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)

Epistemic defeat is standardly understood in either evidentialist or responsibilist terms. The seminal treatment of defeat is an evidentialist one, due to John Pollock, who famously distinguishes between undercutting and rebutting defeaters. More recently, an orthogonal distinction due to Jennifer Lackey has become widely endorsed, between so-called doxastic (or psychological) and normative defeaters. We think that neither doxastic nor normative defeaters, as Lackey understands them, exist. Both of Lackey’s categories of defeat derive from implausible assumptions about epistemic responsibility. Although Pollock’s (...) evidentialist view is superior, the evidentialism per se can be purged from it, leaving a general structure of defeat that can be incorporated in a reliabilist theory that is neither evidentialist nor responsibilist in any way. (shrink)

This project continues our interdisciplinary research into computational and cognitive aspects of narrative comprehension. Our ultimate goal is the development of a computational theory of how humans understand narrative texts. The theory will be informed by joint research from the viewpoints of linguistics, cognitive psychology, the study of language acquisition, literary theory, geography, philosophy, and artificial intelligence. The linguists, literary theorists, and geographers in our group are developing theories of narrative language and spatial understanding that are being tested by the (...) cognitive psychologists and language researchers in our group, and a computational model of a reader of narrative text is being developed by the AI researchers, based in part on these theories and results and in part on research on knowledge representation and reasoning. This proposal describes the knowledge-representation and natural-language-processing issues involved in the computational implementation of the theory; discusses a contrast between communicative and narrative uses of language and of the relation of the narrative text to the story world it describes; investigates linguistic, literary, and hermeneutic dimensions of our research; presents a computational investigation of subjective sentences and reference in narrative; studies children’s acquisition of the ability to take third-person perspective in their own storytelling; describes the psychological validation of various linguistic devices; and examines how readers develop an understanding of the geographical space of a story. This report is a longer version of a project description submitted to NSF. This document, produced in May 2007, is a L ATEX version of Technical Report 89-07 (Buffalo: SUNY Buffalo Department of Computer Science, August 1989), with slightly.. (shrink)

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of (...) incorporating into meetings experts from other disciplines, such as philosophy and history of science. (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.

Background: Emergentism as an ontology of consciousness leaves unanswered the question as to its mechanism. Aim: I aim to solve the Body-Mind problem by explaining how conscious organisms emerged on an evolutionary basis at various times in accordance with an accepted scientific principle, through a mechanism that cannot be understood, in principle. Proposal: The reason for this cloak of secrecy is found in a seeming contradiction in the behaviour of information with respect to the first two laws of thermodynamics. Information, (...) the microstate of particles within an isolated system’s macrostate, can, like first law energy, be neither created nor destroyed, yet the information in the system, like second law entropy, will inevitably increase. To explain information increasing without being created, Laplace’s demon is invoked, able to predict where each particle is destined. This doesn’t work for emerging events like consciousness, which are unpredictable. This can be understood in terms of the derivation of entropy, and the emergence of classical physics, from the Relativistic Transactional Interpretation of Quantum Mechanics. I propose that the increased entropy in a time-irreversible, unpredictable (emergent) isolated system requires the simultaneous deletion of information concerning the steps, or calculations, involved. Conclusion: Thus, the steps leading to consciousness are immediately destroyed and must remain a mystery. Implications include that entropy, not panpsychism, is the Universal principle generative of consciousness, that our being conscious proves that we are not predetermined, and that consciousness requires assuming an “entropy debt” that can only be repaid by living organisms, prohibiting the emergence of conscious machines. (shrink)

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)

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)

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 Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Modern humans are probably a product of social and anatomical preadaptations on the part of our Miocene australopithecine ancestors combined with the increasingly high amplitude, high frequency climate variation of the Pleistocene. The genus Homo first appeared in the early Pleistocene as ice age climates began to grip the earth. We hypothesize that this co-occurrence is causal. The human ability to adapt by cultural means is, in theory, an adaptation to highly variable environments because cultural evolution can better track rapidly (...) changing environments than can genes. High resolution ice and sediment cores published in the early 1990s showed the last ice age was characterized by high amplitude millennial and submillenial scale variation, exactly the sort of variation mathematical models suggest should favor a costly capacity for culture. More recent cores suggest that over the last several 100 thousand year glacial cycles the amount of millennial scale variation has increased rather dramatically in parallel with increases in hominin brain size and sophistication of the artifacts they made. (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)

The precarious rights of senior citizens, especially those who are highly educated and who are expected to counsel and guide the younger generations, has stimulated the creation internationally of advocacy associations and opinion leader groups. The strength of these groups, however, varies from country to country. In some countries, they are supported and are the focus of intense interest; in others, they are practically ignored. For this is reason we believe that the creation of a network of all these associations (...) is essential. The proposed network would act as a support for the already-existing policies of the United Nations’ High Commission for Human Rights, of independent experts, and of the Global Alliance for the Rights of Older People. All three have long ago recommended the creation of a recognized instrument for uniting presently scattered efforts. The proposed network, therefore, will seek to promote the international exchange of relevant expertise, and it will reinforce the commitments and actions that single countries are currently taking to meet these objectives. For example, informative public events can be organised to promote particular support initiatives and to provide an opportunity for new members of the network to be presented. The network will promote health for senior citizens, disease prevention, senior mobility, safe free time for seniors, alimentary education, protection against new risks and dangers, as well as equity in the services necessary for seniors to adopt new information and communication technologies. In the case of retired academic members, the network will promote equality with respect to continuing use of digital technologies (particularly email), continuing access to research libraries, and the guaranteed ability for seniors to fund their own research programs and to deliver free seminars. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Until recently, psychologists have conceptualised and studied trust in God (TIG) largely in isolation from contemporary work in theology, philosophy, history, and biblical studies that has examined the topic with increasing clarity. In this article, we first review the primary ways that psychologists have conceptualised and measured TIG. Then, we draw on conceptualizations of TIG outside the psychology of religion to provide a conceptual map for how TIG might be related to theorised predictors and outcomes. Finally, we provide a research (...) agenda for future empirical work in this area, as well as practical applications for counsellors and religious leaders. (shrink)

You may not know me well enough to evaluate me in terms of my moral character, but I take it you believe I can be evaluated: it sounds strange to say that I am indeterminate, neither good nor bad nor intermediate. Yet I argue that the claim that most people are indeterminate is the conclusion of a sound argument—the indeterminacy paradox—with two premises: (1) most people are fragmented (they would behave deplorably in many and admirably in many other situations); (2) (...) fragmentation entails indeterminacy. I support (1) by examining psychological experiments in which most participants behave deplorably (e.g., by maltreating “prisoners” in a simulated prison) or admirably (e.g., by intervening in a simulated theft). I support (2) by arguing that, according to certain plausible conceptions, character evaluations presuppose behavioral consistency (lack of fragmentation). Possible reactions to the paradox include: (a) denying that the experiments are relevant to character; (b) upholding conceptions according to which character evaluations do not presuppose consistency; (c) granting that most people are indeterminate and explaining why it appears otherwise. I defend (c) against (a) and (b). (shrink)

Although commonly cited as one of the philosophers responsible for the resurgence of interest in pragmatism, Wilfrid Sellars was also the son of Roy Wood Sellars, one of the most dedicated critical realists of the early 20th century. Given his father’s realism and his own ‘scientific realism,’ one might assume that the history of realism – and, despite contemporary interest, not pragmatism – would best serve as the historical background for Wilfrid Sellars’ philosophy. I argue that Wilfrid Sellars, far from (...) being the adherent to classical pragmatism assumed by some, holds more in common with critical realism - specifically, a realism that was framed in opposition to pragmatism – than one finds amongst the writings of Charles Sanders Peirce, William James, or John Dewey. I support this claim by examining Wilfrid Sellars’ adoption of his father’s criticisms of C.I. Lewis, and offer various arguments and historical considerations against thematic accounts that insist on a strong connection between Wilfrid Sellars and pragmatism. (shrink)

In this paper, new evidence is presented for the assumption that the reason-relation reading of indicative conditionals ('if A, then C') reflects a conventional implicature. In four experiments, it is investigated whether relevance effects found for the probability assessment of indicative conditionals (Skovgaard-Olsen, Singmann, and Klauer, 2016a) can be classified as being produced by a) a conversational implicature, b) a (probabilistic) presupposition failure, or c) a conventional implicature. After considering several alternative hypotheses and the accumulating evidence from other studies as (...) well, we conclude that the evidence is most consistent with the Relevance Effect being the outcome of a conventional implicature. This finding indicates that the reason-relation reading is part of the semantic content of indicative conditionals, albeit not part of their primary truth-conditional content. (shrink)

The last twenty-five years or so have seen the emergence of exciting comparative work on Nietzsche and various philosophical traditions beyond the bounds of Europe. So far, however, the emphasis has been primarily on the cultures of India, China and Japan, with an almost exclusive focus on Buddhist, Hindu, Daoist, and Confucian traditions. Surprisingly, little work has been done on Nietzsche and the Islamic tradition. In this paper, I sketch out Nietzsche’s understanding of Islam, the ways in which he uses (...) it as a resource for his critique of Christianity and European modernity and the criticisms he has to make of it as one of the great monotheistic world religions. I then argue for the need to engage Nietzsche with specific Islamic falāsifa of the classical period (9-12th c.) rather than Islam itself, as some recent scholars have attempted to do. Although Nietzsche himself seems to have had no direct familiarity with any of the falāsifa, there are, I argue, many entry points for productive comparison and dialogue. This is at least in part because they share a significant common heritage: both were careful students of classical Greek and Hellenistic thought, and both put the insights they encountered there to work in bold new ways. Indeed, they appropriated, transformed and reanimated Greek ideas in new contexts and towards new ends that their progenitors would scarcely have recognized, and that were often radically challenging to their contemporaries. I focus here on a few select themes—the idea of philosophy as a “way of life,” the ideal of “becoming like God so far as it is possible” and the Platonic figure of the philosopher-ruler, all of which get taken up and re-imagined in radically novel and sometimes antipodal ways. (shrink)

Our folk epistemology says that if someone knows that P and tells you that P, then, given the absence of defeaters, if you believe what they tell you, you will come to know that P as well. A speaker's knowledge that P is then, for the most part, enough for a hearer to come to know that P. But there are counterexamples to this principle: testimonial knowledge does not always transfer from the speaker to the hearer. Why should that be (...) so? Because testimonial knowledge arises through the flow of information--from conclusive grounds--from the speaker through the speaker's assertion to the hearer's state of comprehension as of the speaker's assertion. A speaker's belief can be based on conclusive grounds, but the speaker's assertion may fail to provide conclusive grounds to the hearer. Then the hearer won't acquire knowledge, even from a knowledgeable speaker. Knowledge from testimony then works more like knowledge through perception. But wait, you say, that can't be so because testimony involves free will but perception does not. The essay ends with a broadly Hume inspired reply to this objection. (shrink)

Does epistemic justification aim at truth? The vast majority of epistemologists instinctively answer 'Yes'; it's the textbook response. Joseph Cruz and John Pollock surprisingly say no. In 'The Chimerical Appeal of Epistemic Externalism' they argue that justification bears no interesting connection to truth; justification does not even aim at truth. 'Truth is not a very interesting part of our best understanding' of justification (C&P 2004, 137); it has no 'connection to the truth.' A 'truth-aimed ... epistemology is not entitled to (...) carry the day' (C&P 2004, 138, emphasis added).Pollock and Cruz's argument for this surprising conclusion is of general interest for it is 'out of step with a very common view on the .. (shrink)

With the success of cognitive science's interdisciplinary approach to studying the mind, many theorists have taken up the strategy of appealing to science to address long standing disputes about metaphysics and the mind. In a recent case in point, philosophers and psychologists, including Robert Kane, Daniel C. Dennett, and Daniel M. Wegner, are exploring how science can be brought to bear on the debate about the problem of free will. I attempt to clarify the current debate by considering how empirical (...) research can be useful. I argue that empirical findings don't apply to one basic dimension of the problem, namely the dispute between compatibilism and incompatibilism. However, I show that empirical research can provide constraints in connection with another fundamental dimension, namely the dispute between libertarianism, which claims that indeterminacy is, in certain contexts, sufficient for freedom, and hard determinism and compatibilism, which deny this. I argue that the source of the most powerful constraint is psychological research into the accuracy of introspection. (shrink)

The first sentence of NE I.2 has roughly the form: "If A [there is a universal end] and B, then D [this end will be the best good]". According to some commentators, Aristotle uses B to infer A; but then the sentence is fallacious. According to other commentators, Aristotle does not use B ; but then the sentence is bizarre. Contrary to both sets of commentators, I suggest that Aristotle uses B together with A to infer validly that there is (...) a non-instrumental – and thus unique – universal end. On this interpretation the above two problems disappear, but a subtler problem emerges: not-B does not entail C. (shrink)

A fully developed sophisticated response-dependent account would fill in specifications for B (the beings) and C (the conditions), would probably replace the reference to disapproval with a reference to a more complex response, and might involve a more complex scheme.[ii] For simplicity, however, I shall focus my argument on the above simple scheme of moral wrongness, since added complexities will be irrelevant to my argument.

Although the notion of universal human rights allows for the idea that states (and supranational organizations such as the European Union) can, or even should, control and impose restrictions on migration, both notions clearly do not sit well together. The ensuing tension manifests itself in our ambivalent attitude towards migration, but also affects the border guards who have to implement national and supranational policies on migration. Little has been written on the ethics that has to guide these border guards in (...) their work. Juxtaposing the ethics of border guarding against the ethics of the somewhat related military profession, this article attempts to (a) describe border guarding as a comparatively rule-guided profession; (b) outline the aim and basis of the ethics education that prepares border guards for their work; and (c) propose a research agenda for the future that should further our understanding of (a) and (b), but also help us improve the moral education of border guards. (shrink)

Selective scientific realists disagree on which theoretical posits should be regarded as essential to the empirical success of a scientific theory. A satisfactory account of essentialness will show that the (approximate) truth of the selected posits adequately explains the success of the theory. Therefore, (a) the essential elements must be discernible prospectively; (b) there cannot be a priori criteria regarding which type of posit is essential; and (c) the overall success of a theory, or ‘cluster’ of propositions, not only individual (...) derivations, should be explicable. Given these desiderata, I propose a “unification criterion” for identifying essential elements. (shrink)

I take the debate between the particularists and the principlists to be centered on the issue of whether there are true moral principles. One argument the principlists often appeal to in support of their claim that there are true moral principles is the argument from supervenience. Roughly, the argument is made up of the following three statements: (P1) If the thesis of moral supervenience holds, then there are true moral principles. (P2) The thesis of moral supervenience holds. (C) There are (...) true moral principles, and hence particularism is false. In this paper, I argue that the above argument is not sound by attacking (P1). I hold that no general supervenient/resultance base has a robust enough configuration of contextual features as to ground the existence of true moral principles. If I am right about this, I think it would be indicative of a reason to be less confident about the truth of principlism and more confident about the truth of particularism. (shrink)

This article proposes that oral performance could be a philosophical activity in early China. The focus is on the Huainanzi, a densely rhymed philosophical treatise compiled by Liu An in the second century b.c.e. I show that the tome contains various sound-correlated poetic forms that are intended not only to enable textual performance but also, by means of aural mimesis, to encourage the intuitive understanding of its philosophical messages. Thus scholars of ancient poetry, philosophy, or intellectual history, despite being habituated (...) to reading silently and observing disciplinary boundaries, should be attentive to these sonic patterns in order to do justice to the poetic-cum-philosophical richness and originality of this text. More importantly, I argue that these poetic forms enable readers and audiences to experience, embody, and, above all, enact the Way through textual performance. Thanks to the sound patterns of the Huainanzi, the somatic processes of aural reading and philosophical praxis can occur simultaneously. Vocalization becomes an actionable and repeatable spiritual exercise, which facilitates the intuitive understanding and internalization of philosophical values. In other words, the perennial knowing–doing gap is heroically closed by the Huainanzi. / 淮南子的文本聲景：早期中國的詩歌、表演、哲學與實踐 / 王棕琦 / 本文論證早期中國的文本表演可以是一種具創造性的哲學活動，而非只是以聲音演繹書寫文本的朗讀活動。文中首先指出《淮南子》裏跟聲音有關的詩歌形式不但有助朗誦表演，更能讓讀者直觀感悟書中哲學思想而不落言筌。而 且，這些詩歌形式更讓讀者通過朗讀而實踐、內化書中所述之大道。可以說，《淮南子》對中國哲學的一大貢獻在於它將「知道」、「傳道」和「行道」三者合而為一。. (shrink)

As the title, The Entangled State of God and Humanity suggests, this lecture dispenses with the pre-Copernican, patriarchal, anthropomorphic image of God while presenting a case for a third millennium theology illuminated by insights from archetypal depth psychology, quantum physics, neuroscience and evolutionary biology. It attempts to smash the conceptual barriers between science and religion and in so doing, it may contribute to a Copernican revolution which reconciles both perspectives which have been apparently irreconcilable opposites since the sixteenth century. The (...) published work of C.G. Jung, Wolfgang Pauli, David Bohm and Teilhard de Chardin outline a process whereby matter evolves in increasing complexity from sub-atomic particles to the human brain and the emergence of a reflective consciousness leading to a noosphere evolving towards an Omega point. The noosphere is the envelope of consciousness and meaning superimposed upon the biosphere a concept central to the evolutionary thought of visionary Jesuit palaeontologist Pierre Teilhard de Chardin (The Phenomenon of Man). -/- His central ideas, like those of Jung with his archetypes, in particular that of the Self, provide intimations of a numinous principle implicit in cosmology and the discovery that in and through humanity, evolution becomes not only conscious of itself but also directed and purposive. Although in Jung’s conception it was a “late-born offspring of the unconscious soul”, consciousness has become the mirror which the universe has evolved to reflect upon itself and in which its very existence is revealed. Without consciousness, the universe would not know itself. The implication for process theology is that God and humanity are in an entangled state so that the evolution of God cannot be separated from that of humankind. -/- A process (Incarnational) theology inseminated by the theory of evolution is one in which humankind completes the individuation of God towards the wholeness represented for instance in cosmic mandala symbols (Jung, Collected Works, vol. 11). Jung believed that God needs humankind to become conscious, whole and complete, a thesis explored in my book The Individuation of God: Integrating Science and Religion (Wilmette, IL: Chiron Publications 2012). This process theology like that implicit in the work of Teilhard de Chardin, is panentheistic so that God is immanent in nature though not identical with it (Atmanspacher: 2014: 284). (shrink)

Peter Singer’s famous and influential article is criticised in three main ways that can be considered libertarian, although many non-libertarians could also accept them: 1) the relevant moral principle is more plausibly about upholding an implicit contract rather than globalising a moral intuition that had local evolutionary origins; 2) its principle of the immorality of not stopping bad things is paradoxical, as it overlooks the converse aspect that would be the positive morality of not starting bad things and also thereby (...) conceptually eliminates innocence; and 3) free markets—especially international free trade—have been cogently explained to be the real solution to the global “major evils” of “poverty” and “pollution”, while “overpopulation” does not exist in free-market frameworks; hence charity is a relatively minor alleviant to the problem of insufficiently free markets. There are also various subsidiary arguments throughout. (shrink)

Cognitive penetration of perception is the idea that what we see is influenced by such states as beliefs, expectations, and so on. A perceptual belief that results from cognitive penetration may be less justified than a nonpenetrated one. Inferentialism is a kind of internalist view that tries to account for this by claiming that some experiences are epistemically evaluable, on the basis of why the perceiver has that experience, and the familiar canons of good inference provide the appropriate standards by (...) which experiences are evaluated. I examine recent defenses of inferentialism by Susanna Siegel, Peter Markie, and Matthew McGrath and argue that the prospects for inferentialism are dim. (shrink)

Building on Peter French’s important work, this chapter draws three distinctions that arise in the context of attributions of moral responsibility, understood as the extent to which an agent is blameworthy or praiseworthy. First, the subject of an attribution of responsibility may be an individual agent or a collective agent. Second, the object of the responsibility attribution may be an individual action (or consequence) or a collective action (or consequence). The third distinction concerns the temporal dimension of the responsibility attribution. (...) Sometimes responsibility for an action is attributed to an agent at the time of the action. At other times responsibility for an action is attributed to an agent sometime after the action has taken place. Taken together, these three binary distinctions yield eight types of responsibility attribution. It is argued that a collective agent’s responsibility for a past collective act is properly understood on the same theoretical model as is an individual’s responsibility for a past individual act. While most assume that responsibility over time is a straightforward matter of identity over time, it is argued that instead this is a matter of psychological or attitudinal connectedness. The possibility is considered that this relation also grounds attributions involving an asymmetry between subject and object, such as individual responsibility for past collective action, but a skeptical worry is raised that such attributions entail an unpalatable form of moral luck and should therefore be rejected. (shrink)

"It is difficult not to notice a curious unrest in the philosophic atmosphere of the time, a loosening of old landmarks, a softening of oppositions, a mutual borrowing from one another on the part of systems anciently closed, and an interest in new suggestions, however vague, as if the one thing sure were the inadequacy of extant school-solutions. The dissatisfactions with these seems due for the most part to a feeling that they are too abstract and academic. Life is confused (...) and superabundant, and what the younger generation appears to crave is more of the temperament of life in its philosophy, even though it were at some cost of logical rigor and formal purity." - William James (1904). -/- Abstract: The study of model-based reasoning (MBR) is one of the most interesting recent developments at the intersection of psychology and the philosophy of science. Although a broad and eclectic area of inquiry, one central axis by which MBR connects these disciplines is anchored at one end in theories of internal reasoning (in cognitive science), and at the other, in C.S. Peirce’s semiotics (in philosophy). In this paper, we attempt to show that Peirce’s semiotics actually has more natural affinity on the psychological side with ecological psychology, as originated by James J. Gibson and especially Egon Brunswik, than it does with non-interactionist approaches to cognitive science. In particular, we highlight the strong ties we believe to exist between the triarchic structure of semiotics as conceived by Peirce, and the similar triarchic stucture of Brunswik’s lens model of organismic achievement in irreducibly uncertain ecologies. The lens model, considered as a theory of creative abduction, provides a concrete instantiation of at least one, albeit limited, interpretation of Peirce’s semiotics, one that we believe could be quite fruitful in future theoretical and empirical investigations of MBR in both science an philosophy. (shrink)

Peter Simons has argued that the expression ‘the universe’ is not a genuine singular term: it can name neither a single, completely encompassing individual, nor a collection of individuals. (It is, rather, a semantically plural term standing equally for every existing object.) I offer reasons for resisting Simons’s arguments on both scores.

The link between human nature and human flourishing is undeniable. "A healthy tree cannot bear bad fruit, nor can a diseased tree bear good fruit" (Matt. 7:18). The ontology of the human person will, therefore, ground the nature of human flourishing and thereby sanctification. Spiritual formation is the area of Christian theology that studies sanctification, the Spirit-guided process whereby disciples of Jesus are formed into the image of Jesus (Rom. 8:28-29; 2 Cor. 3:18; 2 Peter 3:18). Until the nineteenth century, (...) there was an overwhelming consensus among Christian thinkers that some form of mind-body (or soul-body) dualism is true of human beings. Recently, that consensus has eroded, and with it the availability of a shared body of knowledge about spiritual formation. Some Christian physicalists argue that dualism is incompatible with central elements of spiritual formation. Neuroscientist Warren Brown and psychologist Brad Strawn offer the only substantive account of spiritual formation from the view of Christian physicalism and its accompanying objections to dualism. It is on their arguments that this chapter focuses. We argue that Brown and Strawn fail to support their incompatibility thesis. Additionally, we argue that Christian physicalism stands in tension with important philosophical and theological foundations of Christian spiritual formation. In doing so we offer a specific form of dualism, the bodily soul view, and explain how this view illuminates the importance of embodiment, our neurological and social development, and hence the important physical aspects of Christian spiritual formation. (shrink)

1. First there is an outline of the libertarian approach taken here. 2. On the assumption of personhood, it is explained how there need be no overall inflicted harm and no proactive killing with abortion and infanticide. This starts with an attached-adult analogy and transitions to dealing directly with the issues. Various well-known criticisms are answered throughout. 3. There is then a more-abstract explanation of how it is paradoxical to assume a duty to do more than avoid inflicting overall harm (...) and, instead, positively benefit. A putative counterexample is explained away. 4. A positive theory of intellectual personhood is defended in principle, but not made precise, which is sufficient to be practical. The greater moral value of intellectual-personhood is defended. An important putative reductio of the potential-personhood argument is refuted. 5. Several further criticisms that apply to both types of defences are answered. 6. Conclusion. (shrink)

Judith Butler’s influential work in feminist theory is significant for its insight that sexist discourse in popular culture affects the agency and consciousness of individuals, but offers an inadequate account of how such discourse might be said to touch, shape, or affect selves. Supplementing Butler’s account of signification with a Deweyan pragmatic account of meaning-making and selective emphasis enables a consistent account of the relationship between discourse and subjectivity with a robust conception of the bodily organism. An analysis of (...) the popular discourse surrounding Hillary Clinton in the 2008 Presidential campaign demonstrates why this hybrid pragmatic/poststructuralist account is necessary. (shrink)

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

Acts 2,5-6 talks of the crowd that gathered in Jerusalem for the annual Pentecost feast. It describes them as ‘devout men from nations under heaven’. This description could be an exaggeration, but it is a literary way of telling the readers that uncountable number of people went for the feast. The presentation posits species from every continent as present. They did not visit Jerusalem to listen to Peter’s preaching about the resurrected Christ. Their visit was an annual pilgrimage for Jewish (...) agricultural feast called ‘Pentecost’. Undoubtedly, they were not interested in stories about Christ who as at the period was regarded as an insurrectionist, a brigand and a robber who died infamously. Truly, perception of an unusual sound necessitated their gathering together but staying on to listen to Peter talk about an infamous man and the historical conversion of about three thousand (3000) men (Acts 2,41) invites a sober reflection on the method used by Peter to pass on his message. If the early Christians were able to move the world at a time when Information Technology and pedagogical methods were not so much in vogue, then the method they adopted is worth being studied. The contemporary era is witnessing the decadence of mainline Churches – Catholicism, Anglicanism, Methodist, Presbyterianism, Lutheranism etc. On the other hand, Pentecostalism and Easter Transcendental Meditation have attractions on a geometrical increase. Evidently therefore, the problem is not with man’s incredulity or nonacceptance of Christocentric method. The submission of this paper is that the problem lies with our method of presentation. Therefore, this work confines itself in the main to an examination of what used to be the case, a look into the present and a suggestion on the way forward. (shrink)

This volume offers very selected papers from the 2014 conference of the “International Association for Computing and Philosophy” (IACAP) - a conference tradition of 28 years. - - - Table of Contents - 0 Vincent C. Müller: - Editorial - 1) Philosophy of computing - 1 Çem Bozsahin: - What is a computational constraint? - 2 Joe Dewhurst: - Computing Mechanisms and Autopoietic Systems - 3 Vincenzo Fano, Pierluigi Graziani, Roberto Macrelli and Gino Tarozzi: - Are Gandy Machines really local? (...) - 4 Doukas Kapantais: - A refutation of the Church-Turing thesis according to some interpretation of what the thesis says - 5 Paul Schweizer: - In What Sense Does the Brain Compute? - 2) Philosophy of computer science & discovery - 6 Mark Addis, Peter Sozou, Peter C R Lane and Fernand Gobet: - Computational Scientific Discovery and Cognitive Science Theories - 7 Nicola Angius and Petros Stefaneas: - Discovering Empirical Theories of Modular Software Systems. An Algebraic Approach. - 8 Selmer Bringsjord, John Licato, Daniel Arista, Naveen Sundar Govindarajulu and Paul Bello: - Introducing the Doxastically Centered Approach to Formalizing Relevance Bonds in Conditionals - 9 Orly Stettiner: - From Silico to Vitro: - Computational Models of Complex Biological Systems Reveal Real-world Emergent Phenomena - 3) Philosophy of cognition & intelligence - 10 Douglas Campbell: - Why We Shouldn’t Reason Classically, and the Implications for Artificial Intelligence - 11 Stefano Franchi: - Cognition as Higher Order Regulation - 12 Marcello Guarini: - Eliminativisms, Languages of Thought, & the Philosophy of Computational Cognitive Modeling - 13 Marcin Miłkowski: - A Mechanistic Account of Computational Explanation in Cognitive Science and Computational Neuroscience - 14 Alex Tillas: - Internal supervision & clustering: - A new lesson from ‘old’ findings? - 4) Computing & society - 15 Vasileios Galanos: - Floridi/Flusser: - Parallel Lives in Hyper/Posthistory - 16 Paul Bello: - Machine Ethics and Modal Psychology - 17 Marty J. Wolf and Nir Fresco: - My Liver Is Broken, Can You Print Me a New One? - 18 Marty J. Wolf, Frances Grodzinsky and Keith W. Miller: - Robots, Ethics and Software – FOSS vs. Proprietary Licenses. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Peter H. Hare (1935-2008) developed informed, original views about the proposition: some published (Hare 1969 and Hare-Madden 1975); some expressed in conversations at scores of meetings of the Buffalo Logic Colloquium and at dinners following. The published views were expository and critical responses to publications by Curt J. Ducasse (1881-1969), a well-known presence in American logic, a founder of the Association for Symbolic Logic and its President for one term.1Hare was already prominent in the University of Buffalo's Philosophy Department in (...) 1969 when I was appointed. Soon after, he became Chair. As his Associate Chair from 1971to 1975, I spent many hours with him in Buffalo and on professional trips .. (shrink)

This reissue of his collection of early essays, Logico-Linguistic Papers, is published with a brand new introduction by Professor Strawson but, apart from minor ...

For more than 200 years scholars have proceeded on the assumption that there was a controversy (in the sense of an argumentative exchange) between the bishop of Cork and Ross, Peter Browne (c. 1665–1735), and his nowadays more famous contemporary, the bishop of Cloyne, George Berkeley (1685–1753) about what we might call ‘the problem of divine attributes’. This problem concerns one of the most vexing issues for 17th /18th century Irish intellectuals. Simply put, it turns on two interconnected questions, namely (...) (1) an ontological question regarding God’s attributes and (2) a semantical question regarding the proper conception of analogy: -/- (1) Do God’s attributes only differ in degree or also in kind from their human counterparts? -/- (2) Is “analogical attribution” only concerned with the structure or the modus of the attribution? That is, is it a separate mode of speech (apart from the metaphorical and literal) or does it just mean we have to use analogies for our divine attributions? -/- In regard to the first question Berkeley argues the attributes of God and humans only differ in degree but not in kind (Alc. 4.22). Browne, on the other hand, is convinced that human and divine attributes differ in kind: “What Knowledge and Goodness are in the Nature of Man, that some inconceivable but correspondent Perfections are in the Nature of God […] which tho’ totally different in Kind from those Properties in us bearing the same Name” (Procedure, 138). Furthermore, Berkeley rejects the notion that analogical attribution is a separate mode of speech in addition to the literal and the metaphorical. Rather, it is an attribution made in the form of an analogy in which the words can be used literally or metaphorically (Alc. 4.21). By contrast, Browne repeatedly insists analogical attribution is more than just using analogies for attributing something to God. He thinks it is a separate mode of speech that ought to be distinguished from literal and metaphorical language (Procedure, 12, 23–29, 123–46). -/- Hence, there can be no doubt that Browne and Berkeley advance conflicting solutions to the problem of divine attributes. Yet, advancing disagreeing positions is not the same as having a (heated) argumentative exchange, i.e., a controversy. In contrast to the controversy-reading, I will defend the following view: Browne surely felt attacked by Berkeley’s elaborations in Alciphron (1732) and reacted to them in his Divine Analogy (1732/3). However, there was no argumentative exchange because Browne’s Procedure (1728) had virtually no influence on Berkeley when he was writing Alciphron. Furthermore, the available evidence suggests that Berkeley was indifferent to the (elaborate) criticisms of Alciphron found in Browne’s Divine Analogy. Thus, while the two bishops have differing positions and Browne reacted to Berkeley there is no reaction on Berkeley’s part and hence there is no argumentative exchange between the two at all, which is why their differing opinions are best described as such and not as a controversy. (shrink)

Not only the direct physical experiences of deployment can severely harm soldiers’ mental health. Witnessing violations of their moral principles by the enemy, or by their fellow soldiers and superiors, can also have a devastating impact. It can cause soldiers’ moral disorientation, increasing feelings of shame, guilt, or hate, and the need for general answers on questions of right and wrong. Various attempts have been made to keep soldiers mentally sane. One is to provide convincing causes for their deployment, which (...) risks an “end justifies the means” way of thinking. The good cause can provide a moral justification for horrible atrocities. Another method, introduced in the USA, Canada, and Australia, aims to strengthen military personnel’s resistance by promoting and maintaining a happy, optimistic state of mind through the use of positive psychology. Alongside making soldiers “morally fit” for all kinds of situations, the focus could also be on moral recovery and forgiveness. Such a care-based military ethics approach, aimed at mutual understanding and interdependence, could help soldiers handle the emotional impact of moral conflicts. This demands that military units reflect on their organizational culture and rethink oaths and codes of conduct that focus mainly on efficiency and readiness, as well as the soldierly self-image with its seemingly still deeply rooted warrior ethos. Today, resilience and positive psychology in the military is apparently mainly geared to assuring its soldiers’ readiness. An appropriate set of virtues and understanding of virtue ethics that are less centered on self-perfection and autonomy could point to a different form of character-building and lead to a better understanding of others. (shrink)

This chapter provides an introduction to higher-order metaphysics as well as to the contributions to this volume. We discuss five topics, corresponding to the five parts of this volume, and summarize the contributions to each part. First, we motivate the usefulness of higher-order quantification in metaphysics using a number of examples, and discuss the question of how such quantifiers should be interpreted. We provide a brief introduction to the most common forms of higher-order logics used in metaphysics, and indicate a (...) number of questions which can be raised in such systems using logical vocabulary alone. Using a further example, we return to applications of higher-order logics in metaphysics. We also mention key developments in the history of higher-order logic as it pertains to metaphysics. Finally, we mention certain arguments which have been raised against the use of higher-order logic, and some ways of responding to them. (shrink)

Confirmation bias is one of the most widely discussed epistemically problematic cognitions, challenging reliable belief formation and the correction of inaccurate views. Given its problematic nature, it remains unclear why the bias evolved and is still with us today. To offer an explanation, several philosophers and scientists have argued that the bias is in fact adaptive. I critically discuss three recent proposals of this kind before developing a novel alternative, what I call the ‘reality-matching account’. According to the account, confirmation (...) bias evolved because it helps us influence people and social structures so that they come to match our beliefs about them. This can result in significant developmental and epistemic benefits for us and other people, ensuring that over time we don’t become epistemically disconnected from social reality but can navigate it more easily. While that might not be the only evolved function of confirmation bias, it is an important one that has so far been neglected in the theorizing on the bias. (shrink)

Philosophical treatments of natural kinds are embedded in two distinct projects. I call these the philosophy of science approach and the philosophy of language approach. Each is characterized by its own set of philosophical questions, concerns, and assumptions. The kinds studied in the philosophy of science approach are projectible categories that can ground inductive inferences and scientific explanation. The kinds studied in the philosophy of language approach are the referential objects of a special linguistic category—natural kind terms—thought to refer directly. (...) Philosophers may hope for a unified account addresses both sets of concerns. This paper argues that this cannot be done successfully. No single account can satisfy both the semantic objectives of the philosophy of language approach and the explanatory projects of the philosophy of science approach. After analyzing where the tensions arise, I make recommendations about assumptions and projects that are best abandoned, those that should be retained, and those that should go their separate ways. I also recommend adopting the disambiguating terminology of “scientific kinds” and “natural kinds” for the different notions of kinds developed in these different approaches. (shrink)

In recent years, it has been argued more than once that situations determine our conduct to a much greater extent than our character does. This argument rests on the findings of social psychologists such as Stanley Milgram, who have popularized the idea that we can all be brought to harm innocent others. An increasing number of philosophers and ethicists make use of such findings, and some of them have argued that this so-called situationist challenge fatally undermines virtue ethics. As virtue (...) ethics is currently the most popular underpinning for ethics education in the military, it is important to know to what extent the claim situationists make is correct. Fortunately, a closer look indicates that an interactionist perspective, with our character and the situation interplaying, is more accurate than the situationist perspective. (shrink)

Members of the field of philosophy have, just as other people, political convictions or, as psychologists call them, ideologies. How are different ideologies distributed and perceived in the field? Using the familiar distinction between the political left and right, we surveyed an international sample of 794 subjects in philosophy. We found that survey participants clearly leaned left (75%), while right-leaning individuals (14%) and moderates (11%) were underrepresented. Moreover, and strikingly, across the political spectrum, from very left-leaning individuals and moderates to (...) very right-leaning individuals, participants reported experiencing ideological hostility in the field, occasionally even from those from their own side of the political spectrum. Finally, while about half of the subjects believed that discrimination against left- or right-leaning individuals in the field is not justified, a significant minority displayed an explicit willingness to discriminate against colleagues with the opposite ideology. Our findings are both surprising and important, because a commitment to tolerance and equality is widespread in philosophy, and there is reason to think that ideological similarity, hostility, and discrimination undermine reliable belief formation in many areas of the discipline. (shrink)