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

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)

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)

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 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)

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)

[[THIS IS THE COMPLETE SECOND ISSUE OF MΕTASCIENCE]] -/- This second issue of the journal Mεtascience continues the char acterization of this new branch of knowledge that is metasci ence. If it is new, it is not in a radical sense since Mario Bunge practiced it in an exemplary way, since logical positivists were accused of practicing only a mere metascience, since scientists have always practiced it implicitly, and since some philosophers no longer practice philosophy but rather metascience, but without (...) characterizing it or theorizing it, that is, without realizing that they have abandoned one general discourse for another. The novelty therefore lies in this aware ness that a general discourse without philosophy is possible: a scien tific general discourse. The twelve contributions gathered in this volume illustrate the metascientific approach to knowledge of the world as well as to knowledge of knowledge of the world, that is, science. And like Bunge’s project, they are neither part of the analytical movement nor the continental movement in philosophy. We will read here studies about the Bungean system, some applications of Bungean thought, some metascientific contributions, and some reflections around meta science. Among metascientific disciplines, ontology occupies a prominent place in this issue of Mεtascience. Metascience differs from philoso phy in its rejection of the fundamental philosophical distinction be tween appearance and reality. Metascientific ontology therefore does not postulate the existence of any metaphysical reality. But metasci entific ontology, no more than philosophical ontology, is a factual sci ence. The first, because it studies scientific constructs and not concrete objects, the second, because it is interested in transcendent or meta physical objects. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) (...) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (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)

Levins and Lewontin have contributed significantly to our philosophical understanding of the structures, processes, and purposes of biological mathematical theorizing and modeling. Here I explore their separate and joint pleas to avoid making abstract and ideal scientific models ontologically independent by confusing or conflating our scientific models and the world. I differentiate two views of theorizing and modeling, orthodox and dialectical, in order to examine Levins and Lewontin’s, among others, advocacy of the latter view. I compare the positions (...) of these two views with respect to four points regarding ontological assumptions: (1) the origin of ontological assumptions, (2) the relation of such assumptions to the formal models of the same theory, (3) their use in integrating and negotiating different formal models of distinct theories, and (4) their employment in explanatory activity. Dialectical is here used in both its Hegelian–Marxist sense of opposition and tension between alternative positions and in its Platonic sense of dialogue between advocates of distinct theories. I investigate three case studies, from Levins and Lewontin as well as from a recent paper of mine, that show the relevance and power of the dialectical understanding of theorizing and modeling. (shrink)

I argue that current projects in ‘naturalized metaphysics’ fail to be properly naturalistic, and thereby fail in their stated aim to take one’s metaphysics from science. I argue that naturalism must involve the idea of taking science seriously, and that this can only be spelled out in terms of taking not only the theories of science seriously, but also its practice and its socio-linguistic situatedness seriously as well. This accords with naturalism because not doing so draws an artificial (non-natural) distinction (...) between the epistemic products of science as essence, and its socio-linguistic and practical features as accidents. The picture of naturalism which falls out of this is a form of pragmatism. Once this is spelled out, the question becomes, what is the appropriate attitude for the pragmatist/naturalist to have toward ontology? It is not the same as that of traditional metaphysics, since such an attitude (that metaphysical theorizing can make positive epistemic contributions) requires a priori commitments which themselves are (1) not subject to empirical review, and (2) are anthropocentric and so potentially distorted. But the pragmatist/naturalist will not go the opposite way, and say that metaphysics is meaningless either, since (true to their pragmatic commitments) ontology does things for the scientist and the layperson. It is a mistake to reject it wholesale, since the task of asserting what there is, exposing such an ontology to criticism, both empirical and logical, and revising it, has both small-scale and large-scale consequences. On the small-scale, ontologies are a guide for thinking—scientists, engineers, and lay people can and do use models of existence to navigate occurent problems in their day-to-day lives. Whether this is posing research hypotheses, developing protocols for generating new materials, or cooling off a cup of coffee, ontology plays a role. Large-scale consequences are more weighty, and more difficult to see. These large-scale consequences have to do with the aims and values which individuals and societies possess, and their interrelation with ontology. This certainly was at the forefront of the earliest ontologies—the Epicureans and Stoics built their moral philosophy on the basis of what ontology they thought was correct. This sort of practice goes on, unabated, today, though with virtually no overt acknowledgement of this important interdependency. How, for the pragmatist, do we make sense of ontological talk, if we are to eschew traditional metaphysics? Ontology—the naturalist/pragmatist declares—is a tool. Ontology helps us do things, whether it be predict behavior, understand phenomena, blame or forgive someone, and hope or despair about a life after this one (for example). Building an ontology is about building our own concepts, and this, in turn is a negotiation between our beliefs, experiences, and commitments, and the beliefs, experiences, and commitments of with whom we’re discursively engaged. (shrink)

This paper is a reply to Richard Lauer’s “Is Social Ontology Prior to Social Scientific Methodology?” (2019) and an attempt to contribute to the meta-social ontological discourse more broadly. In the first part, I will give a rough sketch of Lauer’s general project and confront his pragmatist approach with a fundamental problem. The second part of my reply will provide a solution for this problem rooted in a philosophy of the social sciences in practice.

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)

Ontologies are some of the most central constructs in today's large plethora of knowledge technologies, namely in the context of the semantic web. As their coinage indicates, they are direct heirs to the ontological investigations in the long Western philosophical tradition, but it is not easy to make bridges between them. Contemporary ontological commitments often take causality as a central aspect for the ur-segregation of entities, especially in scientific upper ontologies; theories of causality and philosophical ontological investigations often go (...) hand-in-hand, and were essentially inseparable in medieval thought. This constitutes the foundation for a bridge, and this article analyzes the causality-based ontology of the late medieval philosopher Dietrich of Freiberg from the viewpoint of today's upper-ontology engineering. In this bridging attempt, it offers a translation into English of the first part of Dietrich's De origine (abbreviated title) that is a compromise between traditional scholarly translations of medieval Latin philosophical texts and contemporary ontology. (shrink)

Current controversies about knowledge integration reflect conflicting ideas of what it means to “take Indigenous knowledge seriously”. While there is increased interest in integrating Indigenous and Western scientific knowledge in various disciplines such as anthropology and ethnobiology, integration projects are often accused of recognizing Indigenous knowledge only insofar as it is useful for Western scientists. The aim of this article is to use tools from philosophy of science to develop a model of both successful integration and integration failures. On (...) the one hand, I argue that cross-cultural recognition of property clusters leads to an ontological overlap that makes knowledge integration often epistemically productive and socially useful. On the other hand, I argue that knowledge integration is limited by ontological divergence. Adequate models of Indigenous knowledge will therefore have to take integration failures seriously and I argue that integration efforts need to be complemented by a political notion of ontological self-determination. (shrink)

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 aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species, race, memory, intelligence, depression, or obesity are true or false relative to the choice of a biological, psychological, or medical ontology. Second, I show that ontological choices often depend on non-epistemic values. On (...) the basis of these premises, I argue that it is often neither possible nor desirable to evaluate scientific statements independently of non-epistemic values. Finally, I suggest that considerations of ontological choices do not only challenge the value-free ideal but also help to specify positive roles of non-epistemic values in an often neglected area of scientific practice. (shrink)

I make what I believe is a spirited and lively treatment for the necessary abandonment of scientific materialist ontology in light of numerous difficulties that have arisen within the materialist approach when examined in the light of contemporary physics. Every effort is made to ensure that it is aimed at a non-specialized, intelligent audience (except for this abstract). Within this approach every attempt is made to avoid the jargon employed by specialists, which still remaining accurate. I make a (...) case for the abandonment of materialism in favor of a specific brand of idealism that fits with what cutting edge science requires at its epistemological foundation, but does not lead to disqualifying shortcomings that occasionally accompany some idealist prescriptions. I move from the suggested idealist remedy to how this idealism may mitigate aspects of the arrow of time dilemma. I also suggest this its employment in conjunction with holographic modeling may be especially efficacious in the contemporary scientific endeavor. (shrink)

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find (...) self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. Ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But the ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, ontologies such as the GO are in different respects comparable to scientific theories, to scientific databases, and to scientific journal publications. Such a view implies a new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a new approach to the evaluation of ontologies and to the training of ontologists. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing (...) in abstract fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer (...) science has always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

This paper investigates the nature of scientific realism. I begin by considering the anomalous fact that Bas van Fraassen’s account of scientific realism is strikingly similar to Arthur Fine’s account of scientific non-realism. To resolve this puzzle, I demonstrate how the two theorists understand the nature of truth and its connection to ontology, and how that informs their conception of the realism debate. I then argue that the debate is much better captured by the theory of (...) truthmaking, and not by any particular theory of truth. To be a scientific realist is to adopt a realism-relevant account of what makes true the scientific theories one accepts. The truthmaking approach restores realism’s metaphysical core—distancing itself from linguistic conceptions of the debate—and thereby offers a better characterization of what is at stake in the question of scientific realism. (shrink)

Natural kinds, real kinds, or, following J.S Mill simply, Kinds, are thought to be an important asset for scientific realists in the non-fundamental (or “special”) sciences. Essential natures are less in vogue. I show that the realist would do well to couple her Kinds with essential natures in order to strengthen their epistemic and ontological credentials. I argue that these essential natures need not however be intrinsic to the Kind’s members; they may be historical. I concentrate on assessing the (...) merits of historical essential natures in a paradigm case of Kinds in the non-fundamental sciences: species. I specify two basic jobs for essential natures: 1) offering individuation criteria, and 2) providing a causal explanation of the Kind’s multiple projectable properties. I argue that at least in the case of species historical essences are fit for both tasks. The principled resistance to Kinds with historical essences should also be cleared. (shrink)

Many philosophers have drawn parallels between scientific models and fictions. In this paper I will be concerned with a recent version of the analogy, which compares models to the imagined characters of fictional literature. Though versions of the position differ, the shared idea is that modeling essentially involves imagining concrete systems analogously to the way that we imagine characters and events in response to works of fiction. Advocates of this view argue that imagining concrete systems plays an ineliminable role (...) in the practice of modeling that cannot be captured by other accounts. The approach thus leaves open what we should say about the ontological status of model-systems, and here advocates differ among themselves, defending a variety of realist or anti-realist positions. I argue that this debate over the ontological status of model-systems is misguided. If model-systems are the kinds of objects fictional realists posit, they can play no role in explaining the epistemology of modeling for an advocate of this approach. So they are at best superfluous. Defenders of the approach should focus on developing an account of the epistemological role of imagining model-systems. (shrink)

Abstract: This study explores some theoretical issues in scientific research such as, the nature of experimentation and problems of methodology in scientific practice as well as the question of truth, rationality, objectivity and utility of scientific discoveries. The paper discusses a number of theorizing that have emerged in response to the challenge raised by the above concerns. Epistemological models of science from critical rationalists, like Popper, Kuhn, Feyerabend and the neo-pragmatic methodological orientation of Arthur Fine’s Natural Ontological (...) Attitude (NOA) to Science, have been adopted as points of discussion on what science as an empirical discipline entail. The paper concludes that a rigorous epistemological discussion on the methodology of scientific inquiry is a desideratum for the progress of science. (shrink)

Metascientific ontology differs from philosophical ontologies in its objectives, objects and methods. By an examination of the ontological theories of Mario Bunge, we will show their main objective is a unified representation of the world as known through the sciences, that their objects of study are scientific concepts, and that their methods do not differ from those that one expects to find in any rational activity. Metascientific ontology is therefore not transcendent because it does not seek to (...) represent non-concrete objects alien to the world we inhabit and to the sciences that study it, and therefore does not need special faculties and methods to carry out its research. Metascientific ontology is a general scientific discourse on the world because it was designed by and for the sciences. (shrink)

This paper studies the problem of the arrow of time from the scientific and philosophical perspective. The scientific section (Castagnino) poses the topic according to the instruments of measuring employed in physical theories, specially when they are applied to dynamic chaotic systems in which a temporal asymmetry is shown. From the analysis of “two schools” (epistemological and ontological), the conclusion is favorable to the reality (both ontological and epistemological) of the difference between past and future, with the recourse (...) to Reichenbach’s notion of global system. In the philosophical section (Sanguineti) the content of the scientific part of the article is presented in a qualitative way. The role of some philosophical choices in the scientific field is stressed, taking into account the diversity of a positivistic and realistic view. (shrink)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of (...) individual ontologies, performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (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)

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)

Discussions over whether these natural kinds exist, what is the nature of their existence, and whether natural kinds are themselves natural kinds aim to not only characterize the kinds of things that exist in the world, but also what can knowledge of these categories provide. Although philosophically critical, much of the past discussions of natural kinds have often answered these questions in a way that is unresponsive to, or has actively avoided, discussions of the empirical use of natural kinds and (...) what I dub “activities of natural kinding” and “natural kinding practices”. The natural kinds of a particular discipline are those entities, events, mechanisms, processes, relationships, and concepts that delimit investigation within it—but we might reasonably ask: How are these natural kinds discovered?, How are they made?, Are they revisable?, and Where do they come from? A turn to natural kinding practices reveals a new set of questions open for investigation: How do natural kinds explain through practice?, What are natural kinding practices and classifications and why should we care?, What is the nature of natural kinds viewed as a set of activities?, and How do practice approaches to natural kinds shape and reconfigure scientific disciplines? Natural kinds have traditionally been discussed in terms of how they classify the contents of the world. The metaphysical project has been one which identifies essences, laws, sameness relations, fundamental properties, and clusters of family resemblances and how these map out the ontological space of the world. But actually how this is done has been less important in the discussion than the resultant categories that are produced. I aim to rectify these omissions and suggest a new metaphysical project investigating kinds in practice. (shrink)

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. (...) The paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products? (shrink)

The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles – sometimes overt, sometimes masked – throughout the history of biology, and frequently in very normative ways, also shifting between the biological and the social. Indeed, it has often been presented as a key-concept in life science and the ‘theorization’ of Life, (...) but conversely has also been the target of influential rejections: as just an instrument of transmission for the selfish gene, but also, historiographically, as part of an outdated ‘vitalism’. Indeed, the organism, perhaps because it is experientially closer to the ‘body’ than to the ‘molecule’, is often the object of quasi-affective theoretical investments presenting it as essential, sometimes even as the pivot of a science or a particular approach to nature, while other approaches reject or attack it with equal force, assimilating it to a mysterious ‘vitalist’ ontology of extra-causal forces, or other pseudo-scientific doctrines. This paper does not seek to adjudicate between these debates, either in terms of scientific validity or historical coherence; nor does it return to the well-studied issue of the organism-mechanism tension in biology. Recent scholarship has begun to focus on the emergence and transformation of the concept of organism, but has not emphasized so much the way in which organism is a shifting, ‘go-between’ concept – invoked as ‘natural’ by some thinkers to justify their metaphysics, but then presented as value-laden by others, over and against the natural world. The organism as go-between concept is also a hybrid, a boundary concept or an epistemic limit case, all of which partly overlap with the idea of ‘nomadic concepts’. Thereby the concept of organism continues to function in different contexts – as a heuristic, an explanatory challenge, a model of order, of regulation, etc. – despite having frequently been pronounced irrelevant and reduced to molecules or genes. Yet this perpetuation is far removed from any ‘metaphysics of organism’, or organismic biology. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, (...) diagnosis, prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Consider the most recent Yale-Harvard football game, an event which occurred on 11/20/21 in New Haven, lasting about three hours. This event, like many college football games before, was composed of four quarters, each of which was composed of possessions, each of which was composed of downs, each of which was composed of particular movements, tackles and decisions of the individual players. Each of these parts of the game was itself an event, occurring in a smaller region of space and (...) time than the game itself. Each of these events involved material objects like players, helmets, jerseys, etc. Each had causes and effects, and each instantiated qualitative properties, such as being a kickoff or being a tackle. These are paradigmatic examples of events. Events are many and varied; some other examples include the melting of an ice cube, the birth of a horse, the supernova of a star, the presidential election campaign and a winter snowstorm. Each of these took place in a certain region of spacetime, had other events as parts, involved certain objects, had causes and effects, and instantiated properties. Objects and their properties are not the only furniture in the world. Events are a crucial part of our manifest and scientific pictures of the world. We go to football games, think about and participate in elections, eagerly anticipate the birth of a child, and quantify over and explain such things in our scientific theories. Yet, events have received insufficient attention from metaphysicians. Some philosophers have been skeptical of events, holding that talk of events can be paraphrased away, or that events can be reduced to objects and properties.1 When philosophers have accepted events, their motivations have usually been extrinsic—events are introduced in order to play a role in a larger philosophical system. This tendency has led philosophers to miss a number of interesting features of events. In this paper, I wish to reverse that trend by developing an ontology of events which is not an afterthought with respect to another philosophical project. In so doing, I will provide answers to substantive metaphysical questions about the relations in which events stand and their identity conditions. In the next section, I identify four basic relations in which events stand: parthood, involvement, causation and instantiation, focusing in particular on involvement. Then, I argue that events are individuated by their involvements, and criticize the identity conditions which have been offered by other philosophers, notably Quine, Davidson and Kim. I then conclude. (shrink)

The aim of this article is to discuss the relation between indigenous and scientific kinds on the basis of contemporary ethnobiological research. I argue that ethnobiological accounts of taxonomic convergence-divergence patters challenge common philosophical models of the relation between folk concepts and natural kinds. Furthermore, I outline a positive model of taxonomic convergence-divergence patterns that is based on Slater's [2014] notion of “stable property clusters” and Franklin-Hall's [2014] discussion of natural kinds as “categorical bottlenecks.” Finally, I argue that this (...) model is not only helpful for understanding the relation between indigenous and scientific kinds but also makes substantial contributions to contemporary debates about natural kinds.to contemporary debates about natural kinds. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the (...) class='Hi'>scientific treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, (...) ‘statistical data analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

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)

Fundamental Science is undergoing an acute conceptual-paradigmatic crisis of philosophical foundations, manifested as a crisis of understanding, crisis of interpretation and representation, “loss of certainty”, “trouble with physics”, and a methodological crisis. Fundamental Science rested in the "first-beginning", "first-structure", in "cogito ergo sum". The modern crisis is not only a crisis of the philosophical foundations of Fundamental Science, but there is a comprehensive crisis of knowledge, transforming by the beginning of the 21st century into a planetary existential crisis, which has (...) exacerbated the question of the existence of Humanity and life on Earth. Due to the unsolved problem of justification of Mathematics, paradigm problems in Computational mathematics have arisen. It's time to return ↔ Into Dialectics. The solution to the problem of the foundations of Mathematics, and therefore knowledge in general, is the solution to the problem of modeling (constructing) the ontological basis of knowledge - the ontological model of the primordial generating process. The idea and model of the primordial generating process, its ontological structure directs thinking to the need for the introduction of superconcept → ontological (cosmic, structural) memory, concept-attractor, supercategory, substantial semantic core of the scientific picture of the world of the nuclear-ecological-information age. Model of basic Ideality→ “Space-MatterMemory-Time” [S-MM-T]. (shrink)

Abstract: The following is an outline of an emerging foundation for science that begins to explain living forms and their patterns of movement beyond the sphere of mechanistic interactions. Employing an event ontology based on a convergence of quantum physics and Alfred North Whitehead’s process philosophy, coupled with the controversial yet promising theory of formative causation, this development will explore possible influences on the outcomes of events beyond any combination of external forces, laws of Nature, and chance. If it (...) turns out there are no such additional influences--beyond mechanistic causes--it is difficult to see how agency or free will could exist. Assuming agency exists, as Whitehead apparently does, while committing to an event ontology in which process is fundamental leads to interesting questions about the natures of any entities that might participate in events. Furthermore, what might the purposes and agendas of such entities be based upon, beyond memory traces or DNA code? This ontological model, recognizing processes as fundamental, leads to a revised cosmology where the trajectory of a series of events may be due to more than rearrangement of material bits according to external forces and where goal-directed, recurring processes and the emergence of mind are not so surprising. Just as special relativity reduces to classical treatment when speeds slow down, this scientific model for a living world reduces to mechanistic materialism whenever conditions are more limited. Though this development is based on a philosophy of process, there are some dissimilarities with respect to Whitehead’s particular version. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology consisting of thirty-six classes, designed to support information integration, retrieval, and analysis across all domains of scientific investigation, presently employed in over 350 ontology projects around the world. BFO is a genuine top-level ontology, containing no terms particular to material domains, such as physics, medicine, or psychology. In this paper, we demonstrate how a series of cases illustrating common types of change may be represented by universals, defined (...) classes, and relations employing the BFO framework. We provide discussion of these cases to provide a template for other ontologists using BFO, as well as to facilitate comparison with the strategies proposed by ontologists using different top-level ontologies. (shrink)

Philosophers of science commonly connect ontology and science, stating that these disciplines maintain a two-way relationship: on the one hand, we can extract ontology from scientific theories; on the other hand, ontology provides the realistic content of our scientific theories. In this article, we will critically examine the process of naturalizing ontology, i.e., confining the work of ontologists merely to the task of pointing out which entities certain theories commit themselves to. We will use (...) non-relativistic quantum mechanics as a case study. We begin by distinguishing two roles for ontology: the first would be characterized by cataloging existing entities according to quantum mechanics; the second would be characterized by establishing more general ontological categories in which existing entities must be classified. We argue that only the first step is available for a naturalistic approach; the second step not being open for determination or anchoring in science. Finally, we also argue that metaphysics is still a step beyond ontology, not contained in either of the two tasks of ontology, being thus even farther from science. (shrink)

Systems theory offers a language in which one might formulate a metaphysics (or more specifically an ontology) of problems. This proposal is based upon a conception of systems theory shared by vonBertalanffy, Wiener, Boulding, Rapoport, Ashby, Klir, and others,and expressed succinctly by Bunge, who considered game theory, information theory, feedback control theory, and the like to be attempts to construct an "exact and scientific metaphysics." Our prevailing conceptions of "problems" are concretized yet also fragmented, and in fact dissolved, (...) by the standard reductionist model of science, which cannot provide a general framework for analysis. The idea of a "systems theory," however, suggests the possibility of an abstract and coherent account of the origin and essence of problems. Such an account would constitute a secular theodicy. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

This article addresses ontological negotiations in the Global South through three case studies of community-based research in Brazil and Ghana. We argue that ontological perspectives of Indigenous and other subjugated communities require an ontological pluralism that recognizes the plurality of both representational tools and ways of being in the world. Locating these two readings of ontological pluralism in the politics of the Global South, the article highlights a wider dynamic from ontological paternalism to ontological diversity to ontological decolonization. We conclude (...) by arguing that this dynamic provides important lessons for reorienting agendas in social ontology through Southern Ontologies. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological (...) reality through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop (...) and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The traditional approach to explanation in cognitive neuroscience is realist about psychological constructs, and treats them as explanatory. On the “standard framework,” cognitive neuroscientists explain behavior as the result of the instantiation of psychological functions in brain activity. This strategy is questioned by results suggesting the distribution of function in the brain, the multifunctionality of individual parts of the brain, and the overlap in neural realization of purportedly distinct psychological constructs. One response to this in the field has been to (...) employ the tools of databasing and machine learning to attempt to find and quantify specific correlations between psychological kinds such as ‘memory’ or ‘attention’ (or sub-kinds thereof) and patterns of activity in the brain. I assess the status and prospects of these projects. I argue that current proponents of the project are vague about their aims, vis-à-vis the standard framework, sometimes suggesting substantiation of the framework, sometimes suggesting retaining the framework but revising the ontology of mental constructs, and sometimes suggesting abandonment of the framework. I argue that extant results from within the projects fail to substantiate the standard framework, and propose an alternative. On my view, psychological constructs should not be viewed as explanantia, but instead as heuristic concepts that help us uncover ways that behaviors can vary and the ways that the brain implements those distinctions. I then discuss the normative upshot of these views for databasing and brain mapping projects. (shrink)

The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in (...) many influential ontologies, illustrating our results by reference to examples drawn from the domain of the life sciences. (shrink)

According to the accepted translation-failure interpretation, the problem of incommensurability involves the nature of the meaning-referential relation between scientific languages. The incommensurability thesis is that some competing scientific languages are mutually untranslatable due to the radical variance of meaning or/and reference of the terms they employ. I argue that this interpretation faces many difficulties and cannot give us a tenable, coherent, and integrated notion of incommensurability. It has to be rejected. ;On the basis of two case studies, I (...) find that the confrontations between many classical incommensurable languages are not confrontations between two untranslatable languages with different distribution of truth values, but rather the confrontations between incompatible fundamental presuppositions at the ontological level. We can always identify a truth-value gap between two incommensurable languages. Such a truth-value gap indicates a communication breakdown between the two language communities on the one hand, and is caused by the incompatible fundamental presuppositions underlying them on the other. ;I thereby identify the truth-value functional relationship between sentences, instead of the meaning-referential relationship between terms, as the dominant semantic relation between two incommensurable languages. According to my presuppositional interpretation of incommensurability, the real secret of incommensurability lies in the ontological setup of two competing presuppositional languages. When two presuppositional languages with incompatible factual commitments encounter with each other, the confrontation leads to a truth-value gap, and consequently a communication breakdown between them. Formally put, two scientific languages are incommensurable when core sentences of one language, which have truth values when considered within its own context, lack truth values when considered within the context of the other due to an ontological gap between them. ;The presuppositional interpretation makes many significant contributions to the discussion of the issue of incommensurability and the related metaphysical and epistemological issues: It confirms the existence of the phenomenon of incommensurability and makes it metaphysically and epistemologically significant. It establishes the tenability and integrity of the notion of incommensurability. It avoids many alleged unattractive epistemological and metaphysical consequences of the translation-failure interpretation. (shrink)