Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist (...) and (b) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...) an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies. (shrink)

There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for classifying what the data are about. Unfortunately, such approaches (...) do not yield sustainable results where we are dealing with widely distributed, highly heterogeneous and often changing bodies of data. We argue here that the needed integration requires the use of what we call an lntegrating Semantic Framework (ISF), which provldes a consistent set of categories and relationships that can be reused over and over again to tag successive bodies of data in ways which foster more coherent representation and reasoning. (shrink)

What are words? What makes two token words tokens of the same word-type? Are words abstract entities, or are they (merely) collections of tokens? The ontology of words tries to provide answers to these, and related questions. This article provides an overview of some of the most prominent views proposed in the literature, with a particular focus on the debate between type-realist, nominalist, and eliminativist ontologies of words.

In this paper I wish to connect the recent debate in the philosophy of quantum mechanics concerning the nature of the wave function to the historical debate in the philosophy of science regarding the tenability of scientific realism. Being realist about quantum mechanics is particularly challenging when focusing on the wave function. According to the wave function ontology approach, the wave function is a concrete physical entity. In contrast, according to an alternative viewpoint, namely the primitive ontology approach, the (...) wave function does not represent physical entities. In this paper, I argue that the primitive ontology approach can naturally be interpreted as an instance of the so-called ‘explanationism’ realism, which has been proposed as a response to the pessimistic-meta induction argument against scientific realism. If my arguments are sound, then one could conclude that: (1) contrarily to what is commonly though, if explanationism realism is a good response to the pessimistic-meta induction argument, it can be straightforwardly extended also to the quantum domain; (2) the primitive ontology approach is in better shape than the wave function ontology approach in resisting the pessimistic-meta induction argument against scientific realism. (shrink)

This essay focuses on realism in ontology and on the problem of defining reality. According to the definition given by many realists, reality is independent of our thoughts, conceptual schemes, linguistic practices, etc. Yet, this merely negative definition of reality has some disadvantages: it implies a dualistic view, and it is incompatible with scientific realism. As an alternative, I introduce and discuss the traditional definition of reality as effectiveness, or capability of acting. I then attempt to determine to (...) what extent this definition can be helpful in the debate concerning ontological realism. (shrink)

If there is something (P) that every possible agent is committed to value, and certain actions or attitudes either enhance or diminish P, then normative claims about a range of intentional actions can be objectively and non-trivially evaluated. I argue that the degree of existence as an agent depends on the consistency of reflexive-relating with other individuals of the agent-kind: the ontological thesis. I then show that in intending to act on a reason, every agent is rationally committed to (...) value ‘above all else’ being an agent, what consists in exercising the capacity to act and having the freedom to discriminate between more or less valuable actions: the transcendental thesis. Since the degree of possession of this personal but non-contingent good depends on relating to other agents in a special way, certain actions and attitudes may be objectively right or wrong for all agents. (shrink)

The essay argues that while there is no general agreement on whether moral realism is true, there is general agreement on at least some of the moral obligations that we have if moral realism is true. Given that moral realism might be true, and given that we know some of the things we ought to do if it is true, we have a reason to do those things. Furthermore, this reason is itself an objective moral reason. Thus, (...) if moral realism might be true, then it is true. (shrink)

This essay explores the possibility of constructing a structural realist interpretation of spacetime theories that can resolve the ontological debate between substantivalists and relationists. Drawing on various structuralist approaches in the philosophy of mathematics, as well as on the theoretical complexities of general relativity, our investigation will reveal that a structuralist approach can be beneficial to the spacetime theorist as a means of deflating some of the ontological disputes regarding similarly structured spacetimes.

In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best confirmed (...) theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure. (shrink)

Derek Parfit defended Non-Realist Cognitivism. It is an open secret that this metaethical theory is often thought at best puzzling and at worst objectionably unclear. Employing truthmaker theory, I provide an account of Non-Realist Cognitivism that dispels charges of objectionable unclarity, clarifies how to assess it, and explains why, if plausible, it would be an attractive theory. I develop concerns that the theory involves cheating into an objection that ultimately reveals Non-Realist Cognitivism faces a dilemma. Whether it can escape demands (...) further attention. In bridging metaethics and the truthmaking literature, I illustrate the importance of greater meta-metaphysical reflection in metaethics. (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.

Economists customarily talk about the ‘realism’ of economic models and of their assumptions and make descriptive and prescriptive judgements about them: this model has more realism in it than that, the realism of assumptions does not matter, and so on. This is not the way philosophers mostly use the term ‘realism’ thus there is a major terminological discontinuity between the two disciplines. The following remarks organise and critically elaborate some of the philosophical usages of the term (...) and show some of the ways in which they relate to economists’ concerns. In the philosophy of science, scientific realism is the mainstream position – or rather a heterogeneous collection of positions - that includes ideas about the nature of scientific theories and how they are related to the real world and about the goals and achievements of scientific inquiry. However, most of what philosophers have contributed around these ideas is not designed to deal with the peculiarities of economics, thus some important adjustments are needed to make scientific realism an interesting position for economists. (shrink)

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Amid the wide variety of interpretations of quantum mechanics, the notion of a fully coherent ontological interpretation has seen a promising evolution over the last few decades. Despite this progress, however, the old dualistic categorical constraints of subjectivity and objectivity, correlate with the metrically restricted definition of local and global, have remained largely in place – a reflection of the broader, persistent inheritance of these comfortable strictures throughout the evolution of modern science. If one traces this inheritance back to (...) its ancient roots in Plato and Aristotle, it is clear that the coherence, scientific utility, and historical durability of the various natural philosophies that followed have been directly proportional to their commitment, tacit or explicit, to object-oriented realism. As Simondon might put it, it is a commitment to the primacy of individuated substance over the process of individuation. For Whitehead, it is the misplaced assimilation of becoming to being, of potentiality to actuality. Quantum mechanics has challenged this commitment with a combined breadth and depth of force that far exceeds any other theory in the history of science. The theory’s objectively demonstrable empirical application is manifest only by way of a fundamentally subjective, context-dependent mechanism of measurement. More compelling still, actual system states are always actualizations of locally contextualized yet globally conditioned potential system states, such that “globally objective” reality is no longer merely the object of local measurement, but also its product. Thus, any coherent, ontological interpretation of quantum theory must include a conceptual framework by which objectivity and subjectivity, actuality and potentiality, global and local, being and becoming, individuated fact and process of individuation, are no longer understood as merely epistemic, mutually exclusive category pairs descriptive of an already extant, closed reality – but rather as mutually implicative ontological categories explicative of an ontogenetic, open reality-in-process. (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)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...) We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)

A simple argument against Lewisian modal realism as portrayed in On the Plurality of World arises from its treatment of doxastic modalities. It is easily shown that if it is true, it is impossible to doubt the theory on ontological grounds, or, that, if it is possible to maintain doubt about modal realism’s existential postulate, it has to be false. The argument hinges on the fact that modal realism’s main ontological hypothesis, if true, is necessarily (...) true. (shrink)

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

In order to re-contextualize the otherwise ontologically privileged meaning of metaphysical debates into a more insubstantial form, metaphysical deflationism runs the risk of having to adopt potentially unwanted anti-realist tendencies. This tension between deflationism and anti-realism can be expressed as follows: in order to claim truthfully that something exists, how can deflationism avoid the anti-realist feature of construing such claims singularly in an analytical fashion? One may choose to adopt a Yablovian fallibilism about existential claims, but other approaches can (...) be appealed to as well. Amie Thomasson's Easy Ontology is one such approach, whereby the interaction of empirical as well as analytic features within the construction of its ontological theory affords a role for analytical rules without forsaking a link with empirical reality. The development of these analytical and empirical features has resulted in significant critiques regarding, one, potential reference failure of easy-ontological claims, and two, a circularity in how easy ontology explains the relation between its analytical rules and existential claims. This essay offers a response by showcasing how an easy ontological deflationism can reject these criticisms without succumbing to, one, the anti-realism of pure analyticism, and two, a further critique of wholesale referential indeterminacy in its referring terms. (shrink)

This article aims to provide a new ontological argument for the existence of God. A specific ‘modal’ version of the ontological argument—termed the Modal Realist Ontological Argument—is formulated within the modal realist metaphysical framework of David K. Lewis, Kris McDaniel and Philip Bricker. Formulating this argument within this specific framework will enable the plausibility of its central premise (i.e., the ‘Possibility Premise’) to be established, and allow one to affirm the soundness of the argument—whilst warding off two (...) oft-raised objections against this type of natural theological argument. (shrink)

What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a process that (...) is the bringing into being, sustaining, modifying, or terminating of a mental representation. We conclude by outlining some benefits and applications of this approach. (shrink)

This article examines whether it is possible to uphold one form of deflationism towards metaphysics, ontological pluralism, whilst maintaining metaphysical realism. The focus therefore is on one prominent deflationist who fits the definition of an ontological pluralist, Eli Hirsch, and his self-ascription as a realist. The article argues that ontological pluralism is not amenable to the ascription of realism under some basic intuitions as to what a “realist” position is committed to. These basic intuitions include (...) a commitment to more than a stuff-ontology, and a view that realism carries with it more than a rejection of idealism. This issue is more than merely terminological. The ascription of realism is an important classification in order to understand what sorts of entities can be the truthmakers within a given theory. “Realism” is thus an important term to understand the nature of the entities that a given theory accepts into its ontology. (shrink)

The authors argue that their target is orthogonal to the realism and instrumentalist debate. I argue that it is born directly from it. While the distinction is helpful in illuminating how some ontological commitments demand a theory of implementation, it's less clear whether different views cleanly map onto the epistemic and metaphysical uses defined in the paper.

The question of what ontological insights can be gained from the knowledge of physics (keyword: ontic structural realism) cannot obviously be separated from the view of physics as a science from an epistemological perspective. This is also visible in the debate about 'scientific realism'. This debate makes it evident, in the form of the importance of perception as a criterion for the assertion of existence in relation to the 'theoretical entities' of physics, that epistemology itself is 'ontologically (...) laden'. This is in the form of the assumption that things (or entities) in themselves exist as such and such determined ones (independent of cognition, autonomously). This ontological assumption is not only the basis of our naïve understanding of cognition, but also its indispensable premise, insofar as this understanding is a fundamentally passive, 'receptive' one. Accordingly, just as 'perception' is the foundation, ('objective') description is the aim of cognition, that which cognition is about. In this sense, our idea of cognition and our idea of the things are inseparably linked. Without the ontological premise mentioned we just would not know what cognition is, but it is basically just a kind of image that we have in our minds (an assumption that helps us understand 'cognition'). Epistemology not only shares this basic assumption (which it also shares with metaphysics), but it revolves (unlike metaphysics) entirely around it by making the idea and demand of 'certainty' a condition of 'real' knowledge. As 'certainty' is a subjective criterion this entails the 'remodelling' of the real, holistic cognitive situation (to which metaphysics adheres) into a linear subject-object-relation (which results in the strict 'transcendence' of the objects). And it also establishes, due to its 'expertise' in matters of cognition, the 'primacy of epistemology' over all other sciences. Now, on closer inspection, however, the expertise of epistemology seems not all that dependable, because it basically consists only of paradigms which, from the point of view of the holism of the real cognitive situation itself, are nothing more than relatively simplistic interpretations of this situation. However, we do not yet know what another conception of cognition might look like (which is not surprising given the high rank of the phenomenon of cognition in the hierarchy of phenomena according to their complexity). 'Certainty' as a criterion of cognition is thus excluded from the outset, and thus the linear relational model of cognition appears as what it is, a gross distortion of the real, holistic cognitive situation. The significance of this argumentation with regard to physics is that the linear epistemological model of cognition itself is a major obstacle to an adequate epistemological understanding of physics. This is because it is fixed 'a priori' to an object-related concept of cognition, and to 'description' as the only mode of ('real') cognition. But physics (without questioning our naïve notion of cognition on the level of epistemology) simply works past it and its basic assumptions. Its cognitive concept (alias heuristic) is fundamentally different from that of metaphysics. The acceptance of the real, holistic cognitive situation is, in my opinion, the condition for an adequate understanding of physics' heuristic access to objects, its transcendental, generalizing cognitive concept, as well as its ontological relevance and dimension of its own. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (...) (4) data exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his main conclusions (...) are rejected; rather it is main arguments for them that are the focus. (shrink)

Whitehead’s cosmology centers on the self-creation of actual occasions that perish as they come to be, but somehow do combine to constitute societies that are persistent agents and/or patients. “Instance Ontology” developed by D.W. Mertz concerns unification of relata into facts of relatedness by specific intensions. These two conceptual systems are similar in that they both avoid the substance-property distinction: they differ in their understanding of how basic units combine to constitute complex unities. “Process Structural Realism” (PSR) draws from (...) both of these approaches in developing an account of how combinations of processes may produce ontologically significant coherences. When a group of processes achieves such closure that a set of states recurs continually, the effects of that coherence differ from what would occur in the absence of that closure. Such altered effectiveness is an attribute of the system as a whole, and would have consequences. This indicates that the network of processes, as a unit, has ontological significance. The closed network of processes, together with the conditions that prevail, constitute the form of definiteness of the coherence. That form continues to obtain as long as the coherence persists. Constituents contribute to, rather than share, that characteristic. Aspects of some recent research in systems biology, microeconomics, and social psychology illustrate the application of PSR. (shrink)

In this paper I discuss the ontological status of actants. Actants are argued as being the basic constituting entities of networks in the framework of Actor Network Theory (Latour, 2007). I introduce two problems concerning actants that have been pointed out by Collin (2010). The first problem concerns the explanatory role of actants. According to Collin, actants cannot play the role of explanans of networks and products of the same newtork at the same time, at pain of circularity. The (...) second problem is that if actants are, as suggested by Latour, fundamentally propertyless, then it is unclear how they combine into networks. This makes the nature of actants inexplicable. -/- I suggest that both problems rest on the assumption of a form of object ontology, i.e. the assumption that the ontological basis of reality consists in discrete individual entities that have intrinsic properties. I argue that the solution to this problem consists in the assumption of an ontology of relations, as suggested within the framework of Ontic Structural Realism (Ladyman & Ross, 2007). Ontic Structural Realism is a theory concerning the ontology of science that claims that scientific theories represent a reality consisting on only relation, and no individual entities. -/- Furthermore I argue that the employment of OSR can, at the price of little modification for both theories, solve both of the two problems identified by Collin concerning ANT. -/- Throughout the text I seek support for my claims by referring to examples of application of ANT to the context of networked learning. As I argue, the complexity of the phenomenon of networked learning gives us a convenient vantage point from which we can clearly understand many important aspects of both ANT and OSR. -/- While my proposal can be considered as an attempt to solve Collin's problems, it is also an experiment of reconciliation between analytic and constructivist philosophy of science. -/- In fact I point out that on the one hand Actor Network Theory and Ontic Structural Realism show an interesting number of points of agreement, such as the naturalistic character and the focus on relationality. On the other hand, I argue that all the intuitive discrepancies that originates from the Science and Technology Studies’ criticism against analytic philosophy of science are at a closer look only apparent. (shrink)

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (ETA). We (...) describe here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work. (shrink)

From 1) the main ideas of the Kantian CRP - 2) a reinterpretation of the concept of transcendental subject and - 3) the logical principle of Individuation, we propose a new ontology in which subject and object are of the same reality. We describe the dynamic principle by which the Existence of the subject emerges from formless meta-substance and separates into an animated representation of the world.

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...) purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

There has been much recent debate on the question of whether Kant is to be best understood as a moral realist or a moral constructivist. In an attempt to resolve this debate I examine whether moral constructivism is a form of moral idealism, briefly contrast realism and idealism, and draw on work in social ontology to look at the different accounts of moral ontology implicit in realist and constructivist accounts. As a result of this investigation I conclude that Kant (...) is a moral constructivist. (shrink)

Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the (...) pluralist are mere notational variants of those proposed by the monist, in which case the debate between the two positions would not seem to be substantive. Jason Turner has given an ingenious response to this worry, in terms of a principle that he calls ‘logical realism’. This paper offers a counter-response on behalf of the ‘notationalist’. I argue that, properly applied, the principle of logical realism is no threat to the claim that the languages in question are notational variants. Indeed, there seems to be every reason to think that they are. (shrink)

Realists about mental disorder have been hasty about dismissing social explanations of how mental disorder is constituted. However, many social ontologies are realist ontologies. In order to create a meaningful distinction between realism and social metaphysics about mental disorder, I propose that realism about mental disorder is best understood as Individual Trait Realism (ITR) about them. For ITR, mental disorders exist in virtue of traits. I defend the view that ITR is compatible with social metaphysics, arguing that, (...) in asking whether constituents in the social sphere figure the metaphysics of psychopathology, we are asking questions on three different strata of explanation: the strata of demarcation, instantiation, and individual traits. Distinguishing between these strata allows for nuanced realism that need not reject the social constitution of mental disorder. (shrink)

Scientific realism is the view that our best scientific theories can be regarded as (approximately) true. This is connected with the view that science, physics in particular, and metaphysics could (and should) inform one another: on the one hand, science tells us what the world is like, and on the other hand, metaphysical principles allow us to select between the various possible theories which are underdetermined by the data. Nonetheless, quantum mechanics has always been regarded as, at best, puzzling, (...) if not contradictory. As such, it has been considered for a long time at odds with scientific realism, and thus a naturalized quantum metaphysics was deemed impossible. Luckily, now we have many quantum theories compatible with a realist interpretation. However, scientific realists assumed that the wave-function, regarded as the principal ingredient of quantum theories, had to represent a physical entity, and because of this they struggled with quantum superpositions. In this paper I discuss a particular approach which makes quantum mechanics compatible with scientific realism without doing that. In this approach, the wave-function does not represent matter which is instead represented by some spatio-temporal entity dubbed the primitive ontology: point-particles, continuous matter fields, space-time events. I argue how within this framework one develops a distinctive theory-construction schema, which allows to perform a more informed theory evaluation by analyzing the various ingredients of the approach and their inter-relations. (shrink)

A century after the discovery of quantum mechanics, the meaning of quantum mechanics still remains elusive. This is largely due to the puzzling nature of the wave function, the central object in quantum mechanics. If we are realists about quantum mechanics, how should we understand the wave function? What does it represent? What is its physical meaning? Answering these questions would improve our understanding of what it means to be a realist about quantum mechanics. In this survey article, I review (...) and compare several realist interpretations of the wave function. They fall into three categories: ontological interpretations, nomological interpretations, and the sui generis interpretation. For simplicity, I will focus on non-relativistic quantum mechanics. (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)

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

I outline and defend a limited realism in socio-political conceptual amelioration (RSCA). RSCA claims that, in some cases, socio-political concepts are ameliorated to represent parts of a concept-independent reality more accurately. My main aim is to dissolve a seeming dilemma for RSCA: Whereas social kinds are mind-dependent (i.e. depending on human thought and action), realism implies that the kinds represented are ontologically independent of the concepts representing them. To dissolve this dilemma, I suggest considering two different roles concepts (...) play concerning social kinds. Concepts can both generate social kinds and represent social kinds. Once a concept has generated a social kind, this social kind is part of a concept-independent reality that can be represented by different concepts. Thereby, RSCA allows amelio-rated concepts to represent social kinds (e.g., rape, marriage) more accurately while acknowledging that human actions or concepts have generated these social kinds. (shrink)

We argue that if one wishes to be a realist, one should adopt a Neo-Aristotelian ontology involving tropes instead of a Russellian ontology of property universals and objects. Either Russellian realists should adopt the relata-specific relational tropes of instantiation instead of facts, or convert to Neo-Aristotelian realism with monadic tropes. Regarding Neo-Aristotelian realism, we have two novel points why it fares better than Russellian realism. Instantiation of property universals by tropes and characterization or inherence between tropes and (...) objects are more transparent ontological notions than relational inherence, which is assumed in Russellian realism with the relational tropes of instantiation. Neo-Aristotelian realism makes better sense about abstract universals, which are a more viable option than concrete universals. (shrink)

A scientific theory is successful, according to Stanford (2000), because it is suficiently observationally similar to its corresponding true theory. The Ptolemaic theory, for example, is successful because it is sufficiently similar to the Copernican theory at the observational level. The suggestion meets the scientific realists' request to explain the success of science without committing to the (approximate) truth of successful scientific theories. I argue that Stanford's proposal has a conceptual flaw. A conceptually sound explanation, I claim, respects the (...) class='Hi'>ontological order between properties. A dependent property is to be explained in terms of its underlying property, not the other way around. The applicability of this point goes well beyond the realm of the debate between scientific realists and antirealists. Any philosophers should keep the point in mind when they attempt to give an explanation of a property in their field whatever it may be. (shrink)

This paper distinguishes three concepts of "race": bio-genomic cluster/race, biological race, and social race. We map out realism, antirealism, and conventionalism about each of these, in three important historical episodes: Frank Livingstone and Theodosius Dobzhansky in 1962, A.W.F. Edwards' 2003 response to Lewontin (1972), and contemporary discourse. Semantics is especially crucial to the first episode, while normativity is central to the second. Upon inspection, each episode also reveals a variety of commitments to the metaphysics of race. We conclude by (...) interrogating the relevance of these scientific discussions for political positions and a post-racial future. (shrink)

The paper presents a realist account of the epistemic objectivity of science. Epistemic objectivity is distinguished from ontological objectivity and the objectivity of truth. As background, T.S. Kuhn’s idea that scientific theory-choice is based on shared scientific values with a role for both objective and subjective factors is discussed. Kuhn’s values are epistemologically ungrounded, hence provide a minimal sense of objectivity. A robust account of epistemic objectivity on which methodological norms are reliable means of arriving at the truth is (...) presented. The problem remains that deliberative judgement is required to determine the relevance and relative significance of a range of methodological norms. A role is sketched for cognitive virtues which may be exercised in the course of the deliberative judgement. (shrink)

What is the ultimate nature of reality? This paper defends an answer in terms of informational realism (IR). It does so in three stages. First, it is shown that, within the debate about structural realism (SR), epistemic (ESR) and ontic (OSR) structural realism are reconcilable by using the methodology of the levels of abstractions. It follows that OSR is defensible from a structuralist-friendly position. Second, it is argued that OSR is also plausible, because not all related objects (...) are logically prior to all relational structures. The relation of difference is at least as fundamental as (because constitutive of) any relata. Third, it is suggested that an ontology of structural objects for OSR can reasonably be developed in terms of informational objects, and that Object Oriented Programming provides a flexible and powerful methodology with which to clarify and make precise the concept of “informational object”. The outcome is informational realism, the view that the world is the totality of informational objects dynamically interacting with each other.. (shrink)

It is widely believed that at least two developments in the last third of the 20th century have given dispositionalism—the view that powers, capacities, potencies, etc. are irreducible real properties—new credibility: (i) the many counterexamples launched against reductive analyses of dispositional predicates in terms of counterfactual conditionals and (ii) a new anti-Humean faith in necessary connections in nature which, it is said, owes a lot to Kripke’s arguments surrounding metaphysical necessity. I aim to show in this paper that necessity is, (...) in fact, of little help for the dispositionalists. My argument makes use of one of the above mentioned counterexamples against Humean reduction: antidotes. Turning the tables, I ask how the dispositionalists themselves can deal with antidotes. The result will be to show that if the dispositionalists are to demystify antidote cases, they must make plausible a conceptualisation of dispositions that does not invoke any kind of necessity. I will cautiously suggest that the anti-Humean link dispositions bring to the world has to be thought of in terms of (Newtonian) forces. (shrink)

I present a discussion of some issues in the ontology of spacetime. After a characterisation of the controversies among relationists, substantivalists, eternalists, and presentists, I offer a new argument for rejecting presentism, the doctrine that only present objects exist. Then, I outline and defend a form of spacetime realism that I call event substantivalism. I propose an ontological theory for the emergence of spacetime from more basic entities. Finally, I argue that a relational theory of pre-geometric entities can (...) give rise to substantival spacetime in such a way that relationism and substantivalism are not necessarily opposed positions, but rather complementary. In an appendix I give axiomatic formulations of my ontological views. (shrink)

This chapter examines issues surrounding inference to the best explanation, its justification, and its role in different arguments for scientific realism, as well as more general issues concerning explanations’ ontological commitments. Defending the reliability of inference to the best explanation has been a central plank in various realist arguments, and realists have drawn various ontological conclusions from the premise that a given scientific explanation best explains some phenomenon. This chapter stresses the importance of thinking carefully about the (...) nature of explanation in connection with evaluating realists’ appeals to explanatory reasoning and inference to the best explanation. (shrink)