The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

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)

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)

This essay explores the role of God’s omnipresence in Newton’s natural philosophy, with special emphasis placed on how God is related to space. Unlike Descartes’ conception, which denies the spatiality of God, or Gassendi and Charleton’s view, which regards God as completely whole in every part of space, it is argued that Newton accepts spatial extension as a basic aspect of God’s omnipresence. The historical background to Newton’s spatial ontology assumes a large part of our investigation, but with attention also (...) focused on the details of Newton’s unique approach to these traditional Scholastic conceptions. (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.

Possible worlds models of belief have difficulties accounting for unawareness, the inability to entertain (and hence believe) certain propositions. Accommodating unawareness is important for adequately modelling epistemic states, and representing the informational content to which agents have in principle access given their explicit beliefs. In this paper, I develop a model of explicit belief, awareness, and informational content, along with an sound and complete axiomatisation. I furthermore defend the model against the seminal impossibility result of Dekel, Lipman and Rustichini, according (...) to which three intuitive conditions preclude non-trivial unawareness on any possible worlds model of belief. (shrink)

This paper begins with a puzzle regarding Lewis' theory of radical interpretation. On the one hand, Lewis convincingly argued that the facts about an agent's sensory evidence and choices will always underdetermine the facts about her beliefs and desires. On the other hand, we have several representation theorems—such as those of (Ramsey 1931) and (Savage 1954)—that are widely taken to show that if an agent's choices satisfy certain constraints, then those choices can suffice to determine her beliefs and desires. In (...) this paper, I will argue that Lewis' conclusion is correct: choices radically underdetermine beliefs and desires, and representation theorems provide us with no good reasons to think otherwise. Any tension with those theorems is merely apparent, and relates ultimately to the difference between how 'choices' are understood within Lewis' theory and the problematic way that they're represented in the context of the representation theorems. For the purposes of radical interpretation, representation theorems like Ramsey's and Savage's just aren't very relevant after all. (shrink)

An exploratory pilot study with a small homogenous sample of Christian English speaking participants provided support for an alternative research hypothesis that a Christ consciousness contemplation with Heart Prayer of HeartMath techniques was significantly associated with increasing psychophysiological coherence, sense of coherence, spirituality and health perceptions. Participants described feelings of a peaceful place in oneness and connection with Christ. Integrative findings point towards Christ consciousness as an ultimately non-dual process of sensing vibrational resonance radiating from the human heart. Implications for (...) further research are discussed. (shrink)

This integral investigation explored phenomenological and neurophysiologic, individual and collective dimensions of Christian Trinitarian meditation experiences in a volunteer, convenience sample of 10 practicing Christians, 6 men and 4 women, with a mean age of 48 years and an age range from 21 to 85 years. Participants meditated for a minimum period of 15 minutes, during which neurophysiologic data in the form of electroencephalographic (EEG), electromyographic (EMG), blood volume pulse (BVP) and respiratory activity were recorded. A phenomenological analysis indicated that (...) the meditation process generally involved a movement from body to mind to spirit as evident in reports of an increasingly relaxed, contented and focused state of consciousness characterised by Christian Trinitarian imagery, wonder, surrender, peace, bliss, openness and formlessness. The neuropsychological findings indicated significant increases, from baseline to meditation recordings, in the alpha and beta range, accompanied by increasing mean trends in the theta and gamma range, and decreasing mean trends in the delta range, EMG, BVP and respiration. Integrative findings indicated the practical theological value of small doses of Christian Trinity meditation to enhance spiritual life for those forms of waking, thinking, conscious behaviour needed in everyday world involvement and healing. Findings were discussed in relation to further integrative investigations and interventions with practical theological implications. (shrink)

The research was generally motivated by a dearth of studies on joy, and particularly inspired by a book of joy celebrating the inter-spiritual dialogue between the Dalai Lama and Desmond Tutu. Its aim was to investigate whether the direct contemplation of joy would be associated with improvements in psychophysiological coherence, spirituality and various positive emotions and feelings. Integrative quantitative and qualitative findings emerging from a small pilot study, including a convenience sample of six participants with a mean age of 42 (...) years and age range of 25-69 years, supported the research hypothesis. Significant quantitative increases in psychophysiological coherence, spirituality and positive feelings were coherently and consistently supported by participants' individual and collective experiences. Integrative discussion amplified the paradoxical theme of joy through suffering in human emotional and spiritual life. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

One of the more obscure arguments for Rawls’ difference principle dubbed ‘the Pareto argument for inequality’ has been criticised by G. A. Cohen (1995, 2008) as being inconsistent. In this paper, we examine and clarify the Pareto argument in detail and argue (1) that justification for the Pareto principles derives from rational selfinterest and thus the Pareto principles ought to be understood as conditions of individual rationality, (2) that the Pareto argument is not inconsistent, contra Cohen, and (3) that the (...) kind of bargaining model required to arrive at the particular unequal distribution that the difference principle picks out is a model that is not based on bargaining according to one’s threat advantage. (shrink)

This is, to the best of my knowledge, the first published attempt at a rigorous logical formalization of a passage in Leibniz's Monadology. The method we followed was suggested by Johannes Czermak.

In lieu of an abstract, here is a brief excerpt of the content:Comments on “Moral Complicity in Induced Pluripotent Stem Cell Research”W. Malcolm Byrnes, Ph.D. and Edward J. FurtonIn his article titled “Moral Complicity in Induced Pluripotent Stem Cell Research,” Mark T. Brown (2009) unfortunately mischaracterizes my ethical analysis of the use of induced pluripotent stem (iPS) cells for replacement therapies, or treatments (Byrnes 2008). In my paper, which Brown cites, I argue that, just as it is ethically acceptable for (...) parents to allow their children and themselves to be immunized using vaccines produced by cell lines derived from human fetuses aborted in the past, it is also acceptable for persons in the future to benefit from treatments that use iPS cells validated using human embryonic stem (ES) cell lines [End Page 202] derived in the past. The assumption I make is that iPS cells would have to be shown to be functionally equivalent to human ES cells—i.e., validated—before they could be used for cell replacement treatments. (If it turns out that this assumption is incorrect, and primate or even mouse ES cells can be used for the validation, then all residual ethical problems will disappear and there will be no ethical problems whatsoever associated with iPS cells.) I wrote:... [I]n both cases, the origin of the treatment is in a one-time event: either the one-time use of aborted fetuses to obtain cell lines (e.g., MRC-5 and WI- 38) to grow weakened virus strains for vaccine production, or the one-time destruction of human embryos to validate iPS cells, which then effectively replace embryonic stem cells. In the latter case, if no additional embryonic stem cell lines are derived, then derivation of the existing lines could be considered a “one-time” event in the past, albeit an event that extended over a several-year period(Byrnes 2008, p. 287, emphasis added).Note the phrase “if no additional embryonic stem cell lines are derived.” The derivation of ES cell lines inherently involves destruction of embryos; indeed, that is why many people, including me, are opposed to human ES cell research. In my article, I am arguing that, if no additional ES cell lines are derived, then no additional human embryos will be destroyed, and the destruction of human embryos will lie in the past. In this case, embryo destruction could be considered a past event, just as the abortion of a human fetus from which vaccine-producing cell lines were derived is a past, albeit tragic, event.In the process of building his argument that proponents of iPS cell research are morally complicit in embryo destruction, Brown (2009, p. 15) casts me as being in favor of the “derivation of new embryonic stem [cell lines].” This is the exact opposite of my position. In fact, I am opposed to further destruction of human embryos. I believe that the hundreds of ES cell lines already in existence are more than sufficient to validate iPS cells and so no additional lines need to be derived. This means that no additional human embryos will need to be destroyed.Apparently based on the misperception that I support future destruction of human embryos, Brown concludes that “Byrnes’s endorsement of ongoing iPSC validation studies would seem to implicate him and those who follow his lead in formal and material complicity in what they perceive as moral evil” (p. 16). He writes that “explicit formal complicity would attach because he [Byrnes] knowingly and intentionally recommends that embryos be killed in order to facilitate a transition to a future in which no more embryos need be destroyed” (p. 16). Additionally, my “followers” and I would be guilty of “proximate material complicity” as well as “remote material complicity” (p. 16). Unfortunately, this broad condemnation is based on a misconception of my actual position.An additional problem involves Brown’s use of a quotation he attributes to me: [End Page 203]Once embryonic stem cells are used to successfully validate iPS cells, they will no longer be needed and their association with iPS cells will lie in the past. Is there not an element of sadness and resignation in accepting something (iPS cells) associated with an unjust act (destruction of an... (shrink)

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

In this paper, we present a formalism for handling polysemy in spatial expressions based on supervaluation semantics called standpoint semantics for polysemy (SSP). The goal of this formalism is, given a prepositional phrase, to define its possible spatial interpretations. For this, we propose to characterize spatial prepositions by means of a triplet ⟨ image schema, semantic feature, spatial axis⟩⁠. The core of SSP is predicate grounding theories, which are formulas of a first-order language that define a spatial preposition through the (...) semantic features of its trajector and landmark. Precisifications are also established, which are a set of formulae of a qualitative spatial reasoning formalism that aims to provide the spatial characterization of the trajector with respect to the landmark. In addition to the theoretical model, we also present results of a computational implementation of SSP for the preposition ‘in’. (shrink)

This paper investigates Newton’s ontology of space in order to determine its commitment, if any, to both Cambridge neo-Platonism, which posits an incorporeal basis for space, and substantivalism, which regards space as a form of substance or entity. A non-substantivalist interpretation of Newton’s theory has been famously championed by Howard Stein and Robert DiSalle, among others, while both Stein and the early work of J. E. McGuire have downplayed the influence of Cambridge neo-Platonism on various aspects of Newton’s own spatial (...) hypotheses. Both of these assertions will be shown to be problematic on various grounds, with special emphasis placed on Stein’s influential case for a non-substantivalist reading. Our analysis will strive, nonetheless, to reveal the unique or forward-looking aspects of Newton’s approach, most notably, his critical assessment of substance ontologies, that help to distinguish his theory of space from his neo-Platonic contemporaries and predecessors. (shrink)

J. McTaggart argues that the philosophical conception of time is constituted by the notions of fluid and static time. Since, on his view, neither notion is philosophically viable, he concludes that time is nothing but an illusion that arises from our distorted perception of essentially atemporal reality. In the paper, I argue that despite McTaggart’s failure to prove the unreality of time as such, he does succeed in establishing his lesser claim that the concept of fluid time is without any (...) ontological import whatsoever. (shrink)

This inquiry is addressed to two questions: (1) what if any logical relations might exist between the concepts of desire and action (as they and the distinctions to which they commit us are ensconced in ordinary parlance), and (2) what if any causal or significant non-causal (i.e., material) relations might ever exist between instances of desire and action? -/- It is held that any credible move to deal with such questions must initially, and at some length, specify the employment conditions (...) for the terms 'want' and 'desire'. This is accomplished in the first two chapters wherein a set of premises is generated for the argument of the inquiry which is presented in full and concluded in the third and final chapter. Premises generated devolve from treatment of the following major topics: (a) the grammar of 'want' and 'desire', (b) the ontological status of wants, (c) first-person and third-person want ascriptions, (d) the sorts of things which may be desired (desiderabilia), (e) wants and lacks, (f) wants and wishes, (g) the 'conflicts' of desires and reason and desire, (h) four major candidates for logical relations between wants and acts, (i) the issue of causation, and (j) the placement of Desire in an adequate ontology of persons. -/- It is argued that every major candidate for a logical relation between wants and acts (or our warrant for believing that such a connection exists) breaks down upon analysis; that little warrant exists for construing wants as causes of acts; that wants and acts are related in significant non-logical and non-causal (i.e., material) respects; and that any fully adequate theory of human action must undertake ontology, placing the category of Desire squarely in the foreground. This project represents neither a general theory of desire nor a general theory of human action. It is rather conceived as a propaedeutic to any such inquiry. It is essentially revisionist in intent, setting out on the one hand to challenge existing claims about wants and acts and, on the other hand, proposing a more satisfactory approach to the issue. In no sense is it suggested that recent Anglo-American contributions are without merit. It is rather argued that they are often inadequate contributions vis-a-vis the larger requirements for an adequate theory of human action. (shrink)

This paper reflects on an article that appeared after the death of A.J. Ayer, which complains about what British philosophers focus on. I propose that the content of the philosophy curriculum can be predicted from a rational actor model.

Modern bioethics is clearly dominated by deontologists who believe that we have some way of identifying morally correct and incorrect acts or rules besides taking account of their consequences. Robert M. Veatch is one of the most outspoken of those numerous modern medical ethicists who agree in rejecting all forms of teleological, utilitarian, or consequentialist ethical theories. This paper examines his critique of utilitarianism and shows that the utilitarianism of John Stuart Mill is either not touched at all by his (...) critique or can be defended against it. This article argues that the dominant deontological majority is mistaken and that a utilitarian theory of moral action very much like Mill’s is precisely what is needed by modern medical ethics and by those medical practitioners who are resolved to practice medicine in a reasonable and morally acceptable manner. (shrink)

This paper proposes that there is common ground between H.J. Rose’s A Handbook of Greek Mythology and Robert Graves’s The Greek Myths, in that both seem to think that it is a bad idea to meet a certain demand: to provide a handbook that is reliable, easy to consult, and suitable for students of certain literary tastes.

This paper pays tribute to the distinguished legal and political philosopher Joseph Raz, who recently passed away. I present a response to Donald Davidson on conceptual schemes which tries to imitate Raz’s writing style, which attracts me despite the difficulties it poses. The response includes a definition.

This paper considers whether the saying, “It’s who you know, not what you know” can be used instead of jargon-laden studies of inequality. I argue that it is not a good replacement in some cases and present a challenge to standard Bourdieusian explanations of inequality in some fields. The paper is written as a pastiche of the distinguished political philosopher Joseph Raz.

This paper contains a brief pastiche of analytic philosopher Carrie Ichikawa Jenkins, responding to the sociological theories of Pierre Bourdieu.

Traditional hedonists like Epicurus, Bentham and Sidgwick were quantitative hedonists who assumed that pleasures and pains differ, not just from each other, but also from other pleasures and pains only in such quantitatively measurable ways as intensity, duration, and nearness or remoteness in time. They also differ with respect to their sources or causes. John Stuart Mill introduced an interesting and important complication into the modern theory of hedonism by insisting that pleasures also differ qualitatively as well as quantitatively. This (...) article thoroughly and critically examines Mill’s attempt to explain what qualitative differences might mean, and it proposes, defends, and extends a plausible theory of qualitative differences. (shrink)

J.G. Frazer tells us about a last resort technique which Cambodian hunters use when they have caught nothing in their nets. The “technique” is they act as if they themselves have got caught in the net. Frazer explains this as the consequence of magical thinking, but I propose a different explanation.

This is a one page handout, presenting a puzzle from J.G. Frazer regarding why, to become the priest of Diana at Nemi, one had to first break a bough in the sacred grove.

This paper presents an objection to the theory of names according to which what a name refers to is determined by a description that the speaker or writer associates with that name. Some names are associated with paradoxical descriptions. I use the reputations of Henry Sidgwick and J.M.E. McTaggart to illustrate this problem.

In this paper, I present two puzzles arising from J.M. Coetzee’s novel Elizabeth Costello, a fiction which is closely connected to analytic philosophy.

This is a review of Thomas Jay Oord’s book on The Uncontrolling Love of God in which he develops a very persuasive and highly original process account of how God’s love, power, and providence relate to matters of human freedom, randomness in nature and history, natural laws, miracles, and evil. This review summarizes the main points in each of his eight chapters and offers a few critical and constructive comments on them.

A summary and brief critique of two closely related books by Thomas Jay Oord.

This is an excellent though largely uncritical introduction to, and defence of, Robert Nozick‟s Anarchy, State and Utopia (New York: Basic Books, 1974). It is also quite a good introduction to libertarianism. It is full of good arguments. I shall confine myself to critical remarks. My responses are mainly in the order that matters arise in the book.

This book presents Robert S. Hartman’s formal theory of value and critically examines many other twentieth century value theorists in its light, including A.J. Ayer, Kurt Baier, Brand Blanshard, Paul Edwards, Albert Einstein, William K. Frankena, R.M. Hare, Nicolai Hartmann, Martin Heidegger, G.E. Moore, P.H. Nowell-Smith, Jose Ortega y Gasset, Charles Stevenson, Paul W. Taylor, Stephen E. Toulmin, and J.O. Urmson.

One of the cornerstones of western theology is the doctrine of divine omnipotence. God is traditionally conceived of as an omnipotent or all-powerful being. However, satisfactory analyses of omnipotence are notoriously elusive. In this paper, I first consider some simple attempts to analyze omnipotence, showing how each fails. I then consider two more sophisticated accounts of omnipotence. The first of these is presented by Edward Wierenga; the second by Thomas Flint and Alfred Freddoso. I argue that both of these accounts (...) fail. Finally, I propose and defend a novel account of omnipotence. (shrink)

For decades scholars thought they knew Hume's position on the existence of causes and objects he was a sceptic. However, this received view has been thrown into question by the `new readings of Hume as a sceptical realist. For philosophers, students of philosophy and others interested in theories of causation and their history, The New Hume Debate is the first book to fully document the most influential contemporary readings of Hume's work. Throughout, the volume brings the debate beyond textual issues (...) in Hume to contemporary philosophical issues concerning causation and knowledge of the external world and issues in the history of philosophy, offering the reader a model for scholarly debate. This revised paperback edition includes three new chapters by Janet Broughton, Peter Kail and Peter Millican. Contributors: Kenneth A. Richman, Barry Stroud, Galen Strawson, Kenneth P. Winkler, John P. Wright, Simon Blackburn, Edward Craig, Martin Bell, Daniel Flage, Anne Jaap Jacobson, Rupert Read, Janet Broughton, Peter Millican, Peter Kail. (shrink)

Riječ “intelektualac” francuskog je porijekla, nastala krajem 19. vijeka. Stvorena tokom afere Dreyfus, uglavnom se odnosi na one mislioce koji su spremni da interveniraju u javnom forumu, čak i ako to znači da sebe izlažu riziku (Le Sueur 2001:2). Teoretičari kao što su Edward Said, Paul Ricoeur, Jean-Paul Sartre i Michael Waltzer dali su doprinos diskusiji o intelektualcima: intelektualca Said vidi kao kritički nastrojenog autsajdera, Ricoeur kao političkog edukatora, Sartre kao čovjeka od akcije, a Waltzer kao brižnog insajdera. Opisati intelektualca (...) na ovaj način, pak, ne spominje prostor unutar kojeg intelektualac djeluje, tj. građansko društvo. Upravo se u takvom prostoru ljudskog udruživanja i odnosnih mreža može promovirati kultura dijaloga, tolerancije, umjerenosti i uzajamno korisnog rješavanja sukoba, upravo onakva kultura kakva otjelotvorava stavove i vrijednosti demokratizacije. Mada intelektualac, onakav kakav je gore opisan, igra značajnu ulogu u održavanju dobro razvijenih demokratskih društava, u postkonfliktnim društvima, kakva su i kosovsko i bosanskohercegovačko, pojavljuje se potreba za intelektualcem koji je više od pukog kritičara društva, edukatora, čovjeka od akcije i saosjećajnog pojedinca. I tu na scenu stupa hiperintelektualac. Najupečatljivija karakteristika hiperintelektualca je možda upravo stepen u kojem se intelektualac bavi društvenom kritikom, političkim obrazovanjem, akcijom i “insajderizmom”, ne kao ideolog, već kao nestranačka fi gura. Društvena kritika i političko obrazovanje hiperintelektualca manifestiraju se na nestranački način, tako da se jasno čuje sve što je moguće i napadati i braniti, i sa jedne i sa druge strane. To je poseb-. (shrink)

The author interprets three stories from recently Neolithic cultures (Melanesian, African Bushman, and Inuit) and a fourth story from an oral tradition of Haitian women. All four are about women and perhaps, judging by their content, composed by women. The author trained with Edward Whitmont and developed his interpretation technique in decades of practice with dreams as a Jungian analyst. He adds a new tool, the use of repetition, in which the same point is made by a series of different (...) details. Repetition provides an internal test for the accuracy of an interpretation. The author updates Jung’s concept of archetypes to incorporate an understanding of Darwinian evolution (which Jung lacked), new knowledge of the function of genes, and new knowledge of the emergence of complexity in dynamic and adaptive systems. He compares his interpretations of the four stories with other scholars’ interpretations, in particular the extraordinary work of Michael Wessels on African Bushman legends. Though Wessels criticized Jung for imposing his ‘colonial’ theory of universal archetypes, both Jung and Wessels insisted that interpretation requires a dialogue between two agents in which both are subjects, neither being dominated or objectified. In the four stories, the author shows, symbolic consciousness began with women. The anthropologist Chris Knight proposed something similar in 1991 in his controversial book Blood Relations: Menstruation and the Origins of Culture. (shrink)

Plant diseases are numerous in the world of agriculture. These diseases cause a lot of trouble to most farmers. Among these common diseases, we single out the diseases that affect the Passion fruit, which is affected by about seven diseases, with different symptoms for each disease. Today, technology is facilitating human life in all areas of life, and among these facilities are expert system, a computer program that uses artificial-intelligence methods to solve problems within a specialized domain that ordinarily requires (...) human expertise. The first expert system was developed in 1965 by Edward Feigen Baum and Joshua Lederberg of Stanford University in California, U.S. Dendral, as their expert system was later known, was designed to analyses chemical compounds. Expert systems now have commercial applications in fields as diverse as medical diagnosis, petroleum engineering, and financial investing and other areas, and with reference to expert systems and their importance to humans, an integrated expert system has been created in the agricultural field that diagnoses Passion diseases using CLIPS Expert System language. The system was used to design and implement the proposed expert system. The system facilitates the diagnosis of Passion -related diseases. There is no doubt that this expert system will help farmers and those involved in the agricultural field to diagnose Passion -related diseases. Objectives: is to help farmers diagnose Passion diseases in the correct way and how to treat these diseases. Method: The system contains a program project that diagnoses 7 diseases that affect Passion and the seven diseases are: Brown spot, Septoria spot, Root and crown rot, Fusarium wilt, Anthracnose, Woodiness virus, Scab. Results: The expert system was evaluated by farmers and praised for helping them with it. Conclusion: The expert system for diagnosing Passion diseases is effective and usable. (shrink)

Information can be public among a group. Whether or not information is public matters, for example, for accounts of interdependent rational choice, of communication, and of joint intention. A standard analysis of public information identifies it with (some variant of) common belief. The latter notion is stipulatively defined as an infinite conjunction: for p to be commonly believed is for it to believed by all members of a group, for all members to believe that all members believe it, and so (...) forth. This analysis is often presupposed without much argument in philosophy. Theoretical entrenchment or intuitions about cases might give some traction on the question, but give little insight about why the identification holds, if it does. The strategy of this paper is to characterize a practical-normative role for information being public, and show that the only things that play that role are (variants of) common belief as stipulatively characterized. In more detail: a functional role for “taking a proposition for granted” in non-isolated decision making is characterized. I then present some minimal conditions under which such an attitude is correctly held. The key assumption links this attitude to beliefs about what is public. From minimal a priori principles, we can argue that a proposition being public among a group entails common commitment to believe among that group. Later sections explore partial converses to this result, the factivity of publicity and publicity from the perspective of outsiders to the group, and objections to the aprioricity of the result deriving from a posteriori existential presuppositions. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

In this paper I argue that whether or not a computer can be built that passes the Turing test is a central question in the philosophy of mind. Then I show that the possibility of building such a computer depends on open questions in the philosophy of computer science: the physical Church-Turing thesis and the extended Church-Turing thesis. I use the link between the issues identified in philosophy of mind and philosophy of computer science to respond to a prominent argument (...) against the possibility of building a machine that passes the Turing test. Finally, I respond to objections against the proposed link between questions in the philosophy of mind and philosophy of computer science. (shrink)

The essay reflects on how Hans-Georg Gadamer and Karl Barth view interpretation of the Christian Bible. It proceeds in three main sections. The first contends that Gadamer secularizes Christian theology, and that this has drawbacks for the sort of reading his hermeneutic can give to Christian Scripture. The second part turns to Barth, arguing that the whole structure of his approach to the Bible factors in theological commitment, with benefits for the readings he can deliver. The final part makes a (...) case that contemporary reflection on interpretation can nonetheless glean important insights from Gadamer, especially regarding the readerly reception of texts, because his perspective has a certain sort of richness that Barth’s cannot match. The overall suggestion emerging from the interrogation of these two thinkers is that phenomenology and theology might learn from one another, that they each contribute something valuable to discussions of biblical interpretation. (shrink)

What if your peers tell you that you should disregard your perceptions? Worse, what if your peers tell you to disregard the testimony of your peers? How should we respond if we get evidence that seems to undermine our epistemic rules? Several philosophers have argued that some epistemic rules are indefeasible. I will argue that all epistemic rules are defeasible. The result is a kind of epistemic particularism, according to which there are no simple rules connecting descriptive and normative facts. (...) I will argue that this type of particularism is more plausible in epistemology than in ethics. The result is an unwieldy and possibly infinitely long epistemic rule — an Uber-rule. I will argue that the Uber-rule applies to all agents, but is still defeasible — one may get misleading evidence against it and rationally lower one’s credence in it. (shrink)

Many epistemological problems can be solved by the objective Bayesian view that there are rationality constraints on priors, that is, inductive probabilities. But attempts to work out these constraints have run into such serious problems that many have rejected objective Bayesianism altogether. I argue that the epistemologist should borrow the metaphysician’s concept of naturalness and assign higher priors to more natural hypotheses.

This research aimed to assess the general and technical competency of Technical Vocational Education (TVE) teachers in the schools Division of Aklan. It also determined the competency needs and gaps in teaching TVE in the implementation of the program. The study was participated by 118 TVE teachers. Mixed-methods research design using sequential strategy was employed in this study. The Philippine Professional Standards for Teachers was used as guide for assessing the general level of competency while self-assessment guide of TESDA was (...) used to assess the level of technical competency. The quantitative data were used as bases in the conduct of focus group discussions to triangulate the responses in the survey. The general competency level of TVE teachers was described as “highly proficient” while the technical competency level was reported on the “advanced” level. The gaps identified were: (1) teacher-subject mismatch, (2) inadequate skills in applying math and science principles in technical training, (3) struggle in promoting understanding of global labor markets, (4) inability to lead workplace communication (5) lack of content knowledge and pedagogy, (6) lack of competence in assessment and reporting, (7) insufficient trainings related to area of specialization, and (8) expired and unaligned national certificates (nc).The competency needs identified were:(1) activities that would enhance competency, (2) motivation and opportunities to acquire/enhance, and apply competency, and (3) renewed professionalism and rejuvenated teaching advocacy and calling. (shrink)

If an agent believes that the probability of E being true is 1/2, should she accept a bet on E at even odds or better? Yes, but only given certain conditions. This paper is about what those conditions are. In particular, we think that there is a condition that has been overlooked so far in the literature. We discovered it in response to a paper by Hitchcock (2004) in which he argues for the 1/3 answer to the Sleeping Beauty problem. (...) Hitchcock argues that this credence follows from calculating her fair betting odds, plus the assumption that Sleeping Beauty’s credences should track her fair betting odds. We will show that this last assumption is false. Sleeping Beauty’s credences should not follow her fair betting odds due to a peculiar feature of her epistemic situation. (shrink)

Should philosophers prefer simpler theories? Huemer (Philos Q 59:216–236, 2009) argues that the reasons to prefer simpler theories in science do not apply in philosophy. I will argue that Huemer is mistaken—the arguments he marshals for preferring simpler theories in science can also be applied in philosophy. Like Huemer, I will focus on the philosophy of mind and the nominalism/Platonism debate. But I want to engage with the broader issue of whether simplicity is relevant to philosophy.

How do temporal and eternal beliefs interact? I argue that acquiring a temporal belief should have no effect on eternal beliefs for an important range of cases. Thus, I oppose the popular view that new norms of belief change must be introduced for cases where the only change is the passing of time. I defend this position from the purported counter-examples of the Prisoner and Sleeping Beauty. I distinguish two importantly different ways in which temporal beliefs can be acquired and (...) draw some general conclusions about their impact on eternal beliefs. (shrink)