With Being Me Being You, Samuel Fleischacker provides a reconstruction and defense of Adam Smith’s account of empathy, and the role it plays in building moral consensus, motivating moral behavior, and correcting our biases, prejudices, and tendency to demonize one another. He sees this book as an intervention in recent debates about the role that empathy plays in our morality. For some, such as Paul Bloom, Joshua Greene, Jesse Prinz, and others, empathy, or our capacity for fellow-feeling, tends to (...) misguide us in the best of cases, and more often reinforces faction and tribalism in morals and politics. These utilitarians, as Fleischacker refers to them, propose that empathy take a back seat to cost-benefit analysis in moral decision-making. As an intervention, the book is largely successful. Fleischacker’s defense of empathy is nuanced and escapes the myopic enthusiasm to which many partisans of empathy are prone. Anyone looking to understand the relationship between empathy and morality would do well to grapple with Being Me Being You. Still, Fleischacker overlooks that Smith would most likely be less convinced of the idea that greater empathy can help us overcome the great challenges of our time. (shrink)

In this paper, my aim is to bring together contemporary psychological literature on emotion regulation and the classical sentimentalism of David Hume and Adam Smith to arrive at a plausible account of empathy's role in explaining patterns of moral judgment. Along the way, I criticize related arguments by Michael Slote, Jesse Prinz, and others.

Hume once argued the basic science to be not physics but “the science of man” and the foundation of this science to be the empiricist mechanism of association governed by the law of similarity in appearance—now more popular than ever in the form of artificial neural networks. I update Hume’s picture by showing phenomenology to be centrally concerned with providing a unifying basis for all the sciences (including physics) by going beyond the psychology of associationism (passive synthesis) to reveal phenomena (...) that are irreducibly syntactic (not associative) in structure. I therefore argue that the language of thought (LOT) is the necessary mechanism at the basis of these descriptive phenomena. I conclude by sketching a new picture of all the sciences unified by LOT based on Husserl’s opposition to Galilean “physicomathematical” science vis-à-vis the life-world (Lebenswelt). (shrink)

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (shrink)

Yoshimi has attempted to defuse my argument concerning the identification of network abstraction with empiricist abstraction - thus entailing psychologism - by claiming that the argument does not generalize from the example of simple feed-forward networks. I show that the particular details of networks are logically irrelevant to the nature of the abstractive process they employ. This is ultimately because deep artificial neural networks (ANNs) and dynamical systems theory applied to the mind (DST) are both associationisms - that is, empiricist (...) theories that derive the principles of thought from the causal history of the organism/system. On this basis, I put forward a new aspect of the old argument by noting that ANNs & DST are the causal bases of the phenomena of passive synthesis, whereas the language of thought hypothesis (LOT) and the symbolic computational theory of mind (CTM) are the causal bases of the phenomena of active synthesis. If the phenomena of active synthesis are not distinct in kind from and are thus reducible to those of passive synthesis, psychologism results. Yoshimi’s program, insofar as it denies this fundamental phenomenological distinction, is revealed to be the true anti-pluralist program, by essentially denying the causal efficacy of the mechanistic foundations of active synthesis by referring phenomenology exclusively to associationism for its causal foundation. (shrink)

Our computational metaphysics group describes its use of automated reasoning tools to study Leibniz’s theory of concepts. We start with a reconstruction of Leibniz’s theory within the theory of abstract objects (henceforth ‘object theory’). Leibniz’s theory of concepts, under this reconstruction, has a non-modal algebra of concepts, a concept-containment theory of truth, and a modal metaphysics of complete individual concepts. We show how the object-theoretic reconstruction of these components of Leibniz’s theory can be represented for investigation by means of automated (...) theorem provers and finite model builders. The fundamental theorem of Leibniz’s theory is derived using these tools. (shrink)

The modal account of luck is the predominant account of luck in epistemology and ethics. In the first half of this paper, I discuss three possible interpretations of the modal account and raise objections to each. I then raise an objection to all plausible versions of the modal account, that is, that whether an event is lucky or the extent to which it is a matter of luck will depend on what initial conditions or features of the event one holds (...) constant across nearby possible worlds. However, there is often reasonable disagreement about what the relevant initial conditions of an event are, and the modal account of luck has no means of determining which description of the event is correct. As such, the modal account is subject to a kind of reference class problem, and the view cannot actually tell us the extent to which certain events are a matter of luck. (shrink)

In the article "What Sin Is: A Differential Analysis," Jesse Couenhoven delves into the definitions and categorizations of sin according to various Christian doctrines. The author critically examines traditional definitions, such as those provided by the Westminster Confession and catechisms, and argues that they fail to adequately distinguish between sin and evil, often conflating natural evils with sinful acts. Couenhoven also considers gray areas of ethical behavior, such as the actions of a schizophrenic who curses against God or the mistakes (...) made by medical residents that result in harm to patients, and questions whether these actions should be classified as sin. The primary question driving the article is how sin is differentiated from that which is "merely" evil. To address this, Couenhoven analyzes and evaluates three views of sin, testing their coherence with Christian beliefs and practices. The article aims to provide a more nuanced and sufficient understanding of sin within the Christian tradition, going beyond the necessary elements of the doctrine of sin to better identify and differentiate sin from evil. (shrink)

Nicholas Agar, Jeff McMahan and Allen Buchanan have all expressed concerns about enhancing humans far outside the species-typical range. They argue radically enhanced beings will be entitled to greater and more beneficial treatment through an enhanced moral status, or a stronger claim to basic rights. I challenge these claims by first arguing that emerging technologies will likely give the enhanced direct control over their mental states. The lack of control we currently exhibit over our mental lives greatly contributes to our (...) sense of vulnerability. I then argue moral status should be viewed in terms of vulnerability. The enhanced will slowly gain the ability to command their mental states, reducing their vulnerability. These radically enhanced beings will have greater capacities, and possibly an inner life more valuable than our own. They will also be less vulnerable, and as a result, their moral status will be subordinate to our own. (shrink)

Writers in the propositions literature consider the Benacerraf objection serious, often decisive. The objection figures heavily in dismissing standard theories of propositions of the past, notably set-theoretic theories. I argue that the situation is more complicated. After explicating the propositional Benacerraf problem, I focus on a classic set-theoretic theory of propositions, the possible worlds theory, and argue that methodological considerations influence the objection’s success.

This paper takes under consideration a piece by Roger Crisp in which he questions what the problem of moral luck can teach us about COVID-19 lockdown rule-breakers. Taking the position that although such rule-breakers might seem to be new examples of moral luck, Crisp ends up denying the existence of moral luck and argues that moral luck is an outdated notion in so far as it relies on other questionable aspects of morality, that is, retributivist punishment and blame. Although the (...) author agrees with Crisp that pandemic rule-breaker cases are putative examples of resultant moral luck, he proposes that Crisp has misconstrued what moral luck is and the paper examines in detail what he sees as the numerous problems with Crisp’s claims. The author concludes that Crisp’s analysis of pandemic rule-breaking does not shed any new light on the moral luck debate, and the difficult questions of luck, moral responsibility, and desert are not so easily resolved. -/- . (shrink)

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

It is surprisingly hard to define presentism. Traditional definitions of the view, in terms of tensed existence statements, have turned out not to to be capable of convincingly distinguishing presentism from eternalism. Picking up on a recent proposal by Tallant, I suggest that we need to locate the break between eternalism and presentism on a much more fundamental level. The problem is that presentists have tried to express their view within a framework that is inherently eternalist. I call that framework (...) the Fregean nexus, as it is defined by Frege’s atemporal understanding of predication. In particular, I show that the tense-logical understanding of tense which is treated as common ground in the debate rests on this very same Fregean nexus, and is thus inadequate for a proper definition of presentism. I contrast the Fregean nexus with what I call the original temporal nexus, which is based on an alternative, inherently temporal form of predication. Finally, I propose to define presentism in terms of the original temporal nexus, yielding original presentism. According to original presentism, temporal propositions are distinguished from atemporal ones not by aspects of their content, as they are on views based on the Fregean nexus, but by their form—in particular, by their form of predication. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

It is often assumed that all lucky events are significant. The thought is that a chancy event such as winning the lottery is lucky for you in part because it affects your interests or well-being. But whether you win an Absurdist Raffle in which there are no prizes, is, intuitively, not a matter of luck. This is because this event—even if chancy—is not significant for any subject. However, a few philosophers have recently claimed not only that luck does not necessarily (...) involve a significance condition but that we should not view luck involving claims in terms of significance. After reviewing the literature on this topic, I argue that lucky events are significant. A significance condition is necessary to distinguish between different kinds of luck: practical, epistemic, and moral. All lucky events are significant and chancy, but they can be significant for subjects in different ways. For example, an event is epistemically lucky for you if it is epistemically significant and chancy, but such events need not affect your practical interests or moral standing. Furthermore, I argue that events that are chancy but not significant should be thought of in terms of chance and not luck. (shrink)

Epistemic accounts of luck define luck’s chanciness condition relative to a subject’s epistemic position. This could be put in terms of a subject’s evidence or knowledge about whether the event will occur. I argue that both versions of the epistemic account fail. In §2, I give two types of counterexamples to the evidence-based approach. In §3, I argue—contrary to the knowledge-based view—that an event can be a matter of good or bad luck for a subject even if she knows that (...) it will occur. In §4, I argue that epistemic accounts cannot explain some instances of constitutive luck. Because of these problems, luck’s chanciness condition cannot be adequately defined in epistemic terms. (shrink)

The representations of deep convolutional neural networks (CNNs) are formed from generalizing similarities and abstracting from differences in the manner of the empiricist theory of abstraction (Buckner, Synthese 195:5339–5372, 2018). The empiricist theory of abstraction is well understood to entail infinite regress and circularity in content constitution (Husserl, Logical Investigations. Routledge, 2001). This paper argues these entailments hold a fortiori for deep CNNs. Two theses result: deep CNNs require supplementation by Quine’s “apparatus of identity and quantification” in order to (1) (...) achieve concepts, and (2) represent objects, as opposed to “half-entities” corresponding to similarity amalgams (Quine, Quintessence, Cambridge, 2004, p. 107). Similarity amalgams are also called “approximate meaning[s]” (Marcus & Davis, Rebooting AI, Pantheon, 2019, p. 132). Although Husserl inferred the “complete abandonment of the empiricist theory of abstraction” (a fortiori deep CNNs) due to the infinite regress and circularity arguments examined in this paper, I argue that the statistical learning of deep CNNs may be incorporated into a Fodorian hybrid account that supports Quine’s “sortal predicates, negation, plurals, identity, pronouns, and quantifiers” which are representationally necessary to overcome the regress/circularity in content constitution and achieve objective (as opposed to similarity-subjective) representation (Burge, Origins of Objectivity. Oxford, 2010, p. 238). I base myself initially on Yoshimi’s (New Frontiers in Psychology, 2011) attempt to explain Husserlian phenomenology with neural networks but depart from him due to the arguments and consequently propose a two-system view which converges with Weiskopf’s proposal (“Observational Concepts.” The Conceptual Mind. MIT, 2015. 223–248). (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

In this paper I develop an argument against a type of Non-Analytic Normative Naturalism. This argument, the Normative Property Dualism Argument, suggests that, if Non-Analytic Normative Naturalists posit that normative properties are identical to natural properties and that such identities are a posteriori, they will be forced to posit that these properties which are both normative and natural have higher-order normative properties of their own.

Chalmers (Mind 120(479): 587–636, 2011a) presents an argument against “referentialism” (and for his own view) that employs Bayesianism. He aims to make progress in a debate over the objects of belief, which seems to be at a standstill between referentialists and non-referentialists. Chalmers’ argument, in sketch, is that Bayesianism is incompatible with referentialism, and natural attempts to salvage the theory, Chalmers contends, requires giving up referentialism. Given the power and success of Bayesianism, the incompatibility is prima facie evidence against referentialism. (...) In this paper, I review Chalmers’ arguments and give some responses on behalf of the referentialist. (shrink)

This essay examines the possibility that phenomenological laws might be implemented by a computational mechanism by carefully analyzing key passages from the Prolegomena to Pure Logic. Part I examines the famous Denkmaschine passage as evidence for the view that intuitions of evidence are causally produced by computational means. Part II connects the less famous criticism of Avenarius & Mach on thought-economy with Husserl's 1891 essay 'On the Logic of Signs (Semiotic).' Husserl is shown to reaffirm his earlier opposition to associationist (...) (Humean) and adaptationist (Darwinian) explanations of our thought-machine on the ground that they cannot reconstruct the notion of truth and its syntactic mental preservation in symbolic thought-trains. Part III reveals Husserl's interesting commitment to the idea that descriptive sciences necessarily transform into explanatory sciences on pain of contradicting the essence of science as a rational ideal. Since explanation in relation to phenomenology means causal explanation, and causal explanation in the form of the Denkmaschine accounts for phenomenological intuition, it is inferred that the rationally compelling ideal of explanatory science requires a computationalist reading of the subsequent logical investigations. (shrink)

In this paper I develop an argument against applying a causal theory of mental content to normative concepts. This argument—which I call the Intrapersonal Normative Twin Earth Argument—is inspired by Terry Horgan and Mark Timmons’ Moral Twin Earth Argument. The focus of Horgan and Timmons’ argument is showing that causal theories of mental content conflict with plausible claims about interpersonal normative disagreement. The Intrapersonal Normative Twin Earth Argument, by contrast, is focused on showing that such theories struggle to vindicate plausible (...) claims concerning whether two of an agent’s token normative thoughts have the same or distinct content. (shrink)

We analyse Hutto & Myin's three arguments against computationalism [Hutto, D., E. Myin, A. Peeters, and F. Zahnoun. Forthcoming. “The Cognitive Basis of Computation: Putting Computation In Its Place.” In The Routledge Handbook of the Computational Mind, edited by M. Sprevak, and M. Colombo. London: Routledge.; Hutto, D., and E. Myin. 2012. Radicalizing Enactivism: Basic Minds Without Content. Cambridge, MA: MIT Press; Hutto, D., and E. Myin. 2017. Evolving Enactivism: Basic Minds Meet Content. Cambridge, MA: MIT Press]. The Hard Problem (...) of Content targets computationalism that relies on semantic notion of computation, claiming that it cannot account for the natural origins of content. The Intentionality Problem is targeted against computationalism using non-semantic accounts of computation, arguing that it fails in explaining intentionality. Theion Problem claims that causal interaction between concrete physical processes and abstract computational properties is problematic. We argue that these a... (shrink)

This paper demonstrates the practical and philosophical strengths of adopting Luciano Floridi’s “general definition of information” (GDI) for use in the information sciences (IS). Many definitions of information have been proposed, but little work has been done to determine which definitions are most coherent or useful. Consequently, doubts have been cast on the necessity and possibility of finding a definition. In response to these doubts, the paper shows how items and events central to IS are adequately described by Floridi’s conception (...) of information, and demonstrates how it helps clarify the muddy theoretical framework resulting from the many previous definitions. To this end, it analyzes definitions, popular in IS, that conceive of information as energy, processes, knowledge, and physical objects. The paper finds that each of these definitions produces problematic or counterintuitive implications that the GDI suitably accounts for. It discusses the role of truth in IS, notes why the GDI is preferable to its truth-requiring variant, and ends with comments about the import of such a theory for IS research and practice. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

In response to Petitmengin and Bitbol's recent account of first-person methodologies in the study of consciousness, I provide a revised model of our introspective knowledge of our own conscious experience. This model, which I call the existential constitution model of phenomenal knowledge, avoids the problems that Petitmengin and Bitbol identify with standard observational models of introspection while also avoiding an underlying metaphorical misconception in their own proximity model, which misconstrues first-person knowledge of consciousness in terms of a dichotomous epistemic relationship. (...) The end result is a clearer understanding of the unique nature and epistemic properties of our knowledge of consciousness, as well as the epistemic status of subsequent first-person reports on conscious experience. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

Some feminists hold that surrogacy contracts should be unenforceable or illegal because they contribute to and perpetuate unjust gender inequalities. I argue that in developed countries, surrogacy contracts either wouldn't have these negative effects or that these effects could be mitigated via regulation. Furthermore, the existence of a regulated surrogacy market is preferable on consequentialist grounds.

In this paper I argue against Analytic Normative Naturalism by suggesting that the view cannot capture the way that normative concepts figure in advice. To establish this conclusion, I identify several links between normative concepts and advice and argue that, if Analytic Normative Naturalism were true, these links would not obtain.

In this position paper for the 2019 CSCW workshop Good Systems: Ethical AI for CSCW I propose one tool and one idea for navigating the complex ethical problem space that results from the interaction of human and/or AI agents in shared, hopefully cooperative, computing environments.

Moral metasemantic theories explain how our moral thought and talk are about certain properties. Given the connection between what our moral terms are about and which moral claims are true, it might be thought that metasemantic theorising can justify first-order ethical conclusions, thus providing a novel way of doing moral epistemology. In this paper, we spell out one kind of argument from metasemantic theories to normative ethical conclusions, and argue that it fails to transmit justification from premises to conclusion. We (...) give three reasons for this transmission failure, which together pose a serious challenge to such metasemantic arguments. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (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)

One of the main questions Gillian Brock takes up in Justice for People on the Move (2020) is whether it is morally permissible for states to enact migration policies that discriminate on the basis of religion against those who wish to enter. The main focus of her discussion is on the United States context, and, in particular, the so-called ‘Muslim Ban’ enacted by President Donald Trump in 2017. While Brock offers a powerful critique of this policy, I argue that it (...) is insufficient on its own to support her claim that migration policies that discriminate on the basis of religion in general undermine the legitimacy of the states that enact them. I argue that this claim can be supported within her framework by showing that such policies necessarily display disregard for the human rights of existing members of the discriminating state. I conclude with some reflections on the strength of this account of the moral impermissibility of religious discrimination at the border. (shrink)

In this short paper, we show that a popular view in information science, information-as-thing, fails to account for a common example of information that seems physical. We then demonstrate how the distinction between types and tokens, recently used to analyse Shannon information, can account for this same example by viewing information as abstract, and discuss existing definitions of information that are consistent with this approach. -/- Dans ce court article nous montrons qu'une vision populaire en sciences de l'information, l'information en (...) tant qu’une chose, échoue à rendre compte d'un exemple commun d'information qui semble physique. Nous démontrons ensuite comment la distinction type/token, utilisée récemment pour analyser l'information de Shannon, peut rendre compte de ce même exemple en considérant l'information comme abstraite, et nous discutons des définitions existantes de l’information qui sont compatibles avec cette approche. (shrink)

Introduction and translation of “The Four Phases of Philosophy” by Franz Brentano.

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...) future persons, and to current persons in low-lying and developing countries, by way of their impacts on climate change. When it comes to such large-scale harms, it's easy for the individual to feel helpless. Even if she sincerely wishes things were otherwise, she may wonder what she could possibly do to make them so. In this paper I briefly explore several promising avenues for generating duties in individuals to consume ethically, and develop one in particular: that an individual ought to signal her commitments to others, as a first step in collectivizing to act against unjust global labour practices. (shrink)

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

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Chalmers, responding to Braun, continues arguments from Chalmers for the conclusion that Bayesian considerations favor the Fregean in the debate over the objects of belief in Frege’s puzzle. This short paper gets to the heart of the disagreement over whether Bayesian considerations can tell us anything about Frege’s puzzle and answers, no, they cannot.

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)