The Theory and Practice of Ontology
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The Theory and Practice of Ontology

Leo Zaibert, Leo Zaibert

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The Theory and Practice of Ontology

Leo Zaibert, Leo Zaibert

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About This Book

This book provides close examination of ontology and the work of Professor Barry Smith, one of the most prolific philosophers of the modern day. In this book numerous scholars who have collaborated with Smith explore the various disciplines in which the impact of his work has been felt over the breadth of his career, including biology, computer science and informatics, cognitive science, economics, genetics, geography, law, neurology, and philosophy itself. While offering in-depth perspectives on ontology, the book also expands upon the breadth of Smith's influence. With insights from renowned and influential scholars from many different countries, this book is an informative and enlightening celebration of all Smith has contributed to numerous academic schools of thought.

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Year
2016
ISBN
9781137552785
© The Author(s) 2016
Leo Zaibert (ed.)The Theory and Practice of Ontology10.1057/978-1-137-55278-5_1
Begin Abstract

1. Introduction

Leo Zaibert1  
(1)
Union College, Schenectady, NY, USA
 
 
Leo Zaibert
End Abstract
In one way or another—and often in various ways—all the contributors are indebted to Barry Smith. Some of us were Smith’s students, and took our first steps in academia in the context of collaborative work with him. But even those who have never been, technically speaking, Smith’s students, have nonetheless immensely benefited from his penetrating intelligence. As a matter of fact, in connection to Smith, the categories of “student”, “colleague”, and “collaborator”, exhibit remarkable overlaps. All the contributors are equally grateful to Barry and they dedicate this volume to him, in friendship and in admiration indeed.
In terms of number of publications, Smith is one of the most prolific philosophers of his generation. In addition to his prodigious output, the articles contained in this volume reveal another impressive aspect of his career: the number of disciplines in which the influence of his work has been felt: biology, computer science and informatics, cognitive science, economics, genetics, geography, law, neurology, and philosophy itself. Smith has published important articles in all of these areas, and he has also received prestigious awards by the professional governing bodies of these diverse disciplines. He even holds professorships in six of these fields. Few scholars have ever materialized the real value of interdisciplinarity in anything like the way Smith has. The wide-ranging relevance of his work thus constitutes another, perhaps even more powerful, reason for publishing a volume such as this.
Smith received his BA in mathematics and philosophy (First Class Honours) from Oxford University in 1973—a degree which was subsequently converted to a MA in 1977—and his PhD in philosophy from the University of Manchester in 1976, with a dissertation titled “The Ontology of Reference: Studies in Logic and Phenomenology”. He has held academic posts at the Universities of Sheffield and Manchester, at the International Academy of Philosophy (in Liechtenstein), and, since 1994, at the State University of New York at Buffalo. He has been an invited professor in dozens of universities across the globe, and he is a member of the editorial board of dozens of peer-reviewed publications. His work has been funded by the National Institutes of Health, the National Science Foundation, the Department of Defense, the European Union, the Volkswagen Foundation, and the Alexander von Humboldt Foundation, to name a few. No philosopher comes close to Smith in terms of the number of grants he has received, or in terms of the financial significance of those grants.
Smith’s early interests, captured in the title of his dissertation, have remained at the center of his investigations during his long and fruitful career, and they are key in helping us understand how Smith has been able to contribute to so many diverse disciplines, and indeed how his influence is to be appreciated in the contributions to this volume. Above all, he has been preoccupied with the fundamental structure of the universe: with what philosophers have traditionally called “metaphysics” or “ontology”. Given the ebb and flow of human intellectual pursuits, and given the progressive specialization of human knowledge and the subsequent proliferation of different disciplines and sub-disciplines, this important branch of philosophy became just that—a branch of philosophy, without much connection to the sciences or practical affairs. Interestingly, however, it was nothing other than metaphysics that, say, the early pre-Socratic philosophers thought they were doing—and they did not see this focus as separate from their concern with what throughout different periods in human history have been labeled “purely” scientific endeavors. While in the Renaissance we witness efforts to emphasize the connections between philosophy and the sciences, these connections were particularly significant in the twentieth-century school of phenomenology, particularly in the work of Edmund Husserl. Smith has been greatly influenced by Husserl (he has published considerably on Husserl, and is the co-editor of the authoritative The Cambridge Companion to Husserl). Steeped in this phenomenological tradition, Smith sees his investigations as at once ontological (and thus philosophical) and scientific.
There is, of course, nothing objectionable about projects in, say, the philosophy of medicine, or the philosophy of music, and so on. But it is important to emphasize that this is not what Smith has done. Rather, he has mobilized philosophical tools and methods so that he can contribute to medicine itself, music itself, and so on. It is not that philosophers, qua philosophers, are familiar with the specific facts of medicine or music (etc.)—they are clearly not (hence the need for collaborative approaches such as those which Smith often directs). But philosophers do know better than physicians and musicians (etc.) how to conceptualize some abstract features of these very disciplines, and how to understand the relations between the different entities which fall under the purview of these disciplines. Philosophy, in the sense Smith practices it, is not a meta-discipline that hovers over other disciplines: it is, rather, the quintessential infra-discipline, which lives within these other disciplines.
That philosophers are better equipped to investigate and analyze the fundamental structure of the universe than any other professionals or academics has been Smith’s animating conviction throughout his career. It is, after all, philosophers who are trained to deal with metaphysical or ontological questions. And it is philosophers, too, who are trained in formal logic, and thus likelier than others to approach these ontological questions with the rigor and systematicity that logic presupposes. So, in Smith’s opinion, it is precisely in virtue of their expertise with those essentially philosophical tools that philosophers are so well-suited to come to the help of other disciplines. Smith’s work shows that this help goes much farther than conceptual clarity. The use to which Smith has put the philosophical tools afforded by ontology and logic in the service of other disciplines has been truly revolutionary.
Chronologically listing the title of some of Smith’s influential publications provides hints as to why the preceding assertion is not hyperbolic at all. “The Ontogenesis of Mathematical Objects” (1975), “Logic, Form and Matter” (1981), “The Substitution theory of Art” (1986), “Textual Deference” (1991), “Putting the World Back into Semantics” (1993), “Formal Ontology, Common Sense, and Cognitive Science” (1995), “Geographical Categories: An Ontological Investigation” (2001), “The Metaphysics of Real Estate” (2001), “Husserlian Ecology” (2001), “Quantum Mereotopology” (2002), “Do Mountains Exist? Towards an Ontology of Landforms” (2003), “Biomedical Informatics and Granularity” (2004), “On Carcinomas and Other Pathological Entities” (2005), “Referent Tracking for Digital Rights Management” (2007), “Framework for a Protein Ontology” (2007), “Foundations for a Realist Ontology of Mental Disease” (2010), “Towards an Ontology of Pain (2011), “How to Do Things with Documents” (2012). As can be surmised from the titles above—some of which have appeared in leading publications outside of philosophy—Smith has contributed concrete, in-house advancements in many disciplines.
In addition to the indirect evidence we could glean from these titles and from the sheer output of Smith’s work, consider one example of the sort of strategy which Smith has employed in bringing philosophical tools to bear on other disciplines: the case of medicine, and in particular through the lens of the work of the Institute for Formal Ontology and Medical Information Science (IFOMIS), which Smith founded in 2001, after he was awarded the two million Euros attached to the Wolfgang Paul Prize, with which the Alexander von Humboldt Foundation honored him. Imagine a team of physicians who undertake to collate and systematize data surrounding a certain disease, in order to, for example, develop software that may render the diagnosis and treatment of this disease more efficient. It is of course common knowledge that physicians cannot undertake this project alone—computer scientists would be needed in this enterprise. What is not commonly acknowledged is that a team of physicians and computer scientists working together would still need ontologists—that is, philosophers.
Neither physicians nor musicians (etc.), after all, are likely to understand—and at any rate are not trained to understand—the sometimes subtle but nonetheless important differences between the sorts of relations that may obtain between the fundamental entities with which their disciplines deal. For example, there are important differences between parts and proper parts; and there are important differences between something being either a part or a proper part of something else, on the one hand, and it being caused by that something else, on the other; between two entities overlapping and two entities underlapping, amongst many others. Smith’s efforts in this area have both highlighted the ways in which philosophically uninformed approaches to medicine have failed, and have helped his team of researchers develop conceptual apparatuses better able to capture the ontological foundations of medicine. The results of Smith’s efforts at the helm of IFOMIS can be appreciated not only by looking at the many academic publications that the institute has produced, but by the fact that other organizations—form the Volkswagen Foundation to the National Institute of Health—have continued to support his projects in this area, to the tune of many millions of dollars.
This volume is not conceived only as a celebration of Smith’s work. It is also a stand-alone testament to how genuinely fruitful the work has been, and how the contributors take insights or interests prompted by his work in different directions. While not all of the contributions are about Smith’s work directly, they all resonate well with topics to which he has devoted attention. The general theme that pervades the volume is, of course, connected to ontology. But the range of specific topics covered herein reflects the dizzying breadth of Smith’s own career, and of the value of ontology. Preferring to let them speak for themselves, I shall only offer one-line summaries of the chapters, merely in order to offer at once a glimpse on the richness of the volume.
The volume opens with Peter Simons’s “Ontologia Utens and Beings in Time”, and with his investigation of the connections between “ontology” in the classical Aristotelian sense and the sort of novel applied realms to which Smith, above all, has put it to use. In “Against Fantology Again”, Ingvar Johansson takes on Smith’s attacks on a widespread assumption in contemporary philosophy whereby the fundamental elements of ontology track the fundamental aspects of logical syntax. Achille Varzi, in “On Drawing Lines across the Board”, turns our attention to the implications of Smith’s work on the distinction between fiat and bona fide boundaries, not only regarding geography itself but regarding the surprisingly many other general areas of investigation in which it applies as well.
In “Social Reality, Law, and Justice”, David Koepsell further highlights the scope of Smith’s ontology by exploring its connection to some central worries of jurisprudence and to the burgeoning field of social ontology. Some of these concerns are further explored by Alessandro Salice’s “Acts of Terror as Collective Violent Acts”, in which an analysis of the elusive notion of terrorism is advanced. Maurizio Ferraris, in his “Letter of Pharisaism”, discusses the implications of Heidegger’s Nazism (particularly in light of the recent publication of the Black Notebooks). In “Just Organic Wholes”, Leo Zaibert pays attention to the ways in which what Smith has dubbed the tradition of “Austrian Philosophy” may offer an unusually penetrating lens through which to look at the problem of the justification of punishment.
In “‘Pain’ in SNOMED CT: Is There an Anesthetic?” Werner Ceusters and Jonathan P. Bona offer an example of the sort of practical applications to which ontology can be put to use by examining the ways in which the Systematized Nomenclature of Medicine—Clinical Terms deals with pain. Similarly, in his “The Structure of Standard Musical Notation”, Roberto Casati discusses both some principles that govern the representation of time in standard music notation, and some cognitive consequences of such notation. In her “Attitude: How we Learn to Inhabit the Future”, Mariam Thalos offers a phenomenological account of the perception of time, and of how humans experience it at different stages of their lives. In her “Parental Love and the Meaning of Life” Berit Brogaard discusses some unsavory aspects of motherhood, by considering how motherhood conflicts with other valuable aspects of existence such as autonomy and welfare. And in “Foolishness and the Value of Knowledge” Kevin Mulligan closes the volume by presenting an analysis of foolishness in which it is importantly distinguished from stupidity, and in which it is seen as a form of an intellectual vice.
As it turns out the last note of the last article in the volume can be put to use in concluding this brief introduction as well. For not only does it appropriately conclude Mulligan’s piece, but it offers an invitation to consider some of the multifarious ways in which Smith’s seminal work on ontology—both theoretical and applied—yield fruit in the contributions contained herein.
This tribute to Barry Smith has touched on only a few of the topics he has illuminated over a long and extraordinarily productive career, a career driven by an unusually large range of strong interests pursued in a very determined fashion. Barry Smith, his friends and admirers all agree, is in many ways an epistemic hero.
© The Author(s) 2016
Leo Zaibert (ed.)The Theory and Practice of Ontology10.1057/978-1-137-55278-5_2
Begin Abstract

2. Ontologia Utens and Beings in Time

Peter Simons1
(1)
Trinity College, Dublin, Ireland
Peter Simons
End Abstract

1 Useful Ontology

Ontology, despite the relative newness of its name, goes back to Aristotle’s principal definition of metaphysics as the science of being as being. Christian Wolff divided metaphysics into ontology or general metaphysics on the one hand and three branches of just slightly less general special metaphysics on the other. Husserl renamed the two sides as formal ontology (general) versus regional ontologies (special), while Donald Williams called the former analytic ontology and the latter speculative cosmology. Amid this terminological plethora it is sensible to stay with ontology as the name for the general part. But as the most general part of the most general discipline, how could ontology ever be useful? To see how useful it indeed is when understood sensibly and deployed as a general framework for database ontologies, it suffices to look at Barry Smith’s work, not only his philosophical articles but more particularly his impassioned advocacy of realist philosophical ontology as the best framework in the construction and conceptual structuring of databases in all manner of subjects from genetics, medicine and other biomedical sciences to geography and the military. To achieve this penetration, Smith brought decades of work and experience in philosophy and its history, all conducted from a robust realist perspective and drawing on an encyclopedic knowledge of scientific philosophy from the last 150 years, including many of its less well-known corners.
It would be otiose to add further injunctions to take scientific ontology seriously and apply it as Smith has done to all of his well-argued articles. Those who have benefitted from the sensible and well-designed Basic Formal Ontology (BFO) can attest to the improvements wrought by taking this tool in designing computer ontologies. Since Smith and I agree on nearly all important philosophical matters and likewise on the need to apply ontology in the interest of clean and efficient data, in this paper I shall focus on one area in ontology in which we have a (fairly minor) difference of opinion, namely the relationship between objects that persist in time, continuants and occurrents.

2 Continuants and Occurrents: The Distinction

Consider objects in time. Perhaps there are some that exist instantaneously, for example a particularly shaped shadow cast by two objects that cross in front of one another in the sun, but aside from these, all the objects we encounter (and any of whose existence we can be sure) last for a period of time, even if a very short one. We shall confine attention to these. Following W.E. Johnson, we make a fundamental distinction between two ways in which objects that persist are in time. Some persist by getting longer and longer in temporal extent. These are occurrents, so called because their typical exemplars are events and processes, which occur or happen or go on. A popular kind of occurrent is a race, of which there are many kinds, involving humans, animals and machines: examples of these three genres are respectively a marathon, a greyhound race, and a Formula One motor race. A race lasts for a certain time, from the moment when the competitors are set off to the moment the last competitor to complete the course does so, and the winner is, of course, the competitor that completes the course in the shortest time. That stretch of time gives the clue to the nature of a race: it has a beginning, lasts for a period after that, and comes to an end. The temporal interval from beginning to end is its duration, and this can be subdivided into shorter sub-intervals, such as the first five seconds, or middle third, or the second half. Some of these sub-intervals are arbitrarily like these, others may be determined by physical features of the race, for example the period between the leader starting and completing a certain lap. Races are sometimes abandoned before they finish, for a variety of reasons, and when this happens, the incomplete or abandoned race itself has a duration, which is shorter than would have been the duration had the race proceeded to completion. All of this is well known, but the point is to illustrate the fundamental property of occurrents: that they last for a certain time, or, as Smith and his collaborators say, they span an interval of time. Ontologies dealing with such items are called by them SPAN ontologies.
Because occurrents span intervals, they have longer and shorter parts which span sub-intervals of the total interval. Another way to put this is to say that occurrents have temporal parts, that is to say, parts of the total occurrent which last a shorter time than the whole but which, when they are occurring, comprise all of the occurrent as then ha...

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