Perhaps the question “What is philosophy?” can only be posed late in life, when old age has come, and with it the time to speak in concrete terms. It is a question one poses when one no longer has anything to ask for, but its consequences can be considerable. One was asking the question before, one never ceased asking it, but it was too artificial, too abstract; one expounded and dominated the question, more than being grabbed by it. There are (...) cases in which old age bestows not an eternal youth, but on the contrary a sovereign freedom, a pure necessity where one enjoys a moment of grace between life and death, and where all the parts of the machine combine to dispatch into the future a trait that traverses the ages: Turner, Monet, Matisse. The elderly Turner acquired or conquered the right to lead painting down a deserted path from which there was no return, and that was no longer distinguishable from a final question. In the same way, in philosophy, Kant’s Critique of Judgment is a work of old age, a wild work from which descendants will never cease to flow.We cannot lay claim to such a status. The time has simply come for us to ask what philosophy is. And we have never ceased to do this in the past, and we already had the response, which has not varied: philosophy is the art of forming, inventing, and fabricating concepts. But it was not only necessary for the response to take note of the question; it also had to determine a time, an occasion, the circumstances, the landscapes and personae, the conditions and unknowns of the question. One had to be able to pose the question “between friends” as a confidence or a trust, or else, faced with an enemy, as a challenge, and at the same time one had to reach that moment, between dog and wolf, when one mistrusts even the friend. Gilles Deleuze was professor of philosophy at the University of Paris VIII, Vincennes-St.-Denis, until his retirement in 1987. Among his books translated into English are the two-volume Capitalism and Schizophrenia , the two-volume Cinema , The Logic of Sense , and Expressionism in Philosophy: Spinoza . Daniel W. Smith is a doctoral candidate in philosophy at the University of Chicago. He is at work on a study of the philosophy of Deleuze, and is translating Deleuze’s Francis Bacon: Logique de la sensation. Arnold I. Davidson, executive editor of Critical Inquiry, teaches philosophy at the University of Chicago and is currently Marta Sutton Weeks Fellow at the Stanford Humanities Center. (shrink)

Based on the argumentative analysis, the essential title is interpreted within its entitle as it leaves bias open 'along the lines' as to whether the January 6th insurrection that took place on Capitol Hill was or was not justified or unjustifiably ‘so’ by Jean-Jacques Rousseau’s right to revolution. Detailed evidence to support and prove such intended thesis stretches this theoretical statement as it gambles to reckon with a central paradoxical and unhumored tone that leaves the reader and/or author’s perspective to (...) be ‘centered’ (and left due to a play of ‘centeredness’). As it pertains to the fallout and outcome of how governmental, national, and militaral leadership (given the reality of a sovereign leader or a reign). Presentational style is constructed or structured oddly awakes uncontrollable, uncensored, unmeasurable, and untouchable personification that is nonstop. Such series of quoted citations are pieces of instruction that serve to admire and of acceptability in pursuit of Rousseauian logic as it poses a modest figurative language where its main objective is to attempt to underline the principles and techniques that plague post-modernists within the scope of legislative, executive, or even judicial systems of functionalities. (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)

There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summarizes what (...) is known about Kafka’s relations to the Brentanist movement. It draws on Brentanian ideas on the evidence of inner perception, on oblique consciousness, on active introspection, on correct and incorrect judgment, and on consciousness as a species of inner tribunal, in order to throw light on central features of Kafka’s writings, including stylistic features. Special attention is directed towards Die Verwandlung and Der Prozess, and a reading of the latter is offered according to which the trial of Joseph K. occurs entirely within the mind of K. himself. The revisions in the 1997 version of the paper relate especially to the treatment of Kafka and Brentano in Arnold Heidsieck’s book The Intellectual Contexts of Kafka’s Fiction: Philosophy, Law, Religion of 1994. (shrink)

There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summarizes what (...) is known about Kafka’s relations to the Brentanist movement. It draws on Brentanian ideas on the evidence of inner perception, on oblique consciousness, on active introspection, on correct and incorrect judgment, and on consciousness as a species of inner tribunal, in order to throw light on central features of Kafka’s writings, including stylistic features. Special attention is directed towards Die Verwandlung and Der Prozess, and a reading of the latter is offered according to which the trial of Joseph K. occurs entirely within the mind of K. himself. The revisions in the 1997 version of the paper relate especially to the treatment of Kafka and Brentano in Arnold Heidsieck’s book The Intellectual Contexts of Kafka’s Fiction: Philosophy, Law, Religion, of 1994. (shrink)

We present a dynamic model of the evolution of communication in a Lewis signaling game while systematically varying the degree of common interest between sender and receiver. We show that the level of common interest between sender and receiver is strongly predictive of the amount of information transferred between them. We also discuss a set of rare but interesting cases in which common interest is almost entirely absent, yet substantial information transfer persists in a *cheap talk* regime, and offer a (...) diagnosis of how this may arise. -/- . (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (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)

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)

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

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)

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 development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

Research on research ethics—regarding both the governance and practice of the ethical review of human subjects research—has a tumultuous history in North America and Europe. Much of the academic literature focuses on issues to do with regulating the conduct and quality of ethics review of research protocols by ethics committees (research ethics boards (REBs) in Canada and institutional review boards (IRBs) in the United States). In addition, some of the literature attends to issues particular to the review of qualitative research, (...) and still other literature addresses the challenges posed by and the need for research on REBs/IRBs. It is this third group of literature within which our article is situated. (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)

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)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

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

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (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)

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This paper explores the relation of the theory of time and the theory of truth in Deleuze’s philosophy. According to Deleuze, a mutation in our conception of time occurred with Kant. In antiquity, time had been subordinated to movement, it was the measure or the “number of movement” (Aristotle). In Kant, this relation is inverted: time is no longer subordinated to movement but assumes an independence and autonomy of its own for the first time. In Deleuze’s phrasing, time becomes the (...) pure and empty form of everything that moves and changes — not an eternal form (as in Plato), but precisely the form of what is not eternal. In turn, the theory of time is inextricably linked to the concept of truth, since to say that a proposition is true means that it is true “in all times and in all places.” Truth, in other words, is timeless, eternal, non-temporal. When the form of the true is confronted with the form of time, the concept of truth is necessarily put into crisis, and Deleuze’s argument is that time allows the power of the false to assume an autonomy of its own. The analysis will attempt to show how the liberation of time from movement (the pure and empty form of time) leads to a liberation of the false from the true (the power of the false). (shrink)

The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological (...) and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types—for example in genotypes, phenotypes, and environment types—in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes. (shrink)

Most people will agree that if my brain were made to have within it precisely the same pattern of activity that is in it now but through artificial means, as in its being fed all its stimulation through electrodes as it sits in a vat, an experience would result for me that would be subjectively indistinguishable from that I am now having. In ‘The Story of a Brain’ I ask whether the same subjective experience would be maintained in variations like (...) these: The hemispheres are in different vats but interacting with each other through radio transmission. Smaller chunks - and eventually the individual neurons - are interacting in this way. The hemispheres or the smaller chunks undergo internally the same pattern of activity but without interacting with each other. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

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

We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an important (...) pillar in the infrastructure that is necessary for the accurate and safe delivery of all varieties of knowledge. (shrink)

Imagine that you and a duplicate of yourself are lying unconscious, next to each other, about to undergo a complete step-by-step exchange of bits of your bodies. It certainly seems that at no stage in this exchange of bits will you have thereby switched places with your duplicate. Yet it also seems that the end-result, with all the bits exchanged, will be essentially that of the two of you having switched places. Where will you awaken? I claim that one and (...) the same person possesses both bodies, occupies both places and will experience both awakenings, just as a person whose brain has been bisected must at once experience both of the unconnected fields of awareness, even though each of these will falsely appear to him as the entirety of his experience. I also claim that the more usual apparent boundaries of persons are as illusory as those in brain bisection; personal identity remains unchanged through any variation or multiplication of body or mind. In all conscious life there is only one person - I - whose existence depends merely on the presence of a quality that is inherent in all experience - its quality of being mine, the simple immediacy of it for whatever is having experience. One powerful argument for this is statistical: on the ordinary view of personhood it is an incredible coincidence for you (though not for others) that out of 200,000,000 sperm cells the very one required on each occasion for your future existence was first to the egg in each of the begettings of yourself and all your ancestors. The only view that does not make your existence incredible, and that is not therefore (from your perspective) an incredible view, is that any conscious being would necessarily have been you anyway. It is a consequence that self-interest should extend to all conscious organisms. (shrink)

I critically examine Nietzsche’s argument in The Will to Power that all the detailed events of the world are repeating infinite times (on account of the merely finite possible arrangements of forces that constitute the world and the inevitability with which any arrangement of force must bring about its successors). Nietzsche celebrated this recurrence because of the power of belief in it to bring about a revaluation of values focused wholly on the value of one’s endlessly repeating life. Belief in (...) recurrence would bring joy to those who had achieved excellence in this life and crush those who had not. I point out, however, that this significance of recurrence must be spoiled by the consideration that within each of the long cycles of recurrence there would have to be, as well, countless variations of this life. And I consider the issue of personal identity within such recurrences. Is it the same person or merely resembling but distinct persons in the recurrences or the variations? If it is the same person in precise recurrences, should the subjectively identical experience be thought of as really additional for that person? (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

I argue that a certain type of naturalist should not accept a prominent version of the no-miracles argument (NMA). First, scientists (usually) do not accept explanations whose explanans-statements neither generate novel predictions nor unify apparently disparate established claims. Second, scientific realism (as it appears in the NMA) is an explanans that makes no new predictions and fails to unify disparate established claims. Third, many proponents of the NMA explicitly adopt a naturalism that forbids philosophy of science from using any methods (...) not employed by science itself. Therefore, such naturalistic philosophers of science should not accept the version of scientific realism that appears in the NMA. (shrink)

‘Eruv’ is a Hebrew word meaning literally ‘mixture’ or ‘mingling’. An eruv is an urban region demarcated within a larger urban region by means of a boundary made up of telephone wires or similar markers. Through the creation of the eruv, the smaller region is turned symbolically (halachically = according to Jewish law) into a private domain. So long as they remain within the boundaries of the eruv, Orthodox Jews may engage in activities that would otherwise be prohibited on the (...) Sabbath, such as pushing prams or wheelchairs, or carrying walking sticks. There are eruvim in many towns and university campuses throughout the world. There are five eruvim in Chicago, five in Brooklyn, twenty three in Queens and Long Island, and at least three in Manhattan. The US Supreme Court is (like most other major US Federal Government buildings) located within the eruv of Washington DC. In many cases, not all of those living within or near the area of an actual or proposed eruv will themselves be Orthodox Jews, and this has sometimes led to protests against eruv creation. It is such protests which triggered the writing of this essay. (shrink)

Since anonymous agents can spread misinformation with impunity, many people advocate for greater accountability for internet speech. This paper provides a veritistic argument that accountability mechanisms can cause significant epistemic problems for internet encyclopedias and social media communities. I show that accountability mechanisms can undermine both the dissemination of true beliefs and the detection of error. Drawing on social psychology and behavioral economics, I suggest alternative mechanisms for increasing the trustworthiness of internet communication.

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

History has left a territory composed of two municipalitics, whose shape is unique, belonging partly to the Netherlands and partly to Belgium. Earlier both parts belonged to the former Duchy of Brabant, a tenitory that is now split up into the Dutch province of Noord-Brabant (including Baarle-Nassau) and thc Belgian provinces of Antwerp (which includes Baarle-Hertog), Vlaams Brabant, Brussels, and Brabant-Wallon. People are quite comfortable with this situation, even though it raises many complicated and difficult problems that even the most (...) brilliant jurists are puzzled. Baarle-Hertog is called on older Belgian maps Barle-Duc (Hertog = Duke, fr: duc) and must not be confused with the prefectoral town of Bar-le-Duc, Meuse, France. (shrink)

The Pessimistic Induction over the history of science argues that because most past theories considered empirically successful in their time turn out to be not even approximately true, most present ones probably aren’t approximately true either. But why did past scientists accept those incorrect theories? Kyle Stanford’s ‘Problem of Unconceived Alternatives’ is one answer to that question: scientists are bad at exhausting the space of plausible hypotheses to explain the evidence available to them. Here, I offer another answer, which I (...) call the ‘Problem of Misleading Evidence.’ I argue that this proposal is, in important respects, superior to Stanford’s. (shrink)

Many philosophers accept that, as well as having a right that others not harm us, we also have a right that others not subject us to a risk of harm. And yet, when we attempt to spell out precisely what this ‘right against risk imposition’ involves, we encounter a series of notorious puzzles. Existing attempts to deal with these puzzles have tended to focus on the nature of rights – but I propose an approach that focusses instead on the nature (...) of risk. The key move is to distinguish two different ways in which to conceptualise the risk that a given action presents – one of which is linked to the notion of probability and the other to the notion of normalcy. (shrink)

Many philosophical positions wholly undermine themselves because to possess the truth that they claim for themselves they would have to be false. These are the theories that in one way or another reject the meaningfulness or attainability of objective truth.

Imagine two urns, each with a thousand beads - in one all the beads are blue while in the other only one of the thousand is blue. If one of these urns is pushed forward (based on the toss of a fair coin) and the single bead then randomly drawn from it is blue, we must infer that it is a thousand times more probable that the urn pushed forward is the purely blue one. The hypothesis that this was instead (...) the urn with only one blue bead would require that the occurrence of the evidence, the blue bead being drawn, was something improbable - and it is improbable that something improbable is what has occurred. Next consider an example of only one urn with no prior description. By the same reasoning as above, if all the first beads randomly drawn are blue, it is becoming more and more probable that the beads in the urn are generally blue. (Otherwise something improbable would be happening in another colour not appearing; and what’s improbable is improbable.) It is therefore probable also that the next bead drawn will be blue. This is induction. As Hume would have said, we could not know a priori, given this evidence, that the next bead will be blue. But, as he overlooked, we can know a priori, given this evidence, that it is probable that the next bead will be blue. In neither urn example has the belief regarding the beads been formed as a Humean habit of expectation after many observations of beads. (In the first case there is only one observation. The second could be modified to have all the beads drawn out at once.) Rather the belief is a product of a priori reasoning about probability. Next imagine that a coin has been tossed a thousand times and landed heads every time. There was a fair and a loaded coin. According to the same reasoning, it is overwhelmingly more probable that the coin used was the loaded one. For that the fair coin had so landed is most improbable. The hypothesis that there is no external world makes the orderliness in my current experience improbable - much like getting all heads with a fair coin. (Uncaused sensation would most probably be chaotic.) The most probable hypothesis is that of things like those we believe in causing this orderliness - as the coin’s being loaded would have caused all heads. The hypothesis that my experience has been made to take this pattern by a Cartesian malicious demon or by scientists controlling my brain in a vat can only falsely seem to make the character of the experience probable by sneaking in an inherently improbable ad hoc specification that this sort of pattern of experience was that which they were aiming at producing - like an ad hoc specification that the fair coin was one that by chance landed heads all thousand times. We may thus reject such hypotheses as improbable. So this is the problem of induction solved and scepticism answered through a priori reasoning. (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.

This paper examines the critique of Voegelin in Kelsens "Secular Religion". While Kelsen sets out with the false premise that secular world view can in principle have no religious character, his critique of Voegelin remains largely unimpaired by this mistake. With convincing arguments Kelsen criticises (1) Voegelins interpretation of modernity as an age of gnosticism, (2) Voegelins reinterpretation of enlightened and secular philosopher as gnostics in disguise and (3) Voegelins rejection of modern politics and, to a lesser degree, modern science. (...) I have also uploaded the critical margin notes that some person (unfortunately I do not know any more who) had been so friendly to sent me. The paper was originally written in German, but an English translation is available as well. (shrink)

Suppose one believes that the historical record of discarded scientific theories provides good evidence against scientific realism. Should one adopt Kyle Stanford’s specific version of this view, based on the Problem of Unconceived Alternatives? I present reasons for answering this question in the negative. In particular, Stanford’s challenge cannot use many of the prima facie strongest pieces of historical evidence against realism, namely: superseded theories whose successors were explicitly conceived, and superseded theories that were not the result of elimination-of-alternatives inferences. (...) Attempts to accommodate and within Stanford’s framework are incompatible with other commitments Stanford holds, such as anti-realism being piecemeal instead of global. As separate lines of criticism, I argue that there are problems with Stanford’s claim that the PUA is the most important challenge to realism, and with his view of instrumentalist theory endorsement. (shrink)

For a while in this article it seems impossible to articulate a compelling reason for refraining from killing an innocent stranger with the press of a button when this would earn one a small prize and would be done with absolutely guaranteed immunity from any punishment or other harm (including even an instantaneous elimination of any chance of a guilty memory, achieved through hypnosis, and an ironclad commitment from God not to condemn the killing). After many failed attempts, a compelling (...) reason for not pushing the button is finally articulated. A distinction is demonstrated between merely apparent, mistaken desires and real desires. One might, for example, have merely an apparent, mistaken desire to be drinking the stuff in a mug of hot mud if one mistakenly believed that the stuff was hot chocolate. One would not really desire to be drinking that stuff. A desire, which must always be based on some belief about what its object is like, would always be open to correction along with the belief on which it depended. This realisation leads to the sweeping principle that one can only really desire what one would be desiring with a hypothetical perfect grasp of all that is involved. If one desires something only because of not fully grasping what that thing is, then one does not really desire it. What one really desires, then, regarding this stranger and pushing the button has to be what one would desire if fully experiencing, among other things, the entire value of the stranger's life from his own as well as every other angle along with the small value for oneself of the prize received on killing him. This equal concern for all is morality, and what is compelling in morality is that what it commands is what everyone really desires. (shrink)

Recent scholarship indicates that Quine’s “Truth by Convention” does not present the radical critiques of analytic truth found fifteen years later in “Two Dogmas of Empiricism.” This prompts a historical question: what caused Quine’s radicalization? I argue that two crucial components of Quine’s development can be traced to the academic year 1940–1941, when he, Russell, Carnap, Tarski, Hempel, and Goodman were all at Harvard together. First, during those meetings, Quine recognizes that Carnap has abandoned the extensional, syntactic approach to philosophical (...) analysis, an approach espoused in Carnap’s 1934 Logical Syntax of Language, and which Quine endorsed his entire career. Second, Tarski presents Quine with a philosophically well-motivated reason to think that an apparently analytic discipline, arithmetic, could be synthetic; this reflects one of the central assertions found in “Two Dogmas” but not in “Truth by Convention.” I use this account of Quine’s development to resolve a dispute between Creath and Mancosu concerning the timeline for Quine’s evolving critiques of analyticity. (shrink)