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)

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)

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)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (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)

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)

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

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)

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 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)

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)

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

Information-based epistemology maintains that ‘being informed’ is an independent cognitive state that cannot be reduced to knowledge or to belief, and the modal logic KTB has been proposed as a model. But what distinguishes the KTB analysis of ‘being informed’, the Brouwersche schema (B), is precisely its downfall, for no logic of information should include (B) and, more generally, no epistemic logic should include (B), either.

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)

(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)

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)

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)

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)

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.

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)

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)

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)

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)

Broadening access to both computational and educational resources is crit- ical to diffusing machine learning (ML) innovation. However, today, most ML resources and experts are siloed in a few countries and organizations. In this article, we describe our pedagogical approach to increasing access to applied ML through a massive open online course (MOOC) on Tiny Machine Learning (TinyML). We suggest that TinyML, applied ML on resource-constrained embedded devices, is an attractive means to widen access because TinyML leverages low-cost and globally (...) accessible hardware and encourages the development of complete, self-contained applications, from data collection to deployment. To this end, a collaboration between academia and industry produced a four part MOOC that provides application-oriented instruction on how to develop solutions using TinyML. The series is openly available on the edX MOOC platform, has no prerequisites beyond basic programming, and is designed for global learners from a variety of backgrounds. It introduces real-world applications, ML algorithms, data-set engineering, and the ethi- cal considerations of these technologies through hands-on programming and deployment of TinyML applications in both the cloud and on their own microcontrollers. To facili- tate continued learning, community building, and collaboration beyond the courses, we launched a standalone website, a forum, a chat, and an optional course-project com- petition. We also open-sourced the course materials, hoping they will inspire the next generation of ML practitioners and educators and further broaden access to cutting-edge ML technologies. (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)

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)

This chapter is a work in applied metaphysics. Recent discussions of monism and metaphysical dependence are deployed to develop a view—the doctrine of divine priority (DDP)—that is a viable alternative to the doctrine of divine simplicity (DDS). DDS and the traditional motivation for it are discussed, then DDP is introduced by way of an analogy involving Jonathan Schaffer’s distinction between two forms of monism. It is argued that DDP is an alternative to DDS by showing that it is consistent with (...) the traditional motivation for the latter view, and argued that DDP is a viable alternative by showing that objections to its peculiar implications rest on assumptions that can reasonably be rejected. In the concluding section, the findings of the main discussion are summarized and DDP’s potential theological import is illustrated with a brief discussion of a possible solution to the Problem of the Trinity it affords. (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)

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.

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)

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)

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)

A number of recent historians claim to have defeated what they call the ‘conflict thesis’, the idea that there exists some inevitable conflict between Darwinism and Christianity. This is often thought to be part of a broader ‘warfare thesis’, which posits an inevitable conflict between science and religion. But, all they have defeated is one, relatively uninteresting form of this thesis. There remain other forms of the conflict theses that remain entirely plausible, even in light of the historical record.

This paper argues that Carnap both did not view and should not have viewed Frege's project in the foundations of mathematics as misguided metaphysics. The reason for this is that Frege's project was to give an explication of number in a very Carnapian sense — something that was not lost on Carnap. Furthermore, Frege gives pragmatic justification for the basic features of his system, especially where there are ontological considerations. It will be argued that even on the question of the (...) independent existence of abstract objects, Frege and Carnap held remarkably similar views. I close with a discussion of why, despite all this, Frege would not accept the principle of tolerance. (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)

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)

In The Decline of the West Spengler puts forward a type of philosophical anthropology, an account of the structures of human experiential consciousness and a method of “physiognomic” analysis, which I argue has dimensions that can be understood as akin to existential phenomenology. Humanity, for Spengler, is witness to the creative flux of “Becoming” and constructs a world of phenomena bounded by death, underpinned by the two prime feelings of dread and longing and structured by the two forms of Destiny (...) (Time) and Direction (Space). Human existence, Spengler argues, is future-directed and open in the sense that there is a certain degree of freedom in the ways in which humanity can actualize its existential possibilities. In the course of elaborating the existential implications of this future-orientation, Spengler introduces the concept of care (Sorge), the fundamental experiential structure. (shrink)

Over the past 40 years a tradition of Marx interpretation has built up around a single passage concerning black slavery in an 1853 letter from Marx to Engels, in order to demonstrate that Marx’s support for emancipation was conditional on the level of ‘civilization’ attained by black slaves. I will argue that this interpretation, which attempts to prove Marx’s racist defense of slavery, is overdetermined by an inattention to historical context and a hypersensitivity to Marx’s nineteenth-century epithets. This is important (...) because the alleged anti-black racism of Marx and the place black workers occupy in his historical materialist vision of class struggle are of the utmost significance for properly conceptualizing the relationship between Marxism and black liberation. (shrink)

Recent work on the philosophy of modality has tended to pass over questions about iterated modalities in favour of constructing ambitious metaphysical theories of possibility and necessity, despite the central importance of iterated modalities to modal logic. Yet there are numerous unresolved but fundamental issues involving iterated modalities: Chandler and Salmon have provided forceful arguments against the widespread assumption that all necessary truths are necessarily necessary, for example. The current paper examines a range of ways in which one might seek (...) to identify limited regions within which some of the most well-known principles featuring iterated modalities may safely be assumed. (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)

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

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)

In this paper I first argue against one attractive formulation of the motivation argument, and against one attractive formulation of noncognitivism. I do so by example: I suggest that other-regarding normative judgments do not seem to have motivational powers and do not seem to be desires. After defending these two claims, I argue that other views can accommodate the motivational role of normative judgment without facing this objection. For example, desire-as-belief theories do so, since such theories only say that some (...) normative judgments constitute desires, not that all such judgments do so. In short, I argue that, if we are seeking a theory that explains the motivational role of normative judgement, some theories are better than others insofar as they do so without committing to the claim that all normative judgements play such a motivational role. (shrink)