Function war: An Evaluation of Encode project and Junk DNA in the light of Philosophy of Biology
Keywords:
Philosophy of Biology, Encode Project, Junk DnaAbstract
For a large period of time in biology, it was thought that only 1-2% of the entire human DNA carries protein-making signals, and the remaining 98% of DNA does not carry protein-making signals. They were called junk DNA or non-coding DNA. The Encode Project began in 2003 to explore the function of the remaining 98% of human DNA in the context of human genome research. From the ENCODE project of 2007 and 2012, we know that about 80% of the DNA in the human body is not junk. The subsequent criticisms of the Encode project have been numerous. But no matter the criticism, the results of the Encode Project have always proved true. In this paper I will evaluate the result of Encode project for the case of junk Dna in the light of philosophy of biology.
References
Watson, J. D., & Crick, F. H. (1953). Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 171(4356), 737-738. doi: https://doi.org/10.1038/171737a0
Bateson, W., & Mendel, G. (2013). Mendel's principles of heredity. Courier Corporation.
"What is a gene?: MedlinePlus Genetics". MedlinePlus. 17 September 2020. Retrieved 4 January 2021.
Palazzo, A. F., & Gregory, T. R. (2014). The case for junk DNA. PLoS genetics, 10(5),
e1004351. doi:10.1371/journal.pgen.1004351
Ohno, S. (1972). So much junk DNA in our genome. In Evolution of Genetic Systems, Brookhaven Symp. Biol. (pp. 366-370). PMID: 5065367
Kimura, M., & Maruyama, T. (1966). The mutational load with epistatic gene interactions in fitness. Genetics, 54(6), 1337. doi: 10.1093/genetics/54.6.1337
Fletcher, John (1837). On the functions of organized beings, and their arrangement. Rudiments of physiology, Part 2. On life, as manifested in irritation. John Carfrae & Son. pp. 1–15.
Tipton, J. A. (2014). Philosophical biology in Aristotle's parts of animals. Heidelberg: Springer.
Robert Cummins. (1975) Functional Analysis. The Journal of Philosophy, Vol. 72, No. 20 pp. 741-765
Function without purpose: the uses of causal role function in evolutionary biology.” Biology and Philosophy 9: 443-469 https://doi.org/10.1007/BF00850375.
Ariew, A., Cummins, R., & Perlman, M. (eds.) (2002). Functions: New Essays in the Philosophy of Psychology and Biology. Oxford: Oxford University Press
Griffiths, P. E. (1993). “Functional analysis and proper functions.” British Journal for the Philosophy of Science 44: 409-422.
Millikan, Ruth (1989). "In Defense of Proper Functions". Philosophy of Science. 56 (2): 288–302. https://www.jstor.org/stable/187875
Neander, Karen (1991). "Functions as Selected Effects: The Conceptual Analyst's Defense". Philosophy of Science. 58 (2): 168–184 doi: https://doi.org/10.1086/289610
] Boorse, Christopher (1977). "Health as a Theoretical Concept". Philosophy of Science. 44 (4): 542–573. doi: https://doi.org/10.1086/288768
Bigelow, John; Pargetter, Robert (1987). "Functions". The Journal of Philosophy. 84 (4): 181–196.
Greilhuber J, Doležel J, Lysák M, Bennett MD (2005). "The origin, evolution and proposed stabilization of the terms 'genome size' and 'C-value' to describe nuclear DNA contents". Annals of Botany. 95 (1): 255–60. doi: 10.1093/aob/mci019
T. Cavalier-Smith, “Nuclear Volume Control by Nucleoskeletal DNA, Selection for Cell Volume and Cell Growth Rate, and the Solution of the DNA C-Value Paradox,” Journal of Cell Science 34, (1978): 247-278. doi: 10.1242/jcs.34.1.247
Graur, D. (2017). An upper limit on the functional fraction of the human genome. Genome biology and evolution, 9(7), 1880-1885 doi: https://doi.org/10.1093/gbe/evx121.
Galeota-Sprung, B., Sniegowski, P., & Ewens, W. (2020). Mutational load and the functional fraction of the human genome. Genome biology and evolution, 12(4), 273-281. doi: https://doi.org/10.1093/gbe/evaa040
ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57. doi: https://doi.org/10.1038/nature11247
Ariel, F. D., & Manavella, P. A. (2021). When junk DNA turns functional: Transposon-derived non-coding RNAs in plants. Journal of Experimental Botany, 72(11), 4132-4143. doi: https://doi.org/10.1093/jxb/erab073
Jagannathan, M., Cummings, R., & Yamashita, Y. M. (2018). A conserved function for pericentromeric satellite DNA. Elife, 7, e34122.doi: https://doi.org/10.7554/eLife.34122
Modzelewski, A. J., Shao, W., Chen, J., Lee, A., Qi, X., Noon, M., ... & He, L. (2021). A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell, 184(22), 5541-5558. doi: https://doi.org/10.1016/j.cell.2021.09.021
Statello, L., Guo, C. J., Chen, L. L., & Huarte, M. (2021). Gene regulation by long non-coding RNAs and its biological functions. Nature reviews: Molecular cell biology, 22(2), 96-118. doi:https://doi.org/10.1038/s41580-020-00315-9
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