Experimental philosophers have gathered impressive evidence for the surprising conclusion that philosophers' intuitions are out of step with those of the folk. As a result, many argue that philosophers' intuitions are unreliable. Focusing on the Knobe Effect, a leading finding of experimental philosophy, we defend traditional philosophy against this conclusion. Our key premise relies on experiments we conducted which indicate that judgments of the folk elicited under higher quality cognitive or epistemic conditions are more likely to resemble those of the (...) philosopher. We end by showing how our experimental findings can help us better understand the Knobe Effect. (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 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.

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

A collection of papers presented at the First International Summer Institute in Cognitive Science, University at Buffalo, July 1994, including the following papers: ** Topological Foundations of Cognitive Science, Barry Smith ** The Bounds of Axiomatisation, Graham White ** Rethinking Boundaries, Wojciech Zelaniec ** Sheaf Mereology and Space Cognition, Jean Petitot ** A Mereotopological Definition of 'Point', Carola Eschenbach ** Discreteness, Finiteness, and the Structure of Topological Spaces, Christopher Habel ** Mass Reference and the Geometry of Solids, Almerindo E. (...) Ojeda ** Defining a 'Doughnut' Made Difficult, N .M. Gotts ** A Theory of Spatial Regions with Indeterminate Boundaries, A.G. Cohn and N.M. Gotts ** Mereotopological Construction of Time from Events, Fabio Pianesi and Achille C. Varzi ** Computational Mereology: A Study of Part-of Relations for Multi-media Indexing, Wlodek Zadrozny and Michelle Kim. (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.

RESUMO O trabalho aqui desenvolvido visa analisar por meio de uma revisão de textos os princípios fisiológicos reprodutivos da fêmea equina, aplicados à abordagem da técnica de Inseminação Artificial, como descreve o tema. De maneira, a fazer uma descrição sequencial de toda trajetória da fêmea que será usada para reprodução por meio de Inseminação Artificial, descrevendo os processos que serão utilizados de maneira cuidadosa. Desta forma, o que se pretende é traçar uma linha do tempo detalhando procedimentos e as formas (...) adequadas e mais indicadas de cada um. Assim, o que se busca é entender como todo processo de Inseminação Artificial deve ser conduzido, na expectativa de que o mesmo seja concluído com sucesso com o mínimo de erros e perdas possíveis. Tudo isto, na expectativa de fazer com que a Inseminação Artificial seja melhor acompanhada e difundida nos meios veterinários, indicando em algumas situações que pode ser uma forma de reprodução mais adequada, à depender da necessidade do criador. Assim, para que o processo tenha sucesso, é imprescindível o conhecimento dos profissionais que irão atuar na área, a fim de que não haja perdas, ou erros desnecessários. Palavras-chave: Inseminação Artificial; Fêmea Equina. Fisiologia Animal. ABSTRACT The work developed here aims to analyze, through a review of texts, the reproductive physiological principles of the equine female, applied to the approach of the Artificial Insemination technique, as described in the theme. In order to make a sequential description of the entire trajectory of the female that will be used for reproduction through Artificial Insemination, describing the processes that will be used carefully. In this way, the intention is to draw a timeline detailing procedures and the appropriate and most indicated ways of each one. Thus, what is sought is to understand how the entire Artificial Insemination process should be conducted, in the expectation that it will be successfully completed with the least possible errors and losses. All this, in the hope of making Artificial Insemination better monitored and disseminated in veterinary circles, indicating in some situations that it may be a more adequate form of reproduction, depending on the breeder's needs. Thus, for the process to be successful, the knowledge of professionals who will work in the area is essential, so that there are no losses or unnecessary errors. Keywords: Artificial Insemination; Equine female. Animal Physiology. (shrink)

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.

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)

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.

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)

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)

This commentary examines the role of sustainability in the latest draft of the WHO pandemic accord, highlighting its notable absence from the official list of guiding principles despite being mentioned frequently throughout the text. It argues that sustainability should be explicitly acknowledged as a core principle and given a clear definition tailored to pandemic preparedness, and proposes defining sustainability as ensuring that immediate emergency responses don't compromise future pandemic preparedness and response capabilities. Including sustainability as a guiding principle would serve (...) two key purposes: validating the relevance of ethical principles in the accord's provisions and emphasizing the importance of long-term planning in pandemic preparedness. The commentary notes that while humans naturally discount future consequences, sustainable pandemic planning requires considering impacts beyond the next pandemic. It recommends coupling any reforms, such as intellectual property changes, with alternative innovation incentives to maintain a balanced approach to pandemic preparedness and response. (shrink)

There is, in some quarters, concern about high–level machine intelligence and superintelligent AI coming up in a few decades, bringing with it significant risks for humanity. In other quarters, these issues are ignored or considered science fiction. We wanted to clarify what the distribution of opinions actually is, what probability the best experts currently assign to high–level machine intelligence coming up within a particular time–frame, which risks they see with that development, and how fast they see these developing. We thus (...) designed a brief questionnaire and distributed it to four groups of experts in 2012/2013. The median estimate of respondents was for a one in two chance that high-level machine intelligence will be developed around 2040-2050, rising to a nine in ten chance by 2075. Experts expect that systems will move on to superintelligence in less than 30 years thereafter. They estimate the chance is about one in three that this development turns out to be ‘bad’ or ‘extremely bad’ for humanity. (shrink)

In his latest book, Michael Devitt rejects Chomsky’s mentalist conception of linguistics. The case against Chomsky is based on two principal claims. First, that we can separate the study of linguistic competence from the study of its outputs: only the latter belongs to linguistic inquiry. Second, Chomsky’s account of a speaker’s competence as consisiting in the mental representation of rules of a grammar for his language is mistaken. I shall argue, first, that Devitt fails to make a case for separating (...) the study of outputs from the study of competence, and second, that Devitt mis-characterises Chomsky’s account of competence, and so his objections miss their target. Chomsky’s own views come close to a denial that speaker’s have knowledge of their language. But a satisfactory account of what speakers are able to do will need to ascribe them linguistic knowledge that they use to speak and understand. I shall explore a conception of speaker’s knowledge of language that confirrns Chomsky’s mentalist view of linguistics but which is immune to Devitt’s criticism. (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)

The critic Cyril Connolly once pointed out that diarists don’t make novelists. He went on to describe the problem for the would-be writer. “Writing for oneself: no public. Writing for others: no privacy” (Cyril Connolly, Journal). This paper addresses Connolly's worry about the public ad private: how can we reconcile the inner and conscious dimension of speech with its outer and public dimension? For if what people mean by their words involves, or consists in, what they have in mind when (...) they speak then how can what someone has in mind — the meaning she attaches to her words — be at the same time publicly accessible to others on the basis of her behaviour? The issue is whether there is a notion of the linguistic meaning of an expression that can do justice to both speakers’ inner experience of comprehension and to what is outwardly available in their public practice. (shrink)

[This is the short version of: Müller, Vincent C. and Bostrom, Nick (forthcoming 2016), ‘Future progress in artificial intelligence: A survey of expert opinion’, in Vincent C. Müller (ed.), Fundamental Issues of Artificial Intelligence (Synthese Library 377; Berlin: Springer).] - - - In some quarters, there is intense concern about high–level machine intelligence and superintelligent AI coming up in a few dec- ades, bringing with it significant risks for human- ity; in other quarters, these issues are ignored or considered (...) science fiction. We wanted to clarify what the distribution of opinions actually is, what probability the best experts currently assign to high–level machine intelligence coming up within a particular time–frame, which risks they see with that development and how fast they see these developing. We thus designed a brief questionnaire and distributed it to four groups of experts. Overall, the results show an agreement among experts that AI systems will probably reach overall human ability around 2040-2050 and move on to superintelligence in less than 30 years thereafter. The experts say the probability is about one in three that this development turns out to be ‘bad’ or ‘extremely bad’ for humanity. (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)

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)

Revised version published as Barry Smith and Achille Varzi, “Fiat and Bona Fide Boundaries”, Philosophy and Phenomenological Research, 60: 2 (March 2000), 401–420.

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)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

The new Chomskian orthodoxy denies that our linguistic competence gives us knowledge *of* a language, and that the representations in the language faculty are representations *of* anything. In reply, I have argued that through their intuitions speaker/hearers, (but not their language faculties) have knowledge of language, though not of any externally existing language. In order to count as knowledge, these intuitions must track linguistic facts represented in the language faculty. I defend this idea against the objections Collins has raised to (...) such an account. (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)

Skepticism is one of the most enduring and profound of philosophical problems. With its roots in Plato and the Sceptics to Descartes, Hume, Kant and Wittgenstein, skepticism presents a challenge that every philosopher must reckon with. In this outstanding collection philosophers engage with skepticism in five clear sections: the philosophical history of skepticism in Greek, Cartesian and Kantian thought; the nature and limits of certainty; the possibility of knowledge and related problems such as perception and the debates between objective knowledge (...) and constructivism; the transcendental method as a response to skepticism and the challenge of naturalism; overcoming the skeptical challenge. (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)

Human cognitive acts are directed towards objects extended in space of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. The theory of spatially extended objects should make room not only for the objects of physics but also for objects at higher levels, including the objects of geography and of related disciplines. It should leave room for different types of boundaries, including both the bona fide boundaries which we find in (...) the physical world and the fiat (or human-demarcation-induced) boundaries with which much of geography has to deal. Two distinct axiomatic theories of boundaries are accordingly presented, and the need for both is examined in some detail. The resultant dual framework is shown to have application above all for our understanding of issues involving contact, division, and separation, issues which have posed serious difficulties for the ontological theories of boundaries that have been proposed hitherto. (shrink)

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

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

We propose the beginnings of a general theory of environments, of the parts or regions of space in which organisms live and move. We draw on two sources: on the one hand on recent work on the ontology of space; and on the other hand on work by ecological scientists on concepts such as territory, habitat, and niche. An environment is in first approximation a volume of space; it is a specific habitat, location, or site that is suitable or adequate (...) for given purposes (of foraging, resting, hunting, breeding, nesting, grooming) in the life of an organism or group of organisms. This spatial notion of environment can be drawn closer to biological and ecological science by taking account of the pertinent physical attributes realized within given spatial regions. (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)

This is an informal presentation of the theory of niches understood as ecological contexts. The first part sets out the basic conceptual background. The second part outlines the main principles of the theory and addresses the question of how the theory can be extended to aid our thinking in relation to the special types of causal integrity that characterize niches and niched entities.

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (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)

Cushman, Young, & Greene (2010) urge the consolidation of moral psychology around a dual-system consensus. On this view, a slow, often-overstretched rational system tends to produce consequentialist intuitions and action-tendencies, while a fast, affective system produces virtuous (or vicious) intuitions and action-tendencies that perform well in their habituated ecological niche but sometimes disastrously outside of it. This perspective suggests a habit-corrected-by-reason picture of moral behavior. Recent research, however, has raised questions about the adequacy of dual-process theories of cognition and behavior, (...) which tend to distinguish categorically between fast, affect-laden, automatic, sometimes-unconscious, nearly-incorrigible mental processes and slow, rational, effortful, conscious, corrigible mental processes. Processes of one alleged type often have properties associated with the contrary type. For instance, rational processes can be emotional, and fast thinking can perform logical operations. In addition, the fast-slow binary transforms a continuous temporal scale into a dichotomous one, losing potentially important information along the way. While these problems are beginning to be addressed in some subfields of psychology, moral psychology has yet to grapple with them. In this theoretical paper, we argue that moral psychology needs a framework that accounts for our knowledge of both temporal and spatial (anatomical) dimensions of the brain basis of moral cognition and virtuous decision-making. We argue that methodologies with very fine-grained temporal granularity, such as electroencephalography (EEG), should be used to complement more frequently used methodologies such as functional magnetic resonance imaging (fMRI). We outline how this might be accomplished using generosity, gratitude, and integrity as a case study. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis. Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato’s dialogues, is sfounded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then show (...) how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato’s dialogues by date, more general challenges to historicist interpretations of Plato’s dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

O valor nutritivo do leite de ovelha é superior quando comparado aos leites caprino e bovino, apresentando maior teor proteico, lipídico, minerais e vitaminas. Os humanos evoluíram em estreito contato com a natureza, sendo o leite a primeira fonte de alimento desta espécie ao nascer. Durante milhares de anos, o leite rico em nutrientes, como fonte de alimento, era unicamente materno e só veio a ser consumido pelo homem após idade de amamentação com a domesticação dos animais, primeiramente às ovelhas (...) e as cabras há aproximadamente 13 mil anos, seguido da domesticação das vacas quatro mil anos depois. Desde então o leite tornou-se um alimento indispensável para o homem. O valor nutritivo do leite de ovelha é superior quando comparado aos leites caprino e bovino, apresentando maior teor proteico, lipídico, minerais e vitaminas essenciais para a saúde humana. Este leite apresenta três vezes mais proteínas em relação ao leite de cabra e de vaca, sendo aquelas consideradas proteínas de alto valor biológico contribuindo para uma melhor digestibilidade. Outra característica é a conformação estrutural e a quantidade de micelas de caseína e suas subunidades, que são assim como o leite caprino, menores que as do leite bovino, proporcionando menor sensibilização às pessoas alérgicas. Estudos sugerem que o leite de ovelha pode ser considerado o substituto ideal do leite bovino para pessoas alérgicas ao leite bovino devido ao elevado teor dos principais componentes do leite e minerais. Entretanto, foi verificado que anticorpos IgE de pessoas alérgicas reconhecem as αS1-caseína, αS2-caseína e β-caseína de leite ovino e caprino, mas caseínas do leite bovino são raramente ou não reconhecidas. Além disso, os polimorfismos genéticos das proteínas do leite estão associados com os parâmetros quantitativos e qualitativos e desempenham um papel importante na indução de diferentes graus de reação alérgica. A coloração do leite de ovelha é intensamente branca e homogênea, o que o difere do leite de vaca, pois essa característica está associada à ausência de β-caroteno pigmento precursor do retinol (vitamina A) impedindo que o leite tenha coloração amarelada como no caso do leite bovino. No leite ovino, o β-caroteno apresenta-se na forma convertida da vitamina A que não possui coloração amarelada e essa característica possibilita a produção de diferentes variedades de queijo. A caseína no leite de ovelha compõe 80% do total de proteínas do leite dos ruminantes, enquanto que está presente em 50% da composição proteica do leite equino e em menor porcentagem no leite humano. A caseína do leite de ruminantes difere com relação às características de tamanho, hidratação e mineralização. As micelas de caseína do leite de ovelha possuem maior mineralização e menor hidratação, sendo mais estáveis ao aquecimento quando comparadas à micela de caseína do leite de vaca. Outra importante característica refere-se à conformação molecular e sequencial de aminoácidos com impacto sobre sua digestibilidade, qualidade nutricional e termoestabilidade proteica. As proteínas do leite de ovelha consistem em elevada quantidade de caseínas (resistente ao calor) e proteínas do soro (sensível ao calor) responsáveis pela textura e viscosidade de iogurtes. Tecnologicamente, elas têm propriedades únicas que permitem a fácil conversão do leite em iogurte e queijos, não sendo necessária a adição de sólidos na produção do iogurte, como leite em pó, ou concentração dos sólidos do leite por tecnologia de membrana. Estudos com variantes da caseína do leite ovino representam uma abordagem eficaz para identificar a associação de características de importância econômica e melhorar raças para a produção de proteína do leite específica. As características da caseína no leite de ovelha são particularmente interessantes devido ao número elevado de polimorfismo, alterando a expressão de genes e influenciando o processamento de queijos. Em adição, enzimas presente no leite de ovelha possui atividade proteolítica e lipolítica (quebra de proteínas e lipídios). Elas auxiliam na maturação de queijos - resultando em compostos de aroma e sabor típicos, tornando-os únicos em suas características. O sabor e o aroma do leite de ovelha são suaves e adocicados além de possuir uma textura cremosa devido aos pequenos glóbulos de gordura que apresentam tamanhos menores que 3,5 µm. Esta peculiaridade no tamanho dos glóbulos gordurosos do leite ovino propicia que esse seja digerido mais facilmente. O leite ovino apresenta também altas concentrações de ácidos graxos poli-insaturados com benefícios à saúde como isômeros de ácido linoleico conjugado (CLA) presentes em maior concentração nesta matriz comparado ao leite bovino que são o cis-9 trans-11 e o trans-10 cis-12, responsáveis por ações anticarcinogênica, antiaterogênico e antiobesidade. Ainda com relação aos lipídios do leite de ovelha, as lipases têm um papel importante na produção de leite na glândula mamária. As lipases naturais do leite catalisam e hidrolisam os triglicerídeos, produzindo ácidos graxos livres (AGL). A atividade das lipases, em leite ovino, é cerca de um décimo das do leite bovino. Além disso, o padrão de hidrólise da gordura de leite por ovinos apresenta maior taxa em relação aos triglicerídeos - contendo ácidos graxos de cadeia média em relação aos ácidos graxos de cadeia longa. Os níveis de AGL em queijos de leite ovino são o resultado do processo lipolítico que ocorre durante o período de maturação. Alguns produtos lácteos derivados usando como matéria-prima o leite de ovelha - como iogurte grego e queijos - foram descritos como possuindo peptídeos inibidores da enzima conversora da angiotensina (ECA), sendo a maioria derivada da subunidade β-caseína. Também, alguns peptídeos derivados da κ-caseína, resultante da hidrólise de leite ovino pela pepsina, tripsina e quimotripsina, exercem atividade antioxidante. Em queijos tradicionais derivados de ovelha, como o Scamorza, foram verificados diversos peptídeos com ação inibidora da ECA e ação antibacteriana. Nesse contexto, o leite de ovelha é uma rica fonte de nutrientes e seu principal uso é na produção de queijos devido ao elevado conteúdo de extrato seco total, que contribui com alto rendimento da massa. Todavia, esta matéria-prima permanece inexplorada pela indústria de laticínios com uma visão de alimento funcional, visto que o leite e seus derivados são reconhecidamente ótimos carreadores de fibras prebióticas e bactérias probióticas - que trazem benefícios ao consumidor favorecendo saúde e bem-estar. Nesse contexto, o leite de ovelha apresenta-se como um alimento de grande potencial e uma valiosa alternativa para a indústria de laticínios - que pode aumentar a diversidade de produtos oferecidos ao consumidor. (shrink)

2021 marks Dylan's 80th birthday and his 60th year in the music world. It invites us to look back on his career and the multitudes that it contains. Is he a song and dance man? A political hero? A protest singer? A self-portrait artist who has yet to paint his masterpiece? Is he Shakespeare in the alley? The greatest living exponent of American music? An ironsmith? Internet radio DJ? Poet (who knows it)? Is he a spiritual and religious parking meter? (...) Judas? The voice of a generation or a false prophet, jokerman, and thief? Dylan is all these and none. The essays in this book explore the Nobel laureate’s masks, collectively reflecting upon their meaning through time, change, movement, and age. They are written by wonderful and diverse set of contributors, all here for his 80th birthday bash: celebrated Dylanologists like Michael Gray and Laura Tenschert; recording artists such as Robyn Hitchcock, Barb Jungr, Amy Rigby, and Emma Swift; and 'the professors’ who all like his looks: David Boucher, Anne Margaret Daniel, Ray Monk, Galen Strawson, and more. Read it on your toaster! (shrink)

This volume has been brought together to generate new ideas and provoke discussion about what constitutes arts education in the twenty-first century, both within the institution and beyond. Art, Artists and Pedagogy is intended for educators who teach the arts from early childhood to tertiary level, artists working in the community, or those studying arts in education from undergraduate to Masters or PhD level.

This book presents a (new) attempt to apply the notion of an underlying logic to Aristotle’s Organon and certain passages of the Metaphysics. The author situates his approach as part of a ‘deductio...

We present an interdisciplinary approach to study systematic relations between logical form and attacks between claims in an argumentative framework. We propose to generalize qualitative attack principles by quantitative ones. Specifically, we use coherent conditional probabilities to evaluate the rationality of principles which govern the strength of argumentative attacks. Finally, we present an experiment which explores the psychological plausibility of selected attack principles.

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)