Using models to correct data: paleodiversity and the fossil record
- 66 Downloads
Despite an enormous philosophical literature on models in science, surprisingly little has been written about data models and how they are constructed. In this paper, I examine the case of how paleodiversity data models are constructed from the fossil data. In particular, I show how paleontologists are using various model-based techniques to correct the data. Drawing on this research, I argue for the following related theses: first, the ‘purity’ of a data model is not a measure of its epistemic reliability. Instead it is the fidelity of the data that matters. Second, the fidelity of a data model in capturing the signal of interest is a matter of degree. Third, the fidelity of a data model can be improved ‘vicariously’, such as through the use of post hoc model-based correction techniques. And, fourth, data models, like theoretical models, should be assessed as adequate (or inadequate) for particular purposes.
KeywordsPaleontology Paleobiology Evolution Data Model Suppes Fossil Biodiversity Representation Simulations Climate science Sepkoski Data models
I am grateful to Wendy Parker, Adrian Currie, Mike Benton, and two anonymous referees for helpful comments on an earlier version of this paper. I also thank Demetris Portides for first encouraging me to write this paper and for his patience seeing it through to completion. I gratefully acknowledge the support of the Institute of Advanced Study at Durham University, COFUND Senior Research Fellowship, under EU grant agreement number 609412.
- Alroy, J. (2010b). Fair sampling of taxanomic richness and unbiased estimation of origination and extinction rates. In J. Alroy & G. Hunt (Eds.), Quantitative methods in paleobiology (pp. 55–80). Baltimore: The Paleontological Society.Google Scholar
- Benton, M., Dunhill, A., Lloyd, G., & Marx, F. (2011). Assessing the quality of the fossil record: Insights from vertebrates. In A. McGowan & A. Smith (Eds.), Comparing the geological and fossil records: Implications for biodiversity studies (Vol. 358, pp. 63–94). London: Geological Society.Google Scholar
- Benton, M., & Harper, D. (2009). Introduction to paleobiology and the fossil record. Chichester: Wiley.Google Scholar
- Bokulich, A. (forthcoming). Towards a taxonomy of the model-ladenness of data. In Presentation in Symposium session: Exploring model-data symbiosis in the geosciences. Philosophy of Science Association Biennial Meeting, November 2018, Seattle, WA.Google Scholar
- Brocklehurst, N. (2015). A simulation-based examination of residual diversity estimates as a method of correcting for sampling bias. Palaeontologia Electronica, 18.3.7T, 1–15.Google Scholar
- Currie, A. (2018). Rock, bone, and ruin: An optimist’s guide to the historical sciences. Cambridge, MA: The MIT Press.Google Scholar
- Darwin, C. (1859). On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London: John Murray. Retrieved from https://en.wikisource.org/w/index.php?title=On_the_Origin_of_Species_(1859)&oldid=6512451.
- Edwards, P. (2001). Representing the global atmosphere: Computer models, data, and knowledge about climate change. In C. Miller & P. Edwards (Eds.), Changing the atmosphere: Expert knowledge and environmental governance (pp. 31–65). Cambridge, MA: MIT Press.Google Scholar
- Edwards, P. (2010). A vast machine: Computer models, climate data, and the politics of global warming. Cambridge, MA: MIT Press.Google Scholar
- Eldredge, N., & Gould, S. J. (1972). Punctuated equilibria: An alternative to phyletic gradualism. In T. Schopf (Ed.), Models in paleobiology (pp. 82–115). San Francisco: Freeman, Cooper, and Co.Google Scholar
- Huss, J. (2009). The shape of evolution: The MBL model and clade shape. In D. Sepkoski & M. Ruse (Eds.), The paleobiological revolution: Essays on the growth of modern paleontology. Chicago: University of Chicago Press.Google Scholar
- Lyell, C. (1830). Principles of geology: Being an attempt to explain the former changes of the earth’s surface, by references to causes now in operation. London: John Murray. Retrieved from http://www.esp.org/books/lyell/principles/facsimile/contents/lyell-v1-aa-fm.pdf.
- Magnani, L., & Bertolotti, T. (Eds.). (2017). Springer handbook of model-based science. Dordrecht: Springer.Google Scholar
- Norton, S., & Suppe, F. (2001). Why atmospheric modeling is good science. In C. Miller & P. Edwards (Eds.), Changing the atmosphere: Expert knowledge and environmental governance (pp. 67–105). Cambridge, MA: MIT Press.Google Scholar
- Parker, W., & Bokulich, A. (in preparation). Data models, representation, and adequacy-for-purpose.Google Scholar
- Sepkoski, J. (1982). Compendium of fossil marine families. Milwaukee Public Museum Contributions in Biology and Geology, 51, 1–125.Google Scholar
- Sepkoski, J. (1994). What I did with my research career: Or how research on biodiversity yielded data on extinction. In W. Glenn (Ed.), Mass-extinction debates: How science works in a crisis. Stanford, CA: Stanford University Press.Google Scholar
- Signor, P., III, & Lipps, J. (1982). Sampling bias, gradual extinction patterns and catastrophes in the fossil record. In L. Silver & P. Schultz (Eds.), Geological implications of large asteroids and comets on the earth (Vol. 190, pp. 291–296). Boulder: Geological Society of America.CrossRefGoogle Scholar
- Suppes, P. (1962). Models of data. In E. Nagel, P. Suppes, & A. Tarski (Eds.), Logic, methodology and philosophy of science: Proceedings of the 1960 international congress (pp. 252–261). Stanford: Stanford University Press.Google Scholar
- Upchurch, P., & Barrett, P. (2005). Phylogenetic and taxic perspectives on sauropod diversity. In K. Rogers & J. Wilson (Eds.), The sauropods: Evolution and paleobiology (pp. 104–124). Berkeley: University of California Press.Google Scholar
- Wylie, C. (2009). Preparation in action: Paleontological skill and the role of the fossil preparator. In: M. Brown, J. Kane, & W. Parker (Eds.), Methods in fossil preparation: Proceedings of the first annual fossil preparation and collections symposium (pp. 3–12).Google Scholar
- Wylie, C. (2016). “Overcoming underdetermination” on extinct: The philosophy of palaeontology blog (April 11, 2016). Retrieved August 5, 2017 from http://www.extinctblog.org/extinct/2016/4/11/overcoming-underdetermination.