Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

This paper is a fresh attempt to articulate the role of a theory of truthmakers. We argue that truthmaker theory constitutes a cornerstone of good methodology in metaphysics, but that a conflation of truthmaker theory with the theory of truth has been responsible for certain excesses associated with truthmaker-based approaches in the recent literature. If truthmaker theory is not a component of a theory of truth, then truthmaker maximalism – the view that every truth has a truthmaker – loses its (...) primary motivation. More generally, if the task of truthmaker theory is not to provide a definition or account of truth in truthmaker terms, there is no pressing need for hard, a priori principles stating which truths have truthmakers and which do not. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

A miracle is defined as a violation of or intercession in the laws of nature. Some recent reports of UFO phenomena are such that UFOs may satisfy that definition. In this paper, we ask how Hume’s famous argument in “Of Miracles” relates to UFOs. We argue that his critique fails and that some well corroborated UFO reports are such that they justify a belief in miracles (qua violations of laws of nature).

Le présent article est une tentative nouvelle d’articuler le rôle d’une théorie des vérifacteurs. Nous soutenons que la théorie de la vérifaction constitue une pierre angulaire dans une bonne méthodologie en métaphysique, mais que l’amalgame entre la théorie de la vérifaction et la théorie de la vérité a été responsable de certains excès associés aux approches vérifactionnistes dans la littérature récente. Nous montrons que la théorie de la vérifaction conserve son attrait comme instrument d’investigation métaphysique, et ce, malgré notre accord (...) avec les doctrines déflationnistes telles que celles défendues par Ayer, Quine, Field et Horwich (ou, du moins, malgré notre neutralité à leur égard). Nous soutenons en outre que les intuitions sous-jacentes à la théorie de la vérifaction s’éclairent quand nous les dissocions d’une théorie de la vérité et, par-dessus tout, de la tentative de fournir une définition de la vérité. (shrink)

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-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

This letter addresses the editorial decision to publish the article, “Research on group differences in intelligence: A defense of free inquiry” (Cofnas, 2020). Our letter points out several critical problems with Cofnas's article, which we believe should have either disqualified the manuscript upon submission or been addressed during the review process and resulted in substantial revisions.

We are addressing this letter to the editors of Philosophical Psychology after reading an article they decided to publish in the recent vol. 33, issue 1. The article is by Nathan Cofnas and is entitled “Research on group differences in intelligence: A defense of free inquiry” (2020). The purpose of our letter is not to invite Cofnas’s contribution into a broader dialogue, but to respectfully voice our concerns about the decision to publish the manuscript, which, in our opinion, fails to (...) meet a range of academic quality standards usually expected of academic publications. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

Is the brain really a computer? In particular, is our intelligence a computational achievement: is it because our brains are computers that we get on in the world as well as we do? In this paper I will evaluate an ambitious new argument to the contrary, developed in Landgrebe and Smith (2021a, 2022). Landgrebe and Smith begin with the fact that many dynamical systems in the world are difficult or impossible to model accurately (inter alia, because it is (...) intractable to find exact solutions to the differential equations that describe them—meaning we have to approximate—but at the same time they are such that small differences in starting conditions lead to big differences in final conditions, thwarting accurate approximation). Yet we manage to survive and thrive in a world full of such systems. Landgrebe and Smith argue from these premises that it is not because our brains are computers that we get on as well as we do: instead it is because of the various ways that we dynamically couple with such systems, these couplings themselves impossible to model well enough to emulate in silico. Landgrebe and Smith thus defend a dynamical systems model in the lineage of Gibson (1979), Van Gelder (1995), and Thompson (2007), though their focus is on decisively refuting the computationalist alternatives rather than developing the positive account. Here I will defend the claim that human intelligence is genuinely computational (and that whole brain emulation and others forms of AGI may be possible) against this argument. (shrink)

John Smith was among the first of the Cambridge Platonists. He was therefore in a position to influence not only his contemporaries but all those who followed after him well into the twentieth century and beyond. Well established lines of influence both to and from Whichcote, Cudworth, and More are explored first before moving on to less well-known connections to Bishop Simon Patrick and mathematician Isaac Barrow. Smith’s continued significance for eighteenth century theology is demonstrated through discussion of (...) his inspiration of the doctrines of spiritual sensation developed by Jonathan Edwards and John Wesley. Special notice is also given to Smith’s authority as an interpreter of Biblical prophecy through the eighteenth and nineteenth centuries. The chapter concludes with looks at Smith’s influence on Samuel Taylor Coleridge, Ralph Waldo Emerson, William Ralph Inge, Rufus Jones, Pierre Hadot, and others. This chapter, offers a broad, but highly selective, overview of the reception and influence of Smith’s life and work. It is intended, however, as a call for future research more than as an authoritative presentation of Smith’s legacy. For, if the Cambridge Platonists have been underappreciated until recently, none of them have been unjustly ignored as consistently as Smith. (shrink)

Peter Godfrey-Smith’s Metazoa and Joseph LeDoux’s The Deep History of Ourselves present radically different big pictures regarding the nature, evolution and distribution of consciousness in animals. In this essay review, I discuss the motivations behind these big pictures and try to steer a course between them.

Philosophers of music commonly distinguish performative from critical interpretations. I would like to suggest that the distinction between critical and performative interpretations is well captured by an analogy to legal critics and judges. This parallel draws attention to several features of performative interpretation that are typically overlooked, and deemphasizes epistemic problems with performative interpretations that I believe are typically blown out of proportion and ultimately fail to capture interesting features of performative interpretation. There is an important distinction to be made (...) between critical and performative interpretation, but its source lies in a difference between the authority of critical and performative interpretations. (shrink)

I argue that there can be no such thing as a borderline case of the predicate ‘phenomenally conscious’: for any given creature at any given time, it cannot be vague whether that creature is phenomenally conscious at that time. I first defend the Positive Characterization Thesis, which says that for any borderline case of any predicate there is a positive characterization of that case that can show any sufficiently competent speaker what makes it a borderline case. I then appeal to (...) the familiar claim that zombies are conceivable, and I argue that this claim entails that there can be no positive characterizations of borderline cases of ‘phenomenally conscious’. By the Positive Characterization Thesis, it follows that ‘phenomenally conscious’ can not have any borderline cases. (shrink)

This article explores a concept of artistic transgression I call aesthetic disobedience that runs parallel to the political concept of civil disobedience. Acts of civil disobedience break some law in order to publicly draw attention to and recommend the reform of a conflict between the commitments of a legal system and some shared commitments of a community. Likewise, acts of aesthetic disobedience break some entrenched artworld norm in order to publicly draw attention to and recommend the reform of a conflict (...) between artworld commitments and some shared commitments of a community. Considering artistic transgressions under the concept of aesthetic disobedience highlights often-overlooked features of modern artworld practices. Most significantly, it draws attention to the deliberative participation of a wide variety of citizens of the artworld, including not just artists and performers but also members of audiences, in the transformation of the rules and boundaries of the artworld itself. (shrink)

Advances in forensic techniques have expanded the temporal horizon of criminal investigations, facilitating investigation of historic crimes that would previously have been considered unsolvable. Public enthusiasm for pursuing historic crimes is exemplified by recent high-profile trials of celebrities accused of historic sexual offences. These circumstances give new urgency to the question of how we should decide which historic offences to investigate. A satisfactory answer must take into account the ways in which the passage of time can erode the benefits of (...) criminal investigation, the costs associated with investigating old crimes, and the need to prioritize investigations in the face of limited police resources. This article emphasizes the first of these factors. It begins by considering the moral goals of a criminal justice system and the contribution of criminal investigations to the achievement of these goals, distinguishing between contributions that depend on further steps in the criminal justice process, such as prosecution and punishment, and contributions that can have value independently of these further steps. Using this important distinction, the article then examines a range of factors that relate the passage of time to criminal justice goals, including the seriousness of the crime; deterioration of evidence; death of the offender, victim and others affected by the crime; and diminished psychological connectedness between those affected by the crime and their current selves. While the range and non-uniformity of relevant factors preclude a simple answer to the question of when historic crimes should be investigated and call instead for case-by-case assessment, we find that the analysis does support some general conclusions that can guide such an assessment. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Conservationists have two types of arguments for why we should conserve ecosystems: instrumental and intrinsic value arguments. Instrumental arguments contend that we ought to conserve ecosystems because of the benefits that humans, or other morally relevant individuals, derive from ecosystems. Conservationists are often loath to rely too heavily on the instrumental argument because it could potentially force them to admit that some ecosystems are not at all useful to humans, or that if they are, they are not more useful than (...) alternative configurations of those ecosystems. Consequently, conservationists often resort to an intrinsic value argument, contending that ecosystems are objectively valuable as ends in themselves, rather than merely as means to an end. If ecosystems have intrinsic value, then they have moral standing, which means that we must consider their needs and interests in any decisions we make about them. This paper concerns the significance of this move for... (shrink)

Multiple states are at risk of becoming uninhabitable due to climate change, forcing their populations to flee. While the 1951 Refugee Convention provides the gold standard of international protection, it is only applied to a limited subset of people fleeing their countries, those who suffer persecution, which most people fleeing climate change cannot establish. While many journalists and non-lawyers freely use the term “climate refugees,” governments, and courts, as well as UNHCR and many refugee experts, have excluded most climate refugees (...) from the Convention as a matter of legal interpretation. In our 2015 paper, “Unable to Return in the 1951 Refugee Convention: Stateless Refugees and Climate Change”, we sought to reopen the debate on “climate refugees” by arguing that some climate refugees qualify under the 1951 Convention as it is currently written (even if they are not persecuted): those who are stateless and are unable to return to their country of origin because climate change has rendered it uninhabitable. Our interpretation, however, has been rejected by Goodwin-Gill and McAdam (2021) and by Foster and Lambert (2019), which explicitly responds to our paper. Here, we address and respond to their arguments, and develop a new supplementary one, drawing on the principle of systemic integration, as enshrined in Article 31(3)(c) of the Vienna Convention on the Law of Treaties. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

The literature on the Cambridge Platonists abounds with references to Neoplatonism and the Alexandrian Fathers on general themes of philosophical and theological methodology. The specific theme of the spiritual senses of the soul has received scant attention however, to the detriment of our understanding of their place in this important tradition of Christian speculation. Thus, while much attention has been paid to the clear influence of Plotinus and the Florentine Academy, far less has been given to important theological figures that (...) also form a vital part of the tradition the Cambridge Platonists find irresistible. Similarly, scholarship on the spiritual senses has tended to ignore early modern Protestant developments in this tradition focusing instead on patristic, medieval, and later modern figures. In response to these oversights, the present chapter provides a close reading and analysis of the reception and modification of Origen of Alexandria’s (185-252) doctrine of the spiritual senses in the “Discourse on the True Way or Method of Attaining to Divine Knowledge” by the Cambridge Platonist, John Smith (1618-1652). Although Smith accepted much of the doctrine as he found it in Origen his allegiance to modern notions of methodology, derived especially from Descartes, as well as his Protestantism, made taking the doctrine on authority or antiquity alone unacceptable. Smith therefore offered his own case for the spiritual senses, at once intentionally mimicking the Alexandrian’s interpretive synthesis of Platonism and Scripture (“Origen as model”) and echoing Origen’s own words (“Origen as source”). Whereas Origen made spiritual sensibility intelligible by means of Middle Platonic thought, Smith’s Neoplatonism provided the conceptual tools needed to make sense of biblical passages without suggesting a merely metaphorical meaning for sensory language concerning the awareness of spiritual realities. In this way, both tradition and innovation guide Smith’s reformulation of the doctrine of the spiritual senses. In addition to demonstrating Smith’s debt to patristic thought, this chapter also discusses his influence on such leading figures in modern theology as John Wesley (1703-1791) and Jonathan Edwards (1703-1758). The chapter thus presents an important moment in the development of Christian speculation about the spiritual senses that begins to bridge scholarship on the Patristic and Enlightenment periods. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Conscious states—state that there is something it is like to be in—seem both rich or full of detail and ineffable or hard to fully describe or recall. The problem of ineffability, in particular, is a longstanding issue in philosophy that partly motivates the explanatory gap: the belief that consciousness cannot be reduced to underlying physical processes. Here, we provide an information theoretic dynamical systems perspective on the richness and ineffability of consciousness. In our framework, the richness of conscious experience corresponds (...) to the amount of information in a conscious state and ineffability corresponds to the amount of information lost at different stages of processing. We describe how attractor dynamics in working memory would induce impoverished recollections of our original experiences, how the discrete symbolic nature of language is insufficient for describing the rich and high-dimensional structure of experiences, and how similarity in the cognitive function of two individuals relates to improved communicability of their experiences to each other. While our model may not settle all questions relating to the explanatory gap, it makes progress toward a fully physicalist explanation of the richness and ineffability of conscious experience—two important aspects that seem to be part of what makes qualitative character so puzzling. (shrink)

There is something puzzling about statistical evidence. One place this manifests is in the law, where courts are reluctant to base affirmative verdicts on evidence that is purely statistical, in spite of the fact that it is perfectly capable of meeting the standards of proof enshrined in legal doctrine. After surveying some proposed explanations for this, I shall outline a new approach – one that makes use of a notion of normalcy that is distinct from the idea of statistical frequency. (...) The puzzle is not, however, merely a legal one. Our unwillingness to base beliefs on statistical evidence is by no means limited to the courtroom, and is at odds with almost every general principle that epistemologists have proposed as to how we ought to manage our beliefs. (shrink)

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an effort called (...) Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

Human cognitive acts are directed towards entities of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. A categorial scheme for the objects of human cognition should be (1) critical and realistic. Cognitive subjects are liable to error, even to systematic error of the sort that is manifested by believers in the Pantheon of Olympian gods. Thus not all putative object-directed acts should be recognized as having objects of their own. (...) Broadly, the objects towards which human cognition is directed should be parts of reality in a sense that is at least consistent with the truths of natural science. But such a scheme should also be (2) comprehensive: it should do justice to each sort of object on its own terms, and not attempt to eliminate objects of one sort in favour of objects of other, more favoured sorts. Linguistic and other forms of idealism, as well as Meinongian theories, which assign to each and every referring expression or intentional act an object tailored to fit, yield categorial schemes which fail to satisfy (1). Physicalistic and other forms of reductionism yield categorial schemes which fail to satisfy (2). What follows is a categorial scheme that is both critically realistic and comprehensive. Thus it enjoys some of the benefits of linguistic idealism and physicalism, without (or so it is hoped) the corresponding disadvantages of each. (shrink)

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...) projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments. (shrink)

The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in many influential (...) ontologies, illustrating our results by reference to examples drawn from the domain of the life sciences. (shrink)

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 that there will never be anything like the human will on the part of a machine. This is for mathematical reasons. AI is always and in every case a matter of algorithms; thus of applied mathematics. And algorithms are not the sorts of things that can want or desire or intend to do something. It is the human will of those who work at OpenAI or google or microsoft which have given rise to the new shiny objects of AI (ChatGPT and other Large Language Models). And it is the human will of the users of these shiny objects which gives them the resources and power to work their apparent miracles. (shrink)

The Austrian philosopher Christian von Ehrenfels published his essay "On 'Gestalt Qualities'" in 1890. The essay initiated a current of thought which enjoyed a powerful position in the philosophy and psychology of the first half of this century and has more recently enjoyed a minor resurgence of interest in the area of cognitive science, above all in criticisms of the so-called 'strong programme' in artificial intelligence. The theory of Gestalt is of course associated most specifically with psychologists of the Berlin (...) school such as Max Wertheimer, Wolfgang Kohler and Kurt Koffka. We shall see in what follows, however, that an adequate philosophical understanding of the Gestalt idea and of Ehrenfels' achievement will require a close examination not merely of the work of the Berlin school but also of a much wider tradition in Austrian and German philosophy in general. (shrink)

The discussions which follow rest on a distinction, first expounded by Husserl, between formal logic and formal ontology. The former concerns itself with (formal) meaning-structures; the latter with formal structures amongst objects and their parts. The paper attempts to show how, when formal ontological considerations are brought into play, contemporary extensionalist theories of part and whole, and above all the mereology of Leniewski, can be generalised to embrace not only relations between concrete objects and object-pieces, but also relations between what (...) we shall call dependent parts or moments. A two-dimensional formal language is canvassed for the resultant ontological theory, a language which owes more to the tradition of Euler, Boole and Venn than to the quantifier-centred languages which have predominated amongst analytic philosophers since the time of Frege and Russell. Analytic philosophical arguments against moments, and against the entire project of a formal ontology, are considered and rejected. The paper concludes with a brief account of some applications of the theory presented. (shrink)

Twentieth century philosophers introduced the distinction between “objective rightness” and “subjective rightness” to achieve two primary goals. The first goal is to reduce the paradoxical tension between our judgments of (i) what is best for an agent to do in light of the actual circumstances in which she acts and (ii) what is wisest for her to do in light of her mistaken or uncertain beliefs about her circumstances. The second goal is to provide moral guidance to an agent who (...) may be uncertain about the circumstances in which she acts, and hence is unable to use her standard moral principle directly in deciding what to do. This paper distinguishes two important senses of “moral guidance”; proposes criteria of adequacy for accounts of subjective rightness; canvasses existing definitions for “subjective rightness”; finds them all deficient; and proposes a new and more successful account. It argues that each comprehensive moral theory must include multiple principles of subjective rightness to address the epistemic situations of the full range of moral decision-makers, and shows that accounts of subjective rightness formulated in terms of what it would reasonable for the agent to believe cannot provide that guidance. -/- . (shrink)

Is it right to convict a person of a crime on the basis of purely statistical evidence? Many who have considered this question agree that it is not, posing a direct challenge to legal probabilism – the claim that the criminal standard of proof should be understood in terms of a high probability threshold. Some defenders of legal probabilism have, however, held their ground: Schoeman (1987) argues that there are no clear epistemic or moral problems with convictions based on purely (...) statistical evidence, and speculates that our aversion to such convictions may be nothing more than an irrational bias. More recently, Hedden and Colyvan (2019, section VI) describe our reluctance to convict on the basis of purely statistical evidence as an ‘intuition’, but suggest that there may be no ‘in principle’ problem with such convictions (see also Papineau, forthcoming, section 6). In this paper, I argue that there is, in some cases, an in principle problem with a conviction based upon statistical evidence alone – namely, it commits us to a precedent which, if consistently followed through, could lead to the deliberate conviction of an innocent person. I conclude with some reflections on the idea that the criminal justice system should strive to maximise the accuracy of its verdicts – and the related idea that we should each strive to maximise the accuracy of our beliefs. (shrink)

Epistemic permissivism is the view that it is possible for two people to rationally hold incompatible attitudes toward some proposition on the basis of one body of evidence. In this paper, I defend a particular version of permissivism – unacknowledged permissivism (UP) – which says that permissivism is true, but that no one can ever rationally believe that she is in a permissive case. I show that counter to what virtually all authors who have discussed UP claim, UP is an (...) attractive view: it is compatible with the intuitive motivations for permissivism and avoids a significant challenge to permissivism: the arbitrariness objection. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

Our understanding of subjunctive conditionals has been greatly enhanced through the use of possible world semantics and, more precisely, by the idea that they involve variably strict quantification over possible worlds. I propose to extend this treatment to ceteris paribus conditionals – that is, conditionals that incorporate a ceteris paribus or ‘other things being equal’ clause. Although such conditionals are commonly invoked in scientific theorising, they traditionally arouse suspicion and apprehensiveness amongst philosophers. By treating ceteris paribus conditionals as a species (...) of variably strict conditional I hope to shed new light upon their content and their logic. (shrink)

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)

The theory of document acts is an extension of the more traditional theory of speech acts advanced by Austin and Searle. It is designed to do justice to the ways in which documents can be used to bring about a variety of effects in virtue of the fact that, where speech is evanescent, documents are continuant entities. This means that documents can be preserved in such a way that they can be inspected and modified at successive points in time and (...) grouped together into enduring document complexes. We outline some components of a theory of document acts, and show how it can throw light on certain problems in Searle’s ontology of social reality. (shrink)

This article examines Gilles Deleuze’s concept of the simulacrum, which Deleuze formulated in the context of his reading of Nietzsche’s project of “overturning Platonism.” The essential Platonic distinction, Deleuze argues, is more profound than the speculative distinction between model and copy, original and image. The deeper, practical distinction moves between two kinds of images or eidolon, for which the Platonic Idea is meant to provide a concrete criterion of selection “Copies” or icons (eikones) are well-grounded claimants to the transcendent Idea, (...) authenticated by their internal resemblance to the Idea, whereas “simulacra” (phantasmata) are like false claimants, built on a dissimilarity and implying an essential perversion or deviation from the Idea. If the goal of Platonism is the triumph of icons over simulacra, the inversion of Platonism would entail an affirmation of the simulacrum as such, which must thus be given its own concept. Deleuze consequently defines the simulacrum in terms of an internal dissimilitude or “disparateness,” which in turn implies a new conception of Ideas, no longer as self-identical qualities (the auto kath’hauto), but rather as constituting a pure concept of difference. An inverted Platonism would necessarily be based on a purely immanent and differential conception of Ideas. Starting from this new conception of the Idea, Deleuze proposes to take up the Platonic project anew, rethinking the fundamental figures of Platonism (selection, repetition, ungrounding, the question-problem complex) on a purely differential basis. In this sense, Deleuze’s inverted Platonism can at the same time be seen as a rejuvenated Platonism and even a completed Platonism. (shrink)

Recent work in formal philosophy has concentrated over-whelmingly on the logical problems pertaining to epistemic shortfall - which is to say on the various ways in which partial and sometimes incorrect information may be stored and processed. A directly depicting language, in contrast, would reflect a condition of epistemic perfection. It would enable us to construct representations not of our knowledge but of the structures of reality itself, in much the way that chemical diagrams allow the representation (at a certain (...) level of abstractness) of the structures of molecules of different sorts. A diagram of such a language would be true if that which it sets out to depict exists in reality, i.e. if the structural relations between the names (and other bits and pieces in the diagram) map structural relations among the corresponding objects in the world. Otherwise it would be false. All of this should, of course, be perfectly familiar. (See, for example, Aristotle, Metaphysics, 1027 b 22, 1051 b 32ff.) The present paper seeks to go further than its predecessors, however, in offering a detailed account of the syntax of a working universal characteristic and of the ways in which it might be used. (shrink)

In this paper, we consider two different attempts to make an end run around the experimentalist challenge to the armchair use of intuitions: one due to Max Deutsch and Herman Cappelen, contending that philosophers do not appeal to intuitions, but rather to arguments, in canonical philosophical texts; the other due to Joshua Knobe, arguing that intuitions are so stable that there is in fact no empirical basis for the experimentalist challenge in the first place. We show that a closer attention (...) to philosophical practices reveal, in turn, that we cannot make sense of these philosophical texts as arguments all the way down; and that our methods are so sensitive to error that even a modest amount of instability is enough to raise deep methodological concerns. (shrink)