Ontology, chemistry

Responses to this further question appear to fall into two camps. One prominent metaphysician believes that the question needs to be approached independently of any theories of chemistry and of physics. Robin Le Poidevin has published an extensive article in which he argues in favor of the ontological reduction of chemistry to physics. He does this through what he has termed a combinatorial approach. 

Le Poidevin writes that because the thesis of ontological reduction is about properties, we do have to have a clear conception of what is to count as a chemical property. He then takes the identity of an element, as defined by its position in a periodic ordering, and its associated macroscopic properties to be paradigmatically chemical properties. About these properties we can be unapologetic realists. He also claims that a periodic ordering is a classification rather than a theory, so this conception of chemical properties is as theory-neutral as it can be.v He believes that the question of the ontological reduction of chemistry is the question of whether these paradigmatically chemical properties reduce to more fundamental properties. He then adds,... 

Finally there is a somewhat general objection to the use of combinatorialism in order to ground the ontological reduction of chemistry. Surely the assumption of that fundamental entities combine together to form macroscopic chemical entities ensures from the start that the hoped for asymmetry is present. But it seems to do so in a circular manner. If one assumes that macroscopic chemical entities like elements are comprised of sub-atomic particles then of course it follows that the reverse is not true. The hoped for asymmetry appears to have been written directly into the account, or so it would seem. 

Finally, there are computable properties tliat do not correspond to physical observables. One may legitimately ask about tlie utility of such ontologically indefensible constructs However, one should note that unmeasurable properties long predate computational chemistry - some examples include bond order, aromaticity, reaction concertedness, and isoelec-tronic, -steric, and -lobal behavior. These properties involve conceptual models that have proven sufficiently useful in furthering chemical understanding that they have overcome objections to their not being uniquely defined. 

A. J. Rocke, Convention versus ontology in nineteenth century organic chemistry , in ref. 2, pp. 1-20. 

G. W. Wheland, Theory of Resonance and Its Application to Organic Chemistry (New York J. Wiley and Sons London Chapman and Hall, 1944). The Pauling-Wheland controversy on the ontological status of resonance is described in the contribution of K. Gavroglu and A. Simoes in this volume. 

In this paper we discuss a number of issues which manifest the theoretical particularity of quantum chemistry and which are usually not discussed in an explicit manner either in the historical or in the philosophical studies related to quantum chemistry. We shall focus on five issues the re-thinking of the problem of reductionism, the discourse of quantum chemistry as a confluence of the traditions of physics, chemistry, and mathematics, the role of textbooks in consolidating this discourse, the ontological status of resonance, and the more general problem of the status of the chemical bond. Finally, we shall briefly discuss the impact of large scale computing. 

Textbooks in general are - necessarily - a-historical and only in a very few instances do we find a mention and, in even fewer cases, a discussion of some of the disputes in a discipline s early history. Interestingly, the early textbooks of quantum chemistry could also be read as polemic or partisan texts by proposing and arguing in favor of particular (ontological) hypotheses and approximation methods, each one of them adopts a particular viewpoint on how to answer the question of whether quantum chemistry is an application or use of quantum mechanics for chemical problems. 

In this chapter we shall first describe RDF and OWL, the grammar of the Semantic Web, and then move on to identifiers, the vocabulary of the Semantic Web, and ontologies, which represent the real-world knowledge required to make use of the grammar and vocabulary. We will concentrate on practical chemistry- and biochemistry-orientated deployments of Semantic Web technology rather than the computer science behind it. Then we will cover some case studies Web services, databases, and semantic publishing in the forms of Semantic Eye and RSC Project Prospect. We will briefly cover what the Semantic Web has to offer for experimental data before finishing up with some possible future directions. 

It is worth mentioning that ontologies describe types of things, rather than things you would find in the universe, which are instances of the types. A building ontology would have entries for detached house, apartment, and shed, rather than 23 Acacia Avenue, Framley. For chemistry, a type would be water, and its instance would be a particular molecule of water in the sea or in a cup of coffee. 

Chemistry is some way behind the biomedical sciences in standardization of research protocols. The MIBBI (Minimum Information for Biological and Biomedical Investigations) Project (MIBBI Consortium 2008) aims to bring the various Minimum Information protocols for different sorts of biomedical experiments into line with one another and oversees over a dozen protocols. The mapping of the protocols themselves to stable Semantic Web identifiers is achieved through an ontology. 

The chemistry community, understandably, failed to respond at all, even though Bohmian mechanics probably holds the key to the development of a theory of chemistry, soundly based on quantum theory and relativity. The problem with molecular structure is resolved by the ontological interpretation of quantum-mechanical orbital angular momentum and the key to chemical reactivity and reaction mechanism is provided by the quantum potential function. 

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