Getting clear about the F-word in genomics
Stefan Linquist ,W. Ford Doolittle, Alexander F. Palazzo
Published: April 1, 2020 https://doi.org/10.1371/journal.pgen.1008702
Although biology is generally awash with adaptationist “just-so” stories, the situation in molecular biology and genomics is particularly bad. Various types of non-coding DNA are routinely interpreted as functional without adequate consideration of non-adaptationist alternative hypotheses [1]. Part of the problem is surely due to a failure in these disciplines to appreciate theoretical developments in population genetics, which outline the conditions under which genetic elements are selected [2]. However, as a number of authors have noted, the problem is also partly due to a confusion about the various possible meanings of “function” in biology [3–5]. Our central thesis is that there exists an overlooked dichotomy in the way that researchers see natural selection to be related to function. Traits or genetic elements that are merely under purifying selection have what we call maintenance functions whereas those that have historically been under directional selection have origin functions. We argue that ignoring this distinction encourages a form of pan-adaptationism, where highly plausible non-adaptive explanations for the origins of certain genetic elements or traits are themselves ignored. Thus, our recommendation is for researchers to always clarify which sense of “function” they mean (origin or maintenance) when talking or writing about selected effects.
Citation: Linquist S, Doolittle WF, Palazzo AF (2020) Getting clear about the F-word in genomics. PLoS Genet 16(4): e1008702. https://doi.org/10.1371/journal.pgen.1008702
Editor: Jonathan Flint, University of California Los Angeles, UNITED STATES
Published: April 1, 2020
Copyright: © 2020 Linquist et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Financial support for this research was provided by the Social Sciences and Humanities Research Council of Canada (https://www.sshrc-crsh.gc.ca/, grant #430335) to Stefan Linquist and by the Natural Sciences and Engineering Research Council of Canada (nserc-crsng.gc.ca, grant # GLDSU44989) to W. Ford Doolittle. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
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