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

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

Critical theory has long resisted the notion that an “invisible hand” can operate within the real social dynamics of a free market. But despite the most radical desires of the socially critical imagination, the optimization of that “spontaneous order” or depersonalized way of ordering things known as “the economy” has become the dominant playing field and decisive electoral issue of modern politics. Within this broad contemporary context, Michel Foucault made a strange theoretical intervention that, to this day, continues to baffle (...) readers. During a lecture, he argued that Adam Smith’s invisible hand was, after all, truly and purposively, that is, for technical rather than ideological reasons, “invisible.” This article argues that there is a counter-positivism or tactical irony contained within the logic of such a controversial thesis; namely, that when one acknowledges that the principle of economic competition encourages an efficient self-organizing effect at all times, regardless of context, one is also immediately in a position to appreciate why the art of government should always maintain its political primacy over the spontaneous order of the market. (shrink)

Individualism or communalism? This is a very important question about how societies can live, develop, work and solve problems. Throughout history, this question has been considered from philosophical, sociological, anthropological, psychological, political, economic, and even theological or spiritual perspectives. Perhaps we will not find a solution, and the possibilities of reconciling these two concepts seem slim. Today, with Carolyn Smith-Morris' book, we approach the question from the experience of Indigenous communities. The title of the book is "Indigenous Communalism," but (...) the author will point out several times throughout the book that we cannot fully understand communalism without considering individualism. In her own words, the goal of this book “has been to initiate more overt attention to the individual and communal together, encapsulating (without resolving) the tensions that create human societies, and to value Indigenous communalism as the central feature of Indigeneity that it is” (Smith-Morris, 2020, p. 136). -/- ¿Individualismo o comunalismo? Esta es una pregunta muy importante sobre cómo las sociedades pueden vivir, desarrollarse, trabajar y resolver problemas. A lo largo de la historia, se ha reflexionado sobre este tema desde los puntos de vista filosófico, sociológico, antropológico, psicológico, político, económico, e incluso, teológico o espiritual. Quizás no encontremos ninguna solución y parecen pocas las posibilidades de conciliar estos dos conceptos. Hoy, con el libro de Carolyn Smith-Morris, que se titula en español Comunalismo indígena, abordamos la cuestión desde la experiencia de las comunidades indígenas. En esta línea, la autora señalará varias veces que no podemos entender plenamente el comunalismo sin tener en cuenta el individualismo. En sus propias palabras, se refiere a que su objetivo fue “iniciar un esfuerzo de atención más abierto a lo individual y lo comunal juntos, encapsulando (sin resolver) las tensio-nes que crean las sociedades humanas, y valorar el comunalismo indígena como la característica central de la indigeneidad que es” (Smith-Morris, 2020: 136). (shrink)

Can our beloved cats and dogs love us back? This chapter aims to find a satisfactory theory of love that substantiates the claim that they can. It begins by reconstructing and critically evaluating recent attempts by scientists to show that dogs can love humans back. Although these attempts are argued to be unsuccessful, it is further argued that they illuminate the need for an adequate theory of love and offer us some plausible ideas about love that direct us to two (...) recent philosophical theories of love that support the idea that dogs can love humans back. These two theories are discussed in detail before it is argued that dogs, but not cats, seem capable of loving humans under these theories. These theory-based defenses of the belief that dogs can love humans back are then criticized on the grounds that the theories they use are unsatisfactory because they fail to capture three central truths about love. This leads to a third theory of love that, after some friendly amendments, is argued to be a tentatively adequate theory that provisionally vindicates the claim that dogs, but not cats, can love humans back. (shrink)

This paper focuses on a recently articulated, emergentist conception of ethical naturalism and its commitment to causal efficacy, or the idea that moral properties have causal powers, along with its supporting commitment to moral causation. After I reconstruct the theory, I explain how it offers some interesting theoretical benefits to moral realists in virtue of its commitment to causal efficacy. Then, after locating some examples of moral causation in support of this commitment, I present and respond to five objections to (...) such causation, which all threaten to undermine this support. Lastly, I consider a very serious problem that the theory faces in virtue of positing emergent moral properties as responsible for moral causation – namely, the problem of downward moral causation. I describe this problem in detail and argue that, as it stands, it does not spell doom for the theory. (shrink)

It is common in metaethics today to draw a distinction between “naturalist” and “non-naturalist” versions of moral realism, where the former view maintains that moral properties are natural properties, while the latter view maintains that they are non-natural properties instead. The nature of the disagreement here can be understood in different ways, but the most common way is to understand it as a metaphysical disagreement. In particular, the disagreement here is about the reducibility of moral properties, where the “naturalists” maintain (...) that moral properties are in some way reducible to the lower-level natural properties on which they supervene, while the “non-naturalists” maintain that moral properties are sui generis and robustly irreducible. In this paper I present a novel version of realist ethical naturalism—a view that I call Emergentist Ethical Naturalism—that reveals this common way of understanding the distinction between naturalism and non-naturalism to be flawed by combining a commitment to ethical naturalism with a commitment to the sui generis and robustly irreducible nature of moral properties that typically defines non-naturalism. Then, after presenting the theory and addressing a few worries that one might have about it, I show how it offers some novel, emergence-based responses to the various supervenience challenges that plague moral realism and thereby gives the ethical naturalist a robustly non-reductive option for dealing with these challenges. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

This paper will attempt to assess the primary differences between what I take to be the two primary philosophical "traditions" in contemporary French philosophy, using Derrida (transcendence) and Deleuze (immanence) as exemplary representatives. The body of the paper will examine the use of these terms in three different areas of philosophy on which Derrida and Deleuze have both written: subjectivity, ontology, and epistemology. (1) In the field of subjectivity, the notion of the subject has been critiqued in two manners, either (...) by appealing either to the transcendence of the other (Levinas, Derrida) or to the immanent jlux of experience itself, in relation to which the Ego itself is trancendent (Deleuze, Foucault, Sartre, James). (2) In the field of ontology, a purely "immanent" ontology would be an ontology in which there is neither a "beyond" or an "otherwise" Being, nor "interruptions" in Being, both of which would require an appeal to a formal element of transcendence (Deleuze). Such a "transcendent" and aporetic structure, which can never appear or be present as such within Being, is what lies at the basis of the project of deconstruction, with its attendant aporias (Derrida). (3) This distinction, finally, finds parallels in Kant's epistemology, for whom the possible experience is conditioned by purely immanent criteria (Deleuze), whereas what goes beyond the limits of possible experience is transcendent (Derrida). Drawing on these three thread of analysis, the paper concludes with an assessment of what is at stake in the ethical differences between the two traditions. The question of "transcendence" is "What mast I do?", which is the question of morality (a duty or obligation that is beyond being, an "ought" beyond the "is"). The question of "immanence" is "What can I do?" (my power or capacity as an existing individual within being). For Levinas and Derrida, ethics precedes ontology because it is derived from an element of transcendence (the Other); for Deleuze, ethics is ontology because it is derived from the immanent relation of beings to Being at the level of their existence (Spinoza). (shrink)

This paper addresses the important questions of whether love is possessive and, if so, in what way is it possessive and in what ways is it not. It argues that love is possessive in the way that loyalty is possessive, but it is not possessive in the ways that property-owners are possessive of their mere property, abusers are possessive of their partners, jealousy is possessive of the object it fears losing, or obsession is possessive of its object. By doing so (...) it hopes to shed light on the nature of love as not only possessive, but as loyal and possessive in a loyal way rather than in other ways that might be confused with love. (shrink)

After presenting Kripke’s criticism to Frege’s ideas on context dependence of thoughts, I present two recent attempts of considering cognitive aspects of context dependent expressions inside a truth conditional pragmatics or semantics: Recanati’s non-descriptive modes of presentation (MOPs) and Kaplan’s ways of having in mind (WHIMs). After analysing the two attempts and verifying which answers they should give to the problem discussed by Kripke, I suggest a possible interpretation of these attempts: to insert a procedural or algorithmic level in semantic (...) representations of indexicals. That a function may be computed by different procedures might suggest new possibilities of integrating contextual cognitive aspects in model theoretic semantic. (shrink)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

It’s a truism that love must always be for something. In technical terms, love must have an object. Yet we godless naturalists that disbelieve in all gods and any form of an afterlife, including reincarnation, must then be committed to cases of love without objects insofar as we deny the existence of objects that people genuinely love (namely, God and deceased loved ones). This commitment of ours thus seems inconsistent with the truism about love, and so it seems that we (...) godless naturalists must reject our current beliefs and accept that God and deceased loved ones exist after all. In this paper I explain how we should understand the truism about love needing an object and how, as a result, it doesn’t actually conflict with our commitment to cases of objectless love or demonstrate that we must accept that God and deceased loved ones exist. (shrink)

It has been commonplace to equate Foucault’s 1979 series of lectures at the Collège de France with the claim that for neoliberalism, unlike for classical liberalism, the market needs to be artificially constructed. The article expands this claim to its full expression, taking it beyond what otherwise would be a simple divulgation of a basic neoliberal tenet. It zeroes in on Foucault’s own insight: that neoliberal constructivism is not directed at the market as such, but, in principle, at society, arguing (...) that the value of this insight goes beyond the critique of a neoliberal present. The neoliberal rationale rather helps him to reveal a unique historical architecture, a latent approach to the social dissimilar to the one that has long predominated in the human sciences. The inversion of homo œconomicus in neoliberal theory amounted to the unearthing of a ‘social subject of interest’ within civil society. Such a subject, barely recognized by neoliberals who simply instrumentalize it for the sake of the market, demonstrates that the social is not necessarily the natural product of ethical subjects; that society may also need to be constructed. (shrink)

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

Is it possible to know anything about life we have not yet encountered? We know of only one example of life: our own. Given this, many scientists are inclined to doubt that any principles of Earth’s biology will generalize to other worlds in which life might exist. Let’s call this the “N = 1 problem.” By comparison, we expect the principles of geometry, mechanics, and chemistry would generalize. Interestingly, each of these has predictable consequences when applied to biology. The surface-to-volume (...) property of geometry, for example, limits the size of unassisted cells in a given medium. This effect is real, precise, universal, and predictive. Furthermore, there are basic problems all life must solve if it is to persist, such as resistance to radiation, faithful inheritance, and energy regulation. If these universal problems have a limited set of possible solutions, some common outcomes must consistently emerge. In this chapter, I discuss the N = 1 problem, its implications, and my response (Mariscal 2014). I hold that our current knowledge of biology can justify believing certain generalizations as holding for life anywhere. Life on Earth may be our only example of life, but this is only a reason to be cautious in our approach to life in the universe, not a reason to give up altogether. In my account, a candidate biological generalization is assessed by the assumptions it makes. A claim is accepted only if its justification includes principles of evolution, but no contingent facts of life on Earth. (shrink)

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

Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...) story of three revolutions can provide at best a preliminary orientation, and that Husserl was constantly expanding and revising his philosophical system, integrating views in phenomenology, ontology, epistemology and logic with views on the nature and tasks of philosophy and science as well as on the nature of culture and the world in ways that reveal more common elements than violent shifts of direction. We argue further that Husserl is a seminal figure in the evolution from traditional philosophy to the characteristic philosophical concerns of the late twentieth century: concerns with representation and intentionality and with problems at the borderlines of the philosophy of mind, ontology, and cognitive science. (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)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

Is it right to convict a person of a crime on the basis of purely statistical evidence? Many who have considered this question agree that it is not, posing a direct challenge to legal probabilism – the claim that the criminal standard of proof should be understood in terms of a high probability threshold. Some defenders of legal probabilism have, however, held their ground: Schoeman (1987) argues that there are no clear epistemic or moral problems with convictions based on purely (...) statistical evidence, and speculates that our aversion to such convictions may be nothing more than an irrational bias. More recently, Hedden and Colyvan (2019, section VI) describe our reluctance to convict on the basis of purely statistical evidence as an ‘intuition’, but suggest that there may be no ‘in principle’ problem with such convictions (see also Papineau, forthcoming, section 6). In this paper, I argue that there is, in some cases, an in principle problem with a conviction based upon statistical evidence alone – namely, it commits us to a precedent which, if consistently followed through, could lead to the deliberate conviction of an innocent person. I conclude with some reflections on the idea that the criminal justice system should strive to maximise the accuracy of its verdicts – and the related idea that we should each strive to maximise the accuracy of our beliefs. (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 rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

In this paper, we present one of the main starting points of naturalism in ethics: Geach’s challenge against non-cognitivism. We try to find an answer to Geach’s challenge in the notion of family resemblance applied to ethics. In doing so we recover a not much-discussed influence of Moore on Wittgenstein’s conception of family resemblance, which leads us to define Wittgenstein as non-non-cognitivist in ethics. -/- Pre print (some changes in the published edition).

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)

In this paper I offer a defence of a Russellian analysis of the referential uses of incomplete (mis)descriptions, in a contextual setting. With regard to the debate between a unificationist and an ambiguity approach to the formal treatment of definite descriptions (introduction), I will support the former against the latter. In 1. I explain what I mean by "essentially" incomplete descriptions: incomplete descriptions are context dependent descriptions. In 2. I examine one of the best versions of the unificationist “explicit” approach (...) given by Buchanan and Ostertag. I then show that this proposal seems unable to treat the normal uses of misdescriptions. I then accept the challenge of treating misdescriptions as a key to solving the problem of context dependent descriptions. In 3. I briefly discuss Michael Devitt’s and Joseph Almog’s treatments of referential descriptions, showing that they find it difficult to explain misdescriptions. In 4. I suggest an alternative approach to DD as contextuals, under a normative epistemic stance. Definite descriptions express (i) what a speaker should have in mind in using certain words in a certain context and (ii) what a normal speaker is justified in saying in a context, given a common basic knowledge of the lexicon. In 5. I define a procedure running on contextual parameters (partiality, perspective and approximation) as a means of representing the role of pragmatics as a filter for semantic interpretation. In 6. I defend my procedural approach against possible objections concerning the problem of the boundaries between semantics and pragmatics, relying on the distinction between semantics and theory of meaning. (shrink)

In this paper I respond to Marcello Di Bello’s criticisms of the ‘normic account’ of the criminal standard of proof. In so doing, I further elaborate on what the normic account predicts about certain significant legal categories of evidence, including DNA and fingerprint evidence and eyewitness identifications.

That uses of language not only can, but even normally do, have the character of actions was a fact largely unrealised by those engaged in the study of language before the present century, at least in the sense that there was lacking any attempt to come to terms systematically with the action-theoretic peculiarities of language use. Where the action-character of linguistic phenomena was acknowledged, it was normally regarded as a peripheral matter, relating to derivative or nonstandard aspects of language which (...) could afford to be ignored. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...) and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

Ensayo introductorio para mi traducción del influyente artículo "Essence and Modality" de Kit Fine.

The philosophical conception of mechanistic explanation is grounded on a limited number of canonical examples. These examples provide an overly narrow view of contemporary scientific practice, because they do not reflect the extent to which the heuristic strategies and descriptive practices that contribute to mechanistic explanation have evolved beyond the well-known methods of decomposition, localization, and pictorial representation. Recent examples from evolutionary robotics and network approaches to biology and neuroscience demonstrate the increasingly important role played by computer simulations and mathematical (...) representations in the epistemic practices of mechanism discovery and mechanism description. These examples also indicate that the scope of mechanistic explanation must be re-examined: With new and increasingly powerful methods of discovery and description comes the possibility of describing mechanisms far more complex than traditionally assumed. (shrink)

Basic Formal Ontology was created in 2002 as an upper-level ontology to support the creation of consistent lower-level ontologies, initially in the subdomains of biomedical research, now also in other areas, including defense and security. BFO is currently undergoing revisions in preparation for the release of BFO version 2.0. We summarize some of the proposed revisions in what follows, focusing on BFO’s treatment of material entities, and specifically of the category object.

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)

Performative accounts of personhood argue that group agents are persons, fit to be held responsible within the social sphere. Nonetheless, these accounts want to retain a moral distinction between group and individual persons. That: Group-persons can be responsible for their actions qua persons, but that group-persons might nonetheless not have rights equivalent to those of human persons. I present an argument which makes sense of this disanalogy, without recourse to normative claims or additional ontological commitments. I instead ground rights in (...) the different relations in which performative persons stand in relation to one another. (shrink)

Many moral philosophers have criticized intensive animal farming because it can be harmful to the environment, it causes pain and misery to a large number of animals, and furthermore eating meat and animal-based products can be unhealthful. The issue of industrially farmed animals has become one of the most pressing ethical questions of our time. On the one hand, utilitarians have argued that we should become vegetarians or vegans because the practices of raising animals for food are immoral since they (...) minimize the overall happiness. Deontologists, on the other hand, have argued that the practices of raising animals for food are immoral because animals have certain rights and we have duties toward them. Some virtue ethicists remain unconvinced of deontic and consequentialist arguments against the exploitation of animals and suggest that a virtue-based approach is better equipped to show what is immoral about raising and using animals for food, and what is virtuous about ethical veganism. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

We rely on language to know the minds of others, but does language have a role to play in knowing our own minds? To suppose it does is to look for a connection between mastery of a language and the epistemic relation we bear to our inner lives. What could such a connection consist in? To explore this, I shall examine strategies for explaining self-knowledge in terms of the use we make of language to express and report our mental states. (...) Success in these strategies will depend on the view we take of speakers' understanding of the words they use to speak their minds. The key is to avoid circularity in the account of how they know what they mean; for if knowing what one is saying in speaking a language provides a means of knowing one's own mind, it cannot simply be a part of it. I shall look at ways in which we might proceed here, and examine whether the strategy can make room for a genuinely first-person point of view. But first let me try to motivate the problem of self-knowledge. (shrink)

Goffman’s (1959) dramaturgical identity theory requires modification when theorising about presentations of self on social media. This chapter contributes to these efforts, refining a conception of digital identities by differentiating them from ‘corporatised identities’. Armed with this new distinction, I ultimately argue that social media platforms’ production of corporatised identities undermines their users’ autonomy and digital well-being. This follows from the disentanglement of several commonly conflated concepts. Firstly, I distinguish two kinds of presentation of self that I collectively refer to (...) as ‘expressions of digital identity’. These digital performances (boyd 2007) and digital artefacts (Hogan 2010) are distinct, but often confused. Secondly, I contend this confusion results in the subsequent conflation of corporatised identities – poor approximations of actual digital identities, inferred and extrapolated by algorithms from individuals’ expressions of digital identity – with digital identities proper. Finally, and to demonstrate the normative implications of these clarifications, I utilise MacKenzie’s (2014, 2019) interpretation of relational autonomy to propose that designing social media sites around the production of corporatised identities, at the expense of encouraging genuine performances of digital identities, has undermined multiple dimensions of this vital liberal value. In particular, the pluralistic range of authentic preferences that should structure flourishing human lives are being flattened and replaced by commercial, consumerist preferences. For these reasons, amongst others, I contend that digital identities should once again come to drive individuals’ actions on social media sites. Only upon doing so can individuals’ autonomy, and control over their digital identities, be rendered compatible with social media. (shrink)

There are, familiarly, a range of distinct and competing accounts of the methodological underpinnings of Menger' s work. These include Leibnizian, Kantian, Millian, and even Popperian readings; but they include also readings of an Aristotelian sort, and I have myself made a number of contributions in clarification and defence of the latter. Not only, I have argued, does the historical situation in which Menger found himself point to the inevitability of the Aristotelian reading; this reading fits also very naturally to (...) the text of Menger's works. (shrink)

Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a part of science. Initial evidence for the truth of this proposition (which some will find self-evident) (...) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But these ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, we shall argue, ontologies such as the GO are comparable to scientific theories, to scientific databases, or to scientific journal publications. Such a view implies a radically new conception of what is involved in the authoring, maintenance and application of ontologies in scientific contexts, and therewith also a radically new approach to the evaluation of ontologies and to the training of ontologists. (shrink)

Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review the (...) paper and attempt to assess its significance from the perspective of our current work. We then put the paper in the context of our individual and joint works, which led up to it, and summarize our research trajectories since the paper appeared, pointing out what some of this reveals about spatial ontology in general. We conclude with some remarks on the future of ontological research in geographical information science. (shrink)

The project of growing meat artificially represents for some the next best thing to humanity. If successful, it could be the solution to several problems, such as feed- ing a growing global population while reducing the environmental impact of raising animals for food and, of course, reducing the amount and degree of animal cruelty and suffering that is involved in animal farming. In this paper, I argue that the issue of the morality of such a project has been framed only (...) in terms of the best conse- quences for the environment, animals, and humans, or in terms of deontic princi- ples. I argue that to appreciate how deep and difficult this issue is, it is necessary to consider it in terms of a virtue-oriented approach. Such an approach will reveal aspects that are not apparent, not contemplated by typical approaches, but are essen- tial to our understanding of the morality of lab-grown meat. As I argue, evaluating the issue from a virtue-oriented perspective suggests that the project of in vitro meat should not be supported because it stems from unvirtuous motivations. (shrink)

Both ‘Sachverhalt’ and ‘state of affairs’ seem to have been derived from the juridical ‘status’ in the sense of 'status rerum' meaning: state or constitution of things. ‘Status’ signifies also in an extended sense ‘the way things stand, the condition or peculiarity of a thing in regard to its circumstances, position, order’. We describe the history of usage of ‘Sachverhalt’ from these beginnings, addressing the role of Goclenius, Lotze, Stumpf, Husserl and Adolf Reinach, whose theory of the relations between judgment (...) and Sachverhalt served as one starting point for the development of Reinach’s theory of speech acts in 1913. (shrink)

Entitlement is defined as a sort of epistemic justification that one can possess by default – a sort of epistemic justification that does not need to be earned or acquired. Epistemologists who accept the existence of entitlement generally have a certain anti-sceptical role in mind for it – entitlement is intended to help us resist what would otherwise be compelling radical sceptical arguments. But this role leaves various details unspecified and, thus, leaves scope for a number of different potential conceptions (...) of entitlement. At one extreme there are conceptions that portray entitlement as a weak, attenuated epistemic status and, at the other, we have conceptions that portray entitlement as something potent and strong. Certain intermediate conceptions are also possible. In this paper, I shall argue that the weak and intermediate conceptions of entitlement do not survive careful scrutiny, and the stronger conceptions – while they do, in a way, strain credulity – are the only conceptions that are ultimately viable. (shrink)

Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and (...) the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated. (shrink)