Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (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)

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

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Post-traumatic stress disorder is a “young” disorder formally recognized in the early 1980s, although the symptoms have been noted for centuries particularly in relation to military conflicts. PTSD may develop after a serious traumatic experience that induces feelings of intense fear, helplessness or horror. It is currently characterized by three key classes of symptoms which must cause clinically significant distress or impairment of functioning: persistent and distressing re-experiencing of the trauma; persistent avoidance of stimuli associated with the trauma and numbing (...) of general responsiveness; and persistent symptoms of hyper-arousal. One of the possible symptoms within the second class is difficulty in remembering an important aspect of the traumatic event.PTSD is not an uncommon condition, with an estimated lifetime prevalence of about 7-9% based on studies conducted in the United States and Canada, with women at higher risk than men. While not everyone who experiences a significant trauma will go on to develop PTSD, about a third will do so. Sexual assault, along with other forms of assaultive violence, pose a comparatively high risk of PTSD. (shrink)

This paper articulates and defends a novel hybrid account of well-being. We will call our view a Robust Hybrid. We call it robust because it grants a broad and not subservient role to both objective and subjective values. In this paper we assume, we think plausibly but without argument, that there is a significant objective component to well-being. Here we clarify what it takes for an account of well-being to have a subjective component. Roughly, we argue, it must allow that (...) favoring attitudes that are not warranted by the lights of objective values can ground benefits. Given this understanding, we show that there is an important and unrecognized expansion in the resources available to fully objectivist views: namely that such views can help themselves to the value of warranted love of objective goods. Such a move by the objectivist can help them respond to concerns that, on their view, a person’s well-being can be too alien to them. We next argue that, nonetheless, such objectivist views are still unconvincing due to their lack of a subjective component. This motivates a move from fully objective accounts to hybrid accounts. We show that many prominent hybrid theories in the literature are inadequate because they implausibly minimize the subjective component. This motivates a move to a robust hybrid view that has an expanded subjectivist component. We conclude with some remarks about the interrelation between the subjective and objective components in the hybrid account that we favor and a role for resonance in a theory of well-being other than serving as a hard constraint on any benefit. (shrink)

The Standard View of personal identity says that someone who exists now can exist at another time only if there is continuity of her mental contents or capacities. But no person is psychologically continuous with a fetus, for a fetus, at least early in its career, has no mental features at all. So the Standard View entails that no person was ever a fetus--contrary to the popular assumption that an unthinking fetus is a potential person. It is also mysterious what (...) does ordinarily happen to a human fetus, if it does not come to be a person. Although an extremely complex variant of the Standard View may allow one to persist without psychological continuity before one becomes a person but not afterwards, a far simpler solution is to accept a radically non-psychological account of our identity. (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)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

In this paper, we argue that promoting patient values is a legitimate goal of medicine. Our view offers a justification for certain current practices, including birth control and living organ donation, that are widely accepted but do not fit neatly within the most common extant accounts of the goals of medicine. Moreover, we argue that recognising value promotion as a goal of medicine will expand the scope of medical practice by including some procedures that are sometimes rejected as being outside (...) the scope of acceptable medical practice, such as certain forms of physician-assisted death. We then rebut some common and possible objections to this view. Our aim is not to argue that other accounts are mistaken—except when they argue for a single goal that does not include patient values—but rather to show that value promotion should play a more central role in discussions about the goals of medicine. (shrink)

The overwhelming majority of those who theorize about implicit biases posit that these biases are caused by some sort of association. However, what exactly this claim amounts to is rarely specified. In this paper, I distinguish between different understandings of association, and I argue that the crucial senses of association for elucidating implicit bias are the cognitive structure and mental process senses. A hypothesis is subsequently derived: if associations really underpin implicit biases, then implicit biases should be modulated by counterconditioning (...) or extinction but should not be modulated by rational argumentation or logical interventions. This hypothesis is false; implicit biases are not predicated on any associative structures or associative processes but instead arise because of unconscious propositionally structured beliefs. I conclude by discussing how the case study of implicit bias illuminates problems with popular dual-process models of cognitive architecture. (shrink)

Conscious states—state that there is something it is like to be in—seem both rich or full of detail and ineffable or hard to fully describe or recall. The problem of ineffability, in particular, is a longstanding issue in philosophy that partly motivates the explanatory gap: the belief that consciousness cannot be reduced to underlying physical processes. Here, we provide an information theoretic dynamical systems perspective on the richness and ineffability of consciousness. In our framework, the richness of conscious experience corresponds (...) to the amount of information in a conscious state and ineffability corresponds to the amount of information lost at different stages of processing. We describe how attractor dynamics in working memory would induce impoverished recollections of our original experiences, how the discrete symbolic nature of language is insufficient for describing the rich and high-dimensional structure of experiences, and how similarity in the cognitive function of two individuals relates to improved communicability of their experiences to each other. While our model may not settle all questions relating to the explanatory gap, it makes progress toward a fully physicalist explanation of the richness and ineffability of conscious experience—two important aspects that seem to be part of what makes qualitative character so puzzling. (shrink)

Moorean arguments are a popular and powerful way to engage highly revisionary philosophical views, such as nihilism about motion, time, truth, consciousness, causation, and various kinds of skepticism (e.g., external world, other minds, inductive, global). They take, as a premise, a highly plausible first-order claim (e.g., cars move, I ate breakfast before lunch, it’s true that some fish have gills) and conclude from it the falsity of the highly revisionary philosophical thesis. Moorean arguments can be used against nihilists in ethics (...) (error theorists), too. Recently, error theorists have recognized Moorean arguments as a powerful challenge and have tried to meet it. They’ve argued that moral Moorean premises seem highly credible to us, but aren’t, by offering various debunking explanations. These explanations all appeal to higher-order evidence—evidence of error in our reasoning. I argue that drawing attention to higher-order evidence is a welcome contribution from error theorists, but that the higher-order evidence actually counts further against error theoretic arguments—including their debunking explanations—and further in favor of Moorean arguments and the commonsense views they support. Along the way I answer a few prominent objections to Moorean arguments: that they are objectionably question-begging, rely on categorizing some facts as “Moorean Facts”, and that reports of one’s credence in a proposition bears no interesting relation to that proposition’s credibility. (shrink)

At some point in the future – perhaps within the next few decades – it will be possible for foetuses to develop completely outside the womb. Ectogenesis, as this technology is called, raises substantial issues for the abortion debate. One such issue is that it will become possible for a woman to have an abortion, in the sense of having the foetus removed from her body, but for the foetus to be kept alive. We argue that while there is a (...) right to an abortion, there are reasons to doubt that there is a right to the death of the foetus. Our strategy in this essay is to consider and reject three arguments in favour of this latter right. The first claims that women have a right not to be biological mothers, the second that women have a right to genetic privacy, and the third that a foetus is one's property. Furthermore, we argue that it follows from rejecting the third claim that genetic parents also lack a right to the destruction of cryopreserved embryos used for in vitro fertilization. The conclusion that a woman possesses no right to the death of the foetus builds upon the claims that other pro-choice advocates, such as Judith Jarvis Thomson, have made. (shrink)

In this paper, I develop a novel account of concept acquisition for an atomistic theory of concepts. Conceptual atomism is rarely explored in cognitive science because of the feeling that atomistic treatments of concepts are inherently nativistic. My model illustrates, on the contrary, that atomism does not preclude the learning of a concept.

The guiding thread of the paper is the diagnosis that the advanced division of cognitive labor (that is, intellectual specialization) engenders a set of perennial, political and epistemic challenges (Millgram 2015) that, simultaneously, also generate opportunities for philosophy. In this paper, I re-characterize the nature of synthetic philosophy as a means to advance and institutionalize philosophy. For my definition of synthetic philosophy see section 2. In section 1, I treat Plato’s Republic as offering two models to represent philosophy's relationship to (...) the other sciences within the advanced division of labor. I highlight that for Plato intellectual specialization is central not just to economic, but also to political life. And, yet, that the very dispersion of scientific expertise, and its esoteric nature, also generates non-trivial challenges to the recognition and political utilization of knowledge. From Plato we can infer that in imperfect circumstances, philosophy’s self-constitution is, in part, a response to these challenges in political epistemology. However, how philosophy is institutionalized differs through time. In section 2, I re-introduce my conceptualization of synthetic philosophy and restate it. This makes visible that synthetic philosophy is already widely practiced in the profession as philosophy of the special sciences, PPE, formal modelling, public philosophy, etc. I use recent work by Dorst (2023) to illustrate synthetic philosophy and to identify some of the processes that give rise to the need for it. In sections 2-3, I contrast my account with the evolving ways that Philip Kitcher has conceptualized synthetic philosophy in order to make more precise the version promoted here. I do so not just because Kitcher and I use the same term, ‘synthetic philosophy,’ but because the temptations inherent in Kitcher’s approach should be resisted. -/- . (shrink)

One of the deepest and longest-lasting debates in ethics concerns a version of the Euthyphro question: are choiceworthy things choiceworthy because agents have certain attitudes toward them or are they choiceworthy independent of any agents’ attitudes? Reasons internalists, such as Bernard Williams, Michael Smith, Mark Schroeder, Sharon Street, Kate Manne, Julia Markovits, and David Sobel answer in the first way. They think that all of an agent’s normative reasons for action are grounded in facts about that agent’s pro-attitudes (e.g., her (...) desires, valuing states, normative judgments). According to the most popular brand of internalism, idealizing internalism, an agent’s reasons are grounded, not in her actual pro-attitudes, but rather in what her pro-attitudes would be in suitably idealized conditions. Idealizing internalists presuppose that, for any agent with an irrational set of attitudes, there is one uniquely rational set that that agent would have if she were to undergo the relevant idealizing process. I argue that this assumption is false and that it raises two puzzles for idealizing internalism: one about the existence of practical reasons and another about their normative weight. I argue that idealizing internalists have an adequate solution to the first puzzle but not the second. Indeed, when they try to solve the second puzzle, they confront a dilemma. This second puzzle and the associated dilemma thus constitutes a powerful, but so far unnoticed, difficulty for idealizing internalism. (shrink)

Metaphors have computable semantics. A program called NETMET both generates metaphors and produces partial literal interpretations of metaphors. NETMET is based on Kittay's semantic field theory of metaphor and Black's interaction theory of metaphor. Input to NETMET consists of a list of literal propositions. NETMET creates metaphors by finding topic and source semantic fields, producing an analogical map from source to topic, then generating utterances in which terms in the source are identified with or predicated of terms in the topic. (...) Given a metaphor, NETMET utilizes if-then rules to generate the implication complex of that metaphor. The literal leaves of the implication complex comprise a partial literal interpretation. (shrink)

According to one interpretation of Aristotle’s famous thesis, to say that action is the conclusion of practical reasoning is to say that action is itself a judgment about what to do. A central motivation for the thesis is that it suggests a path for understanding the non-observational character of practical knowledge. If actions are judgments, then whatever explains an agent’s knowledge of the relevant judgment can explain her knowledge of the action. I call the approach to action that accepts Aristotle’s (...) thesis so understood Normativism. There are many reasons to doubt Normativism. My aim in this paper is to defend Normativism from a pair of arguments that purport to show that a normative judgment could not constitute an event in material reality and also the knowledge of such a happening. Both highlight a putative mismatch between the natures of, on the one hand, an agent’s knowledge of her normative judgment and, on the other, her knowledge of her own action. According to these objections, knowledge of action includes (a) perceptual knowledge and (b) knowledge of what one has already done. But knowledge of a normative judgment includes neither. Hence knowledge of action cannot simply be knowledge of a normative judgment. (shrink)

“What is the structure of thought?” is as central a question as any in cognitive science. A classic answer to this question has appealed to a Language of Thought (LoT). We point to emerging research from disparate branches of the field that supports the LoT hypothesis, but also uncovers diversity in LoTs across cognitive systems, stages of development, and species. Our letter formulates open research questions for cognitive science concerning the varieties of rules and representations that underwrite various LoT-based systems (...) and how these variations can help researchers taxonomize cognitive systems. (shrink)

Whole Brain Emulation has been championed as the most promising, well-defined route to achieving both human-level artificial intelligence and superintelligence. It has even been touted as a viable route to achieving immortality through brain uploading. WBE is not a fringe theory: the doctrine of Computationalism in philosophy of mind lends credence to the in-principle feasibility of the idea, and the standing of the Human Connectome Project makes it appear to be feasible in practice. Computationalism is a popular, independently plausible theory, (...) and Connectomics a well-funded empirical research program, so optimism about WBE is understandable. However, this optimism may be misplaced. This article argues that WBE is, at best, no more compelling than any of the other far-flung routes to achieving superintelligence. Similarly skeptical conclusions are found regarding immortality. The essay concludes with some positive considerations in favor of the Biological Theory of consciousness, as well as morals about the limits of Computationalism in both artificial intelligence and the philosophy of mind more generally. (shrink)

An analysis of a valenced corpus of English words revealed that words that rhyme with slurs are rated more poorly than their synonyms. What at first might seem like a bizarre coincidence turns out to be a robust feature of slurs, one arising from their phonetic structure. We report novel data on phonaesthetic preferences, showing that a particular class of phonemes are both particularly disliked, and overrepresented in slurs. We argue that phonaesthetic associations have been an overlooked source of some (...) of the more peculiar, arational aspects of slurs. We conclude by drawing broader morals about the evolution of the lexicon. (shrink)

Traditionally, a scientific model is thought to provide a good scientific explanation to the extent that it satisfies certain scientific goals that are thought to be constitutive of explanation. Problems arise when we realize that individual scientific models cannot simultaneously satisfy all the scientific goals typically associated with explanation. A given model’s ability to satisfy some goals must always come at the expense of satisfying others. This has resulted in philosophical disputes regarding which of these goals are in fact necessary (...) for explanation, and as such which types of models can and cannot provide explanations. Explanatory monists argue that one goal will be explanatory in all contexts, while explanatory pluralists argue that the goal will vary based on pragmatic considerations. In this paper, I argue that such debates are misguided, and that both monists and pluralists are incorrect. Instead of any goal being given explanatory priority over others in a given context, the different goals are all deeply dependent on one another for their explanatory power. Any model that sacrifices some explanatory goals to attain others will always necessarily undermine its own explanatory power in the process. And so when forced to choose between individual scientific models, there can be no explanatory victors. Given that no model can satisfy all the goals typically associated with explanation, no one model in isolation can provide a good scientific explanation. Instead we must appeal to collections of models. Collections of models provide an explanation when they satisfy the web of interconnected goals that justify the explanatory power of one another. (shrink)

On an intellectualist approach to belief, the intellectual endorsement of a proposition (such as “The working poor deserve as much respect as the handsomely paid”) is sufficient or nearly sufficient for believing it. On a pragmatic approach to belief, intellectual endorsement is not enough. Belief is behaviorally demanding. To really, fully believe, you must also “walk the walk.” This chapter argues that the pragmatic approach is preferable on pragmatic grounds: It rightly directs our attention to what matters most in thinking (...) about belief. (shrink)

PDF with introduction and front and back materials. Abstract: A provocative examination of the consequences of Levinas’s and Adorno’s thought for contemporary ethics and political philosophy. This book unfolds a dialogue between Emmanuel Levinas and Theodor W. Adorno, using their thought to address contemporary environmental and social-political situations. Eric S. Nelson explores the “non-identity thinking” of Adorno and the “ethics of the Other” of Levinas with regard to three areas of concern: the ethical position of nature and “inhuman” material (...) others such as environments and animals; the bonds and tensions between ethics and religion and the formation of the self through the dynamic of violence and liberation expressed in religious discourses; and the problematic uses and limitations of liberal and republican discourses of equality, liberty, tolerance, and their presupposition of the private individual self and autonomous subject. Thinking with and beyond Levinas and Adorno, this work examines the possibility of an anarchic hospitality and solidarity between material others and sensuous embodied life. -/- “This is an extremely impressive, original, and thorough treatment of two key twentieth-century thinkers and their applicability to the most pressing social and political issues of our time.” — Jeffrey A. Bernstein, author of Leo Strauss on the Borders of Judaism, Philosophy, and History -/- “This book is an excellent and timely contribution to political and environmental philosophy, located around a nuanced historical and philosophical approach to Levinas and Adorno. It will be of great interest to anyone concerned with these figures or with the current moment.” — Martin Shuster, author of Autonomy after Auschwitz: Adorno, German Idealism, and Modernity. (shrink)

Why Human Rights? addresses universal human rights as moral mandates – rights to justice that all m persons have by virtue of their humanity alone. These are not the legal rights of statutes and treaties, but moral rights of the kind Gandhi, King, and Mandela invoked to oppose unjust laws. All such rights presuppose three claims: (1) that some duties of justice apply universally, (2) that all human beings have equal moral status, and (3) that states must protect or serve (...) certain individual interests regardless of the societal impact of doing so. -/- Can these three premises be justified? Is the human equality claim, for example, rationally supportable, or is it no less faith-based than hierarchical doctrines like caste? This book explores the case for these foundational claims along with other philosophical controversies pertaining to human rights. Because these issues lie at the heart of moral and political philosophy, readers will also obtain a broad appreciation of these disciplines and their leading theorists, including Mill, Kant, Rawls, Sandel, Nozick, Rorty, and many others. Written in concise, jargon-free language, this book presents a high-relief map of the philosophical issues surrounding human rights. (shrink)

A Bayesian mind is, at its core, a rational mind. Bayesianism is thus well-suited to predict and explain mental processes that best exemplify our ability to be rational. However, evidence from belief acquisition and change appears to show that we do not acquire and update information in a Bayesian way. Instead, the principles of belief acquisition and updating seem grounded in maintaining a psychological immune system rather than in approximating a Bayesian processor.

A common view in the philosophy of mind and philosophy of psychology is that there is an ideally correct way of categorizing the structures and operations of the mind, and that the goal of neuroscience and psychology is to find this correct categorizational scheme. Categories which cannot find a place within this correct framework ought to be eliminated from scientific practice. In this paper, I argue that this general idea runs counter to productive scientific practices. Such a view ignores the (...) plurality of aims and goals that neuroscientists and psychologists have in studying mental phenomena, and the necessity of employing distinct classificatory frameworks to achieve them. (shrink)

Most philosophers are familiar with the metaphysical puzzle of the statue and the clay. A sculptor begins with some clay, eventually sculpting a statue from it. Are the clay and the statue one and the same thing? Apparently not, since they have different properties. For example, the clay could survive being squashed, but the statue could not. The statue is recently formed, though the clay is not, etc. Godehart Link 1983’s highly influential analysis of the count/mass distinction recommends that English (...) draws a distinction between uncountable “stuff” and countable “things”. There are two mereological relations, related in specific ways. Our primary question here is whether an empirically adequate account of the mass/count distinction really does require distinguishing “things” from “stuff”, and thus postulating two corresponding mereological relations, or if instead positing only one sort of entity and corresponding mereological relation is sufficient, as other semantic theories would have it. This question is meant to be one of what we call natural language mereology. We are asking about the mereological commitments of English, or perhaps competent speakers of English, and not about ultimate reality as such. There is no pretense that we will definitively solve the metaphysical puzzle of the statue and clay. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The empirical study of belief is emerging at a rapid clip, uniting work from all corners of cognitive science. Reliance on belief in understanding and predicting behavior is widespread. Examples can be found, inter alia, in the placebo, attribution theory, theory of mind, and comparative psychological literatures. Research on belief also provides evidence for robust generalizations, including about how we fix, store, and change our beliefs. Evidence supports the existence of a Spinozan system of belief fixation: one that is automatic (...) and independent of belief rejection. Independent research supports the existence of a system of fragmented belief storage: one that relies on large numbers of causally isolated, context-sensitive stores of belief in memory. Finally, empirical and observational data support at least two systems of belief change. One system adheres, mostly, to epistemological norms of updating; the other, the psychological immune system, functions to guard our most centrally held beliefs from potential inconsistency with newly formed beliefs. Refining our under- standing of these systems can shed light on pressing real-world issues, such as how fake news, propaganda, and brainwashing exploit our psychology of belief, and how best to construct our modern informational world. (shrink)

Do university ethics classes influence students’ real-world moral choices? We aimed to conduct the first controlled study of the effects of ordinary philosophical ethics classes on real-world moral choices, using non-self-report, non-laboratory behavior as the dependent measure. We assigned 1332 students in four large philosophy classes to either an experimental group on the ethics of eating meat or a control group on the ethics of charitable giving. Students in each group read a philosophy article on their assigned topic and optionally (...) viewed a related video, then met with teaching assistants for 50-minute group discussion sections. They expressed their opinions about meat ethics and charitable giving in a follow-up questionnaire (1032 respondents after exclusions). We obtained 13,642 food purchase receipts from campus restaurants for 495 of the students, before and after the intervention. Purchase of meat products declined in the experimental group (52% of purchases of at least $4.99 contained meat before the intervention, compared to 45% after) but remained the same in the control group (52% both before and after). Ethical opinion also differed, with 43% of students in the experimental group agreeing that eating the meat of factory farmed animals is unethical compared to 29% in the control group. We also attempted to measure food choice using vouchers, but voucher redemption rates were low and no effect was statistically detectable. It remains unclear what aspect of instruction influenced behavior. (shrink)

For a period of several years the philosopher of science Hasok Chang has promoted various inter-related views including pluralism, pragmatism, and an associated view of natural kinds. He has also argued for what he calls the persistence of everyday terms in the scientific view. Chang claims that terms like phlogiston were never truly abandoned but became transformed into different concepts that remain useful. On the other hand, Chang argues that some scientific terms such as acidity have suffered a form of (...) “rupture”, especially in the case of the modern Lewis definition of acids. Chang also complains that the degree of acidity of a Lewis acid cannot be measured using a pH meter and seems to regard this as a serious problem. The present paper examines some of these views, especially what Chang claims to be a rupture in the definition of acidity. It is suggested that there has been no such rupture but a genuine generalization, on moving from the Brønsted-Lowry theory to the Lewis theory of acidity. It will be shown how the quantification and measurement of Lewis acidity can easily be realized through the use of equilibrium theory and the use of stability constants. (shrink)

Carine Defoort, Mario Wenning, and Kai Marchal offer three ways of engaging with Chinese and Buddhist Philosophy in Early Twentieth-Century German Thought and the philosophical, hermeneutical, and historical issues it attempted to articulate and address.1 This work is historical with a contemporary philosophical intent: to reexamine a tumultuous contested epoch of philosophy’s past in order to reconsider its existing limitations and alternative possibilities. One dimension of this book is the investigation of constellations and entanglements of historical forces and concepts for (...) the sake of articulating critical models and alternatives for the present.2 In the book, I contested the modern self-image of philosophy... (shrink)

In some recent works, Crupi and Iacona have outlined an analysis of ‘if’ based on Chrysippus’ idea that a conditional holds whenever the negation of its consequent is incompatible with its antecedent. This paper presents a sound and complete system of conditional logic that accommodates their analysis. The soundness and completeness proofs that will be provided rely on a general method elaborated by Raidl, which applies to a wide range of systems of conditional logic.

This Derridean reading of Freud asks the question of how we should read Freud with respect to sexual difference and what Derrida considers a radicalized concept of trace, a "scene of writing" of differance ---that is, how we should read Freud with respect to phallogocentrism. Throughout I consider the possible relationships between the "mainstyles" of various psychoanalyses, deconstructions, and feminisms. By analyzing what is most original for Freud---the cause of hysteria, the navel of the dream, the perceptual identity, the primal (...) phantasies, for example---I find that Freud consistently seeks a single origin, a "caput Nili," on which to base a grand narrative. At first this narrative is an etiology of hysteria, but it evolves into a masterplot of sexual development and later into one of humanity. The establishment of an oedipal origin and telos, and the masterplot based on them, moves psychoanalysis toward a totalizing theory, and therefore its openness to chance and something beyond what that theory can master is greatly reduced. ;I approach these topics in terms of a question of the ethics of psychoanalysis. This appropriative or reductive process of Freud's masterplotting is based on what Derrida calls "castration-truth" in his reading of Lacan, "Le facteur de la verite." In contrast to some theorists who appeal to the radical spirit of Freudian theory as a basis for their radicalization of psychoanalysis---specifically Barnaby B. Barratt's Psychoanalysis and the Postmodern Impulse---I argue that Lacan's phallogocentric "return to Freud" is actually a more faithful one since I find both "mainstyles" of these psychoanalyses based on a logic of lack or "castration-truth." I argue throughout that the radical spirit of Freud is at times overemphasized or exaggerated by Derridean theorists---and even Derrida himself, though rarely---and that the dominant specter of Freud is an "establishment" or appropriative one, rather than one which is radical or "other-wise." I connect this trend of Derridean thinkers claiming too much debt to psychoanalysis to these thinkers not taking seriously Freud's commitment and interest in an idealized phylogenetics: "phylo-'genetics.'" Since my establishment of this establishment specter of Freud as the "mainstyle" of Freudian theory itself risks reproducing exactly the kind of appropriative discourse I hope to problematize, I attempt to avoid such a reproduction by considering what remains of the radical spirit of Freudian theory in what might be called a deconstructive "technology of iterability;" a "cyborg-analysis;" or what I call "post-psychoanalysis.". (shrink)

You can survive after death in various kinds of artifacts. You can survive in diaries, photographs, sound recordings, and movies. But these artifacts record only superficial features of yourself. We are already close to the construction of programs that partially and approximately replicate entire human lives (by storing their memories and duplicating their personalities). A digital ghost is an artificially intelligent program that knows all about your life. It is an animated auto-biography. It replicates your patterns of belief and desire. (...) You can survive after death in a digital ghost. We discuss a series of digital ghosts over the next 50 years. As time goes by and technology advances, they are progressively more perfect replicas of the lives of their original authors. (shrink)

The mainstream tradition in recent Anglophone Zhuangzi interpretation treats spontaneous skillful responsiveness – similar to the spontaneous responsiveness of a skilled artisan, athlete, or musician – as a, or the, Zhuangzian ideal. However, this interpretation is poorly grounded in the Inner Chapters. On the contrary, in the Inner Chapters, this sort of skillfulness is at least as commonly criticized as celebrated. Even the famous passage about the ox-carving cook might be interpreted more as a celebration of the knife’s passivity than (...) as a celebration of the cook’s skillfulness. (shrink)

Abstract: Longtermist Effective Altruists (EAs) aim to mitigate the risk of existential catastrophes. In this paper, I have three goals. First, I identify a catastrophic risk that EAs have completely ignored. I call it religious catastrophe: the threat that (as Christians and Muslims have warned for centuries) billions of people stand in danger of going to hell for all eternity. Second, I argue that, even by secular EA lights, religious catastrophe is at least as bad and at least as probable (...) and, therefore, at least as important as many of the standard EA catastrophic risks (e.g., catastrophic climate change, nuclear winter). Third, I present the following dilemma for secular EAs: either adopt religious catastrophe as an EA cause or ignore religious catastrophe but also ignore catastrophic risks whose mitigation has a similar or lower expected value (i.e., most or all of them). Business as usual—ignoring religious catastrophe while championing the typical EA causes—is not an option consistent with longtermist EA principles. (shrink)

Rationalization, in our intended sense of the term, occurs when a person favors a particular conclusion as a result of some factor (such as self-interest) that is of little justificatory epistemic relevance, if that factor then biases the person’s subsequent search for, and assessment of, potential justifications for the conclusion. Empirical evidence suggests that rationalization is common in people’s moral and philosophical thought. We argue that it is likely that the moral and philosophical thought of philosophers and moral psychologists is (...) also pervaded by rationalization. Moreover, although rationalization has some benefits, overall it would be epistemically better if the moral and philosophical reasoning of people, including professional academics, were not as heavily influenced by rationalization as it likely is. We discuss the significance of our arguments for cognitive management and epistemic responsibility. (shrink)

This paper explores the current obstacles that a cognitive theory of humor faces. More specifically, I argue that the nebulous and ill-defined nature of humor makes it difficult to tell what counts as clear instances of, and deficits in, the phenomenon.Without getting clear on this, we cannot identify the underlying cognitive mechanisms responsible for humor. Moreover, being too quick to draw generalizations regarding the ubiquity of humor, or its uniqueness to humans, without substantially clarifying the phenomenon and its occurrences is (...) not only unwise but can actually be a detriment to our study of humor. As such, these sorts of claims must be resisted. I conclude the paper by pointing the way forward to addressing these obstacles. -/- . (shrink)

I follow standard mathematical practice and theory to argue that the natural numbers are the finite von Neumann ordinals. I present the reasons standardly given for identifying the natural numbers with the finite von Neumann's (e.g., recursiveness; well-ordering principles; continuity at transfinite limits; minimality; and identification of n with the set of all numbers less than n). I give a detailed mathematical demonstration that 0 is { } and for every natural number n, n is the set of all natural (...) numbers less than n. Natural numbers are sets. They are the finite von Neumann ordinals. (shrink)

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)

Some key political challenges today, e.g. climate change, are future oriented. The intergenerational setting differs in some notable ways from the intragenerational one, creating obstacles to theorizing about intergenerational justice. One concern is that as the circumstances of justice do not pertain intergenerationally, intergenerational justice is not meaningful. In this paper, I scrutinize this worry by analysing the presentations of the doctrine of the circumstances of justice by David Hume and John Rawls. I argue that we should accept the upshot (...) of their idea, that justice is context sensitive, even if this at first sight seems to invalidate intergenerational justice. On the basis of moral constructivism, I subsequently provide a fresh reading of the doctrine according to which it conveys the idea that justice is the solution to a practical problem. However, as the problem background is evolving, we need to properly characterize the relevant practical problem in order to make ethical theorizing relevant. Contrary to what has been claimed, the circumstances of justice do not then clash with intergenerational justice, but are the necessary presuppositions for its advancement. (shrink)

There is a long-standing debate in the philosophy of mind and philosophy of science regarding how best to interpret the relationship between neuroscience and psychology. It has traditionally been argued that either the two domains will evolve and change over time until they converge on a single unified account of human behaviour, or else that they will continue to work in isolation given that they identify properties and states that exist autonomously from one another (due to the multiple-realizability of psychological (...) states). In this paper, I argue that progress in psychology and neuroscience is contingent on the fact that both of these positions are false. Contra the convergence position, I argue that the theories of psychology and the theories of neuroscience are scientifically valuable as representational tools precisely because they cannot be integrated into a single account. However, contra the autonomy position, I propose that the theories of psychology and neuroscience are deeply dependent on one another for further refinement and improvement. In this respect, there is an irreconcilable codependence between psychology and neuroscience that is necessary for both domains to improve and progress. The two domains are forever linked while simultaneously being unable to integrate. (shrink)

Among the most widely discussed of William of Ockham’s texts on ethics is his Quodlibet III, q. 14. But despite a large literature on this question, there is no consensus on what Ockham’s answer is to the central question raised in it, specifically, what obligations one would have if one were to receive a divine command to not love God. (Surprisingly, there is also little explicit recognition in the literature of this lack of consensus.) Via a close reading of the (...) text, I argue, contrary to much of the literature, that Ockham believes that if one were given this command, one would be obligated to refrain from loving God and would also be able to fulfill this obligation without any moral wrongdoing. Among other results, this study will help clarify Ockham’s much-discussed claim that loving God is “a necessarily virtuous act.”. (shrink)

In this article, I argue that intentional psychology (i.e. the interpretation of human behaviour in terms of intentional states and propositional attitudes) plays an essential role in the sciences of the mind. However, this role is not one of identifying scientifically respectable states of the world. Rather, I argue that intentional psychology acts as a type of phenomenological model, as opposed to a mechanistic one. I demonstrate that, like other phenomenological models in science, intentional psychology is a methodological tool with (...) its own benefits and insights that complements our mechanistic understanding of systems. As a result, intentional psychology's distinctive scientific benefit is its ability to model systems in unique, non-mechanistic, ways. This allows us to generate predictions that we cannot otherwise generate using the mechanistic models of neuroscience and cognitive psychology necessary for various scientific tasks. (shrink)