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                                            philosophy of biology

Stefan Linquist  homepage

contact: linquist@uoguelph.ca

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Research Statement

I think of philosophy generally as the identification and analysis of foundational assumptions. Every human practice depends on certain assumptions, whether we are aware of them or not. You might be making art, raising children, participating in a social movement, or doing science. In each case you are relying on assumptions about the nature of the world and how to best interact with it. Philosophy involves the identification and questioning of those assumptions, usually within a specific area.

Currently, my two primary areas of interest are the sciences of ecology and genomics. Both are fairly young disciplines. Both have enjoyed rapid success. Both are important for humanity. My research examines the foundations on which these sciences are based. Below is a diagram followed by an explanation of how my work on these and other topics fits together.

One of my main areas of investigation concerns the science of ecology and how it differs from other disciplines such as evolutionary biology. What is distinctive about an ecological approach to the world? Only by answering this question can we develop a theory of what it means to do ecology well or poorly. I am also interested in the status of ecological generalizations or "laws" and their roles in explanation, prediction, and ecosystem management. This ties in with questions about the nature and value of biodiversity. Why should we value species and ecosystems? Should  they sometimes be conserved on aesthetic grounds alone? Here are some representative publications on these topics - see my CV for a more expansive list.

  • Linquist, S. (2019), "Why ecology and evolution occupy distinct epistemic niches." Philosophical Topics 47(1):143-166.  (pdf)
  • Linquist, S. (2019), "Two (and a half) arguments for conserving biodiversity on aesthetic grounds." Biology & Philosophy 35: 6 (pdf)
  • Linquist, S. Gregory, T.R. Elliott, T.A. Saylor, B. Kremer, S.C. Cottenie K. (2016),  "Yes! There are resilient generalizations (or "laws") in ecology." The Quarterly Review of Biology, 91. (pdf)
  • Linquist, S. (2015), "Against Lawton's contingency thesis, or, why the reported demise of community ecology is greatly exaggerated." Philosophy of Science, 82: 1104-1115.  (pdf)

My interest in genomics focuses on three related issues. First, I am somewhat concerned about the rise of Big Biology and its relationship to biomedicine. Projects like the Human Genome Project and ENCODE change the intellectual landscape in ways that might not be good for the accumulation of knowledge. Second, I am interested in how the concepts of function and junk DNA have been modified in recent years, partly to suit the goals of these large biomedical projects. Specifically, I think it is a mistake to divorce functional genomics from the study of genome evolution. Finally, I am concerned about the hype surrounding epigenetics. Although some very impressive and important work is being done on the regulation of genes by non-genic entities, I suspect that the significance of these entities for organismal evolution and development tends to be overstated. Here are some publications on these topics. 

  • Linquist, S. and Fullerton, B. (2021), "Transposon dynamics and the epigenetic switch hypothesis." Theoretical Medicine and Bioethics, forthcoming (pdf)
  • Linquist, S. Doolittle, W. F. and Palazzo, A.F. (2020), "Getting clear about the F-word in genomics." PLOS Genetics: e1008702 (pdf
  • Elliott, T.A. Linquist, S. Gregory, T.R. (2014), "Conceptual and empirical challenges of ascribing functions to transposable elements." The American Naturalist, 184: 14-24.  (pdf)

I also work at the interface between genomics and ecology. An emerging discipline called genome-level ecology applies ecological thinking to mobile strands of DNA. Transposable elements or "jumping genes" are viewed in this discipline as miniature organisms in their own right. The cellular structures with which they interact are regarded as the local environment. Concepts, models, and methods borrowed from population and community ecology are then applied to "ecological" processes within the cell. My contributions to this discipline have been in collaboration with scientists at the University of Guelph. Here are some publications. Again, my CV goes into more detail.

  • Kremer, S. C. Linquist, S. Saylor, B. Elliott, T.E. Gregory, T.R. (2020), "Transposable element persistence via potential genome-level ecosystem engineering." BMC Genomics, 21: 1. (pdf)
  • Linquist, S. Cottenie, K. Elliott, T.A. Saylor, B. Kremer, S.C. and Gregory, T.R. (2015), "Applying ecological models to communities of genetic elements: the case of neutral theory." Molecular Ecology, 24: 3232-3242. (pdf)
  • Linquist, S. Saylor, B. Cottenie, K. Elliott, T.A. Kremer, S.C. Gregory, T.R. (2013), "Distinguishing ecological from evolutionary approaches to transposable elements." Biological Reviews 88(3): 573-584. (pdf)

My previous work has explored issues in cultural evolution, the nature of human emotion, and the concept of innateness. I have also written on the topic of public aquariums, arguing that they should be viewed as "plexiglass dinosaurs." I am proud of some of this research and will provide a few examples below. However, at the moment most of my energy goes to ecology, genomics, and the overlap between them. I am most  interested in supervising grad students in these areas. But if you are enthusiastic about cultural evolution or the philosophy of emotion, for example, let me know. Perhaps we can work together.

  • Linquist, S. (2016), "Which evolutionary model best explains the culture of honour?" Biology & Philosophy 31(2): 213-235. (pdf)
  • Linquist, S. and Bartol, J. (2013), "Two myths about somatic markers." British Journal for the Philosophy of Science, 64(3): 455-484.  (pdf)

  • Linquist, S. (2007), "Prospects for a dual inheritance model of emotional evolution." Philosophy of Science, 74: 848-859.  (pdf)
  • Linquist, S. (2018), "Today's awe-inspiring design, tomorrow's Plexiglas dinosaur." In B.A. Minteer, J. Maienschein, J.P. Collins (Eds.) The Ark and Beyond: The Evolution of Zoo and Aquarium Conservation. Chicago University Press. (pp. 329-343) (pdf)

Finally, I am involved in an ongoing research project on social dynamics in the Gloomy Octopus (
O. tetricus). Here are some example papers.

  • Scheel, D. Godfrey-Smith, P. Linquist, S. Chancellor, S. Hing, M. Lawrence, M. (2017), "Octopus engineering, intentional and inadvertent." Communicative and Integrative Biology, doi.org/10.1080/19420889.2017.1395994 (pdf)

    Scheel, D. Chancellor, S. Hing, M.Lawrence, M. Linquist, S. Godfrey-Smith, P. (2017) "A second site occupied by Octopus tetricus at high densities, with notes on their ecology and behavior." Marine and Freshwater Behavior and Physiology. (pdf)