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 Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

This chapter contains sections titled: Etching Awesomeness on the Top Tube in Three Pedal Strokes Free Riding with the Bhagavad Gita Coming Full Circle Notes.

Focusing on cases which involve binding into epistemic modals with definite descriptions and quantifiers, I raise some new problems for standard approaches to all of these expressions. The difficulties are resolved in a semantic framework that is dynamic in character. I close with a new class of problems about de re readings within the scope of modals.

Epistemic modal operators give rise to something very like, but also very unlike, Moore's paradox. I set out the puzzling phenomena, explain why a standard relational semantics for these operators cannot handle them, and recommend an alternative semantics. A pragmatics appropriate to the semantics is developed and interactions between the semantics, the pragmatics, and the definition of consequence are investigated. The semantics is then extended to probability operators. Some problems and prospects for probabilistic representations of content and context are explored.

The view that actually has a reading on which it is a two-dimensional indexical modal operator has some problems.

Plato, Allan Bloom wrote, is "the most erotic of philosophers," and his Symposium is one of the greatest works on the nature of love ever written. This new edition brings together the English translation of the renowned Plato scholar and translator, Seth Benardete, with two illuminating commentaries on it: Benardete's "On Plato's _Symposium_" and Allan Bloom's provocative essay, "The Ladder of Love." In the _Symposium,_ Plato recounts a drinking party following an evening meal, where the guests include the poet (...) Aristophanes, the drunken Alcibiades, and, of course, the wise Socrates. The revelers give their views on the timeless topics of love and desire, all the while addressing many of the major themes of Platonic philosophy: the relationship of philosophy and poetry, the good, and the beautiful. (shrink)

Deontologists have long been upbraided for lacking an account of justified decision- making under risk and uncertainty. One response is to develop a deontological decision theory—a set of necessary and sufficient conditions for an act’s being permissible given an agent’s imperfect information. In this article, I show that deontologists can make more use of regular decision theory than some might have thought, but that we must adapt decision theory to accommodate agent- centered options—permissions to favor or sacrifice our own interests, (...) when doing so is overall morally worse. Accommodating options requires more than just amend- ing the decision-theoretic ‘value function’. We must change the decision rule as well. (shrink)

When I tell you that it’s raining, I describe a way the world is—viz., rainy. I say something whose truth turns on how things are with the weather in the world. Likewise when I tell you that the weatherman thinks that it’s raining. Here the truth of what I say turns on how things are with the weatherman’s state of mind in the world. Likewise when I tell you that I think that it’s raining. Here the truth of what I (...) say turns on how things are with my state of mind in the world. (shrink)

This volume is a tribute to the thought of Seth Benardete by contributors who had the rare good fortune of studying with him or those who discovered the treasure of his writings. Benardete was fully immersed in the world of the ancients, starting with Homer, but their works opened up for him a way to the fundamental questions-about justice and love, nature and law, human and divine. Finding "the problem of the human good grounded in the city, and the (...) problem of being in god," he was led to the conclusion that "Political philosophy is the eccentric core of philosophy." While Benardete wrote this statement reflecting on the theological-political issue in the work of his teacher, Leo Strauss, the paradoxical notion of an "eccentric core," in giving this volume its title, is meant to capture a characteristic of his own way of thinking. The essays in this collection-on the Bible and Homer, the pre-Socratics, Plato, Aristotle, and the Roman writers-indicate the range of Benardete's studies and teaching. The centrality of Plato is evident at the same time in those pieces as well as in the reviews of Benardete's books included here, along with three of his own previously unpublished essays. Book jacket. (shrink)

By leveraging the case of Hindu sati, this paper elucidates the ways in which structure and culture condition suicidal behavior by way of social psychological and emotional dynamics. Conventionally, sati falls under Durkheim's discussion of altruistic suicides, or the self-sacrifice of underindividuated or excessively integrated peoples like widows in traditional societies. In light of the fact that Durkheim's interpretation was based on uneven data, nineteenth century Eurocentric beliefs, and a theoretical framework that can no longer resist modification and elaboration, by (...) reconsidering sati it is possible to sketch a new model that strengthens Durkheim's theory by making it more robust and generalizable. The following model is built on five principles. First, integration and regulation are not distinct causal forces, but overlapping contextual conditions. Second, to better explain the variation in suicidality across time and space, we must also pay attention to culture as it provides the underlying meanings of suicide that can increase the odds a person or class of persons become suicidal or are protected against suicidality. Third, structure still matters, but in many cases, the role power and power-differentials play must be considered. Fourth, understanding why and how people choose suicide depends on incorporating identity and status processes. Fifth, because the expression of social emotions like shame are patterned by structural and cultural conditions, to understand how suicidality is socioculturally patterned we must further explore the link between identity/status, social emotions, and structure and culture. (shrink)

Many new mothers question the nature of their motherly love after birth. This affectionate relationship towards the infant is commonly called bonding in everyday speech, clinical practice and research. Bonding may not sufficiently describe the mother’s emotional response to the infant and does not capture the ambivalence and struggle to develop maternal affection of many women. This study aims to explore the phenomenon of disturbed maternal affection through the clinical case of one mother who experienced severe and prolonged disturbances. Two (...) in-depth interviews led to a descriptive phenomenological analysis. The mother developed depressive symptoms from not feeling enough for her child, not the opposite, as is often hypothesized. We describe and discuss crucial constituents of her experience, such as ambivalence, remoteness, boredom, guilt, and the looming repetition of parenting patterns, and a solution resulting from therapy-enhanced reflection on motherhood vis-à-vis early life patterns, sociocultural expectations and existential predicaments. (shrink)

People often think that their special relationships with family, friends, comrades and compatriots, can ground moral reasons. Among these reasons, they understand some to be duties – pro tanto requirements that have genuine weight when they conflict with other considerations. In this paper I ask: what is the underlying moral structure of associative duties? I first consider and reject the orthodox Teleological Welfarist account, which first observes that special relationships are fundamental for human well-being, then claims that we cannot have (...) these relationships, if we do not recognise associative duties, before concluding that we should therefore recognise associative duties. I then introduce a nonteleological alternative, grounded in the Appropriate Response approach to ethical theory. (shrink)

I provide a novel, non-reductive, action-first skill-based account of active imagining. I call it the Skillful Action Account of Imagining (the skillful action account for short). According to this account, to actively imagine something is to form a representation of that thing, where the agent’s forming that representation and selecting its content together constitute a means to the completion of some imaginative project. Completing imaginative projects stands to the active formation of the relevant representations as an end. The account thus (...) bakes in the means-end order that some in action theory take to be definitional of intentional action. Moreover, in the spirit of this conception of intentional action, I hold that a central feature of the means-end order exhibited in active imagining is the agent’s direct non-observational knowledge both of her act of imagining and of its having this order. The agent knows that she’s actively imagining (that-)p and knows why she actively imagines this–to carry on the pretense, engage in the fiction, predict another’s behavior, reason about possibility or necessity, reason about contingent matters of fact, just imagine for its own sake, and so on. I show that the account accounts for the possibility of misimagining while holding onto the idea that we imagine what we intend to imagine. I likewise show that the account unifies imagining across types of imaginative project like those just listed in a way that tolerates conflict in the roles that imagining plays in the mental economy across those projects. Finally, I show that the account can accommodate passive imagining like involuntary and automatic imagining as well as mind wandering. -/- Acknowledgments: I'd like to thank Amy Kind, Robert Brandom, Colin Allen, Peter Langland-Hassan, Alison Springle, Daniel Munro, Nick Wiltsher, and Andrew Rubner for excellent comments on earlier drafts from which this paper greatly benefited. I'd also like to thank two anonymous reviewers for extremely helpful comments. And I'd like to thank participants of the 2022 Simulationism Conference hosted by the Centre for Philosophy of Memory and the 4th Annual Conference [Online/Virtual] for Imagination Domination (COVID) hosted by Amy Kind for excellent feedback on earlier versions of the paper. (shrink)

The temporal structure for motivating, monitoring, and making sense of agency depends on encoding, maintaining, and accessing the right contents at the right times. These functions are facilitated by memory. Moreover, in informing action, memory is itself often active. That remembering is essential to and an expression of agency and is often active suggests that it is a type of action. Despite this, Galen Strawson (Proceedings of the Aristotelian Society, 103, 227–257, 2003) and Alfred Mele (2009) deny that remembering is (...) an action. They claim that memory fails to admit of control. Remembering is automatic—once remembering starts, the process can neither be stopped nor intervened on. Moreover, the agent does not initiate remembering. An agent has control over an event or process if and only if she has the capacity and opportunity to initiate and intervene on that event or process. Actions are events over which an agent has control. Since it is automatic, we fail to have control over remembering. Thus, remembering is not an action. In this paper, I draw out an assumption of Strawson’s and Mele’s accounts: an event-type whose tokens exhibit automaticity cannot, for that reason, be an action (§2). Against this assumption, I draw parallels between skilled bodily action and memory. I show that memory exhibits two defining features of skill: it can be learned with practice and it admits of attributions of excellence (§3). These features reveal how intelligent control is exerted in the exercise of skill despite apparent automaticity—control is gained over time (§4). Since exercises of skill are by definition actions and since memory exemplifies the defining features of skill, memory is a skill and instances of remembering are actions too. (shrink)

It is generally agreed that using lethal or otherwise serious force in self-defense is justified only when three conditions are satisfied: first, there are some grounds for the defender to give priority to his own interests over those of the attacker (whether because the attacker has lost the protection of his right to life, for example, or because of the defender’s prerogative to prefer himself to others); second, the harm used is proportionate to the threat thereby averted; third, the harm (...) is necessary to avert that threat. The first and second conditions have been exhaustively discussed, but the third has been oddly neglected. Meanwhile a prominent school of thought has arisen, in the ethics of war, which seeks to ground the justification of killing in war in principles of individual self-defense. They too have failed to offer any substantive analysis of necessity, while at the same time appealing to it when it suits them to do so. In this paper, I attempt a detailed analysis of the necessity constraint on defensive force, and explore the implications of that analysis for the attempt to transpose principles of individual self-defense into the context of warfare. (shrink)

This paper defends a counterexample to Modus Tollens, and uses it to draw some conclusions about the logic and semantics of indicative conditionals and probability operators in natural language. Along the way we investigate some of the interactions of these expressions with 'knows', and we call into question the thesis that all knowledge ascriptions have truth-conditions.

Purpose This paper aims to formalize long-term trajectories of human civilization as a scientific and ethical field of study. The long-term trajectory of human civilization can be defined as the path that human civilization takes during the entire future time period in which human civilization could continue to exist. -/- Design/methodology/approach This paper focuses on four types of trajectories: status quo trajectories, in which human civilization persists in a state broadly similar to its current state into the distant future; catastrophe (...) trajectories, in which one or more events cause significant harm to human civilization; technological transformation trajectories, in which radical technological breakthroughs put human civilization on a fundamentally different course; and astronomical trajectories, in which human civilization expands beyond its home planet and into the accessible portions of the cosmos. -/- Findings Status quo trajectories appear unlikely to persist into the distant future, especially in light of long-term astronomical processes. Several catastrophe, technological transformation and astronomical trajectories appear possible. -/- Originality/value Some current actions may be able to affect the long-term trajectory. Whether these actions should be pursued depends on a mix of empirical and ethical factors. For some ethical frameworks, these actions may be especially important to pursue. (shrink)

Philosophers, psychologists, economists and other social scientists continue to debate the nature of human well-being. We argue that this debate centers around five main conceptualizations of well-being: hedonic well-being, life satisfaction, desire fulfillment, eudaimonia, and non-eudaimonic objective-list well-being. Each type of well-being is conceptually different, but are they empirically distinguishable? To address this question, we first developed and validated a measure of desire fulfillment, as no measure existed, and then examined associations between this new measure and several other well-being measures. (...) In addition, we explored associations among all five types of well-being. We found high correlations among all measures of well-being, but generally correlations did not approach unity, even when correcting for unreliability. Furthermore, correlations between well-being and related constructs (e.g., demographics, personality) depended on the type of well-being measured. We conclude that empirical findings based on one type of well-being measure may not generalize to all types of well-being. (shrink)

The standard behavioral index for human consciousness is the ability to report events with accuracy. While this method is routinely used for scientific and medical applications in humans, it is not easy to generalize to other species. Brain evidence may lend itself more easily to comparative testing. Human consciousness involves widespread, relatively fast low-amplitude interactions in the thalamocortical core of the brain, driven by current tasks and conditions. These features have also been found in other mammals, which suggests that consciousness (...) is a major biological adaptation in mammals. We suggest more than a dozen additional properties of human consciousness that may be used to test comparative predictions. Such homologies are necessarily more remote in non-mammals, which do not share the thalamocortical complex. However, as we learn more we may be able to make “deeper” predictions that apply to some birds, reptiles, large-brained invertebrates, and perhaps other species. (shrink)

The complexity, subtlety, interlinking, and scale of many problems faced individually and collectively in today's rapidly changing world requires an epistemology--a way of thinking about our knowing--capable of facilitating new kinds of responses that avoid recapitulation of old ways of thinking and living. Epistemology, which implicitly provides the basis for engagement with the world via the fundamental act of distinction, must therefore be included as a central facet of any practical attempts at self/world transformation. We need to change how we (...) think, not just what we think. The new epistemology needs to be of a higher order than the source of the problems we face. -/- This theoretical, transdisciplinary dissertation argues that such a new epistemology needs to be recursive and process-oriented. This means that the thoughts about thinking that it produces must explicitly follow the patterns of thinking by which those thoughts are generated. The new epistemology is therefore also phenomenological, requiring the development of a reflexivity in thinking that recursively links across two levels of order--between content and process. The result is an epistemology that is of (and for) the whole human being. It is an enacted (will-imbued) and aesthetic (feeling-permeated) epistemology (thinking-penetrated) that is sensitive to and integrative of material, soul, and spiritual aspects of ourselves and our world. I call this kind of epistemology aesthetic, because its primary characteristic is found in the phenomenological, mutually fructifying and transformative marriage between the capacity for thinking and the capacity for feeling. -/- Its foundations are brought forward through the confluence of multiple domains: cybernetic epistemology, the esoteric epistemology of anthroposophy (the spiritual science of Rudolf Steiner), and the philosophy of the implicit as developed by Eugene Gendlin. -/- The practice of aesthetic epistemology opens new phenomenal domains of experience, shedding light on relations between ontology and epistemology, mind and body, logic and thinking, as well as on the formation (and transformation) of identity, the immanence of thinking in world-processes, the existence of different types of logic, and the nature of beings, of objects, and most importantly of thinking itself and its relationship to spirit. (shrink)

The ability to understand both the self and others as purposeful agents — with thoughts, beliefs, and desires — seems to be central to the emergence of cultural processes both phylo- and ontogenetically. This ability has been termed second-order intentionality or “theory of mind” and has been conceptualized as a species-specific “trait” which is genetically predetermined, naturally selected and the resident of a dedicated module within the mind. Alternatively, we see it emerging out of a more general process — symbolization. (...) The paper discusses the emergence of the symbolic function from previously existing forms of communication by analyzing the structures and functions of different kinds of signs used in human and non-human vocal communication. We reinterpret evidence from the study of non-human primate vocalizations and suggest that these vocalizations embody a semiotic type that, like all signs, is more highly developed than a signal, but is not catalogued within the basic Peircean triad of sign types . This form, the double indexical, is intermediary between indexes and symbols. We speculate on what structural and functional reorganization is required to establish a developmental continuity from signals through the various types of signs to the well-known structure of the symbol — and possibly beyond. (shrink)

Artificial intelligence experts are currently divided into “presentist” and “futurist” factions that call for attention to near-term and long-term AI, respectively. This paper argues that the presentist–futurist dispute is not the best focus of attention. Instead, the paper proposes a reconciliation between the two factions based on a mutual interest in AI. The paper further proposes realignment to two new factions: an “intellectualist” faction that seeks to develop AI for intellectual reasons and a “societalist faction” that seeks to develop AI (...) for the benefit of society. The paper argues in favor of societalism and offers three means of concurrently addressing societal impacts from near-term and long-term AI: advancing societalist social norms, thereby increasing the portion of AI researchers who seek to benefit society; technical research on how to make any AI more beneficial to society; and policy to improve the societal benefits of all AI. In practice, it will often be advantageous to emphasize near-term AI due to the greater interest in near-term AI among AI and policy communities alike. However, presentist and futurist societalists alike can benefit from each others’ advocacy for attention to the societal impacts of AI. The reconciliation between the presentist and futurist factions can improve both near-term and long-term societal impacts of AI. (shrink)

Cancer biology features the ascription of normal functions to parts of cancers. At least some ascriptions of function in cancer biology track local normality of parts within the global abnormality of the aberration to which those parts belong. That is, cancer biologists identify as functions activities that, in some sense, parts of cancers are supposed to perform, despite cancers themselves having no purpose. The present paper provides a theory to accommodate these normal function ascriptions—I call it the Modeling Account of (...) Normal Function (MA). MA comprises two claims. First, normal functions are activities whose performance by the function-bearing part contributes to the self-maintenance of the whole system and, thereby, results in the continued presence of that part. Second, MA holds that models of system-level activities that are (partly) constitutive of self-maintenance are improved by including a representation of the relevant function-bearing part and by making reference to the activity/activities that part performs which contribute(s) to those system-level activities. I contrast MA with two other accounts that seek to explicate the ascription of normal functions in biology, namely, the organizational account and the selected effects account. Both struggle to extend to cancer biology. However, I offer ecumenical readings which allow them to recover some ascriptions of normal function to parts of cancers. So, though I contend that MA excels in this respect, the purpose of this paper is served if it provides materials for bridging the gap between cancer biology, philosophy of cancer, and the literature on function. (shrink)

this paper advances a novel account of part of what justifies killing in war, grounded in the duties we owe to our loved ones to protect them from the severe harms with which war threatens them. It discusses the foundations of associative duties, then identifies the sorts of relationships, and the specific duties that they ground, which can be relevant to the ethics of war. It explains how those associa- tive duties can justify killing in theory—in particular how they can (...) justify overrid- ing the rights to life of some of those who must be killed to win a war. It then shows how these duties can be operationalised in practice: first, showing how soldiers who fight on behalf of their community can act on reasons that apply to the members of that community; second, showing that the argument from associative duties does not prove too much—in particular, that it does not license the intentional killing of noncombatants in war. (shrink)

A recent report by Persaud et al. [Persaud, N., McLeod, P. & Cowey, A. . Post-decision wagering objectively measures awareness. Nature Neuroscience 10, 257–261] addresses a fundamental issue in consciousness science: the experimental measurement of conscious content. The authors propose a novel technique, ‘post-decision wagering’, in which subjects place bets on the correctness of decisions or discriminations. In this note, I critique the authors’ claim that their method “measures awareness directly”.

This is a study in the meaning of natural language probability operators, sentential operators such as probably and likely. We ask what sort of formal structure is required to model the logic and semantics of these operators. Along the way we investigate their deep connections to indicative conditionals and epistemic modals, probe their scalar structure, observe their sensitivity to contex- tually salient contrasts, and explore some of their scopal idiosyncrasies.

We investigate a basic probabilistic dynamic semantics for a fragment containing conditionals, probability operators, modals, and attitude verbs, with the aim of shedding light on the prospects for adding probabilistic structure to models of the conversational common ground.

Killing in War presents the Moral Equality of Combatants with serious, and in my view insurmountable problems. Absent some novel defense, this thesis is now very difficult to sustain. But this success is counterbalanced by the strikingly revisionist implications of McMahan’s account of the underlying morality of killing in war, which forces us into one of two unattractive positions, contingent pacifism, or near-total war. In this article, I have argued that his efforts to mitigate these controversial implications fail. The reader (...) is left stranded: to reach plausible conclusions, Walzer deployed an implausible conception of our rights to life; McMahan’s more rigorous account of those rights generates untenable conclusions. Absent new developments, it seems that the prospects for grounding the ethics of war in individual rights are poor: any theory of our rights to life that is sufficiently indiscriminate to work in the chaos of war is not discriminating enough to be a plausible theory of our rights to life. Perhaps by rejecting the ideal of the rights-respecting war altogether we might develop an alternative theory of justified warfare, which marries theoretical soundness with conclusions that we can more confidently support. (shrink)

In this paper, we suggest that affect meets the traditional definition of “cognition” such that the affect–cognition distinction is phenomenological, rather than ontological. We review how the affect–cognition distinction is not respected in the human brain, and discuss the neural mechanisms by which affect influences sensory processing. As a result of this sensory modulation, affect performs several basic “cognitive” functions. Affect appears to be necessary for normal conscious experience, language fluency, and memory. Finally, we suggest that understanding the differences between (...) affect and cognition will require systematic study of how the phenomenological distinction characterising the two comes about, and why such a distinction is functional. (shrink)