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A process ontology approach in biochemistry: the case of GPCRs and biosignaling

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Abstract

According to process ontology in the philosophy of biology, the living world is better understood as processes rather than as substantial individuals. Within this perspective, an organism does not consist of a hierarchy of structures like a machine, but rather a dynamic hierarchy of processes, dynamically maintained and stabilized at different time scales. With this respect, two processual approaches on enzymes by Stein (Hyle Int J Philos Chem 10(4):5–22, 2004, Process Stud 34:62–80, 2005, Found Chem 8:3–29, 2006) and by Guttinger (Everything Flows: Towards a Processual Philosophy of Biology, Oxford University Press, Oxford, 2018) allows to think of macromolecules as relational and processual entities. In this work, I propose to extend their arguments to another case study within the biochemical domain, which is the case of ligand receptors and receptor-mediated biosignaling. The aim of this work is to analyze the case of G Protein-Coupled Receptors and biosignaling under the consideration of a processual ontology. I will defend that the processual ontology framework is adequate for the biochemical domain and that it allows accounting for the current biochemical knowledge related to the case study.

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Notes

  1. This is not an exhaustive list of process philosophers.

  2. During this time, the demonstration that ferments were proteins was achieved by the crystallization of urease by James Sumner and of pepsin by John Northrop (Morange 2007).

  3. Supramolecular chemistry, as it was firstly defined by the chemist Jean Marie Lehn in 1988 (Lehn 1988), is the chemistry of non-covalent intermolecular bonds, which studies the structures and functions of entities formed by two or more chemical species.

  4. For more details on the discussion around protein microstructuralism, see Slater (2009), Tobin (2010), Goodwin (2011), Havstad (2018), Tahko (2020).

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Acknowledgements

I would like to thank to the Secretary of Science and Technology of the National University of Patagonia San Juan Bosco (Argentina), for financial support of this work.

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    Fiorela Alassia

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Alassia, F. A process ontology approach in biochemistry: the case of GPCRs and biosignaling. Found Chem 24, 405–422 (2022). https://doi.org/10.1007/s10698-022-09443-w

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