Is it possible a processual ontology of biochemical entities? Considerations on the case of cell receptors and cell signaling
DOI:
https://doi.org/10.17533/udea.ef.345867Keywords:
Ontology, Biochemistry, Receptors, Cell signaling, individuals, processesAbstract
Biological macromolecules, considered as the items of the biochemical domain, are typically conceived under the ontological category of substantial individuals. In this paper, I will argue that the philosophical framework of process ontology, according to which the living world is not populated by individuals but by a dynamic hierarchy of processes, is more adequate to account for the structure and functioning of macromolecules. In particular, I will analyze its application to the phenomenon of cell signaling and to one of its key concepts, cell receptors. Current knowledge in biochemistry allows us to conceive receptors as processual and dynamic entities, relationally stabilized and not separated from the biochemical phenomenon of which they are part.
Downloads
References
Avendaño, C. (2001). Introducción a la química farmacéutica (2o ed.). Madrid.
Bartol, J. (2016). Biochemical kinds. The British journal for the philosophy of science, 67(2),
-551. https://doi.org/10.1093/bjps/axu046
Bensaude-Vincent, B. (2014). Philosophy of chemistry or philosophy with chemistry. HYLE:
International Journal for Philosophy of Chemistry, 20, 58-76.
Berg, K. A. & Clarke, W. P. (2018). Making sense of pharmacology: inverse agonism and functional selectivity. International
Journal of Neuropsychopharmacology, 21(10), 962-977. https:// doi.org/10.1093/ijnp/pyy071
Cobb, J.B. (1988). Ecology, science, and religion: toward a postmodern worldview. In D.R. Griffin (Ed.), The Reenchantment of Science (99-114). State University of New York Press.
Córdoba, M. y Zambon, A. (2017). How to handle nanomaterials? The re-entry of individuals into the philosophy of chemistry. Foundations of Chemistry, 19(3), 185-196. https://doi. org/10.1007/s10698-017-9283-6
Curtis, H., Barnes, S., Schnek, A. y Massarini, A. (2013). Curtis Biología, Séptima edición. Buenos Aires.
Davis, C. M., Gruebele, M. & Sukenik, S. (2018). How does solvation in the cell affect protein folding and binding? Current opinion in structural biology, 48, 23-29. https://doi. org/10.1016/j.sbi.2017.09.003
Dupré, J. (2012). Processes of life: essays in the philosophy of biology. Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199691982.001.0001
Dupré, J. (2021). The metaphysics of biology (elements in the philosophy of biology). Cambridge University Press. https://doi.org/10.1017/9781009024297
Dupré, J. & Nicholson, D. (2018). A manifesto for a processual philosophy of biology. In D. Nicholson & J. Dupré (Ed.), Everything flows: towards a processual philosophy of biology (pp. 3-45). Oxford University Press.
Dyson, H.J. & Wright, P.E. (2005). Intrinsically unstructured proteins and their functions. Nature Reviews Molecular Cell Biology, 6, 197-208. https://doi.org/10.1038/nrm1589
French, S. & Krause, D. (2006). Identity in physics: a historical, philosophical and formal analysis. Oxford University Press.
Gillett, C. (2007). Understanding the new reductionism: the metaphysics of science and compositional reduction. The Journal of Philosophy, 104, 193–216. https://doi. org/10.5840/jphil2007104427
Gillett, C. (2010). Moving beyond the subset model of realization: the problem of qualitative distinctness in the metaphysics of science. Synthese, 177, 165–92. https://doi. org/10.1007/s11229-010-9840-1
Goodwin, W. (2011). Structure, function, and protein taxonomy. Biology & Philosophy, 26(4), 533-545. https://doi.org/10.1007/s10539-011-9252-8
Grouleff, J., Irudayam S.J., Skeby, K.K. & Schiøtt, B. (2015). The influence of cholesterol on membrane protein structure, function, and dynamics studied by molecular dynamics simulations. Biochim Biophys Acta (BBA) — Biomembr. 1848(9), 1783-1795. https://doi. org/10.1016/j.bbamem.2015.03.029
Guttinger, S. (2018). A process ontology for macromolecular biology. In D. Nicholson & J. Dupré (Ed.), Everything flows: towards a processual philosophy of biology (pp. 303-320). Oxford University Press. https://doi.org/10.1093/oso/9780198779636.003.0015
Guttinger, S. (2021). Process and practice: understanding the nature of molecules. HYLE: International Journal for Philosophy of Chemistry, 27, 47-66. http://www.hyle.org/ journal/issues/27-1/guttinger.htm
Havstad, J. C. (2018). Messy chemical kinds. British Journal for the Philosophy of Science, 69, 719–43. https://doi.org/10.1093/bjps/axw040
Hendry, R. (2008). Microstructuralism: problems and prospects. In J. van Brakel & K. Ruthenberg (Eds.), Stuff – The nature of chemical substances (pp. 107-121). Würzburg: Königshauen & Neumann.
Hipp, M. S., Kasturi, P. & Hartl, F. U. (2019). The proteostasis network and its decline in ageing. Nature reviews Molecular cell biology, 20(7), 421-435. https://doi.org/10.1038/s41580- 019-0101-y
Huberts, D. H. & van der Klei, I. J. (2010). Moonlighting proteins: an intriguing mode of multitasking. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1803(4), 520–525. https://doi.org/10.1016/j.bbamcr.2010.01.022
Jeffery, C. (2014). An introduction to protein moonlighting. Biochemical Society Transactions, 42(6), 1679–1683. https://doi.org/10.1042/BST20140226
Kaiser, M.I. & Trappes, R. (2021). Broadening the problem agenda of biological individuality: individual differences, uniqueness and temporality. Biology & Philosophy, 36(15). https:// doi.org/10.1007/s10539-021-09791-5
Krause, D. & Arenhart, J.R.B. (2016). Individuality, quantum physics, and a metaphysics of non-individuals. The role of the formal. In A. Guay & T. Pradeu (Eds.), Individuals Across the Sciences (pp 61–84). Oxford University Press. https://doi.org/10.1093/acprof:o so/9780199382514.003.0005
Kopel, J. (2019). A note regarding relational ontology in chemistry. Process Studies, 48(1), 59-66. https://doi.org/10.5840/process20194815
Lewowicz, L. & Lombardi, O. (2013). Stuff versus individuals. Foundations of Chemistry, 15(1), 65-77. https://doi.org/10.1007/s10698-012-9152-2
Lowe, E.J. (2003). Individuation. In M.J. Loux & D.W. Zimmerman, (Eds.), The Oxford Handbook of Metaphysics (pp. 75–95). Oxford University Press.
Lowe, E.J. (2016), Non-individuals. In A. Guay & T. Pradeu (Eds.), Individuals Across the Sciences (pp 49–60). Oxford University Press. https://doi.org/10.1093/acprof:o so/9780199382514.003.0004
Martínez González, J. C., y Córdoba, M. (2016). El problema de las clases naturales en química: algunas dificultades para el microestructuralismo. Crítica (México, DF), 48(144), 89-117. https://doi.org/10.22201/iifs.18704905e.2016.214
Manglik, A. & Kobilka, B. (2014). The role of protein dynamics in GPCR function: insights from the β2AR and rhodopsin.
Current opinion in cell biology, 27, 136-143. https://doi. org/10.1016/j.ceb.2014.01.008
Needham, P. (2003). Continuants and Processes in Macroscopic Chemistry. In J. Seibt (Eds.), Process Theories (237-265). Springer. https://doi.org/10.1007/978-94-007-1044-3_10
Nicholson, D. y Dupré, J. (Eds.). (2018). Everything flows: towards a processual philosophy of biology. Oxford University Press. https://doi.org/10.1093/oso/9780198779636.001.0001
Ruthenberg, K. & van Brakel, J. (Eds.). (2008). Stuff. The Nature of Chemical Substances. Königshauen & Neumann.
Santos, G., Vallejos, G. & Vecchi, D. (2020). A relational-constructionist account of protein macrostructure and function. Foundations of Chemistry 22, 363–382. https://doi. org/10.1007/s10698-020-09373-5
Seibt, J. (2018). Ontological tools for the process turn in biology some basic notions of general process theory. In D. Nicholson & J. Dupré (Eds.), Everything flows: towards a processual philosophy of biology (pp. 113-136). Oxford University Press. https://doi.org/10.1093/ oso/9780198779636.003.0006
Seibt, J. (2021). Process Philosophy. In E. N. Zalta (Ed.), The Stanford Encyclopedia of Philosophy (Fall 2021 Edition). https://plato.stanford.edu/archives/fall2021/entries/process- philosophy/.
Schummer, J. (1998). The chemical core of chemistry I: a conceptual approach. HYLE: International Journal for Philosophy of Chemistry, 4, 129-162.
Slater, M. H. (2009). Macromolecular pluralism. Philosophy of Science, 76(5), 851-863. https:// doi.org/10.1086/605817
Silverman, R. B. & Holladay, M. W. (2004). The organic chemistry of drug design and drug action. Academic press.
Stein, R. L. (2004). Towards a process philosophy of chemistry. HYLE: International Journal for Philosophy of Chemistry, 10(4), 5–22.
Stein, R. L. (2006). A process theory of enzyme catalytic power – the interplay of science and metaphysics. Foundations of Chemistry, 8, 3–29. https://doi.org/10.1007/s10698- 005-7907-8
Tahko, T. E. (2020). Where do you get your protein? Or: biochemical realization. The British journal for the philosophy of science, 71(3), 799-825. https://doi.org/10.1093/bjps/axy044
Tobin, E. (2010). Microstructuralism and macromolecules: the case of moonlighting proteins. Foundations of Chemistry, 12(1), 41-54. https://doi.org/10.1007/s10698-009-9078-5
Voet, D. & Voet, J. (2004). Bioquímica. Médica Panamericana.
Wang, Y., Bugge, K., Kragelund, B. B. & Lindorff-Larsen, K. (2018). Role of protein dynamics in transmembrane receptor signalling. Current opinion in structural biology, 48, 74-82. https://doi.org/10.1016/j.sbi.2017.10.017
Wennerström, H., Estrada, E. V., Danielsson, J. & Oliveberg, M. (2020). Colloidal stability of the living cell. Proceedings of the National Academy of Sciences, 117(19), 10113-10121. https://doi.org/10.1073/pnas.1914599117
Wright, P. E. & Dyson, H. J. (1999). Intrinsically unstructured proteins: re-assessing the protein structurefunction paradigm. Journal of Molecular Biology, 293(2), 321–331. https://doi. org/10.1006/jmbi.1999.3110
Yang, J., Gao, M., Xiong, J., Su, Z. & Huang, Y. (2019). Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding. Protein Science, 28(11), 1952-1965. https://doi.org/10.1002/pro.3718
Published
How to Cite
Issue
Section
Categories
License
Copyright (c) 2021 Fiorela Alassia
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Authors who publish with this journal agree to the following terms:
1. The Author retains copyright in the Work, where the term "Work" shall include all digital objects that may result in subsequent electronic publication or distribution.
2. Upon acceptance of the Work, the author shall grant to the Publisher the right of first publication of the Work.
3. The Author shall grant to the Publisher a nonexclusive perpetual right and license to publish, archive, and make accessible the Work in whole or in part in all forms of media now or hereafter known under a Creative Commons Attribution-NoCommercia-ShareAlike (CC BY-NC-SA 4.0), or its equivalent, which, for the avoidance of doubt, allows others to copy, distribute, and transmit the Work under the following conditions: (a) Attribution: Other users must attribute the Work in the manner specified by the author as indicated on the journal Web site;(b) Noncommercial: Other users (including Publisher) may not use this Work for commercial purposes;
4. The Author is able to enter into separate, additional contractual arrangements for the nonexclusive distribution of the journal's published version of the Work (e.g., post it to an institutional repository or publish it in a book), as long as there is provided in the document an acknowledgement of its initial publication in this journal;
5. Authors are permitted, and Estudios de Filosofía promotes, to post online the preprint manuscript of the Work in institutional repositories or on their Websites prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (see The Effect of Open Access). Any such posting made before acceptance and publication of the Work is expected be updated upon publication to include a reference to the Estudios de Filosofía's assigned URL to the Article and its final published version in Estudios de Filosofía.
