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. (shrink)

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. (shrink)

The present paper attempts to demonstrate semiotic arguments against the sequence → structure → function paradigm in protein studies. The unidirectional deterministic thinking in biological processes has been challenged by several disciplines of life sciences (epigenetics, proteomics, etc.) and philosophy (process philosophy). Biosemiotics comprehends living organisms as actively participating in their present and somehow creating or shaping their future, having a plurality of options for acting. Determinism and unidirectionality are in contradiction with a biosemiotic approach towards life, mostly when considering (...) Peirce’s triadic concept of semiosis. In this paper, a Peircean biosemiotic approach is applied to proteins and to the process of protein folding. Two main concepts are presented to support the arguments against the SSF paradigm in protein studies: the NonReduction Theorem and the notion of folded continuum. A processual approach is proposed as the most suitable for descriptions of proteins and their functions. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

Had more philosophers of science come from chemistry, their thinking would have been different. I begin by looking at a typical chemical paper, in which making something is the leitmotif, and conjecture/refutation is pretty much irrelevant. What in fact might have been, might be, different? The realism of chemists is reinforced by their remarkable ability to transform matter; they buy into reductionism where it serves them, but make no real use of it. Incommensurability is taken without a blink, and actually (...) serves. The preeminence of synthesis in chemistry could have led philosophers of science to take more seriously questions of aesthetics within science, and to find a place in aesthetics for utility. The necessary motion twixt macroscopic and microscopic views of matter in modern chemistry leads to the coexistence of symbolic and iconic representations. And in another way to the deliberate, creative violation of categories. (shrink)

During the past two decades, philosophers of biology have increasingly turned their attention to mechanisms of biological phenomena. Through analyses of mechanistic proposals advanced by biologists, the goal of these philosophers is to understand what a mechanism is and how mechanisms explain. These analyses have generally focused on mechanistic proposals for phenomenon that occur at the cellular or sub-cellular level, such as synapse firing, protein synthesis, or metabolic pathway operation. Little is said about the mechanisms of the macromolecular reactions that (...) underpin these phenomena. These reactions comprise a diverse family of reaction types, and include protein folding, macromolecular complex formation, receptor-ligand interactions, and enzyme catalysis. In this paper, I develop an account of mechanism that focuses exclusively on macromolecular reactions. I begin by reviewing how mechanism is understood in enzymology, and how mechanistic concepts of enzymology apply to macromolecular reactions in general. We will see that the mechanism of a macromolecular reaction is most accurately described as a progression of reaction intermediates, where the evolution of intermediates, from one to the next, is characterized by an energetic coupling between chemistry and protein dynamics. I then make the case that this description necessitates a grounding in a process ontology. To describe the mechanism by which a macromolecular reaction occurs is to describe a process. (shrink)

Starting from common-sense notions of ‘furniture of the world’ a process ontology is developed in which prospective is an integral part. Technology as configurations that work (precariously) embodies expectations which structure further development. Examples (a cloned puppy, hotel keys, DC airplanes, stem cells, and overpasses on Long Island) are used to develop the notion of material narratives that are “written”, not just by engineers and designers/producers, but also by users: “reading” implies some further “writing”. In contrast to prevailing notions of (...) technological control (through manipulation of building blocks), the “writing” of nanotechnology is modulation of the invisible and impredictable - an extreme example of unruly technology and repair work after the fact, where in practice control is a gesture not so different from magic. Because ontology cannot be other than prospective, it is political throughout. Thus, prospective technology highlights ontological politics. (shrink)

Despite the currently perceived urgent need among contemporary philosophers of chemistry for adjudicating between two rival metaphysical conceptual frameworks—is chemistry primarily a science of substances or processes?—this essay argues that neither provides us with what we need in our attempts to explain and comprehend chemical operations and phenomena. First, I show the concept of a chemical property can survive the abandoning of the metaphysical framework of substance. While this abandonment means that we will need to give up essential properties, contingent (...) properties can give us all the stability we need to account for chemical continuity as well as change. I then go on to show that this attention to clusters of contingent properties does not force us into the arms of an alternative process metaphysical framework either. Finally, I sketch a view I call particularism with respect to chemical properties on analogy with moral particularism. I conclude by sketching some of the implications for the field of philosophy of chemistry of my proposal that we abandon our interest in the metaphysical question of what chemistry is primarily about in favor of a broadly scientific particularism with respect to kinds and properties. (shrink)