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)

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.

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)

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.

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)

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)

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)

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.

(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)

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)

In the worlds of philosophy, linguistics, and communications theory, a view has developed which understands conscious experience as experience which is 'reflected' back upon itself through language. This indicates that the consciousness we experience is possible only because we have culturally invented language and subsequently evolved to accommodate it. This accords with the conclusions of Daniel Dennett (1991), but the 'hermeneutic objection' would go further and deny that the objective sciences themselves have escaped the hermeneutic circle. -/- The consciousness we (...) humans experience is developed only within the context of crossing the 'symbolic threshold' (Percy 1975; Deacon 1997) and one of the earliest and most important symbols we acquire is that of the self, or 'the subject of experience'. It is only when we achieve self-awareness that the world, as such, comes to exist for us as an object (which contains categories and sub-categories of objects). Any consciousness imputed to prelinguistic stages of development is based on projection and guesswork, since we can know nothing directly of it. It can be said that any experience which does not separate an inner subject from an outer world is probably a continuum of sensation in which environmental stimulus and instinctive response are experienced as a unity; it may be 'lived experience' but it is experience 'lived' non-consciously. -/- Speech requires assertion and by learning to speak we find ourselves asserting, in essence, our selves into the world. The narrative form of language allows us to develop life stories, self-knowledge, and, most important, narrative memory coincident with narrative time. All this is made possible with the intersubjective 'net' of language which allows us to know ourselves by first identifying with the viewpoint of others; and, later, such allows us to identify with other minds as we anticipate their reception our communication. These three, assertion, narrative, and intersubjectivity are the essence of what language is and are the keystones that make culture possible outside of nature. (shrink)

This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 MIE meeting (...) in Geneva. (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)

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

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)

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)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (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 Joint Battle Management Language (JBML) is an XML-based language designed to allow Command and Control (C2) systems to interface easily with Modeling and Simulation (M&S) systems. While some of the XML-tags defined in this language correspond to types of entities that exist in reality, others are mere syntactic artifacts used to structure the messages themselves. Because these two kinds of tags are not formally distinguishable, JBML messages in effect confuse data with what the data represent. In this paper we (...) show how a realism-based ontology combined with a rule language can be used to make these distinctions explicit. The approach allows storage of the contents of JBML messages in a Referent Tracking System in a format that mimics the structure of reality thereby providing an aid to message validation. (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)

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 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)

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.

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)

Advances in artificial intelligence and neuroscience claim to have begun to undermine the assumptions of the arts and educational theory community by explaining consciousness through either a reduction to mathematical functionalism or an excrescence of brain biology. I suggest that the worldview behind such reductionism is opposed to the worldview assumed by many educational practitioners and theorists. I then go on to outline a few common positions taken in the burgeoning field of consciousness studies that suggest that—though many attributes of (...) consciousness have been identified and explained—individual consciousness itself remains as much of an enigma to scientists as to the rest of us who experience it. However, I do suggest the necessity of intersubjectivity for conscious evolution. (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)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

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

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)

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)

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 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)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (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)

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)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

Why is there a long-standing debate about paraphrase in poetry? Everyone agrees that paraphrase can be useful; everyone agrees that paraphrase is no substitute for the poem itself. What is there to disagree about? Perhaps this: whether paraphrase can specify everything that counts as a contribution to the meaning of a poem. There are, we say, two ways to take the question; on one way of taking it, the answer is that paraphrase cannot. Does this entail that there is meaning (...) mysteriously locked in a poem, meaning that cannot be represented in any way other than via the poem itself? If that were so it would have profound implications for poetry’s capacity to convey insight. We suggest reasons for thinking that the entailment does not hold. Throughout, we connect the traditional debate over paraphrase, which has largely been conducted within the fields of philosophy and literary theory, with recent empirically oriented thinking about the communicability of meaning, represented by work in pragmatics. We end with a suggestion about what is to count as belonging to meaning, and what as merely among the things that determine meaning. (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)

Charles Mills' philosophical position has undergone a number of subtle shifts over the past 30 years. Nevertheless, there has been a relative consistency in his thought over the past two decades, at least since The Racial Contract of 1997. That consistency consists in his turn towards social contract theory and its liberal values and away from Marxism with its focus on class and political economy. Mills notes that this turn does not constitute a “a complete repudiation of Marxism, since I (...) do think that a modified historical materialism might be able to carry out an adequate conceptualization of the significance of race.” Some of the claims Mills makes about Marx and Engels, however, should be challenged; they (or their views) are not as “white” as Mills attests. Indeed, Marx and Engels made a considerable start at theorizing white supremacy as an outgrowth of modern capitalism. (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.

This paper argues against the common justification for the necessity of the state through the particular difficulty of private property right. Instead, I argue that the necessity of the state is internal to the concept of right in general. In order to show this, I point out how Kants adoption of hylomorphic language for the concept of right, where there is a formal and material aspect of right, allows us to understand the Rechtslehre as progressing through a syllogistic deduction from (...) innate right (major), private right (minor) to public right (conclusion). Material right is made necessary through its subsumption under formal right in the civil condition. (shrink)

Certain states in the Global North have responded to refugees seeking safety on their territories through harmful practices of border violence, detention, encampment and containment that serve to prevent and deter refugee arrivals. These practices are ostensibly justified through an appeal to a right to control borders. This paper therefore assesses whether these harmful practices can indeed be morally justified by a state’s right to control borders. It analyses whether Christopher Heath Wellman’s account of a state’s right to freedom of (...) association, which represents the most restrictive account of a state’s right to control borders available in the literature, can extend to justify current harmful practices against refugees. If not, then no available justification will be able to do so, and thus contemporary harmful practices used against refugees cannot be justified by a state’s right to control borders. (shrink)

ABSTRACT This article examines the under-researched figure A.W. Rehberg in his exchange with Kant over the relationship between theory and practice in the philosophy of right. I argue that Rehberg raises, what I call, two problems of political matter which attempt to show that Kant's overly formal approach to political theory cannot justifiably determine political practice. The first problem is the problem of positive determinations of right, rather than merely negative prohibitions. Rehberg takes this to mean that Kant cannot determine (...) us to a specific form of constitution. I argue that Kant's innovation of intelligible property functions as a response to this critique in that it provides the possibility of synthetic propositions of right a priori. Second, Rehberg insists that an a priori system of right cannot relate to already formed historical communities. Here Kant's response comes close to agreeing with Rehberg as Kant takes prudential or historical reasoning to harmonize with the demands of a priori right in order to applied to the sensible world. Kant, in this instance, comes closer to Rehberg by denying centralized enlightened monarchy and the reliance on natural and historical development for the application of right. (shrink)