The in­ten­tion of this pa­per is to po­int out a tr­o­u­ble­so­me si­tu­a­tion in con­tem­po­rary Ser­bian on­to­lo­gi­cal ter­mi­no­logy, and al­so to in­di­ca­te the ways and pre-con­di­ti­ons in terms of hi­story of phi­lo­sophy, hi­story of lan­gu­a­ge and met­ho­do­logy in se­ar­ching for pos­si­ble so­lu­ti­ons. We are al­so trying to cast so­me light on the pr­o­blem of re­la­ti­on­ship bet­we­en lan­gu­a­ge and phi­lo­sop­hi­cal thin­king.

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

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)

The growth of self-tracking and personal surveillance has given rise to the Quantified Self movement. Members of this movement seek to enhance their personal well-being, productivity, and self-actualization through the tracking and gamification of personal data. The technologies that make this possible can also track and gamify aspects of our interpersonal, romantic relationships. Several authors have begun to challenge the ethical and normative implications of this development. In this article, we build upon this work to provide a detailed ethical analysis (...) of the Quantified Relationship. We identify eight core objections to the QR and subject them to critical scrutiny. We argue that although critics raise legitimate concerns, there are ways in which tracking technologies can be used to support and facilitate good relationships. We thus adopt a stance of cautious openness toward this technology and advocate the development of a research agenda for the positive use of QR technologies. (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)

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)

Practical wisdom is the intellectual virtue that enables a person to make reliably good decisions about how, all-things-considered, to live. As such, it is a lofty and important ideal to strive for. It is precisely this loftiness and importance that gives rise to important questions about wisdom: Can real people develop it? If so, how? What is the nature of wisdom as it manifests itself in real people? I argue that we can make headway answering these questions by modeling wisdom (...) on expert skill. Presenting the main argument for this expert skill model of wisdom is the focus of this paper. More specifically, I’ll argue that wisdom is primarily the same kind of epistemic achievement as expert decision-making skill in areas such as firefighting. Acknowledging this helps us see that, and how, real people can develop wisdom. It also helps to resolve philosophical debates about the nature of wisdom. For example, philosophers, including those who think virtue should be modeled on skills, disagree about the extent to which wise people make decisions using intuitions or principled deliberation and reflection. The expert skill model resolves this debate by showing that wisdom includes substantial intuitive and deliberative and reflective abilities. (shrink)

In attempting to form rational personal probabilities by direct inference, it is usually assumed that one should prefer frequency information concerning more specific reference classes. While the preceding assumption is intuitively plausible, little energy has been expended in explaining why it should be accepted. In the present article, I address this omission by showing that, among the principled policies that may be used in setting one’s personal probabilities, the policy of making direct inferences with a preference for frequency information for (...) more specific reference classes yields personal probabilities whose accuracy is optimal, according to all proper scoring rules, in situations where all of the relevant frequency information is point-valued. Assuming that frequency information for narrower reference classes is preferred, when the relevant frequency statements are point-valued, a dilemma arises when choosing whether to make a direct inference based upon relatively precise-valued frequency information for a broad reference class, R, or upon relatively imprecise-valued frequency information for a more specific reference class, R*. I address such cases, by showing that it is often possible to make a precise-valued frequency judgment regarding R* based on precise-valued frequency information for R, using standard principles of direct inference. Having made such a frequency judgment, the dilemma of choosing between and is removed, and one may proceed by using the precise-valued frequency estimate for the more specific reference class as a premise for direct inference. (shrink)

In a pair of recent articles, Brian Leftow and Eleonore Stump offer independent, although similar, accounts of the metaphysics of the Incarnation. Both believe that their Aquinas-inspired theories can offer solutions to the kind of Leibniz’s Law problems that can seem to threaten the logical possibility of this traditional Christian doctrine. In this paper, I’ll have a look at their compositional account of the nature of God incarnate. In the end, I believe their position can be seen to have unacceptable (...) philosophical and theological implications, and that is it inadequate to solve the Leibniz’s law problems that motivate it in the first place. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (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)

In this issue, Ahmadi1 reports on the practice of hymenoplasty—a surgical intervention meant to restore a presumed physical marker of virginity prior to a woman's marriage. As Mehri and Sills2 have stated, these women ‘want to ensure that blood is spilled on their wedding night sheets.’ Although Ahmadi's research was carried out in Iran specifically, this surgery is becoming increasingly popular in a number of Western countries as well, especially among Muslim populations.3 What are the ethics of hymen restoration?Consider the (...) role of the physician. Two of the doctors interviewed by Ahmadi reported being in ‘a perpetual state of guilt because of the surgery's inherent aim at deceiving the groom’ and noted their ‘personal conflict’ at being involved in this deception. Yet: "None of the doctors believed that the surgery was unethical, arguing that the girl could be ‘abused’ and ‘can even die’ if she is discovered not … ". (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 badness of having conflicting emotions is a familiar theme in academic ethics, clinical psychology, and commercial self-help, where emotional harmony is often put forward as an ideal. Many philosophers give emotional harmony pride of place in their theories of practical reason.1 Here we offer a defense of a particular species of emotional conflict, namely, ambivalence. We articulate an conception of ambivalence, on which ambivalence is unresolved inconsistent desire (§1) and present a case of appropriate ambivalence (§2), before considering two (...) alternative defenses of emotional conflict (§3). We then argue that inconsistent desires can be fitting (§4) and that it can be reasonable not to resolve inconsistent desires (§5), before considering an objection (§6) and concluding the discussion (§7). (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.

What would be the consequence of embracing skepticism about free will and/or desert-based moral responsibility? What if we came to disbelieve in moral responsibility? What would this mean for our interpersonal relationships, society, morality, meaning, and the law? What would it do to our standing as human beings? Would it cause nihilism and despair as some maintain? Or perhaps increase anti-social behavior as some recent studies have suggested (Vohs and Schooler 2008; Baumeister, Masicampo, and DeWall 2009)? Or would it rather (...) have a humanizing effect on our practices and policies, freeing us from the negative effects of what Bruce Waller calls the “moral responsibility system” (2014, p. 4)? These questions are of profound pragmatic importance and should be of interest independent of the metaphysical debate over free will. As public proclamations of skepticism continue to rise, and as the mass media continues to run headlines announcing free will and moral responsibility are illusions, we need to ask what effects this will have on the general public and what the responsibility is of professionals. (shrink)

Obóz Kultury 2.0 Mirosław Filiciak, Alek Tarkowski, Agata Jałosińska, Andrzej Klimczuk, Maciej Rynarzewski, Jacek Seweryn, Stunża M., D. Grzegorz, Marcin Wilkowski & Anna Orlik .

The applicability of Bayesian conditionalization in setting one’s posterior probability for a proposition, α, is limited to cases where the value of a corresponding prior probability, PPRI(α|∧E), is available, where ∧E represents one’s complete body of evidence. In order to extend probability updating to cases where the prior probabilities needed for Bayesian conditionalization are unavailable, I introduce an inference schema, defeasible conditionalization, which allows one to update one’s personal probability in a proposition by conditioning on a proposition that represents a (...) proper subset of one’s complete body of evidence. While defeasible conditionalization has wider applicability than standard Bayesian conditionalization (since it may be used when the value of a relevant prior probability, PPRI(α|∧E), is unavailable), there are circumstances under which some instances of defeasible conditionalization are unreasonable. To address this difficulty, I outline the conditions under which instances of defeasible conditionalization are defeated. To conclude the article, I suggest that the prescriptions of direct inference and statistical induction can be encoded within the proposed system of probability updating, by the selection of intuitively reasonable prior probabilities. (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)

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)

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)

Dombrowski and Murdoch offer versions of the ontological argument which aim to avoid two types of objection – those concerned with the nature of the divine, and those concerned with the move from an abstract concept to a mind-independent reality. For both, the nature of the concept of God/Good entails its instantiation, and both supply a supporting argument from experience. It is only Murdoch who successfully negotiates the transition from an abstract concept to the instantiation of that concept, however, and (...) this is achieved by means of an ontological argument from moral experience which, in a reversal of the Kantian doctrine, depends ultimately on a form of the cosmological argument. (shrink)

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

Given the importance of theoretical wisdom in Aristotle’s account of the human good, it is striking that contemporary virtue ethicists have been virtually silent about this intellectual virtue and what contribution it makes – or could make – toward human flourishing. In this paper, I examine, and respond to, two main worries that account for theoretical wisdom’s current marginality. Along the way, I sketch a neo-Aristotelian conception of theoretical wisdom, and argue that this intellectual virtue is more central to the (...) concerns of contemporary virtue ethicists than it has perhaps so far seemed. (shrink)

In this paper I argue for a version of the Total Evidence view according to which the rational response to disagreement depends upon one's total evidence. I argue that perceptual evidence of a certain kind is significantly weightier than many other types of evidence, including testimonial. Furthermore, what is generally called "The Uniqueness Thesis" is actually a conflation of two distinct principles that I dub "Evidential Uniqueness" and "Rationality Uniqueness." The former principle is likely true but the latter almost certainly (...) false. Seeing why the Rationality Uniqueness fails opens the door to seeing how mutual reasonable disagreement is possible even among those who share the same evidence. (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 argues that Sartre’s work as both a literary critic and social philosopher is deeply indebted to his early commitment to phenomenology. The first part of the paper examines the nature of reading and writing in the account of literary meaning that is presented in the transitional text, 'Qu’est-ce que la littérature?' While acknowledging the political turn that occurs in Sartre’s work, we then discuss how the theme of history emerges in the later essay, 'Questions de méthode,' as one (...) that opens up a “double reading” of human motivation. Our conclusion maintains that the Marxist phase of Sartre’s work is based on the hermeneutical notion of comprehension, which provides an anthropological grounding for his existential philosophy. (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)

Does the soul have powers? If so, what general account can philosophy give of powers of the soul? One can broach some of Thomas Aquinas’s more obscure teachings concerning the soul and its powers, such as that the soul alone is the subject of some powers and that powers flow from the soul, by asking these broad questions. Many commentators have preferred, however, to focus on specific powers of the soul, which has resulted in detailed studies of, for example, the (...) intellect and the will. Here, however, I take up powers of the soul in general and, through a causal analysis of their being, articulate what they are. (shrink)

This dissertation discusses the work of Thomas Hobbes, and has two main themes. The first is Hobbes's materialism, and the second is Hobbes's relationships to other philosophers, in particular his place in the mechanist movement that is said to have replaced Aristotelianism as the dominant philosophy in the seventeenth century. -/- I argue that Hobbes does not, for most of his career, believe the general materialist view that bodies are the only substances. He believes, rather, that ideas, which are our (...) main mechanism for thinking about the world, allow us to understand many bodies, but not to understand every thing we recognize to exist. The incomprehensible things include God---and, early in Hobbes's career, the human mind. Discussing materialism and our knowledge of God leads me to engage with the debate over Hobbes's alleged atheism. I argue that the evidence for Hobbes's atheism is weak at best. Hobbes is a sincere theist, though his view is sometimes unusual. -/- My discussion of Hobbes's relationships to other philosophers has three parts. In chapter five I argue that Hobbes's views about method are in important ways similar to Zabarella's. In chapter six I look at Hobbes's rejection of the view, held by some scholastic Aristotelians, that accidents can sometimes exist without inhering in substances. Thus we see two sides of Hobbes's interaction with the Aristotelian tradition. Sometimes that interaction is just rejection, but at other times Hobbes takes over views from that tradition. Then in chapter seven I consider whether, and in what sense, Hobbes is a mechanist. I argue that the narrative of mechanism and Aristotelianism is a less powerful explanation than it has seemed to some to be, because it is hard to see what mechanists have in common. (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)

(v.3) In this paper it is argued that Barad's Agential Realism, an approach to quantum mechanics originating in the philosophy of Niels Bohr, can be the basis of a 'theory of everything' consistent with a proposal of Wheeler that 'observer-participancy is the foundation of everything'. On the one hand, agential realism can be grounded in models of self- organisation such as the hypercycles of Eigen, while on the other agential realism, by virtue of the 'discursive practices' that constitute one aspect (...) of the theory, implies the possibility of the generation of physical phenomena through acts of specification originating at a more fundamental level. This kind of order stems from the association of persisting structures with special mechanisms for sustaining such structures. Included in phenomena that may be generated by these mechanisms are the origin and evolution of life, and human capacities such as mathematical and musical intuition. (shrink)

The focus of this paper is showing that meditation is becoming aware of awareness itself...and this awareness is a field phenomena.

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)

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 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)

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)