Democratic governance of genomics: the case of UK Biobank

Biobanks are collections of human biological tissue used for genomics research. This promises a better understanding of the gene-based contribution to common disease and development of a more personalized approach to healthcare with safer drugs and more effective treatment. However, biobanks are also controversial owing to the ethical, legal, social and political issues raised about their collection and use of biological samples. Therefore, their democratic governance is not only a normative challenge but also an empirical one. This paper is concerned with both challenges: it attempts to “evaluate” processes of democratic governance of genomics by focusing on the case of UK Biobank. The overall argument is that although the UK Biobank performs well in terms of general democratic governance structures, there are epistemological and practical limits to specific democratic governance processes.     

Life Sciences and the web: a new era for collaboration

The World Wide Web has revolutionized how researchers from various disciplines collaborate over long distances. This is nowhere more important than in the Life Sciences, where interdisciplinary approaches are becoming increasingly powerful as a driver of both integration and discovery. Data access, data quality, identity, and provenance are all critical ingredients to facilitate and accelerate these collaborative enterprises and it is here where Semantic Web technologies promise to have a profound impact. This paper reviews the need for, and explores advantages of as well as challenges with these novel Internet information tools as illustrated with examples from the biomedical community.     

Realizing the promise of population biobanks: a new model for translation

The promise of science lies in expectations of its benefits to societies and is matched by expectations of the realisation of the significant public investment in that science. In this paper, we undertake a methodological analysis of the science of biobanking and a sociological analysis of translational research in relation to biobanking. Part of global and local endeavours to translate raw biomedical evidence into practice, biobanks aim to provide a platform for generating new scientific knowledge to inform development of new policies, systems and interventions to enhance the public’s health. Effectively translating scientific knowledge into routine practice, however, involves more than good science. Although biobanks undoubtedly provide a fundamental resource for both clinical and public health practice, their potentiating ontology—that their outputs are perpetually a promise of scientific knowledge generation—renders translation rather less straightforward than drug discovery and treatment implementation. Biobanking science, therefore, provides a perfect counterpoint against which to test the bounds of translational research. We argue that translational research is a contextual and cumulative process: one that is necessarily dynamic and interactive and involves multiple actors. We propose a new multidimensional model of translational research which enables us to imagine a new paradigm: one that takes us from bench to bedside to backyard and beyond, that is, attentive to the social and political context of translational science, and is cognisant of all the players in that process be they researchers, health professionals, policy makers, industry representatives, members of the public or research participants, amongst others.     

Emotions as infectious diseases in a large social network: the SISa model

Human populations are arranged in social networks that determine interactions and influence the spread of diseases, behaviours and ideas. We evaluate the spread of long-term emotional states across a social network. We introduce a novel form of the classical susceptible–infected–susceptible disease model which includes the possibility for ‘spontaneous’ (or ‘automatic’) infection, in addition to disease transmission (the SISa model). Using this framework and data from the Framingham Heart Study, we provide formal evidence that positive and negative emotional states behave like infectious diseases spreading across social networks over long periods of time. The probability of becoming content is increased by 0.02 per year for each content contact, and the probability of becoming discontent is increased by 0.04 per year per discontent contact. Our mathematical formalism allows us to derive various quantities from the data, such as the average lifetime of a contentment ‘infection’ (10 years) or discontentment ‘infection’ (5 years). Our results give insight into the transmissive nature of positive and negative emotional states. Determining to what extent particular emotions or behaviours are infectious is a promising direction for further research with important implications for social science, epidemiology and health policy. Our model provides a theoretical framework for studying the interpersonal spread of any state that may also arise spontaneously, such as emotions, behaviours, health states, ideas or diseases with reservoirs.     

The quest for a message: budding yeast, a model organism to study the control of pre-mRNA splicing

Removal of introns during pre-mRNA splicing is a critical processin gene expression, and understanding its control at both single-geneand genomic levels is one of the great challenges in Biology.Splicing takes place in a dynamic, large ribonucleoprotein complexknown as the spliceosome. Combining Genetics and Biochemistry,Saccharomyces cerevisiae provides insights into its mechanisms,including its regulation by RNA–protein interactions.Recent genome-wide analyses indicate that regulated splicingis broad and biologically relevant even in organisms with arelatively simple intronic structure, such as yeast. Furthermore,the possibility of coordination in splicing regulation at genomiclevel is becoming clear in this model organism. This shouldprovide a valuable system to approach the complex problem ofthe role of regulated splicing in genomic expression.      

嗜热四膜虫——具有发展潜力的功能基因组学研究模型

在真核生物的分子生物学和遗传学研究方面,纤毛类原生动物嗜热四膜虫(Tetrahymenathermophila)已经被证明是一种有价值的生物学模型。通过对它的研究,人们发现并且掌握了核酶的分子机制、RNA的自我拼接、端粒的结构和功能、DNA序列重组等机理。这种原生动物的基因组功能分别由两个细胞核执行,即二倍体的小核与生殖过程有关,而多倍体的大核决定细胞的基因转录,并为转化基因的表达提供了强有力的手段。     

Variable conceptions of population in community resource genetic projects: a challenge for governance

In recent years, human genetic research has developed rapidly, and the cost of sequencing and computational technology continues to decline. This research has also been pushed forward by a major organizational innovation: the development of large, open-access databases of human gene sequences or biospecimens known as community resource projects. This article describes a challenge for the governance of these projects: conceptions of population vary significantly across organizational contexts. This makes it difficult to manage risk appropriately, as measures intended to address hazards to one kind of population may be inadequate for others. Unstable conceptions of population may also make it difficult to identify the stakeholders interested in the governance of these projects. This argument is developed by examining two cases, the International HapMap Project and 1000 Genomes Project, which make use of at least six distinct conceptions of population in different organizational segments.     

The psychology of primate cooperation and competition: a call for realigning research agendas

Cooperation and competition are two key components of social life. Current research agendas investigating the psychological underpinnings of competition and cooperation in non-human primates are misaligned. The majority of work on competition has been done in the context of theory of mind and deception, while work on cooperation has mostly focused on collaboration and helping. The current impression that theory of mind is not necessarily implicated in cooperative activities and that helping could not be an integral part of competition might therefore be rather misleading. Furthermore, theory of mind research has mainly focused on cognitive aspects like the type of stimuli controlling responses, the nature of representation and how those representations are acquired, while collaboration and helping have focused primarily on motivational aspects like prosociality, common goals and a sense of justice and other-regarding concerns. We present the current state of these two bodies of research paying special attention to how they have developed and diverged over the years. We propose potential directions to realign the research agendas to investigate the psychological underpinnings of cooperation and competition in primates and other animals.     

DigiPINS: a database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies

Single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variations in numerous organisms, have emerged as important tools for the study of complex genetic traits and deciphering of genome evolution. High-throughput genome sequencing projects worldwide provide an unprecedented opportunity for whole-genome SNP analysis in a variety of species. To facilitate SNP discovery in vertebrates, we have developed a web-based, user-friendly, and fully automated application, DigiPINS, for genome-wide identification of exonic SNPs from EST data. Currently, the database can be used to the mining of exonic SNPs in six complete genomes (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus and Danio rerio). In addition to providing information on sequence conservation, DigiPINS allows compilation of comprehensive sets of polymorphisms within cancer candidate genes or identification of novel cancer markers, making it potentially useful for cancer association studies. The DigiPINS server is available via the internet at http://pbil.univ-lyon1.fr/gem/DigiPINS/query_DigiPINS.php.     

Fundulus as the premier teleost model in environmental biology: opportunities for new insights using genomics

A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms.     

Online Islamophobia and the politics of fear: manufacturing the green scare

Negative attitudes and explicit racism against Muslims are increasingly visible in public discourse throughout Europe. Right-wing populist parties have strengthened their positions by focusing on the ‘Islamic threat’ to the West. Concurrently, the Internet has facilitated a space where racist attitudes towards Muslims are easily disseminated into the public debate, fuelling animosity against European Muslims. This paper explores part of the online Islamophobic network and scrutinizes the discursive strategies deployed by three ‘prominent’ online actors. By combining social network analysis and critical discourse analysis, the study shows that Islamophobic web pages constitute a dynamic network with ties to different political and geographical milieus. They create a seemingly mainstream political position by framing racist standpoints as a defence of Western values and freedom of speech. The study also shows that Islamophobic discourse is strengthened by xenophobic currents within mass media, and by the legitimization of intellectuals and political actors.     

The vitality of social media for establishing a research agenda on black lives and the movement

Social media provides scholars with important portals into the lives of marginalized communities and the movements organized to combat issues of race and racism in society. However, how to incorporate the seemingly unwieldy amount of social media data for research in our fields can pose challenges to further clarify how people navigate our social world and the issues with in it, but also how they organize to push for social change and equality. In what follows, the authors discuss how social media data can be used to enhance our studies of black lives in reflection of the burgeoning Black Lives Matter movement on issues such as gun violence, public health, and higher education.     

绿色参与式社区：加强城市景观的社会行动

介绍了位于洛哈市西南的提阿拉斯·科罗拉达斯（Tierras Coloradas）街区绿地和城市形象提升项目。以风景园林参与式设计方法为基础,该方法分5个阶段开展,从民众的主观批判精神开始,构成了参与行动的原动力。整个过程是在社区普及教学的进程中制定的,妇女是必须的参与者,共同找出邻里的问题和可能的解决办法。为此,普及教学是很有必要的,有助于未来社区项目的执行。重要的成果是,我们对部分城市街区进行了重新造林,改变了城市景观的形象,强化了社区体系, 促使社区在改善公共人行步道绿地方面开展合作。从专业的角度认为其主要效果是引导民众打破主观社区的非个人主观限制,为项目开展和参与打下基础。项目的整个社区干预过程是在高校、社区警察局、市政府等公共机构的支持下进行的,发挥着真正的协同作用,并齐心协力致力于该区块邻里间的自我发展,为未来与自然环境的友好关系奠定基础,这些都将影响社区的生活质量。     

A collaborative model for large‐scale riparian restoration in the western United States

In 2009, a group of practitioners took action to restore 175 miles of riparian habitat impaired by invasive plants along the Dolores River in southwestern Colorado and eastern Utah. Recognizing the magnitude of ecological, jurisdictional, and management challenges associated with this large‐scale initiative, this group of managers built trust and relationships with key partners to foster collaboration across boundaries and cultivate consensus of a variety of perspectives and forms of knowledge. What emerged was a network of individuals, organizations, and agencies dedicated to restoring the Dolores River riparian corridor while sharing information and learning from one another. This public–private collaboration, called the Dolores River Restoration Partnership (DRRP), has been successful in creating a process by which financial, technical, and human resources are shared across boundaries to restore a riparian corridor. Specifically, the DRRP developed effective planning documents, a responsive governance structure, monitoring protocols, and a shared mindset for extracting lessons learned that have been instrumental in making progress toward its shared restoration goals and addressing a wide variety of restoration challenges. The tools developed by the partnership and lessons learned from their utility are outlined in this case study as a means to inform other collaborative restoration efforts.     

GRASS: a server for the graphical representation and analysis of structures

GRASS (Graphical Representation and Analysis of Structures Server), a new web-based server, is described. GRASS exploits many of the features of the GRASP program and is designed to provide interactive molecular graphics and quantitative analysis tools with a simple interface over the World-Wide Web. Using GRASS, it is now possible to view many surface features of biological macromolecules on either standard workstations used in macromolecular analysis or personal computers. The result is a World-Wide Web-based, platform-independent, easily used tool for macromolecular visualization and structure analysis.     

Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system

Bumble bees are a longstanding model system for studies on behaviour, ecology and evolution, due to their well‐studied social lifestyle, invaluable role as wild and managed pollinators, and ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of bumble bee biology have remained enigmatic until the rise of the genetic and, more recently, genomic eras. Here, we review and synthesize new insights into the ecology, evolution and behaviour of bumble bees that have been gained using modern genetic and genomic techniques. Special emphasis is placed on four areas of bumble bee biology: the evolution of eusociality in this group, population‐level processes, large‐scale evolutionary relationships and patterns, and immunity and resistance to pesticides. We close with a prospective on the future of bumble bee genomics research, as this rapidly advancing field has the potential to further revolutionize our understanding of bumble bees, particularly in regard to adaptation and resilience. Worldwide, many bumble bee populations are in decline. As such, throughout the review, connections are drawn between new molecular insights into bumble bees and our understanding of the causal factors involved in their decline. Ongoing and potential applications to bumble bee management and conservation are also included to demonstrate how genetics‐ and genomics‐enabled research aids in the preservation of this threatened group.     

Exploring the population dynamics of waterfowl hunters using a mark-recapture approach

The number of waterfowl hunters in the United States has declined since the 1980s despite relatively abundant waterfowl populations and liberal hunting regulations. Programs focused on recruiting, retaining, and reactivating (R3) waterfowl hunters have become important to avoid further losses in traditional revenue for habitat management and protection and political support for waterfowl conservation and management. We focus on 4 waterfowl hunter population vital rates (i.e., recruitment rate, retention probability, license purchase probability, realized population growth rate), which can be used to improve the effectiveness of waterfowl hunter R3 activities and initiatives by providing a deeper understanding of waterfowl hunter population dynamics to determine who programs should target, where programs should be targeted, and finally the evaluation of programs. To do so, we analyzed Nebraska state electronic license data from 2012–2019 using Pradel survival and recruitment models in a mark-recapture framework. Female waterfowl hunter recruitment was higher than males; however, retention and license purchase probabilities were lower. Recruitment was highest in younger generations and retention highest in older generations. License purchase probabilities were highest among those in the oldest and youngest generations. The availability of hunting opportunity increased license purchase probabilities but had a minimal influence on retention and no association with recruitment. There were weak relationships between rurality and recruitment, and retention and license purchase probabilities. Finally, belonging to Ducks Unlimited was positively associated with higher license purchase and retention probabilities. Targeting an increase in license purchase probability by promoting social support for hunters through conservation organization membership should be a focus of waterfowl hunter R3 efforts to have the greatest influence on increasing waterfowl hunter participation.