structure of a laboratory report (generalized from Italian, Chinese and US sources), we distill a fifth flavor, the givens, whose flip side is the freedoms or tangibles of an experiment. (Stated in terms of computer science, we are trying to find inputs and outputs, but these turn out to be surprisingly vague in chemistry.) Then, in the service of a white-boxing ethos (which sounds less severe than ‘anti black-boxing’), we establish a movable boundary between givens and tangibles, with implications for (...) ‘ontological attitudes’ and for the future of chemistry. Next, in revisiting a 2002 exchange between Schummer and Laszlo, which might be paraphrased as the chemist-as-philosopher versus chemist-as-artisan, we apply a second kind of sliding scale which seems to harmonize the discussion. Finally, on a possibly quixotic note, we look briefly at a third kind of sliding scale, now aimed squarely at ontology itself. For illustrative purposes, we adopt an atomocentric viewpoint (as distinct from atomistic), and assign it the provisional name ‘Fuzzy CH4 Ontology’. (shrink)

If nature is by definition the object of the natural sciences, then the dichotomy ‘natural’ versus ‘chemical’, held by both chemists and nonchemists, suggests an idiosyncrasy of chemistry. The first part of the paper presents a selective historical analysis of the main notions of nature in chemistry, as developed in early Christian views of chemical crafts, alchemy, iatrochemistry, mechanical philosophy, organic chemistry, and contemporary drug research. I argue that the dichotomy as well as quasi-moral judgments of chemistry have been based (...) on static and teleological notions of nature throughout history and that chemists, unlike physicists, have neglected the dynamic notion of nature. The second part provides a philosophical criticism of the former notions and argues for the latter as well as for an explicit discourse about values in chemistry.Author Keywords: History and philosophy of chemistry; Notion of nature; Alchemy; Mechanical philosophy; Synthetic organic chemistry; Contemporary drug research. (shrink)

The problem of the peculiarcharacter of chemical laws and theories is a central topic in philosophy of chemistry. Oneof the most characteristic and, at the sametime, most puzzling examples in discussions onchemical laws and theories is Mendeleev''speriodic law. This law seems to be essentiallydifferent in its nature from the exact laws ofclassical physics, the latter being usuallyregarded as a paradigm of science byphilosophers. In this paper the main argumentsconcerning the peculiar character of chemicallaws and theories are examined. The laws ofchemistry (...) are natural laws to the same extentas are the laws of physics. The law discoveredby Mendeleev is a normal law of nature. It isnot a law of physics, nevertheless, it is exactin the same philosophical sense as are the lawsof physics. The periodic system of chemicalelements was established by constructing anidealized system of idealized elements. Thefundamental idealization substantiated byexperimental chemistry was the chemicalelement as a place in the periodicsystem. (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 exploration of chemical periodicity over the past 250 years led to the development of the Periodic System of Elements and demonstrates the value of vague ideas that ignored early scientific anomalies and instead allowed for extended periods of normal science where new methodologies and concepts are developed. The basic chemical element provides this exploration with direction and explanation and has shown to be a central and historically adaptable concept for a theory of matter far from the reductionist frontier. This (...) is explored in the histories of Prout’s hypothesis, Döbereiner Triads, element inversions necessary when ordering chemical elements by atomic weights, and van den Broeck’s ad-hoc proposal to switch to nuclear charges instead. The development of more accurate methods to determine atomic weights, Rayleigh and Ramsey’s gas separation and analytical techniques, Moseley’s X-ray spectroscopy to identify chemical elements, and more recent accelerator-based cold fusion methods to create new elements at the end of the Periodic Table point to the importance of methodological development complementing conceptual advances. I propose to frame the crossover from physics to chemistry not as a loss of accuracy and precision but as an increased application of vague concepts such as similarity which permit classification. This approach provides epistemic flexibility to adapt to scientific anomalies and the continued growth of chemical compound space and rejects the Procrustean philosophy of reductionist physics. Furthermore, it establishes chemistry with its explanatory and operational autonomy epitomized by the periodic system of elements as a gateway to other experimental sciences. (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)

Though complex networks have been widely applied in the research of chemistry, there is hardly any introduction about the establishment of networks using chemical bonds. In this paper, we consider chemical elements as a system linked by chemical bonds and create the undirected chemical bond network by abstracting nodes from elements and undirected edges from bonds. Connectivity, heterogeneity, small world and disassortativity of this network show the macro structural rationality of this system. The degree and k-order neighbors of an element, (...) which represent the micro topology of this network, can be used to measure its chemical reactivity and detect how many kinds of compounds it can form. The similarity between two elements is measured by the Jaccard index and the VOS mapping technique, results of which are similar to well-known similarities between elements shown by the periodic table. The establishment and topological analysis of this network provide another way to understand and study elements and bonds, and more chemical properties of elements and bonds can be studied by complex networks. (shrink)

According to ‘standard histories’ of nanotechnology, the colorful pictures of atoms produced by scanning probe microscopists since the 1980s essentially inspired visions of molecular nanotechnology. In this paper, I provide an entirely different account that, nonetheless, refers to aesthetic inspiration, First, I argue that the basic idea of molecular nanotechnology, i.e., producing molecular devices, has been the goal of supramolecular chemistry that emerged earlier, without being called nanotechnology. Secondly, I argue that in supramolecular chemistry the production of molecular devices was (...) inspired by an aesthetic phenomenon of gestalt switch, by certain images that referred to both molecules and ordinary objects, and thus symbolically bridged the two worlds. This opened up a new way of perceiving and drawing molecular images and new approaches to chemical synthesis. Employing Umberto Eco’s semiotic theory of aesthetics, I analyze the gestalt switch and the inspiration to build molecular devices and to develop a new sign language for supramolecular chemistry. More generally, I argue that aesthetic phenomena can play an important role in directing scientific research and that aesthetic theories can help understand such dynamics, such that they need to be considered in philosophy of science. (shrink)

We argue for an account of chemical reactivities as chancy propensities, in accordance with the ‘complex nexus of chance’ defended by one of us in the past. Reactivities are typically quantified as proportions, and an expression such as “A + B → C” does not entail that under the right conditions some given amounts of A and B react to give the mass of C that theoretically corresponds to the stoichiometry of the reaction. Instead, what is produced is a fraction (...) α < 1 of this theoretical amount, and the corresponding percentage is usually known as the yield, which expresses the relative preponderance of its reaction. This is then routinely tested in a laboratory against the observed actual yields for the different reactions. Thus, on our account, reactivities ambiguously refer to three quantities at once. They first refer to the underlying propensities effectively acting in the reaction mechanisms, which in ‘chemical chemistry’ (Schummer in Hyle 4:129–162, 1998) are commonly represented by means of Lewis structures. Besides, reactivities represent the probabilities that these propensities give rise to, for any amount of the reactants to combine as prescribed. This last notion is hence best understood as a single case chance and corresponds to a theoretical stoichiometric yield. Finally, reactivities represent the actual yields observed in experimental runs, which account for and provide the requisite evidence for/against both the mechanisms and single case chances ascribed. (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)

Charles S. Peirce's epistemological theory of mental diagrams forms the theoretical basis of his attempt to analyze diagrammatic reasoning. Two examples, one from science and another from art, are examined to test the scope of this theory. While the first example shows how scientific diagrams form part of translation processes, similar processes are demonstrated in how paintings are received. The article attempts to connect Peirce and A. J. Greimas's theory of narrative. Relating the two proves useful in allowing Peirce's theory (...) of the connection between the three normative sciences to be discussed on a new basis. (shrink)

Chemists do not aim at testing preconceptions or theoretical hypotheses only; they first and foremost produce and determine the object of chemical investigation: they learn through making. They never cease to create and stabilize heterogeneous devices, methods, models, and theories in order to act upon the world. Chemical bodies cannot be studied in isolation; their properties constitutively depend on what surrounds and acts upon them. Starting from the specificity of chemical practices, this paper investigates the meaning of consistency, inconsistency, and (...) that of the ceteris paribus clause, in this domain of science. In so doing, it defends the idea that studying what we call ‘a lack of consistency’ should always include the scrutiny of: the way a particular scientific practice is stabilized, and the ontological or pragmatic assumptions about the entities and processes upon which this practice revolves. (shrink)

We analyze the connections of Lavoisier system of nomenclature with Leibniz’s philosophy, pointing out to the resemblance between what we call Leibnizian and Lavoisian programs. We argue that Lavoisier’s contribution to chemistry is something more subtle, in so doing we show that the system of nomenclature leads to an algebraic system of chemical sets. We show how Döbereiner and Mendeleev were able to develop this algebraic system and to find new interesting properties for it. We pointed out the resemblances between (...) Leibniz program and Lavoisier legacy, particularly regarding the lingua philosophica for understanding and thinking Nature, in this particular case, chemistry. In the second part we discuss, from the linguistic viewpoint, how Lavoisian algebraic system may be taken further to build a language. We study the constituents of such a chemical language. Finally, we formalize some of the ideas here presented by using elements of network theory and discrete mathematics. (shrink)

The rich and ongoing debate about constructivism in chemistry education includes questions about the relationship, for better or worse, between applications of the theory in pedagogy and in epistemology. This paper presents an examination of the potential to use connections of epistemological and pedagogical constructivism to one another. It examines connections linked to the content, processes, and premises of science with a goal of prompting further research in these areas.

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)

This paper argues for the theoretical and practical validity of similarity as a useful epistemological tool in scientific knowledge generation, specifically in chemistry. Classical analyses of similarity in philosophy of science do not account for the concept’s practical significance in scientific activities. We recur to examples from chemistry to counter the claim of authors like Quine or Goodman to the effect that similarity must be excluded from scientific practices . In conclusion we argue that more recent conceptualizations of the notion (...) of similarity, particularly Giere’s one, are appropriate for a philosophical analysis that considers scientific practices on equal terms with scientific theory. (shrink)

Traditionally the study of chemical elements has been limited to well-known concepts like the periodic properties and chemical families. However, current information shows a new and rich language that allows us to observe relations in the elements that are not limited to their positions in the table. These relations are evident when reactions are represented through networks, as in the case of similar reactivity of organic compounds sharing functional groups. For the past two decades, it has been argued that network (...) reactions may be considered the core of chemistry. This network, which constitutes the basic set of chemical knowledge, provides the basis for classification and delivers routes to obtain new and known substances. In order to provide an example, we constructed and analyzed a network of chemical elements from the formation of stoichiometric binary compounds, providing to the chemistry, a formal structure of extracting the chemical knowledge. Thus, we explored all possible presence of relationships among elements. Concepts like degree centrality and centralization, the relationships among metals, semimetal and nonmetal classes, blocks, and chemical families were analyzed. We observed that the network structure had a small core set of elements of high reactivity and also a peripheral set of elements of low reactivity. The classes, blocks and families show the following increasing order of reactivity: nonmetals > semimetals > metals; p > s > d > f; and families: boron, carbon, pnictogens, chalcogens, halogens, lanthanoids > other families. This example shows, from the network perspective, that the elements and their classifications exhibit properties such as the reactivity, order, and similarity. (shrink)

Me circunscribo a la química, en cuanto ciencia empírica natural. Aquélla comprende el mundo como totalidad de fenómenos químicos y abstrae de estos los objetos químicos. Examino los confines de la química, entendidos como límites estructurales, cognitivos y a priori. Ahora bien, la investigación química se realiza en campos de experimentación observacional, donde interactúan el observador químico, el lenguaje científico de la química, los sensores químicos y los fenómenos químicos. Por lo tanto, examino los confines de cada uno de estos (...) factores. I restrict myself to Chemistry, as a natural empirical science. That one understands the world as a totality of chemical phenomena and it abstracts from these one the chemical objects. I examine the boundaries of Chemistry, as structural, cognitive and a priori limits. Now then, chemical research takes place as observation-experimentation fields, where chemical observer, scientific language of Chemistry, chemical sensors and phenomena interact. Therefore, I examine the boundaries of everyone of these factors. (shrink)

Philosophie ist konkret und abstrakt. Sie ist konkret im Gespür für Probleme, die jeden – oder jeden in einem bestimmten Bereich – betreffen. Sie ist abstrakt in der kritischen Formulierung und Lösung von Problemen, indem sie von besonderen Bedingungen und Voreingenommenheiten abstrahiert. Philosophie erfordert Kreativität, Phantasie und die Bereitschaft zu Unkonventionellem in der Wahl der Problemzugangsweisen. Wie alle Wissenschaften ist sie als Methode lehr- und entwickelbar, sofern ein gewisses Talent vorhanden ist. Philosophie beginnt dort, wo Wissenschaftler nicht mehr weiter fragen. (...) Was heute Philosophie ist, kann morgen Wissenschaft sein – Naturwissenschaft, Sozialwissenschaft oder Geisteswissenschaft –, Philosophie hat keine Vorlieben. (shrink)