Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

The lack of gender parity in philosophy has garnered serious attention recently. Previous empirical work that aims to quantify what has come to be called “the gender gap” in philosophy focuses mainly on the absence of women in philosophy faculty and graduate programs. Our study looks at gender representation in philosophy among undergraduate students, undergraduate majors, graduate students, and faculty. Our findings are consistent with what other studies have found about women faculty in philosophy, but we were able to add (...) two pieces of new information. First, the biggest drop in the proportion of women in philosophy occurs between students enrolled in introductory philosophy classes and philosophy majors. Second, this drop is mitigated by the presence of more women philosophy faculty. (shrink)

Many of us agree that we ought not to wrong future people, but there remains disagreement about which of our actions can wrong them. Can we wrong individuals whose lives are worth living by taking actions that result in their very existence? The problem of justifying an answer to this question has come to be known as the non-identity problem.[1] While the literature contains an array of strategies for solving the problem,[2] in this paper I will take what I call (...) the harm-based approach, and I will defend an account of harming—which I call the existence account of harming—that can vindicate this approach. -/- Roughly put, the harm-based approach holds that, by acting in ways that result in the existence of individuals whose lives are worth living, we can harm and thereby wrong those individuals. An initially plausible way to try to justify this approach is to endorse the non-comparative account of harming, which holds that an event harms an individual just in case it causes her to be in a bad state, such that the state’s badness does not derive from a comparison between that state and some alternative state that the individual would or could have been in. However, many philosophers argue that the non-comparative account of harming is inadequate,[3] and one might be tempted to infer from this that any harm-based approach to the non-identity problem will fail. My proposal, which I call the existence account of harming, will show that this inference is faulty: we can vindicate the harm-based approach without relying on the non-comparative account of harming. (shrink)

This chapter offers an overview of the philosophy of Robert S. Sokolowski with a focus on his account of what philosophy is, how philosophy arises out of pre-philosophical life, and how it is related back to pre-philosophical life. It also situates Sokolowsk’s achievements in articulating the relationship between Husserlian phenomenology and modern and pre-modern styles of philosophizing.

Suffering can make sacred, so it may partly be nature, and not culture alone, that leads us to apprehend a sacred aspect in victims of oppression. Those who recognize this sacredness show piety—a special form of respect—toward members of oppressed groups. The result is a system of social constructions often dismissed as “identity politics.” This essay starts with an analysis of the intentionality of piety and sacredness and how they relate to suffering, sacrifice, sanctions, pollution, and purification. It then argues (...) that the sacralization of oppressed groups is an expression of the perennial human disposition to acknowledge sacredness and to respond piously. The essay then analyzes this sacred status as socially constructed. Based on the sacred-making power of suffering, the sacred status elicits piety, gives its bearers special authority, surrounds them with sanctions, and calls for symbolic sacrificial punishments of the impious. By dissecting sacrificial politics as a system of social constructions, we see that, although the oppressed groups are made sacred, certain people in the oppressor groups—“the Pious”—continue to exercise fundamental power. This essay, by displaying the inner logic of this cultural phenomenon, helps us both to sympathize with and to critique the system and then to pose questions about what good or bad the system might be doing. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

A complete theory of harming must have both a substantive component and a formal component. The substantive component, which Victor Tadros (2014) calls the “currency” of harm, tells us what I interfere with when I harm you. The formal component, which Tadros calls the “measure” of harm, tells us how the harm to you is related to my action. In this chapter I survey the literature on both the currency and the measure of harm. I argue that the currency of (...) harm is well-being and that the measure of harming is best captured by a causal account on which harming is causing a harm. A harm for you is the presence of something intrinsically bad for you or the absence of something intrinsically good for you. Thus, although a counterfactual account of the measure of harm need not distinguish between an harm and a harmful event, the causal account reserves the term ‘harm’, not for a harmful event, but only for its effect. Finally, I show how a complete theory of harming can help us to answer questions about whether we can harm people with speech, whether we can harm the dead, and how it is possible to harm future generations. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

According to various “harm-based” approaches to the non-identity problem, an action that brings a particular child into existence can also harm that child, even if his or her life is worth living. In the third chapter of The Non-Identity Problem and the Ethics of Future People, David Boonin surveys a variety of harm-based approaches and argues that none of them are successful. In this paper I argue that his objections to these various approaches do not impugn a harm-based approach that (...) Boonin does not consider, an approach I call the “existence solution to the non-identity problem.” I also argue that the existence solution is more plausible than Boonin’s own proposed solution. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

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)

Husserl’s philosophy of culture relies upon a person’s body being expressive of the person’s spirit, but Husserl’s analysis of expression in Logical Investigations is inadequate to explain this bodily expressiveness. This paper explains how Husserl’s use of “expression” shifts from LI to Ideas II and argues that this shift is explained by Husserl’s increased understanding of the pervasiveness of sense in subjective life and his increased appreciation for the unity of the person. I show how these two developments allow Husserl (...) to better describe the bodily expressiveness that is the source of culture. Husserl’s account of culture is thoroughly intentionalistic, but it does not emphasize thought at the expense of embodiment. Culture originates not in an abstract subjectivity, but by persons’ expressing themselves physically in the world. By seeing how Husserl develops his mature position on bodily expressiveness, we can better appreciate the meaningfulness and the bodily concreteness of cultural objects. (shrink)

This chapter defends a deontological approach to both the non-identity problem and what is referred to as the “inconsequentiality problem.” Both problems arise in cases where, although the actions of presently living people appear to have harmful consequences for future people, it is difficult to explain why there are moral reasons against such actions. The deontological response to both problems appeals to a distinction between causal and non-causal consequences. By acknowledging the moral importance of such a distinction, deontologists can vindicate (...) the judgment that, collectively and individually, we have harm-based reasons against bringing about bad consequences for future people. (shrink)

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms that are (...) designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain. (shrink)

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)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

What types of unity and disunity belong to a group of people sharing a culture? Husserl illuminates these communities by helping us trace their origin to two types of interpersonal act—cooperation and influence—though cultural communities are distinguished from both cooperative groups and mere communities of related influences. This analysis has consequences for contemporary concerns about multi- or mono-culturalism and the relationship between culture and politics. It also leads us to critique Husserl’s desire for a new humanity, one that is rational, (...) cooperatively united, and animated by a universal philosophical culture. Reflecting on culture, a spiritually shaped and shared domain of the world, draws us to reflect also on ourselves as social and rational animals, and to ask, what should we reasonably hope for—and aim for—in a human culture that expresses and supports our shared lives of reason? Aristotle is used for occasional comparisons and contrasts. (shrink)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (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)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

The crucial distinction for ethics is between the good and the apparent good, between being and seeming. Tradition is useful for developing our ability to make this distinction and to live ethically or in self-responsibility, but it is also threatening to this ability. The phenomenology of Husserl and of others in the Husserlian tradition, especially Robert Sokolowski, are helpful in spelling out how tradition works; how the difference between the apparent good and the good is bridged in the experience of (...) moral truth but also a permanent, challenging feature of human life; what ethics requires regarding self-responsibility or authenticity; and what the proper voice of tradition is in the ethical or moral life. (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)

This paper discusses the rhetorical problems teachers face in presenting Socratic activity to students, and it then argues that parallel problems arise in presenting liberal education to many academic colleagues. Given the nature of philosophy and the nature of expertise in today’s academy, most academics will not understand, and perhaps be hostile to, philosophy, and philosophers may sometimes seem to them both arrogant and ignorant. The contemporary academy, dominated by assumptions Weber articulates in "Science as a Vocation," does not make (...) room for philosophical activity and practitioners of philosophy in the classroom (in various departments) must adopt rhetorically appropriate postures in order to create safe spaces for Socratic activity. (shrink)

In this dissertation, I explicate some of the moral duties we have to future humans. I defend the view that (DV1) we have pro tanto duties of nonmaleficence and beneficence to and regarding at least some future humans; (DV2) in the present circumstances, this duty of nonmaleficence grounds reasons for us to refrain from damaging certain features of the natural environment; and (DV3) in the present circumstances, this duty of beneficence grounds reasons for at least some of us to bring (...) future humans into existence. I refer to the view consisting of (DV1) - (DV3) as the Duties to Future Humans View (DV). In defense of DV1, I argue that future humans have moral standing, and that their having moral standing is sufficient for our having pro tanto duties of nonmaleficence and beneficence to and regarding them. I take a duty of nonmaleficence to be a duty to refrain from harming and a duty of beneficence to be a duty to benefit. In defense of DV2, I argue that increases in the concentration of carbon dioxide in the atmosphere and numerous species extinctions are harms for future humans. In defense of DV3, I argue that having a life worth living is a benefit to the person who lives that life. One objection to DV is the non-identity problem. In response, I defend substantive accounts of harming and benefiting. The account of harming holds that for any individual having moral standing, S, and any state of affairs, A, (1) A is a harm for S just in case if it were true that both S existed and A did not obtain, then S would have a higher level of lifetime well-being; (2) an action or event harms S just in case it causes a harm for S to obtain; (3) other things being equal, the reason against harming S is stronger, the more similar the world would be if A did not obtain. I argue for a similar account of benefiting. I also argue for a metaphysical distinction between causes and mere conditions. (shrink)

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding, melting. Among this plethora of what we can think of as ‘mere dispositions’ is a subset of dispositions in whose realizations we have an interest – a car responding well when driven on ice, a rabbit’s lungs responding well when it is chased by a wolf, and so on. We (...) call the latter ‘capabilities’ and we attempt to provide an ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are being collected in siloed fashion. (shrink)

Daniel Dennett provides many compelling reasons to question the existence of phenomenal experiences in his paper titled Quining Qualia, however, from the perspective of the individual, qualia appear to be an inherent feature of consciousness. The act of reflecting on one’s experiences suggests that subjective feelings and sensations are a necessary element of human life, as personal opinions on various artistic works are apt to demonstrate. This paper argues that by considering subjective experiences from a naturalized functionalist perspective, a comprehensive (...) explanation for qualia can be provided given its origins in evolutionary biology. As information passing through the nervous system, qualia serve to guide the behaviour of individuals to ultimately facilitate survival. Specifically, qualia are representations of environmental features, existing as information messages supported by neural physiology and encoded in electrochemical formats. In addition to addressing the Hard Problem of Consciousness and clarifying the four properties Dennett associates with qualia, this theoretical foundation enables further metaphysical discussion on the nature of consciousness more generally. Although many outstanding questions on the contents of subjective experiences are apt to linger given the explanatory gap, a robust theory for the existence of qualia can be developed through the integration of ideas and concepts from a variety of domains. (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)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

Does ?ought? imply ?can? for collectives' obligations? In this paper I want to establish two things. The first, what a collective obligation means for members of the collective. The second, how collective ability can be ascertained. I argue that there are four general kinds of obligation, which devolve from collectives to members in different ways, and I give an account of the distribution of obligation from collectives to members for each of these kinds. One implication of understanding collective obligation and (...) ability in the proposed way is that a group can be blameworthy for failing to realize its obligation even when no member of the group is blameworthy for failing to realize her obligation. (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)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...) future persons, and to current persons in low-lying and developing countries, by way of their impacts on climate change. When it comes to such large-scale harms, it's easy for the individual to feel helpless. Even if she sincerely wishes things were otherwise, she may wonder what she could possibly do to make them so. In this paper I briefly explore several promising avenues for generating duties in individuals to consume ethically, and develop one in particular: that an individual ought to signal her commitments to others, as a first step in collectivizing to act against unjust global labour practices. (shrink)

Climate change appears to be a classic aggregation problem, in which billions of individuals perform actions none of which seem to be morally wrong taken in isolation, and yet which combine to drive the global concentration of greenhouse gases (GHGs) ever higher toward environmental (and humanitarian) catastrophe. When an individual can choose between actions that will emit differing amounts of GHGs―such as to choose a vegan rather than carnivorous meal, to ride a bike to work rather than drive a car, (...) or to take a reusable bag to the supermarket rather than send another plastic bag to landfill―does she have any reason to choose the lower-emitting actions? In this chapter I'll reject the claim that individuals don't make a difference when it comes to climate change. I first discuss making a difference with every action, as a way of getting clearer about how individuals' actions impact causally on the harms resulting from climate change, making a distinction so far overlooked in the climate ethics discussion between 'macro' thresholds like ice-cap melt, and 'micro' thresholds like severe weather events. I set aside making a difference with every action as implausible, and then move on to discuss both low probability of major difference, and high probability of minor difference. I argue that both of these are plausible characterizations of individuals' causal contributions to climate change. I conclude by noting some policy implications of having (probabilistic) individual difference-making back in play. (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)

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey- (...) class='Hi'>Smith puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concepts such as kind, species, part, whole, function, process, fragment, sequence, expression, (...) boundary, locus, environment, system, and so on. Concepts which belong to the implicit stock of knowledge of every biologist. They amount to a dimension of biological reality which remains constant in the course of biological evolution and whose theoretical treatment requires contemporary analogues of the tools developed in traditional Aristotelian metaphysics. To provide the necessary theories and definitions is a task for philosophy, which is thus called upon to play an important role as intermediary between biology and informatics. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

In her ‘On the apparent paradox of ideal theory’, Laura Valentini combines three supposedly plausible premises to derive the paradoxical result that ideal theory is both unable to, and indispensable for, guiding action. Her strategy is to undermine one of the three premises by arguing that there are good and bad kinds of ideal theory, and only the bad kinds are vulnerable to the strongest version of their opponents’ attack. By undermining one of the three premises she releases ideal theorists (...) from the paradox, which is as follows. (1) Any sound theory of justice is action-guiding. (2) Any sound theory of justice is ideal. (3) Any ideal theory fails to be action-guiding. Here I shall respond to Valentini in two ways. First, I shall show that both (1) and (2) are false. The falsity of either is sufficient to release ideal theorists from the paradox. Second, I shall show that Valentini’s response to (3) can be extended, because her bad kinds of ideal theory do not necessarily fail to guide action. The cumulative effect of my arguments further strengthens Valentini’s support of ideal theory. I will deal with premises (1) and (2) in Sections I and II, and (3) in Section III. (shrink)