The way in which knowledge progresses, and especially our scientific knowledge, is by unjustified anticipations, by guesses, by tentative solutions to our problems, by conjectures. These conjectures are controlled by criticism: that is, by attempted refutations, which include severely critical tests. They may survive these tests; but they can never be positively justified: they can neither be established as certainly true nor even as 'probable'. Criticism of our conjectures is of decisive importance: by bringing out our mistakes it makes us (...) understand the difficulties of the problems which we try to solve. This is how we become better acquainted with our problem, and able to propose more mature solutions: the very refutation of a theory - that is, of a tentative solution to our problem - is always a step forward that takes us nearer the truth. And this is how we can learn from our mistakes. As we learn from our mistakes our knowledge grows, even though we may never know - that is, know for certain. Since our knowledge can grow, there can be no reason here for despair of reason. And since we can never know for certain, the can be no authority here for any claim to authority, for conceit over our knowledge, or for smugness. The essays and lectures of which this book is composed apply this thesis to many topics, ranging from problems of the philosophy and history of the physical and social sciences to historical and political problems. (shrink)

_This sweeping discussion of the philosophy of evolutionary biology is based on the revolutionary idea that species are not kinds of organisms but wholes composed of organisms._.

E. J. Lowe, a prominent figure in contemporary metaphysics, sets out and defends his theory of what there is. His four-category ontology is a metaphysical system which recognizes four fundamental categories of beings: substantial and non-substantial particulars and substantial and non-substantial universals. Lowe argues that this system has an explanatory power which is unrivalled by more parsimonious theories and that this counts decisively in its favour. He shows that it provides a powerful explanatory framework for a unified account of causation, (...) dispositions, natural laws, natural necessity and many other related matters, thus constituting a full metaphysical foundation for natural science. (shrink)

Husserls »Logische Untersuchungen« sind eines der folgenreichsten Werke der neueren Philosophiegeschichte. Mit dem ersten Erscheinen in den Jahren 1900 und 1901 (Max Niemeyer Verlag, Halle/Saale) nimmt jene Schule ihren Anfang, deren Name im Untertitel des zweiten Bandes zum ersten Mal sinnfällig wird: die Phänomenologie. Husserl sah damals in diesem Werk »Versuche zur Neubegründung der reinen Logik und Erkenntnistheorie«, die den Grund zu einem größeren Gedankengebäude zu legen imstande waren. Sie wollten freilich kein bloßes Programm sein, sondern »Fundamentalarbeit an den unmittelbar (...) erschauten und ergriffenen Sachen« darstellen. Die weitere Arbeit an der Ausprägung der phänomenologischen Philosophie führte schon nach wenigen Jahren zu neuen Problemen, zu vertieften Erkenntnissen und zu schärferen Formulierungen. Ihnen trägt die zweite, zum Teil tiefgreifend umgearbeitete Auflage Rechnung, deren Text seither in unveränderter Form immer wieder nachgedruckt wurde. (shrink)

At least 22 concepts of species are in use today and many of these are notably incompatible in their accounts of biological diversity. Much of the traditional turmoil embodied in the species problem ultimately derives from the packaging of inappropriate criteria for species into a single concept. This results from a traditional conflation of function of concepts with their applications, definitions with concepts, taxonomic categories with groups, and the ontological status of real species with teleological approaches to recover them. Analogous (...) to classifications of supraspecific taxa, our forging inappropriate and ambiguous information relating to theoretical and operational discussions of species ultimately results in a trade-off between convenience, accuracy, precision, and the successful recovery of natural biological diversity. Hence, none of these expectations or intentions of species or classifications is attainable through composite, and possibly discordant, concepts of biological diversity or its descent. Reviewing and evaluating the concepts of species for their theoretical and operational qualities illustrates that a monistic, primary concept of species, applicable to the various entities believed to be species, is essential. This evaluation reveals only one theoretical concept as appropriate for species, the Evolutionary Species Concept. This conceptualization functions as a primary concept and is essential in structuring our ideas and perceptions of real species in the natural world. The remaining concepts are secondary, forming a hierarchy of definitional guidelines subordinate to the primary concept, and are essential to the study of species in practice. Secondary concepts should be used as operational tools, where appropriate, across the variance in natural diversity to discover entities in accord with the primary concept. Without this theoretical and empirical structuring of concepts of species our mission to achieve reconciliation and understanding of pattern and process of the natural world will fail. (shrink)

Like the latter, it unites into one and the same function the possibility of giving things a sign, of representing one thing by another, and the possibility of causing a sign to shift in relation to what it designates. The four functions that define the ...

Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...) story of three revolutions can provide at best a preliminary orientation, and that Husserl was constantly expanding and revising his philosophical system, integrating views in phenomenology, ontology, epistemology and logic with views on the nature and tasks of philosophy and science as well as on the nature of culture and the world in ways that reveal more common elements than violent shifts of direction. We argue further that Husserl is a seminal figure in the evolution from traditional philosophy to the characteristic philosophical concerns of the late twentieth century: concerns with representation and intentionality and with problems at the borderlines of the philosophy of mind, ontology, and cognitive science. (shrink)

Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in (...) which all clinically salient particulars – from the concrete disorder on the side of the patient and the body parts in which it occurs to the concrete treatments given – should be uniquely identified. This will allow us to achieve interoperability among different systems of records at the level where it really matters: in regard to what is happening in the real world. It will also allow us to keep track of particular disorders and of the effects of particular treatments in a precise and unambiguous way. We discuss the ontological and epistemological aspects of our claim and describe a scenario for implementation within EHR systems. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...) they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship (...) between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities. (shrink)

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...) are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto. (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)

The essay surveys recent developments in ontology and defends a strategy for improvement of ontologies based on ontological realism. As a thought experiment, we consider central theses of Aristotelian metaphysics, and show how they fall short of what we believe to be the requirements of ontology today. Above all, Aristotle provides us with no strategy for the reconciliation of common-sense realism and scientific realism where these diverge. We focus specifically on shortfalls in Aristotle’s treatment of individual accidents, especially in regard (...) to the category of place. We then show how Aristotle’s metaphysics needs to be supplemented by a theory of holes, of fiat boundaries, of granularity, and of vagueness. (shrink)

The human body is a system made of systems. The body is divided into bodily systems proper, such as the endocrine and circulatory systems, which are subdivided into many sub-systems at a variety of levels, whereby all systems and subsystems engage in massive causal interaction with each other and with their surrounding environments. Here we offer an explicit definition of bodily system and provide a framework for understanding their causal interactions. Medical sciences provide at best informal accounts of basic notions (...) such as system, process, and function, and while such informality is acceptable in documentation created for human beings, it falls short of what is needed for computer representations. In our analysis we will accordingly provide the framework for a formal definition of bodily system and of associated notions. (shrink)

Die analytische Philosophie hat selbst da, wo sie explizit an Kant anschließt, erhebliche Schwierigkeiten mit dessen Idee eines synthetischen Wissens a priori. Damit verliert sie eine ganze Dimension der philosophischen Tradition. Das vorliegende Buch gewinnt diese Idee zurück, indem es gerade den Anschauungsbezug und damit den Zeitbezug des menschlichen Denkens zum Gegenstand einer logischen Untersuchung macht. Nur wenn man die Zeit als inneres und formbildendes Merkmal des menschlichen Aussagens erkennt, versteht man den Begriff empirischer Wahrheit und sinnlich vermittelter Erkenntnis. In (...) diesem Gedanken, so zeigt sich, liegt die Einheit einer philosophischen Tradition, die Aristoteles mit Kant und beide mit dem späten Wittgenstein verbindet. (shrink)

We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it (...) provides an account of how cells and subcells relate to objects in reality. We define a notion of well-formedness for partitions, and we give an account of what it means for a partition to project onto objects in reality. We continue by classifying partitions along three axes: (a) in terms of the degree of correspondence between partition cells and objects in reality; (b) in terms of the degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) in terms of the degree of completeness with which a partition represents this domain. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...) and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

Mereotopology faces problems when its methods are extended to deal with time and change. We offer a new solution to these problems, based on a theory of partitions of reality which allows us to simulate (and also to generalize) aspects of set theory within a mereotopological framework. This theory is extended to a theory of coarse- and fine-grained histories (or finite sequences of partitions evolving over time), drawing on machinery developed within the framework of the so-called ‘consistent histories’ interpretation of (...) quantum mechanics. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these are (...) two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine. (shrink)

According to immanent realism, there are universals in the spatiotemporal world quite independently of language and the mind. The existence of these universals, furthermore, is not dependent upon there being Platonic universals existing outside the spatiotemporal world. In this paper I will try to show that immanent realism holds not only for many determinate universals, but for some determinable universals as well. In other words, there are ontological determinables as well as conceptual determinables.

Given the fundamental role that concepts play in theories of cognition, philosophers and cognitive scientists have a common interest in concepts. Nonetheless, there is a great deal of controversy regarding what kinds of things concepts are, how they are structured, and how they are acquired. This chapter offers a detailed high-level overview and critical evaluation of the main theories of concepts and their motivations. Taking into account the various challenges that each theory faces, the chapter also presents a novel approach (...) to concepts that is organized around two ideas. The first is a pluralistic view of differing types of conceptual structure. The second is a model that treats concepts as atomic representations that are linked to various types of conceptual structures. (shrink)

The classic, influential essay in 'descriptive metaphysics' by the distinguished English philosopher.

Traditionally, species have been treated as classes. In fact they may be considered individuals. The logical term “individual” has been confused with a biological synonym for “organism.” If species are individuals, then: 1) their names are proper, 2) there cannot be instances of them, 3) they do not have defining properties, 4) their constituent organisms are parts, not members. “ Species " may be defined as the most extensive units in the natural economy such that reproductive competition occurs among their (...) parts. Species are to evolutionary theory as firms are to economic theory: this analogy resolves many issues, such as the problems of “reality” and the ontological status of nomenclatorial types. (shrink)

Intelligent systems are faced with the problem of securing a principled (ideally, veridical) relationship between the world and its internal representation. I propose a unified approach to visual representation, addressing both the needs of superordinate and basic-level categorization and of identification of specific instances of familiar categories. According to the proposed theory, a shape is represented by its similarity to a number of reference shapes, measured in a high-dimensional space of elementary features. This amounts to embedding the stimulus in a (...) low-dimensional proximal shape space. That space turns out to support representation of distal shape similarities which is veridical in the sense of Shepard's (1968) notion of second-order isomorphism (i.e., correspondence between distal and proximal similarities among shapes, rather than between distal shapes and their proximal representations). Furthermore, a general expression for similarity between two stimuli, based on comparisons to reference shapes, can be used to derive models of perceived similarity ranging from continuous, symmetric, and hierarchical, as in the multidimensional scaling models (Shepard, 1980), to discrete and non-hierarchical, as in the general contrast models (Tversky, 1977; Shepard and Arabie, 1979). (shrink)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

The Renaissance architect, moral philosopher, cryptographer, mathematician, Papal adviser, painter, city planner and land surveyor Leon Battista Alberti provided the theoretical foundations of modern perspective geometry. Alberti’s work on perspective exerted a powerful influence on painters of the stature of Albrecht Dürer, Leonardo da Vinci and Piero della Francesca. But his Della pittura of 1435–36 contains also a hitherto unrecognized ontology of pictorial projection. We sketch this ontology, and show how it can be generalized to apply to representative devices in (...) general, including maps and spatial and non-spatial databases. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

The world of ontology development is full of mysteries. Recently, ISO Standard 15926 (“Lifecycle Integration of Process Plant Data Including Oil and Gas Production Facilities”), a data model initially designed to support the integration and handover of large engineering artefacts, has been proposed by its principal custodian for general use as an upper level ontology. As we shall discover, ISO 15926 is, when examined in light of this proposal, marked by a series of quite astonishing defects, which may however provide (...) general lessons for the developers of ontologies in the future. (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)

Relevance logic has become ontologically fertile. No longer is the idea of relevance restricted in its application to purely logical relations among propositions, for as Dunn has shown in his (1987), it is possible to extend the idea in such a way that we can distinguish also between relevant and irrelevant predications, as for example between “Reagan is tall” and “Reagan is such that Socrates is wise”. Dunn shows that we can exploit certain special properties of identity within the context (...) of standard relevance logic in a way which allows us to discriminate further between relevant and irrelevant properties, as also between relevant and irrelevant relations. The idea yields a family of ontologically interesting results concerning the different ways in which attributes and objects may hang together. Because of certain notorious peculiarities of relevance logic, however,1 Dunn’s idea breaks down where the attempt is made to have it bear fruit in application to relations among entities which are of homogeneous type. (shrink)

The winning entry in David Stove's Competition to Find the Worst Argument in the World was: “We can know things only as they are related to us/insofar as they fall under our conceptual schemes, etc., so, we cannot know things as they are in themselves.” That argument underpins many recent relativisms, including postmodernism, post-Kuhnian sociological philosophy of science, cultural relativism, sociobiological versions of ethical relativism, and so on. All such arguments have the same form as ‘We have eyes, therefore we (...) cannot see’, and are equally invalid. (shrink)

I demonstrate here that it is possible for an event to be identical with one of its proper parts, refuting the key premise in Lawrence Lombard's argument for the essentiality of an event's time. I also propose and defend an alternative to his criterion of event identity.

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...) projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments. (shrink)

There are five individually plausible and jointly incompatible assumptions underlying four familiar puzzles about material constitution. The problem of material constitution just is the fact that these five assumptions are both plausible and incompatible. I will begin by providing a very general statement of the problem. I will present the five assumptions and provide a short argument showing how they conflict with one another. Then, in subsequent sections, I will go on to show how these assumptions underlie each of the (...) four puzzles. I will conclude by providing an exhaustive taxonomy of possible solutions to the problem. (shrink)

The question "Why?" that is deployed in these exchanges evidently bears the "special sense" Elizabeth Anscombe has linked to the concepts of intention and of a reason for action; it is the sort of question "Why?" that asks for what Donald Davidson later called a "rationalization".2 The special character of what is given, in each response, as formulating a reason ── a description, namely, of the agent as actually doing something, and, moreover, as..

I analyze a number of widespread misconceptions concerning species. The species category, defined by a concept, denotes the rank of a species taxon in the Linnaean hierarchy. Biological species are reproducing isolated from each other, which protects the integrity of their genotypes. Degree of morphological difference is not an appropriate species definition. Unequal rates of evolution of different characters and lack of information on the mating potential of isolated populations are the major difficulties in the demarcation of species taxa.

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.