The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

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)

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)

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)

A collection of papers presented at the First International Summer Institute in Cognitive Science, University at Buffalo, July 1994, including the following papers: ** Topological Foundations of Cognitive Science, Barry Smith ** The Bounds of Axiomatisation, Graham White ** Rethinking Boundaries, Wojciech Zelaniec ** Sheaf Mereology and Space Cognition, Jean Petitot ** A Mereotopological Definition of 'Point', Carola Eschenbach ** Discreteness, Finiteness, and the Structure of Topological Spaces, Christopher Habel ** Mass Reference and the Geometry of Solids, Almerindo (...) E. Ojeda ** Defining a 'Doughnut' Made Difficult, N .M. Gotts ** A Theory of Spatial Regions with Indeterminate Boundaries, A.G. Cohn and N.M. Gotts ** Mereotopological Construction of Time from Events, Fabio Pianesi and Achille C. Varzi ** Computational Mereology: A Study of Part-of Relations for Multi-media Indexing, Wlodek Zadrozny and Michelle Kim. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

BioéthiqueOnline was launched in March 2012 as a non-peer reviewed journal with the aim of providing a platform to facilitate and encourage the development of a bilingual bioethics community in Canada and internationally. In light of discussions amongst the Editorial Committee over the past few months regarding the growth of the journal, we have decided to move to a peer-reviewed process for articles submitted to the journal.

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

Certain states in the Global North have responded to refugees seeking safety on their territories through harmful practices of border violence, detention, encampment and containment that serve to prevent and deter refugee arrivals. These practices are ostensibly justified through an appeal to a right to control borders. This paper therefore assesses whether these harmful practices can indeed be morally justified by a state’s right to control borders. It analyses whether Christopher Heath Wellman’s account of a state’s right to freedom (...) of association, which represents the most restrictive account of a state’s right to control borders available in the literature, can extend to justify current harmful practices against refugees. If not, then no available justification will be able to do so, and thus contemporary harmful practices used against refugees cannot be justified by a state’s right to control borders. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

Evidential Uniqueness is the thesis that, for any batch of evidence, there’s a unique doxastic state that a subject with that evidence should have. One of the most common kinds of objections to views that violate Evidential Uniqueness are arbitrariness objections – objections to the effect that views that don’t satisfy Evidential Uniqueness lead to unacceptable arbitrariness. The goal of this paper is to examine a variety of arbitrariness objections that have appeared in the literature, and to assess the extent (...) to which these objections bolster the case for Evidential Uniqueness. After examining a number of different arbitrariness objections, I’ll conclude that, by and large, these objections do little to bolster the case for Evidential Uniqueness. (shrink)

A volume of papers inspired by the work of George E. Smith on confirmation and evidence in advanced science—from Newton's gravitation theory to the physics of molecules.

Major Research Paper Abstract -/- A Part of This World: Deleuze & The Logic Of Creation. -/- Is there a particular danger in following Deleuze’s philosophy to its end result? According to Peter Hallward and Alain Badiou, Deleuze’s philosophy has some rather severe conclusions. Deleuze has been known as a vitalist thinker of life and affirmation. Hallward & Badiou seek to challenge the accepted view of Deleuze; showing that these accepted norms in Deleuzian scholarship should be challenged; and that initially (...) Deleuze calls for the evacuation of political action in order to remain firm in the realm of pure contemplation. I intend to investigate and defend Deleuze’s philosophy and against critics like Badiou and Hallward; and that not only is Deleuze’s philosophy creative and vital but also highly revolutionary and ‘a part of this world.’ I will look at several works in Deleuze’s corpus, as well as look at Deleuzian scholars whom defend Deleuze’s position -/- Hallward sees Deleuze as a theophantic thinker of the one and like Spinoza an individual mode must align oneself with the intellectual love of god, so that creativity and expressivity may mediate through them. Thus, according to Hallward the major theme of Deleuze’s philosophy is creativity; and a subject or a creature must tap into this vital spark of creation, which, is also a form of creatural confinement. Hallward states this creative act can only occur in the realm of the virtual, by lines of flight leading 'out of this world'. The subject is then re-introduced to an extra-worldly existence of contemplation and remains further away from decisions and lived experience. Deleuze, according to Hallward, falls prey to a cosmological pantheism. -/- Badiou has similar concerns. Deleuze’s philosophy is too systematic and abstract. The entirety of Deleuzes’ work is surrounded by metaphysics of the one; and essentially its repercussions lead to an overt asceticism. Badiou notes that Deleuze wants us all to surrender thought to a renewed concept of the one. Through the surrender of the one, the multiple is lost and incorporated into the realm of simulacra. Everything in this Deleuzian world is ‘always-already’ in the infinite and inhuman totality of the one. According to Badiou, this entire process is articulated in the power of inorganic life that operates through all of us. Like Hallward, Badiou sees Deleuze demolishing the subject, who is stuck between machinery and exteriority. Subjects are forced to transcend and go beyond their limits, slowly collapsing into an infinite virtuality. Badiou believes this is a powerful metaphor for a philosophy of death. Thus the conditions of Deleuzian thought are contingent upon asceticism, making a Deleuzian world a sort of ‘crowned anarchy’. Badiou sees Deleuze’s ascetic mission intimately linked with a philosophy of death, and like Hallward we should pay careful attention to the outcome of such an aristocratic philosophy. Death according to Badiou, symbolizes Deleuzian thought, not only making it dangerous, but also actualizing it as an ineffective position. Badiou also points out that Deleuze’s conceptual sources are not only limited but also repeated time and time again through a monotonous selection of concepts. Is this a fair critique and representation of Deleuzian thought? -/- Eugene Holland states, that both Hallward and Badiou have misrepresented Deleuze. Deleuze does invoke the creation of a new earth but one which we all fully believe in. The only world Deleuze wants to get out of is the world of habits, conformity, power; and forces that block creative being. According to Holland, Hallward presents us a Deleuze that inhibits an engagement with the world. However Deleuze’s creative enterprise is insistent on forming concepts that can change and transform our world. -/- So the question arises where does the problem of misrepresentation begin? It begins with both Badiou and Hallward having an erroneous account of the actual/virtual distinction in Deleuze’s Philosophy. According to Protevi, Hallward posits a dualism between the actual and the virtual, denying the role of the intensive. Hallward initially sees the relationship between the intensive and the virtual, ignoring the fact that the intensive has its own ontological register that mediates both the virtual and the actual. However, Protevi notes if one could not accept the intensive for an ontological register and had to place it with one or the other; you would have to accept an interrelationship between the actual and the intensive. Hallward places it in the realm of the virtual, thus, leading us to his major claim that Deleuze’s philosophy leads us out of the world. Protevi states, intensive processes happen in our world they are a part of this world. Hallward completely empties all creativity from the actual, thus depending on the virtual and its slippery slope. Both Hallward and Badiou have missed the point altogether. We live in an intensive/actual world and the main point about Deleuze’s politics has to do with experimentation and social interaction and the transformation and intervention of the concept. As Daniel W. Smith states, unlike Badiou, Deleuze is not searching for an axiomatic approach to the world, one that is prone to reductionism but rather with problematic, inventive and creative methods to transform a society. (shrink)

In this paper I argue that Christopher Kutz misapplies his theory of joint action when he attributes shareowners responsibilities on the basis of their intentional participation in the corporations in which they invest. Instead I propose that his theory of joint action should be used to attribute shareowners responsibilities on the basis of their intentional participation in the stock market. If shareholders’ accountability is grounded in their intentional participation in the stock market, then shareholders cannot take responsibility for corporation’s (...) individual actions. Instead they are solely responsible for the benefits they gain from holding shares if these are a result of moral wrongdoing and for this they should be held accountable. (shrink)

This volume brings together a range of influential essays by distinguished philosophers and political theorists on the issue of global justice. Global justice concerns the search for ethical norms that should govern interactions between people, states, corporations and other agents acting in the global arena, as well as the design of social institutions that link them together. The volume includes articles that engage with major theoretical questions such as the applicability of the ideals of social and economic equality to the (...) global sphere, the degree of justified partiality to compatriots, and the nature and extent of the responsibilities of the affluent to address global poverty and other hardships abroad. It also features articles that bring the theoretical insights of global justice thinkers to bear on matters of practical concern to contemporary societies, such policies associated with immigration, international trade, and climate change. -/- Contents: Introduction; Part I Standards of Global Justice: (i) Assistance-Based Responsibilities to the Global Poor: Famine, affluence and mortality, Peter Singer; We don't owe them a thing! A tough-minded but soft-hearted view of aid to the faraway needy, Jan Narveson; Does distance matter morally to the duty to rescue? Frances Myrna Kamm. (ii) Contribution-Based Responsibilities to the Global Poor: 'Assisting' the global poor, Thomas Pogge; Should we stop thinking about poverty in terms of helping the poor?, Alan Patten; Poverty and the moral significance of contribution, Gerhard Øverland. (iii)Cosmopolitans, Global Egalitarians, and its Critics: The one and the many faces of cosmopolitanism, Catherine Lu; Cosmopolitan justice and equalizing opportunities, Simon Caney; The problem of global justice, Thomas Nagel; Against global egalitarianism, David Miller; Egalitarian challenges to global egalitarianism: a critique, Christian Barry and Laura Valentini. Part II Pressing Global Socioeconomic Issues: (i) Governing the Flow of People: Immigration and freedom of association, Christopher Wellman; Democratic theory and border coercion: no right to unilaterally control your own borders, Arash Abizadeh; Justice in migration: a closed borders utopia?, Lea Ypi. (ii) Climate Change: Global environment and international inequality, Henry Shue; Valuing policies in response to climate change: some ethical issues, John Broome; Saved by disaster? Abrupt climate change, political inertia, and the possibility of an intergenerational arms race, Stephen M. Gardiner; Polycentric systems for coping with collective action and global environmental change, Elinor Ostrom. (iii) International Trade: Responsibility and global labor justice, Iris Marion Young; Property rights and the resource curse, Leif Wenar; Fairness in trade I: obligations arising from trading and the pauper-labor argument, Mathias Risse; Name index. -/- See: www.ashgate.com/default.aspx?page=637&calctitle=1&pageSubject=483&sort=pubdate&forthcoming=1&title_i d=9958&edition_id=13385. (shrink)

This paper challenges (in a shorter version than the also listed 2002 LSE discussion paper) the first Gettier counterexample to the tripartite account of knowledge. Noting that 'the man who will get the job' is a description and invoking Donnellan's distinction between their 'referential' and 'attributive' uses, I argue that Smith does not actually believe that the man who will get the job has ten coins in his pocket. Smith's ignorance about who will get the job shows that (...) the belief cannot be understood referentially, his ignorance of the coins in his pocket shows that it cannot be understood attributively. An explanation for why Smith appeared to have justified true belief is given by distinguishing between 'belief' and 'belief in truth'. Smith believes the sentence 'the man who will get the job has ten coins in his pocket' to be true (he mistakenly believes that Jones will get the job, of whom he knows that he has ten coins in his pocket) (hence his 'belief'), the sentence is true (hence 'truth'), and he has sufficient reason to assent to it (hence his 'justification'). But he does not believe the proposition expressed. Hence he does not know it either. (shrink)

This paper challenges the first Gettier counterexample to the tripartite account of knowledge. Noting that 'the man who will get the job' is a description and invoking Donnellan's distinction between their 'referential' and 'attributive' uses, I argue that Smith does not actually believe that the man who will get the job has ten coins in his pocket. Smith's ignorance about who will get the job shows that the belief cannot be understood referentially, his ignorance of the coins in (...) his pocket shows that it cannot be understood attributively. An explanation for why Smith appeared to have justified true belief is given by distinguishing between 'belief' and 'belief in truth'. Smith believes the sentence 'the man who will get the job has ten coins in his pocket' to be true (he mistakenly believes that Jones will get the job, of whom he knows that he has ten coins in his pocket) (hence his 'belief'), the sentence is true (hence 'truth'), and he has sufficient reason to assent to it (hence his 'justification'). But he does not believe the proposition expressed. Hence he does not know it either. (shrink)

Giubilini and Minerva argue that the permissibility of abortion entails the permissibility of infanticide. Proponents of what we refer to as the Birth Strategy claim that there is a morally significant difference brought about at birth that accounts for our strong intuition that killing newborns is morally impermissible. We argue that strategy does not account for the moral intuition that late-term, non-therapeutic abortions are morally impermissible. Advocates of the Birth Strategy must either judge non-therapeutic abortions as impermissible in the later (...) stages of pregnancy or conclude that they are permissible on the basis of premises that are far less intuitively plausible than the opposite conclusion and its supporting premises. (shrink)

The Realist that investigates questions of ontology by appeal to the quantificational structure of language assumes that the semantics for the privileged language of ontology is externalist. I argue that such a language cannot be (some variant of) a natural language, as some Realists propose. The flexibility exhibited by natural language expressions noted by Chomsky and others cannot obviously be characterized by the rigid models available to the externalist. If natural languages are hostile to externalist treatments, then the meanings of (...) natural language expressions serve as poor guides for ontological investigation, insofar as their meanings will fail to determine the referents of their constituents. This undermines the Realist’s use of natural languages to settle disputes in metaphysics. (shrink)

In the quantum-Bayesian approach to quantum foundations, a quantum state is viewed as an expression of an agent’s personalist Bayesian degrees of belief, or probabilities, concerning the results of measurements. These probabilities obey the usual probability rules as required by Dutch-book coherence, but quantum mechanics imposes additional constraints upon them. In this paper, we explore the question of deriving the structure of quantum-state space from a set of assumptions in the spirit of quantum Bayesianism. The starting point is the representation (...) of quantum states induced by a symmetric informationally complete measurement or SIC. In this representation, the Born rule takes the form of a particularly simple modification of the law of total probability. We show how to derive key features of quantum-state space from (i) the requirement that the Born rule arises as a simple modification of the law of total probability and (ii) a limited number of additional assumptions of a strong Bayesian flavor. (shrink)

If non-human animals have high moral status, then we commit a grave moral error by eating them. Eating animals is thus morally risky, while many agree that it is morally permissible to not eat animals. According to some philosophers, then, non-animal ethicists should err on the side of caution and refrain from eating animals. I argue that this precautionary argument assumes a false dichotomy of dietary options: a diet that includes farm-raised animals or a diet that does not include animals (...) of any kind. There is a third dietary option, namely, a diet of plants and non-traditional animal protein, and there is evidence that such a diet results in the least amount of harm to animals. It follows therefore that moral uncertainty does not support the adoption of a vegetarian diet. (shrink)

The probabilities a Bayesian agent assigns to a set of events typically change with time, for instance when the agent updates them in the light of new data. In this paper we address the question of how an agent's probabilities at different times are constrained by Dutch-book coherence. We review and attempt to clarify the argument that, although an agent is not forced by coherence to use the usual Bayesian conditioning rule to update his probabilities, coherence does require the agent's (...) probabilities to satisfy van Fraassen's [1984] reflection principle (which entails a related constraint pointed out by Goldstein [1983]). We then exhibit the specialized assumption needed to recover Bayesian conditioning from an analogous reflection-style consideration. Bringing the argument to the context of quantum measurement theory, we show that "quantum decoherence" can be understood in purely personalist terms---quantum decoherence (as supposed in a von Neumann chain) is not a physical process at all, but an application of the reflection principle. From this point of view, the decoherence theory of Zeh, Zurek, and others as a story of quantum measurement has the plot turned exactly backward. (shrink)

In this paper, I try to cause some good-natured trouble. The issue is, when will we ever stop burdening the taxpayer with conferences devoted to the quantum foundations? The suspicion is expressed that no end will be in sight until a means is found to reduce quantum theory to two or three statements of crisp physical (rather than abstract, axiomatic) significance. In this regard, no tool appears better calibrated for a direct assault than quantum information theory. Far from a strained (...) application of the latest fad to a time-honoured problem, this method holds promise precisely because a large part---but not all---of the structure of quantum theory has always concerned information. It is just that the physics community needs reminding. (shrink)

According to QBism, quantum states, unitary evolutions, and measurement operators are all understood as personal judgments of the agent using the formalism. Meanwhile, quantum measurement outcomes are understood as the personal experiences of the same agent. Wigner’s conundrum of the friend, in which two agents ostensibly have different accounts of whether or not there is a measurement outcome, thus poses no paradox for QBism. Indeed the resolution of Wigner’s original thought experiment was central to the development of QBist thinking. The (...) focus of this paper concerns two very instructive modifications to Wigner’s puzzle: One, a recent no-go theorem by Frauchiger and Renner, and the other a thought experiment by Baumann and Brukner. We show that the paradoxical features emphasized in these works disappear once both friend and Wigner are understood as agents on an equal footing with regard to their individual uses of quantum theory. Wigner’s action on his friend then becomes, from the friend’s perspective, an action the friend takes on Wigner. Our analysis rests on a kind of quantum Copernican principle: When two agents take actions on each other, each agent has a dual role as a physical system for the other agent. No user of quantum theory is more privileged than any other. In contrast to the sentiment of Wigner’s original paper, neither agent should be considered as in “suspended animation.” In this light, QBism brings an entirely new perspective to understanding Wigner’s friend thought experiments. (shrink)

In the Bayesian approach to quantum mechanics, probabilities—and thus quantum states—represent an agent’s degrees of belief, rather than corresponding to objective properties of physical systems. In this paper we investigate the concept of certainty in quantum mechanics. Particularly, we show how the probability-1 predictions derived from pure quantum states highlight a fundamental difference between our Bayesian approach, on the one hand, and Copenhagen and similar interpretations on the other. We first review the main arguments for the general claim that probabilities (...) always represent degrees of belief. We then argue that a quantum state prepared by some physical device always depends on an agent’s prior beliefs, implying that the probability-1 predictions derived from that state also depend on the agent’s prior beliefs. Quantum certainty is therefore always some agent’s certainty. Conversely, if facts about an experimental setup could imply agent-independent certainty for a measurement outcome, as in many Copenhagen-like interpretations, that outcome would effectively correspond to a preexisting system property. The idea that measurement outcomes occurring with certainty correspond to preexisting system properties is, however, in conflict with locality. We emphasize this by giving a version of an argument of Stairs [(1983). Quantum logic, realism, and value-definiteness. Philosophy of Science, 50, 578], which applies the Kochen–Specker theorem to an entangled bipartite system. (shrink)

The appearance of negative terms in quasiprobability representations of quantum theory is known to be inevitable, and, due to its equivalence with the onset of contextuality, of central interest in quantum computation and information. Until recently, however, nothing has been known about how much negativity is necessary in a quasiprobability representation. Zhu :120404, 2016) proved that the upper and lower bounds with respect to one type of negativity measure are saturated by quasiprobability representations which are in one-to-one correspondence with the (...) elusive symmetric informationally complete quantum measurements. We define a family of negativity measures which includes Zhu’s as a special case and consider another member of the family which we call “sum negativity.” We prove a sufficient condition for local maxima in sum negativity and find exact global maxima in dimensions 3 and 4. Notably, we find that Zhu’s result on the SICs does not generally extend to sum negativity, although the analogous result does hold in dimension 4. Finally, the Hoggar lines in dimension 8 make an appearance in a conjecture on sum negativity. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

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

This is a contribution to a Book symposium on The Limits of Free Will: Selected Essays by Paul Russell. Russell provides replies to three critics of The Limits of Free Will. The first reply is to Robert Wallace and focuses on the question of whether there is a conflict between the core compatibilist and pessimist components of the "critical compatibilist" position that Russell has advanced. The second reply is to Angela Smith's discussion of the "narrow" interpretation of moral responsibility (...) responsibility (as defended by R. Jay Wallace) and how best to respond to it. The third and last reply is concerned with Christopher Bennett's criticism of Russell's views concerning "motivational scepticism" and the possibility of pure practical reasons. (shrink)

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

The 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)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

A growing number of epistemologists have endorsed the Ignorance Norm for Inquiry. Roughly, this norm says that one should not inquire into a question unless one is ignorant of its answer. I argue that, in addition to ignorance, proper inquiry requires a certain kind of knowledge. Roughly, one should not inquire into a question unless one knows it has a true answer. I call this the Knowledge Norm for Inquiry. Proper inquiry walks a fine line, holding knowledge that there is (...) an answer in the left hand and ignorance of the answer in the right. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

A long line of epistemologists including Sosa (2021), Feldman (2002), and Chisholm (1977) have argued that, at least for a certain class of questions that we take up, we should (or should aim to) close inquiry iff by closing inquiry we would meet a unique epistemic standard. I argue that no epistemic norm of this general form is true: there is not a single epistemic standard that demarcates the boundary between inquiries we are forbidden and obligated to close. In short, (...) such norms are false because they are insensitive to the potentially ambitious epistemic goals that agents may permissibly bring to bear on an inquiry. Focusing particularly on knowledge-oriented versions of the norm, I argue that ignorance has a positive role to play in epistemic life by licensing prolonged inquiry into questions that we especially care about. (shrink)

Every quantum state can be represented as a probability distribution over the outcomes of an informationally complete measurement. But not all probability distributions correspond to quantum states. Quantum state space may thus be thought of as a restricted subset of all potentially available probabilities. A recent publication (Fuchs and Schack, arXiv:0906.2187v1, 2009) advocates such a representation using symmetric informationally complete (SIC) measurements. Building upon this work we study how this subset—quantum-state space—might be characterized. Our leading characteristic is that the inner (...) products of the probabilities are bounded, a simple condition with nontrivial consequences. To get quantum-state space something more detailed about the extreme points is needed. No definitive characterization is reached, but we see several new interesting features over those in Fuchs and Schack (arXiv:0906.2187v1, 2009), and all in conformity with quantum theory. (shrink)

There is something puzzling about statistical evidence. One place this manifests is in the law, where courts are reluctant to base affirmative verdicts on evidence that is purely statistical, in spite of the fact that it is perfectly capable of meeting the standards of proof enshrined in legal doctrine. After surveying some proposed explanations for this, I shall outline a new approach – one that makes use of a notion of normalcy that is distinct from the idea of statistical frequency. (...) The puzzle is not, however, merely a legal one. Our unwillingness to base beliefs on statistical evidence is by no means limited to the courtroom, and is at odds with almost every general principle that epistemologists have proposed as to how we ought to manage our beliefs. (shrink)

We present a theory of truth in fiction that improves on Lewis's [1978] ‘Analysis 2’ in two ways. First, we expand Lewis's possible worlds apparatus by adding non-normal or impossible worlds. Second, we model truth in fiction as belief revision via ideas from dynamic epistemic logic. We explain the major objections raised against Lewis's original view and show that our theory overcomes them.

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

According to a captivating picture, epistemic justification is essentially a matter of epistemic or evidential likelihood. While certain problems for this view are well known, it is motivated by a very natural thought—if justification can fall short of epistemic certainty, then what else could it possibly be? In this paper I shall develop an alternative way of thinking about epistemic justification. On this conception, the difference between justification and likelihood turns out to be akin to the more widely recognised difference (...) between ceteris paribus laws and brute statistical generalisations. I go on to discuss, in light of this suggestion, issues such as classical and lottery-driven scepticism as well as the lottery and preface paradoxes. (shrink)

One famous scene in The Wolf of Wall Street (2013) is the dialogue between the young Jordan Belfort (Leonardo DiCaprio) and the expert trader Mark Hanna (Matthew McConaughey). Hanna is complaining that the stock market is unpredictable; it’s “fugazi … it’s fairy dust. It doesn’t exist. It’s never landed. It is not matter. It’s not on the element chart. It’s not real”. But the fact that something is unpredictable and non-physical does not imply that it does not exist. On the (...) other hand, its unpredictability, non-physicality, and the fact that the stock market trend is largely determined by investors’ beliefs, do make its nature difficult to grasp. -/- This special issue of Rivista di Estetica aims to explore the financial sector from an ontological point of view. While the ontology of money has been extensively studied, few scholars have focused on the stock market and, more generally, on those entities belonging to the investment landscape. Matters are made more complicated by the fact that the financial sector is characterized by an ever-increasing use of digital technology, including software elements that trade in the market themselves. We believe that a careful study of this phenomenon may help us better to understand the role of artificial agents in the social world. (shrink)

Bayesian classifiers perform well when each of the features is completely independent of the other which is not always valid in real world applications. The aim of this study is to implement and compare the performances of each variant of the Bayesian classifier (Multinomial, Bernoulli, and Gaussian) on anomaly detection in network intrusion, and to investigate whether there is any association between each variant’s assumption and their performance. Our investigation showed that each variant of the Bayesian algorithm blindly follows its (...) assumption regardless of feature property, and that the assumption is the single most important factor that influences their accuracy. Experimental results show that Bernoulli has accuracy of 69.9% test (71% train), Multinomial has accuracy of 31.2% test (31.2% train), while Gaussian has an accuracy of 81.69% test (82.84% train). Going deeper, we investigated and found that each Naïve Bayes variants performances and accuracy is largely due to each classifier assumption, Gaussian classifier performed best on anomaly detection due to its assumption that features follow normal distributions which are continuous, while multinomial classifier have a dismal performance as it simply assumes discreet and multinomial distribution. (shrink)

According to the principle of Conjunction Closure, if one has justification for believing each of a set of propositions, one has justification for believing their conjunction. The lottery and preface paradoxes can both be seen as posing challenges for Closure, but leave open familiar strategies for preserving the principle. While this is all relatively well-trodden ground, a new Closure-challenging paradox has recently emerged, in two somewhat different forms, due to Backes :3773–3787, 2019a) and Praolini :715–726, 2019). This paradox synthesises elements (...) of the lottery and the preface and is designed to close off the familiar Closure-preserving strategies. By appealing to a normic theory of justification, I will defend Closure in the face of this new paradox. Along the way I will draw more general conclusions about justification, normalcy and defeat, which bear upon what Backes :2877–2895, 2019b) has dubbed the ‘easy defeat’ problem for the normic theory. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries (...) yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (shrink)

Distinguishes two senses of 'judgment' on the one hand as meaning a state of 'conviction' or 'belief', and on the other hand as meaning an act of 'affirmation' or 'assertion'. Certainly conviction and assertion stand in close relation to each other, but they delineate two heterogeneous logical spheres, and thereby divide the total field of the theory of judgment into two neighbouring but separate sub-fields. Once this is done it is shown to have implications for our understanding especially of the (...) phenomenon of negation, and of the distinction between negation as affirmation of a negative state of affairs, and negation as act of contradicting the judgment someone else has made. (shrink)

A de minimis risk is defined as a risk that is so small that it may be legitimately ignored when making a decision. While ignoring small risks is common in our day-to-day decision making, attempts to introduce the notion of a de minimis risk into the framework of decision theory have run up against a series of well-known difficulties. In this paper, I will develop an enriched decision theoretic framework that is capable of overcoming two major obstacles to the modelling (...) of de minimis risk. The key move is to introduce, into decision theory, a non-probabilistic conception of risk known as normic risk. (shrink)

I offer a new argument for the elimination of ‘beliefs’ from cognitive science based on Wimsatt’s concept of robustness and a related concept of fragility. Theoretical entities are robust if multiple independent means of measurement produce invariant results in detecting them. Theoretical entities are fragile when multiple independent means of detecting them produce highly variant results. I argue that sufficiently fragile theoretical entities do not exist. Recent studies in psychology show radical variance between what self-report and non-verbal behaviour indicate about (...) participants’ beliefs. This is evidence that ‘belief’ is fragile, and is thus a strong candidate for elimination. 1 Introduction2 Robustness and Fragility2.1 A historical example of robustness2.2 Fragility and elimination3 The Received View4 Evidence for the Fragility of Belief4.1 Contamination and fragility4.2 Implicit association tests and fragility5 Attempts to Preserve the Belief Category for Cognitive Science5.1 Beliefs and aliefs5.2 Contradictory beliefs5.3 In-between beliefs and the unity assumption5.4 Belief sub-classes5.5 Self-deception6 Alternative Mental States7 Conclusion. (shrink)

Recently, a number of epistemologists (notably Feldman [2007], [2009] and White [2005], [2013]) have argued for the rational uniqueness thesis, the principle that any set of evidence permits only one rationally acceptable attitude toward a given proposition. In contrast, this paper argues for extreme rational permissivism, the view that two agents with the same evidence may sometimes arrive at contradictory beliefs rationally. This paper identifies different versions of uniqueness and permissivism that vary in strength and range, argues that evidential peers (...) with different interests need not rationally endorse all the same hypotheses, argues that evidential peers who weigh the theoretic virtues differently can sometimes rationally endorse contradictory conclusions, and finally defends the permissivist appeal to standards against objections in the works of Feldman and White. (shrink)