Abstract According to Russellianism, the content of a Russellian thought, in which a person ascribes a monadic property to an object, can be represented as an ordered couple of the object and the property. A consequence of this is that it is not possible for a person to believe that a is F and not to believe b is F, when a=b. Many critics of Russellianism suppose that this is possible and thus that Russellianism is false. Several arguments for this (...) claim are criticized and it is argued that Russellians need not appeal to representational notions in order to defeat them. Contrary to popular opinion, the prospects for a pure Russellianism, a Russellianism without representations, are in fact very good. (shrink)

Moritz Schlick, Rudolf Carnap and Herbert Feig are the most prominent of the positivists to formulate views on the mind-body problem (aside from Hempel’s one-off treatment in 1935). While their views differed from each other and changed over time they were all committed to some form of scientific physicalism, though a linguistic or conceptual rather than ontological form of it. In focus here are their views during the heyday of logical positivism and its immediate aftermath, though some initial scene-setting of (...) Schlick’s and Carnap’s pre-positivist views will help to understand the final opposing positions of Carnap and Feigl. (shrink)

This paper seeks to answer the question: Can contemporary forms of artificial intelligence be creative? To answer this question, I consider three conditions that are commonly taken to be necessary for creativity. These are novelty, value, and agency. I argue that while contemporary AI models may have a claim to novelty and value, they cannot satisfy the kind of agency condition required for creativity. From this discussion, a new condition for creativity emerges. Creativity requires curiosity, a motivation to pursue epistemic (...) goods. I argue that contemporary AI models do not satisfy this new condition. Because they lack both agency and curiosity, it is a mistake to attribute the same sort of creativity to AI that we prize in humans. Finally, I consider the question of whether these AI models stand to make human creativity in the arts and sciences obsolete, despite not being creative themselves. I argue, optimistically, that this is unlikely. (shrink)

In this paper I articulate a view of doxastic control that helps defend the legitimacy of our practice of blaming people for their beliefs. I distinguish between three types of doxastic control: intention-based, reason-based, and influence-based. First I argue that, although we lack direct intention-based control over our beliefs, such control is not necessary for legitimate doxastic blame. Second, I suggest that we distinguish two types of reason-responsiveness: sensitivity to reasons and appreciation of reasons. I argue that while both capacities (...) are necessary for satisfying the control condition, neither is sufficient. Finally, I defend an influence-based view of doxastic control according to which we have the capacity to execute intentions to engage in reflection that causally influences our beliefs in positive epistemic ways. This capacity is both necessary and sufficient for satisfying the control condition for legitimate doxastic blame. I end by defending the view from two objections: that reflection is not necessary for meeting the control condition, and that it is not sufficient. (shrink)

In this paper, I solve a puzzle generated by three conflicting claims about the relationship between faith, belief, and control: according to the Identity Thesis, faith is a type of belief, and according to Fideistic Voluntarism, we sometimes have control over whether or not we have faith, but according to Doxastic Involuntarism, we never have control over what we believe. To solve the puzzle, I argue that the Identity Thesis is true, but that either Fideistic Voluntarism or Doxastic Voluntarism is (...) false, depending on how we understand "control." I distinguish two notions of control: direct intention-based control and indirect reflective control. I argue that though we have direct intention-based control over neither belief nor faith, we have indirect reflective control over each of them. Moreover, indirect reflective control helps explain how we can be held accountable for each. (shrink)

In this chapter, we explore whether agents have an epistemic duty to eradicate implicit bias. Recent research shows that implicit biases are widespread and they have a wide variety of epistemic effects on our doxastic attitudes. First, we offer some examples and features of implicit biases. Second, we clarify what it means to have an epistemic duty, and discuss the kind of epistemic duties we might have regarding implicit bias. Third, we argue that we have an epistemic duty to eradicate (...) implicit biases that have negative epistemic impact. Finally, we defend this view against the objection that we lack the relevant control over implicit bias that’s required for such a duty. We argue that we have a kind of reflective control over the implicit biases that we are duty-bound to eradicate. And since, as we show, we have this control over a wide variety of implicit biases, there are a lot of implicit biases that we have epistemic duties to eradicate. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Eleonore Stump insightfully develops Aquinas’s theodicy to account for a significant source of human suffering, namely the undermining of desires of the heart. Stump argues that what justifies God in allowing such suffering are benefits made available to the sufferer through her suffering that can defeat the suffering by contributing to the fulfillment of her heart’s desires. We summarize Stump’s arguments for why such suffering requires defeat and how it is defeated. We identify three problems with Stump’s account of how (...) such suffering is defeated and offer solutions to each. We defend and strengthen Stump’s response to the hardest cases for her view, and explain what her view demands of God. (shrink)

One of the most compelling questions still unanswered in neuroscience is how consciousness arises. In this article, we examine visual processing, the parietal lobe, and contralateral neglect syndrome as a window into consciousness and how the brain functions as the mind and we introduce a mechanism for the processing of visual information and its role in consciousness. We propose that consciousness arises from integration of information from throughout the body and brain by the thalamus and that the thalamus reimages visual (...) and other sensory information from throughout the cortex in a default three-dimensional space in the mind. We further suggest that the thalamus generates a dynamic default three-dimensional space by integrating processed information from corticothalamic feedback loops, creating an infrastructure that may form the basis of our consciousness. Further experimental evidence is needed to examine and support this hypothesis, the role of the thalamus, and to further elucidate the mechanism of consciousness. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

Numerous studies of the beliefs of people with anorexia nervosa (AN) suggest that a subset of such individuals may experience delusions. We first describe what makes a belief delusional and conclude that such characteristics can be appropriately applied to some beliefs of people with AN. Next, we outline how delusional beliefs may relate to the broader psychopathological process in AN, including: (1) they may be epiphenomenal; (2) they may be an initial partial cause of AN; (3) they may be caused (...) by aspects of AN; or (4) they may be sustaining causes, possibly involved in reciprocal causal relations with aspects of AN. We argue that there is good reason to believe that delusional beliefs of people with AN are not merely epiphenomenal, but rather that they’re causally connected to AN. Because of this, empirical studies can be designed to test for the presence of causal relations. We describe how these studies should be designed. The results of such studies have important implications for understanding the experience of individuals with AN and for the treatment of AN. We outline these implications. (shrink)

Understanding the autonomic nervous system and homeostatic changes associated with emotions remains a major challenge for neuroscientists and a fundamental prerequisite to treat anxiety, stress, and emotional disorders. Based on recent publications, the inter-relationship between respiration and emotions and the influence of respiration on autonomic changes, and subsequent widespread membrane potential changes resulting from changes in homeostasis are discussed. We hypothesize that reversing homeostatic alterations with meditation and breathing techniques rather than targeting neurotransmitters with medication may be a superior method (...) to address the whole body changes that occur in stress, anxiety, and depression. Detrimental effects of stress, negative emotions, and sympathetic dominance of the autonomic nervous system have been shown to be counteracted by different forms of meditation, relaxation, and breathing techniques. We propose that these breathing techniques could be used as firstline and supplemental treatments for stress, anxiety, depression, and some emotional disorders. (shrink)

In a recent study, we found a negative association between psychopathy and violence against genetic relatives. We interpreted this result as a form of nepotism and argued that it failed to support the hypothesis that psychopathy is a mental disorder, suggesting instead that it supports the hypothesis that psychopathy is an evolved life history strategy. This interpretation and subsequent arguments have been challenged in a number of ways. Here, we identify several misunderstandings regarding the harmful dysfunction definition of mental disorder (...) as it applies to psychopathy and regarding the meaning of nepotism. Furthermore, we examine the evidence provided by our critics that psychopathy is associated with other disorders, and we offer a comment on their alternative model of psychopathy. We conclude that there remains little evidence that psychopathy is the product of dysfunctional mechanisms. (shrink)

According to Russellianism (or Millianism), the two sentences ‘Ralph believes George Eliot is a novelist’ and ‘Ralph believes Mary Ann Evans is a novelist’ cannot diverge in truth-value, since they express the same proposition. The problem for the Russellian (or Millian) is that a puzzle of Kaplan’s seems to show that they can diverge in truth-value and that therefore, since the Russellian holds that they express the same proposition, the Russellian view is contradictory. I argue that the standard Russellian appeal (...) to “ways of thinking” or “propositional guises” is not necessary to solve the puzzle. Rather than this retrograde concession to Fregeanism, appeal should be made to second-order belief. The puzzle is solved, and the contradiction avoided, by maintaining that both sentences are indeed true in addition to the sentence ‘Ralph (mistakenly) believes that he does not believe Mary Ann Evans/George Eliot is a novelist’. (shrink)

The identity theory’s rise to prominence in analytic philosophy of mind during the late 1950s and early 1960s is widely seen as a watershed in the development of physicalism, in the sense that whereas logical behaviourism proposed analytic and a priori ascertainable identities between the meanings of mental and physical-behavioural concepts, the identity theory proposed synthetic and a posteriori knowable identities between mental and physical properties. While this watershed does exist, the standard account of it is misleading, as it is (...) founded in erroneous intensional misreadings of the logical positivists’—especially Carnap’s—extensional notions of translation and meaning, as well as misinterpretations of the positivists’ shift from the strong thesis of translation-physicalism to the weaker and more liberal notion of reduction-physicalism that occurred in the Unity of Science programme. After setting the historical record straight, the essay traces the first truly modern identity theory to Schlick’s pre-positivist views circa 1920 and goes on to explore its further development in Feigl, arguing that the fundamental difference between the Schlick-Feigl identity theory and the more familiar and influential Place-Smart-Armstrong identity theory has resurfaced in the deep and seemingly unbridgeable gulf in contemporary philosophy of consciousness between inflationary mentalism and deflationary physicalism. (shrink)

The human eyes and brain, which have finite boundaries, create a ‘‘virtual’’ space within our central nervous system that interprets and perceives a space that appears boundless and infinite. Using insights from studies on the visual system, we propose a novel fast processing mechanism involving the eyes, visual pathways, and cortex where external vision is imperceptibly processed in our brain in real time creating an internal representation of external space that appears as an external view. We introduce the existence of (...) a three-dimension default space consisting of intrapersonal body space that serves as the framework where visual and non-visual sensory information is sensed and experienced. We propose that the thalamus integrates processed information from corticothalamic feedback loops and fills-in the neural component of 3D default space with an internal visual representation of external space, leading to the experience of visual consciousness. This visual space inherently evades perception so we have introduced three easy clinical tests that can assist in experiencing this visual space. We also review visual neuroanatomical pathways, binocular vision, neurological disorders, and visual phenomenon to elucidate how the representation of external visible space is recreated within the mind. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

Propositionalism is the view that intentional attitudes, such as belief, are relations to propositions. Propositionalists argue that propositionalism follows from the intuitive validity of certain kinds of inferences involving attitude reports. Jubien (2001) argues powerfully against propositions and sketches some interesting positive proposals, based on Russell’s multiple relation theory of judgment, about how to accommodate “propositional phenomena” without appeal to propositions. This paper argues that none of Jubien’s proposals succeeds in accommodating an important range of propositional phenomena, such as the (...) aforementioned validity of attitude-report inferences. It then shows that the notion of a predication act-type, which remains importantly Russellian in spirit, is sufficient to explain the range of propositional phenomena in question, in particular the validity of attitude-report inferences. The paper concludes with a discussion of whether predication act-types are really just propositions by another name. (shrink)

Respiration influences various pacemakers and rhythms of the body during inspiration and expiration but the underlying mechanisms are relatively unknown. Understanding this phenomenon is important, as breathing disorders, breath holding, and hyperventilation can lead to significant medical conditions. We discuss the physiological modulation of heart rhythm, blood pressure, sympathetic nerve activity, EEG, and other changes observed during inspiration and expiration. We also correlate the intracellular mitochondrial respiratory metabolic processes with real-time breathing and correlate membrane potential changes with inspiration and expiration. (...) We propose that widespread minor hyperpolarization occurs during inspiration and widespread minor depolarization occurs during expiration. This depolarization is likely a source of respiratory drive. Further knowledge of intracellular and extracellular ionic changes associated with respiration will enhance our understanding of respiration and its role as a modulator of cellular membrane potential. This could expand treatment options for a wide range of health conditions, such as breathing disorders, stress-related disorders, and further our understanding of the Hering–Breuer reflex and respiratory sinus arrhythmia. (shrink)

Quine introduced a famous distinction between the ‘notional’ sense and the ‘relational’ sense of certain attitude verbs. The distinction is both intuitive and sound but is often conflated with another distinction Quine draws between ‘dyadic’ and ‘triadic’ (or higher degree) attitudes. I argue that this conflation is largely responsible for the mistaken view that Quine’s account of attitudes is undermined by the problem of the ‘exportation’ of singular terms within attitude contexts. Quine’s system is also supposed to suffer from the (...) problem of ‘suspended judgement with continued belief’. I argue that this criticism fails to take account of a crucial presupposition of Quine’s about the connection between thought and language. The aim of the paper is to defend the spirit of Quine’s account of attitudes by offering solutions to these two problems. (shrink)

In this article, we examine phantom limb syndrome to gain insights into how the brain functions as the mind and how consciousness arises. We further explore our previously proposed consciousness model in which consciousness and body schema arise when information from throughout the body is processed by corticothalamic feedback loops and integrated by the thalamus. The parietal lobe spatially maps visual and non-visual information and the thalamus integrates and recreates this processed sensory information within a three-dimensional space termed the ‘‘3D (...) default space.’’ We propose that phantom limb syndrome and phantom limb pain arise when the afferent signaling from the amputated limb is lost but the neural circuits remain intact. In addition, integration of conflicting sensory information within the default 3D space and the loss of inhibitory afferent feedback to efferent motor activity from the amputated limb may underlie phantom limb pain. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

The existence of object-dependent thoughts has been doubted on the grounds that reference to such thoughts is unnecessary or 'redundant' in the psychological explanation of intentional action. This paper argues to the contrary that reference to object-dependent thoughts is necessary to the proper psychological explanation of intentional action upon objects. Section I sets out the argument for the alleged explanatory redundancy of object-dependent thoughts; an argument which turns on the coherence of an alternative 'dual-component' model of explanation. Section II rebuts (...) this argument by showing the dual-component model to be incoherent precisely because of its exclusion of object-dependent thoughts. Section III concludes with a conjecture about the further possible significance of object-dependent thoughts for the prediction of action. (shrink)

The received view in the history of the philosophy of psychology is that the logical positivists—Carnap and Hempel in particular—endorsed the position commonly known as “logical” or “analytical” behaviourism, according to which the relations between psychological statements and the physical-behavioural statements intended to give their meaning are analytic and knowable a priori. This chapter argues that this is sheer legend: most, if not all, such relations were viewed by the logical positivists as synthetic and knowable only a posteriori. It then (...) traces the origins of the legend to the logical positivists’ idiosyncratic extensional or at best weakly intensional use of what are now considered crucially strongly intensional semantic notions, such as “translation,” “meaning” and their cognates, focussing on a particular instance of this latter phenomenon, arguing that a conflation of explicit definition and analyticity may be the chief source of the legend. (shrink)

The brain is considered to be the primary generator and regulator of emotions; however, afferent signals originating throughout the body are detected by the autonomic nervous system (ANS) and brainstem, and, in turn, can modulate emotional processes. During stress and negative emotional states, levels of cardiorespiratory coherence (CRC) decrease, and a shift occurs toward sympathetic dominance. In contrast, CRC levels increase during more positive emotional states, and a shift occurs toward parasympathetic dominance. Te dynamic changes in CRC that accompany different (...) emotions can provide insights into how the activity of the limbic system and afferent feedback manifest as emotions. The authors propose that the brainstem and CRC are involved in important feedback mechanisms that modulate emotions and higher cortical areas. That mechanism may be one of many mechanisms that underlie the physiological and neurological changes that are experienced during pranayama and meditation and may support the use of those techniques to treat various mood disorders and reduce stress. (shrink)

The paper presents a new theory of perceptual demonstrative thought, the property-dependent theory. It argues that the theory is superior to both the object-dependent theory (Evans, McDowell) and the object-independent theory (Burge).

In Making it Explicit Robert Brandom claims that perspectivally hybrid de re attitude ascriptions explain what an agent actually did, from the point of view of the ascriber, whether or not that was what the agent intended to do. There is a well-known problem, however, first brought to attention by Quine, but curiously ignored by Brandom, that threatens to undermine the role of de re ascriptions in the explanation of action, a problem that stems directly from the fact that, unlike (...) de dicto ascriptions, they permit the attribution of inconsistent attitudes to agents. I propose a solution to the problem which I believe is consistent with Brandom’s approach to the nature of intentionality and the explanation of action. (shrink)

This paper argues for an account of the relation between thought ascription and the explanation of action according to which de re ascriptions and de dicto ascriptions of thought each form the basis for two different kinds of action explanations, nonrationalizing and rationalizing ones. The claim that de dicto ascriptions explain action is familiar and virtually beyond dispute; the claim that that de re ascriptions are explanatory of action, however, is not at all familiar and indeed has mostly been denied (...) by philosophers. I explain how de re ascriptions enter into non-rationalizing explanations of action and how attention to their distinctive explanatory nature reveals flaws in an alternative “dual-component” view about action explanation. (shrink)

The theory of object-dependent singular thought is outlined and the central motivation for it, turning on the connection between thought content and truth conditions, is discussed. Some of its consequences for the epistemology of thought are noted and connections are drawn to the general doctrine of externalism about thought content. Some of the main criticisms of the object-dependent view of singular thought are outlined. Rival conceptions of singular thought are also sketched and their problems noted.

The theory of object-dependent singular thought is outlined and the central motivation for it, turning on the connection between thought content and truth conditions, is discussed. Some of its consequences for the epistemology of thought are noted and connections are drawn to the general doctrine of externalism about thought content. Some of the main criticisms of the object-dependent view of singular thought are outlined. Rival conceptions of singular thought are also sketched and their problems noted.

A number of traditional roles that propositions are supposed to play are outlined. Philosophical theories of the nature of propositions are then surveyed, together with considerations for and against, with an eye on the question whether any single notion of a proposition is suited to play all or any of these roles. Approaches discussed include: (1) the structureless possible-worlds theory; (2) the structured Russellian theory; and (3) the structured Fregean theory. It is noted that it is often unclear whether these (...) are accounts of what propositions are, ontologically speaking, or whether they are accounts of how propositions are best represented in a formal semantic theory. (shrink)

This paper argues that Twin Earth twins belong to the same psychological natural kind, but that the reason for this is not that the causal powers of mental states supervene on local neural structure. Fodor’s argument for this latter thesis is criticized and found to rest on a confusion between it and the claim that Putnamian and Burgean type relational psychological properties do not affect the causal powers of the mental states that have them. While it is true that Putnamian (...) and Burgean type relational psychological properties do not affect causal powers, it is false that no relational psychological properties do. Examples of relational psychological properties that do affect causal powers are given and psychological laws are sketched that subsume twins in virtue of them instantiating these relational properties rather than them sharing the narrow contents of their thoughts. (shrink)

This article is about a very important metaphysical concept, macrocosm/microcosm and its appearance in Doric thought which in turn influenced Socrates and Plato. But since this concept has been gainsaid and negated in recent articles and distorted by some ancient thinkers it will be necessary to conduct reconstructive surgery to restore it to its pristine condition. Hopefully, this paper will illustrate how metaphysics is done with the use of the Mind's eye, in the reading of reality that was part and (...) parcel of the Greek mind but also in understanding the ancient Greeks themselves and their culture especially in the creation of the classical republican form of government. This account will discuss what macrocosm/microcosm is, its part in the Cosmos and hence its centrality in the Natural Law and in philosophy (wisdom). Second, it will prove the concept thru another natural law principle, righteousness. Third, point out it's provenance in Doric thought. In a corollary, it points to what the impact macrocosm/microcosm has on the true meaning "to be a lover of wisdom" and its importance in the concept of theosis. More than a research/academic article, this paper is also an exposition in which it will attempt to demonstrate the use and the mechanics of this principle by using a saying of Homer and the tripartite paradigm of the family. (shrink)

v. 1. Foundations -- v. 2. The mind-body problem -- v. 3. Intentionality -- v. 4. Consciousness.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

Stress profoundly impacts quality of life and may lead to various diseases and conditions. Understanding the underlying physiological and neurological processes that take place during stress and meditation techniques may be critical for effectively treating stress-related diseases. The article examines a hypothetical physiological homeostatic response that compares and contrasts changes in central and peripheral oscillations during stress and meditation, and relates these to changes in the autonomic system and neurological activity. The authors discuss how cardiorespiratory synchronization, which occurs during the (...) parasympathetic response and meditation, influences and modulates activity and oscillations of the brain and autonomic nervous system. Evidence is presented on how synchronization of cardiac and respiratory rates during meditation may lead to a homeostatic increase in cellular membrane potentials in neurons and other cells throughout the body. These potential membrane changes may underlie the reduced activity in the amygdala, and other cortical areas during meditation, and research examining these changes may foster better understanding of the restorative properties and health benefits of meditation. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

This is a review of Uriah Kriegal's book on intentionality, The Sources of Intentionality.

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

How do concert pianists commit to memory the structure of a piece of music like Bach’s Italian Concerto, learning it well enough to remember it in the highly charged setting of a crowded performance venue, yet remaining open to the freshness of expression of the moment? Playing to this audience, in this state, now, requires openness to specificity, to interpretation, a working dynamicism that mere rote learning will not provide. Chaffin, Imreh and Crawford’s innovative and detailed research suggests that (...) the key to this skill is a declarative mental roadmap aiding musical performance. This hypothesis is neatly and unintentionally summarized by professional pianist Imreh, who states when learning a new piece of music “My fingers were playing the notes just fine. The practice I needed was in my head. I had to learn to keep track of where I was. It was a matter of learning exactly what I needed to be thinking of as I played, and at exactly what point. (shrink)

Kate Crawford presents AI as “both reflecting and producing social relations and understandings of the world”; or again, as “a form of exercising power, and a way of seeing… as a manifestation of highly organized capital backed by vast systems of extraction and logistics, with supply chains that wrap around the entire planet”. I interpret these material insights through a Marxist understanding of ideology, with reference to Marx/Engels, Guy Debord and Louis Althusser. In the German Ideology, Marx and Engels (...) present ideology as the alienated and alienating discourse of exchange, dissimulating the material forces of production and its science. Guy Debord presents the spectacle as the further representation of capital. The spectacle is a total Weltanschauung, pure appearance, where “whatever appears is good and where what is good, appears.” Above all, the spectacle is ideology, representing “the impoverishment, enslavement and negation of real life”. Louis Althusser presents ideology as essential for the reproduction of labor-power and capital. His notion of “interpellation” explains the subjective uptake of ideology, how we respond, “yes!” to its call. The algorithms of AI are enactments of surplus value generating capital as data. The AI data-world is the spectacle, “the autonomous movement of non-life” (Debord) where the proletariat/consumer is the producer of their own ideological subjection. Is resistance possible? What form might it take? And if AI is understood as ideology, i.e. as a language that obscures the true conditions of real life, then what are those true conditions? What is “real life”? (shrink)

In Frege’s Puzzle (1986), Salmon analyzed ‘a withholds believing p’ in terms of a ternary relation BEL of x believing a proposition p under a guise g. The proposed analysis is the following: There is a proposition guise g such that a grasps p by means of g but a does not stand in BEL to p and g. Sean Crawford has made a proposal for Millians to evade propositional guises through second-order belief. Specifically, in effect, Crawford’s proposes (...) to analyze the crucial notion of withheld belief instead as believing that one does not believe: a believes that a does not believe p. Crawford’s clever proposal thus avoids explicit quantification over guises. However, it is shown that the proposal is inadequate to avoid guises. The resulting notion is too weak to capture the relevant notion of withheld belief. (shrink)