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. The NCRO ontology is free and open to all users. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (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)

Explaining the maintenance of communicative behavior in the face of incentives to deceive, conceal information, or exaggerate is an important problem in behavioral biology. When the interests of agents diverge, some form of signal cost is often seen as essential to maintaining honesty. Here, novel computational methods are used to investigate the role of common interest between the sender and receiver of messages in maintaining cost-free informative signaling in a signaling game. Two measures of common interest are defined. These quantify (...) the divergence between sender and receiver in their preference orderings over acts the receiver might perform in each state of the world. Sampling from a large space of signaling games finds that informative signaling is possible at equilibrium with zero common interest in both senses. Games of this kind are rare, however, and the proportion of games that include at least one equilibrium in which informative signals are used increases monotonically with common interest. Common interest as a predictor of informative signaling also interacts with the extent to which agents’ preferences vary with the state of the world. Our findings provide a quantitative description of the relation between common interest and informative signaling, employing exact measures of common interest, information use, and contingency of payoff under environmental variation that may be applied to a wide range of models and empirical systems. © 2013 Godfrey-Smith, Martínez. (shrink)

Is Popper's philosophy alive or dead? If we make a judgment based on recent discussion in academic philosophy of science, he definitely seems to be fading. Popper is still seen as an important historical figure, a key part of the grand drama of 20th century thinking about science. He is associated with an outlook, a mindset, and a general picture of scientific work. His name has bequeathed us an adjective, "Popperian," that is well established. But the adjective is used for (...) very general ideas that, according to most current philosophers, Popper did not develop convincingly. His detailed account is often seen as attractive on first impression, but full of holes that become bigger rather than smaller as discussion continues. The picture and the name remain, which is more than 1 most philosophers can hope for. But the name attaches more and more to a set of instincts and intuitions, less and less to views that are seeing ongoing philosophical development. Inside science itself, Popper's standing is quite different. He continues to be just about the only philosopher who can seize the imagination and command the loyalty of successful professional scientists. And he is popular within science not only for purposes of general commentary and public relations. Popper's philosophy is a resource drawn on by scientists in their internal debates about scientific matters. This has been especially marked in some parts of biology (Hull 1999). From the point of view of philosophers, this affection on the part of scientists may have an unflattering explanation. Popper offers a rather heroic view of the scientific character, featuring an appealing combination of creativity and hard-headedness. It is no surprise that scientists like to be described this way. It is no surprise that they prefer this picture to the one often (though inaccurately) associated with Hempel and Carnap – the scientist as a sort of logic-driven pattern-recognition machine. The same applies to the picture associated with Kuhn, who presents the normal scientist as a narrow-minded, indoctrinated member of a peculiar collective enterprise, an enterprise devoted to solving tiny puzzles most of the time but prone to occasional fits of crisis and chaos.. (shrink)

The author posits that the value of individual freedom is best realized within the context of the Moral Imagination concept of philosopher Rudolph Steiner and that when freedom is seen more as a licence for deception and exploitation not only does the greater community suffer but also the party itself suffers character destruction. Thus, laissez-faire capitalism, as exemplified by the mortgage banking meltdown of 2008 and subsequent debt-based unemployment crisis, has not only impoverished millions, destroyed savings and bankrupted long-established investment (...) firms, but also has further bonded the perpetrators to the morally undeveloped self-centredness of Lawrence Kohlberg’s least advanced moral stage (Kohlberg, 1981). Following a discussion of the folly and futility of the consumerist culture, the author argues that the solution lies in practicing the time tested values of caring and social responsibility on the part of government and mortgage bankers coupled with self-restraint and moderation on the part of investors and borrowers. (shrink)

ABSTRACT The destruction of the environment is a matter for moral concern and cannot be halted in the long term by appeals to human utility. However, the inadequacy and naïvety of humanist styles of ethical argument become apparent when attempts are made to extend them to environmental issues. They usually abstract certain supposed features of natural objects, e.g. sentience, and reify these as essential characteristics which operate to carry or ground ethical values. These arguments necessarily lead to the exclusion of (...) objects which are, in fact, ethically valued or entail an unacceptably expansive egalitarianism. Such egalitarianism is often followed by a return to human‐centred prejudices opposed to the originally stated aims of ‘biocentric’ethicists like Taylor. Similarly, those physical and ecological holisms which rely not upon shared ‘natural’features, but upon sharing in nature itself cannot solve this dilemma as they are incapable of explaining differential ethical values. The attempt to place boundaries on moral considerability should be abandoned in favour of an ethical pluralism which places emphasis on the context of valuations. (shrink)

Introduction: Foundations of faith described -- Christian history : a brief overview -- The Apostolic Age (ca. A.D. 30-100 -- The Patristic Age (ca. A.D. 100-500) -- The Medieval Age (ca. A.D. 500-1500) -- The Reformation/counter-Reformation Age -- The Modern Age (ca. A.D. 1600-1950) -- The Postmodern Age (ca. A.D. 1950-present) -- Mormon and evangelical theology : a comparison -- Scripture and revelation -- God and humanity -- Church and temple -- Salvation and the afterlife -- Moral and social standards (...) -- Mormonism and Christianity -- Sociological foundations of faith -- Question 9: Who was or is the greatest influence on your religious beliefs? -- Question 10: What were the religious beliefs of your family when you were growing up? -- Question 13: How much do you associate with people that hold to other religious beliefs? -- Question 15: What would be the social consequences for you if you converted to another religion? -- Sociological foundations of faith : conclusion -- Spiritual foundations of faith -- Question 4: To what extent has spiritual or religious -- Question 6: Mormons and Evangelicals claim to have the witness of the Holy Ghost/Holy Spirit in their hearts confirming the Mormons and Evangelicals -- Truth of their faith : how do you know that the assurance you have in your heart is from God? -- Question 8: What do you think of the religious experiences of people outside your religion, especially those which seem to confirm their religious beliefs to them? -- Rational foundations of faith -- Question 16: To what extent do you have faith because you think that Mormonism/Evangelicalism is reasonable? -- Question 18: What do you consider to be the best proof or evidence for Mormonism/Evangelicalism? -- Question 19: Would you believe that Mormonism/Evangelicalism is true even if most of the evidence were against it? -- Question 20: How has your assurance changed over time? -- Question 21: What has caused your faith to become stronger or weaker over time? -- Question 22: To what extent do you ever doubt that Mormonism/Evangelicalism is true? -- Question 23: If you sometimes doubt that your beliefs are true, what causes you to doubt? -- Question 24: How do you respond to or deal -- Conversion stories -- Conclusion: Foundations of faith prescribed. (shrink)

Perceptions of justice in decision outcomes and processes increases trust, support for authorities, and satisfaction with unfavorable outcomes (Lind and Tyler 1988). However, very little research has been done to apply justice concepts to natural resource decision making contexts (an exception is Lauber and Knuth 1997; 1998). In the study presented here, two rounds of focus groups with public participants in the Northern Lower Michigan Ecosystem Management Project were conducted. Participants were asked to describe their experiences with and attitudes toward (...) different types of public participation. They were also asked what criteria they use when judging the fairness of a natural resource agency decision. Themes emerging in the answers included the importance of representation, voice, consideration, logic, and desired outcomes. These are very similar to justice principles documented in other fields. This suggests managers would be wise to focus less on public participation techniques and more on achieving fair decision-making processes. (shrink)

When Donna Rice, who was brought into the public limelight as a companion to ex-presidentiaI candidate Gary Hart, appeared at a university ethics seminar, her statement, and the subsequent coverage, raised three troubling questions for journalists: the nature of academic inquiry, journalistic practices, and the right of people to define themselves.

In each of Parts 1A, IB and II of the Philosophy Tripos, there is an Essay paper in which you are asked to write for three hours on a single topic. In these notes I offer some suggestions about how to tackle this paper, and try to answer some Frequently Asked Questions. The notes are based (in the second half, very closely indeed) on notes written by Jane Heal -- I'm very grateful to her for allowing me to snaffle some (...) of her best suggestions, though she is not responsible for the final result. Do note, though, that the result is still just one view ... Consult other supervisors/directors of studies for additional advice. (shrink)

Our massive tampering with the world's interdependent web of life-coupled with the environmental damage inflicted by deforestation, species loss, and climate change-could trigger widespread adverse effects, including unpredictable collapses of critical biological systems whose interactions and dynamics we only imperfectly understand. Uncertainty over the extent of these effects cannot excuse complacency or delay in facing the threats ... We the undersigned, senior members of the world's scientific community, hereby warn all humanity of what lies ahead. A great change in our (...) stewardship of the earth and the life on it is required, if vast human misery is to be avoided and our global home on this planet is not to be irretrievably mutilated. (Union of Concerned Scientists, 1992). (shrink)

such as to affect an election result. As I understand, this is acknowledged by the Joint Standing Committee on Electoral lvlatters, and remains the view of my Govemrnent, as supported by recent State election experiences. In the absence of such evidence, any proposal to tighten voter eligibility by insisting on validating the proof of identity of electors against driver's licence details or supplementary documentation will only operate to disenfranchise many rural and indigenous Australian electors and potentially those people in society (...) who do not have a driver's licence. More rigorous identity tests may also considerably increase the time taken for electors to submit or update.. (shrink)

Many social theorists assert that in leading sectors and regions of the contemporary economy a transition is occurring from 'Fordism' to the 'lean production' system of production and distribution. The present paper considers the contemporary significance of Volume Two of Capital in light of the alleged rise of lean production. The first task is to sketch briefly the nature of the transition in question.