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)

It is a fundamental cornerstone of thermodynamics that entropy (SU,V\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$S_{U,V}$$\end{document}) increases in spontaneous processes in isolated systems (often called closed or thermally closed systems when the transfer of energy as work is considered to be negligible) and achieves a maximum when the system reaches equilibrium. But with a different sign convention entropy could just as well be said to decrease to a minimum in spontaneous constant U, V processes. It would then (...) change in the same direction as the thermodynamic potentials in spontaneous processes. This article discusses but does not advocate such a change. (shrink)

We provide a detailed history of the concepts of atomic number and isotopy before the discovery of protons and neutrons that draws attention to the role of evolving interplays of multiple aims and criteria in chemical and physical research. Focusing on research by Frederick Soddy and Ernest Rutherford, we show that, in the context of differentiating disciplinary projects, the adoption of a complex and shifting concept of elemental identity and the ordering role of the periodic table led to a relatively (...) coherent notion of atomic number. Subsequent attention to valency, still neglected in the secondary literature, and to nuclear charge led to a decoupling of the concepts of elemental identity and weight and allowed for a coherent concept of isotopy. This concept received motivation from empirical investigations on the decomposition series of radioelements and their unstable chemical identity. A new model of chemical order was the result of an ongoing collaboration between chemical and physical research projects with evolving aims and standards. After key concepts were considered resolved and their territories were clarified, chemistry and physics resumed autonomous projects, yet remained bound by newly accepted explanatory relations. It is an episode of scientific collaboration and partial integration without simple, wholesale gestalt switches or chemical revolutions. (shrink)

Many philosophers attribute extraordinary importance to the idea of natural kinds seemingly intimating that the very possibility of certain kinds of activity are ontologically beholden to the existence of kinds. Specifically, regarding chemistry, Brian Ellis intimated that the success of any plausible metaphysical essentialism depends upon its “reliance on examples from chemistry.” Ellis’s view is representative of a tradition in analytic philosophy that has utilized chemical examples as paradigmatic natural kinds. In this regard, Kripke and Putnam emerge as the architects (...) of an entrenched research program dedicated to the chemical tradition of natural kinds in analytic philosophy. The emergence of a critical body of literature by philosophers of chemistry and others has shattered the complacent reliance upon chemical examples as exemplary kinds. On the basis of this emerging critical literature, I will critically explore the way in which chemical practice and inquiry affects the natural kind debate. So, instead of the pretense that we simply carve nature at its joints, we need to become better grounded in the practice of science, and especially with regard to the debate about natural kinds in chemical practice. Consistent with this orientation, we need to make the practice turn, that is, eradicate the fantasy of logical reconstruction and become involved with the interpretative and historical challenges of understanding the nuances of practice. The point here is quite clear, metaphysical questions regarding natural kind should be imminent to scientific practice. Indeed, any legitimate metaphysics of natural kinds should be appropriately informed and grounded in practice and not operate on the basis of a priori sovereignty. I will insert this critical discussion within the analytical context of the notion of interpretive communities and make the case that philosophers should not assume that appeals to the purity of philosophy can substitute for the complexity and practical orientation of chemical practice. (shrink)

The aim of the series of the three articles entitled “Name game…” is to present the historical information about nomenclature history of every known chemical element. The process of naming each chemical element is analyzed, with particular emphasis on the first publication with a given name. It turned out that in many cases this information is not obvious and unambiguous, and the published data are even contradictory. In a few cases, the names of the elements were changed even several times. (...) Moreover, even when the author of a given element name is known, it is sometimes not entirely clear in which publication he/she first used it. Therefore, the series of three articles are an attempt to sort out the issue of first publishing of the names of all 118 chemical elements known so far, based on original source texts, available thanks to the digitization of a number of collections of scientific literature. The articles are divided according to the time of discoveries: (1) research till the end of the 18th century, (2) discoveries in the 19th century, (3) discoveries and syntheses of elements in the 20th and 21st centuries. This particular article presents the history of naming of the first 37 elements: known from antiquity, discovered in nature and named in 17th and 18th century. (shrink)

Formal charge and oxidation state are two means of estimating the charge of an atom in a molecule. Though these concepts have very different origins—formal charge is derived from the ball-and-hook model of bonding and oxidation state is based on the ionic approximation of molecules—they are used to predict reactivity and other molecular properties through their properties as charges. In this submission, it is shown that formal charge and oxidation state are two extreme descriptions of bonding: formal charge represents zero (...) charge transfer between atoms while oxidation state represents complete charge transfer in each bond. These ‘localised electron approximations’ form an incomplete picture of atomic charge. Electronegativity measures the extent of polarity in real bonds; this concept can be introduced to polarise bonds relative to the ‘equal sharing model’. It is shown that the various electronegativity models are fundamentally related. We chose two models to demonstrate numerically that polar bonds yield charges intermediate between the localised electron approximations: Pauling and Mulliken. It is shown that probabilistic interpretation of the Pauling scale (‘scaled Pauling’ method) and use of asymmetric chemical potential (‘modified Mulliken’ method) lead to atomic charges that closely approximate experimental values using simple ‘back of the envelope’ calculations. It is seen that formal charge, oxidation state, and electronegativity-interpolated charge lie on a continuum and are mathematically related. It is therefore concluded that electronegativity introduces (quantum) delocalisation to the localised (classical) picture of electron bonding. (shrink)