Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey- (...) class='Hi'>Smith puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms. (shrink)

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...) partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain. (shrink)

Mystical Theology and Platonism in the Time of Cusanus engages with the history of mystical theology and Neoplatonic philosophy through the lens of the 15th century philosopher and theologian, Nicholas of Cusa. The volume comprises nineteen essays that break down the barriers between medieval and Renaissance studies, reinterpreting Cusanus’ place in the history of thought by exploring the archive that informed his thinking, while also interrogating his works by exploring them from the standpoint of their later reception by modern philosophers (...) and theologians. The volume also offers tribute to the career of Donald F. Duclow, a leading scholar in the field of Cusanus studies in particular and of the history of mystical theology and Neoplatonic philosophy more generally. (shrink)

Objective: Compassion has been associated with eudaimonia and prosocial behavior, and has been regarded as a virtue, both historically and cross-culturally. However, the psychological study of compassion has been limited to laboratory settings and/or standard survey assessments. Here, we use an experience sampling method (ESM) to compare naturalistic assessments of compassion with standard assessments, and to examine compassion, its variability, and associations with eudaimonia and prosocial behavior. -/- Methods: Participants took a survey which included standard assessments of compassion and eudaimonia. (...) Then, over four days, they were repeatedly asked about their level of compassion, eudaimonia, and situational factors within the moments of daily life. Finally, prosocial behavior was tested using the Dual Gamble Task and an opportunity to donate task winnings. -/- Results: Analyses revealed within-person associations between ESM compassion and eudaimonia. ESM compassion also predicted eudaimonia at the next ESM time point. While not impervious to situational factors, considerable consistency was observed in ESM compassion in comparison with eudaimonia. Further, ESM compassion along with eudaimonia predicted donating behavior. Standard assessments did not. -/- Conclusion: Consistent with virtue theory, some individual’s reports displayed a probabilistic tendency toward compassion, and ESM compassion predicted ESM eudaimonia and prosocial behavior toward those in need. (shrink)

This chapter offers a new criticism of the Mind argument that is both decisive and instructive. It introduces a plausible principle (γ) that places a requirement on one’s having a choice about an event whose causal history includes only other events. Depending on γ’s truth-value, the Mind argument fails in such a way that one or the other of the two main species of libertarianism is the best approach to the metaphysics of freedom. Libertarians argue the compatibility of freedom and (...) indeterminism, and their biggest obstacle is the Mind argument that argues an incompatibility between the two. The chapter aims to build a case for the truth of γ, and so for nonreductive libertarianism. This is achieved by defending it from the best objections that have been brought to light, thereby emphasizing γ’s prima facie plausibility. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

In De interpretatione 9, Aristotle argues against the fatalist view that if statements about future contingent singular events (e.g. ‘There will be a sea battle tomorrow,’ ‘There will not be a sea battle tomorrow’) are already true or false, then the events to which those statements refer will necessarily occur or necessarily not occur. Scholars have generally held that, to refute this argument, Aristotle allows that future contingent statements are exempt from either the principle of bivalence, or the law of (...) excluded middle. This paper offers a new interpretation of Aristotle’s refutation of fatalism. According to this interpretation, each member of a pair of contradictory future contingent statements, in virtue of expressing modal necessity, is simply false. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

This paper attempts to explain the conceptual connections between happiness and well-being. It first distinguishes episodic happiness from happiness in the personal attribute sense. It then evaluates two recent proposals about the connection between happiness and well-being: (1) the idea that episodic happiness and well-being both have the same fundamental determinants, so that a person is well-off to a particular degree in virtue of the fact that they are happy to that degree, and (2) the idea that happiness in the (...) personal attribute sense can serve as a ‘‘proxy’’ for well-being, i.e., that a person’s degree of deep or robust happiness approximates their degree of well-being. It is argued that happiness in both these senses is conceptually, metaphysically, and empirically distinct from well- being. A new analysis of welfare, well-being as agential flourishing, can explain welfare’s real connection to happiness in both the episodic and personal attribute senses. It predicts that such happiness is only directly beneficial when it is valued, when it is a form of valuing, or when it underwrites (i.e., serves as the causal basis for) the disposition to realize one’s values. It is therefore a necessary—but not sufficient—condition for especially high levels of well-being. This analysis of welfare integrates many insights from the eudaimonic tradition of welfare and happiness research in psychology, and also addresses common criticisms of these eudaimonic models. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

In “On the Teachings of Gotama Buddha” (1925) and “Socrates-Buddha” (1926), Edmund Husserl claims that the Buddha achieves a transcendental view of consciousness by performing the epoché. Yet, states Husserl, the Buddha fails to develop a purely theoretical and universal science of consciousness, i.e., phenomenology, because his purely practical goal of Nibbāna limits knowledge of consciousness. I evaluate Husserl’s claims by examining the Buddha’s Majjhima Nikāya. I argue that Husserl correctly identifies an epoché and transcendental viewpoint in the Buddha’s teachings. (...) However, I contend that Husserl’s distinction between pure theory and pure praxis leads him to misconstrue the function of the Buddha’s epoché, the extent of knowledge that the Buddha gains from the transcendental viewpoint, and the nature of Nibbāna. I finally suggest that the Buddha presents a way of studying consciousness that is a way of life, meaning that any distinction between pure theory and pure praxis is dissolved. (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)

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)

In this paper, I argue that what counts as the proper function of a trait is a matter of the de facto perspective that the biological system, itself, possesses on what counts as proper functioning for that trait. Unlike non-perspectival accounts, internal perspectivalism does not succumb to generality problems. But unlike external perspectivalism, internal perspectivalism can provide a fully naturalistic, mind-independent grounding of proper function and natural norms. The attribution of perspectives to biological systems is intended to be neither metaphorical (...) nor anthropomorphic: I do not mean to imply that such systems thereby must possess agency, cognition, intentions, concepts, or mental or psychological states. Instead, such systems provide the grounding for norms of performance when they internally enforce their own standard of (i.e., their own perspective on) what constitutes proper functioning or malfunctioning. By operating with a fixed, determinate level of generality, such systems provide the basis for an account of proper function that is immune to generality problems. (shrink)

Since Descartes, the nature of doubt has played a central role in the development of metaphysics both positively and negatively. Despite this fact, there has been very little discussion centering round the specific nature of doubt which led, for example, to the Cartesian discovery of the cogito. Certainly, the role of doubt has been well recognized: through doubt Descartes arrives at his indubitable first principle. But what can it mean to doubt the existence of the sensible world? This would seem (...) to rest upon the assumption that we have clear and distinct knowledge of the precise nature of what it means to exist and indeed of what it means to be. As it stands, Descartes’ initiates his Meditations upon certain definite assumptions that demand more thorough interrogation. In this paper and presentation, I examine the possible assumptions inherent in the Cartesian method of doubt within the first and second meditation and the manner in which this leads to the discovery of the cogito. I consider a number of essential questions in light of this: What presuppositions lie at bottom to Cartesian doubt? What is the precise nature of metaphysical doubt? What can it mean to doubt the existence of the sensible world? (shrink)

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

Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...) future persons, and to current persons in low-lying and developing countries, by way of their impacts on climate change. When it comes to such large-scale harms, it's easy for the individual to feel helpless. Even if she sincerely wishes things were otherwise, she may wonder what she could possibly do to make them so. In this paper I briefly explore several promising avenues for generating duties in individuals to consume ethically, and develop one in particular: that an individual ought to signal her commitments to others, as a first step in collectivizing to act against unjust global labour practices. (shrink)

We first argue that there are cases of “blameless non-belief.” That is, some people—through no fault of their own—fail to enter into a conscious relationship with God. But if so, then it would be unjust of God to make certain particular goods depend upon one having a conscious relationship with God. So, given that God is just, then despite what some theists believe, a relationship with God cannot be a necessary condition for the attainment of these goods; there might, e.g., (...) be atheists in heaven, even assuming that theism is true. This implies that religion is a far less important component of people’s lives than many might think. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (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)

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)

Aristotle rightly holds that the constitution of a city is not entirely captured by its written documents or official political structures. More fundamentally, the constitution of a city is made up of its real and deep habits, customs, relations, expectations, aspirations, and ideals of the people who live there. The aim here is to articulate five values that together constitute what I will call close-knit cities: a) ecological resiliency; b) intimate proximity; c) social heterogeneity; d) fairness; e) social trust. I (...) give a brief account of each of these values alone, along the way showing how each value needs the others to be fully realised, and ultimately argue that at least most cities should aspire to become close-knit cities because they simultaneously realise environmental stewardship and enable human flourishing. (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)

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.

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

Los teóricos de la democracia dejaron de lado la pregunta de quién legalmente forma parte del "pueblo" autorizado, pregunta que atraviesa a todas las teoría de la democracia y continuamente vivifica la práctica democrática. Determinar quién constituye el pueblo es un dilema inabordable e incluso imposible de responder democráticamente; no es una pregunta que el pueblo mismo pueda decidir procedimentalmente porque la propia premisa subvierte las premisas de su resolución. Esta paradoja del mandato popular revela que el pueblo para ser (...) mejor comprendido como una demanda política, como un proceso de subjetivación, surge y se desarrolla en distintos contextos democráticos. En Estados Unidos el disputado poder para hablar en beneficio del pueblo deriva de un excedente constitutivo heredado de la era revolucionaria, a partir del hecho de que desde la Revolución el pueblo ha sido por vez primera encarnado por la representación y como exceso de cualquier forma de representación. La autoridad posrevolucionaria del vox populi deriva de esa continuamente reiterada pero nunca realizada referencia a la soberanía del pueblo a partir de la representación, legitimidad a partir de la ley, espíritu a partir de la letra, la palabra a través de la palabra. Este ensayo examina la emergencia histórica de este exceso de democracia en el período revolucionario, y cómo este habilita a una subsecuente historia de "momentos constituyentes", momentos cuando subautorizados -radicales, entidades autocreadas-, se apoderan del manto de la autoridad, cambiando las reglas de la autoridad en ese proceso. Estos pequeños dramas de reclamos de autoridad política para hablar en nombre del pueblo son felices, aun cuando explícitamente rompan con los procedimientos o reglas estatuidas para representar la voz popular. -/- Momentos constituyentes: paradojas y poder popular en los Estados Unidos de América posrevolucionarios [traducción], Revista Argentina de Ciencia Política, N°15, EUDEBA, Buenos Aires, Octubre 2012, pp. 49-74. ISSN: 0329-3092. Introducción de “Constituent Moments: Enacting the People in Postrevolutionary America”, de Jason Frank [Ed.: Duke University Press Books, enero de 2010. ISBN-10: 0822346753; ISBN-13: 978-0822346753]. (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)

This paper concerns “human symbolic output,” or strings of characters produced by humans in our various symbolic systems; e.g., sentences in a natural language, mathematical propositions, and so on. One can form a set that consists of all of the strings of characters that have been produced by at least one human up to any given moment in human history. We argue that at any particular moment in human history, even at moments in the distant future, this set is finite. (...) But then, given fundamental results in recursion theory, the set will also be recursive, recursively enumerable, axiomatizable, and could be the output of a Turing machine. We then argue that it is impossible to produce a string of symbols that humans could possibly produce but no Turing machine could. Moreover, we show that any given string of symbols that we could produce could also be the output of a Turing machine. Our arguments have implications for Hilbert’s sixth problem and the possibility of axiomatizing particular sciences, they undermine at least two distinct arguments against the possibility of Artificial Intelligence, and they entail that expert systems that are the equals of human experts are possible, and so at least one of the goals of Artificial Intelligence can be realized, at least in principle. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

This paper explores the difference it makes to incorporate the multi-focal conception of violence that has emerged in peace studies over recent decades into the discourse of non-violent direct action (Galtung 1969, 1990; Uvin 2003; Springs 2015b). I argue that non-violent action can and should incorporate and deploy the distinctions between direct, cultural, and structural forms of violence. On one hand, these analytical distinctions can facilitate forms of self-reflexive critical analysis that guard against certain violent conceptual and practical implications of (...) non-violence, however inadvertent those may be. At the same time, these lenses help reconceptualise non-violent action in ways that open up an array of strategies and tools not previously prevalent among activists committed to non-violence. Non-violent action may itself be either complicit in, or might be enabled to illuminate and cut against, forms of violence that infuse social, political, and economic structures (i.e. structural violence). Appeals to non-violence and the actions with which they interweave may be complicit in, or might be enabled to illuminate and cut against, religious, ideological, aesthetic, and even scientific understandings and conceptual frames that underpin and support structural violence (i.e. cultural violence). In each case, non- violence must be critically examined with all these possibilities in mind. I first define and contextualize a multidimensional account of violence in terms of direct, structural, and cultural violence. I then consider two examples of how it challenges thinking about non-violence. (shrink)

Is the institutionalization of religious freedom through human rights jurisprudence simply a means by which the modern nation-state manufactures and regulates “religion”? Is the discourse of religious freedom principally a technology of state governance? These questions challenge the ways that scholars conceptualize the relation between states, nationalism, human rights, and religious freedom. This article forwards an approach to human rights and methodological nationalism that both counters and explores alternatives to the prevailing conceptions of human rights, nationalism, and state sovereignty in (...) the discourse on the putative impossibility—and, by some accounts, insidiousness—of religious freedom. I first explicate the interpretive and contestatory dimensions of human rights discourse concerning religious freedom. I then explore cross-cutting ambivalences within the nationalisms that states need and cultivate in effort to transmute their monopoly upon coercive force (i.e. power) into legitimated authority. I argue that these provide two dimensions in and through which state sovereignty may be opposed, criticized, held accountable, and subject to change. (shrink)

In this essay, I take up the question of why so many of the movies made by Hollywood are endless sequels, “prequels,” and remakes of prior blockbuster hits and so many are based on comic books (X-men, Superman, Batman, and so on). I tie the explanation in part to the aforementioned 1950 Supreme Court ruling prohibiting production companies, and in part to broader cultural changes. In particular, I argue that precisely because film producers can no longer make money from the (...) concessions (i.e., the purchases within the theater), but only of the ticket sales, the producers keep producing remakes of known popular movies, rather than make deeply original movies. (shrink)

In this paper I introduce the idea of a higher-order modal logic—not a modal logic for higher-order predicate logic, but rather a logic of higher-order modalities. “What is a higher-order modality?”, you might be wondering. Well, if a first-order modality is a way that some entity could have been—whether it is a mereological atom, or a mereological complex, or the universe as a whole—a higher-order modality is a way that a first-order modality could have been. First-order modality is modeled in (...) terms of a space of possible worlds—a set of worlds structured by an accessibility relation, i.e., a relation of relative possibility—each world representing a way that the entire universe could have been. A second-order modality would be modeled in terms of a space of spaces of (first-order) possible worlds, each space representing a way that (first-order) possible worlds could have been. And just as there is a unique actual world which represents the way that things actually are, there is a unique actual space which represents the way that first-order modality actually is. -/- One might wonder what the accessibility relation itself is like. Presumably, if it is logical or metaphysical modality that is being dealt with, it is reflexive; but is it also symmetric, or transitive? Especially in the case of metaphysical modality, the answer is not clear. And whichever of these properties it may or may not have, could that itself have been different? Could at least some rival modal logics represent different ways that first-order modality could have been? -/- To be clear, the idea behind my proposal is not just that some things which are possible or necessary might not have been so at the first order, as determined by the actual accessibility relation, but also that the actual accessibility relation, and hence the nature or structure of actual modality, could have been different at some higher order of modality. Even if the accessibility relation is actually both symmetric and transitive, perhaps it could (second-order) have been otherwise: There is a (second-order) possible space of worlds in which it is different, where it fails to be symmetric, or transitive. We must, therefore, introduce the notion of a higher-order accessibility relation, one that in this case relates spaces of first-order worlds. The question then arises as to whether that relation is symmetric, or transitive. We can then consider third-order modalities, spaces of spaces of spaces of possible worlds, where the second-order accessibility relation differs from how it actually is. I can see no reason why there should be a limit to this hierarchy of higher-order modalities, any more than I can see a reason why there should be a limit to the hierarchy of higher-order properties. There will thus be an infinity of orders, one for each positive integer, and each order will have an accessibility relation of its own. To keep things as clear as possible, a space of first-order points (i.e., of possible worlds) shall be called a galaxy, a space of second-order points, a universe, and a space of any higher order, a cosmos. However, to keep things as simple as possible, in what follows I will deal with but a single cosmos, and hence will not deal with modalities higher than the third order. -/- The accessibility relation is not the only thing that might be thought to vary between spaces of worlds: Perhaps the contents of the spaces can vary as well. While I presume that the contents of the worlds themselves remain constant—it makes doubtful sense to suppose that in one space some entity e exists in a world w and in another space e doesn’t exist in that same world w—we may suppose that different spaces differ as to which worlds they contain, just as different worlds may differ as to which objects they contain. Thus we might have a higher-order analogue of a variable-domain modal logic. There seem, then, to be three ways in which spaces can differ: First, as to the properties of the accessibility relation; second, as to which worlds the relation relates; and third, as to which worlds or spaces are parts of their domains. -/- The paper will be structured as follows. In Section 2 I provide some reasons why one might want to pursue this kind of project in the first place. In Section 3 I outline the syntax and semantics of my proposed logic. Section 4 covers semantic tableaux for this system; and after giving the rules for their construction, I construct a few of them myself to establish some logical consequences of the system and give the reader a feel for how it works. In Sections 5, 6 and 7 I explore some of its potential philosophical implications for areas besides logic, namely the philosophy of language; metaphysics, including the metaphysics of modality and the philosophy of time, and finally the philosophy of religion, before concluding the paper in Section 8. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...) they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

A response to critical commentaries. Crookston begins her commentary by noting that my book would have been better with answers to “the following three questions: (1) Why is the harm principle the right principle upon which to base a theory of toleration? (2) How is Cohen thinking of the concept of volenti? (p. x ) Is interference (i.e., the abandonment of toleration) ever morally required by the harm principle?” (p. x ). She is right, and I address these questions below (...) in Sections 2, 3, and 4. That is the bulk of this essay. I then turn to Kelley's issues in Sections 6, 7, and 8; these have to do with “the link between toleration and relativism,” the way I distinguish “the concepts of toleration and endurance,” and a “question about moral toleration” (p. x ). Despite much agreement, there are points of contention and I try to make my position clearer in response . (shrink)

Some recent work in philosophy of religion addresses what can be called the “axiological question,” i.e., regardless of whether God exists, would it be good or bad if God exists? Would the existence of God make the world a better or a worse place? Call the view that the existence of God would make the world a better place “Pro-Theism.” We argue that Pro-Theism is not implausible, and moreover, many Theists, at least, (often implicitly) think that it is true. That (...) is, many Theists think that various good outcomes would arise if Theism is true. We then discuss work in cognitive science concerning human cognitive bias, before discussing two noteworthy attempts to show that at least some religious beliefs arise because of cognitive bias: Hume’s, and Draper’s and Nichols’s. We then argue that, as a result of certain cognitive biases that result when good outcomes might be at stake, Pro-Theism causes many Theists to inflate the epistemic probability that God exists, and as a result, Theists should lower the probability they assign to God’s existence. Finally, based our arguments, we develop a novel objection to Pascal’s wager. (shrink)

We formulate a sort of "generic" cosmological argument, i.e., a cosmological argument that shares premises (e.g., "contingent, concretely existing entities have a cause") with numerous versions of the argument. We then defend each of the premises by offering pragmatic arguments for them. We show that an endorsement of each premise will lead to an increase in expected utility; so in the absence of strong evidence that the premises are false, it is rational to endorse them. Therefore, it is rational to (...) endorse the cosmological argument, and so rational to endorse theism. We then consider possible objections. (shrink)

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

This essay is my review of economist Mark Skousen’s book, The Big Three in Economics. In it, he discusses the economic work of Adam Smith, Karl Marx, and John Maynard Keynes. He gives even-handed treatments of the major contributions of each, for example, Smith’s reputation refutation of mercantilist policies and Smith’s crucial insight into the role that division of labor plays in economic growth. My only complaint is that Skousen doesn’t adequately explain his choice of Marx as (...) a great economist. What enduring contributions did he make to the field? Why name him rather than (say) David Ricardo? (shrink)

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task of ensuring that the right sorts of information gets to the right sorts of people remains. We argue that the many efforts underway to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations. This in turn requires that the management of information and knowledge within healthcare (...) organizations be combined with models of resources and processes of patient care that are based on a general ontology of social interaction. The Health Level 7 (HL7) is one of several ANSI-accredited Standards Developing Organizations operating in the healthcare arena. HL7 has advanced a widely used messaging standard that enables healthcare applications to exchange clinical and administrative data in digital form. HL7 focuses on the interface requirements of the entire healthcare system and not exclusively on the requirements of one area of healthcare such as pharmacy, medical devices, imaging or insurance transactions. This has inspired the development of a powerful abstract model of patient care called the Reference Information Model (RIM). The present paper begins with an overview of the core classes of the HL7 (Version 3) RIM and a brief discussion of its “actcentered” view of healthcare. Central to this account is what is called the life cycle of events. A clinical action may progress from defined, through planned and ordered, to executed. These modalities of an action are represented as the mood of the act. We then outline the basis of an ontology of organizations, starting from the theory of speech Acts, and apply this ontology to the HL7 RIM. Special attention is given to the sorts of preconditions that must be satisfied for the successful performance of a speech act and to the sorts of entities to which speech acts give rise (e.g. obligations, claims, commitments, etc.). Finally we draw conclusions for the efficient communication and management of medical information and knowledge within and between healthcare organizations, paying special attention to the role that medical documents play in such organizations. (shrink)

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

While there has been significant discussion in the health sciences and ethics literatures about problems associated with publication practices (e.g., ghost- and gift-authorship, conflicts of interest), there has been relatively little practical guidance developed to help researchers determine how they should fairly allocate credit for multi-authored publications. Fair allocation of credit requires that participating authors be acknowledged for their contribution and responsibilities, but it is not obvious what contributions should warrant authorship, nor who should be responsible for the quality and (...) content of the scientific research findings presented in a publication. In this paper, we review arguments presented in the ethics and health science literatures, and the policies or guidelines proposed by learned societies and journals, in order to explore the link between author contribution and responsibility in multi-author multidisciplinary health science publications. We then critically examine the various procedures used in the field to help researchers fairly allocate authorship. (shrink)