I propose and defend a novel view called “de se consequentialism,” which is noteworthy for two reasons. First, it demonstrates—contra Doug Portmore, Mark Schroeder, Campbell Brown, and Michael Smith, among others—that agent-neutral consequentialism is consistent with agent-centered constraints. Second, it clarifies the nature of agent-centered constraints, thereby meriting attention from even dedicated nonconsequentialists. Scrutiny reveals that moral theories in general, whether consequentialist or not, incorporate constraints by assessing states in a first-personal guise. Consequently, de se consequentialism enacts constraints through (...) the very same feature that nonconsequentialist theories do. (shrink)

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

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

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

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

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

Our approach is based on a tri-partite method of integrating psychodynamic hypotheses, cognitive subliminal processes, and psychophysiological alpha power measures. We present ten social phobic subjects with three individually selected groups of words representing unconscious conflict, conscious symptom experience, and Osgood Semantic negative valence words used as a control word group. The unconscious conflict and conscious symptom words, presented subliminally and supraliminally, act as primes preceding the conscious symptom and control words presented as supraliminal targets. With alpha power as a (...) marker of inhibitory brain activity, we show that unconscious conflict primes, only when presented subliminally, have a unique inhibitory effect on conscious symptom targets. This effect is absent when the unconscious conflict primes are presented supraliminally, or when the target is the control words. Unconscious conflict prime effects were found to correlate with a measure of repressiveness in a similar previous study (Shevrin et al., 1992, 1996). Conscious symptom primes have no inhibitory effect when presented subliminally. Inhibitory effects with conscious symptom primes are present, but only when the primes are supraliminal, and they did not correlate with repressiveness in a previous study (Shevrin et al., 1992, 1996). We conclude that while the inhibition following supraliminal conscious symptom primes is due to conscious threat bias, the inhibition following subliminal unconscious conflict primes provides a neurological blueprint for dynamic repression: it is only activated subliminally by an individual's unconscious conflict and has an inhibitory effect specific only to the conscious symptom. These novel findings constitute neuroscientific evidence for the psychoanalytic concepts of unconscious conflict and repression, while extending neuroscience theory and methods into the realm of personal, psychological meaning. (shrink)

Background: Current practice frequently fails to provide care consistent with the preferences of decisionally-incapacitated patients. It also imposes significant emotional burden on their surrogates. Algorithmic-based patient preference predictors (PPPs) have been proposed as a possible way to address these two concerns. While previous research found that patients strongly support the use of PPPs, the views of surrogates are unknown. The present study thus assessed the views of experienced surrogates regarding the possible use of PPPs as a means to help make (...) treatment decisions for decisionally-incapacitated patients. -/- Methods: This qualitative study used semi-structured interviews to determine the views of experienced surrogates [n=26] who were identified from two academic medical centers and two community hospitals. The primary outcomes were respondents’ overall level of support for the idea of using PPPs and the themes related to their views on how a PPP should be used, if at all, in practice. -/- Results: Overall, 21 participants supported the idea of using PPPs. The remaining five indicated that they would not use a PPP because they made decisions based on the patient’s best interests, not based on substituted judgment. Major themes which emerged were that surrogates, not the patient’s preferences, should determine how treatment decisions are made, and concern that PPPs might be used to deny expensive care or be biased against minority groups. -/- Conclusions: Surrogates, like patients, strongly support the idea of using PPPs to help make treatment decisions for decisionally-incapacitated patients. These findings provide support for developing a PPP and assessing it in practice. At the same time, patients and surrogates disagree over whose preferences should determine how treatment decisions are made, including whether to use a PPP. These findings reveal a fundamental disagreement regarding the guiding principles for surrogate decision-making. Future research is needed to assess this disagreement and consider ways to address it. (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)

Next SectionThis article argues against two dominant accounts of the nature of nostalgia. These views assume that nostalgia depends, in some way, on comparing a present situation with a past one. However, neither does justice to the full range of recognizably nostalgic experiences available to us – in particular, ‘Proustian’ nostalgia directed at involuntary autobiographical memories. Therefore, the accounts in question fail. I conclude by considering an evaluative puzzle raised by Proustian nostalgia when it is directed at memories that the (...) nostalgist herself regards as non-veridical. (shrink)

It has recently been argued that when one conducts an inquiry into some question one ought to suspend belief with respect to that question. But what about hunches? In this short note, a hunch about the cause of a phenomenon is described. The hunch plays a role in the inquiry into the cause of the phenomenon. It appears that the hunch constitutes a belief that need not be suspended during the inquiry even though belief about the precise cause of the (...) phenomenon is suspended. (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)

The chapter introduces and characterizes the notion of fittingness. It charts the history of the relation and its relevance to contemporary debates in normative and metanormative philosophy and proceeds to survey issues to do with fittingness covered in the volume’s chapters, including the nature and epistemology of fittingness, the relations between fittingness and reasons, the normativity of fittingness, fittingness and value theory, and the role of fittingness in theorizing about responsibility. The chapter concludes with a brief discussion of issues to (...) do with fittingness that aren’t covered extensively by the volume’s chapters in order to indicate avenues for further research. (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)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

This note poses a dilemma for scientific realism which stems from the apparent conflict between science and common sense. On the one hand, we may accept scientific realism and agree that there is a conflict between science and common sense. If we do this, we remove the evidential basis for science and have no reason to accept science in the first place. On the other hand, we may accept scientific realism and endorse common sense. If we do this, we must (...) reject the conflict between science and common sense. The dilemma is to be resolved by distinguishing between basic common sense and widely held beliefs. Basic common sense survives the advance of science and may serve as the evidential basis for science. (shrink)

In this dialogue, we discuss the contrast between inexorable physical laws and the semiotic freedom of life. We agree that material and symbolic structures require complementary descriptions, as do the many hierarchical levels of their organizations. We try to clarify our concepts of laws, constraints, rules, symbols, memory, interpreters, and semiotic control. We briefly describe our different personal backgrounds that led us to a biosemiotic approach, and we speculate on the future directions of biosemiotics.

This paper explores the relationship between scepticism and epistemic relativism in the context of recent history and philosophy of science. More specifically, it seeks to show that significant treatments of epistemic relativism by influential figures in the history and philosophy of science draw upon the Pyrrhonian problem of the criterion. The paper begins with a presentation of the problem of the criterion as it occurs in the work of Sextus Empiricus. It is then shown that significant treatments of epistemic relativism (...) in recent history and philosophy of science (critical rationalism, historical philosophy of science and the strong programme) draw upon the problem of the criterion. It is briefly suggested that a particularist response to the problem of the criterion may be put to good use against epistemic relativism. (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.

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (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)

This article examines where Kant stands on the question of the redistribution of wealth and income both nationally and globally. Kant is rightly seen as a radical reformer of the world order from a political standpoint seeking a republican, federative worldwide system; can he also be seen as wanting to bring about an equally dramatic shift from an economic perspective? To answer this question we have first of all to address the question of whether he is an egalitarian or an (...) inegalitarian at the national level. Certainly there are certain social and material inequalities within a civil society Kant is prepared to accept and there are some he is not. This would imply that he would affirm certain inequalities at an international level and that there are others upon which he would recommend action. Thus the question arises as to whether or not it is appropriate for Kantians to regard the current enormous inequalities in wealth and income between individuals living in different parts of the globe as scandalous and in need of change. The paper throughout relates the problem of distributive justice within the state to the problem of distributive justice amongst states, arguing that this approach is warranted by Kant's own method. Particular attention is paid to how Kant's own approach to political philosophy may be deployed to underpin a change to a distinctive type of international distributive justice. (shrink)

This paper presents a particularist and naturalist response to epistemic relativism. The response is based on an analysis of the source of epistemic relativism, according to which epistemic relativism is closely related to Pyrrhonian scepticism. The paper starts with a characterization of epistemic relativism. Such relativism is explicitly distinguished from epistemological contextualism. Next the paper presents an argument for epistemic relativism that is based on the Pyrrhonian problem of the criterion. It then considers a response to the problem of the (...) criterion proposed by Roderick Chisholm, which is based on epistemological particularism. After sketching Chisholm’s approach, a response to epistemic relativism is presented which combines Chisholm’s particularism with epistemic naturalism and reliabilism. A number of objections to the position are then considered. The paper ends with remarks about the relationship between particularism and the naturalistic response proposed to epistemic relativism. (shrink)

The New Zealand philosopher, Robert Nola (1940-2022), has died. He was a kind man, a good friend, and a fine philosopher. Here is how I remember him.

In this short essay, we sketch a theory of faith that features resilience in the face of challenges to relying on those in whom you have faith. We argue that it handles a variety of both religious and secular faith-data, e.g., the value of faith in relationships of mutual faith and faithfulness, how the Christian and Hebrew scriptures portray pístis and ʾĕmûnāh, and the character of faith as it is often expressed in popular secular venues.

I argue that the self is simple metaphysically, whilst being complex psychologically and that the persona that links these moments might be dubbed ”creativity’ or ”imagination’. This theory is trinitarian because it ascribes to the self these three ”features’ or ”moments’ and they bear at least some analogy with the Persons of the Trinity, as understood within the neo- platonic, Augustinian tradition.

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.

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

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)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The 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)

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 paper presents a naturalistic response to the challenge of epistemic relativism. The case of the Azande poison oracle is employed as an example of an alternative epistemic norm which may be used to justify beliefs about everyday occurrences. While a distinction is made between scepticism and relativism, an argument in support of epistemic relativism is presented that is based on the sceptical problem of the criterion. A response to the resulting relativistic position is then provided on the basis of (...) a particularist response to scepticism combined with a naturalistic approach to the warrant of epistemic norms. It is argued that it is possible to comparatively assess the ability of epistemic norms to lead to epistemic aims. As against the epistemic relativist, it is possible to provide an objective basis for the choice between alternative epistemic norms. (shrink)

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

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)

This is a brief exploration of the notion of an objective fact. The form of objectivity at issue is distinct from epistemic objectivity or objectivity about truth. It is an ontological form of objectivity. Objective facts may obtain whether or not we know, believe or are aware of them. They depend upon objects, for example, on the properties that objects have or the relationships into which objects enter. Setting scepticism to one side, there is a perfectly mundane sense in which (...) we may come to have knowledge or fail to have knowledge of such facts. We must perceive objective facts from a perspective, but this does not enter into the facts. Nor does the fact that we must describe facts using language mean that facts are language-dependent. (shrink)

The contemporary debate between scientific realism and anti-realism is conditioned by a polarity between two opposing arguments: the realist’s success argument and the anti-realist’s pessimistic induction. This polarity has skewed the debate away from the problem that lies at the source of the debate. From a realist point of view, the historical approach to the philosophy of science which came to the fore in the 1960s gave rise to an unsatisfactory conception of scientific progress. One of the main motivations for (...) the scientific realist appeal to the success of science was the need to provide a substantive account of the progress of science as an increase of knowledge about the same entities as those referred to by earlier theories in the history of science. But the idea that a substantive conception of progress requires continuity of reference has faded from the contemporary debate. In this paper, I revisit the historical movement in the philosophy of science in an attempt to resuscitate the original agenda of the debate about scientific realism. I also briefly outline the way in which the realist should employ the theory of reference as the basis for a robust account of scientific progress which will satisfy realist requirements. (shrink)

This article examines the controversy that has arisen concerning the interpretation of Immanuel Kant's account of European colonialism. One the one hand there are those interpreters such as Robert Bernasconi who see Kant's account as all of a piece with his earlier views on race which demonstrate a certain narrow mindedness in relation to black and coloured people and, on the other hand, there are those such as Pauline Kleingeld and Allen Wood who argue that the earlier writings on race (...) are not wholly typical of Kant's approach and suggest that Kant's later discussions of colonialism in Perpetual Peace and the Metaphysics of Morals provide a better indication of Kant's progressive views on the treatment of non-European societies. The article draws attention to the very strong evidence of Kant's dislike for the pattern of European expansion to other parts of the globe and indicates that within Kant's writings there are the seeds of a wholly unconventional critical understanding of western colonialism that have yet to be developed fully. The article suggests that this critical understanding surpasses the unsystematic objections made to colonialism in post - modernist thought and also the critique proffered by the determinist Marxist account. (shrink)

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

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)

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)

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

This is the original English version of the introduction to Ciencia, Realidad y Racionalidad (University of Cauca Press, 2015), which is a collection of my essays translated into Spanish by Juan Carlos Aguirre Garcia.

In Anti-Oedipus, Deleuze and Guattari claim that a general theory of society must be a generalised theory of flows. This is hardly a straightforward claim, and this paper attempts to examine the grounds for it. Why should socio-political theory be based on a theory of flows rather than, say, a theory of the social contract, or a theory of the State, or the questions of legitimation or revolution, or numerous other possible candidates? The concept of flow (and the related notions (...) of code and stock), I argue, is derived from contemporary economic theory, and most notably John Maynard Keynes. Deleuze and Guattari remained Marxists, not only because they held that contemporary political philosophy must inevitably be centred on the analysis of capitalism, but also because they held, following Marx himself, that the Marxist analysis of capital must constantly be transformed and adapted to new conditions. Thus, while certain aspects of Marx's analysis disappear from Capitalism and Schizophrenia, they are supplemented by the addition of new concepts adequate to the contemporary state of capitalism. The paper concludes, then, with an analysis of the role played by the concepts of flow, code and stock in Deleuze and Guattari's political philosophy. (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)

I present and defend (1) an account of ethical judgments as judgments about our reasons to feel specific motivationally laden attitudes, (2) an account of what an agent should do in terms of what would achieve ends that she has reason to be motivated to pursue, and (3) an account of an agent’s reasons for motivation (and thus action) in terms of the prescriptions of the most fundamental principles that guide her deliberations. Using these accounts, I explain the connection between (...) ethics and reasons for action, how ethical judgments are both descriptive and intrinsically motivating, and how ethical facts arise from facts about agents’ deliberations. (shrink)

This book presents a critical analysis of the semantic incommensurability thesis of Thomas Kuhn and Paul Feyerabend. In putting forward the thesis of incommensurability, Kuhn and Feyerabend drew attention to complex issues concerning the phenomenon of conceptual change in science. They raised serious problems about the semantic and logical relations between the content of theories which deploy unlike systems of concepts. Yet few of the more extreme claims associated with incommensurability stand scrutiny. The argument of this book is as follows. (...) The terms of theories with different concepts diverge semantically and the vocabularies of such theories may not be fully intertranslatable. Given the possibility of referential overlap between the terms of conceptually divergent theories, it does not follow that the content of such theories is incomparable. Nor, given the distinction between understanding a language and translation from one language into another, does it follow that the proponents of mutually untranslatable theories are unable to communicate. Neither is it the case that the shift between conceptually divergent theories involves a discontinuous transition between theories which have no common reference or that refer to distinct worlds of their own making. The semantic differences resulting from conceptual variance may be embraced within a thoroughly realist framework on which they are construed as diverse linguistic relations to a fixed and independent reality. -/- The book, which was originally published in 1994, has now been re-issued in the Routledge Revivals series. -/- . (shrink)