We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We (...) examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

In this paper, we develop an organizational account that defines biological functions as causal relations subject to closure in living systems, interpreted as the most typical example of organizationally closed and differentiated self-maintaining systems. We argue that this account adequately grounds the teleological and normative dimensions of functions in the current organization of a system, insofar as it provides an explanation for the existence of the function bearer and, at the same time, identifies in a non-arbitrary way the norms that (...) functions are supposed to obey. Accordingly, we suggest that the organizational account combines the etiological and dispositional perspectives in an integrated theoretical framework. IntroductionDispositional ApproachesEtiological TheoriesBiological Self-maintenance Closure, teleology, and normativityOrganizational differentiationFunctions C1: Contributing to the maintenance of the organization C2: Producing the functional trait Implications and Objections Functional versus useful Dysfunctions, side effects, and accidental contributionsProper functions and selected effectsReproductionRelation with other ‘unitarian’ approachesConclusions. (shrink)

Many years ago, C.B. Martin drew our attention to the possibility of ‘finkish’ dispositions: dispositions which, if put to the test would not be manifested, but rather would disappear. Thus if x if finkishly disposed to give response r to stimulus s, it is not so that if x were subjected to stimulus r, x would give response z; so finkish dispositions afford a counter‐example to the simplest conditional analysis of dispositions. Martin went on to suggest that finkish dispositions required (...) a theory of primitive causal powers; there, I think, he was mistaken. All that they require is an improved conditional analysis, and this improved analysis can be built upon whatever treatments of properties and of laws we may favour on other grounds. (shrink)

Objects have dispositions. As Nelson Goodman put it, “a thing is full of threats and promises”. But sometimes those threats go unfulfilled, and the promises unkept. Sometimes the dispositions of objects fail to manifest themselves, even when their conditions of manifestation obtain. Pieces of wood, disposed to burn when heated, do not burn when heated in a vacuum chamber. And pastries, disposed to go bad when left lying around too long, won’t do so if coated with lacquer and put on (...) display in a baker ’s window. Any account of what a disposition is, or of what it takes for an object to have a disposition, should be compatible with these commonplace observations. To date, I believe, no adequate account of dispositions has been given, and the aim of this paper is to defend one. (shrink)

This is the first philosophical study of artifacts that is book length. In it Randall Dipert develops a theory of what artifacts are and applies it extensively to one of the most complex and intriguing kind of artifacts, art works. He presents his own account of what agents, intentions, and actions are, then uses these notions to clarify what it is for an agent to "make" something. From this starting point, he develops a full theory of artifacts and other artificial (...) things - and, especially, a theory of art works and performances of art works as artifacts. He proposes a theory of nature and of the value of nature as what is essentially nonartificial. Two chapters are devoted to value considerations: merit in artifacts generally, and the evaluation of art works and performance art as artifacts or intentional gestures. Believing that a developed theory of action and philosophy of mind is necessary for a developed aesthetics and philosophy of art, Dipert relies on classical and contemporary research on agency, actions, and intentions, and on the intentionalist theory of mental objects of Brentano and Meinong. Dipert considers artifacts to be physical entities, but he also includes in the definition thoughts, utterances, and performances. This vast category encompasses everyday household objects and tools, streets and edifices, as well as communicative and artistic artifacts. Especially with regard to artistic artifacts, Dipert proposes a theory of expression and communication as actions and extensively discusses the problems of interpreting and recognizing actions, artifacts, and art works. (shrink)

Formulations of the essential commitment of the etiological theory of functions have varied significantly, with some individual authors' formulations even varying from one place to another. The logical geography of these various formulations is different from what is standardly assumed; for they are not stylistic variants of the same essential commitment, but stylistic variants of two non-equivalent versions of the etiological theory. I distinguish these “strong” and “weak” versions of the etiological theory (which differ with respect to the role of (...) selection in their definitions of function), draw out their respective implications, and argue that the weak version is to be preferred to the strong. (shrink)

In this paper I discuss a recent theory on functions called Organizational Account. This theory seeks to provide a new definition of function that overcomes the distinction between etiological and dispositional accounts and that could be used in biology as well as in technology. I present a definition of function that I think captures the intuitions of Organizational Accounts and consider several objections.

Philosophers of evolutionary biology favor the so-called etiological concept of function according to which the function of a trait is its evolutionary purpose, defined as the effect for which that trait was favored by natural selection. We term this the selected effect (SE) analysis of function. An alternative account of function was introduced by Robert Cummins in a non-evolutionary and non-purposive context. Cummins''s account has received attention but little support from philosophers of biology. This paper will show that a similar (...) non-purposive concept of function, which we term causal role (CR) function, is crucial to certain research programs in evolutionary biology, and that philosophical criticisms of Cummins''s concept are ineffective in this scientific context. Specifically, we demonstrate that CR functions are a vital and ineliminable part of research in comparative and functional anatomy, and that biological categories used by anatomists are not defined by the application of SE functional analysis. Causal role functions are non-historically defined, but may themselves be used in an historical analysis. Furthermore, we show that a philosophical insistence on the primary of SE functions places practicing biologists in an untenable position, as such functions can rarely be demonstrated (in contrast to CR functions). Biologists who study the form and function of organismal design recognize that it is virtually impossible to identify the past action of selection on any particular structure retrospectively, a requirement for recognizing SE functions. (shrink)

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

The great philosopher and historian of philosophy, Etienne Gilson, sets out to show that final causality or purposiveness and formal causality are principles for those who think hard and carefully about the world, including the world of biology. Gilson insists that a completely rational understanding of organisms and biological systems requires the philosophical notion of teleology, the idea that certain kinds of things exist and have ends or purposes the fulfillment of which are linked to their natures-in other words, formal (...) and final causes. His approach relies on philosophical reflection on the facts of science, not upon theology or an appeal to religious authorities such as the Church or the Bible. (shrink)

In recent decades, the analysis of causal relations has become a topic of central importance in analytic philosophy. More recently, dispositional properties have also become objects of intense study. Both of these phenomena appear to be intimately related to counterfactual conditionals and other modal phenomena such as objective chance, but little work has been done to directly relate them. This collection contains ten essays by scholars working in both metaphysics and in philosophy of science, examining the relation between dispositional and (...) causal concepts. (shrink)

In Aristotle's teleological view of the world, natural things come to be and are present for the sake of some function or end. Whereas much of recent scholarship has focused on uncovering the physical underpinnings of Aristotle's teleology and its contrasts with his notions of chance and necessity, this book examines Aristotle's use of the theory of natural teleology in producing explanations of natural phenomena. Close analyses of Aristotle's natural treatises and his Posterior Analytics show what methods are used for (...) the discovery of functions or ends that figure in teleological explanations, how these explanations are structured, and how well they work in making sense of phenomena. The book will be valuable for all who are interested in Aristotle's natural science, his philosophy of science, and his biology. (shrink)

Preface by Daniel C. Dennett Beginning with a general theory of function applied to body organs, behaviors, customs, and both inner and outer representations, ...

This volume takes on both issues and examines the relationship between organisms and artifacts from the perspective of functionality.

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)

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. (shrink)

Medical science conceives the human body as a system comprised of many subsystems at a variety of levels. At the highest level are bodily systems proper, such as the endocrine system, which are central to our understanding of human anatomy, and play a key role in diagnosis and in dynamic modeling as well as in medical pedagogy and computer visualization. But there is no explicit definition of what a bodily system is; such informality is acceptable in documentation created for human (...) beings, but falls short of what is needed for computer representations. Our analysis is intended as a first step towards filling this gap. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...) thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

John Searle began to discuss his recently published book `The Construction of Social Reality' with Anthony Freeman, and they ended up talking about God. The book itself and part of their conversation are introduced and briefly reflected upon by Anthony Freeman. Many familiar social facts -- like money and marriage and monarchy -- are only facts by human agreement. They exist only because we believe them to exist. That is the thesis, at once startling yet obvious, that philosopher John Searle (...) explores in The Construction of Social Reality. (shrink)

This article gives a general overview of recent metaphysical work on dispositional properties and causal relations. It serves as an introduction to the edited volume, Dispositions and Causes.

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