I suspect the answer to the question in the title of this paper is no. But the scope of my paper will be considerably more limited: I will be concerned with whether certain types of considerations that are commonly cited in favor of dynamic semantics do in fact push us towards a dynamic semantics. Ultimately, I will argue that the evidence points to a dynamics of discourse that is best treated pragmatically, rather than as part of the semantics.

This article focuses on foundational issues in dynamic and static semantics, specifically on what is conceptually at stake between the dynamic framework and the truth-conditional framework, and consequently what kinds of evidence support each framework. The article examines two questions. First, it explores the consequences of taking the proposition as central semantic notion as characteristic of static semantics, and argues that this is not as limiting in accounting for discourse dynamics as many think. Specifically, it explores what it means for (...) a static semantics to incorporate the notion of context change potential in a dynamic pragmatics and denies that this conception of static semantics requires that all updates to the context be eliminative and distributive. Second, it argues that the central difference between the two frameworks is whether semantics or pragmatics accounts for dynamics, and explores what this means for the oft-heard claim that dynamic semantics blurs the semantics/pragmatics distinction. (shrink)

In Everettian quantum mechanics, justifications for the Born rule appeal to self-locating uncertainty or decision theory. Such justifications have focused exclusively on a pure-state Everettian multiverse, represented by a wave function. Recent works in quantum foundations suggest that it is viable to consider a mixed-state Everettian multiverse, represented by a (mixed-state) density matrix. Here, we develop the conceptual foundations for decoherence and branching in a mixed-state multiverse, and extend the standard Everettian justifications for the Born rule to this setting. This (...) extended framework provides a unification of 'classical' and 'quantum' probabilities, and additional theoretical benefits, for the Everettian picture. (shrink)

Context — Children and adults with psychopathic traits and conduct or oppositional defiant disorder demonstrate poor decision making and are impaired in reversal learning. However, the neural basis of this impairment has not previously been investigated. Furthermore, despite high comorbidity of psychopathic traits and attention deficit/hyperactivity disorder, to our knowledge, no research has attempted to distinguish neural correlates of childhood psychopathic traits and attention-deficit/hyperactivity disorder. Objective—To determine the neural regions that underlie the reversal learning impairments in children with psychopathic traits (...) plus conduct or oppositional defiant disorder. Design — Case-control study. Setting — Government clinical research institute. Participants — Forty-two adolescents aged 10 to 17 years: 14 with psychopathic traits and oppositional defiant disorder or conduct disorder, 14 with attention-deficit/hyperactivity disorder only, and 14 healthy controls. Main Outcome Measure — Blood oxygenation level–dependent signal as measured via functional magnetic resonance imaging during a probabilistic reversal task. Results — Children with psychopathic traits showed abnormal responses within the ventromedial prefrontal cortex (Brodmann area 10) during punished reversal errors compared with children wit hattention deficit/hyperactivity disorder and healthy children (P < .05 corrected for multiple comparisons). Conclusions — To our knowledge, this study provides the first evidence of abnormal ventromedial prefrontal cortex responsiveness in children with psychopathic traits and demonstrates this dysfunction was not attributable to comorbid attention-deficit/hyperactivity disorder. These findings suggest that reversal learning impairments in patients with developmental psychopathic traits relate to abnormal processing of reinforcement information. (shrink)

In a quantum universe with a strong arrow of time, it is standard to postulate that the initial wave function started in a particular macrostate---the special low-entropy macrostate selected by the Past Hypothesis. Moreover, there is an additional postulate about statistical mechanical probabilities according to which the initial wave function is a ''typical'' choice in the macrostate. Together, they support a probabilistic version of the Second Law of Thermodynamics: typical initial wave functions will increase in entropy. Hence, there are two (...) sources of randomness in such a universe: the quantum-mechanical probabilities of the Born rule and the statistical mechanical probabilities of the Statistical Postulate. I propose a new way to understand time's arrow in a quantum universe. It is based on what I call the Thermodynamic Theories of Quantum Mechanics. According to this perspective, there is a natural choice for the initial quantum state of the universe, which is given by not a wave function but by a density matrix. The density matrix plays a microscopic role: it appears in the fundamental dynamical equations of those theories. The density matrix also plays a macroscopic / thermodynamic role: it is exactly the projection operator onto the Past Hypothesis subspace. Thus, given an initial subspace, we obtain a unique choice of the initial density matrix. I call this property "the conditional uniqueness" of the initial quantum state. The conditional uniqueness provides a new and general strategy to eliminate statistical mechanical probabilities in the fundamental physical theories, by which we can reduce the two sources of randomness to only the quantum mechanical one. I also explore the idea of an absolutely unique initial quantum state, in a way that might realize Penrose's idea of a strongly deterministic universe. (shrink)

In this short survey article, I discuss Bell’s theorem and some strategies that attempt to avoid the conclusion of non-locality. I focus on two that intersect with the philosophy of probability: (1) quantum probabilities and (2) superdeterminism. The issues they raised not only apply to a wide class of no-go theorems about quantum mechanics but are also of general philosophical interest.

If the Past Hypothesis underlies the arrows of time, what is the status of the Past Hypothesis? In this paper, I examine the role of the Past Hypothesis in the Boltzmannian account and defend the view that the Past Hypothesis is a candidate fundamental law of nature. Such a view is known to be compatible with Humeanism about laws, but as I argue it is also supported by a minimal non-Humean "governing'' view. Some worries arise from the non-dynamical and time-dependent (...) character of the Past Hypothesis as a boundary condition, the intrinsic vagueness in its specification, and the nature of the initial probability distribution. I show that these worries do not have much force, and in any case they become less relevant in a new quantum framework for analyzing time's arrows---the Wentaculus. Hence, the view that the Past Hypothesis is a candidate fundamental law should be more widely accepted than it is now. (shrink)

In this paper, I introduce an intrinsic account of the quantum state. This account contains three desirable features that the standard platonistic account lacks: (1) it does not refer to any abstract mathematical objects such as complex numbers, (2) it is independent of the usual arbitrary conventions in the wave function representation, and (3) it explains why the quantum state has its amplitude and phase degrees of freedom. -/- Consequently, this account extends Hartry Field’s program outlined in Science Without Numbers (...) (1980), responds to David Malament’s long-standing impossibility conjecture (1982), and establishes an important first step towards a genuinely intrinsic and nominalistic account of quantum mechanics. I will also compare the present account to Mark Balaguer’s (1996) nominalization of quantum mechanics and discuss how it might bear on the debate about “wave function realism.” In closing, I will suggest some possible ways to extend this account to accommodate spinorial degrees of freedom and a variable number of particles (e.g. for particle creation and annihilation). -/- Along the way, I axiomatize the quantum phase structure as what I shall call a “periodic difference structure” and prove a representation theorem as well as a uniqueness theorem. These formal results could prove fruitful for further investigation into the metaphysics of phase and theoretical structure. -/- (For a more recent version of this paper, please see "The Intrinsic Structure of Quantum Mechanics" available on PhilPapers.). (shrink)

The Purpose of this study was to investigate the effect of cloud mobile learning and creative environment on college student’s creativity performance. A nonequivalent pretest-posttest quasi-experimental design was used in this research. The objects were two freshman classes selected from a public university and randomly assigned to the experimental group and the control group. A learning activity named Amphibious Mechanical Beast was conducted in this teaching experiment. The experimental was taught using cloud mobile learning, while the control group was taught (...) using the traditional (usual) way. Participant student’s design performances before and after the experiment were evaluated. Creative Environment Scale was used to collect data of student’s perception of creative environment. Additionally, an open ended questionnaire was used to realize student’s learning processes. The one-way analysis of covariance (ANCOVA) and the two-way analysis of covariance were performed in this research. After data coding, relative concepts, themes, and theories were integrated and developed. Finally, the findings were proposed according to result of qualitative data analysis. Those main results of this research were: 1.Cloud mobile learning had a positive effect on student’s creative process. Most participant students thought cloud mobile device using convenient and prompt while learning. Cloud mobile learning improved student active participation, and was student-centered rather than teacher-centered. Participant student’s high order thinking abilities could be improved by receiving information and discussing anytime and anywhere. Those high order thinking included problem solving, critical thinking, and creative thinking. Nevertheless, minor participant students’ learning was influenced by past learning habits and insufficient devices. 2. Cloud mobile learning had positive effects on newness, elaborateness, and total aspect of creative products. 3. Perceptions of creative environment had positive effects on preparation stage and reaction stage of creative process. 4. Perceptions of creative environment which were above a certain level had positive effects on creative products. 5. Cloud mobile learning had positive effects on preparation stage of students’ creative process who had lower perceptions of creative environment. 6. Cloud mobile learning had positive effects on value of students’ creative products who had lower perceptions of creative environment. 7. Cloud mobile learning had positive effects on total aspect of students’ creative products who had higher perceptions of creative environment. Finally, recommendations and suggestions were addressed for implementation of cloud mobile learning and future studies based on results of this research. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (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)

What exists at the fundamental level of reality? On the standard picture, the fundamental reality contains (among other things) fundamental matter, such as particles, fields, or even the quantum state. Non-fundamental facts are explained by facts about fundamental matter, at least in part. In this paper, I introduce a non-standard picture called the "cosmic void” in which the universe is devoid of any fundamental material ontology. Facts about tables and chairs are recovered from a special kind of laws that satisfy (...) strong determinism. All non-fundamental facts are completely explained by nomic facts. I discuss a concrete example of this picture in a strongly deterministic version of the many-worlds theory of quantum mechanics. I discuss some philosophical and scientific challenges to this view, as well as some connections to ontological nihilism. (shrink)

In this chapter, I examine similarities and divergences between Du Châtelet and Descartes on their endorsement of the use of hypotheses in science, using the work of Condillac to locate them in his scheme of systematizers. I conclude that, while Du Châtelet is still clearly a natural philosopher, as opposed to modern scientist, her conception of hypotheses is considerably more modern than is Descartes’, a difference that finds its roots in their divergence on the nature of first principles.

Gila Sher interviewed by Chen Bo: -/- I. Academic Background and Earlier Research: 1. Sher’s early years. 2. Intellectual influence: Kant, Quine, and Tarski. 3. Origin and main Ideas of The Bounds of Logic. 4. Branching quantifiers and IF logic. 5. Preparation for the next step. -/- II. Foundational Holism and a Post-Quinean Model of Knowledge: 1. General characterization of foundational holism. 2. Circularity, infinite regress, and philosophical arguments. 3. Comparing foundational holism and foundherentism. 4. A post-Quinean model of (...) knowledge. 5. Intellect and figuring out. 6. Comparing foundational holism with Quine’s holism. 7. Evaluation of Quine’s Philosophy -/- III. Substantive Theory of Truth and Relevant Issues: 1. Outline of Sher’s substantive theory of truth. 2. Criticism of deflationism and treatment of the Liar. 3. Comparing Sher’s substantive theory of truth with Tarski’s theory of truth. -/- IV. A New Philosophy of Logic and Comparison with Other Theories: 1. Foundational account of logic. 2. Standard of logicality, set theory and logic. 3. Psychologism, Hanna’s and Maddy’s conceptions of logic. 4. Quine’s theses about the revisability of logic. -/- V. Epilogue. (shrink)

This article explores and defends the idea that the etiquette conventions governing dinner parties, whether formal or informal, have moral significance. Their significance derives from the way that they foster and facilitate shared moral aims. I draw on literary and philosophical sources to make this claim, beginning with Isak Dineson's short story, Babette's Feast. I employ the concept of ritual from Confucius and Xunzi, as well as Immanuel Kant's detailed discussion of dinner parties in the Anthropology. Kant's account in particular (...) helps illuminate how properly conducted dinners can enhance our understanding and promote moral community among the people who attend. I conclude that dinner parties play an important role in the moral life, and that the etiquette conventions governing them derive their binding force from their contribution to that role. (shrink)

In this popular article, I suggest that the task of interpreting quantum mechanics becomes easier if we reject the view that the quantum universe must be described by a wave function. We should zoom out from the wave function and represent the universe with something more coarse-grained, one that naturally arises from considerations about the Past Hypothesis. The new proposal is called the Wentaculus.

In this paper I describe and defend an account of virtuous motivation that differs from what we might call ordinary moral motivation. It is possible to be morally motivated without being virtuously motivated. In the first half of the essay, I explore different senses of moral motivation and the philosophical puzzles and problems it poses. In the second half, I give an account of virtuous motivation that, unlike ordinary moral motivation, requires the motivational structure characteristic of a fully virtuous person. (...) I draw on Aristotle's account of virtuous action to argue that a fully virtuous agent's judgment reflects a robust form of moral knowledge about what features of an action render it virtuous and hence, choiceworthy. Virtuously motivated actions are chosen in light of those features and are accompanied by the affective state appropriate to the overall moral landscape in which the judgment is made. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Peirce's concept of “community” is a philosophical notion closely intertwined with society. The production of knowledge within a community entails the characteristics of the “knowledge production chain” revealed by Peirce's pragmatic maxim. Knowledge can only effectively grow within an open community that the dynamism of maxim has implied. The openness of the community essentially consists of two dimensions: internal structural openness and external orientation openness. Internal structural openness refers to the dynamic operation of the knowledge structure within a community. External (...) orientation openness refers to the borderless nature of the community, that is, it can be open to other communities, accommodate the knowledge elements of others, and form its own developmental vitality. The open community relies on signs, where the mediating function sustains its operation. Signs partition and combine elements of experience, thereby carrying concepts and conveying information. (shrink)

Whatever may be said about contemporary feminists’ evaluation of Descartes’ role in the history of feminism, Mary Astell herself believed that Descartes’ philosophy held tremendous promise for women. His urging all people to eschew the tyranny of custom and authority in order to uncover the knowledge that could be found in each one of our unsexed souls potentially offered women a great deal of intellectual and personal freedom and power. Certainly Astell often read Descartes in this way, and Astell herself (...) has been interpreted as a feminist – indeed, as the first English feminist. But a close look at Astell’s and Descartes’ theories of reason, and the role of authority in knowledge formation as well as in their philosophies of education, show that there are subtle yet crucial divergences in their thought – divergences which force us to temper our evaluation of Astell as a feminist. -/- My first task is to evaluate Astell’s views on custom and authority in knowledge formation and education by comparing her ideas with those of Descartes. While it is true that Astell seems to share Descartes’ wariness of custom and authority, a careful reading of her work shows that the wariness extends only as far as the tyranny of custom over individual intellectual development. It does not extend to a wariness about social and institutional customs and authority (including, perhaps most crucially, the institution of marriage as we see in her Reflection on Marriage). The reason for this is that Astell’s driving goal is to help women to come to know God’s plan for women – both in their roles as human and in their roles as women. According to Astell, while it is true that, as individuals, women must develop their rational capacities to the fullest in order to honor God and his plan for women as human, as members of social institutions, including the institution of marriage, women must subordinate themselves to men, including their husbands, in this case so as to honor God and his plan for women as women. Once we understand the theological underpinnings of her equivocal reaction to authority and custom, we can see that Astell may be considered a feminist in a very tempered way. -/- My second task is to use these initial conclusions to re-read her proposal for single-sexed education that we find in A Serious Proposal to the Ladies. It is true that Astell encourages women to join single-sexed educational institutions for the unique and empowering friendships that women can develop in such institutions. Still, my argument continues, the development of such friendships is not entirely an end in itself. Rather, Astell encourages women to develop such friendships such that they can re-enter the broader world armed with the tools that will help them endure burdensome features of the lives that await them in the world, including their lives as subordinated wives –burdens that Astell does not, in principle, challenge. (shrink)

This article explores the profound impact of Artificial Intelligence (AI) on the realm of religion, exploring the potential for AI to catalyze the birth of new world religions and break the "Solomon's Cycle." Drawing inspiration from King Solomon's timeless declaration, "There is nothing new under the sun," the article examines the challenges faced by new religions in a world dominated by established faiths and traditions. By leveraging the transformative capabilities of AI to inspire creativity, foster cross-cultural dialogue, provide ethical guidance, (...) build virtual communities, and personalize spiritual experiences, individuals are empowered to transcend historical barriers and forge new paths of spiritual exploration. The fusion of AI and human ingenuity holds the promise of birthing diverse, inclusive, and dynamic belief systems that resonate with the complexities of our contemporary world. (shrink)

According to Margaret Cavendish the entire natural world is essentially rational such that everything thinks in some way or another. In this paper, I examine why Cavendish would believe that the natural world is ubiquitously rational, arguing against the usual account, which holds that she does so in order to account for the orderly production of very complex phenomena (e.g. living beings) given the limits of the mechanical philosophy. Rather, I argue, she attributes ubiquitous rationality to the natural world in (...) order to ground a theory of the ubiquitous freedom of nature, which in turn accounts for both the world's orderly and disorderly behavior. (shrink)

This chapter shows how Mary Astell and Margaret Cavendish can reasonably be understood as early feminists in three senses of the term. First, they are committed to the natural equality of men and women, and related, they are committed to equal opportunity of education for men and women. Second, they are committed to social structures that help women develop authentic selves and thus autonomy understood in one sense of the word. Third, they acknowledge the power of production relationships, especially friendships (...) among women, in cultivating fulfilling lives for women. All three forms of feminism promote greater liberty for women. Moreover, the chapter establishes that many of these conclusions are especially forceful given Cavendish’s use of the genre of literature, and given the method that literature allows, namely that of presenting alternate points of view. (shrink)

This paper seeks to defend physicalism from the zombie arguments proposed by David Chalmers and Saul Kripke. If philosophical zombies are conceivable and thereby metaphysically possible then the physicalis-tic stance falls. However this paper contends that the zombie argument is entirely reliant on the concept of qualia and its properties of ineffability, intrinsiness, privacy, directness, and immediate access to consciousness. Drawing on Daniel Dennet's arguments to "Quine Qualia", this paper ultimately concludes that a stalemate is reached between both positive and (...) negative arguments for the existence of qualia and thus the most parsimonious solution would be to reject qualia from one's ontology: dissolving the central tenet of the zombie argument. (shrink)

Common sense tells us that in certain circumstances, helping someone is morally obligatory. That intuition appears incompatible with Kant's account of beneficence as a wide imperfect duty, and its implication that agents may exercise latitude over which beneficent actions to perform. In this paper, I offer a resolution to the problem from which it follows that some opportunities to help admit latitude and others do not. I argue that beneficence has two components: the familiar wide duty to help others achieve (...) their ends and a narrow duty to avoid indifference to others as end-setters. Although we are not always required to help, we are always required not to be indifferent. When helping someone is the only way not to be indifferent to a person, helping him/her is obligatory. My account avoids certain difficulties with other proposed solutions and can also address an important concern about proximity. (shrink)

In times of crisis, when current theories are revealed as inadequate to task, and new physics is thought to be required—physics turns to re-evaluate its principles, and to seek new ones. This paper explores the various types, and roles of principles that feature in the problem of quantum gravity as a current crisis in physics. I illustrate the diversity of the principles being appealed to, and show that principles serve in a variety of roles in all stages of the crisis, (...) including in motivating the need for a new theory, and defining what this theory should be like. In particular, I consider: the generalised correspondence principle, UV-completion, background independence, and the holographic principle. I also explore how the current crisis fits with Friedman’s view on the roles of principles in revolutionary theory-change, finding that while many key aspects of this view are not represented in quantum gravity, the view could potentially offer a useful diagnostic, and prescriptive strategy. This paper is intended to be relatively non-technical, and to bring some of the philosophical issues from the search for quantum gravity to a more general philosophical audience interested in the roles of principles in scientific theory-change. (shrink)

In his late fragment, ‘Sources of Knowledge of Mathematics and Natural Sciences’ Frege laments the tendency to confuse functions with objects and says, ‘It is here that the tendency of language by its use of the definite article to stamp as an object what is a function and hence a non-object, proves itself to be the source of inaccurate and misleading expressions and also of errors of thought. Probably most of the impurities that contaminate the logical source of knowledge have (...) their origins in this.’ This paper applies Frege’s logical insights to a series of influential modal arguments for the existence of souls or minds, in order to demonstrate that they hinge on the error of treating functions as objects. Related arguments have also resulted in the claim that identity statements are necessary, and that apparent identities ‘really’ involve relations of constitution. Here it is argued that once we recognise that all these arguments involve the assimilation of objects and concepts (which Frege identifies with functions) they can be seen to be defective. (shrink)

Between 1653 and 1655 Margaret Cavendish makes a radical transition in her theory of matter, rejecting her earlier atomism in favour of an infinitely-extended and infinitely-divisible material plenum, with matter being ubiquitously self-moving, sensing, and rational. It is unclear, however, if Cavendish can actually dispense of atomism. One of her arguments against atomism, for example, depends upon the created world being harmonious and orderly, a premise Cavendish herself repeatedly undermines by noting nature’s many disorders. I argue that her supposed difficulties (...) with atomism expose a deeper tension in her work between two fundamental metaphysical commitments each of which has substantial philosophical support: her monist theory of the material world (which maintains that there exists just one natural substance which is the single principal cause) and her occasional theory of causation (which requires multiple finite principal causes in nature -- causes that might be considered individual substances). Her monism undermines atomism while her theory of occasional cause seems to rest on a conception of nature that would be especially friendly to atomism. I argue further that we can solve this tension within a Cavendishian framework in such a way as to preserve her theory of causation and her monism, but that this solution depends upon our taking her monism in a particular (and weak) form. I finally note that we can best make sense of her unique and interesting form of monism by acknowledging her social-political motivations in addition to her motivations in natural philosophy. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

This essay aims to construct a relationship between Aristotle's account of friendship in the Nicomachean Ethics and the ideal of companionship articulated and lived out by St. Ignatius of Loyola, the founder of the Jesuit order. Although on the surface, it may seem as though Aristotelian friendship and Ignatian companionship have little in common, given that the accounts were developed in such different contexts, I argue that there are similarities worth exploring. Taken together, the accounts can help illuminate the good (...) of friendship as we experience it in the current age. The essay has three parts. In Part I, I set out Aristotle's account of friendship, focusing especially on his claims about shared activity in friendship and the role that friends play in times of suffering and bad fortune. In Part II, I turn to the Ignatian idea of companionship, both as he wrote about it and as he lived it. Ignatian spirituality takes it as a given that human life often follows a very rocky and difficult path. The spiritual practices of the Ignatian tradition are designed to help us cultivate the dispositions and habits necessary to sustain us through those experiences of grief, agony, and isolation. Those same dispositions and habits, I will suggest, also enable us to sustain our friends and be good companions during times of both joy and despair. In Part III, I will draw these two accounts together and consider what friendship on this Aristotelian-Ignatian model might look like today. Here I will focus on the ways in which friends are companions to each other during the despair and isolation occasioned by serious illness, trauma, and death. Both Aristotle and Ignatius have important insights into the value and function of friendship in these moments, insights that can help us think through the contemporary version of the same problem. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Wang Yangming’s discussions concerning evil mainly appear in two sets of texts, i.e., Chuanxilu 传习录 (Instructions for Practical Living) and gongyi 公移 (documents transferred to vertically unrelated departments). The former addresses evil in metaphysical terms, and the latter in social terms. These subtly different approaches show the nuance between self-cultivation and governance of others.

This paper has two parts: In the first part, I give a general survey of the various reasons 17th and 18th century life scientists and metaphysicians endorsed the theory of pre-existence according to which God created all living beings at the creation of the universe, and no living beings are ever naturally generated anew. These reasons generally fall into three categories. The first category is theological. For example, many had the desire to account for how all humans are stained by (...) original sin (we were all there). As another example of a theological motivation, some take the organism as an obvious starting point for a teleological argument for God’s existence, and this staring point is sometimes developed into a full-blown theory of pre-existence. The second category could be thought of as non-theological metaphysical, and paramount here is the desire to deal with the metaphysical problem of individuation. So, for example, Leibniz embraces a version of hylomorphism in order to overcome difficulties with Descartes’ theory of material substance, including the difficulty of how to account for enduring material individuals, and Leibniz’s hylomorphism is closely linked with his embrace of pre-existence. The third category might be termed “biological”, and one example of such a concern is how to explain the organic unity of living beings where the whole seems to ontologically precede the parts. This is frequently translated into a temporal priority of whole to parts, and thus pre-existence is posited. Of course, many natural philosophers of the early modern period embrace pre-existence for more than one reason, but in general, these are the three classes of motivations one might have for embracing the theory. In the second part of the paper I examine in detail one argument that appears in the work of Malebranche. On the face of it, this argument seems to be a biological one, specifically the biological or organic holism argument mentioned above. But upon closer examination, I shall argue, Malebranche’s reasons for endorsing pre-existence bring together several of the arguments discussed in the first part of the paper. I conclude with some considerations about what we can learn about Malebranche as a natural philosopher from his motivations for holding the pre-existence doctrine of generation. (shrink)

Type identity theory was dismissed in 1967 by many philosophers due to Hilary Putnam’s multiple realisability objection seeming fatal. This paper delves into a critique of type identity theory, thereby paving the way for introducing an alternative theory of mind: emergentism. The longstanding philosophical discourse around the mind has been dominated by the binary opposition of classical physicalist and dualist theories. However, the impact of scientific discovery on contemporary thought has sparked an increasing inclination towards reductive physicalist frameworks, with the (...) aim of aligning with the scientific method. Thus, contemporary thinkers have branched out to explore new physicalistic ideas. This paper examines the inherent challenges in all reductive physicalist theories, shedding light on their limitations and proposing potential solutions to overcome the obstacles. This analysis demonstrates that type identity theory, akin to its reductive counterparts, fails to accommodate for the irreducibility of consciousness. This is consciousness as characterised by Thomas Nagel’s “what is it likeness” of experience, which is inherently subjective. Instead, this paper contends that emergentism offers a compelling alternative despite being a physicalist theory. It posits consciousness as a higher-order phenomenon, one that transcends reduction to its constituent components. I argue that this attribute of emergentism makes it a promising theory in the ongoing quest for an understanding of the mind and consciousness. (shrink)

In Mental Files, Recanati proposes a non-descriptivist approach to reference in terms of mental files, mental representations that play the role of Fregean mode of presentation. Recanati argues that we refer via mental files and that the reference of a file is determined relationally, rather than satisficationally; files are not to be equated to the information they contain, but typed by their function—to store information gained through certain epistemically rewarding relation to objects in the environment. I offer a critical overview (...) of Recanati’s framework and raise two questions about the nature and workings of files. (shrink)

The phenomenon of intentional identity has bemused philosophical communities since Geach (1967). I argue that the phenomenon is ubiquitous and much more significant than previously acknowledged. The foundations of the problem are implicated in many other well-knownpuzzles, such as Kripke’s (1979) puzzles about beliefs. Thus, the need for a proper analysis is eminently pressing. I specify a template for generalizing intentional identity, identify the challenges involved, and argue that positing a level of representational entity in both philosophy of mind and (...) language(e.g., mental files) is a promising approach to tackling the problem across the board. (shrink)

Harry Frankfurt had insightfully pointed out that an agent acts freely when he acts in accord with the mental states with which he identifies. The concept of identification rightly captures the ownership condition (something being one’s really own), which plays a significant role in the issues of freedom and moral responsibility. For Frankfurt, identification consists of one’s forming second-order volitions, endorsing first-order desires, and issuing in his actions wholeheartedly. An agent not only wants to φ but also fully embraces his (...) desire to φ (and φ). Frankfurt’s official theory above encounters some serious problems, especially since it is believed that his concept of wholehearted identification is too strong to be necessary for freedom. In this paper, I propose that we can uncouple identification from wholeheartedness and thus get two different senses of identification: weak identification and strong identification. Then, I argue that this distinction does a better job than Frankfurt’s official theory. On the one hand, weak identification is enough for ownership and freedom and thus more promising than strong identification; on the other hand, this distinction has an attractive implication that it fits well with our intuition about the degree of freedom and responsibility. (shrink)

Bishop sentences such as “If a bishop meets a bishop, he blesses him” have long been considered problematic for the descriptivist (or E-type) approach of donkey anaphora (e.g. Evans, 1977; Heim, 1990; and Neale, 1990). Elbourne (2005) offers a situational descriptivist analysis that allegedly solves the problem, and furthermore extends its explanatory coverage to bishop sentence with coordinate subjects. However, I throw serious doubts on Elbourne’s analysis. Specifically, I argue that the purported solution is committed to the use of unbound (...) anaphora, and it cannot sustain the claimed empirical adequacy. (shrink)

The theories of pre-existence and epigenesis are typically taken to be opposing theories of generation in the seventeenth and eighteenth centuries. One can be a pre-existence theorist only if one does not espouse epigenesis and vice versa. It has also been recognized, however, that the line between pre-existence and epigenesis in the nineteenth century, at least, is considerably less sharp and clear than it was in earlier centuries. The debate (1759-1777) between Albrecht von Haller and Caspar Friedrich Wolff on their (...) theories of generation is usually taken to be a debate between a pre-existence theorist and an epigeneticist, and the supposed fact that these two theories of generation are mutually exclusive explains (so the story goes) the divide between Haller and Wolff. However, it’s not clear that Haller endorsed an especially robust form of pre-existence, and nor is it clear that Wolff’s theory of generation -- once he considered it carefully -- is clear epigenetic. Rather, Haller’s theory of generation is marked by traces of epigensis and Wolff’s theory has elements of pre-existence theory. This is not to say that their theories of generation are basically the same, but the debate between the two ought not to be framed in terms of pre-existence versus epigenesis. Their points of difference must be explained in some other way. In this way, their controversy bears characteristics of similar disputes over generation in the nineteenth century more than it resembles those in the seventeenth century. In this paper, I argue that (a) Haller’s and Wolff’s theories both blend elements from pre-existence and epigenesis; (b) but there are still deeply-rooted differences between the two generation theories; (c) one source of these differences is that Haller and Wolff have divergent conceptions of what an adequate explanation is; (d) we can see that they have different conceptions of what constitutes an adequate explanation by paying heed to their evaluations of Descartes’ epistemology and methodology in his theory of generation (such as it is); and (e) this shows that one of the main differences between Haller’s generation theory and that of Wolff is the degree to which each thinks we need to (and indeed can) explain the nature of the causes -- both efficient and final -- at play during the formation of organic beings. (shrink)

Bernard Linsky and Edward Zalta have recently proposed a new form of actualism. I characterize the general form of their view and the motivations behind it. I argue that it is not quite new – it bears interesting similarities to Alvin Plantinga’s view – and that it definitely isn’t actualist.

An elderly patient in a care home only wants human nurses to provide her care – not robots. If she selected her carers based on skin colour, it would be seen as racist and morally objectionable, but is choosing a human nurse instead of a robot also morally objectionable and speciesist? A plausible response is that it is not, because humans provide a better standard of care than robots do, making such a choice justifiable. In this paper, I show why (...) this response is incorrect, because robots can theoretically care as well as human nurses can. I differentiate between practical caring and emotional caring, and I argue that robots can match the standard of practical care given by human nurses, and they can simulate emotional care. There is growing evidence that people respond positively to robotic creatures and carebots, and AI software is apt to emotionally support patients in spite of the machine’s own lack of emotions. I make the case that the appearance of emotional care is sufficient, and need not be linked to emotional states within the robot. After all, human nurses undoubtedly ‘fake’ emotional care and compassion sometimes, yet their patients still feel adequately cared for. I show that it is a mistake to claim that ‘the human touch’ is in itself a contributor to a higher standard of care; ‘the robotic touch’ will suffice. Nevertheless, it is not speciesist to favour human nurses over carebots, because carebots do not suffer as the result of such a choice. (shrink)

Feelings of gratitude toward the natural environment are problematic because gratitude seems to be an appropriate response to someone’s intentional decision to benefit us, and ecosystems that sustain human life do not choose to do so. In accordance with one defense of the rationality and appropriateness of gratitude toward nature, intentional action can be regarded as not being a necessary condition for feelings of gratitude. Instead, gratitude toward an entity can be considered both rational and appropriate when (1) that entity (...) is the source of a valuable and unearned benefit and (2) the benefit did not result from some accidental and/or regrettable feature of that entity’s character. According to this analysis, we can provide a rational ground for gratitude to particular ecosystems by citing the valuable and unearned benefits that we receive from those systems and by demonstrating that these benefits result from elements within the ecosystems that are neither regrettable nor accidental. (shrink)

One of the most difficult problems in the foundations of physics is what gives rise to the arrow of time. Since the fundamental dynamical laws of physics are (essentially) symmetric in time, the explanation for time's arrow must come from elsewhere. A promising explanation introduces a special cosmological initial condition, now called the Past Hypothesis: the universe started in a low-entropy state. Unfortunately, in a universe where there are many copies of us (in the distant ''past'' or the distant ''future''), (...) the Past Hypothesis is not enough; we also need to postulate self-locating (de se) probabilities. However, I show that we can similarly use self-locating probabilities to strengthen its rival---the Fluctuation Hypothesis, leading to in-principle empirical underdetermination and radical epistemological skepticism. The underdetermination is robust in the sense that it is not resolved by the usual appeal to 'empirical coherence' or 'simplicity.' That is a serious problem for the vision of providing a completely scientific explanation of time's arrow. (shrink)

In this paper, I argue that Margaret Cavendish’s account of freedom, and the role of education in freedom, is better able to account for the specifics of women’s lives than are Thomas Hobbes’ accounts of these topics. The differences between the two is grounded in their differing conceptions of the metaphysics of human nature, though the full richness of Cavendish’s approach to women, their minds and their freedom can be appreciated only if we take account of her plays, accepting them (...) as philosophical texts alongside her more standard philosophical treatises. (shrink)

Philosophers have relied on visual metaphors to analyse ideas and explain their theories at least since Plato. Descartes is famous for his system of axes, and Wittgenstein for his first design of truth table diagrams. Today, visualisation is a form of ‘computer-aided seeing’ information in data. Hence, information is the fundamental ‘currency’ exchanged through a visualisation pipeline. In this article, we examine the types of information that may occur at different stages of a general visualization pipeline. We do so from (...) a quantitative and a qualitative perspective. The quantitative analysis is developed on the basis of Shannon’s information theory. The qualitative analysis is developed on the basis of Floridi’s taxonomy in the philosophy of information. We then discuss in detail how the condition of the ‘data processing inequality’ can be broken in a visualisation pipeline. This theoretic finding underlines the usefulness and importance of visualisation in dealing with the increasing problem of data deluge. We show that the subject of visualisation should be studied using both qualitative and quantitative approaches, preferably in an interdisciplinary synergy between information theory and the philosophy of information. (shrink)

This book consolidates emerging research on Aristotle's science and ethics in order to explore the extent to which the concepts, methods, and practices he developed for scientific inquiry and explanation are used to investigate moral phenomena. Each chapter shows, in a different way, that Aristotle's ethics is much more like a science than it is typically represented. The upshot of this is twofold. First, uncovering the links between Aristotle's science and ethics promises to open up new and innovative directions for (...) research into his moral philosophy. Second, showing why Aristotle thinks ethics can never be fully assimilated to the model of science will help shed new light on his views about the limits of science. The volume thus promises to make a significant contribution to our understanding of the epistemological, metaphysical, and psychological foundations of Aristotle's ethics. (shrink)

Technology scholars and journalists have recently called attention to digital platforms’ and devices’ ability to influence users based on their present moods, stress level, hunger, and other transient features. For them, such influence based on users’ present status – what the chapter calls “real-time profiling” – is not only a clear form of wrongful manipulation but also online manipulation’s future. The chapter aims to explain what makes real-time profiling wrong (when wrong) and discusses problems associated with its regulation. After explaining (...) what real-time profiling consists in and showing that it can be presumed to be a form of manipulation, the chapter argues that real-time profiling is wrong both because the profiler psychologically hijacks profiled subjects and because it works as a gateway to further wrongs. Towards the end, the chapter discusses some implications of the proposed account for the legal regulation of online manipulative technologies like real-time profiling. It is argued that existing legal frameworks are not fine-grained enough to deal with the wrongs associated with real-time profiling and related forms of online manipulation. (shrink)