Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

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

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)

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)

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)

Recent research has relied on trolley-type sacrificial moral dilemmas to study utilitarian versus nonutili- tarian modes of moral decision-making. This research has generated important insights into people’s attitudes toward instrumental harm—that is, the sacrifice of an individual to save a greater number. But this approach also has serious limitations. Most notably, it ignores the positive, altruistic core of utilitarianism, which is characterized by impartial concern for the well-being of everyone, whether near or far. Here, we develop, refine, and validate a (...) new scale—the Oxford Utilitarianism Scale—to dissociate individual differences in the ‘negative’ (permissive attitude toward instrumental harm) and ‘positive’ (impartial concern for the greater good) dimensions of utilitarian thinking as manifested in the general population. We show that these are two independent dimensions of proto-utilitarian tendencies in the lay population, each exhibiting a distinct psychological profile. Empathic concern, identification with the whole of humanity, and concern for future generations were positively associated with impartial beneficence but negatively associated with instrumental harm; and although instrumental harm was associated with subclinical psychopathy, impartial beneficence was associated with higher religiosity. Importantly, although these two dimensions were independent in the lay population, they were closely associated in a sample of moral philosophers. Acknowledging this dissociation between the instrumental harm and impartial beneficence components of utilitarian thinking in ordinary people can clarify existing debates about the nature of moral psychology and its relation to moral philosophy as well as generate fruitful avenues for further research. (shrink)

Theoretical ethics includes both metaethics (the meaning of moral terms) and normative ethics (ethical theories and principles). Practical ethics involves making decisions about every day real ethical problems, like decisions about euthanasia, what we should eat, climate change, treatment of animals, and how we should live. It utilizes ethical theories, like utilitarianism and Kantianism, and principles, but more broadly a process of reflective equilibrium and consistency to decide how to act and be.

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.

Recent research has begun treating the perennial philosophical question, “what makes a person the same over time?” as an empirical question. A long tradition in philosophy holds that psychological continuity and connectedness of memories are at the heart of personal identity. More recent experimental work, following Strohminger & Nichols (2014), has suggested that persistence of moral character, more than memories, is perceived as essential for personal identity. While there is a growing body of evidence supporting these findings, a critique by (...) Starmans & Bloom (2018) suggests that this research program conflates personal identity with mere similarity. To address this criticism, we explore how loss of someone’s morality or memories influence perceptions of identity change, and perceptions of moral duties towards the target of the change. We present participants with a classic ‘body switch’ thought experiment and after assessing perceptions of identity persistence, we present a moral dilemma, asking participants to imagine that one of the patients must die (Study 1) or be left alone in a care home for the rest of their life (Study 2). Our results highlight the importance of the continuity of moral character, suggesting lay intuitions are tracking (something like) personal identity, not just mere similarity. (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 requirements of rationality are fundamental in practical and theoretical philosophy. Nonetheless, there exists no correct account of what constitutes rational requirements. This paper attempts to provide a correct constitutive account of ‘rationality requires’. I argue that rational requirements are grounded in ‘necessary explanations of subjective incoherence’, as I shall put it. Rationality requires of you to X if and only if your rational capacities, in conjunction with the fact that you not-X, explain necessarily why you have a non-maximal degree (...) of subjective coherence. (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)

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)

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)

“Love hurts”—as the saying goes—and a certain amount of pain and difficulty in intimate relationships is unavoidable. Sometimes it may even be beneficial, since adversity can lead to personal growth, self-discovery, and a range of other components of a life well-lived. But other times, love can be downright dangerous. It may bind a spouse to her domestic abuser, draw an unscrupulous adult toward sexual involvement with a child, put someone under the insidious spell of a cult leader, and even inspire (...) jealousy-fueled homicide. How might these perilous devotions be diminished? The ancients thought that treatments such as phlebotomy, exercise, or bloodletting could “cure” an individual of love. But modern neuroscience and emerging developments in psychopharmacology open up a range of possible interventions that might actually work. These developments raise profound moral questions about the potential uses—and misuses—of such anti-love biotechnology. In this article, we describe a number of prospective love-diminishing interventions, and offer a preliminary ethical framework for dealing with them responsibly should they arise. (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)

Numerous high-profile ethics scandals, rising inequality, and the detrimental effects of climate change dramatically underscore the need for business schools to instill a commitment to social purpose in their students. At the same time, the rising financial burden of education, increasing competition in the education space, and overreliance on graduates’ financial success as the accepted metric of quality have reinforced an instrumentalist climate. These conflicting aims between social and financial purpose have created an existential crisis for business education. To resolve (...) this impasse, we draw on the concept of moral self-awareness to offer a system-theoretical strategy for crowding-in a culture of ethics within business schools. We argue that to do so, business schools will need to (1) reframe the purpose of business, (2) reframe the meaning of professional success, and (3) reframe the ethos of business education itself. (shrink)

A core challenge for contemporary bioethics is how to address the tension between respecting an individual’s autonomy and promoting their wellbeing when these ideals seem to come into conflict (Not...

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

There is growing concern that a global economic system fueled predominately by financial incentives may not maximize human flourishing and social welfare externalities. If so, this presents a challenge of how to get economic actors to adopt a more virtuous motivational mindset. Relying on historical, psychological, and philosophical research, we show how such a mindset can be instilled. First, we demonstrate that historically, financial self-interest has never in fact been the only guiding motive behind free markets, but that markets themselves (...) are representations of our individual and collective moral identities. Building on this understanding, we review the research on how economic incentives crowd out virtue-oriented concerns. We then introduce the concept of moral self-awareness (MSA), an evolving mindset informed by reflection on moral identity, namely what one’s actions say about oneself given the impacts on others or society that one’s action may effect. MSA comprises three fundamental aspects of virtue-oriented reasoning: pride, shame, and guilt. Finally, we offer a four-stage model anchored in systems theory, yielding ever more refined motivating strategies for maximizing human flourishing and social welfare externalities. (shrink)

Extant research suggests that individuals employ traditional moral heuristics to support their observed altruistic behavior; yet findings have largely been limited to inductive extrapolation and rely on relatively few traditional frames in so doing, namely, deontology in organizational behavior and virtue theory in law and economics. Given that these and competing moral frames such as utilitarianism can manifest as identical behavior, we develop a moral framing instrument—the Philosophical Moral-Framing Measure (PMFM)—to expand and distinguish traditional frames associated and disassociated with observed (...) altruistic behavior. The validation of our instrument based on 1015 subjects in 3 separate real stakes scenarios indicates that heuristic forms of deontology, virtue-theory, and utilitarianism are strongly related to such behavior, and that egoism is an inhibitor. It also suggests that deontic and virtue-theoretical frames may be commonly perceived as intertwined and opens the door for new research on self-abnegation, namely, a perceived moral obligation toward suffering and self-denial. These findings hold the potential to inform ongoing conversations regarding organizational citizenship and moral crowding out, namely, how financial incentives can undermine altruistic behavior. (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)

Can we employ the property of rationality in establishing what rationality requires? According to a central and formal thesis of John Broome’s work on rational requirements, the answer is ‘no’ – at least if we expect a precise answer. In particular, Broome argues that (i) the property of full rationality (i.e. whether or not you are fully rational) is independent of whether we formulate conditional requirements of rationality as having a wide or a narrow logical scope. That is, (ii) by (...) replacing a wide-scope requirement with a corresponding narrow-scope requirement (or vice versa), we do not alter the situations in which a person is fully rational. As a consequence, (iii) the property of full rationality is unable to guide us in determining whether a rational requirement has a wide or a narrow logical scope. We cannot resolve the wide/narrow scope debate by appealing to a theory of fully rational attitudes. This paper argues that (i), (ii) and (iii) are incorrect. Replacing a wide- with a corresponding narrow-scope requirement (or vice versa) can alter the set of circumstances in which a person is fully rational. The property of full rationality is therefore not independent of whether we formulate conditional requirements of rationality as having a wide or a narrow logical scope. As a consequence, the property of full rationality can guide us in determining what rationality requires – even in cases where we expect a precise answer. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (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)

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)

Many of us assume that all the free editing and sorting of online content we ordinarily rely on is carried out by AI algorithms — not human persons. Yet in fact, that is often not the case. This is because human workers remain cheaper, quicker, and more reliable than AI for performing myriad tasks where the right answer turns on ineffable contextual criteria too subtle for algorithms to yet decode. The output of this work is then used for machine learning (...) purposes to generate algorithms constructed from large data sets containing thousands of correctly coded observations. The fact that ghost workers are treated as consumers distorts the basic logic of the employment relationship, effectively placing the worker-as-consumer in the worst of both worlds, in which they hold the legal rights of neither group. This puts them in a regulatory limbo position in which they have little or no protection, control, or guarantee of return on investment. This is because the platforms that facilitate ghost work have orchestrated a three-way virtual relationship that absolves all parties of responsibility, while placing nearly all the risks and opportunity costs squarely on the shoulders of the workers. As a result, we believe such a work arrangement as it stands, does not uphold basic standards of Rawlsian justice as fairness. (shrink)

Our rapidly increasing reliance on frictionless AI interactions may increase cognitive and emotional distance, thereby letting our adaptive resilience slacken and our ethical virtues atrophy from disuse. Many trends already well underway involve the offloading of cognitive, emotional, and ethical labor to AI software in myriad social, civil, personal, and professional contexts. Gradually, we may lose the inclination and capacity to engage in critically reflective thought, making us more cognitively and emotionally vulnerable and thus more anxious and prone to manipulation (...) from false news, deceptive advertising, and political rhetoric. In this article, I consider the overarching features of this problem and provide a framework to help AI designers tackle it through system enhancements in smartphones and other products and services in the burgeoning internet of things (IoT) marketplace. The framework is informed by two ideas: psychologist Daniel Kahneman’s cognitive dual process theory and moral self-awareness theory, a four-level model of moral identity that I developed with Benjamin M. Cole. (shrink)

The intellectual culture of scientism clouds our understanding of science itself. What’s more, it eclipses alternative ways of knowing — chiefly the philosophical — that can actually yield greater certainty than the scientific. While science and philosophy do at times overlap, they are fundamentally different approaches to understanding. So philosophers should not add to the conceptual confusion that subsumes all knowledge into science. Rather, we should underscore the fact that various disciplines we ordinarily treat as science are at least as (...) — if not more —philosophical than scientific. (shrink)

Michael Goldhaber, who popularized the term the attention economy, said of the US Capitol insurrection: “It felt like an expression of a world in which everyone is desperately seeking their own audience and fracturing reality in the process. I only see that accelerating.” If we don’t do something about this, American democracy may not survive. For when there is no longer any common ground of evidence and reason, history shows that misinformation will eventually overwhelm public discourse and authoritarianism can take (...) over. That is precisely what dictators across the world gleefully anticipate will happen in the US. The Biden administration could combat this by establishing a digital fairness doctrine for the twenty-first century. This would not mean setting up a government agency as the arbiter of truth. The purpose of such a doctrine is simply to preserve the possibility of a functioning national discourse on critical issues of public interest. It would not run afoul of First Amendment free speech guarantees, given that it would do nothing to block speech itself. In fact, it would expand and enrich national conversations, by preventing echo chambers prone to systematic bias. (shrink)

It is beyond doubt that the legal system established by the Nazi government in Germany between 1933-1945 represented a gross departure from the rule of law: the Nazis eradicated legal security and certainty; allowed for judicial and state arbitrariness; blocked epistemic access to what the law requires; issued unpredictable legal requirements; and so on. This introduction outlines the distorted nature of the Nazi legal system and looks at the main factors that contributed to this grave divergence.

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)

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)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

: 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)

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.

Recent advances in the Super Linguistics of pictures have laid the Super Semantic foundation for modelling the phenomena of narrative sequencing and co-reference in pictorial and mixed linguistic-pictorial discourses. We take up the question of how one arrives at the pragmatic interpretations of such discourses. In particular, we offer an analysis of: (i) the discourse composition problem: how to represent the joint meaning of a multi-picture discourse, (ii) observed differences in narrative sequencing in prima facie equivalent linguistic vs pictorial discourses, (...) and (iii) the phenomenon of co-referencing across pictures. We extend Segmented Discourse Representation Theory to spell out a formal Super Pragmatics that applies to linguistic, pictorial and mixed discourses, while respecting the particular ‘genius’ of either medium and computing their distinctive pragmatic interpretations. (shrink)

We offer an argument for the extended mind based on considerations from brain development. We argue that our brains develop to function in partnership with cognitive resources located in our external environments. Through our cultural upbringing we are trained to use artefacts in problem solving that become factored into the cognitive routines our brains support. Our brains literally grow to work in close partnership with resources we regularly and reliably interact with. We take this argument to be in line with (...) complementarity or “second-wave” defences of the extended mind that stress the functional differences between biological elements and external, environmental resources in putative cases of extended cognition. Complementarity defences argue that many of the kinds of cognition humans excel at can only be accomplished by brains working together with a body that directly manipulates and acts on the world [Rowlands (1999); Menary (2007); Sutton (2010)]. We argue that complementarity and functionalist defences of the extended mind aren’t opposed, but that complementarity considerations can provide much needed and hitherto under exploited leverage in defending EMT. Moreover, the developmental work we will describe adds extra weight to the complementarity case for EMT. (shrink)

Most prominent arguments favoring the widespread discretionary business practice of sending jobs overseas, known as ‘offshoring,’ attempt to justify the trend by appeal to utilitarian principles. It is argued that when business can be performed more cost-effectively offshore, doing so tends, over the longterm, to achieve the greatest good for the greatest number. This claim is supported by evidence that exporting jobs actively promotes economic development overseas while simultaneously increasing the revenue of the exporting country. After showing that offshoring might (...) indeed be justified on utilitarian grounds, I argue that according to Rawlsian social-contract theory, the practice is nevertheless irrational and unjust. For it unfairly expects the people of a given society to accept job-gain benefits to peoples of other societies as outweighing job-loss hardships it imposes on itself. Finally, I conclude that contrary to socialism, which relies much more on government control, capitalism constitutes a social contract that places a particularly strong moral obligation on corporations themselves to refrain from offshoring. (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)

Delusions have traditionally been considered the hallmark of mental illness, and their conception, diagnosis and treatment raise many of the fundamental conceptual and practical questions of psychopathology. One of these fundamental questions is whether delusions are understandable. In this paper, we propose to consider the question of understandability of delusions from a philosophy of language perspective. For this purpose, we frame the question of how delusions can be understood as a question about the meaning of delusional utterances. Accordingly, we ask: (...) “what meaning(s) can delusional utterances possibly have?”. We argue that in the current literature, there is a standard approach to the meaning of delusional utterances, namely the descriptive account which assumes that a delusional utterance “p” means that p is the case. Drawing on Speech Act Theory, we argue that solely relying on the descriptive account disregards essential ways of how linguistic meaning is constituted. Further, we show that Speech Act Theory can prove a helpful addition to the theoretical and clinical “toolbox” used for attempting to understand delusional utterances. This, we believe, may address some of the theoretical and clinical shortcomings of using only the currently predominant descriptive account. (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)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

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)

To pursue the cultivation of a compassionate disposition is often perceived as an external demand, constraining one's individual freedom. Some might think of it as a necessary burden for the benefit of society, while others may exercise it only in the most convenient occasions. This most common view is gravely impoverished. Compassion is in fact a cognitive disposition with a certain historical life that actually frees us from our own perceptive constraints.