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)

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)

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)

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)

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)

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)

In lieu of an abstract, here is a brief excerpt of the content:Plato on Knowledge as a Power1Nicholas D. SmithAt 471C4 in Plato’s Republic, the argument takes a sudden turn when Glaucon becomes impatient with all of the specific prescriptions Socrates has been making, and asks to return to the issue Socrates had earlier set aside—whether or not the city he was describing could ever be brought into being. In response to Glaucon’s impatient question, Socrates articulates his “third wave of (...) paradox” (472ag–7), namely, that the ills of the cities will never be ended until either philosophers become rulers or rulers become philosophers (473c11–d6). Glaucon immediately responds that such a view is likely to be greeted with violence and scorn (473e6–474a4), and so Socrates must hasten to explain his odd claim. His explanation, it turns out, is that true philosophers have an enormous cognitive advantage over non-philosophers—philosophers have and use knowledge (ἐπιστήμη), whereas non-philosophers have and use only opinion (δόξα).2 This distinction, between επιστήμη and δόξα, turns out: to be a distinction between two different cognitive powers (δυνάμεις—477d7–e3). And different powers, Plato clearly tells us, apply to or take as their objects (Plato says they are “ἐπί”) different things (477dl).In this paper, I shall argue that the relationship between the cognitive powers and their various objects has been fundamentally misunderstood, which has led scholars into one or more misinterpretations of important and explicit features of the text. At the heart of these misunderstandings, I claim, is [End Page 145] their shared misconception of the relation between the cognitive power and its objects as interpretable in terms of the relationship between a cognitive stale and what the content of that state is of or about.3 One consequence of the view for which I shall argue is that what has come to be known as the “two-worlds theory”4 of Plato’s epistemology is seriously mistaken, but no less mistaken than the alternatives given by its recent critics. Another consequence that I shall draw from my argument is that Plato should be understood neither as a kind of foundationalist with regard to knowledge and warrant, as some have supposed him to be,5 nor as a coherentist, as others have supposed,6 but, rather, as a kind of causal reliabilist. [End Page 146]1. KNOWLEDGE AS A POWERScholarly interpretations of Plato’s epistemology have routinely sought to understand the relationships between each cognitive power of Republic Book V and the objects of the ἐφ’ ᾦ (“what it is related to”) condition by which it is differentiated from other δυνάμεις as Plato’s way of telling us what each sort of cognition is of or aboul. 7 So, for example, we find Gail Fine using the expressions “belief [δόξα] is set over [Fine’s translation of Plato’s ἐπί] …” and “knowledge is set over …” interchangeably with “belief is of …” or “belief is about…” and “knowledge is of …” or “knowledge is about …”8 Against the “two-worlds theory,” Fine argues that, for Plato, there can be knowledge of sensibles and beliefs about Forms. Accordingly, since she assimilates the power-ἐπί-object set of relations to the cognilion-of/about-object relation, she concludes—in order to account for knowledge of sensibles and beliefs about Forms—that the objects of knowledge and opinion must be propositions. Plato’s claims that knowledge is ἐπί what is, whereas opinion is ἐπί what is and is not, Fine understands as, “One can only know true propositions; one can believe both true and false propositions.”9 We shall see later that this “veridical” understanding of what Plato means to identify as “what is,” and “what is and is not” fails to account for important and explicit elements of Plato’s exposition of the epistemological and metaphysical distinctions he is making. For now, it is enough to note that Fine understands the ἐφ’ᾦ) relation in terms of our cognition-of/about-object relation. One finds the same assimilation made by those who advance existential readings of Plato’s “is” and “is not,”10 as [End Page 147] well as those who have urged that we adopt predicative readings of “is” and “is not.”11But I think there are very serious problems with this assimilation. Plato is very... (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)

The ten original studies included in this Research Topic investigate selected assumptions and predictions of parochial altruism theory in detail. We, the editors, are convinced that their highly instructive findings will help researchers interested in parochial altruism, but also in intergroup psychology more generally, to gain a much more fine-grained understanding of the interplay of altruistic and spiteful motives in human decision making in the context of intergroup relations. The broad range of disciplines represented by the authors contributing (...) to this Research Topic and the variety of methods used in their studies are representative for the current interdisciplinary interest in parochial altruism. The most important insight that, in our view, can be derived from the works collected here is that human decision making in intergroup contexts is more complex than suggested by current theory. Thus, we hope that future theorizing on parochial altruism will be stimulated by the evidence gathered in this Research Topic. In this editorial, we briefly highlight central findings reported here, which, to us, appear most informative for prospective enhancements of parochial altruism theory. (shrink)

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)

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 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)

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

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)

We can use radically different reference‐schemes to generate the same truth‐conditions for the sentences of a language. In this paper, we do three things. (1) Distinguish two arguments that deploy this observation to derive different conclusions. The first argues that reference is radically indeterminate: there is no fact of the matter what ordinary terms refer to. This threat is taken seriously and most contemporary metasemantic theories come with resources intended to rebut it. The second argues for radical parochialism about reference: (...) it's a reflection of our parochial interests, rather than the nature of the subject matter, that our theorizing about language appeals to reference rather than another relation that generates the same truth‐conditions. Rebuttals of the first argument cut no ice against the second, because radical parochialism is compatible with reference being determinate. (2) Argue that radical parochialism, like radical indeterminacy, would be shocking if true. (3) Argue that the case for radical parochialism turns on the explanatory purposes of “reference”‐talk: on relatively “thin” conceptions, the argument goes through, and radical parochialism is (shockingly!) true; on richer conceptions, the argument can be blocked. We conclude that non‐revisionists must endorse, and justify, a relatively rich conception of the explanatory purposes of “reference”‐talk. (shrink)

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an effort called (...) Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up. (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)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (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 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)

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)

Philosophers often consider problems of free will and moral luck in isolation from one another, but both are about control and moral responsibility. One problem of free will concerns the difficult task of specifying the kind of control over our actions that is necessary and sufficient to act freely. One problem of moral luck refers to the puzzling task of explaining whether and how people can be morally responsible for actions permeated by factors beyond their control. This chapter (...) explicates and assesses skeptical, compatibilist, and libertarian approaches to moral luck. First, I argue that what makes the above problems of free will and moral luck distinct is largely their emphasis on different kinds of luck. Second, I describe and evaluate skeptical arguments from constitutive and circumstantial luck that it is impossible to act freely. Third, I explicate and assess various support and implication relationships between various kinds of compatibilism and libertarianism, on the one hand, and causal, constitutive, circumstantial, and resultant moral luck, on the other. (shrink)

According to the Free Will Explanation of a traditional view of hell, human freedom explains why some people are in hell. It also explains hell’s punishment and finality: persons in hell have freely developed moral vices that are their own punishment and that make repentance psychologically impossible. So, even though God continues to desire reconciliation with persons in hell, damned persons do not want reconciliation with God. But this moral vice explanation of hell’s finality is implausible. I argue that (...) God can and would make direct or indirect alterations in their character to give them new motivational reasons that re-enable their freedom to repent. Subsequently, I argue that it is probable that each damned person will be saved eventually, because there is a potential infinity of opportunities for free repentance. Thus, if the Free Will Explanation’s descriptions of hell and divine love are correct, it is highly probable that each person in hell escapes to heaven. (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)

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)

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)

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 national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to this model can be seen at (...) work today in Quebec and in Ireland, it underpins much of the rhetoric of the P.L.O., and was certainly to some degree involved as a motivating factor in much of the ethnic cleansing which took place in Bosnia in recent times. The question to be addressed in what follows is: to what extent could inter-group disputes be more peacefully resolved, and ethnic cleansing avoided, if political leaders, diplomats and others involved in the resolution of such disputes could be brought to accept weaker geometrical constraints on the shapes of nations? A number of associated questions then present themselves: What sorts of administrative and logistical problems have been encountered by existing non contiguous nations and by perforated nations, and by other nations deviating in different ways from the received geometrical ideal? To what degree is the desire for continuity and simple connectedness a rational desire, and to what degree does it rest on species of political rhetoric which might be countered by, for example, philosophical argument? These and a series of related questions will form the subject- matter of the present essay. (shrink)

The book’s core argument is that an artificial intelligence that could equal or exceed human intelligence—sometimes called artificial general intelligence (AGI)—is for mathematical reasons impossible. It offers two specific reasons for this claim: Human intelligence is a capability of a complex dynamic system—the human brain and central nervous system. Systems of this sort cannot be modelled mathematically in a way that allows them to operate inside a computer. In supporting their claim, the authors, Jobst Landgrebe and Barry Smith, marshal (...) evidence from mathematics, physics, computer science, philosophy, linguistics, and biology, setting up their book around three central questions: What are the essential marks of human intelligence? What is it that researchers try to do when they attempt to achieve "artificial intelligence" (AI)? And why, after more than 50 years, are our most common interactions with AI, for example with our bank’s computers, still so unsatisfactory? Landgrebe and Smith show how a widespread fear about AI’s potential to bring about radical changes in the nature of human beings and in the human social order is founded on an error. There is still, as they demonstrate in a final chapter, a great deal that AI can achieve which will benefit humanity. But these benefits will be achieved without the aid of systems that are more powerful than humans, which are as impossible as AI systems that are intrinsically "evil" or able to "will" a takeover of human society. (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)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

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

As central as the method of forcing is within set theory, it has yet to be incorporated into the philosopher's toolbox. That strikes me as a shame, since it may well have important applications within philosophy. One barrier is that typical presentations of forcing are overly dry and technical and make it seem inherently bound up with its applications within set theory. The purpose of this note is to try to rectify this. In particular, I will explain how the (...) method of forcing can be seen as a way of constructing a certain kind of intensional model that philosophers are already interested in: namely, possibility models. (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)

An interview by Alex Thomson of UKColumn on Landgrebe and Smith's book: Why Machines Will Never Rule the World. The subtitle of the book is Artificial Intelligence Without Fear, and the interview begins with the question of the supposedly imminent takeover of one profession or the other by artificial intelligence. Is there truly reason to be afraid that you will lose your job? The interview itself is titled 'Where this is no will there is no way', (...) drawing on one thesis of the book to the effect that there will never be anything like the human will on the part of a machine. This is for mathematical reasons. AI is always and in every case a matter of algorithms; thus of applied mathematics. And algorithms are not the sorts of things that can want or desire or intend to do something. It is the human will of those who work at OpenAI or google or microsoft which have given rise to the new shiny objects of AI (ChatGPT and other Large Language Models). And it is the human will of the users of these shiny objects which gives them the resources and power to work their apparent miracles. (shrink)

Climate change appears to be a classic aggregation problem, in which billions of individuals perform actions none of which seem to be morally wrong taken in isolation, and yet which combine to drive the global concentration of greenhouse gases (GHGs) ever higher toward environmental (and humanitarian) catastrophe. When an individual can choose between actions that will emit differing amounts of GHGs―such as to choose a vegan rather than carnivorous meal, to ride a bike to work rather than drive a (...) car, or to take a reusable bag to the supermarket rather than send another plastic bag to landfill―does she have any reason to choose the lower-emitting actions? In this chapter I'll reject the claim that individuals don't make a difference when it comes to climate change. I first discuss making a difference with every action, as a way of getting clearer about how individuals' actions impact causally on the harms resulting from climate change, making a distinction so far overlooked in the climate ethics discussion between 'macro' thresholds like ice-cap melt, and 'micro' thresholds like severe weather events. I set aside making a difference with every action as implausible, and then move on to discuss both low probability of major difference, and high probability of minor difference. I argue that both of these are plausible characterizations of individuals' causal contributions to climate change. I conclude by noting some policy implications of having (probabilistic) individual difference-making back in play. (shrink)

The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build is the domain mid-level (...) ontologies. However, thus far there has been no mid-level manufacturing ontology that is based on BFO. The IOF has recently released the IOF Core version 1 beta to fill this gap. This paper documents the development process and gives an overview of the current content of the IOF Core. Finally, the paper describes how the IOF Core can be used as the basis for a more domain-specific Supply Chain Ontology. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata (...) registries, thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

What should we do when we won't do as we ought? Suppose it ought to be that the procrastinating professor accept the task of reviewing a book, and actually review the book. It seems clear that given he won't review it, he ought not to accept the task. That is a genuine moral obligation in light of less than perfect circumstances. I want to entertain the possibility that a set of such obligations form something like a 'practical morality'; that which (...) we ought to do given that we're unlikely or unwilling to do much of what ideal morality demands. If it is possible to give a coherent account of these kinds of obligations, then it is possible to entertain the idea that these obligations are in fact what morality demands. The conceptual truths about justice (good, right, fairness) that come from ideals are one thing; the actions that morality demands of people given their actual circumstances are quite another. In this paper I will ask about the kinds of facts that can be used to establish a more circumscribed set of obligations than we get from the orthodox view about moral obligation. (shrink)

In her ‘On the apparent paradox of ideal theory’, Laura Valentini combines three supposedly plausible premises to derive the paradoxical result that ideal theory is both unable to, and indispensable for, guiding action. Her strategy is to undermine one of the three premises by arguing that there are good and bad kinds of ideal theory, and only the bad kinds are vulnerable to the strongest version of their opponents’ attack. By undermining one of the three premises she releases ideal theorists (...) from the paradox, which is as follows. (1) Any sound theory of justice is action-guiding. (2) Any sound theory of justice is ideal. (3) Any ideal theory fails to be action-guiding. Here I shall respond to Valentini in two ways. First, I shall show that both (1) and (2) are false. The falsity of either is sufficient to release ideal theorists from the paradox. Second, I shall show that Valentini’s response to (3) can be extended, because her bad kinds of ideal theory do not necessarily fail to guide action. The cumulative effect of my arguments further strengthens Valentini’s support of ideal theory. I will deal with premises (1) and (2) in Sections I and II, and (3) in Section III. (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

The politics of climate change is marked by the fact that countries are dragging their heels in doing what they ought to do; namely, creating a binding global treaty, and fulfilling the duties assigned to each of them under it. Many different agents are culpable in this failure. But we can imagine a stylised version of the climate change case, in which no agents are culpable: if the bad effects of climate change were triggered only by crossing a particular threshold, (...) and it was reasonably, but mistakenly, believed by each country that insufficiently many other countries were willing to cooperate in order for that threshold to remain uncrossed, no country would be required to make a unilateral contribution. Yet even without culpability, we can diagnose a moral ill: the world has gone other than it should have. If not for the mistaken beliefs, there would have been a global climate treaty, and all the avoidance of future suffering that would come with it. In this article I argue that this moral ill has implications for the non-culpable agents, in that it generates duties to disgorge actual holdings over and above the counterpart holdings in the relevant counterfactual: those holdings the agents would have had, were the world to have gone as it should. (shrink)

St. Anselm is a master of philosophical prose. His writings on God, truth, and free will are models of clarity born of unflagging concern for argumentative precision. He is especially adept at using analogies to cinch his readers' understanding of these recondite matters. Who could forget the light shed upon the concept of existence by the Painter Analogy in the Ontological Argument or how his River Analogy illumines the unification of the Holy Trinity? Such intellectual insights could only be (...) gifts of the Holy Ghost for the edification of Holy Mother Church. I shall discuss here the three splendid analogies that St. Anselm draws in De Concordia in order to reconcile grace and free will, fostering an understanding of co-operation according to which divine assistance must accentuate, rather than nullify, exercises of human freedom. Central to my discussion is The Father of Scholasticism's four-fold distinction between a power, its exercises, the effects of those exercises, and opportunities to bring about those effects. (shrink)

St. Anselm is a master of philosophical prose. His writings on God, truth, and free will are models of clarity born of unflagging concern for argumentative precision. He is especially adept at using analogies to cinch his readers' understanding of these recondite matters. Who could forget the light shed upon the concept of existence by the Painter Analogy in the Ontological Argument or how his River Analogy illumines the unification of the Holy Trinity? Such intellectual insights could only be (...) gifts of the Holy Ghost for the edification of the Holy Mother Church. I shall discuss here the three splendid analogies that St. Anselm draws in De Concordia in order to reconcile grace and free will, fostering an understanding of cooperation according to which divine assistance must accentuate, rather than nullify, exercises of human freedom. Central to my discussion is The Father of Scholasticism's four-fold distinction between a power, its exercises, the effects of those exercises, and opportunities to bring about those effects. (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 _Principle of Indifference_ was once regarded as a linchpin of probabilistic reasoning, but has now fallen into disrepute as a result of the so-called _problem of multiple of partitions_. In ‘Evidential symmetry and mushy credence’ Roger White suggests that we have been too quick to jettison this principle and argues that the problem of multiple partitions rests on a mistake. In this paper I will criticise White’s attempt to revive POI. In so doing, I will argue that (...) what underlies the problem of multiple partitions is a fundamental tension between POI and the very idea of _evidential incomparability_. (shrink)

Where does the mind begin and end? Most philosophers and cognitive scientists take the view that the mind is bounded by the skull or skin of the individual. Robert Wilson, in this provocative and challenging 2004 book, provides the foundations for the view that the mind extends beyond the boundary of the individual. The approach adopted offers a unique blend of traditional philosophical analysis, cognitive science, and the history of psychology and the human sciences. The companion volume, Genes and (...) the Agents of Life, explores the theme in the biological sciences. Written with verve and clarity, this ambitious book will appeal to a broad swathe of professionals and students in philosophy, psychology, cognitive science, and the history of the behavioural and human sciences. You can download the table of contents here. (shrink)

Based on the argumentative analysis, the essential title is interpreted within its entitle as it leaves bias open 'along the lines' as to whether the January 6th insurrection that took place on Capitol Hill was or was not justified or unjustifiably ‘so’ by Jean-Jacques Rousseau’s right to revolution. Detailed evidence to support and prove such intended thesis stretches this theoretical statement as it gambles to reckon with a central paradoxical and unhumored tone that leaves the reader and/or author’s perspective to (...) be ‘centered’ (and left due to a play of ‘centeredness’). As it pertains to the fallout and outcome of how governmental, national, and militaral leadership (given the reality of a sovereign leader or a reign). Presentational style is constructed or structured oddly awakes uncontrollable, uncensored, unmeasurable, and untouchable personification that is nonstop. Such series of quoted citations are pieces of instruction that serve to admire and of acceptability in pursuit of Rousseauian logic as it poses a modest figurative language where its main objective is to attempt to underline the principles and techniques that plague post-modernists within the scope of legislative, executive, or even judicial systems of functionalities. (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.

In recent years, a growing discussion about how we should design our cities has emerged, particularly for the more controversial modes of design such as “defensive,” “hostile,” or “disciplinary” architecture (i.e., benches on which one cannot sleep, or metal studs on which one cannot skate). Although this debate is relatively mature, many studies have argued that these design notions are undertheorized and are, thus, challenging to study from an empirical and normative perspective. In this paper, I will defne the (...) most common terms used in the literature and show how they are interconnected by utilizing a set of “conditions of adequacy” from philosophy to facilitate a more transparent and well-grounded discussion of them. Terms such as “hostile” and “defensive” design are underlined by several diferent phenomena, not just one as is sometimes commonly assumed. I will also show that these phenomena and their conceptualizations require—and sometimes force us to use—diferent moral reasons when justifying the utilization of diferent designs. (shrink)