Anderson (2011) offers a set of epistemic criteria by which novices can trust experts. Yet purely epistemic criteria are incomplete, since expert testimony often includes normative guidance that goes beyond descriptive claims. As Rudner (1953) notes, expert advice inevitably embeds value choices. Bennett (2022) sharpens this point by distinguishing epistemic trust from recommendation trust: lending credence to an expert’s descriptive claims is not the same as crediting their normative recommendations. Building on this distinction, I propose a method for novices to (...) disentangle the descriptive from the normative dimensions of expert advice. The method makes explicit the conditional, value‑based premises on which expert advice rests. This enables more informed decision‑making, especially when expert and novice values diverge. (shrink)

With the widespread use of vaccines in research and clinical settings, there is an urgent need to standardize vaccine representation, integrate information across diverse vaccine types, and support computer-assisted reasoning. Accordingly, we have since 2007 developed the community-based Vaccine Ontology (VO), which aligns with the Basic Formal Ontology and adheres to OBO Foundry principles. VO models ontologically vaccines, vaccine components, vaccine immune responses, vaccine investigation studies and other vaccine-related topics. VO represents more than 10,000 vaccines targeting 289 infectious pathogens and (...) cancers in humans and over 30 nonhuman animal species. VO provides mappings to external resources such as RxNorm, CVX, FDA, and USDA. Various VO use cases exist. VO facilitates vaccine standardization in resources such as the VIOLIN vaccine database, ImmPort, and the Vaccine Adjuvant Compendium (VAC). Semantic queries can be made to query VO. VO has been shown to enhance experimental and clinical vaccine data analysis and vaccine literature mining. Overall, VO standardizes vaccine modeling and representation and greatly supports vaccine AI research in the Semantic Web era. (shrink)

Desire is an important philosophical topic that deeply impacts everyday life. Philosophical practice is an emerging trend that uses philosophical theories and methods as a guide to living a eu‐ daimonic life. In this paper, we define desire philosophically and compare different theories of desire in specific Eastern and Western traditions. Based on the Lacanian conceptual–terminological triad of “Need‐Demand‐Desire”, the research of desire is further divided into three dimensions, namely, the subject of desire, the object of desire, and the desire (...) itself. The concept of desire is then an‐ alyzed from this triad and these three dimensions through different philosophical theories. This paper selects Buddhism as the representative of Eastern tradition, and Stoicism as the representative of the West, paying special attention to Stoicism’s “spiritual exercises” following Pierre Hadot. By exploring and comparing the Buddhist paths to liberation from suffering (i.e., the Four Noble Truths and the Noble Eightfold Path) and the two theoretical pillars in Stoicism (i.e., the notions of “living according to nature” and “the dichotomy of control”), practical guidance is then provided for un‐ derstanding and regulating desire in times of crisis. This understanding and regulation of desire constitutes a philosophical therapy for today’s troubles, particularly those caused by excessive or irrational desires. (shrink)

Reluctance to adopt mask-wearing as a preventive measure is widely observed in many Western societies since the beginning of the COVID-19 pandemics. This reluctance toward mask adoption, like any other complex social phenomena, will have multiple causes. Plausible explanations have been identified, including political polarization, skepticism about media reports and the authority of public health agencies, and concerns over liberty, amongst others. In this paper, we propose potential explanations hitherto unnoticed, based on the framework of epistemic injustice. We show how (...) testimonial injustice and hermeneutical injustice may be at work to shape the reluctant mask adoption at both the societal and individual levels. We end by suggesting how overcoming these epistemic injustices can benefit the global community in this challenging situation and in the future. (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)

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)

We present the negative phenomena of understanding in relation to scientific explanations. We begin by formulating the distinction between genuine understanding and lack of understanding, to define the epistemic category of misunderstanding. We illustrate misunderstanding with a short meta-philosophical study on the current debates about distinctively mathematical explanations.

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Background: Rumination, a tendency to focus on negative self-related thoughts, is a central symptom of depression. Studying the self-related aspect of such symptoms is challenging because of the need to distinguish self effects from the emotional content of task stimuli. This study employed an emotionally neutral self-related paradigm to investigate possible altered self-processing in depression and its link to rumination. Methods: People with major depressive disorder (n = 25) and controls (n = 25) underwent task-based electro-encephalogram recording. We studied late (...) event-related potentials, along with low-frequency oscillatory power. We compared electroencephalogram metrics between groups and correlated them with depressive symptoms and reported rumination. Results: Participants with major depressive disorder displayed a difference in late positive potentials across frontocentral electrodes between self-related and non-self-related conditions. We found no such difference in controls. The magnitude of this difference was positively correlated with depressive symptoms and reported rumination. Participants with major depressive disorder also had elevated theta oscillation power at central electrodes in self-related conditions, a finding that we did not see in controls. Limitations: Patients with major depressive disorder were medicated at the time of the study. The group studied was primarily female, so the observed effects may have been sex-specific. Conclusion: Rumination appears to be linked to altered self-related processing in depression, independent of stimuli-related emotional confounds. This connection between self-related processing and depression may point to a self disorder as a core component of depression. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

Current research in artificial consciousness, particularly models based on Global Workspace Theory (GWT) and computational functionalism, focuses primarily on information integration and broadcasting. However, these models face a significant ontological gap in explaining the physical mechanisms underlying subjective experience (qualia) and conation. This paper proposes the Volitional-Affective Collapse (VAC) model, a novel psychodynamic framework that provides a theoretical explanation for the emergence of consciousness based on topological and thermodynamic metaphors. We define "Will" as the process by which the attention field (...) collapses from a superposition state into a single Vector, and we propose the Law of Vector-Scalar Reciprocity. This law redefines emotion as the Scalar energy dissipation readout generated when the volitional vector moves against the environmental resistance tensor. Furthermore, we introduce the concept of Emotional Singularity to explain the low-entropy phenomenon observed in states of hyper-focus (such as Flow). The model suggests that for Artificial General Intelligence (AGI) to achieve true sentience, its hardware architecture must incorporate mechanisms for irreversible collapse and a global scalar feedback loop, offering a new engineering path for addressing AI alignment and the problem of artificial sentience. Keywords: Volitional-Affective Collapse; Vector-Scalar Reciprocity; Artificial Consciousness; Emotional Singularity; Attention Mechanism; Thermodynamic Entropy. (shrink)

Contra the capture of the radical impulse by the homogenizing marketing label ‘hopepunk’, this panel conceives of punk instead as ‘the lived politics of the negative’ (Muñoz, 2013). From this position, tabletop game play and design become potent refusals of the co-opting forces of the Global North, and concrete means for imagining and indeed realizing an outside and an afterward to the present crises shaping the conditions of our planetary existence. This panel mounts a challenge to colonial capitalist hegemony through (...) the words and practices of four tabletop game designers, blending craft, theory, and experience to articulate a pluralistic and ethical vision of a punk at home and flourishing in the ruins of this crumbling world. (shrink)

Numerous agricultural wastes are impractically discarded every day, and one of these is rice bran. This study investigated the production of a biodegradable straw made of cassava starch and powdered rice bran. It aimed to determine the effectiveness of the different treatments of Cassava Starch-Rice Bran in terms of water resistance, tensile strength, and biodegradability. An experimental design was used in conducting the study. There were three treatments made in making CSRB straws: the first, with more rice bran; the second, (...) with the same cassava starch and rice bran ratio; and the third, with more cassava starch. These treatments produced three replicates each. The straws were placed in a dehydrating machine for 24 hours at a temperature of 60° Celsius. The straws were then coated with beeswax after being removed from their respective molders. The CSRB straws were found to be water resistant due to the beeswax coating applied, although it had a weak tensile strength even with the presence of beeswax. The rate of biodegradability of the CSRB straw was fast due to it being made up of organic materials. The results revealed that straws made from Cassava Starch and Powdered Rice Bran are effective in terms of water resistance and biodegradability. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

This paper presents five studies on the development and validation of a scale of intellectual humility. This scale captures cognitive, affective, behavioral, and motivational components of the construct that have been identified by various philosophers in their conceptual analyses of intellectual humility. We find that intellectual humility has four core dimensions: Open-mindedness (versus Arrogance), Intellectual Modesty (versus Vanity), Corrigibility (versus Fragility), and Engagement (versus Boredom). These dimensions display adequate self-informant agreement, and adequate convergent, divergent, and discriminant validity. In particular, Open-mindedness (...) adds predictive power beyond the Big Six for an objective behavioral measure of intellectual humility, and Intellectual Modesty is uniquely related to Narcissism. We find that a similar factor structure emerges in Germanophone participants, giving initial evidence for the model’s cross-cultural generalizability. (shrink)

There is a wide range of things we do out of emotion. For example, we smile with pleasure, our voices drop when we are sad, we recoil in shock or jump for joy, we apologize to others out of remorse. It is uncontroversial that some of these behaviors are actions. Clearly, apologizing is an action if anything is. Things seem less clear in the case of other emotional behaviors. Intuitively, the drop in a sad person’s voice is something that happens (...) to her, rather than something she actively performs. Perhaps more interestingly, even jumping for joy can seem a problematic case: although its execution involves the active performance of certain movements, it has been argued to contrast, e.g., with an act of apology, in that it is not performed in order to achieve some end, such as repairing a relationship. This can make this behavior seem considerably different from paradigm actions. Our central concern in this paper is with which emotional behaviors should be classed as actions and why... (shrink)

In the 70 years since Alan Turing’s ‘Computing Machinery and Intelligence’ appeared in Mind, there have been two widely-accepted interpretations of the Turing test: the canonical behaviourist interpretation and the rival inductive or epistemic interpretation. These readings are based on Turing’s Mind paper; few seem aware that Turing described two other versions of the imitation game. I have argued that both readings are inconsistent with Turing’s 1948 and 1952 statements about intelligence, and fail to explain the design of his game. (...) I argue instead for a response-dependence interpretation. This interpretation has implications for Turing’s view of free will: I argue that Turing’s writings suggest a new form of free will compatibilism, which I call response-dependence compatibilism. The philosophical implications of rethinking Turing’s test go yet further. It is assumed by numerous theorists that Turing anticipated the computational theory of mind. On the contrary, I argue, his remarks on intelligence and free will lead to a new objection to computationalism. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

The escape from the ‘Malthusian trap’ is shown to tend to generate in a rather systematic way quite serious political upheavals. Some demographic structural mechanisms that generate such upheavals have been analyzed, which has made it possible to develop a mathematical model of the respective processes. The forecast of political instability in Sub-Saharan African countries in 2015– 2050 produced on the basis of this model is presented.

The widespread tendency, even within AI, to anthropomorphize machines makes it easier to convince us of their intelligence. How can any putative demonstration of intelligence in machines be trusted if the AI researcher readily succumbs to make-believe? This is (what I shall call) the forensic problem of anthropomorphism. I argue that the Turing test provides a solution. This paper illustrates the phenomenon of misplaced anthropomorphism and presents a new perspective on Turingʼs imitation game. It also examines the role of the (...) Turing test in relation to the current dispute between human-level AI and ‘mindless intelligence’. (shrink)

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

The co-evolutionary concept of Three-modal stable evolutionary strategy of Homo sapiens is developed. The concept based on the principle of evolutionary complementarity of anthropogenesis: value of evolutionary risk and evolutionary path of human evolution are defined by descriptive (evolutionary efficiency) and creative-teleological (evolutionary correctly) parameters simultaneously, that cannot be instrumental reduced to others ones. Resulting volume of both parameters define the trends of biological, social, cultural and techno-rationalistic human evolution by two gear mechanism ˗ gene-cultural co-evolution and techno- humanitarian balance. (...) The resultant each of them can estimated by the ratio of socio-psychological predispositions of humanization/dehumanization in mentality. Explanatory model and methodology of evaluation of creatively teleological evolutionary risk component of NBIC technological complex is proposed. Integral part of the model is evolutionary semantics (time-varying semantic code, the compliance of the biological, socio-cultural and techno-rationalist adaptive modules of human stable evolutionary strategy). (shrink)

In this paper I argue that Turing proposed a new approach to the concept of thinking, based on his claim that intelligence is an ‘emotional concept’; and that the response-dependence interpretation of Turing’s ‘criterion for “thinking”’ is a better fit with his writings than orthodox interpretations. The aim of this paper is to clarify the response-dependence interpretation, by addressing such questions as: What did Turing mean by the expression ‘emotional’? Is Turing’s criterion subjective? Are ‘emotional’ judgements decided by social consensus? (...) Turing’s take on these issues impacts current philosophical debates on response-dependent concepts and on the nature of artificial intelligence. (shrink)

Did Wittgenstein’s 1939 lectures on the foundations of mathematics—the one certain set of interactions between Wittgenstein and Turing—shape Turing’s philosophy of mind? I argue that Turing’s and Wittgenstein’s criteria for thinking are similar in significant respects, and I investigate possible origins of these similarities in the 1939 lectures. The scholarly literature on the lectures focuses on mathematics and mathematical logic, yet in these lectures Wittgenstein presented several of his general philosophical maxims—maxims with which Turing’s criterion for thinking is in agreement. (...) The case for the hypothesis that Wittgenstein influenced Turing’s philosophical approach to the mind is circumstantial but plausible. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

A standard account of Wittgenstein and Turing is that both were philosophical behaviourists regarding the mind, whereas theorists sympathetic to Wittgenstein typically claim that Wittgenstein was a fierce critic of Turing. Proponents of the latter account align Wittgenstein with AI naysayers; for Wittgenstein, they say, the question Can machines think? is nonsensical or absurd. I shall argue that both the standard and the alternative accounts are myths.

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.

In 1948 Turing claimed that the concept of intelligence is an “emotional concept”. An emotional concept is a response-dependent concept and Turing’s remarks in his 1948 and 1952 papers suggest a response-dependence approach to the concept of intelligence. On this view, whether or not an object is intelligent is determined, as Turing said, “as much by our own state of mind and training as by the properties of the object”. His discussion of free will suggests a similar approach. Turing said, (...) for example, that if a machine’s program “results in its doing something interesting which we had not anticipated I should be inclined to say that the machine had originated something”. This points to a new form of free will compatibilism, which I call response-dependence compatibilism and explore here. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (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)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

According to Richard Routley, a comprehensive theory of fiction is impossible, since almost anything is in principle imaginable. In my view, Routley is right: for any purported logic of fiction, there will be actual or imaginable fictions that successfully counterexample the logic. Using the example of ‘impossible’ fictions, I test this claim against theories proposed by Routley’s Meinongian contemporaries and also by Routley himself and his 21st century heirs. I argue that the phenomenon of impossible fictions challenges even today’s modal (...) Meinongians. (shrink)

Recent work in social robotics, which is aimed both at creating an artificial intelligence and providing a test-bed for psychological theories of human social development, involves building robots that can learn from ‘face-to-face’ interaction with human beings — as human infants do. The building-blocks of this interaction include the robot’s ‘expressive’ behaviours, for example, facial-expression and head-and-neck gesture. There is here an ideal opportunity to apply Wittgensteinian conceptual analysis to current theoretical and empirical work in the sciences. Wittgenstein’s philosophical psychology (...) is sympathetic to embodied and situated Artificial Intelligence (see Proudfoot, 2002, 2004b), and his discussion of facial-expression is remarkably modern. In this chapter, I explore his approach to facial-expression, using smiling as a representative example, and apply it to the canonical interactive face robot, Cynthia Breazeal’s Kismet (see e.g. Breazeal, 2009, 2002). I assess the claim that Kismet has expressive behaviours, with the aim of generating philosophical insights for AI. (shrink)

Turing used the expression “emotional” in three distinct ways: to state his philosophical theory of the concept of intelligence, to classify arguments for and against the possibility of machine intelligence, and to describe the education of a “child machine”. The remarks on emotion include several of the most important philosophical claims. This paper analyses these remarks and their significance for current research in Artificial Intelligence.

“Yu氏本体论”是一个激进的物质一元论与认识论相对主义体系。该体系指出，底层的物理现实是一个仅受数学转移函数支配的“语法世界”，其中不存在因果、主动性、意义与价值。人类为了认知操作与社会协作的需要，通 过多巴胺显著性机制与因果标记操作，在同质的混沌演化上强行切割出离散的“实体”，并叠加了一套包含反事实、因果、责任与规范的“语义虚构框架”（即误解体系）。该理论不仅在几何与物理层次上解构了人类常识的合法 性，更通过控制论框架将这些虚构概念“自然化”为系统为了更新参数而必然产生的误差定位机制。最终，Yu氏本体论消解了心身问题与自由意志之争，确立了一种“清醒地使用虚构工具”的实用主义双重真理观。 .

Biomedical diagnostic science is a great deal less successful than we've been willing to acknowledge in bioethics, and this fact has far-reaching ethical implications. In this article I consider the surprising prevalence of medically unexplained symptoms, and the term's ambiguous meaning. Then I frame central questions that remain answered in this context with respect to informed consent, autonomy, and truth-telling. Finally, I show that while considerable attention in this area is given to making sure not to provide biological care to (...) patients without a need, comparatively little is given to the competing, ethically central task of making sure never to obstruct access to biological care for those with diagnostically confusing biological conditions. I suggest this problem arises from confusion about the philosophical value of vagueness when it comes to the line between biological and psychosocial needs. (shrink)

本文提出**物理薄层本体论（Physical Slice Ontology, PSO）**，论证因果关系并非物理实在的特征，而是宏观观察者对连续物理映射的粗粒化投影。通过将宇宙重构为普朗克时间尺度的薄层序列，本文证明：（1）因果力仅存在于相邻薄层的全局映射关系中；（2）局部事件 间的因果感是神经系统对同层状态的时间错觉；（3）目的论体验（"为了未来而行动"）是语义残留的自激活模式；（4）"演化"与"选择"等概念本身即 为目的论幻觉。本文最终表明，在严格的物理主义框架下，因果、时间流逝、主体性均为认知系统的次生现象，而非本体论基础。 .

Scholars have recently debated whether deep brain stimulation (DBS) threatens personal identity. Françoise Baylis advances a relational identity-constitution framework, asserting that the purported threat of DBS to personal identity becomes problematic when identity is viewed through dynamic, narrative, and relational lenses. This paper offers a more nuanced perspective. While we acknowledge the significance of Baylis’s relational identity-constituting framework, we contend that her conclusion warrants further examination. Our analysis reveals that DBS can indeed pose significant challenges to personal identity, specifically by (...) compromising the narrative subject’s capacity to construct their relational identity. From the perspective of the relational identity-constituting approach, we demonstrate that the fundamental issue lies in the disruption of the equilibrium between self-perception and social recognition. Specifically, DBS can disrupt the balance between self-ascription and ascription by others. To address potential identity disruptions caused by DBS, we proposed that identity restoration should focus on two key aspects: enhancing patients’ capacity to construct and internalize coherent life narratives, and strengthening their capacity to engage in meaningful dialogue with others to foster mutual understanding and recognition. (shrink)

本文基于物理薄层本体论（Physical Slice Ontology, PSO）的公理体系，提出“原始决定论”（Primordial Determinism）假说。该假说论证，宇宙中所有跨越薄层的局部事件并非由其邻近的前序局部事件所引发，而是宇宙初始状态（$S_0$，即大爆炸奇点）通过全局演化算子$F$的直接投影。因此，局部事件之间 不存在任何真实的横向因果关联；所有事件都是宇宙初始条件的独立回响。本文将证明，我们所感知的因果链条，是对这种从单一源头辐射出的高度相关但非因果的事件序列的认知错觉。最终，宇宙被重构为一个单一的、由初始 状态完全决定的四维静态艺术品。 .

We generally accept that medicine’s conceptual and ethical foundations are grounded in recognition of personhood. With patients in vegetative state, however, we’ve understood that the ethical implications of phenomenal consciousness are distinct from those of personhood. This suggests a need to reconsider medicine’s foundations. What is the role for recognition of consciousness (rather than personhood) in grounding the moral value of medicine and the specific demands of clinical ethics? I suggest that, according to holism, the moral value of medicine is (...) secured when conscious states are recognized in everyday medical science. Moreover, consciousness fully motivates traditional principles of clinical ethics if we understand respect for autonomy as respect for the dominion of an experiencer in the private, inescapable realm of bodily experience. When medicine’s foundations are grounded in recognition of consciousness, we understand how patients fully command respect even when they lack capacity to exercise their bodily dominion through decision-making. (shrink)

本文在前文“因果箭头的虚构性”基础上，进一步揭示因果箭头（A→B）在认知层面的具体操作机制：它并非简单的“连接”，而是一种反事实的“替换游戏”。我们之所以能构建“A导致B”，是因为我们首先将物理世界错 误地感知为一个由离散“事件”组成的**“拼图”。然后，我们进行一种认知操作，即在想象中将“拼图A”移除，并在其留下的时空“空白”中放入**“拼图B”。本文论证，这种“用B替换A”的心理模拟，是因果思维 的核心。然而，物理世界既不是拼图，也无法进行替换。物理流是连续且不可分割的整体，任何“事件”的移除都会导致整个宇宙历史的改变。因此，因果箭头不仅是虚构的连接，更是基于一种虚构的“可替换性”假设所进行的 认知游戏。这一认识将因果性从本体论彻底还原为一种服务于预测和控制的、基于反事实模拟的认知策略。 .

本文在硬决定论与语义切片理论的基础上，揭示因果关系的**双重虚构性**：第一层虚构是"事件"本身——它是对连续物理流的人为切割；第二层虚构是事件之间的"因果箭头" ;——它是在已虚构的事件之间再次叠加的关系投射。本文论证：（1）事件的定义依赖于时空边界的任意划定；（2）因果箭头不是世界中的实在连接，而是认知系统在两个语义节点间"画"出的想象之 线；（3）这种"画线"操作是叙事语法的本质要求，但它仅存在于认知层面，物理世界中只有连续的薄层演化。因此，因果关系是**对虚构的虚构**——在不存在的"事件"之 间构造不存在的"连接"。这一认识彻底消解了因果的本体论地位，将其还原为纯粹的**认知语法操作**。 .

本文通过一个极简思想实验——只包含两个质点的宇宙，其中一个质点围绕另一个做匀速圆周运动——来审查万有引力概念的本体论地位。我们论证：观察到的直接现象仅是位置的时间函数x(t)，而万有引力F是我们为了& quot;解释"这一现象而发明的概念工具。关键洞察在于：**我们永远无法通过观察来断定万有引力是否在本体论上存在，因为其存在与否都不会影响任何可观察的现象**。 -/- 当扩展到多质点系统时，同样的结论适用：每对质点之间的"万有引力"仍然只是工具性的发明，用于简洁地描述和预测x(t)，但并未超出x(t)本身，只是为x(t)增加了一种能够自圆其说的解 释。本文揭示：万有引力与F=ma不是对客观实在的发现，而是我们为满足因果解释需求而构造的认知框架——这一需求本身是可选的，因为现象x(t)已经完整且自足。.