This is the story of Lisa 1 —a woman like so many others who has been abused—and of her healing journey using music and creative arts experiences. It is also a story about how music, song, poetry, art, and dance awakened her to a new consciousness and provided the necessary empowerment she needed in order to reclaim the woman she had been before experiencing the trauma of abuse. While the question of how utilization of music and the creative arts encourages (...) personal transformation and healing is also deserving of a theoretical exploration, in this article I have chosen to foreground Lisa's story as narrative, in order to also engage the reader with the transformative potential of empowerment that comes through listening. I have chosen an approach that foregrounds Lisa's experience over theory explicitly, for, it is with the process of "finding voice" and of engaging the listener in that process, that transformation of consciousness and empowerment occurs. (shrink)

Few medievalists today would deny that the massive social and economic changes of the central Middle Ages affected the character and institutions of medieval Christianity. Generations of scholars, especially those influenced by the Annales school, have explored the social and economic roots of religious change. Despite widespread acceptance of the connection between socioeconomic factors and religious change, detailed explanations of exactly how social and economic development transformed medieval Christianity are still lacking for numerous important issues. My goal here is to (...) address one such issue: the connection between the emergence of new social groups and the development of new kinds of ecclesiastical institutions. (shrink)

Next SectionBiodefence, broadly understood as efforts to prevent or mitigate the damage of a bioterrorist attack, raises a number of ethical issues, from the allocation of scarce biomedical research and public health funds, to the use of coercion in quarantine and other containment measures in the event of an outbreak. In response to the US bioterrorist attacks following September 11, significant US policy decisions were made to spur scientific enquiry in the name of biodefence. These decisions led to a number (...) of critical institutional changes within the US federal government agencies governing scientific research. Subsequent science policy discussions have focused largely on ‘the dual use problem’: how to preserve the openness of scientific research while preventing research undertaken for the prevention or mitigation of biological threats from third parties. We join others in shifting the ethical debate over biodefence away from a simple framing of the problem as one of dual use, by demonstrating how a dual use framing distorts the debate about bioterrorism and truncates discussion of the moral issues. We offer an alternative framing rooted in social epistemology and institutional design theory, arguing that the ethical and policy debates regarding ‘dual use’ biomedical research ought to be reframed as a larger optimisation problem across a plurality of values including, among others: (1) the production of scientific knowledge; (2) the protection of human and animal subjects; (3) the promotion and protection of public health (national and global); (4) freedom of scientific enquiry; and (5) the constraint of government power. (shrink)

Older adults often have long-term relationships, and many of their goals are intertwined with their respective partners. Joint goals can help or hinder goal progress. Little is known about how accurately older adults assess if a goal is joint, the role of over-reporting in these perceptions, and how joint goals and over-reporting may relate to older partners' relationship satisfaction and physical health. Two-hundred-thirty-six older adults from 118 couples listed their three most important goals and whether they thought of them as (...) goals they had in common with and wanted to achieve together with their partner. Two independent raters classified goals as “joint” if both partners independently listed open-ended goals of the same content. Goal progress and relationship satisfaction were assessed 1 week later. Allostatic load was calculated using nine different biomarkers. Results show that 85% self-reported at least one goal as joint. Over-reporting– the perception that a goal was joint when in fact it was not mentioned among the three most salient goals of the spouse – occurred in one-third of all goals. Multilevel models indicate that the number of externally-rated joint goals was related to greater goal progress and lower allostatic load, but only for adults with little over-reporting. More joint goals and higher over-reporting were each linked with more relationship satisfaction. In conclusion, joint goals are associated with goal progress, relationship satisfaction, and health, but the association is dependent on the domain of functioning. (shrink)

The debate over how to best guide HIV-infected mothers in resource-poor settings on infant feeding is more than two decades old. Globally, breastfeeding is responsible for approximately 300,000 HIV infections per year, while at the same time, UNICEF estimates that not breastfeeding (formula feeding with contaminated water) is responsible for 1.5 million child deaths per year. The largest burden of these infections and deaths occur in Sub-Saharan Africa. Using this region as an example of the burden faced more generally in (...) other resource-poor settings, we contrast the evolution of the clinical standard of care for infant feeding with HIV-infected mothers in high-income countries to the current international clinical guidelines for HIV-infected mothers and infant feeding in resource-poor settings. While the international guidelines of exclusive breastfeeding for a 6-month period seem to offer the least-worst strategy for reducing mother-to-child transmission of HIV during infancy while conferring some immunity through breastfeeding post-6 months, we argue that the impact of the policy on mothers and healthcare workers on the ground is not well understood. The harm reduction approach on the level of health policy translates into a complicated, painful moral dilemma for HIV-positive mothers and those offering them guidance on infant feeding. We argue that the underlying socio-economic disparities that continue to fuel the need for a harm reduction policy on infant feeding and the harm to women and children justify: (1) that higher priority be given to solving the infant feeding dilemma with improved data on safe feeding alternatives, and (2) support of innovative, community-driven solutions that address the particular economic and cultural challenges that continue to result in HIV-transmission to children within these communities. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

Background Achieving meaningful consent can be challenging, particularly in contexts of diminished literacy, yet is a vital part of participant protection in global health research. Method We explored the challenges and potential solutions of achieving meaningful consent through a qualitative study in a predominantly hill tribe ethnic minority population in northern Thailand, a culturally distinctive population with low literacy. Semi-structured interviews were conducted with 37 respondents who had participated in scrub typhus clinical research, their family members, researchers and other key (...) informants. A thematic analysis was conducted. Results Our analysis identified four interrelated themes surrounding participants’ ability to give consent: varying degrees of research understanding, limitations of using informal translators, issues impacting decisions to join research, and voluntariness of consent. Suggestions for achieving more meaningful consent included the use of formal translators and community engagement with research populations. Conclusions Participant’s agency in decision making to join research should be supported, but research information needs to be communicated to potential participants in a way that they can understand. We found that improved understanding about the study and its potential benefits and harms goes beyond literacy or translation and requires attention to social and cultural factors. (shrink)

Microbial model systems have a long history of fruitful use in fields that include evolution and ecology. In order to develop further insight into modelling practice, we examine how the competitive exclusion and coexistence of competing species have been modelled mathematically and materially over the course of a long research history. In particular, we investigate how microbial models of these dynamics interact with mathematical or computational models of the same phenomena. Our cases illuminate the ways in which microbial systems and (...) equations work as models, and what happens when they generate inconsistent findings about shared targets. We reveal an iterative strategy of comparative modelling in different media, and suggest reasons why microbial models have a special degree of epistemic tractability in multimodel inquiry. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

BackgroundWhen conducting research with Indigenous populations consent should be sought from both individual participants and the local community. We aimed to search and summarise the literature about methods for seeking consent for research with Indigenous populations.MethodsA systematic literature search was conducted for articles that describe or evaluate the process of seeking informed consent for research with Indigenous participants. Guidelines for ethical research and for seeking consent with Indigenous people are also included in our review.ResultsOf 1447 articles found 1391 were excluded (...) ; 56 were relevant and included. Articles were categorised into original research that evaluated the consent process or publications detailing the process of seeking consent and guidelines for ethical research. Guidelines were categorised into international ; national and state/regional/local guidelines. In five studies based in Australia, Canada and The United States of America the consent process with Indigenous people was objectively evaluated. In 13 other studies interpreters, voice recording, videos, pictures, flipcharts and “plain language” forms were used to assist in seeking consent but these processes were not evaluated. Some Indigenous organisations provide examples of community-designed resources for seeking consent and describe methods of community engagement, but none are evaluated. International, national and local ethical guidelines stress the importance of upholding Indigenous values but fail to specify methods for engaging communities or obtaining individual consent. In the ‘Grey literature’ concerns about the consent process are identified but no solutions are offered.ConclusionConsultation with Indigenous communities is needed to determine how consent should be sought from the community and the individual, and how to evaluate this process. (shrink)

The consent and community engagement process for research with Indigenous communities is rarely evaluated. Research protocols are not always collaborative, inclusive or culturally respectful. If participants do not trust or understand the research, selection bias may occur in recruitment, affecting study results potentially denying participants the opportunity to provide more knowledge and greater understanding about their community. Poorly informed consent can also harm the individual participant and the community as a whole. Invited by local Aboriginal community leaders of the Fitzroy (...) Valley, the Kimberley, Western Australia, The Picture Talk project explores the consent process for research. Focus groups of Aboriginal community members were conducted to establish preferences for methods of seeking individual consent. Transcripts were analysed through NVivo10 Qualitative software using grounded theory with inductive and deductive coding. Themes were synthesised with quotes highlighted. Focus groups with Aboriginal community members were facilitated by a Community Navigator as a cultural guide and interpreter and a researcher. Participants were recruited from all main language groups of the Fitzroy Valley – Gooniyandi, Walmajarri, Wangkatjungka, Bunuba and Nikinya. Participants were aged ≥18 years, with 5 female groups and one male group. Themes identified include: Reputation and trust is essential; The Community Navigator is key; Pictures give the words meaning – milli milli versus Pictures; Achieving consensus in circles; Signing for consent; and Research is needed in the Valley. Aboriginal communities of the Fitzroy Valley recommend that researchers collaborate with local leaders, develop trust and foster a good reputation in the community prior to research. Local Aboriginal researchers should be employed to provide cultural guidance throughout the research process and interpret local languages especially for elders. Pictures are preferred to written text to explain research information and most prefer to sign for consent. The Fitzroy Valley welcomes research when collaborative and for the benefit of the community. Future research could include exploring how to support young people, promote health screening and improve understanding of medical knowledge. (shrink)

Intended for introductory classes focusing on philosophy of mind, 'Theories of Mind' includes readings from primary sources, edited to suit the needs of the beginner. Selections focus on vivid examples and counterexamples, and give instructors concerned with assigning accessible primary source material a foundation for more advanced studies in philosophy. Selections from David Armstrong, Ned Block, David Chalmers, Patricia Churchland, Paul Churchland, Andy Clark, Daniel C. Dennett, René Descartes, Jerry A. Fodor, Keith Gunderson, Frank Jackson, David Lewis, Barbara Montero, Thomas (...) Nagel, Gilbert Ryle, John Searle, J. J. C. Smart, and Alan M. Turing are included. (shrink)

How has reason, believed since the Enlightenment to be the ally of freedom in the search for a better, more humanly satisfying world, been reduced to a technical rationality that has actually impoverished the bases of human freedom? What might be the options and obligations for sociologists who wish to restore reason to its proper status? -/- Working within the tradition of C. Wright Mills and Jurgen Habermas, Frank Hearn sets out to answer these questions. He surveys the treatment of (...) the relation between reason and freedom in both the classical tradition (especially the writings of Saint-Simon, Comte, Durkheim, Marx, Weber, and Freud) and an increasingly significant segment of social thought and criticism (and, for example, in the contrasting visions of Daniel Bell and Christopher Lasch.) He then analyses both the concrete social and historical forms of expression taken by what Mills calls 'rationality without reason' and their impact on individual autonomy and the freedoms associated with democratic politics. Finally, he develops Mills's and Habermas's claims that the cultivation of democratic publics and a critical social theory committed to a vibrant public life are indispensable to the protection and revitalization of the values of reason and freedom and of the practices they entail. -/- This book updates and enriches Mills's influential argument by demonstrating its affinity with critical theory, by showing its contributions to a critical understanding of the classical tradition, and by showing its implications for contemporary social, political, and economic developments. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to this (...) controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn’s account may capture aspects of the pattern of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn’s application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. (shrink)

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)

The eukaryote cell is one of the most radical innovations in the history of life, and the circumstances of its emergence are still deeply contested. This paper will outline the recent history of attempts to reveal these origins, with special attention to the argumentative strategies used to support claims about the first eukaryote cell. I will focus on two general models of eukaryogenesis: the phagotrophy model and the syntrophy model. As their labels indicate, they are based on claims about metabolic (...) relationships. The first foregrounds the ability to consume other organisms; the second the ability to enter into symbiotic metabolic arrangements. More importantly, however, the first model argues for the autogenous or self-generated origins of the eukaryote cell, and the second for its exogenous or externally generated origins. Framing cell evolution this way leads each model to assert different priorities in regard to cell-biological versus molecular evidence, cellular versus environmental influences, plausibility versus evolutionary probability, and irreducibility versus the continuity of cell types. My examination of these issues will conclude with broader reflections on the implications of eukaryogenesis studies for a philosophical understanding of scientific contestation. (shrink)

Recent discoveries of geographical patterns in microbial distribution are undermining microbiology’s exclusively ecological explanations of biogeography and their fundamental assumption that ‘everything is everywhere: but the environment selects’. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will (...) trace the conceptual history of Beijerinck’s claim that ‘everything is everywhere’ in relation to a more general account of its theoretical, experimental and institutional context. His principle also needs to be situated in relationship to plant and animal biogeography, which, this paper will argue, forms a continuum of thought with microbial biogeography. Finally, a brief overview of the contemporary microbiological research challenging ‘everything is everywhere’ reveals that philosophical issues from Beijerinck’s era of microbiology still provoke intense discussion in twenty-first century investigations of microbial biogeography. (shrink)

Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses – not usually considered to be organisms – would merely be part of the environment. Since the late 1980s, however, a growing stream of micrographic, experimental, molecular, and model-based (theoretical) research has been investigating how and why viruses should be understood as ecological actors of the most important sort. Viruses, especially phage, have been revealed as participants in the (...) planet's most crucial food webs, even though viruses technically consume nothing (they do not metabolize by themselves). Even more impressively, viruses have been identified as regulators of planetary biogeochemistry, in which they control cycles such as carbon, nitrogen and phosphorus – cycles on which all life depends. Although much biogeochemical research black-boxes the entities filling functional roles, it is useful to focus a little more closely to understand how viruses can be held responsible for the global processes of life. This paper will give a brief overview of the history of virus ecology and tease out the implications of large-scale ecological modelling with viruses. This analysis suggests that viruses should be conceptualized as ecological actors that are at least comparable and possibly equal to organismal actors. Ecological agency can therefore be distinguished from standard interpretations of biological agency. (shrink)

Although the cell is commonly addressed as the unit of life, historians and philosophers have devoted relatively little attention to this concept in comparison to other fundamental concepts of biology such as the gene or species. As a partial remedy to this neglect, we introduce the cell as a major point of connection between various disciplinary approaches, epistemic strategies, technological vectors and overarching biological processes such as metabolism, growth, reproduction and evolution. We suggest that the role of the cell as (...) a nexus forms the basis for a new philosophical and historical appreciation of cell biology. This perspective focuses less on the cell as a well-defined, stable object and places more emphasis on its role as a mediator of fundamental biological processes. (shrink)

My aim in this article is to introduce readers to the topic of exploratory experimentation and briefly explain how the three articles that follow, by Richard Burian, Kevin Elliott, and Maureen O'Malley, advance our understanding of the nature and significance of exploratory research. I suggest that the distinction between exploratory and theory-driven experimentation is multidimensional and that some of the dimensions are continuums. I point out that exploratory experiments are typically theory-informed even if they are not theory-driven. I also (...) distinguish between research programs and experiments. Research programs that are largely exploratory, such as the ones discussed in these case studies, can involve both exploratory and theory-driven experimentation. (shrink)