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… 
Postgenomics function monism.
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    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
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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.
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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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References

SHOWING 1-10 OF 84 REFERENCES
Is junk DNA bunk? A critique of ENCODE
  • W. Doolittle
  • Biology, Medicine
    Proceedings of the National Academy of Sciences
  • 2013
TLDR
Older arguments for junk grounded in the C-value paradox are reviewed, and a thought experiment is proposed to challenge ENCODE’s ontology.
PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION
TLDR
It is argued that easy popular appellations such as “selfish DNA’ and “junk DNA” may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism.
Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
TLDR
It is argued that many genome-wide studies dealing with TE exaptation in recent lineages of mammals are still inconclusive and that the hypothesis of rapid transcriptional regulatory rewiring mediated by TE mobilization must be taken with caution.
On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE
TLDR
The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks and it is detailed the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome.
Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis
TLDR
It is proposed that the evolution of these repair proteins is likely to have been shaped by their interactions with Ty elements, where critical genes like those involved in DNA repair are also subject to selective pressures imposed by mobile elements and could favor alleles that might be otherwise deleterious for their normal roles related to genome stability.
PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION
TLDR
It is argued that easy popular appellations such as “selfish DNA’ and “junk DNA” may be either inaccurate or misleading and that a more enlightened view of the transposable element‐host relationship encompasses a continuum from extreme parasitism to mutualism.
Can ENCODE tell us how much junk DNA we carry in our genome?
  • D. Niu, Li Jiang
  • Biology, Medicine
    Biochemical and biophysical research communications
  • 2013
TLDR
This work has suggested that Knockout may be the most effective means of distinguishing functional sequences from junk DNA.
Molecular domestication of transposable elements: From detrimental parasites to useful host genes
Abstract.Transposable elements (TEs) are commonly viewed as molecular parasites producing mainly neutral or deleterious effects in host genomes through their ability to move. However, during the past
Molecular domestication of transposable elements : From detrimental parasites to useful host genes
Transposable elements (TEs) are commonly viewed as molecular parasites producing mainly neutral or deleterious effects in host genomes through their ability to move. However, during the past two
GENOMICS IN THE LIGHT OF EVOLUTIONARY TRANSITIONS
TLDR
This article argues for a Darwinian multilevel selection interpretation for the origin of the genome based on the multileVEL selection theory of hypercycles of cooperative interacting genes and predictions that gene‐level trade‐offs in viability and reproduction can help drive evolutionary transitions.
...
1
2
3
4
5
...