Is it possible a processual ontology of biochemical entities? Considerations on the case of cell receptors and cell signaling

Authors

DOI:

https://doi.org/10.17533/udea.ef.345867

Keywords:

Ontology, Biochemistry, Receptors, Cell signaling, individuals, processes

Abstract

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.

|Abstract
= 1419 veces | PDF (ESPAÑOL (ESPAÑA))
= 200 veces| | HTML (ESPAÑOL (ESPAÑA))
= 98 veces|

Downloads

Download data is not yet available.

Author Biography

Fiorela Alassia, UNPSJB

is research professor at the Faculty of Natural Sciences and Health Sciences of the UNPSJB (Argentina). She is a Biochemist (UNPSJB), Specialist in University Teaching (UNPSJB) and Master in Epistemology and History of Science (UNTREF). She is starting his Doctorate in Philosophy at the University of Buenos Aires. His current areas of work are the philosophy of biochemistry and health sciences.

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

2022-01-31

How to Cite

Alassia, F. (2022). Is it possible a processual ontology of biochemical entities? Considerations on the case of cell receptors and cell signaling. Estudios De Filosofía, (65), 153–175. https://doi.org/10.17533/udea.ef.345867

Issue

Section

Original or Research articles

Categories