Conceptual and Empirical Challenges of Ascribing Functions to Transposable Elements

@article{Elliott2014ConceptualAE,
  title={Conceptual and Empirical Challenges of Ascribing Functions to Transposable Elements},
  author={Tyler A. Elliott and Stefan Linquist and T. Ryan Gregory},
  journal={The American Naturalist},
  year={2014},
  volume={184},
  pages={14 - 24}
}
Media attention and the subsequent scientific backlash engendered by the claim by spokespeople for the Encyclopedia of DNA Elements (ENCODE) project that 80% of the human genome has a biochemical function highlight the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function concepts that have been developed in the philosophy of science—the causal role concept and the selected effects concept—and their relevance to ENCODE. Unlike… 
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Postgenomics function monism.
  • Z. Brzović, Predrag Šustar
  • Medicine, Computer Science
    Studies in history and philosophy of biological and biomedical sciences
  • 2020
TLDR
The ENCODE controversy is examined in terms of the distinction between function monism and pluralism and a weak etiological account to genomic function ascriptions is proposed, which enables the main difficulties of CR, as well as SE's overdependence on natural selection, while still preserving an evolutionary-constrained notion of biological functions.
Conceptual and empirical investigations of eukaryotic transposable element evolution
TLDR
It is argued, with empirical evidence from the literature, that the multi-level approach advocated by the classic ―selfish DNA‖ papers of 1980 has become less commonly invoked over the past 35 years, in a favour of a strictly organism-centric view.
Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements
TLDR
Here, general arguments for the importance of selection at levels above that of organisms in evolution are reviewed, and developed further for a common genomic feature: the carriage of transposable elements (TEs).
Transposon dynamics and the epigenetic switch hypothesis.
TLDR
A large sample of scientific publications on the topics of epigenetics and transposons over the past fifty years is surveyed, finding that enthusiasm for epigenetics is often inversely related to interest in transposon dynamics across the four disciplines it was examined.
Getting clear about the F-word in genomics
TLDR
It is argued that there exists an overlooked dichotomy in the way that researchers see natural selection to be related to function, and 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.
Transposon Ecology: The Power of Community Ecology Methods on Genomic Transposable Element Data
TLDR
This thesis represents the first systematic application of ecological methods per se to genomic TE data and assessment of their utility, and lays the groundwork for many future studies in transposon ecology.
On causal roles and selected effects: our genome is mostly junk
The idea that much of our genome is irrelevant to fitness—is not the product of positive natural selection at the organismal level—remains viable. Claims to the contrary, and specifically that the…
The Case for Junk DNA
TLDR
The excitement and subsequent backlash of the ENCODE claims served to illustrate the widespread interest among scientists and nonspecialists in determining how much of the human genome is functionally significant at the organism level.
Selfish genetic elements
TLDR
Though long dismissed as genetic curiosities, with little relevance for evolution, they are now recognized to affect a wide swath of biological processes, ranging from genome size and architecture to speciation.
Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells
TLDR
Roles of TEs as enhancers in mouse embryonic and trophoblast stem cells are tested by combining bioinformatic analyses with genetic and epigenetic editing experiments, and it is suggested that a small proportion ofTEs contribute to the mouse pluripotency regulatory network.
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