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)

Although during the last decades the philosophy of chemistry has greatly extended its thematic scope, the main difficulties appear in the attempt to link the chemical description of atoms and molecules and the description supplied by quantum mechanics. The aim of this paper is to analyze how the difficulties that threaten the continuous conceptual link between molecular chemistry and quantum mechanics can be overcome or, at least, moderated from the perspective of BM. With this purpose, in “The quantum-mechanical challenges” section (...) the foundational incompatibility between chemical and SQM descriptions will be briefly recalled. “Bohmian mechanics” section will be devoted to explain the main features of BM. In “Empirical equivalence and underdetermination” section, the consequences of the empirical equivalence between SQM and BM will be discussed. Finally, in the Conclusion, we will stress the scope of the obtained conclusions and the philosophical difficulties that still remain even after adopting BM for foundational purposes. (shrink)

When young Kant meditated upon the distinction between his right and left hands, he could not foresee that the problem of incongruent counterparts would revive in the twentieth century under a new form. In the early days of quantum chemistry, Friedrich Hund developed the so-called Hund paradox that arises from the supposed inability of quantum mechanics to account for the difference between enantiomers. In this paper, the paradox is expressed as a case of quantum measurement, stressing that decoherence does not (...) offer a way out of the problem. The main purpose is to argue for the need to adopt a clear interpretation of quantum mechanics in order to solve the paradox. In particular, I claim that the Modal-Hamiltonian Interpretation, which conceives measurement as a breaking-symmetry process, supplies the tools required to explain the dextro-rotation or levo-rotation properties of optical isomers. (shrink)

The general question to be considered in this paper points to the nature of the world described by chemistry: what is macro-chemical ontology like? In particular, we want to identify the ontological categories that underlie chemical discourse and chemical practice. This is not an easy task, because modern Western metaphysics was strongly modeled by theoretical physics. For this reason, we attempt to answer our question by contrasting macro-chemical ontology with the mainstream ontology of physics and of traditional metaphysics. In particular, (...) we introduce the distinction between stuff-ontology, proper of chemistry, and individual-ontology, proper of physics. These two ontologies differ from each other in the basic categories of their own structures. On this basis, we characterize individual-ontology in such a way that the features of stuff-ontology will arise by contrast with it. (shrink)

The analysis of the concept of orbital allows us to argue that—in opposition to a recent position in philosophy of science—it is impossible to defend the autonomy of the chemical reality in regard to physical reality, appealing to the idea that there is a conceptual rupture among a chemical interpretation and a quantuminterpretation of the concept. This is the case because there are not two different interpretations of the concept of orbital. On the contrary, the concept involved in structural chemistry (...) and in quantum chemistry comes from quantum mechanics.El análisis del concepto de orbital permite argumentar—en oposición a una propuesta reciente en filosofía de la química—que no es posible defender la autonomía ontológica de la realidad química respecto de la física, sobre la base de una ruptura conceptual entre una interpretación química del concepto y otra propia de la mecánica cuántica. Esto es así porque no existen tales interpretaciones distintas del concepto de orbital, sino que, por el contrario, este concepto en química cuántica y en química estructural proviene de la mecánica cuántica. (shrink)

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)

A los cristales se los describe como a una red de átomos que puede vibrar alrededor de su posición de equilibrio. Sin embargo, el hecho de que la energía de estas ondas esté cuantificada sugiere una analogía con el campo electromagnético. En analogía con el fotón se define al fonón. Generalmente se concibe al fonón como a una cuasi-partícula, es decir, como a un instrumento matemático útil en los cálculos pero sin una existencia propia. En este trabajo estudiamos el estatuto (...) ontológico del fonón y argumentaremos en favor de la idea de considerarlo como una partícula real. (shrink)

The problem of the 3N dimensions of the wave function is of particular interest in the philosophy of physics. In this work, we will recall the main positions about the nature and dimensionality of the wave function and we will introduce a new perspective, coming from quantum chemistry. For this, we will bring to light the formal operations that underlie the independent electron approximation. On this basis, we will point out how quantum chemistry can offer new arguments that contribute to (...) the debate about the ontology of wave function. (shrink)

The present work is a comment of a recent paper by Fortin and coauthors in which the authors propose the introduction of Bohmian mechanics in the philosophy of chemistry and the use of standard quantum mechanics as a mere instrument of prediction. This way would allow overcoming the obstacles found in linking molecular chemistry and quantum mechanics. Starting from some remarks on the orbital concept, we highlight and discuss some general issues that need to be taken into account when two (...) scientific theories coexist within the same investigation field, i.e. SQM and BM. (shrink)

The many-faced relationship between chemistry and physics is one of the most discussed topics in the philosophy of chemistry. In his recent book Reducing Chemistry to Physics. Limits, Models, Consequences, Hinne Hettema conceives this relationship as a reduction link, and devotes his work to defend this position on the basis of a “naturalized” concept of reduction. In the present paper I critically review three kinds of issues stemming from Hettema’s argumentation: philosophical, scientific and methodological.

By moving away from the traditional reductionist reading of the quantum theory of atoms in molecules, in this paper we analyze the role played by QTAIM in the relationship between molecular chemistry and quantum mechanics from an emergentist perspective. In particular, we show that such a relationship involves two steps: an intra-domain emergence and an inter-domain emergence. Intra-domain emergence, internal to quantum mechanics, results from the fact that the electron density, from which all the other QTAIM’s concepts are defined, arises (...) from the wavefunction as a coarse-grained magnitude. Inter-domain emergence involves an analogical link, a mapping, between QTAIM’s entities, such as topological atoms and bond paths, and the entities that populate the molecular-chemistry domain, such as chemical atoms and chemical bonds. (shrink)

Recent discussions about the microstructure of materials generally focus on the ontological aspects of the molecular structure. However, there are many types of substances that cannot be studied by means of the concept of molecule, for example, salts. For the quantum treatment of these substances, a new particle, called phonon, is introduced. Phonons are generally conceived as a pseudo-particle, that is, a mathematical device necessary to perform calculations but which does not have a "real" existence. In this context, the aim (...) of this paper will be to analyze the ontological status of phonons. For such purposes we will critically analyze the arguments that would account for the presumed nonexistence of phonons. Finally, having already demonstrated that there are not enough reasons to consider phonons as non-existing entities, we will explore some possibilities that allow us to elucidate their ontological status. (shrink)

According to classical molecular chemistry, molecules have a structure, that is, they are sets of atoms with a definite arrangements in space and held together by chemical bonds. The concept of molecular structure is central to modern chemical thought given its impressive predictive power. It is also a very useful concept in chemistry education, due to its role in the rationalization and visualization of microscopic phenomena. However, such a concept seems to find no place in the ontology described by quantum (...) mechanics, since it appeals to classical notions such as the position of the atomic nuclei or the individuality of electrons. Although this problem has attracted the attention of several authors, the discussion is far from settled. Some authors adopt an explicitly reductionist position and advocate to reconstruct the concept of molecular structure within the framework of the quantum theory. Others, although acknowledging the conceptual discontinuity between quantum mechanics and molecular chemistry, keep the hope of future reduction alive. From an explicitly non-reductionist position, on the contrary, others authors conceive molecular structure as an emergent phenomenon. The purpose of this article is to propose a different line of argumentation to address this problem. By contrast to reduction and emergence, the admission of a multiplicity of ontologies, not necessarily linked by hierarchical connections, cancels the need of finding a relation of dependence between the molecular level and the quantum level. This ontologically pluralist position can be applied to the issue of molecular structure, in order to argue that it is possible to admit the existence of structure in the ontology of molecular chemistry, in spite of the fact that it does not exist in the quantum world. (shrink)

Although during the last decades the philosophy of chemistry has greatly extended its thematic scope, the main difficulties appear in the attempt to link the chemical description of atoms and molecules and the description supplied by quantum mechanics. The aim of this paper is to analyze how the difficulties that threaten the continuous conceptual link between molecular chemistry and quantum mechanics can be overcome or, at least, moderated from the perspective of BM. With this purpose, in “The quantum-mechanical challenges” section (...) the foundational incompatibility between chemical and SQM descriptions will be briefly recalled. “Bohmian mechanics” section will be devoted to explain the main features of BM. In “Empirical equivalence and underdetermination” section, the consequences of the empirical equivalence between SQM and BM will be discussed. Finally, in the Conclusion, we will stress the scope of the obtained conclusions and the philosophical difficulties that still remain even after adopting BM for foundational purposes. (shrink)