The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Conventional wisdom has had it that the naturalist Alfred Russel Wallace and his colleague Henry Walter Bates journeyed to the Amazon in 1848 with two intentions in mind: to collect natural history specimens, and to consider evidential materials that might reveal the causal basis of organic evolution. This understanding has been questioned recently by the historian John van Wyhe, who points out that with regard to the second matter, at least, there appears to be no evidence of a “smoking (...) gun” variety proving it so. In the present essay the circumstances of Wallace’s interest in the matter are reviewed, and van Wyhe is taken to task with alternate explanations for the facts he introduces in his argument. The conclusion is that Wallace almost certainly did have the second objective in mind when he left for both the Amazon, and the Far East. Keywords: Alfred Russel Wallace, Henry Walter Bates, evolution, natural selection. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

F. H. Bradley has assured us that where all is bad it must be good to know the worst. In the case before us the worst is that Jonathan Edwards, from whatever perspective he is viewed, represents an imposing enigma. I confess at the outset that the enigma is one I am unable entirely to dispel, although I am confident that I can explain what is enigmatic about his thought, his approach, his caste of mind, and that I can do (...) so "not through a glass darkly." The central problem is this: Edwards, on the one hand, accepted totally the tradition established by the Reformers with respect to the absolute primacy and authority of the Bible, and he could approach the biblical writings with that conviction of their inerrancy and literal truth which one usually associates with Protestant fundamentalism. On the other hand, Edwards insisted vigorously on the criteria of reason and experience, and he was without equal on the American scene up to the time of Charles Peirce in his capacity for philosophical analysis, for sustaining a logical argument, and for expressing his conclusions with the most painstaking attention to subtle nuances of meaning and rhetorical effectiveness. Moreover, he insisted on the use of philosophical concepts and principles in considering the "things of religion" and his speculations about creation, his estheticism, and pantheism caused deep anxiety in the minds of traditional Calvinists, whose theology was as literal as their biblical exegesis. This double-barrelled character of his approach has led critics to define him as a reactionary and "medieval" thinker who had lost touch with those currents of thought which would eventually lead to the "modern" point of view. Without pausing to evaluate that charge at this point, one thing at least is clear: in relation to his contemporaries Edwards was alone in his attempt to make the religious tradition intelligible in those philosophical terms first laid down by Augustine and Anselm in their enterprise of "faith seeking understanding.". (shrink)

The article examines John McDowell's attempt to rehabilitate the classical idea of the rational animal and Hubert Dreyfus's criticisms of that attempt. After outlining the 'engaged' conception of rationality which, in McDowell's view, enables the idea of the rational animal to shake off its intellectualist appearance, the objections posed by Dreyfus are presented that such a conception of rationality is inconsistent with the phenomena of everyday coping, characterised by non-conceptual 'involvement', and expertise, characterised by non-conceptual 'absorption'. Drawing on Michael (...) Fried's reflections on the representation of absorption in Douglas Gordon and Philippe Parreno's film Zidane, and invoking other considerations concerning the 'mindedness' of skilful activity, the sharp contrast between conceptuality and rationality on the one side and absorption and skilled coping on the other that frames Dreyfus's position in the debate is questioned. The paper concludes by suggesting that in order to see why Dreyfus is so firmly committed to that contrast, we need to widen the lens so that a broader range of philosophical motivations comes into view. For it is not just that there are phenomena that go missing or are mis-described in McDowell's account, according to Dreyfus; there are ideals and excellences that go missing too. (shrink)

From John Maynard Keynes’s prediction of a fifteen-hour workweek to present-day speculation about automation, we have not stopped forecasting the end of work. Critical theory and political philosophy have turned their attention away from the workplace to focus on other realms of domination and emancipation. But far from coming to an end, work continues to occupy a central place in our lives. This is not only because of the amount of time people spend on the job. Many of our (...) deepest hopes and fears are bound up in our labor—what jobs we perform, how we relate to others, how we might flourish. The Return of Work in Critical Theory presents a bold new account of the human significance of work and the human costs of contemporary forms of work organization. A collaboration among experts in philosophy, social theory, and clinical psychology, it brings together empirical research with incisive analysis of the political stakes of contemporary work. The Return of Work in Critical Theory begins by looking in detail at the ways in which work today fails to meet our expectations. It then sketches a phenomenological description of work and examines the normative premises that underlie the experience of work. Finally, it puts forward a novel conception of work that can renew critical theory’s engagement with work and point toward possibilities for transformation. Inspired by Max Horkheimer’s vision of critical theory as empirically informed reflection on the sources of social suffering with emancipatory intent, The Return of Work in Critical Theory is a lucid diagnosis of the malaise and pathologies of contemporary work that proposes powerful remedies. (shrink)

Integrating concepts of maintenance and of origins is essential to explaining biological diversity. The unified theory of evolution attempts to find a common theme linking production rules inherent in biological systems, explaining the origin of biological order as a manifestation of the flow of energy and the flow of information on various spatial and temporal scales, with the recognition that natural selection is an evolutionarily relevant process. Biological systems persist in space and time by transfor ming energy from one state (...) to another in a manner that generates structures which allows the system to continue to persist. Two classes of energetic transformations allow this; heat-generating transformations, resulting in a net loss of energy from the system, and conservative transformations, changing unusable energy into states that can be stored and used subsequently. All conservative transformations in biological systems are coupled with heat-generating transformations; hence, inherent biological production, or genealogical proesses, is positively entropic. There is a self-organizing phenomenology common to genealogical phenomena, which imparts an arrow of time to biological systems. Natural selection, which by itself is time-reversible, contributes to the organization of the self-organized genealogical trajectories. The interplay of genealogical (diversity-promoting) and selective (diversity-limiting) processes produces biological order to which the primary contribution is genealogical history. Dynamic changes occuring on times scales shorter than speciation rates are microevolutionary; those occuring on time scales longer than speciation rates are macroevolutionary. Macroevolutionary processes are neither redicible to, nor autonomous from, microevolutionary processes. (shrink)

v. 1. Nicomachean ethics. Politics. The Athenian Constitution. Rhetoric. On Poetics.--v. 2. Logic.--v. 3. Physics. Metaphysics. On the soul. Short physical treaties.--v. 4. On the heavens. On generation and corruption. Meteorology. Biological treatises.

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

This book provides practical and research-based chapters that offer greater clarity about the particular kinds of teacher reflection that matter and avoids talking about teacher reflection generically, which implies that all kinds of reflection are of equal value.

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Deception in Psychological ResearchJohn P. Gluck and Stephen Hahn-SmithMadam: In the March 1995 issue of the KIEJ, Sissela Bok adds meaningfully to her consistent and important analysis of the harms associated with deception in biomedical and behavioral research. She reminds us that investigator and review committee domination of the analysis of costs and benefits deprives the prospective research subjects of the opportunity to apply their unique sense of values (...) and preferences, an obligation that flows from an authentic respect for persons and a recognition of the importance of autonomy.She also correctly points out that the American Psychological Association (APA) is unique in that it acknowledges the harms of deception by requiring scientific [End Page 386] justification, limiting the scope of what factors can be part of the deception, and supporting minimal duration of deception, at the same time as it maintains a very permissive stance toward its use. For example, the APA code of conduct requires that alternatives to deception be implemented only when they are deemed to be "equally effective."What Bok omits in her critique is that a common justification for the use of deception by psychologists is the belief that many research subjects actually benefit from being deceived. This impression is based on studies that interview subjects at some point in time after their experimental experience. For example, Smith and Richardson (1983, p. 1080) concluded that: "In general, respondents who have been deceived while participating in psychological research did not report negative effects of their experience. In fact, they perceived their experiences more positively that did respondents who had not participated in studies employing deception." Christensen (1988, p. 668), after reviewing the literature on subject reaction to deception, states that the evidence supports the notion that deception experiments are perceived as "more enjoyable and beneficial than nondeception experiments." He goes on to say that in the face of these data it may be that deception has gotten its bad name from philosophers!Basing the acceptability of deception on direct sampling of subjects' highly personal reactions assumes that the procedure yields responses that are valid on their face. If this is true, it would seem to undermine the typical justification for deception in the first place, which is that subjects when asked for personal information are likely to respond in misleading ways. It is important to note that evidence suggests that if subjects are queried about the acceptability of deception prior to actual participation, substantial proportions of subjects judge deception to be unacceptable (Korn 1987). These results are consistent with our own recently completed research, which shows that subjects asked about their reactions following participation in a deception experiment did indeed tend to indicate its acceptability. However, when asked to make a judgment about what reactions other students had to the same experiment, they expressed concern that others may have been harmed by the deception.For psychologists to selectively disregard the distinct possibility of dynamically motivated minimization of harm in order to justify deceptive research practices further supports Bok's characterization of today's competitive research environment and the standards of personal integrity that it challenges.Stephen Hahn-SmithDepartment of Psychology The University of New Mexico Albuquerque, NMReferencesChristensen, Larry. 1988. Deception in Psychological Research: When is it Justified? Personality and Social Psychology Bulletin 14: 664-75. Google ScholarKorn, James H. 1987. Judgements of Acceptability of Deception in Psychological Research. Journal of General Psychology 114: 205-6. [End Page 387]Google ScholarSmith, Steven S., and Richardson, Deborah. 1983 Amelioration of Deception and Harm in Psychological Research: The Important Role of Debriefing. Journal of Personality and Social Psychology 44: 1075-82. [End Page 388]Google ScholarCopyright © 1995 The Johns Hopkins University Press... (shrink)

1 Evidence-based policy requires researchers to provide the answers to ecological questions that are of interest to policy makers. To find out what those questions are in the UK, representatives from 28 organizations involved in policy, together with scientists from 10 academic institutions, were asked to generate a list of questions from their organizations. 2 During a 2-day workshop the initial list of 1003 questions generated from consulting at least 654 policy makers and academics was used as a basis for (...) generating a short list of 100 questions of significant policy relevance. Short-listing was decided on the basis of the preferences of the representatives from the policy-led organizations. 3 The areas covered included most major issues of environmental concern in the UK, including agriculture, marine fisheries, climate change, ecosystem function and land management. 4 The most striking outcome was the preference for general questions rather than narrow ones. The reason is that policy is driven by broad issues rather than specific ones. In contrast, scientists are frequently best equipped to answer specific questions. This means that it may be necessary to extract the underpinning specific question before researchers can proceed. 5 Synthesis and applications. Greater communication between policy makers and scientists is required in order to ensure that applied ecologists are dealing with issues in a way that can feed into policy. It is particularly important that applied ecologists emphasize the generic value of their work wherever possible. (shrink)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)

ObjectiveMost young adults diagnosed with breast or gynecologic cancers experience adverse reproductive or sexual health outcomes due to cancer and its treatment. However, evidence-based interventions that specifically address the RSH concerns of young adult and/or LGBTQ+ survivor couples are lacking. Our goal is to develop a feasible and acceptable couple-based intervention to reduce reproductive and sexual distress experience by young adult breast and gynecologic cancer survivor couples with diverse backgrounds.MethodsWe systematically adapted an empirically supported, theoretically grounded couple-based intervention to address (...) the RSH concerns of young couples coping with breast or gynecologic cancer through integration of stakeholder perspectives. We interviewed 11 couples with a history of breast or gynecologic cancer to review and pretest intervention materials. Three of these couples were invited to review and comment on intervention modifications. Content experts in RSH and dyadic coping, clinicians, and community advisors participated throughout the adaptation process.ResultsFindings confirmed the need for an online, couple-based intervention to support young couples experiencing RSH concerns after breast or gynecologic cancer. Qualitative themes suggested intervention preferences for: A highly flexible intervention that can be tailored to couples’ specific RSH concerns; Active steps to help members of a dyad “get on the same page” in their relationship and family building plans; A specific focus on raising partners’ awareness about how cancer can affect body image and physical intimacy; and Accessible, evidence-based information about RSH for both partners. These results, along with feedback from stakeholders, informed adaptation and finalization of the intervention content and format. The resulting virtual intervention, Opening the Conversation, includes five weekly sessions offering training to couples in communication and dyadic coping skills for addressing RSH concerns.ConclusionThe systematic adaptation process yielded a theory-informed intervention for young adult couples facing breast and gynecological cancers, which will be evaluated in a randomized controlled trial. The long-term goal is to implement and disseminate Opening the Conversation broadly to reach young adult couples with diverse backgrounds who are experiencing RSH concerns in cancer survivorship. (shrink)

Physicists regularly invoke universal laws, such as those of motion and electromagnetism, to explain events. Biological and medical scientists have no such laws. How then do they acquire a reliable body of knowledge about biological organisms and human disease? One way is by repeatedly returning to, manipulating, observing, interpreting, and reinterpreting certain subjects—such as flies, mice, worms, or microbes—or, as they are known in biology, “model systems.” Across the natural and social sciences, other disciplinary fields have developed canonical examples that (...) have played a role comparable to that of biology’s model systems, serving not only as points of reference and illustrations of general principles or values but also as sites of continued investigation and reinterpretation. The essays in this collection assess the scope and function of model objects in domains as diverse as biology, geology, and history, attending to differences between fields as well as to epistemological commonalities. Contributors examine the role of the fruit fly Drosophila and nematode worms in biology, troops of baboons in primatology, box and digital simulations of the movement of the earth’s crust in geology, and meteorological models in climatology. They analyze the intensive study of the prisoner’s dilemma in game theory, ritual in anthropology, the individual case in psychoanalytic research, and Athenian democracy in political theory. The contributors illuminate the processes through which particular organisms, cases, materials, or narratives become foundational to their fields, and they examine how these foundational exemplars—from the fruit fly to Freud’s Dora—shape the knowledge produced within their disciplines. Contributors Rachel A. Ankeny Angela N. H. Creager Amy Dahan Dalmedico John Forrester Clifford Geertz Carlo Ginzburg E. Jane Albert Hubbard Elizabeth Lunbeck Mary S. Morgan Josiah Ober Naomi Oreskes Susan Sperling Marcel Weber M. Norton Wise. (shrink)

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

The question 'Why should I obey the law?' introduces a contemporary puzzle that is as old as philosophy itself. The puzzle is especially troublesome if we think of cases in which breaking the law is not otherwise wrongful, and in which the chances of getting caught are negligible. Philosophers from Socrates to H.L.A. Hart have struggled to give reasoned support to the idea that we do have a general moral duty to obey the law but, more recently, the greater number (...) of learned voices has expressed doubt that there is any such duty, at least as traditionally conceived. (shrink)

For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two other seminal figures in this development: H.L.A. Hart (...) and John Rawls. We show that all three thinkers tend to assume that there is but one type of normativity within the realm of social institutions – roughly, the sort of normativity that is involved in following the results of chess – and that they thereby neglect features that are of crucial significance for an adequate understanding of social reality. (shrink)

A clearly written, authoritative introduction to Taylor's work.