Beyond the genome: Reconstituting the new genetics

The mapping and sequencing of the human genome has been the 'Holy Grail' of the new genetics, and its publication marks a turning point in the development of modern biotechnology. However, the question remains: what has been the impact of this discovery on how biotechnology develops in science, and in society at large? Using concepts developed in the social studies of science and technology, the paper begins by rehearsing the historical development of the Human Genome Project (HGP), and suggests that its translation into genomics has been achieved through a process of 'black-boxing' to ensure stabilization. It continues by exploring the extent to which the move to genomics is part of a paradigm shift in biotechnology resulting from the conceptual and organizational changes that have occurred following the completion of HGP. The discussion then focuses on whether genomics can be seen as part of the development of socially robust knowledge in late modernity. The paper suggests that there is strong evidence that a transformation is indeed taking place. It concludes by sketching a social scientific agenda for investigating the reconstitution of the new genetics in a post-genomic era using a 'situated' analytic approach based on an understanding of techno-scientific change as both emergent and contingent.     

The human genome as public: Justifications and implications

Since the human genome was decoded, great emphasis has been placed on the unique, personal nature of the genome, along with the benefits that personalized medicine can bring to individuals and the importance of safeguarding genetic privacy. As a result, an equally important aspect of the human genome – its common nature – has been underappreciated and underrepresented in the ethics literature and policy dialogue surrounding genetics and genomics. This article will argue that, just as the personal nature of the genome has been used to reinforce individual rights and justify important privacy protections, so too the common nature of the genome can be employed to support protections of the genome at a population level and policies designed to promote the public's wellbeing. In order for public health officials to have the authority to develop genetics policies for the sake of the public good, the genome must have not only a common, but also a public, dimension. This article contends that DNA carries a public dimension through the use of two conceptual frameworks: the common heritage (CH) framework and the common resource (CR) framework. Both frameworks establish a public interest in the human genome, but the CH framework can be used to justify policies aimed at preserving and protecting the genome, while the CR framework can be employed to justify policies for utilizing the genome for the public benefit. A variety of possible policy implications are discussed, with special attention paid to the use of large‐scale genomics databases for public health research.     

Genomics research in the UK—the social science agenda

Abstract

We sketch the development of UK genetics and genomics research, and emphasize the UK's key role in the international genetics and genomics research community. We highlight in particular the part played by the UK's Research Councils and other funders. With the move from genomics to post-genomics research, the field is diversifying, and interdisciplinarity becomes increasingly important, as traditional disciplinary boundaries become blurred, or break down, in the face of newly emerging sciences. We consider the changing nature of health and ill health in the developed and developing world, and questions about the complex nature of the relationships between genes and the environment, and their future implications for human health and human populations. We describe the ESRC's activities, stressing the importance of both the social, ethical and legal issues raised by these emerging disciplines, and of public engagement. Finally, we link the data handling and analysis issues raised by these emerging sciences, with other new research areas, in particular the UK's e-Science programme.     

J. B. S. Haldane,Ernst Mayr and the Beanbag Genetics Dispute

Starting from the early decades of the twentieth century, evolutionary biology began to acquire mathematical overtones. This took place via the development of a set of models in which the Darwinian picture of evolution was shown to be consistent with the laws of heredity discovered by Mendel. The models, which came to be elaborated over the years, define a field of study known as population genetics. Population genetics is generally looked upon as an essential component of modern evolutionary theory. This article deals with a famous dispute between J. B. S. Haldane, one of the founders of population genetics, and Ernst Mayr, a major contributor to the way we understand evolution. The philosophical undercurrents of the dispute remain relevant today. Mayr and Haldane agreed that genetics provided a broad explanatory framework for explaining how evolution took place but differed over the relevance of the mathematical models that sought to underpin that framework. The dispute began with a fundamental issue raised by Mayr in 1959: in terms of understanding evolution, did population genetics contribute anything beyond the obvious? Haldane’s response came just before his death in 1964. It contained a spirited defense, not just of population genetics, but also of the motivations that lie behind mathematical modelling in biology. While the difference of opinion persisted and was not glossed over, the two continued to maintain cordial personal relations.     

Current Status of Genetics and Genomics of Reared Penaeid Shrimp: Information Relevant to Access and Benefit Sharing

At present, research and progress in shrimp genomics and genetics show significant developments. Shrimp genetics and genomics also show immense potential for an increased production in a way that meets shrimp culture progress goals for the third millennium. This review article aims to provide an overview of its current status and future direction, discusses questions that need focused research to address them, and summarizes areas where genetics and genomics knowledge can make a positive difference to shrimp culture sustainability. Sustainable progress of penaeid shrimps will depend upon feasible solutions for environmental, research, economic, consumer problems, proper development, and planning policy enforcement. It is recommended that increased funding for biotechnology research and progress be directed to expand worldwide commercial shrimp culture and address environmental and public health issues. For any researcher or shrimp company member who has attempted to or whom would like to thoroughly search the literature to gain a complete understanding of the current state of shrimp genetics and genomics, this publication will be an invaluable source of reference materials, some of which is reported here for the first time.     

Ten years of pathway analysis: current approaches and outstanding challenges

Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces complexity and has increased explanatory power. We discuss the evolution of knowledge base-driven pathway analysis over its first decade, distinctly divided into three generations. We also discuss the limitations that are specific to each generation, and how they are addressed by successive generations of methods. We identify a number of annotation challenges that must be addressed to enable development of the next generation of pathway analysis methods. Furthermore, we identify a number of methodological challenges that the next generation of methods must tackle to take advantage of the technological advances in genomics and proteomics in order to improve specificity, sensitivity, and relevance of pathway analysis.     

Technoscientific bespoking: Animals,publics and the new genetics

This paper examines the public understanding of science, especially biotechnology and the new genetics, in light of the symbolic roles of animals in the constitution of cultural identities. As such, the paper expands on the critical approach to public understanding of science, with its emphasis upon the way local identities impact upon the apprehension of, and trust in, science and scientific institutions. In particular, the new genetics raises issues about what sorts of broader public identities are mobilized. It is argued that, on the one hand, the complex symbolic role of animals is linked to a wide and contradictory range of modern Western identities, and thus potentially to volatility in the public's response to such biotechnological innovation. On the other, technoscientific bespoking, by rendering animals 'ready-to-order', might catastrophically curtail the symbolic role of animals in human identities, and thus provoke a general anxiety toward new genetics. Some political and research implications of the analysis are briefly explored.     

Sustainable forest management reporting in Australia

Criteria and indicators are used in a number of sectors to assess progress towards specified goals or targets. The adoption by the Australian Government of a modified set of Montreal Process criteria and indicators to report Australia's progress towards sustainable forest management, at national and sub-national levels, has improved the ability to report comprehensively and consistently, on economic, environmental and social values. The establishment of Australia's Montreal Process Implementation Group, with members from all States and Territories representing forest conservation, production, public and private forest management, provides a strong regional ownership and guidance of the framework. The adoption of the framework by State government agencies, involved in both production and conservation forests, for reporting sustainable forest management demonstrates the framework's relevance at national and sub-national levels. A major development was the implementation, for the first time, of Australia's sustainable forest management reporting framework in Australia's State of the Forest Report 2003. The implementation process revealed issues of relevance to indicators at national and regional levels, data availability, duplication, ambiguity and gaps between some indicators. A national review of the framework is underway to improve the reporting of progress towards sustainable forest management reporting in Australia.     

Crowdsourcing indicators for cultural ecosystem services: A geographically weighted approach for mountain landscapes

Integrating cultural dimensions into the ecosystem service framework is essential for appraising non-material benefits stemming from different human–environment interactions. This study investigates how the actual provision of cultural services is distributed across the landscape according to spatially varying relationships. The final aim was to analyse how landscape settings are associated to people's preferences and perceptions related to cultural ecosystem services in mountain landscapes. We demonstrated a spatially explicit method based on geo-tagged images from popular social media to assess revealed preferences. A spatially weighted regression showed that specific variables correspond to prominent drivers of cultural ecosystem services at the local scale. The results of this explanatory approach can be used to integrate the cultural service dimension into land planning by taking into account specific benefiting areas and by setting priorities on the ecosystems and landscape characteristics which affect the service supply. We finally concluded that the use of crowdsourced data allows identifying spatial patterns of cultural ecosystem service preferences and their association with landscape settings.     

Molecular approaches in pig breeding to improve meat quality.

This article reviews the advances in molecular genetics that have led to the identification of genes and markers associated with meat quality in pig. The development of a considerable number of annotated livestock genome sequences represents an incredibly rich source of information that can be used to identify candidate genes responsible for complex traits and quantitative trait loci effects. In pig, the huge amount of information emerging from the study of the genome has helped in the acquisition of new knowledge concerning biological systems and it is opening new opportunities for the genetic selection of this specie. Among the new fields of genomics recently developed, functional genomics and proteomics that allow considering many genes and proteins at the same time are very useful tools for a better understanding of the function and regulation of genes, and how these participate in complex networks controlling the phenotypic characteristics of a trait. In particular, global gene expression profiling at the mRNA and protein level can provide a better understanding of gene regulation that underlies biological functions and physiology related to the delivery of a better pig meat quality. Moreover, the possibility to realize an integrated approach of genomics and proteomics with bioinformatics tools is essential to obtain a complete exploitation of the available molecular genetics information. The development of this knowledge will benefit scientists, industry and breeders considering that the efficiency and accuracy of the traditional pig selection schemes will be improved by the implementation of molecular data into breeding programs.     

SpectralNET – an application for spectral graph analysis and visualization

Background  

Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks.     

The Gellnerian modality revisited: towards a ‘genealogy’ of cultural homogenization and nation-state congruency

This paper re-evaluates Ernest Gellner's theory of nations and nationalism and particularly his conceptions of cultural homogenization and congruency. The paper shows how Gellner's historical and epistemological stance naturalizes homogenization processes and rationalizes modern history as an inevitable trajectory of congruency making of states and nations. The paper proposes, nonetheless, to deploy a critical framework and read Gellner's notions of congruency and cultural homogenization as a ‘social imaginary’/‘fantasy’. That is, understanding congruency as a sociopolitical project that idealizes a certain imaginary as positive, necessary and inevitable – a ‘fantasy’ that sets to secure and stabilize discursively the contingency of social relations. It is suggested, moreover, to deploy a Foucauldian genealogical technique in an attempt to de-naturalize congruency and homogenization practices and expose the conditions of their emergence in modern history.     

Autobiologies on YouTube: narratives of direct-to-consumer genetic testing

Despite a growing personal genomics market, little is known about how people engage with the possibilities offered by direct-to-consumer (DTC) genetic testing. In order to help address this gap, this study deploys narrative analysis of YouTube videos posted by individuals who have purchased DTC genetic testing for disease. Genetic testing is said to be contributing to new states of illness, where individuals may become “patients-in-waiting.” In the videos analyzed, we found a new form of storytelling about this ambiguous state of illness, which we refer to as autobiology. Autobiology – the study of, and story about, one's own biology – concerns narratives of sense-making through forms of biological practice, as well as wayfaring narratives which interweave genetic markers and family histories of disease. These autobiologies – part of a broader shift toward public stories about genetics and other healthcare technologies – exhibit playfulness, as well as being bound with consumerist practices.     

SenseLab: new developments in disseminating neuroscience information

This article presents the latest developments in neuroscience information dissemination through the SenseLab suite of databases: NeuronDB, CellPropDB, ORDB, OdorDB, OdorMapDB, ModelDB and BrainPharm. These databases include information related to: (i) neuronal membrane properties and neuronal models, and (ii) genetics, genomics, proteomics and imaging studies of the olfactory system. We describe here: the new features for each database, the evolution of SenseLab's unifying database architecture and instances of SenseLab database interoperation with other neuroscience online resources.     

Evo-devo and the evolution of social behavior

The integration of evolutionary biology with developmental genetics into the hybrid field of 'evo-devo' resulted in major advances in understanding multicellular development and morphological evolution. Here we show how insights from evo-devo can be applied to study the evolution of social behavior. We develop this idea by reviewing studies that suggest that molecular pathways controlling feeding behavior and reproduction in solitary insects are part of a 'genetic toolkit' underlying the evolution of a particularly complex form of social behavior, division of labor among workers in honeybee colonies. The evo-devo approach, coupled with advances in genomics for non-model genetic organisms, including the recent sequencing of the honeybee genome, promises to advance our understanding of the evolution of social behavior.     

Molecular links between mitochondrial dysfunctions and schizophrenia

Schizophrenia is a complex neuropsychiatric disorder with both neurochemical and neurodevelopmental components in the pathogenesis. Growing pieces of evidence indicate that schizophrenia has pathological components that can be attributable to the abnormalities of mitochondrial function, which is supported by the recent finding suggesting mitochondrial roles for Disrupted-in-Schizophrenia 1 (DISC1). In this minireview, we briefly summarize the current understanding of the molecular links between mitochondrial dysfunctions and the pathogenesis of schizophrenia, covering recent findings from human genetics, functional genomics, proteomics, and molecular and cell biological approaches.     

Templates and exclusions: victim centrism in Canada's Truth and Reconciliation Commission on Indian residential schools

In this article I use an ethnographic approach to consider the causes and consequences of a focus on ‘survivor’ experience in Canada's Truth and Reconciliation Commission (TRC) on Indian residential schools. In this Truth Commission, the interconnected concepts of ‘survivor’, ‘cultural genocide’, ‘trauma’, and ‘healing’ became reference points for much of the testimony that was presented and the ways the schools were represented. Canada's Truth Commission thus offers an example of the consequences of ‘victim centrism’, including the ways that ‘truth‐telling’ can be influenced by the affirmation of particular survivor experiences and the wider goal of reforming the dominant historical narrative of the state through public education. Canada's TRC was limited by its mandate to a particular kind of institution and scope of collective harm. It was at the same time active in its creation of narrative templates, which guided the expression of traumatic personal experience and affirmed the category of residential school ‘survivor’ as the focal point for understanding policy‐driven loss of language, tradition, and political integrity.