We are not our genes: Considerations about the molecular definition of gene
Keywords:
Function, Structure, Causal Agency, Causal Specificity
Abstract
The molecular concept of gene has been subject, in recent decades, to a constant process of theoretical deconstruction. Despite of the many criticisms received, this concept still exists today as the main work stereotype. The objective of this paper will be to try to evaluate the validity and scope of the molecular concept of gene in light of the current state of biology. In order to do so, the work will be structured in three sections. In the first section the basic characteristics of the molecular concept of gene will be established. These characteristics will be articulated under four basic parameters: 1. Structural definition. 2. Functional definition. 3. Causal agency. 4. Causal specificity. In the second section, a detailed analysis of the structural and functional definition of the molecular concept will be carried out. In the third section, the points concerning agency and causal specificity will be examined. From these considerations two conclusions can be drawn. Firstly, it is necessary to suspend the unrestricted validity of the molecular concept of gene. Secondly, that it is necessary to embrace more open definitions that allow dealing with the inherent complexity of biological phenomena.
References
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Dounce, Alexander (1952). «Duplicating Mechanism for Peptide Chain and Nucleic Acid Synthesis». Enzymologia 15: pp. 503-507.
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Hall, Brian (2001). «The Gene is not Dead, merely Orphaned and seeking a Home». Evolution & Development 3 (4): pp. 225-228. doi: https://doi.org/10.1046/j.1525-142x.2001.003004225.x
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Hull, David (1972). «Reduction in Genetics –Biology or Philosophy?». Philosophy of Science 39 (4): pp. 491-499. doi: https://doi.org/10.1086/288470
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Jacob, François y Monod, Jacques (1961). «Genetic Regulatory Mechanisms in the Synthesis of Proteins». J. Molec. Biol. 3: pp. 318-356. doi: https://doi.org/10.1016/S0022-2836(61)80072-7
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Jeffery, Constance (1999). «Moonlighting proteins». TiBS 24 (1): pp. 8-11. doi: https://doi.org/10.1016/s0968-0004(98)01335-8
Jeffery, Constance (2003). «Multifunctional proteins: examples of gene sharing». Ann. Med. 35: pp. 28-35. doi: https://doi.org/10.1080/07853890310004101
Jiménez, Luis y Merchant, Horacio (coords.) (2003). Biología celular y molecular. México: Pearson.
Johannsen, Wilhelm (1909). Elemente der exakten Erblichkeitslehre. Jena: Gustav Fischer.
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Morange, Michel (2002). The Misunderstood Gene. Cambridge: Harvard University Press.
Morgan, Thomas (1934). «The relation of genetics to physiology and medicine». En: Nobel Lectures, Physiology or Medicine 1922-1941. Amsterdam: Elsevier, 1965, pp. 313-328.
Müller, Hermann (1922). «Variation due to change in the individual gene». The American Naturalist 56: pp. 32-50.
Müller, Hermann (1927). «Artificial transmutation of the gene». Science 66: pp. 84-87. doi: https://doi.org/10.1126/science.66.1699.84
Noble, Denis (2006). The Music of Life. Biology beyond Genes. New York: Oxford University Press.
Noble, Denis (2017). Dance to the Tune of Life. Biological Relativity. Cambridge: Cambridge University Press. doi: https://doi.org/10.1017/9781316771488
Oyama, Susan.; Griffiths, Paul y Gray, Russell (eds.) (2001). Cycles of Contingency. Developmental Systems and Evolution. Cambridge: The MIT Press.
Portin, Peter (1993). «The Concept of the Gene: Short History and Present Status». The Quaterly Review of Biology 68 (2): pp. 173-223. doi: https://doi.org/10.1086/418039
Rheinberger, Hans-Jörg (1995). «Genes: A Desunified View from the Perspective of Molecular Biology». En: Gene Concepts and Evolution (Workshop). Preprint nº18, editado por Peter Beurton, Wolfgang Lefèvre y Hans-Jörg Rheinberger. Berlin: Max Planck Institute for the History of Science, pp. 7-13.
Rheinberger, Hans-Jörg y Müller-Wille, Staffan (2017). The Gene. From Genetics to Postgenomics. Chicago: The University of Chicago Press.
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Waters, Kenneth (1994). «Genes made Molecular». Philosophy of Science 61: pp. 163-185. doi: https://doi.org/10.1086/289794
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Woodward, James (2003). Making Things Happen. A Theory of Causal Explanation. New York: Oxford University Press. doi: 10.1093/0195155270.001.0001
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Bürglin, Thomas (2006). «Genome Analysis and Developmental Biology: The Nematode Caenorhabditis elegans as a Model System». En: Genes in Development. Re-reading the Molecular Paradigm, editado por Eva Neumann-Held y Christoph Rehmann-Sutter. Durham: Duke University Press, pp. 15-38. doi: https://doi.org/10.1215/9780822387336-002
Burian, Richard (1995). «Too many kinds of genes? Some problems posed by discontinuities in gene concepts and the continuity of the genetic material». En: Gene Concepts and Evolution (Workshop). Preprint nº18, editado por Peter Beurton, Wolfgang Lefèvre y Hans-Jörg Rheinberger. Berlin: Max Planck Institute for the History of Science, pp. 54-51.
Burian, Richard (2004). «Molecular Epigenesis, Molecular Pleiotropy, and Molecular Gene Definitions». Hist. Phil. Life. Sci. 26: pp. 59-80. doi: https://doi.org/10.1080/03919710412331341641
Crick, Francis (1958). «On Protein Synthesis». Symposium of the Society of Experimental Biology 12: pp. 138-163.
Crick, Francis (1966). Of Molecules and Men. Seattle: University of Washington Press.
Culp, Sylvia y Kitcher, Philip (1989). «Theory Structure and Theory Change in Contemporary Molecular Biology». Brit. J. Phil. Sci. 40: pp. 459-483. doi: https://doi.org/10.1093/bjps/40.4.459
Dounce, Alexander (1952). «Duplicating Mechanism for Peptide Chain and Nucleic Acid Synthesis». Enzymologia 15: pp. 503-507.
Duret, Laurent.; Chureau, Corinne.; Samain, Sylvie.; Weissenbach, Jean y Avner, Philip (2006). «The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene». Science 312: pp. 1653-1655. doi: https://doi.org/10.1126/science.1126316
Eisenberg, Eli y Levanon, Erez (2018). «A-to-I RNA editing –immune protector and transcriptome diversifier». Nature Review Genetics 19 (8): pp. 473-490. doi: https://doi.org/10.1038/s41576-018-0006-1
Ereshefsky, Marc (2001). The Poverty of Linnean Hierarchy. A Philosophical Study of Biological Taxonomy. Cambridge: Cambridge University Press. doi: https://doi.org/10.1017/CBO9780511498459
Falk, Raphael (1995). «The Gene: From an Abstract to Material Entity and Back». En: Gene Concepts and Evolution (Workshop). Preprint nº18, editado por Peter Beurton, Wolfgang Lefèvre y Hans-Jörg Rheinberger. Berlin: Max Planck Institute for the History of Science, pp. 21-30.
Falk, Raphael (2009). Genetic Analysis. A History of Genetic Thinking. Cambridge: Cambridge University Press.
Gamow, George (1954). «Possible Relation between Deoxyribonucleic Acid and Protein Structures». Nature 173: pp. 318. doi: https://doi.org/10.1038/173318a0
Gayon, Jean (1995). «From Measure to Order: A Philosophical Scheme for the History of the Concept of Heredity». En: Gene Concepts and Evolution (Workshop). Preprint nº18, editado por Peter Beurton, Wolfgang Lefèvre y Hans-Jörg Rheinberger. Berlin: Max Planck Institute for the History of Science, pp. 53-60.
Gerstein, Mark.; Bruce, Can.; Rozowsky, Joel.; Zheng, Deyou.; Du, Jiang.; Korbel, Jan.; Emanuelsson, Olof.; Zhang, Zhengdong.; Weissman, Sherman y Snyder, Michael (2007). «What is a Gene, post-Encode? History and Updated Definition». Genome Research 17 (6): pp. 669-681. doi: https://doi.org/10.1101/gr.6339607
Gilbert, Walter (1992). «Vision of the Grail». En: The Code of Codes, editado por Daniel Kevles y Leroy Hood. Cambridge: Harvard University Press, pp. 83-97.
Gilbert, Scott (2000). «Genes Classical and Genes Developmental: The Different Use of Genes in Evolutionary Syntheses». En: The Concept of the Gene in Development and Evolution, editado por Peter Beurton, Raphael Falk y Hans-Jörg Rheinberger. Cambridge: Cambridge University Press, pp. 178-192. doi: https://doi.org/10.1017/CBO9780511527296.010
Gluckman, Peter.; Hanson, Mark.; Beedle, Alan.; Buklijas, Tatjana y Low, Felicia (2011) «Epigenetics of Human Disease». En: Epigenetics: Linking Genotype and Phenotype in Development and Evolution, editado por Benedikt Hallgrímsson y Brian Hall. Berkeley: University of California Press, pp. 398-423.
Godfrey-Smith, Peter (1999). «Genes and Codes: Lessons from the Philosophy of Mind?». En: Where Biology meets Psychology: Philosophical Essays, editado por Valerie Hardcastle. Cambridge: The MIT Press, pp. 305-331.
Griffiths, Paul y Stotz, Karola (2006). «Genes in the Postgenomic Era». Theoretical Medicine and Bioethics 27 (6): pp. 499-521. doi: https://doi.org/10.1007/s11017-006-9020-y
Griffiths, Paul y Stotz, Karola (2013). Genetics and Philosophy. An Introduction. Cambridge: Cambridge University Press. doi: https://doi.org/10.1017/CBO9780511744082
Hall, Brian (2001). «The Gene is not Dead, merely Orphaned and seeking a Home». Evolution & Development 3 (4): pp. 225-228. doi: https://doi.org/10.1046/j.1525-142x.2001.003004225.x
Hall, Brian (2003a). «Evo-Devo: Evolutionary Developmental Mechanisms». Int. J. Dev. Biol. 47: pp. 491-495.
Hall, Brian (2003b). «Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units». Biology and Philosophy 18: pp. 219-247. doi: https://doi.org/10.1023/A:1023984018531
Hall, Brian (2011). «A brief History of the Term and Concept Epigenetics». En: Epigenetics: Linking Genotype and Phenotype in Development and Evolution, editado por Benedikt Hallgrímsson y Brian Hall. Berkeley: University of California Press, pp. 9-13.
Hull, David (1972). «Reduction in Genetics –Biology or Philosophy?». Philosophy of Science 39 (4): pp. 491-499. doi: https://doi.org/10.1086/288470
Hüttemann, Andreas y Love, Alan (2011). «Aspects of Reductive Explanation in Biological Science: Intrinsicality, Fundamentality, and Temporality». British Journal for Philosophy of Science 62: pp. 519-549. doi: https://doi.org/10.1093/bjps/axr006
Jablonka, Eva y Raz, Gal (2009). «Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution». The Quaterly Review of Biology 84 (2): pp. 131-176. doi: https://doi.org/10.1086/598822
Jacob, François (1970). La logique du vivant. Une histoire de l’hérédité. Paris: Gallimard. [Trad. cast.: La lógica de lo viviente. Una historia de la herencia. Trad. de Joan Senent y M. Rosa Soler. Barcelona: Tusquets, 2014].
Jacob, François y Monod, Jacques (1961). «Genetic Regulatory Mechanisms in the Synthesis of Proteins». J. Molec. Biol. 3: pp. 318-356. doi: https://doi.org/10.1016/S0022-2836(61)80072-7
Janzen, F y Phillips, P (2006). «Exploring the evolution of environmental sex determination, especially in reptiles». J. Evol. Biol. 19 (6): pp. 1775-1784. doi: https://doi.org/10.1111/j.1420-9101.2006.01138.x
Jeffery, Constance (1999). «Moonlighting proteins». TiBS 24 (1): pp. 8-11. doi: https://doi.org/10.1016/s0968-0004(98)01335-8
Jeffery, Constance (2003). «Multifunctional proteins: examples of gene sharing». Ann. Med. 35: pp. 28-35. doi: https://doi.org/10.1080/07853890310004101
Jiménez, Luis y Merchant, Horacio (coords.) (2003). Biología celular y molecular. México: Pearson.
Johannsen, Wilhelm (1909). Elemente der exakten Erblichkeitslehre. Jena: Gustav Fischer.
Kampourakis, Kostas (2017). Making Sense of Genes. Cambridge: Cambridge University Press. doi: https://doi.org/10.1017/9781316422939
Keller, Evelyn Fox (2000). The Century of the Gene. Cambridge: Harvard University Press
Keller, Evelyn Fox (2006). «Beyond the gene but beneath the skin». En: Genes in Development. Re-reading the Molecular Paradigm, editado por Eva Neumann-Held y Christoph Rehmann-Sutter. Durham: Duke University Press, pp. 290-312. doi: https://doi.org/10.1215/9780822387336-012
Kitcher, Philip (1984). «1953 and all that. A Tale of Two Sciences». The Philosophical Review 93 (3): pp. 335-373. doi: https://doi.org/10.2307/2184541
Lewontin, Richard (1998). Gene, organismo e ambiente. Roma: Laterza & Figli. [Trad. cast.: Genes, organismo y ambiente. Las relaciones de causa y efecto en biología. Trad. de. Alberto Bixio. Barcelona: Gedisa, 2000].
Lodish, Harvey.; Berk, Arnold.; Kaiser, Chris.; Krieger, Monty.; Bretscher, Anthony.; Ploegh, Hidde.; Amon, Angelika y Scott, Matthew (2000). Molecular Cell Biology. New York: W. H. Freeman and Company. [Trad. cast.: Biología Celular y Molecular. Trad. de Silvia Fernández Castelo, Fiorella Magani, Andrea Méndez y Sofía Pfeiffer. Buenos Aires: Panamericana, 2016].
Martín Villuendas, Mariano (2019). «Una discusión en torno a los límites del concepto especie». Revista de Humanidades de Valparaíso 14: pp. 241-273. doi: https://doi.org/10.22370/rhv2019iss14pp241-273
Morange, Michel (2002). The Misunderstood Gene. Cambridge: Harvard University Press.
Morgan, Thomas (1934). «The relation of genetics to physiology and medicine». En: Nobel Lectures, Physiology or Medicine 1922-1941. Amsterdam: Elsevier, 1965, pp. 313-328.
Müller, Hermann (1922). «Variation due to change in the individual gene». The American Naturalist 56: pp. 32-50.
Müller, Hermann (1927). «Artificial transmutation of the gene». Science 66: pp. 84-87. doi: https://doi.org/10.1126/science.66.1699.84
Noble, Denis (2006). The Music of Life. Biology beyond Genes. New York: Oxford University Press.
Noble, Denis (2017). Dance to the Tune of Life. Biological Relativity. Cambridge: Cambridge University Press. doi: https://doi.org/10.1017/9781316771488
Oyama, Susan.; Griffiths, Paul y Gray, Russell (eds.) (2001). Cycles of Contingency. Developmental Systems and Evolution. Cambridge: The MIT Press.
Portin, Peter (1993). «The Concept of the Gene: Short History and Present Status». The Quaterly Review of Biology 68 (2): pp. 173-223. doi: https://doi.org/10.1086/418039
Rheinberger, Hans-Jörg (1995). «Genes: A Desunified View from the Perspective of Molecular Biology». En: Gene Concepts and Evolution (Workshop). Preprint nº18, editado por Peter Beurton, Wolfgang Lefèvre y Hans-Jörg Rheinberger. Berlin: Max Planck Institute for the History of Science, pp. 7-13.
Rheinberger, Hans-Jörg y Müller-Wille, Staffan (2017). The Gene. From Genetics to Postgenomics. Chicago: The University of Chicago Press.
Sakai, Daisuke y Trainor, Paul (2009). «Treacher Collins syndrome: Unmasking the role of Tcof1/Treacle». The International Journal of Biochemistry & Cell Biology 41 (6): pp. 1229-1232. doi: https://doi.org/10.1016/j.biocel.2008.10.026
Stotz, Karola.; Griffiths, Paul y Knight, Rob (2004). «How Biologists Conceptualize Genes: An Empirical Study». Studies in History and Philosophy of Biological and Biomedical Sciences 35 (4): pp. 647-673. doi: https://doi.org/10.1016/j.shpsc.2004.09.005
Valdez, Benigno.; Henning, Dale.; So, Rolando.; Dixon, Jill y Dixon, Michael (2004). «The Treacher Collins syndrome (TCOF1) gene product is involved in ribosomal DNA gene transcription by interacting with upstream binding factor». PNAS 101 (29): pp. 10709-10714. doi: https://doi.org/10.1073/pnas.0402492101
Waters, Kenneth (1994). «Genes made Molecular». Philosophy of Science 61: pp. 163-185. doi: https://doi.org/10.1086/289794
Waters, Kenneth (2007). «Causes that Make a Difference». The Journal of Philosophy 104 (11): pp. 551-579. doi: https://doi.org/10.5840/jphil2007104111
Watson, James y Crick, Francis (1953a). «Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid». Nature 171: pp. 737-738. doi: https://doi.org/10.1038/171737a0
Watson, James y Crick, Francis (1953b). «Genetical Implications of the Structure of Deoxyribonucleic Acid». Nature 171: pp. 964-967. doi: https://doi.org/10.1038/171964b0
Weber, Marcel (2006). «The Central Dogma as a Thesis of Causal Specificity». Hist. Phil. Life. Sci. 28: pp. 595-610.
Woodward, James (2003). Making Things Happen. A Theory of Causal Explanation. New York: Oxford University Press. doi: 10.1093/0195155270.001.0001
Published
2021-03-30
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Martín-Villuendas, M. 2021. We are not our genes: Considerations about the molecular definition of gene. Disputatio. 10, 16 (Mar. 2021), 103-137. DOI:https://doi.org/10.5281/zenodo.4678992.
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