I propose and defend a novel view called “de se consequentialism,” which is noteworthy for two reasons. First, it demonstrates—contra Doug Portmore, Mark Schroeder, Campbell Brown, and Michael Smith, among others—that agent-neutral consequentialism is consistent with agent-centered constraints. Second, it clarifies the nature of agent-centered constraints, thereby meriting attention from even dedicated nonconsequentialists. Scrutiny reveals that moral theories in general, whether consequentialist or not, incorporate constraints by assessing states in a first-personal guise. Consequently, de se consequentialism enacts constraints through (...) the very same feature that nonconsequentialist theories do. (shrink)

Some rules seem more important than others. The moral rule to keep promises seems more important than the aesthetic rule not to wear brown with black or the pool rule not to scratch on the eight ball. A worrying number of metaethicists are increasingly tempted to explain this difference by appealing to something they call “authoritative normativity” – it’s because moral rules are “authoritatively normatively” that they are especially important. The authors of this chapter argue for three claims concerning “authoritative (...) normativity”: (1) that motivation for it originates in a parochial conception of “normative flavours”; (2) that arguments against alternative ways of explaining e.g., morality’s importance are overblown; and (3) that there are strong reasons against theorizing in terms of “authoritative normativity”. The overarching aim is not to show that “authoritative normativity” is incoherent or entirely unmotivated. Rather, it is to discuss some of “authoritative normativity’s” deeper commitments to correct the impression that is it largely benign or that it is entailed by familiar and popular “metanormative” positions. Authoritative normativity, it seems to us, is a solution in search of a problem. (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)

While it is tempting to suppose that an act has moral worth just when and because it is motivated by sufficient moral reasons, philosophers have, largely, come to doubt this analysis. Doubt is rooted in two claims. The first is that some facts can motivate a given act in multiple ways, not all of which are consistent with moral worth. The second is the orthodox view that normative reasons are facts. I defend the tempting analysis by proposing and defending a (...) heterodox account of both normative and motivating reasons that is inspired by Donald Davidson’s primary reasons. We should adopt the heterodox view, I argue, because it addresses an overlooked but fatal defect in the orthodox conception of reasons, of which challenges to the tempting analysis are a special case. (shrink)

Throughout his career, Derek Parfit made the bold suggestion, at various times under the heading of the "Normativity Objection," that anyone in possession of normative concepts is in a position to know, on the basis of their competence with such concepts alone, that reductive realism in ethics is not even possible. Despite the prominent role that the Normativity Objection plays in Parfit's non-reductive account of the nature of normativity, when the objection hasn't been ignored, it's been criticized and even derided. (...) We argue that the exclusively negative attention that the objection has received has been a mistake. On our reading, Parfit's Normativity Objection poses a serious threat to reductivism, as it exposes the uneasy relationship between our a priori knowledge of a range of distinctly normative truths and the typical package of semantic commitments that reductivists have embraced since the Kripkean revolution. (shrink)

I defend the widely-held view that morally worthy action need not be motivated by a desire to promote rightness as such. Some have recently come to reject this view, arguing that desires for rightness as such are necessary for avoiding a certain kind of luck thought incompatible with morally worthy action. I show that those who defend desires for rightness as such on the basis of this argument misunderstand the relationship between moral worth and the kind of luck that their (...) argument employs. Consequently, the argument provides no reason to doubt the popular view that a desire for rightness as such is no part of virtue. I conclude by suggesting that a family of worries about merely accidentally right action presuppose one side of the recent debate about objectivism and perspectivism about moral rightness. (shrink)

Inflicting harm is generally preferable to inflicting death. If you must choose between the two, you should generally choose to harm. But prenatal harm seems different. If a mother must choose between harming her fetus or aborting it, she may choose either, at least in many cases. So it seems that prenatal harm is particularly objectionable, sometimes on a par with death. This paper offers an explanation of why prenatal harm seems particularly objectionable by drawing an analogy to the all-or-nothing (...) problem. It then argues that this analogy offers independent support for the ‘voluntarist’ view that at least some parental role obligations are grounded in the choice to be a parent. (shrink)

Normal 0 false false false EN-CA X-NONE X-NONE The purpose of this paper is to reconstruct Hilary Kornblith’s argument for excluding conceptual analysis from epistemological inquiry, and then provide three objections to it. More specifically, Kornblith argues that epistemological properties such as ‘knowledge’ reduce to natural kinds which can only be discovered and investigated using the a posteriori methods of the natural sciences. Thus, he continues, conceptual analysis can’t properly illuminate the target domain. The three objections to Kornblith’s argument which (...) I present are as follows: Multiple Realizeability, Psychological Explanation, Starting Points. On strength of these objections, I conclude that Kornblith’s brand of a posteriori epistemology both eliminates our ability to make epistemic evaluations in general, and also implies a strong form of scepticism. /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}. (shrink)

Philosophers have recently come to focus on explaining the phenomenon of ​bad beliefs,​ beliefs that are apparently true and well-evidenced but nevertheless objectionable. Despite this recent focus, a consensus is already forming around a particular explanation of these beliefs’ badness called ​moral encroachment​, according to which, roughly, the moral stakes engendered by bad beliefs make them particularly difficult to justify. This paper advances an alternative account not just of bad beliefs but of bad attitudes more generally according to which bad (...) beliefs’ badness originates not in a failure of sufficient evidence but in a failure to respond adequately to reasons. I motivate this alternative account through an analogy to recent discussions of moral worth centered on the well-known grocer case from Kant’s ​Groundwork​, and by showing that this analogy permits the proposed account to generalize to bad attitudes beyond belief. The paper concludes by contrasting the implications of moral encroachment and of the proposed account for bad attitudes’ blameworthiness. (shrink)

The wrong kind of reason (WKR) problem is a problem for attempts to analyze normative properties using only facts about the balance of normative reasons, a style of analysis on which the ‘Reasons First’ programme depends. I argue that this problem cannot be solved if the orthodox view of reasons is true --- that is, if each normative reason is numerically identical with some fact, proposition, or state-of-affairs. That’s because solving the WKR problem requires completely distinguishing between the right- and (...) wrong-kind reasons for an attitude. I argue that some facts give both right- and wrong-kind reasons for an attitude. Consequently, no such distinction between the two types of reasons is complete if reasons are facts or the like. I conclude by suggesting that reasons and facts are related by constitution, not identity. (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)

There’s a long but relatively neglected tradition of attempting to explain why many researchers working on the nature of phenomenal consciousness think that it’s hard to explain.1 David Chalmers argues that this “meta-problem of consciousness” merits more attention than it has received. He also argues against several existing explanations of why we find consciousness hard to explain. Like Chalmers, we agree that the meta-problem is worthy of more attention. Contra Chalmers, however, we argue that there’s an existing explanation that is (...) more promising than his objections suggest. We argue that researchers find phenomenal consciousness hard to explain because phenomenal concepts are complex demonstratives that encode the impossibility of explaining consciousness as one of their application conditions. (shrink)

Eleven top Deleuze scholars reclaim Deleuzian philosophy as moral philosophy Ethics plays a crucial, if subtle, role in Gilles Deleuze's philosophical project. Michel Foucault claimed that Anti-Oedipus was `a book of ethics, the first book of ethics to be written in France in quite a long time'. But what is the nature of the immanent ethics that is developed in Deleuze's thought? How does it differ from previous conceptions of ethics? And what paths does it open for future thought, given (...) the ethical challenges facing humanity in so many domains? Each of the eleven essays in this collection explores the ethical dimension of Deleuze's thought along a new and singular trajectory, and in so doing, attempts to reclaim his philosophy as an ethical philosophy. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (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)

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)

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

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)

Contemporary discourse is littered with nasty and derailed disagreements. In this paper we hope to help clean things up. We diagnose two patterns of thought that often plague and exacerbate controversy. We illustrate these patterns and show that each involves both a logical mistake and a failure of intellectual charity. We also draw upon recent work in social psychology to shed light on why we tend to fall into these patterns of thought. We conclude by suggesting how the intellectual virtues (...) can militate against these fallacies, focusing on the virtues of charity and humility. (shrink)

We have witnessed the athleticization of political discourse, whereby debate is treated like an athletic contest in which the aim is to vanquish one's opponents. When political discourse becomes a zero-sum game, it is characterized by suspicions, accusations, belief polarization, and ideological entrenchment. Unfortunately, athleticization is ailing the classroom as well, making it difficult for educators to prepare students to make valuable contributions to healthy civic discourse. Such preparation requires an educational environment that fosters the intellectual virtues that characterize an (...) examined life. This, in turn, requires an amicable and hospitable atmosphere in which a student enjoys the freedom to discover and articulate what she believes, how well her beliefs hang together, and what underlying assumptions or biases might be at work—without the fear that her self-disclosure will trigger immediate accusations and pigeonholing from fellow students. Educating for intellectual virtue is crucial for meeting these challenges and in this chapter we contribute to this strategy by offering some tools and guidance for promoting productive discussion of controversial issues. In the first two sections, we identify and explain two fallacious patterns of thought that often encumber discussion of controversial issues: assailment-by-entailment and the attitude-to-agent fallacy. In effect, these sections diagnose two diseases of discourse. We conclude each section with practical suggestions—in the form of thinking routines—for curing these ills. We will argue that part of the cure is to be found in the intellectual virtues. In particular, we will discuss how the virtues of intellectual charity, humility and carefulness can inoculate the mind against the fallacies we identify. (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 present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing ontologies where appropriate” is (...) critically important (Wright et al., 2020, p. 17). Our remaining concerns with BCIO relate directly to these two principles. First, we identify a number of issues with some of the classifications and definitions in BCIO that seem to be in tension with the just-mentioned principle . Second, we note some reservations about the reuse of certain classes in BCIO, namely from the Gazetteer (GAZ), the Ontology of Medically Related Social Entities (OMRSE), and the Information Artifact Ontology (IAO). While the latter principle of “reuse” is important, it is also important not to let the reuse of existing classes (or their corresponding definitions) compromise the logical integrity or the realist nature of one’s ontology. (shrink)

In the Republic, Socrates argues that morality (justice) is valuable both for itself and for what comes from it. In contemporary moral theory, this view is not widely accepted. However, contemporary empirical research in psychology reveals that what we experience is also what we come to expect. It follows from this that if we act in an immoral fashion, we will expect the same from others. The more often we act immorally, the more suspicion will be ingrained within us. Suspicion (...) quickly pervades our minds, corrodes our relationships, and increases our levels of stress, thereby dramatically decreasing our quality of life. Moral action, on the other hand, has the ability to strengthen our faith in others and create strong human relationships. Therefore,morality should be classified as having the highest type of value, just as Socrates contends.Moral behavior allows for healthy relations between persons (intrinsic value) and the wellbeing of the individual (extrinsic value). (shrink)

Independently of whether an object of experience becomes a candidate for being a part of the self or a part of the external world, it is always given to us as just an object of experience. The observer-observed relation can be seen as a type of relation with many instances, both between the self and different objects of experience and between any given object of experience and different selves. The self is situated in a spatial grid, where the latter can (...) be characterised as an array of relations, of which the relata include both observers and observed. The world, understood as independent existence, including the self, is empty. However, Paolo Bozzi’s method for identifying the self and delimiting its independent existence from the external world has taught us just the opposite lesson. Bozzi’s project is to teach us how to use them, and to recognise that they allow a self to be situated in a world of objects. (shrink)

In December 2013, the Nonhuman Rights Project (NhRP) filed a petition for a common law writ of habeas corpus in the New York State Supreme Court on behalf of Tommy, a chimpanzee living alone in a cage in a shed in rural New York (Barlow, 2017). Under animal welfare laws, Tommy’s owners, the Laverys, were doing nothing illegal by keeping him in those conditions. Nonetheless, the NhRP argued that given the cognitive, social, and emotional capacities of chimpanzees, Tommy’s confinement constituted (...) a profound wrong that demanded remedy by the courts. Soon thereafter, the NhRP filed habeas corpus petitions on behalf of Kiko, another chimpanzee housed alone in Niagara Falls, and Hercules and Leo, two chimpanzees held in research facilities at Stony Brook University. Thus began the legal struggle to move these chimpanzees from captivity to a sanctuary, an effort that has led the NhRP to argue in multiple courts before multiple judges. The central point of contention has been whether Tommy, Kiko, Hercules, and Leo have legal rights. To date, no judge has been willing to issue a writ of habeas corpus on their behalf. Such a ruling would mean that these chimpanzees have rights that confinement might violate. Instead, the judges have argued that chimpanzees cannot be bearers of legal rights because they are not, and cannot be persons. In this book we argue that chimpanzees are persons because they are autonomous. (shrink)

First published in 1995. Routledge is an imprint of Taylor & Francis, an informa company.

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)

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)

In this brief, we argue that there is a diversity of ways in which humans (Homo sapiens) are ‘persons’ and there are no non-arbitrary conceptions of ‘personhood’ that can include all humans and exclude all nonhuman animals. To do so we describe and assess the four most prominent conceptions of ‘personhood’ that can be found in the rulings concerning Kiko and Tommy, with particular focus on the most recent decision, Nonhuman Rights Project, Inc v Lavery.

We submit this brief in support of the Nonhuman Rights Project’s efforts to secure habeas corpus relief for the elephant named Happy. The Supreme Court, Bronx County, declined to grant habeas corpus relief and order Happy’s transfer to an elephant sanctuary, relying, in part, on previous decisions that denied habeas relief for the NhRP’s chimpanzee clients, Kiko and Tommy. Those decisions use incompatible conceptions of ‘person’ which, when properly understood, are either philosophically inadequate or, in fact, compatible with Happy’s personhood.

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)

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)

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)

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)

http://www.uni-bielefeld.de/ZIF/Publikationen/books/10_Baurmann_NormsAndValues.html.

How can a business institution function as an ethical institution within a wider system if the context of the wider system is inherently unethical? If the primary goal of an institution, no matter how ethical it sets out to be, is to function successfully within a market system, how can it reconcile making a profit and keeping its ethical goals intact? While it has been argued that some ethical businesses do exist, e.g., Johnson and Johnson, the argument I would like (...) to put forth is that no matter how ethical a business institution is, or how ethical its goals are, its capacity to act in an ethical manner is restricted by the wider system in which it must operate, the market system. Unless there is a fundamental change in the notion of the market system itself, the capacity for individual businesses to act in an ethical manner will always be restricted. My argument is divided into two parts. The first part is to show the inherent bias towards unethical outcomes that is inherent in the market system. The second part is to suggest how to reorient the general economic framework in order to make ethical institutions more possible. The question then becomes, how to define economic behavior in terms other than competition for profit. (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)

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 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)

This book presents Robert S. Hartman’s formal theory of value and critically examines many other twentieth century value theorists in its light, including A.J. Ayer, Kurt Baier, Brand Blanshard, Paul Edwards, Albert Einstein, William K. Frankena, R.M. Hare, Nicolai Hartmann, Martin Heidegger, G.E. Moore, P.H. Nowell-Smith, Jose Ortega y Gasset, Charles Stevenson, Paul W. Taylor, Stephen E. Toulmin, and J.O. Urmson.

The republican tradition has long been ambivalent about markets and commercial society more generally: from the contrasting positions of Rousseau and Smith in the eighteenth century to recent neorepublican debates about capitalism, republicans have staked out diverse positions on fundamental issues of political economy. Rather than offering a systematic historical survey of these discussions, this chapter will instead focus on the leading neo-republican theory—that of Philip Pettit—and consider its implications for market society. As I will argue, Pettit’s theory is (...) even friendlier to markets than most have believed: far from condemning commercial society, his theory recognizes that competitive markets and their institutional preconditions are an alternative means to limit arbitrary power across the domestic, economic, and even political spheres. While most republican theorists have focused on political means to limit such power—including both constitutional means (e.g., separation of powers, judicial review, the rule of law, federalism) and participatory ones (democratic elections and oversight)—I will examine here an economic model of republicanism that can complement, substitute for, and at times displace the standard political model. Whether we look at spousal markets, labor markets, or residential markets within federal systems, state policies that heighten competition among their participants and resource exit from abusive relationships within them can advance freedom as non-domination as effectively or even more effectively than social-democratic approaches that have recently gained enthusiasts among republicans. These conclusions suggest that democracy, be it social or political, is just one means among others for restraining arbitrary power and is consequently less central to (certain versions of) republicanism than we may have expected. So long as they counteract domination, economic inroads into notionally democratic territory are no more worrisome than constitutional ones. (shrink)

The current economic/political system, neoliberalism, has touched every aspect of life globally. The doctrine of neoliberalism consists of three central propositions, that the market is real and part of the natural universal law; that unlimited economic growth is both possible and even desirable; and that human nature is coincident with market values and based solely on self-interest. All three of these propositions are seriously flawed and have caused immense human suffering and staggering environmental destruction. This paper is a reminder of (...) the failures of neoliberal policy and an appeal for change to a new institutional arrangement in which development trumps economic growth. This position is in contrast to Francis Fukuyama’s end-of-history thesis. He alleges there are no economic/political ideologies to compete with neoliberalism, the “TINA principle: There Is No Alternative”: the West has won. It is time to reintroduce Henry David Thoreau’s, and to a lesser extent, Adam Smith’s moral economies. Both have encourgaging insights, often overlooked by current academic economists, which could figure prominently in the conception of a new economy. (shrink)

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)