Stefan Linquist | College of Arts

Stefan Linquist
Associate Professor
Mackinnon 358


I am a philosopher of biology with research interests in ecology, genomics, evolution, and psychology. Much of my work is at the interface between these disciplines.  See below for brief descriptions of my current projects.  Despite the diversity of these pursuits some common themes unify my work. Philosophically, I am a naturalist. I take this to mean that philosophical reasoning should be informed by the best available scientific theories and results. However, I also consider it the job of philosophy to challenge science. For example, my work on innateness in psychology, on contingency in ecology, and on function in genomics challenges the ways that some scientists employ these concepts.

Graduate Students

I interested in working with graduate students or talented undergrads in areas related to my research interests. Currently I am supervising the PhD theses of Brady Fullerton, Josh Grant-Young and Stefan Schneider.


I see philosophy as a skill with immense practical value. Undergraduate students train up on texts that can seem obscure and distantly removed from the problems of daily life. But those skills are highly transferrable. In most of my teaching I strive to equip students with problem solving and reasoning strategies that will assist them in whatever field they ultimately pursue.

Perhaps my favourite undergraduate course is one that I developed shortly after arriving at the University of Guelph. The Philosophy Field Course involves a field component where students engage first hand with community stakeholders over some contested issue.  For the past several years I have taught this course on location in Clayoquot Sound  – where environmentalists, industry representatives, First Nations, and government agencies often conflict over resource issues. To learn more about the Philosophy Field Course see here or here.

Each year I co-teach a graduate seminar in the philosophy of biology with T. Ryan Gregory – my colleague from the department of Integrative Biology.  This course explores a different theme each year.  But it tends to cover a standard range of topics including adaptation, levels of selection, gene centrism, the nature of species, and the relationship between evolution and development. Approximately 2/3rds of the students in this course are biology majors, many of whom are taking philosophy for the first time. This mix of students from different backgrounds enriches the discussion during seminar.  Students also develop a deeper understanding of their own fields by engaging with peers from a neighbouring discipline.


PhD  Philosophy,  Duke University.

MSc  Biology,  State University of New York, Binghamton.

B.A. Philosophy,  Simon Fraser University


I am engaged in several different research projects at the moment. Here are some brief descriptions. For more info see my website.

Philosophy of Genomics

Scientists disagree radically about how much of the human genome is functional, with estimates ranging from as little as two percent to as much as eighty percent. These disagreements have implications for the ways that researchers invest their time, energy and funding.  Of particular interest are competing ideas about transposable elements (TEs) or "jumping genes." Simply put, these genetic elements are copied and pasted into new genomic locations over the lifetime of an organism. Amazingly, as much as 60% of the human genome descends from this type of mobile DNA. Some researchers regard TEs as genomic parasites and attempt to understand their evolution in terms of host-parasite dynamics. Others view transposons as "genomic switches" which have evolved to "re-wire" the genome and help organisms adapt to changing environments. Both theories are popular; and yet they are at odds  How could the same element -a jumping gene- be both selfish parasite and essential switch at the same time? Itis perhaps no surprise that researchers from these two camps disagree about such fundamental issues as the meaning of "function" and the minimal evidence for functionality. My work attempts to understand and ultimately resolve these disputes. To this end, I see genome-level ecology as a promising new direction. It attempts to view TEs not as parasites or switches, but rather as organism-like entities inhabiting a cellular ecosystem. More generally, this project aims to combine philosophical theories of function with a close look at the scientific practice of genomics. One of my goals is to foster collaborations between scientists and philosophers on these issues.

Philosophy of Ecology and Enviornment

I am interested in a variety of theoretical issues in ecology, especially those with direct relevance to public policy. In collaboration with Jay Odenbaugh I am editing a special edition of Philosophical Topics dedicated to the philosophy of ecology. Currently, I am studying the ways that different researchers conceptualize biodiversity. I am also working on a general philosophical account of the discipline of ecology and how it differs from evolutionary biology. I have published articles on ecological generalization (or "laws" in ecology), neutral theory, and genome-level ecology. Recently, I co-authored a book on the value of biodiversity.  

Nature, Nurture and the Cultural Evolution of Emotion

Everyone agrees that the nature/nurture dichotomy is a false one. Yet, there is a stubborn tendency both in everyday conversation and in scientific discourse to retain these categories. For example, behaviours are categorized as either innate or learned, or as biological or cultural. This project investigates how and why people employ these categories, and proposes strategies for transcending them. One aspect of this research critically examines the claim, popularized by neurobiologist Antonio Damasio in his book Descartes’ Error, that good practical judgment is guided by emotion. This idea is interesting but extremely vague. I have developed strategies for calrifying different versions of the  "somatic marker hypothesis"  and identified the kinds of data required to test them. Another aspect of my emotion research attempts to move beyond the (rather stale) debate between biological and social constructionist theories. Currently, I am looking at the Culture of Honour hypothesis as a case study for emotional cultural evolution. This work involves, in part, a cross cultural analysis of data drawn from the Human Relations Area File.

Complex Social Behaviour in Octopuses

I have recently joined an exciting research project examining the social behaviour of the "gloomy" octopus (O. tetricus). In January, 2015, we mounted three underwater cameras around a high-activity site located in Jervis Bay, Australia. The video is still being analyzed so our results are not yet available. But some of our work is discussed here 1, 2,).


Here are my publications over the past five years. More can be found on my website:


Journal Articles

  • Kremer, S. C., S. Linquist, B. Saylor, T.A. Elliott, T.R. Gregory, K. Cottenie (forthcoming), "Transposable element persistence via potential genome-level ecosystem engineering. BMC Genomics   pdf

  • Linquist, S. W.F. Doolittle, A.F. Palazzo (2020), "Getting clear about the F-word in genomics."  PLOS Genetics: e1008702.

  • Linquist, S. G. Varner, J.E. Newman (2020), "Precis of Defending Biodiversity." Biology & Philosophy: 35:14.  pdf

  • Linquist, S. (2019), "Why ecology and evolution occupy distinct epistemic niches". Philosophical Topics 47.

  • Linquist, S. (2019), "Two (and a half) arguments for conserving biodiversity on aesthetic grounds." Biology & Philosophy: 35:6  pdf

  • Linquist, S. (2018), "The conceptual critique of innateness." Philosophy Compass, e12492   pdf

  • Schneider, S., G.W. Taylor, S. Linquist, S.C. Kremer (2018), "Past, present and future approaches using computer vision for animal re-identification from camera trap data." Methods in Ecology and Evolution 10: 461-470.  pdf 

  • Scheel, D., S. Chancellor, M. Hing, M. Lawrence, S. Linquist, P. Godfrey-Smith (2017), "A second site occupied by Octopus tetricus at high densityies, with notes on their ecology and behavior." Marine and Freshwater Behaviour and Physiology 50: 285-291.  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." Quarterly Review of Biology, 91(2): 119-131. pdf

  • Linquist, S. (2016),  "Which evolutionary model best explains the culture of honour?" Biology & Philosophy, 31(2): 213-235. 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. (2015), "Against Lawton's contingency thesis, or, whyt the reported demise of community ecology is greatly exaggerated." Philosophy of Science 82 S1104-1118. 

Book Chapters 

  • Machery, E., P.E. Griffiths, S. Linquist, K. Stotz (2019), "Scientists' conception of innateness: evolution or attraction?" In D.A. Wilkenfeld & R. Samuels (Ed.s) Advances in Experimental Philosophy of Science. N.Y.: Blumsbury Academic (pp 172-204).  pdf

  • Linquist, S. (2018), "Today's awe inspiring design, tomorrow's Plexiglas dinosaur. How public aquariums contradict their conservation mandate in pursuit of immersive underwater displays." In The Ark and Beyond: The Evolution of Zoo and Aquarium Conservation. B.A. Minteer, J. Maienschein, J.P. Collins (Eds). University of Chicago Press. p.p. 329-343.  pdf



2016- 2020 Social Sciences and Humanities Reserach Council, Insight Grant: "The use and abuse of function concepts in genomics." ($85,279).


2016- University of Guelph Faculty Association, "Distinguished Professor Award for Excellence in Teaching."