In this new edition, a hypothesis is put forward for the first time to unify the Big Bang theory and the evolutionary theory by showing both events following the same set of fundamental interrelationships. As the evolution of life is a part of the evolutions of the universe, these two events express many fundamental similarities (this is self-similarity, which means a part of the system is similar to the whole system). Based on the same principle, the evolution of multicellular organisms, (...) social evolution, development of the human body, and human technological development are all a part of the evolution of life. Thus, they all follow the same set of rules that all life follows and, at the fundamental level, the interrelationships that the Big Bang follows. Therefore, all of these events follow the fundamental interrelationships and express fundamental similarities. In other words, all these events are the specific expressions of those fundamental interrelationships – the fundamental mechanism that governs everything in the universe. -/- Upon these interrelationships, new approaches to study social development and technological development are employed. By using the knowledge of the medical sciences, including the structures (anatomy and histology), functions (physiology) and development (embryology) of a human body; knowledge of the evolution of life; and the concept of fundamental interrelationships, we can see the future beyond the horizon. Using the nerve system in parallel as a model, we can comprehensively understand the development of the information revolution. Based upon parallel interrelationships, we can see that the transformation of society due to individuals’ power increase brought by new technologies bears great similarities with the transformation from the solid state of ice to the liquid state of water due the individual molecules’ kinetic energy increase. -/- As the fundamental interrelationships govern social evolution, all events in human civilisation are simply specific expressions of those rules in which significant social events not only changed the course of civilisation but left so many unanswered mysteries: how did the Greeks build such brilliant civilisations; why did the Scientific Revolution originate from the West rather than the East such as in China; why did the Chinese society remain in feudalism for such a long time while the Western society had evolved into a higher level – industrialization and modern society; why did the Chinese civilisation fall from its ancient glory in the modern time but rapidly re-rise again to a super power in the last few decades? All these mysteries remain unanswered because of the lack of fundamental laws of physics and evolutionary biology used in the traditional methodologies of social science. As the fundamental laws of physics are the fundamental mechanism for everything and these mysteries are a part of the evolution of life, the fundamental laws of physics and evolutionary biology are used in tackling these unanswered issues. For example, upon parallel relationship, Chinese civilisation is compared with the transition from unicellular organisms to multicellular organisms. From how unicellular organisms aggregate and evolve new rules to organise themselves, we can much better understand how human individuals aggregate to form societies and evolve new cultures to organise themselves in social evolution. Furthermore, transformation from the solid state of ice to the liquid state of water is used to analyze Chinese social evolution. With these approaches the mysteries in Chinese civilisation have been answered. -/- Ultimately, all these discussions in this book have demonstrated that the Interrelationships Model has unified social science with natural science, and furthermore, science with philosophy. This is an important attempt in answering the most fundamental and intriguing question of all – the Theory of Everything. -/- Currently, this book is for FREE download. (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)

1. Biomedical sciences are fast-growing fields with unprecedented speed of research outputs, especially in the quantities of papers. Philosophers aiming to study ongoing biomedical changes face cha...

R Core Team. (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing. Supplement to Occipital and left temporal instantaneous amplitude and frequency oscillations correlated with access and phenomenal consciousness. Occipital and left temporal instantaneous amplitude and frequency oscillations correlated with access and phenomenal consciousness move from the features of the ERP characterized in Occipital and Left Temporal EEG Correlates of Phenomenal Consciousness (Pereira, 2015) towards the instantaneous amplitude and frequency of event-related changes correlated with a (...) contrast in access and in phenomenology. Occipital and left temporal instantaneous amplitude and frequency oscillations correlated with access and phenomenal consciousness proceed as following. In the first section, empirical mode decomposition (EMD) with post processing (Xie, G., Guo, Y., Tong, S., and Ma, L., 2014. Calculate excess mortality during heatwaves using Hilbert-Huang transform algorithm. BMC medical research methodology, 14, 35) Ensemble Empirical Mode Decomposition (postEEMD) and Hilbert-Huang Transform (HHT). -/- In the second section, calculated the variance inflation factor (VIF). In the third section, partial least squares regression (PLSR): the minimal root mean squared error of prediction (RMSEP). In the last section, partial least squares regression (PLSR): significance multivariate correlation (sMC) statistic. (shrink)

Given the hard problem of consciousness, there are no brain electrophysiological correlates of the subjective experience (the felt quality of redness or the redness of red, the experience of dark and light, the quality of depth in a visual field, the sound of a clarinet, the smell of mothball, bodily sensations from pains to orgasms, mental images that are conjured up internally, the felt quality of emotion, the experience of a stream of conscious thought, or the phenomenology of thought). However, (...) there are occipital and left temporal brain electrophysiological correlates of the subjective experience. Notwithstanding, as an evoked signal, the change in event-related brain potential phase (frequency is the change in phase over time) is instantaneous, that is, the frequency will transiently be infinite: a transient peak in frequency (positive or negative), if any, is instantaneous in electroencephalogram averaging or filtering that the event-related brain potentials required and the underlying structure of the event-related brain potentials in the frequency domain cannot be accounted for, for example, by the Wavelet Transform or the Fast Fourier Transform analysis, because they require that frequency be derived by convolution rather than by differentiation. However, as I show, one suitable method for analysing the instantaneous change in event-related brain potential phase and accounting for a transient peak in frequency (positive or negative), if any, in the underlying structure of the event-related brain potentials is the Empirical Mode Decomposition with post-processing Ensemble Empirical Mode Decomposition. (shrink)

The present first part about the eventual completeness of mathematics (called “Hilbert mathematics”) is concentrated on the Gödel incompleteness (1931) statement: if it is an axiom rather than a theorem inferable from the axioms of (Peano) arithmetic, (ZFC) set theory, and propositional logic, this would pioneer the pathway to Hilbert mathematics. One of the main arguments that it is an axiom consists in the direct contradiction of the axiom of induction in arithmetic and the axiom of infinity in (...) set theory. Thus, the pair of arithmetic and set are to be similar to Euclidean and non-Euclidean geometries distinguishably only by the Fifth postulate now, i.e. after replacing it and its negation correspondingly by the axiom of finiteness (induction) versus that of finiteness being idempotent negations to each other. Indeed, the axiom of choice, as far as it is equivalent to the well-ordering “theorem”, transforms any set in a well-ordering either necessarily finite according to the axiom of induction or also optionally infinite according to the axiom of infinity. So, the Gödel incompleteness statement relies on the logical contradiction of the axiom of induction and the axiom of infinity in the final analysis. Nonetheless, both can be considered as two idempotent versions of the same axiom (analogically to the Fifth postulate) and then unified after logicism and its inherent intensionality since the opposition of finiteness and infinity can be only extensional (i.e., relevant to the elements of any set rather than to the set by itself or its characteristic property being a proposition). So, the pathway for interpreting the Gödel incompleteness statement as an axiom and the originating from that assumption for “Hilbert mathematics” accepting its negation is pioneered. A much wider context relevant to realizing the Gödel incompleteness statement as a metamathematical axiom is consistently built step by step. The horizon of Hilbert mathematics is the proper subject in the third part of the paper, and a reinterpretation of Gödel’s papers (1930; 1931) as an apology of logicism as the only consistent foundations of mathematics is the topic of the next second part. (shrink)

The two greatest mathematicians of the early twentieth century, David Hilbert and Henri Poincaré transformed the mathematics of their time. Their personal interaction was infrequent, until Hilbert invited Poincaré to deliver the first Wolfskehl Lectures in Göttingen in the spring of 1909. A correspondence ensued, which fixed the content and timing of the lecture series. A close reading of the exchange throws light on what Hilbert wanted Poincaré to talk about, and on what Poincaré wanted to present (...) to Hilbert and his colleagues. To answer the latter question, reference is made to the published version of Poincaré’s six talks, with a focus on two of them, concerning the propagation of Hertzian waves, and the theory of relativity. (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)

A survey of color science and color vision.

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)

Arthur Clark and Michael Kube–McDowell (“The Triger”, 2000) suggested the sci-fi idea about the direct transformation from a chemical substance to another by the action of a newly physical, “Trigger” field. Karl Brohier, a Nobel Prize winner, who is a dramatic persona in the novel, elaborates a new theory, re-reading and re-writing Pauling’s “The Nature of the Chemical Bond”; according to Brohier: “Information organizes and differentiates energy. It regularizes and stabilizes matter. Information propagates through matter-energy and mediates the interactions of (...) matter-energy.” Dr Horton, his collaborator in the novel replies: “If the universe consists of energy and information, then the Trigger somehow alters the information envelope of certain substances –“. “Alters it, scrambles it, overwhelms it, destabilizes it” Brohier adds. There is a scientific debate whether or how far chemistry is fundamentally reducible to quantum mechanics. Nevertheless, the fact that many essential chemical properties and reactions are at least partly representable in terms of quantum mechanics is doubtless. For the quantum mechanics itself has been reformulated as a theory of a special kind of information, quantum information, chemistry might be in turn interpreted in the same terms. Wave function, the fundamental concept of quantum mechanics, can be equivalently defined as a series of qubits, eventually infinite. A qubit, being defined as the normed superposition of the two orthogonal subspaces of the complex Hilbert space, can be interpreted as a generalization of the standard bit of information as to infinite sets or series. All “forces” in the Standard model, which are furthermore essential for chemical transformations, are groups [U(1),SU(2),SU(3)] of the transformations of the complex Hilbert space and thus, of series of qubits. One can suggest that any chemical substances and changes are fundamentally representable as quantum information and its transformations. If entanglement is interpreted as a physical field, though any group above seems to be unattachable to it, it might be identified as the “Triger field”. It might cause a direct transformation of any chemical substance by from a remote distance. Is this possible in principle? (shrink)

A survey of arguments for and against the view that colors are physical properties.

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)

Synthetic biology (SynBio) covers two main areas: application engineering, exemplified by metabolic engi- neering, and the design of life from artificial building blocks. As the general public is often reluctant to embrace synthetic approaches, preferring nature to artifice, its immediate future will depend very much on the public’s reaction to the unmet needs created by the pervasive demands of sustainability. On the other hand, this reluctance should not have a negative impact on research that will now take into account the (...) existence of the multiple transitions that cells face over time. The ages of life—birth, development, maturation, senescence and death—reflect specific key transitions and have, until now, rarely been taken into account in SynBio designs. This results in a mismatch between novelty and the very long evolutionary time that led to the existing chassis [remember that this is the common term used to describe the cellular framework as seen by synthetic biologists (de Lorenzo & Danchin, 2008)]. It also implies that, in general, transitions between growth stages will be taken into account with the appro- priate embodiment of highly specific processes. This is particularly important when adapting new models to their host, whether natural or artificial. Adaptation fol- lows two stages, short-term accommodation of new entities and long-term assimilation into the cell as a whole. This requires discrimination between classes of entities. We suggest that proteins playing the essential role of Maxwell’ demons, here named Maxwell’s dis- criminators (MxDs) to refer to their original function, will permit the assimilation and accommodation of artificial constructs. As a consequence, we can foresee that class discrimination, beyond mere recognition, will be implemented in SynBio 2.0, leading to an authentic par- adigm shift (Kuhn, 1996), based on conceptions that embody information as a genuine currency of reality. (shrink)

Color-vision defects constitute a spectrum of disorders with varying degrees and types of departure from normal human color vision. One form of color-vision defect is dichromacy; by mixing together only two lights, the dichromat can match any light, unlike normal trichromatic humans, who need to mix three. In a philosophical context, our titular question may be taken in two ways. First, it can be taken at face value as a question about visible properties of external objects, and second, it may (...) be interpreted as the more intangible question of “what it’s like” to be color-blind. (shrink)

The human faculty of moral judgment is not well suited to address problems, like climate change, that are global in scope and remote in time. Advocates of ‘moral bioenhancement’ have proposed that we should investigate the use of medical technologies to make human beings more trusting and altruistic, and hence more willing to cooperate in efforts to mitigate the impacts of climate change. We survey recent accounts of the proximate and ultimate causes of human cooperation in order to assess the (...) prospects for bioenhancement. We identify a number of issues that are likely to be significant obstacles to effective bioenhancement, as well as areas for future research. (shrink)

Abstract: For the last two decades, land and land-related problems are more complicated ever before. Especially the proliferation of large-scale rural land investments and the vulnerability of the local communities in land abundant developing countries instigated researchers, human right activists, and international and regional organizations to proposed governance guidelines, principles, and codes of conduct for large-scale land investments. To identify policy flaws on the protection of local community rights under the governance process of large-scale rural land investment in Amhara National (...) Regional State Ethiopia the commonalities of those international and regional accepted governance guiding lines and principles are taken as a point of reference to examine the land governance policies of the region through the approach of document analysis. The result shows all legislation with regard to the governance of large-scale rural land investment is flawed throughout the land policy reform processes and identified five ways in which the de jure land-related rights of the local communities are compromised and exacerbated the vulnerability of their livelihoods. (shrink)

This paper critically examines color relationalism and color relativism, two theories of color that are allegedly supported by variation in normal human color vision. We mostly discuss color relationalism, defended at length in Jonathan Cohen's The Red and the Real, and argue that the theory has insuperable problems.

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)

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)

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)

Social scientists have paid insufficient attention to the role of law in constituting the economic institutions of capitalism. Part of this neglect emanates from inadequate conceptions of the nature of law itself. Spontaneous conceptions of law and property rights that downplay the role of the state are criticized here, because they typically assume relatively small numbers of agents and underplay the complexity and uncertainty in developed capitalist systems. In developed capitalist economies, law is sustained through interaction between private agents, courts (...) and the legislative apparatus. Law is also a key institution for overcoming contracting uncertainties. It is furthermore a part of the power structure of society, and a major means by which power is exercised. This argument is illustrated by considering institutions such as property and the firm. Complex systems of law have played a crucial role in capitalist development and are also vital for developing economies. (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)

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)

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)

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)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (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)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

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)

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)

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)

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)

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

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)

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)

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.

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 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)

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)

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

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

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

Name der Zeitschrift: Nietzsche-Studien Jahrgang: 44 Heft: 1 Seiten: 494-497.