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)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (shrink)

It is argued, on the basis of ideas derived from Wittgenstein's Tractatus and Husserl's Logical Investigations, that the formal comprehends more than the logical. More specifically: that there exist certain formal-ontological constants (part, whole, overlapping, etc.) which do not fall within the province of logic. A two-dimensional directly depicting language is developed for the representation of the constants of formal ontology, and means are provided for the extension of this language to enable the representation of certain materially necessary relations. The (...) paper concludes with a discussion of the relationship between formal logic, formal ontology, and mathematics. (shrink)

J. N. (Jitendra Nath) Mohanty (1928–2023). -/- Professor J. N. Mohanty has characterized his life and philosophy as being both “inside” and “outside” East and West, i.e., inside and outside traditions of India and those of the West, living in both India and United States: geographically, culturally, and philosophically; while also traveling the world: Melbourne to Moscow. Most of his academic time was spent teaching at the University of Oklahoma, The New School Graduate Faculty, and finally Temple University. Yet his (...) preeminent work in Husserlian phenomenology developed alongside his eminent work in Indian philosophy: describing his interests as “a fusion of disparate horizons.” -/- J. N. Mohanty was born September 26, 1928, in Cuttack (Odisha, East India). After graduating from high school, he went on to study both Indian and Western philosophy in Calcutta, earning bachelor’s and master’s degrees. There he read Whitehead and Kant’s First Critique; although he wanted to include mathematics in his curriculum, he was led instead to include Indian philosophy and Sanskrit. On the shelves of his teacher, Ras Vihar Das, he came upon a copy of the English translation (Ideas I, 1931) of Edmund Husserl’s classic Ideen I (1913), which presented Husserl’s ground-breaking conception of phenomenology. In 1952–1954 he left India for the first time, reaching Göttingen to study mathematics and philosophy, which earned him a doctorate in mathematics and “philosophy of mathematical sciences” (in his own words). In Göttingen, Mohanty found the powerful mathematical world that Husserl himself had earlier interacted with, where several Husserl students had formed the Göttingen school of phenomenology. During these years Mohanty studied primarily mathematics, alongside Kant and also Vedic Sanskrit. From his friend Günter Patzig, interpreter of Aristotle and Frege, Mohanty was drawn to Frege in relation to mathematical logic. He attended lectures of Heidegger, intrigued by his ontological thinking. Yet, despite the Husserlian legacy, Mohanty was completely self-taught in his studies of Husserl (as he has reported). With a doctorate in mathematics, and ideas from Kant and Frege in his philosophical background, Mohanty set about crafting his own conception of philosophy grounded in phenomenology, drawing on Husserl’s extensive work, critically sifting through Husserl’s texts and their emerging concepts of intentionality, meaning, subject, intersubjectivity, and world. In between he wrote his first book-length study: on phenomenological insights in Nicolai Hartmann and A. N. Whitehead (1958). -/- Over many decades Mohanty formulated and argued, in analytical detail, for a conception of phenomenology and its place in philosophy, later presented in a clear and concise book titled Transcendental Phenomenology: An Analytic Account (1989). Over these very decades the same scholar explored classical and recent Indian philosophy, thinking through kindred ideas of consciousness, self, and knowledge drawn from the Indian philosophical contexts. While writing on Nyāya theory of truth, he also pondered whether the world and finite individual are illusory or real, and whether Marx, Arendt, Gandhi (whom he heard speak in Calcutta), or Vinoba Bhave (with whom he marched across India for the land-grant movement) could best navigate post-Independent India’s social and svarāj or self-rule reforms. The two Mohantys, thinking through a vision of self and world, turned out to be “non-different” or “non-dual” as they each practiced critical phenomenology from both inside and outside the respective philosophical and cultural traditions. Numerous students, fellows, and colleagues or collaborators have benefited immensely from this infusion and unified approach to diversity in philosophical thought. In the 2000s, moving into retirement, Mohanty wrote two long books devoted to his understanding of Husserl and phenomenology and the calling of philosophy itself. This two-volume study shows Mohanty himself thinking through Husserl, critically, in The Philosophy of Edmund Husserl: A Historical Introduction (2008), and Edmund Husserl’s Freiburg Years: 1916–1938. As Mohanty worked on Husserl, he carefully indicated where he agreed and where he rejected or changed ideas, all part of his practice in phenomenology of “description and interpretation.” It was the same pattern he used in addressing the thought of Husserl vis-à-vis Kant or Frege or even Quine. -/- As Mohanty developed his understanding of phenomenology over the years, he wrote books on theory of meaning and the concept of intentionality, developing a model of ideal meaning and its foundation in intentionality, drawing on Husserl’s results. He followed these with the book Husserl and Frege (1982), linking the thought of those foundational figures for the “continental” and “analytic” traditions, respectively, in twentieth-century Western philosophy. Over his long career Mohanty addressed both traditions in his clear and accessible writing style. While developing his views on phenomenology, Mohanty regularly looked to “Husserl and his others,” evaluating views in Heidegger, Sartre, Merleau-Ponty, Ricoeur, and then Derrida and others in the wake of Husserl. With his background in Kant, Mohanty also looked toward Heidegger and Hegel in relation to Husserl’s later work in the Crisis (1935–38). Similarly, he looked to contemporary analytic philosophers, adjudicating his own, oft-wise Husserlian views in relation to Frege, Nagel, and others. Amid his active scholarly career, Mohanty co-founded the journal Husserl Studies, and was editorial advisor to Philosophy & Phenomenological Research, Philosophy East & West, Journal of Indian Philosophy, Sophia, among others. -/- Yet all this while Mohanty was also thinking and writing about Indian philosophy and its relation to phenomenology. In his own retrospective, Indian philosophy is “the permanent background” of his Husserlian thinking, while Kant is the recurrent Western background of his Husserlian phenomenology. Mohanty’s form of “transcendental phenomenology” evolved, in his own perspective, against the background of his studies of Navya-Nyāya on logic and Vedānta on consciousness, in Indian philosophy, and against the background of Kant’s First Critique on the transcendental, in Western philosophy. Accordingly, Mohanty’s study of logical form and of the intentionality of consciousness seeks a fusion of East and West in the conception of transcendental phenomenology. (Cf. Mohanty’s apt response to critics in The Empirical and the Transcendental (2000).) Even in the context of North American Husserl scholarship, Mohanty has exercised an earnest fusion of East and West. For the so-called East Coast and West Coast interpretations of Husserl’s crucial notion of noema both find a sympathetic spirit in J. N. Mohanty’s careful and nuanced interpretation of Husserlian transcendental phenomenology. With Mohanty the two faces of the noema are the logical (Fregean) and the phenomenal (Kantian), and these views of intentional structure join in consciousness—in a way resonant with Indian thought. -/- - David Woodruff Smith (UC Irvine) and Purushottama Bilimoria (SFSU, San Francisco; University of Melbourne) -/- For photo of Prof Mohanty visit APA online memorial_minutes2023 Courtesy of APA Memorial Minutes (& Proceedings) 2023 . (shrink)

The authors outline the way in which documents as social objects have evolved from their earliest forms to the electronic documents of the present day. They note that while certain features have remained consistent, processes regarding document authentication are seriously complicated by the easy reproducibility of digital entities. The authors argue that electronic documents also raise significant questions concerning the theory of ‘documentality’ advanced by Maurizio Ferraris, especially given the fact that interactive documents seem to blur the distinctions between the (...) static documents (or ‘inscriptions’) which form Ferraris’s starting point, and dynamic software processes. The authors argue further that the Ferraris view as applied to legal documents is flawed because of the fact that courts may treat contractual obligations as enduring even in spite of a complete absence of enduring inscriptions. Finally, the authors note that traces in brains, another important family of inscriptions (as Ferraris conceives them), differ significantly from genuinely documentary inscriptions by their lack of public inspectability. (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)

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

John Searle’s The Construction of Social Reality and Hernando de Soto’s The Mystery of Capital shifted the focus of current thought on capital and economic development to the cultural and conceptual ideas that underpin market economies and that are taken for granted in developed nations. This collection of essays assembles 21 philosophers, economists, and political scientists to help readers understand these exciting new theories.

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

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding, melting. Among this plethora of what we can think of as ‘mere dispositions’ is a subset of dispositions in whose realizations we have an interest – a car responding well when driven on ice, a rabbit’s lungs responding well when it is chased by a wolf, and so on. We (...) call the latter ‘capabilities’ and we attempt to provide an ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are being collected in siloed fashion. (shrink)

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)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (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.

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

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)

The question of whether lies by those who govern are acceptable receives a clear focus and an ideal case in the Republic. Against C. D. C. Reeve, and T. C. Brickhouse and N. D Smith, I argue that the Republic’s apparent recommendation of administrative lies is incoherent. While lies may be a necessary part of the City’s administration, the process and practice of lying undermines that nature which is necessary for any suitable ruler – rendering the ideal impossible. I (...) argue that this analysis, while concerned with an ideal case, also applies to the political realist’s regrettable-but-necessary defence of such practices. (shrink)

Brought to you by: Crop X editors: Jonathan Alexander Perez, Harmony Smith, Corinne Tendorf, David Turturo, and Derek Rahn Williams. Faculty Advisor: David Turturo; Crop X team included: Chaimae Alehyane, Zachary S. Casey, Suzanna Brinez, Jacob Brown, Elizabeth George, Francisco Javier Muniz Ituarte, Brodey Myers. -/- Credits: Huckabee College of Architecture; Graphic Designers: Studio BLDG (Blossom Liu + Danny Gray); English Editor: Luke Studebaker; Spanish Translator: Jessie Forbes; Printer: Die Keure. Cover Photo: Derek Williams. -/- Generously supported (...) by the Graham Foundation for Advanced Studies in the Fine Arts and the Huckabee College of Architecture, Texas Tech University. (shrink)

Machine learning algorithms may radically improve our ability to diagnose and treat disease. For moral, legal, and scientific reasons, it is essential that doctors and patients be able to understand and explain the predictions of these models. Scalable, customisable, and ethical solutions can be achieved by working together with relevant stakeholders, including patients, data scientists, and policy makers.

[First published in Italian as: “L’irreligione e lo spettatore imparziale nel sistema morale di Adam Smith”, in Rivista di Filosofia 3 (3):375-403 (2005). -/- Translated by E. Lecaldano.] -/- A number of commentators on Smith’s philosophy have observed that the relationship between his moral theory and his theological beliefs is “exceedingly difficult to unravel.” The available evidence, as generally presented, suggests that although Smith was not entirely orthodox by contemporary standards, he has no obvious or significant irreligious (...) commitments or orientation. Contrary to this view of things, this essay argues that behind the veneer of orthodoxy that covers Smith’s discussion in The Theory of the Moral Sentiments there are significant irreligious themes present in his work. -/- . (shrink)

We propose a formal framework for interpretable machine learning. Combining elements from statistical learning, causal interventionism, and decision theory, we design an idealised explanation game in which players collaborate to find the best explanation for a given algorithmic prediction. Through an iterative procedure of questions and answers, the players establish a three-dimensional Pareto frontier that describes the optimal trade-offs between explanatory accuracy, simplicity, and relevance. Multiple rounds are played at different levels of abstraction, allowing the players to explore overlapping causal (...) patterns of variable granularity and scope. We characterise the conditions under which such a game is almost surely guaranteed to converge on a optimal explanation surface in polynomial time, and highlight obstacles that will tend to prevent the players from advancing beyond certain explanatory thresholds. The game serves a descriptive and a normative function, establishing a conceptual space in which to analyse and compare existing proposals, as well as design new and improved solutions. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

To the extent that dualism is even taken to be a serious option in contemporary discussions of personal identity and the philosophy of mind, it is almost exclusively either Cartesian dualism or property dualism that is considered. The more traditional dualism defended by Aristotelians and Thomists, what I call hylemorphic dualism, has only received scattered attention. In this essay I set out the main lines of the hylemorphic dualist position, with particular reference to personal identity. First I argue that overemphasis (...) of the problem of consciousness has had an unhealthy effect on recent debate, claiming instead that we should emphasize the concept of form. Then I bring in the concept of identity by means of the notion of substantial form. I continue by analyzing the relation between form and matter, defending the traditional theses of prime matter and of the unicity of substantial form. I then argue for the immateriality of the substantial form of the human person, viz. the soul, from an account of the human intellect. From this follows the soul's essential independence of matter. Finally, although the soul is the immaterial bearer of personal identity, that identity is still the identity of an essentially embodied being. I explain how these ideas are to be reconciled. Footnotesa I am grateful to Stephen Braude, John Cottingham, John Haldane, David Jehle, Joel Katzav, Eduardo Ortiz, and Fred Sommers for helpful comments and discussion of a draft of this essay. I would also like to thank Ellen Paul, whose suggestions have helped greatly to improve the essay's style and content. (shrink)

Corruptionism is the view that following physical death, the human being ceases to exist but their soul persists in the afterlife. Survivalism holds that both the human being and their soul persist in the afterlife, as distinct entities, with the soul constituting the human. Each position has its defenders, most of whom appeal both to metaphysical considerations and to the authority of St Thomas Aquinas. Corruptionists claim that survivalism violates a basic principle of any plausible mereology, while survivalists tend to (...) reject the principle, though without as much detail as one would like. In this paper I examine both the key exegetical issues and the mereological question, arguing that Aquinas cannot be shown to have supported the principle in question, and that the principle should be rejected on independent grounds. If correct, some key planks in support of survivalism are established, with others to await further examination. (shrink)

Many scholars have argued that the Protestant Reformation generally departed from virtue ethics, and this claim is often accepted by Protestant ethicists. This essay argues against such discontinuity by demonstrating John Calvin’s reception of ethical concepts from Augustine and Aristotle. Calvin drew on Augustine’s concept of eudaimonia and many aspects of Aristotle’s Nicomachean Ethics , including concepts of choice, habit, virtue as a mean, and the specific virtues of justice and prudence. Calvin also evaluated the problem of pagan virtue in (...) light of traditional Augustinian texts discussed in the medieval period. He interpreted the Decalogue as teaching virtue, including the cardinal virtues of justice and temperance. Calvin was not the harbinger of an entirely new ethical paradigm, but rather a participant in the mainstream of Christian thinkers who maintained a dual interest in Aristotelian and Augustinian eudaimonist virtue ethics. (shrink)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to happen, (...) the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

There is a tension between the reasonable desire not to be judgmental of other people’s behaviour or character, and the moral necessity of making negative judgments in some cases. I sketch a way in which we might accommodate both, via an evaluation of the good of reputation and the ethics of judgment of other people’s character and behaviour. I argue that a good reputation is a highly valuable good for its bearer, akin to a property right, and not to be (...) damaged without serious reason deriving from the demands of justice and the common welfare. Rash judgment wrongfully damages reputation and is sometimes a seriously immoral act. Rashness is not merely about lack of evidence, but involves lack of charity and is to be avoided even in some cases where the evidence of bad character or action is epistemically sufficient for judgment. I argue that the desirability of a good name for its holder, whether the reputation is deserved or not, means that in all but a relatively narrow range of cases it is always wrong to think badly of someone, even if they are bad. (shrink)

This is a brief introduction to the origin and development of Protestant ethical works in the tradition of Aristotle’s Nicomachean Ethics.

Michael Slote’s Moral Sentimentalism is a wonderful model of a particular, under-appreciated philosophical method. It demonstrates that exciting, original work can be created by putting old ideas to new uses, proving once again that the classics of moral and political philosophy offer too rich an array of intellectual resources to leave to historians alone. Whenever one is reclaiming old ideas, however, the most important decision is which ideas to reclaim, and which to leave in the dustbin of history. Slote makes (...) use of many ideas drawn from history’s greatest moral sentimentalist, David Hume, but he rejects many others. The work of Hume’s closest friend and greatest sentimentalist ally, Adam Smith, is rejected without adequate explanation. Smith is mentioned, but quickly dismissed. Yet even though Smith makes little contribution to Slote’s own version of sentimentalism, I think he deserved greater discussion in this book. Smith and Slote address many of the same subjects, using the same basic sentimentalist approach, but they come to very different conclusions. It is thus possible to construct a fruitful debate between them—a debate in which, since he can no longer speak on his own behalf, I will be taking Smith’s side. (shrink)

Richard Baxter, one of the most famous Puritans of the seventeenth century, is generally known as a writer of practical and devotional literature. But he also excelled in knowledge of medieval and early modern scholastic theology, and was conversant with a wide variety of seventeenth-century philosophies. Baxter was among the early English polemicists to write against the mechanical philosophy of René Descartes and Pierre Gassendi in the years immediately following the establishment of the Royal Society. At the same time, he (...) was friends with Robert Boyle and Matthew Hale, corresponded with Joseph Glanvill, and engaged in philosophical controversy with Henry More. In this book, David Sytsma presents a chronological and thematic account of Baxter's relation to the people and concepts involved in the rise of mechanical philosophy in late-seventeenth-century England. -/- Drawing on largely unexamined works, including Baxter's Methodus Theologiae Christianae (1681) and manuscript treatises and correspondence, Sytsma discusses Baxter's response to mechanical philosophers on the nature of substance, laws of motion, the soul, and ethics. Analysis of these topics is framed by a consideration of the growth of Christian Epicureanism in England, Baxter's overall approach to reason and philosophy, and his attempt to understand creation as an analogical reflection of God's power, wisdom, and goodness, understood as vestigia Trinitatis. Baxter's views on reason, analogical knowledge of God, and vestigia Trinitatis draw on medieval precedents and directly inform a largely hostile, though partially accommodating, response to mechanical philosophy. (shrink)

This essay is my brief review of Nicholas Phillipson’s biography of Adam Smith. I discuss the highlights of his treatment of Smith’s fascinating life. Phillipson does a beautiful job of surveying Smith’s academic career. Especially useful is Phillipson’s discussion of the influence David Hume had on Smith’s thought, as well as the influences of Montesquieu, Samuel Johnson, Voltaire, Rousseau, and others.

This essay examines the development of Reformed treatments of the affections in the period of early orthodoxy (ca. 1565-1640). I argue that discussion of the affections during this period grew within the broad framework of the Aristotelian psychology and certain polemical concerns initially established by early Reformed theologians. With the advent of Protestant universities and academies, Reformed ethicists and theologians treated the affections in greater detail, with a majority drawing on a generally Thomistic approach to the nature and division of (...) the affections, although not without a dissenting Scotistic minority. (shrink)

This critical edition is the first ever publication of Hale's Of the Law of Nature, which previously existed only in manuscript form. After discussing and defining the law in general, Hale examines the natural law in particular, its discovery and divine origin, and how it relates to both biblical and human laws. Hale's treatise, which was likely written as part of his personal meditations, and was circulated among English lawyers after his death, reveals not only the close relationship between law (...) and theology in his thought, but also the importance of natural law to early modern legal thought. (shrink)

A sentimentalist theory of morality explains all moral evaluations as manifestations of certain emotions, ones that David Hume and Adam Smith, in their related but divergent accounts, call moral sentiments. The two theories have complementary successes and failures in capturing familiar features of the experience of making moral evaluations. Thinking someone courageous or dishonest need not involve having goals or feelings of desire, and Hume’s theory captures that well; but its account of how our moral evaluations are about (...) or directed toward people or actions is deficient. Smith’s theory readily explains how moral sentiments can be about things (and which things they are about), but at the cost of construing some central moral evaluations as goal-directed desires that are simply not like that. Present-day sentimentalists also face the challenge of combining these two desiderata. (shrink)

I contend that Adam Smith and David Hume offer re-interpretations of Aristotle’s notion of greatness of soul, focusing on the kind of magnanimity Aristotle attributes to Socrates. Someone with Socratic magnanimity is worthy of honor, responds moderately to fortune, and is virtuous—just and benevolent. Recent theorists err in claiming that magnanimity is less important to Hume’s account of human excellence than benevolence. In fact, benevolence is a necessary ingredient for the best sort of greatness. Smith’s “Letter to (...) Strahan” attributes this greatness to Hume. It encourages us to admire Hume as an exemplar of human excellence, to seek Hume’s virtues for ourselves, and to approve of the “love of literary fame” which Hume calls his “ruling passion.”. (shrink)

Corcoran’s 27 entries in the 1999 second edition of Robert Audi’s Cambridge Dictionary of Philosophy [Cambridge: Cambridge UP]. -/- ancestral, axiomatic method, borderline case, categoricity, Church (Alonzo), conditional, convention T, converse (outer and inner), corresponding conditional, degenerate case, domain, De Morgan, ellipsis, laws of thought, limiting case, logical form, logical subject, material adequacy, mathematical analysis, omega, proof by recursion, recursive function theory, scheme, scope, Tarski (Alfred), tautology, universe of discourse. -/- The entire work is available online free at more than (...) one website. Paste the whole URL. http://archive.org/stream/RobertiAudi_The.Cambridge.Dictionary.of.Philosophy/Robert.Audi_The.Cambrid ge.Dictionary.of.Philosophy -/- The 2015 third edition will be available soon. Before you think of buying it read some reviews on Amazon and read reviews of its competition: For example, my review of the 2008 Oxford Companion to Philosophy, History and Philosophy of Logic,29:3,291-292. URL: http://dx.doi.org/10.1080/01445340701300429 -/- Some of the entries have already been found to be flawed. For example, Tarski’s expression ‘materially adequate’ was misinterpreted in at least one article and it was misused in another where ‘materially correct’ should have been used. The discussion provides an opportunity to bring more flaws to light. -/- Acknowledgements: Each of these entries was presented at meetings of The Buffalo Logic Dictionary Project sponsored by The Buffalo Logic Colloquium. The members of the colloquium read drafts before the meetings and were generous with corrections, objections, and suggestions. Usually one 90-minute meeting was devoted to one entry although in some cases, for example, “axiomatic method”, took more than one meeting. Moreover, about half of the entries are rewrites of similarly named entries in the 1995 first edition. Besides the help received from people in Buffalo, help from elsewhere was received by email. We gratefully acknowledge the following: José Miguel Sagüillo, John Zeis, Stewart Shapiro, Davis Plache, Joseph Ernst, Richard Hull, Concha Martinez, Laura Arcila, James Gasser, Barry Smith, Randall Dipert, Stanley Ziewacz, Gerald Rising, Leonard Jacuzzo, George Boger, William Demopolous, David Hitchcock, John Dawson, Daniel Halpern, William Lawvere, John Kearns, Ky Herreid, Nicolas Goodman, William Parry, Charles Lambros, Harvey Friedman, George Weaver, Hughes Leblanc, James Munz, Herbert Bohnert, Robert Tragesser, David Levin, Sriram Nambiar, and others. -/- . (shrink)

Franz Brentano’s attempt to distinguish mental from physical phenomena by employing the scholastic concept of intentional inexistence is often cited as reintroducing the concept of intentionality into mainstream philosophical discussion. But Brentano’s own claims about intentional inexistence are much misunderstood. In the second half of the 20th century, analytical philosophers in particular have misread Brentano’s views in misleading ways.1 It is important to correct these misunderstandings if we are to come to a proper assessment of Brentano’s worth as a philosopher (...) and his position in the history of philosophy. Good corrections have been made in the recent analytic literature by David Bell (1990), Dermot Moran (1996), and Barry Smith (1994) among others. But there is also another, more purely philosophical lesson to be learned from the proper understanding of Brentano’s views on this matter. This is that Brentano’s struggles with the concept of intentionality reveal a fundamental division between different ways of thinking about intentionality, an division which Brentano himself does not make fully clear. Making the nature of this division explicit is the aim of this paper. (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)

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors (...) and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

What happens when someone acts? A familiar answer goes like this. There is something that the agent wants, and there is an action that he believes conducive to its attainment. His desire for the end, and his belief in the action as a means, justify taking the action, and they jointly cause an intention to take it, which in turn causes the corresponding movements of the agent's body. I think that the standard story is flawed in several respects. The flaw (...) that will concern me in this paper is that the story fails to include an agent-or, more precisely, fails to cast the agent in his proper role. (shrink)

The eighteenth century philosopher David Hume was much influenced by Greek philosophy and literature. His favourite writer was the satirist Lucian. What is David Hume’s thanatotherapy (therapy of the fear of death)? Is he an Epicurean or Pyrrhonian thanatotherapist? I argue that, while he is in part an Epicurean who is sceptical about his Epicureanism, he is primarily a Lucianic thanatotherapist. A Lucianic thanatotherapist uses self and other deprecating irony as a form of therapy. He also ruthlessly satirises (...) religious consolations. I use Hume’s deathbed allusions to Lucian’s Kataplous (floating downwards) and the Dialogues of the Dead to explain my view. (shrink)

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

The agent portrayed in much philosophy of action is, let's face it, a square. He does nothing intentionally unless he regards it or its consequences as desirable. The reason is that he acts intentionally only when he acts out of a desire for some anticipated outcome; and in desiring that outcome, he must regard it as having some value. All of his intentional actions are therefore directed at outcomes regarded sub specie boni: under the guise of the good. This agent (...) is conceived as being capable of intentional action—and hence as being an agent—only by virtue of being a pursuer of value. I want to question whether this conception of agency can be correct. Surely, so general a capacity as agency cannot entail so narrow a cast of mind. Our moral psychology has characterized, not the generic agent, but a particular species of agent, and a particularly bland species of agent, at that. It has characterized the earnest agent while ignoring those agents who are disaffected, refractory, silly, satanic, or punk. I hope for a moral psychology that has room for the whole motley crew. I shall begin by examining why some philosophers have thought that the attitudes motivating intentional actions involve judgments of value. I shall then argue that their conception of these attitudes is incorrect. Finally, I shall argue that practical reason should not be conceived as a faculty for pursuing value. (shrink)