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)

Reinterpretation of our data concerning sleep onset, motivated by the desire to pay close attention to “intra-individual regularities,” suggests that the experience of control might be a key factor in determining the subjective sense that sleep has begun. This loss of control seems akin to what Frith and others have described as “passivity experiences,” which also occur in schizophrenia. Although clearly sleep onset is not a schizophrenic episode, this similarity might help to explain other features of sleep onset. We further (...) speculate that we could build upon the discovery of various “intra-individual regularities” to construct a model of sleep onset and other forms of sleep mentation. (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)

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)

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)

A number of analytical philosophers have recently endorsed the view that the world itself is indeterminate in some respect. Intriguingly, ideas similar to the view are expressed by thinkers from Chinese Madhyamaka Buddhism, which may shed light on the current discussion of worldly indeterminacy. Using as a basis Chinese Madhyamaka thought, together with Jessica Wilson’s account of indeterminacy, I develop an ontological conception of indeterminacy, termed ontic indeterminacy, which centres on two complementary ideas—conclusive indeterminability and provisional determinability. I show that (...) OI is well-equipped to tackle several issues of worldly indeterminacy. My overarching aim is to present a viable and sustainable perspective on the subject of indeterminacy to enrich analytical philosophers’ insights into the intricate nature of reality. (shrink)

A number of traditional philosophers and religious thinkers advocated an ineffability thesis to the effect that the ultimate reality cannot be expressed as it truly is by human concepts and words. However, if X is ineffable, the question arises as to how words can be used to gesture toward it. We can't even say that X is unsayable, because in doing so, we would have made it sayable. In this article, I examine the solution offered by the fifth-century Indian grammarian-philosopher (...) Bhartrhari and develop it into a linguistic strategy based on the imposition-cum-negation method. The purpose is to show how we can non-contradictorily say, or rather indicate, the unsayable. (shrink)

In his essay “Things Do Not Move,” Sengzhao (374?−414 CE), a prominent Chinese Buddhist philosopher, argues for the thesis that the myriad things do not move in time. This view is counter-intuitive and seems to run counter to the Mahayana Buddhist doctrine of emptiness. In this book chapter, I assess Sengzhao’s arguments for his thesis, elucidate his stance on the change/nonchange of things, and discuss related problems. I argue that although Sengzhao is keen on showing the plausibility of the thesis, (...) he actually views the myriad things as both changing and unchanging and upholds the nonduality of motion and rest. In fact, the nonmoving thesis follows from the discernment that things change from moment to moment without there being any enduring stuff in the process. Among philosophical works that confer a higher ontological status on nonchange over change, Sengzhao’s essay is unique and well worth pondering. (shrink)

For Bhartrhari, a fifth-century Indian grammarian-philosopher, all conscious beings—beasts, birds and humans—are capable of what he called pratibha, a flash of indescribable intuitive understanding such that one knows what the present object “means” and what to do with it. Such an understanding, if correct, amounts to a mode of knowing that may best be termed knowing-what, to distinguish it from both knowing-that and knowing-how. This paper attempts to expound Bhartrhari’s conception of pratibha in relation to the notions of meaning, understanding, (...) and knowing. First, I touch briefly on Bhartrhari’s views of consciousness and language, and examine at some length his indescribability thesis concerning the intuitive meaning of a sentence. Then, I delineate the general features of pratibha as intuitive understanding and discuss its probable range in relation to expert intuition and sense perception. Thereafter, I relate pratibha to the notion of knowing-what and show why these two notions are to be differentiated from knowing-that and knowing-how. The paper concludes with some remarks on the contemporary relevance of Bhartrhari’s conception of pratibha. (shrink)

For Jizang (549−623), a prominent philosophical exponent of Chinese Madhyamaka, all things are empty of determinate form or nature. Given anything X, no linguistic item can truly and conclusively be applied to X in the sense of positing a determinate form or nature therein. This philosophy of ontic indeterminacy is connected closely with his notion of the Way (dao), which seems to indicate a kind of ineffable principle of reality. However, Jizang also equates the Way with nonacquisition as a conscious (...) state of freedom from any attachment and definite understanding whatsoever. The issue then becomes pressing as to how we are to understand Jizang's notion of the Way. Does it indicate some metaphysical principle or reality? Is it actually a skilful expedient to lead one to the consummate state of complete spiritual freedom? How is this issue related to Jizang's conception of ontic indeterminacy? In this book chapter, I examine Jizang's key writings in an attempt to clarify his ontological position. (shrink)

Chinese Chan or Zen Buddhism is renowned for its improvisational, atypical, and perplexing use of words. In particular, the tradition’s encounter dialogues, which took place between Chan masters and their interlocutors, abound in puzzling, astonishing, and paradoxical ways of speaking. In this chapter, we are concerned with Chan’s use of paradoxical language. In philosophical parlance, a linguistic paradox comprises the confluence of opposite or incongruent concepts in a way that runs counter to our common sense and ordinary rational thinking. One (...) naturally wonders about Chan masters’ rationales for their use of paradox. There are also concerns about whether the use violates the logical principle of noncontradiction to the effect that nothing can be both P and not-P all over in the same way at the same time. Chan became a viable Chinese Buddhist tradition during the Tang dynasty (618−907) and continued to develop for several centuries. The tradition had produced a huge literature; consequently, our investigation of its use of paradox cannot but be limited and selective. In the second section, I first sketch key ideas of Chan that are pertinent to our investigation and then examine the use of paradox in the sermons associated with certain Tang masters of the southern Chan. In the third section, I analyze the presence of paradoxical language in post-Tang encounter dialogues. The fourth section concludes. (shrink)

A number of contemporary philosophers think that the unqualified statement “X is unspeakable” faces the danger of self-referential absurdity: if this statement is true, it must simultaneously be false, given that X is speakable by the predicate word “unspeakable.” This predicament is in this chapter formulated as an argument that I term the “ineffability paradox.” After examining the Buddhist semantic theory of apoha (exclusion) and an apoha solution to the issue, I resort to a few Chinese Buddhist and Hindu philosophical (...) materials to rationally reconstruct a strategy for resolving the paradox. By introducing the mode of expression termed “indication,” together with the relevant notions of superimposition and of gesturing beyond the horizon, I show that expressing the ineffable does not necessarily involve irresoluble contradiction. It is also suggested that philosophers may need to acknowledge the relevance of the notion of ineffability for contemporary philosophizing. (shrink)

This paper reconstructs Sartre’s account of the “circuit of ipseity” as an integral theory of the experiential, agentive and normative aspects of self-consciousness. At the core of this theory is a conception of human (self-)consciousness as lacking, and the correlation between lacking and ideal. In Section 1, I show how this theory manages to satisfy the apparently incompatible requirements generated by the idea of a pre-reflective cogito. Section 2 discusses practical self-consciousness, in particular the agent’s consciousness of herself as self-determined (...) in the projection and pursuit of ends, and how this is accounted for in Sartre’s theory by the correlation of lack and ideal. Section 3 first clarifies the Sartrean conception of the ideal by comparing it with Korsgaard’s, and then reconstructs Sartre’s account of practical normativity by showing how it can be read as emerging from a critical engagement with Heidegger. (shrink)

Mahayana Buddhist philosophers’ attitude toward language is notoriously negative. The transcendental reality is often said to be ineffable. One’s obsession to apprehend the truth through words is an intellectual disease to be cured Attachment to verbal and conceptual proliferation enslaves oneself in the afflictive circle of life and death. Nevertheless, no Buddhist can afford to overlook the significance of language in preaching Buddhist dharmas as well as in day-to-day transactions. The point is not that of keeping silence. Rather, one should (...) understand and use language in such a way that one alludes to the unsayable reality and somehow escapes the bewitchment of language. Perhaps with this realization in mind, Mahayana Buddhist metaphysicians had fostered the penchant for using, at the sentential level, denials, negations and paradoxes to couch their views. In a similar vein but mainly at the word level, Dignaga (ca. 480-540 CE) the Yogacara epistemologist’ offered us a theory of language known as apoha doctrine in his landmark work Pramiinasamuccaya (henceforth PS). It is the purpose of this article to construe the doctrine. (shrink)

Especially over the past twenty years, a number of analytic philosophers have embraced the idea that the world itself is vague or indeterminate in one or more respects. The issue then arises as to whether it can be the case that the world itself is indeterminate in all respects. Using as a basis Chinese Madhyamaka Buddhist thought, I offer two reasons for the coherence and intelligibility of the thesis that all concrete things are themselves indeterminate with respect to the ways (...) they are. The first reason draws on a notion reminiscent of the picture of reality as an amorphous lump, while the second reason makes use of the relativity of conceptual perspectives and determinations. Assuming that the world is the mere totality of all concrete things, I show that there is a genuine metaphysical possibility of the world’s being indeterminate in all respects. (shrink)

In this article, I first introduce an Indian Madhyamaka Buddhist critique of causality and discuss critically a contemporary Humean interpretation of the critique. After presenting a Chinese Madhyamaka interpretation, I resort to an ontological conception of indeterminacy, termed ontic indeterminacy, which draws on Chinese Madhyamaka thought together with Jessica Wilson’s account of metaphysical indeterminacy, to show that the conception is well equipped to unravel two puzzling issues that arise from the critique. I suggest that a world that consists of things (...) that are indeterminate with respect to certain ways they are is sufficient for it to embody causal phenomena. (shrink)

In his essay “Things Do Not Move,” Sengzhao, a prominent Chinese Buddhist philosopher, argues for the thesis that the myriad things do not move in time. This view is counter-intuitive and seems to run counter to the Mahayana Buddhist doctrine of emptiness. I assess Sengzhao’s arguments for his thesis, elucidate his stance on the change/nonchange of things, and discuss related problems. I argue that although Sengzhao is keen on showing the plausibility of the thesis, he actually views the myriad things (...) as both changing and unchanging and upholds the nonduality of motion and rest. In fact, the nonmoving thesis follows from the discernment that things change from moment to moment without there being any enduring stuff in the process. Among philosophical works that confer a higher ontological status on nonchange over change, Sengzhao’s essay is unique and well worth pondering. (shrink)

John Harris recently argues that the moral bioenhancement proposed by Persson and Savulescu can damage moral agency by depriving the recipients of their freedom to fall (freedom to make wrongful choices) and therefore should not be pursued. The link Harris makes between moral agency and the freedom to fall, however, implies that all forms of moral enhancement, including moral education, that aim to make the enhancement recipients less likely to “fall” are detrimental to moral agency. In this paper, I present (...) a new moral agency-based critique against the moral bioenhancement program envisaged by Persson and Savulescu. I argue that the irresistible influences exerted by the bioenhancement program harms our capabilities for conducting accurate self-reflection and forming decisions that truly express our will, which subsequently undermine our moral agency. (shrink)

Sleep onset is associated with marked changes in behavioral, physiological, and subjective phenomena. In daily life though subjective experience is the main criterion in terms of which we identify it. But very few studies have focused on these experiences. This study seeks to identify the subjective variables that reflect sleep onset. Twenty young subjects took an afternoon nap in the laboratory while polysomnographic recordings were made. They were awakened four times in order to assess subjective experiences that correlate with the (...) (1) appearance of slow eye movement, (2) initiation of stage 1 sleep, (3) initiation of stage 2 sleep, and (4) 5 min after the start of stage 2 sleep. A logistic regression identified control over and logic of thought as the two variables that predict the perception of having fallen asleep. For sleep perception, these two variables accurately classified 91.7% of the cases; for the waking state, 84.1%. (shrink)

Artificial intelligence (AI) systems are increasingly adopted to make decisions in domains such as business, education, health care, and criminal justice. However, such algorithmic decision systems can have prevalent biases against marginalized social groups and undermine social justice. Explainable artificial intelligence (XAI) is a recent development aiming to make an AI system’s decision processes less opaque and to expose its problematic biases. This paper argues against technical XAI, according to which the detection and interpretation of algorithmic bias can be handled (...) more or less independently by technical experts who specialize in XAI methods. Drawing on resources from feminist epistemology, we show why technical XAI is mistaken. Specifically, we demonstrate that the proper detection of algorithmic bias requires relevant interpretive resources, which can only be made available, in practice, by actively involving a diverse group of stakeholders. Finally, we suggest how feminist theories can help shape integrated XAI: an inclusive social-epistemic process that facilitates the amelioration of algorithmic bias. (shrink)

Although Chan, or Zen, Buddhism traditionally claimed itself as a special transmission outside doctrinal teachings that eschews the written word, it has long been praised for its improvisational, atypical, intriguing, and intricate use of words. Prominent Chan masters are characteristically skillful in employing paradoxical and aporetic phrases, figurative and poetic expressions, negations, questions, repetitions, and so forth, to express their thoughts, indicate their awakened states of mind, cut off the interlocutor’s habitual dualistic thinking, or evoke in him or her an (...) experience of awakening. This fact, among others, has led some contemporary scholars to claim that the Chan experience of awakening does not... (shrink)

This paper approaches Husserl’s analysis of time-consciousness from a mereological perspective. Taking as inspiration Bergson’s idea that pure durée is a multiplicity of interpenetration, I will show, from within Husserlian phenomenology, that the absolute flow can indeed be described as a whole of interpenetrating parts. This mereological perspective will inform my re-consideration of the much-discussed issue of Husserl’s self-criticism concerning the schema of content and apprehension. It will also reveal a fundamental similarity between Husserl’s conception of the absolute flow and (...) Sartre’s conception of lived temporality. This paper consists of four sections. Section 2 presents the basic elements of Husserl’s mereology. Section 3 introduces the difficulty encountered by Husserl’s early account of time that makes use of the schema. I will examine Barry Dainton’s criticism of Husserl’s theory of time-consciousness against the background of the older debate between Meinong and Stern, a debate that has informed Husserl’s own account. Section 4 distinguishes two common criticisms of the schema from Husserl’s own self-criticism, which is in turn divided into two steps. It is shown how the second step of this self-criticism implies the interpenetration of the absolute flow and responds to Dainton’s criticism. Finally, Sect. 5 concludes with some comparative remarks. I will show how Husserl’s notion of absolute flow, as mereologically interpreted, anticipates Sartre’s conception of consciousness as self-transcendence, as well as how it accommodates the apparently conflicting mereological intuitions of Aristotle and Bergson. (shrink)

Theorists who advocate worldly (metaphysical or ontological) indeterminacy—the idea that the world itself is indeterminate in one or more respects—should address how we understand the signifying nature and function of language in light of worldly indeterminacy. I first attend to Sengzhao and Jizang, two leading thinkers in Chinese Sanlun Buddhism, to reconstruct a Chinese Madhyamaka notion of ontic indeterminacy. Then, I draw on the thinkers’ views to propose a provisional (non-definitive) understanding of the nature and use of language. Under this (...) understanding, an expression signifying a thing is provisional in that the expression connotes no determinate feature of the thing. (shrink)

Can an agent deliberating about an action A hold a meaningful credence that she will do A? 'No', say some authors, for 'Deliberation Crowds Out Prediction' (DCOP). Others disagree, but we argue here that such disagreements are often terminological. We explain why DCOP holds in a Ramseyian operationalist model of credence, but show that it is trivial to extend this model so that DCOP fails. We then discuss a model due to Joyce, and show that Joyce's rejection of DCOP rests (...) on terminological choices about terms such as 'intention', 'prediction', and 'belief'. Once these choices are in view, they reveal underlying agreement between Joyce and the DCOP-favouring tradition that descends from Ramsey. Joyce's Evidential Autonomy Thesis (EAT) is effectively DCOP, in different terminological clothing. Both principles rest on the so-called 'transparency' of first-person present-tensed reflection on one's own mental states. (shrink)

There is a long-standing disagreement in the philosophy of probability and Bayesian decision theory about whether an agent can hold a meaningful credence about an upcoming action, while she deliberates about what to do. Can she believe that it is, say, 70% probable that she will do A, while she chooses whether to do A? No, say some philosophers, for Deliberation Crowds Out Prediction (DCOP), but others disagree. In this paper, we propose a valid core for DCOP, and identify terminological (...) causes for some of the apparent disputes. (shrink)

In this article, I analyze the evolution of Husserl's view on the normativity of logic and the corresponding changes in his phenomenological analysis of judgment. Initially, in the Prolegomena, Husserl claimed that the laws of pure logic are ideal and acquire normative status only as a result of application. Later, however, he revised this position and claimed that the same laws are at once ideal and normative. Sections 1 and 2 present textual evidence for attributing such a change of position (...) to Husserl, which is not generally acknowledged in the literature. Section 3 critically examines Husserl's early position, with specific attention to the model of instantiation. Sections 4–6 identify three key stages in the development of Husserl's theory of judgment that lead to the normative conception of pure logic: (1) the critique of the dissociation of ideal content and assertive force; (2) the rejection of the instantiation model of proposition and the development of a new account in terms of identification; (3) the genetic‐phenomenological interpretation of proposition and the elaboration of the three‐layer structure of pure logic. (shrink)

ABSTRACT In a Buddhist treatise from around the fourth century CE there is a very remarkable story which serves as a thought experiment calling us to question the nature of self and the identity of persons. Lost in Sanskrit, the passage is fortunately preserved in a Chinese translation, the Dà zhìdù lùn. We here present the first reliable translation directly from the Classical Chinese, and discuss the philosophical significance of the story in its historical and literary context. We emphasise the (...) philosophical importance of embedding the story in two framing narratives, and demonstrate that the story taps a range of intuitions, and indeed fears, about the survival of the self which have also played a large role in the history of the topic in the West, and which continue to be of great contemporary concern. (shrink)

This paper aims to provide a clarification of the long debate on whether enhancement will or will not diminish authenticity. It focuses particularly on accounts provided by Carl Elliott and David DeGrazia. Three clarifications will be presented here. First, most discussants only criticise Elliott’s identity argument and neglect that his conservative position in the use of enhancement can be understood as a concern over social coercion. Second, Elliott’s and DeGrazia’s views can, not only co-exist, but even converge together as an (...) autonomy based theory of authenticity. Third, the current account of autonomy provided by DeGrazia fails to address the importance of rationality and the ability of self-correction, which, as a result impedes the theory to provide a fully developed account for authenticity. In conclusion, a satisfactory account of authenticity cannot focus only on identity or subjective preference. (shrink)

The issue of the use of the Nachlass material has been much debated in Nietzsche scholarship in recent decades. Some insist on the absolute interpretative priority of his published writings over those unpublished and suggest that an extensive engagement with the Nachlass is harmful because it is something Nietzsche rejected. To verify this claim, they appeal to the story of Nietzsche asking his landlord in Sils-Maria to burn some of his notes. Since the notes that were ultimately retrieved are purportedly (...) incorporated into the compilation The Will to Power, the story also leads some to conclude that Nietzsche rejected his project on the will to power. However, the reliability of this story has been questioned. In this manuscript I first present the decisive piece of evidence that will settle the controversy over the story’s authenticity. After showing that it is true that in 1888 Nietzsche wanted some of his notes burned, I address the question of what we can conclude from this story. I argue that it neither suggests the abandonment of the will to power project, nor warrants a devaluation of the Nachlass. Finally, I will discuss the methodological problem of the use of Nietzsche’s Nachlass in general. (shrink)

This study attempts to reconstruct Nietzsche’s reading of Aristotle in the 1860s and 1870s—the years before he left his career as a philologist. Against the popular view that Nietzsche read only one book by Aristotle, namely the Rhetoric, the present study hopes to show that he had direct knowledge of several of Aristotle’s main works, while much of his interest in Aristotle centred on the latter’s account of art. The particular aim of this study is to explore how Nietzsche’s reading (...) of Aristotle contributed to the formation of The Birth of Tragedy. It will show that, although Nietzsche mentions Aristotle in his first book only en passant, his theory of tragedy should be understood against the background of Aristotelian poetics, especially as interpreted by such contemporaries as Jacob Bernays, Joseph Hubert Reinkens, and Gustav Teichmüller. (shrink)

The article will be divided into three parts: 1. Explain the literary origins of the nesting pattern and its relationship to cinema narrative, and analyse the nesting tactics commonly used in films under Hollywood’s classical narrative. 2. Describe the variations in nested structures in films made in the 1990s, focusing on self-reflexive nesting, which emerged as a new model beyond conventional nesting during this period. 3. Distinguish the literary style of embedded narratives from the visual recognition mode and provide an (...) example of how the latter is used in films to create impossible puzzles. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

The rare but severe cerebral venous thrombosis occurring in some AstraZeneca vaccine recipients has prompted some governments to suspend part of their COVID-19 vaccination programmes. Such suspensions have faced various challenges from both scientific and ethical angles. Most of the criticisms against such suspensions follow a consequentialist approach, arguing that the suspension will lead to more harm than benefits. In this paper, I propose a rights-based argument against the suspension of the vaccine rollouts amid this highly time-sensitive combat of COVID-19. (...) I argue that by suspending a vaccine rollout, a government infringes people's right to take the risks they deem worth taking for their health. I also consider four potential objections to my argument and explain why none of them undermines my argument. (shrink)

Name der Zeitschrift: Nietzsche-Studien Jahrgang: 44 Heft: 1 Seiten: 516-531.

This thesis contributes to a better conceptual understanding of how self-organized control works. I begin by analyzing the control problem and its solution space. I argue that the two prominent solutions offered by classical cognitive science (centralized control with rich commands, e.g., the Fodorian central systems) and embodied cognitive science (distributed control with simple commands, such as the subsumption architecture by Rodney Brooks) are merely two positions in a two-dimensional solution space. I outline two alternative positions: one is distributed control (...) with rich commands, defended by proponents of massive modularity hypothesis; the other is centralized control with simple commands. My goal is to develop a hybrid account that combines aspects of the second alternative position and that of the embodied cognitive science (i.e., centralized and distributed controls with simple commands). Before developing my account, I discuss the virtues and challenges of the first three. This discussion results in a set of criteria for successful neural control mechanisms. Then, I develop my account through analyzing neuroscientific models of decision-making and control with the theoretical lenses provided by formal decision and social choice theories. I contend that neural processes can be productively modeled as a collective of agents, and neural self-organization is analogous to democratic self-governance. In particular, I show that the basal ganglia, a set of subcortical structures, contribute to the production of coherent and intelligent behaviors through implementing “democratic" procedures. Unlike the Fodorian central system—which is a micro-managing “neural commander-in-chief”—the basal ganglia are a “central election commission.” They delegate control of habitual behaviors to other distributed control mechanisms. Yet, when novel problems arise, they engage and determine the result on the basis of simple information (the votes) from across the system with the principles of neurodemocracy, and control with simple commands of inhibition and disinhibition. By actively managing and taking advantage of the wisdom-of-the-crowd effect, these democratic processes enhance the intelligence and coherence of the mind’s final "collective" decisions. I end by defending this account from both philosophical and empirical criticisms and showing that it meets the criteria for successful solution. (shrink)

Name der Zeitschrift: Nietzsche-Studien Jahrgang: 46 Heft: 1 Seiten: 242-242.

This paper addresses the issue of finite versus countable additivity in Bayesian probability and decision theory -- in particular, Savage's theory of subjective expected utility and personal probability. I show that Savage's reason for not requiring countable additivity in his theory is inconclusive. The assessment leads to an analysis of various highly idealised assumptions commonly adopted in Bayesian theory, where I argue that a healthy dose of, what I call, conceptual realism is often helpful in understanding the interpretational value of (...) sophisticated mathematical structures employed in applied sciences like decision theory. In the last part, I introduce countable additivity into Savage's theory and explore some technical properties in relation to other axioms of the system. (shrink)

Lack of a historical sense is the hereditary defect of philosophers. … So what is needed from now on is historical philosophizing, and with it the virtue of modesty.

This paper primarily investigates the following questions: The first question：What is the basic structure of consciousness? I proposed that objects moving at the speed of light form the fundamental structure of consciousness. The second question:How is the unified field of the conscious self formed? The study suggests that countless particles moving at the speed of light, through quantum entanglement, form the unified field of each individual's consciousness. Each individual's unified field consists of countless particles originating from a source, which can (...) be referred to as the "soul quantum." The third question:What is the mechanism underlying the formation of different forms of imagery (images, sounds, and bodily sensations)? The study posits that when the wave-particle duality of quantum mechanics collapses, it results in different forms of imagery. (shrink)

The notion of comparative probability defined in Bayesian subjectivist theory stems from an intuitive idea that, for a given pair of events, one event may be considered “more probable” than the other. Yet it is conceivable that there are cases where it is indeterminate as to which event is more probable, due to, e.g., lack of robust statistical information. We take that these cases involve indeterminate comparative probabilities. This paper provides a Savage-style decision-theoretic foundation for indeterminate comparative probabilities.

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

Two types of formal models - landscape search tasks and two-armed bandit models - are often used to study the effects that various social factors have on epistemic performance. I argue that they can be understood within a single framework. In this unified framework, I develop a model that may be used to understand the effects of functional and demographic diversity and their interaction. Using the unified model, I find that the benefit of demographic diversity is most pronounced in a (...) functionally homogeneous group, and decreases with the increase of functional diversity. (shrink)

In the literature on expert trust, it is often assumed that track records are the gold standard for evaluating expertise, and the difficulty of expert identification arises from either the lack of access to track records, or the inability to assess them. I show, using a computational model, that even in an idealized environment where agents have a God’s eye view on track records, they may fail to identify experts. Under plausible conditions, selecting testimony based on track records ends up (...) reducing overall accuracy, and preventing the community from identifying the real experts. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Background: The concept of digital twins has great potential for transforming the existing health care system by making it more personalized. As a convergence of health care, artificial intelligence, and information and communication technologies, personalized health care services that are developed under the concept of digital twins raise a myriad of ethical issues. Although some of the ethical issues are known to researchers working on digital health and personalized medicine, currently, there is no comprehensive review that maps the major ethical (...) risks of digital twins for personalized health care services. Objective: This study aims to fill the research gap by identifying the major ethical risks of digital twins for personalized health care services. We first propose a working definition for digital twins for personalized health care services to facilitate future discussions on the ethical issues related to these emerging digital health services. We then develop a process-oriented ethical map to identify the major ethical risks in each of the different data processing phases. Methods: We resorted to the literature on eHealth, personalized medicine, precision medicine, and information engineering to identify potential issues and developed a process-oriented ethical map to structure the inquiry in a more systematic way. The ethical map allows us to see how each of the major ethical concerns emerges during the process of transforming raw data into valuable information. Developers of a digital twin for personalized health care service may use this map to identify ethical risks during the development stage in a more systematic way and can proactively address them. Results: This paper provides a working definition of digital twins for personalized health care services by identifying 3 features that distinguish the new application from other eHealth services. On the basis of the working definition, this paper further layouts 10 major operational problems and the corresponding ethical risks. Conclusions: It is challenging to address all the major ethical risks that a digital twin for a personalized health care service might encounter proactively without a conceptual map at hand. The process-oriented ethical map we propose here can assist the developers of digital twins for personalized health care services in analyzing ethical risks in a more systematic manner. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

Balancing a hermeneutic of trust with a hermeneutic of suspicion, this article develops a phenomenological description of imagination that highlights its alethic ambiguity. Imagination is an act of disclosure, without which the world of fiction and pure possibility cannot be constituted. Imagination is also an act of self-indulgence and narcissism, the source of much concealment and untruth. It is not the one or the other, but both at the same time, essentially ambiguous because of its phenomenological constitution. In this article, (...) I will take some steps towards clarifying this essential ambiguity of the imagination by drawing on the insights of Husserl and Sartre. Beginning with Husserl’s parallel treatment of imagination and perception as intuitive, objectifying acts, I will argue, drawing on insights from Sartre, that there is an important discrepancy between them with respect to the role of desire. While the constitution of perceptual presence is inseparable from a desire for truth, the desire involved in the constitution of imaginary presence has an ambiguous character, both epistemic and magical. This duplicity of desire partly accounts for the ambiguity of imagination, which is all the more pronounced the more the imagination demands the full emotional involvement of the imagining subject. (shrink)

Name der Zeitschrift: Nietzsche-Studien Jahrgang: 47 Heft: 1 Seiten: 364-366.