Morgan, M. S. 2003. “Experiments without Material Intervention: Model Experiments, Virtual Experiments and Virtually Experiments.” In The Philosophy of Scientific Experimentation, ed. Radder, Hans, 216–35. Pittsburgh: University of Pittsburgh Press.Google Scholar
Radder, Hans 2005. “Experiments versus Models: New Phenomena, Inference and Surprise.” Journal of Economic Methodology 12:317–29.Google Scholar
Morgan, Mary S., and Morrison, Margaret, eds. 1999. Models as Mediators. Cambridge: Cambridge University Press.10.1017/CBO9780511660108CrossRefGoogle Scholar
O’Malley, Maureen. 2007. “Exploratory Experimentation and Scientific Practice: Metagenomics and the Proteorhodopsin Case.” History and Philosophy of the Life Sciences 29:335–58.Google ScholarPubMed
Park, Thomas. 1948. “Experimental Studies of Interspecies Competition. I. Competition between Populations of the Flour Beetles, Tribolium Confusum Duvall and Tribolium Castaneum Herbst.” Ecological Monographs 18:267–307.10.2307/1948641CrossRefGoogle Scholar
Parker, Wendy S. 2009. “Does Matter Really Matter? Computer Simulations, Experiments, and Materiality.” Synthese 169:483–96.10.1007/s11229-008-9434-3CrossRefGoogle Scholar
Plutynski, Anya. 2001. “Modeling Evolution in Theory and Practice.” Philosophy of Science 68 (Proceedings): S225–S236.10.1086/392911CrossRefGoogle Scholar
Ratcliff, William C., Denison, R. Ford, Borrello, Mark, and Travisano, Michael. 2012. “Experimental Evolution of Multicellularity.” Proceedings of the National Academy of Sciences 109:1595–600.10.1073/pnas.1115323109CrossRefGoogle ScholarPubMed
Rheinberger, Hans-Jörg. 1997. Toward a History of Epistemic Things: Synthesizing Proteins in the Test Tube. Stanford, CA: Stanford University Press.Google Scholar
Shou, W., Ram, S., and Vilar, J. M. G.. 2007. “Synthetic Cooperation in Engineered Yeast Populations.” Proceedings of the National Academy of Sciences 104:1877–82.10.1073/pnas.0610575104CrossRefGoogle ScholarPubMed
Timoféeff-Ressovsky, N. W. 1934. “Über den Einfluss des genotypischen Milieus und der Aussenbedingungen auf die Realisation des Genotyps.” Nachrichten der Gesellschaft der Wissenschaften zu Göttingen, Biologie, N.F. 1:53–106.Google Scholar
Volterra, Vito. 1926. “Fluctuations in the Abundance of a Species Considered Mathematically.” Nature 118:558–60.CrossRefGoogle Scholar
Waters, C. Kenneth. 2012. “Experimental Modeling as a Form of Theoretical Modeling.” Paper presented at PSA 2012, San Diego, November 15–17.Google Scholar
Weber, Marcel. 2005. Philosophy of Experimental Biology. Cambridge: Cambridge University Press.Google Scholar
Weber, Marcel 2012. “Experiment in Biology.” In Stanford Encyclopedia of Philosophy, ed. Zalta, Edward N.. Stanford, CA: Stanford University. http://plato.stanford.edu/entries/biology-experiment/.Google Scholar
Weisberg, Michael. 2007. “Who Is a Modeler?” British Journal for the Philosophy of Science 58:207–33.10.1093/bjps/axm011CrossRefGoogle Scholar
Weisberg, Michael 2013. Simulation and Similarity: Using Models to Understand the World. Oxford: Oxford University Press.CrossRefGoogle Scholar
Winsberg, Eric. 2009. “A Tale of Two Methods.” Synthese 169:575–92.10.1007/s11229-008-9437-0CrossRefGoogle Scholar