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Epigenetic this, epigenetic that: comparing two digital humanities methods for analyzing a slippery scientific term

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We compared two digital humanities methods in the analysis of a contested scientific term. “Epigenetics” is as enigmatic as it is popular. Some authors argue that its meaning has diluted over time as this term has come to describe a widening range of entities and mechanisms (Haig, International Journal of Epidemiology 41:13–16, 2012). Others propose both a Waddingtonian “broad sense” and a mechanistic “narrow sense” definition to capture its various scientific uses (Stotz and Griffiths, History and Philosophy of the Life Sciences 38:22, 2016). We evaluated these proposals by first replicating a recent analysis by (Linquist and Fullerton, Theoretical Medicine and Bioethics 42:137–154, 2021). We analyzed the 1100 most frequently cited abstracts on epigenetics across four disciplines: proximal biology, biomedicine, general biology, and evolution. Each abstract was coded for its heritability commitments (if any) and functional interpretation. A second study applied LDA topic modelling to the same corpus, thus providing a useful methodological comparison. The two methods converged on a discipline-relative ambiguity. Within such disciplines as biomedicine or molecular biology that focus on proximate mechanisms, “epigenetic(s)” refers to a range of molecular structures while specifying nothing in particular about their heritability. This proximal conception was primarily associated with the functions of gene regulation and disease. In contrast, a second relatively uncommon sense of “epigenetic(s)” is restricted to a small proportion of evolutionary abstracts. It refers to many of the same molecular structures, but regards them as trans-generationally inherited and associated with adaptive phenotypic plasticity. This finding underscores the benefit of digital tools in complementing traditional conceptual analysis. Philosophers should be cautious not to conflate the relatively uncommon evolutionary sense of epigenetics with the more widely used proximal conception.
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Synthese (2023) 202:68
https://doi.org/10.1007/s11229-023-04265-5
ORIGINAL RESEARCH
Epigenetic this, epigenetic that: comparing two digital
humanities methods for analyzing a slippery scientific term
Stefan Linquist1·Brady Fullerton1·Akashdeep Grewal2
Received: 31 March 2022 / Accepted: 6 July 2023 / Published online: 22 August 2023
© The Author(s), under exclusive licence to Springer Nature B.V. 2023
Abstract
We compared two digital humanities methods in the analysis of a contested scien-
tific term. “Epigenetics” is as enigmatic as it is popular. Some authors argue that its
meaning has diluted over time as this term has come to describe a widening range
of entities and mechanisms (Haig, International Journal of Epidemiology 41:13–16,
2012). Others propose both a Waddingtonian “broad sense” and a mechanistic “nar-
row sense” definition to capture its various scientific uses (Stotz and Griffiths, History
and Philosophy of the Life Sciences 38:22, 2016). We evaluated these proposals by
first replicating a recent analysis by (Linquist and Fullerton, Theoretical Medicine and
Bioethics 42:137–154, 2021). We analyzed the 1100 most frequently cited abstracts
on epigenetics across four disciplines: proximal biology, biomedicine, general biol-
ogy, and evolution. Each abstract was coded for its heritability commitments (if any)
and functional interpretation. A second study applied LDA topic modelling to the
same corpus, thus providing a useful methodological comparison. The two methods
converged on a discipline-relative ambiguity. Within such disciplines as biomedicine
or molecular biology that focus on proximate mechanisms, “epigenetic(s)” refers to a
range of molecular structures while specifying nothing in particular about their heri-
tability. This proximal conception was primarily associated with the functions of gene
regulation and disease. In contrast, a second relatively uncommon sense of “epige-
netic(s)” is restricted to a small proportion of evolutionary abstracts. It refers to many
of the same molecular structures, but regards them as trans-generationally inherited
and associated with adaptive phenotypic plasticity. This finding underscores the benefit
of digital tools in complementing traditional conceptual analysis. Philosophers should
be cautious not to conflate the relatively uncommon evolutionary sense of epigenetics
with the more widely used proximal conception.
BStefan Linquist
linquist@uoguelph.ca
1Department of Philosophy, University of Guelph, Guelph, ON, Canada
2Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
123
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