I argue that there is nothing about truth as such that prevents contradictions from being true. I argue this by considering the main standard accounts of truth, and showing that they are quite compatible with the existence of true contradictions. Indeed, in many cases, they are actually friendly to the idea.

It is often supposed that Confucianism is opposed to the idea of equality insofar as the key ideals to which it is committed, such as meritocracy and li , are incompatible with equality. Sympathetic commentators typically defend Confucianism by saying that (a) the Confucian person is not a free-standing individual but a social being embedded in a social structure with different and unequal roles, and (b) social inequality has to be traded in for other values. This paper argues that (...) in advocating meritocracy, Confucianism does not abandon the idea of equality. Indeed, invoking Aristotle's account of equality in the Nicomachean Ethics , it can be argued that the unequal distribution of rights and benefits reflects one aspect of equality, namely the vertical aspect, or the unequal treatment of unequals. (shrink)

Although fairness is a key moral trait, limited research focuses on participants' observed fairness behavior because moral traits are generally measured through self-report. This experiment focused on day-to-day interpersonal fairness rather than impersonal justice, and fairness was assessed as observed behavior. The experiment investigated whether a self-reported fairness trait would moderate a situational influence on observed fairness behavior, such that individuals with a stronger fairness trait would be less affected by a situational influence than those with a weaker fairness trait. (...) We used an iterated resource game in which participants could withdraw resources as they chose, and we manipulated the number of resources bogus players withdrew. The number of resources participants withdrew was the behavioral measure of fairness. Results confirmed the expected moderation of the unfairness manipulation by a fairness trait on observed behavior. Those reporting a stronger fairness trait were unaffected by the manipulation, whereas those reporting a weaker fairness trait were more strongly influenced. (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)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

Hilary Putnam and Nelson Goodman are two of the twentieth century's most persuasive critics of metaphysical realism, however they disagree about the consequences of rejecting metaphysical realism. Goodman defended a view he called irrealism in which minds literally make worlds, and Putnam has sought to find a middle path between metaphysical realism and irrealism. I argue that Putnam's middle path turns out to be very elusive and defend a dichotomy between metaphysical realism and irrealism.

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.

In this paper I show how the conserved quantity theory, or more generally the process theory of Wesley Salmon and myself, provides a sufficient condition in an analysis of causation. To do so I will show how it handles the problem of alleged 'misconnections'. I show what the conserved quantity theory says about such cases, and why intuitions are not to be taken as sacrosanct.

Consider the following denumerably infinite sequence of sentences: (s1) For all k > 1, sk is not true. (s2) For all k > 2, sk is not true. (s3) For all k > 3, sk is not true.

Some forms of envy and resentment are centrally connected with a concern for justice and so should not be morally condemned but accepted. Envy and resentment enable us to discern and respond to injustices against ourselves and others. I argue that whereas envy and resentment as character traits or dispositions may be ethically deplorable, as episodic emotions they can be both moral responses to injustice and lead to action against injustice.

"The Tao Encounters in West" by Chenyang Li is reviewed.

Avicenna (d. 1037) bequeathed the Arabic philosophical tradition with an aporia : self-knowledge is conceived, at times, in terms of intellection, at other times, in terms of apperception. In his Book of Discussions and Book of Notes, Avicenna has lengthy discussions on apperception, defined as a direct ontological mode of knowledge. Heir to this tradition, Shihāb al-Dīn al-Suhrawardī (d. 1191) moved away from the first conception of self-knowledge as intellection to adopt the second conception of an apperception of the (...) self as a direct, intuitive and "presential (hcombining dot belowudcombining dot belowūrī)" perception, and which he defended with four types of arguments. (shrink)

Why did Levinas choose Isaiah 45:7 ("I make peace and create evil: I the Lord do all that") as a superscription of his essay on evil? This article explores the role of evil in Levinas's religious ethics. The author discusses the structure of evil as revealed phenomenologically and juxtaposes it to the structure of subjectivity found in the writings of Levinas. The idea of the "ethical anthropic principle," modeled upon the cosmic anthropic principle, is then used to link evil to (...) the responsibility of the subject. The link is subsequently extended to God. This is proposed as one way of understanding the meaning of Isaiah 45:7. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Epicurus notoriously argued that death at no time is a harm because before death there is no harm and after death there is no victim. The denial that death can be a harm to the one who dies has been challenged by various claims including (1) death is eternally bad for the victim (Feldman), (2) it is before death that it is bad for the victim (Feinberg and Pitcher), (3) death is bad for the victim but at no particular time (...) (Nagel), and (4) it is at the time of death that death is bad for the victim (Lamont). Nagel's account is more plausible and is consistent with the view that the temporal location of the harm of untimely death is best understood as the time when the decedent might otherwise have lived. (edited). (shrink)

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