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)

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)

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)

This work attempts to respond to Tomas Aquinas' Cosmological Argument in a way that combines Set Theory with the idea of the ‘Book of Change’. The study defines the ith Cause Set on which to operate on, which leads to the ontological commitment of austerity that the ‘First Cause's Compromise with emergence’ cannot be avoided. It is argued in the present paper that the concept that ‘emergence only consists of Synchronic Emergence and Diachronic Emergence’ should be extended to a broader (...) notion of emergence, which is made up of the two discussed elements and a third one ‘No-Boundary Emergence’ (beyond the time dimension). The article defines the concept of No-Boundary Emergence, proves why it is a type of emergence that differs from the traditional two types, and asserts that it underlies the bottom layer of the cosmos. This study describes the common feature of all emergence as communication protocols between layers. The assemblage of all emergences behaves similar to a distributed system that cannot be restricted by Gödel's theorem. The paper provides evidence (in Big Bang Cosmology, Conformal Cyclic Cosmology, Superstring Theory, Quantum Gravity) for this point of view, and notes that emergence (in the context of No-Boundary Emergence) is not only a simple scientific theory but also a progressive scientific research programme that can spontaneously grow from scientific theory based on Platonism at the expense of a degenerating shift to the ontological commitment of austerity. This paper proposes an improved model of Schrödinger Cat that provides a new explanation for quantum measurement and argues that there must be a forbidden zone of thought experiments. The study also introduces the implications of ancient Chinese thoughts (namely, the ‘Book of Change’ and Confucius). The paper comes to the conclusion that emergence (crossing the gap between ‘being’ and ‘nothing’, while ignoring the forbidden zone of thought experiments) relieves ‘cosmological insufficiency’ in the sense of Neo-Aristotelism. (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)

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)

This summary is not exactly the way I would have done it myself but I must admit that my writing is sometimes a challenge to read. So I asked an AI to do this summary expecting that it will give an easily understandable although not totally accurate view on Ontology of Knowledge and from this general understanding help the reader to read the original papers. Jean-Louis Boucon’s works, "Introduction to the Ontology of Knowledge" and "Time, Space, and World as (...) Knowledge," delve into the intricate nature of reality, meaning, and the process of knowing. Boucon challenges traditional dichotomies in philosophy and science, presenting a cohesive framework where the knowing subject and the world are intertwined aspects of a single dynamic reality. His ideas provide a robust foundation for exploring ontological and epistemological questions, including the interpretation of quantum mechanics. (shrink)

The Fundamental Interrelationships Model – An Alternative Approach to the Theory of Everything, Part 4 Subtitle: The Nature of Beauty and Fundamental Interrelationships -/- Abstract: This article is Chapter 21, titled The Nature of Beauty and the Fundamental Interrelationships, from the book Behind Civilization. It posits that the nature of beauty is rooted in one of the fundamental interrelationships: order. Beauty is perceived as a response in the human brain to this fundamental interrelationship. This article provides evidence that the order (...) theory uniquely explains all forms of beauty and reaffirms the IRM's ability to offer a comprehensive framework for the Theory of Everything. (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)

A prominent version of emotional cognitivism is the view that emotions are preceded by awareness of value. In a recent paper, Jonathan Mitchell (2019) has attacked this view (which he calls the content-priority view). According to him, extant suggestions for the relevant type of pre-emotional evaluative awareness are all problematic. Unless these problems can be overcome, he argues, the view does not represent a plausible competitor to rivaling cognitivist views. As Mitchell supposes, the view is not mandatory since its core (...) motivations can be accommodated by competing views, too. I argue that Mitchell's case against the content-priority view is unconvincing as it misconceives the principal motivation for the view. As I show, properly reconstructed, this motivation provides a strong case for the indispensability of the view to any adequate cognitivist treatment of emotion. Moreover, Mitchell's survey of candidates for pre-emotional value awareness can be seen to rest on problematic phenomenological assumptions. (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)

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)

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 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)

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)

The Dominican theologian Durand of Saint-Pourçain (ca. 1275–1334), breaking from the wide consensus, made a two-pronged attack on concurrentism (i.e., the theory according to which God does more than conserving creatures in existence and co-causes all their actions). On the one hand, he shows that the concurrentist position leads to the unacceptable consequence that God is the direct cause of man’s evil actions. On the other hand, he attacks the metaphysical foundations of concurrentism, first in the version offered by Thomas (...) Aquinas and Giles of Rome, and then in a more general way. Against Thomas and Giles, he challenges Neoplatonic assumptions about causality and being. More generally, he establishes that God’s action and a creature’s action can be neither identical nor different, and thus cannot both be direct causes of the same effect. Without claiming that Durand’s series of objections are definitely unanswerable, we may at least observe that they have generally been underestimated (which earned him the lowly role of the mere foil of the concurrentist view in the history of philosophy) and are able to do considerable damage to concurrentism. (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 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)

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)

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)

Robert Sparrow recently argues that state-driven moral bioenhancement is morally problematic because it inevitably invites moral perfectionism. While sharing Sparrow’s worry about state-driven moral bioenhancement, I argue that his anti-perfectionism argument is too strong to offer useful normative guidance. That is, if we reject state-driven moral bioenhancement because it cannot remain neutral between different conceptions of the good, we might have to conclude that all forms of moral enhancement program ought not be made compulsory, including the least controversial and most (...) popular state-driven program: compulsory (moral) education. -/- In this paper, I argue that instead, the spirit of Sparrow’s worry should be recast in the language of the capability approach – an approach that strives to enhance people’s capabilities to develop their own conceptions of the good by restricting itself from endorsing thick conceptions of the good. The distinction made regarding thick and thin conceptions of the good helps better capture sentiments against state-driven bioenhancement programs without falling prey to the issues I raise against Sparrow’s anti-perfectionist arguments. (shrink)

In todays educational landscape, adapting teaching methods to the digital age is important. While traditional approaches remain essential, they may not fully engage students in multimedia-rich environments. This study evaluates multimedia tools effectiveness in teaching Filipino subjects to Grade 10 learners at Tikalaan National High School for School Year 2023-2024. It examines the impact of such tools on academic performance and student attitudes by comparing pretest and posttest results between control and experimental groups and its implications in teaching Filipino to (...) Grade 10 learners. The study involves Grade 10 students divided into two groups of thirty-five (35) both the Control Group and the Experimental Group. Data collection involved the Division-Based Quarterly Assessment for both pretest and posttest evaluations to measure academic progress. Additionally, a researcher-created survey is made to assess students attitudes towards multimedia tools. Respondents were selected through purposive sampling, focusing on characteristics relevant to the studys objectives. A quasi-experimental design was used, comparing the pretest and posttest results of both groups to determine multimedia tools effectiveness. Statistical analyses, including T-test, ANOVA, and F-test, were used to evaluate the significance of observed differences. The study reveals significant improvement in academic performance and a positive shift in attitudes towards multimedia tools among the experimental group. These findings suggest that multimedia tools can enhance learners academic performance and foster greater student engagement. It underscores the importance of integrating multimedia tools into educational practices to improve teaching and learning outcomes. Recommendations include incorporating multimedia into the curriculum and providing professional development for educators to maximize these tools effectiveness. (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)

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

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

It is widely accepted that a liberal state has a general duty to protect its people from undue health risks. However, the unprecedented emergent measures against the COVID-19 pandemic taken by governments worldwide give rise to questions regarding the extent to which this duty may be used to justify suspending a vaccine rollout on marginal safety grounds. -/- In this chapter, I use the case of vaccination to argue that while a liberal state has a general duty to protect its (...) people’s health, there is a limit to the measures this duty can be used to justify. First, I argue that since every available option involves different risks and benefits, the incommensurability of the involved risks and benefits forbids the prioritisation of a particular vaccine. Second, I argue that given epistemic limitations and uncertainty, policies that favour certain vaccines are not only epistemically ill-founded but also morally unacceptable. I conclude that in a highly uncertain situation such as the unfolding pandemic, the duty a liberal state ought to uphold is to properly communicate the knowns and unknowns to the general public and help people decide which option to choose for themselves. I call this duty the duty to facilitate risk-taking. (shrink)

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

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)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

The aim of this paper is to clarify the role of category theory in the foundations of mathematics. There is a good deal of confusion surrounding this issue. A standard philosophical strategy in the face of a situation of this kind is to draw various distinctions and in this way show that the confusion rests on divergent conceptions of what the foundations of mathematics ought to be. This is the strategy adopted in the present paper. It is divided into 5 (...) sections. We first show that already in the set theoretical framework, there are different dimensions to the expression foundations of. We then explore these dimensions more thoroughly. After a very short discussion of the links between these dimensions, we move to some of the arguments presented for and against category theory in the foundational landscape. We end up on a more speculative note by examining the relationships between category theory and set theory. (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)

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)

Name der Zeitschrift: Nietzsche-Studien Jahrgang: 46 Heft: 1 Seiten: 235-235.

The text “The Ontology of Knowledge, Logic, Arithmetic, Set Theory, and Geometry” by Jean-Louis Boucon explores a deeply philosophical interpretation of knowledge, its logical structure, and the foundational elements of mathematical and scientific reasoning. -/- Here’s an overview condensed by an AI of the key themes and ideas, summarized into a quite general conceptual structure. These two pages are instructive on their own, but their main purpose is to facilitate the reading of the entire article, allowing the reader to (...) situate in the coherence of the whole both the meaning and the usefulness of each proposed idea. (shrink)

Supra-Bayesianism is the Bayesian response to learning the opinions of others. Probability pooling constitutes an alternative response. One natural question is whether there are cases where probability pooling gives the supra-Bayesian result. This has been called the problem of Bayes-compatibility for pooling functions. It is known that in a common prior setting, under standard assumptions, linear pooling cannot be nontrivially Bayes-compatible. We show by contrast that geometric pooling can be nontrivially Bayes-compatible. Indeed, we show that, under certain assumptions, geometric and (...) Bayes-compatible pooling are equivalent. Granting supra-Bayesianism its usual normative status, one upshot of our study is thus that, in a certain class of epistemic contexts, geometric pooling enjoys a normative advantage over linear pooling as a social learning mechanism. We discuss the philosophical ramifications of this advantage, which we show to be robust to variations in our statement of the Bayes-compatibility problem. (shrink)

In this paper, we try to establish that some mathematical theories, like K-theory, homology, cohomology, homotopy theories, spectral sequences, modern Galois theory (in its various applications), representation theory and character theory, etc., should be thought of as (abstract) machines in the same way that there are (concrete) machines in the natural sciences. If this is correct, then many epistemological and ontological issues in the philosophy of mathematics are seen in a different light. We concentrate on one problem which immediately follows (...) the recognition of the particular status of these theories: the demarcation problem between ‘natural kinds’ and ‘artefacts’. (shrink)

This article explores the use of model organisms in studying the cognitive phenomenon of decision-making. Drawing on the framework of biological control to develop a skeletal conception of decision-making, we show that two core features of decision-making mechanisms can be identified by studying model organisms, such as E. coli, jellyfish, C. elegans, lamprey, and so on. First, decision mechanisms are distributed and heterarchically structured. Second, they depend heavily on chemical information processing, such as that involving neuromodulators. We end by discussing (...) the implications for studying distinctively human decision-making. (shrink)

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)

Both Husserl and Sartre speak of quasi-presence in their descriptions of the lived experience of imagination, and for both philosophers, accounting for quasi-presence means developing an account of the hyle proper to imagination. Guided by the perspective of fulfillment, Husserl’s theory of imaginary quasi-presence goes through three stages. Having experimented first with a depiction-model and then a perception-model, Husserl’s mature theory appeals to his innovative conception of inner consciousness. This elegant account nevertheless fails to do justice to the facticity and (...) bodily involvement of our imaginary experience. Sartre’s theory of analogon, based on his conception of imaginary quasi-presence as ‘magical’ self-affection, embodies important insights on these issues. Kinesthetic sensations and feelings are the modes in which we make use of own body to possess and be possessed by the imaginary object, thus lending it a semblance of bodily presence. (shrink)

This article reconstructs Sartre’s theory of selfhood against the background of the contemporary debate between minimal-self theories and narrative-self theories. I argue that Sartre’s theory incorporates both an emphasis on the singular first-person perspective, which is characteristic of minimal-self theories, and an emphasis on the practical intelligibility of experience, which is characteristic of narrative-self theories. The distinctiveness of the Sartrean combination of these motifs consists in its idea of the necessary ideal-relatedness of consciousness. According to Sartre, the logical structure of (...) the pre-reflective cogito requires the haunting presence of an ideal of self-coincidence, which determines for consciousness the meaning of its lived experiences. Consciousness exists as a question to itself due to this ideal-relatedness, and it answers this question by projecting its possibilities as creative and symbolic realizations of this ideal. Establishing the connection between Sartre’s theory of imagination and his theory of selfhood, I suggest that both the ideal and the possibility of consciousness are lived in the manner of the imaginary. (shrink)

This thesis provides an account of acquaintance with abstract objects. The notion of acquaintance is integral to theorising on reference and singular thought, since it is generally taken to be the relation that must exist between a subject and an object, in order for the subject to refer to, and entertain singular thoughts about the object. The most common way of understanding acquaintance is as a form of causal connection. However, this implies a problem. We seem to be able to (...) refer and have singular thoughts about abstract objects. But given that abstract objects are causally inert, this would mean that we are unable to become acquainted with them. This problem shall be the focus of this thesis. I first argue that these traditional causal interpretations of acquaintance are lacking. Instead, I show that acquaintance is dependent to some degree on factors internal to the subject, namely the skills that they possess. From doctors to sommeliers to mathematicians (and possibly even philosophers!) – these subjects seem to succeed in becoming acquainted with certain objects precisely in virtue of their respective skills. Thus, building off from Evans’ The Varieties of Reference, I present a novel account of acquaintance, which I term as Skill-based Acquaintance (SBA). On SBA, a subject is said to be acquainted with an object when they possess discriminating knowledge of that object, gained through the use of their capacities and skills. The SBA account is applied to virtual (Ch.3), fictional (Ch.4), and mathematical objects (Ch.5), as well as God (Ch.6). SBA is successful in explaining how subjects can indeed become acquainted with these problematic categories of objects - some of which are abstract – thus being able to refer and entertain singular thoughts about them. Overall, then, SBA is shown to have greater explanatory power than competing accounts and should thus be preferred. (shrink)

Knowledge of the subject only ever speaks to the subject himself and of nothing more than the subject himself. And yet, when due to their mode of emergence, objects of this knowledge seem to occupy part of a space (whatever it may be) which would contain them, it is tempting for the subject to give this space the name of Reality. The conventional western philosophies (and science) gave in to this temptation. They came to distinguish the Subject {place-of-the-mind} from the (...) Reality {place-of-the-objects} whereas Reality is only the "objectified" or rather "objectivized" aspect of knowledge of the subject. From this artificial distinction followed a great confusion, a dispute that lasted for centuries, and still does, between different -isms with infinitesimal differences, from which the most influential parties emerge victorious each at his turn. In reaction to this confusion a "pivotal" re-orientation is suggested, considering the way objects of knowledge emerge and are organized, not in correlation with objects of Reality but with the subject for himself and knowledge for itself. For this re-orientation the OK proposes to transcend the subject's mind to reveal its logical principles. That's the specific subject I would like to delve into here : the transcendence of meaning. This is necessary for understanding the OK and could be beneficial to “mental health counseling”. (shrink)

This paper shows that the NMA eluding the knowing subject would be nothing more than a profession of faith. Then it re-introduces the subject with the help of Ontology of Knowledge Using the example of the theory of Relativity it shows the difficulties resulting from the elision of the subject and propose a solution to include the subject into the NMA.