The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice (...) of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7. (shrink)

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags accounting for 2266 restriction fragments on the homoeologous group 3 chromosomes of hexaploid wheat. Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the (...) chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes ∼21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected. (shrink)

To localize wheat ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and (...) least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin. (shrink)

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid wheat genome. Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection. Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of (...) ESTs into contigs. These contigs plus singletons were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5′ and 3′ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics. (shrink)

The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into (...) two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop. (shrink)

Beginning with an examination of the relationship between Hegel and Goethe, Löwith discusses how Hegel's students, particularly Marx and Kierkegaard, interpreted--or reinterpreted--their master's thought, and proceeds with an in-depth assessment of the other important philosophers, from Feuerbach, Stirner, and Schelling to Nietzsche.

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat, to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci (...) in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes. (shrink)

A total of 944 expressed sequence tags generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat. EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and ID with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms (...) was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences, where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses. (shrink)

In some cases people judge it morally acceptable to sacrifice one person’s life in order to save several other lives, while in other similar cases they make the opposite judgment. Researchers have identified two general factors that may explain this phenomenon at the stimulus level: (1) the agent’s intention (i.e. whether the harmful event is intended as a means or merely foreseen as a side-effect) and (2) whether the agent harms the victim in a manner that is relatively “direct” or (...) “personal”. Here we integrate these two classes of findings. Two experiments examine a novel personalness/directness factor that we call personal force, present when the force that directly impacts the victim is generated by the agent’s muscles (e.g., in pushing). Experiments 1a and b demonstrate the influence of personal force on moral judgment, distinguishing it from physical contact and spatial proximity. Experiments 2a and b demonstrate an interaction between personal force and intention, whereby the effect of personal force depends entirely on intention. These studies also introduce a method for controlling for people’s real-world expectations in decisions involving potentially unrealistic hypothetical dilemmas. (shrink)

We report on the deliberations of an interdisciplinary group of experts in science, law, and philosophy who convened to discuss novel ethical and policy challenges in stem cell research. In this report we discuss the ethical and policy implications of safety concerns in the transition from basic laboratory research to clinical applications of cell-based therapies derived from stem cells. Although many features of this transition from lab to clinic are common to other therapies, three aspects of stem cell biology pose (...) unique challenges. First, tension regarding the use of human embryos may complicate the scientific development of safe and effective cell lines. Second, because human stem cells were not developed in the laboratory until 1998, few safety questions relating to human applications have been addressed in animal research. Third, preclinical and clinical testing of biologic agents, particularly those as inherently complex as mammalian cells, present formidable challenges, such as the need to develop suitable standardized assays and the difficulty of selecting appropriate patient populations for early phase trials. We recommend that scientists, policy makers, and the public discuss these issues responsibly, and further, that a national advisory committee to oversee human trials of cell therapies be established. **NB we did not reccommend a NAC, we think it might be appropriate**. (shrink)

When we perceive an object, we perceive the object from a perspective. As a consequence of the perspectival nature of perception, when we perceive, say, a circular coin from different angles, there is a respect in which the coin looks circular throughout, but also a respect in which the coin's appearance changes. More generally, perception of shape and size properties has both a constant aspect—an aspect that remains stable across changes in perspective—and a perspectival aspect—an aspect that changes depending on (...) one's perspective on the object. How should we account for the perspectival aspect of spatial perception? We present a framework within which to discuss the perspectival aspect of perception and put forward three desiderata that any account of the perspectival aspect of perception should satisfy. We discuss views on which the perspectival aspect of perception is analyzed in terms of constitutively mind-dependent appearance properties as well as views on which the perspectival aspect of perception is analyzed in terms of representations of mind-independent perspectival properties. (shrink)

Quilty-Dunn et al.'s wide-ranging defense of the Language of Thought Hypothesis (LoTH) argues that vision traffics in abstract, structured representational formats. We agree: Vision, like language, is compositional – just as words compose into phrases, many visual representations contain discrete constituents that combine in systematic ways. Here, we amass evidence extending this proposal, and explore its implications for how vision interfaces with the rest of the mind.

When the COVID-19 surge hit New York City hospitals, the Division of Medical Ethics at Weill Cornell Medical College, and our affiliated ethics consultation services, faced waves of ethical issues sweeping forward with intensity and urgency. In this article, we describe our experience over an eight-week period (16 March through 10 May 2020), and describe three types of services: clinical ethics consultation (CEC); service practice communications/interventions (SPCI); and organizational ethics advisement (OEA). We tell this narrative through the prism of time, (...) describing the evolution of ethical issues and trends as the pandemic unfolded. We delineate three phases: anticipation and preparation, crisis management, and reflection and adjustment. The first phase focused predominantly on ways to address impending resource shortages and to plan for remote ethics consultation, and CECs focused on code status discussions with surrogates. The second phase was characterized by the dramatic convergence of a rapid increase in the number of critically ill patients, a growing scarcity of resources, and the reassignment/ redeployment of staff outside their specialty areas. The third phase was characterized by the recognition that while the worst of the crisis was waning, its medium- and long-term consequences continued to pose immense challenges. We note that there were times during the crisis that serving in the role of clinical ethics consultant created a sense of dis-ease as novel as the coronavirus itself. In retrospect we learned that our activities far exceeded the familiar terrain of clinical ethics consultation and extended into other spheres of organizational life in novel ways that were unanticipated before this pandemic. To that end, we defined and categorized a middle level of ethics consultation, which we have termed service practice communication intervention (SPCI). This is an underappreciated dimension of the work that ethics consult services are capable of in times of crisis. We believe that the pandemic has revealed the many enduring ways that ethics consultation services can more robustly contribute to the ethical life of their institutions moving forward. (shrink)

This book updates and adds to the classic Social Movements of the Sixties and Seventies, showing how social movement theory has grown and changed.

G. E. Moore observed that to assert, 'I went to the pictures last Tuesday but I don't believe that I did' would be 'absurd'. Over half a century later, such sayings continue to perplex philosophers. In the definitive treatment of the famous paradox, Green and Williams explain its history and relevance and present new essays by leading thinkers in the area.

Although the primary meaning of Max Weber’s concept of disenchantment is as a sociological condition (the retreat of magic and myth from social life through processes of secularization and rationalization), as Weber himself makes clear in his address, “Science as a Vocation,” disenchantment can also be a philosophical act: an unusual form of moral discourse that derives new ethical direction out of the very untenability of a previously robust moral tradition. The philosophical variant of disenchantment is significant both because it (...) contradicts numerous elements of the sociological version and because it suggests there are forms of cognition unique to moral philosophy (insofar as the derivation of a moral teaching from the very absence of one is foreign to both a religious and ascientific mindset). (shrink)

If stem cell-based therapies are developed, we will likely confront a difficult problem of justice: for biological reasons alone, the new therapies might benefit only a limited range of patients. In fact, they might benefit primarily white Americans, thereby exacerbating long-standing differences in health and health care.

We represent shape in both sight and touch, but how do these abilities relate to one another? This issue has been discussed in the context of Molyneux's question of whether someone born blind could, upon being granted sight, identify shapes visually. Some have suggested that we might look to real‐world cases of sight restoration to illuminate the relation between visual and tactual shape representations. Here, I argue that newly sighted perceivers should not be relied on in this way because they (...) are unlikely to form the kinds of shape representations responsible for cross‐modal recognition in normally sighted perceivers. I then argue that the available evidence makes a compelling case for the type identity view, on which the visual and tactual representations responsible for cross‐modal recognition are type‐identical. (shrink)

Christopher Hill's Perceptual experience is a must‐read for philosophers of mind and cognitive science. Here I consider Hill's representationalist account of spatial perception. I distinguish two theses defended in the book. The first is that perceptual experience does not represent the enduring, intrinsic properties of objects, such as intrinsic shape or size. The second is that perceptual experience does represent certain viewpoint‐dependent properties of objects—namely, Thouless properties. I argue that Hill's arguments do not establish the first thesis, and then I (...) raise questions about the Thouless‐property view and its role in Hill's defense of representationalism. (shrink)

Many have held that when a person visually attends to an object, her visual system deploys a representation that designates the object. Call the referential link between such representations and the objects they designate attentive visual reference. In this article I offer an account of attentive visual reference. I argue that the object representations deployed in visual attention—which I call attentive visual object representations —refer directly, and are akin to indexicals. Then I turn to the issue of how the reference (...) of an AVOR is determined relative to a context. After raising problems for existing accounts, I propose a mechanism of reference determination that is both causal and descriptive: For an AVOR to refer to a particular object, the object must appropriately cause the deployment of the AVOR, and the AVOR must be associated with descriptive information about some of the object's geometrical and mereological properties. (shrink)

This volume is a collection of essays by various contributors in honor of the late Laurence Berns, Richard Hammond Elliot Tutor Emeritus at St. John's College, Annapolis. The essays address the literary, political, theological, and philosophical themes of his life's work as a scholar, teacher, and constant companion of the "great books.".

ABSTRACT:A wide range of research uses patterns of genetic variation to infer genetic similarity between individuals, typically referred to as genetic ancestry. This research includes inference of human demographic history, understanding the genetic architecture of traits, and predicting disease risk. Researchers are not just structuring an intellectual inquiry when using genetic ancestry, they are also creating analytical frameworks with broader societal ramifications. This essay presents an ethics framework in the spirit of virtue ethics for these researchers: rather than focus on (...) rule following, the framework is designed to build researchers’ capacities to react to the ethical dimensions of their work. The authors identify one overarching principle of intellectual freedom and responsibility, noting that freedom in all its guises comes with responsibility, and they identify and define four principles that collectively uphold researchers’ intellectual responsibility: truthfulness, justice and fairness, anti-racism, and public beneficence. Researchers should bring their practices into alignment with these principles, and to aid this, the authors name three common ways research practices infringe these principles, suggest a step-by-step process for aligning research choices with the principles, provide rules of thumb for achieving alignment, and give a worked case. The essay concludes by identifying support needed by researchers to act in accord with the proposed framework. (shrink)

G. E. Moore famously observed that to assert ‘I went to the pictures last Tuesday but I do not believe that I did’ would be ‘absurd’. Moore calls it a ‘paradox’ that this absurdity persists despite the fact that what I say about myself might be true. Krista Lawlor and John Perry have proposed an explanation of the absurdity that confines itself to semantic notions while eschewing pragmatic ones. We argue that this explanation faces four objections. We give a better (...) explanation of the absurdity both in assertion and in belief that avoids our four objections. (shrink)

Let’s say that an act requires Person-Affecting Justification if and only if some alternative would have been better for someone. So, Lucifer breaking Xavier’s back requires Person-Affecting Justification because the alternative would have been better for Xavier. But the story continues: While Lucifer evades justice, Xavier moves on and founds a school for gifted children. Xavier’s deepest values become identified with the school and its community. When authorities catch Lucifer, he claims no Person-Affecting Justification is needed: because the attack set (...) Xavier on his life’s path, it’s no longer true that the alternative would have been better by the standard of what Xavier now values most. An unappealingly paternalistic way to hold Lucifer to account is to discount Xavier’s preferences as merely adaptive. Instead, I propose understanding the persons of Person-Affecting Justification to be not persons but person stages. This allows us to hold Lucifer to account without having to discount Xavier’s actual preferences, and has interesting implications for compensatory justice, including making sense of reparations for historical wrongs. (shrink)

Suppose that Depletion will reduce the well-being of future people. Many of us would like to say that Depletion is wrong because of the harm to future people. However, it can easily be made to seem that Depletion is actually harmless – this is the non-identity problem. I discuss a particularly ingenious attempt by Melinda Roberts to attribute a harm to Depletion. I will argue that the magnitude of Roberts's harm is off target by many orders of magnitude: it is (...) just too tiny to explain the intuitive wrong of Depletion. (shrink)

This paper details a “metadisciplinary” applied ethics course jointly taught and pioneered by a biologist, psychologist, and ethicist on the subject of Assisted Reproduction. Contrasted with a transdisciplinary approach (whose content involves themes or issues that span traditional disciplinary lines) and a multidisciplinary approach (which involves experts from several disciplines working side by side), a metadisciplinary approach involves both of these former characteristics while incorporating a continuous, critical appreciation for the strengths and weaknesses of the contrasting methods and scopes of (...) each discipline’s methods of inquiry. This paper details the kinds of subjects that lend themselves to metadisciplinary approaches (e.g. applied ethics subjects which are real-world, complex, and studied by various disciplines), staffing guidelines for a smoothly functioning core team, how to plan and prepare the day-to-day of such a course to prevent a diffuse lesson structure, assignment and evaluation guidelines, and an appraisal of the value of such a class. The authors argue that while fundamental research may be conducted along traditional disciplinary lines, solutions to the complex problems of contemporary society require people who are equipped with problem-solving skills whose relevance spans disciplinary boundaries. (shrink)

How do we thrive in our behaviors and experiences? Positive neuroscience research illuminates the brain mechanisms that enable human flourishing. Supported by the John Templeton Foundation's Positive Neuroscience Project, which Martin E. P. Seligman established in 2008, Positive Neuroscience provides an intersection between neuroscience and positive psychology.In this edited volume, leading researchers describe the neuroscience of social bonding, altruism, and the capacities for resilience and creativity. Part I describes the mechanisms that enable humans to connect with one another. Part II (...) focuses on the neural mechanisms underlying the human ability and willingness to confer costly benefits on others. Part III examines the mechanisms by which human brains overcome adversity, create, and discover. Specific topics include: a newly discovered nerve type that appears to be specialized for emotional communication; the effects of parenting on the male brain; how human altruism differs from that of other primates; the neural features of extraordinary altruists who have donated kidneys to strangers; and distinctive patterns of brain wiring that endow some people with exceptional musical abilities. Accessible to a broad academic audience, from advanced undergraduates to senior scholars, these subjects have generated a fascinating and highly convergent set of ideas and results, shaping our understanding of human nature. (shrink)

The attribution of sentience or consciousness to plants is currently a topic of debate among biologists and philosophers. The claim that plants are conscious is based on three arguments: (i) plants, like all living organisms, are sentient (biopsychism); (ii) there is a strong analogy between the phloem transport system of plants and the nervous system of animals; and (iii) plants are the cognitive equals of sentient animals. On the basis of a model of consciousness that spells out criteria for assigning (...) sentience to a living organism and presents a diagnostic evolutionary marker of consciousness, we argue that these arguments are flawed and discuss some of the ethical issues they raise. (shrink)