New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage‐specific genes. It was recently reported that an excess of primate‐specific and human‐specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in (...) both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under‐characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality (...) through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We (...) use statistical methods and formal ontological principles as a first step towards finding answers to this question. (shrink)

MicroRNAs are non‐coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts (...) decisively to improve the accuracy of miRNAome annotations. We encourage genome annotation teams to do it right or not at all. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. (...) Such annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential (...) in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

The major transcript variants of human protein‐coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes—they can be protein‐coding, noncoding, or pseudogenes—and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced (...) micro‐exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re‐assignments. The emerging human pan‐genome is necessitating distinctive annotations incorporating differences between individuals and between populations. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...) the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

NCG 4.0 is the latest update of the Network of Cancer Genes, a web-based repository of systems-level properties of cancer genes. In its current version, the database collects information on 537 known (i.e. experimentally supported) and 1463 candidate (i.e. inferred using statistical methods) cancer genes. Candidate cancer genes derive from the manual revision of 67 original publications describing the mutational screening of 3460 human exomes and genomes in 23 different cancer types. For all 2000 cancer genes, duplicability, evolutionary origin, expression, (...) functional annotation, interaction network with other human proteins and with microRNAs are reported. In addition to providing a substantial update of cancer-related information, NCG 4.0 also introduces two new features. The first is the annotation of possible false-positive cancer drivers, defined as candidate cancer genes inferred from large-scale screenings whose association with cancer is likely to be spurious. The second is the description of the systems-level properties of 64 human microRNAs that are causally involved in cancer progression (oncomiRs). Owing to the manual revision of all information, NCG 4.0 constitutes a complete and reliable resource on human coding and non-coding genes whose deregulation drives cancer onset and/or progression. NCG 4.0 can also be downloaded as a free application for Android smart phones. (shrink)

We present an annotated bibliography of peer reviewed scientific research highlighting the human health, animal welfare, and environmental risks associated with genetic modification. Risks associated with the expression of the transgenic material include concerns over resistance and non-target effects of crops expressing Bt toxins, consequences of herbicide use associated with genetically modified herbicide-tolerant plants, and transfer of gene expression from genetically modified crops through vertical and horizontal gene transfer. These risks are not connected to the technique of genetic (...) modification as such, but would be present for any conventionally produced crops with the same heritable traits. In contrast, other risks are a direct consequence of the method used in gene manipulation. These come about because of the unstable nature of the transgene and vectors used to insert it, and because of unpredictable interactions between the transgene and the host genome. The debate over the release of genetically modified organisms is not merely a scientific one; it encompasses economics, law, ethics, and policy. Any discussion on these levels does, however, need to be informed by sound science. We hope that the scientific references provided here will provide a useful starting point for further debate. (shrink)

The purpose of this article is to update and defend syntax-based gene concepts. I show how syntax-based concepts can and have been extended to accommodate complex cases of processing and gene expression regulation. In response to difficult cases and causal parity objections, I argue that a syntax-based approach fleshes out a deflationary concept defining genes as genomic sequences and organizational features of the genome contributing to a phenotype. These organizational features are an important part of accepted molecular explanations, (...) provide the theoretical basis for a large number of experimental techniques and practical applications, and play a crucial role in in annotating the genome, deriving predictions and constructing bioinformatics models. (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)

This study is the most comprehensive account to date of modern treatments of the love commandment. Gene Outka examines the literature on agape from Nygren's Agape and Eros in 1930. Both Roman Catholic and Protestant writings are considered, including those of D'Arcy, Niebuhr, Ramsey, Tillich, and above all, Karl Barth. The first seven chapters focus on the principal treatments in the theological literature as they relate to major topics in ethical theory. The last chapter explores further the basic normative (...) content of agape and discusses some of the most characteristic problems. "The book is in my judgment the best recent work in religious ethics. Outka brings together analytic moral philosophy and theological ethics, providing a masterly survey of views and issues arising in the past forty years.... I can think of few books of interest to scholars in both philosophy and theology, but Outka's is one. Unlike some scholars who are at home in continental theology, Outka is also at home in secular analytic philosophy; he brings them together in a mutually illuminating way."--Donald Evans "Outka has mastered this vast literature on love, and has brought a critical and clarifying analysis to bear upon it. This is a most important book on a most important subject, and brings the whole discussion into a new phase."--John Macquarrie "The first thing to be said about Outka's book quite simply is that it is excellent; in fact, it is probably the very best available book about contemporary Christian ethical theory."--The Humanities Association Review. (shrink)

This experimental study evaluated the influence of stated organizational concern for ethical conduct upon managerial behavior. Using an in-basket to house the manipulation, a sample of 113 MBA students with some managerial experience reacted to scenarios suggesting illegal conduct and others suggesting only unethical behavior. Stated organizational concern for ethical conduct was varied from none (control group) to several other situations which included a high treatment consisting of a Code of Ethics, an endorsement letter by the CEO and specific sanctions (...) for managerial misconduct. Only in the case of suggested illegal behavior tempered by high organizational concern were managers influenced by organizational policy to modify the morality of their actions. However, the responses to the illegal scenarios were significantly more ethical than the reactions given to the unethical (but not illegal) situations. The implications of these findings are then discussed. (shrink)

Abstract:This study examined the relationship between the individual difference variables of personal moral philosophy, locus of control, Machiavellianism, and just world beliefs and ethical judgments and behavioral intentions. A sample of 602 marketing practitioners participated in the study. Structural equation modeling was used to test hypothesized relationships. The results either fully or partially supported hypothesized direct effects for idealism, relativism, and Machiavellianism. Findings also suggested that Machiavellianism mediated the relationship between individual difference variables and ethical judgments/behavioral intentions.

The Ethical Journalist gives aspiring journalists the tools they need to make responsible professional decisions. Provides a foundation in applied ethics in journalism Examines the subject areas where ethical questions most frequently arise in modern practice Incorporates the views of distinguished print, broadcast and online journalists, exploring such critical issues as race, sex, and the digitalization of news sources Illustrated with 24 real-life case studies that demonstrate how to think in 'shades of gray' rather than 'black and white' Includes questions (...) for class discussion and guides for putting important ethical concepts to use in the real world Accompanying website includes model course schedules, discussion guides, PowerPoint slides, sample quiz and exam questions and links to additional readings online: www.wiley.com/go/foreman. (shrink)

ONE OF THE MOST prominent theorists of anarcho-capitalism is Hans- Hermann Hoppe. In what is perhaps his most famous result, the argumentation ethic for libertarianism, he purports to establish an a priori defense of the justice of a social order based exclusively on pri- vate property. Hoppe claims that all participants in a debate must presuppose the libertarian principle that every person owns himself, since the principle underlies the very concept of argumentation. Some libertarians (e.g., Rothbard 1988) have celebrated Hoppe’s (...) argument as the final nail in the coffin for collectivism of any type; following Hoppe, they believe that to deny the libertarian ethic is not only wrong, but also internally contradictory. On the other hand, a number of other prominent libertarians characterized Hoppe’s initial statement of his case as “one muddle after another” (Steele 1988, p. 47) or “a tissue of bald assertions” (Yeager 1988, p. 45). (shrink)

This paper begins by examining several potentially unethical recent marketing practices. Since most marketing managers face ethical dilemmas during their careers, it is essential to study the moral consequences of these decisions. A typology of ways that managers might confront ethical issues is proposed. The significant organizational, personal and societal costs emanting from unethical behavior are also discussed. Both relatively simple frameworks and more comprehensive models for evaluating ethical decisions in marketing are summarized. Finally, the fact that organizational commitment to (...) fostering ethical marketing decisions can be accomplished by top management leadership, codes of ethics, ethics seminars/programs and ethical audits is examined. (shrink)

Peter Winch famously critiqued Michael Oakeshott's view of human conduct. He argued that Oakeshott had missed the fact that truly human conduct is conduct that 'follows a rule.' This paper argues that, as is sometimes the case with Oakeshott, what seems, on the surface, to be a disagreement with another, somewhat compatible thinker about a matter of detail in some social theory in fact turns out to point to a deeper philosophical divide. In particular, I contend, Winch, as typical of (...) those who only picked up on Oakeshott's work in the 1940s and 1950s, when Oakeshott became known for his critique of rationalism, failed to understand the idealist metaphysics underlying that critique. (shrink)

The political systems of the Roman Republic were based almost entirely on tradition, “the way of the ancestors”, rather than on a written constitution. While the founders of the American Republic looked to ancient Rome as a primary model for their enterprise, nevertheless, in line with the rationalist spirit of their age, the American founders attempted to create a rational set of rules that would guide the conduct of American politics, namely, the US Constitution.These two examples offer a striking case (...) of the ideal types, famously delineated by Michael Oakeshott in “Rationalism in Politics” and elsewhere, between politics as a practice grounded in tradition and politics as a system based on principles flowing from abstract reasoning.This book explores how the histories of the two republics can help us to understand Oakeshott’s claims about rational versus traditional politics. Through examining such issues we may come to understand better not only Oakeshott’s critique of rationalism, but also modern constitutional theory, issues in the design of the European Union, and aspects of the revival of republicanism. (shrink)

This volume centers on debates about how far moral judgments bind across traditions and epochs. Nowadays such debates appear especially volatile, both in popular culture and intellectual discourse: although there is increasing agreement that the moral and political criteria invoked in human rights documents possess cross-cultural force, many modern and postmodern developments erode confidence in moral appeals that go beyond a local consensus or apply outside a particular community. Often the point of departure for discussion is the Enlightenment paradigm of (...) a common morality, in which it is assumed that certain unchanging beliefs inhere in the structure of human reason. Whereas some thinkers continue to defend this paradigm, others modify it in diverse ways without abandoning entirely the attempt to address a universal audience, and still others jettison virtually all of its distinguishing features. Exhibiting a range of positions Western participants take in these debates, this volume seeks to advance the substance of the debates themselves without prejudging the outcome. Rival assessments of the Enlightenment paradigm are offered from various philosophical and theological points of view. In addition to the editors, the contributors include Robert Merrihew Adams, Annette C. Baier, Alan Donagan, Margaret A. Farley, Alan Gewirth, David Little, Richard Rorty, Jeffrey Stout, and Lee H. Yearley. (shrink)

The role of imagery in encoding event-based prospective memories has yet to be fully clarified. Herein, it is argued that imagery augments a cue-to-context association that supports event-based prospective memory performance. By this account, imagery encoding not only improves prospective memory performance but also reduces interference to intention-related information that occurs outside of context. In the current study, when lure words occurred outside of the appropriate responding context, the use of imagery encoding strategies resulted in less interference when compared with (...) a standard event-based intention condition. This difference was eliminated when participants were not given a specific context to associate their intention . These results support a cue-to-context association account of how imagery operates in certain event-based prospective memory tasks. (shrink)

While self-report data is a staple of modern psychological studies, they rely on participants accurately self-reporting. Two constructs that impede accurate results are insufficient effort responding and response styles. These constructs share conceptual underpinnings and both utilized to reduce cognitive effort when responding to self-report scales. Little research has extensively explored the relationship of the two constructs. The current study explored the relationship of the two constructs across even-point and odd-point scales, as well as before and after data cleaning procedures. (...) We utilized IRTrees, a statistical method for modeling response styles, to examine the relationship between IER and response styles. To capture the wide range of IER metrics available, we employed several forms of IER assessment in our analyses and generated IER factors based on the type of IER being detected. Our results indicated an overall modest relationship between IER and response styles, which varied depending on the type of IER metric being considered or type of scale being evaluated. As expected, data cleaning also changed the relationships of some of the variables. We posit the difference between the constructs may be the degree of cognitive effort participants are willing to expend. Future research and applications are discussed. (shrink)

A number of social theorists have contended that the essence of historical analysis is the employment of ideal types to comprehend past goings-on. But, while acknowledging that the study of history through ideal types can yield genuine insight, we may still ask if it represents the full emancipation of historical understanding from other modes of conceiving the past. This paper follows Michael Oakeshott's work on the philosophy of history in arguing that explaining the historical past by means of ideal types, (...) even though offering a coherent and fruitful enterprise, nevertheless falls short of fully embodying the characteristics that differentiate historical understanding. -/- This dispute involves fundamental issues regarding the nature of the social sciences. Furthermore, I suggest that it is of more than purely theoretical interest, in that social theorists who have accepted the Weberian view of historical inquiry will tend to be unaware of the defects inherent in all attempts to capture the nature of past events in a net of generalizations, and thus may be lead to ignore the inherent partiality of the understanding of historical happenings provided by ideal typification. (shrink)

: The medical and clinical promise of stem cell research is widely heralded, but moral judgments about it collide. This article takes general stock of such judgments and offers one specific resolution. It canvasses a spectrum of value judgments on sources, complicity, adult stem cells, and public and private contexts. It then examines how debates about abortion and stem cell research converge and diverge. Finally, it proposes to extend the principle of "nothing is lost" to current debates. This extension links (...) historic discussions of the ethics of direct killing with unprecedented possibilities that in vitro fertilization procedures yield. A definite normative region to inhabit is located, within a larger range of rival value judgments. The creation of embryos for research purposes only should be resisted, yet research on "excess" embryos is permissible by virtue of an appeal to the "nothing is lost" principle. (shrink)

The paper aims to explore what it means for something to be a social cycle, for a theory to be a social cycle theory, and to offer a suggestion for a simple, yet, we believe, fundamentally grounded schema for categorizing them. We show that a broad range of cycle theories can be described within the concept of disruption and adjustments. Further, many important cycle theories are true endogenous social cycle theories in which the theory provides a reason why the cycle (...) should recur. We find that many social cycle theories fit with a two-population disruption and adjustment model similar to the well-known predator-prey model. This implies that a general modeling framework could be established for creating agent-based models of many social cycle theories. (shrink)

This volume centers on debates about how far moral judgments bind across traditions and epochs. Nowadays such debates appear especially volatile, both in popular culture and intellectual discourse: although there is increasing agreement that the moral and political criteria invoked in human rights documents possess cross-cultural force, many modern and postmodern developments erode confidence in moral appeals that go beyond a local consensus or apply outside a particular community. Often the point of departure for discussion is the Enlightenment paradigm of (...) a common morality, in which it is assumed that certain unchanging beliefs inhere in the structure of human reason. Whereas some thinkers continue to defend this paradigm, others modify it in diverse ways without abandoning entirely the attempt to address a universal audience, and still others jettison virtually all of its distinguishing features. Exhibiting a range of positions Western participants take in these debates, this volume seeks to advance the substance of the debates themselves without prejudging the outcome. Rival assessments of the Enlightenment paradigm are offered from various philosophical and theological points of view. In addition to the editors, the contributors include Robert Merrihew Adams, Annette C. Baier, Alan Donagan, Margaret A. Farley, Alan Gewirth, David Little, Richard Rorty, Jeffrey Stout, and Lee H. Yearley. (shrink)

Often different schools or styles of doing economics are seen as inevitably at odds with each other, so that one must be crowned 'correct' and the others vanquished as defective. However, if they actually represent alternative but potentially enlightening views of economic phenomena, then it will be foolish exclusively to pursue one approach at the expense of all others. This paper argues that the latter is a more accurate view of economics than is the former.

A themed issue on the work of Michael Oakeshott.

Recent work by Jaegwon Kim and others suggest that functionalism leaves mental properties causally inefficacious in some sense. I examine three lines of argument for this conclusion. The first appeals to Occam's Razor; the second appeals to a ban on overdetermination; and the third charges that the kind of response I favor to these arguments forces me to give up "the homogeneity of mental and physical causation". I show how each argument fails. While I concede that a positive theory of (...) mental causation is desirable, there is no reason to think that functionalism renders such a theory unattainable. (shrink)

The advance of technology has influenced marketing in a number of ways that have ethical implications. Growth in use of the Internetand e-commerce has placed electronic “cookies,” spyware, spam, RFIDs, and data mining at the forefront of the ethical debate. Some marketers have minimized the significance of these trends. This overview paper examines these issues and introduces the two articles that follow. It is hoped that these entries will further the important “marketing and technology” ethical debate.

The advance of technology has influenced marketing in a number of ways that have ethical implications. Growth in use of the Internetand e-commerce has placed electronic “cookies,” spyware, spam, RFIDs, and data mining at the forefront of the ethical debate. Some marketers have minimized the significance of these trends. This overview paper examines these issues and introduces the two articles that follow. It is hoped that these entries will further the important “marketing and technology” ethical debate.

Research findings on addiction are contradictory. According to biographical records and widely used diagnostic manuals, addicts use drugs compulsively, meaning that drug use is out of control and independent of its aversive consequences. This account is supported by studies that show significant heritabilities for alcoholism and other addictions and by laboratory experiments in which repeated administration of addictive drugs caused changes in neural substrates associated with reward. Epidemiological and experimental data, however, show that the consequences of drug consumption can significantly (...) modify drug intake in addicts. The disease model can account for the compulsive features of addiction, but not occasions in which price and punishment reduced drug consumption in addicts. Conversely, learning models of addiction can account for the influence of price and punishment, but not compulsive drug taking. The occasion for this target article is that recent developments in behavioral choice theory resolve the apparent contradictions in the addiction literature. The basic argument includes the following four statements: First, repeated consumption of an addictive drug decreases its future value and the future value of competing activities. Second, the frequency of an activity is a function of its relative (not absolute) value. This implies that an activity that reduces the values of competing behaviors can increase in frequency even if its own value also declines. Third, a recent experiment (Heyman & Tanz 1995) shows that the effective reinforcement contingencies are relative to a frame of reference, and this frame of reference can change so as to favor optimal or suboptimal choice. Fourth, if the frame of reference is local, reinforcement contingencies will favor excessive drug use, but if the frame of reference is global, the reinforcement contingencies will favor controlled drug use. The transition from a global to a local frame of reference explains relapse and other compulsive features of addiction. (shrink)