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.

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.

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.

Being an "untimely review", this paper reviews Aristotle's 'Categories' as if they were published today, in the era of computerised information, where categorisation becomes more and more essential for information retrieval. I suggest a systematic ordering of Aristotle's list of categories and argue that Aristotle's discussion of ontological dependency and his focus on concrete entities are still a source of new insight and can indeed be read as a contribution to the emerging field of applied ontology and ontological engineering.

Darwinists classify biological traits either by their ancestry (homology) or by their adaptive role. Only the latter can provide traditional natural kinds, but only the former is practicable. Process structuralists exploit this embarrassment to argue for non-Darwinian classifications in terms of underlying developmental mechanisms. This new taxonomy will also explain phylogenetic inertia and developmental constraint. I argue that Darwinian homologies are natural kinds despite having historical essences and being spatio-temporally restricted. Furthermore, process structuralist explanations of biological form require an unwarranted (...) assumption about the space of developmental possibility. (shrink)

In theMetaphysics, Aristotle pointed out that some activities are engaged in for their own sake, while others are directed at some end. The test for distinguishing between them is to ask, ‘At any time during a period in which someone is Xing, is it also true that they have Xed?’ If both are true, the activity is being done for its own sake. If not, it is being done for the sake of some end other than itself. For example, if (...) I am thinking, it is true that I have thought. But if I’m making a blouse, it is not true that I have made a blouse, at least not this particular blouse. That’s not true until I have completed the project.There have been a number of attempts to deepen our understanding of this distinction. Anthony Kenny devoted a chapter of Action, Emotion, and Will to this issue, exploring the effect tense has on implication relations, and using that as a basis for dividing verbs of action into state-verbs, activity-verbs and performance-verbs. In more recent years the trend has been to generalize these categories so as to include occurrences other than actions, i.e., occurrences which do not involve intentions. While interest in this area tends to focus primarily on linguistic issues, such as the categorization of verbs, or on the logical analysis of sentences, there has been some interest in related metaphysical issues. In 1978 Alexander Mourelatos published ‘Events, Processes, and States,’ a paper which has turned out to be quite influential, in which he proposes an ontological trichotomy of occurrences. In his view, processes and events form distinct categories within the general category of occurrences. In this paper I will examine the reasoning underlying Mourelatos’s claim, arguing that the differences between processes and events cannot provide the basis for an ontological subcategorization of occurrences. (shrink)

This is a book about how we see: the environment around us (its surfaces, their layout, and their colors and textures); where we are in the environment; whether or not we are moving and, if we are, where we are going; what things are good for; how to do things (to thread a needle or drive an automobile); or why things look as they do.The basic assumption is that vision depends on the eye which is connected to the brain. The (...) author suggests that natural vision depends on the eyes in the head on a body supported by the ground, the brain being only the central organ of a complete visual system. When no constraints are put on the visual system, people look around, walk up to something interesting and move around it so as to see it from all sides, and go from one vista to another. That is natural vision—and what this book is about. (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)

Since its publication in 1959, Individuals has become a modern philosophical classic. Bold in scope and ambition, it continues to influence debates in metaphysics, philosophy of logic and language, and epistemology. Peter Strawson's most famous work, it sets out to describe nothing less than the basic subject matter of our thought. It contains Strawson's now famous argument for descriptive metaphysics and his repudiation of revisionary metaphysics, in which reality is something beyond the world of appearances. Throughout, Individuals advances some highly (...) influential and controversial ideas, such as 'non-solipsistic consciousness' and the concept of a person a 'primitive concept'. (shrink)

Argues for the primacy of the phylogenetic system as the general reference system in biology. This book, first published in 1966, generated significant controversy and opened possibilities for evolutionary biology.

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 ...

In this important new book Nagel, one of the most distinguished philosophers writing in English today, presents a sustained defence of reason against the attacks of subjectivism. He offers systematic rebuttals of relativistic claims with respect to language, logic, science, and ethics.

_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._.

What makes a biological entity an individual? Jack Wilson shows that past philosophers have failed to explicate the conditions an entity must satisfy to be a living individual. He explores the reason for this failure and explains why we should limit ourselves to examples involving real organisms rather than thought experiments. This book explores and resolves paradoxes that arise when one applies past notions of individuality to biological examples beyond the conventional range and presents an analysis of identity and persistence. (...) The book's main purpose is to bring together two lines of research, theoretical biology and metaphysics, which have dealt with the same subject in isolation from one another. Wilson explains an alternative theory about biological individuality which solves problems which cannot be addressed by either field alone. He presents a more fine-grained vocabulary of individuation based on diverse kinds of living things, allowing him to clarify previously muddled disputes about individuality in 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, ...

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)

A systematic overview of modern metaphysics, A Survey of Metaphysics covers all of the most important topics in the field. It adopts the fairly traditional conception of metaphysics as a subject that deals with the deepest questions that can be raised concerning the fundamental structure of reality as a whole. The book is divided into six main sections that address the following themes: identity and change, necessity and essence, causation, agency and events, space and time, and universals and particulars. It (...) focuses on contemporary views and issues throughout, rather than on the history of metaphysics. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

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)

There are various puzzles that set our intuitions about composition and identity against one another. Four that are particularly well known are the Growing Argument, the Ship of Theseus Puzzle, the Body-minus Argument, and Allan Gibbard’s puzzle about Lumpl and Goliath. Such puzzles have received a great deal of attention in the literature over the past thirty years, and there is an impressive and growing variety of solutions available for each of them. Surprisingly, however, no one has really discussed how (...) all of the different puzzles, and their solutions, are interrelated. On the surface, they seem to raise different problems; but clearly the puzzles are related somehow. They raise similar questions and generate similar sets of possible solutions. But, as yet, nothing has been said about how far the similarities extend. (shrink)

Both and agree that there are universals—that qualities are universals. To say that the quality white is a universal is to say, in part, that one and the same thing is connected in some way to both Plato and Socrates and accounts for the truth of the sentences "Plato is white" and "Socrates is white." To put it another way, the term "white" in both sentences refers to the same entity. What arguments are there for such a view? Russell elegantly (...) put forth the classic argument in "On the Relations of Universals to Particulars." To deny universals is to assert that the quality attributed to Socrates is not one and the same with the quality attributed to Plato. The quality "in" each is numerically distinct and, furthermore, no one thing accounts for these distinct qualities being of the same kind. [I mention this latter point since one might, on a version of, hold that there are particular qualities as well as universal qualities. The former account for the whiteness of particular patches; the latter for such particular whitenesses being just that.] One must then hold that such particular qualities are related in some way, since they are the entities in virtue of which we truly assert that both things are white. One must then specify such a relation. The obvious point is that such a relation will either be taken as a universal or a particular instance. If a particular then the original problem recurs when we introduce a third white patch or a pair of black patches. If admitted as a universal then the view finally accepts universals, albeit relational ones. No other alternative can answer the original question—to account for Socrates and Plato having the same color. That is, no alternative acknowledging only individuals—that denies the two patches are connected, in some way, to one and the same entity—can prevent the recurrence of exactly the same kind of question we started out with. Let us consider the case of particulars. One may argue that just as universals account for the sameness of quality, something must account for the difference of two patches which, conceivably, have all their nonrelational qualities in common. This something, the ground of numerical difference, is considered to be a substratum which stands in a unique relation or connection with universals to form or constitute facts and the things we started out with, Plato and Socrates. These ordinary things are thought of as composed of a substratum and universals connected together. Facts about such things may be composed of the substratum and one universal. The facts are about the things since the same substratum is a constituent of both sorts of entities. Such substrata account for the difference of the two patches; for there being two and not one thing. These substrata, in turn, are held to be simply different. At this point one may balk. If substrata are held to be simply different, why bother with them at all? Why not hold that Socrates and Plato are composites, not classes, of universals, and that they are different composites of the same universals? They just simply differ. If substrata can simply differ, why may not composites of universals simply differ? The proponent of substrata must retort that since Plato and Socrates are composite entities they cannot simply differ but must be held to differ in a constituent. Only simple entities can simply differ. Let me call this assertion the axiom of difference. The first point to note is that it is a necessary assumption in the argument to establish the need for substrata in an adequate ontology. We must then inquire why some accept, implicitly or explicitly, such an axiom. (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)

Ontology as a branch of philosophy is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality. ‘Ontology’ in this sense is often used by philosophers as a synonym of ‘metaphysics’ (a label meaning literally: ‘what comes after the Physics’), a term used by early students of Aristotle to refer to what Aristotle himself called ‘first philosophy’. But in recent years, in a development hardly noticed by philosophers, the (...) term ‘ontology’ has gained currency in the field of computer and information science, and in information-driven research in bioinformatics and related areas. We examine these new developments in applied ontology, and show what lessons they might have for both philosophers and information scientists. (shrink)

Die biomedizinische Forschung hat ein Kommunikationsproblem. Um die Ergebnisse ihrer Arbeit darzustellen, greifen einzelne Forschergruppen auf unterschiedliche und oft inkompatible Terminologien zurück. Für den Fortschritt der modernen Biomedizin ist die Integration dieser Ergebnisse jedoch unabdingbar.

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (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.