The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, some of (...) which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (shrink)

In this paper, I develop and defend a new adverbial theory of perception. I first present a semantics for direct-object perceptual reports that treats their object positions as supplying adverbial modifiers, and I show how this semantics definitively solves the many-property problem for adverbialism. My solution is distinctive in that it articulates adverbialism from within a well-established formal semantic framework and ties adverbialism to a plausible semantics for perceptual reports in English. I then go on to present adverbialism as a (...) theory of the metaphysics of perception. The metaphysics I develop treats adverbial perception as a directed activity: it is an activity with success conditions. When perception is successful, the agent bears a relation to a concrete particular, but perception need not be successful; this allows perception to be fundamentally non-relational. The result is a novel formulation of adverbialism that eliminates the need for representational contents, but also treats successful and unsuccessful perceptual events as having a fundamental common factor. (shrink)

Recent research has relied on trolley-type sacrificial moral dilemmas to study utilitarian versus nonutili- tarian modes of moral decision-making. This research has generated important insights into people’s attitudes toward instrumental harm—that is, the sacrifice of an individual to save a greater number. But this approach also has serious limitations. Most notably, it ignores the positive, altruistic core of utilitarianism, which is characterized by impartial concern for the well-being of everyone, whether near or far. Here, we develop, refine, and validate a (...) new scale—the Oxford Utilitarianism Scale—to dissociate individual differences in the ‘negative’ (permissive attitude toward instrumental harm) and ‘positive’ (impartial concern for the greater good) dimensions of utilitarian thinking as manifested in the general population. We show that these are two independent dimensions of proto-utilitarian tendencies in the lay population, each exhibiting a distinct psychological profile. Empathic concern, identification with the whole of humanity, and concern for future generations were positively associated with impartial beneficence but negatively associated with instrumental harm; and although instrumental harm was associated with subclinical psychopathy, impartial beneficence was associated with higher religiosity. Importantly, although these two dimensions were independent in the lay population, they were closely associated in a sample of moral philosophers. Acknowledging this dissociation between the instrumental harm and impartial beneficence components of utilitarian thinking in ordinary people can clarify existing debates about the nature of moral psychology and its relation to moral philosophy as well as generate fruitful avenues for further research. (shrink)

In December 2013, the Nonhuman Rights Project (NhRP) filed a petition for a common law writ of habeas corpus in the New York State Supreme Court on behalf of Tommy, a chimpanzee living alone in a cage in a shed in rural New York (Barlow, 2017). Under animal welfare laws, Tommy’s owners, the Laverys, were doing nothing illegal by keeping him in those conditions. Nonetheless, the NhRP argued that given the cognitive, social, and emotional capacities of chimpanzees, Tommy’s confinement constituted (...) a profound wrong that demanded remedy by the courts. Soon thereafter, the NhRP filed habeas corpus petitions on behalf of Kiko, another chimpanzee housed alone in Niagara Falls, and Hercules and Leo, two chimpanzees held in research facilities at Stony Brook University. Thus began the legal struggle to move these chimpanzees from captivity to a sanctuary, an effort that has led the NhRP to argue in multiple courts before multiple judges. The central point of contention has been whether Tommy, Kiko, Hercules, and Leo have legal rights. To date, no judge has been willing to issue a writ of habeas corpus on their behalf. Such a ruling would mean that these chimpanzees have rights that confinement might violate. Instead, the judges have argued that chimpanzees cannot be bearers of legal rights because they are not, and cannot be persons. In this book we argue that chimpanzees are persons because they are autonomous. (shrink)

Basic Emotion Theory, or BET, has dominated the affective sciences for decades (Ekman, 1972, 1992, 1999; Ekman and Davidson, 1994; Griffiths, 2013; Scarantino and Griffiths, 2011). It has been highly influential, driving a number of empirical lines of research (e.g., in the context of facial expression detection, neuroimaging studies and evolutionary psychology). Nevertheless, BET has been criticized by philosophers, leading to calls for it to be jettisoned entirely (Colombetti, 2014; Hufendiek, 2016). This paper defuses those criticisms. In addition, it shows (...) that we have good reason to retain BET. Finally, it reviews and puts to rest worries that BET’s commitment to affect programs renders it outmoded. We propose that, with minor adjustments, BET can avoid such criticisms when conceived under a radically enactive account of emotions. Thus, rather than leaving BET behind, we show how its basic ideas can be revised, refashioned and preserved. Hence, we conclude, our new BET is still a good bet. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

Sexual abuse of minors by Catholic priests has been a persistent and widespread problem in the Church. Although more than 80 percent of victims have been boys, prior studies have rejected the idea that the abuse is related to homosexuality among priests. Available data show, however, that the proportion of homosexual men in the priesthood is correlated almost perfectly with the percentage of male victims and with the overall incidence of abuse. Data also show that while the incidence of abuse (...) is lower today than it was three decades ago, it has not declined as much as is commonly believed, and has recently begun to rise amid signs of episcopal complacency about procedures for the protection of children. (shrink)

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

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

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Identification of factors that predict recurrent antisocial behavior is integral to the social sciences, criminal justice procedures, and the effective treatment of high-risk individuals. Here we show that error-related brain activity elicited during performance of an in- hibitory task prospectively predicted subsequent rearrest among adult offenders within 4 y of release (N =96). The odds that an offender with relatively low anterior cingulate activity would be rearrested were approximately double that of an offender with high activity in this region, holding (...) constant other observed risk factors. These results suggest a potential neurocognitive biomarker for persistent antisocial behavior. (shrink)

In this paper, we propose a new concept named the uniform single valued neutrosophic graph. An illustrative example and some properties are examined. Next, we develop an algorithmic approach for computing the complement of the single valued neutrosophic graph. A numerical example is demonstrated for computing the complement of single valued neutrosophic graphs and uniform single valued neutrosophic graph.

This paper focuses on invasive therapeutic procedures, defined as procedures requiring the introduction of hands, instruments, or devices into the body via incisions or punctures of the skin or mucous membranes performed with the intent of changing the natural history of a human disease or condition for the better. Ethical and methodological concerns have been expressed about studies designed to evaluate the effects of invasive therapeutic procedures. Can such studies meet the same standards demanded of those, for example, evaluating pharmaceutical (...) agents? This paper describes a research project aimed at examining the interplay and sometimes apparent conflict between ethical standards for human research and standards for methodological rigor in trials of invasive procedures. The paper discusses how the authors plan to develop a set of consensus standards that, if met, would result in substantial and much-needed improvements in the methodological and ethical quality of such trials. (shrink)

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

We investigate claims about the frequency of "know" made by philosophers. Our investigation has several overlapping aims. First, we aim to show what is required to confirm or disconfirm philosophers’ claims about the comparative frequency of different uses of philosophically interesting expressions. Second, we aim to show how using linguistic corpora as tools for investigating meaning is a productive methodology, in the sense that it yields discoveries about the use of language that philosophers would have overlooked if they remained in (...) their "armchairs of an afternoon", to use J.L. Austin’s phrase. Third, we discuss facts about the meaning of "know" that so far have been ignored in philosophy, with the aim of reorienting discussions of the relevance of ordinary language for philosophical theorizing. (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)

Background: Recent literature on addiction and judgments about the characteristics of agents has focused on the implications of adopting a ‘brain disease’ versus ‘moral weakness’ model of addiction. Typically, such judgments have to do with what capacities an agent has (e.g., the ability to abstain from substance use). Much less work, however, has been conducted on the relationship between addiction and judgments about an agent’s identity, including whether or to what extent an individual is seen as the same person after (...) becoming addicted. Methods: We conducted a series of vignette-based experiments (total N = 3,620) to assess lay attitudes concerning addiction and identity persistence, systematically manipulating key characteristics of agents and their drug of addiction. Conclusions: In Study 1, we found that US participants judged an agent who became addicted to drugs as being closer to ‘a completely different person’ than ‘completely the same person’ as the agent who existed prior to the addiction. In Studies 2-6, we investigated the intuitive basis for this result, finding that lay judgments of altered identity as a consequence of drug use and addiction are driven primarily by perceived negative changes in the moral character of drug users, who are seen as having deviated from their good true selves. (shrink)

Patient centred diagnosis is best practised through shared decision making; an iterative dialogue between doctor and patient, whichrespects a patient’s needs, values, preferences, and circumstances. -/- Shared decision making for diagnostic situations differs fundamentally from that for treatment decisions. This has important implications when considering its practical application. -/- The nature of dialogue should be tailored to the specific diagnostic decision; scenarios with higher stakes or uncertainty usually require more detailed conversations.

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)

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

We develop a conceptually clear, intuitive, and feasible decision procedure for testing satisfiability in the full multi\-agent epistemic logic \CMAELCD\ with operators for common and distributed knowledge for all coalitions of agents mentioned in the language. To that end, we introduce Hintikka structures for \CMAELCD\ and prove that satisfiability in such structures is equivalent to satisfiability in standard models. Using that result, we design an incremental tableau-building procedure that eventually constructs a satisfying Hintikka structure for every satisfiable input set of (...) formulae of \CMAELCD\ and closes for every unsatisfiable input set of formulae. (shrink)

Transoral laser microsurgery applies to the piecemeal removal of malignant tumours of the upper aerodigestive tract using the CO2 laser under the operating microscope. This method of surgery is being increasingly popularised as a single modality treatment of choice in early laryngeal cancers (T1 and T2) and occasionally in the more advanced forms of the disease (T3 and T4), predomi- nantly within the supraglottis. Thomas Kuhn, the American physicist turned philosopher and historian of science, coined the phrase ‘paradigm shift’ in (...) his groundbreaking book The Structure of Scientific Revolutions. He argued that the arrival of the new and often incompatible idea forms the core of a new paradigm, the birth of an entirely new way of thinking. This article discusses whether Steiner and col- leagues truly brought about a paradigm shift in oncological surgery. By rejecting the principle of en block resection and by replacing it with the belief that not only is it oncologically safe to cut through the substance of the tumour but in doing so one can actually achieve better results, Steiner was able to truly revolutionise the man- agement of laryngeal cancer. Even though within this article the repercussions of his insight are limited to the upper aerodigestive tract oncological surgery, his willingness to question other peoples’ dogma makes his contribution truly a genuine paradigm shift. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Background Analysis of aphasic narratives can be a challenge for clinicians. Previous studies have mainly employed measures that categorized speech samples at the word level. They included quantification of the use and misuse of different word classes, presence and absence of narrative contents and errors, paraphasias, and perseverations, as well as morphological structures and errors within a narrative. In other words, a great amount of research has been conducted in the aphasiology literature focusing on micro-linguistic structures of oral narratives. Aspects (...) of macro- linguistic structures, such as the analysis of content information by a speaker, consistency of using cohesive devices to present information within a narrative, and order of presenting information necessary to form a coherent discourse, have not been extensively investigated. The current investigation proposes a clinical analytic system to target three aspects of macro-linguistic structures in narratives among speakers with aphasia. Specifically, (1) the presence of search events (i.e., the mentioning of key events that allow the listener to understand; Capilouto, Wright, &Wagovich, 2006) within a narrative, (2) the sequence of the mentioned events, and (3) the informativeness (i.e., the fulfillment of lexical items that allow the user to understand what the event is detailing) of the event contents, were focused in the proposed framework. Method Ten controls transcripts from were selected from the AphasiaBank (MacWhinney, Fromm, Forbes, & Holland, 2011). Three narrative tasks, including sequential picture description of ‘Refused Umbrella’, procedural narrative of making a ‘Peanut Butter and Jelly Sandwich’, and telling of ‘Cinderella’ story, were used to establish normative data for the basis of analysis. Specifically, the Search Events (e) and Informative Words (i) used by at least 70% of the speakers were listed for each genre. The sequential order of mentioning the Search Events, i.e., common order of events in 90% of the speakers, (s.total) was determined. Twelve speakers with aphasia (nine fluent and three non-fluent) were recruited and administered the Western Aphasia Battery and Object and Action Naming Battery. Their performance in the above three discourse tasks were orthographically transcribed and analyzed using the following measures: e.total, e.matched with norm, e.missed, e.irrlevant, e.extra, s.total, i.pb&j, i.umbr, i.cind, and i.total. Three samples were randomly chosen to be re-analyzed for inter- and intra-rater reliability. Results Results of an independent t-test suggested significant differences between the fluent and non-fluent subjects in sequential order of Search Events for all genres (s.total) and i.total, suggesting sensitivity of this framework to differentiate between the two fluency groups. Results of Pearson product-moment correlations revealed significant relation between Informative Words and WAB spontaneous speech scores, AQ, as well as OAB scores, for both aphasic groups. The mean value of coefficients for intra-rater reliability (0.992), with significant correlations on e.match, e.miss, and e.extra, was higher than that of inter-rater reliability (0.897). Discussion Based on our preliminary results, this objective framework allowed clinical evaluation of impairment in macro-linguistic structures present in aphasic discourse. Further extension should involve more subjects encompassing a wider range of severity with different types of aphasia. (shrink)

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)

A theory of cognitive systems individuation is presented and defended. The approach has some affinity with Leonard Talmy's Overlapping Systems Model of Cognitive Organization, and the paper's first section explores aspects of Talmy's view that are shared by the view developed herein. According to the view on offer -- the conditional probability of co-contribution account (CPC) -- a cognitive system is a collection of mechanisms that contribute, in overlapping subsets, to a wide variety of forms of intelligent behavior. Central to (...) this approach is the idea of an integrated system. A formal characterization of integration is laid out in the form of a conditional-probabilitybased measure of the clustering of causal contributors to the production of intelligent behavior. I relate the view to the debate over extended and embodied cognition and respond to objections that have been raised in print by Andy Clark, Colin Klein, and Felipe de Brigard. (shrink)

Simple regression (regression analysis with a single explanatory variable), and multiple regression (regression models with multiple explanatory variables), typically correspond to very different biological questions. The former use regression lines to describe univariate associations. The latter describe the partial, or direct, effects of multiple variables, conditioned on one another. We suspect that the superficial similarity of simple and multiple regression leads to confusion in their interpretation. A clear understanding of these methods is essential, as they underlie a large range of (...) procedures in common use in biology. Beyond simple and multiple regression in their most basic forms, understanding the key principles of these procedures is critical to understanding, and properly applying, many methods, such as mixed models, generalised models, and causal inference using graphs (including path analysis and its extensions). A simple, but careful, look at the distinction between these two analyses is valuable in its own right, and can also be used to clarify widely-held misconceptions about collinearity (correlations among explanatory variables). There is no general sense in which collinearity is a problem. We suspect that the perception of collinearity as a hindrance to analysis stems from misconceptions about interpretation of multiple regression models, and so we pursue discussions about these misconceptions in this light. In particular, collinearity causes multiple regression coefficients to be less precisely estimated than corresponding simple regression coefficients. This should not be interpreted as a problem, as it is perfectly natural that direct effects should be harder to characterise than univariate associations. Purported solutions to the perceived problems of collinearity are detrimental to most biological analyses. (shrink)

Descartes has been accused of reasoning in a circle since the publication of the Meditations. The Circle is easy to point out: it seems that Descartes employs clear and distinct perceptions to demonstrate God’s existence and benevolence, and the latter, in turn, validates the use of clear and distinct perceptions. But is Descartes really guilty of fallacious argument, or can we break the arc somehow?

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)

R.G. Collingwood (1889-1943) was an English philosopher, historian and practicing archaeologist. His work, particularly in the philosophy of action and history, has been profoundly influential in the 20th and 21st century. Although the importance of his work is indisputable, this is the first book to consider how and why it actually matters. Giussepina D'oro considers the importance of Collingwood as a thinker who thinks kaleidoscopically and, unlike lots of contemporary philosophers, refuses to focus on narrow, technical interests but instead, observes (...) the whole world of thought. Why Collingwood Matters revives Collingwood's conception of the role and character of philosophical analysis and shows how it informs his understanding of the mind, what it means to act, and what it means to understand the past historically. It also argues for the relevance of his metaphilosophical approach to the challenge posed by the Anthropocene and the global environmental crisis. Both an elucidation of Collingwood's thought and a lively exploration of it's contemporary relevance, Why Collingwood Matters provides a much-needed examination of a 20th-century polymath. (shrink)

Philosophers have rightly condemned lookism—that is, discrimination in favor of attractive people or against unattractive people—in education, the justice system, the workplace and elsewhere. Surprisingly, however, the almost universal preference for attractive romantic and sexual partners has rarely received serious ethical scrutiny. On its face, it’s unclear whether this is a form of discrimination we should reject or tolerate. I consider arguments for both views. On the one hand, a strong case can be made that preferring attractive partners is bad. (...) The idea is that choosing partners based on looks seems essentially similar to other objectionable forms of discrimination. (In particular, the preference for attractive partners is arguably both unfair and harmful to a significant degree.) One can try to resist this conclusion in several ways. I consider three possible replies. The first has to do with the possibility of controlling our partner preferences. The second pertains to attractiveness and “good genes”. The last attempts to link certain aspects of attractiveness to a prospective partner’s personality and values. I argue that the first two replies fail conclusively, while the third only amounts to a limited defense of a particular kind of attractiveness preference. So the idea that we should often avoid preferring attractive partners is compelling. (shrink)

“Do Anthropocene narratives confuse an important distinction between the natural and the historical past?” asks Giuseppina D’Oro. D’Oro defends the view that the concept of the historical past is sui generis and distinct from that of the geological past against a new, Anthropocene-inspired challenge to the possibility of a humanistically oriented historiography. She argues that the historical past is not a short segment of geological time, the time of the human species on Earth, but the past investigated from the perspective (...) of a distinctive kind of interest, that of uncovering the norms which governed historical agents in different periods of time. The past for the Egyptologist, or for the Roman historian, is not the same past studied by the palaeontologist or the geologist, not because it is infinitesimal short in comparison to geological time, but because the questions asked by historians concerned with the Egyptian or Roman civilization are not the same kind of questions asked by empirically minded scientists. She argues that the accusation that the distinction between the historical and the natural/geological past, rests on unacceptable form of human exceptionalism is based on the conflation of the concept of the historical past with that of the human past and that keeping alive the nature/culture distinction has important implications for praxis. If the distinction between nature and culture is collapsed, and the corollary that historical agents are not distinct in kind from natural agents (such as yeast and microbes) is accepted, then “the anticipation of the future would become a mere spectator’s sport analogous to the activity of predicting the weather”: collapsing the nature culture distinction, D’Oro argues, undermines the possibility of political action against the very threat (climate change) that motivates Anthropocene narratives in the first instance. (shrink)

We discuss potential biorisks from large language models (LLMs). AI assistants based on LLMs such as ChatGPT have been shown to significantly reduce barriers to entry for actors wishing to synthesize dangerous, potentially novel pathogens and chemical weapons. The harms from deploying such bioagents could be further magnified by AI-assisted misinformation. We endorse several policy responses to these dangers, including prerelease evaluations of biomedical AIs by subject-matter experts, enhanced surveillance and lab screening procedures, restrictions on AI training data, and access (...) controls on biomedical AI. We conclude with a suggestion about future research directions in bioethics. (shrink)

Defense of an account of intrinsic properties in terms of (what is now called) grounding rather than naturalness.

For more than four decades, George Atwood and I have been absorbed in rethinking psychoanalysis as a form of phenomenological inquiry. In the course of this work, I repeatedly made the claim that phenomenology led us inexorably to relationality, but until now I did not offer an explanation of this inexorability. In this article, I show that emotional phenomenology and relationality always already form an indissoluble unity, because relationality is constitutive of emotional experience.

This essay argues that Schelling's late transition from Negative to Positive Philosophy constitutes a pointed inversion of the path of systematic ascent mapped by Hegel for the first time in the Phenomenology's Preface, which itself establishes Hegel's development out of and beyond Schelling's early philosophy; that a key notion to inspire the Hegelian vision articulated in the Preface returns to cap off the critique implicit in Schelling's late inversion, where this notion emerges from their divergent readings of Aristotle's Metaphysics; and (...) finally, that while Hegel's theorization of the end of all philosophizing represents his innovative enlargement from within the framework he finds in Aristotle, Schelling's vision of this same end facilitates the crisis of reason which opens unto revelation, and so is akin to the vision which carries Aquinas beyond Aristotle, albeit in Schelling's post‐Spinozist mode of thought. (shrink)

Multidimensional adjectives are ubiquitous in natural language. An adjective F is multidimensional just in case whether F applies to an object or pair of objects depends on how those objects stand with respect to multiple underlying dimensions of F-ness. Developing a semantics for multidimensional adjectives requires us to address the problem of dimensional aggregation: how do the application conditions of an adjective F in its positive and comparative forms depend on its underlying dimensions? Here we develop a semantics for multidimensional (...) adjectives that incorporates aggregation functions. We then explore an analogy between dimensional aggregation and preference aggregation, bringing results from social choice theory to bear on the number and kind of aggregation functions that are admissible in a context. These results suggest that, for any given adjective, there will often be multiple aggregation functions admissible, meaning that multidimensional comparatives are often vague. (shrink)

David Stove reviews Selwyn Grave's History of Philosophy in Australia, and praises philosophers for thinking harder about the bases of science, mathematics and medicine than the practitioners in the field. The review is reprinted as an appendix to James Franklin's Corrupting the Youth: A History of Philosophy in Australia.

The paper looks at the semantics and ontology of dispositions in the light of recent work on the subject. Objections to the simple conditionals apparently entailed by disposition statements are met by replacing them with so-called 'reduction sentences' and some implications of this are explored. The usual distinction between categorical and dispositional properties is criticised and the relation between dispositions and their bases examined. Applying this discussion to two typical cases leads to the conclusion that fragility is not a real (...) property and that, while both temperature and its bases are, this does not generate any problem of overdetermination. (shrink)

According to a widespread view in metaphysics and philosophy of science, all explanations involve relations of ontic dependence between the items appearing in the explanandum and the items appearing in the explanans. I argue that a family of mathematical cases, which I call “viewing-as explanations”, are incompatible with the Dependence Thesis. These cases, I claim, feature genuine explanations that aren’t supported by ontic dependence relations. Hence the thesis isn’t true in general. The first part of the paper defends this claim (...) and discusses its significance. The second part of the paper considers whether viewing-as explanations occur in the empirical sciences, focusing on the case of so-called fictional models. It’s sometimes suggested that fictional models can be explanatory even though they fail to represent actual worldly dependence relations. Whether or not such models explain, I suggest, depends on whether we think scientific explanations necessarily give information relevant to intervention and control. Finally, I argue that counterfactual approaches to explanation also have trouble accommodating viewing-as cases. (shrink)

Pain may appear to undermine the radically intentionalist view that the phenomenal character of any experience is entirely constituted by its representational content. That appearance is illusory. After categorizing versions of pain intentionalism along two dimensions, I argue that an 'objectivist' and 'non-mentalist' version is the most promising, if it can withstand two objections concerning what we say when in pain, and the distinctiveness of pain. I rebut these objections, in a way available to both opponents of and adherents to (...) the view that experiential content is entirely conceptual. (shrink)

This is a greatly expanded version of my article "Anarchism and the Beats," which was published in the book, The Philosophy of the Beats, by the University Press of Kentucky in 2012. It is both an historical and a philosophical analysis of the postwar American counterculture. It charts the historical origins of the postwar American counterculture from the anarchists and romantic poets of the early nineteenth century to a complex network of beat poets and pacifist anarchists in the early decades (...) after World War II. The beat poets understood themselves to be religious prophets of a new form of liberated consciousness. Poetry was both a means to achieve this new form of consciousness and a means to express that consciousness once it was achieved by other means including travel, psychedelic drugs, sex or meditation. The transformation of consciousness sought by the beats was therefore primarily religious in nature, not political or ideological. However, that does not mean that the beats believed that the transformation of consciousness they sought had no political or social implications. On the contrary, the beats were almost all anarchists. It merely means that, for them, political ideology follows consciousness, not the reverse. (shrink)

ABSTRACT: This article explores the role of principal leadership in creating a thinking school. It contributes to the school leadership literature by exploring the intersection of two important areas of study in education  school leadership and education for thinking  which is a particularly apt area of study, because effective school leadership is crucial if students are to learn to be critical and creative thinkers, yet this connection has not be widely investigated. We describe how one principal, Hinton, turned (...) around an underperforming school by using critical and creative philosophical thinking as the focus for students, staff and parents. Then, drawing on the school leadership literature, the article describes seven attributes of school leadership beginning with four articulated by Leithwood and colleagues (2006) (building vision and setting direction; redesigning the organisation; understanding and developing people; managing the teaching and learning program), and adding three others (influence; self-development; and responding to context). This framework is then used in a case study format in a collaboration between practitioner and researchers to first explore evidence from empirical studies and personal reflection about Hinton’s leadership of Buranda State School, and second to illuminate how these general features of school leadership apply to creating a thinking school. Based on the case study and using the general characteristics of school leadership, a framework for leading a thinking school is described. Because the framework is based on a turnaround school, this framework has wide applicability: to schools that are doing well as an indication of how to implement a contemporary approach to curriculum and pedagogy; and to schools that are underperforming and want a rigorous, high expectation and contemporary way to improve student learning. (shrink)

In this paper I show that we have strong empirical and theoretical reasons to treat the verbs we use in our semantic theorizing—particularly ‘refers to ’, ‘applies to ’, and ‘is true of ’—as intensional transitive verbs. Stating our semantic theories with intensional vocabulary allows us to partially reconcile two competing approaches to the nature and subject-matter of semantics: the Chomskian approach, on which semantics is non-relational, internalistic, and concerns the psychology of language users, and the Lewisian approach, on which (...) semantics is fully relational, specifies truth-conditions, and has metaphysical implications. ITVs have two readings: an intensional, de dicto reading, and a relational, de re reading. A semantic theory stated with the de dicto readings of our semantic verbs captures the core insights of the Chomskian approach to semantics, in part because it allows us to assign extremely fine-grained semantic values to expressions, even when those expressions are empty. On the other hand, the de re reading yields a theory that is fully relational, and issues in truth-conditions. The resulting theories are related—and compatible—in that they are expressed by two different readings of the very same semantic vocabulary, and plausibly, the distinction between these two readings is one of scope. (shrink)

Philosophers of science since Nagel have been interested in the links between intertheoretic reduction and explanation, understanding and other forms of epistemic progress. Although intertheoretic reduction is widely agreed to occur in pure mathematics as well as empirical science, the relationship between reduction and explanation in the mathematical setting has rarely been investigated in a similarly serious way. This paper examines an important particular case: the reduction of arithmetic to set theory. I claim that the reduction is unexplanatory. In defense (...) of this claim, I offer evidence from mathematical practice, and I respond to contrary suggestions due to Steinhart, Maddy, Kitcher and Quine. I then show how, even if set-theoretic reductions are generally not explanatory, set theory can nevertheless serve as a legitimate foundation for mathematics. Finally, some implications of my thesis for philosophy of mathematics and philosophy of science are discussed. In particular, I suggest that some reductions in mathematics are probably explanatory, and I propose that differing standards of theory acceptance might account for the apparent lack of unexplanatory reductions in the empirical sciences. (shrink)

There is good reason to think that, in every case of perceptual consciousness, there is something of which we are conscious; but there is also good reason to think that, in some cases of perceptual consciousness—for instance, hallucinations—there is nothing of which we are conscious. This paper resolves this inconsistency—which we call the presentation problem—by (a) arguing that ‘conscious of’ and related expressions function as intensional transitive verbs and (b) defending a particular semantic approach to such verbs, on which they (...) have readings that lack direct objects or themes. The paper further argues that this approach serves not only as a linguistic proposal about the semantics of ‘conscious of’, but also as a proposal about the metaphysics of conscious states. (shrink)