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/) 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)

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)

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)

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)

Research on the use of propranolol as a pharmacological memory dampening treatment for post-traumatic stress disorder is continuing and justifies a second look at the legal and ethical issues raised in the past. We summarize the general ethical and legal issues raised in the literature so far, and we select two for in-depth reconsideration. We address the concern that a traumatized witness may be less effective in a prosecution emerging from the traumatic event after memory dampening treatment. We analyze this (...) issue in relation to sexual assault, where the suggestion that corroborating evidence may remedy any memory defects is less likely to be helpful. We also consider the clinical ethical question about a physician's obligation to discuss potential legal consequences of memory dampening treatment. We conclude that this latter question reflects a general problem related to novel medical treatments where the broader socio-legal consequences may be poorly understood, and suggest that issues of this sort could usefully be addressed through the promulgation of practice guidelines. (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.

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)

Aristotle's treatment of the choice between the political and contemplative lives (in EN I 5 and X 7-8) can seem awkward. To offer one explanation of this, I argue that when he invokes self-sufficience (autarkeia) as a criterion for this choice, he appeals to two different and incompatible specifications of "lacking nothing." On one specification, suitable to a human being living as a political animal and thus seeking to realize his end as an engaged citizen of a polis, a person (...) lacks nothing by possessing a wide range of goods that directly require other people. On the other, more suitable to a god or a beast, a person lacks nothing by having no need of goods that directly require other people. The ambiguity of this criterion renders the choice between the political and contemplative lives difficult. (shrink)

Except for a patina of twenty-first century modernity, in the form of logic and language, philosophy is exactly the same now as it ever was; it has made no progress whatsoever. We philosophers wrestle with the exact same problems the Pre-Socratics wrestled with. Even more outrageous than this claim, though, is the blatant denial of its obvious truth by many practicing philosophers. The No-Progress view is explored and argued for here. Its denial is diagnosed as a form of anosognosia, a (...) mental condition where the affected person denies there is any problem. The theories of two eminent philosophers supporting the No-Progress view are also examined. The final section offers an explanation for philosophy 's inability to solve any philosophical problem, ever. The paper closes with some reflections on philosophy 's future. (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.

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)

Foundational theories of mental content seek to identify the conditions under which a mental representation expresses, in the mind of a particular thinker, a particular content. Normativists endorse the following general sort of foundational theory of mental content: A mental representation r expresses concept C for agent S just in case S ought to use r in conformity with some particular pattern of use associated with C. In response to Normativist theories of content, Kathrin Glüer-Pagin and Åsa Wikforss propose a (...) dilemma, alleging that Normativism either entails a vicious regress or falls prey to a charge of idleness. In this paper, I respond to this argument. I argue that Normativism can avoid the commitments that generate the regress and does not propose the sort of explanation required to charge that its explanation has been shown to be problematically idle. The regress-generating commitment to be avoided is, roughly, that tokened, contentful mental states are the product of rule-following. The explanatory task Normativists should disavow is that of explaining how it is that beliefs and other contentful mental states are produced. I argue that Normativism, properly understood as a theory of content, does not provide this kind of psychological explanation, and therefore does not entail that such explanations are to be given in terms of rule-following. If this is correct, Normativism is not the proper target of the dilemma offered by Glüer-Pagin and Wikforss. Understanding why one might construe Normativism in the way Glüer-Pagin and Wikforss must, and how, properly understood, it avoids their dilemma, can help us to appreciate the attractiveness of a genuinely normative theory of content and the importance of paying careful attention to the sort of normativity involved in norm-based theories of content. (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)

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.

After presenting evidence about categorization behavior, this paper argues for the following theses: 1) that there is a border between perception and cognition; 2) that the border is to be characterized by perception being modular (and cognition not being so); 3) that perception outputs conceptualized representations, so views that posit that the output of perception is solely non-conceptual are false; and 4) that perceptual content consists of basic-level categories and not richer contents.

According to the analysis of concessive conditionals suggested by Crupi and Iacona, a concessive conditional \(p{{\,\mathrm{\hookrightarrow }\,}}q\) is adequately formalized as a conjunction of conditionals. This paper presents a sound and complete axiomatic system for concessive conditionals so understood. The soundness and completeness proofs that will be provided rely on a method that has been employed by Raidl, Iacona, and Crupi to prove the soundness and completeness of an analogous system for evidential conditionals.

This is a study of Plato's use of the character Socrates to model what philosophy is. The study focuses on the Apology, and finds that philosophy there is the love of wisdom, where wisdom is expertise about how to live, of the sort that only gods can fully have, and where Socrates loves wisdom in three ways, first by honoring wisdom as the gods' possession, testing human claims to it, second by pursuing wisdom, examining himself as he examines others, to (...) achieve a more well justified set of beliefs about how to live, and third by trying to live wisely, insofar as he can, which includes exhorting others to care about living wisely than anything else. The essay also includes some suggestions about how Plato criticizes and revises this model of philosophy outside the Apology. (shrink)

This essay attempts to clarify the nature and structure of aliefs. First I distinguish between a robust notion of aliefs and a deflated one. A robust notion of aliefs would introduce aliefs into our psychological ontology as a hitherto undiscovered kind, whereas a deflated notion of aliefs would identify aliefs as a set of pre-existing psychological states. I then propose the following dilemma: one the one hand, if aliefs have propositional content, then it is unclear exactly how aliefs differ from (...) psychological states we already countenance, in which case there is no robust notion of aliefs; on the other, if aliefs just contain associative content, then they cannot do the explanatory work set out for them, in which case there is no reason to posit aliefs at all. Thus, it appears that we have little reason to posit the novel category of robust aliefs. (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)

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)

“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)

I describe a phenomenon that has not yet been described in the epistemology literature. I label this phenomenon expression-style exclusion. Expression-style exclusion is an example of how s...

Advocates of dynamic systems have suggested that higher mental processes are based on continuous representations. In order to evaluate this claim, we first define the concept of representation, and rigorously distinguish between discrete representations and continuous representations. We also explore two important bases of representational content. Then, we present seven arguments that discrete representations are necessary for any system that must discriminate between two or more states. It follows that higher mental processes require discrete representations. We also argue that discrete (...) representations are more influenced by conceptual role than continuous representations. We end by arguing that the presence of discrete representations in cognitive systems entails that computationalism (i.e., the view that the mind is a computational device) is true, and that cognitive science should embrace representational pluralism. (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)

This paper argues for a noncognitiveist computationalism in the philosophy of mind. It further argues that both humans and computers have intentionality, that is, their mental states are semantical -- they are about things in their worlds.

I argue that the Stoics were right to portray Socrates as a cosmopolitan, because this portrait is fully consistent with the Socrates of Plato's Socratic dialogues. His rejection of ordinary political engagement in favor of an extraordinary way of doing the political work of improving others lives by examining them is also the rejection of locally engaged politics in favor of benefiting human beings as such. It is less clear whether his cosmopolitanism is moderate (admitting special obligations to benefit compatriots (...) alongside general obligations to benefit humans as such) or strict (denying the special obligations), but I argue that the evidence of Socrates' attachment to Athens, in the Crito and elsewhere, is compatible with his being a strict cosmopolitan. (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)

Éric Delassus | : Selon Fabienne Brugère, un point de rencontre existe entre l’éthique spinoziste et les éthiques du care, le care pouvant être envisagé comme une réactualisation du conatus spinoziste. Cet article vise à démontrer que cette convergence peut s’établir à partir d’une éthique narrative inspirée de la pensée de Paul Ricoeur. Cela concerne principalement la perception que l’on peut avoir de soi en tant que corps et esprit, dans la mesure où l’esprit est défini par Baruch Spinoza comme (...) « idée du corps ». L’éthique spinoziste invite à se rendre utile aux autres pour augmenter notre puissance d’être et nous libérer d’une servitude qui n’est pas sans rapport avec la vulnérabilité telle que définie dans les éthiques du care. L’humain.e vulnérable a besoin pour se sentir exister d’avoir une idée cohérente de son corps, et le récit est l’une des voies lui permettant de progresser dans cette direction. Encore faut-il, pour y parvenir, trouver des pourvoyeuses et pourvoyeurs de care disposé.e.s à écouter, aptes à susciter en soi le désir de se raconter. | : According to Fabienne Brugère, there is common ground between Spinoza’s ethics and the ethics of care, which can be regarded as a renewal of the Spinozan concept of ‘conatus.’ This article aims to demonstrate that this form of convergence can be based upon a narrative ethic as inspired by Paul Ricoeur’s thought. It is mainly about how people can perceive themselves both as mind and body, insofar as “mind” is defined by Spinoza as the “idea of the body.” The Spinozan ethic leads us to make ourselves useful to other people in order to expand our capacity to be and to free ourselves from a form of servitude that is somewhat linked to vulnerability as it is defined in the ethics of care. Therefore, vulnerable people each need to develop consistent ideas of their bodies if they wish to feel that they do exist. Narrative is one of the many ways of advancing in that direction. However, vulnerable people should not be alone; they must be accompanied by care providers who have a sympathetic ear and who can arouse in them the desire to tell and share their stories. (shrink)

Consider the following three claims. (i) There are no truths of the form ‘p and ~p’. (ii) No one holds a belief of the form ‘p and ~p’. (iii) No one holds any pairs of beliefs of the form {p, ~p}. Irad Kimhi has recently argued, in effect, that each of these claims holds and holds with metaphysical necessity. Furthermore, he maintains that they are ultimately not distinct claims at all, but the same claim formulated in different ways. I find (...) his argument suggestive, if not entirely transparent. I do think there is at least an important kernel of truth even in (iii), and that (i) ultimately explains what’s right about the other two. Consciousness of an impossibility makes belief in the obtaining of the corresponding state of affairs an impossibility. Interestingly, an appreciation of this fact brings into view a novel conception of inference, according to which it consists in the consciousness of necessity. This essay outlines and defends this position. A central element of the defense is that it reveals how reasoners satisfy what Paul Boghossian calls the Taking Condition and do so without engendering regress. (shrink)

What is a concept? Philosophers have given many different answers to this question, reflecting a wide variety of approaches to the study of mind and language. Nonetheless, at the most general level, there are two dominant frameworks in contemporary philosophy. One proposes that concepts are mental representations, while the other proposes that they are abstract objects. This paper looks at the differences between these two approaches, the prospects for combining them, and the issues that are involved in the dispute. We (...) argue that powerful motivations have been offered in support of both frameworks. This suggests the possibility of combining the two. Unlike Frege, we hold that the resulting position is perfectly coherent and well worth considering. Nonetheless, we argue that it should be rejected along with the view that concepts are abstract objects. (shrink)

Much attention has been drawn to the cognitive basis of innovation. While interesting in many ways, this poses the threat of falling back to traditional internalist assumptions with regard to cognition. We oppose the ensuing contrast between internal cognitive processing and external public practices and technologies that such internal cognitive systems might produce and utilize. We argue that innovation is best understood from the gibsonian notion of affordance, and that many innovative practices emerge from the external scaffolding of cognitive processes. (...) The public engageability that allows the disclosure of hidden affordances is not only –not even primarily– a property of cognitive products, but of cognitive processes. We elaborate on this claims by drawing on Dutilh Novaes’ account of formal languages as cognitive technologies and Hutto’s Narrative Practice Hypothesis. This paves the way to sketch some general principles on how to strategically seek for innovation by targeting hidden affordances. (shrink)

Belief storage is often modeled as having the structure of a single, unified web. This model of belief storage is attractive and widely assumed because it appears to provide an explanation of the flexibility of cognition and the complicated dynamics of belief revision. However, when one scrutinizes human cognition, one finds strong evidence against a unified web of belief and for a fragmented model of belief storage. Using the best available evidence from cognitive science, we develop this fragmented model into (...) a nascent theory of the cognitive architecture of belief storage. (shrink)

Reduplicative approaches to the incarnation attempt to avoid the charge of incoherence by employing a qua-operator that operates on an entire assertion. The main objection to this approach is that it still yields a contradiction. Recently, two new reduplicative approaches have been offered that purport to avoid contradiction, one that offers a novel analysis of negative predications and the other which prevents conjoining divine and human predicates into a meaningful sentence. In this paper, I argue that these newer approaches either (...) fail to provide a distinctive solution or do not show whether the model is genuinely possible. (shrink)

This chapter presents the reception of Leo Strauss by analytic philosophers after Strauss’s emigration to the United States. It gives a brief survey of the polemics against Strauss and his school by analytic philosophers, which aided in the self-constitution of analytic philosophy as a rival school of thought in philosophy. But most of the chapter is devoted to recovering the significance and influence of a criticism of Strauss by Ernest Nagel. The chapter argues that this response is of intrinsic interest (...) because it involves the relationship between science and values. Nagel’s response was foundational to Felix Oppenheim’s political philosophy or what Oppenheim called his project of ‘conceptual reconstruction.’ Lurking in Oppenheim’s response to Strauss are questions about the role of the principle of sufficient reason in philosophy. Rge chapter argues that an opportunity was missed to clarify questions pertaining to the inductive risk of philosophy more than a half century before these issues became fashionable again. (shrink)

Expanded reprint of the WIREs Science of Belief paper for Julien Musolino, Joseph Sommer, and Pernille Hemmer's The Science of Beliefs: A Multidisciplinary Approach. Cambridge University Press.

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)

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)

There is a prevalent notion among cognitive scientists and philosophers of mind that computers are merely formal symbol manipulators, performing the actions they do solely on the basis of the syntactic properties of the symbols they manipulate. This view of computers has allowed some philosophers to divorce semantics from computational explanations. Semantic content, then, becomes something one adds to computational explanations to get psychological explanations. Other philosophers, such as Stephen Stich, have taken a stronger view, advocating doing away with semantics (...) entirely. This paper argues that a correct account of computation requires us to attribute content to computational processes in order to explain which functions are being computed. This entails that computational psychology must countenance mental representations. Since anti-semantic positions are incompatible with computational psychology thus construed, they ought to be rejected. Lastly, I argue that in an important sense, computers are not formal symbol manipulators. (shrink)

This paper has two main aims. The first is to present a general approach for understanding “dispositional” and “categorical” properties; the second aim is to use this approach to criticize Russellian Monism. On the approach I suggest, what are usually thought of as “dispositional” and “categorical” properties are really just the extreme ends of a spectrum of options. The approach allows for a number of options between these extremes, and it is plausible, I suggest, that just about everything of scientific (...) interest falls in this middle ground. I argue that Russellian Monism depends for its plausibility on the unarticulated assumption that there are no properties in the middle ground. (shrink)

How do you know what you want? Philosophers have lately developed sophisticated accounts of the practical and doxastic knowledge that are rooted in the point of view of the subject. Our ability to just say what we are doing or what we believe—that is, to say so authoritatively, but not on the basis of observation or evidence—is an aspect of our ability to reason about the good and the true. However, no analogous route to orectic self-knowledge is feasible. Knowledge of (...) desire is distinctive in being a matter of our affective response to imagined prospects. An examination of this idea yields the following thesis: I know what I want just in case the object pursued in anticipation of a certain pleasure actually yields the anticipated pleasure. (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)

This paper takes a fresh look at the nativism–empiricism debate, presenting and defending a nativist perspective on the mind. Empiricism is often taken to be the default view both in philosophy and in cognitive science. This paper argues, on the contrary, that there should be no presumption in favor of empiricism (or nativism), but that the existing evidence suggests that nativism is the most promising framework for the scientific study of the mind. Our case on behalf of nativism has four (...) parts. (1) We characterize nativism’s core commitments relative to the contemporary debate between empiricists and nativists, (2) we present the positive case for nativism in terms of two central nativist arguments (the poverty of the stimulus argument and the argument from animals), (3) we respond to a number of influential objections to nativist theories, and (4) we explain the nativist approach to the conceptual system. (shrink)

In statistics, there are two main paradigms: classical and Bayesian statistics. The purpose of this article is to investigate the extent to which classicists and Bayesians can agree. My conclusion is that, in certain situations, they cannot. The upshot is that, if we assume that the classicist is not allowed to have a higher degree of belief in a null hypothesis after he has rejected it than before, then he has to either have trivial or incoherent credences to begin with (...) or fail to update his credences by conditionalization. (shrink)

Based on three recently published books on climate justice, this article reviews the field of climate ethics in light of developments of international climate politics. The central problem addressed is how idealised normative theories can be relevant to the political process of negotiating a just distribution of the costs and benefits of mitigating climate change. I distinguish three possible responses, that is, three kinds of non-ideal theories of climate justice: focused on (1) the injustice of some agents not doing their (...) part; (2) the policy process and aiming to be realistic; and (3) grievances related to the transition to a clean-energy economy. The methodological discussion underpinning each response is innovative and should be of interest more generally, even though it is still underdeveloped. The practical upshot, however, is unclear: even non-ideal climate justice may be too disconnected from the fast-moving and messy climate circus. (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)

For some reason, participants hold agents more responsible for their actions when a situation is described concretely than when the situation is described abstractly. We present examples of this phenomenon, and survey some attempts to explain it. We divide these attempts into two classes: affective theories and cognitive theories. After criticizing both types of theories we advance our novel hypothesis: that people believe that whenever a norm is violated, someone is responsible for it. This belief, along with the familiar workings (...) of cognitive dissonance theory, is enough to not only explain all of the abstract/concrete paradoxes, but also explains seemingly unrelated effects, like the anthropomorphization of malfunctioning inanimate objects. (shrink)

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)

In recent years, the idea has been gaining ground that our traditional conceptions of knowledge and cognition are unduly limiting, in that they privilege what goes on inside the ‘skin and skull’ of an individual reasoner. Instead, it has been argued, knowledge and cognition need to be understood as embodied, situated, and extended. Whether these various interrelations and dependencies are ‘merely’ causal, or are in a more fundamental sense constitutive of knowledge and cognition, is as much a matter of controversy (...) as the degree to which they pose a challenge to ‘traditional’ conceptions of cognition, knowledge and the mind. In this paper we argue that when the idea of ‘extendedness’ is applied to a core concept in epistemology and the philosophy of science—namely, scientific evidence—things appear to be on a much surer footing. The evidential status of data gathered through extended processes—including its utility as justification or warrant—do not seem to be weakened by virtue of being extended, but instead are often strengthened because of it. Indeed, it is often precisely by virtue of this extendedness that scientific evidence grounds knowledge claims, which individuals may subsequently ascribe to themselves. The functional equivalence between machine-based gathering, filtering, and processing of data and human interpretation and assessment is the crucial factor in deciding whether evidence has been gathered, rather than the distinction between intra- and extracranial processes or individual and social processes. To prioritize biological processes here, and to assert the superiority of human cognitive capacities seems both arbitrary and unwarranted with respect to gathering evidence, and ultimately would lead to an unattractive skepticism about many of the methods used in science to gather evidence. In other words, conceiving of scientific evidence as ‘impersonal’ not only better captures the character of evidence-gathering in practice, but also makes sense of a large amount of evidence-gathering that ‘personal’ accounts fail to either acknowledge or accurately describe. Whilst we suggest it is likely that all internally-distributed evidence-gathering processes are merely contingently internal processes, a significant number of externally-distributed evidence-gathering processes are necessarily externally-distributed. Some evidence can only be gathered by extended epistemic agents. (shrink)

Is it impossible for a person to do something intentionally without knowing that she is doing it? The phenomenon of self-deceived agency might seem to show otherwise. Here the agent is not lying, yet disavows a correct description of her intentional action. This disavowal might seem expressive of ignorance. However, I show that the self-deceived agent does know what she's doing. I argue that we should understand the factors that explain self-deception as masking rather than negating the practical knowledge characteristic (...) of intentional action. This masking takes roughly the following form: when we are deceiving ourselves about what we are intentionally doing, we don't think about our action because it's painful to do so. (shrink)