• University at Buffalo
    Department of Philosophy
    Biomedical Informatics
    Computer Science and Engineering
    Distinguished Professor, Julian Park Chair
University of Manchester
Department of Philosophy
PhD, 1976
APA Eastern Division
Buffalo, New York, United States of America
  • Book reviews (review)
    with Maria J. Frapolli, Ignacio Angelelli, Curt C. Christian, K. Misiuna, Albent C. Lewis, J. B. Gould, A. Urquhart, E. L. Lowe, L. Kreiser, G. Roussopoulos, H. L. L. Busard, Wolfe Mays, Miriam Franchella, Rezensiert Von Dominik Perler, Michele Di Francesco, Donald Felipe, and R. Smith
    History and Philosophy of Logic 16 (1): 127-156. 1995.
    Daniel Laurier and Francois Lepage, Essais sur le langage et Vintentionalité. Montréal; Bellarmin:Paris; Vrin: 1992. 366 pp. Can $34.95 Dino Buzzetti, Maurizio Ferriani and Andrea Tabarroni...
  •  20
    Gene Ontology annotations: What they mean and where they come from
    with David P. Hill, Monica S. McAndrews-Hill, and Judith A. Blake
    BMC Bioinformatics 9 (5): 1-9. 2008.
    The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of…Read more
  •  40
    Where there’s no will, there’s no way
    with Alex Thomson and Jobst Landgrebe
    Ukcolumn. 2023.
    An interview by Alex Thomson of UKColumn on Landgrebe and Smith's book: Why Machines Will Never Rule the World. The subtitle of the book is Artificial Intelligence Without Fear, and the interview begins with the question of the supposedly imminent takeover of one profession or the other by artificial intelligence. Is there truly reason to be afraid that you will lose your job? The interview itself is titled 'Where this is no will there is no way', drawing on one thesis of the book to the effect …Read more
  • Ontology
    In Guillermo Hurtado & Oscar Nudler (eds.), The Furniture of the World: Essays in Ontology and Metaphysics, Editions Rodopi. 2012.
  •  50
    Quantum sensing and quantum engineering: a strategy for acceleration via metascience
    with Charles Clark, Mayur Gosai, Terry Janssen, Melissa LaDuke, Jobst Landgrebe, and Lawrence Pace
    Proceedings of Spie: Quantum Sensing, Imaging, and Precision Metrology 12447. 2023.
    Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It pr…Read more
  •  47
    A new framework for host-pathogen interaction research
    with Hong Yu, Li Li, Anthony Huffman, John Beverley, Junguk Hur, Eric Merrell, Hsin-hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang, Pengpai Li, Zhiping Liu, Zhigang Wang, Xiangyan Zhang, Xianwei Ye, Samuel K. Handelman, Jonathan Sexton, Kathryn Eaton, Gerry Higgins, Gilbert S. Omenn, Brian Athey, Luonan Chen, and Yongqun He
    Frontiers in Immunology 13. 2022.
    COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host…Read more
  •  104
    Sam Harris and the Myth of Artificial Intelligence
    In Sam Harris: Critical Responses, Open Universe. pp. 153-61. 2023.
    Sam Harris is a contemporary illustration of the difficulties standing in the way of coherent interdisciplinary thinking in an age where science and the humanities have drifted so far apart. We are here with Harris’s views on AI, and specifically with his view according to which, with the advance of AI, there will evolve a machine superintelligence with powers that far exceed those of the human mind. This he sees as something that is not merely possible, but rather a matter of inevitability. If,…Read more
  •  123
    Transcript of an Interview on the podcast Irreverend: Faith and Current Affairs
  •  21
    The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – and this…Read more
  •  52
    What is a service?
    with Peter Koch
    The Eighth Joint Ontology Workshops (JOWO’22), August 15-19, 2022, Jönköping University, Sweden. 2022.
    When governments collect data relating to economic activity they commonly employ a distinction between goods and services. Both goods and services have economic value. Goods (cars, houses, bottles of milk) are, very roughly, independent continuants which can be alienated (sold, gifted, rented, and so forth). Services (hairdressing, gardening, teaching) are, again very roughly, occurrents. They are occurrents which are further often said to be marked by the fact that production and consumption co…Read more
  •  46
    Model-induced escape
    Facing the Future, Facing the Screen: 10Th Budapest Visual Learning Conference. 2022.
    We can illustrate the phenomenon of model-induced escape by examining the phenomenon of spam filters. Spam filter A is, we can assume, very effective at blocking spam. Indeed it is so effective that it motivates the authors of spam to invent new types of spam that will beat the filters of spam filter A. An example of this phenomenon in the realm of philosophy is illustrated in the work of Nyíri on Wittgenstein's political beliefs. Nyíri writes a paper demonstrating convincingly that there are s…Read more
  •  111
    The Industrial Ontologies Foundry (IOF) Core Ontology
    with Milos Drobnjakovic, Boonserm Kulvatunyou, Farhad Ameri, Chris Will, and Albert Jones
    FOMI 2022: 12th International Workshop on Formal Ontologies Meet Industry, September 12-15, 2022, Tarbes, France. 2022.
    The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build i…Read more
  •  48
    A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
    with Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, and Brian Athey
    Journal of Biomedical Semantics 13 (1): 25. 2022.
    The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integ…Read more
  •  378
    Why AI will never rule the world (interview)
    with Luke Dormehl and Jobst Landgrebe
    Digital Trends. 2022.
    Call it the Skynet hypothesis, Artificial General Intelligence, or the advent of the Singularity — for years, AI experts and non-experts alike have fretted (and, for a small group, celebrated) the idea that artificial intelligence may one day become smarter than humans. According to the theory, advances in AI — specifically of the machine learning type that’s able to take on new information and rewrite its code accordingly — will eventually catch up with the wetware of the biological brain. In t…Read more
  •  133
    Unsterblichkeit 2.0
    In Ludger Jansen & Rebekka A. Klein (eds.), Seele digital? Mind uploading, virtuelles Bewusstsein und christliche Auferstehungshoffnung, Verlag Friedrich Pustet. pp. 69-83. 2022.
    Das in diesem Aufsatz vorgebrachte Argumentationsmuster hat folgende Schritte: 1. Der menschliche Geist ist vom Körper nicht trennbar, sie bilden ein Kontinuum. 2. Unser Bewusstsein und alle darauf aufbauenden geistigen Phänomene sind die Emanation eines materiellen Prozesses, den ein komplexes System verursacht. 3. Komplexe Systeme lassen sich mathematisch nicht modellieren und nicht kausal verstehen. 4. Computer sind Turing-Maschinen. Sie können nur mathematische Modelle berechnen. Es wird nie…Read more
  •  1147
    The book’s core argument is that an artificial intelligence that could equal or exceed human intelligence—sometimes called artificial general intelligence (AGI)—is for mathematical reasons impossible. It offers two specific reasons for this claim: Human intelligence is a capability of a complex dynamic system—the human brain and central nervous system. Systems of this sort cannot be modelled mathematically in a way that allows them to operate inside a computer. In supporting their claim, the …Read more
  •  176
    Philosophical foundations of intelligence collection and analysis: a defense of ontological realism
    with William Mandrick
    Intelligence and National Security 38. 2022.
    There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for …Read more
  •  87
    Ontocommons in the standardization environment
    with Rita Giuffrida
    OntoCommons. 2022.
    Ontologies and standards are strongly interrelated and can often be seen as two sides of the same coin. Indeed, standards reflect consensus on the semantics of terms, though different standards might employ different ways to explain the same or very similar concepts semantically. Given the crucial role played by both aspects in OntoCommons, we have interviewed Barry Smith, SUNY Distinguished Professor of Philosophy at the University at Buffalo and one of the External Advisory Board (EAB) members…Read more
  •  80
    The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
    with Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J. Mungall, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Nigam Shah, Patricia L. Whetzel, and Suzanna Lewis
    Nature Biotechnology 25 (11): 1251-1255. 2007.
    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Ex…Read more
  •  165
    The Space Domain Ontologies
    with Alexander P. Cox, C. K. Nebelecky, R. Rudnicki, W. A. Tagliaferri, and J. L. Crassidis
    In National Symposium on Sensor & Data Fusion Committee, . 2021.
    Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of li…Read more
  •  124
    An Introduction to Hard and Soft Data Fusion via Conceptual Spaces Modeling for Space Event Characterization
    with Jeremy Chapman, David Kasmier, John L. Crassidis, James L. Llinas, and Alex P. Cox
    In National Symposium on Sensor & Data Fusion (NSSDF), Military Sensing Symposia (MSS). 2021.
    This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic …Read more
  •  283
    Gestalt Theory and Its Reception: An Annotated Bibliography
    In Barry Smith (ed.), Foundations of Gestalt Theory, Philosophia Verlag. pp. 227-478. 1988.
    The list which follows is intended as a comprehensive bibliographical survey of the wider Gestalt tradition from Graz and Berlin to Padua, Frankfurt and New York. It presents diagrammatically the main influence and teacher-pupil relationships also groupings into schools. It includes the classical texts of the Gestalt psychological tradition, together with the more important translations and reprints thereof. Special attention is paid to works on the following topics: - the concept of Prägnanz o…Read more
  •  552
    The birth of ontology
    Journal of Knowledge Structures and Systems 3 (1): 57-66. 2022.
    This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of these diagraphs are: 1. that they do not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for their content.
  •  107
    Implementing Dempster-Shafer Theory for property similarity in Conceptual Spaces modeling
    with Jeremy R. Chapman, John L. Crassidis, James Llinas, and David Kasmier
    Sensor Systems and Information Systems IV, American Institute of Aeronautics and Astronautics (AIAA) SCITECH Forum 2022. 2022.
    Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptua…Read more
  •  132
    Ontology of plays for autonomous teaming and collaboration
    with David Kasmier, Eric Merrell, Robert Kelly, Curtis Heisey, Donald Evan Maki, Marc Brittain, Ronald Ankner, and Kevin Bush
    Proceedings of the 14th Seminar on Ontology Research in Brazil (ONTOBRAS 2021), CEUR 3050, 9-22. forthcoming.
    We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to…Read more
  •  467
    We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that a water pump has the function to pump …Read more
  •  216
    The bridge between philosophy and information-driven science.
    Journal of Knowledge Structures and Systems 2 (2): 47-55. 2021.
    This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.