Barry Smith

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account.

The paper uses the tools of mereotopology (the theory of parts, wholes and boundaries) to work out the implications of certain analogies between the 'ecological psychology' of J. J Gibson and the phenomenology of Edmund Husserl. It presents an ontological theory of spatial boundaries and of spatially extended entities. By reference to examples from the geographical sphere it is shown that both boundaries and extended entities fall into two broad categories: those which exist independently of our cognitive acts (for example, the planet Earth, its exterior surface); and those which exist only in virtue of such acts (for example: the equator, the North Sea). The visual field, too, can be conceived as an example of an extended entity that is dependent in the sense at issue. The paper suggests extending this analogy by postulating entities which would stand to true judgments as the visual field stands to acts of visual perception. The judgment field is defined more precisely as that complex extended entity which comprehends all entities which are relevant to the truth of a given (true) judgment. The work of cognitive linguists such as Talmy and Langacker, when properly interpreted, can be shown to yield a detailed account of the structures of the judgment fields corresponding to sentences of different sorts. A new sort of correspondence-theoretic definition of truth for sentences of natural language can then be formulated on this basis

For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two other seminal figures in this development: H.L.A. Hart and John Rawls. We show that all three thinkers tend to assume that there is but one type of normativity within the realm of social institutions – roughly, the sort of normativity that is involved in following the results of chess – and that they thereby neglect features that are of crucial significance for an adequate understanding of social reality.

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research.

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria.

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.

It is argued, on the basis of ideas derived from Wittgenstein's Tractatus and Husserl's Logical Investigations, that the formal comprehends more than the logical. More specifically: that there exist certain formal-ontological constants (part, whole, overlapping, etc.) which do not fall within the province of logic. A two-dimensional directly depicting language is developed for the representation of the constants of formal ontology, and means are provided for the extension of this language to enable the representation of certain materially necessary relations. The paper concludes with a discussion of the relationship between formal logic, formal ontology, and mathematics.

The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types—for example in genotypes, phenotypes, and environment types—in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes.

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies in anatomy, physiology and pathology.

The object of the present paper is the philosophical commentary, a form of literature that once predominated in all major philosophical cultures from classical Greece to Renaissance Italy, but which has more recently fallen into comparative disuse. Commentaries on the writings of German thinkers such as Kant, Hegel, Marx and Heidegger have, certainly, kept the form alive to some extent in recent centuries; in the tradition of philosophy that was initiated by Descartes and Locke, however, and which constitutes the contemporary mainstream, the commentary genre has been utilized in systematic ways hardly at all, almost always by those concerned with other traditions, most especially with the philosophy of classical Greece. Why, then , should what has earlier proved so vital a plant in the literature of philosophy be so conspicuously absent from the philosophy of today? And why, uniquely among the canonical texts of contemporary analytic philosophy, should it be the writings of Wittgenstein that have spawned the growth of a commentary literature?

This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 MIE meeting in Geneva.

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

French translation of "Truth-Makers" (1984). A realist theory of truth for a class of sentence holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. The authors uphold the mutual independence of logical and ontological complexity. The theory is compared with that of Wittgenstein’s Tractatus, and the authors outline formal principles of truthmaking taking account of both kinds of complexity and suggesting how to overcome Wittgenstein’s problem of negation.

Revised version of chapter in J. N. Mohanty and W. McKenna (eds.), Husserl’s Phenomenology: A Textbook, Lanham: University Press of America, 1989, 29–67. Logic for Husserl is a science of science, a science of what all sciences have in common in their modes of validation. Thus logic deals with universal laws relating to truth, to deduction, to verification and falsification, and with laws relating to theory as such, and to what makes for theoretical unity, both on the side of the propositions of a theory and on the side of the domain of objects to which these propositions refer. This essay presents a systematic overview of Husserl’s views on these matters as put forward in his Logical Investigations. It shows how Husserl’s theory of linguistic meanings as species of mental acts, his formal ontology of part, whole and dependence, his theory of meaning categories, and his theory of categorial intuition combine with his theory of science to form a single whole. Finally, it explores the ways in which Husserl’s ideas on these matters can be put to use in solving problems in the philosophy of language, logic and mathematics in a way which does justice to the role of mental activity in each of these domains while at the same time avoiding the pitfalls of psychologism.

Much recent work on the intellectual background of Austrian economics reveals an unfortunate lack of awareness of the distinct nature of the Austrian contribution to philosophy, from which the Austrian economists drew many of their ideas. The present essay offers a sketch of this contribution, contrasting Austrian philosophy especially with the modes of philosophy dominant in Germany. This makes it possible to throw new light on the relations on Mises, Kant and the Vienna circle, and it allows us also to establish the extent to which Austrian economics might properly be seen as being allied to the German hermeneutic tradition of Dilthey, Gadamer, et al. The essay concludes with a criticism of the hermeneutic relativism recently canvassed by some Austrian economists, concentrating especially on the work of Don Lavoie, whose writing are treated as symptomatic of a wider and somewhat regrettable trend.

From the point of view of Brentano’s philosophy, contemporary philosophy of mind presupposes an over-crude theory of the internal structures of mental acts and states and of the corresponding types of parts, unity and dependence. We here describe Brentano’s own account of the part-whole structures obtaining in the mental sphere, and show how it opens up new possibilities for mereological investigation. One feature of Brentano’s view is that the objects of experience are themselves parts of mind, so that there is a sense in which for him (as e.g. for Leibniz) ontology is a proper part of rational or descriptive psychology.

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.

Dieses Buch betritt Neuland. Es ist eine Einführung in das neue Gebiet der angewandten Ontologie, jenem multidisziplinären Arbeitsgebiet, in dem Philosophen gemeinsam mit Informatikern und Vertretern der jeweils thematischen Wissenschaftsbereiche, in unserem Fall mit Biologen und Medizinern, daran arbeiten, wissenschaftliches Wissen informationstechnisch zu repräsentieren. Es zeigt, wie Philosophie eine praktische Anwendung findet, die von zunehmender Wichtigkeit nicht nur in den heutigen Lebenswissenschaften ist. Und so richtet sich dieses Buch an Philosophen, aber auch an interessierte Biologen, Mediziner und Informatiker.

We presuppose a position of scientific realism to the effect (i) that the world exists and (ii) that through the working out of ever more sophisticated theories our scientific picture of reality will approximate ever more closely to the world as it really is. Against this background consider, now, the following question: 1. Do the empirical theories with the help of which we seek to approximate a good or true picture of reality rest on any non-empirical presuppositions? One can answer this question with either a 'yes' or a 'no'. 'No' is the preferred answer of most contemporary methodologists -- Murray Rothbard is one distinguished counterexample to this trend -- who maintain that empirical theories are completely free of non-empirical ('a priori') admixtures and who see science as a matter of the gathering of pure 'data' obtained through simple observation. From such data scientific propositions are then supposed to be somehow capable of being established.

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

Human cognitive acts are directed towards objects extended in space of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. The theory of spatially extended objects should make room not only for the objects of physics but also for objects at higher levels, including the objects of geography and of related disciplines. It should leave room for different types of boundaries, including both the bona fide boundaries which we find in the physical world and the fiat (or human-demarcation-induced) boundaries with which much of geography has to deal. Two distinct axiomatic theories of boundaries are accordingly presented, and the need for both is examined in some detail. The resultant dual framework is shown to have application above all for our understanding of issues involving contact, division, and separation, issues which have posed serious difficulties for the ontological theories of boundaries that have been proposed hitherto.

Building on the writings of Wittgenstein on rule-following and deviance, Kristóf Nyíri advanced a theory of creativity as consisting in a fusion of conflicting rules or disciplines. Only such fusion can produce something that is both intrinsically new and yet capable of being apprehended by and passed on to a wider community. Creativity, on this view, involves not the breaking of rules, or the deliberate cultivation of deviant social habits, but rather the acceptance of enriched systems of rules, the adherence to which presupposes simultaneous immersion in disciplines hitherto seen as being unrelated. The paper presents a demonstration of the fruitfulness of this theory by means of an account of some of the political, cultural and intellectual peculiarities of the Habsburg Monarchy.

The paper seeks to indicate ways in which the crude distinction between Anglo-Saxon and Continental philosophy may have to be amended in light of recent developments in Eastern Europe. As is well known, the philosophy of science is to no small part a product of the universities of the Habsburg Empire (in Vienna, Prague, Lemberg/Lwow, etc.). Logic, too, has played a more significant role in Eastern Europe (not least in Poland) than in the philosophical cultures of Germany or France. For these and other reasons, a shift in the center of gravity of Continental philosophy is currently being realized, as younger Eastern European philosophers in newly liberalized institutions begin to return to their roots in their native pre-Communist intellectual traditions.