Things strike me in a variety ways. F and F# sound slightly different, ripe and unripe tomatoes neither look nor taste nor smell the same, and silk feels smoother than corduroy. In each case, I distinguish an experience of something on the basis of what it is like to be its subject. That is to say, in philosophical parlance, if not quite the vernacular, its “quale,” leads me to categorize it and, thus, respond appropriately to its stimulus. The function of (...) a quale being established, we must define it along with its subject and, as Sartre maintained, their relation. How should we understand the subject and predicate terms and the copula in sentences such as ‘He is listening to Chopin’ or ‘She is seeing the sights of Paris’? Elaborating upon adverbialism, I shall argue that the subject of experiencing is a hylomorphic compound that is temporarily identical to the 'accidental compound' that it forms along with a qualified passion. I begin by explicating the adverbialist’s treatment of qualitative consciousness and defending it against the charge of circularity. (shrink)

A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.

In this paper, I examine Emest Sosa’s defense of Conceptual Relativism: the view that what exists is a function of human thought. My examination reveals that his defense entails an ontology that is indistinguishable from that of the altemative he labels less “sensible,” viz., Absolutism: the view that reality exists independently of our thinking. I conclude by defending Absolutism against Sosa’s objections.

This is a contribution to a Book symposium on The Limits of Free Will: Selected Essays by Paul Russell. Russell provides replies to three critics of The Limits of Free Will. The first reply is to Robert Wallace and focuses on the question of whether there is a conflict between the core compatibilist and pessimist components of the "critical compatibilist" position that Russell has advanced. The second reply is to Angela Smith's discussion of the "narrow" interpretation of moral (...) responsibility responsibility (as defended by R. Jay Wallace) and how best to respond to it. The third and last reply is concerned with Christopher Bennett's criticism of Russell's views concerning "motivational scepticism" and the possibility of pure practical reasons. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, and dispositions, (...) to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined in (Arp, Smith, and (...) Spear 2015). BCIO uses as its top-level ontology Basic Formal Ontology (BFO). The methods outlined in Wright, et al. are a valuable contribution to the field, especially the use of formal mechanisms for literature annotation and expert stakeholder review, and the BCIO will certainly play an important role in the extension of OBO Foundry ontologies into the behavioural domain. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (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)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

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

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

For the greater part of the last 50 years, it has been common for philosophers of mind and cognitive scientists to invoke the notion of realization in discussing the relationship between the mind and the brain. In traditional philosophy of mind, mental states are said to be realized, instantiated, or implemented in brain states. Artificial intelligence is sometimes described as the attempt either to model or to actually construct systems that realize some of the same psychological abilities that we and (...) other living creatures possess. The claim that specific psychological. (shrink)

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)

Sleep has long been a topic of fascination for artists and scientists. Why do we sleep? What function does sleep serve? Why do we dream? What significance can we attach to our dreams? We spend so much of our lives sleeping, yet its precise function is unclear, in spite of our increasing understanding of the processes generating and maintaining sleep. We now know that sleep can be accompanied by periods of intense cerebral activity, yet only recently has experimental data started (...) to provide us with some insights into the type of processing taking place in the brain as we sleep. There is now strong evidence that sleep plays a crucial role in learning and in the consolidation of memories. Once the preserve of psychoanalysts, 'dreaming' is now a topic of increasing interest amongst scientists. With research into sleep growing, this volume is both timely and valuable in presenting a unique study of the relationship between sleep, learning, and memory. It brings together a team of international scientists researching sleep in both human and animal subjects. Aimed at researchers within the fields of neuroscience, cognitive neuroscience, psychiatry, and neurology, this book will be an important first step in developing a full scientific understanding of the most intriguing state of consciousness. (shrink)

An intuitive view regarding the epistemic significance of disagreement says that when epistemic peers disagree, they should suspend judgment. This abstemious view seems to embody a kind of detachment appropriate for rational beings; moreover, it seems to promote a kind of conciliatory inclination that makes for irenic and cooperative further discussion. Like many strategies for cooperation, however, the abstemious view creates opportunities for free-riding. In this essay, the authors argue that the believer who suspends judgment in the face of peer (...) disagreement is vulnerable to a kind of manipulation on the part of more tenacious peers. The result is that the abstemious view can have the effect of encouraging dogmatism. (shrink)

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

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

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

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

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

When modern economists use the notions of sympathy or empathy, they often claim that their ideas have their roots in Adam Smith's Theory of Moral Sentiments, while sometimes complaining that Smith fails to distinguish clearly enough between the two concepts. Recently, Philippe Fontaine has described various forms of sympathy and empathy, and has explored their respective roles in Smith's work. My objective in this paper is to argue that Smith's analysis of how people's sentiments impinge on (...) one another involves a concept of fellow-feeling that is distinct from both sympathy and empathy. Unlike sympathy and empathy, fellow-feeling does not fit into the ontological framework of rational choice theory – which may explain why it tends to be overlooked by modern readers of Smith. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

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

As so often with his published texts, the experience of reading Nietzsche’s notebooks is at once mesmerising and infuriating. One is in the presence of a thinker who, on the one hand, meditates deeply on fundamental issues in philosophy and psychology but who, on the other, refuses to be pinned down. The fact that Nietzsche’s style is so elusive can account for the enormously disparate interpretations of his work and it is no surprise that his notebooks have been read in (...) the most extreme fashion. The notebooks have a chequered history having been variously touted as the crowning achievement of his philosophy, and as not repaying the effort of reading. (shrink)

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)

P.F. Strawson’s account of moral responsibility in “Freedom and Resentment” has been widely influential. In both that paper and in the contemporary literature, much attention has been paid to Strawson’s account of blame in terms of reactive attitudes like resentment and indignation. The Strawsonian view of praise in terms of gratitude has received comparatively little attention. Some, however, have noticed something puzzling about gratitude and accountability. We typically understand accountability in terms of moral demands and expectations. Yet gratitude does not (...) express or enforce moral demands or expectations. So, how is it a way to hold an agent accountable? In a more general manner, we might ask if there is even sense to be made of the idea that agents can be accountable—i.e., “on the hook”—in a positive way. In this paper, I clarify the relationship between gratitude and moral accountability. I suggest that accountability is a matter of engaging with others in a way that is basically concerned with their feelings and attitudes rather than solely a matter of moral demands. Expressions of gratitude are a paradigmatic form of this concerned engagement. I conclude by defending my view from the objection that it leads to an overly generous conception of holding accountable and suggest in reply that moral responsibility skeptics may not help themselves to as many moral emotions as they might have thought. (shrink)

The thesis that an analysis of property rights is essential to an adequate analysis of the state is a mainstay of political philosophy. The contours of the type of government a society has are shaped by the system regulating the property rights prevailing in that society. Views of this sort are widespread. They range from Locke to Nozick and encompass pretty much everything else in between. Defenders of this sort of view accord to property rights supreme importance. A state that (...) does not sufficiently respect property rights is likely to be a totalitarian state, and will also be likely to fail to respect rights of other sorts. (shrink)

P.F. Strawson’s compatibilism has had considerable influence. However, as Watson has argued in “Responsibility and the Limits of Evil”, his view appears to have a disturbing consequence: extreme evil exempts an agent from moral responsibility. This is a reductio of the view. Moreover, in some cases our emotional reaction to an evildoer’s history clashes with our emotional expressions of blame. Anyone’s actions can be explained by his or her history, however, and thereby can conflict with our present blame. Additionally, we (...) too might have been evil if our history had been like the unlucky evildoer’s. Thus, our emotional responses to the evildoer compromise our standing to blame them. Since Strawson’s view demarcates moral responsibility by moral emotional responses, his view appears to be self-defeating. In this paper, I defend the Strawsonian view from the reductio and self-defeat problems. I argue that two emotions, disgust and elevation, can be moral reactive attitudes in Strawson’s sense. First, moral disgust expresses neither blame nor exemption from responsibility. Instead, moral disgust presupposes blameworthiness but is instead a distinct response to the extreme wrongdoer. Secondly, moral disgust involves self-directed attitudes that explain away our apparent lack of standing to blame the evil agent. The structure of disgust as a reactive attitude is mirrored along the positive dimension by the emotion that Haidt has called “elevation”, a feeling of moral inspiration. I conclude by defending my view from objections about the moral appropriateness of disgust. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

Sumário. Apresentação. PARTE I. 1. O legado filosófico de P. F. Strawson, Itamar Luís Gelain e Jaimir Conte; 2 . Strawson e o caso dos metafísicos descritivos, Itamar Luís Gelain; 3. Metafísica e linguagem comum: sobre uma conturbada herança wittgensteiniana de Strawson, Jônadas Techio; 4. Strawson e Descartes, Albertinho Luiz Gallina; 5. Strawson: sobre Kant e Berkeley, Robert Calabria; 6. O empirismo pós-kantiano de Strawson, Wenceslao J. González; 7. Reabilitando Strawson, Marco Antonio Franciotti; 8. Strawson e o ceticismo em (...) Individuals, Plínio Junqueira Smith; 9. Strawson e a causação visível, João Paulo Monteiro; 10. A verdade dos fatos, Susana Badiola; 11. Estabelecer limites: implicações epistemológicas da lógica, Roberta Corvi; 12. Referência e termos singulares, Carlos E. Caorsi; 13. Strawson: da experiência possível para a ação possível, Márlon Henrique Teixeira; 14. Atitudes reativas e responsabilidade moral, Cristina de Moraes Nunes; 15. Strawson e Hume: uma comparação a propósito de “Moralidade social e ideal individual”, Amán Rosales Rodríguez; PARTE II. 16. Liberdade e ressentimento, P. F. Strawson. Tradução: Jaimir Conte; 17. Moralidade social e ideal individual, P. F. Strawson, Tradução: Jaimir Conte. Seleção bibliográfica. (shrink)

This article examines the fundamental question of philosophy. The author proposes to amend its classical scheme, developed by F. Engels, one of the founders of dialectical materialism, by adding a third side. This third side of the MQP should be the question of “the concrete representation of matter in nature (matter of nature)”. This is the fundamental question of physics and all natural science. The solution to this question is simple, clear, unambiguous: “the content of elementary particles is “pure”, concrete (...) matter of nature”. (shrink)

The argument of this paper, written by an ethicist and a philosopher, is that self-interest economics is fundamentally flawed and needs to be replaced by a spiritual economics or a value based economics. Its argument contains two interwoven threads. One thread is an attempt to show why the fundamental philosophical notions of Adam Smith, taken as an illustration of self-interest economics, cannot lead to an equitable society. Smith’s Wealth of Nations, according to Jacob Viner, ‘ became a significant (...) factor in determining the course of national policy not only in Britain but in other countries as well. This is much more than any other economic work has ever achieved; and Smith probably has had much more influence than any other economist.’ One wonders if it is Smith that Keynes had in mind when he famously quipped that all of us are slaves of some defunct economist. This despite Schumpeter’s trumpeted dictum that ‘the Wealth of Nationsdoes not contain a single analyticidea, principle or method that was entirely new in 1776.’. (shrink)

Representational pictures and sculptures both present their objects visually: to grasp what they represent is in some sense to see, not only the representation before one, but the object represented. But is the form of visual presentation the same? Or does a deep difference lie at the heart of our experience of these representations, a difference in how each presents us with its object? Almost all philosophical discussion of pictures and 3D representations has assumed or implied a negative answer to (...) this question. The notable exception is M.G.F.Martin’s account of pictures in terms of an ‘image’, a pure visibile that presents the represented object and its features without exemplifying them. In order to interpret Martin’s view so as to bring out its plausibility, I relate it to the somewhat similar position advocated by Lambert Wiesing’s account of pictures and our experience of them. That done, I ask whether a position drawing on both these positions can justify drawing a fundamental distinction between the ways in which pictures and sculptures present what they represent. (shrink)

Historically, republicans were of different minds about markets: some, such as Rousseau, reviled them, while others, like Adam Smith, praised them. The recent republican resurgence has revived this issue. Classical liberals such as Gerald Gaus contend that neo-republicanism is inherently hostile to markets, while neo-republicans like Richard Dagger and Philip Pettit reject this characterization—though with less enthusiasm than one might expect. I argue here that the right republican attitude toward competitive markets is celebratory rather than acquiescent and that republicanism (...) demands such markets for the same reason it requires the rule of law: because both are essential institutions for protecting individuals from arbitrary interference. I reveal how competition restrains—and in the limit, even eradicates—market power and thereby helps us realize “market freedom,” i.e., freedom as non-domination in the context of economic exchange. Finally, I show that such freedom necessitates “Anglo-Nordic” economic policies. (shrink)

The article addresses the treatment given to the notion of subject in Slavoj Žižek and Robert Kurz. Without aiming at a synthesis between the two radically opposed positions, they are played against one another in order to reveal the unidimensional stances and false steps in the field of the constitution of the struggle for a concrete negation of capitalist society.

Robert Kimball, in “What’s Wrong with Argumentum Ad Baculum?” (Argumentation, 2006) argues that dialogue-based models of rational argumentation do not satisfactorily account for what is objectionable about more malicious uses of threats encountered in some ad baculum arguments. We review the dialogue-based approach to argumentum ad baculum, and show how it can offer more than Kimball thinks for analyzing such threat arguments and ad baculum fallacies.

Commercial republicanism is the idea that a properly-structured commercial society can serve the republican end of minimizing the domination of citizens by states (imperium) and of citizens by other citizens (dominium). Much has been written about this idea in the last half-century, including analyses of individual commercial republicans (e.g., Adam Smith and Immanuel Kant) as well as discussions of national traditions of the same (e.g., in America, Britain, France, the Netherlands, and Italy). In this chapter, I review five kinds (...) of arguments that have been historically offered for how commercial society so understood advances the republican ideal of non-domination: first, by simply realizing non-dominating relationships in the marketplace itself (Instantiation); second, by encouraging the growth of a wide middle class that can offer a counterweight to other, dominating classes (Internal Check-and-Balance); third, by increasing the wealth and power of republics vis-à-vis other, dominating states in the international arena (External Check-and-Balance); fourth, by helpfully nurturing bourgeois-civic virtues in republican citizens (Cultivating Virtue); and finally, by transforming dangerous passions into more readily regulable, even socially beneficial material interests (Sublimating Vice). I end the chapter by briefly considering commercial republicanism’s prospects as a continuing research program. (shrink)

The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...) reality and re-entering the matrix. Not only does reason compel us to admit the existence of the external world, it also requires us to face this world, to build for ourselves meaningful lives within it, and to engage, as adults, in the serious business of living. (shrink)

This public philosophy piece examines moral responsibility and alternatives to angry blame as exemplified in the TV show Avatar: The Last Airbender. Abstract: Many contemporary philosophers believe that there is an important connection between holding someone responsible and being angry at them. The British philosopher P.F. Strawson argued that to blame someone‐to hold them responsible for a wrongdoing‐is just to feel and express certain kinds of moral anger toward them. Classical Buddhist thought suggests that anger is one of the poisons (...) in our nature, something that gives rise to pain and suffering. Angry blame plays an important role in some of its most important positive moments‐Katara confronting Pakku and Iroh defending the moon spirit, for instance. But Avatar: The Last Airbender ( ATLA ) highlights that people can choose not to be angry with wrongdoers. Media for children and young adults have an important role to play here, even for adults. In this role, ATLA succeeds in many ways. (shrink)