The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

A vexing problem in contemporary epistemology—one with origins in Plato’s Meno—concerns the value of knowledge, and in particular, whether and how the value of knowledge exceeds the value of mere true opinion. The recent literature is deeply divided on the matter of how best to address the problem. One point, however, remains unquestioned: that if a solution is to be found, it will be at the personal level, the level at which states of subjects or agents, as such, appear. We (...) take exception to this orthodoxy, or at least to its unquestioned status. We argue that subpersonal states play a significant—arguably, primary—role in much epistemically relevant cognition and thus constitute a domain in which we might reasonably expect to locate the “missing source” of epistemic value, beyond the value attached to mere true belief. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, (...) Henry Stapp. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

The Axis II Work Group of the Task Force on Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) has expressed concern that antisocial personality disorder (APD) criteria are too long and cumbersome and that they focus on antisocial behaviors rather than personality traits central to traditional conceptions of psychopathy and to international criteria. R. D. Hare et al describe an alternative to the approach taken in the DSM-III—Revised (DSM-III—R; American Psychiatric Association, 1987), namely, the revised Psychopathy Checklist. The authors also (...) discuss the multisite APD field trials designed to evaluate and compare 4 criteria sets: the DSM-III—R criteria, a shortened list of these criteria, the criteria for dyssocial personality disorder from the 10th edition of the International Classification of Diseases (World Health Organization, 1990), and a 10-item criteria set for psychopathic personality disorder derived from the revised Psychopathy Checklist. (PsycINFO Database Record (c) 2015 APA, all rights reserved). (shrink)

D. M. Armstrong famously claims that deterministic laws of nature are contingent relations between universals and that his account can also be straightforwardly extended to irreducibly probabilistic laws of nature. For the most part, philosophers have neglected to scrutinize Armstrong’s account of probabilistic laws. This is surprising precisely because his own claims about probabilistic laws make it unclear just what he takes them to be. We offer three interpretations of what Armstrong-style probabilistic laws are, and argue that all three interpretations (...) are incompatible either with some feature of Armstrong’s broader metaphysics or with essential features of his account of laws (or both). (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (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)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

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 Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...) reality and re-entering the matrix. Not only does reason compel us to admit the existence of the external world, it also requires us to face this world, to build for ourselves meaningful lives within it, and to engage, as adults, in the serious business of living. (shrink)

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

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

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

Recently it has been argued that autocatalytic theory could be applied to the origin of culture. Here possible application to a theory of meaning in the philosophy of language, called radical interpretation, is commented upon and compared to previous applications.

It is argued that colour name strategy, object name strategy, and chunking strategy in memory are all aspects of the same general phenomena, called stereotyping, and this in turn is an example of a know-how representation. Such representations are argued to have their origin in a principle called the minimum duplication of resources. For most the subsequent discussions existence of colour name strategy suffices. It is pointed out that the BerlinA- KayA universal partial ordering of colours and the frequency of (...) traffic accidents classified by colour are surprisingly similar; a detailed analysis is not carried out as the specific colours recorded are not identical. Some consequences of the existence of a name strategy for the philosophy of language and mathematics are discussed: specifically it is argued that in accounts of truth and meaning it is necessary throughout to use real numbers as opposed to bi-valent quantities; and also that the concomitant label associated with sentences should not be of unconditional truth, but rather several real-valued quantities associated with visual communication. The implication of real-valued truth quantities is that the Continuum Hypothesis of pure mathematics is side-stepped, because real valued quantities occur ab initio. The existence of name strategy shows that thought/sememes and talk/phonemes can be separate, and this vindicates the assumption of thought occurring before talk used in psycho-linguistic speech production models. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

This booklet is a Korean adaptation and translation of Part VIII of forall x: Calgary (Fall 2021 edition), which is intended to be introductory material for modal logic. The original text is based on Robert Trueman's A Modal Logic Primer, which is revised and expanded by Richard Zach and Aaron Thomas-Bolduc in forall x: Calgary. (forall x: Calgary is based on forall x: Cambridge by Tim Button, which is in turn based on forall x by P. D. Magnus, and (...) also includes material from forall x: Lorain County Remix by Cathal Woods and J. Robert Loftis.) This booklet is licensed under a Creative Commons Attribution 4.0 license. (shrink)

Proponents of the view which I call ‘moral antitheodicy’ call for the theistic discourse of theodicy to be abandoned, because, they claim, all theodicies involve some form of moral impropriety. Three arguments in support of this view are examined: the argument from insensitivity, the argument from detachment, and the argument from harmful consequences. After discussing the merits of each argument individually, I attempt to show that they all must presuppose what they are intended to establish, namely, that the set of (...) premises advanced in any given theodicy will be untenable. I conclude by discussing what uses there might be for the moral critique of theodicy, if it cannot be used to ground a global rejection of theodical practice. (shrink)

This book presents Robert S. Hartman's formal theory of value and critically examines many other twentieth century value theorists in its light, including A.J. Ayer, Kurt Baier, Brand Blanshard, Paul Edwards, Albert Einstein, William K. Frankena, R.M. Hare, Nicolai Hartmann, Martin Heidegger, G.E. Moore, P.H. Nowell-Smith, Jose Ortega y Gasset, Charles Stevenson, Paul W. Taylor, Stephen E. Toulmin, and J.O. Urmson. Open Access funding for this volume has been provided by the Robert S. Hartman Institute.

The project of a naive physics has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as Kohler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit from a (...) knowledge of these historical roots of their discipline, which are shown to imply above all a critique of the set-theory-based models of reality typically presupposed by contemporary work in common-sense ontology. (shrink)

La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui (...) existent indépendamment de nos actes cognitifs (par exemple: la planète Terre, sa surface extérieure); et des objets qui existent seulement grâce à ces actes (par exemple: l'équateur, la Mer du Nord). Le champ visuel, lui aussi, peut être conçu comme un exemple d'une entité à extension spatiale qui est dépendante dans le sens proposé ci-dessus. L'étude présente suggère une extension de cette analogie en postulant les entités qui, pour les vrais jugements, seraient ce que le champ visuel est pour les actes de perception visuelle. Le champ de jugement est défini plus précisément comme une entité étendue complexe, contenant toutes les entités essentielles pour la vérité d'un (vrai) jugement donné. Il est possible de démontrer que le travail des linguistes cognitifs tel Talmy ou Langacker, si l'on l'interprète convenablement, produit une explication détaillée des structures des champs de jugement correspondant aux phrases de sortes différentes. Un genre nouveau de définition de la vérité en tant que correspondance pour les expressions de la langue naturelle peut donc être formulé sur cette base. (shrink)

Augustine′s conversion to Christianity in A.D. 386 is a pivotal moment not only in his own life, but in Christian and world history, for the theology of Augustine set the course of theological and cultural development in the western Christian church. But to what exactly was Augustine converted? Scholars have long debated whether he really converted to Christianity in 386, whether he was a Platonist, and, if he adhered to both Platonism and Christianity, which dominated his thought. The debate of (...) the last thirteen decades spans an immense body of literature in multiple languages. In this literature, four major views on Augustine′s conversion may be discerned. The first view is associated with Gaston Boissier and Adolph von Harnack, and was famously championed by Prosper Alfaric: that Augustine in 386 converted to neo-Platonism but not to Christianity. Second, there is the view recently promoted by Catherine Conybeare: that Augustine in 386 converted to Christianity and rejected neo-Platonism. Third, there is the view that he converted to Christianity and was also a neo-Platonist; the most famous adherents of this view are Robert J. O′Connell and Pierre Courcelle. Finally, there is the view recently promoted by Carol Harrison: that Augustine committed to Christianity in 386, yet did not utterly reject neo-Platonism; rather, he aimed to develop a Christian faith that was informed by neo-Platonic insight. In this article, I first explain and distinguish these four general views, and then I explain why I prefer the fourth view. -/- More Info: This is the pre-peer reviewed version of Boone, Mark, "The Role of Platonism in Augustine's 386 Conversion to Christianity," Religion Compass 9.5 (May 2015), 151-61. This article has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/rec3.12149/abstract. (shrink)

This paper engages critically with anti-representationalist arguments pressed by prominent enactivists and their allies. The arguments in question are meant to show that the “as-such” and “job-description” problems constitute insurmountable challenges to causal-informational theories of mental content. In response to these challenges, a positive account of what makes a physical or computational structure a mental representation is proposed; the positive account is inspired partly by Dretske’s views about content and partly by the role of mental representations in contemporary cognitive scientific (...) modeling. (shrink)

This essay joins Wilhelm Dilthey’s conception of the metaphysical impulse as a flight from the tragedy of human finitude with Ludwig Wittgenstein’s understanding of how language bewitches intelligence. We contend that there are features of the phenomenology of language that play a constitutive and pervasive role in the formation of metaphysical illusion.

This paper evaluates the Natural-Kinds Argument for cognitive extension, which purports to show that the kinds presupposed by our best cognitive science have instances external to human organism. Various interpretations of the argument are articulated and evaluated, using the overarching categories of memory and cognition as test cases. Particular emphasis is placed on criteria for the scientific legitimacy of generic kinds, that is, kinds characterized in very broad terms rather than in terms of their fine-grained causal roles. Given the current (...) state of cognitive science, I conclude that we have no reason to think memory or cognition are generic natural kinds that can ground an argument for cognitive extension. (shrink)

I argue that there is a flaw in the way that response-dependence has been formulated in the literature, and this flawed formulation has been correctly attacked by Mark Johnston’s Missing Explanation Argument (1993, 1998). Moving to a better formulation, which is analogous to the move from behaviourism to functionalism, avoids the Missing Explanation Argument.

In this paper, I claim that extant empirical data do not support a radically embodied understanding of the mind but, instead, suggest (along with a variety of other results) a massively representational view. According to this massively representational view, the brain is rife with representations that possess overlapping and redundant content, and many of these represent other mental representations or derive their content from them. Moreover, many behavioral phenomena associated with attention and consciousness are best explained by the coordinated activity (...) of units with redundant content. I finish by arguing that this massively representational picture challenges the reliability of a priori theorizing about consciousness. (shrink)

The recent literature on mental causation has not been kind to nonreductive, materialist functionalism (‘functionalism’, hereafter, except where that term is otherwise qualified). The exclusion problem2 has done much of the damage, but the epiphenomenalist threat has taken other forms. Functionalism also faces what I will call the ‘problem of metaphysically necessary effects’ (Block, 1990, pp. 157-60, Antony and Levine, 1997, pp. 91-92, Pereboom, 2002, p. 515, Millikan, 1999, p. 47, Jackson, 1998, pp. 660-61). Functionalist mental properties are individuated partly (...) by their relation to the very effects those properties’ instantiations are thought to cause. Consequently, functionalist causal generalizations would seem to have the following problematical structure: The state of being, among other things, a cause of e (under such-andsuch conditions) causes e (under those conditions).3 The connection asserted lacks the contingency one would expect of a causal generalization. Mental states of the kind in question are, by metaphysical necessity, causes of e; any state that does not cause e is thereby a different kind of state. Yet, a mental state’s being the sort of state it is must play some causal role if functionalism is to account for mental causation.4 In what follows, I first articulate more fully the problem of metaphysically necessary effects. I then criticize three functionalist attempts to solve the problem directly. Given the failure of functionalist efforts to meet the problem head-on, I consider less direct strategies: these involve formulating functionalism or its causal claims in such a way that they appear not to generate the problem of metaphysically necessary effects. I argue against these indirect solutions, in each case concluding either that the problem still arises or that avoiding it requires the adoption of an unorthodox form of functionalism (itself a surprising result). In the final.. (shrink)

A theory of cognitive systems individuation is presented and defended. The approach has some affinity with Leonard Talmy's Overlapping Systems Model of Cognitive Organization, and the paper's first section explores aspects of Talmy's view that are shared by the view developed herein. According to the view on offer -- the conditional probability of co-contribution account (CPC) -- a cognitive system is a collection of mechanisms that contribute, in overlapping subsets, to a wide variety of forms of intelligent behavior. Central to (...) this approach is the idea of an integrated system. A formal characterization of integration is laid out in the form of a conditional-probabilitybased measure of the clustering of causal contributors to the production of intelligent behavior. I relate the view to the debate over extended and embodied cognition and respond to objections that have been raised in print by Andy Clark, Colin Klein, and Felipe de Brigard. (shrink)

This volume considers challenges to forgiveness in the most difficult circumstances, such as in criminal justice contexts, when the victim is dead or when bystanders disagree, and when anger and resentment seem preferable and important. Contributing philosophers include Myisha Cherry, Jonathan Jacobs, Barrett Emerick, Alice MacLachlan, David McNaughton and Eve Garrard. Contributing psychologists include Pumla Gobodo-Madikizela, Robert D. Enright and Mary Jacqueline Song, C. Ward Struthers, Joshua Guilfoyle, Careen Khoury, Elizabeth van Monsjou, Joni Sasaki, Curtis Phills, Rebecca Young, and (...) Zdravko Marjanovic. (shrink)

Philosophers of mind commonly draw a distinction between the personal level – the distinctive realm of conscious experience and reasoned deliberation – and the subpersonal level, the domain of mindless mechanism and brute cause and effect. Moreover, they tend to view cognitive science through the lens of this distinction. Facts about the personal level are given a priori, by introspection, or by common sense; the job of cognitive science is merely to investigate the mechanistic basis of these facts. I argue (...) that this view misrepresents the structure of cognitive-scientific enquiry. Taken at face value, cognitive science makes no commitment to the existence of a distinctive level at which persons or selves appear. Thus, in the age of cognitive science, we should not expect to find the self in an ontologically distinct realm. Instead, we should expect to locate it in cognitive-scientific models themselves. In closing, I indicate likely results of this approach. (shrink)

Laws of nature seem to take two forms. Fundamental physics discovers laws that hold without exception, ‘strict laws’, as they are sometimes called; even if some laws of fundamental physics are irreducibly probabilistic, the probabilistic relation is thought not to waver. In the nonfundamental, or special, sciences, matters differ. Laws of such sciences as psychology and economics hold only ceteris paribus – that is, when other things are equal. Sometimes events accord with these ceteris paribus laws (c.p. laws, hereafter), but (...) sometimes the laws are not manifest, as if they have somehow been placed in abeyance: the regular relation indicative of natural law can fail in circumstances where an analogous outcome would effectively refute the assertion of strict law. Many authors have questioned the supposed distinction between strict laws and c.p. laws. The brief against it comprises various considerations: from the complaint that c.p. clauses are void of meaning to the claim that, although understood well enough, they should appear in all law-statements. These two concerns, among others, are addressed in due course, but first, I venture a positive proposal. I contend that there is an important contrast between strict laws and c.p. laws, one that rests on an independent distinction between combinatorial and noncombinatorial nomic principles.2 Instantiations of certain properties, e.g., mass and charge, nomically produce individual forces, or more generally, causal influences,3 in accordance with noncombinatorial.. (shrink)

This essay presents the conditional probability of co-contribution account of the individuation of cognitive systems (CPC) and argues that CPC provides an attractive basis for a theory of the cognitive self. The argument proceeds in a largely indirect way, by emphasizing empirical challenges faced by an approach that relies entirely on predictive processing (PP) mechanisms to ground a theory of the cognitive self. Given the challenges faced by PP-based approaches, we should prefer a theory of the cognitive self of the (...) sort CPC offers, one that accommodates variety in the kinds of mechanism that, when integrated, constitute a cognitive system (and thus the cognitive self), to a theory according to which the cognitive self is composed of essentially one kind of thing, for instance, prediction-error minimization mechanisms. The final section focuses on one of the central functions of the cognitive self: to engage in conscious reasoning. It is argued that the phenomenon of conscious, deliberate reasoning poses an apparently insoluble problem for a PP-based view, one that seems to rest on a structural limitation of predictive-processing models. In a nutshell, conscious reasoning is a single-stream phenomenon, but, in order for PP to apply, two streams of activity must be involved, a prediction stream and an input stream. Thus, with regard to the question of the nature of the self, PP-based views must yield to an alternative approach, regardless of whether proponents of the predictive processing, as a comprehensive theory of cognition, can handle the various empirical challenges canvassed in the preceding section. (shrink)

This book demonstrates how the authors have experienced the power of phenomenology in their therapeutic work with patients, especially those struggling with horrific trauma; in their encounters with psychological and philosophical theories; and in their efforts to comprehend destructive ideologies and the collective traumas that give rise to them. The Power of Phenomenology presents the trajectory of this work. Each chapter begins with a contribution written by one or both authors, extending the power of phenomenological inquiry to one or more (...) of these diverse contexts. The contributions are followed, one or two at a time, by a dialogue between the authors, illustrating the dialectical process of their long collaboration. The unusual format seeks to bring the phenomenology of their collaborative efforts to life for the reader. (shrink)

This paper asks about the ways in which embodimentoriented cognitive science contributes to our understanding of phenomenal consciousness. It is first argued that central work in the field of embodied cognitive science does not solve the hard problem of consciousness head on. It is then argued that an embodied turn toward neurophenomenology makes no distinctive headway on the puzzle of consciousness; for neurophenomenology either concedes dualism in the face of the hard problem or represents only a slight methodological variation on (...) extant cognitive-scientific approaches to the easy problems of consciousness. The paper closes with the positive suggestion that embodied cognitive science supports a different approach to phenomenal consciousness, according to which the mind is massively representational, cognitive science has no use for the personal-level posits that tend to drive philosophical theorizing about consciousness and mind, and the hard problem is illusory. (shrink)

In this essay, it is argued that naturalism of an even moderate sort speaks strongly against a certain widely held thesis about the human mental (and cognitive) architecture: that it is divided into two distinct levels, the personal and the subpersonal, about the former of which we gain knowledge in a manner that effectively insulates such knowledge from the results of scientific research. -/- An empirically motivated alternative is proposed, according to which the architecture is, so to speak, flattened from (...) above. On this flattened view, although the states and processes typically associated with the personal level likely appear in our best models of the production of human behavior, they appear alongside states and processes normally associated with the subpersonal level. Moreover, the success of such models depends nowise on a levels-based distinction between the various causal contributors. It is argued that the flattened view has methodological implications of significant import. (shrink)

This essay develops the thesis that the essence of psychoanalysis lies in emotional phenomenology.

The psychiatric diagnostic system, as exemplified by the DSM, is a pseudo-scientific framework for diagnosing sick Cartesian isolated minds. As such, it completely overlooks the exquisite context sensitivity and radical context dependence of human emotional life and of all forms of emotional disturbance. In Descartes’s vision, the mind is a “thinking thing,” ontologically decontextualized, fundamentally separated from its world. Heidegger’s existential phenomenology mended this Cartesian subject-object split, unveiling our Being as always already contextualized, a Being-in-the-world. Here I offer a critique (...) of studies in “phenomenological psychopathology” that presuppose the validity of the psychiatric diagnostic system and leave it unchallenged. In this vein, I contend that all emotional disturbances are constituted in an indissoluble context of human interrelatedness. Specifically, I claim that all emotional disturbances, including those objectified by the DSM, take form in relational contexts of severe emotional trauma. There are no psychiatric entities, only devastating contexts. Additionally, I show that Heidegger’s analyses of Angst, world-collapse, uncanniness, and thrownness into Being-toward-death provide extraordinary philosophical tools for grasping the existential significance of such contexts of emotional trauma. Applying Heidegger’s concept of authenticity, I suggest that emotional health entails an ease of passage—i.e., an absence of dissociation—between the world of trauma and the world of everydayness. (shrink)

For more than four decades, George Atwood and I have been absorbed in rethinking psychoanalysis as a form of phenomenological inquiry. In the course of this work, I repeatedly made the claim that phenomenology led us inexorably to relationality, but until now I did not offer an explanation of this inexorability. In this article, I show that emotional phenomenology and relationality always already form an indissoluble unity, because relationality is constitutive of emotional experience.

When faced with the complexity of an intersubjective system, in which one is oneself implicated, an epistemic humility that recognizes and respects the finitude of knowing is essential.