The ‘triumph of the anti-phlogistians’ is a familiar story to the historians and philosophers of science who characterize the Chemical Revolution as a broad conceptual shift. The apparent “incommensurability” of the paradigms across the revolutionary divide has caused much anxiety. Chemists could identify phlogiston and oxygen, however, only with different sets of instrumental practices, theoretical schemes, and philosophical commitments. In addition, the substantive counterpart to phlogiston in the new chemistry was not oxygen, but caloric. By focusing on the changing (...) visions of chemical body across the revolutionary divide with a more sensitive probe into the historical actors’ material manipulations and linguistic usage, we can historicize their laboratory realities and philosophical agenda. An archeology of chemical bodies that configures the fragile stability of the material worlds chemists created in succession promises a philosophical horizon that would recognize our hybrid (natural–artificial) environment as an evolving investigative object of science. (shrink)

In the problem of the relationship between chemistry and physics, many authors take for granted the ontological reduction of the chemical world to the world of physics. The autonomy of chemistry is usually defended on the basis of the failure of epistemological reduction: not all chemical concepts and laws can be derived from the theoretical framework of physics. The main aim of this paper is to argue that this line of argumentation is not strong enough for eliminate the (...) idea of a hierarchical dependence of chemistry with respect to physics. The rejection of the secondary position of chemistry and the defense of the legitimacy of the philosophy of chemistry require a radically different philosophical perspective that denies not only epistemological reduction but also ontological reduction. Only on the basis of a philosophically grounded ontological pluralism it is possible to accept the ontological autonomy of the chemical world and, with this, to reverse the traditional idea of the ‘superiority’ of physics in the context of natural sciences. (shrink)

A chemical substance is instantiated in the material world by a number of quantities of such substance, placed in different locations. A change of location implies a change in the net of relationships entertained by the QCS with the region wherein it is found. This fact entails changes of the ontological status of the CS, as this is not fully determined by the inherent features of the CS and includes a relevant relational contribution. In order to demonstrate this thesis, (...) we have chosen to analyse the status of quantities of a same CS that are synchronically located in different spacetime regions: a synthetic lab, a lab where the QCS is turned into a material, an industrial plant, the market where the QCS gets a price and a dump waste where the QCS is discarded, respectively: Chemical substance Open image in new window material Open image in new window product Open image in new window goods Open image in new window wasteThe use of first-order predicate logic, mereology and locative logic allows carrying out a regimentation process that highlights the ontological commitments implied by the formal expressions through which each element of the aforementioned series can be described. The presence of relational properties discloses the systemic nature of the CS instantiated within a spacetime region. The implications of such an aspect are discussed. (shrink)

Although Boyle has been regarded as a champion of the seventeenth century Cartesian mechanical philosophy, I defend the position that Boyle’s views conciliate between a strictly mechanistic conception of fundamental matter and a non-reductionist conception of chemical qualities. In particular, I argue that this conciliation is evident in Boyle’s ontological distinction between fundamental corpuscles endowed with mechanistic properties and higher-level corpuscular concretions endowed with chemical properties. Some of these points have already been acknowledged by contemporary scholars, and I (...) actively engage with their ideas in this paper. However I attempt to contribute to the debate over Boyle’s mechanical philosophy by arguing that Boyle’s writings suggest an emergentist, albeit still mechanistic, notion of chemical properties. I contrast Boyle’s views against those of strict reductionist mechanical philosophers, focusing on the famous debate with Spinoza over the redintegration of niter, and argue that Boyle’s complex chemical ontology provides a more satisfactory understanding of chemical phenomena than is provided by a strictly reductionist and Cartesian mechanical philosophy. (shrink)

Quine, taking the molecular constitution of matter as a paradigmatic example, offers an account of the relation between theory confirmation and ontology. Elsewhere, he deploys a similar ontological methodology to argue for the existence of mathematical objects. Penelope Maddy considers the atomic/molecular theory in more historical detail. She argues that the actual ontological practices of science display a positivistic demand for “direct observation,” and that fulfillment of this demand allows us to distinguish molecules and other physical objects from mathematical (...) abstracta. However, the confirmation of the atomic/molecular theory and the development of scientists’ ontological attitudes towards atoms was more complicated and subtle than even Maddy supposes. The present paper argues that the history of the theory in fact supports neither Quine’s and Maddy’s accounts of scientific ontology. There was no general demand from scientists to “see” atoms before they were reckoned to be real; but neither did the indispensable appearance of atoms in the best theory of chemical combination suffice to convince scientists of their reality. (shrink)

This essay proposes to discuss the manner in which Jan Baptista van Helmont helped to transform the Neoplatonic notions of vital spirit and of ferment by giving these notions an unambiguously chemical interpretation, thereby influencing the eventual naturalization of these ideas in the work of late seventeenth century chymists. This chemical interpretation of vital spirit and ferment forms part of Helmont’s hybrid ontology, which fuses a corpuscular conception of minima naturalia with a non-corporeal conception of semina rerum. (...) For Helmont, chemical alterations involve the minima as physical units but also depend upon ferments that are contained in the semina, which function as formative spiritual agents. Helmont’s nuanced ontology ultimately contributes to the development of modern corpuscularian theory by explaining many chemical reactions in fundamentally corpuscular terms, as the addition and subtraction of particles. (shrink)

In his book, 'History as a Science and the System of the Sciences', Thomas Seebohm articulates the view that history can serve to mediate between the sciences of explanation and the sciences of interpretation, that is, between the natural sciences and the human sciences. Among other things, Seebohm analyzes history from a phenomenological perspective to reveal the material foundations of the historical human sciences in the lifeworld. As a preliminary to his analyses, Seebohm examines the formal and material presuppositions of (...) phenomenological epistemology, as well as the emergence of the human sciences and the traditional distinctions and divisions that are made between the natural and the human sciences. -/- As part of this examination, Seebohm devotes a section to discussing Husserl’s formal mereology because he understands that a reflective analysis of the foundations of the historical sciences requires a reflective analysis of the objects of the historical sciences, that is, of concrete organic wholes (i.e., social groups) and of their parts. Seebohm concludes that Husserl’s mereological ontology needs to be altered with regard to the historical sciences because the relations between organic wholes and their parts are not summative relations. Seebohm’s conclusion is relevant for the issue of the reducibility of organic wholes such as social groups to their parts and for the issue of the reducibility of the historical sciences to the lower-order sciences, that is, to the sciences concerned with lower-order ontologies. -/- In this paper, I propose to extend Seebohm’s conclusion to the ontology of chemical wholes as object of quantum chemistry and to argue that Husserl’s formal mereology is descriptively inadequate for this regional ontology as well. This may seem surprising at first, since the objects studied by quantum chemists are not organic wholes. However, my discussion of atoms and molecules as they are understood in quantum chemistry will show that Husserl’s classical summative and extensional mereology does not accurately capture the relations between chemical wholes and their parts. This conclusion is relevant for the question of the reducibility of chemical wholes to their parts and of the reducibility of chemistry to physics, issues that have been of central importance within the philosophy of chemistry for the past several decades. (shrink)

Following Kripke and Putnam, the received view of chemical kinds has been a microstructuralist one. To be a microstructuralist about chemical kinds is to think that membership in said kinds is conferred by microstructural properties. Recently, the received microstructuralist view has been elaborated and defended, but it has also been attacked on the basis of complexities, both chemical and ontological. Here, I look at which complexities really challenge the microstructuralist view; at how the view itself might be (...) made more complicated in order to accommodate such challenges; and finally, at what this increasingly complicated picture implies for our standard assessment of chemical kindhood—primarily, for the widespread assumption that chemical kinds in general are more neat and tidy than those messy biological ones. _1_ The Received View _2_ A Taxonomy of Chemical Kinds _3_ Atomic Number _4_ H2O, H3O+, OH−, and More _5_ Complicating the Microstructuralist Picture _6_ Concrete and Other Mixtures _7_ Macromolecules, Especially Proteins _8_ Abandoning Sameness of Elemental Composition _9_ Not So Different after All. (shrink)

Given the rich diversity of research fields usually ascribed to chemistry in a broad sense, the present paper tries to dig our characteristic parts of chemistry that can be conceptually distinguished from interdisciplinary, applied, and specialized subfields of chemistry, and that may be called chemistry in a very narrow sense, or 'the chemical core of chemistry'. Unlike historical, ontological, and 'anti-reductive' approaches, I use a conceptual approach together with some methodological implications that allow to develop step by step a (...) kind of cognitive architecture for chemistry, which basically contains: (1) systematic chemical knowledge on the experimental level; (2) clarification of chemical species; (3) chemical classification systems; (4) theoretical foundation through the chemical theory of structural formulas. In a succeeding paper the results will be checked for resisting physicalistic reduction. (shrink)

This book examines the way in which Robert Boyle seeks to accommodate his complex chemical philosophy within the framework of a mechanistic theory of matter. More specifically, the book proposes that Boyle regards chemical qualities as properties that emerged from the mechanistic structure of chymical atoms. Within Boyle’s chemical ontology, chymical atoms are structured concretions of particles that Boyle regards as chemically elementary entities, that is, as chemical wholes that resist experimental analysis. Although this interpretation (...) of Boyle’s chemical philosophy has already been suggested by other Boyle scholars, the present book provides a sustained philosophical argument to demonstrate that, for Boyle, chemical properties are dispositional, relational, emergent, and supervenient properties. This argument is strengthened by a detailed mereological analysis of Boylean chymical atoms that establishes the kind of theory of wholes and parts that is most consistent with an emergentist conception of chemical properties. The emergentist position that is being attributed to Boyle supports his view that chemical reactions resist direct explanation in terms of the mechanistic properties of fundamental particles, as well as his position regarding the scientific autonomy of chymistry from mechanics and physics. (shrink)

In this paper, I explore a seldom-recognized connection between the ontology of abstract objects and a current issue in the philosophy of chemistry. Specifically, I argue that realism with regard to universals implies a view of chemical elements similar to F.A. Paneth’s thesis about the dual nature of the concept of element.

The debate between ontological reductionists and emergentists in chemistry has revolved around quantum mechanics. What Franklin and Seifert (BJPS 2020) add to the long-running dispute is an attention to the measurement problem. They contend that all three realist interpretations of the quantum formalism capable of resolving the measurement problem also obviate any need for chemical emergence. I push their argument further, arguing that the realist interpretations of quantum mechanics actually subvert the basis for reduction as well, by undercutting the (...) idea that fundamental physical particles are actual parts of molecules. With both reduction and traditional synchronic emergence pictures ruled out, the only option for realists about quantum chemistry is strong Thomistic emergence. (shrink)

Some philosophers have claimed that kinds can be construed as mereologically complex structural properties. This essay examines several strategies aimed at construing a certain class of natural kinds, namely isomeric chemical kinds, in accordance with this view. In particular, the essay examines views which posit structural proper parts in addition to micro-constitutive parts to individuate isomeric chemical kinds. It then goes on to argue that the phenomenon of chirality in stereochemistry gives the proponent of kinds-as-complex-properties evidence for positing (...) the existence of causal-cum-dispositional individuating proper parts, in addition to structural parts, for chemical enantiomeric kinds. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic (...) expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

In the characterization of the ArCl2 'van der Waals complex', a recognizable pattern of well-defined peaks is observed in the microwave absorption spectrum. In the control of chaos in a chemical oscillatory reaction the power spectrum progressively becomes simpler, at length yielding a single peak. Since both of these cases generate coherences that are centers of agency, they should be considered to produce new chemical entities. Applicability of this ontological approach to coherences of wider societal interest is suggested.

In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all such isomers yield precisely (...) the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment. Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei. (shrink)

Combinations of molecules, of biological individuals, or of chemical processes can produce effects that are not simply attributable to the constituents. Such non-redundant causality warrants recognition of those coherences as ontologically significant whenever that efficacy is relevant. With respect to such interaction, the effective coherence is more real than are the components. This ontological view is a variety of structural realism and is also a kind of process philosophy. The designation ‘process structural realism’ (PSR) seems appropriate.

The sixteenth and seventeenth centuries marks a period of transition between the vitalistic ontology that had dominated Renaissance natural philosophy and the Early Modern mechanistic paradigm endorsed by, among others, the Cartesians and Newtonians. This paper will focus on how the tensions between vitalism and mechanism played themselves out in the context of sixteenth and seventeenth century chemistry and chemical philosophy, particularly in the works of Paracelsus, Jan Baptista Van Helmont, Robert Fludd, and Robert Boyle. Rather than argue (...) that these natural philosophers each embraced either fully vitalistic or fully mechanistic ontologies, I hope to demonstrate that these thinkers adhered to complicated and nuanced ontologies that cannot be described in either purely vitalistic or purely mechanistic terms. A central feature of my argument is the claim that a corpuscularian theory of matter does not entail a strictly mechanistic and reductionistic account of chemical properties. I also argue that what marks the shift from pre-modern vitalistic chemical philosophy to the modern chemical philosophy that marked the Chemical Revolution is not the victory of mechanism and reductionism in chemistry but, rather, the shift to a physicalistic and naturalistic account of chemical properties and vital spirits. (shrink)

A novel non-classical mereological concept built up by blending the Metaphysics of Xavier Zubiri and the Quantum Theory of Atoms in Molecules of R. F. W. Bader is proposed. It is argued that this philosophical concept is necessary to properly account for what happens in a chemical reaction. From the topology of the gradient of the laplacian of the electronic charge density, \\) within the QTAIM framework, different “atomic graphs” are found for each atom depending on the molecular context, (...) reflecting how the whole molecule affects each atom. In this way, the whole molecular system imposes certain geometry onto each atom, and every atom exhibits different ontological modality. On the Metaphysical side, for X. Zubiri real things are system of different notes. The physical essence is the subsystem of essential notes with a coherence unity. Every note is grounded on the essence. The unity of the system is present somehow in every note-of beforehand, and every essential note-of turns towards the other. The essence determines the position of each note within the system, and hence is the grounding for modality of the notes. By conflating both “theories” and taking the atoms as essential notes, we propose the concept of “Molecule in atoms-of” or “atoms-of in Molecules”. Within the course of a chemical reaction the atoms-of modified their “of” as required by the new molecular unity being formed, and eventually change their modality. The validity to the Zubiri’s statements, is attained by evaluating necessity and possibility in a set-up of finite accessible “possible worlds”. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry (...) ontology that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

This paper defends an ontology of weak entity realism for homeostatic property cluster (HPC) theories of natural kinds, adapted from Bird’s (Synthese 195(4):1397–1426, 2018) taxonomy of such theories. Weak entity realism about HPC kinds accepts the existence of natural kinds. Weak entity realism denies two theses: that (1) HPC kinds have mind-independent essences, and that (2) HPC kinds reduce to entities, such as complex universals, posited only by metaphysical theories. Strong entity realism accepts (1) and (2), whereas moderate entity (...) realism accepts only (1). Given its commitment to (2), strong entity realism is more theoretically complex than weak entity realism, with little explanatory payoff. Given their commitment to (1), moderate and strong entity realisms cannot explain how the identity conditions of HPC kinds are to be straightforwardly knowable. I argue that weak entity realism avoids such epistemic difficulties. I further rebut two plausible criticisms of weak entity realism, namely that weak entity realism cannot account for quantification over kinds, and that weak entity realism cannot provide identity conditions for HPC kinds which are both scientifically useful and objective. Given the theoretical costs of strong and moderate entity realism, and weak entity realism’s adequate response to its most plausible challenges, weak entity realism about HPCs is to be preferred, especially for biological and chemical kinds. (shrink)

This paper establishes that Robert Boyle’s complex chemical ontology implies a non-reductionistic conception of chemical qualities and, more specifically, a conception of chemical qualities as being dispositional and relational. Though Peter Anstey has already shown that that Boyle considered sensible qualities to be dispositional and relational, this moves beyond Anstey’s work by extending his arguments to chemical properties. These arguments are, however, merely a first step in establishing a non-reductionistic interpretation of Boyle’s chemical (...) class='Hi'>ontology. A further argument will show that Boyle regards chemical and other higher-level properties as being emergent and supervenient properties. These arguments are supported by substantial textual evidence from Boyle’s writings, which show that he clearly conceived of chemical substances as functional wholes whose properties emerge not only from the microstructural ordering of their parts but also from their relationship with other chemical substances within the context of experimental practice. (shrink)

The "hard problem" of today's consciousness studies is subjective experience: understanding why some brain processing is accompanied by an experienced inner life. Recent scientific advances offer insights for understanding the physiological and chemical phenomenology of consciousness. But by leaving aside the internal experiential nature of consciousness in favor of mapping neural activity, such science leaves many questions unanswered. In Ontology of Consciousness, scholars from a range of disciplines -- from neurophysiology to parapsychology, from mathematics to anthropology and indigenous (...) non-Western modes of thought -- go beyond these limits of current neuroscience research to explore insights offered by other intellectual approaches to consciousness. These scholars focus their attention on such philosophical approaches to consciousness as Tibetan Tantric Buddhism, North American Indian insights, pre-Columbian Mesoamerican civilization, and the Byzantine Empire. Some draw on artifacts and ethnographic data to make their point. Others translate cultural concepts of consciousness into modern scientific language using models and mathematical mappings. Many consider individual experiences of sentience and existence, as seen in African communalism, Hindi psychology, Zen Buddhism, Indian vibhuti phenomena, existentialism, philosophical realism, and modern psychiatry. Some reveal current views and conundrums in neurobiology to comprehend sentient intellection. Contributors: Karim Akerma, Matthijs Cornelissen, Antoine Courban, Mario Crocco, Christian de Quincey, Thomas B. Fowler, Erlendur Haraldsson, David. J. Hufford, Pavel B. Ivanov, Heinz Kimmerle, Stanley Krippner, Armand J. Labbé, James Maffie, Hubert Markl, Graham Parkes, Michael Polemis, E Richard Sorenson, Mircea Steriade, Thomas Szasz, Mariela Szirko, Robert A.F. Thurman, Edith L.B. Turner, Julia Watkin, Helmut Wautischer. (shrink)

The 16th and 17th centuries marked a period of transition from the vitalistic ontology that had dominated Renaissance natural philosophy to the Early Modern mechanistic paradigm endorsed by, among others, the Cartesians and Newtonians. This paper focuses on how the tensions between vitalism and mechanism played themselves out in the context of 16th and 17th century chemistry and chemical philosophy. The paper argues that, within the fields of chemistry and chemical philosophy, the significant transition that culminated in (...) the 18th century Chemical Revolution was not a transition from vitalism to full-blown mechanism. Rather, chemical philosophy shifted from a vitalistic theory of matter and spirits to a naturalistic, physicalistic, and corpuscularian conception of chemical properties and reactions. Despite being naturalistic, physicalistic, and corpuscularian, however, this theory was not fully mechanistic. Special attention is paid to the contributions made by Paracelsus, Sebastien Basso, Jan Baptista van Helmont, and Robert Boyle to this ontological transition. (shrink)

While temporal considerations are of prime importance for chemical reactions, as well as for molecular stability, most chemical concepts are not explicitly formulated on a diachronic basis. It will be argued here that a formulation explicitly incorporating temporal and epistemological considerations enables us to treat chemical reactions and chemical substances on ontologically equivalent terms, instead of assigning a more fundamental status to the latter. After all, in collision theory, a chemical substance is just a collision (...) complex that takes too long. How long qualifies as “too long”, and “too long” in relation to what, are crucial questions that distinguish chemical substances from chemical reactions, and reversible reactions from irreversible ones, thereby introducing anthropocentric considerations into these distinctions. Too long for a lab chemist is very different from too long for an astrochemist studying chemical reactions between chemical substances in inter-stellar space on cosmological timescales. Examining several physical and chemical properties on the basis of which chemical substances are distinguished from one another, the role of temporal and anthropocentric considerations in defining molecular properties is emphasized. I conclude with some observations on the much-debated reduction of chemistry to other disciplines, arguing that such reduction depends on our aesthetic choices as to what kinds of observations demand explanation, and what kinds of explanation are acceptable. (shrink)

The concept of fields available in physics will be considered for application to unravel the mysteries of form, structure and function of human consciousness and mind. The sameness of functions of human consciousness and mind in language acquisition and communication and also acquiring knowledge of various kinds and its will be discussed. In the light of this the limitations of concepts of pure physics and modern physics probes will be discussed. -/- The information and ideas available in the Upanishads in (...) the form of Brahmajnaana will be applied to understand the physical nature of human consciousness and mind and their functions. This information and translation into modern and cognitive scientific terms would be correlated with brainwaves concept of modern physiology. The physiochemical, physical and chemical natures of experiences, purport, meanings, ideas, thoughts and expressions will be presented based on Upanishadic insight thus acquired. The advantage of this alternative probe, method and model to understand the functions of human consciousness and mind will be demonstrated. -/- This model of human consciousness and mental functions is also correlated to brain wave EEG frequency changes. -/- . (shrink)

The problem raised in the article is actualized not by the artificial attachment of the topic of ecology to the existential problems of humankind, but by the urgent need to conceptualize the dangers of a growing gap between the further development of civilization and ignoring the primary nature of its existence, the analysis of modern specific dangers of wildlife, flora and fauna, catastrophic climatic phenomena, desertification, and chemical pollution of the land. The posed problem of the conceptualization of wild (...) nature logically continues the intention of the authors to turn to the human-dimensional characteristics of the entire natural environment. At the level of socio-philosophical analysis, the meaning of a new model of relations between society and nature is revealed, and alternative concepts of nature protection to modern practices are comprehended. The importance of wildlife in its narrowed (terrestrial) space for social development on the established ideological principles of the most careful attitudes to wildlife, taking into account the reverse dangerous impact of the destructible habitat on humanity, has been proved. (shrink)

The widespread mistrust of metaphysics-the main obstacle to the unification of physics and philosophy-is based on the myth that metaphysical claims cannot be falsified or verified, because they are supposedly true independently of empirical knowledge. This is not true of metaphysical naturalism, whose approach is to critically reflect on the theories and findings of all the empirical disciplines and abstract from them a theory about such general features of reality that no single empirical discipline can be the authority on. Causation (...) is such a feature, since its instances include anything from planetary motions to particle interactions, chemical reactions, biological functions, and closing a door. Consequently, a general account of causation is beyond any particular empirical discipline. Metaphysical naturalism takes a meta-perspective on the results of the empirical sciences and attempts to figure out how it fits together in a coherent whole, e.g. by offering a general account of causation. General accounts of this kind are falsifiable in so far as the theories are falsifiable from which they are generalizations. The paper also discusses some fundamental metaphysical principles implicitly assumed by the sciences generally, and why they imply that unification is methodologically virtuous. (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)

One of several important issues that inform contemporary philosophy of chemistry is the issue of structural explanation, precisely because modern chemistry is primarily concerned with microstructure. This paper argues that concern over microstructure, albeit understood differently than it is today, also informs the chemical philosophy of Robert Boyle. According to Boyle, the specific microstructure of ‘chymical atoms’, understood in geometric terms, accounts for the unique essential properties of different chemical substances. Because he considers the microstructure of ‘chymical atoms’ (...) as semi-permanent, Boyle considers these stable entities as operationally irreducible, even if they are not ontologically fundamental. While it is generally believed that our contemporary concern over structural explanation is a function of modern chemistry’s emphasis on microstructure, this discussion of structural explanation in Boyle will serve as a case study to illustrate the manner in which many of our contemporary concerns have deeply historical origins and the manner in which the history of chemistry can substantively inform issues in contemporary philosophy of chemistry. (shrink)

One of several important issues that inform contemporary philosophy of chemistry is the issue of structural explanation, precisely because modern chemistry is primarily concerned with microstructure. This paper argues that concern over microstructure, albeit understood differently than it is today, also informs the chemical philosophy of Robert Boyle (1627–1691). According to Boyle, the specific microstructure of ‘chymical atoms’, understood in geometric terms, accounts for the unique essential properties of different chemical substances. Because he considers the microstructure of ‘chymical (...) atoms’ as semi-permanent, Boyle considers these stable entities as operationally irreducible, even if they are not ontologically fundamental. While it is generally believed that our contemporary concern over structural explanation is a function of modern chemistry’s emphasis on microstructure, this discussion of structural explanation in Boyle will serve as a case study to illustrate the manner in which many of our contemporary concerns have deeply historical origins and the manner in which the history of chemistry can substantively inform issues in contemporary philosophy of chemistry. (shrink)

This paper examines whether classical extensional mereology is adequate for formalizing the whole–parts relation in quantum chemical systems. Although other philosophers have argued that classical extensional and summative mereology does not adequately formalize whole–parts relation within organic wholes and social wholes, such critiques often assume that summative mereology is appropriate for formalizing the whole–parts relation in inorganic wholes such as atoms and molecules. However, my discussion of atoms and molecules as they are conceptualized in quantum chemistry will establish that (...) standard mereology cannot adequately fulfill this task, since the properties and behavior of such wholes are context-dependent and cannot simply be reduced to the summative properties of their parts. To the extent that philosophers of chemistry have called for the development of an alternative mereology for quantum chemical systems, this paper ends by proposing behavioral mereology as a promising step in that direction. According to behavioral mereology, considerations of what constitutes a part of a whole is dependent upon the observable behavior displayed by these entities. Thus, relationality and context-dependence are stipulated from the outset and this makes behavioral mereology particularly well-suited as a mereology of quantum chemical wholes. The question of which mereology is appropriate for formalizing the whole–parts relation in quantum chemical systems is relevant to contemporary philosophy of chemistry, since this issue is related to the more general questions of the reducibility of chemical wholes to their parts and of the reducibility of chemistry to physics, which have been of central importance within the philosophy of chemistry for several decades. More generally, this paper puts contemporary discussions of mereology within the philosophy of chemistry into a broader historical and philosophical context. In doing so, this paper also bridges the gap between formal mereology, conceived as a branch of formal ontology, and “applied” mereology, conceived as a branch of philosophy of science. (shrink)

In this article I examine several related views expressed by Robin Hendry concerning molecular structure, emergence and chemical bonding. There is a long-standing problem in the philosophy of chemistry arising from the fact that molecular structure cannot be strictly derived from quantum mechanics. Two or more compounds which share a molecular formula, but which differ with respect to their structures, have identical Hamiltonian operators within the quantum mechanical formalism. As a consequence, the properties of all such isomers yield precisely (...) the same calculated quantities such as their energies, dipole moments etc. The only means through which the difference between the isomers can be recovered is to build their structures into the quantum mechanical calculations, something that is carried out by the application of the Born-Oppenheimer approximation. Consequently, it has been argued by many authors that molecular structure is written in ‘by hand’ rather than derived. Robin Hendry is one such author, but he goes a great deal further by proposing that this situation implies the existence of emergence and downward causation. In the current article I argue that there are alternative explanations which render emergence and downward causation redundant. Such an alternative lies in the notion of quantum decoherence and the appeal to work in the foundations of physics, which posits that the various isomers exist as a superposition until their wavefunctions are collapsed either by observation or by interacting with their environment.Hendry also alludes to a debate among chemists as to whether chemical bonds are real or not, in the sense of directional connections between two or more nuclei in any given molecule. I reject this view and propose that the structural and energetic views of chemical bonding, that have been discussed by some philosophers of chemistry including Hendry, do not refer to any essential ontological differences. I agree that chemists view bonding in a more realistic fashion and may consider bonds to be in some senses real, while physicists may consider bonding in more abstract energetic terms. However, I do not believe that such differences in scientific practice and attitudes should be considered to offer a window as to the ontological status of bonding or whether bonding is real. Finally, I discuss the kinetic energy school of chemical bonding which would seem to challenge any notion of bonds as directional entities, since bonding is no longer regarded as being primarily due to the build-up of electron density between nuclei. (shrink)

An Aristotelian philosophy of nature offers an alternative to reduction for the conception of the inter-theoretical relationships between molecular chemistry and quantum mechanics. A basic ingredient for such an approach is an ontology of fundamental causal powers, and this work aims to develop such an ontology by drawing on quantum-chemical entities, particularly, the electron density. This notion is central to the Quantum Theory of Atoms in Molecules, a theory of molecular structure developed by Richard F. W. Bader, (...) which describes molecules and atoms in terms precisely of the electron density. Then, by identifying a philosophical tension in Bader’s discourse about the nature of electron density, the work will analyze this central notion in terms of the categorical/dispositional distinction regarding properties. The central idea is that electron density can be conceived as categorical and dispositional at once, and this very characterization can avoid Bader’s philosophical tension. (shrink)

This essay critically considers the issue of natural kind essentialism. More specifically, the essay critically probes the philosophical use of chemical examples to support realism about natural kinds. My simple contention is that the natural kind debate can be understood in terms of two different cultures of academic production. These two cultures will be conceptualized using Thomas Kasulis’s distinction between intimacy and integrity as cultural orientations. Acknowledging Kasulis’s contention that, “What is foreground in one culture may be background in (...) another”, it may very well be the case that philosophers writing about chemistry place chemical practice in the background, thereby adopting the orientation of integrity. Chemists and philosophers of chemistry, on the other hand, place chemical practice at the foreground of their work, thereby adopting the orientation of intimacy. Because the intimacy orientation is grounded in chemical practice, it is preferable to the integrity orientation. Understanding the natural kinds debate from this perspective highlights the fact that the misuse of chemical examples by certain philosophers is informed by an orientation of detachment from actual chemical practice. This underscores the importance of an intimate understanding of chemical practice when deploying chemical examples in the context of philosophical discussions about ontology and metaphysics. (shrink)

There are several ontological and consequently also methodological mistakes in contemporary mainstream economics. Among them, the so-called ergodic axiom is play significant role. It is understandable that the real economy elaborated as formalized mental model looks like dynamic system on first sight. However, that is right only of dynamical systems in mathematical formalism. Economy that is in our understanding societal and/or collective economy is complex evolving organism. If we imagine such organism in the form of dynamical system that is as (...) clear mathematical formalism, we are losing their crucial authentic character. The significant irredeemable attribute of societal economy is lying in his complex evolving network process character created by large population of people with different decision-making and complex realizing among them. Going from these imaginations the two entities in a question that is dynamical system with their ergodicity and societal economic organism as complex evolving network are qualitative very different ones. That is the reason why we cannot accede with endeavours to draw on living economy straitjacket of ergodic axiom. To articulate that cause by other words ergodic dynamical systems are applicable for physical and partly for chemical entities and only scarcely are fit for living organisms. On the other hand however, as clear method the ergodic dynamical system have good applying for didactical approaches in economics where helping in better understanding some types of complexities in dynamics. The purpose of that essay is to discuss problems around usability of ergodic dynamical system theory and methods in economics in the age of advanced ICT knowledge based society. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

Reductionism remains the dominant philosophical framework of modern science. Within reductionism, the universe is conceived as a probabilistic and deterministic system guided solely by the laws of physics and mathematics. Under the guidance of reductionist thought, the development of the modern atomic theory and quantum mechanics has drastically changed science, medicine, and philosophy. In particular, the standard model of particle physics remains the crowning achievement of over three hundred years of reductionist thought in both physics and chemistry. Yet developments within (...) chemistry suggest a new paradigm is required to overcome the limitations of reductionism and provide chemists a more fruitful model. This article will argue that a version of relational ontology provides an avenue for elucidating and predicting chemical and atomic phenomena. In relational ontology, the ontological status of an enduring entity in any moment is viewed as a composite of its own inherited properties and the influences of other entities, especially those closely related to it within a system. This view encompasses the causal aspects of the world without denying its dynamic and creative nature while providing a richer understanding of chemistry and other scientific fields. (shrink)

resumo: Este artigo pretende mostrar que sem a influência de uma filosofia construtivista que eu denomino boa, representada principalmente por Bruno Latour, a elucidação das substâncias químicas teria sido virtualmente impossível. Sem a noção de materiais “artefatuais” cunhada por eles, a Química Moderna seria impensável a partir dos metaparadigmas em uso no campo atual da história e da filosofia da ciência. A tese central que defendo aqui é a de que o construtivismo, tal como definido pelos antropológos da ciência, é (...) uma maneira disfarçada de colocar a histórica filosofia materialista na trilha da discussão histórica e filosófica das ciências e tecnologias e que isso restaura o papel desempenhado pelos materiais usados pelos cientistas para que sejam exatamente o que são. abstract: This paper aims to show that without the influence of a constructivist philosophy I call good, mainly represented by Bruno Latour, the ontological elucidation of the chemical substances would have been virtually impossible. Without the notion of artifactual materials given by them, would be Modern Chemistry unthinkable from the metaparadigms in use in the present field of history and philosophy of science. The central thesis I defended here is that constructivism as defined by the anthropologists of science is a disguised way of sliding historical materialist philosophy into the mainline of philosophical and historical discussion of the sciences and technologies and that those restore the role played by the materials used by sciences to be exactly what they are. (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)

On November 28, 2009, as part of events marking the twenty-fifth anniversary of the disaster at the Union Carbide plant in Bhopal, gas survivors protested the contents of the report prepared by government scientists that mocked their complaints about contamination. The survivors shifted from the scientific document to a mediated lunch invitation performance, purporting to serve the same chemicals as food that the report had categorized as having no toxic effects. I argue that the lunch spread, consisting of soil and (...) water from the pesticide plant, explicitly front-staged and highlighted the survivor’s forced intimate relationship with such chemicals, in order to reshape public perception of risks from toxins. Chemical matter like sevin tar and naphthol tar bound politicians, scientists, corporations, affected communities, and activists together, as these stakeholders debated the potential effects of toxic substances. This gave rise to an issue-based “chemical public.” Borrowing from such theoretical concepts as “ontologically heterogeneous publics” and “agential realism,” I track the existing and emerging publics related to the disaster and the campaigns led by the International Campaign for Justice in Bhopal advocacy group. (shrink)

It is often assumed that chemistry was a typical positivistic science as long as chemists used atomic and molecular models as mere fictions and denied any concern with their real existence. Even when they use notions such as molecular orbitals chemists do not reify them and often claim that they are mere models or instrumental artefacts. However a glimpse on the history of chemistry in the longue durée suggests that such denials of the ontological status of chemical entities do (...) not testify for any specific allegiance of chemists to positivism. Rather it suggests that the dilemma positivism vs realism is inappropriate for characterizing the ontology of chemistry. This alternative shaped at the turn of the twentieth century in the context of controversies about atomic physics does not take into account the major concern of chemists, i.e. making up things. Only by considering what matters for chemists, their matters of concern rather than their matter theories, can we expect to get an insight on their ontological assumptions. The argumentation based on historical data is twofold. Generating new substances out of initial ingredients which is the raison d’être of chemistry raised a vexing puzzle which has been alternatively solved with the Aristotelian notion of mixt and the Lavoisieran notion of compound. I will argue that an essential tension remains intrinsic in chemistry between the two conceptual frameworks. But how are we to make sense of the long tradition of ontological non-commitment in chemistry? I argue that what is usually considered as a denial of the existence of the basic units of matter is better characterized as a focus on more important actors on the chemical stage. (shrink)

This paper approaches the problem of the ontology of the photographic image ‘post-digitalization’ historically, via a conception of photography as the historical totality of photographic forms. It argues, first, that photography is not best understood as a particular art or medium, but rather in terms of the form of the image it produces; second, that the photographic image is the main social form of the digital image ; and third, that there is no fundamental ontological distinction regarding indexicality between (...) photographically generated digital images and those of chemically based photography. ‘The anxiety about the real’ produced by digital imagery has its origins elsewhere, in the ontological peculiarities of the social form of value in societies based on relations of exchange. Distinguishing between the ‘event of capture’ and the ‘event of visualization’, it is argued that it is in its potential for an infinite multiplication of visualizations that the distinctiveness of the digital image lies. In the digital image, the infinite possibilities for social exchange generated by the abstraction of value from use finds an equivalent visual form. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, (...) and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

The main goal of this article is to use the epistemological framework of a specific version of Cognitive Constructivism to address Piaget’s central problem of knowledge construction, namely, the re-equilibration of cognitive structures. The distinctive objective character of this constructivist framework is supported by formal inference methods of Bayesian statistics, and is based on Heinz von Foerster’s fundamental metaphor of objects as tokens for eigen-solutions. This epistemological perspective is illustrated using some episodes in the history of chemistry concerning the definition (...) or identification of chemical elements. Some of von Foerster’s epistemological imperatives provide general guidelines of development and argumentation. (shrink)

Does chemistry reduce to physics? If this means ‘Can we derive the laws of chemistry from the laws of physics?’, recent discussions suggest that the answer is ‘no’. But sup posing that kind of reduction—‘epistemological reduction’—to be impossible, the thesis of ontological reduction may still be true: that chemical properties are determined by more fundamental properties. However, even this thesis is threatened by some objections to the physicalist programme in the philosophy of mind, objections that generalize to the (...) class='Hi'>chemical case. Two objections are discussed: that physicalism is vacuous, and that nothing grounds the asymmetry of dependence which reductionism requires. Although it might seem rather surprising that the philosophy of chemistry is affected by shock waves from debates in the philosophy of mind, these objections show that there is an argumentative gap between, on the one hand, the theoretical connection linking chemical properties with properties at the sub-atomic level, and, on the other, the philosophical thesis of ontological reduction. The aim of this paper is to identify the missing premises (among them a theory of physical possibility) that would bridge this gap. Introduction: missing elements and the mystery of discreteness The refutation of physicalism A combinatorial theory of physical possibilia Combinatorialism and the Bohr model Objections The missing premises and a disanalogy with mind. (shrink)

Ellis argues that certain essential properties of objects in the world not only determine the nature of these objects but also how they will behave in any situation. In this paper I will critique Ellis's essentialism from the perspective of the philosophy of chemistry, arguing that our current knowledge of chemistry in fact does not lend itself to essentialist interpretations and that this seriously undercuts Ellis's project. In particular I will criticize two key distinctions Ellis draws between internal vs. external (...) properties and essential vs. accidental properties, showing that at the chemical level such distinctions are insupportable. If essential properties only exist at the level of sub-atomic physics, then Ellis's hopes that essentialism will provide a theoretical basis for a philosophy of chemistry are at best hopes for a very distant future, since the argument that chemical structure and dynamics can be explained at the quantum level derived is purely from analogy to much simpler systems than those chemists actually study. This suggests that we have very little scientific evidence that scientific essentialism is a viable ontology. †To contact the author, please write to: Department of Philosophy, University of Notre Dame, Notre Dame, IN 46556; e-mail: [email protected]. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is (...) linked to multiple clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)