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)

In this paper, I show that we should understand the direction of fit of beliefs and desires in normative terms. After rehearsing a standard objection to Michael Smith’s analysis of direction of fit, I raise a similar problem for Lloyd Humberstone’s analysis. I go on to offer my own account, according to which the difference between beliefs and desires is determined by the normative relations such states stand in. I argue that beliefs are states which we have reason to (...) change in light of the world, whereas desires are states that give us reason to change the world. After doing this, I show how the view avoids various objections, including two from David Sobel and David Copp. The paper ends by briefly discussing the relevance of the view to the Humean theory of motivation. (shrink)

This paper examines the status of naturalism in the philosophies of Edmund Husserl and John Dewey. Despite the many points of overlap and agreement between Husserl’s and Dewey’s philosophical projects, there remains one glaring difference, namely, the place and status of naturalism in their approaches. For Husserl, naturalism is an enemy to be vanquished. For Dewey, naturalism is the only method that can put philosophy back in touch with the concerns of human beings. This paper will demonstrate the remarkable similarities (...) between Husserl’s and Dewey’s thought before contending that Dewey’s “naturalistic humanism” offers a conception of naturalism which is compatible with Husserlian phenomenology. Furthermore, reading these two philosophers together, this paper argues, can point the way forward to a naturalism which avoids the dismissal of the contributions made by knowing subjects carried out by dominant contemporary strains of reductive naturalism. (shrink)

Verbal irony constitutes a rough class of indirect intentional communication involving a complex interaction of language-specific and communication-general phenomena. Conversationalists use verbal irony in conjunction with paralinguistic signals such as speech prosody. Researchers examining acoustic features of speech communication usually focus on how prosodic information relates to the surface structure of utterances, and often ignore prosodic phenomena associated with implied meaning. In the case of verbal irony, there exists some debate concerning how these prosodic features manifest themselves in conversation. A (...) form-function approach can provide a valuable tool for understanding speakers' varied vocal strategies in this domain. Here I describe several ways conversationalists employ prosodic contrasts, laughter, and other speech characteristics in their attempts to communicate effectively and efficiently. The presented examples, culled from spontaneous conversation recordings, reveal just a small sample of the enormous variation in delivery styles speakers adopt when communicating with ironic language. (shrink)

Sumantra Ghoshal’s condemnation of “bad management theories” that were “destroying good management practices” has not lost any of its salience, after a decade. Management theories anchored in agency theory (and neo-classical economics generally) continue to abet the financialization of society and undermine the functioning of business. An alternative approach (drawn from a more classic institutional, new ecological, and refocused ethical approaches) is reviewed.

Throughout his career, Jean-Paul Sartre had a contentious theoretical relationship with psychoanalysis. Nowhere is this more evident than in his criticisms of the concept of the unconscious. For him, the unconscious represents a hidden psychological depth that is anathema to the notion of human freedom. In this paper, I argue that Lacan’s conception of the unconscious-structured-like-a-language overcomes many of Sartre’s most damning objections. I demonstrate that Lacan shares with Sartre a concern to rid the psyche of hidden depths. Both thinkers (...) therefore reject the depth psychological conception of the unconscious and arrive at strikingly similar positions on the nature of the unconscious. In this way, I show that the conceptual analogues that Sartre develops in order to avoid the psychoanalytic unconscious lead him to a position on the unconscious with which Lacan could be in agreement. This indicates that Sartre’s philosophical position is not as at odds with Freudian-Lacanian psychoanalysis as is typically thought. (shrink)

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

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

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

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

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

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

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

Philip Goff has recently argued that due to the ‘subject-summing problem’, panpsychism cannot explain consciousness. The subject-summing problem is a problem which is analogous to the physicalist's explanatory gap; it is a gap between the micro-experiential facts and the macro-experiential facts. Goff also suggests that there could be a solution by way of a ‘phenomenal bonding relation’, but believes that this solution is not up to scratch because we cannot form a positive not-merely-role-playing concept of this relation. In this paper, (...) I argue that the phenomenal bonding solution is up to scratch. I argue that the panpsychist, by carefully inspecting their phenomenology and scrutinising their concepts, can form a positive concept of the phenomenal bonding relation. By doing this they can start to get around their explanatory gap. (shrink)

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

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

The field of of imprecise probability has matured, in no small part because of Teddy Seidenfeld’s decades of original scholarship and essential contributions to building and sustaining the ISIPTA community. Although the basic idea behind imprecise probability is (at least) 150 years old, a mature mathematical theory has only taken full form in the last 30 years. Interest in imprecise probability during this period has also grown, but many of the ideas that the mature theory serves can be difficult to (...) apprehend to those new to the subject. Although these fundamental ideas are common knowledge in the ISIPTA community, they are expressed, when they are expressed at all, obliquely, over the course of years with students and colleagues. -/- A single essay cannot convey the store of common knowledge from any research community, let alone the ISIPTA community. But, this essay nevertheless is an attempt to guide those familiar with the basic Bayesian framework to appreciate some of the elegant and powerful ideas that underpin the contemporary theory of lower previsions, which is the theory that most people associate with the term ‘imprecise probabilities’. (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)

(Updated 5/23/24) This unpublished paper, which readers should feel free to cite, is posted primarily for the historical record. In recent work that has, deservedly, received some attention, Paul R. Daniels presents and defends a non-standard theory of persistence that he dubs transdurantism, according to which persisting objects are temporally extended simples. This is exactly what I do in work dating back to Spring 2004. (This work includes this version of this paper, as well as later version that was presented (...) to the University of Rochester's Philosophy Department in 2005.) While this might be a total coincidence, I doubt that it is, especially given that 'transdurantism' appears as a name for a theory of persistence associated with me in at least two places in the literature, one of which includes a citation of this paper. The paper begins with a discussion of what I call 'locative relations' (the relations borne by material objects to the regions of space and time they occupy), which draws relevant distinctions that others have failed to draw. The results of this discussion are then used in constructing spatial analogues for the three established theories of persistence--endurantism, perdurantism, and exdurantism--as well as for transdurantism. Next, these four views concerning persistence are explicitly formulated and a defense of their formulation is offered. Finally, transdurantism's advantages and disadvantages relative to the other theories are discussed. The main goal of the paper is to challenge the trichotomy between the established theories by arguing that transdurantism is also a viable view concerning persistence through time. [Note: Befitting its status as a historical document, with the exception of some light editing to fix typos that might impede understanding, no changes have been made to the paper.]. (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)

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

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

When comparing alternative courses of action, modern military decision makers often must consider both the military effectiveness and the ethical consequences of the available alternatives. The basis, design, calibration, and performance of a principles-based computational model of ethical considerations in military decision making are reported in this article. The relative ethical violation (REV) model comparatively evaluates alternative military actions based upon the degree to which they violate contextually relevant ethical principles. It is based on a set of specific ethical principles (...) deemed by philosophers and ethicists to be relevant to military courses of action. A survey of expert and non-expert human decision makers regarding the relative ethical violation of alternative actions for a set of specially designed calibration scenarios was conducted to collect data that was used to calibrate the REV model. Perhaps unsurprisingly, the survey showed that people, even experts, disagreed greatly amongst themselves regarding the scenarios’ ethical considerations. Despite this disagreement, two significant results emerged. First, after calibration the REV model performed very well in terms of replicating the ethical assessments of human experts for the calibration scenarios. The REV model outperformed an earlier model that was based on tangible consequences rather than ethical principles, that earlier model performed comparably to human experts, the experts outperformed human non-experts, and the non-experts outperformed random selection of actions. All of these performance comparisons were measured quantitatively and confirmed with suitable statistical tests. Second, although humans tended to value some principles over others, none of the ethical principles involved—even the principle of not harming civilians—completely overshadowed all of the other principles. (shrink)

Nico Silins (2012, 2013, 2020) argues that conscious judgments justify self-attribution of belief in the content judged. In defending his view, he makes use of Moore’s Paradox, seeking to show how his theory can explain what seems irrational or absurd about sentences of the form, ‘p and I do not believe that p’. I show why his argument strategy is not available to defend the view that conscious judgments can justify the self-attribution of belief in the content judged. I then (...) propose an amended version of his theory, which holds that sincerely asserting a proposition—whether aloud or silently—justifies self-ascribing belief in the proposition expressed. In doing so, I draw on an argument which I made in Gregory (2018) that there is something it is like to make a sincere assertion which is different from what it is like to make an insincere assertion. The phenomenology of sincere assertion provides immediate justification for self-ascription of belief in a proposition which has been sincerely asserted; nonetheless, it may be that we need to interpret our own assertions in order to determine which propositions they express. This paves the way for showing how two competing schools of thought about self-knowledge—one which holds that self-knowledge is immediate and one which holds that self-knowledge is inferential—might be combined. (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)

This paper presents a new objection to the buck-passing account of value. I distinguish the buck-passing account of predicative value from the buck-passing account of attributive value. According to the latter, facts about attributive value reduce to facts about reasons and their weights. But since facts about reasons’ weights are themselves facts about attributive value, this account presupposes what it is supposed to explain. As part of this argument, I also argue against Mark Schroeder's recent account of the weights of (...) reasons, which purports to explain the weights of reasons in terms of further reasons without circularity. I then argue that if we abandon the buck-passing account of attributive value, it would be ad hoc and unjustifiable to continue to endorse the buck-passing account of predicative value. In short, there seems to be little hope for the buck-passing account in either form. The paper ends by sketching a novel alternative theory according to which reasons are analysed in terms of the attributive value of motives. I suggest that a normative reason to is something that would be a good motive for -ing. At least at first glance, this view has numerous merits and few problems. (shrink)

Philosophy of technology was not initially considered a consolidated field of inquiry. However, under the influence of sociology and pragmatist philosophy, something resembling a consensus has emerged in a field previously marked by a lack of agreement amongst its practitioners. This has given the field a greater sense of structure and yielded interesting research. However, the loss of the earlier “messy” state has resulted in a limitation of the field’s scope and methodology that precludes an encompassing view of the problematic (...) issues inherent in the question of technology. It is argued that the heterodox disunity and diversity of earlier philosophy of technology was not a mark of theoretical immaturity but was necessitated by the field’s complex subject matter. It is further argued that philosophy of technology should return to its pluralistic role as a meta-analytical structure linking insights from different fields of research. (shrink)

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

Human aesthetic practices show a sensitivity to the ways that the appearance of an artefact manifests skills and other qualities of the maker. We investigate a possible origin for this kind of sensibility, locating it in the need for co-ordination of skill-transmission in the Acheulean stone tool culture. We argue that our narrative supports the idea that Acheulian agents were aesthetic agents. In line with this we offer what may seem an absurd comparison: between the Acheulian and the Quattrocento. In (...) making it we display some hidden richness in what counts as an aesthetic response to an artefact. We conclude with a brief review of rival explanations—biological and/or cultural—of how this skills-based sensibility became a regular feature of human aesthetic practices. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

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

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (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)

Defences of inference to the best explanation (IBE) frequently associate IBE with scientific realism, the idea that it is reasonable to believe our best scientific theories. I argue that this linkage is unfortunate. IBE does not warrant belief, since the fact that a theory is the best available explanation does not show it to be (even probably) true. What IBE does warrant is acceptance: taking a proposition as a premise in theoretical and/or practical reasoning. We ought to accept our best (...) scientific theories since they are the theories that are most likely to lead to the goal of science, which is that of knowledge. In support of this claim I invoke Bill Lycan's Panglossian reflections regarding Mother Nature.1. (shrink)

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

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)

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)

: 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 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)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

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

The 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)

Hud Hudson has argued that if MaxCon, Ned Markosian's favored answer to the Simple Question, is true, then there couldn't be gunky objects. If Hudson's argument succeeds, then those who believe that gunky objects are possible have a good reason to reject MaxCon. However, I show that Hudson's argument relies on substantive metaphysical claims that a proponent of MaxCon need not accept. Thus, one who endorses MaxCon need not reject the possibility of gunky objects and those who believe that gunky (...) objects are possible need not reject MaxCon. (shrink)

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

Pereira’s “The Projective Theory of Consciousness” is an experimental statement, drawing on many diverse sources, exploring how consciousness might be produced by a projective mechanism that results both in private selves and an experienced world. Unfortunately, pulling together so many unrelated sources and methods means none gets full attention. Furthermore, it seems to me that the uncomfortable breadth of this paper unnecessarily complicates his project; in fact it may hide what it seeks to reveal. If this conglomeration of diverse sources (...) and methods were compared to trees, the reader may feel like the explorer who cannot see the forest for the trees. Then again, it may be the author who is so preoccupied with foreground figures that the everpresent background is ultimately obscured. (shrink)

_Theurgy and the Soul_ is a study of Iamblichus of Syria, whose teachings set the final form of pagan spirituality prior to the Christianization of the Roman Empire. Gregory Shaw focuses on the theory and practice of theurgy, the most controversial and significant aspect of Iamblichus's Platonism. Theurgy literally means "divine action." Unlike previous Platonists who stressed the elevated status of the human soul, Iamblichus taught that the soul descended completely into the body and thereby required the performance of (...) theurgic rites—revealed by the gods—to unite the soul with the One. Iamblichus was once considered one of the great philosophers whose views on the soul and the importance of ritual profoundly influenced subsequent Platonists such as Proclus and Damascius. The Emperor Julian followed Iamblichus's teachings to guide the restoration of traditional pagan cults in his campaign against Christianity. Although Julian was unsuccessful, Iamblichus's ideas persisted well into the Middle Ages and beyond. His vision of a hierarchical cosmos united by divine ritual became the dominant world view for the entire medieval world and played an important role in the Renaissance Platonism of Marsilio Ficino. Even Ralph Waldo Emerson wrote that he expected a reading of Iamblichus to cause a "revival in the churches." But modern scholars have dismissed him, seeing theurgy as ritual magic or "manipulation of the gods." Shaw, however, shows that theurgy was a subtle and intellectually sophisticated attempt to apply Platonic and Pythagorean teachings to the full expression of human existence in the material world. (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)

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