The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

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

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)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

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

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

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)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical (...) presentation including signs and symptoms. (shrink)

Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons. We obtain the following spin-offs. First, the generated tree turns out to be an organismal tree of life. Second, this organismal tree is homeomorphic to the phylogenetic Hennigian species tree of life, implying the discovery of a multi-level tree of life: (...) this phylogenetic tree can be obtained by zooming out from the organismal tree, or conversely, the organismal tree of life can be generated by expanding the phylogenetic nodes into unary trees. Finally, the definition of the organismal tree allows an efficient algorithmic transformation of a given genealogical network into its corresponding phylogenetic species tree of life. The latter will be presented in a separate paper. (shrink)

A fundamental question asked in modal logic is whether a given theory is consistent. But consistent with what? A typical way to address this question identifies a choice of background knowledge axioms (say, S4, D, etc.) and then shows the assumptions codified by the theory in question to be consistent with those background axioms. But determining the specific choice and division of background axioms is, at least sometimes, little more than tradition. This paper introduces generic theories for propositional modal logic (...) to address consistency results in a more robust way. As building blocks for background knowledge, generic theories provide a standard for categorical determinations of consistency. We argue that the results and methods of this paper help to elucidate problems in epistemology and enjoy sufficient scope and power to have purchase on problems bearing on modalities in judgement, inference, and decision making. (shrink)

There are numerous theoretical reasons which are usually said to undermine the case for mental causation. But in recent years, Libet‘s experiment on readiness potentials (Libet, Wright, and Gleason 1982; Libet, Gleason, Wright, and Pearl 1983), and a more recent replication by a research team led by John Dylan Haynes (Soon, C.S., Brass, M., Heinze, H.J., and Haynes, J.-D. [2008]) are often singled out because they appear to demonstrate empirically that consciousness is not causally involved in our choices and actions. (...) In this paper, an alternative interpretation of these studies is offered; one which is in accordance both with the empirical evidence and also with the phenomenology of the will, demonstrating that the two opposing views of agency – both the ones that deny the reality of free will and the ones that affirm it – are equally compatible with the outcomes of these two experiments. On this basis, it is shown that the claim that the results on the timing of readiness potential tip the scales in favour of one or the other view cannot be justified - neither from a neurological, nor from a philosophical perspective. (shrink)

In discussions of the Aharonov-Bohm effect, Healey and Lyre have attributed reality to loops $\sigma_0$ (or hoops $[\sigma_0]$), since the electromagnetic potential $A$ is currently unmeasurable and can therefore be transformed. I argue that $[A]=[A+d\lambda]_{\lambda}$ and the hoop $[\sigma_0]$ are related by a meaningful duality, so that however one feels about $[A]$ (or any potential $A\in[A]$), it is no worse than $[\sigma_0]$ (or any loop $\sigma_0\in[\sigma_0]$): no ontological firmness is gained by retreating to the loops, which are just as flimsy (...) as the potentials. And one wonders how the unmeasurability of one entity can invest another with physical reality; would an eventual observation of $A$ dissolve $\sigma_0$, consigning it to a realm of incorporeal mathematical abstractions? The reification of loops rests on the potential's ''gauge dependence''; which in turn rests on its unmeasurability; which is too shaky and arbitrary a notion to carry so much weight. (shrink)

We argue that C. Darwin and more recently W. Hennig worked at times under the simplifying assumption of an eternal biosphere. So motivated, we explicitly consider the consequences which follow mathematically from this assumption, and the infinite graphs it leads to. This assumption admits certain clusters of organisms which have some ideal theoretical properties of species, shining some light onto the species problem. We prove a dualization of a law of T.A. Knight and C. Darwin, and sketch a decomposition result (...) involving the internodons of D. Kornet, J. Metz and H. Schellinx. A further goal of this paper is to respond to B. Sturmfels’ question, “Can biology lead to new theorems?”. (shrink)

"In the programs of Logic and History of Philosophy in the FHUCE study and introduction to logic is always done on the basis of Western classical Greek tradition, and its development is still exclusively through Western culture. This presentation aims to provide a path parallel to the West is the tradition of Nyaya-Vaisesika schools, which arise in the S. V B.C. like a response to the anti-Vedic Buddhist nihilism, and reached an important technical development at the beginning of S. II (...) D.C. when you know the Nyāyasutras attributed to Aksapada Gautama, and are considered the founding text of Nyāya tradition of Indian philosophy. The great virtue of the achievement of these schools is that although the system has Vaisesika been described as "a synthesis between philosophy of nature, ethics and soteriology" , which also applies to school Nyāya in the latter we are also a great emphasis on epistemology and the rules must be observed in philosophical debates. In their synthesis, Nyāya -Vaisesika system gets his language and jargon will be adopted by all who wish to discuss logical issues in India (especially in discussions Vedanta / Buddhism) without the need to adopt such language should assume his ontological, moral and religious premises. (shrink)

This paper defends the Principle of Sufficient Reason, taking Baumgarten as its guide. The primary aim is not to vindicate the principle, but rather to explore the kinds of resources Baumgarten originally thought sufficient to justify the PSR against its early opponents. The paper also considers Baumgarten’s possible responses to Kant’s pre-Critical objections to the proof of the PSR. The paper finds that Baumgarten possesses reasonable responses to all these objections. While the paper notes that in the absence of a (...) response to Kant’s Critical discussion of the PSR, this result does not vindicate the principle, it shows how this discussion provides a deeper understanding of what, according to Baumgarten, the PSR really assumes and intends, and prepares the way for a more responsible discussion of Kant’s critical objections to Baumgarten’s supposed proof. (shrink)

A new translation and edition of Aristotle's Protrepticus (with critical comments on the fragments) -/- Welcome -/- The Protrepticus was an early work of Aristotle, written while he was still a member of Plato's Academy, but it soon became one of the most famous works in the whole history of philosophy. Unfortunately it was not directly copied in the middle ages and so did not survive in its own manuscript tradition. But substantial fragments of it have been preserved in several (...) works by Iamblichus of Chalcis, a third century A.D. neo-Pythagorean philosopher and educator. On the basis of a close study of Iamblichus' extensive use and excerption of Aristotle's Protrepticus, it is possible to reconstruct the backbone of the lost work, and then to flesh it out with the other surviving reports about the work from antiquity (for example in Alexander of Aphrodisias and other ancient commentators on Aristotle). It is also possible to identify several papyrus fragments of the work, and many references and literary allusions in later authors, especially Cicero, whose own lost dialogue Hortensius was a defense of philosophy modeleld on Aristotle's. (shrink)

Part 1 of 2, this is an introductory critical review of Michelle Alexander's "The New Jim Crow: Mass Incarceration In The Age of Colorblindness" (The New Press, 2010). See part 2: "Toward Détournement of The New Jim Crow" for an advanced critical reading.

SUMMARY. The works of Alexander of Aphrodisias were written a few decades after the publication of the most successful -astrology hand- book in antiquity, Ptolemy's Tetrabiblos Syntaxis, which attempts to naturalize astrology, i.e. to make it agree with Aristotelian theory of science. A comparison of the doctrines between the Tetrabiblos and some passages of Alexander'p works on fate demostrates a noteworthy con¬vergere of the two scholars, and probably a dependence of the lasi great greek Aristotle's exegete on the (...) theories of Ptolemaic astrology, at least in reference to three points: theory of fate; justification of de- vining as a technical and naturai conjecture about man's fate; ana¬lysis of the stars' influence on the sublunary world in physical and phi¬losophical terms. (shrink)

Discussion of the relevance of grounding to substantiveness, theory-choice, and “location problems” in metaphysics.

Introduction -- What is personal responsibility? -- Ordinary language -- Common conceptions -- What do philosophers mean by responsibility? -- Personally responsible for what? -- What do philosophers think? part I -- Causes -- Capacity -- Control -- Choice versus brute luck -- Second-order attitudes -- Equality of opportunity -- Deservingness -- Reasonableness -- Reciprocity -- Equal shares -- Combining criteria -- What do philosophers think? part II -- Utility -- Self-respect -- Autonomy -- Human flourishing -- Natural duties and (...) special obligations -- A matter of perspectives -- Combining values -- What do politicians think? -- A brief typology -- International comparisons -- Welfare reform -- Healthcare reform -- Rights and responsibilities -- On the responsibilities of politicians -- What do ordinary people think? -- Why ask? -- Attitudes to welfare claimants -- When push comes to shove -- Perceptions and reality -- Further international comparisons -- The trouble with opinion surveys -- Four contemporary issues in focus -- Unemployment -- Health -- Drug abuse -- Personal debt and financial rewards -- So how do we decide? -- Getting the public involved -- Citizens juries -- Answering some potential criticisms. (shrink)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the reduction or emergence of molecular structure (...) cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

Can there be grounding without necessitation? Can a fact obtain wholly in virtue of metaphysically more fundamental facts, even though there are possible worlds at which the latter facts obtain but not the former? It is an orthodoxy in recent literature about the nature of grounding, and in first-order philosophical disputes about what grounds what, that the answer is no. I will argue that the correct answer is yes. I present two novel arguments against grounding necessitarianism, and show that grounding (...) contingentism is fully compatible with the various explanatory roles that grounding is widely thought to play. (shrink)

ABSTRACT It has become standard to conceive of metalinguistic disagreement as motivated by a form of negotiation, aimed at reaching consensus because of the practical consequences of using a word with one content rather than another. This paper presents an alternative motive for expressing and pursuing metalinguistic disagreement. In using words with given criteria, we betray our location amongst social categories or groups. Because of this, metalinguistic disagreement can be used as a stage upon which to perform a social identity. (...) The ways in which metalinguistic disagreements motivated in this way diverge in character from metalinguistic negotiations are described, as are several consequences of the existence of metalinguistic disagreements motivated in this way. (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)

I propose an approach to liar and Curry paradoxes inspired by the work of Roger Swyneshed in his treatise on insolubles (1330-1335). The keystone of the account is the idea that liar sentences and their ilk are false (and only false) and that the so-called ''capture'' direction of the T-schema should be restricted. The proposed account retains what I take to be the attractive features of Swyneshed's approach without leading to some worrying consequences Swyneshed accepts. The approach and the resulting (...) logic (called ''Swynish Logic'') are non-classical, but are consistent and compatible with many elements of the classical picture including modus ponens, modus tollens, and double-negation elimination and introduction. It is also compatible with bivalence and contravalence. My approach to these paradoxes is also immune to an important kind of revenge challenge that plagues some of its rivals. (shrink)

Can an agent's intelligence level be negative? We extend the Legg-Hutter agent-environment framework to include punishments and argue for an affirmative answer to that question. We show that if the background encodings and Universal Turing Machine (UTM) admit certain Kolmogorov complexity symmetries, then the resulting Legg-Hutter intelligence measure is symmetric about the origin. In particular, this implies reward-ignoring agents have Legg-Hutter intelligence 0 according to such UTMs.

According to ontological nihilism there are, fundamentally, no individuals. Both natural languages and standard predicate logic, however, appear to be committed to a picture of the world as containing individual objects. This leads to what I call the \emph{expressibility challenge} for ontological nihilism: what language can the ontological nihilist use to express her account of how matters fundamentally stand? One promising suggestion is for the nihilist to use a form of \emph{predicate functorese}, a language developed by Quine. This proposal faces (...) a difficult objection, according to which any theory in predicate functorese will be a notational variant of the corresponding theory stated in standard predicate logic. Jason Turner (2011) has provided the most detailed and convincing version of this objection. In the present paper, I argue that Turner's case for the notational variance thesis relies on a faulty metasemantic principle and, consequently, that an objection long thought devastating is in fact misguided. (shrink)

In 1937 Joan Robinson proposed that “when capitalism is rightly understood, the rate of interest will be set at zero and the major evils of capitalism will disappear”. A permanent zero rate would abolish capitalist profit except in limited cases, leaving nearly all output to be claimed by labour as wages. It would allow capital to be allocated on the basis of prospective social benefit rather than short-term profitability and a collateral basis that favours the wealthy. It would remove some (...) of the economic pressure to use resources unsustainably. So why not do this? I argue that the few available philosophical arguments for positive interest rates are unsatisfactory. Those who want a just and sustainable form of capitalism should target net zero for the interest rate. (shrink)

This article argues that economic crises are incompatible with the realisation of non-domination in capitalist societies. The ineradicable risk that an economic crisis will occur undermines the robust security of the conditions of non-domination for all citizens, not only those who are harmed by a crisis. I begin by demonstrating that the unemployment caused by economic crises violates the egalitarian dimensions of freedom as non-domination. The lack of employment constitutes an exclusion from the social bases of self-respect, and from a (...) practice of mutual social contribution crucial to the intersubjective affirmation of one’s status. While this argument shows that republicans must be concerned about economic crises, I suggest a more powerful argument can be grounded in the republican requirement that freedom must be robust. The systemic risk of economic crisis constitutes a threat to the conditions of free citizenship that cannot be nullified using policy mechanisms. As a result, republicans appear to be faced with the choice of revising their commitments or rejecting the possibility that republican freedom can be robustly secured in capitalist societies. (shrink)

When people suffer they always suffer as a whole human being. The emotional, cognitive and spiritual suffering of human beings cannot be completely separated from all other kinds of suffering, such as from harmful natural, ecological, political, economic and social conditions. In reality they interact with each other and influence each other. Human beings do not only suffer from somatic illnesses, physical pain, and the lack of decent opportunities to satisfy their basic vital, social and emotional needs. They also suffer (...) when they are not able to experience and grasp any meaning of life even if such suffering is not quite as obvious as most forms of physical, social and emotional suffering. Suffering from the lack for the sense of the meaning of life is a special form of emotional, cognitive, and spiritual suffering. Although all human beings share the same basic human need for some meaning of life, the fulfilment of this need is highly individual and personal. Although all forms of human suffering can be a challenge to the meaning of life, the personal conditions of suffering usually are a stronger challenge for the meaning of life. Among the personal conditions of human suffering, the Grenzsituationen cannot be cancelled or raised at all, but only accepted and coped with as existential aspects of the conditio humana. According to Karl Jaspers these are: death, suffering, struggling, guilt, and failing. The challenge for human beings to cope with these Grenzsituationen is a way to move from the mere Being-there to true human Existence. (shrink)

A counterpossible is a counterfactual with an impossible antecedent. Counterpossibles present a puzzle for standard theories of counterfactuals, which predict that all counterpossibles are semantically vacuous. Moreover, counterpossibles play an important role in many debates within metaphysics and epistemology, including debates over grounding, causation, modality, mathematics, science, and even God. In this article, we will explore various positions on counterpossibles as well as their potential philosophical consequences.

Recent metaphysics has turned its focus to two notions that are—as well as having a common Aristotelian pedigree—widely thought to be intimately related: grounding and essence. Yet how, exactly, the two are related remains opaque. We develop a unified and uniform account of grounding and essence, one which understands them both in terms of a generalized notion of identity examined in recent work by Fabrice Correia, Cian Dorr, Agustín Rayo, and others. We argue that the account comports with antecedently plausible (...) principles governing grounding, essence, and identity taken individually, and illuminates how the three interact. We also argue that the account compares favorably to an alternative unification of grounding and essence recently proposed by Kit Fine. (shrink)

A number of bioethicists have been critical of the power of the family to “veto” a patient’s decision to posthumously donate her organs within opt-in systems of organ procurement. One major objection directed at the family veto is that when families veto the decision of their deceased family member, they do something wrong by violating or failing to respect the autonomy of that deceased family member. The goal of this paper is to make progress on answering this objection. I do (...) this in two stages. First, I argue that the most plausible interpretation of what happens when a person registers as an organ donor in an opt-in system is that she gives her consent to the state to posthumously remove her organs for transplantation purposes. Call this the Authorization Account. Second, given the Authorization Account, I argue by analogy that when families veto an individual’s decision to donate and the individual’s organs are not in the end removed, neither the doctors nor the family violate the individual’s autonomy in any morally objectionable sense. Call this the Nonremoval Thesis. I argue that since the Nonremoval Thesis is true, we do not violate or fail to respect the autonomy of registered donors when we fail to remove their organs because their family has objected. (shrink)

International regulation of autonomous weapon systems (AWS) is increasingly conceived as an exercise in risk management. This requires a shared approach for assessing the risks of AWS. This paper presents a structured approach to risk assessment and regulation for AWS, adapting a qualitative framework inspired by the Intergovernmental Panel on Climate Change (IPCC). It examines the interactions among key risk factors—determinants, drivers, and types—to evaluate the risk magnitude of AWS and establish risk tolerance thresholds through a risk matrix informed by (...) background knowledge of event likelihood and severity. Further, it proposes a methodology to assess community risk appetite, emphasizing that such assessments and resulting tolerance levels should be determined through deliberation in a multistakeholder forum. The paper highlights the complexities of applying risk-based regulations to AWS internationally, particularly the challenge of defining a global community for risk assessment and regulatory legitimization. (shrink)

Otto Neurath’s empiricist methodology of economics and his contributions to politi- cal economy have gained increasing attention in recent years. We connect this research with contemporary debates regarding the epistemological status of thought experiments by reconstructing Neurath’s utopias as linchpins of thought experiments. In our three reconstructed examples of different uses of utopias/dystopias in thought experiments we employ a reformulation of Häggqvist’s model for thought experiments and we argue that: (1) Our reformulation of Häggqvist’s model more adequately complies with many (...) uses of thought experiments, especially with the open-ended discussions of utopias and dys- topias in thought experiments. (2) As a strict logical empiricist, Neurath is committed to a strictly empiricist account of thought experiments. John Norton’s empiricist argument view can indeed account for the justifications of empirical beliefs and genuine discoveries targeted by scientific utopianism in three distinct (yet connected) ways, all of which Neur- ath already contemplated: (2.I) Dealing with utopias and thought experiments on a regular basis increases creativity and inventiveness. (2.II) Particular ways of presenting knowl- edge facilitate scientific discovery and social progress. (2.III) The use of utopias in thought experiments can prompt conceptual change and allow access to new phenomena. We con- clude by highlighting that, even though thought experiments support a positive attitude for exploring new social possibilities, Neurath points out that active decisions are unavoidable. The exploration of alternatives and the awareness of a need for decisions in policy discus- sion avert a technocratic outlook in social science. (shrink)

Kant’s accounts of the Highest Good and the moral argument for God and immortality are central features of his philosophy. But both involve lingering puzzles. In this entry, we first explore what the Highest Good is for Kant and the role it plays in a complete account of ethical life. We then focus on whether the Highest Good involves individuals only, or whether it also connects with Kant’s doctrines about the moral progress of the species. In conclusion, we look into (...) three ways of articulating the moral argument for God and immorality that take our commitment to the Highest Good as their point of departure. (shrink)

Pattern-based reasons are reasons for action deriving not from the features of our own actions, but from the features of the larger patterns of action in which we might be participating. These reasons might relate to the patterns of action that will actually be carried out, or they might relate to merely hypothetical patterns. In past work, I have argued that accepting merely hypothetical pattern-based reasons, together with a plausible account of how to weigh these reasons, can lead to disastrous (...) consequences. However, in this article, I argue that this problem is not limited to hypothetical pattern-based reasons: it turns out that there are analogous issues for reasons deriving from actual patterns. I then suggest that we can avoid this problem by adopting a different account of the weight of pattern-based reasons. (shrink)

Kant and Fichte developed the concept of a worldview as a way of reflecting on experience as a whole. But what does it mean to form a worldview? And what role did it play in the German Idealist tradition? This paper seeks to answer these questions through a detailed analysis of the form of a philosophical worldview and its historical portent, both of which remain unexplored in the literature. The dearth of attention is partially to blame on Kant’s desultory development (...) of it, as well as its place in Fichte’s understudied lectures on religion. In this paper, I first reconstruct Kant’s conception as the starting point and then trace it to Fichte who went on to evolve it further. Fichte endorses the basic conceptual shape pioneered by Kant, namely, a reflective process of positing an idea and then checking the coherence of necessary judgments relative to it. However, Fichte came to realize that its philosophical function needed expanding. Beyond recognizing the possibility for alternative worldviews, Fichte further fleshed out how worldview creation could lead to human flourishing. The common feature between both thinkers is that the formation of a worldview aims to turn philosophy into a life-orienting exercise. (shrink)

While it is a point of agreement in contemporary republican political theory that property ownership is closely connected to freedom as non-domination, surprisingly little work has been done to elucidate the nature of this connection or the constraints on property regimes that might be required as a result. In this paper, I provide a systematic model of the boundaries within which republican property systems must sit and explore some of the wider implications that thinking of property in these terms may (...) have for republicans. The boundaries I focus on relate to the distribution of property and the application of types of property claims over particular kinds of goods. I develop this model from those elements of non-domination most directly related to the operation of a property regime: (a) economic independence, (b) limiting material inequalities, and (c) the promotion of common goods. The limits that emerge from this analysis support intuitive judgments that animate much republican discussion of property distribution. My account diverges from much orthodox republican theory, though, in challenging the primacy of private property rights in the realization of economic independence. The value of property on republican terms can be realized without private ownership of the means of production. (shrink)

Verteilungsgerechtigkeit befasst sich mit der Verteilung von Gütern innerhalb einer Gruppe, wobei verschiedene Verteilungsprinzipien und -ergebnisse als mögliche Ideale einer solchen Verteilung verhandelt werden. Diese normativen Ansätze sind oft rein verbal formuliert, wodurch ihre Anwendung auf unterschiedliche konkrete Verteilungssituationen, die hinsichtlich ihrer Gerechtigkeit beurteilt werden sollen, häufig schwer fällt. Eine Möglichkeit, fein abgestufte Gerechtigkeitsbeurteilungen verschiedener Verteilungen präzise erfassen zu können, besteht in der formalen Modellierung solcher Ideale durch Maße oder Indizes. Die Auswahl eines geeigneten Maßes, das ein gewisses Ideal abbilden (...) soll, muss ihrerseits eine Fundierung erfahren, was durch die Forderung von begründeten Axiomen erreicht werden kann, denen ein Maß genügen soll. In der vorliegenden Arbeit werden solche Axiome für Maße der Verteilungsgerechtigkeit am Beispiel von Bedarfsgerechtigkeit eingeführt. Ferner werden exemplarische Maße der Bedarfsgerechtigkeit vorgestellt. Damit wird für die Beurteilung und Modellierung von Maßen der Verteilungsgerechtigkeit eine erste diskutable Grundlage gelegt. (shrink)

In this paper, I explore a fundamental but under-appreciated distinction between two ways of understanding the desire-satisfaction theory of well-being. According to proactive desire satisfactionism, a person is benefited by the acquisition of new satisfied desires. According to reactive desire satisfactionism, a person can be benefited only by the satisfaction of their existing desires. I first offer an overview of this distinction. I then canvass several ways of developing a general formulation of desire satisfactionism that would capture the reactive view, (...) and argue that all come with significant costs. (shrink)

This is an introduction to the volume "Explanation Beyond Causation: Philosophical Perspectives on Non-Causal Explanations", edited by A. Reutlinger and J. Saatsi (OUP, forthcoming in 2017). -/- Explanations are very important to us in many contexts: in science, mathematics, philosophy, and also in everyday and juridical contexts. But what is an explanation? In the philosophical study of explanation, there is long-standing, influential tradition that links explanation intimately to causation: we often explain by providing accurate information about the causes of the (...) phenomenon to be explained. Such causal accounts have been the received view of the nature of explanation, particularly in philosophy of science, since the 1980s. However, philosophers have recently begun to break with this causal tradition by shifting their focus to kinds of explanation that do not turn on causal information. The increasing recognition of the importance of such non-causal explanations in the sciences and elsewhere raises pressing questions for philosophers of explanation. What is the nature of non-causal explanations - and which theory best captures it? How do non-causal explanations relate to causal ones? How are non-causal explanations in the sciences related to those in mathematics and metaphysics? This volume of new essays explores answers to these and other questions at the heart of contemporary philosophy of explanation. The essays address these questions from a variety of perspectives, including general accounts of non-causal and causal explanations, as well as a wide range of detailed case studies of non-causal explanations from the sciences, mathematics and metaphysics. (shrink)

Journal of Political Philosophy, EarlyView.