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)

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)

Der berühmte Ameisenmann E.O. Wilson war schon immer einer meiner Helden - nicht nur ein hervorragender Biologe, sondern eine der winzigen und verschwindenden Minderheit von Intellektuellen, die es zumindest wagt, die Wahrheit über unsere Natur anzudeuten, die andere nicht verstehen oder, soweit sie es verstehen, aus politischen Gründen unermüdlich vermeiden. Leider beendet er seine lange Karriere auf äußerst schäbige Weise als Partei eines ignoranten und arroganten Angriffs auf die Wissenschaft, der zumindest teilweise durch die religiöse Inbrunst seiner Harvard-Kollegenmotiviertist. Es zeigt (...) die abscheulichen Folgen, wenn Universitäten Geld von religiösen Gruppen annehmen, Wissenschaftszeitschriften von großen Namen so bewundert sind, dass sie eine ordnungsgemäße Peer Review vermeiden und wenn Egos außer Kontrolle geraten dürfen. Es führt uns in die Natur der Evolution, die Grundlagen der wissenschaftlichen Methodik, wie Mathematik mit Wissenschaft zusammenhängt, was eine Theorie ausmacht, und sogar, welche Einstellungen zu Religion und Großzügigkeit angemessen sind, wenn wir uns unaufhaltsam dem Zusammenbruch der industriellen Zivilisation nähern. Ich fand Abschnitte in 'Conquest' mit dem üblichen prägnanten Kommentar (obwohl nichts wirklich Neues oder Interessantes, wenn man seine anderen Werke gelesen hat und auf biologie im Allgemeinen ist) in der oftgestylten Prosa, die sein Markenzeichen ist, aber war ziemlich überrascht, dass der Kern des Buches seine Ablehnung inklusiver Fitness (die seit über 50 Jahren ein Standbein der Evolutionsbiologie ist) zugunsten der Gruppenauswahl ist. Man nimmt an, dass von ihm kommen und mit den articles er bezieht sich auf veröffentlicht von sich selbst und Harvard Mathematik Kollege Nowak in großen Peer-Review-Zeitschriften wie Nature, muss es ein wesentlicher Fortschritt sein,, trotz der Tatsache, dass ich wusste, Gruppenauswahl wurde fast überall abgelehnt, da mit jeder großen Rolle in der Evolution. Ich habe zahlreiche Rezensionen im Netz gelesen und viele haben gute Kommentare, aber die, die ich am meisten sehen wollte, war, dass von renommierten Wissenschaftsautor und Evolutionsbiologe Richard Dawkins. Im Gegensatz zu den meisten von Fachleuten, die in Zeitschriften nur für diejenigen mit Zugang zu einer Universität zur Verfügung stehen, ist es leicht im Netz verfügbar, obwohlanscheinend, entschied er sich, es nicht in einer Zeitschrift zu veröffentlichen, da es angemessen abscheulich ist. Leider findet man eine vernichtende Ablehnung des Buches und den acerbic Kommentar über einen wissenschaftlichen Kollegen, den ich je von Dawkins gesehen habe -- über alles in seinem vielen Austausch mit dem verstorbenen und unbeklagten Demagogen und Pseudowissenschaftler Stephan Jay Gould. Obwohl Gould für seine persönlichen Angriffe auf seinen Harvard-Kollegen Wilson berüchtigt war, stellt Dawkins fest, dass ein Großteil von "Conquest" einen unbequem an Goulds häufige Verfehlungen in "bland, unfocussed ecumenicalis" erinnert. Dasselbe gilt mehr oder weniger für Wilsons populäres Schreiben, einschließlich seines jüngsten Buches "The Meaning of Human Existence" – eine weitere schamlose Eigenwerbung seiner diskreditierten Ideen zu Inklusiver Fitness (IF). Dawkins weist darauf hin, dass das berüchtigte 2010-Papier von Nowak, Tarnita und Wilson in Nature von über 140 Biologen, die einen Brief unterzeichnet haben, fast überall abgelehnt wurde und dass es in Wilsons Buch kein Wort darüber gibt. Auch in den folgenden 4 Jahren mit Artikeln, Vorträgen und mehreren Büchern haben sie dies nicht korrigiert. Es gibt keine andere Wahl, als Dawkins trenchant Kommentar zuzustimmen: "Für Wilson nicht zu zugeben, dass er für sich selbst gegen die große Mehrheit seiner professionellen Kollegen spricht - es schmerzt mich, dies von einem lebenslangen Helden zu sagen -- ein Akt mutwilligen Arroganz." Angesichts von Nowaks späterem Verhalten muss man ihn auch einbeziehen. Ich habe das Gefühl, dass einer der fassungslosen Menschen, die man im Fernsehen sieht, interviewt wird, nachdem der nette Mann von nebenan, der seit 30 Jahren alle Kinder babysitten, als Serienmörder entlarvt wird. Dawkins weist auch darauf hin (wie er und andere seit vielen Jahren), dass inklusive Fitness mit dem Neo-Darwinismus (d.h. logischerweise folgt) entsteht und nicht abgelehnt werden kann, ohne die Evolution selbst abzulehnen. Wilson erinnert uns erneut an Gould, der Kreationisten von der einen Seite seines Mundes anprangerte, während er ihnen Trost spendete, indem er endlosen ultraliberalen marxistisch gefärbten Kauderwelsch über Spandrels, unterbrochenes Gleichgewicht und Evolutionspsychologie von der anderen ausspeist. Die Unbestimmtheit und mathematische Opazität (für die meisten von uns) der Mathematik der Gruppen- oder Mehrebenenauswahl ist genau das, was die Sanftmütigen ihnen ermöglichen wollen, dem rationalen Denken in ihren endlosen antiwissenschaftlichen Gerüchten und (in der Wissenschaft) postmodernen Wortsalate zu entkommen. Schlimmer noch, Wilsons "Eroberung" ist ein schlecht durchdachtes und schlampig geschriebenes Durcheinander voller Nonsequiturs, vager Streifzüge, Verwirrungen und Inkohärenz. Eine gute Bewertung, die einige davon im Detail ist, dass von Absolvent Gerry Carter, die Sie im Netz finden können. Wilson hat auch nichts mit unserem gegenwärtigen Verständnis der Evolutionspsychologie (EP) zu tun (siehe z.B. die letzten 300 Seiten von Pinkers 'The Better Angels of our Nature'). Wenn Sie eine seriöse Buchlänge Bericht über die soziale Evolution und einige relevante EP von einem Experten wollen, siehe 'Principles of Social Evolution' von Andrew F.G. Bourke, oder ein nicht ganz so ernster und zugegebenermaßen fehlerhafter und irrender Bericht, aber ein Muss,das Robert Trivers dennoch lesen muss—'The Folly of Fools: The Logic of Deceit and Self-Deception in Human Life' und ältere, aber immer noch aktuelle und durchdringende Werke wie 'The Evolutionof Cooperation':Revised Edition by Robert Axelrod and 'The Biology ofMoral Systems' von Richard Alexander. (shrink)

In this paper, we analyse how GPS-based navigation systems are transforming some of our intellectual virtues and then suggest two strategies to improve our practices regarding the use of such epistemic tools. We start by outlining the two main approaches in virtue epistemology, namely virtue reliabilism and virtue responsibilism. We then discuss how navigation systems can undermine five epistemic virtues, namely memory, perception, attention, intellectual autonomy, and intellectual carefulness. We end by considering two possible interlinked ways of trying to remedy (...) this situation: [i] redesigning the epistemic tool to improve the epistemic virtues of memory, perception, and attention; and [ii] the cultivation of cognitive diligence for wayfinding tasks scaffolding intellectual autonomy and carefulness. (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)

Emotion development research centrally concerns capacities to produce emotions and to think about them. We distinguish these enterprises and consider a novel account of how they might be related. On one recent account, the capacity to have emotions of various kinds comes by way of the acquisition of emotion concepts. This account relies on a constructionist theory of emotions and an embodied theory of emotion concepts. We explicate these elements, then raise a challenge for the approach. It appears to be (...) incompatible with various familiar ways in which cognitions about one’s own emotions can come apart from episodes of emotion. (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)

The use of the symbol ∨for disjunction in formal logic is ubiquitous. Where did it come from? The paper details the evolution of the symbol ∨ in its historical and logical context. Some sources say that disjunction in its use as connecting propositions or formulas was introduced by Peano; others suggest that it originated as an abbreviation of the Latin word for “or,” vel. We show that the origin of the symbol ∨ for disjunction can be traced to Whitehead and (...) Russell’s pre-Principia work in formal logic. Because of Principia’s influence, its notation was widely adopted by philosophers working in logic (the logical empiricists in the 1920s and 1930s, especially Carnap and early Quine). Hilbert’s adoption of ∨ in his Grundzüge der theoretischen Logik guaranteed its widespread use by mathematical logicians. The origins of other logical symbols are also discussed. (shrink)

Tasks, tools, and techniques that we perform, use, and acquire, define the elements of expertise which we value as the hallmarks of goal-driven behavior. Somehow, the creation of tools enables us to define new tasks, or is it that the envisioning of new tasks drives us to invent new tools? Or maybe it is that new tools engender new techniques which then result in new tasks? This jumble of issues will be explored and discussed in this diverse collection of papers. (...) Individually, few of the papers are related to each other by topic or by techniques of analysis. Collectively, all focus on tasks performed using tools and discuss the techniques of tool use which enable differences in performance and expertise across individuals, societies, and (even) species. -/- . (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 first-order temporal logics with □ and ○ of time structures isomorphic to ω (discrete linear time) and trees of ω-segments (linear time with branching gaps) and some of its fragments are compared: the first is not recursively axiomatizable. For the second, a cut-free complete sequent calculus is given, and from this, a resolution system is derived by the method of Maslov.

forall x: Calgary is a full-featured textbook on formal logic. It covers key notions of logic such as consequence and validity of arguments, the syntax of truth-functional propositional logic TFL and truth-table semantics, the syntax of first-order (predicate) logic FOL with identity (first-order interpretations), symbolizing English in TFL and FOL, and Fitch-style natural deduction proof systems for both TFL and FOL. It also deals with some advanced topics such as modal logic, soundness, and functional completeness. Exercises with solutions are available. (...) It is provided in PDF (for screen reading, printing, and a special version for dyslexics), HTML, and in LaTeX source code. (shrink)

It is shown that the infinite-valued first-order Gödel logic G° based on the set of truth values {1/k: k ε w {0}} U {0} is not r.e. The logic G° is the same as that obtained from the Kripke semantics for first-order intuitionistic logic with constant domains and where the order structure of the model is linear. From this, the unaxiomatizability of Kröger's temporal logic of programs (even of the fragment without the nexttime operator O) and of the authors' temporal (...) logic of linear discrete time with gaps follows. (shrink)

Control measures, such as “lockdowns”, have been widely used to suppress the COVID-19 pandemic. Under some conditions, they prevent illness and save lives. But they also exact an economic toll. How should we balance the impact of such policies on individual lives and livelihoods (and other dimensions of concern) to determine which is best? A widely used method of policy evaluation, benefit–cost analysis (BCA), answers these questions by converting all the effects of a policy into monetary equivalents and then summing (...) them up. A different method, social welfare analysis, proceeds by determining the effects of a policy on individual wellbeing and then applying an aggregation formula to them to evaluate the overall effects of a policy. In this chapter, we survey these methods and argue that social welfare analysis has important advantages. One crucial advantage is that it enables ethical considerations relating to the impact of policies on individual wellbeing and its distribution to be incorporated into policy assessments in a transparent way. We illustrate this with a simple numerical model for evaluating pandemic policies that vary in terms of the stringency of the controls that they impose on individual behaviour, showing how the evaluation depends on the ethical significance accorded to their impact on the wellbeing of different age and income groups. (shrink)

The COVID-19 crisis has forced a difficult trade-off between limiting the health impacts of the virus and maintaining economic activity. Welfare economics offers tools to conceptualize this trade-off so that policy-makers and the public can see clearly what is at stake. We review four such tools: the Value of Statistical Life (VSL); the Value of Statistical Life Years (VSLYs); Quality-Adjusted Life-Years (QALYs); and social welfare analysis, and argue that the latter are superior. We also discuss how to choose policies that (...) differentially affect people’s wellbeing. We argue in favor of evaluating policies using a Social Welfare Function (SWF), which evaluates the possible distributions of wellbeing across individuals that may result from a policy. Such a function, we argue, should regard increases in the wellbeing of the less well-off as especially valuable. We then use a model to illustrate how such a framework can help evaluate two broad policy types in response to the pandemic: eradication of the virus, and more lenient control of the spread. Our model reveals how such evaluations depend on many empirical facts but also on key value judgments about the relative importance of health and on the extent of special concern for the worse off. The purpose of this brief is not to make precise recommendations, as conditions vary widely across countries and over time, but to provide a methodology. (shrink)

It is proposed that our memory is made up of individual, unconnected Records, to each of which is attached a Heading. Retrieval of a Record can only be accomplished by addressing the attached Heading, the contents of which cannot itself be retrieved. Each Heading is made up of a mixture of content in more or less literal form and context, the latter including specification of environment and of internal states (e.g. drug states and mood). This view of memory allows an (...) easy account of a number of natural memory phenomena as well as a variety of laboratory findings such as the differences between recall and recognition. The theory further proposes that Headed Records can neither be deleted nor modified. Data apparently against such a hypothesis can be accounted for in terms of the retrieval process. (shrink)

Livro-texto de introdução à lógica, com (mais do que) pitadas de filosofia da lógica, produzido como uma versão revista e ampliada do livro Forallx: Calgary. Trata-se da versão de 13 de outubro de 2022. Comentários, críticas, correções e sugestões são muito bem-vindos.

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)

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)

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)

Rirchard Rorty has criticized the rigiditiy of the classical ethics of Kant, and he claims that we do not have absolute and universal moral norms.

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)

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)

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

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.

This paper argues that higher-order doubt generates an epistemic dilemma. One has a higher-order doubt with regards to P insofar as one justifiably withholds belief as to what attitude towards P is justified. That is, one justifiably withholds belief as to whether one is justified in believing, disbelieving, or withholding belief in P. Using the resources provided by Richard Feldman’s recent discussion of how to respect one’s evidence, I argue that if one has a higher-order doubt with regards to (...) P, then one is not justified in having any attitude towards P. Otherwise put: No attitude towards the doubted proposition respects one’s higher-order doubt. I argue that the most promising response to this problem is to hold that when one has a higher-order doubt about P, the best one can do to respect such a doubt is to simply have no attitude towards P. Higher-order doubt is thus much more rationally corrosive than non-higher-order doubt, as it undermines the possibility of justifiably having any attitude towards the doubted proposition. (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)

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)

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)

Political parties have been the subject of a recent resurgent interest among political philosophers, with prominent contributions spanning liberal to socialist literatures arguing for a more positive appraisal of the role of parties in the operation of democratic representation and public deliberation. In this article, I argue for a similar re-evaluation of the role of political parties within contemporary republicanism. Contemporary republicanism displays a wariness of political parties. In Philip Pettit’s paradigmatic account of republican democracy, rare mentions of political parties (...) often stress their tendency to lead to factionalism or corruption. Others working in the republican tradition such as Richard Bellamy and Ian Shapiro provide more extended discussion of the role of parties, but limit their theoretical function to enabling electoral competition. I argue that political parties play a far more significant role in promoting non-domination than this. In addition to enabling electoral competition, I show that political parties are also essential to the effective operation of two other components of republican democracy: contestation and interest-formation. I further argue that understanding political parties in these terms is compatible with republican democracy more generally, addressing the worry that parties will produce factional rather than common-good oriented public decisions. (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)

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)

In the recent philosophical literature on inquiry, epistemologists point out that their subject has often begun at the point at which you already have your evidence and then focussed on identifying the beliefs for which that evidence provides justification. But we are not mere passive recipients of evidence. While some comes to us unbidden, we often actively collect it. This has long been recognised, but typically epistemologists have taken the norms that govern inquiry to be practical, not epistemic. The recent (...) literature challenges this assumption and uncovers a rich range of questions about the epistemic normativity of inquiry. In this paper, I approach these questions from the formal side of epistemology. Developing out of the philosophy of science, as it did, this branch of epistemology has long discussed inquiry. And, building on the insights of Janina Hosiasson (1931), David Blackwell (1951), and I. J. Good (1967), it has produced a reasonably well-developed framework in which to understand norms of inquiry, both epistemic and practical. In the first half of the paper, I will present the pragmatic versions of this framework due to Hosiasson, Blackwell, and Good, and the epistemic version due to Graham Oddie (1997); in the second half of the paper, I put this framework to work, turning to some of the questions from the recent debate about inquiry and asking how the framework can help us answer them. Questions include: When should we initiate an inquiry, when should we continue it, when should we conclude it, and when should we reopen it? How do epistemic norms of inquiry relate to epistemic norms of belief or credence, and can they conflict, as Jane Friedman (2020) contends? How should we resolve the apparent puzzle raised by Friedman's example of counting the windows in the Chrysler Building? How should we direct our attention, as Georgi Gardiner (2022) asks? How should we choose and reason after receiving evidence we'd rather not have received? And how should we understand the epistemic error that occurs when someone is resistant to evidence in the way Mona Simion (2023) describes? (shrink)

The pantheist ontology of Baruch Spinoza (b.1632 – d.1677) is an attempt to deny the accountability of political evil. -/- Spinoza’s instinct for statist control and his distrust of the common man are displayed in Theological-Political Treatise (published 1670). His masterwork, Ethics (published posthumously in 1677), is a bold attempt (in the guise of ontology) to classify minds and bodies as attributes of the State. -/- In Ethics, Spinoza ‘outlaws’ any vantage point from which we can address or protest the (...) kind of ‘perfect power’ -- and its attendant evils -- that constitute the essence and existence of the State. (shrink)

A dispositional property is a tendency, or potency, to manifest some characteristic behaviour in some appropriate context. The mainstream view in the twentieth century was that such properties are to be explained in terms of more fundamental non-dispositional properties, together with the laws of nature. In the last few decades, however, a rival view has become popular, according to which some properties are essentially dispositional in nature, and the laws of nature are to be explained in terms of these fundamental (...) dispositions. The supposed ability of fundamental dispositions to ground natural laws is one of the most attractive features of the dispositional essentialist position. In this paper, however, I cast doubt on the ability of dispositional essences to ground the laws of nature. In particular I argue that the dispositional essentialist position is not able to coherently respond—sympathetically or otherwise—to Cartwright's challenge that there are no true general laws of nature. (shrink)

This paper discusses the question whether it is possible to explain the notion of a singular term without invoking the notion of an object or other ontological notions. The framework here is that of Michael Dummett's discussion in Frege: Philosophy of Language. I offer an emended version of Dummett's conditions, accepting but modifying some suggestions made by Bob Hale, and defend the emended conditions against some objections due to Crispin Wright. This paper dates from about 1989. It originally formed part (...) of a very early draft of what became my Ph.D. dissertation. I rediscovered it and began scanning it, when I had nothing better to do, in Fall 2001, making some minor editing changes along the way. Suffice it to say that it no longer represents my current views. I hope, however, that it remains of some small interest. (shrink)

이 책자는 형식 논리의 일종인 양상논리에 입문하고 싶으신 분들을 위한 짧은 교재입니다. “양상논리 맛보기” 라는 말마따나, 이 책자는 양상논리에 관심은 있지만 아직 본격적으로 공부를 시작하진 않은 분들께서 ‘맛보기’를 하기에 적합한 안내 책자입니다. 아무쪼록 이 책자가 양상논리를 공부해나가시는데 유용한 첫 발판이 될 수 있기를 바랍니다. / This booklet is a Korean adaptation and translation of Part VIII of forall x: Calgary (Fall 2021 edition), which is intended to be introductory material for modal logic. The original text is based on Robert Trueman's (...) A Modal Logic Primer, which is revised and expanded by Richard Zach and Aaron Thomas-Bolduc in forall x: Calgary. (forall x: Calgary is based on forall x: Cambridge by Tim Button, which is in turn based on forall x by P. D. Magnus, and also includes material from forall x: Lorain County Remix by Cathal Woods and J. Robert Loftis.) This booklet is licensed under a Creative Commons Attribution 4.0 license. (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)

Freud, kendini Kopernik ve Darwin’in de dahil olduğu merkezsizleştirici düşünce hareketi içinde görmekteydi. Ünlü bir pasajında, psikanalizin, “egoya kendi evinin bile efendisi olmadığını, ancak aklında, bilinçten uzak bir biçimde olup bitenlerin kıt bilgisi ile yetinmesi gerektiğini kanıtlamaya çabaladığını” söyler. Kendimizin önemli olduğu hissi veya özdenetim duygumuz, gerçekten kendimize karşı şeffaf olduğumuz inancına mı dayanmaktadır? Bilinç dışının keşfi neden arzularımızın keşfine değersizlik eklemek zorundadır?Freud thought of himself as part of the same “decentering” movement of thought to which Copernicus and Darwin belonged. (...) In a famous passage, he says that psychoanalysis “seeks to prove to the ego that it is not even master in its own house, but must content itself with scanty information of what is going on unconsciously in its mind.” Does our sense of our importance, or our capacity for self-control, really depend on the belief that we are transparent to ourselves? Why should the discovery of the unconscious add humiliation to the discovery of the passions? (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)

J’ai lu de nombreuses discussions récentes sur les limites du calcul et de l’univers en tant qu’ordinateur, dans l’espoir de trouver quelques commentaires sur le travail étonnant du physicien polymathe et théoricien de la décision David Wolpert, mais n’ont pas trouvé une seule citation et je présente donc ce résumé très bref. Wolpert s’est avéré quelques théoricaux d’impossibilité ou d’incomplétude renversants (1992 à 2008-voir arxiv dot org) sur les limites de l’inférence (computation) qui sont si généraux qu’ils sont indépendants de (...) l’appareil faisant le calcul, et même indépendamment des lois de la physique, ainsi ils s’appliquent à travers les ordinateurs, la physique, et le comportement humain. Ils utilisent la diagonalisation de Cantor, le paradoxe menteur et les worldlines (lignes du monde) pour fournir ce qui peut être le théorème ultime dans Turing Machine Theory, et apparemment fournir des aperçus de l’impossibilité, l’incomplétude, les limites du calcul, et l’univers comme ordinateur, dans tous les univers possibles et tous les êtres ou mécanismes possibles, générant, entre autres, un principe d’incertitude mécanique non quantique et une preuve de monothéisme. Il existe des connexions évidentes à l’œuvre classique de Chaitin, Solomonoff, Komolgarov et Wittgenstein et à l’idée qu’aucun programme (et donc aucun dispositif) ne peut générer une séquence (ou un dispositif) avec une plus grande complexité qu’il ne possède. On pourrait dire que cet ensemble de travaux implique l’athéisme puisqu’il ne peut y avoir d’entité plus complexe que l’univers physique et du point de vue wittgensteinien, « plus complexe » n’a aucun sens (n’a pas de conditions de satisfaction, c’est-à-dire véridique ou test). Même un « Dieu » (c’est-à-dire un « dispositif » avec un temps/ espace et une énergie illimité) ne peut pas déterminer si un « nombre » donné est « aléatoire», ni trouver un certain moyen de montrer qu’une « formule » donnée, un « théorème » ou une « phrase » ou un « dispositif » (tous ces jeux de langage complexes) fait partie d’un « système » particulier. Ceux qui souhaitent un cadre complet à jour pour le comportement humain de la vue moderne de deux systemes peuvent consulter mon livre 'The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle' 2nd ed (2019). Ceux qui s’intéressent à plus de mes écrits peuvent voir 'Talking Monkeys --Philosophie, Psychologie, Science, Religion et Politique sur une planète condamnée --Articles et revues 2006-2019 2ème ed (2019) et Suicidal Utopian Delusions in the 21st Century 4th ed (2019) et autres. (shrink)

Après un demi-siècle dans l’oubli, la nature de la conscience est maintenant le sujet le plus chaud dans les sciences du comportement et la philosophie. Commençant par le travail pionnier de Ludwig Wittgenstein dans les années 1930 (les Livres Bleus et Brown) et des années 50 à nos jours par son successeur logique John Searle, j’ai créé la table suivante comme un heuristique pour la poursuite de cette étude. Les lignes montrent divers aspects ou façons d’étudier et les colonnes montrent (...) les processus involontaires et les comportements volontaires comprenant les deux systèmes (deux processus) de la Structure Logique de la Conscience (LSC), qui peuvent également être considérés comme la structure logique de la rationalité (LSR-Searle), du comportement (LSB), de la personnalité (LSP), de la réalité (LSOR), de l’intentionnalité (LSI) - le terme philosophique classique, la psychologie détative , la psychologie descriptive de la pensée (DPT) - ou mieux, le langage de la psychologie descriptive de la pensée (LDPT), termes introduits ici et dans mes autres écrits très récents. Ceux qui souhaitent un cadre complet à jour pour le comportement humain de la vue moderne de deuxemssyst peuvent consulter mon livre 'The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle' 2nd ed (2019). Ceux qui s’intéressent à plus de mes écrits peuvent voir «Talking Monkeys --Philosophie, Psychologie, Science, Religion et Politique sur une planète condamnée --Articles et revues 2006-2019 3e ed (2019) et Suicidal Utopian Delusions in the 21st Century 4th ed (2019) et autres. (shrink)

Richard Rorty’s conception of literature has been criticised more than acclaimed. While Rorty certainly has impacted literary studies, a comprehensive account of his understanding of literature is still lacking. Moreover, while literature is seen as significant to his later work, the philosophical role this plays in Rortyan thought is underexamined and underappreciated. This paper aims to provide an account of the role of literature and the “literary” in Rorty’s philosophy and the functions he assigns to literature and poetry – (...) in a broad and narrow sense – in democratic cultures. Beginning with an account of Rorty’s conceptions of metaphor and “unfamiliar” language, it draws on this to explain Rorty’s parallel view of literature in the “narrower sense” as playing the same role in culture as metaphors do in language. “Stimulating” literature unsettles settled selves and beliefs and expands human imagination. Using Rorty’s readings of Lolita and 1984 as examples, it shows that to him, literature not only plays a part in increasing empathy and solidarity but has a distinct therapeutic epistemological task: it helps individuals and societies adopt a more pluralist, ironist, post-metaphysical outlook. Both are important democratic functions. For these reasons, Rorty recommends that we work to realise a “literary” culture that rejects any ontologically inflected distinctions between kinds of texts, where philosophy becomes comparative “literary” criticism, and we see literature in the “narrower sense” as equally necessary material for making selves, communities and just institutions as any philosophical or political treatise. (shrink)

This paper examines 18th-century Annamese Neo-Confucian discourse on conceptual issues related to zhongguo and the hua-yi dichotomy as expressed across a diversity of 18th-century writings. I engage with Huang Chun-chieh’s theory of “contextual turn” and localized subjectivity in 18th-century East Asian Confucianisms by arguing that 18th-century Annamese Neo-Confucianism operated along a dissimilar ideological trajectory which affirmed “geographic China, political China, and cultural China” as a transdynastic and singular zhongguo from which Annam received its politico-cultural legitimation and prestige. This discourse of (...) dependence on institutional recognition and geographical connection to the Chinese zhongguo distinguished 18th-century Annamese literati not only from contemporaneous modes of Confucian intellectuality in Japan and Joseon, but also from foundational conceptions of Vietic statehood characteristic of the early Le dynasty. My analysis of metaphysical theories invoked by 18th-century Annamese literati in their discussions of zhongguo and the rise of human civilization engages with both Huang Chun-chieh’s theory of a philological turn away from the metaphysical commitments in 18th-century East Asian Confucianisms and Alexander Woodside’s theory of pre-modern Vietnamese Confucianism being characterized by a non-metaphysical “classical primordialism.”. (shrink)

The Homeostatic Property Cluster (HPC) account of natural kinds has become popular since it was proposed by Richard Boyd in the late 1980s. Although it is often taken as a defining natural kinds as such, it is easy enough to see that something's being a natural kind is neither necessary nor sufficient for its being an HPC. This paper argues that it is better not to understand HPCs as defining what it is to be a natural kind but instead (...) as providing the ontological realization of (some) natural kinds. (shrink)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his work was (...) disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

Это отличный обзор генов / окружающей среды взаимодействия на поведение и, несмотря на то, немного от, это легко и стоит читать. Они начинаются с двойных исследований, которые показывают подавляющее влияние генетики на поведение. Они отмечают все более известные исследования Джудит Харрис, которые расширяют и обобщают факты, которые разделяют домашнюю среду, почти не влияет на поведение и что приемные дети вырастают такими же разными от своих сводных братьев и сестер, как люди, выбранные случайным образом. Один из основных моментов, что они (и (...) почти все, кто обсуждает поведенческой генетики) не отметить, что сотни (тысячи в зависимости от вашей точки зрения) человеческих поведенческих универсалий, в том числе все основы нашей личности, на 100% определяется нашими генами, без каких-либо изменений в нормах. Каждый видит дерево как дерево, а не камень, ищет и ест пищу, сердится и ревнует и т.д. Таким образом, то, что они в основном говорят о том, сколько окружающей среды (культура) может повлиять на степень, в которой различные черты показаны, а не их внешний вид. Наконец, они обсуждают евгеники в обычной политически корректной моды, не заметив, что мы и все организмы являются продуктами евгеники природы и что попытки победить естественный отбор с медициной, сельского хозяйства и цивилизации в целом, являются катастрофическими для любого общества, которое сохраняется в этом. До 50% всех зачатий, или около 100 миллионов/год, заканчиваются ранним спонтанным абортом, почти все без того, чтобы мать знала об этом. Это естественное выбраковка дефектных генов стимулирует эволюцию, сохраняет нас относительно генетически здоровыми и делает возможным общество. Дисгении достаточно, чтобы уничтожить цивилизацию, но перенаселенность будет do его впервую очередь. Те, кто желает всеобъемлющего до современных рамок для человеческого поведения из современных двух systEms зрения могут проконсультироваться с моей книгой"Логическая структура философии, психологии, Минd иязык в Людвиг Витгенштейн и Джон Сирл"2-й ред (2019). Те, кто заинтересован в более моих работ могут увидеть "Говоря обезьян - -Философия, Психология, Наука, Религия и Политика на обреченной планете - Статьи и обзоры 2006-2017' 3rd ed (2019) и другие. (shrink)