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)

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

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

This dissertation examines the relationship that exists between two distinct and seemingly incompatible bodies of scholarship within the field of contemporary philosophy of technology. The first, as argued by postmodern pragmatist Barry Allen, posits that our tools and what we make with them are epistemically important; disputing the idea that knowledge is strictly sentential or propositional, he claims instead that knowledge is the product of a performance that is both superlative and artefactual, rendering technology importantly world-constituting. The second, as (...) argued by Heidegger and his inheritors, is that technology is ontologically problematic; rather than technology being evidence of performative knowledge, it is instead existentially threatening by virtue of the fact that it changes the tenor of our relationship with the world-as-given. Despite the fact that these claims seem prima facie incompatible, I argue that they may be successfully reconciled by introducing a third body of scholarship: the philosophy of photography. For it is the case, I argue, that although we, qua human beings, occupy lifeworlds that are necessarily constituted by technology, technology also induces a kind of phenomenological scepticism: a concern that mediated action precludes us from the possibility of authentic experience. Arguing in favour of the sentiment that photographs serve as a kind of phenomenal anchor—a kind of machine for living—I claim that photographic images provide a panacea to this existential concern: despite being epistemically problematic, it is this selfsame epistemic “specialness” of photographs that forces us to phenomenologically recommit, if only temporarily, to the world in a serious way. Consequently, it is my belief that an analysis of our artefacts and the way they function is fundamentally incomplete without an analysis of the epistemic and ontological problems introduced of the photographic image; as I will demonstrate, the photographic image casts an extremely long shadow over the philosophy of technology. (shrink)

In this paper we apply the popular Best System Account of laws to typical eternal worlds – both classical eternal worlds and eternal worlds of the kind posited by popular contemporary cosmological theories. We show that, according to the Best System Account, such worlds will have no laws that meaningfully constrain boundary conditions. It’s generally thought that lawful constraints on boundary conditions are required to avoid skeptical arguments. Thus the lack of such laws given the Best System Account may seem (...) like a severe problem for the view. We show, however, that at eternal worlds, lawful constraints on boundary conditions do little to help fend off skeptical worries. So with respect to handling these skeptical worries, the proponent of the Best System Account is no worse off than their competitors. (shrink)

Coronavirus disease 2019 can lead to respiratory failure. Some patients require extracorporeal membrane oxygenation support. During the current pandemic, health care resources in some cities have been overwhelmed, and doctors have faced complex decisions about resource allocation. We present a case in which a pediatric hospital caring for both children and adults seeks to establish guidelines for the use of extracorporeal membrane oxygenation if there are not enough resources to treat every patient. Experts in critical care, end-of-life care, bioethics, and (...) health policy discuss if age should guide rationing decisions. (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)

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)

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)

This paper applies the ontological framework developed by Roman Ingarden in his Controversy over the Existence of the World to the domain of mathematics, concluding with some remarks on parallels between the mode of existence of mathematical entities on the one hand and of values on the other.

In her paper, “The cost of conscience: Kant on conscience and conscientious objection,” Jeanette Kennett argues that a Kantian view of conscientious objection in medicine would bar physicians from refusing to perform certain practices based on conscience. I offer a response in the following manner: First, I reconstruct her main argument; second, I present a more accurate picture of Kant’s view of conscience. I conclude that, given a Kantian framework, a physician should be allowed to refuse to perform practices that (...) break the moral law and, thus, refuse practices that violate her conscience. (shrink)

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

According to the most important objection to the existence of moral beauty, true judgements of moral beauty are not possible as moral judgements require being motivated to act in line with the moral judgement made, and judgements of beauty require not being motivated to act in any way. Here, I clarify the argument underlying the objection, and show that it does not show that moral beauty does not exist. I present two responses: namely, that the beauty of moral beauty does (...) not lie in the moral goodness per se (the “adjacent properties” response); and that only a dispositional motivation to act is required for the moral judgements that are typically made as part of judgements of moral beauty, whereas aesthetic judgements only rule out state motivations to act (the “equivocation of motivation required” response). In addressing the objection, I show how moral beauty is consistent with disinterestedness, and so should be accepted more widely; and also clarify where the beauty in moral beauty resides, and how the moral-aesthetic distinction should be drawn. (shrink)

DNA sequencers, Twitter, MRIs, Facebook, particle accelerators, Google Books, radio telescopes, Tumblr: what do these things have in common? According to the evangelists of “data science,” all of these are instruments for observing reality at unprecedentedly large scales and fine granularities. This perspective ignores the social reality of these very different technological systems, ignoring how they are made, how they work, and what they mean in favor of an exclusive focus on what they generate: Big Data. But no data, big (...) or small, can be interpreted without an understanding of the process that generated them. Statistical data science is applicable to systems that have been designed as scientific instruments, but is likely to lead to confusion when applied to systems that have not. In those cases, a historical inquiry is preferable. (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)

In a development that has still been hardly noticed by philosophers, a conception of ontology has been advanced in recent years in a series of extra-philosophical disciplines as researchers in linguistics, psychology, geography and anthropology have sought to elicit the ontological commitments (‘ontologies’, in the plural) of different cultures or disciplines. Exploiting the terminology of Quine, researchers in psychology and anthropology have sought to establish what individual human subjects, or entire human cultures, are committed to, ontologically, in their everyday cognition, (...) in much the same way in which philosophers of science have attempted to elicit the ontological commitments of the natural sciences. Thus they have engaged in inquiries designed to establish how folk ontologies (or folk biologies, folk theories of physics, folk psychologies, and so on) develop through infancy and childhood, or to establish the degree to which given elements of folk ontologies reflect universal features of the human cognitive system. In a parallel development, researchers in biomedicine developed what they called 'ontologies' as controlled vocabularies to ensure interoperability of the way in which, for example, genomic data is described in different biological disciplines. We describe in what follows some of the relations between these efforts and the more traditional concerns of philosophers. (shrink)

Why are moral actions beautiful, when indeed they are? This paper assesses the view, found most notably in Schiller, that moral actions are beautiful just when they present the appearance of freedom by appearing to be the result of internal harmony (the Schillerian Internal Harmony Thesis). I argue that while this thesis can accommodate some of the beauty involved in contrasts of the ‘continent’ and the ‘fully’ virtuous, it cannot account for all of the beauty in such contrasts, and so (...) needs to be weakened considerably (to the Internal Harmony Thesis). To account for the remaining beauty that cannot be fully accommodated even by this revised thesis, as well as the beauty contained in contrasts that involve agents who experience internal conflict as a result of being sensitive to different sources of moral value to an appropriate extent, a number of further theses need to be posited: namely, that the beauty of some moral actions is to be accommodated in terms of internal disharmony (the Internal Disharmony Thesis), and in terms of a felt harmony between the appreciator of the action and the executor of the action (the Affective Harmony Thesis). As such, in contrast to Schiller, I suggest that we need to take a pluralist and context-sensitive approach to accommodating the beauty of moral actions. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries (...) yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (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)

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the (...) relation between fetus and mother (connection, parthood, dependence). (shrink)

ABSTRACT We have previously argued that there are forms of greenhouse gas offsetting for which, when one emits and offsets, one imposes no risk. Orri Stefansson objects that our argument fails to distinguish properly between the people who stand to be harmed by one’s emissions and the people who stand to be benefited by one’s offsetting. We reply by emphasizing the difference between acting with a probability of making a difference to the distribution of harm and acting in a way (...) that worsen’s someone’s prospect. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (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)

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...) projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments. (shrink)

The puzzle of petitionary prayer: if we ask for the best thing, God was already going to do it, and if we ask for something that's not the best, God's not going to grant our request. In this paper, we give a new solution to the puzzle.

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)

Bilateral proof systems, which provide rules for both affirming and denying sentences, have been prominent in the development of proof-theoretic semantics for classical logic in recent years. However, such systems provide a substantial amount of freedom in the formulation of the rules, and, as a result, a number of different sets of rules have been put forward as definitive of the meanings of the classical connectives. In this paper, I argue that a single general schema for bilateral proof rules has (...) a reasonable claim to inferentially articulating the core meaning of all of the classical connectives. I propose this schema in the context of a bilateral sequent calculus in which each connective is given exactly two rules: a rule for affirmation and a rule for denial. Positive and negative rules for all of the classical connectives are given by a single rule schema, harmony between these positive and negative rules is established at the schematic level by a pair of elimination theorems, and the truth-conditions for all of the classical connectives are read off at once from the schema itself. (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)

When governments collect data relating to economic activity they commonly employ a distinction between goods and services. Both goods and services have economic value. Goods (cars, houses, bottles of milk) are, very roughly, independent continuants which can be alienated (sold, gifted, rented, and so forth). Services (hairdressing, gardening, teaching) are, again very roughly, occurrents. They are occurrents which are further often said to be marked by the fact that production and consumption coincide. Social services under both headings typically involve combinations (...) of service provision. The patterns in question are primarily those of the family (where the patterns to be maintained or restored are, roughly, those characteristic of a healthy family life) and of the child (patterns characteristic of healthy development, provided by child protective services, who work to prevent child abuse). (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)

In this article, robust evidence is provided showing that an individual’s moral character can contribute to the aesthetic quality of their appearance, as well as being beautiful or ugly itself. It is argued that this evidence supports two main conclusions. First, moral beauty and ugliness reside on the inside, and beauty and ugliness are not perception-dependent as a result; and, second, aesthetic perception is affected by moral information, and thus moral beauty and ugliness are on the outside as well.

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

Business and Economic textbooks warn against committing the Sunk Cost Fallacy: you, rationally, shouldn't let unrecoverable costs influence your current decisions. In this paper, I argue that this isn't, in general, correct. Sometimes it's perfectly reasonable to wish to carry on with a project because of the resources you've already sunk into it. The reason? Given that we're social creatures, it's not unreasonable to care about wanting to act in such a way so that a plausible story can be told (...) about you according to which your diachronic behavior doesn't reveal that you've suffered, what I will call, diachronic misfortune. Acting so as to hide that you've suffered diachronic misfortune involves striving to make yourself easily understood while disguising any shortcomings that might damage your reputation as a desirable teammate. And making yourself easily understood to others while hiding your flaws will, sometimes, put pressure on you to honor sunk costs. (shrink)

This paper attempts to fill an epistemological gap in our theorizing about love with a sketch of an epistemology of love that unfolds by addressing Whitney Houston’s famous epistemological questions pertaining to how we can know whether another loves us. After arguing for three possible sources of the knowledge of love, it offers initial answers to how the knowledge of the presence or absence of another’s love can be acquired from the relevant possible sources previously established. These initial answers, though, (...) are unsatisfying because they invite more difficult questions that are then addressed, such as those pertaining to the kinds of things that constitute love’s expressions along with how to detect these expressions given the possibility of false positives. Addressing these questions ultimately leads to a sharpened, Aristotle-inspired account of how to acquire the knowledge of the presence or absence of another’s love by inferring it, respectively, from the successful or failed detection of love’s expressions. (shrink)

Bioethics, Volume 36, Issue 1, Page 54-62, January 2022.

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)

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)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The paper uses the tools of mereotopology (the theory of parts, wholes and boundaries) to work out the implications of certain analogies between the 'ecological psychology' of J. J Gibson and the phenomenology of Edmund Husserl. It presents an ontological theory of spatial boundaries and of spatially extended entities. By reference to examples from the geographical sphere it is shown that both boundaries and extended entities fall into two broad categories: those which exist independently of our cognitive acts (for example, (...) the planet Earth, its exterior surface); and those which exist only in virtue of such acts (for example: the equator, the North Sea). The visual field, too, can be conceived as an example of an extended entity that is dependent in the sense at issue. The paper suggests extending this analogy by postulating entities which would stand to true judgments as the visual field stands to acts of visual perception. The judgment field is defined more precisely as that complex extended entity which comprehends all entities which are relevant to the truth of a given (true) judgment. The work of cognitive linguists such as Talmy and Langacker, when properly interpreted, can be shown to yield a detailed account of the structures of the judgment fields corresponding to sentences of different sorts. A new sort of correspondence-theoretic definition of truth for sentences of natural language can then be formulated on this basis. (shrink)

Michael Ryan's Literary Theory: A Practical Introduction, Second Edition introduces students to the full range of contemporary approaches to the study of literature and culture, from Formalism, Structuralism, and Historicism to Ethnic Studies, Gender Studies, and Global English. Introduces readings from a variety of theoretical perspectives, on classic literary texts. Demonstrates how the varying perspectives on texts can lead to different interpretations of the same work. Contains an accessible account of different theoretical approaches An ideal resource for use in (...) introductory courses on literary theory and criticism. Designed to function both as a stand-alone text and a companion to Rivkin and Ryan’s Literary Theory: An Anthology, Second Edition. (shrink)

There is a famous and important dictum reminiscent of the medieval age posited by Carl Jung in Alchemical Studies, the thirteenth volume of his collected works: in sterquiliniis invenitur—in filth it shall be found (35). Translated for modern society this might be better understood as “that which is most valuable will be found in the place you least want to look.” If there is one source in the corpus of popular culture that best typifies “the last place we would want (...) to look” for masculine values, it would be Mads Mikkelsen’s portrayal of Hannibal Lector, particularly Lector’s relationship with FBI profiler Will Graham during the first two seasons of the HBO series Hannibal. By stripping away the perverse horror of Lector’s actions toward Graham, and treating their relationship as an absolute value, I systematically explore the series’ portrayal of masculine nurturing in a way that reveals potentially praiseworthy facets relevant to modern masculinity. (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 piece of wax takes on the form of the seal; but this occurs in a way that is largely indifferent to the particular constitution of the seal. Similarly, Aristotle says, ‘the sense is affected by what is coloured or flavoured or sounding, but it is indifferent as to what in each case the substance is’. We show that Brentano takes this Aristotelian account of the relation between sense and its objects as the basis for his theory of mind in (...) the Psychology from an Empirical Standpoint. (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”.

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it (...) provides an account of how cells and subcells relate to objects in reality. We define a notion of well-formedness for partitions, and we give an account of what it means for a partition to project onto objects in reality. We continue by classifying partitions along three axes: (a) in terms of the degree of correspondence between partition cells and objects in reality; (b) in terms of the degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) in terms of the degree of completeness with which a partition represents this domain. (shrink)

Which traits are beautiful? And is their beauty perceptual? It is argued that moral virtues are partly beautiful to the extent that they tend to give rise to a certain emotion— ecstasy—and that compassion tends to be more beautiful than fair-mindedness because it tends to give rise to this emotion to a greater extent. It is then argued, on the basis that emotions are best thought of as a special, evaluative, kind of perception, that this argument suggests that moral virtues (...) are partly beautiful to the extent that they tend to give rise to a certain kind of evaluative perceptual experience. (shrink)