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)

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)

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)

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

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

In philosophy of aesthetics, scholars commonly express a commitment to the premise that there is a distinctive type of judgment that can be meaningfully labeled “aesthetic”, and that these judgments are distinctively different from other types of judgments. We argue that, within an Aristotelian framework, there is no clear avenue for meaningfully differentiating “aesthetic” judgment from other types of judgment, and, as such, we aim to question the assumption that aesthetic judgment does in fact constitute a distinctive kind of judgment (...) that is in need of, or can be subject to, distinctive theorizing. We advance our argument primarily through demonstrating that leading contemporary accounts of aesthetic judgment do not successfully distinguish a type of judgment in that they do not tell us how making an aesthetic judgment differs substantially from judging that 2 + 3 = 5, that football is entertaining, or that today is Tuesday. (shrink)

One way in which philosophers have often sought to distinguish moral judgments from non-moral judgments is by using the “moral-conventional” distinction. I seek to raise serious questions about the significance of the moral-conventional distinction, at least for philosophers interested in moral judgment. I survey recent developments in the fields of philosophy, psychology, and cognitive science that have led many to the conclusion that moral judgment is not a distinctive kind of judgment or the result of a specific, identifiable cognitive process. (...) I argue that if this conclusion is largely correct, the moral-conventional distinction loses significance. If moral judgment does not correspond to a distinctive cognitive process, it is unclear how distinguishing between types of norms tracks anything of significance to human judgment formation. I then discuss the implications of abandoning the distinction for research in the field of moral psychology and tentatively propose a more modest way of conceiving of norm significance. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

While environmental claims are increasingly used by companies to appeal consumers, they also attract greater scrutiny from independent parties interested in consumer protection. Consumers are now able to compare corporate environmental claims against external, often disconfirming, information to form their brand attitudes and purchase intentions. What remains unclear is how the level of information specificity of both the environmental claims and external disconfirming information interact to influence consumer reactions. Two experiments address this gap in the CSR communication literature. When specific (...) claims are countered by specific external information, consumers report more negative brand attitudes and lower purchase intentions. The effect is serially mediated by skepticism toward the claims and lack of corporate credibility. We conclude by discussing strategies that firms can utilize to avoid information dilution and ensure that external disconfirming information percolates to consumers as specific. (shrink)

Various philosophers discuss perlocutionary silencing, but none defend an account of perlocutionary silencing. This gap may exist because perlocutionary success depends on extralinguistic effects, whereas silencing interrupts speech, leaving theorists to rely on extemporary accounts when they discuss perlocutionary silencing. Consequently, scholars assume perlocutionary silencing occurs but neglect to explain how perlocutionary silencing harms speakers as speakers. In relation to that shortcoming, I defend a novel account of perlocutionary silencing. I argue that speakers experience perlocutionary silencing when they are illegitimately (...) deprived of perlocutionary influence on a conversation in which they are active participants, where perlocutionary influence on the conversation relates to speech-related perlocutionary goals meant to influence the conversation or conversational direction. Thus, this account grounds perlocutionary silencing in linguistic phenomena and characterizes perlocutionary silencing in a way that explains why those who experience perlocutionary silencing are harmed as speakers. Moreover, this account explains how perlocutionary silencing harms speakers as conversational participants in a way that cannot be captured by illocutionary or locutionary silencing, for a speaker may be perlocutionarily silenced despite illocutionary success. Consequently, the account explains why “All Lives Matter” silences Black Lives Matter and “Not All Men” silences women sharing experiences of sexual harassment. (shrink)

Daniel Dennett has offered a set of necessary and sufficient conditions for something's being the proper object of our moral commitment, that is, for something's being a person. Strict application of these largely pragmatic conditions, however, would result in a moral community with quite a surprising membership roster, because of both who is on it and who isn't. The problem is that "your" being a person should amount to more than a function of "my" goals and cleverness.

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

A defense of the value of studying what Aristotle, in the Politics, refers to as useless things, and thereby a defense of the 'uselessness' of the study of the liberal arts.

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

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana głównie za pomocą prostych przykładów z biologii, ale pojęcie niszy należy rozumieć — podobnie jak pojęcia części, granicy (...) i położenia — jako pojęcie strukturalne, znajdujące zastosowanie w obszernym zakresie różnych dziedzin. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

In this paper we argue that Socrates is a cognitivist about emotions, but then ask how the beliefs that constitute emotions can come into being, and why those beliefs seem more resistant to change through rational persuasion than other beliefs.

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

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

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

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

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)

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

• Aggregates of previously isolated cells of Hydra are capable, under suitable solvant conditions, of regeneration forming complete animals. In a first stage, ecto- and endodermal cells sort out, producing the bilayered hollow structure characteristic of Hydra tissue; thereafter, heads are formed (even if the original cell preparation contained no head cells), eventually leading to the separation of normal animals with head, body column and foot. Hydra appears to be the highest type of organism that allows for regeneration of the (...) entire structure from random cell aggregates. The system is particularly useful for studying cell interactions, tissue polarity, pattern formation, and cell differentiation. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

In uttering a sentence we are often taken to assert more than its literal meaning — though we sometimes assert less. Robyn Carston and others take this phenomenon to show that what is said or asserted by a speaker on an occasion of utterance is usually a contextuallyenriched version of the semantic content of the sentence. I shall argue that we can resist this conclusion if we recognize that what we think we are asserting, or take others to be asserting, (...) involves selective attention to one of the ways a sentence could be true and neglects others. Most of the time people converge in their selective attention and so communication is not impaired. Though in the case of sentences involving predicates of taste, people’s attention to different aspect of the truth conditions leads to seemingly intractable disputes. I will propose a treatment of such cases on which speakers mean the same by a sentence, assert no more than its semantic content, hold conflicting opinions about its truth-value, and are both right. (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)

Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review the (...) paper and attempt to assess its significance from the perspective of our current work. We then put the paper in the context of our individual and joint works, which led up to it, and summarize our research trajectories since the paper appeared, pointing out what some of this reveals about spatial ontology in general. We conclude with some remarks on the future of ontological research in geographical information science. (shrink)

Long-standing neglect of the chemical senses in the philosophy of perception is due, mostly, to their being regarded as ‘lower’ senses. Smell, taste, and chemically irritated touch are thought to produce mere bodily sensations. However, empirically informed theories of perception can show how these senses lead to perception of objective properties, and why they cannot be treated as special cases of perception modelled on vision. The senses of taste, touch, and smell also combine to create unified perceptions of flavour. The (...) nature of these multimodal experiences and the character of our awareness of them puts pressure on the traditional idea that each episode of perception goes one or other of the five senses. Thus, the chemical senses, far from being peripheral to the concerns of the philosophy of perception, may hold important clues to the multisensory nature of perception in general. (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)

What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a process that (...) is the bringing into being, sustaining, modifying, or terminating of a mental representation. We conclude by outlining some benefits and applications of this approach. (shrink)

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries (...) yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (shrink)

Transdisciplinary research knits together knowledge from diverse epistemic communities in addressing social-environmental challenges, such as biodiversity loss, climate crises, food insecurity, and public health. This paper reflects on the roles of philosophy of science in transdisciplinary research while focusing on Indigenous and other subaltern forms of knowledge. We offer a critical assessment of demarcationist approaches in philosophy of science and outline a constructive alternative of transdisciplinary philosophy of science. While a demarcationist focus obscures the complex relations between epistemic communities, transdisciplinary (...) philosophy of science provides resources for meeting epistemic and political challenges of collaborative knowledge production. (shrink)

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

We propose as a UCGIS research priority the topic of “Ontological Foundations for Geographic Information.” Under this umbrella we unify several interrelated research subfields, each of which deals with different perspectives on geospatial ontologies and their roles in geographic information science. While each of these subfields could be addressed separately, we believe it is important to address ontological research in a unitary, systematic fashion, embracing conceptual issues concerning what would be required to establish an exhaustive ontology of the geospatial domain, (...) issues relating to the choice of appropriate methods for formalizing ontologies, and considerations regarding the design of ontology-driven information systems. This integrated approach is necessary, because there is a strong dependency between the methods used to specify an ontology, and the conceptual richness, robustness and tractability of the ontology itself. Likewise, information system implementations are needed as testbeds of the usefulness of every aspect of an exhaustive ontology of the geospatial domain. None of the current UCGIS research priorities provides such an integrative perspective, and therefore the topic of “Ontological Foundations for Geographic Information Science” is unique. (shrink)

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

Do mountains exist? The answer to this question is surely: yes. In fact, ‘mountain’ is the example of a kind of geographic feature or thing most commonly cited by English speakers (Mark, et al., 1999; Smith and Mark 2001), and this result may hold across many languages and cultures. But whether they are considered as individuals (tokens) or as kinds (types), mountains do not exist in quite the same unequivocal sense as do such prototypical everyday objects as chairs or (...) people. (shrink)

Response to the paper “The Biomedical Ethics Ontology Proposal: Excellent Aims, Questionable Methods" by James DuBois, published in the Journal of Empirical Research on Human Research Ethics.

This article addresses ontological negotiations in the Global South through three case studies of community-based research in Brazil and Ghana. We argue that ontological perspectives of Indigenous and other subjugated communities require an ontological pluralism that recognizes the plurality of both representational tools and ways of being in the world. Locating these two readings of ontological pluralism in the politics of the Global South, the article highlights a wider dynamic from ontological paternalism to ontological diversity to ontological decolonization. We conclude (...) by arguing that this dynamic provides important lessons for reorienting agendas in social ontology through Southern Ontologies. (shrink)

ABSTRACT Objectives There is little research on moral uncertainties and distress of palliative and hospice care providers (PHCPs) working in jurisdictions anticipating legalising voluntary assisted dying (VAD). This study examines the perception and anticipated concerns of PHCPs in providing VAD in the State of Queensland, Australia prior to legalisation of the practice in 2021. The findings help inform strategies to facilitate training and support the health and well-being of healthcare workers involved in VAD. Design The study used a qualitative approach (...) to examine and analyse the perception and anticipated concerns of PHCPs regarding challenges of providing assisted dying in Queensland. Fourteen PHCPs were recruited using a purposive sampling strategy to obtain a broad representation of perspectives including work roles, geographical locations and workplace characteristics. Data were collected via one in-depth interview per participant. The transcripts were coded for patterns and themes using an inductive analysis approach following the tradition of Grounded Theory. Setting The study was conducted in hospital, hospice, community and residential aged care settings in Queensland, Australia. These included public and private facilities, secular and faith-based facilities, and regional/rural and urban facilities. Participants Interviews were conducted with fourteen PHCPs: 10 nurses and 4 physicians; 11 female and 3 male. The median number of years of palliative care practice was 17, ranging from 2 to 36 years. For inclusion, participants had to be practising palliative and hospice care providers. Results PHCPs are divided on whether VAD should be considered part of palliative care. Expectations of moral distress and uncertainty about practising VAD were identified in five areas: handling requests, assessing patient capacity, arranging patient transfers and logistical issues, managing unsuccessful attempts, and dealing with team conflicts and stigma. Conclusions The possibility of having to practise VAD causes moral distress and uncertainty for some PHCPs. Procedural clarity can address some uncertainties; moral and psychological distress, however, remains a source of tension that needs support to ensure ongoing care of both patients and PHCPs. The introduction of VAD post-legalisation may present an occasion for further moral education and development of PHCPs. (shrink)

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing in abstract (...) fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

In uttering a sentence we are often take to assert more than its literal meaning - though sometimes we assert less. This phenomenon is taken by many to show that what is said or asserted by a speaker on an occasion is a contextually enriched or developed version of the semantic content of the words uttered. I argue that we can resist this conclusion by recognizing that what we think we are asserting, or take others to assert, involves selective attention (...) to just one of the ways a sentence could be true and neglects others. In most conversations people converge in their selective attention and communication is not impaired. Though in the case of sentences involving predicates of personal taste, people's attention to aspects of what is claimed differs and this can lead to intractable disputes. I offer a diagnosis of such disputes where speakers can disagree about the same claim and both be right. (shrink)

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