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

In this paper, I provide a descriptive definition of art that is able to accommodate the existence of bad art, while illuminating the value of good art. This, I argue, is something that existing definitions of art fail to do. I approach this task by providing an account according to which what makes something an artwork is the institutional process by which it is made. I argue that Searle’s account of institutions and institutional facts shows that the existence of all (...) institutions is due to their being perceived by their participants to perform some humanly valuable function. I then identify the functions to which the existence of art institutions is due. I then use these functions to provide a reductive institutional definition of art. Finally, in section seven, I examine the account’s consequences for the value of good art. (shrink)

While scientific inquiry crucially relies on the extraction of patterns from data, we still have a far from perfect understanding of the metaphysics of patterns—and, in particular, of what makes a pattern real. In this paper we derive a criterion of real-patternhood from the notion of conditional Kolmogorov complexity. The resulting account belongs to the philosophical tradition, initiated by Dennett :27–51, 1991), that links real-patternhood to data compressibility, but is simpler and formally more perspicuous than other proposals previously defended in (...) the literature. It also successfully enforces a non-redundancy principle, suggested by Ladyman and Ross, that aims to exclude from real-patternhood those patterns that can be ignored without loss of information about the target dataset, and which their own account fails to enforce. (shrink)

There is a variety of epistemic roles to which photographs are better suited than non-photographic pictures. Photographs provide more compelling evidence of the existence of the scenes they depict than non-photographic pictures. They are also better sources of information about features of those scenes that are easily overlooked. This chapter examines several different attempts to explain the distinctive epistemic value of photographs, and argues that none is adequate. It then proposes an alternative explanation of their epistemic value. The chapter argues (...) that photographs play the epistemic roles they do because they are typically rich sources of depictively encoded information about the scenes they depict, and reliable depictive representations of those scenes. It then explains why photographs differ from non-photographic pictures in both respects. (shrink)

One of the most prominent ethical concerns regarding emerging neurotechnologies is mental privacy. This is the idea that we should have control over access to our neural data and to the information about our mental processes and states that can be obtained by analyzing it. A key issue is whether this information needs more stringent protection than other kinds of personal information. I will articulate and support the view, underlying recent regulatory frameworks, that mental privacy requires a special treatment because (...) of its relation to relevant aspects of personal identity. It has been suggested that this approach could be supported by the idea that mental privacy constitutes a fundamental psychological dimension of privacy. The connection between this psychological view of privacy and identity can be traced back to Irwin Altman’s idea that privacy is an interpersonal boundary regulation process. However, it is not clear whether this notion of privacy can be associated with a conception of identity that is relevant in contemporary neuroethics. I will suggest that the narrative and relational approach to identity, a prominent view in recent ethical discussions of neurotechnology, lines up with key aspects of Altman’s proposal. I suggest that if mental privacy is an essential component of identity, the latter could be affected by technological mind-reading. (shrink)

A uniform construction for sequent calculi for finite-valued first-order logics with distribution quantifiers is exhibited. Completeness, cut-elimination and midsequent theorems are established. As an application, an analog of Herbrand’s theorem for the four-valued knowledge-representation logic of Belnap and Ginsberg is presented. It is indicated how this theorem can be used for reasoning about knowledge bases with incomplete and inconsistent information.

It is generally recognised that an adequate resemblance-based account of depiction must specify some standard of correctness which explains how a picture’s content differs from the content we would attribute to it purely on the basis of resemblance. For example, an adequate standard should explain why stick figure drawings do not depict emaciated beings with gargantuan heads. Most attempts to specify a standard of correctness appeal to the intentions of the picture’s maker. However, I argue that the most detailed such (...) attempt to date is incomplete. I argue that an adequate standard can be given only if one construes a picture’s content as being pictorially implicated, in a way analogous to that in which Grice explains an utterance’s meaning as being conversationally implicated. I propose a theory of pictorial implicature and use it as the basis for an intention-based standard of correctness. I show how this standard is able to explain both the ways in which the content of pictures differs from the content we would attribute to them solely on the basis of resemblance, and how we are able to apply an intention-based standard of correctness even though we lack any independent knowledge of the intentions of pictures’ makers. (shrink)

In this paper, I discuss the influential view that depiction, like language, depends on arbitrary conventions. I argue that this view, however it is elaborated, is false. Any adequate account of depiction must be consistent with the distinctive features of depiction. One such feature is depictive generativity. I argue that, to be consistent with depictive generativity, conventionalism must hold that depiction depends on conventions for the depiction of basic properties of a picture’s object. I then argue that two considerations jointly (...) preclude depiction from being governed by such conventions. Firstly, conventions must be salient to those who employ them. Secondly, those parts of pictures that depict basic properties of objects are not salient to the makers and interpreters of pictures. (shrink)

The aim of this paper is to emphasize the fact that for all finitely-many-valued logics there is a completely systematic relation between sequent calculi and tableau systems. More importantly, we show that for both of these systems there are al- ways two dual proof sytems (not just only two ways to interpret the calculi). This phenomenon may easily escape one’s attention since in the classical (two-valued) case the two systems coincide. (In two-valued logic the assignment of a truth value and (...) the exclusion of the opposite truth value describe the same situation.). (shrink)

In this paper, I discuss the account of depiction proposed by Robert Hopkins in his book Picture, Image and Experience. I first briefly summarise Hopkins’s account, according to which we experience depictions as resembling their objects in respect of outline shape. I then ask whether Hopkins’s account can perform the explanatory tasks required of an adequate account of depiction. I argue that there are at least two reasons for which Hopkins’s account of depiction is inadequate. Firstly, the notion of outline (...) shape, as Hopkins presents it, is inconsistent. Moreover, I argue that, while a consistent construal of outline shape is possible, Hopkins’s account becomes indistinguishable from previous accounts of depiction under any such construal. Second, I argue that, however it is construed, the notion of outline shape is unable to explain one of the central features which Hopkins himself insists any successful account of depiction must explain. (shrink)

As systems based on opaque Artificial Intelligence (AI) continue to flourish in diverse real-world applications, understanding these black box models has become paramount. In response, Explainable AI (XAI) has emerged as a field of research with practical and ethical benefits across various domains. This paper not only highlights the advancements in XAI and its application in real-world scenarios but also addresses the ongoing challenges within XAI, emphasizing the need for broader perspectives and collaborative efforts. We bring together experts from diverse (...) fields to identify open problems, striving to synchronize research agendas and accelerate XAI in practical applications. By fostering collaborative discussion and interdisciplinary cooperation, we aim to propel XAI forward, contributing to its continued success. Our goal is to put forward a comprehensive proposal for advancing XAI. To achieve this goal, we present a manifesto of 27 open problems categorized into nine categories. These challenges encapsulate the complexities and nuances of XAI and offer a road map for future research. For each problem, we provide promising research directions in the hope of harnessing the collective intelligence of interested stakeholders. (shrink)

According to proponents of the extended mind, bio-external resources, such as a notebook or a smartphone, are candidate parts of the cognitive and mental machinery that realises cognitive states and processes. The present chapter discusses three areas of ethical concern associated with the extended mind, namely mental privacy, mental manipulation, and agency. We also examine the ethics of the extended mind from the standpoint of three general normative frameworks, namely, consequentialism, deontology, and virtue ethics.

The paper introduces a special issue of the journal Philosophical Problems in Science (ZFN) on the topic of the nature and norms of scientific explanation.

I defend Christopher Peacocke's and Robert Hopkins's experienced resemblance accounts of depiction against criticisms put forward by Gavin McIntosh in a recent article in this journal. I argue that, while there may be reasons for rejecting Peacocke's and Hopkins's accounts, McIntosh fails to provide any.

The first-order temporal logics with □ and ○ of time structures isomorphic to ω (discrete linear time) and trees of ω-segments (linear time with branching gaps) and some of its fragments are compared: the first is not recursively axiomatizable. For the second, a cut-free complete sequent calculus is given, and from this, a resolution system is derived by the method of Maslov.

Autonomy has been central to moral and political philosophy for millenia, and has been positioned as a critical aspect of both justice and wellbeing. Research in psychology supports this position, providing empirical evidence that autonomy is critical to motivation, personal growth and psychological wellness. Responsible AI will require an understanding of, and ability to effectively design for, human autonomy (rather than just machine autonomy) if it is to genuinely benefit humanity. Yet the effects on human autonomy of digital experiences are (...) neither straightforward nor consistent, and are complicated by commercial interests and tensions around compulsive overuse. This multi-layered reality requires an analysis that is itself multidimensional and that takes into account human experience at various levels of resolution. We borrow from HCI and psychological research to apply a model (“METUX”) that identifies six distinct spheres of technology experience. We demonstrate the value of the model for understanding human autonomy in a technology ethics context at multiple levels by applying it to the real-world case study of an AI-enhanced video recommender system. In the process we argue for the following three claims: 1) There are autonomy-related consequences to algorithms representing the interests of third parties, and they are not impartial and rational extensions of the self, as is often perceived; 2) Designing for autonomy is an ethical imperative critical to the future design of responsible AI; and 3) Autonomy-support must be analysed from at least six spheres of experience in order to approriately capture contradictory and downstream effects. (shrink)

We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...) pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research. (shrink)

All first-order Gödel logics G_V with globalization operator based on truth value sets V C [0,1] where 0 and 1 lie in the perfect kernel of V are axiomatized by Ciabattoni’s hypersequent calculus HGIF.

It is shown that the infinite-valued first-order Gödel logic G° based on the set of truth values {1/k: k ε w {0}} U {0} is not r.e. The logic G° is the same as that obtained from the Kripke semantics for first-order intuitionistic logic with constant domains and where the order structure of the model is linear. From this, the unaxiomatizability of Kröger's temporal logic of programs (even of the fragment without the nexttime operator O) and of the authors' temporal (...) logic of linear discrete time with gaps follows. (shrink)

Although arguments for and against competing theories of vagueness often appeal to claims about the use of vague predicates by ordinary speakers, such claims are rarely tested. An exception is Bonini et al. (1999), who report empirical results on the use of vague predicates by Italian speakers, and take the results to count in favor of epistemicism. Yet several methodological difficulties mar their experiments; we outline these problems and devise revised experiments that do not show the same results. We then (...) describe three additional empirical studies that investigate further claims in the literature on vagueness: the hypothesis that speakers confuse ‘P’ with ‘definitely P’, the relative persuasiveness of different formulations of the inductive premise of the Sorites, and the interaction of vague predicates with three different forms of negation. (shrink)

A new strategy for moving forward in the characterization of the Global Neuronal Workspace (GNW) is proposed. According to Dehaene, Changeux and colleagues, broadcasting is the main function of the GNW. However, the dynamic network properties described by recent graph-theoretic GNW models are consistent with many large-scale communication processes that are different from broadcasting. We propose to apply a different graph-theoretic approach, originally developed for optimizing information dissemination in communication networks, which can be used to identify the pattern of frequency (...) and phase-specific directed functional connections that the GNW would exhibit only if it were a broadcasting network. (shrink)

We present a general framework for representing belief-revision rules and use it to characterize Bayes's rule as a classical example and Jeffrey's rule as a non-classical one. In Jeffrey's rule, the input to a belief revision is not simply the information that some event has occurred, as in Bayes's rule, but a new assignment of probabilities to some events. Despite their differences, Bayes's and Jeffrey's rules can be characterized in terms of the same axioms: "responsiveness", which requires that revised beliefs (...) incorporate what has been learnt, and "conservativeness", which requires that beliefs on which the learnt input is "silent" do not change. To illustrate the use of non-Bayesian belief revision in economic theory, we sketch a simple decision-theoretic application. (shrink)

During much of the past century, it was widely believed that phonemes--the human speech sounds that constitute words--have no inherent semantic meaning, and that the relationship between a combination of phonemes (a word) and its referent is simply arbitrary. Although recent work has challenged this picture by revealing psychological associations between certain phonemes and particular semantic contents, the precise mechanisms underlying these associations have not been fully elucidated. Here we provide novel evidence that certain phonemes have an inherent, non-arbitrary emotional (...) quality. Moreover, we show that the perceived emotional valence of certain phoneme combinations depends on a specific acoustic feature--namely, the dynamic shift within the phonemes' first two frequency components. These data suggest a phoneme-relevant acoustic property influencing the communication of emotion in humans, and provide further evidence against previously held assumptions regarding the structure of human language. This finding has potential applications for a variety of social, educational, clinical, and marketing contexts. (shrink)

The question of the cognitive role of fictionality is this: what is the correct cognitive attitude to take to p, when it is fictional that p? We began by considering one answer to this question, implicit in the work of Kendall Walton, that the correct response to a fictional proposition is to imagine that proposition. However, this approach is silent in cases of fictional incompleteness, where neither p nor its negation are fictional. We argue that that Waltonians should embrace a (...) pluralistic account of the cognitive role of fictional incompleteness: in some cases of fictional incompleteness, we are permitted to resolve the incompleteness during our engagement with the target fiction, and in other cases, we are obliged not to resolve the incompleteness. But though pluralism is accommodated by Walton’s wider account of fictionality, it puts tension on his motivating idea that fictionality stands to the imagination as truth stands to belief. And so we develop a rival conception of the cognitive role of fictionality that is built around a different analogy: on this evidentialist approach, (known) fictionality stands to the imagination as evidence stands to credence. (shrink)

The genre to which an artwork belongs affects how it is to be interpreted and evaluated. An account of genre and of the criteria for genre membership should explain these interpretative and evaluative effects. Contrary to conceptions of genres as categories distinguished by the features of the works that belong to them, I argue that these effects are to be explained by conceiving of genres as categories distinguished by certain of the purposes that the works belonging to them are intended (...) to serve. (shrink)

The use of the symbol ∨for disjunction in formal logic is ubiquitous. Where did it come from? The paper details the evolution of the symbol ∨ in its historical and logical context. Some sources say that disjunction in its use as connecting propositions or formulas was introduced by Peano; others suggest that it originated as an abbreviation of the Latin word for “or,” vel. We show that the origin of the symbol ∨ for disjunction can be traced to Whitehead and (...) Russell’s pre-Principia work in formal logic. Because of Principia’s influence, its notation was widely adopted by philosophers working in logic (the logical empiricists in the 1920s and 1930s, especially Carnap and early Quine). Hilbert’s adoption of ∨ in his Grundzüge der theoretischen Logik guaranteed its widespread use by mathematical logicians. The origins of other logical symbols are also discussed. (shrink)

Tasks, tools, and techniques that we perform, use, and acquire, define the elements of expertise which we value as the hallmarks of goal-driven behavior. Somehow, the creation of tools enables us to define new tasks, or is it that the envisioning of new tasks drives us to invent new tools? Or maybe it is that new tools engender new techniques which then result in new tasks? This jumble of issues will be explored and discussed in this diverse collection of papers. (...) Individually, few of the papers are related to each other by topic or by techniques of analysis. Collectively, all focus on tasks performed using tools and discuss the techniques of tool use which enable differences in performance and expertise across individuals, societies, and (even) species. -/- . (shrink)

A construction principle for natural deduction systems for arbitrary, finitely-many-valued first order logics is exhibited. These systems are systematically obtained from sequent calculi, which in turn can be automatically extracted from the truth tables of the logics under consideration. Soundness and cut-free completeness of these sequent calculi translate into soundness, completeness, and normal-form theorems for natural deduction systems.

A general class of labeled sequent calculi is investigated, and necessary and sufficient conditions are given for when such a calculus is sound and complete for a finite -valued logic if the labels are interpreted as sets of truth values. Furthermore, it is shown that any finite -valued logic can be given an axiomatization by such a labeled calculus using arbitrary "systems of signs," i.e., of sets of truth values, as labels. The number of labels needed is logarithmic in the (...) number of truth values, and it is shown that this bound is tight. (shrink)

An adequate account of the nature of genre and of the criteria for genre membership is essential to understanding the nature of the various categories into which comics can be classified. Because they fail adequately to distinguish genre categories from other ways of categorizing works, including categorizations according to medium or according to style, previous accounts of genre fail to illuminate the nature of comics categories. I argue that genres are sets of conventions that have developed as means of addressing (...) particular interpretative and/or evaluative concerns, and have a history of co‐instantiation within a community, such that a work’s belonging to some genre generates interpretative and evaluative expectations among the members of that community. Genres are distinct from styles in consisting of conventions, and are distinct from media both in consisting of conventions and in generating interpretative and evaluative expectations. (shrink)

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

Investigation of neural and cognitive processes underlying individual variation in moral preferences is underway, with notable similarities emerging between moral- and risk-based decision-making. Here we specifically assessed moral distributive justice preferences and non-moral financial gambling preferences in the same individuals, and report an association between these seemingly disparate forms of decision-making. Moreover, we find this association between distributive justice and risky decision-making exists primarily when the latter is assessed with the Iowa Gambling Task. These findings are consistent with neuroimaging studies (...) of brain function during moral and risky decision-making. This research also constitutes the first replication of a novel experimental measure of distributive justice decision-making, for which individual variation in performance was found. Further examination of decision-making processes across different contexts may lead to an improved understanding of the factors affecting moral behaviour. (shrink)

It is shown that Gqp↑, the quantified propositional Gödel logic based on the truth-value set V↑ = {1 - 1/n : n≥1}∪{1}, is decidable. This result is obtained by reduction to Büchi's theory S1S. An alternative proof based on elimination of quantifiers is also given, which yields both an axiomatization and a characterization of Gqp↑ as the intersection of all finite-valued quantified propositional Gödel logics.

A key strength of connectionist modelling is its ability to simulate both intact cognition and the behavioural effects of neural damage. We survey the literature, showing that models have been damaged in a variety of ways, e.g. by removing connections, by adding noise to connection weights, by scaling weights, by removing units and by adding noise to unit activations. While these different implementations of damage have often been assumed to be behaviourally equivalent, some theorists have made aetiological claims that rest (...) on nonequivalence. They suggest that related deficits with different aetiologies might be accounted for by different forms of damage within a single model. We present two case studies that explore the effects of different forms of damage in two influential connectionist models, each of which has been applied to explain neuropsychological deficits. Our results indicate that the effect of simulated damage can indeed be sensitive to the way in which damage is implemented, particularly when the environment comprises subsets of items that differ in their statistical properties, but such effects are sensitive to relatively subtle aspects of the model’s training environment. We argue that, as a consequence, substantial methodological care is required if aetiological claims about simulated neural damage are to be justified, and conclude more generally that implementation assumptions, including those concerning simulated damage, must be fully explored when evaluating models of neurological deficits, both to avoid over-extending the explanatory power of specific implementations and to ensure that reported results are replicable. (shrink)

All disciplines must define their basic units and core processes. In evolutionary biology, the core process is natural selection and the basic unit of selection and adaptation is the individual. To operationalize the theory of natural selection we must count individuals, as they are the bearers of fitness. While canonical individuals have often been taken to be multicellular organisms, the hierarchy of life shows that new kinds of individuals have evolved. A variety of criteria have been used to define biological (...) individuality. Some criteria rely on the presence/absence of a particular property while others advocate an approach that reflects the process of natural selection. The plethora of approaches to classifying individuality has resulted in confusion regarding how to study individuality in a given taxon. (shrink)

forall x: Calgary is a full-featured textbook on formal logic. It covers key notions of logic such as consequence and validity of arguments, the syntax of truth-functional propositional logic TFL and truth-table semantics, the syntax of first-order (predicate) logic FOL with identity (first-order interpretations), symbolizing English in TFL and FOL, and Fitch-style natural deduction proof systems for both TFL and FOL. It also deals with some advanced topics such as modal logic, soundness, and functional completeness. Exercises with solutions are available. (...) It is provided in PDF (for screen reading, printing, and a special version for dyslexics), HTML, and in LaTeX source code. (shrink)

Fourteen philosophers share their experience teaching Peirce to undergraduates in a variety of settings and a variety of courses. The latter include introductory philosophy courses as well as upper-level courses in American philosophy, philosophy of religion, logic, philosophy of science, medieval philosophy, semiotics, metaphysics, etc., and even an upper-level course devoted entirely to Peirce. The project originates in a session devoted to teaching Peirce held at the 2007 annual meeting of the Society for the Advancement of American Philosophy. The session, (...) organized by James Campbell and Richard Hart, was co-sponsored by the American Association of Philosophy Teachers. (shrink)

We present a new understanding of Christ’s real presence in the Eucharist on the model of Stump’s account of God’s omnipresence and Green and Quan’s account of experiencing God in Scripture. On this understanding, Christ is derivatively, rather than fundamentally, located in the consecrated bread and wine, such that Christ is present to the believer through the consecrated bread and wine, thereby making available to the believer a second-person experience of Christ, where the consecrated bread and wine are the way (...) in which she shares attention with him. The consecrated bread and wine are then, in a sense, icons of Christ. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Nomophobia (no-mobile-phone phobia) is the fear and anxiety of being without a mobile phone. This study pioneers the investigation of nomophobia in Afghanistan using the Nomophobia Questionnaire (NMP-Q), addressing a crucial gap in the field. We collected statistical data from 754 undergraduate medical students, comprising men (56.50 %) and women (43.50 %), and analyzed the dimensions of nomophobia. While results revealed that all but two participants were nomophobic, they identified three significant dimensions affecting the level of nomophobia among participants: (a) (...) gender, (b) age, and (c) marital status. The study's contributions are precious, given the peculiarity of Afghan political turmoil, security, and human rights issues, especially for women. For example, the study's data collection was abruptly halted in December 2022 due to the Taliban regime's decision to make it illegal for women to enroll in universities as students. Therefore, while examining the characteristics of nomophobia across societies is imperative, it is also vital to investigate what is true of one society, Afghanistan, at one point in time and space. The study concludes by emphasizing the need to broaden participants' scope in future studies to better understand the prevalence of nomophobia across broader societal contexts and forces. (shrink)

This updated essay expands on the author's analysis of the complex social and psychological reasons for the inadequate response to the climate emergency. Recent reports by climate scientists quoted in the article suggest that the pace of climate change has already reached the point of irreversibility, triggering multiple tipping points with catastrophic implications for the future of life on this planet. Yet climate change denial, which as the author explains, takes many forms itself, both aggressive and passive, remains common at (...) all levels of human society, hindering effective action. Nevertheless, citing the growing number of legal cases being brought against both fossil fuel industries and state governments for not taking sufficient and verifiable measures for dealing with the crisis, the author finds positive signs that justice may be finally catching up with the culpable parties in both sectors. (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)

Angell's logic of analytic containment AC has been shown to be characterized by a 9-valued matrix NC by Ferguson, and by a 16-valued matrix by Fine. We show that the former is the image of a surjective homomorphism from the latter, i.e., an epimorphic image. The epimorphism was found with the help of MUltlog, which also provides a tableau calculus for NC extended by quantifiers that generalize conjunction and disjunction.

In his wide-ranging study of architecture and cultural evolution, Chris Abel argues that, despite progress in sustainable development and design, resistance to changing personal and social identities shaped by a technology-based and energy-hungry culture is impeding efforts to avert drastic climate change. The book traces the roots of that culture to the coevolution of Homo sapiens and technology, from the first use of tools as artificial extensions of the human body to the motorized cities spreading around the world, whose uncontrolled (...) effects are fast changing the planet itself. Advancing a new concept of the meme, called the 'technical meme', as the primary agent of cognitive extension and technical embodiment, Abel proposes a theory of the 'extended self' as a complex and diffuse outcome of that coevolution. Challenging conventional ideas of the self as a separate and autonomous being, the extended self, he explains, encompasses material and spatial as well as psychological and social elements, including the built environment and artifacts, and now reaches out into the virtual world of cyberspace. Drawing upon research into extended cognition and embodied minds from philosophy, psychology and the neurosciences, the book presents a new approach to environmental and cultural studies. N.B. This book was the winner of the International Committee of Architectural Critics 2017 Bruno Zevi Book Award by unanimous decision of the international jury. (shrink)

Expanding his collected essays on architectural theory and criticism, Chris Abel pursues his explorations across disciplinary and regional boundaries in search of a deeper understanding of architecture in the evolution of human culture and identity formation. From his earliest writings predicting the computer-based revolution in customised architectural production, through his novel studies on 'tacit knowing' in design or hybridisation in regional and colonial architecture, to his radical theory of the 'extended self', Abel has been a consistently fresh and provocative thinker, (...) contesting both conventions and intellectual fashions. This revised third edition includes a new introduction and six additional chapters by the author covering a broad range of related topics, up to recent concerns with genetic design methods and virtual selves. Together with the former essays, the book presents a unique global perspective on the changing cultural issues and technologies shaping human identities and the built environment in diverse parts of the world, both East and West (from the book cover). (shrink)