Getting clear about the F-word in genomics


Autoři: Stefan Linquist aff001;  W. Ford Doolittle aff002;  Alexander F. Palazzo aff003
Působiště autorů: Department of Philosophy, University of Guelph, Guelph, Ontario, Canada aff001;  Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada aff002;  Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada aff003
Vyšlo v časopise: Getting clear about the F-word in genomics. PLoS Genet 16(4): e32767. doi:10.1371/journal.pgen.1008702
Kategorie: Opinion Piece
doi: 10.1371/journal.pgen.1008702


Zdroje

1. Sarkar S. The genomic challenge to adaptationism. Brit J for the Philos Sci 66: 505–536.

2. Lynch M. The origins of genome architecture. Sunderland MA: Sinauer Associates; 2007.

3. Doolittle WF. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 2013; 110:5294–5300. doi: 10.1073/pnas.1221376110 23479647

4. Elliott TA, Linquist S, Gregory TR. Conceptual and empirical challenges of ascribing functions to transposable elements. The American Naturalist 2014; 184: 14–2. doi: 10.1086/676588 24921597

5. Brunet TDP, Doolittle WF. Getting “function” right. Proc Natl Acad Sci USA 2014; 111: E3365. doi: 10.1073/pnas.1409762111 25107292

6. Graur D, Zheng Y, Price N, Azvedo RBR, Zufall RA, Elhaik E. On the immortality of television sets: “Function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013; 5: 578–590. doi: 10.1093/gbe/evt028 23431001

7. Rosenberg A, Neander K. Are homologies (selected effect or causal role) function free? Phil Sci 2009; 76: 307–334.

8. Eddy S. The ENCODE project: Missteps overshadowing a success. Current Biology 2013; 23: R259–R261. doi: 10.1016/j.cub.2013.03.023 23578867

9. Mattick J.S. Dinger M.E. The extent of functionality in the human genome. HUGO J 2013; 7, 2 doi: 10.1186/1877-6566-7-2

10. Lee H., Zhang Z., and Krause H. M. (2019). Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners? TRENDS in Genetics. 2019; doi.org/10.1016/j.tig.2019.09.006

11. Ponting C. P. Biological function in the twilight zone of sequence conservation. BMC Biology. 2017; 15: 71. doi: 10.1186/s12915-017-0411-5 28814299

12. Palazzo A.F. Lee E.S. Non-coding RNA: what is functional and what is junk? Frontiers in Genetics. 2015; 6: 1–11. doi: 10.3389/fgene.2015.00001 25674101

13. Garson J. A critical overview of biological functions. New York: Springer Briefs in Philosophy; 2016.

14. Godfrey-Smith P. A modern history theory of functions. In: Linquist S, editor. Philosophy of Evolutionary Biology, volume 1. New York: Routledge; 2016.

15. Maynard Smith J. Overview—unsolved evolutionary problems. In: Dover GA, Flavell RB, editors. Genome evolution. London: Academic Press; 1982.

16. Gould SJ, Vrba ES. Exaptation—a missing term in the science of form. Paleobiology 1982; 8: 4–15.

17. Stoltzfus A. On the possibility of constructive neutral evolution. J Mol Evol. 1999;49: 169–181. doi: 10.1007/pl00006540 10441669

18. Akins R. A. Lambowitz A. M. A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative therof. Cell 1987; 50: 331–345. doi: 10.1016/0092-8674(87)90488-0 3607872

19. Lukes J. Archibald J.M. Keeling P.J. Doolittle W.F. Gray M.W. How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 2011; 63: 528–537. doi: 10.1002/iub.489 21698757

20. Doolittle WF. A ratchet for protein complexity. Nature 2010; 481:270–271.

21. Lane N, Martin W. The energetics of genome complexity. Nature 2010; 467:929–934. doi: 10.1038/nature09486 20962839

22. Naito T, Kusano K, Kobayashi I. Selfish behavior of restriction-modification systems. Science 1995;267: 897–899. doi: 10.1126/science.7846533 7846533

23. Palazzo AF, Gregory TR. The case for junk DNA. PLOS Genetics 2014;10: e1004351. doi: 10.1371/journal.pgen.1004351 24809441

24. Palazzo AF, Lee ES. Sequence determinants for nuclear retention and cytoplasmic export of mRNAs and lncRNAs. Front Genet. 2018; 9:440. doi: 10.3389/fgene.2018.00440 30386371

25. Brunet TDP, Doolittle WF. The generality of constructive neutral evolution. Biol Philos. 2018;33:2.

26. Gould SJ, Lewontin RC. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist paradigm. Proc R Soc Lond B. 1979; 205:581–598. doi: 10.1098/rspb.1979.0086 42062

27. Craver C.F. Functions and mechanisms: A perspectivalist view. Huneman P. (ed) Function: Selection and Mechanisms, Springer, pp 1331–58.

Štítky
Genetika Reprodukční medicína

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