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Stefan Linquist (Univ. of Guelph, Canada), Genome-level ecology, a novel approach to the functional analysis of junk DNA

19 June | 17 h 00 min - 18 h 30 min

Stefan Linquist (Associate Professor of Philosophy, University of Guelph, Canada)

Abstract:
Why is the size of an onion’s genome five times larger than that of a human? And if only 10% of a human’s DNA performs some functional role, what explains the origin and maintenance of the remaining 90 %?  Historically, such questions have been approached from an organism-centric perspective. On this view, surplus DNA is either disregarded as “junk” because it does nothing for the organism, or else it is presumed to have some unknown function. The first option fails to explain patterns in the abundance and distribution of non-coding DNA among species. The second option leads to a syndrome that I dub “causal role myopia,” where hypotheses about the putative organismal benefits of non-coding DNA are easily generated but difficult to falsify. In recent years, a novel approach has emerged in genomics that potentially avoids the “function versus junk” dilemma. Genome-level ecology promises to explain patterns in non-coding DNA as the result of intra-cellular ecological processes. This perspective also potentially allows one to discriminate among genomic regions as more or less likely to have some organismal function. In this talk, I will clarify the foundational assumptions of genome-level ecology, demonstrate some applications, and evaluate its explanatory prospects.

 

Video of the talk:

 

Description

Stefan is a philosopher of biology with research interests in ecology, genomics, and evolution. He works on a wide range of projects often at the interface between these disciplines. Some of his previous work has focused on the nature/nurture distinction, looking for ways to transcend this false dichotomy. He has also worked on cultural evolution, looking at whether cultures of honour evolve in response to specific environmental variables. More recently, his research focuses on theoretical issues in genomics and ecology.

Education

PhD  Philosophy,  Duke University.

MSc  Biology,  State University of New York, Binghamton.

B.A. Philosophy,  Simon Fraser University

 

Current Research Projects

Why is Biodiversity Valuable?

Most of us take it for granted that biodiversity has value and ought to be conserved. In many situations, however, decision makers face trade offs that require weighing different types of diversity againts each other or risking the loss biodiversity altogether. These choices require us to be explicit about why biodiversity is valuable. My work in this area critically evaluates some of the commonly touted scientific benefits of biodiversity such as the idea that it provides various ecosystem services. I also investigate ethical arguments for the suggestion that biodiversity has moral standing. Of particular interest is the question of whether the sheer beauty of biodiversity –its aesthetic value– provides a legitimate basis for conservation.

Function, Junk, and the Ecological Genome.  

Scientists disagree about how much of the human genome is functional with estimates ranging from 2% to 80%. These disagreements impact the ways that researchers invest their time, energy and funding. Of particular interest are competing ideas about transposable elements (TEs) or “jumping genes”. By rapidly copying and reinserting themselves into new chromosomal locations these elements have become the most common type of DNA in plant and animal genomes. Yet, there is deep scientific disageeement about their function. Some researchers regard TEs as genomic parasites that colonize genomes like an invasive species, while others view them as “genomic switches” that help organisms adapt to changing environments. Both theories are popular; and yet they are at odds. How could the same strand of DNA be both selfish parasite and an organismal switch? Some of my work attempts to resolve this dispute by thinking carefully about the nature of genomic function and how to empirically distinguish junk from functional DNA. I am also exploring a third alternative that views TEs as neither parts nor parasites, but rather as organism-like entities inhabiting a cellular ecosystem.

Complex Social Behaviour in Octopuses

Octopuses have a reputation as asocial animals that does not square easily with their advanced cognitive abilities. If the main behavioural tasks for an octopus involve foraging under predation threat, then why have they evoled such a large brain and flexible behaviour? More commonly, these traits evolve in response to social complexity. I am part of a research group investigating social behaviour in the gloomy octopus (Octopus tetricus). In a population of gloomy octopuses located in Jervis Bay, Australia individuals engaged in frequent socially directed movements and exhibit a range of different types of social interaction. This reserach has implications not only for our understanding of the evolution of complex learning but also on the animal welfare policies surrounding the treatment of octopuses in aquariums, research labs, and aquaculture.

 

Publications

Here is a selection of publications from the past few years.

Book

Journal Articles

  • Linquist, S. Fullerton, B. Grewal, A. (2023) “Epigenetic this, epigenetic that: comparing two digital humanities methods for investigating a slippery scientific term.” Synthese 202(3): 1-55. https://doi.org/10.1007/s11229-023-04265-5
  • Linquist, S. (2022) “Causal role myopia and the functional investigation of junk DNA.” Biology and Philosophy 37(28). https://doi.org/10.1007/s10539-022-09853-2
  • Linquist, S. and Fullerton, B. (2021),”Transposon dynamics and the epigenetic switch hypothesis.” Theoretical Medicine and Bioethics, 42:137-154. https://doi.org/10.1007/s11017-021-09548-x
  • Kremer, S.C. Linquist, S. Saylor, B. Elliott, T.A. Gregory, T.R. Cottenie, K. (2021), “Long term TE persistence even without beneficial insertion.” BMC Genomics 42: 137-154. doi: 10.1186/s12864-021-07568-4
  • Kremer, S. C., S. Linquist, B. Saylor, T.A. Elliott, T.R. Gregory, K. Cottenie (2021), “Transposable element persistence via potential genome-level ecosystem engineering.” BMC Genomics.  https://doi.org/10.1186/s12864-020-6763-1
  • Linquist, S. W.F. Doolittle, A.F. Palazzo (2020), “Getting clear about the F-word in genomics.”  PLOS Genetics: e1008702.  https://doi.org/10.1371/journal.pgen.1008702
  • 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, why the reported demise of community ecology is greatly exaggerated.” Philosophy of Science 82 S1104-1118. 

Book Chapters and Encyclopedia Entries

  • The distinction between innate and acquired characteristics.  Stanford Encyclopedia of Philosophy. https://plato.stanford.edu/entries/innate-acquired/
  • 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

Funding

2020-2023 “Barriers and opportunities surrounding gene-editing technologies for the dairy and beef industry,” Genome Canada – Genomics in Society Interdisciplinary Research Initiatives. Co-Investigator, ($1,424, 374).

2016- 2020  “The use and abuse of function concepts in genomics,” Social Sciences and Humanities Reserach Council of Canada. Principal Investigator, Insight Grant ($85,279).

Awards

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

Details

Date:
19 June
Time:
17 h 00 min - 18 h 30 min
Event Categories:
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