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)

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)

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 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)

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)

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)

Integrity is often conceived as a heroic ideal: the person of integrity sticks to what they believe is right, regardless of the consequences. In this article, I defend a conception of ordinary integrity, for people who either do not desire or are unable to be moral martyrs. Drawing on the writings of seventeenth century thinker Huang Zongxi, I propose refocussing attention away from an abstract ideal of integrity, to instead consider the institutional conditions whereby it is made safe not (...) to be servile. (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)

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)

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)

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.

From Dialectic to Black Hole, The Definition of Time in Plato’s View.

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)

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)

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

The Protein Ontology (PRO) 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)

This paper explicates the influential Confucian view that “people” and not “institutional rules” are the proper sources of good governance and social order, as well as some notable Confucian objections to this position. It takes Xunzi 荀子, Hu Hong 胡宏, and Zhu Xi 朱熹 as the primary representatives of the “virtue-centered” position, which holds that people’s good character and not institutional rules bear primary credit for successful governance. And it takes Huang Zongxi 黃宗羲 as a major advocate for the (...) “institutionalist” position, which holds that institutional rules have some power to effect success independently of improvements in character. Historians have often called attention to this debate but left the major arguments and positions relatively unspecified. As I show, the Confucian virtue-centered view is best captured in two theses: first, that reforming people is far more demanding than reforming institutional rules; second, that once the rules have reached a certain threshold of viability, further improvements in those rules are unlikely to be effective on their own. Once we specify the theses in this way, we can catalogue the different respects and degrees to which the more virtue-centered political thinkers endorse virtue-centrism in governance. Zhu Xi, for example, turns out to endorse a stronger version of virtue-centrism than Hu Hong. I also use this account of the major theses to show that Huang Zongxi, who is sometimes regarded as historical Confucianism’s foremost institutionalist, has more complicated and mixed views about the power of institutional reform than scholars usually assume. (shrink)

Given the hard problem of consciousness (Chalmers, 1995) 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 brain occipital and left temporal electrophysiological correlates of the subjective experience (Pereira, 2015). Notwithstanding, as evoked signal, the change in event-related brain potentials 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 example, by the Wavelet Transform (WT) or the Fast Fourier Transform (FFT) analysis, because they require that frequency is derived by convolution rather than by differentiation. However, as I show in the current original research report, one suitable method for analyse the instantaneous change in event-related brain potentials phase and accounted 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 (Xie et al., 2014) Ensemble Empirical Mode Decomposition (postEEMD) and Hilbert-Huang Transform (HHT). (shrink)

Huang and Bargh’s definition of goals is ambiguous between ‘specific goals’ – the end-state of a token action I am about to perform – and ‘unspecific goals’ – the end-state of an action-type (without specifying how this would be achieved). The analogy with selfish genes pushes the authors towards the former interpretation, but the latter would provide a more robust theoretical framework.

Confucius gave counsel that is notoriously hard to follow: "What you do not wish for yourself, do not impose on others" (Huang 1997: 15.24). People tend to be concerned with themselves and to be indifferent to most others. We are distinct from others so our self-concern does not include them, or so it seems. Were we to realize this distinctness is merely apparent--that our true self includes others--Confucius's counsel would be easier to follow. Concern for our true self would (...) extend concern beyond the narrow selves we appear to be. The neo-Confucians held just such a view. They espoused an identity with the universe and everything in it, arguing that this identity explains a natural concern for everyone and everything, not just for our narrow selves. However, many things in the universe differ from each other, that is, some have qualities others lack. If they are all one and the same thing then that one thing differs from itself. I will suggest that the objection can be answered with some metaphysical innovation. I will address the objection by sketching a theory--call it the theory of aspects--that explains how numerically identical things can differ qualitatively. (shrink)

Addressing concerns about the treatment of psychopaths, Grant Gillett and Flora Huang (2013) argue that we ought to accept a relational or holistic view of psychopathy and APSD rather than the default biomedical-deficit model since the latter “obscures moral truths about the psychopath”. This change in approach to the psychopath will both mitigate at least some of their moral responsibility for the harms they cause, and force communities to incur special obligations, so they claim, because the harms endured by (...) psychopaths will be understood as part of the cause for the harms they are guilty of committing. However, as I will argue, even if we accept that a relational or holistic approach is better suited to understand psychopathy (which is itself contentious), it does not follow that their responsibility is mitigated in a way that causes communities to have special obligations to them as Gillett and Huang suggest. A diagnosis of APSD or psychopathy does not, prima facie, exculpate an agent or suggest a different way of treating them. My discussion will focus on the widely accepted excusing conditions one must meet for responsibility to me mitigated and conclude, contra Gillett and Huang, that psychopaths are no different from you or I with regards to having a causal history that leads to action. Outside forces play a role in all of our behavior. If the psychopath is owed anything because of the way they have come to understand the world then we all are owed that same debt. (shrink)

Rorty, Pragmatism, and Confucianism, a collection of twelve essays on the work of Richard Rorty and its relation to Confucian thought, arose out of a conference in Shanghai in 2004, where participants were granted access to several of Rorty’s unpublished manuscripts. In his introduction, the editor Yong Huang states his desire to outline areas of shared interest in Rortian and Confucian thought. He notes, for example, the similarities between Rorty’s view that sentiment is “central to the moral consciousness” (p. (...) 2) and the early Confucian tradition’s stress on the enhancement and appropriate directing of feeling; in Rorty’s words, a more moral world is best created by telling a “long, sad, sentimental .. (shrink)