Linquist and Fullerton – Epigenetics and Transposon Dynamics – DS² 2021
Channel: CEFISES at UCLouvain
Date: 2021-03-16

The talk “The rise of epigenetics and the neglect of transposon dynamics across disciplines” by Stefan Linquist and Brady M. Fullerton (University of Guelph), recorded at the DS² 2021 online conference, March 15, 2021.



The recent explosion of interest in epigenetics is often portrayed as the dawning of a scientific revolution that promises to transform biomedical science along with developmental and evolutionary biology. This paper argues that some of this enthusiasm might be due to the failure of epigenetics researchers to embrace a certain form of evolutionary reasoning. A dominant theme in epigenetics involves an expansion of the entities that are classified as functional. Prior to the rise of epigenetics, protein-coding genes were the primary functional units in genomics and molecular biology. However, these disciplines are becoming increasingly interested in the functions of such non-genic entities as methylation patterns, histone modifications, transcription-factor binding sites, and non-coding RNA. Perhaps the most widely discussed example of this expansion in functional classification surrounds the ENCODE project. In 2012, ENCODE researchers came under scrutiny because of their controversial statement that over 80% of the human genome has a “biochemical function.” Critics argued that ENCODE’s functional proxies ignored the fact that upwards of 60% of human DNA descends from parasitic mobile elements (i.e. transposons). The first part of this paper spells out this objection in simple terms. We briefly explain what transposons are and why they often masquerade as functional entities. Thinking in terms of transposon-host coevolutionary dynamics reveals that ENCODE’s criteria for epigenetic functions were too liberal. This raises some interesting questions about the reception of epigenetics across scientific disciplines. We predicted that epigenetics as a topic would be most popular in disciplines where evolutionary thinking is relatively uncommon. We also predicted that the rise of epigenetics over time would correspond, in certain disciplines, with declining interest in transposons. Bibliometric analyses of “epigenetic” and “transposon” over the past five decades provides support for both predictions. Specifically, we compared the relative frequencies of these terms across the disciplines of biomedical science, proximal biology (which included developmental and molecular biology), general biology, and evolutionary biology. Using digital tools supplied by Web of Science, we found that although there has been a general increase in the popularity of epigenetics since 2000, within evolutionary biology its popularity is more delayed and less pronounced compared to other disciplines. Most striking perhaps, although interest in transposons has generally increased over the past five decades, within biomedicine and molecular biology -disciplines that show strong interest in epigenetics— interest in transposons has declined roughly since the rise in popularity of epigenetics. This trend is especially surprising given that our scientific understanding of transposons and their roles in causing harmful mutations has increased over this period. These findings prompted a further analysis to determine whether the term “epigenetic” is used univocally across these disciplines. A qualitative analysis of the top 25 most frequently cited abstracts from the past three decades revealed some interesting patterns. Abstracts in biomedicine and proximal biology use this term similarly to each other. Specifically, both disciplines assigned relatively modest heritability commitments (e.g. mitotic inheritance) and only moderately controversial functional interpretations (e.g. in gene regulation or disease) to epigenetic marks. In contrast, evolutionary publications assigned more controversial heritability commitments (open-ended meiotic inheritance) and even more speculative functional interpretations (epigenetic switches for adaptive phenotypic change) to epigenetic marks. Putting the two sets of results together, we find that the reception of epigenetics as a topic has been relatively delayed and muted in evolutionary biology compared to other disciplines, but that those evolutionary biologists who do discuss epigenetics embrace even more controversial hypotheses than scientists in other disciplines. Hopefully, our findings will inspire further interest in transposon dynamics, especially among researchers drawn to the idea of an epigenetic revolution. This work might also help to inform philosophers of science, who often take their cues from scientists, where certain disciplinary biases might lie.