L'ontologie d'entreprise établit une distinction claire entre le niveau de données, le niveau d'information et le niveau essentiel des transactions blockchain et des contrats intelligents. La méthodologie OntoClean analyse des ontologies basées sur des propriétés formelles, indépendantes des domaines (méta-propriétés), constituant la première tentative de formalisation des concepts d'analyse ontologique pour des systèmes informatiques. Les notions sont extraites de l'ontologie philosophique. DOI: 10.13140/RG.2.2.12557.49120 .

Some scientific categories seem to correspond to genuine features of the world and are indispensable for successful science in some domain; in short, they are natural kinds. This book gives a general account of what it is to be a natural kind and puts the account to work illuminating numerous specific examples.

The paper looks at the semantics and ontology of dispositions in the light of recent work on the subject. Objections to the simple conditionals apparently entailed by disposition statements are met by replacing them with so-called 'reduction sentences' and some implications of this are explored. The usual distinction between categorical and dispositional properties is criticised and the relation between dispositions and their bases examined. Applying this discussion to two typical cases leads to the conclusion that fragility is not a real (...) property and that, while both temperature and its bases are, this does not generate any problem of overdetermination. (shrink)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices (...) in modeling, some of which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories (...) identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

Ontologies are being used by information scientists in order to facilitate the sharing of meaningful information. However, computational ontologies are problematic in that they often decontextualize information. The semantic content of information is dependent upon the context in which it exists and the experience through which it emerges. For true semantic interoperability to occur among diverse information systems, within or across domains, information must remain contextualized. In order to bring more context to computational ontologies, we introduce culture (...) as an essential concept for information science. Culture helps to focus our attention on and make meaning of relevant extrapersonal structures and their qualities and dimensions that comprise the context and background of the world. In our approach, culture is integral to the study of semantics and, consequently, the study of ontologies and information technologies. The meaning we make of entities and phenomena in the world is always shaped by our cultural experience. If we understand culture as the emergent interplay of intrapersonal cognitive structures and extrapersonal structures of the world, then the notion of cognitive and cultural schemas becomes essential to understanding ontology and the ways in which we might achieve authentic semantic interoperability among diverse information systems. We explore the nature of ontologies and reconceptualize them as cultural schemas. Our proposal is an alternative to the historical path from philosophical ontology to computational ontologies as one that adheres primarily to the notion of ontology as a categorization and classification system. The obvious implication for ontology as categorization is that there is a single objective world that exists and that it can be described as entirely separate from the person observing it. We draw upon Heidegger’s examination of ontology to ground ontology in a phenomenological perspective, enabling it to remain flexible and adaptable and to accommodate context. (shrink)

The paper points out that the modern formulation of Bohm’s quantum theory known as Bohmian mechanics is committed only to particles’ positions and a law of motion. We explain how this view can avoid the open questions that the traditional view faces according to which Bohm’s theory is committed to a wave-function that is a physical entity over and above the particles, although it is defined on configuration space instead of three-dimensional space. We then enquire into the status of the (...) law of motion, elaborating on how the main philosophical options to ground a law of motion, namely Humeanism and dispositionalism, can be applied to Bohmian mechanics. In conclusion, we sketch out how these options apply to primitive ontology approaches to quantum mechanics in general. (shrink)

This paper motivates taking seriously the possibility that brains are basically protean: that they make use of neural structures in inventive, on-the-fly improvisations to suit circumstance and context. Accordingly, we should not always expect cognition to divide into functionally stable neural parts and pieces. We begin by reviewing recent work in cognitive ontology that highlights the inadequacy of traditional neuroscientific approaches when it comes to divining the function and structure of cognition. Cathy J. Price and Karl J. Friston, and Colin (...) Klein identify the limitations of relying on forward and reverse inferences to cast light on the relation between cognitive functions and neural structures. There is reason to prefer Klein’s approach to that of Price and Friston’s. But Klein’s approach is neurocentric - it assumes that we ought to look solely at neural contexts to fix cognitive ontology. Using recent work on mindreading as a case study, we motivate adopting a radically different approach to cognitive ontology. Promoting the Protean Brain Hypothesis, we posit the possibility that we may need to look beyond the brain when deciding which functions are being performed in acts of cognition and in understanding how the brain contributes to such acts by adapting to circumstance. (shrink)

When we ask what natural kinds are, there are two different things we might have in mind. The first, which I’ll call the taxonomy question, is what distinguishes a category which is a natural kind from an arbitrary class. The second, which I’ll call the ontology question, is what manner of stuff there is that realizes the category. Many philosophers have systematically conflated the two questions. The confusion is exhibited both by essentialists and by philosophers who pose their accounts in (...) terms of similarity. It also leads to misreading philosophers who do make the distinction. Distinguishing the questions allows for a more subtle understanding of both natural kinds and their underlying metaphysics. (shrink)

Humans think and communicate in very flexible and schematic ways, and a Spatial Data Infrastructure (SDI) for the Amazon and associated information system ontologies should reflect this flexibility and the adaptive nature of human cognition in order to achieve semantic interoperability. In this paper I offer a conceptual investigation of SDI and explore the nature of cultural schemas as expressions of indigenous ontologies and the challenges of semantic interoperability across cultures. Cultural schemas are, in essence, our ontologies, (...) but they are markedly different than classical formal ontologies. They shape our ontological commitments to what exists in the world as well as the ways in which we approach and engage the world. And while they help structure our understanding of the world in which we are embedded, they are associative and flexible. They help to focus our attention to particular details of our experiences and give them salience, yet they cannot be simply reduced to a series of extracted features. They allow us to make meaning of the contextualized, cultural experience in which we are always immersed. An SDI is a shared social-technological-informational structure that, if it is to be useful and successful for sustainability in the Amazon, must incorporate and use indigenous cultural schemas. Indigenous communities must have the ability to contribute to the collection of geospatial data and their contributions recognized as legitimate forms of knowledge. In order for the SDI to work, it must recognize the larger cultural landscape to which cultural schemas can connect to the ready-to-hand elements of salient cultural experiences. (shrink)

The conspicuous similarities between interpretive strategies in classical statistical mechanics and in quantum mechanics may be grounded on their employment of common implementations of probability. The objective probabilities which represent the underlying stochasticity of these theories can be naturally associated with three of their common formal features: initial conditions, dynamics, and observables. Various well-known interpretations of the two theories line up with particular choices among these three ways of implementing probability. This perspective has significant application to debates on primitive ontology (...) and to the quantum measurement problem. (shrink)

Some philosophers understand natural kinds to be the categories which are constraints on enquiry. In order to elaborate the metaphysics appropriate to such an account, I consider the complicated history of scurvy, citrus, and vitamin C. It may be tempting to understand these categories in a shallow way (as mere property clusters) or in a deep way (as fundamental properties). Neither approach is adequate, and the case instead calls for middle-range ontology: starting from categories which we identify in the world (...) and elaborating their structure, but not pretending to jump ahead to a complete story about fundamental being. (shrink)

N.T. Wright has offered Christian philosophers a proposal where it is apparently possible to hold the belief in the intermediate state-resurrection of the body and an ontological holism in the same sense at the same time. I argue that this not only creates a basic contradiction in Wright’s ontological paradigm, but also it is not a coherent and tenable proposal despite the fact one might eventually find a potential solution to such a quandary.

In this paper I will address the specifics of Peirce’s concept of qualia. Peirce is the first philosopher to ever use the term qualia as philosophical, but his understanding of it differs considerably from the contemporary philosophy of mind. There are certain tendencies to present Peirce in this regard as a forerunner of contemporary debates. Although such an interpretation is not unfounded, I believe that it does not do full justice to the significance of the concept for Peirce’s thought. I (...) will try to elucidate its importance with an adequate web of synonyms, that is, the other important concepts in Peirce’s philosophy. The main idea of the paper is that Peirce’s concept of qualia is not a technical term meant to tackle a finite group of problems within an already accepted ontology, but one of the concepts that Peirce uses to build his ontology. (shrink)

Dombrowski and Murdoch offer versions of the ontological argument which aim to avoid two types of objection – those concerned with the nature of the divine, and those concerned with the move from an abstract concept to a mind-independent reality. For both, the nature of the concept of God/Good entails its instantiation, and both supply a supporting argument from experience. It is only Murdoch who successfully negotiates the transition from an abstract concept to the instantiation of that concept, however, and (...) this is achieved by means of an ontological argument from moral experience which, in a reversal of the Kantian doctrine, depends ultimately on a form of the cosmological argument. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Upon what philosophical foundation are semantic network graphs based? Does this foundation allow for the legitimization of other semantic networks and ontological diversity? How can we design our computational and informational systems to accommodate this ontological diversity and the variety of semantic networks? Are semantic networks segmentations of larger semantic landscapes? This paper explores semantic networks from a Heideggerian existentialist and phenomenological perspective. The analysis presented uses cultural schema theory to bridge the syntactic and lexical elements to the semantic and (...) conceptual dimensions of semantic network graphs and offers reasons why the viability of such graphs as they are currently constructed are insufficient for creating semantic interoperability for our informationtechnologies. Reconceptualizing semantic networks as cultural landscapes offers us. (shrink)

The axiological tenet of scientific realism, “science seeks true theories,” is generally taken to rest on a corollary epistemological tenet, “we can justifiably believe that our successful theories achieve (or approximate) that aim.” While important debates have centered on, and have led to the refinement of, the epistemological tenet, the axiological tenet has suffered from neglect. I offer what I consider to be needed refinements to the axiological postulate. After showing an intimate relation between the refined postulate and ten theoretical (...) desiderata, I argue that the axiological postulate does not depend on its epistemological counterpart; epistemic humility can accompany us in the quest for truth. Upon contrasting my axiological postulate against the two dominant non-realist alternatives and the standard realist postulate, I contend that its explanatory and justificatory virtues render it, among the axiologies considered, the richest account of the scientific enterprise. (shrink)

Concerning abortion and infanticide, ethics has always seen to each one as quite puzzling an issue. The dilemma expectedly goes like this: “Are they morally good, permissible or acceptable, or are they not?” All three major approaches in ethics, viz. virtue ethics, deontology and consequentialism, have fervently exerted themselves in order to settle both. A virtue ethicist is expected to approach the issue wondering: “Is performing abortion and infanticide indicative of virtues, to wit of character traits that the virtuous agent (...) possesses?” A deontologist would bring the dilemma up for discussion asking: “Is conducting abortion and infanticide in accordance with some moral rule or principle?” To an act utilitarian, on the other hand, the same question would strike as: “Do abortion and infanticide promote the best consequences, to wit those in which happiness is maximized?” All three approaches have been applied to the subject matter ever since the classic era, sadly with no remarkable success and, most of the times, even without the slightest suspicion of the promised rigor. (shrink)

Many philosophers are impressed by the progress achieved by physical sciences. This has had an especially deep effect on their ontological views: it has made many of them physicalists. Physicalists believe that everything is physical: more precisely, that all entities, properties, relations, and facts are those which are studied by physics or other physical sciences. They may not all agree with the spirit of Rutherford's quoted remark that 'there is physics; and there is stamp-collecting',' but they all grant physical science (...) a unique ontological authority: the authority to tell us what there is. Physicalism is now almost orthodox in much philosophy, notably in much recent philosophy of mind. But although often invoked, it is rarely explicitly defined. It should be. The claim that everything is physical is not as clear as it seems. In this paper, we examine a number of proposed definitions of physicalism and reasons for being a physicalist. We will argue both that physicalism lacks a clear and credible definition, and that in no non-vacuous interpretation is it true. We are concerned here only with physicalism as a doctrine about the empirical world. In particular, it should not be confused with nominalism, the doctrine that there are no universals.2 Nominalism and physicalism are quite independent doctrines. Believers in universals may as consistently assert as deny that the only properties and relations are those studied by physical science. And nominalists may with equal consistency assert or deny that physical science could provide enough predicates to describe the world. That is the question which concerns physicalists, not whether physical predicates name real universals. (We will for brevity write as if they do, but we do not need that assumption.). (shrink)

Reportedly ever since Pythagoras, but possibly much earlier, humans have been concerned about the way non human animals (henceforward “animals” for convenience) should be treated. By late antiquity all main traditions with regard to this issue had already been established and consolidated, and were only slightly modified during the centuries that followed. Until the nineteenth century philosophers tended to focus primarily on the ontological status of animals, to wit on whether – and to what degree – animals are actually rational (...) beings; accordingly they allowed – or denied – them some kind of moral standing. This modus operandi was for the first time seriously questioned by Jeremy Bentham, who put the issue on a different track. If the question, as Bentham suggested, is not if animals can think or speak, but if they can suffer1, then it seems plausible that moral agents ought to abstain from inflicting unnecessary suffering on animals; in other words, humans might have at least one – even limited – moral duty towards animals. And if this, in turn, is true, then animals should arguably be allowed the commensurate moral right, namely the right not to be inflicted unnecessary pain. Then, if animals possess this right, they could probably possess others, as well. This is how grosso modo the issue of animal rights became a pivotal part of the discussion concerning animal ethics. Bentham himself, of course, wouldn’t have gone that far; to him even the idea of human rights sounded like “simple… rhetorical nonsense upon stilts”.2 It was mostly due to his views, however, that the debate was moved from the way things actually are to the way things should ideally be – thus merging into what, in my view, should always have been: one primarily concerning ethics. (shrink)

Part of a book symposium on Anjan Chakravartty's Scientific ontology: integrating naturalized metaphysics and voluntarist epistemology (Oxford University Press, 2017).

The accepted narrative treats John Stuart Mill’s Kinds as the historical prototype for our natural kinds, but Mill actually employs two separate notions: Kinds and natural groups. Considering these, along with the accounts of Mill’s nineteenth-century interlocutors, forces us to recognize two distinct questions. First, what marks a natural kind as worthy of inclusion in taxonomy? Second, what exists in the world that makes a category meet that criterion? Mill’s two notions offer separate answers to the two questions: natural groups (...) for taxonomy and Kinds for ontology. This distinction is ignored in many contemporary debates about natural kinds and is obscured by the standard narrative that treats our natural kinds just as a development of Mill’s Kinds. (shrink)

The Homeostatic Property Cluster (HPC) account of natural kinds has become popular since it was proposed by Richard Boyd in the late 1980s. Although it is often taken as a defining natural kinds as such, it is easy enough to see that something's being a natural kind is neither necessary nor sufficient for its being an HPC. This paper argues that it is better not to understand HPCs as defining what it is to be a natural kind but instead as (...) providing the ontological realization of (some) natural kinds. (shrink)

Mario Bunge’s Causality and Modern Science is arguably one of the best treatments of the causal realist tradition ever to have been written, one that defends the place of causality as a category in the conceptual framework of modern science. And yet in the current revival of causal realism in contemporary metaphysics, there is very little awareness of Bunge’s work. This paper seeks to remedy this, by highlighting one particular criticism Bunge levels at the Aristotelian view of causation and illustrating (...) its relevance for contemporary powers-based accounts. Roughly, the Aristotelian view depicts interactions between objects as involving a unidirectional exertion of influence of one object upon another. This idea of unidirectional action is central to the Aristotelian distinction between active and passive powers, and its corresponding distinction between active and passive objects. As Bunge points out, modern physics does not recognise the existence of any unidirectional actions at all; all influence comes in the form of reciprocal action, or interaction. If this is right, all notions deriving from or influenced by the idea of unidirectional actions—such as the concept of mutual manifestation and reciprocal disposition partners—risk being false by the same measure. Bunge drew the conclusion that the Aristotelian view is ontologically inadequate, but still advocated its use as the most useful approximation available in science. He considered, but ultimately rejected the possibility of a modified view of causation built on reciprocal action, because, in his view, it couldn’t account for the productivity of causation. Bunge’s critique of this particular aspect of the Aristotelian view cannot be overlooked in contemporary metaphysics, but it is possible to construe a modified view of causation that takes the reciprocity of interactions seriously without loss of productivity. (shrink)

Prima facie it would seem that the traditional scholastic debates about entia rationis (“beings of reason”) may be easily brought into dialogue with debates about nonexistent objects in contemporary analytical metaphysics. It turns out, however, that the scholastic debates about beings of reason are placed within a very different ontological framework or paradigm, so that bringing scholastic and analytical authors into common discussion about this topic is not trivial. In this paper I make the first step toward establishing such discussion (...) by describing the ontological framework presupposed by the scholastic debates about beings of reason, and by identifying the roles that beings of reason were supposed to play in it. (shrink)

Spinoza’s attitude toward nonhuman animals is uncharacteristically cruel. This essay elaborates upon this ostensible idiosyncrasy in reference to Hasana Sharp’s commendable desire to revitalize a basis for animal ethics from within the bounds of his system. Despite our favoring an ethics beginning from animal affect, this essay argues that an animal ethic adequate to the demands of our historical moment cannot be developed from within the confines of strict adherence to Spinoza’s system—and this is not yet to speak of a (...) more robust animal ethics which would advocate actual care and compassion for the animals themselves. We argue that on the assumption of Spinoza’s ontological biocentrism, in the presence of Spinozist determinism and the absence of an axiological biocentrism, an anthropocentric axiology necessarily follows. Any Spinozist animal ethic must fall back, therefore, upon appeals to the maximization of human pleasure and power; hence Spinoza’s ruthless injunction to “use (the animals) at our pleasure.” These are the very ontological and ethical assumptions which have incited human self-exaltation in the modern period, in pursuit of power and pleasure even despite the destructive long-term consequences for all the living. We suggest that an adequate animal ethic would require either an abandonment of Spinoza’s ontological biocentrism or the adoption of an axiological biocentrism. (shrink)

Many philosophers are impressed by the progress achieved by physical sciences. This has had an especially deep effect on their ontological views: it has made many of them physicalists. Physicalists believe that everything is physical: more precisely, that all entities, properties, relations and facts are those which are studied by physics or other physical sciences...

Jag tror att det är ett misstag att kräva av humanvetenskaperna (d.v.s. humaniora, samhälls- och beteendevetenskaperna) att de imiterar naturvetenskapernas forskningsmetodik. Humanvetenskaperna studerar meningsfulla fenomen vilkas natur är på ett grundläggande sätt annorlunda än de blott fysiska fenomen som naturvetenskapen studerar. Den största skillnaden är att meningsfulla fenomen inte uppenbarligen är lagbundna på samma sätt som fysiska fenomen och uppvisar därför inte samma regelbundenhet och förutsägbarhet som fysiska fenomen. För att studera meningsfulla fenomen krävs därför andra forskningsmetoder. Trots att humanvetenskaperna (...) studerar fenomen som inte är lagbundna och är på ett visst sätt subjektiva, så vill jag mena att de studerar objektivt verkliga fenomen och kan få giltig kunskap om dem. Att subjektiva fenomen också kan vara objektivt verkliga kan låta märkligt för vissa läsare, varför jag rundar av med en diskussion om vad det egentligen innebär för något att vara objektivt verkligt. Enligt den definition jag föreslår så framstår att meningsfulla fenomen, också de som kallas ”sociala konstruktioner”, kan förstås som objektivt verkliga företeelser trots att de på ett betydelsefullt sätt också är subjektiva. (shrink)

Philosophers of mind commonly draw a distinction between the personal level – the distinctive realm of conscious experience and reasoned deliberation – and the subpersonal level, the domain of mindless mechanism and brute cause and effect. Moreover, they tend to view cognitive science through the lens of this distinction. Facts about the personal level are given a priori, by introspection, or by common sense; the job of cognitive science is merely to investigate the mechanistic basis of these facts. I argue (...) that this view misrepresents the structure of cognitive-scientific enquiry. Taken at face value, cognitive science makes no commitment to the existence of a distinctive level at which persons or selves appear. Thus, in the age of cognitive science, we should not expect to find the self in an ontologically distinct realm. Instead, we should expect to locate it in cognitive-scientific models themselves. In closing, I indicate likely results of this approach. (shrink)

Cover songs are a familiar feature of contemporary popular music. Musicians describe their own performances as covers, and audiences use the category to organize their listening and appreciation. However, until now philosophers have not had much to say about them. This book explores how to think about covers, appreciating covers, and the metaphysics of covers and songs. Along the way, it explores a range of issues raised by covers, from the question of what precisely constitutes a cover, to the history (...) and taxonomy of the category, the various relationships that hold between songs, performances, and tracks, and the appreciation and evaluation of covers. (shrink)

Phenomenology, as propounded by Edmond Husserl, is an important movements in the modern western philosophy, while sÅÙkhya and its application yoga are the ancient Indian philosophical disciplines or dar±ana. This is a comparative study of phenomenology with sÅÙkhya and yoga. As per my present understanding this project is now completed. I have organized the outcome of my study in the following four papers preceded by prolegomena: Prolegomena to the comparative study of Phenomenology and SaÙkhya 1, Consciousness in Phenomenology and SÅÙkhya (...) 2. ‘Nature’ (ontology) in Phenomenology and SÅÙkhya 3. Structures (cosmology) in Phenomenology and SÅÙkhya 4. ‘Terminal Transcendental Teleological Cause’ in Phenomenology and SÅÙkhya -/- The parallelism between the philosophical disciplines, so far removed historically, geographically and culturally from each other, which this study brought out, was not only fascinating but also extensive. Certain differences also have been critically brought out. Viewing phenomenology through the grid of sÅÙkhya, I found, elucidates phenomenology. In being viewed from the perspective of a philosophical school, as modern as that of phenomenology, the ancient Indian disciplines also stand to benefit. The comparative study can hope to introduce sÅÙkhya to those acquainted with phenomenology and vice versa. This presentation is an attempt to share the flavor of my findings. (shrink)

Classical Greek philosophy in its struggle to grasp the material world from its very beginning has been marked by the – sometimes undercurrent, some others overt and even intense, but never idle – juxtaposition between the mind and the senses, logos and perception or, if the anachronism is allowed, between realism and idealism. Parmenides is reportedly the first philosopher to insistently assert that thought and being are the same by his famous aphorism τὸ γὰρ αὐτὸ νοεῖν ἐστί τε καὶ εἶναι, (...) and that the “way of truth”, as opposed to the “way of opinion”, only runs through the intellect, since the truth is unattainable by the illusory senses. Thus, true may be only what our intellect can firmly grasp, and – by an easy, though not equally sound step – vice versa: that which our intellect can firmly grasp is necessarily true. In this paper I intend to set off Parmenides’ apparent influence on Anselm with regard to the latter’s celebrated ontological argument concerning the existence of God, and the influence of both on Spinoza’s Ethica, which is founded on the key tenet that not only does God necessarily exist – since God is intellectually conceivable –, but that God also by necessity is an utterly good one. (shrink)

In this paper, I explore and defend the idea that musical works are historical individuals. Guy Rohrbaugh (2003) proposes this for works of art in general. Julian Dodd (2007) objects that the whole idea is outré metaphysics, that it is too far beyond the pale to be taken seriously. Their disagreement could be seen as a skirmish in the broader war between revisionists and reactionaries, a conflict about which of metaphysics and art should trump the other when there is a (...) conflict. That dispute is a matter of philosophical methodology as much as it is a dispute about art. I argue that the ontology of works as individuals need not be dunked in that morass. My primary strategy is to show, contra Dodd's accusation, that historical individuals are familiar parts of the world. Although the ontological details are open to debate, it is the standard opinion of biologists is that biological species are historical individuals. So there is no conflict here between fidelity to art and respectable metaphysics. What suits species will fit musical work as well. (shrink)

The most habitual and common use of the term natural corresponds to that which is – or could be – property of our experience, irrespective of whether that experience is mental or physical, viz. whatever can be known, perceived, determined and categorized by human mind, after it has bumped into and passed through the channels of our senses. The cooperation between our intellectual and sensual capabilities in relation to the usurpation of what is considered to be “natural”, is extremely crucial (...) for us to presume something as such, even if we are not familiar with – or sympathetic to – the duality of the Kantian Theory of Knowledge. That is inasmuch as the human mind, to be specific, is characterized by the intrinsic ability to conceive and contemplate on beings or events, which anything but belong to the natural order of things, beings such as Pegasus or the Valkyries, for instance, and counterfactual realities like the Purgatory or the Valhalla. (shrink)

What makes some acts morally right and others morally wrong? Traditionally, philosophers have thought that in order to answer this question we must find and formulate exceptionless moral principles—principles that capture all and only morally right actions. Utilitarianism and Kantianism are paradigmatic examples of such attempts. In recent years, however, there has been a growing interest in a novel approach—Particularism—although its precise content is still a matter of controversy. In this paper I develop and motivate a new formulation of particularism (...) as a research program and I show that my formulation is not vulnerable to the most common objections to particularism. Moreover, I argue that the particularist research program shows enough promise to warrant further exploration. (shrink)

Daniel Dennett (1996) has disputed David Chalmers' (1995) assertion that there is a "hard problem of consciousness" worth solving in the philosophy of mind. In this paper I defend Chalmers against Dennett on this point: I argue that there is a hard problem of consciousness, that it is distinct in kind from the so-called easy problems, and that it is vital for the sake of honest and productive research in the cognitive sciences to be clear about the difference. But I (...) have my own rebuke for Chalmers on the point of explanation. Chalmers (1995, 1996) proposes to "solve" the hard problem of consciousness by positing qualia as fundamental features of the universe, alongside such ontological basics as mass and space-time. But this is an inadequate solution: to posit, I will urge, is not to explain. To bolster this view, I borrow from an account of explanation by which it must provide "epistemic satisfaction" to be considered successful (Rowlands, 2001; Campbell, 2009), and show that Chalmers' proposal fails on this account. I conclude that research in the science of consciousness cannot move forward without greater conceptual clarity in the field. (shrink)

This paper sets mathematics among the sciences, despite not being empirical, because it studies relations of various sorts, like the sciences. Each empirical science studies the relations among objects, which relations determining which science. The mathematical science studies relations as such, regardless of what those relations may be or be among, how relations themselves are related. This places it at the extreme among the sciences with no objects of its own (A Subject with no Object, by J.P. Burgess and G. (...) Rosen). Examples are discussed. The historical development of written mathematics from algorithms on clay tablets to theorems with proofs is said to show that application of algorithms to specific problems and theorems to scientific objects is like allegorical interpretation. Mathematics fits into the modern scientific context because the sciences, beginning with Galileo, have been constructed in imitation of mathematics. Viewing mathematics this way does not solve any ontological problems, but it does show how mathematics avoids them. Epistemological problems, insuperable for object realism, are simplified. For example, we have access to relations among any objects that we can consider objectively, first physical objects and then mathematical objects of greater and greater abstraction. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of (...) protein research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The psychiatric diagnostic system, as exemplified by the DSM, is a pseudo-scientific framework for diagnosing sick Cartesian isolated minds. As such, it completely overlooks the exquisite context sensitivity and radical context dependence of human emotional life and of all forms of emotional disturbance. In Descartes’s vision, the mind is a “thinking thing,” ontologically decontextualized, fundamentally separated from its world. Heidegger’s existential phenomenology mended this Cartesian subject-object split, unveiling our Being as always already contextualized, a Being-in-the-world. Here I offer a critique (...) of studies in “phenomenological psychopathology” that presuppose the validity of the psychiatric diagnostic system and leave it unchallenged. In this vein, I contend that all emotional disturbances are constituted in an indissoluble context of human interrelatedness. Specifically, I claim that all emotional disturbances, including those objectified by the DSM, take form in relational contexts of severe emotional trauma. There are no psychiatric entities, only devastating contexts. Additionally, I show that Heidegger’s analyses of Angst, world-collapse, uncanniness, and thrownness into Being-toward-death provide extraordinary philosophical tools for grasping the existential significance of such contexts of emotional trauma. Applying Heidegger’s concept of authenticity, I suggest that emotional health entails an ease of passage—i.e., an absence of dissociation—between the world of trauma and the world of everydayness. (shrink)

The Fifth Element (1997) is a French science-fiction film in English, directed and co-written by Luc Besson. The title and the plot of the film refer to a central notion of Greek philosophy, that is, pemptousia, or quintessence. Pre-Socratic philosophers such as Thales, Anaxagoras, Anaximenes and others, were convinced that all natural beings – in fact, nature itself – consist in four primary imperishable elements or essences (ousiai), i.e., fire, earth, water, and air. To these four, Aristotle added aether, a (...) fifth essence (pemptousia). The introduction of aether gave birth to a great tradition in late Antique and Medieval philosophy, and eventually it came to signify not an additional primary element, but the core-essence of all beings, their fundamental ontological structure. Besson’s film draws its inspiration on this philosophical tradition but its cinematographic rendering of the concept of Quintessence is typical of the contemporaneous views on the core characteristics of matters. The modernity that stimulates the film is equally anti-transcendentalist and anti-essentialist. Thus, the fifth element of the film is existentially personified and genderized making the traditional philosophical significance of the term to be adjusted by modernity in an immanent and temporal context where in addition aesthetics plays a crucial role. (shrink)

Action can only be spontaneous and impulsive if not guided by contemplation; contemplation, on the other hand, may only be luxurious playfulness if not either purposed - or suitable - to motivate action. This volume seeks to prove what may seem self-evident to common sense, but adhering to common sense is never pointless nor excessive. Next to this, Thinking in Action is the offspring of friendship, respect and commitment between two academic communities, the Hellenic and the Serbian philosophical communities, that (...) admittedly have a lot in common, especially with regard to philosophy, and hopefully as many differences as needed in order to secure a long-lasting and fertile exchange of ideas; it is also the natural-born child of necessity: philosophy is about argumentation, debate and confrontation. Thinking in Action inaugurates Hellenic-Serbian Philosophical Dialogue Series that entertains no hesitation in being as ambitious as any philosophical series could be: it seeks to establish a permanent, wide and rich channel of fruitful philosophical interaction between the two philosophical communities. Having high aspirations is one thing; meeting these aspirations as well as the expectations of the reader is a totally different one. We wish Thinking in Action, the first volume of the Hellenic-Serbian Philosophical Dialogue Series, apart from being the initial step of a long journey, will also be a fascinating one to the reader. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these (...) goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

The ontological paradigms of Schelling and the late Merleau-Ponty bear striking resemblances to Spinoza’s ontology. Both were developed in response to transcendental models of a Cartesian mold, resisting tendencies to exalt the human ego to the neglect or the detriment of the more-than-human world. As such, thinkers with environmental concerns have sought to derive favorable ethical prescriptions on their basis. We begin by discerning a deadlock between two such thinkers: Ted Toadvine and Sean McGrath. With ecological responsibility in mind, both (...) actually resist Spinozist reduction of the human being to the status of a mere mode among modes. But despite having the same general aim, they end up endorsing contrary practical conclusions. Our objective is to pinpoint the reasons behind this deadlock, indicative of two strands of post-Spinozist environmental thought which stand in tension, and to begin to propose an integrative way forward. The ethical weight afforded by Toadvine to the notion of resistance in the work of the late Merleau-Ponty, namely nature’s resistance to harmonizing, unifying pretensions, invites inquiry into two Merleau-Pontean notions he does not address: the barbarian principle, and the proposal to “Do a Psychoanalysis of Nature.” We trace these to their origins in the works of Schelling’s middle period, arguing that the Schellingian location of resistance in Spirit’s dark ground—alternately conceived as primordial Dionysiac madness, bottled-up within the substratum of consciousness—lends to an understanding of the human, and human responsibility, that harbors favorable implications for environmental ethics. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates (...) to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated (...) the development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (...) (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

The in­ten­tion of this pa­per is to po­int out a tr­o­u­ble­so­me si­tu­a­tion in con­tem­po­rary Ser­bian on­to­lo­gi­cal ter­mi­no­logy, and al­so to in­di­ca­te the ways and pre-con­di­ti­ons in terms of hi­story of phi­lo­sophy, hi­story of lan­gu­a­ge and met­ho­do­logy in se­ar­ching for pos­si­ble so­lu­ti­ons. We are al­so trying to cast so­me light on the pr­o­blem of re­la­ti­on­ship bet­we­en lan­gu­a­ge and phi­lo­sop­hi­cal thin­king.