Adam Smith sought to explain the persistence of slavery as an institution in Wealth of Nations and Lectures on Jurispridence. In order to accomplish this he also drew on arguments he had developed in the Theory of Moral Sentiments. The result was a sophisticated explanation which bridged economic, psychological, and moral considerations. After presenting Smith’s explanation I will consider a discussion of the moral wrong of slavery in Ottobah Cugoano, the author of the incisive criticism of the slave (...) trade Thoughts and Sentiments on the Evil of Slavery (1787). I will suggest that Cugoano’s account of what is morally wrong in slavery shows an important lacuna in Smith‘s views. (shrink)

Commentators such as Kemp Smith (1941), Mendelbaum (1974), and Bricke (1980) have taken the distinctions of reason to pose either a counterexample to or a limitation of scope on the Separability Principle. This has been convincingly addressed by various accounts such as Garrett (1997), Hoffman (2011), and Baxter (2011). However, I argue in this paper that there are two notions of ‘distinction of reason’, one between particular instantiations (token distinctions of reason) and one between general ideas (type distinctions (...) of reason). Discussion of the distinctions of reason in the secondary literature has without fail focused on token distinctions of reason, but I will argue that type distinctions of reason prove problematic for Hume’s Separability Principle. I find a way around this problem that is consonant with Hume’s account of general ideas, but which can hardly be said to be an account which he explicitly or even implicitly endorsed. (shrink)

The ancient theory of substance and accident is supposed to make sense of complex unities in a way that respects both their unity and their complexity. On Hume’s view such complex unities are only fictitiously unities. This result follows from his thoroughgoing critique of the theory of substance. I will characterize the theory Hume is critiquing as it is presented in Locke, presupposing what Bennett calls the “Leibnizian interpretation.” Locke uses the word ‘substance’ in two senses. Call substance in the (...) first sense “individual substance” and in the second sense “pure substance.” I will discuss the seven main parts of Hume’s view: (I) that we have no idea of pure substance, (II) that there is no complex individual substance, except in a loose sense, (III) that the fiction of complex individual substance arises in a way parallel to that of the fiction of identity through time, and (IV) results in the fiction of pure substance, (V) that simple qualities and perceptions satisfy the definition of individual substance, (VI) that there is no such thing as inherence, and (VII) that there is no such thing as pure substance. Hume’s views on substance are often mentioned without being discussed in detail. Kemp Smith, Stroud, and Garrett, for example, mostly summarize various claims of Hume in the course of expounding on his theory of the idea of personal identity. In contrast, I will attempt to present a systematic treatment of Hume on substance as a refutation of Locke. (shrink)

Weak particularism about reasons is the view that the normative valency of some descriptive considerations varies, while others have an invariant normative valency. A defence of this view needs to respond to arguments that a consideration cannot count in favour of any action unless it counts in favour of every action. But it cannot resort to a global holism about reasons, if it claims that there are some examples of invariant valency. This paper argues for weak particularism, and presents a (...) framework for understanding the relationships between practical reasons. A central part of this framework is the idea that there is an important kind of reason-a 'presumptive reason'-which need not be conclusive, but which is neither pro tanto nor prima facie. /// [Richard Holton] Should particularists about ethics claim that moral principles are never true? Or should they rather claim that any finite set of principles will not be sufficient to capture ethics? This paper explores and defends the possibility of embracing the second of these claims whilst rejecting the first, a position termed 'principled particularism'. The main argument that particularists present for their position-the argument that holds that any moral conclusion can be superseded by further considerations-is quite compatible with principled particularism; indeed, it is compatible with the idea that every true moral conclusion can be shown to follow deductively from a finite set of premises. Whilst it is true that these premises must contain implicit ceteris paribus clauses, this does not render the arguments trivial. On the contrary, they can do important work in justifying moral conclusions. Finally the approach is briefly applied to the related field of jurisprudence. (shrink)

What is involved in weighing normative reasons against each other? One attractive answer offers us the following Simple Picture: a fact is a reason for action when it bears to an action the normative relation of counting in its favour; this relation comes in different strengths or weights; the weights of the reasons for and against an action can be summed; the reasons for performing the action are sufficient when no other action is more strongly supported, overall; the reasons are (...) decisive when it is most strongly supported; one ought to perform the action there is most reason to perform; rational deliberation is weighing reasons correctly; and acting rationally is doing what one has sufficient reasons to do. This chapter investigates various ways in which, on examination, this Simple Picture appears to require modification and refinement. It examines some of the ways in which talk of the weight of a reason may need improvement, looks more closely at the relationship between reasons and rationality, and asks whether there are ways in which a reason can be defeated which are not kinds of outweighing. The conclusion is that while in some respects the Simple Picture does need to be corrected, in others the jury is out. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

Aristotle claims that in some extenuating circumstances, the correct response to the wrongdoer is sungnōmē rather than blame. Sungnōmē has a wide spectrum of meanings that include aspects of sympathy, pity, fellow-feeling, pardon, and excuse, but the dominant interpretation among scholars takes Aristotle’s meaning to correspond most closely to forgiveness. Thus, it is commonly held that the virtuous Aristotelian agent ought to forgive wrongdoers in specific extenuating circumstances. Against the more popular forgiveness interpretation, I begin by defending a positive account (...) of sungnōmē as the correct judgment that a wrongdoer deserves excuse since she was not blameworthy. I then argue that since sungnōmē is merited on the grounds of fairness, this shows that both the forgiveness interpretation and a third, alternative interpretation of sungnōmē as sympathy mischaracterize both the justification for sungnōmē and its nature. Moreover, I argue that Aristotle not only lacks an account of forgiveness but in fact, that his account of blame is incompatible with forgiveness altogether. (shrink)

There have been several recent lawsuits in which problem gamblers (or those affected by problem gambling) have sued casinos or other gaming companies for damages relating to bankruptcies, suicides, and other negative consequences of compulsive gambling. Although the legal cases have been decided in favor of the gaming companies, it can seem as though there is a moral residue in some of these cases: perhaps some of the actions of the gaming companies, though legal, have been morally problematic. This case (...) invites students to explore this possibility by introducing them to the facts surrounding the lawsuits and highlighting some of the most salient moral considerations. Students will also be asked to reflect on the public policy implications, if any, of their findings. (shrink)

Are the wishes of the dead more important than the needs of the living? This question is prompted by consideration of the Hershey Trust Company, a perpetual charitable trust that not only owns and operates the Milton Hershey School in Pennsylvania, but also owns a controlling interest in various Hershey-related for-profit entities. This unusual arrangement, and the conditions under which it was formed, have produced a situation in which a small, private boarding school for low-income students has an endowment of (...) $12 billion (in addition to its other corporate and real estate interests). The trust has been operating according to its founder’s wishes for decades, but some have wondered whether its resources could be put to better use for more urgent needs. This case will invite students to consider the question of how we should weigh the needs of the living against the wishes of the dead. (shrink)

Ever since the hard problem of consciousness (Chalmers, 1996, 1995) first entered the scene in the debate over consciousness many have taken it to show the limitations of a scientific or naturalist explanation of consciousness. The hard problem is the problem of explaining why there is any experience associated with certain physical processes, that is, why there is anything it is like associated with such physical processes? The character of one’s experience doesn’t seem to be entailed by physical processes and (...) so an explanation which can overcome such a worry must (1) explain how physical processes give rise to experience (explain the entailment), (2) give an explanation which doesn’t rely on such physical processes, or (3) show why the hard problem is misguided in some sense. Recently, a rather ambitious and novel theory of consciousness has entered the scene – Integrated Information Theory (IIT) of Consciousness (Oizumi et al., 2014; Tononi, 2008; Tononi et al., 2016) – and proposes that consciousness is the result of a specific type of information processing, what those developing the theory call integrated information. The central aim of this dissertation is to philosophically investigate IIT and see whether it has the ability to overcome the hard problem and related worries. I then aim to use this philosophical investigation to answer a set of related questions which guide this dissertation, which are the following: Is it possible to give an information-theoretic explanation of consciousness? What would the nature of such an explanation be and would it result in a novel metaphysics of consciousness? In this dissertation, I begin in chapter one by first setting up the hard problem and related arguments against the backdrop of IIT (Mindt, 2017). I show that given a certain understanding of structural and dynamical properties IIT fails to overcome the hard problem of consciousness. I go on in chapter two to argue that a deflationary account of causation is the best view for IIT to overcome the causal exclusion problem (Baxendale and Mindt, 2018). In chapter three, I explain IIT’s account of how the qualitative character of our experience arises (qualia) and what view of intentionality (the directedness of our mental states) IIT advocates. I then move on in chapter four to show why the hard problem mischaracterizes structural and dynamical properties and misses important nuances that may shed light on giving a naturalized explanation of consciousness. In the last and fifth chapter, I outline a sketch of a novel metaphysics of consciousness that takes the conjunction of Neutral Monism and Information-Theoretic Structural Realism to give what I call Information-Theoretic Neutral-Structuralism. (shrink)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

The Ockhamist claims that our ability to do otherwise is not endangered by God’s foreknowledge because facts about God’s past beliefs regarding future contingents are soft facts about the past—i.e., temporally relational facts that depend in some sense on what happens in the future. But if our freedom, given God’s foreknowledge, requires altering some fact about the past that is clearly a hard fact, then Ockhamism fails even if facts about God’s past beliefs are soft. Recent opponents of Ockhamism, including (...) David Widerker and Peter van Inwagen, have argued along precisely these lines. Their arguments, if successful, would undermine Ockhamism while avoiding the controversy over the alleged softness of facts about God’s past beliefs. But these arguments do not succeed. The past facts they rely on must be clear and uncontroversial examples of hard facts about the past, and these facts must be such that an ability to refrain from the relevant future action implies an ability to alter the relevant hard fact. We demonstrate the flaw in these arguments by showing how they rely on past facts that do not satisfy these criteria. The Ockhamist may have troubles, but this type of argument is not one of them. (shrink)

What requirements does morality impose on us in relation to climate change? This question can be asked of individuals, of the entire global population, and of groups of various sizes in between. Given the case for accepting that we all collectively ought to be causing less climate-affecting pollution than we do, what follows from that about the moral status of the actions of members of the larger group? I examine two main ways in which moral requirements on group members can (...) derive from requirements that apply to the larger group. But neither of them seems to apply to the case of climate-affecting pollution. Perhaps this is a case where we together act wrongly, although no-one’s contribution to our doing so is wrong. (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)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

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

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Game theory involves deliberating about what to do in light of what other people are likely to do. One of the central frameworks of game theory is the prisoner’s dilemma, in which participants who make rational choices end up in suboptimal outcomes. Using the prisoner’s dilemma to model competition between firms sets the stage for a new and promising approach to business ethics: the market failures approach.

Causalists about explanation claim that to explain an event is to provide information about the causal history of that event. Some causalists also endorse a proportionality claim, namely that one explanation is better than another insofar as it provides a greater amount of causal information. In this chapter I consider various challenges to these causalist claims. There is a common and influential formulation of the causalist requirement – the ‘Causal Process Requirement’ – that does appear vulnerable to these anti-causalist challenges, (...) but I argue that they do not give us reason to reject causalism entirely. Instead, these challenges lead us to articulate the causalist requirement in an alternative way. This alternative articulation incorporates some of the important anti-causalist insights without abandoning the explanatory necessity of causal information. For example, proponents of the ‘equilibrium challenge’ argue that the best available explanations of the behaviour of certain dynamical systems do not appear to provide any causal information. I respond that, contrary to appearances, these equilibrium explanations are fundamentally causal, and I provide a formulation of the causalist thesis that is immune to the equilibrium challenge. I then show how this formulation is also immune to the ‘epistemic challenge’ – thus vindicating (a properly formulated version of) the causalist thesis. (shrink)

There can be situations in which, if I contribute to a pool of resources for helping a large number of people, the difference that my contribution makes to any of the people helped from the pool will be imperceptible at best, and maybe even non-existent. And this can be the case where it is also true that giving the same amount directly to one of the intended beneficiaries of the pool would have made a very large difference to her. Can (...) non-contribution to the pool be morally justified on this ground? I argue that it cannot. For, first, this line of thought leaves unaffected any reasons for holding that failing to perform the direct action of benefiting someone greatly would be wrong. But the pooling system of helping people is often better than a system separating the help which is given — better because of the perceptible difference it makes to its beneficiaries. If so, failing to contribute to the pool will be at least as wrong as failing to have helped directly would have been. The paper clarifies and defends an argument of this form, showing how it can be formulated in a way that avoids apparent counterexamples, and identifying the assumptions on which it rests. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

Edwards’s views on the nature of the human will demonstrate his unique ability to unite philosophical rigor and theological fervor. Edwards was a staunch defender of the Reformed doctrines of absolute divine sovereignty and meticulous providence, but he was also a proponent of the intellectual tools and methods of early modern philosophy (and of John Locke in particular). His ultimate statement of his doctrinal position, Freedom of the Will, is the masterful result of these dual commitments.

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

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

Moral discourse contains judgements of two prominent kinds. It contains deontic judgements about rightness and wrongness, obligation and duty, and what a person ought to do. As I understand them, these deontic judgements are normative: they express conclusions about the bearing of normative reasons on the actions and other responses that are available to us. And it contains evaluative judgements about goodness and badness. Prominent among these are the judgements that evaluate the quality of our responsiveness to morally relevant reasons. (...) We have a rich vocabulary for making such evaluations – our vocabulary of aretaic terms. Aretaic terms are those which can be used to attribute virtues: terms such as “kind”, “honest”, “fair”, “tolerant” and “reliable”. However, while they can be used to attribute virtues, they have other uses too; and they can be applied not only to persons but also to various states of persons, to actions and other responses, and to patterns of response. In this paper, I offer an account of the relationship between some of the principal uses of aretaic terms; and I show how a useful taxonomy of moral virtues can be generated from the thought that these are ways of being well oriented to morally relevant reasons. (shrink)

Local miracle compatibilists claim that we are sometimes able to do otherwise than we actually do, even if causal determinism obtains. When we can do otherwise, it will often be true that if we were to do otherwise, then an actual law of nature would not have been a law of nature. Nevertheless, it is a compatibilist principle that we cannot do anything that would be or cause an event that violates the laws of nature. Carl Ginet challenges this nomological (...) principle, arguing that it is not always capable of explaining our inability to do otherwise. In response to this challenge, I point out that this principle is part of a defense against the charge that local miracle compatibilists are committed to outlandish claims. Thus it is not surprising that the principle, by itself, will often fail to explain our inability to do otherwise. I then suggest that in many situations in which we are unable to do otherwise, this can be explained by the compatibilist’s analysis of ability, or his criteria for the truth of ability claims. Thus, the failure of his nomological principle to explain the falsity of certain ability claims is no strike against local miracle compatibilism. (shrink)

This case examines the rise and fall of WeWork—a company that experienced one of the most dramatic changes of fortune in technology company history. For several years, WeWork was a Silicon Valley darling, growing at breakneck speed with visionary Adam Neumann at the helm. By some estimates, Neumann’s company was worth $47 billion in January of 2019. But when the company filed paperwork in preparation for going public later that year, investors balked at the details revealed in the documents: billions (...) of dollars in losses and lots of questionable behavior on the part of Neumann (including numerous conflicts of interest involving his personal business dealings). The IPO was postponed and later withdrawn; Neumann was forced to step down as CEO; and by May of 2020 the company’s valuation had dropped to $3 billion. Exploring this recent history will provide an opportunity to ask what lessons can be drawn from the rise and fall of WeWork, and from the economic and social context that enabled its growth. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

After an intensive 4-year process, the World Medical Association (WMA) has revised its International Code of Medical Ethics (ICoME). In their report outlining this process, Parsa-Parsi et al not only describe how the WMA sought to ‘cultivat[e] international agreement’ on a ‘global medical ethos’, but also outline the philosophical framework of the ICoME: how the WMA, as the ‘global representation of the medical profession’, created and revised the ICoME through the process of international professional self-regulation.1 However, there is a significant (...) tension to be found in this framework—one which contrasts the international scope of the ICoME with the supposed source of its legitimacy. Here, we seek to characterise this tension and the doubt which it casts on the legitimacy of the ICoME. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

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

Traditional views about God and about deliberation seem to imply that we need a deliberation restriction on the concept of divine omniscience. I will argue, however, that this deliberation restriction is both irrelevant and unnecessary. It is irrelevant because there is no time at which God needs to deliberate; and it is unnecessary because even if God does deliberate, it’s possible for him to do so while knowing what the results of that deliberation will be. And because this possibility of (...) deliberating despite knowing the results holds for deliberation in general, my argument provides useful (and perhaps surprising) results not only for discussions of the divine attributes, but also for broader discussions of deliberation itself. (shrink)

A familiar part of ordinary moral thought is this idea: when other people are doing something worthwhile together, there is a reason for you to join in on the same terms as them. Morality does not tell you that you must always do this; but it exerts some pressure on you to join in. Suppose we take this idea seriously: just how should it be developed and applied? More particularly, just which groups and which actions are the ones with respect (...) to which you have participatory moral reasons? And just when is it wrong not to join in? I present answers to these questions, and discuss the implications—including for joint action on a very large scale, like global efforts to address climate change or fight a pandemic. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In August 2017, Google executives found themselves in a difficult position. An internal memo written by a disgruntled software engineer, James Damore, had just gone viral. In this memo, Damore claimed that the relatively small number of women in the tech industry was partly due to biological factors, and that many of Google’s diversity efforts were therefore counterproductive. The contents of this memo were offensive to many (and thus were having a negative impact on the overall workplace environment), but the (...) executives were aware that the wrong reaction to it would at least partially vindicate Damore’s claims about the lack of open discussion at Google. In the end, after two days of controversy, Google leadership decided to fire Damore on the grounds that he had violated the company’s code of conduct. This case gives students an opportunity to explore the numerous issues raised by Damore’s memo and the controversy surrounding it. Did Google handle this case properly? Was firing Damore the right thing to do? How could the situation have been handled more effectively? (shrink)

According to the argument from gratuitous evil, if God were to exist, then gratuitous evil wouldn’t; but gratuitous evil does exist, so God doesn’t. We can evaluate different views of divine providence with respect to the resources they are able to bring to bear when encountering this argument. By these lights, theological determinism is often seen as especially problematic: the determinist is seen as having an impoverished set of resources to draw from in her attempts to respond to the argument (...) from gratuitous evil. In particular, there is an important resource – an appeal to free will – that many have claimed is unavailable to the determinist. I argue that the determinist does not in fact suffer from this particular resource deficit. I do so by examining some recent work on determinist responses to the problem of evil, analyzing some of the ways in which they fall short, and proposing a new response that is informed by those shortcomings. This new response is built on an appeal to the reactive attitudes. (shrink)

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)

Standard ways of conceptualizing moral development and measuring pedagogical interventions in ethics classes privilege the growth of moral judgment over moral sensitivity, moral motivation, and moral habits by too often conflating improvement in moral judgment with holistic moral development. I argue here that if we care about students’ construction and cultivation of their ethical selves, our assessment design principles ought to take seriously the transformative possibilities of philosophy as a way of life and be based on a more robust and (...) holistic account of moral development. I illustrate these principles of assessment design through an examination of the Character Project, which I created to help students engage in their own deliberate ethical transformation through self-directed, individualized, and concentrated practice. Finally, I conclude with a discussion about how to appropriately and fairly assess this kind of deeply personal learning. (shrink)

For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two other seminal figures in this development: H.L.A. Hart (...) and John Rawls. We show that all three thinkers tend to assume that there is but one type of normativity within the realm of social institutions – roughly, the sort of normativity that is involved in following the results of chess – and that they thereby neglect features that are of crucial significance for an adequate understanding of social reality. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Should we kill animals to save animals? This question lies at the heart of this case study. Sovereign nations have an interest in protecting and conserving their natural resources, and in particular their distinctive flora and fauna. As they seek to promote these interests, they inevitably face the economic question of how they are going to finance their conservation efforts. One way of answering this question is to engage in the practice of selling big game hunting licenses and using the (...) revenues to fund conservation programs. This strategy is counterintuitive (and to some, morally repellent); but it has a partial track record of success in places such as Namibia, South Africa, and the United States. Despite its successes, there are some who believe that the moral objections to such a strategy outweigh any potential benefits. This case study provides the student with an opportunity to explore the tension between the desire to save endangered animals and the possibility that the best way to do that involves killing some of them. (shrink)

For Aristotle, some wrongdoers do not deserve blame, and the virtuous judge should extend sungnōmē, a correct judgment about what is equitable, under the appropriate excusing circumstances. Aristotle’s virtuous judge, however, does not forgive; the wrongdoer is excused from blame in the first place, rather than being forgiven precisely because she is blameworthy. Additionally, the judge does not fail to blame because she wishes to be merciful or from natural feeling, but instead, because that is the equitable action to take (...) under the circumstances. Moreover, while Aristotle does claim in his discussions of the virtues of megalopsychia and praotēs that the virtuous person will sometimes fail to become angry at blameworthy wrongdoers, Aristotle’s reasons for repudiating anger or forestalling blame have little to do with the sorts of reasons that one would or could be forgiving for. Although an Aristotelian virtuous agent does let go of anger for her own reasons, she does not forgive. As a result, I argue that since Aristotle’s account of equity entails that forgiveness is positively vicious, forgivingness is not merely a virtue left out of Aristotle’s account, but is in fact incompatible with his account. (shrink)

The failure to understand the needs, beliefs, and values of others is widely blamed on a lack of empathy, which has been touted in recent years as the necessary ingredient for bringing us together and ultimately for tackling issues of social justice and harmony. In this essay, I explore whether empathy really can serve the role it has been tasked with. To answer this question, I will first identify what empathy is and why its champions believe it plays such an (...) essential role in social life. With this in mind, I contend that promoting empathy on its own may make solidarity among diverse populations more difficult to achieve and undermine social reconciliation. Instead, I argue for a different approach that begins with acknowledging our self-oriented perspective and how it shapes what we see, appreciate, and interpret, before turning to others with a kind of loving attention. Unlike empathy, loving attention allows us to see others as they really are, not as we imagine we would be in their shoes, and is that kind of perception that is necessary for bridging divides and building solidarity in our contemporary world. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Examining Seneca’s account of friendship produces an interpretative puzzle: if the good of the Stoic sage is already both complete and self-sufficient, how can friendship be a good? I reject the solution that friendship is simply a preferred indifferent instead of a good and argue that though Seneca’s account can consistently explain both why friendship’s nature as a good does not threaten the completeness or the self-sufficiency of the sage, Stoic friends must choose between intimate friendships that leave them vulnerable (...) or impersonal friendships that lack intimacy but do not undermine their happiness. The consistent Stoic must choose the latter, but I argue that this conflict shows why we ought to reject the Stoic model of friendship. (shrink)

In the one-for-one business model, a purchaser of, for example, a pair of shoes simultaneously purchases a pair of shoes for a child in need. This model, popularized by TOMS shoe company in 2006, has been remarkably successful. The driving force behind the success is most likely the emotional appeal of the one-for-one idea. The TOMS model has been criticized, however—not just for being less effective than advertised, but for arguably doing more harm than good. Whether or not this latter (...) charge is true, the TOMS story serves as an illustrative starting point for an exploration of the ways in which commonsense thinking about charity and philanthropy is often wrong. Examining these criticisms will set the stage for an examination of the influential “effective altruism” movement and invite the reader to think more deeply about different ways of doing good in the world. (shrink)