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)

In June 2002, Arthur Andersen LLP became the first accounting firm in history to be criminally convicted. The repercussions were immense. From a position as one of the leading professional services firms in the world, with 85,000 staff in 84 countries and revenues in excess of $9 billion, Andersen effectively ceased to exist within a matter of months. Although Andersen’s conviction related specifically to a charge of obstructing justice, public attention focused on the audit relationship between Andersen and its major (...) client, Enron Corporation, particularly the actions (and inactions) that had allowed Enron to post spectacular year-on-year earnings and profit growth. As well as examining events leading up to the demise of Andersen, the case provides an opportunity to consider the broader controversy over accounting and corporate governance practices and, more generally, the pressures found within organisations that can foster unethical conduct. The case was prepared from public sources. (shrink)

Atheists have tacitly conceded the field to theists in the area of philosophical cosmology, specifically, in the enterprise of explaining why the universe exists. The theistic hypothesis is that the reason the universe exists lies in God’s creative choice, but atheists have not proposed any reason why the universe exists. I argue that quantum cosmology proposes such an atheistic reason, namely, that the universe exists because it has an unconditional probability of existing based on a functional law of nature. This (...) law of nature (“the wave function of the universe”) is inconsistent with theism and implies that God does not exist. I criticize the claims of Alston, Craig, Deltete and Guy, Oppy and Plantinga that theism is consistent with quantum cosmology. (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.

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

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)

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)

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.

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)

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)

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.

Quentin Smith argues that if God exists, He had a duty to ensure life's existence; and He couldn't rationally have done so and made a big bang unless a counter-factual like "If God had made a big bang, there would have been life," was true pre-creation. But such counter-factuals are not true pre-creation. I argue that God could have made a big bang without irrationality; and that He could have ensured life without making big bangs non-random. Further, a proper (...) understanding of the truth-conditions of counter-factuals like the one above lets them have determinate truth-values pre-creation. But the explanation of how the above counter-factual can be true pre-creation is more complicated than that offered by William Lane Craig. (shrink)

Given his view that the modern world is ‘radically evil’, Adorno is an unlikely contributor to business ethics. Despite this, we argue that his work has a number of provocative implications for the field that warrant wider attention. Adorno regards our social world as damaged, unfree, and false and we draw on this critique to outline why the achievement of good work is so rare in contemporary society, focusing in particular on the ethical demands of roles and the ideological nature (...) of management’s self-understanding. Nevertheless, we show that Adorno’s comments on activities such as art and philosophy mean that it is possible to draw on his work in a way that contributes constructively to the conversation about good and meaningful work within business ethics. (shrink)

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

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

In the bitcoin whitepaper, Satoshi Nakamoto (2008: 2) defines an electronic coin as a chain of digital signatures. Many have since defined a bitcoin as a chain of digital signatures. This latter definition continues to appear in reports from central banks, advocacy centers, and governments, as well as in academic papers across the disciplines of law, economics, computer science, cryptography, management, and philosophy. Some have even used it to argue that what we now call bitcoin is not the real bitcoin. (...) The definition fails, however. This is important because the Chain Definition obscures Satoshi’s solution to a dilemma in the design of electronic cash, as well as the truth about bitcoin’s privacy and fungibility. In this article, I explain why the Chain Definition fails and what Satoshi likely endorsed instead. Along the way, I untangle some issues around bitcoin fungibility and clarify some others around the ontology of digital assets. (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

In this article I present an original interpretation of Roy Bhaskar’s project in Dialectic: The Pulse of Freedom. His major move is to separate an ontological dialectic from a critical dialectic, which in Hegel are laminated together. The ontological dialectic, which in Hegel is the self-unfolding of spirit, becomes a realist and relational philosophical anthropology. The critical dialectic, which in Hegel is confined to retracing the steps of spirit, now becomes an active force, dialectical critique, which interposes into the ontological (...) dialectic at the ‘fourth dimension’ of a naturalistically reconfigured account of relational human nature, agency. This account allows Bhaskar to explain and vindicate the crucial role social criticism must play in any realistic project of self-emancipation, and to create a space that didn’t exist in Hegel for an open-ended concrete utopianism. Freedom is thus the actualization of human nature, but is not automatic: the relation of human nature to freedom is mediated historically through dialectical critique, which, informed by concrete utopianism, can have emancipatory power. Content Type Journal Article Category Article Pages 13-44 Authors Craig Reeves, Brunel University Journal Journal of Critical Realism Online ISSN 1572-5138 Print ISSN 1476-7430 Journal Volume Volume 12 Journal Issue Volume 12, Number 1 / 2013. (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)

Drunk drivers and other culpably incapacitated wrongdoers are often taken to pose a problem for reasons-responsiveness accounts of moral responsibility. These accounts predicate moral responsibility upon an agent having the capacities to perceive and act upon moral reasons, and the culpably incapacitated wrongdoers lack exactly those capacities at the time of their wrongdoing. Many reasons-responsiveness advocates thus expand their account of responsibility to include a tracing condition: The culpably incapacitated wrongdoer is blameworthy despite his incapacitation precisely because he is responsible (...) for becoming incapacitated. As some skeptics have suggested, it is not clear that we need tracing. Here, however, I make a stronger case against tracing: I show that tracing gets things wrong. I consider a new sort of case, the case of the Odysseus agent, whose incapacitation is non-culpable (sometimes merely permissible and sometimes praiseworthy). Tracing would have us hold responsible and therefore blame unlucky Odysseus agents, Odysseus agents who commit a wrongdoing in the throes of their non-culpably induced incapacitation. But we should not hold these unlucky Odysseus agents responsible for their incapacitated wrongdoing. Because tracing gets these cases wrong, we should reject tracing. (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)

The article examines from an historical perspective some of the key ideas used in contemporary bioethics debates both for and against the practices of assisted suicide and euthanasia. Key thinkers examined--spanning the Ancient, Medieval and Modern periods--include Plato, Aristotle, Augustine, Aquinas, Hume, Kant, and Mill. The article concludes with a synthesizing summary of key ideas that oppose or defend assisted suicide and euthanasia.

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

The 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)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

In Eichmann in Jerusalem , Hannah Arendt struggled to defend the possibility of judgment against the obvious problems encountered in attempts to offer legally valid and morally meaningful judgments of those who had committed crimes in morally bankrupt communities. Following Norrie, this article argues that Arendt’s conclusions in Eichmann are equivocal and incoherent. Exploring her perspectival theory of judgment, the article suggests that Arendt remains trapped within certain Kantian assumptions in her philosophy of history, and as such sees the question (...) of freedom in a binary way. The article argues that Adorno’s philosophy of freedom provides the resources to diagnose and overcome Arendt’s shortcomings. Adorno’s position provides a way of embracing the antinomical character of judgment, by emphasising the need for elements of reason and nature in the phenomenon of freedom. In Adorno’s lights, judgment becomes an attempt to express a ‘spirit of solidarity’ with the tragic status of the potentially free but actually unfree subject of modernity. (shrink)

This paper aims to demonstrate the contemporary relevance of Adorno’s thought for business ethicists working in the critical tradition by showing how his critique of modern social life anticipated, and offers continuing illumination of, recent technological transformations of capitalism. It develops and extrapolates Adorno’s thought regarding three central spheres of modern society, which have seen radical changes in light of recent technological developments: work, in which employee monitoring has become ever more sophisticated and intrusive; leisure consumption, in which the algorithmic (...) developments of the culture industry have paved the way for entertainment products to dominate us; and political discourse, in which social media has exacerbated the anti-democratic tendencies Adorno warned of in the mid-twentieth century. We conclude by presenting, as a rejoinder to these developments, the contours of an Adornian ethics of resistance to the reification and dehumanisation of such developments. (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)

One of the most intriguing claims in Sven Rosenkranz’s Justification as Ignorance is that Timothy Williamson’s celebrated anti-luminosity argument can be resisted when it comes to the condition ~K~KP—the condition that one is in no position to know that one is in no position to know P. In this paper, I critically assess this claim.

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)

In this paper I argue that Theodor W. Adorno 's philosophy of freedom needs an ontological picture of the world. Adorno does not make his view of natural order explicit, but I suggest it could be neither the chaotic nor the strictly determined ontological images common to idealism and positivism, and that it would have to make intelligible the possibility both of human freedom and of critical social science. I consider two possible candidates, Nancy Cartwright 's ‘patchwork of laws’, and (...) Roy Bhaskar 's critical realism. Arguing that Cartwright 's position conflicts with the spirit of Adorno 's philosophy, I suggest that Bhaskar 's realism is compatible with and to a significant extent implicit in Adorno 's position. Whilst Adorno is clearly not a critical realist, Bhaskar 's position does provide the best overall account of the ontological commitments of Adorno 's critical theory. It becomes possible in turn to locate Bhaskar 's arguments in a broader critical tradition and give fuller expression to the concerns that structure his work, in particular by locating the epistemic fallacy in the narrative account of the natural history of subjective reason and its tendency towards ‘identity thinking ’. The discussion goes on to consider the interdependence of reason, nature and freedom in the idea of emancipatory critique, confirming the deeper affinities between critical realism and critical theory. (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 paper is a critical review of *Big Bang Cosmology* by Quentin Smith and William Lane Craig. (The book is a collection of previously published papers; most are concerned, in one way or another, with kalam cosmological arguments for the existence of God.).

The argument from illusion attempts to establish the bold claim that we are never perceptually aware of ordinary material objects. The argument has rightly received a great deal critical of scrutiny. But here we develop a criticism that, to our knowledge, has not hitherto been explored. We consider the canonical form of the argument as it is captured in contemporary expositions. There are two stages to our criticism. First, we show that the argument is invalid. Second, we identify premises that (...) can be used to make the argument valid. But we argue that the obvious fixes are problematic. If our arguments are successful, we show that the argument from illusion is even more difficult to defend than is commonly acknowledged. (shrink)

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

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)

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”.

Many epistemologists have responded to the lottery paradox by proposing formal rules according to which high probability defeasibly warrants acceptance. Douven and Williamson present an ingenious argument purporting to show that such rules invariably trivialise, in that they reduce to the claim that a probability of 1 warrants acceptance. Douven and Williamson’s argument does, however, rest upon significant assumptions – amongst them a relatively strong structural assumption to the effect that the underlying probability space is both finite and uniform. In (...) this paper, I will show that something very like Douven and Williamson’s argument can in fact survive with much weaker structural assumptions – and, in particular, can apply to infinite probability spaces. (shrink)

The counterfactual mental state of negligent criminal activity invites skepticism from those who see mental states as essential to responsibility. Here, I offer a revision of the mental state of criminal negligence, one where the mental state at issue is actual and not merely counterfactual. This revision dissolves the worry raised by the skeptic and helps to explain negligence’s comparatively reduced culpability.

Many contemporary theorists charge that naïve realists are incapable of accounting for illusions. Various sophisticated proposals have been ventured to meet this charge. Here, we take a different approach and dispute whether the naïve realist owes any distinctive account of illusion. To this end, we begin with a simple, naïve account of veridical perception. We then examine the case that this account cannot be extended to illusions. By reconstructing an explicit version of this argument, we show that it depends critically (...) on the contention that perceptual experience is diaphanous, or more minimally and precisely, that there can be no difference in phenomenal properties between two experiences without a difference in the scenes presented in those experiences. Finding no good reason to accept this claim, we develop and defend a simple, naïve account of both veridical perception and illusion, here dubbed Simple, Austere Naïve Realism. (shrink)

Duress is a defense in both law and morality. The bank teller who provides an armed robber with the bank vault combination, the innocent suspect who fabricates a story after hours of interrogation, the Good Samaritan who breaks into a private cabin in the woods to save a stranded hiker, and the father who drives at high speed to rush his injured child to the hospital—in deciding how to respond to agents like these, we should take into account that they (...) have acted under duress. In this paper, I offer a new duress defense, which I call “distinctive duress.” The distinctive-duress defense is neither ordinary justification nor ordinary excuse. Rather, it is a defense available to agents who act wrongly because they are appropriately insensitive to certain reasons. In the distinctive-duress cases, an agent’s normative sensitivities are rightly directed elsewhere, leading them awry. (shrink)

Jaakko Nevasto has offered a number of thoughtful criticisms of our attempt to show that Adorno’s work can fruitfully be brought to bear on topics in business ethics. After welcoming his constructive clarifications, we attempt to defuse Nevasto’s main objections and defend our application of Adorno, focusing in particular on the topics of moral epistemology, needs, and the possibility of genuine activity – and thus good work – within capitalist society.

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 On What Matters, Derek Parfit enters the debate between actualists and possibilists. This debate concerns mere possibilia, possible but non-actual things such as golden mountains and talking donkeys. Roughly, possibilism says that there are such things, and actualism says that there are not. Parfit not only argues for possibilism but also argues that some self-proclaimed actualists are, in fact, unwitting possibilists. -/- I argue that although Parfit’s arguments do not fully succeed, they do highlight a tension within the frameworks (...) of many actualists. Many actualists conscript abstract objects into the role of "possible worlds" to avoid quantifying over mere possibilia. But, in doing so, actualists must quantify over mere possibilia anyway. When we alleviate this tension, a Parfit-friendly form of actualism arguably remains. This form of actualism says that while everything that exists is actual, it is also true in some sense that there are mere possibilia. (shrink)

Visual experiences seem to exhibit phenomenological particularity: when you look at some object, it – that particular object – looks some way to you. But experiences exhibit generality too: when you look at a distinct but qualitatively identical object, things seem the same to you as they did in seeing the first object. Naïve realist accounts of visual experience have often been thought to have a problem with each of these observations. It has been claimed that naïve realist views cannot (...) account for the generality of visual experiences, and that the naïve realist explanation of particularity has unacceptable implications for self- knowledge: the knowledge we have of the character of our own experiences. We argue in this paper that neither claim is correct: naïve realism can explain the generality of experiences, and the naïve realist explanation of particularity raises no problems for our self-knowledge. (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)