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 dynamical hypothesis states that cognitive systems are dynamical systems. While dynamical systems play an important role in many cognitive phenomena, the dynamical hypothesis as stated applies to every system and so fails both to specify what makes cognitive systems distinct and to distinguish between proposals regarding the nature of cognitive systems. To avoid this problem, I distinguish several different types of dynamical systems, outlining four dimensions along which dynamical systems can vary: total-state versus partial-state, internal versus external, macroscopic versus (...) microscopic, and systemic versus componential, and illustrate these with examples. I conclude with two illustrations of partial-state, internal, microscopic, componential dynamicism. (shrink)

In this essay, David Hildebrand connects Democracy and Education to Dewey's wider corpus. Hildebrand argues that Democracy and Education's central objective is to offer a practical and philosophical answer to the question, What is needed to live a meaningful life, and how can education contribute? He argues, further, that this work is still plausible as “summing up” Dewey's overall philosophy due to its focus upon “experience” and “situation,” crucial concepts connecting Dewey's philosophical ideas to one another, to education, and (...) to democracy. He opens the essay with a brief synoptic analysis of Democracy and Education's major philosophical ideas, moves on to sections devoted to experience and situation, and then offers a brief conclusion. Some mention is made throughout about the surprisingly significant role art and aesthetics can play in education. (shrink)

Tomasello offers an evolutionary, palaeoanthropological account of the human origin of objects and objectivity. Husserl gives a phenomenological account of the constitution of objects by intersubjectivity. Comparing the two, I claim that Tomasello’s “naturalized” approach closely parallels Husserl’s transcendental approach.

Overview of challenges facing philosophical analyses of experience in the face of life with constant connection, social media, and data mining.

Language defines human existence. Yet defining language is a fraught project. I use the term "language" to refer to a specific mode of information transfer. First, it is a communicative mode. By communication I mean the information transfer serves a function, that is, an activity that occurs because it has increased the evolutionary fitness of ancestors. Secondly, while all communication is governed by norms, human communication, as opposed to biological communication, is governed by norms that have evolved within the learned (...) traditions of individual cultures. The meaning of an assertion in a culture’s language is the set of commitments to which that culture holds its speakers when they utter that assertion. Syntax has appeared in recent evolution to facilitate and enrich the communicative function, but it is a secondary aspect of language. The defining characteristic of human communication, of "language," -- is its capacity to constitute meaning. (shrink)

Modern selfhood presents itself as autonomous, overcoming emotion by following cognitive, moral and linguistic norms on the basis of clear, rational principles. It is difficult to imagine how such normative creatures could have evolved from their purely biological, non-normative, primate ancestors. I offer a just-so story to make it easier to imagine this transition. Early hominins learned to cooperate by developing group identities based on tribal norms. Group identity constituted proto-selves as normative creatures. Such group identity was not based on (...) autonomous selfhood – such an explanation would be anachronistic -- but on emotional patterning. By imitation, music, dance, ritual and other emotional practices, proto-selves learned how to bind themselves to the norms of their culture. Such conformity was a transitional evolutionary stage between primates and selves. Emotion and rationality are not incompatible: even contemporary selfhood remains rooted in emotional identity. (shrink)

The temporal unity of the self cannot be accounted for by the continuity of causal, factual, or contiguous relations between independently definable mental events, as proposed by Locke and Parfit. The identity of the self over time is normative: it depends on the institutional context of social rules external to the self that determine the relationship between past commitments and current responsibilities. (2005).

Four philosophers, Husserl, Wittgenstein, Dennett, and Hegel, who hold for the most part radically different philosophies, all agree on rejecting the notion of atomic entities, of “things-in-themselves,” and insist that objects only make sense – can only be what they are -- in a context.

Against the concept that objects are defined by their self-contained essence – “thing-in-themselves” – Husserl and Foucault claim they are defined by intersubjectivity or social institutions. I argue that biological and even physical (complex) systems can constitute the unity and meaning of objects.

A self is a temporal unity in which responsibility for past commitments modifies how the present world is experienced and evaluated. This structure is analogous (a) to biological evolutionary changes in perception and (b) to how changes in a computer program determine how it will respond in the future. Responsibility is not an add-on to a self, but the mode of its integration over time. (Presented at Royal Institute of Philosophy Annual Conference, Narrative and Understanding Persons, University of Hertfordshire, UK, (...) 2005). (shrink)

Why should anyone be bound by cognitive norms, such as the norms of reason or mathematics? To become a mathematician is to learn to obey the norms of the mathematical community. A self becomes intentional by binding itself to communal norms. Only then can it have the freedom to think or make assertions about the community’s objects -- triangles or imaginary numbers, for example. Norms do not bind selves from the outside: being bound by norms is what constitutes a self.

Biological organisms, languages and selves are normative entities, so must be understood in terms of norms. Mechanistic understanding is based on causal necessity, but normative understanding relies on a grasp of the contingencies of evolution, history and personal experience.

The self is not a metaphysical object but a mode of temporal organization unified by responsibility. Learning to be responsible constitutes the self as a self-identical entity over time. Responsibility depends on the current self interpreting previous events, attributing them to itself and thereby committing itself for the future. (2004) .

What makes us persons? Is it our bodies, our minds, or our consciousness? For centuries, philosophers have sought to answer these questions. While some believe humans are physical or biological, others claim we have an immaterial soul. This book proposes a new alternative. Selves were formed in evolution through connections and commitments to others when early hominins lived in tribal groups and developed languages. As humans learned to fulfill these commitments, they not only cultivated relationships but also created their personal (...) identities. Their habits of responsibility established their characters and therefore their reputations within their communities. This naturalistic approach proposes that a self is defined by the history of its commitments to cultural and personal norms. While brain processes are required, the self is not some internal, private mind but primarily a role within its community. As technology advances, selfhood could in the future be enabled by electronic, quantum, or other non-biological means. So if a self is formed through norms, could artificial intelligence evolve to have self-identity? (shrink)

Methodological and philosophical foundations in the anthropology of Ruth Benedict and Margaret Mead.

Exactly how do the sign/symbol/token systems of endo- and exo-biosemiosis differ from those of cognitive semiosis? Do the biological messages that integrate metabolism have conceptual meaning? Semantic information has two subsets: Descriptive and Prescriptive. Prescriptive information instructs or directly produces nontrivial function. In cognitive semiosis, prescriptive information requires anticipation and “choice with intent” at bona fide decision nodes. Prescriptive information either tells us what choices to make, or it is a recordation of wise choices already made. Symbol systems allow recordation (...) of deliberate choices and the transmission of linear digital prescriptive information. Formal symbol selection can be instantiated into physicality using physical symbol vehicles (tokens). Material symbol systems (MSS) formally assign representational meaning to physical objects. Even verbal semiosis instantiates meaning into physical sound waves using an MSS. Formal function can also be incorporated into physicality through the use of dynamically-inert (dynamically-incoherent or -decoupled) configurable switch-settings in conceptual circuits. This paper examines the degree to which biosemiosis conforms to the essential formal criteria of prescriptive semiosis and cybernetic management. (shrink)

The central objective of Dewey’s Democracy and Education is to explain ‘what is needed to live a meaningful life and how can education contribute?’ While most acquainted with Dewey’s educational philosophy know that ‘experience’ plays a central role, the role of ‘situations’ may be less familiar or understood. This essay explains why ‘situation’ is inseparable from ‘experience’ and deeply important to Democracy and Education’s educational methods and rationales. First, a prefatory section explores how experience is invoked and involved in pedagogical (...) practice, especially experience insofar as it is (a) experimental, (b) direct, and (c) social-moral in character. The second and main section on situations follows. After a brief introduction to Dewey’s special philosophical use of ‘situation’, I examine how situations are implicated in (a) student interest and motivation; (b) ‘aims’ and ‘criteria’ in problem-solving; and (c) moral education (habits, values, and judgements). What should become abundantly clear from these examinations is that there could be no such thing as meaningful education, as Dewey understood it, without educators’ conscious, intentional, and imaginative deployment of experience and situations. (shrink)

Abstract: For most people, mobile phones and various forms of personal information technology (PIT) have become standard equipment for everyday life. Recent theorists such as Sherry Turkle raise psychological and philosophical questions about the impact of such technologies and practices, but deeper further philosophical work is needed. This paper takes a pragmatic approach to examining the effects of PIT practices upon experience. After reviewing several main issues with technology raised by Communication theorists, the paper looks more deeply at Turkle’s analysis (...) of technology's impacts upon solitude and conversation. Because Turkle only raises but doesn’t pursue the philosophical dimensions of these issues, the work on experience of John Dewey, William James, and John J. McDermott is utilized to provide concepts and methods by which PIT’s effects might be judged. Finally, pragmatist aesthetics is introduced and consulted as a source of constructive ideals which might guide future amelioration of PIT’s more significant drawbacks. (shrink)

Failure to recognize the "realistic" motivations for Putnam's commitment to internal realism has led to a widely shared misunderstanding of Putnam's arguments against metaphysical realism. Realist critics of these arguments frequently offer rebuttals that fail to confront his arguments. Simply put, Putnam's arguments --the brains in a vat argument as well as the model-theoretic argument -- are "reductios" that are intended to show that "metaphysical realism itself is not sufficiently realistic". If that claim can be substantiated then Putnam can go (...) on to argue that his own view is, by comparison, more realistic than metaphysical realism. (shrink)

The Human Eros is an outstanding accomplishment, a work of genuine wisdom. It combines meticulous scholarship with an enviable mastery of cultural and philosophical history to address pressing concerns of human beings, nature, and philosophy itself. While comprised of essays spanning over two decades, the book presents a powerfully coherent philosophical vision which Alexander names, alternately, “eco-ontology,” “humanistic naturalism,” and “ecological humanism.” Whatever the name, the approach is humane and intellectually compelling, offering insight and direction to pragmatism, aesthetics, existentialism, environmental (...) philosophy, and anyone in search of wisdom. It is an immensely readable book, too. (shrink)

Recent writings by Hilary Putnam indicate the seriousness with which he has moved toward pragmatism. Putnam has not only characterized his own position as similar to pragmatism, he has written a number of essays presenting the views of the classical pragmatists, especially James, Dewey, and Peirce. “Putnam, Pragmatism, and Dewey” examines fundamental problems with Putnam’s recent efforts, especially as they pertain to Dewey’s epistemology.

Thought is not based on an image that is isomorphic to the object. Descartes, Husserl, Frege, Wittgenstein and Brandom progressively overcome this Aristotelian misconception of the intentionality of thinking.

Comment on Robin Tapley's paper on whether or not the sexual aspect of sexual harms adds anything to the harm done. I argue it does not based on the grounds Tapley provides.

For Charles Peirce, the project of inquiry is a social one. Though inquiry, the passage from genuine doubt to settled belief, can be described on the individual level, its significance as a human activity is manifested in collective action. For any individual, Truth transcends experience and inquiry. But it does not transcend experience and inquiry altogether: is a fixed limit, an ideal, towards which a properly functioning community converges. What, in principle, makes the cohesion of such a community possible? Why (...) did Peirce believe that convergence towards an ultimate conclusion was the necessary end of unlimited scientific inquiry? This essay examines Peirce's notion of community to answer these questions and suggests that the presence of genuine doubt not only makes convergence possible, but also constitutes the starting point for almost all inquiry. The exception is philosophical inquiry. (shrink)

The undergraduate philosophy major is often seen as an irrelevant degree. While this may be attributed to a number of causes, it is also occasion for academic philosophers to reevaluate pedagogical methods at the undergraduate level. The author evaluates typical pedagogical methods and argues that overemphasizing epistemological goals of philosophical investigation (e.g. truth and justification) instrumentalizes the process of inquiry and stifles students’ philosophical imagination, resulting in the impression of philosophy’s irrelevance. An alternative model is offered on the basis of (...) John Dewey’s pattern of inquiry. It is argued that a pedagogy that attends to Dewey’s five phases of inquiry promotes greater attention to the process of inquiry itself, which emphasizes knowledge as social, open to revision, and pertinent to students’ needs and interests. The author concludes by considering the philosophical implications of implementing such a pedagogy. (shrink)

Kenneth Burke's recent death has spurred academics in a variety of disciplines to reassess the import of his prolific output. As a specialist in American philosophy, I have begun to make inroads on a question I have heard thus far only in English and Communication departments: Should Kenneth Burke be considered a pragmatist. This paper seeks to persuade specialists in Pragmatism and American Philosophy that Burke's work has enough in common with the epistemological and metaphysical doctrines of Classical Pragmatism to (...) merit renewed consideration by philosophers. (shrink)

In "The Incoherence of Whitehead’s Theory of Perception" (PS 9:94-104), Robert H. Kimball tries to show how Alfred North Whitehead’s account of perception is a failed attempt to reconcile two traditional theories of perception: phenomenological (or sense-data) theory and causal (or physiological) theory. Whitehead fails, Kimball argues, in two main ways. First because his notion of symbolic reference requires the simultaneous enjoyment of perceptions in the mode of presentational immediacy and causal efficacy. Kimball believes this experience is, in principle, impossible (...) and supports this claim by attacking Whitehead’s conception of causal efficacy and the experiential evidence used to support it. Whitehead’s second failure results from the first: Whitehead’s erroneous belief in the simultaneous enjoyment of the two modes of perception leads him to construct a theory of perception which is composed of two contradictory parts: realism and mediatism. In this essay, I will examine Kimball’s attack on causal efficacy and symbolic reference and show why Whitehead’s theory of perception is not susceptible to Kimball’s charge of incoherence. (shrink)

Explanation is a human activity. Teleological, causal, and evolutionary explanations are all valid forms of responding to particular puzzlements. Reductionism incorrectly assumes there is one absolute explanation. While causal explanation appeals primarily to necessity, evolutionary explanation is based largely on contingency.

The sameness and difference of entities depend on context or horizon and these horizons may be either synchronous or diachronic. Money and qualia are examples of identity within synchronic contexts. Music, biological functions, and cultural roles are defined by their diachronic horizons. The diachronic cultural and narrative contexts of selves are what makes them distinctively different.

Kosgaard claims that selves/agents self-constitute during actions by relying on principles such as Kant’s Categorical Imperative. This intellectualist approach neglects the body. Merleau-Ponty considers the “lived body” and its perceptual world as the source of the unity of action, an approach that I extrapolate to all biological organisms.

Jacobs, in Choosing Character, seems to assume that there are selves already capable of voluntary choice who then choose their character by developing habits. I argue that selves, choice, responsibility and character form a conceptual and practical hermeneutic circle, a whole without which selfhood makes no sense. There can be no selfhood prior to responsible character.

The received Cognitive Science paradigm holds that the brain manipulates mental representations of reality. This position is problematic. My alternative to representationalism is that each organism lives in its own "world" made up of objects defined by reference to the organism’s perceptual systems. These objects act as supervenient causes on organisms without the mediation of mental representations. (1992).

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In recent years, a genre of introduction to philosophical figures and movements for non-specialists has gained in popularity; these introductions aim to be neither too cursory nor too laden with academic detail. Oxford’s “Very Short Introductions” and the “Wadsworth Notes” series are examples of the cursory type, while academic monographs are examples of the detailed type. Steven Fesmire’s Dewey is a welcome and unique contribution to the new introductory genre, joining similar efforts such as Raymond Boisvert’s John Dewey Rethinking Our (...) Time and my own Dewey A Beginner’s Guide. Dewey possesses a number of helpful features. (shrink)

Gilbert Harman’s famous principle of Clutter Avoidance commands that “one should not clutter one’s mind with trivialities". Many epistemologists have been inclined to accept Harman’s principle, or something like it. This is significant because the principle appears to have robust implications for our overall picture of epistemic normativity. Jane Friedman (2018) has recently argued that one potential implication is that there are no genuine purely evidential norms on belief revision. In this paper, we present some new objections to a suitably (...) formulated version of the clutter principle qua norm on belief revision. Moreover, we argue that the clutter principle is best understood as a norm on non-doxastic stages of inquiry. In our view, it is a norm of asking and considering questions rather than a norm of settling on an answer to a question by forming a belief. (shrink)

Congdon (2017), Giladi (2018), and McConkey (2004) challenge feminist epistemologists and recognition theorists to come together to analyze epistemic injustice. I take up this challenge by highlighting the failure of recognition in cases of testimonial and hermeneutical injustice experienced by victims of sexual harassment and sexual assault. I offer the #MeToo movement as a case study to demonstrate how the process of mutual recognition makes visible and helps overcome the epistemic injustice suffered by victims of sexual harassment and sexual assault. (...) I argue that in declaring “me too,” the epistemic subject emerges in the context of a polyphonic symphony of victims claiming their status as agents who are able to make sense of their own social experiences and able to convey their knowledge to others. (shrink)

In this open peer commentary, we categorize the possible “neuroscience in national security” definitions of misuse of science and identify which, if any, are uniquely presented by advances in neuroscience. To define misuse, we first define what we would consider appropriate use: the application of reasonably safe and effective technology, based on valid and reliable scientific research, to serve a legitimate end. This definition presents distinct opportunities for assessing misuse: misuse is the application of invalid or unreliable science, or is (...) the use of reliable scientific methods to serve illegitimate ends. Ultimately, we conclude that while national security is often a politicized issue, assessing the state of scientific progress should not be. (shrink)

Social epistemologists use the term hermeneutical injustice to refer to a form of epistemic injustice in which a structural prejudice in the economy of collective interpretive resources results in a person’s inability to understand his/her/their own social experience. This essay argues that the phenomenon of unacknowledged date rapes, that is, when a person experiences sexual assault yet does not conceptualize him/her/their self as a rape victim, should be regarded as a form of hermeneutical injustice. The fact that the concept of (...) date rape has been widely used for at least three decades indicates the intractability of hermeneutical injustices of this sort and the challenges with its overcoming. (shrink)

In this paper, I consider the topic of racism in America, the Christian Church, and in Pentecostalism. Historically there has been a tepid response to racism by the Christian. Although many individuals who are Christian’s have voiced and demonstrated opposition to the practice of racism the Christian as a whole has not actively supported the rights of black people to be equal citizens in the United States. I examine the actions and words of whites from an historical and religious perspective (...) with a focus on Pentecostalism. My discussion shows that while Pentecostalism is not a movement that promotes racism some individuals from the Clergy to the pew who profess to be Pentecostals and recipients of the ‘second blessing’ embrace and practice racism. (shrink)

Whether in the form of testimonial injustice, hermeneutical injustice, or contributory injustice, epistemic injustice is characterised an injustice rather than simply an epistemic harm because it is often motivated by an identity prejudice and exacerbates existing social disadvantages and inequalities. I argue that epistemic injustice can also be utlised against some members of privileged social identity groups in order to preserve the dominant status of the group as a whole. As a case-study, I analyze how the harms to male victims (...) of sexual violence is exacerbated by the failure of the law to recognise the rape of men as a crime and the failure of other people to recognise the testimony of male rape victims as credible. Analyzing shifts in the legal concept of rape and examples from Project Unbreakable, I uncover how these failures of recognition undermine the victims’ status as legal, moral, and epistemic subjects and inflict epistemic injustice against them. (shrink)

Friendship between professors and students have the potential for hurting those involved and can be hurtful to the larger society in which they occur. This paper examines what sort of boundary lines can be drawn for appropriate faculty-student relationships by considering three arguments against faculty-student friendships. After rejecting these arguments on the grounds that they rely upon a flawed conceptualization of friendship, the paper, drawing on William Rawlins’s theory of friendship, argues that faculty-student relationships are neither desirable nor undesirable per (...) se. However, if such relationships do arise, it is possible that they can be conducted in an ethically responsible and professionally appropriate way. (shrink)