In "Rational Capacities" Michael Smith outlines the sense of capacity he believes to be required before blame is appropriate. I question whether this sense of capacity is required. In so doing, I consider different ways in which blame might be conditioned.

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (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)

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)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

In the classical Turing test, participants are challenged to tell whether they are interacting with another human being or with a machine. The way the interaction takes place is not direct, but a distant conversation through computer screen messages. Basic forms of interaction are face-to-face and embodied, context-dependent and based on the detection of reciprocal sensorimotor contingencies. Our idea is that interaction detection requires the integration of proprioceptive and interoceptive patterns with sensorimotor patterns, within quite short time lapses, so that (...) they appear as mutually contingent, as reciprocal. In other words, the experience of interaction takes place when sensorimotor patterns are contingent upon one’s own movements, and vice versa. I react to your movement, you react to mine. When I notice both components, I come to experience an interaction. Therefore, we designed a “minimal” Turing test to investigate how much information is required to detect these reciprocal sensorimotor contingencies. Using a new version of the perceptual crossing paradigm, we tested whether participants resorted to interaction detection to tell apart human from machine agents in repeated encounters with these agents. In two studies, we presented participants with movements of a human agent, either online or offline, and movements of a computerized oscillatory agent in three different blocks. In each block, either auditory or audiovisual feedback was provided along each trial. Analysis of participants’ explicit responses and of the implicit information subsumed in the dynamics of their series will reveal evidence that participants use the reciprocal sensorimotor contingencies within short time windows. For a machine to pass this minimal Turing test, it should be able to generate this sort of reciprocal contingencies. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

Donald Davidson opens ‘Actions, Reasons, and Causes’ by asking, ‘What is the relation between a reason and an action when the reason explains the action by giving the agent's reason for doing what he did?’ His answer has generated some confusion about reasons for action and made for some difficulty in understanding the place for the agent's own reasons for acting, in the explanation of an action. I offer here a different account of the explanation of action, one that, though (...) minimal and formal, preserves the proper role for the agent's own reasons for acting. (shrink)

A good number of people currently thinking and writing about reasons identify a reason as a consideration that counts in favor of an action or attitude.1 I will argue that using this as our fundamental account of what a reason is generates a fairly deep and recalcitrant ambiguity; this account fails to distinguish between two quite different sets of considerations that count in favor of certain attitudes, only one of which are the “proper” or “appropriate” kind of reason for them. (...) This ambiguity has been the topic of recent discussion, under the head “the wrong kind of reasons problem.”2 I will suggest that confusion about “the wrong kind of reason” will be dispelled by changing our account of what a reason is. While I agree both that reasons are considerations and that certain.. (shrink)

Many assume that we can be responsible only what is voluntary. This leads to puzzlement about our responsibility for our beliefs, since beliefs seem not to be voluntary. I argue against the initial assumption, presenting an account of responsibility and of voluntariness according to which, not only is voluntariness not required for responsibility, but the feature which renders an attitude a fundamental object of responsibility (that the attitude embodies one’s take on the world and one’s place in it) also guarantees (...) that it could not be voluntary. It turns out, then, that, for failing to be voluntary, beliefs are a central example of the sort of thing for which we are most fundamentally responsible. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

A common line of thought claims that we are responsible for ourselves and our actions, while less sophisticated creatures are not, because we are, and they are not, self-aware. Our self-awareness is thought to provide us with a kind of control over ourselves that they lack: we can reflect upon ourselves, upon our thoughts and actions, and so ensure that they are as we would have them to be. Thus, our capacity for reflection provides us with the control over ourselves (...) that grounds our responsibility. I argue that this thought is subtly, but badly, confused. It uses, as its model for the control that grounds our responsibility, the kind of control we exercise over ordinary objects and over our own voluntary actions: we represent to ourselves what to do or how to change things, and then we bring about that which we represent. But we cannot use this model to explain our responsibility for ourselves and our actions: if there is a question about why or how we are responsible for ourselves and our actions, it cannot be answered by appeal to a sophisticated, self-directed action. There must be some more fundamental account of how or why we are responsible. I replace the usual account with a novel but natural view: responsible mental activity can be modeled, not as an ordinary action, but as the settling of a question. This shift will require abandoning the tempting but troublesome thought that responsible activity involves discretion and awareness—which, I argue, we must abandon in any case. (shrink)

I suggest that Fischer concedes too much to the consequence argument when he grants that we may not make a difference. I provide a broad sketch of (my take on) the dispute between compatibilists and incompatibilists, while suggesting that some of the discussion may have confused the freedom required for moral responsibility with a very different notion of autonomy. I introduce that less usual notion of autonomy and suggest that those who are autonomous, in this sense, do make a difference.

In this paper I consider fairness of blaming a wrongdoer. In particular, I consider the claim that blaming a wrongdoer can be unfair because blame has a certain characteristic force, a force which is not fairly imposed upon the wrongdoer unless certain conditions are met--unless, e.g., the wrongdoer could have done otherwise, or unless she is someone capable of having done right, or unless she is able to control her behavior by the light of moral reasons. While agreeing that blame (...) has a characteristic force, I am skeptical of this charge of unfairness. My skepticism concerns itself less with the particular conditions of fairness proposed than with the idea that blame can be rendered unfair by its characteristic force. If to blame a person were simply to perform certain intentional actions, then, as we will see, blame could be rendered unfair by its force. But to blame a person is not just to act in certain ways. It is, at least in large part, to make certain judgments or adopt certain attitudes. However, it is unclear how these attitudes or judgments carry "force"? and also unclear whether they can be rendered unfair by their force. Examining these issues, I will suggest that much of the force of blame is found in a set of judgments--most centrally, the judgment that one person failed to show proper regard for others. But, I will argue, once it is granted that such judgments are true, their characteristic force cannot render them unfair. (shrink)

I argue to a conclusion I find at once surprising and intuitive: although many considerations show trust useful, valuable, important, or required, these are not the reasons for which one trusts a particular person to do a particular thing. The reasons for which one trusts a particular person on a particular occasion concern, not the value, importance, or necessity of trust itself, but rather the trustworthiness of the person in question in the matter at hand. In fact, I will suggest (...) that the degree to which you trust a particular person to do a particular thing will vary inversely with the degree to which you must rely, for the motivation or justification of your trusting response, on reasons that concern the importance, or value, or necessity of having such a response. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

There seems to be widespread agreement that to be responsible for something is to be deserving of certain consequences on account of that thing. Call this the “merited-consequences” conception of responsibility. I think there is something off, or askew, in this conception, though I find it hard to articulate just what it is. The phenomena the merited-consequences conception is trying to capture could be better captured, I think, by noting the characteristic way in which certain minds can rightly matter to (...) other such minds—the way in which certain minds can carry a certain kind of importance, made manifest in certain sorts of responses. Mattering, not meriting, seems to me central. However, since I cannot yet better articulate an alternative, I continue in the merit-consequences framework. I focus on a particular class of consequences: those that are non-voluntary, in a sense explained. The non-voluntariness of these reactions has two important upshots. First, questions about their justification will be complex. Second, they are not well thought of as consequences voluntarily imposed upon the wrongdoer by the responder. By focusing on merited consequences and overlooking non-voluntariness, we risk misunderstanding the significance of moral criticism and of certain reactions to moral failure. (shrink)

I first present what Peter Strawson calls his “Social Naturalism,” as applied to ethics. I then briefly present the way in which his Naturalism allows Strawson to resist skepticism about moral responsibility and free will, as argued in “Freedom and Resentment.” His way of resisting this kind of skepticism opens his Naturalism to another challenge: it can seem objectionably relativistic. I have provided a response to this challenge, on Strawson’s behalf, in the final chapter of my _Freedom, Resentment, and the (...) Metaphysics of Morals_ (2020). In this paper I expand upon that response—in particular, on the way in which the introduction of admittedly contested ideals might provide sufficient critical purchase to avoid objectionable relativism while remaining broadly naturalistic. (shrink)

A moral requirement R1 is said to be lexically prior to a moral requirement R2 just in case we are morally obliged to uphold R1 at the expense of R2 – no matter how many times R2 must be violated thereby. While lexical priority is a feature of many ethical theories, and arguably a part of common sense morality, attempts to model it within the framework of decision theory have led to a series of problems – a fact which is (...) sometimes spun as a ‘decision theoretic critique’ of lexical priority. In this paper, I develop an enriched decision theoretic framework that is capable of modelling lexical priority while avoiding all extant problems. This will involve introducing several new ingredients into the standard decision theoretic framework, including multidimensional utilities, de minimis risks, and the means to represent two different conceptions of risk. (shrink)

According to ‘Excluders’, descriptive uncertainty – but not normative uncertainty – matters to what we ought to do. Recently, several authors have argued that those wishing to treat normative uncertainty differently from descriptive uncertainty face a dependence problem because one's descriptive uncertainty can depend on one's normative uncertainty. The aim of this paper is to determine whether the phenomenon of dependence poses a decisive problem for Excluders. I argue that existing arguments fail to show this, and that, while stronger ones (...) can be found, Excluders can escape them. (shrink)

This chapter presents two contrasting pictures of the will. On the first, “the will” is a psychological structure or module within a person that originates spontaneous or endogenous activity, independently of external influence. On the second, “the will” is that collection of ordinary states of mind (cares, concerns, beliefs, desires, commitments, fears, etc.) that generates intentional, or voluntary, or responsible activity—it is the functioning together of those aspects of mind that account for human activity. A challenge is posed for each. (...) The challenge for the first is to say how the outputs of this module are the activity of the person. The challenge for the second is to say how psychological activity that might be entirely explained by a person’s history and environment can nonetheless be free and responsible activity. The replies take up an important question about the role of consciousness, in each picture. (shrink)

I here defend an account of the will as practical reason —or, using Kant's phrase, as " reason in its practical employment"—as against a view of the will as a capacity for choice, in addition to reason, by which we execute practical judgments in action. Certain commonplaces show distance between judgment and action and thus seem to reveal the need for a capacity, in addition to reason, by which we execute judgment in action. However, another ordinary fact pushes in the (...) other direction: the activities of the will are activities for which the person is answerable in a very particular sort of way. This answerability is most easily understood if willing involves settling a question. Settling a question seems to be a capacity of reason. Thus it can seem that activities of will are activities of our capacity for reasoning. I will suggest that we can accommodate the commonplaces while still understanding the will as reason in its practical employment, by abandoning the assumption that practical reasoning concludes in a judgment. Rather, reasoning which concludes in a judgment—reasoning directed at the question of whether p—is theoretical reasoning. In its practical employment, reason is directed at the question of whether to x; it concludes, not in a judgment about x-ing, but rather in an intention to x. (shrink)

In 1982, when T. M. Scanlon published “Contractualism and Utilitarianism,” he noted that, despite the widespread attention to Rawls’ A Theory of Justice, the appeal of contractualism as a moral theory had been under appreciated. In particular, the appeal of contractualism’s account of what he then called “moral motivation” had been under appreciated.1 It seems to me that, in the intervening quarter century, despite the widespread discussion of Scanlon’s work, the appeal of contractualism, in precisely this regard, has still been (...) under appreciated—even though Scanlon makes what he once called “moral motivation” central, throughout his work. My first aim, then, is to do my best to draw out and make vivid this appeal. I will do this by first considering the two questions that Scanlon thinks must be addressed by any moral theory, what he once called “the question of subject matter” and “the question of motivation.” I will spend some time first locating and explicating the second question, of motivation, and then displaying Scanlon’s answer to it—it is this answer which provides contractualism with its under-appreciated appeal. I will then return to the question of subject matter—which will, by that point, have been revealed as not wholly distinct from the question of motivation, as Scanlon understands it. But it is as an answer to this question that Scanlon’s theory is most often.. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Many think of reasons as facts, propositions, or considerations that stand in some relation (or relations) to attitudes, actions, states of affairs. The relation may be an explanatory one or a “normative” one—though some are uncomfortable with irreducibly “normative” relations. I will suggest that we should, instead, see reasons as items in pieces of reasoning. They relate, in the first instance, not to psychological states or events or states of affairs, but to questions. That relation is neither explanatory nor “normative.” (...) If we must give it a label, we could call it “rational”—but that will mean, I think, only that the consideration bears on the question. By thus putting reasoning first, we not only avoid a handful of difficulties that have plagued thinking about reasons, but we also bring back to center-stage the importance of rational agency. (shrink)

I here press an often overlooked question: Why does the fairness of a sanction require an adequate opportunity to avoid it? By pressing this question, I believe I have come to better understand something that has long puzzled me, namely, what philosophers (and others) might have in mind when they talk about “true moral responsibility,” or the “condemnatory force” of moral blame, or perhaps even “basic desert.” In presenting this understanding of “condemnation” or of “basic desert,” I am presenting an (...) idea that I do not, myself, endorse—one to which I am, myself, opposed. I present and defend it, hoping that, if what I say accurately captures what people have in mind, it will also show how condemnation or desert, in this sense, can be left behind. (shrink)

Recently, there has been an insurgence of corporations that bioprospect in Third World countries (going into these areas in hopes of utilizing traditional knowledge about local natural resources so as to eventually develop a synthetic alternative that they can then market). Although this type of bioprospecting does not encounter the problem of depleting environmental resources, other problems arise. Two primary problems are: (1) determining who has legal ownership of these resources, and (2) who should share in the profits that were (...) derived, in part, from these resources. Despite the attention that these problems have received, there has been little attention focused on the issue that I believe underlies these problems -- the differing views of nature between corporations (who consider nature to be an individually owned resource) and Third World communities (many of whom consider nature to be a communally owned resource). In this paper, I present what I believe is an additional useful tool for policy makers in resolving the current problems regarding bioprospecting in Third World countries. The tool I have in mind is a set of method components that can be used as guidelines as well as a test for inclusiveness. To arrive at these components, I will look to James D. Proctor's methodological proposal for resolving conflicts between those with differing views of nature. Because he presents this methodology in a limited context (as a means of resolving the Ancient Forest debate), I will clarify and expand his methodology so as to arrive at a set of methods that I believe can be helpful in arriving at a fair global policy regarding bioprospecting in Third World countries. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (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)

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

This paper proposes an intermediate account of personhood, based on the capacity to participate in intersubjective interactions. We articulate our proposal as a reply to liberal and restrictive accounts, taking Mark Rowlands’ and Stephen Darwall’s proposals as contemporary representatives of each view, respectively. We argue that both accounts fall short of dealing with borderline cases and defend our intermediate view: The criteria of personhood based on the second-person perspective of mental state attribution. According to it, a person should be able (...) to participate in intersubjective interactions. We apply our proposal to the borderline cases of non-human primates and human infants. (shrink)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

I consider Paulina Sliwa’s fruitful account of “taking responsibility” as “owning the normative footprint” of a wrong. Unlike most, Sliwa approaches the topic without concern for what I call “responsible agency.” I raise the possibility that this is virtue. I then question whether the “footprint” is simply given with the wrong or whether it must instead be made determinate through subsequent interaction, perhaps through conversation. I next distinguish two different kinds of conversation: a cooperative negotiation and a low-level power struggle. (...) The later is often part of what I call “the blame game.” I suggest that the “blame” of the blame game is the blame of ordinary life, to be distinguished from the technical term in the current philosophical literature, and I give an account of it. I note that one may sometimes opt out of the blame game simply by owning a generous interpretation of the footprint, something Sliwa discusses. I note that doing so is sometimes, but not always, virtuous. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

For centuries it has been a mainstay of European and American moral thought that keeping promises—and the allied activity of upholding contracts—is one of the most important requirements of morality. On some historically powerful views the obligation to uphold promises or contracts not only regulates private relationships, but also provides the moral foundation for our duty to support and obey legitimate governments. Some theorists believe that the concept of keeping promises has gradually moved to center stage in European moral thought. (...) They see this movement as part of an historical shift from a moral conception in which an individual’s duties are mainly externally imposed and unalterable, to a conception in which duties are largely chosen by the individual. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

In this paper I defend an eudaimonistic reading of Spinoza’s ethical philosophy. Eudaimonism refers to the mainstream ethical tradition of the ancient Greeks, which considers happiness a naturalistic, stable, and exclusively intrinsic good. Within this tradition, we can also draw a distinction between weak eudaimonists and strong eudaimonists. Weak eudaimonists do not ground their ethical conceptions of happiness in complete theories of metaphysics, epistemology, or psychology. Strong eudaimonists, conversely, build their conceptions of happiness around an overall philosophical system that extends (...) far beyond ethics, while nevertheless being directed at the promotion of a happy life. I will show that Spinozistic happiness is not only naturalistic, stable, and exclusively intrinsically good, but that Spinoza is also a strong eudaimonist because his ethical account of happiness is incomprehensible without appeal to metaphysical, epistemological, and psychological doctrines. As well, I will explain how the apparent subjective and relativistic features of Spinoza’s ethics do not undermine the eudaimonistic reading, because both Spinoza and the ancient eudaimonists grant that the beliefs/feelings of the subject play a necessary (but insufficient) role in happiness as the highest good. (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)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

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

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

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