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)
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