The purpose of this paper is to provide an account of the epistemology and metaphysics of universe creation on a computer. The paper begins with F.J.Tipler's argument that our experience is indistinguishable from the experience of someone embedded in a perfect computer simulation of our own universe, hence we cannot know whether or not we are part of such a computer program ourselves. Tipler's argument is treated as a special case of epistemological scepticism, in a similar vein to `brain-in-a-vat' arguments. (...) It is argued that the hypothesis that our universe is a program running on a digital computer in another universe generates empirical predictions, and is therefore a falsifiable hypothesis. The computer program hypothesis is also treated as a hypothesis about what exists beyond the physical world, and is compared with Kant's metaphysics of noumena. It is proposed that a theory about what exists beyond the physical world should be formulated with the precise concepts of mathematics, and should generate physical predictions. It is argued that if our universe is a program running on a digital computer, then our universe must have compact spatial topology, and the possibilities of observationally testing this prediction are considered. The possibility of testing the computer program hypothesis with the value of the density parameter Omega_0 is also analysed. The informational requirements for a computer to represent a universeexactly and completely are considered. Consequent doubt is thrown upon Tipler's claim that if a hierarchy of computer universes exists, we would not be able to know which `level of implementation' our universe exists at. It is then argued that a digital computer simulation of a universe cannot exist as a universe. However, the paper concludes with the acknowledgement that an analog computer simulation can be objectively related to the thing it represents, hence an analog computer simulation of a universe could, in principle, exist as a universe. (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics (...) domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

The main aim of this paper is to characterize Maurizio Ferraris’ New Realism as a metaphilosophical account that develops Peter Strawson’s project of a descriptive metaphysics. The paper consists of two sections. The former outlines Strawson’s descriptive metaphysics by highlighting its realist commitments. The latter characterizes New Realism as a way of turning Strawson’s metaphysics into a metaphilosophy. New Realism moves from Strawson’s metaphysical description of the world we share through our experience to the metaphilosophical claim that philosophy should primarily (...) consist in this kind of description. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

The discipline of ontology has enjoyed a checkered history since 1606, with a significant expansion in recent years. We focus here on those developments in the recent history of philosophy which are most relevant to the understanding of the increased acceptance of ontology, and especially of realist ontology, as a valuable method also outside the discipline of philosophy.

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the (...) relation between fetus and mother (connection, parthood, dependence). (shrink)

The philosophy of information (PI) is a new area of research with its own field of investigation and methodology. This article, based on the Herbert A. Simon Lecture of Computing and Philosophy I gave at Carnegie Mellon University in 2001, analyses the eighteen principal open problems in PI. Section 1 introduces the analysis by outlining Herbert Simon's approach to PI. Section 2 discusses some methodological considerations about what counts as a good philosophical problem. The discussion centers on Hilbert's famous analysis (...) of the central problems in mathematics. The rest of the article is devoted to the eighteen problems. These are organized into five sections: problems in the analysis of the concept of information, in semantics, in the study of intelligence, in the relation between information and nature, and in the investigation of values. (shrink)

Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artificial (...) intelligence encouraged by these successes, especially in the domain of language processing. We then show an alternative approach to language-centric AI, in which we identify a role for philosophy. (shrink)

Do Web devices (addresses, tags, networks, and the rest) have counterparts in classical ontology? Yes, but they allow us also to introduce more refined distinctions. In addition, their dynamic use could inspire a dynamic reconception of classical ontology. In the process of making explicit ontological types, different types can be undistinguished at the first step (considered as “floating types”) to be defined only in a further step, one in which their function as distinguishers of other kinds of entities has to (...) be made explicit. The fact that the ontological import of some node in a network of tags and addresses could evolve with the transformation of the network can most easily find an interpretation in this dynamic conception of ontology. (shrink)

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...) geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (shrink)

Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those who (...) created them, and unable to serve as inputs for automated reasoning. This volume shows, in a nontechnical way and using examples from medicine and biology, how the rigorous application of theories and insights from philosophical ontology can improve the ontologies upon which information management depends. (shrink)

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)

This paper explores the possibility of building a coherent knowledge base for philosophyof design in IS research. After identifying and categorizing what is considered as designissues in the IS field, we propose a taxonomy of design abstractions in the form of a meta-theoretical structure. Based on the proposed hierarchical taxonomy, we have conducteda concept-centric literature review on four leading IS research journals publishedbetween January 2011 and July 2016. Our result shows that the IS field struggles withmisalignment of philosophy of design (...) issues, including constructing design theory,research positioning, and an inconsistent knowledge base in design subject areas such asethics and aesthetics. It is suggested that integrating philosophy of design into IS researchcould contribute to the development of a coherent body of design knowledge. We concludeby proposing a model both to study and integrate philosophy of design into the ISresearch field. (shrink)

Cognitive sciences as an interdisciplinary field, involving scientific disciplines (such as computer science, linguistics, psychology, neuroscience, economics, etc.), philosophical disciplines (philosophy of language, philosophy of mind, analytic philosophy, etc.) and engineering (notably knowledge engineering), have a vast theoretical and practical content, some even conflicting. In this interdisciplinary context and on computational modeling, ontologies play a crucial role in communication between disciplines and also in a process of innovation of theories, models and experiments in cognitive sciences. We propose a model for (...) this process here. An ontological commitment is advocated as the framework of a scientific realism, which leads computational modeling to search for more realistic models, for a complex systems perspective of nature and cognition. In that way multiagent modeling of complex systems has been fulfilling an important role. (shrink)

Do mountains exist? The answer to this question is surely: yes. In fact, ‘mountain’ is the example of a kind of geographic feature or thing most commonly cited by English speakers (Mark, et al., 1999; Smith and Mark 2001), and this result may hold across many languages and cultures. But whether they are considered as individuals (tokens) or as kinds (types), mountains do not exist in quite the same unequivocal sense as do such prototypical everyday objects as chairs or people.

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński.

Attempts to trace a unifying thread of ontological realism extending through 1. my early writings on Frege, Brentano, Husserl, Wittgenstein, Ingarden and (with Kevin Mulligan and Peter Simons) on truthmakers; 2. work on formal theories of the common-sense world, and on mereotopology, fiat objects, geographical categories, and environments (with David Mark, Roberto Casati, Achille Varzi), to 3. current work on applied ontology in biology and medicine, and on the theory of document acts and on the ontology of information artifacts.

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

Initially the problems of data integration, for example in the field of medicine, were resolved in case by case fashion. Pairs of databases were cross-calibrated by hand, rather as if one were translating from French into Hebrew. As the numbers and complexity of database systems increased, the idea arose of streamlining these efforts by constructing one single benchmark taxonomy, as it were a central switchboard, into which all of the various classification systems would need to be translated only once. By (...) serving as a lingua franca for database integration this benchmark taxonomy would ensure that all databases calibrated in its terms would be automatically compatible with each other. We describe one strategy for creating such a lingua franca, in which philosophical ontology plays a central role. (shrink)

The paper assumes that to be of practical interest process must be understood as physical action that takes place in the world rather than being an idea in the mind. It argues that if an ontology of process is to accommodate actuality, it must be represented in terms of relative probabilities. Folk physics cannot accommodate this, and so the paper appeals to scientific culture because it is an emergent knowledge of the world derived from action in it. Process is represented (...) as a contradictory probability distribution that does not depend on a spatio-temporal frame. An actuality is a probability density that grounds the values of probabilities to constitute their distributions. Because probability is a conserved value, probability distributions are subject to the constraint of symmetry and must be zero-sum. An actuality is locked-in by other actualities to become a zero-sum symmetry of probability values. It is shown that the locking-in of actualities constructs spatio-temporal locality, lends actualities specificity, and makes them a contradiction. Localization is the basis for understanding empirical observation. Because becoming depends on its construction of being, processes exist as trajectories. The historical trajectories of evolution and revolution as well as the non-historical trajectory of strong emergence are how processes are observed to exist. (shrink)

In this article, I introduce the notion of horizon for scientific practice (HSP), representing limits or boundaries within which scientists ply their trade, to facilitate analysis of scientific discovery and progress. The notion includes not only constraints that delimit scientific practice, e.g. of bringing experimentation to a temporary conclusion, but also possibilities that open up scientific practice to additional scientific discovery and to further scientific progress. Importantly, it represents scientific practice as a dynamic and developmental integration of activities to investigate (...) and analyze the natural world. I use the discovery of the clotting factor, thrombin, and the experiments conducted by the Johns Hopkins physiologist, William Howell, on the enzymatic nature of thrombin to illustrate the notion of HSP. In a concluding section, I compare the notion of HSP to other notions for scientific practice proposed in the history and philosophy of science literature. (shrink)

The application of digital humanities techniques to philosophy is changing the way scholars approach the discipline. This paper seeks to open a discussion about the difficulties, methods, opportunities, and dangers of creating and utilizing a formal representation of the discipline of philosophy. We review our current project, the Indiana Philosophy Ontology (InPhO) project, which uses a combination of automated methods and expert feedback to create a dynamic computational ontology for the discipline of philosophy. We argue that our distributed, expert-based approach (...) to modeling the discipline carries substantial practical and philosophical benefits over alternatives. We also discuss challenges facing our project (and any other similar project) as well as the future directions for digital philosophy afforded by formal modeling. (shrink)

We describe an ontology of philosophy that is designed to aid navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is oriented around what philosophical literature (...) is about. (shrink)

The basic elements of faceted thesauri are described, together with a review of their origins and some prominent examples. Their use in browsing and searching applications is discussed. Faceted thesauri are distinguished from faceted classification schemes, while acknowledging the close similarities. The paper concludes by comparing faceted thesauri and related knowledge organization systems to ontologies and discussing appropriate areas of use.

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (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)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...) andere im Bereich der Biologie und Biomedizin von der OBO Foundry. Es soll aufgezeigt werden, wie die Verpflichtung zu speziellen Kriterien der Ontologieentwicklung die Nützlichkeit und Effektivität der Ontologien positiv beeinflusst, indem die Pflege der terminologischen Systeme und ihre Interoperabilität vereinfacht werden. -/- Ergebnisse: SNOMED CT und die OBO Foundry unterscheiden sich grundlegend in ihren Ansätzen und Zielen. Unabhängig davon kann jedoch ein allgemeiner Trend zur strengeren Formalisierung und Fokussierung auf Interoperabilität zwischen unterschiedlichen Domänen und ihren Repräsentationen beobachtet werden. (shrink)

Este trabajo ofrece los bosquejos de una teoría no representacional del conocimiento. Para ello en §1 se presentan los rasgos básicos de una teoría representacional del conocimiento y se señala su dependencia de metáforas visuales, en §2 se expone el giro idealista en que culmina dicha teoría y se revisan teorías representacionales que intentan abandonar la idea de imagen, en §3 se presenta una crítica de la razón visual y una defensa de formas de razón no visual, en §4 y (...) §5 se responden ciertas objeciones teóricas contra la teoría no representacional, a partir de una distinción entre conocimiento y producción de representaciones cognitivas, y en §6 se responden posibles objeciones escépticas. (shrink)

The purpose of this paper is to provide an account of the epistemology and metaphysics of universe creation on a computer. The paper begins with F.J.Tipler's argument that our experience is indistinguishable from the experience of someone embedded in a perfect computer simulation of our own universe, hence we cannot know whether or not we are part of such a computer program ourselves. Tipler's argument is treated as a special case of epistemological scepticism, in a similar vein to `brain-in-a-vat' arguments. (...) It is argued that the hypothesis that our universe is a program running on a digital computer in another universe generates empirical predictions, and is therefore a falsifiable hypothesis. The computer program hypothesis is also treated as a hypothesis about what exists beyond the physical world, and is compared with Kant's metaphysics of noumena. It is proposed that a theory about what exists beyond the physical world should be formulated with the precise concepts of mathematics, and should generate physical predictions. It is argued that if our universe is a program running on a digital computer, then our universe must have compact spatial topology, and the possibilities of observationally testing this prediction are considered. The possibility of testing the computer program hypothesis with the value of the density parameter Omega_0 is also analysed. The informational requirements for a computer to represent a universeexactly and completely are considered. Consequent doubt is thrown upon Tipler's claim that if a hierarchy of computer universes exists, we would not be able to know which `level of implementation' our universe exists at. It is then argued that a digital computer simulation of a universe cannot exist as a universe. However, the paper concludes with the acknowledgement that an analog computer simulation can be objectively related to the thing it represents, hence an analog computer simulation of a universe could, in principle, exist as a universe. (shrink)