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)

This volume asks how and why the concept of nature has changed its meaning in modernity and whether a rearticulation of premodern ideas about nature is possible. Building on the work of Voegelin, Strauss, Lonergan, Finnis, and others, the book compares and contrasts classical, medieval, and modern conceptions of nature.

Modern thought is sometimes presented as introducing a “turn to the subject” absent from ancient and medieval thought, although the schools of thought associated with Bernard Lonergan, Eric Voegelin, Leo Strauss, and the new natural law theory often find subjectivity already operative in the older forms. In this volume, sixteen leading scholars examine the turn to the subject in modern philosophy and consider its historical antecedents in ancient and medieval thought.

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes from 26 Triticeae cDNA libraries, were mapped to wheat homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported (...) elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases. (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)

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)

In their article “The Rise of Citizen Science in Health and Biomedical Research,” Wiggins and Wilbanks (2019) present a new typology for understanding the complex landscape of health and biomedical...

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)

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)

There is a thematic unity to these essays on Newton's thought: they are concerned with the central categories of Newton's metaphysics of nature (matter, causation, force, space, time) and the ways in which Newton's work relates to cultural themes such as providence and creation. Focusing on questions of tradition and innovation and Newton's engaged response to the broader patterns of his contemporary culture, they present a unified, interpretive stance that often challenges the scholarly orthodoxies. The essays contain a large body (...) of unpublished manuscript material that is related exegetically to the corpus of Newton's published writings. Accordingly, they provide a fresh basis for understanding and clarifying the inner dynamics of Newton's thought. Audience: Historians, philosophers and sociologists of early modern thought, and those who have an interest in the intellectual achievements of Isaac Newton. (shrink)

Descartes's works are often treated as a unified, unchanging whole. But in Descartes's Changing Mind, Peter Machamer and J. E. McGuire argue that the philosopher's views, particularly in natural philosophy, actually change radically between his early and later works--and that any interpretation of Descartes must take account of these changes. The first comprehensive study of the most significant of these shifts, this book also provides a new picture of the development of Cartesian science, epistemology, and metaphysics. No changes in (...) Descartes's thought are more significant than those that occur between the major works The World and Principles of Philosophy. Often seen as two versions of the same natural philosophy, these works are in fact profoundly different, containing distinct conceptions of causality and epistemology. Machamer and McGuire trace the implications of these changes and others that follow from them, including Descartes's rejection of the method of abstraction as a means of acquiring knowledge, his insistence on the infinitude of God's power, and his claim that human knowledge is limited to that which enables us to grasp the workings of the world and develop scientific theories. (shrink)

Manuscript Add. 3965, section 13, folios 541r–542r and 545r–546r is in the Portsmouth Collection of manuscripts and housed in the University Library, Cambridge. These drafts contain a careful account, in Newton's hand, of his views on place, time, and God. They are part of a large number of drafts relating to the three official editions of the Principia published in Newton's lifetime.

Drawing on a landscape analysis of existing data-sharing initiatives, in-depth interviews with expert stakeholders, and public deliberations with community advisory panels across the U.S., we describe features of the evolving medical information commons. We identify participant-centricity and trustworthiness as the most important features of an MIC and discuss the implications for those seeking to create a sustainable, useful, and widely available collection of linked resources for research and other purposes.

This study considers Newton's views on space and time with respect to some important ontologies of substance in his period. Specifically, it deals in a philosophico-historical manner with his conception of substance, attribute, existence, to actuality and necessity. I show how Newton links these “features” of things to his conception of God's existence with respect of infinite space and time. Moreover, I argue that his ontology of space and time cannot be understood without fully appreciating how it relates to the (...) nature of Divine existence. In order to establish this, the ontology embodied in Newton's theory of predication is analysed, and shown to be different from the presuppositions of the ontological argument. From the historical point of view Gassendi's influence is stressed, via the mediation of Walter Charleton. Furthermore, Newton's thought on these matters is contrasted with Descartes's and Spinoza's. In point of fact, in his earliest notebook Newton recorded observations on Descartes's version of the ontological argument. Soon, however, he was to oppose the Cartesian conception of the actuality of Divine existence by means of arguments similar to those of Gassendi. Lastly, I suggest that the nature and extent of Henry More's influence on Newton's conception of how God relates to absolute space and time bears further examination. (shrink)

In this paper, we explore the perspectives of expert stakeholders about who owns data in a medical information commons and what rights and interests ought to be recognized when developing a governance structure for an MIC. We then examine the legitimacy of these claims based on legal and ethical analysis and explore an alternative framework for thinking about participants' rights and interests in an MIC.

Isaac Newton wrote the manuscript Questiones quaedam philosophicae at the very beginning of his scientific career. This small notebook thus affords rare insight into the beginnings of Newton's thought and the foundations of his subsequent intellectual development. The Questiones contains a series of entries in Newton's hand that range over many topics in science, philosophy, psychology, theology, and the foundations of mathematics. These notes, written in English, provide a very detailed picture of Newton's early interests, and record his critical appraisal (...) of contemporary issues in natural philosophy. Written predominantly in 1664-5, they give a significant perspective on Newton's thought just prior to his annus mirabilis, 1666. This volume provides a complete transcription of the Questiones, together with an 'expansion' into modern English, and a full editorial commentary on the content and significance of the notebook in the development of Newton's thought. It will be essential reading for all those interested in Newton and the intellectual foundations of science. (shrink)

As a result, the works of Popper, Kuhn, Quine, and Lakatos, as well as Heidegger, Gadamer, Nietzsche, Foucault, and Feyerabend, are called into play.

: This article is concerned with Newton's appropriation of Descartes' ontology of true and immutable natures in developing his theory of infinitely extended space. It contends that unless the part played by the Platonic distinction between "being a nature" and "having a nature" in Newton's thinking is properly appreciated the foundation of his doctrine of space in relation to God will not be fully understood. It also contends that Newton's Platonism is consistent with his empiricism once the mediating role is (...) made clear that the geometry of moving loci play in grounding his intuitions concerning infinite natures. (shrink)

This essay explores the role of God’s omnipresence in Newton’s natural philosophy, with special emphasis placed on how God is related to space. Unlike Descartes’ conception, which denies the spatiality of God, or Gassendi and Charleton’s view, which regards God as completely whole in every part of space, it is argued that Newton accepts spatial extension as a basic aspect of God’s omnipresence. The historical background to Newton’s spatial ontology assumes a large part of our investigation, but with attention also (...) focused on the details of Newton’s unique approach to these traditional Scholastic conceptions. (shrink)

While the bioethics literature demonstrates that the field has spent substantial time and thought over the last four decades on the goals, methods, and desired outcomes for service and training in bioethics, there has been less progress defining the nature and goals of bioethics research and scholarship. This gap makes it difficult both to describe the breadth and depth of these areas of bioethics and, importantly, to gauge their success. However, the gap also presents us with an opportunity to define (...) this scope of work for ourselves and to help shape the broader conversation about the impact of academic research. Because of growing constraints on academic funding, researchers and scholars in many fields are being asked to demonstrate and also forecast the value and impact of their work. To do that, and also to satisfy ourselves that our work has meaningful effect, we must understand how our work can motivate change and how that change can be meaningfully measured. In a field as diverse as bioethics, the pathways to and metrics of change will likewise be diverse. It is therefore critical that any assessment of the impact of bioethics research and scholarship be informed by an understanding of the nature of the work, its goals, and how those goals can and ought to be furthered. In this paper, we propose a conceptual model that connects individual bioethics projects to the broader goals of scholarship, describing the translation of research and scholarly output into changes in thinking, practice, and policy. One of the key implications of the model is that impact in bioethics is generally the result of a collection of projects rather than of any single piece of research or scholarship. Our goal is to lay the groundwork for a thoroughgoing conversation about bioethics research and scholarship that will advance and shape the important conversation about their impact. (shrink)

Descartes is always concerned about knowledge. However, the Galileo affair in 1633, the reactions to his Discourse on method, and later his need to reply to objections to his Meditations provoked crises in Descartes’s intellectual development the import of which has not been sufficiently recognized. These events are the major reasons why Descartes’s philosophical position concerning how we know and what we may know is radically different at the end of his life from what it was when he began. We (...) call this later position Descartes’s epistemic stance and contrast it with his earlier methodological, metaphysical realism. Yet Descartes’s epistemic views cannot be separated from other aspects of his work, for example, his views concerning God, causality, metaphysics, and the nature of science. A further meta-implication is that serious errors await any scholar who cites early Cartesian texts in support of late Cartesian positions, or who uses later texts in conjunction with early ones to support a reading of Descartes’s philosophy.Keywords: René Descartes; Nature; Motion; Method; Knowledge. (shrink)

Interest in science and math plays an important role in encouraging STEM motivation and career aspirations. This interest decreases for girls between late childhood and adolescence. Relatedly, positive mentoring experiences with female teachers can protect girls against losing interest. The present study examines whether visitors to informal science learning sites differ in their expressed science and math interest, as well as their science and math stereotypes following an interaction with either a male or female educator. Participants were visitors to one (...) of four ISLS in the United States and United Kingdom. Following an interaction with a male or female educator, they reported their math and science interest and responded to math and science gender stereotype measures. Female participants reported greater interest in math following an interaction with a female educator, compared to when they interacted with a male educator. In turn, female participants who interacted with a female educator were less likely to report male-biased math gender stereotypes. Self-reported science interest did not differ as a function of educator gender. Together these findings suggest that, when aiming to encourage STEM interest and challenge gender stereotypes in informal settings, we must consider the importance of the gender of educators and learners. (shrink)

One of the earliest and most influential treatises on the subject of this volume is Aristotle's Categories. Aristotle's title is a form of the Greek verb for speaking against or submitting an accusation in a legal proceeding. By the time of Aristotle, it also meant: to signify or to predicate. Surprisingly, the "predicates" Aristotle talks about include not only bits of language, but also such nonlinguistic items as the color white in a body and the knowledge of grammar in a (...) man's soul. (Categories I/ii) Equally surprising are such details as Aristotle's use of the terms 'homonymy' and 'synonymy' in connection with things talked about rather than words used to talk about them. Judging from the evidence in the Organon, the Metaphysics, and elsewhere, Aristotle was both aware of and able to mark the distinction between using and men tioning words; and so we must conclude that in the Categories, he was not greatly concerned with it. For our purposes, however, it is best to treat the term 'predication' as if it were ambiguous and introduce some jargon to disambiguate it. Code, Modrak, and other authors of the essays which follow use the terms 'linguistic predication' and 'metaphysical predication' for this. (shrink)

Background Citizen science is increasingly prevalent in the biomedical sciences, including the field of human genomics. Genomic citizen science initiatives present new opportunities to engage individuals in scientific discovery, but they also are provoking new questions regarding who owns the outputs of the research, including intangible ideas and discoveries and tangible writings, tools, technologies, and products. The legal and ethical claims of participants to research outputs become stronger—and also more likely to conflict with those of institution-based researchers and other stakeholders—as (...) participants become more involved, quantitatively and qualitatively, in the research process. It is not yet known, however, how genomic citizen science initiatives are managing the interests of their participants in accessing and controlling research outputs in practice. To help fill this gap, we conducted an in-depth review of relevant policies and practices of U.S.-based genomic citizen science initiatives. Methods We queried the peer-reviewed literature and grey literature to identify 22 genomic citizen science initiatives that satisfied six inclusion criteria. A data collection form was used to capture initiative features, policies, and practices relevant to participants’ access to and control over research outputs. Results This analysis revealed that the genomic citizen science landscape is diverse and includes many initiatives that do not have institutional affiliations. Two trends that are in apparent tension were identified: commercialization and operationalization of a philosophy of openness. While most initiatives supported participants’ access to research outputs, including datasets and published findings, none supported participants’ control over results via intellectual property, licensing, or commercialization rights. However, several initiatives disclaimed their own rights to profit from outputs. Conclusions There are opportunities for citizen science initiatives to incorporate more features that support participants’ access to and control over research outputs, consistent with their specific objectives, operations, and technical capabilities. (shrink)

We argue that Isaac Newton really is best understood as being in the tradition of the Mechanical Philosophy and, further, that Newton saw himself as being in this tradition. But the tradition as Newton understands it is not that of Robert Boyle and many others, for whom the Mechanical Philosophy was defined by contact action and a corpuscularean theory of matter. Instead, as we argue in this paper, Newton interpreted and extended the Mechanical Philosophy's slogan “matter and motion” in reference (...) to the long and distinguished tradition of mixed mathematics and the study of simple machines. (shrink)

Increasingly, genomic analysis is being utilized to diagnose children with developmental delay or dysmorphic facial features suggestive of a congenital disorder. Genetic testing has rapidly evolved, and the genome-wide tests that we use today are significantly different from the more targeted single-gene tests of the last decade. Chromosomal microarray analysis is now a first line test for children with multiple birth defects, children with intellectual impairment, and children with an unusual constellation of symptoms that do not fit with a known (...) disease. There are three types of CMA that are currently clinically available. CMA by oligonucleotide array-based comparative genomic hybridization compares the hybridization signal from the patient's DNA to that of a reference DNA sample for each oligonucleotide on the array. Depending on the specific array, this can range from tens of thousands to hundreds of thousands of oligonucleotides. (shrink)