In this eleventh book of scilogs – called in-turns and out-turns –, one may find new and old questions and solutions, referring mostly to topics on Neutrosophy, but also Multispace, with miscellaneous addition of topics on Physics, Mathematics, or Sociology – email messages to research colleagues, or replies, notes about authors, articles, or books, spontaneous ideas, and so on. -/- Exchanging ideas with Prem Kumar Singh, Feng Liu, Nicolae Bălașa, Jimmy Quellet, Minodora Rușchița, Frank Gelli, A. R. Vătuiu, Victor Christianto, (...) Vladimir I. Rogozhin, Robert Neil Boyd, Akira Kanda, Stefan Spaarmann, Oliver Consa, Yabin Shao, Junle Zhuo, Nivetha Martin, Said Broumi, Jean Dezert, Erick González, Tomasz Witczak, B. De Baets, I. Couso, D. Dubois, L. Good, Mihaela Colhon, Atiqe Ur Rahman, Muhammad Saeed, Muhammad Ihsan, Edeline Nancy, Shawkat Alkhazaleh, Shazia Rana, Vasantha Kandasamy, Santanu Acharjee, Mohamed Al-Shmrani, Parimala Manie, Mehmet Unver, Murat Olgun, Adel Aleidhri, Akira Kanda, Ilanthenral Kandasamy, Mircea Zărnescu, R. Tayebi Khorami, Arsham Borumand Saeid, Maisam Jdid, M. Abobala, Riad Hamido, Rafael Rojas, Esmaeil Zarei, Faisal Khan, Rouzbeh Abbassi, Adel Al-Odhari, Henry Garrett, Ackbar Rezaei, Saeid Jafari, Karthika Muthusamy, Harish Garg, Huda E. Khalid, Gonca D. Güngör, Muslim A. Noah Zainal, Fakhry Asad Agusfrianto, Madeleine Al-Tahan, Mariam Hariri, Yudi Mahatma, Masoud Ghods, Marco Brigliadori, Luis Enrique Aponte Pérez, Amr Mohammed, M. Aslam (in order of reference in the book). (shrink)

In this ninth book of scilogs collected from my nest of ideas, one may find new and old questions and solutions, – in email messages to research colleagues, or replies, and personal notes, some handwritten on the planes to, and from international conferences, about topics on Neutrosophy and its applications, such as: Neutrosophic Bipolar Set, Linguistic Neutrosophic Set, Neutrosophic Resonance Frequency, n-ary HyperAlgebra, n-ary NeutroHyperAlgebra, n-ary AntiHyperAlgebra, Plithogenic Crisp Graph, Plithogenic Fuzzy Graph, Plithogenic Intuitionistic Fuzzy Graph, Plithogenic Neutrosophic Graph, Plithogenic (...) Real Number Graph, Plithogenic Complex Number Graph, Plithogenic Neutrosophic Number Graph, and many more. -/- Exchanging ideas with: Tareq Al-Shami, Riad Khidr Al-hamido, Mohammad Akram, B. De Baets, Robert Neil Boyd, Said Broumi, Terman Frometa-Castillo, Yilmaz Ceven, D. Dubois, Harish Garg, L. Godo, Erik Gonzalez, Yanhui Guo, Mohammad Hamidi, E. Hüllermeier, W. B. Vasantha Kandasamy, Mary Jansi, Nivetha Martin, Mani Parimala, Akbar Rezaei, Bouzina Salah, Christy Vincent, Jun Ye.‬‬‬. (shrink)

The purpose of this article is to present several immediate consequences of the introduction of a new constant called Lambda in order to represent the object ``nothing" or ``void" into a standard set theory. The use of Lambda will appear natural thanks to its role of condition of possibility of sets. On a conceptual level, the use of Lambda leads to a legitimation of the empty set and to a redefinition of the notion of set. It lets also clearly appear (...) the distinction between the empty set, the nothing and the ur-elements. On a technical level, we introduce the notion of pre-element and we suggest a formal definition of the nothing distinct of that of the null-class. Among other results, we get a relative resolution of the anomaly of the intersection of a family free of sets and the possibility of building the empty set from ``nothing". The theory is presented with equi-consistency results . On both conceptual and technical levels, the introduction of Lambda leads to a resolution of the Russell's puzzle of the null-class. (shrink)

The debates on the scientificity of social sciences in general, and sociology in particular, are recurring. From the original methodenstreitat the end the 19th Century to the contemporary controversy on the legitimacy of “regional epistemologies”, a same set of interrogations reappears. Are social sciences really scientific? And if so, are they sciences like other sciences? How should we conceive “research programs” Lakatos (1978) or “research traditions” for Laudan (1977) able to produce advancement of knowledge in the field of social and (...) human phenomena? Is the progress of knowledge in social sciences similar to the one generally observed in natural sciences? Is it possible to evaluate the relative merits of each one of these research programs? -/- These debates are important vectors of social and intellectual polarization. The historical divide between the positivist and the hermeneutics poles precedes the structure of the contemporary debate around the epistemic space of social sciences, It is not only a question of renewing the opposition between a monist view of sciences (e.g. McIntyre, 1996) and a dualistic one (e.g. Geertz, 1973) or even a trialist view of sciences (e.g. Lepenies, 1985). It is also a question of asserting dichotomies transformed into framework (including when it is a question of exceeding them): nature-culture, nomothetic-idiographic, models-narrative, structure-history, cause-reason, explanation-comprehension. -/- In this short introduction, we provide, in section 2, a first overview of this epistemological debate in social science. Section 3 proposes a different standpoint on the same questions, by introducing both ontological and methodological aspects in this basic epistemological debate. Namely, following (Hollis, 1994) oppositions of the explanation - understanding, causes - meaning, etc., types discussed in the firsts ection are comparatively examined together with oppositions of the structure - action, holism - individualism types. This allows us to discus show multi-agent design, by integrating various dimensions and standpoints in the same framework (Phan, Amblard, 2007, Chapters 1, 5, 14) can help us to shift these boundaries, and to bypass these oppositions. As model building and ontology design are at the core of this process (Phan, Amblard, 2007, Chapter 12), Section4 discusses various issues of the art of modelling, starting both from economists’ and sociologists’ current standpoints. (shrink)

This article-testimony can be seen as an example of a maybe new discipline that could be called "scientific metaphysics" made of thoughts experiments, definitions, some proofs, some explanations, some conjectures. Of course, to be called science, the discipline needs some possibility of "verification" too. We will see if it can be considered. -/- We start from a thought experiment: -/- Can the universe defined as U_Def be aware conscious of itself as whole? -/- This question is a variant of the (...) more familiar: -/- Can the universe be aware conscious? -/- We can distinguish two main approaches in human history in the attempts at answering this second question: 1) the approach by the bottom with a weak version of consciousness: it includes "panpsychic" like theories. 2) the approach by the head with a strong version of consciousness: it includes "holistic" theories. Spinoza's "Pantheism", for example, can be considered as one of them, even if some interpretations of Spinoza's metaphysics are not satisfied with the equation "god = universe". -/- The purpose developed in this article belongs to the second kind of approach. After a definition of the universe \emph{U}$_{\textit{Def}} $ in 7 points and the introduction of 3 premisses, one of them being devoted to our definition of "strong consciousness", we suggest an answer to the initial question and we draw the most important among numerous consequences: - semantical jump by META-abstraction and introduction of the holistic semantics; - extension of the natural language to a supra-natural language; - highlighting of a higher-order solipsism; - etc. -/- We devote some attention to the notion of "model" in its logical and philosophical acceptation and we introduce the notion of evolutional self-modelization. (shrink)

This article consists in two parts that are complementary and autonomous at the same time. -/- In the first one, we develop some surprising consequences of the introduction of a new constant called Lambda in order to represent the object ``nothing" or ``void" into a standard set theory. On a conceptual level, it allows to see sets in a new light and to give a legitimacy to the empty set. On a technical level, it leads to a relative resolution of (...) the anomaly of the intersection of a family free of sets. -/- In the second part, we show the interest of introducing an operator of potentiality into a standard set theory. Among other results, this operator allows to prove the existence of a hierarchy of empty sets and to propose a solution to the puzzle of "ubiquity" of the empty set. -/- Both theories are presented with equi-consistency results (model and interpretation). -/- Here is a declaration of intent : in each case, the starting point is a conceptual questionning; the technical tools come in a second time\\[0.4cm] \textbf{Keywords:} nothing, void, empty set, null-class, zero-order logic with quantifiers, potential, effective, empty set, ubiquity, hierarchy, equality, equality by the bottom, identity, identification. (shrink)

A key source of support for the view that challenging people’s beliefs about free will may undermine moral behavior is two classic studies by Vohs and Schooler (2008). These authors reported that exposure to certain prompts suggesting that free will is an illusion increased cheating behavior. In the present paper, we report several attempts to replicate this influential and widely cited work. Over a series of five studies (sample sizes of N = 162, N = 283, N = 268, N (...) = 804, N = 982) (four preregistered) we tested the relationship between (1) anti-free-will prompts and free will beliefs and (2) free will beliefs and immoral behavior. Our primary task was to closely replicate the findings from Vohs and Schooler (2008) using the same or highly similar manipulations and measurements as the ones used in their original studies. Our efforts were largely unsuccessful. We suggest that manipulating free will beliefs in a robust way is more difficult than has been implied by prior work, and that the proposed link with immoral behavior may not be as consistent as previous work suggests. (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)

Consider the concept combination ‘pet human’. In word association experiments, human subjects produce the associate ‘slave’ in relation to this combination. The striking aspect of this associate is that it is not produced as an associate of ‘pet’, or ‘human’ in isolation. In other words, the associate ‘slave’ seems to be emergent. Such emergent associations sometimes have a creative character and cognitive science is largely silent about how we produce them. Departing from a dimensional model of human conceptual space, this (...) article will explore concept combinations, and will argue that emergent associations are a result of abductive reasoning within conceptual space, that is, below the symbolic level of cognition. A tensor-based approach is used to model concept combinations allowing such combinations to be formalized as interacting quantum systems. Free association norm data is used to motivate the underlying basis of the conceptual space. It is shown by analogy how some concept combinations may behave like quantum-entangled particles. Two methods of analysis were presented for empirically validating the presence of non-separable concept combinations in human cognition. One method is based on quantum theory and another based on comparing a joint probability distribution with another distribution based on a separability assumption using a chi-square goodness-of-fit test. Although these methods were inconclusive in relation to an empirical study of bi-ambiguous concept combinations, avenues for further refinement of these methods are identified. (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)

Similarity-based cognition is commonplace. It occurs whenever an agent or system exploits the similarities that hold between two or more items—e.g., events, processes, objects, and so on—in order to perform some cognitive task. This kind of cognition is of special interest to cognitive neuroscientists. This paper explicates how similarity-based cognition can be understood through the lens of radical enactivism and why doing so has advantages over its representationalist rival, which posits the existence of structural representations or S-representations. Specifically, it is (...) argued that there are problems both with accounting for the content of S-representations and with understanding how neurally-based structural similarities can work as representations in guiding intelligent behavior. Finally, with these clarifications in place, it is revealed how radical enactivism can commit to an account of similarity-based cognition in its understanding of neurodynamics. (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)

IPCC SPECIAL REPORT ON CLIMATE CHANGE AND LAND (SRCCL) -/- Chapter 3: Climate Change and Land: An IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems.

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)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

The 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)

In terms of validity in Kripke frames, a modal formula expresses a universal monadic second-order condition. Those modal formulae which are equivalent to first-order conditions are called elementary. Modal formulae which have a certain persistence property which implies their validity in all canonical frames of modal logics axiomatized with them, and therefore their completeness, are called canonical. This is a survey of a recent and ongoing study of the class of elementary and canonical modal formulae. We summarize main ideas and (...) results, and outline further research perspectives. (shrink)

Do laypeople think that moral responsibility is compatible with determinism? Recently, philosophers and psychologists trying to answer this question have found contradictory results: while some experiments reveal people to have compatibilist intuitions, others suggest that people could in fact be incompatibilist. To account for this contradictory answers, Nichols and Knobe (2007) have advanced a ‘performance error model’ according to which people are genuine incompatibilist that are sometimes biased to give compatibilist answers by emotional reactions. To test for this hypothesis, we (...) investigated intuitions about determinism and moral responsibility in patients suffering from behavioural frontotemporal dementia. Patients suffering from bvFTD have impoverished emotional reaction. Thus, the ‘performance error model’ should predict that bvFTD patients will give less compatibilist answers. However, we found that bvFTD patients give answers quite similar to subjects in control group and were mostly compatibilist. Thus, we conclude that the ‘performance error model’ should be abandoned in favour of other available model that best fit our data. (shrink)

A dilemma exists when a doctor is faced with a child or young person who refuses medically indicated treatment. The Gillick case has been interpreted by many to mean that a child of sufficient age and intelligence could validly consent or refuse consent to treatment. Recent decisions of the Court of Appeal on a child's refusal of medical treatment have clouded the issue and undermined the spirit of the Gillick decision and the Children Act 1989. It is now the case (...) that a child patient whose competence is in doubt will be found rational if he or she accepts the proposal to treat but may be found incompetent if he or she disagrees. Practitioners are alerted to the anomalies now exhibited by the law on the issue of children's consent and refusal. The impact of the decisions from the perspectives of medicine, ethics, and the law are examined. Practitioners should review each case of child care carefully and in cases of doubt seek legal advice. (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)

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)

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.

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)

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)

This article is a preliminary presentation of conjunctive paraconsistency, the claim that there might be non-explosive true contradictions, but contradictory propositions cannot be considered separately true. In case of true ‘p and not p’, the conjuncts must be held untrue, Simplification fails. The conjunctive approach is dual to non-adjunctive conceptions of inconsistency, informed by the idea that there might be cases in which a proposition is true and its negation is true too, but the conjunction is untrue, Adjunction fails. While (...) non-adjunctivism is a well-known option, the other view is not so much studied nowadays, but it was not unknown in the tradition, and there are some positive suggestions, in recent literature, that the position is plausible and deserves to be developed. The article compares conjunctivism, non-adjunctivism and dialetheism, then focuses on some possible justifications, costs and benefits of the conjunctive view. (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)

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)

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)

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)

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)

The verb 'imagine' admits of perspectival modification: we can imagine things from above, from a distant point of view, or from the point of view of a Russian. But in such cases, there need be no person, either real or imagined, who is above or distant from what is imagined, or who has the point of view of a Russian. We call this the puzzle of perspectival displacement. This paper sets out the puzzle, shows how it does not just concern (...) language, but also states of imagining themselves, and then presents a solution. The solution draws on the idea that many reports of imagining conceal a distinctive kind of question, and such concealed questions have an extra argument place for (what we will call) an experiencer from whose perspective things are imagined. This solution has a range of advantages over other proposals in the literature, and helps to advance two debates concerning perspectival engagement with fiction. (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)

Susan Schneider (2019) has proposed two new tests for consciousness in AI (artificial intelligence) systems, the AI Consciousness Test and the Chip Test. On their face, the two tests seem to have the virtue of proving satisfactory to a wide range of consciousness theorists holding divergent theoretical positions, rather than narrowly relying on the truth of any particular theory of consciousness. Unfortunately, both tests are undermined in having an ‘audience problem’: Those theorists with the kind of architectural worries that motivate (...) the need for such tests should, on similar grounds, doubt that the tests establish the existence of genuine consciousness in the AI in question. Nonetheless, the proposed tests constitute progress, as they could find use by some theorists holding fitting views about consciousness and perhaps in conjunction with other tests for AI consciousness. (shrink)

Prior’s puzzle is standardly taken to be the puzzle of why, given the assumption that that-clauses denote propositions, substitution of “the proposition that P” for “that P” within the complements of many propositional attitude verbs is invalid. I show that Prior’s puzzle is much more general than is ordinarily supposed. There are two variants on the substitutional form of the puzzle—a quantificational variant and a pronominal variant—and all three forms of the puzzle arise in a wide range of grammatical positions, (...) rather than merely in the complements of propositional attitude verbs. The generalized puzzle shows that a range of proposed solutions to the original puzzle fail, or are radically incomplete, and also reveals the connections between Prior’s puzzle and debates over the nature of semantic types and higher-order quantification. I go on to develop a novel, higher-order solution to the generalized form of the puzzle, and I argue that this higher-approach is superior to its first-order alternatives. (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)

Ramsification is a well-known method of defining theoretical terms that figures centrally in a wide range of debates in metaphysics. Prior's puzzle is the puzzle of why, given the assumption that that-clauses denote propositions, substitution of "the proposition that P" for "that P" within the complements of many propositional attitude verbs sometimes fails to preserve truth, and other times fails to preserve grammaticality. On the surface, Ramsification and Prior's puzzle appear to have little to do with each other. But Prior's (...) puzzle is much more general than is ordinarily appreciated, and Ramsification requires a solution to the generalized form of Prior's puzzle. Without such a solution, a wide range of theories will either fail to imply their Ramsey sentences, or have Ramsey sentences that are ill-formed. As a consequence, definitions of theoretical terms given using the Ramsey sentence will be either incorrect or nonsensical. I present a partial solution to the puzzle that requires making use of a neo-Davidsonian language for scientific theorizing, but the would-be Ramsifier still faces serious challenges. (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)

Mathematicians distinguish between proofs that explain their results and those that merely prove. This paper explores the nature of explanatory proofs, their role in mathematical practice, and some of the reasons why philosophers should care about them. Among the questions addressed are the following: what kinds of proofs are generally explanatory (or not)? What makes a proof explanatory? Do all mathematical explanations involve proof in an essential way? Are there really such things as explanatory proofs, and if so, how do (...) they relate to the sorts of explanation encountered in philosophy of science and metaphysics? (shrink)

This paper argues that the concept and role of ‘institutional racism’ in contemporary discussions of race should be reconsidered. It starts by distinguishing between ‘intrinsic institutional racism’, which holds that institutions are racist in virtue of their constitutive features, and ‘extrinsic institutional racism’, which holds that institutions are racist in virtue of their negative effects. It accepts intrinsic institutional racism, but argues that a ‘disparate impact’ conception of extrinsic conception faces a number of objections, the most serious being that it (...) has no plausible account of what it is that makes extrinsically racist institutions racist. It also argues that claims about the explanatory indispensability of institutional racism are overstated (individual racism is at least as important), critiques structural approaches to racial inequality, and suggests that there is reason to doubt whether institutional reform can provide us with all that morality may require in the racial domain. (shrink)

The many-property problem has traditionally been taken to show that the adverbial theory of perception is untenable. This paper first shows that several widely accepted views concerning the nature of perception---including both representational and non-representational views---likewise face the many-property problem. It then presents a solution to the many-property problem for these views, but goes on to show how this solution can be adapted to provide a novel, fully compositional solution to the many-property problem for adverbialism. Thus, with respect to the (...) many-property problem, adverbialism and several widely accepted views in the philosophy of perception are on a par, and the problem is solved. (shrink)

Vendler’s :161–173, 1979) puzzle about imagination is that the sentences ‘Imagine swimming in that water’ and ‘Imagine yourself swimming in that water’ seem at once semantically different and semantically the same. They seem semantically different, since the first requires you to imagine ’from the inside’, while the second allows you to imagine ’from the outside.’ They seem semantically the same, since despite superficial dissimilarity, there is good reason to think that they are syntactically and lexically identical. This paper sets out (...) the puzzle and offers a novel solution. Our proposal is that, just as there is knowledge-wh, there is also imagining-wh and that the inside/outside distinction Vendler points to is properly understood as a distinction within imagining-wh. In particular, to imagine swimming from the inside is to imagine what it feels like to swim, while to imagine swimming from the outside is to imagine what it looks like to swim. We show that this proposal is well grounded in both the semantics and syntax of ‘imagine.’ We also argue it makes better sense than its rivals of the data Vendler found so puzzling. (shrink)

Following neo-Aristotelians Alasdair MacIntyre and Martha Nussbaum, we claim that humans are story-telling animals who learn from the stories of diverse others. Moral agents use rational emotions, such as compassion which is our focus here, to imaginatively reconstruct others’ thoughts, feelings and goals. In turn, this imaginative reconstruction plays a crucial role in deliberating and discerning how to act. A body of literature has developed in support of the role narrative artworks (i.e. novels and films) can play in allowing us (...) the opportunity to engage imaginatively and sympathetically with diverse characters and scenarios in a safe protected space that is created by the fictional world. By practising what Nussbaum calls a ‘loving attitude’, her version of ethical attention, we can form virtuous habits that lead to phronesis (practical wisdom). In this paper, and taking compassion as an illustrative focus, we examine the ways that students’ moral education might usefully develop from engaging with narrative artworks through Philosophy for Children (P4C), where philosophy is a praxis, conducted in a classroom setting using a Community of Inquiry (CoI). We argue that narrative artworks provide useful stimulus material to engage students, generate student questions, and motivate philosophical dialogue and the formation of good habits which, in turn, supports the argument for philosophy to be taught in schools. (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)

In this paper I present an empirical solution to the puzzle of Macbeth's dagger. The puzzle of Macbeth's dagger is the question of whether, in having his fatal vision of a dagger, Macbeth sees a dagger. I answer this question by addressing a more general one: the question of whether perceptual verbs are intensional transitive verbs (ITVs). I present seven experiments, each of which tests a collection of perceptual verbs for one of the three features characteristic of ITVs. One of (...) these features is Nonexistence: the failure of sentences involving transitive verbs to entail the existence of their direct objects. The experiments reveal that with respect to all three of these features, "see" behaves much more like a paradigmatically extensional verb than an intensional one. But surprisingly, unlike "see", "perceive" behaves much more like a paradigmatically intensional verb. This shows that the category of perceptual verbs is not uniform with respect to the features of intensionality; while Macbeth does not see a dagger, he may still perceive one. (shrink)

Gauss’s quadratic reciprocity theorem is among the most important results in the history of number theory. It’s also among the most mysterious: since its discovery in the late 18th century, mathematicians have regarded reciprocity as a deeply surprising fact in need of explanation. Intriguingly, though, there’s little agreement on how the theorem is best explained. Two quite different kinds of proof are most often praised as explanatory: an elementary argument that gives the theorem an intuitive geometric interpretation, due to Gauss (...) and Eisenstein, and a sophisticated proof using algebraic number theory, due to Hilbert. Philosophers have yet to look carefully at such explanatory disagreements in mathematics. I do so here. According to the view I defend, there are two important explanatory virtues—depth and transparency—which different proofs (and other potential explanations) possess to different degrees. Although not mutually exclusive in principle, the packages of features associated with the two stand in some tension with one another, so that very deep explanations are rarely transparent, and vice versa. After developing the theory of depth and transparency and applying it to the case of quadratic reciprocity, I draw some morals about the nature of mathematical explanation. (shrink)

“Philosophy as a way of life” has its roots in ancient ethics and has attracted renewed interest in recent decades. The aim in this paper is to construct a contemporized image of Socrates, consistent with the textual evidence. The account defers concern over analytical/theoretical inquiry into virtue, in favor of a neo-existentialist process of self-examination informed by the virtue of what is called “moral seriousness.” This process is modeled on Frankfurt’s hierarchical account of self-identification, and the paper suggests an expansion (...) of Frankfurt’s concept of a person to include “full” personhood, in which the apprehended “meaning” of one’s “whole life” is taken as a necessary condition for eudaimonia (meaning of life) and is characterized by phenomenological transcendence. In addition, the importance of the informed scrutiny of a community of philosophers to the self-examination process is discussed. (shrink)

This article discusses the adequacy of Rawls’ theory of justice as a tool for racial justice. It is argued that critics like Charles W Mills fail to appreciate both the insights and limits of the Rawlsian framework. The article has two main parts spread out over several different sections. The first is concerned with whether the Rawlsian framework suffices to prevent racial injustice. It is argued that there are reasons to doubt whether it does. The second part is concerned with (...) whether a Rawlsian framework has the resources to rectify past racial injustice. It is argued that it has more resources to do this than Mills allows. This second part of the article centers on two Rawlsian ideas: ideal theory and the fair equality of opportunity principle. It is argued that ideal theory is essential for the kind of rectificatory work that Mills wants nonideal theory to do, and that where there is a socioeconomic legacy of past injustice, it is hard to see how FEO could be implemented if it did no rectificatory work, a result which means that there is less need to turn to nonideal theory at all. (shrink)