Background Genomic research on neurodevelopmental disorders (NDDs), particularly involving minors, combines and amplifies existing research ethics issues for biomedical research. We performed a review of the literature on the ethical issues associated with genomic research involving children affected by NDDs as an aid to researchers to better anticipate and address ethical concerns. Results Qualitative thematic analysis of the included articles revealed themes in three main areas: research design and ethics review, inclusion of (...) class='Hi'>research participants, and communication of research results. Ethical issues known to be associated with genomic research in general, such as privacy risks and informed consent/assent, seem especially pressing for NDD participants because of their potentially decreased cognitive abilities, increased vulnerability, and stigma associated with mental health problems. Additionally, there are informational risks: learning genetic information about NDD may have psychological and social impact, not only for the research participant but also for family members. However, there are potential benefits associated with research participation, too: by enrolling in research, the participants may access genetic testing and thus increase their chances of receiving a (genetic) diagnosis for their neurodevelopmental symptoms, prognostic or predictive information about disease progression or the risk of concurrent future disorders. Based on the results of our review, we developed an ethics checklist for genomic research involving children affected by NDDs. Conclusions In setting up and designing genomic research efforts in NDD, researchers should partner with communities of persons with NDDs. Particular attention should be paid to preventing disproportional burdens of research participation of children with NDDs and their siblings, parents and other family members. Researchers should carefully tailor the information and informed consent procedures to avoid therapeutic and diagnostic misconception in NDD research. To better anticipate and address ethical issues in specific NDD studies, we suggest researchers to use the ethics checklist for genomic research involving children affected by NDDs presented in this paper. (shrink)

Research studies increasingly use genomic sequencing to draw inferences based on comparisons between the genetic data of a set of purportedly related individuals. As use of this method progresses, it will become much more common to discover that the assumed biological relationships between the individuals are mistaken. Consequently, researchers will have to grapple with decisions about whether to return incidental findings of misattributed parentage on a much larger scale than ever before. In this paper we provide an extended (...) argument for the view that the default position for researchers ought to be the non-disclosure of misattributed parentage. (shrink)

As the international genomic research community moves from the tool-making efforts of the Human Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work – and for understanding who we are as biological organisms. In this essay we focus on the Human Microbiome Project as one such translational initiative. The HMP is a new ‘metagenomic’ research effort to sequence the genomes of human microbiological flora, in order (...) to pursue the interesting hypothesis that our ‘microbiome’ plays a vital and interactive role with our human genome in normal human physiology. Rather than describing the human genome as the ‘blueprint’ for human nature, the promoters of the HMP stress the ways in which our primate lineage DNA is interdependent with the genomes of our microbiological flora. They argue that the human body should be understood as an ecosystem with multiple ecological niches and habitats in which a variety of cellular species collaborate and compete, and that human beings should be understood as ‘superorganisms’ that incorporate multiple symbiotic cell species into a single individual with very blurry boundaries. These metaphors carry interesting philosophical messages, but their inspiration is not entirely ideological. Instead, part of their cachet within genome science stems from the ways in which they are rooted in genomic research techniques, in what philosophers of science have called a ‘tools-to-theory’ heuristic. Their emergence within genome science illustrates the complexity of conceptual change in translational research, by showing how it reflects both aspirational and methodological influences. (shrink)

An increasing number of European research projects return, or plan to return, individual genomic research results (IRR) to participants. While data access is a data subject’s right under the General Data Protection Regulation (GDPR), and many legal and ethical guidelines allow or require participants to receive personal data generated in research, the practice of returning results is not straightforward and raises several practical and ethical issues. Existing guidelines focusing on return of IRR are mostly project-specific, only (...) discuss which results to return, or were developed outside Europe. To address this gap, we analysed existing normative documents identified online using inductive content analysis. We used this analysis to develop a checklist of steps to assist European researchers considering whether to return IRR to participants. We then sought feedback on the checklist from an interdisciplinary panel of European experts (clinicians, clinical researchers, population-based researchers, biobank managers, ethicists, lawyers and policy makers) to refine the checklist. The checklist outlines seven major components researchers should consider when determining whether, and how, to return results to adult research participants: 1) Decide which results to return; 2) Develop a plan for return of results; 3) Obtain participant informed consent; 4) Collect and analyse data; 5) Confirm results; 6) Disclose research results; 7) Follow-up and monitor. Our checklist provides a clear outline of the steps European researchers can follow to develop ethical and sustainable result return pathways within their own research projects. Further legal analysis is required to ensure this checklist complies with relevant domestic laws. (shrink)

When the Human Genome Project (HGP) was launched, our genome was presented as our ‘blueprint’, a metaphor reflecting a genetic deterministic epistemology. Eventually, however, the HGP undermined rather than strengthened the understanding of genomes as blueprints and of genes as ultimate causal units. A symbolical turning point was the discovery that the human genome only contains 22,500 genes. Initially, this was seen as a narcissistic offence. Gradually, however, it strengthened the shift from traditional genetics and biotechnology (i.e., gene-oriented approaches) to (...) genomics, i.e. genome-oriented or systems approaches, emphasizing complexity. The 20th century can be regarded as the century of biotechnology and of the gene. Its history demonstrated that the will to know (notably: to know ourselves) has never been a disinterested affair: it is driven by a will to improve (notably: to improve ourselves). In this article it is claimed that, as genomics takes us beyond a genetic deterministic understanding of life, this must have consequences for societal research and debate as well. Policies for self-improvement will increasingly rely on the use of complex interpretation. Therefore, the emphasis must shift from issues such as genetic manipulation and human enhancement to issues involved in governance of novel forms of information. (shrink)

Mehlman and Li offer a framework for approaching the bioethical issues raised by the military use of genomics that is compellingly grounded in both the contemporary civilian and military ethics of medical research, arguing that military commanders must be bound by the two principles of paternal- ism and proportionality. I agree fully. But I argue here that this is a much higher bar than we may fully realize. Just as the principle of proportionality relies upon a thorough assessment of (...) harms caused and military advantage gained, the use of genomic research, on Mehlman and Li’s view, will require an accurate understanding of the connection between genotypes and phenotypes – accurate enough to ameliorate the risk undertaken by our armed forces in being subject to such research. Recent conceptual work in evolutionary theory and the philosophy of biology, however, renders it doubtful that such knowledge is forthcoming. The complexity of the relationship between genotypic factors and realized traits (the so-called ‘G→P map’) makes the estimation of potential military advantage, as well as potential harm to our troops, incredibly challenging. Such fundamental conceptual challenges call into question our ability to ever satisfactorily satisfy the demands of a sufficiently rigorous ethical standard. (shrink)

The Human Genome Project is regarded by many as one of the major scientific achievements in recent science history, a large-scale endeavour that is changing the way in which biomedical research is done and expected, moreover, to yield considerable benefit for society. Thus, since the completion of the human genome sequencing effort, a debate has emerged over the question whether this effort merits to be awarded a Nobel Prize and if so, who should be the one to receive it, (...) as no more than three individuals can be selected. In this article, the HGP is taken as a case study to consider the ethical question to what extent it is still possible, in an era of big science, of large-scale consortia and global team work, to acknowledge and reward individual contributions to important breakthroughs in biomedical fields. Is it still viable to single out individuals for their decisive contributions in order to reward them in a fair and convincing way? Whereas the concept of the Nobel prize as such seems to reflect an archetypical view of scientists as solitary researchers who, at a certain point in their careers, make their one decisive discovery, this vision has proven to be problematic from the very outset. Already during the first decade of the Nobel era, Ivan Pavlov was denied the Prize several times before finally receiving it, on the basis of the argument that he had been active as a research manager rather than as a researcher himself. The question then is whether, in the case of the HGP, a research effort that involved the contributions of hundreds or even thousands of researchers worldwide, it is still possible to “individualise” the Prize? The “HGP Nobel Prize problem” is regarded as an exemplary issue in current research ethics, highlighting a number of quandaries and trends involved in contemporary life science research practices more broadly. (shrink)

The involvement of the public in the governance of genomics has become a topic of growing interest among scholars, practitioners and policy-makers. The implementation of public involvement programmes may be quite expensive, and the design and evaluation of public participation is a matter of controversy. Thus, this paper examines the justifications for public participation in the governance of genomic research to help understand whether public involvement is worthwhile and to provide a guide to the design of public participation. (...) I identify four primary justifications in support of public involvement. I argue that three of them have serious flaws: neither an increase in the stability of institutions, nor the positive effects on the virtues of individuals, nor the epistemic merits of participatory activities provide a solid ground for the engagement of the public in the governance of genomics. However, the ideal of legitimacy in the exercise of coercive power appears to lend strong support to public involvement programmes. Given that the reasons why public involvement is sought shape the design of the participatory activities, restricting the range of valid justifications promises to simplify the task of designing and evaluating public involvement. (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)

Michael Crichton (1942–2008) was a prolific writer of “science novels”, portraying the psychodynamics and sociodynamics of genomics and other NBIC (Nanotechnology, Biotechnology, Information technology and Cognitive science) fields, fostering critical reflection on their societal dimensions. Science novels may serve as “literary experiments”, as windows into the (future) impacts of current research. Although on the surface level Crichton’s books may be seen as entertaining bestsellers, an in-depth reading allows them to emerge as exploratory exercises, usable as course material for science (...) students. To open up this “deeper” dimension, I read Crichton’s work from a psychoanalytic angle, focusing on typical scenes and themes, such as the idea of a scientific crisis, geneticization and gender role reversal. The core question of a typical Crichton novel usually is: what will happen when a new laboratory research field suddenly comes out into the open? Notably, the gender dimension reflects and exemplifies the fascinations and concerns with contemporary technoscience addressed by him. (shrink)

In various documents the view emerges that contemporary biotechnosciences are currently experiencing a scientific revolution: a massive increase of pace, scale and scope. A significant part of the research endeavours involved in this scientific upheaval is devoted to understanding and, if possible, ameliorating humankind: from our genomes up to our bodies and brains. New developments in contemporary technosciences, such as synthetic biology and other genomics and “post-genomics” fields, tend to blur the distinctions between prevention, therapy and enhancement. An important (...) dimension of this development is “biomimesis”: i.e. the tendency of novel technologies and materials to mimic or plagiarize nature on a molecular and microscopic level in order to optimise prospects for the embedding of technological artefacts in natural systems such as human bodies and brains. In this paper, these developments are read and assessed from a psychoanalytical perspective. Three key concepts from psychoanalysis are used to come to terms with what is happening in research laboratories today. After assessing the general profile of the current revolution in this manner, I will focus on a particular case study, a line of research that may serve as exemplification of the vicissitudes of contemporary technosciences, namely viral biomaterials. Viral life forms can be genetically modified (their genomes can be rewritten) in such a manner that they may be inserted in human bodies in order to produce substances at specific sites such as hormones (testosterone), neurotransmitters (dopamine), enzymes (insulin) or bone and muscle tissue. Notably, certain target groups such as top athletes, soldiers or patients suffering from degenerative diseases may become the pioneers serving as research subjects for novel applications. The same technologies can be used for various purposes ranging from therapy up to prevention and enhancement. (shrink)

This year’s topic is “Genomics and Philosophy of Race.” Different researchers might work on distinct subsets of the six thematic clusters below, which are neither mutually exclusive nor collectively exhaustive: (1) Concepts of ‘Race’; (2) Mathematical Modeling of Human History and Population Structure; (3) Data and Technologies of Human Genomics; (4) Biological Reality of Race; (5) Racialized Selves in a Global Context; (6) Pragmatic Consequences of ‘Race Talk’ among Biologists.

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 framework and the common resource 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. (shrink)

This article analyzes a number of recently published autobiographies by leading participants in the Human Genome Project (HGP), in order to determine to what extent they may further our understanding of the history, scientific significance and societal impact of this major research endeavor. Notably, I will focus on three publications that fall under this heading, namely The common thread by John Sulston (2002/2003), The language of God (2006) by Francis Collins and A life decoded by Craig Venter (2007).1 What (...) may we learn from these autobiographical sources about the dynamics of scientific change? What is their added value in understanding science in general and the HGP in particular? These questions will be elaborated in three directions: on the level of knowledge (epistemology), power (politics) and the Self (ethics). On the epistemological level, genomics is often presented as a paradigm shift in the life sciences, a tremendous up-scaling of research, an “informatization” of life. Autobiographies may reveal how this shift – usually discussed in more general terms from a philosophy of science or science studies perspective – manifests itself on an individual scale, on a micro- epistemological level. On the political level, autobiographies may inform us about the micro-politics of scientific change. Finally, on the level of Self, autobiographies may allow us to analyze how researchers, through practices of Self, are actively engaged in constituting themselves as responsible subjects in the face of unpredictable dynamics and unforeseen dilemmas. (shrink)

Since the completion of the human genome project in 2003, genomic sequencing, analysis, and interpretation have become staples of research in medicine and the life sciences more generally. While much ink has been spilled concerning genomics’ precipitous rise, there is little agreement among scholars concerning its meaning, both in general and with respect to our current moment. Some claim genomics is neither new, nor noteworthy; others claim it is a novel and worrisome instrument of newgenics. Contrary to the (...) approaches of Foucault scholars in both camps, in this paper I utilize research in philosophy of disability to argue that genomics is indeed noteworthy as a unique form of biopower and that its primary function is to precisify impairments in contradistinction to disability. I call the force at play in this process genopower. (shrink)

Appropriate information and consent has been one of the most intensely discussed topics within the context of biobank research. In parallel to the normative debate, many socio-empirical studies have been conducted to gather experiences, preferences and views of patients, healthy research participants and further stakeholders. However, there is scarcity of literature which connects the normative debate about justifications for different consent models with findings gained in empirical research. In this paper we discuss findings of a limited review (...) of socio-empirical research on patients’ and healthy research participants’ experiences and views regarding consent to biobank research in light of ethical principles for appropriate information and consent. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in (...) biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

In this article, we discuss epistemological limitations relating to the use of ethnoracial categories in biomedical research as devised by the Office of Management and Budget’s institutional guidelines. We argue that the obligation to use ethnoracial categories in genomics research should be abandoned. First, we outline how conceptual imprecision in the definition of ethnoracial categories can generate epistemic uncertainty in medical research and practice. Second, we focus on the use of ethnoracial categories in medical genetics, particularly genomics-based (...) precision medicine, where ethnoracial identity is understood as a proxy for medically relevant differences among individuals. Notably, extensive criticisms have been made already against the genetic interpretation of races, but, nonetheless, the concept of race remains a key element of contemporary genomics. This motivates us to explore possible reasons why such criticisms may have been ineffective in redirecting attention to other (non-race-based) ways of controlling for human variability. We contend that popular arguments against the idea that human races have a genetic basis, though convincing in many respects, are not sufficient to exclude the pragmatic use of race and ethnicity as proxies for genetic variability related to complex phenotypes. Finally, we provide two further arguments to support the idea that ethnoracial categories are unlikely to provide meaningful insights into medical genetics, which implies that even the interpretation of race as a useful tool to stratify disease risk is unwarranted. (shrink)

From 1900 onwards, scientists and novelists have explored the contours of a future society based on the use of “anthropotechnologies” (techniques applicable to human beings for the purpose of performance enhancement ranging from training and education to genome-based biotechnologies). Gradually but steadily, the technologies involved migrated from (science) fiction into scholarly publications, and from “utopia” (or “dystopia”) into science. Building on seminal ideas borrowed from Nietzsche, Peter Sloterdijk has outlined the challenges inherent in this development. Since time immemorial, and at (...) least since the days of Plato’s Academy, human beings have been interested in possibilities for (physical or mental) performance enhancement. We are constantly trying to improve ourselves, both collectively and individually, for better or for worse. At present, however, new genomics-based technologies are opening up new avenues for self-amelioration. Developments in research facilities using animal models may to a certain extent be seen as expeditions into our own future. Are we able to address the bioethical and biopolitical issues awaiting us? After analyzing and assessing Sloterdijk’s views, attention will shift to a concrete domain of application, namely sport genomics. For various reasons, top athletes are likely to play the role of genomics pioneers by using personalized genomics information to adjust diet, life-style, training schedules and doping intake to the strengths and weaknesses of their personalized genome information. Thus, sport genomics may be regarded as a test bed where the contours of genomics-based self-management are tried out. (shrink)

The rise of molecular epigenetics over the last few years promises to bring the discourse about the sociality and susceptibility to environmental influences of the brain to an entirely new level. Epigenetics deals with molecular mechanisms such as gene expression, which may embed in the organism “memories” of social experiences and environmental exposures. These changes in gene expression may be transmitted across generations without changes in the DNA sequence. Epigenetics is the most advanced example of the new postgenomic and context-dependent (...) view of the gene that is making its way into contemporary biology. In my article I will use the current emergence of epigenetics and its link with neuroscience research as an example of the new, and in a way unprecedented sociality of contemporary biology. After a review of the most important developments of epigenetic research, and some of its links with neuroscience, in the second part I reflect on the novel challenges that epigenetics presents for the social sciences for a re-conceptualization of the link between the biological and the social in a postgenomic age. Although epigenetics remains a contested, hyped, and often uncritical terrain, I claim that especially when conceptualized in broader non-genecentric frameworks,. (shrink)

Current debate and policy surrounding the use of genetic editing in humans often relies on a binary distinction between therapy and human enhancement. In this paper, we argue that this dichotomy fails to take into account perhaps the most significant potential uses of CRISPR-Cas9 gene editing in humans. We argue that genetic treatment of sporadic Alzheimer’s disease, breast- and ovarian-cancer causing BRCA1/2 mutations and the introduction of HIV resistance in humans should be considered within a new category of genetic protection (...) treatments. We find that if this category is not introduced, life-altering research might be unnecessarily limited by current or future policy. Otherwise ad hoc decisions might be made, which introduce a risk of unforeseen moral costs, and might overlook or fail to address some important opportunities. (shrink)

Cancer research is experiencing ‘paradigm instability’, since there are two rival theories of carcinogenesis which confront themselves, namely the somatic mutation theory and the tissue organization field theory. Despite this theoretical uncertainty, a huge quantity of data is available thanks to the improvement of genome sequencing techniques. Some authors think that the development of new statistical tools will be able to overcome the lack of a shared theoretical perspective on cancer by amalgamating as many data as possible. We think (...) instead that a deeper understanding of cancer can be achieved by means of more theoretical work, rather than by merely accumulating more data. To support our thesis, we introduce the analytic view of theory development, which rests on the concept of plausibility, and make clear in what sense plausibility and probability are distinct concepts. Then, the concept of plausibility is used to point out the ineliminable role played by the epistemic subject in the development of statistical tools and in the process of theory assessment. We then move to address a central issue in cancer research, namely the relevance of computational tools developed by bioinformaticists to detect driver mutations in the debate between the two main rival theories of carcinogenesis. Finally, we briefly extend our considerations on the role that plausibility plays in evidence amalgamation from cancer research to the more general issue of the divergences between frequentists and Bayesians in the philosophy of medicine and statistics. We argue that taking into account plausibility-based considerations can lead to clarify some epistemological shortcomings that afflict both these perspectives. (shrink)

In this article, we analyse how researchers use the categories of race and ethnicity with reference to genetics and genomics. We show that there is still considerable conceptual “messiness” (despite the wide-ranging and popular debate on the subject) when it comes to the use of ethnoracial categories in genetics and genomics that among other things makes it difficult to properly compare and interpret research using ethnoracial categories, as well as draw conclusions from them. Finally, we briefly reconstruct some of (...) the biases of reductionism to which geneticists (as well as other researchers referring to genetic methods and explanations) are particularly exposed to, and we analyse the problem in the context of the biologization of ethnoracial categories. Our work constitutes a novel, in-depth contribution to the debate about reporting race and ethnicity in biomedical and health research. First, we reconstruct the theoretical background assumptions about racial ontology which researchers implicitly presume in their studies with the aid of a sample of recent papers published in medical journals about COVID-19. Secondly, we use the typology of the biases of reductionism to the problem of biologization of ethnoracial categories with reference to genetics and genomics. (shrink)

Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By (...) reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy (...) to advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

As opposed to a ‘one size fits all’ approach, precision medicine uses relevant biological, medical, behavioural and environmental information about a person to further personalize their healthcare. This could mean better prediction of someone’s disease risk and more effective diagnosis and treatment if they have a condition. Big data allows for far more precision and tailoring than was ever before possible by linking together diverse datasets to reveal hitherto-unknown correlations and causal pathways. But it also raises ethical issues relating to (...) the balancing of interests, viability of anonymization, familial and group implications, as well as genetic discrimination. This article analyses these issues in light of the values of public benefit, justice, harm minimization, transparency, engagement and reflexivity and applies the deliberative balancing approach found in theEthical Framework for Big Data in Health and Research to a case study on clinical genomic data sharing. Please refer to that article for an explanation of how this framework is to be used, including a full explanation of the key values involved and the balancing approach used in the case study at the end. Our discussion is meant to be of use to those involved in the practice as well as governance and oversight of precision medicine to address ethical concerns that arise in a coherent and systematic manner. (shrink)

During the past decades, our image ofHomo neanderthalensishas changed dramatically. Initially, Neanderthals were seen as primitive brutes. Increasingly, however, Neanderthals are regarded as basically human. New discoveries and technologies have led to an avalanche of data, and as a result of that it becomes increasingly difficult to pinpoint what the difference between modern humans and Neanderthals really is. And yet, the persistent quest for a minimal difference which separates them from us is still noticeable in Neanderthal research. Neanderthal discourse (...) is a vantage point from which the logic of ‘us’ versus ‘other’ is critically reconsidered. Studying contemporary academic literature and science autobiographies from an oblique perspective, focusing not on Neanderthals as objects, but on the dynamics of interaction between Neanderthal researchers and their finds, basic convictions at work in this type of research are retrieved. What is at issue is not the actual distinction between modern humans and Neanderthals, but rather the dualistic construction of human and nonhuman. Neanderthal understanding is affected by the desire to safeguard human uniqueness. The overall trend is to identify the human mark or spark, which defines us as favoured ‘winners’. The paradoxes emerging in contemporary Neanderthal discourse are symptomatic of the fact that a dualistic style of thinking is no longer tenable. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In (...) the naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

In various writings Michel Foucault has shown how, in the beginning of the 19th century, in settings such as army barracks, psychiatric hospitals and penitentiary institutions, the modern human sciences were ‹born› as an ensemble of disciplines (medical biology, psychiatry, psychology, criminology, and the like) From the beginning, the nature-nurture de- bate has been one of its key disputes. Are human individuals malleable by environmental factors (such as psychiatric treatments or disciplinary regimes), or do they rather display inborn predispositions for (...) delin- quency and other forms of antisocial behaviour? In the current era of genetic testing, in behavioural genomics and neuroscience, this issue is as controversial and topical as ever. Büchner’s unfinished drama Woyzeck (written in 1836) is a remarkable anticipation of this debate, staging the birth of the human individual as a research subject. It is the story of a destitute soldier who, according to his superiors, displays er- rant behaviour and is therefore recruited to serve as a research subject in an experiment. His army physician turns him into a ‹case›, which can be meticulously monitored and studied so as to record the genesis of a crime. In this paper, Büchner’s unsettling play is analysed in detail as one of the great anticipatory literary documents of the 19th century, ex- ploring the idea of predictive psychiatry and the quest for genetic pre- dispositions: a primal scene as it were of the nature-nurture debate as it unfolds from predictive criminology up to behavioural genomics. (shrink)

Health data processing fields face ethical and legal problems regarding fundamental rights. As we know, patients can benefit in the Digital Era from having health or medical information available, and medical decisions can be more effective with a better understanding of clinical histories, medical and health data thanks to the development of Artificial Intelligence, Internet of Things and other Digital technologies. However, at the same time, we need to guarantee fundamental rights, including privacy ones. The complaint about ethical and legal (...) requirements – including constitutional ones – is particularly relevant in the processing of health data. This paper is focused on the problem of the consent required to the processing of health data and the exceptions established in the new European Union General Data Regulation, which cover the processing of this special data -within other aims- for scientific, historical and statistical research as legitimate purposes, which include biomedical research. The conclusion is that these open concepts are problematic both for the protection of privacy rights and for the legal security/certainty of research. On one hand there are several interpretation problems, regarding the processing of health data and the protection of information privacy. On the other hand, professionals must follow the Multilevel legal framework and to guarantee fundamental rights in the processing of health data, so there are also problems of interpretation for researchers. Therefore, we need a clearer legal framework for biomedical research. (shrink)

A commentary on “Models of Consent to Return of Incidental Findings in Genomic Research,” by Paul S. Appelbaum, Erik Parens, Cameron R. Waldman, Robert Klitzman, Abby Fyer, Josue Martinez, W. Nicholson Price II, and Wendy K. Chung, in the July‐August 2014 issue.

The metaphor of “gene editing” has been employed widely in popular discussions of CRISPR technology. The editing metaphor obscures the physical mechanism of action in CRISPR techniques, and understates the present frequency of off-target effects. However, the editing metaphor may be a useful means to think about approaches to regulating the future use of CRISPR. Conceiving of CRISPR as an information technology recalls the highly computational, information-oriented context of genomic research in which CRISPR has emerged. More importantly, the (...) editing metaphor, while currently inaccurate, anticipates a future moment when CRISPR technology will be ubiquitous and extremely reliable. Contemporary deliberations about the regulation of CRISPR should keep in mind that the technology may become more powerful—and more susceptible to misuse—as the overall state of genomic science advances and applications of CRISPR become less expensive and more refined. (shrink)

This paper presents results found through searching publicly available U.S. data sources for information about how to handle incidental fndings (IF) in human subjects research, especially in genetics and genomics research, neuroimaging research, and CT colonography research. We searched the Web sites of 14 federal agencies, 22 professional societies, and 100 universities, as well as used the search engine Google for actual consent forms that had been posted on the Internet. Our analysis of these documents showed (...) that there is very little public guidance available for researchers as to how to deal with incidental fndings. Moreover, the guidance available is not consistent. (shrink)

The Centre for Society and Genomics (CSG) was established in 2004, funded by NGI (the Netherlands Genomics Initiative). Funding was continued in 2008. This report summarises the basic outcomes of almost a decade of interactive societal research, in close collaboration with the other centres of the NGI network. There are two reasons for presenting these results. First of all, at the end of this year, the CSG Next programme (2008-2013), encompassing more than 50 research projects conducted at 10 (...) Dutch universities, will be completed. Moreover, we are currently preparing ourselves for the years to come. The network of principal investigators, together with the research communities they represent and the societal and international networks they are involved in, have agreed to continue to work together, on the basis of mutual learning, transdisciplinary collaboration and collegial support. Notably, we offer our networks, experiences and expertise to help prepare the ground for promoting Responsible Research and Innovation (RRI) in the context of Horizon2020, together with our European colleagues. This report summarises what our type of research can achieve and how we want to continue our activities in the future. After a concise sketch of the life sciences landscape as it has evolved during the past seven decades or so, we explain how CSG came about and what kind of approach we have developed. Subsequently, we list our main results, notably in the form of project vignettes, so as to make the harvest of the CSG Next programme as tangible and concrete as possible. Finally, we explain how we see our role in the future. As is already indicated by the title: this is not merely a retrospective summary of our results (CSG harvest), but an invitation to readers (from academia, industry, policy and civil society) to reassemble and to optimally prepare ourselves for things to come, by strengthening and broadening our collaborative efforts, building on what we have achieved so far. (shrink)

Francis Collins had an impressive track record as a gene hunter (cystic fibrosis, neurofibromatosis, Huntington’s disease) when he was appointed Director of the Human Genome Project (HGP) in 1993. In June 2000, together with Craig Venter and President Bill Clinton, he presented the draft version of the human genome sequence to a worldwide audience during a famous press conference. And in 2009, President Barack Obama nominated him as director of the National Institutes of Health (NIH), the largest Tfunding agency for (...) biomedical research in the world. s The In 2006, Collins published his book The Language of God,3 an autobiographical account of the HGP and its scientific, historical, and societal significance, with special attention paid to the impact of the human sequence on the way we see our world and ourselves.4 Now, by way of a sequel, he has written The Language of Life. Wherea Language of God focused on the genome sequence of mankind in general, and on the HGP as a “revolution” in biomedicine, the new book, as indicated by its subtitle, is oriented towards “the revolution in personalized medicine”, the impact of the genomics revolution on the personal lives of individuals. Before subjecting Collins’ book to a closer reading, I first of all would like to explain how I will read it and from what perspective. Why is genomics in general, and the HGP and its aftermath in particular, a subject of interest to a philosopher like me? Why did I become interested in assessing the HGP and in studying the work and views of some of its key contributors? (shrink)

Current research on the origin of DNA and RNA, viruses, and mobile genetic elements prompts a re-evaluation of the origin and nature of genetic material as the driving force behind evolutionary novelty. While scholars used to think that novel features resulted from random genetic mutations of an individual’s specific genome, today we recognize the important role that acquired viruses and mobile genetic elements have played in introducing evolutionary novelty within the genomes of species. Viral infections and subviral RNAs can (...) enter the host genome and persist as genetic regulatory networks. Persistent viral infections are also important to understand the split between great apes and humans. Nearly all mammals and nonhuman primates rely on olfaction, i.e., chemoreception as the basis of the sense of smell for social recognition, group membership, and the coordination of organized social life. Humans, however, evolved other means to establish social bonding, because several infection waves by endogenous retroviruses caused a loss of odor receptors in human ancestors. The human independence from olfaction for social recognition was in turn one driver of the rather abrupt human transition to dependence on visual information, gesture production, and facial recognition that are at the roots of language-based communication. (shrink)

ABSTRACT The philosophical tradition approaches to morals have their grounds predominantly on metaphysical and theological concepts and theories. Among the traditional ethics concepts, the most prominent is the Divine Command Theory (DCT). As per the DCT, God gives moral foundations to the humankind by its creation and through Revelation. Morality and Divinity are inseparable since the most remote civilization. These concepts submerge in a theological framework and are largely accepted by most followers of the three Abrahamic traditions: Judaism, Christianity, and (...) Islam: the greatest part of the human population. Holding faith and Revelation for its grounds, the Divine Command Theories are not strictly subject to the demonstration. The opponents to the Divine Command conception of morals, grounded in the impossibility of demonstration of its metaphysical and religious assumptions, have tried for many centuries (albeit unsuccessfully) to devalue its importance. They held the argument that it does not show material evidence and logical coherence and, for this reason, cannot be taken into account for scientific nor philosophical purposes. It is just a belief and, as so, should be understood. Besides these extreme oppositions, many other concepts contravene the Divine Command theories, in one or another way, in part or in full. Many philosophers and social scientists, from the classic Greek philosophy up to the present date, for instance, sustain that morality is only a construct, and thus culturally relative and culturally determined. However, this brings many other discussions and imposes the challenge to determine what is the meaning of culture, which elements of culture are morally determinant, and finally, what are the boundaries of such relativity. Moral determinists claim that everything related to human behavior, including morality, is determined, once free will does not exist. More recently, modern thinkers argued that there is a strict science of morality. However, the scientific method alone, despite explaining several facts and evidence, cannot enlighten the entire content and full meaning of ethics. Morals’ understanding requires a broader perception, and an agreement among philosophers, which they have never achieved. All of these questions have many different configurations depending on each philosophical strand, and start complex analysis and endless debates, as long as many of them are reciprocally conflictive. The universe and the atmosphere involving this thesis are the dominions of all these conceptual conflicts, observed from an objective and evolutionary standpoint. Irrespective of this circumstance and its intrinsic importance, however, these questions are far distant from the methodological approach of an analytical discussion on objective morals, what is, indeed, the aim and scope of this work. We should briefly revisit these prominent traditional theories because this thesis shelters a comparative study, and its assumptions at least differ profoundly from all traditional theories. Therefore, it becomes necessary offering direct and specific elements of comparison to the reader, for the right criticism, dispensing interruptive researches. However, even revisiting the traditional theories, for this comparative and critical exposure purpose, they will be kept by the side of our main concerns, as “aliena materia.” Irrespective of the validity of any or all of the elements of this discussion, and their meaning as the philosophical universe of this thesis, the purpose of this work is demonstrating and justifying the existence and meaning of prehistoric moral archetypes arisen directly from the very first social needs and efforts for survival. These archetypes are the definition of the essential foundation of ethics, its aggregation to the collective unconscious and corresponding logic organization and transmission to evolutionary stages of the human genome and different relations space-time, irrespective of any contemporary experience of the individuals. The system defined by these archetypes composes an evolutionary human social model. Is this a metaethical position? Yes, it is. Moreover, as in any metaethical reasoning, we should look carefully for the best and coherent routes, as the Analytical Philosophy offers them. Thus, this work should reasonably demonstrate that morals are not a cultural product of the civilized men or modern societies and that despite being subject to several cultural relative aggregations and subtractions, its essential foundations are archetypal and have never structurally changed. This reasoning induces that morality is an original attribute of the “homo sapiens”; it is not a property and nor an accident: it integrates the human essence and belongs to the realm of the ontological human identity. The human phenomena is a continuing process, playing its role between random determination and free will, and we need to question how morality began and how did it come to us in the present. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant (...) science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This (...) review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

Since the ENCODE project published its final results in a series of articles in 2012, there is no consensus on what its implications are. ENCODE’s central and most controversial claim was that there is essentially no junk DNA: most sections of the human genome believed to be «junk» are functional. This claim was met with many reservations. If researchers disagree about whether there is junk DNA, they have first to agree on a concept of function and how function, given a (...) particular definition, can be discovered. The ENCODE debate centered on a notion of function that assumes a strong dichotomy between evolutionary and non-evolutionary function and causes, prevalent in the Modern Evolutionary Synthesis. In contrast to how the debate is typically portrayed, both sides share a commitment to this distinction. This distinction is, however, much debated in alternative approaches to evolutionary theory, such as the EES. We show that because the ENCODE debate is grounded in a particular notion of function, it is unclear how it connects to broader debates about what is the correct evolutionary frame- work. Furthermore, we show how arguments brought forward in the controversy, particularly arguments from mathematical population genetics, are deeply embedded in their particular disciplinary contexts, and reflect substantive assumptions about the evolution of genomes. With this article, we aim to provide an anatomy of the ENCODE debate that offers a new perspective on the notions of function both sides employed, as well as to situate the ENCODE debate within wider debates regarding the forces operating in evolution. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Research in pharmacogenomics and precision medicine has recently introduced the concept of Polygenic Scores (PGSs), namely, indexes that aggregate the effects that many genetic variants are predicted to have on individual disease risk. The popularity of PGSs is increasing rapidly, but surprisingly little attention has been paid to the idealisations they make about phenotypic development. Indeed, PGSs rely on quantitative genetics models and methods, which involve considerable theoretical assumptions that have been questioned on various grounds. This comes with epistemological (...) and ethical concerns about the use of PGSs in clinical decision-making. In this paper, I investigate to what extent idealisations in genetics models can impact the data gathering and clinical interpretation of genomics findings, particularly the calculation and predictive accuracy of PGSs. Although idealisations are considered ineliminable components of scientific models, they may be legitimate or not depending on the epistemic aims of a model. I thus analyse how various idealisations have been introduced in classical models and progressively readapted throughout the history of genetic theorising. Notably, this process involved important changes in the epistemic purpose of such idealisations, which raises the question of whether they are legitimate in the context of contemporary genomics. (shrink)

Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations (...) at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology. (shrink)

Rapid advances in genome editing and its potential application in medicine and enhancement have been hotly debated by scientists and ethicists. Although it has been proposed that germline gene editing be discouraged for the time being1, the use of gene editing in somatic human cells in the clinical context remains controversial, particularly for interventions aimed at enhancement2. In a report on human genome editing, the US National Academies of Sciences, Engineering, and Medicine (NAS; Washington, DC) notes that “important questions raised (...) with respect to genome editing include how to incorporate societal values into salient clinical and policy considerations”3. We report here our research that opens a window onto what the public thinks about these issues. (shrink)

This study takes off from the ethical problem that racism grounded in population genetics raises. It is an analysis of four standard scientific responses to the problem of genetically motivated racism, seen in connection with the Human Genome Diversity Project (HGDP): (1) Discriminatory uses of scientific facts and arguments are in principle ‘misuses’ of scientific data that the researcher cannot be further responsible for. (2) In a strict scientific sense, genomic facts ‘disclaim racism’, which means that an epistemically correct (...) grasp of genomics should be ethically justified. (3) Ethical difficulties are issues to be ‘resolved’ by an ethics institution or committee, which will guarantee the ethical quality of the research scrutinized. (4) Although population genetics occasionally may lead to racism, its overall ‘value’ for humankind justifies its cause as a desirable pursuit. I argue that these typical responses to genetically motivated racism supervene on a principle called the ‘ethic of knowledge’, which implies that an epistemically correct account has intrinsic ethical value. This principle, and its logically related ideas concerning the ethic of science, effectively avoids a deeper ethical question of responsibility in science from being raised. (shrink)

One interesting aspect of the Hwang-case has been the way in which this affair was assessed by academic journals such as Nature. Initially, Hwang’s success was regarded as evidence for the detrimental effects of research ethics, slowing down the pace of research in Western countries. Eventually, however, Hwang’s debacle was seen as evidence for the importance of ethics in the life sciences. Ironically, it was concluded that the West maintains its prominence in science (as a global endeavour) precisely (...) because it has its ethics in place. Bioethics was now seen as an indispensable part of quality control. In this article, I will claim that the Hwang case rather reveals that there is no reason for complacency and that there are substantial challenges awaiting us. They have to do with major transformations in the way knowledge is produced and research in the life sciences is conducted (such as the increase in pace and scale, globalisation and the growing importance of ICT and bioinformation). These transformations call for a different kind of bioethics. The focus must shift from duties of autonomous researchers concerning visible research subjects (“micro-ethics”) to responsibilities of institutionalised research networks in managing and processing large amounts of bioinformation (“macro-ethics”). Concepts such as transparency, reliability and benefit-sharing will become more important than concepts such as informed consent. Basically, it is a resurgence of the tension between the Kantian and the Hegelian view of ethics. The contours of macro-ethics will be elaborated notably as it is emerging in bioethical debates over biobanking and genetic databanks. (shrink)

Why conduct research concerning human genome or proving the existence of Higgs particle? What makes these problems significant or worthy of investigation? In recent epistemological discussions one can find at least two conceptions of the problem of epistemic significance: research question or cognitive problem can be practically significant or intrinsically epistemically significant, in a way that depends on the consideration whether reasons that support the significance of the problem are practical or epistemic. In this paper I am dealing (...) with the question of the possibility of determining the significance of the problem from the purely epistemic perspective. In that regard I argue that (under suitable interpretation of the problem of epistemic significance) there are no pure epistemic reasons that could determine the importance of the cognitive problem. The argument is based on three objections: (1) epistemic duty is unjustifiably identified with epistemic justification, (2) the dependence of epistemic reasons on conceputal schemes is not taken into consideration, and (3) the infinite justificatory potential of evidence is being disregarded. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In (...) particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an oppor- tunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would sug- gest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to imple- ment novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engi- neering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engi- neering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)