We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry (...) ontology that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

contents -/- ONT vol 1 i. short review: Beyond the Black Rainbow ii. as you die, hold one thought iii. short review: LA JETÉE -/- ONT vol 2 i. maya means ii. short review: SANS SOLEIL iii. vocab iv. eros has an underside v. short review: In the Mood for Love -/- ONT vol 3 i. weed weakens / compels me ii. an Ender's Game after-party iii. playroom is a realm of the dead iv. a precise german History v. short (...) review: STATUES ALSO DIE vi. Kenneth Clark, curator for Fascism vii. a protest poem, in industry lit viii. Lawrence and the English Romance -/- ONT vol 4 i. short review: The Eyes of Tammy Faye ii. vR is efficient R iii. all thru Asia, robes for monks iv. same of God, and of the one God sent v. i thought of the Messiah / muse would be vi. conscience is strong vii. a monk's exalted end -/- ONT vol 5 -/- i. for Shakespeare's Richard the Third ii. the truth is i pass over so many words iii. the boori nazar / nadhar iv. i've awe for jihaad v. short review: Hail, Caesar! vi. a minute of Nothing, gone from YouTube vii. we were rivalrous friends, again viii. my bardo pdf ix. within i'm a weak old mandarin -/- ONT vol 6 i. short review: The Intern ii. the confusion of Chinatown iii. we'll remember water, in Theology iv. Respironics versus ResMed v. i'd bet my life for what vi. the Mad Max deity vii. they'd kill my rat, not heal him -/- ONT vol 7 i. Austen would eroticize all life ii. Merchant/Ivory, a name oddly right iii. Ellie Arroway / Agent Starling iv. abattoir / l’abattoir / laboratoire v. von Neumann's brain an anomaly vi. was terrified of death, delighted in the a-bomb vii. the Greatest Brain is variously named -/- ONT vol 8 i. the day they shot the sacrifice ii. Yay or Nay, on Animal Testing iii. an ought is an is / an is is an ought iv. Behaviorism is for zombies v. a finding from the neuro-lab, on empathy vi. i’ve never had discernible abs vii. a cowardice i'm assenting to perpetually -/- ONT vol 9 i. Day of the Locust / Triffids ii. we're wide on a Paramount soundstage iii. HOLLYWOOD, an ecologic history iv. yet one more site of end-time art v. he's "a bookworm with bulging lobes" vi. apartment is my state of being apart vii. enlightenment means a weight's release -/- ONT lates and xtras i. re Gödel's ontological argument ii. deep in pi's numeric noise iii. from Nothing, something iv. endless in the wrong direction, tragic v. they give you all Eternity to answer vi. what of God's mercy? vii. informed consent and prayer viii. i won't live on. a deed i've done may ix. my selective memory x. Janus means: in close-up foam, two faces xi. a liveable world is a readable world xii. what Supervenes from this? xiii. at each extreme our naming is anachronism xiv. Cat is a collapsing of the wave-function xv. diminishing returns in the history of Experiment xvi. all those undershared Nobels xvii. ice preserves the Cold from heat xviii. a desert spreads xix. Pinker's wit, on jokes xx. Rome surrounds St. Paul / Paul is now the center xxi. each is a gathering Ministry xxii. white boy shot execution-style xxiii. the McDonald's Statement of Claim xxiv. first & last: Don Quixote / Ulysses xxv. The Summer of Rave xxvi. this electro is intrinsically anonymous xxvii. all thru Asia, Drake-Rihanna xxviii. WHO IS BETTER: PLATON OR KANT? (shrink)

Daniel Dennett (1996) has disputed David Chalmers' (1995) assertion that there is a "hard problem of consciousness" worth solving in the philosophy of mind. In this paper I defend Chalmers against Dennett on this point: I argue that there is a hard problem of consciousness, that it is distinct in kind from the so-called easy problems, and that it is vital for the sake of honest and productive research in the cognitive sciences to be clear about the difference. But I (...) have my own rebuke for Chalmers on the point of explanation. Chalmers (1995, 1996) proposes to "solve" the hard problem of consciousness by positing qualia as fundamental features of the universe, alongside such ontological basics as mass and space-time. But this is an inadequate solution: to posit, I will urge, is not to explain. To bolster this view, I borrow from an account of explanation by which it must provide "epistemic satisfaction" to be considered successful (Rowlands, 2001; Campbell, 2009), and show that Chalmers' proposal fails on this account. I conclude that research in the science of consciousness cannot move forward without greater conceptual clarity in the field. (shrink)

This paper contributes to the debate in the philosophy of psychiatry regarding the relation between thought insertion in schizophrenia and the sense of selfhood. Some scholars have suggested that thought insertion presents a case where the sense of selfhood is lacking. Other scholars have disputed this by proposing that a form of minimal selfhood is a necessary feature of consciousness that is still present in thought insertion, albeit in a disturbed manner. Herein, I argue that the notion of minimal selfhood (...) that is used by these scholars is ambiguous between two meanings. The first is an ontological notion concerning the first-person individuation of consciousness. The second is a phenomenological notion concerning how a conscious experience is experienced as being given to the first-person subject. I argue that the former ontological notion is indeed a necessary feature of conscious experience, but the latter phenomenological notion is only a contingent feature. Therefore, even if it is possible that thought insertion presents a case where the feeling of first-person givenness is lacking or disturbed, the first-person individuation of consciousness remains present and undisturbed. As well as further clarifying the connection between consciousness and selfhood, this philosophical analysis reveals the extent to which schizophrenia can and cannot be said to comprise a disorder of selfhood. (shrink)

This paper examines the need for static dispositions within the basic ontology of the powers view of properties. To lend some focus, Neil Williams’s well developed case for static dispositions is considered. While his arguments are not necessarily intended to address fundamental ontology, they still provide a useful starting point, a springboard for diving into the deeper metaphysical waters of the dispositionalist approach. Within that ontological context, this paper contends that Williams’s arguments fail to establish the need to (...) posit static dispositions, or at least any sort not already well appreciated by advocates of the powers view. The paper then proceeds to suggest an alternative motivation for positing static dispositions, the success of which depends greatly on which ontological approach to objects is paired with the powers view. (shrink)

We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within (...) a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework. (shrink)

This paper investigates the connection between temporal attitudes (attitudes characterised by a concern (or lack thereof) about future and past events), beliefs about temporal ontology (beliefs about the existence of future and past events) and temporal preferences (preferences regarding where in time events are located). Our aim is to probe the connection between these preferences, attitudes, and beliefs, in order to better evaluate the normative status of these preferences. We investigate the hypothesis that there is a three-way association between (...) (a) being present-biased (that is, preferring that positive events are located in the present, and negative events are located in the non-present), (b) believing that past and future events do not exist and (c) tending to have present-focused rather than non-present-focused temporal attitudes. We find no such association. This suggests that insofar as temporal preferences and temporal attitudes are connected to the ways we represent time, they are not connected to the ways we represent temporal ontology; rather, they are more likely connected to the ways we represent relative movement in, or of, time. This has important consequences for, first, explaining why we exhibit these preferences and, second, for their normative evaluation. (shrink)

In this article, the results of conceptualization of the definition of mind as an object of interdisciplinary applied research are described. The purpose of the theoretical analysis is to generate a methodological discourse suitable for a functional understanding of the mind in the context of the problem of natural language processing as one of the components of developments in the field of artificial intelligence. The conceptual discourse was realized with the help of the author's method of structural-ontological analysis, and developed (...) in the mainstream of the system-methodological tradition of the school of G.P. Shchedrovitsky and intended for descriptive research of subject areas of interdisciplinary objects of scientific study. As a result of the structural and ontological analysis of the super-system, the relevant place and role of the directly studied system (mind) are determined, and its primary process and material are localized and structural and functional connections are described. At the basic level, the mind is conceptualized as an energy process unfolding in a spatio-temporal environment and accompanied by archetypal structuring of neural impulses into images. The genesis of the system is separately analyzed by constructing a structural-ontological matrix that reflects the initial stage of the development of the mind. The primary process is concretized with the help of hetero- and homeostatic dichotomy, and also the most significant features of the consistent transformation of the material of the system and its ascent to verbal morphology are described. The structural-ontological comparison of the functioning of the verbal intelligence with the preverbal level has been carried out. The transformation of neural impulses of needs into words, as verbal units fixing semiotic values is analyzed. Structural-ontological connections that determine the reactive and prospective characteristics of the functioning of the system are disclosed. The position of the chronological primacy of "semiotic readiness" for language with respect to the debut of the latter as an information-sign model of the environment is argued. The hypothesis of domination at the initial stage of the development of the mind of exopsychic functions over endopsychic ones is formulated. The theoretical substantiation of the hypothesis of the inevitability of the ontology of language in the functional understanding of the mind is given, corresponding structural and ontological arguments are given, including those based on the ideas about the information relationship between affects and needs, according to the views of P.V. Simonov. The arguments are presented in favor of the non-alternative methodology of A. Turing in studies of artificial intelligence. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. (...) Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...) the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

In my paper, I establish an Ingardenian phenomenological ontology of "virtualized ficta", i.e., fictional entities introduced to virtual gaming. The first Section of my paper provides an ontology of virtualized ficta, focusing primarily on their ‘‘existential moments’’. But in order to have a firm grasp of the ontological aspects grounding the virtual work, it’s important to engage its strata. This is what I attempt to do in Section 1.2. Virtualized ficta’s intentional dependencies are strongly manifest in what I (...) call the ‘‘strata of the virtual work’’. That is, I repurpose Ingarden’s strata of the literary work, the picture, and the film to showcase that virtualized ficta, from the bottom up (i.e., from their pure ontology to aesthetics) are purely intentional entities. In short, I argue for a purely intentional account of virtualized ficta as ficta-made-virtualia, whose ontological status is determined by the creative acts of game developers and gamers. (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)

John Bell proposed an ontology for the GRW modification of quantum mechanics in terms of flashes occurring at space- time points. This article spells out the motivation for this ontology, inquires into the status of the wave function in it, critically examines the claim of its being Lorentz invariant, and considers whether it is a parsimonious but nevertheless physically adequate ontology.

This article questions the place of negative Forms in Plato’s ontology. And it does so against appearances to the contrary, given that Plato himself seems to acknowledge both positive Forms and negative Forms, that is to say, both good ones and bad ones. He may not say so outright, but he invokes both and rejects neither. The apparent finality of this impression is so strong that it creates a lack of direct interest in the subject: Plato scholars do not (...) give negative Forms much thought except where the prospect relates to something else they happen to be doing. Yet when they do give the matter any thought at all, typically for the sake of a prior concern, they try either to support the textual evidence or to contradict it, indicating that the evidence does not stand on its own. The aim of this article is to determine why they tend to affirm or deny the obvious, how they try to confirm or dispute it, and what this says about Plato’s position. The strategic vehicle is a comparative case study. The confirmation comes from Debra Nails (2013), who needs to embrace negative Forms to demonstrate that the unhypothetical first principle of everything is not identical to the Form of the Good, something she cannot do unless Plato recognizes negative Forms. The contradiction comes from Holger Thesleff (2013), who needs to reject negative (Ideal) Forms because the defining feature of his (Ideal) Forms is the possession of positive intrinsic value, which cannot be predicated of anything negative. Despite defending opposite views, or perhaps because of this, they jointly make up for any lack of interest in the scholarly community. I appreciate both yet side with Thesleff. (shrink)

Nihilism is the thesis that no composite objects exist. Some ontologists have advocated abandoning nihilism in favor of deep nihilism, the thesis that composites do not existO, where to existO is to be in the domain of the most fundamental quantifier. By shifting from an existential to an existentialO thesis, the deep nihilist seems to secure all the benefits of a composite-free ontology without running afoul of ordinary belief in the existence of composites. I argue that, while there are (...) well-known reasons for accepting nihilism, there appears to be no reason at all to accept deep nihilism. In particular, deep nihilism draws no support either from the usual arguments for nihilism or from considerations of parsimony. (shrink)

According to Lowe’s Four-Category Ontology, the general nature of the entities belonging to the four fundamental categories is determined by the basic formal ontological relations (instantiation and characterization) that they bear to other entities. I argue that, in closer analysis, instead of one formal relation of characterization, this category system introduces two, one connecting particulars and another universals. With regard to the characterization relation connecting particulars, it remains an open issue whether it would need further analysis. By contrast, the (...) status of instantiation as an internal relation is comparatively clear. Nevertheless, because of holding by virtue of the essences of particulars, the holding of instantiation between universals and particulars rules out the possibility of kind change and entails that particulars are essentially rigidly dependent on universals. Finally, Lowe’s analysis of necessary exemplification gives us some reasons to suspect that some property universals need not have any instances in order to exist. (shrink)

Performative accounts of personhood argue that group agents are persons, fit to be held responsible within the social sphere. Nonetheless, these accounts want to retain a moral distinction between group and individual persons. That: Group-persons can be responsible for their actions qua persons, but that group-persons might nonetheless not have rights equivalent to those of human persons. I present an argument which makes sense of this disanalogy, without recourse to normative claims or additional ontological commitments. I instead ground rights in (...) the different relations in which performative persons stand in relation to one another. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of (...) the ontology within the ACGT project thus far. (shrink)

Individualists about social ontology hold that social facts are “built out of” facts about individuals. In this paper, I argue that there are two distinct kinds of individualism about social ontology, two different ways individual people might be the metaphysical “builders” of the social world. The familiar kind is ontological individualism. This is the thesis that social facts supervene on, or are exhaustively grounded by, facts about individual people. What I call anchor individualism is the alternative thesis that (...) facts about individuals put in place the conditions for a social entity to exist, or the conditions for something to have a social property. Examples include conventionalist theories of the social world, such as David Hume’s theories of promises, money, and government, and collective acceptance theories, such as John Searle’s theory of institutional facts. Anchor individualism is often conflated with ontological individualism. But in fact, the two theses are in tension with one another: if one of these kinds of individualism is true, then the other is very unlikely to be. My aim in this paper is to clarify both, and argue that they should be sharply distinguished from one another. (shrink)

Scientific realists don’t standardly discriminate between, say, biology and fundamental physics when deciding whether the evidence and explanatory power warrant the inclusion of new entities in our ontology. As such, scientific realists are committed to a lush rainforest of special science kinds (Ross, 2000). Viruses certainly inhabit this rainforest – their explanatory power is overwhelming – but viruses’ properties can be explained from the bottom up: reductive explanations involving amino acids are generally available. However, reduction has often been taken (...) to lead to a metaphysical downgrading, so how can viruses keep their place in the rainforest? In this paper, we show how the inhabitants of the rainforest can be inoculated against the eliminative threat of reduction: by demonstrating that they are emergent. According to our account, emergence involves a screening off condition as well as novelty. We go on to demonstrate that this account of emergence, which is compatible with theoretical reducibility, satisfies common intuitions concerning what should and shouldn’t count as real: viruses are emergent, as are trout and turkeys, but philosophically gerrymandered objects like trout-turkeys do not qualify. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer (...) hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

The ontology of marketing, particularly the question of what products and brands are, is still largely unexplored. The ontological status of brands hinges on their relationship with products. Idealists about brands see perceptual or cognitive acts of consumers grouped under the heading ‘brand awareness’ or ‘brand image’ as constitutive for the existence of brands so that, in their view, tools of the marketing mix can influence relevant mental dispositions and attitudes. Brand realists, on the other hand, reject the view (...) of brands as mere marks or names and interpret them as emergent products with properties that afford branding in the sense of Gibson’s ecological psychology. Brand strength is a function of the degree to which brands occupy defensible niches in product space. Branding as a process involves changing external or internal boundaries of products. Several arguments are proposed in favor of brand realism. The fragments of an ontology of marketing are developed in a broadly Aristotelian framework. Brand realism has significant implications for a new understanding of issues ranging from the effects of advertising to financial brand valuation, the nature of trademarks, and marketing strategy in general. It permits one to treat brand equity as a real phenomenon not dependent on associations, attitudinal states such as brand loyalty, or spurious constructs such as brand character or personality. (shrink)

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better (...) formulated as quasi-Newtonian, via the postulation of forces proportional to acceleration; advocates of the guidance approach defend the notion that the theory is essentially first-order and incorporates some concepts akin to those of Aristotelian physics. Here I analyze whether the desideratum of an interpretation of Bohmian mechanics that is both explanatorily adequate and not committed to configuration space realism favors one of these two approaches to the theory over the other. Contrary to some recent claims in the literature, I argue that the quasi-Newtonian approach based on the idea of a quantum potential does not come out the winner. (shrink)

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is (...) an essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

Part of a book symposium on Anjan Chakravartty's Scientific ontology: integrating naturalized metaphysics and voluntarist epistemology (Oxford University Press, 2017).

This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes.

According to a number of influential views in penal theory, 1 one of the primary goals of the criminal justice system is to rehabilitate offenders. Rehabilitativemeasures are commonly included as a part of a criminal sentence. For example, in some jurisdictions judges may order violent offenders to attend anger management classes or to undergo cognitive behavioural therapy as a part of their sentences. In a limited number of cases, neurointerventions — interventions that exert a direct biological effect on the brain (...) — have been used as aids to rehabilitation, typically being imposed as part of criminal sentences, separate treatment orders, or conditions of parole. Examples of such interventions include medications intended to attenuate addictive desires in substance-abusing offenders and agents intended to suppress libido in sex offenders.This chapter reviews some of the ethical issues raised by the use of neurointerventions as aids to rehabilitation. (shrink)

Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recom- mended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are they representations of (...) such real things in information artifacts? We here outline the problems faced by HL7 in providing answers to such questions, problems which arise because of the lack of anything like a coherent ontology in the HL7 standard, and we make some recommendations for future improvements. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...) But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

Notions such as śūnyatā, catuṣkoṭi, and Indra's net, which figure prominently in Buddhist philosophy, are difficult to readily accommodate within our ordinary thinking about everyday objects. Famous Buddhist scholar Nāgārjuna considered two levels of reality: one called conventional reality, and the other ultimate reality. Within this framework, śūnyatā refers to the claim that at the ultimate level objects are devoid of essence or "intrinsic properties", but are interdependent by virtue of their relations to other objects. Catuṣkoṭi refers to the claim (...) that four truth values, including contradiction, are admissible in reasoning. Indra's net refers to the claim that every part of a whole is reflective of the whole. Here we present category theoretic constructions that are reminiscent of these Buddhist concepts. The universal mapping property definition of mathematical objects, wherein objects of a universe of discourse are defined not in terms of their content, but in terms of their relations to all objects of the universe is reminiscent of śūnyatā. The objective logic of perception, with perception modeled as [a category of] two sequential processes (sensation followed by interpretation), and with its truth value object of four truth values, is reminiscent of the Buddhist logic of catuṣkoṭi. The category of categories, wherein every category has a subcategory of sets with zero structure within which every category can be modeled, is reminiscent of Indra's net. Our thorough elaboration of the parallels between Buddhist philosophy and category theory can facilitate better understanding of Buddhist philosophy, and bring out the broader philosophical import of category theory beyond mathematics. (shrink)

This paper elaborates on relationalism about space and time as motivated by a minimalist ontology of the physical world: there are only matter points that are individuated by the distance relations among them, with these relations changing. We assess two strategies to combine this ontology with physics, using classical mechanics as example: the Humean strategy adopts the standard, non-relationalist physical theories as they stand and interprets their formal apparatus as the means of bookkeeping of the change of the (...) distance relations instead of committing us to additional elements of the ontology. The alternative theory strategy seeks to combine the relationalist ontology with a relationalist physical theory that reproduces the predictions of the standard theory in the domain where these are empirically tested. We show that, as things stand, this strategy cannot be accomplished without compromising a minimalist relationalist ontology. (shrink)

Do we suddenly become justified in treating robots like humans by positing new notions like “artificial moral agency” and “artificial moral responsibility”? I answer no. Or, to be more precise, I argue that such notions may become philosophically acceptable only after crucial metaphysical issues have been addressed. My main claim, in sum, is that “artificial moral responsibility” betokens moral responsibility to the same degree that a “fake orgasm” betokens an orgasm.

After some suggestions about how to clarify the confused metaphysical distinctions between dispositional and non-dispositional or categorical properties, I review some of the main interpretations of QM in order to show that – with the relevant exception of Bohm’s minimalist interpretation – quantum ontology is irreducibly dispositional. Such an irreducible character of dispositions must be explained differently in different interpretations, but the reducibility of the contextual properties in the case of Bohmian mechanics is guaranteed by the fact that the (...) positions of particles play the role of the categorical basis, a role that in other interpretations cannot be filled by anything else. In Bohr’s and Everett-type interpretations, dispositionalism is instrumentalism in disguise. (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)

Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? This question is, we believe, central to the entire domain of social ontology. We argue that the recorded game is a special sort of quasi-abstract pattern, something that is: (i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at (...) the same time, (ii) through its association with specific players and a specific occasion, tied to time and history. We discover other abstract patterns of this sort especially in the domains of law and commerce. This essay draws on the work in social ontology, we of Hernando de Soto and of John Searle to develop an ontology of the social world based on an analysis of the peculiar interdependence between quasi-abstract patterns and their representations in documents of different sorts. (shrink)

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...) geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (shrink)

Intellectual history still quite commonly distinguishes between the episode we know as the Scientific Revolution, and its successor era, the Enlightenment, in terms of the calculatory and quantifying zeal of the former—the age of mechanics—and the rather scientifically lackadaisical mood of the latter, more concerned with freedom, public space and aesthetics. It is possible to challenge this distinction in a variety of ways, but the approach I examine here, in which the focus on an emerging scientific field or cluster of (...) disciplines—the ‘life sciences’, particularly natural history, medicine, and physiology —is, not Romantically anti-scientific, but resolutely anti-mathematical. Diderot bluntly states, in his Thoughts on the interpretation of nature, that “We are on the verge of a great revolution in the sciences. Given the taste people seem to have for morals, belles-lettres, the history of nature and experimental physics, I dare say that before a hundred years, there will not be more than three great geometricians remaining in Europe. The science will stop short where the Bernoullis, the Eulers, the Maupertuis, the Clairauts, the Fontaines and the D’Alemberts will have left it.... We will not go beyond.” Similarly, Buffon in the first discourse of his Histoire naturelle speaks of the “over-reliance on mathematical sciences,” given that mathematical truths are merely “definitional” and “demonstrative,” and thereby “abstract, intellectual and arbitrary.” Earlier in the Thoughts, Diderot judges “the thing of the mathematician” to have “as little existence in nature as that of the gambler.” Significantly, this attitude—taken by great scientists who also translated Newton or wrote careful papers on probability theory, as well as by others such as Mandeville—participates in the effort to conceptualize what we might call a new ontology for the emerging life sciences, very different from both the ‘iatromechanism’ and the ‘animism’ of earlier generations, which either failed to account for specifically living, goal-directed features of organisms, or accounted for them in supernaturalistic terms by appealing to an ‘anima’ as explanatory principle. Anti-mathematicism here is then a key component of a naturalistic, open-ended project to give a successful reductionist model of explanation in ‘natural history’, a model which is no more vitalist than it is materialist—but which is fairly far removed from early modern mechanism. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

In the Netherlands and Belgium, it is lawful for voluntary euthanasia to be offered on the grounds of psychiatric suffering. A recent case that has sparked much debate is that of Aurelia Brouwers, who was helped to die in the Netherlands on account of her suffering from borderline personality disorder. It is sometimes claimed that whether or not a mentally ill person’s wish to die is valid hinges on whether or not that wish is a symptom of the person’s mental (...) disorder. This article addresses the philosophical problems raised by this claim, with a specific focus on the diagnosis of borderline personality disorder. After considering descriptivist and causal conceptualizations of mental disorder, I argue that the current approach to borderline personality disorder in psychiatry precludes the possibility of dissociating the wish to die from the disorder. I then examine the implications of this analysis for the question of whether or not the request for voluntary euthanasia in the case of borderline personality disorder can be considered valid. Ultimately, I conclude that the inability to dissociate the wish to die from the disorder does not invalidate the wish in the case of borderline personality disorder. (shrink)

The hard problem of consciousness arises in most incarnations of present day physicalism. Why should certain physical processes necessarily be accompanied by experience? One possible response is that physicalism itself should be modified in order to accommodate experience: But, modified how? In the present work, we investigate whether an ontology derived from quantum field theory can help resolve the hard problem. We begin with the assumption that experience cannot exist without being accompanied by a subject of experience (SoE). While (...) people well versed in Indian philosophy will not find that statement problematic, it is still controversial in the analytic tradition. Luckily for us, Strawson has elaborately defended the notion of a thin subject—an SoE which exhibits a phenomenal unity with different types of content (sensations, thoughts etc.) occurring during its temporal existence. Next, following Stoljar, we invoke our ignorance of the true physical as the reason for the explanatory gap between present day physical processes (events, properties) and experience. We are therefore permitted to conceive of thin subjects as related to the physical via a new, yet to be elaborated relation. While this is difficult to conceive under most varieties of classical physics, we argue that this may not be the case under certain quantum field theory ontologies. We suggest that the relation binding an SoE to the physical is akin to the relation between a particle and (quantum) field. In quantum field theory, a particle is conceived as a coherent excitation of a field. Under the right set of circumstances, a particle coalesces out of a field and dissipates. We suggest that an SoE can be conceived as akin to a particle—a SelfOn—which coalesces out of physical fields, persists for a brief period of time and then dissipates in a manner similar to the phenomenology of a thin subject. Experiences are physical properties of selfons with the constraint (specified by a similarity metric) that selfons belonging to the same natural kind will have similar experiences. While it is odd at first glance to conceive of subjects of experience as akin to particles, the spatial and temporal unity exhibited by particles as opposed to fields and the expectation that selfons are new kinds of particles, paves the way for cementing this notion. Next, we detail the various no-go theorems in most versions of quantum field theory and discuss their impact on the existence of selfons. Finally, we argue that the time is ripe for a rejuvenated Indian philosophy to begin tackling the three-way relationship between SoEs (which may become equivalent to jivas in certain Indian frameworks), phenomenal content and the physical world. With analytic philosophy still struggling to come to terms with the complex worlds of quantum field theory and with the relative inexperience of the western world in arguing the jiva-world relation, there is a clear and present opportunity for Indian philosophy to make a worldcentric contribution to the hard problem of experience. (shrink)

This paper puts Searle’s social ontology together with an understanding of the human person as inclined openly toward the truth. Institutions and their deontology are constituted by collective Declarative beliefs, guaranteeing mind-world adequation. As this paper argues, often they are constituted also by collective Assertive beliefs that justify (rather than validate intrainstitutionally) institutional facts. A special type of Status Function-creating ‘Assertive Declarative’ belief is introduced, described, and used to shore up Searle’s account against two objections: that, as based on (...) collective acceptance, Searlean social ontology cannot make sense of dissenters, and that it, as its deontology is all game-like, implies a legal positivism and thus cannot make proper sense of the moral import of sociopolitical institutions. This change is necessary to deepen social ontology’s understanding of human societies and to accurately describe many social, religious, and political institutions as constituted from the perspectives of participants and dissidents. (shrink)

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been (...) little effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. We describe our efforts towards developing an Emotion Ontology (EMO) to serve the affective science community. We here focus on conformity to the BFO upper ontology and disambiguation of polysemous terminology. (shrink)