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.

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.

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”.

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)

ObjectiveTo examine measurement agreement between a vocabulary test that is administered in the standardized manner and a version that is administered with a brain-computer interface.MethodThe sample was comprised of 21 participants, ages 9–27, mean age 16.7 years, 61.9% male, including 10 with congenital spastic cerebral palsy, and 11 comparison peers. Participants completed both standard and BCI-facilitated alternate versions of the Peabody Picture Vocabulary Test - 4. The BCI-facilitated PPVT-4 uses items identical to the unmodified PPVT-4, but each quadrant forced-choice item (...) is presented on a computer screen for use with the BCI.ResultsMeasurement agreement between instruments was excellent, including an intra-class correlation coefficient of 0.98, and Bland-Altman plots and tests indicating adequate limits of agreement and no systematic test version bias. The mean standard score difference between test versions was 2.0 points.ConclusionThese results demonstrate that BCI-facilitated quadrant forced-choice vocabulary testing has the potential to measure aspects of language without requiring any overt physical or communicative response. Thus, it may be possible to identify the language capabilities and needs of many individuals who have not had access to standardized clinical and research instruments. (shrink)

Spoken word recognition involves a perceptual tradeoff between the reliance on the incoming acoustic signal and knowledge about likely sound categories and their co-occurrences as words. This study examined how adult second language (L2) learners navigate between acoustic-based and knowledge-based spoken word recognition when listening to highly variable, multi-talker truncated speech, and whether this perceptual tradeoff changes as L2 listeners gradually become more proficient in their L2 after multiple months of structured classroom learning. First language (L1) Mandarin Chinese listeners and (...) L1 English-L2 Mandarin adult listeners took part in a gating experiment. The L2 listeners were tested twice—once at the start of their intermediate/advanced L2 language class and again two months later. L1 listeners were only tested once. Participants were asked to identify syllable-tone words that varied in syllable token frequency (high/low according to a spoken word corpus) and syllable-conditioned tonal probability (most probable/least probable in speech given the syllable). The stimuli were recorded by 16 different talkers and presented at eight gates ranging from onset-only (gate 1) through onset+40 ms increments (gates 2 through 7) to the full word (gate 8). Mixed-effects regression modeling was used to compare performance to our previous study which used single-talker stimuli (Wiener, Lee, & Tao, 2019). The results indicated that multi-talker speech caused both L1 and L2 listeners to rely greater on knowledge-based processing of tone. L1 listeners were able to draw on distributional knowledge of syllable-tone probabilities in early gates and switch to predominantly acoustic-based processing when more of the signal was available. In contrast, L2 listeners, with their limited experience with talker range normalization, were less able to effectively transition from probability-based to acoustic-based processing. Moreover, for the L2 listeners, the reliance on such distributional information for spoken word recognition appeared to be conditioned by the nature of the acoustic signal. Single-talker speech did not result in the same pattern of probability-based tone processing, suggesting that knowledge-based processing of L2 speech may only occur under certain acoustic conditions, such as multi-talker speech. (shrink)

Cancer biologists ascribe normal functions to parts of cancer. Normal functions are activities that parts of systems are in some minimal sense supposed to perform. Cancer biologists’ finding normality within the abnormality of cancer pose difficulties for two main approaches to normal function. One approach claims that normal functions are activities that parts are selected for. However, some parts of cancers that have normal functions aren’t selected to perform them. The other approach claims that normal functions are part-activities typical for (...) the system and that contribute to survival/reproduction. However, cancers are too heterogeneous to establish what’s typical across a type. (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)

Institutional differentiation has been one of the central concerns of sociology since the days of Auguste Comte. However, the overarching tendency among institutionalists such as Durkheim or Spencer has been to treat the process of differentiation from a macro, "outside in" perspective. Missing from this analysis is how institutional differentiation occurs from the "inside out, "or through the efforts and struggles of individual and corporate actors. Despite the recent efforts of the "new institutionalism" to fill in this gap, a closer (...) look at the literature will uncover the fact that (1) it has tended to conflate macro-level institutions and meso-level organizations and (2) this has led to a taken for granted approach to institutional dynamics. This article seeks to develop a general theory of institutional autonomy; autonomy is a function of the degree to which specialized corporate units are structurally and symbolically independent of other corporate units. It is argued herein that the process by which these "institutional entrepreneurs" become independent can explain how institutions become differentiated from the "inside out." Moreover, this article offers five dimensions that can be operationalized, measuring the degree to which institutions are autonomous. (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.

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)

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)

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.

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)

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)

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.

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)

Understanding human behaviour, thoughts, and emotional expressions can be challenging in the global context. Due to cultural differences, the study of psychology cannot be de-contextualised. This calls for unearthing of the explanatory systems that exist in Africa to understand and account for behaviour, emotions, and cognition of Africans. This call is addressed through the emergence of African Psychology (AP) or Indigenous Psychology in Africa (IPA) as a legitimate science of human experience. This Element discusses the motivations for AP, centrality of (...) culture, demarcations of AP, and the different strands within AP. It highlights issues related to African philosophy, African cultural anthropology, African philosophy of science, and suitable methodological approaches for AP research. It also discusses some selected theoretical contributions and applications of AP. The Element concludes that AP researchers and practitioners need to pursue interdisciplinarity and avoid meaningless rejection of good ideas from other cultural settings. (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)

This paper discusses means for promoting artificial intelligence that is designed to be safe and beneficial for society. The promotion of beneficial AI is a social challenge because it seeks to motivate AI developers to choose beneficial AI designs. Currently, the AI field is focused mainly on building AIs that are more capable, with little regard to social impacts. Two types of measures are available for encouraging the AI field to shift more toward building beneficial AI. Extrinsic measures impose constraints (...) or incentives on AI researchers to induce them to pursue beneficial AI even if they do not want to. Intrinsic measures encourage AI researchers to want to pursue beneficial AI. Prior research focuses on extrinsic measures, but intrinsic measures are at least as important. Indeed, intrinsic factors can determine the success of extrinsic measures. Efforts to promote beneficial AI must consider intrinsic factors by studying the social psychology of AI research communities. (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)

Materialist metaphysicians want to side with physics, but not to take sides within physics.If we took literally the claim of a materialist that his position is simply belief in the claim that all is matter, as currently conceived, we would be faced with an insoluble mystery. For how would such a materialist know how to retrench when his favorite scientific hypotheses fail? How did the 18th century materialist know that gravity, or forces in general, were material? How did they know (...) in the 19th century that the electromagnetic field was material, and persisted in this conviction after the aether had been sent packing?The doctrine of physicalism casts a long shadow in contemporary philosophy, configuring all kinds of philosophical issues and projects. Unsurprisingly, its proponents argue that physicalism has all the obvious features necessary for a scientific hypothesis to be in what we will call ‘good standing,’ i.e. being worthy of serious scientific investigation. In fact, many claim much more, arguing that physicalism is a well-confirmed hypothesis and possibly amongst the best of our theories. But, as our second opening passage makes clear, a persistent worry has been that physicalism, or ‘materialism’ as van Fraassen terms it, is an edifice built on sand. For many philosophers question whether the ‘physical’ can be specified at all, or at least in a manner that will produce a physicalism that would be in good standing. (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)

In the pediatric heart-failure population, severity of illness often forces therapeutic decisions to be made under time-pressure, such that mechanical circulatory support (MCS) can be offered as a...

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.

Although Jacques Rancière and Jürgen Habermas share several important commitments, they interpret various core concepts differently, viewing politics, democracy, communication, and disagreement in conflicting ways. Rancière articulates his democratic vision in opposition to important elements of Habermas’s approach. Critics contend that Habermas cannot account for the dynamics of command, exclusion, resistance, and aesthetic transformation involved in Rancière’s understanding of politics. In particular, the prominent roles Habermas affords to communicative rationality and consensus have led people to think that he cannot grasp (...) the radical forms of political disagreement Rancière describes. While some have viewed Rancière as offering a trenchant challenge to Habermas, I will contend that Rancière’s critique is less compelling than some have thought. Habermasian understandings of third personal speech and aesthetic expression are nuanced and adaptable enough to evade Rancière’s criticisms. I conclude by suggesting that Habermasian theorists have also developed crucial forms of social and political critique that Rancière’s theory systematically excludes. (shrink)

In this article we explore the two emotional experiences of hypervigilance and attention. These emotions are associated with both military training and with posttraumatic stress among other disorders. We consider the way that these emotions can be experienced after exposure to combat as well as grievous bodily injury, and seek to untangle situations in which they are artifacts of military training and identity rather than symptoms. The data for this article are drawn from interviews and observations with former patients of (...) the US Armed Forces Amputee Patient Care Program at the Walter Reed National Military Medical Center. An experience like hypervigilance is often treated as a symptom of posttraumatic stress disorder (PTSD) or mild traumatic brain injury. Some experts place the number of returning service members with either or both of these disorders in the hundreds of thousands. While some participants in our study have received diagnoses of either PTSD or mild traumatic brain injury, in many cases they experience emotions like hypervigilance, differently. Rather than being troubled by hypervigilance, they experience it as a valued legacy of their military training and an important characteristic that distinguishes them from civilians. (shrink)