New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell (...) division and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology. (shrink)

Advances in biochemistry, chemistry and engineering have enabled the development of a new gene expression assay. This ‘chip‐based’ approach utilizes microscopic arrays of cDNAs printed on glass as high‐density hybridization targets. Fluorescent probe mixtures derived from total cellular messenger RNA (mRNA) hybridize to cognate elements on the array, allowing accurate measurement of the expression of the corresponding genes. Array densities of >1,000 cDNAs per cm2 enable quantitative expression monitoring of a large number of genes in a single hybridization. A two‐color (...) fluorescence detection scheme allows rapid and simultaneous differential expression analysis of independent biological samples. Mass‐produced microarrays provide a new tool for genome expression analysis that may revolutionize genetic dissection, drug discovery and human disease diagnostics. (shrink)

The phenomenal proliferation of scientific studies into the nature of induced pluripotent stem (iPS) cells following publication of the findings of Takahashi and Yamanaka little more than 2 years ago, have significantly expanded our understanding of cellular mechanisms relating to cell lineage, differentiation, and proliferation. While the full potential of iPS cell lineages for both scientific tool and therapeutic applications is as yet unclear, findings from several lines of investigation suggests that multipotential and terminally differentiated cells from an array of (...) cell types are competent to undergo epigenetic reprogramming to a pluripotential state. The nature of this pluripotential state appears to be similar to, but not identical with that previously described for embryonic stem (ES) cells. Understanding the nature of this induced reprogrammed state will be critical to determining the full potential of iPS cells. Recently, this issue has been examined through an integrated analysis of the genome in fully and partially reprogrammed iPS cell lineages. These results provide a window onto the temporal components of reprogramming and suggest mechanisms by which the efficacy of reprogramming can be enhanced. (shrink)

Delivering high quality genomics-informed care to patients requires accurate test results whose clinical implications are understood. While other actors, including state agencies, professional organizations, and clinicians, are involved, this article focuses on the extent to which the federal agencies that play the most prominent roles — the Centers for Medicare and Medicaid Services enforcing CLIA and the FDA — effectively ensure that these elements are met and concludes by suggesting possible ways to improve their oversight of genomic testing.

It is probable that, increasingly, genome investigations are going to be based on statistical formalization. This review summarizes the state of art and potentiality of using statistics in microbial genome analysis. First, I focus on recent advances in functional genomics, such as finding genes and operons, identifying gene conversion events, detecting DNA replication origins and analysing regulatory sites. Then I describe how to use phylogenetic methods in genome analysis and methods for genome‐wide scanning for (...) positively selected amino acids. I conclude with speculations on the future course of genome statistical modeling. BioEssays 25:266–273, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

As evidenced by high-throughput sequencers, genomic technologies have recently undergone radical advances. These technologies enable comprehensive sequencing of personal genomes considerably more efficiently and less expensively than heretofore. These developments present a challenge to the conventional framework of biomedical ethics; under these changing circumstances, each research project has to develop a pragmatic research policy. Based on the experience with a new large-scale project—the Genome Science Project—this article presents a novel approach to conducting a specific policy for personal genome (...) research in the Japanese context. In creating an original informed-consent form template for the project, we present a two-tiered process: making the draft of the template following an analysis of national and international policies; refining the draft template in conjunction with genome project researchers for practical application. Through practical use of the template, we have gained valuable experience in addressing challenges in the ethical review process, such as the importance of sharing details of the latest developments in genomics with members of research ethics committees. We discuss certain limitations of the conventional concept of informed consent and its governance system and suggest the potential of an alternative process using information technology. (shrink)

The introduction of genomics and biobanking methodologies to the African research context has also introduced novel ways of doing science, based on values of sharing and reuse of data and samples. This shift raises ethical challenges that need to be considered when research is reviewed by ethics committees, relating for instance to broad consent, the feedback of individual genetic findings, and regulation of secondary sample access and use. Yet existing ethics guidelines and regulations in Africa do not successfully regulate research (...) based on sharing, causing confusion about what is allowed, where and when. In order to understand better the ethics regulatory landscape around genomic research and biobanking, we conducted a comprehensive analysis of existing ethics guidelines, policies and other similar sources. We sourced 30 ethics regulatory documents from 22 African countries. We used software that assists with qualitative data analysis to conduct a thematic analysis of these documents. Surprisingly considering how contentious broad consent is in Africa, we found that most countries allow the use of this consent model, with its use banned in only three of the countries we investigated. In a likely response to fears about exploitation, the export of samples outside of the continent is strictly regulated, sometimes in conjunction with regulations around international collaboration. We also found that whilst an essential and critical component of ensuring ethical best practice in genomics research relates to the governance framework that accompanies sample and data sharing, this was most sparingly covered in the guidelines. There is a need for ethics guidelines in African countries to be adapted to the changing science policy landscape, which increasingly supports principles of openness, storage, sharing and secondary use. Current guidelines are not pertinent to the ethical challenges that such a new orientation raises, and therefore fail to provide accurate guidance to ethics committees and researchers. (shrink)

Large-scale whole genome sequencing (WGS) studies promise to revolutionize cancer research by identifying targets for therapy and by discovering molecular biomarkers to aid early diagnosis, to better determine prognosis and to improve treatment response prediction. Such projects raise a number of ethical, legal, and social (ELS) issues that should be considered. In this study, we set out to discover how these issues are being handled across different jurisdictions.

High‐capacity sequencing technologies have dramatically reduced both the cost and time required to generate complete human genome sequences. Besides expanding our knowledge about existing diversity, the nature of these technologies makes it possible to extend knowledge in yet another dimension: time. Recently, the complete genome sequence of a 4,000‐year‐old human from the Saqqaq culture of Greenland was determined to 20‐fold coverage. These data make it possible to investigate the population affinities of this enigmatic culture and, by identifying several (...) phenotypic traits of this individual, provide a limited glimpse into how these people may have looked. While undoubtedly a milestone in ancient DNA research, the cost to generate an ancient genome, even from such an exceptionally preserved specimen, remains out of reach for most. Nonetheless, recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large‐scale genome‐wide analysis of ancient human diversity a reality, providing a fresh look at human population history. (shrink)

Background The rise in genomic and biobanking research worldwide has led to the development of different informed consent models for use in such research. This study analyses consent documents used by investigators in the H3Africa (Human Heredity and Health in Africa) Consortium. Methods A qualitative method for text analysis was used to analyse consent documents used in the collection of samples and data in H3Africa projects. Thematic domains included type of consent model, explanations of genetics/genomics, data sharing and feedback (...) of test results. Results Informed consent documents for 13 of the 19 H3Africa projects were analysed. Seven projects used broad consent, five projects used tiered consent and one used specific consent. Genetics was mostly explained in terms of inherited characteristics, heredity and health, genes and disease causation, or disease susceptibility. Only one project made provisions for the feedback of individual genetic results. Conclusion H3Africa research makes use of three consent models—specific, tiered and broad consent. We outlined different strategies used by H3Africa investigators to explain concepts in genomics to potential research participants. To further ensure that the decision to participate in genomic research is informed and meaningful, we recommend that innovative approaches to the informed consent process be developed, preferably in consultation with research participants, research ethics committees and researchers in Africa. (shrink)

Whether, and to what degree, do patents granted on human genes cast a shadow of uncertainty over genomics and its applications? Will owners of patents on individual genes or clusters of genes sue those performing whole-genome analyses on human samples for patent infringement? These are related questions that have haunted molecular diagnostics companies and services, coloring scientific, clinical, and business decisions. Can the profusion of whole-genome analysis methods proceed without fear of patent infringement liability?Whole-genome sequencing is (...) proceeding apace. Academic centers have been performing whole-genome and -exome sequencing in research for at least five years, and academic clinical laboratories with national reach have been doing sequencing for clinical applications for almost as long. Companies have also been offering WGS and WES as a clinical service for a few years now. So far as we know, no one has been sued for infringement of “gene patents” for performing WGS. (shrink)

In this post‐sequencing era, geneticists can focus on functional genomics on a much larger scale than ever before. One goal is the discovery and elucidation of the intricate genetic networks that co‐ordinate transcriptional activation in different regulatory circuitries. High‐throughput gene expression measurement using DNA arrays has thus become routine strategy. This approach, however, does not directly identify gene loci that belong to the same regulatory group; e.g., those that are bound by a common (set of) transcription factor(s). Working in yeast, (...) two groups have recently published an elegant method that could circumvent this problem, by combining chromatin immunoprecipitation and DNA microarrays.(1,2) The method is likely to provide a powerful tool for the dissection of global regulatory networks in eukaryotic cells. BioEssays 23:473–476, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct.

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called “omic” techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe the taxonomic structure (...) of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the ‘omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel ‘omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment. (shrink)

A clear, introductory overview of the issues surrounding gene patenting.

Human heritable genome editing (HHGE) involves editing the genes of human gametes and/or early human embryos. Whilst ‘identity’ is a key concept underpinning the current HHGE debate, there is a lack of inclusive analysis on different concepts of ‘identity’ which renders the overall debate confusing at times. This paper first contributes to reviewing the existing literature by consolidating how ‘identity’ has been discussed in the HHGE debate. Essentially, the discussion will reveal an ontological and empirical understanding of identity (...) when different types of identity are involved. Here, I discuss genetic, numerical, qualitative and narrative and how each of them is relevant in the HHGE context. Secondly, given the different types of identity, the paper explores how we could navigate these different interpretations of identity in a way that promotes an inclusive and informed discussion between primary stakeholders and the general public in the HHGE debate. Here, I argue for and refine a multi-faceted concept of identity as a suitable framework for discussing the ethical and societal implications of HHGE because it not only could integrate different understandings of identity but also highlight the interconnectedness between these different understandings. (shrink)

Whole-genome analysis and whole-exome analysis generate many more clinically actionable findings than traditional targeted genetic analysis. These findings may be relevant to research participants themselves as well as for members of their families. Though researchers performing genomic analyses are likely to find medically significant genetic variations for nearly every research participant, what they will find for any given participant is unpredictable. The ubiquity and diversity of these findings complicate questions about disclosing individual genetic test results. We (...) outline an approach for disclosing a select range of genetic results to the relatives of research participants who have died, developed in response to relatives? requests during a pilot study of large-scale medical genetic sequencing. We also argue that studies that disclose individual research results to participants should, at a minimum, passively disclose individual results to deceased participants? relatives. (shrink)

The power of the scientific enterprise presents multiple avenues for harnessing and increasingly controlling biological phenomena and instituting interventions in different areas of biomedicine (Af...

I analyze Ojibway objections to genomics and genetics research on wild rice. Although key academic and industry participants in this research have dismissed their objections out of hand, my analysis supports the conclusion that the objections merit serious consideration, even by those who do not share the Ojibway’s religious beliefs.

New techniques in genome editing have led to a controversial debate about the opportunities and uncertainties they present for agricultural food production and consumption. In July 2018, the Court of Justice of the European Union defined genome editing as a new process of mutagenesis, which implies that the resulting organisms count as genetically modified and are subject, in principle, to the obligations of EU Directive 2001/18/EG. This paper examines how key protagonists from academia, politics, and the economy strategically (...) framed the debate around genome editing in agriculture in Germany prior to its legal classification by the Court of Justice. It is based on an analysis of 96 official statements, including position papers, press releases, and information brochures. Our study reveals eight strategic frames used in the discourse on genome editing and uncovers the strategies used to disconnect from or connect with the previous discourse on green genetic engineering in the 1970s, 1980s and 1990s. Building on competitive framing theory, the study provides explanations for the use and emergence of counter-framing strategies and their success or failure in the debate around genome editing. (shrink)

The vast majority (> 95%) of single-gene mutations in yeast affect not only the expression of the mutant gene, but also the expression of many other genes. These data suggest the presence of a previously uncharacterized ‘gene expression network’—a set of interactions between genes which dictate gene expression in the native cell environment. Here, we quantitatively analyze the gene expression network revealed by microarray expression data from 273 different yeast gene deletion mutants.(1) We find that gene expression interactions form a (...) robust, error-tolerant ‘scale-free’ network, similar to metabolic pathways(2) and artificial networks such as power grids and the internet.(3-5) Because the connectivity between genes in the gene expression network is unevenly distributed, a scale-free organization helps make organisms resistant to the deleterious effects of mutation, and is thus highly adaptive. The existence of a gene expression network poses practical considerations for the study of gene function, since most mutant phenotypes are the result of changes in the expression of many genes. Using principles of scale-free network topology, we propose that fragmenting the gene expression network via ‘genome-engineering’ may be a viable and practical approach to isolating gene function. BioEssays 24:267–274, 2002. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/bies.10054. (shrink)

Genomic research results and incidental findings with health implications for a research participant are of potential interest not only to the participant, but also to the participant's family. Yet investigators lack guidance on return of results to relatives, including after the participant's death. In this paper, a national working group offers consensus analysis and recommendations, including an ethical framework to guide investigators in managing this challenging issue, before and after the participant's death.

In this paper I claim that the goal of mapping and sequencing the human genome is not wholly new, but rather is an extension of an older project to map genes, a central aim of genetics since its birth. Thus, the discussion about the value of the HGP should not be posed in global terms of acceptance or rejection, but in terms of how it should be developed. The first section of this paper presents a brief history of the (...) project. The second section distinguishes among four kinds of issues relevant to an evaluation of the HGP: those economic and organizational issues related to the feasibility of the project; the ethical questions arising in the development of the project and the application of the data gathered; the empirical issues relevant to the scientific value of the project; and conceptual issues like reductionism and determinism relevant to understand the nature and scope of the project. In a third section, I analyze in detail whether the HGP and, more generally, molecular biology is reductionistic. (shrink)

Danchin argues that if scientists can reach a level of understanding of genomes, they will be able to resolve the major biological puzzle of the 21st century: the enigma of the living machine that creates the living machine.

Large-scale sequencing tests, including whole-exome and whole-genome sequencing, are rapidly moving into clinical use. Sequencing is already being used clinically to identify therapeutic opportunities for cancer patients who have run out of conventional treatment options, to help diagnose children with puzzling neurodevelopmental conditions, and to clarify appropriate drug choices and dosing in individuals. To evaluate and support clinical applications of these technologies, the National Human Genome Research Institute and National Cancer Institute have funded studies on clinical and research (...) sequencing under the Clinical Sequencing Exploratory Research program as well as studies on return of results. Most of these studies use sequencing in real-world clinical settings and collect data on both the application of sequencing and the impact of receiving genomic findings on study participants. They are occurring in the context of controversy over how to obtain consent for exome and genome sequencing. (shrink)

As Next Generation Sequencing technologies are increasingly implemented in biomedical research and care, the number of study participants and patients who ask for release of their genomic raw data is set to increase. This raises the question whether research participants and patients have a legal and moral right to receive their genomic raw data and, if so, how this right should be implemented into practice. In a first step we clarify some central concepts such as “raw data”; in a second (...) step we sketch the international legal framework. The third step provides an extensive ethical analysis which comprehends two parts: an evaluation of whether there is a prima facie moral right to receive one’s raw data, and a contextualization and discussion of the right in light of potentially conflicting interests and rights of the data subject herself and third parties; in a last fourth step we emphasize the main practical consequences of the ethical analyses and propose recommendations for the release of raw data. In several legislations like the new European General Data Protection Regulation, patients do in principle have the right to receive their raw data. However, the procedural implementation of this right and whether it involves genetic counselling is at the discretion of the Member States. Even more questions remain with respect to the research context. The ethical analysis suggests that patients and research subjects have a moral right to receive their genomic raw data and addresses aspects which are also of relevance for the legal discussion such as the costs of release of raw data and its impact on academic freedom. Taking into account the specific nature and implications of genomic raw data and the contexts of research and health care, several concerns and potentially conflicting interests of the data subjects themselves and involved researchers, physicians, biomedical institutions and relatives arise. Instead of using them to argue in favor of restrictions of the data subjects’ legal and moral right to genomic raw data, the concerns should be addressed through provision of information and other measures. To this end, we propose relevant recommendations. (shrink)

In 2021, the WHO Expert Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing (the ‘Committee’) published its policy recommendations. It proposes, inter alia, a set of nine values and principles to inform the governance of human genome editing (HGE) and makes recommendations regarding how HGE can be regulated. While these proposals contain valuable contributions to the discourse on the global governance of HGE, they also contain elements that call for heightened attention to (...) the risks of the technology, and a countervailing focus on the potential benefits of the technology is missing. The Committee ostensibly prioritises restricting HGE technology in the interest of society as a collective but, in doing so, neglects to consider the interests and rights of individuals. In this article, we suggest that this approach is imbalanced insofar as it fails to give sufficient weight to the promise of this technology in considering the regulation of risks and disregards the importance of the fundamental liberties underlying the use of HGE in its discussion of values and principles that should guide governance. How this is problematic is illustrated with reference to the Committee's openness to using patents as HGE governance tools and its blanket rejection of ‘eugenics’. It is concluded that while the Committee makes some sensible recommendations on global governance, the Committee's approach of emphasising restrictions on HGE without also giving weight to the value of an open and liberal policy space is not something that liberal democratic states ought to follow. (shrink)

There is growing interest for a communitarian approach to the governance of genomics, and for such governance to be grounded in principles of justice, equity and solidarity. However, there is a near absence of conceptual studies on how communitarian-based principles, or values, may inform, support or guide the governance of genomics research. Given that solidarity is a key principle in Ubuntu, an African communitarian ethic and theory of justice, there is emerging interest about the extent to which Ubuntu could offer (...) guidance for the governance of genomics research in Africa. To this effect, we undertook a conceptual analysis of Ubuntu with the goal of identifying principles that could inform equity-oriented governance of genomics research. Solidarity, reciprocity, open sharing, accountability, mutual trust, deliberative decision-making and inclusivity were identified as core principles that speak directly to the different macro-level ethical issues in genomics research in Africa such as: the exploitation of study populations and African researchers, equitable access and use of genomics data, benefit sharing, the possibility of genomics to widen global health inequities and the fair distribution of resources such as intellectual property and patents. We use the identified the principles to develop ethical guidance for genomics governance in Africa. (shrink)

Homology searches between DNA sequences of evolutionary distant species (phylogenetic footprinting) offer a fast detection method for regulatory sequences. Because of the small size of their genomes, tetraodontid species such as the Japanese pufferfish and green spotted pufferfish have become attractive models for comparative genomics. A disadvantage of the tetraodontid species is, however, that they cannot be bred and manipulated routinely under laboratory conditions, so these species are less attractive for developmental and genetic analysis. In contrast, an increasing arsenal (...) of transgene techniques with the developmental model species zebrafish and medaka are being used for functional analysis of cis regulatory sequences. The main disadvantage is the much larger genome. While comparison between many loci proved the suitability of phylogenetic footprinting using fish and mammalian sequences, fast rate of change in enhancer structure and gene duplication within teleosts may obscure detection of homologies. Here we discuss the contribution and potentials provided by different teleost models for the detection and functional analysis of conserved cis‐regulatory elements. BioEssays 24:564–572, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

High‐throughput DNA analyses are increasingly being used to detect rare mutations in moderately sized genomes. These methods have yielded genome mutation rates that are markedly higher than those obtained using pre‐genomic strategies. Recent work in a variety of organisms has shown that mutation rate is strongly affected by sequence context and genome position. These observations suggest that high‐throughput DNA analyses will ultimately allow researchers to identify trans‐acting factors and cis sequences that underlie mutation rate variation. Such work should (...) provide insights on how mutation rate variability can impact genome organization and disease progression. (shrink)

The complete sequencing of the genome of the fruit fly Drosophila melanogaster offers the prospect of detailed functional analysis of the extensive gene families in this genetic model organism. Comprehensive functional analysis of family members is facilitated by access to a robust, stable and inducible expression system in a fly cell line. Here we show how the Schneider S2 cell line, derived from the Drosophila embryo, provides such an expression system, with the bonus that radioligand binding studies, (...) second messenger assays, ion imaging, patch‐clamp electrophysiology and gene silencing can readily be applied. Drosophila is also ideal for the study of new control strategies for insect pests since the receptors and ion channels that many new animal health drugs and crop protection chemicals target can be expressed in this cell line. In addition, many useful orthologues of human disease genes are emerging from the Drosophila genome and the study of their functions and interactions is another area for postgenome applications of S2 cell lines. BioEssays 24:1066–1073, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

With the arrival of new methods of genome editing, especially CRISPR/cas 9, new perspectives on germline interventions have arisen. Supporters of germ line genome editing claim that the procedure could be used as a means of disease prevention. As a possible life-saving therapy, it provides benefits that outweigh its risks. Opponents of GGE claim that the medical and societal risks, especially the use of GGE for genetic enhancement, are too high. In our paper, we analyze the risks and (...) benefits of GGE. We show that the medical risk on an individual level might be reduced by further research in the near future so that they may be outweighed by the benefits. We also show that the societal risks of the procedure, i.e. genetic enhancement, are manageable by establishing a regulative framework before the GGE is implemented. Since the effects of modifying genes for the genepool of a given population are extremely difficult to model, the medical risks on the population level might be too high. (shrink)

A central problem for the international governance of heritable germline gene editing is that there are important differences in attitudes and values as well as ethical and health care considerations around the world. These differences are reflected in a complicated and diverse regulatory landscape. Several publications have discussed whether reproductive uses would be legally permissible in individual countries and whether clinical applications could emerge in the context of regulatory gaps and gray areas. Systematic comparative studies that explore issues related to (...) the governance of this technology from different national and international perspectives are needed to address the lack of knowledge in this area. In this research report, we contribute to filling this gap by presenting views of stakeholders in the United Kingdom on challenges to the governance of heritable genome editing. We present findings from a multistakeholder study conducted in the United Kingdom between October 2016 and January 2018 and funded by the Wellcome Trust. This research included interviews, literature analysis, and a workshop. We involved leading U.K. scientists, in vitro fertilization clinicians, and representatives from regulatory bodies, patient organizations, and other civil societal organizations, as well as fertility companies. Part one of this article explores stakeholder perceptions of possible global developments in heritable genome editing and associated risks and governance challenges. Part two presents a range of policy options that were generated during the workshop in relation to the challenges discussed in part one. (shrink)

The genomics “revolution” is spreading. Originating in the molecular life sciences, it initially affected a number of biomedical research fields such as cancer genomics and clinical genetics. Now, however, a new “wave” of genomic bioinformation is transforming a widening array of disciplines, including those that address the social, historical and cultural dimensions of human life. Increasingly, bioinformation is affecting “human sciences” such as psychiatry, psychology, brain research, behavioural research (“behavioural genomics”), but also anthropology and archaeology (“bioarchaeology”). Thus, bioinformatics is having (...) an impact on how we define and understand ourselves, how identities are formed and constituted, and, finally, on how we (on the basis of these redefined identities) assess and address some of the more concrete societal issues involved in genomics governance in various settings. This article explores how genomics and bioinformation, by influencing research agendas in the human sciences and the humanities, are affecting our self-image, our identity, the way we see ourselves. The impact of bioinformation on self-understanding will be assessed on three levels: (1) the collective level (the impact of comparative genomics on our understanding of human beings as a species), (2) the individual level (the impact of behavioural genomics on our understanding of ourselves as individuals), and (3) the genealogical level (the impact of population genomics on our understanding of human history, notably early human history). This threefold impact will be assessed from two seemingly incompatible philosophical perspectives, namely a “humanistic” perspective (represented in this article by Francis Fukuyama) and a “post-humanistic” one (represented by Peter Sloterdijk). On the basis of this analysis it will be concluded that, rather than focussing on human “enhancement” by adding or deleting genes, genome-oriented practices of the Self will focus on using genomics information in the context of identity-formation. Genomic bioinformation will increasingly be built into our self-images and used in order to tailor and adapt our practices of Self to our “personalised” genome. We will keep working on ourselves, no doubt, not by modifying our genomes, but rather by fine-tuning our behaviour. What we are experiencing is a bioinformatisation of the life-world. Genomics-based technologies will increasingly pervade our daily lives, our autobiographies and narratives, as well as our anthropologies, rather than our genomes as such. (shrink)

Genome editing enables very accurate alterations to DNA. It promises profound and potentially disruptive changes in healthcare, agriculture, industry, and the environment. This paper presents a multidisciplinary analysis of the contemporary development of genome editing and the tension between continuity and change. It draws on the idea that actors involved in innovation are guided by “sociotechnical regimes” composed of practices, institutions, norms, and cultural beliefs. The analysis focuses on how genome editing is emerging in different (...) domains and whether this marks continuity or disruption of the established biotechnology regime. In conclusion, it will be argued that genome editing is best understood as a technology platform that is being powerfully shaped by this existing regime but is starting to disrupt the governance of biotechnology. In the longer term is it set to converge with other powerful technology platforms, which together will fundamentally transform the capacity to engineer life. (shrink)

We have refined entropy theory to explore the meaning of the increasing sequence data on nucleic acids and proteins more conveniently. The concept of selection constraint was not introduced, only the analyzed sequences themselves were considered. The refined theory serves as a basis for deriving a method to analyze non-coding regions (NCRs) as well as coding regions. Positions with maximal entropy might play the most important role in genome functions as opposed to positions with minimal entropy. This method was (...) tested in the well-characterized coding regions of 12 strains of Classical Swine Fever Virus (CSFV) and non-coding regions of 20 strains of CSFV. It is suitable to analyze nucleic acid sequences of a complete genome and to detect sensitive positions for mutagenesis. As such, the method serves to formulate the basis for elucidating the functional mechanism. (shrink)

Extensive conflicts of interest at both individual and institutional levels are identifiable in scientific research and healthcare in China, as in many other parts of the world. A prominent new case from China is He Jiankui’s experiment that produced the world’s first gene-edited babies and that raises numerous ethical, political, socio-cultural, and transnational questions. Serious financial and other COI were involved in He’s genetic adventure. Using He’s infamous experiment as a case study, this paper explores the wider issue of financial (...) and other COI in scientific research and healthcare in China, especially institutional conflict of interest and policy-related COI. Taking a socio-ethical perspective, it examines China’s state policies and its massive efforts to transform and commercialize scientific research, the lack of policies and oversight mechanisms for regulating COI, as well as major ethical issues arising from COI including the undermining of public trust. Some practical suggestions are offered for institutional reform and institutional development so that COI, particularly ICOI, can be avoided or more effectively managed in scientific research in China. (shrink)

This paper applies the conceptual toolkit of Evolutionary Developmental Biology (evo‐devo) to the evolution of the genome and the role of the genome in organism development. This challenges both the Modern Evolutionary Synthesis, the dominant view in evolutionary theory for much of the 20th century, and the typically unreflective analysis of heredity by evo‐devo. First, the history of the marginalization of applying system‐thinking to the genome is described. Next, the suggested framework is presented. Finally, its application (...) to the evolution of genome modularity, the evolution of induced mutations, the junk DNA versus ENCODE debate, the role of drift in genome evolution, and the relationship between genome dynamics and symbiosis with microorganisms are briefly discussed. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Human Genome Research in an Interdependent WorldAlexander Morgan Capron (bio)This has been the year of agenda-setting conferences for the ambitious ELSI (ethical, legal and social issues) program of the Human Genome Project (HGP). But of the dozen or more major meetings of this sort held across the country, the one held at the National Institutes of Heakh (NIH) in Bethesda, MD, June 2-4, 1991, was distinctive in (...) several respects.1As its name implies, "Human Genome Research in an Interdependent World" was a global look at the issues raised by gene mapping and sequencing. Unlike previous conferences, however, this meeting looked beyond a comparative analysis of clinical and domestic legal issues, and concentrated on topics that may require responses on a truly international level if they are to be successfully resolved.The meeting's organizers gathered an impressive group of more than seventy participants from fifteen countries, including the first significant contingent of Soviet and Japanese scientists, physicians, and philosophers at an ELSI meeting. In addition to talks by the heads of the genome projects in the Soviet Union, Japan, and the United States, the meeting was keynoted by Dr. James Wyngaarden, director general of the Human Genome Organization (HUGO), and I had the honor of serving as its general chairman.The goal of the meeting was to consider an array of issues that scientists, philosophers, and lawyers from around the world suggested might have international significance, with an eye to deciding three things: (1) Does the issue deserve further attention? (2) Is the issue best addressed in an international or domestic context? and (3) Do structures exist to which the issue can be referred for resolution? In the final sessions, the entire group debated proposed resolutions on the various topics and narrowed the list needing further, intensive exploration.To provide an international framework for this process, the conference [End Page 247] established a Global Steering Committee on Ethical and Social Issues in Genome Research, which will coordinate the efforts of several task forces charged with refining the tentative resolutions adopted by the conference participants on June 4. The task forces are expected to be able to complete work on some topics by the time of the steering committee's first meeting, which was described by one participant as a "check point," probably within the coming year; on other topics, the task forces will provide interim reports and arrange to continue their analysis. Several topics—less complex or more embryonic—were referred directly to the steering committee. On all issues, a major objective will be to ascertain what existing or newly created structure or structures are capable of implementing the group's recommendations and then to monitor the issue to ensure that appropriate implementation is occurring.Issues to be Explored by Task ForcesInsurance and EmploymentWhile individuals may derive medically useful information from the expanded range of genetic tests that will flow from the HGP, they could also be harmed if test results become a basis for discrimination. An area of particular concern at the conference in Bethesda was whether genetic information should be used to decide eligibility for employment or the scope and cost of health and life insurance. The complexity of this issue is increased as barriers to worker migration fall (especially in Europe) and as more firms carry on business internationally. Furthermore, questions arise about the limits of required testing and whether individuals may decline to be informed of the results of tests.The task force will not only gather information on practices and legal standards throughout the world—especially in light of the differences among nations with regard to the linkage of employment and various forms of insurance—but will also examine international anti-discrimination laws as a possible means of supplementing domestic statutes and regulations. As a starting point, the Bethesda meeting agreed on a set of principles for the task force to refine.2ForensicsAlthough their legal status is not fully resolved, DNA tests are being used increasingly in judicial proceedings and civil and criminal investigations as a highly probative means to identify people. Most forensic uses of "DNA fingerprints" are domestic, but international cooperation among investigative bodies... (shrink)

This paper examines the promise of science and its role in shaping research policy. The promise of science is characterized by expectations of science, which are embedded in promissory discourses that envision futures made possible through advances in promising science. Through a single case study of the origins of Genome Canada, the research was guided by the question: How did expectations of genomics shape the creation of Genome Canada? A conceptualization of discursive power and expectations of genomics storylines (...) provide the theoretical and analytical basis for an in-depth examination of the ideational effects and material impacts on research policy decisions over three years that culminated in the creation of Genome Canada. Expectations of genomics storylines functioned in a complex interplay of discursive practices and dynamics among diverse policy actors within a genomics discourse-coalition to produce a range of ideational and material impacts. The expectations of genomics storylines produced powerful genomics subject-positions from which policy actors perceived their interests, identities and preferences and gained agency, which led to various material impacts, such as mobilizing support and funding, coordinating activities and transforming Canada’s research policy framework. With the increasing importance of research policy to a range of broader policy priorities underpinned by expectations that science will resolve societal challenges and contribute to socio-economic benefits, this paper sheds light on how complex research policy decisions are made; it further contributes to understanding the role of promissory discourses in shaping those decisions. (shrink)

While scientific terms lack the stability of physical objects, they are generally far more stable than the various meanings associated with them. As a consequence, they tend to carry older conceptions alongside those more recently acquired, thereby exerting an effective drag against conceptual change. I illustrate this claim with an analysis of the shifting meanings of the term genome, originally used to refer to a collectivity of genes, but more recently to an organism’s complement of DNA. While genes (...) were originally regarded as effectively autonomous formal agents, and DNA as collections of genes, contemporary research suggests that an organism’s DNA constitutes a far more complex system designed to adapt and respond to the environment in which it finds itself. (shrink)

BackgroundGenetic/genomic testing (GGT) are useful tools for improving health and preventing diseases. Still, since GGT deals with sensitive personal information that could significantly impact a patient’s life or that of their family, it becomes imperative to consider Ethical, Legal and Social Implications (ELSI). Thus, ELSI studies aim to identify and address concerns raised by genomic research that could affect individuals, their family, and society. However, there are quantitative and qualitative discrepancies in the literature to describe the elements that provide content (...) to the ELSI studies and such problems may result in patient misinformation and harmful choices.MethodsWe analyzed the major international documents published by international organizations to specify the parameters that define ELSI and the recognized criteria for GGT, which may prove useful for researchers, health professionals and policymakers. First, we defined the parameters of the ethical, legal and social fields in GGT to avoid ambiguities when using the acronym ELSI. Then, we selected nine documents from 44 relevant publications by international organizations related to genomic medicine.ResultsWe identified 29 ELSI sub-criteria concerning to GGT, which were organized and grouped within 10 minimum criteria: two from the ethical field, four from the legal field and four from the social field. An additional analysis of the number of appearances of these 29 sub-criteria in the analyzed documents allowed us to order them and to determine 7 priority criteria for starting to evaluate and propose national regulations for GGT.ConclusionsWe propose that the ELSI criteria identified herein could serve as a starting point to formulate national regulation on personalized genomic medicine, ensuring consistency with international bioethical requirements. (shrink)

Interventions in the human germline have been regarded as a red line in genetic engineering up to now. However, with the recent progress in genome editing techniques, first and foremost CRISPR-based methods, the tide seems to be turning. The therapeutic benefits in particular are brought forward as an argument in favor of germline genome editing. According to this view, the main benefit of GGE is disease prevention. The procedure could be used to prevent monogenetic conditions for which no (...) treatment is available so far. This leads many commentators to the view that the benefits of GGE outweigh the risks. In this article, I examine the status and ethical implications of GGE as a means of disease prevention. I intend to show that the notion of GGE as disease prevention is only true for one specific application. Instead of being preventive treatments, most applications of GGE are advanced techniques of assisted reproduction. As such, they can be thought of as wish-fulfilling medicine, that is the use of medical techniques for non-medically indicated purposes. Thus, it is necessary to reconsider the risk-benefit analysis of GGE for most of its applications. (shrink)