Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

Stereotypes are commonly alleged to be false or inaccurate views of groups. For shorthand, I call this the falsity hypothesis. The falsity hypothesis is widespread and is often one of the first reasons people cite when they explain why we shouldn’t use stereotypic views in cognition, reasoning, or speech. In this essay, I argue against the falsity hypothesis on both empirical and ameliorative grounds. In its place, I sketch a more promising view of stereotypes—which avoids the falsity hypothesis—that joins my (...) earlier work on stereotypes in individual psychology with the work of Patricia Hill Collins on cultural stereotypes. According to this two-part hybrid theory, stereotypes are controlling images or ideas that enjoy both a psychological and cultural existence, which serve a regulative social function. (shrink)

I explore the question of whether Kant's theory in the _Critique of Judgment_ can account for judgments of taste regarding the ugly. While there has been much debate regarding this issue in recent decades, many scholars consider the harmonious free play of the faculties to be central to this question. Harmony between the imagination and understanding is stressed in a series of articles regarding pure judgments of taste of the ugly beginning in the mid-1990s and extending into the 2000s. I (...) investigate the status of harmony in relation to judgments of taste and assess whether harmony among these faculties is necessary to free play. In order to do so, I compare three cases and consider how they relate to cognitive activity: judgments of taste of the beautiful, sublime experience, and judgments of taste regarding works of genius. I argue that pure judgements of taste of the ugly are indeed possible by analyzing the cognitive activity produced in the aforementioned cases. These instances show that in Kant's system, cognitive harmony may not be necessary to free play. Rather, disharmony can also be produced by our aesthetic experience with the sublime, works of genius, and the ugly. I argue that in spite of the contrapurposiveness and disharmony that experience with the ugly spurs, it nonetheless can serve to further cognitive activity and quicken the mind, cultivate taste, and develop community, thus revealing a higher, and perhaps unexpected, purposiveness. (shrink)

This paper raises questions concerning Ted Morris’ interpretation of Hume’s notion of meaning and investigates the private and public aspects of Hume’s notion of meaning.

Samuel Butler is usually remembered for Erewhon, widely considered among the best English satires. He also contributed to philosophical biology in works that collectively compose the nineteenth century's finest statement of the evolutionary argument associated with the name of Lamarck. In writing on evolution, Butler was not presenting science for a popular audience but deliberately intervening in the scientific argument about Darwinism. Surprised by the success of his first venture in philosophical biology, Life and Habit, Butler committed himself to the (...) project of developing an alternative to Darwinism, which he did in three additional volumes, and these are the works canvassed in this “delayed book review.”. (shrink)

How do individuals and communities respond to negative aesthetic experience? Historically, philosophical aesthetics has devoted much thought to positive aesthetic experience, including the beautiful, agreeable, charming, and tasteful. But this is only a partial picture. Some aesthetic experience displeases: the ugly, disgusting, and horrific are but a few examples with which aestheticians have grappled in recent decades. The aversive and visceral nature of disgust has generated particular interest. But as Carolyn Korsmeyer points out in _Savoring Disgust: The Foul & the (...) Fair in Aesthetics_, there is also a paradoxical attraction to that which arouses disgust. Following Kant and Korsmeyer from the Western philosophical tradition, I claim that the aversive-attractive response is integral to disgust’s power to motivate aesthetic engagement. On the one hand, people might feel its force and refuse to engage with that which disgusts. On the other hand, unshakeable interest may spur active responses including the exchange of judgments of taste; protests of a given artist, work, or exhibition; or even violent actions intended to damage or destroy a particular work. While the negative dimension of disgust response is often regarded as a liability from an aesthetic standpoint, disgust also has a corresponding productive dimension that has important implications for communities. In this chapter, I coin the term “generative disgust” in order to explain the productive capacity of disgust to inspire communal, often subcultural, activity. On my view, generative disgust has two orientations – destructive and constructive. Both forms activate the community in question based upon the valence of the group’s comportment towards a particular work of art. As such, destructive generative disgust galvanizes the community and spurs increased activity based upon negative response to art, whereas constructive generative disgust galvanizes the community and spurs increased activity based upon positive response to art. I explore two examples that reveal the dual character of generative disgust in communities: Andres Serrano’s _Immersion (Piss Christ)_ (destructive deployment) and Bryan Fuller’s _Hannibal_ (constructive deployment). In the case of _Piss Christ_, the intensity of generative disgust spurred some Christians to police moral-religious boundaries and restrict aesthetic expression in order to protect a community. Their activity culminated in vandalism and destruction of Serrano’s photograph. In the case of Hannibal, the intensity of generative disgust, combined with hedonic ambivalence inspired the “Fannibals” (the Hannibal fandom) to forge community, make art, and to try to find the show a new home when it was not renewed by NBC. Both instances manifest how generative disgust can incite aesthetic engagement and increase organized activity on the part of subcultural groups. (shrink)

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 biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

An account of the specific ill of Native American mascots—that is, the particular racism of using Native Americans as mascots, as distinct from other racist portrayals of Native Americans—requires a fuller account of the function of mascots as such than has previously been offered. By analyzing the history of mascots in the United States, this article argues that mascots function as symbols that draw into an artificial unity 1) a variety of teams existing over a period of time and thereby (...) 2) a community of individuals who are thus able to use that team as their own symbolic locus of unification. This unification of teams and their concomitant communities is accomplished by appeal to a symbol that facilitates a particular fantasy of collective identity. The usage of Native American mascots is racist not only because it involves stereotypical portrayals of Native Americans, but because it treats Native persons simply as a means to symbolic unification—and not, importantly, as members of the community they thus serve. In other words, in these cases mascots work as unifying signifiers precisely by being the purely instrumental facilitator of a group's collective fantasy of itself. (shrink)

ABSTRACT We have previously argued that there are forms of greenhouse gas offsetting for which, when one emits and offsets, one imposes no risk. Orri Stefansson objects that our argument fails to distinguish properly between the people who stand to be harmed by one’s emissions and the people who stand to be benefited by one’s offsetting. We reply by emphasizing the difference between acting with a probability of making a difference to the distribution of harm and acting in a way (...) that worsen’s someone’s prospect. (shrink)

This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In an (...) appendix, however, Brentano puts forward an even more radical suggestion, inspired by the physics of Kelvin. According to this final view, space itself is an accident of a deeper substance: the present time. (shrink)

In Faces of Inequality: A Theory of Wrongful Discrimination, Sophia Moreau embarks on a classic philosophical journey. It’s what philosophers nowadays call an explanatory project. The goal of explanatory projects is to deepen our understanding of wrongful actions and what they share in common. In this review essay, I argue that Moreau’s book embodies a valuable explanatory project and contribution to discrimination theory that ought to be on the radar of lawyers, legal theorists, and philosophers. After sketching the book’s arguments, (...) I explain why they are so refreshing. The remainder of the essay proceeds in a more critical mode. First, I argue that book’s explanatory aspirations fall short, and I sketch a framework for a more radically pluralistic theory of wrongful discrimination. This framework has the power to embrace Moreau’s compelling view that discrimination wrongs people by failing to treat them as equals while also recognizing a rich array of other discriminatory wrongs found in lived experience. Second, I argue that Faces of Inequality will disappoint readers looking for a truly inclusive account of wrongful discrimination. I end by emphasizing the book’s contribution to political philosophy and its ambition to provide a truly liberatory theory of what we owe to each other as moral and political equals. (shrink)

Some provisions of the UN’s Convention on the Elimination of Discrimination Against Women (CEDAW) are clearly important from the perspective of business ethics, particularly those calling for equal rights for women to employment and financial security. Some other provisions of CEDAW are equally as important for ethical business practices and Corporate Social Responsibility (CSR), but are frequently overlooked because of the presumption that they are not strictly business concerns: the rights of women to participation in public life, marriage, and family (...) rights; the rights of rural women to adequate living conditions; and general rights to equality. This chapter will discuss the conceptual commitments that underlie the assumption of a clear demarcation between work and life concerns, and examine the criticisms of this assumption made by feminism. It will, in particular, be interested in: -/- • The public/private distinction • The meaning of “work” or “labor” • The relationship between CSR and care ethics • Fostering a broader understanding of the family or familial relations • Examining the connection between fair wages and work/life integration -/- These discussions suggest that the ability for businesses worldwide to uphold the tenets of CEDAW is dependent upon a reconsideration of the character of the Ideal Worker and a nuanced understanding of the effects of workplace policies on the wider communities in which businesses operate. In particular, though work/life integration is not strictly speaking a “women’s issue,” the ethical and policy considerations addressed herein currently have disproportionately negative effects for women; thus, addressing them is crucial for achieving the aims of gender equality. (shrink)

This paper is a contribution to the historical roots of the analytical tradition. As Michael Dummett points out in his Origins of Analytic Philosophy, many tendencies in Central European thought contributed to the early development of analytic philosophy. Dummett himself concentrates on just one aspect of this historical complex, namely on the relationship between the theories of meaning and reference developed by Frege and by Husserl in the years around the turn of the century. It is to this specific issue (...) that the present essay is devoted, though we attempt a more sympathetic reading of Husserl's views on these matters than is to be found in Dummett’s work. Topics covered include Husserl’s theory of intentionality, his view of meanings as types or essences of mental acts, of the relation between meaning and expression, of states of affairs, and of indexicality. (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

In “Stereotyping as Discrimination: Why Thoughts Can Be Discriminatory,” I propose that stereotyping someone—even if you manage to keep your thoughts hidden and don’t act on them—can constitute a form of discrimination (2021b). What, Alex Madva asks, are the practical implications of this claim? Even if I am correct that stereotyping constitutes a form of discriminatory treatment, it’s still possible that people should keep on speaking and acting as if “discrimination” refers exclusively to behaviors and policies. He invites me to (...) explore the “potential payoffs and perils” of referring to thoughts and perceptions as discriminatory, especially as they relate to legal practice and social-scientific inquiry (2021, 46). (shrink)

We rely on language to know the minds of others, but does language have a role to play in knowing our own minds? To suppose it does is to look for a connection between mastery of a language and the epistemic relation we bear to our inner lives. What could such a connection consist in? To explore this, I shall examine strategies for explaining self-knowledge in terms of the use we make of language to express and report our mental states. (...) Success in these strategies will depend on the view we take of speakers' understanding of the words they use to speak their minds. The key is to avoid circularity in the account of how they know what they mean; for if knowing what one is saying in speaking a language provides a means of knowing one's own mind, it cannot simply be a part of it. I shall look at ways in which we might proceed here, and examine whether the strategy can make room for a genuinely first-person point of view. But first let me try to motivate the problem of self-knowledge. (shrink)

This chapter is an extended version (almost 2x in length) of an essay first published in Australasian Philosophical Review. -/- Abstract: In On Female Body Experience, Iris Marion Young argues that a central aim of feminist and queer theory is social criticism. The goal is to understand oppression and how it functions: know thy enemy, so as to better resist. Much of Sally Haslanger’s work shares this goal, and her newest article, “Cognition as a Social Skill,” is no exception. In (...) this essay, I will specify what I believe is special and insightful about Haslanger’s theory of oppression and her most recent addition to it. However, I also explore what it is missing, namely, an account of what Young calls “individual [embodied] experience, subjectivity, and identity.” Echoing a chorus of critical voices, I argue that this omission undermines Haslanger’s ability to effectively theorize group oppression and how to resist it. The core problem is this. Haslanger privileges a third-person methodology that prioritizes social structures over all else. I conclude by amplifying a collective call to action: any adequate theory of oppression must attend to both the lived experiences of individuals and to social structures, that is, to the broad institutional and cultural underpinnings of oppression. A theory that does only one, or the other, will fail. Through this analysis, the chapter contributes to an overall aim of this volume, namely, to advance our understanding of racial and gender-based group oppressions by paying closer attention to facts about embodiment. (shrink)

We argue that a modified version of Mill’s method of agreement can strongly confirm causal generalizations. This mode of causal inference implicates the explanatory virtues of mechanism, analogy, consilience, and simplicity, and we identify it as a species of Inference to the Best Explanation (IBE). Since rational causal inference provides normative guidance, IBE is not a heuristic for Bayesian rationality. We give it an objective Bayesian formalization, one that has no need of principles of indifference and yields responses to the (...) Voltaire objection, van Fraassen’s Bad Lot objection, and John Norton’s recent objection to IBE. (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)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

Judith Butler’s influential work in feminist theory is significant for its insight that sexist discourse in popular culture affects the agency and consciousness of individuals, but offers an inadequate account of how such discourse might be said to touch, shape, or affect selves. Supplementing Butler’s account of signification with a Deweyan pragmatic account of meaning-making and selective emphasis enables a consistent account of the relationship between discourse and subjectivity with a robust conception of the bodily organism. An analysis of the (...) popular discourse surrounding Hillary Clinton in the 2008 Presidential campaign demonstrates why this hybrid pragmatic/poststructuralist account is necessary. (shrink)

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, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

People attribute resistance to bodies in Spinoza's physics. It's not always clear what they mean when they do this, or whether they are entitled to. This article clarifies what it would mean, and examines the evidence for attributing resistance. The verdict: there's some evidence, but not nearly as much as people think.

Spinoza reasons about impossibilities on a regular basis. But he also says they're unthinkable and that reasoning is a mental process. How can he do this? The paper defends a linguistic account of counterpossible inferences in Spinoza's geometrical method.

Autobiography of Barry Smith; emphasizes the role of Dummett and Husserl, Austrian philosophy and economics, and the Munich-Göttingen-Kraków school of realist phenomenology.

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 authors, Jobst Landgrebe and Barry Smith, marshal (...) evidence from mathematics, physics, computer science, philosophy, linguistics, and biology, setting up their book around three central questions: What are the essential marks of human intelligence? What is it that researchers try to do when they attempt to achieve "artificial intelligence" (AI)? And why, after more than 50 years, are our most common interactions with AI, for example with our bank’s computers, still so unsatisfactory? Landgrebe and Smith show how a widespread fear about AI’s potential to bring about radical changes in the nature of human beings and in the human social order is founded on an error. There is still, as they demonstrate in a final chapter, a great deal that AI can achieve which will benefit humanity. But these benefits will be achieved without the aid of systems that are more powerful than humans, which are as impossible as AI systems that are intrinsically "evil" or able to "will" a takeover of human society. (shrink)

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.

The paper investigates the role played by ethical deliberation and ethical judgment in Wittgenstein's early thought in the light of twentieth?century German legal philosophy. In particular the theories of the phenomenologists Adolf Reinach, Wilhelm Schapp, and Gerhart Husserl are singled out, as resting on ontologies which are structurally similar to that of the Tractatus: in each case it is actual and possible Sachverhalte which constitute the prime ontological category. The study of the relationship between the states of affairs depicted, e.g., (...) in the sentences of a legal trial and prior fact?complexes to which these may correspond suggests one possible connecting link between the logical and ontological sections of the Tractatus and the ethical reflections appearing at the end. It is argued that the latter can best be understood in terms of the idea of a ?last judgment? (with its associated ethical rewards and punishments) which would relate to the world as a whole as a penal trial relates to individual complexes of facts. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Frank Cabrera argues that informational explanatory virtues—specifically, mechanism, precision, and explanatory scope—cannot be confirmational virtues, since hypotheses that possess them must have a lower probability than less virtuous, entailed hypotheses. We argue against Cabrera’s characterization of confirmational virtue and for an alternative on which the informational virtues clearly are confirmational virtues. Our illustration of their confirmational virtuousness appeals to aspects of causal inference, suggesting that causal inference has a role for the explanatory virtues. We briefly explore this possibility, delineating a (...) path from Mill’s method of agreement to Inference to the Best Explanation (IBE). (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (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 translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

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 strong signals of a conservative strain of thought in the writings of Wittgenstein. This has initially a tiny effect; but then a more significant effect sets in as the authors of Wittgenstein secondary literature, consciously or unconsciously, draw attention to features of Wittgenstein which cast the conservatism thesis in a negative light. This is an example of what I call model-induced escape: the Nyíri model of Wittgenstein initiates a process which undermines the Nyíri model of Wittgenstein. -/- Wittgenstein, as obiectum philosophiae, is reduced to a constantly mutating set of interpretations of a certain body of work. -/- Perhaps this is what makes philosophy so problematic when viewed from the perspective of results, or in other words of signs of progress commonly accepted across the discipline. There are just too many ways of inducing escape from any given putative discovery; too many dimensions along which an interpretative or definitional arms race can be triggered. (shrink)

We outline Brentano’s theory of boundaries, for instance between two neighboring subregions within a larger region of space. Does every such pair of regions contain points in common where they meet? Or is the boundary at which they meet somehow pointless? On Brentano’s view, two such subregions do not overlap; rather, along the line where they meet there are two sets of points which are not identical but rather spatially coincident. We outline Brentano’s theory of coincidence, and show how he (...) uses it to resolve a number of Zeno-like paradoxes. (shrink)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (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)

This paper examines Spinoza’s view on the consistency of mental representation. First, I argue that he departs from Scholastic tradition by arguing that all mental states—whether desires, intentions, beliefs, perceptions, entertainings, etc.—must be logically consistent. Second, I argue that his endorsement of this view is motivated by key Spinozistic doctrines, most importantly the doctrine that all acts of thought represent what could follow from God’s nature. Finally, I argue that Spinoza’s view that all mental representation is consistent pushes him to (...) a linguistic account of contradiction. (shrink)

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, because these (...) are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (shrink)

Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...) story of three revolutions can provide at best a preliminary orientation, and that Husserl was constantly expanding and revising his philosophical system, integrating views in phenomenology, ontology, epistemology and logic with views on the nature and tasks of philosophy and science as well as on the nature of culture and the world in ways that reveal more common elements than violent shifts of direction. We argue further that Husserl is a seminal figure in the evolution from traditional philosophy to the characteristic philosophical concerns of the late twentieth century: concerns with representation and intentionality and with problems at the borderlines of the philosophy of mind, ontology, and cognitive science. (shrink)

Of Chisholm’s many signal contributions to analytic metaphysics, perhaps the most important is his treatment of boundaries, a category of entity that has been neglected, to say the least, in the history of ontology. We can gain some preliminary idea of the sorts of problems which the Chisholmian ontology of boundaries is designed to solve, if we consider the following Zeno-inspired thought-experiment.

Material things have material (spatial) parts. Acts, events, occurrences, have phases, which we can view as their temporal parts. Spatial surfaces and volumes, stretches of time, they all have parts again; they can all be considered "extended". Entities, on the other hand, such as directions, numbers, temperatures, colors, tones, fictional characters, prices, numbers, values, ideologies, goals, are all unextended; they are partless. Let us call such non-extended objects “nodes”, in order to express the fact that we have a tendency to (...) grasp them as pure correlates of our thinking, often at the same time viewing them effectively as placeholders within systems of coordinates in various intellectual and social domains. My aim, here, is to clarify this rough idea of “node” for the purpose of providing a corresponding clarification of Ingarden's idea of a purely intentional object. I first consider purely intentional objects in general, and then focus in particular on fictional examples. (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)

Plato’s partition argument infers that the soul has parts from the fact that the soul experiences mental conflict. We consider an ambiguity in the concept of mental conflict. According to the first sense of conflict, a soul is in conflict when it has desires whose satisfaction is logically incompatible. According to the second sense of conflict, a soul is in conflict when it has desires which are logically incompatible even when they are unsatisfied. This raises a dilemma: if the mental (...) conflict is supposed to be the latter kind of conflict, then the partition argument is valid but is likely unsound; if it’s supposed to be the former kind, then the partition argument has true premises but is invalid. We explain this dilemma in detail and defend a dispositionalist solution to it. (shrink)

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

Some defenders of so-called `artificial intelligence' believe that machines can understand language. In particular, Søgaard has argued in his "Understanding models understanding language" (2022) for a thesis of this sort. His idea is that (1) where there is semantics there is also understanding and (2) machines are not only capable of what he calls `inferential semantics', but even that they can (with the help of inputs from sensors) `learn' referential semantics. We show that he goes wrong because he pays insufficient (...) attention to the difference between language as used by humans and the sequences of inert symbols which arise when language is stored on hard drives or in books in libraries. (shrink)

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

Despite the prevalence of human rights discourse, the very idea or concept of a human right remains obscure. In particular, it is unclear what is supposed to be special or distinctive about human rights. In this paper, we consider two recent attempts to answer this challenge, James Griffin’s “personhood account” and Charles Beitz’s “practice-based account”, and argue that neither is entirely satisfactory. We then conclude with a suggestion for what a more adequate account might look like – what we call (...) the “structural pluralist account” of human rights. (shrink)