"The author tells a history of the study of cancer-causing viruses from the early twentieth century to the development of an HPV vaccine for cervical cancer in 2006. He profiles the "cancer virus hunters" who made breakthroughs in tumor virology"--.

College of Medicine, University of South Alabama Mobile, AL 36688-0002, USA wbp501{at}jaguar1.usouthal.edu ' + u + '@' + d + ' '//--> Abstract Recent work in viral genomics has shown that bacteriophages exhibit a high degree of mosaicism, which is most likely due to a long history of prolific horizontal gene transfer (HGT). Given these findings, we argue that each of the most plausible attempts to properly classify bacteriophages into distinct species fail. Mayr's biological species concept fails because there is (...) no useful viral analog to sexual reproduction. Phenetic species concepts fail because they obscure the mosaicism and the rich reticulated viral histories. Phylogenetic species concepts, even when extended to take into account reticulation, fail because there is no non-arbitrary distinction between recombination events that create a new viral species and those that do not. There is good reason to think that bacteriophages, arguably the Earth's most abundant biological agent, evolve without forming species. Introduction The Biology of Viruses 2.1 Bacteriophage life cycles 2.2 Mechanisms of HGT The Species Problem and Species Concepts 3.1 Phenetic species concepts 3.2 The biological species concept 3.3 Phylogenetic species concepts 3.4 The ecological species concept 3.5 Homeostatic property cluster species Viruses and Species Taxonomy Reticular Phylogenies Conclusion CiteULike Connotea Del.icio.us What's this? (shrink)

In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency Thesis” by counterexample. Beatty argues that there are no distinctly biological laws because the outcomes of the evolutionary processes are contingent. I argue that the heart of the Caspar–Klug theory of virus structure—that spherical virus capsids consist of 60T subunits (where T = k 2 + hk + h 2 and h and k are integers)—is a distinctly biological law even if the existence of spherical (...) viruses is evolutionarily contingent. (shrink)

Recent work in viral genomics has shown that bacteriophages exhibit a high degree of mosaicism, which is most likely due to a long history of prolific horizontal gene transfer (HGT). Given these findings, we argue that each of the most plausible attempts to properly classify bacteriophages into distinct species fail. Mayr's biological species concept fails because there is no useful viral analog to sexual reproduction. Phenetic species concepts fail because they obscure the mosaicism and the rich reticulated viral histories. Phylogenetic (...) species concepts, even when extended to take into account reticulation, fail because there is no non-arbitrary distinction between recombination events that create a new viral species and those that do not. There is good reason to think that bacteriophages, arguably the Earth's most abundant biological agent, evolve without forming species.1. Introduction2. The Biology of Viruses2.1. Bacteriophage life cycles2.2. Mechanisms of HGT3. The Species Problem and Species Concepts3.1. Phenetic species concepts3.2. The biological species concept3.3. Phylogenetic species concepts3.4. The ecological species concept3.5. Homeostatic property cluster species4. Viruses and Species Taxonomy5. Reticular Phylogenies6. Conclusion. (shrink)

The recent conception of biodiversity proposed by James Maclaurin and Sterelny was developed mostly with macrobiological life in mind. They suggest that we measure biodiversity by dividing life into natural units (typically species) and quantifying the differences among units using phenetic rather than phylogenetic measures of distance. They identify problems in implementing quantitative phylogenetic notions of difference for non-prokaryotic species. I suggest that if we focus on microbiological life forms that engage in frequent, promiscuous lateral gene transfer (LGT), and their (...) associated reticulated phylogenies, we need to rethink the notion of species as the natural unit, and we discover additional problems with phylogenetic notions of distance. These problems suggest that a phenetic approach based on morphospaces has just as much appeal, if not more, for microbes as they do for multi-cellular life. Facts about LGT, however, offer no new insight into the additional challenge of reconciling units and differences into a single measure of biodiversity. (shrink)

In his Particles and Waves, Peter Achinstein gives a precise probabilistic version of theoretical coherence inspired by William Whewell's somewhat vague notion of coherence. Whewell believed that as theoretical science proceeds, it becomes more coherent and rejects false incoherent theories. Achinstein offers a challenge: try to make Whewell's idea more precise while maintaining the properties that Whewell claimed coherence to have. This chapter argues (1) that Achinstein's probabilistic rendition of coherence fails to capture Whewell's notion since the probabilistic rendition of (...) coherence is not an a priori sign of truth and (2) that Achinstein's approach is better seen as a critique of Whewell's central methodological claims than as an interpretation of Whewell's ideas. (shrink)

In this paper I consider Kenneth Schaffner''s(1998) rendition of ''''developmentalism'''' from the point of viewof bacteriophage biology. I argue that the fact that a viablephage can be produced from purified DNA and host cellularcomponents lends some support to the anti-developmentalist, ifthey first show that one can draw a principled distinctionbetween genetic and environmental effects. The existence ofhost-controlled phage host range restriction supports thedevelopmentalist''s insistence on the parity of DNA andenvironment. However, in the case of bacteriophage, thedevelopmentalist stands on less firm (...) ground than when organismswith nervous systems, such as Schaffner''s C. elegans, areconsidered. (shrink)

In this, the first book devoted to Peter Achinstein's influential work in philosophy of science, twenty distinguished philosophers, including four Lakatos award winners, address various aspects of Achinstein's influential views on the nature of scientific evidence, scientific explanation, and scientific realism. It includes short essays by Steve Gimbel and Jeff Maynes, Nancy Cartwright, Jordi Cat, Victor DiFate, Jerry Doppelt, Adam Goldstein, Philip Kitcher, Fred Kronz, Deborah Mayo, Greg Morgan, Helen Longino, John Norton, Michael Ruse, Bas van Fraassen, Stathis Psillos, (...) Larry Laudan, Richard Richards, Kent Staley, and Jim Woodward with replies to each contributor from Peter Achinstein. Readers will come away with an understanding of the current debate in multiple areas of philosophy of science and how various contemporary issues are connected. (shrink)

In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.

Should judgments of beauty play a guiding role in theoretical science even if beauty is not a sign of truth? In this paper I argue that they should in certain cases. If we analyze the rationality of theoretical pursuit using decision theory, a theory’s beauty can influence the utilities of the various options confronting the researcher. After considering the views of Pierre Duhem and Thomas Kuhn on aesthetics in science, I suggest that because we value freedom of inquiry we rightly (...) allow scientists some choice in how they value aesthetic properties of theories and thus some freedom to use beauty to guide their research program. (shrink)

In 1962, Donald Caspar and Aaron Klug published their classic theory of virus structure. They developed their theory with an explicit analogy between spherical viruses and Buckminster Fuller's geodesic domes. In this paper, I use the spherical virus-geodesic dome case to develop an account of analogy and deductive analogical inference based on the notion of an isomorphism. I also consider under what conditions there is a good reason to claim an experimentally untested analogy is plausible.

The use of Big Data—however the term is defined—involves a wide array of issues and stakeholders, thereby increasing numbers of complex decisions around issues including data acquisition, use, and sharing. Big Data is becoming a significant component of practice in an ever-increasing range of disciplines; however, since it is not a coherent “discipline” itself, specific codes of conduct for Big Data users and researchers do not exist. While many institutions have created, or will create, training opportunities to prepare people to (...) work in and around Big Data, insufficient time, space, and thought have been dedicated to training these people to engage with the ethical, legal, and social issues in this new domain. Since Big Data practitioners come from, and work in, diverse contexts, neither a relevant professional code of conduct nor specific formal ethics training are likely to be readily available. This normative paper describes an approach to conceptualizing ethical reasoning and integrating it into training for Big Data use and research. Our approach is based on a published framework that emphasizes ethical reasoning rather than topical knowledge. We describe the formation of professional community norms from two key disciplines that contribute to the emergent field of Big Data: computer science and statistics. Historical analogies from these professions suggest strategies for introducing trainees and orienting practitioners both to ethical reasoning and to a code of professional conduct itself. We include two semester course syllabi to strengthen our thesis that codes of conduct can be harnessed to support the development of ethical reasoning in, and a sense of professional identity among, Big Data practitioners. (shrink)

ABSTRACT Rosalind Franklin is best known for her informative X-ray diffraction patterns of DNA that provided vital clues for James Watson and Francis Crick's double-stranded helical model. Her scientific career did not end when she left the DNA work at King's College, however. In 1953 Franklin moved to J. D. Bernal's crystallography laboratory at Birkbeck College, where she shifted her focus to the three-dimensional structure of viruses, obtaining diffraction patterns of Tobacco mosaic virus (TMV) of unprecedented detail and clarity. During (...) the next five years, while making significant headway on the structural determination of TMV, Franklin maintained an active correspondence with both Watson and Crick, who were also studying aspects of virus structure. Developments in TMV research during the 1950s illustrate the connections in the emerging field of molecular biology between structural studies of nucleic acids and of proteins and viruses. They also reveal how the protagonists of the “race for the double helix” continued to interact personally and professionally during the years when Watson and Crick's model for the double-helical structure of DNA was debated and confirmed. (shrink)

ABSTRACT Rosalind Franklin is best known for her informative X-ray diffraction patterns of DNA that provided vital clues for James Watson and Francis Crick's double-stranded helical model. Her scientific career did not end when she left the DNA work at King's College, however. In 1953 Franklin moved to J. D. Bernal's crystallography laboratory at Birkbeck College, where she shifted her focus to the three-dimensional structure of viruses, obtaining diffraction patterns of Tobacco mosaic virus (TMV) of unprecedented detail and clarity. During (...) the next five years, while making significant headway on the structural determination of TMV, Franklin maintained an active correspondence with both Watson and Crick, who were also studying aspects of virus structure. Developments in TMV research during the 1950s illustrate the connections in the emerging field of molecular biology between structural studies of nucleic acids and of proteins and viruses. They also reveal how the protagonists of the “race for the double helix” continued to interact personally and professionally during the years when Watson and Crick's model for the double-helical structure of DNA was debated and confirmed. (shrink)

Reinhold Niebuhr (1892-1971) may have been the most influential and insightful American thinker of the twentieth century. In dealing with the intricacies of human nature, society, politics, ethics, theology, racism and international relations, Niebuhr the teacher, preacher, philosopher, social critic and ethicist, was highly influential and difficult to ignore during the Second World War and Cold War eras because of his intellectual heft and the novel manner in which he addressed the economic, spiritual, social and political problems of his time. (...) This book distils Niebuhr's disparate and now difficult to access work into one volume, making it more easily accessible than ever before, at the same time bringing his work into the twenty first century. It argues that if he were alive today Niebuhr would be a champion of the U.N, a supporter of globalization, a fierce opponent of America's 2003 Iraq War (for all the reasons he opposed the Vietnam War), an advocate of the Responsibility to Protect, and a pragmatic hawk on China as it rises today. It also highlights his many contributions to international relations theory, from Realism to Liberalism to existentialism to the English School to constructivism. This is the first book that focuses exclusively on the international relations thought of Reinhold Niebuhr, one of Classical Realism's most important figures, one whom diplomat and Realist George Kennan called, "the father of us all.". (shrink)

The focus of this book is to explore teachers' evolving personal epistemologies, or the beliefs we hold about the origin and development of knowledge in the context of teaching. The chapters focus on a range of conceptual frameworks about how university and field-based experiences influence the connections between teachers' personal epistemologies and teaching practice. In an earlier volume we investigated ways in which we might change preservice teachers' beliefs and teaching practice (Brownlee, Schraw and Berthelsen, 2011). While we addressed the (...) nature of teachers' personal epistemology, learning and teaching practices, and approaches for changing beliefs throughout teacher education programs, the volume did not address conceptual frameworks for the development of teacher's personal epistemologies. The book is focused on teacher educators, teachers and teacher education programmers in universities with an overall aim of highlighting how we might support students to engage in learning that is challenging and to engage in professional experiences that promote changes in teaching practice. We argue that students need to be encouraged to question their beliefs and develop increasingly sophisticated beliefs about their knowledge and their students' knowledge that facilitate learning and intellectual growth. (shrink)

Introduction: Vulnerability is a poorly understood concept in research ethics, often aligned to autonomy and consent. A recent addition to the literature represents a taxonomy of vulnerability developed by Kipnis, but this refers to the conduct of clinical trials rather than qualitative research, which may raise different issues. Aim: To examine issues of vulnerability in cancer and palliative care research obtained through qualitative interviews. Method: Secondary analysis of qualitative data from 26 black Caribbean and 19 white British patients with advanced (...) cancer. Results: Four domains of vulnerability derived from Kipnis’s taxonomy were identified and included: (i) communicative vulnerability, represented by participants impaired in their ability to communicate because of distressing symptoms; (ii) institutional vulnerability, which referred to participants who existed under the authority of others—for example, in hospital; (iii) deferential vulnerability, which included participants who were subject to the informal authority or the independent interests of others; (iv) medical vulnerability, which referred to participants with distressing medical conditions; and (v) social vulnerability, which included participants considered to belong to an undervalued social group. Participants from both ethnic groups populated all these domains, but those who were black Caribbean were more present among the socially vulnerable. Conclusions: Current classifications of vulnerability require reinterpretation when applied to qualitative research at the end of life. We recommend that researchers and research ethics committees reconceptualise vulnerability using the domains identified in this study and consider the research context and interviewers’ skills. (shrink)

Findlay & Walker give voice to several common lines of thought regarding oculomotor control but do not provide sufficient detail for a critical evaluation of their theory. I argue that arbitrary spatial and temporal saccade metrics can be produced simply by manipulating the initial activation values in their model – values that the authors never specify. This lack of detail makes it difficult to anticipate the model's specific oculomotor behavior, or to compare this behavior to models opting for a more (...) quantitative framework. (shrink)

Karl Jaspers was one of the greatest European philosophers and humanists of the twentieth century. He demonstrated a broad range of philosophical thinking that makes his work relevant for the twenty-first century. Coming to philosophy from medicine and psychiatry, Jaspers's views encompass a vast and creative range of empirical, philosophical, social, historical, and poltical ideas. Hannah Arendt described Jaspers as one of the greatest interpreters of Kant in the German tradition. In the 1950s, Jaspers spoke of his "philosophy of reason" (...) and his debt to Nietzsche, Kierkegaard, Weber, and others. His philosophy, however, has often been misunderstood by Anglophone readers and interpreters, both with respect to his so-called existentialism, as well as to the originality, creativity, depth, and scope of this thinking and method. The contributors to this fascinating volume offer fresh expositions and interpretations of Jaspers's philosophy. All are prominent experts in Jaspers research from three continents (Europe, North America, and Asia). Six major parts reveal the significant contribution of Jaspers's thought to the philosophy of psychiatry and science, philosophy of history, metaphysics, philosophy of education, philosophy of humanity, philosophy of politics, philosophy of religion, and intercultural philosophy. Key concepts of Jaspers's philosophy are highlighted and interpreted from a fresh and timely perspective: "boundary situations," existential communication, existential truth, transcendence, philosophical faith, the axial age in world history, new politics and the role of a moral and political conversion, the idea of the university, and Jaspers's fascination with and interpretation of Asian thought. The accessible essays will help readers overcome the intimidation often felt when faced with the work of a major German philosopher. The editors introduce and summarize Jaspers's published works, while offering an overview of his basic themes and concerns. New readers and researchers alike will find this collection instrumental in understanding recent developments in the interpretation of Jaspers. (shrink)

Most of what has been written about Buber and education tend to be studies of two kinds: theoretical studies of his philosophical views on education, and specific case studies that aim at putting theory into practice. The perspective taken has always been to hold a dialogue with Buber's works in order to identify and analyse critically Buber's views and, in some cases, to put them into practice; that is, commentators dialogue with the text. In this article our aims are of (...) a different kind. First and fundamentally, we demonstrate the political and social ontological basis of Buber's thought; that is, we show that Buber, the philosopher of dialogue, held an authentic dialogue with his time, and demonstrate that Buber's work, in this case I and Thou, holds a dialogue with its Zeitgeist; that is the text dialogues with its Zeitgeist. This approach leads us to our second aim, which is to demonstrate that Buber's thought remains relevant to our times, particularly when it serves as a dialogical educational tool with which to resolve conflict of all types and to aid dialogue towards peace in inter‐community relations. (shrink)

This article is a response to Frank Hindriks’ “Restructuring Searle’s Making the Social World.”.

This article discusses John Searle’s status function account of human rights and Åsa Burman’s “A Critique of the Status Function Account of Human Rights.” While recognizing the validity of part of the critique, based on the distinction between types and tokens, the author argues that, nonetheless, one is not compelled to accept Burman’s conclusion, that “one must give up the status function account of human rights to explain how a human right can exist without collective recognition”. Specifically, the author accepts (...) Burman’s critique of Searle’s attempt to preserve the intuition that human rights have existed without collective recognition, but concludes offering three ways to understand human rights even in the absence of collective recognition, all of which preserve the status function account. (shrink)

_ Source: _Volume 28, Issue 2, pp 132 - 148 A striking feature of Thomas Hobbes’s account of political obligation is his discussion of the Fool, who thinks it reasonable to adopt a policy of selective, self-interested covenant breaking. Surprisingly, scholars have paid little attention to the potential of a psychological defense of Hobbes’s controversial claim that the Fool behaves irrationally. In this paper, I first describe Hobbes’s account of the Fool and argue that the kind of Fool most worth (...) considering is the covert, long-term Fool. Then I advance and critically assess two psychological arguments according to which the Fool’s policy of self-interested covenant breaking is prudentially irrational. The first argument holds that, taken together, the deep guilt from early-stage covenant breaking, the cumulative guilt from continued covenant breaking, and the high statistical risk of detection during high-volume covenant breaking render the Fool’s policy irrational. The second argument holds that the Fool’s policy is irrational because it puts him at risk of adopting a psychologically intolerable view of his fellow covenanters and, specifically, the extent to which they can be trusted. (shrink)

This accessible book gives a new, detailed and elementary explanation of the Gödel incompleteness theorems and presents the Chaitin results and their relation to the da Costa-Doria results, which are given in full, but with no ...

Surprisingly few articles have focused on Aquinas’s particular conception of necessary beings in the Third Way, and many scholars have espoused inaccurate or incomplete views of that conception. My aim in this paper is both to offer a corrective to some of those views and, more importantly, to provide compelling answers to the following two questions about the necessary beings of the Third Way. First, how exactly does Aquinas conceive of these necessary beings? Second, what does Aquinas seek to accomplish (...) in the third stage of the Third Way? In answering these questions, I challenge prominent contemporary understandings of the necessary beings of the Third Way. (shrink)

This article introduces the Normative Representativeness Requirement (NRR) on any moral objection to a decentralized, profit-oriented system of political economy. I develop and defend the NRR and then show why the most important recent critique of the profit system—which I call The Moderate Critique (developed by, for instance, Elizabeth Anderson)—fails to meet the NRR. This article also defends the radical claim that no objection to the profit system itself, rather than just key aspects or salient instances of it, succeeds in (...) meeting the NRR. Critics of the profit system should not seek an alternative to the profit system, but, at most, an alternative within it. (shrink)