1900 was a remarkable year for science. Several ground-breaking events took place, in physics, biology and psychology. Planck introduced the quantum concept, the work of Mendel was rediscovered, and Sigmund Freud published The Interpretation of Dreams . These events heralded the emergence of completely new areas of inquiry, all of which greatly affected the intellectual landscape of the 20 th century, namely quantum physics, genetics and psychoanalysis. What do these developments have in common? Can we discern a family likeness, a (...) basic affinity between them, so that we can use the one to deepen our understanding of the other? One common denominator is that they open up realms of inquiry that are significantly different from the world of everyday experience, namely the realm of elementary particles, of genes and genomes, and of the unconscious. But to what extent can we meaningfully argue, for instance, that the genome is the biological unconscious, and the unconscious the psychic genome? To address these questions, I will build on the work of two key intellectual figures who have explored the affinities of these developments in depth, namely Erwin Schrödinger (a quantum physicist and avid reader of Schopenhauer who initiated molecular biology) and Jacques Lacan (who reframed the specificity of psychoanalysis with the help of 20 th century science: the era of structural linguistics, but also of quantum physics, molecular biology, bioinformatics and DNA). (shrink)

In this paper I argue that some human reproductive genome editing interventions can be therapeutic in nature, and thus that it is false that all such interventions just create healthy individuals. I do this by showing that the conditions established by a therapy definition are met by certain reproductive genome editing interventions. I then defend this position against two objections: (a) reproductive genome editing interventions do not attain one of the two conditions for something to be a therapy, and (b) (...) some reproductive genome editing interventions are therapeutic but in a nonstandard way. In the Conclusion I call for a more nuanced discussion of the nature of reproductive genome editing interventions. (shrink)

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...) epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

In this paper, I will present the empirical version of the slippery slope argument (SSA) in the field of genome editing. According to the SSA, if we adopt germline manipulation of embryos we will eventually end up performing or allowing something morally reprehensible, such as new coercive eugenics. I will investigate the actual possibility of sliding towards eugenics: thus, I will examine enhancement and eugenics both in the classical and liberal versions, through the lens of SSA. In the first part, (...) I will discuss the classical eugenics from a historical perspective and conclude that classical eugenics is morally deplorable; but by currently accepting genome editing I argue that it is not possible to ‘slip’ into classical eugenics. Then, I will analyze liberal eugenics: I will consider Habermas’ and Sandel’s objections to liberal eugenics and genetic human enhancement. Subsequently, I will reply to these arguments affirming that, although it is not possible to refuse any form of genetic enhancement, liberal eugenics would not consider the principles of justice, non-maleficence, and non-instrumentalization; hence, it should be considered not morally acceptable. In addition, I will support the thesis according to which the possibility of relapsing into liberal eugenics is more likely than relapsing into classical eugenics. Then, I will present a strategy that, while avoiding falling into the undesirable scenarios related to SSA, still accepts some application of germline genome editing of embryos and gametes. In such a way, I will show that even if we accept the plausibility of a certain slip into an undesirable scenario, SSA does not offer conclusive reasons to forbid any use of germline genome editing technique in both therapeutic and enhancement fields. (shrink)

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during (...) stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general. (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)

In 1990 the Human Genome Project (HGP) was launched as an important historical marker, a pivotal contribution to the time-old quest for human self-knowledge. However, when in 2001 two major publications heralded its completion, it seemed difficult to make out how the desire for self-knowledge had really been furthered by this endeavor (IHGSC 2001; Venter et al. 2001). In various ways mankind seems to stand out from other organisms as a unique type of living entity, developing a critical perspective on (...) its own behavior and consciously engaged in building a complex society of its own making—and therefore increasingly able to determine the conditions of its own evolution. However, this uniqueness is not easily and .. (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)

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)

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)

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)

Biologists are nearing the creation of the first fully synthetic eukaryotic genome. Does this mean that we still soon be able to create genomes that are parts of an existing genetic lineage? If so, it might be possible to bring back extinct species. But do genomes that are synthetically assembled, no matter how similar they are to native genomes, really belong to the genetic lineage on which they were modelled? This article will argue that they are situated within the same (...) genetic lineage. To see why requires closely examining whether material overlap between parents and offspring is a necessary feature of biological reproduction. The processes used to create synthetic genomes shows that these processes are a form of scaffolded reproduction because they use external machinery and take ownership of the material parts used to create synthetic genomes. Closely examining these processes also reveals, surprisingly, that ‘synthetic reproduction’ can take place between entities that don’t participate in the same biological lineages. 1Introduction2The Argument for Lineage-less Genomes3Synthetic Eukaryotic Chromosomes and Material Overlap4Biological Reproduction, Material, and Information5Synthetic Reproductive Processes and Their Implications. (shrink)

Natural genome editing from a biocommunicative perspective is the competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing integrates both natural editing of genetic code and epigenetic marking that determines genetic reading patterns. As agents that edit genetic code and epigenetically mark genomic structures, viral and subviral agents have been suggested because they may be (...) evolutionarily older than cellular life. This hypothesis that viruses and viral-like agents edit genetic code is developed according to three well investigated examples that represent key evolutionary inventions in which non-lytic viral swarms act symbiotically in a persistent lifestyle within cellular host genomes: origin of eukaryotic nucleus, adaptive immunity, placental mammals. Additionally an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on the genetic code. Most of these RNA agents such as transposons, retroposons and small non-coding RNAs act consortially and are remnants of persistent viral infections that now act as co-opted adaptations in cellular key processes. (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.

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)

Volume 19, Issue 7, July 2019, Page 39-40.

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)

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)

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 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)

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)

In this commentary paper, we are taking one step further in questioning the central assumptions in the bioethical debates about reproductive technologies. We argue that the very distinction between “person affecting” and “identity affecting” interventions is based on a questionable form of material-origin essentialism. Questioning of this form of essentialist approach to human identity allows treating genome editing and genetic selection as more similar than they are taken to be in the standard approaches. It would also challenge the idea that (...) normative reasons we have in these two types of cases markedly differ in strength. (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)

According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...) a novel criterion for ‘causal primacy’, one that is grounded in the ontology of the unique causal role of dispositional properties. This paper argues that, if the genome is conceptualised as realising dispositional properties that are “directed toward” phenotypic traits, the parity of ‘causal roles’ between genetic and extra-genetic factors is no longer apparent, and further, that the causal primacy of the genome is both plausible and defensible. (shrink)

Everyone in biology keeps predicting that the next few years will bring answers to some of the major open questions in evolutionary biology, but there seems to be disagreement on what, exactly, those questions are. Enthusiasts of the various “-omics” (genomics, proteomics, transcriptomics, metabolomics, and even phenomics) believe, as Michael Lynch puts it in the final chapter of The Origins of Genome Architecture, that “we can be confident of two things: the basic theoretical machinery for understanding the evolutionary process (...) is well established, and we will soon be effectively unlimited by the availability of information at the DNA level.”. (shrink)

Excerpt: 1. Introduction This chapter provides insight into the diverse ethical debates on genetics and epigenetics. Much controversy surrounds debates about intervening into the germline genome of human embryos, with catchwords such as genome editing, designer baby, and CRISPR/Cas. The idea that it is possible to design a child according to one’s personal preferences is, however, a quite distorted view of what is actually possible with new gene technologies and gene therapies. These are much more limited than the editing and (...) design metaphors suggest. Such metaphors are therefore highly problematic phrases in the context of new gene technologies, for two reasons. On one hand, to design a child of choice by modifying the genome would require modifying any gene of choice, which is more than can be done with current gene technologies, such as CRISPR/Cas. On the other hand, a modification of genes would need to be enough to create any characteristic of choice in the future child. The latter presupposes the assumption of genetic determinism. Moreover, the CRISPR/Cas technology can not only be used in a potentially therapeutic manner at the germline level. In addition, there is the (more likely) scenario of a future clinical therapeutic use of these new gene technologies for modifying the DNA sequence of other cells of the body (somatic genome editing). There is also the option of modifying the epigenome, that is, the spatial configuration of DNA (epigenome editing) (see table 1). Like genetics and genome editing, epigenetics has been at the center of recent popular scientific and ethical discourse as well as scientific debates. The concept of epigenetics has given rise to very different notions of inheritability and responsibility for health, which, however, are oftentimes based on scientifically controversial basic assumptions. That there continues to be covert genetic determinism in the form of epigenetic determinism (see table 2) in debates about epigenetics has been pointed out in ethical analyses of epigenetics. Neither genetic determinism nor epigenetic determinism has been confirmed scientifically. It is therefore important to recognize the concepts that are discussed (and sometimes harshly criticized) in debates about genome editing and epigenetics—for example, concepts about the causal role of DNA for our own life course. This importance is based on the fact that if we understand such controversial concepts, we will be able to remain critical when evaluating scientific knowledge and ethical arguments about genome editing and epigenetics. This chapter, therefore, explains some of these concepts. For an ethical analysis of epigenetics as well as of genome editing, it is necessary to understand and critically reflect upon the underlying concepts of genetic determinism and other, related -isms. The following section offers a detailed introduction to these -isms (section 2; see also table 2). Section 3 provides an ethical analysis of genome editing and epigenetics based on the explanations in section 2. Section 3 focuses on inheritability and responsibility, justice, safety, the problem of consent, and the effects of genome editing and epigenetics on embryos and future generations. This section does not discuss in detail further points that can be found in ethical debates about epigenetics as well as in ethical debates about genome editing. These points include (among others): • fear that the findings of epigenetics and that the methods of genome editing are misused—this also with respect to eugenics and enhancement; • naturalness—an issue we mention in passing a few times in the following analysis; • a possible connection between the genome/epigenome and the concept of human dignity, and the derived danger of instrumentalization and infringement of autonomy when intervening in the genome or epigenome. Since current discourse about ethical issues associated with genome editing focuses mainly on germline interventions, which are, for instance, interventions into a human embryo’s genome, we mainly focus on germline interventions when comparing the debates on genome editing and on epigenetics in section 3. (shrink)

Personalized genomics companies (PG; also called ‘direct-to-consumer genetics’) are businesses marketing genetic testing to consumers over the Internet. While much has been written about these new businesses, little attention has been given to their roles in science communication. This paper provides an analysis of the gene concept presented to customers and the relation between the information given and the science behind PG. Two quite different gene concepts are present in company rhetoric, but only one features in the science. To (...) explain this, we must appreciate the delicate tension between PG, academic science, public expectation, and market forces. (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)

Assisted reproductive technologies have greatly increased our control over reproductive choices, leading some bioethicists to argue that we face unprecedented moral obligations towards progeny. Several models attempting to balance the principle of procreative autonomy with these obligations have been proposed. The least demanding is the minimal threshold model (MTM), according to which every reproductive choice is permissible, except creating children whose lives will not be worth living. Hence, as long as the future child is likely to have a life worth (...) living, prospective parents may be allowed to use preimplantation genetic diagnosis (PGD) to select embryos with genetic diseases or disabilities. Assuming a consequentialist person‐affecting view of morality, this paper investigates whether the MTM is an appropriate tool to guide procreative decisions given the continuous development of reproductive genetic technologies. In particular, I consider germline genome editing (GGE) and I argue that its application in human reproduction, unlike PGD, should be conceived as person‐affecting towards future progeny. I claim that even if we assume the plausibility of the MTM within PGD, we are committed to accepting that a greater moral obligation towards progeny should guide procreative decisions if GGE were available. In this case, the MTM should no longer be considered an appropriate instrument to guide procreative choices. Finally, I investigate when we face this greater moral obligation, concluding that it applies only when prospective parents have already engaged in the in vitro fertilization process. (shrink)

The guiding premise from which this special report begins is the conviction and hope that justice is at the normative heart of medicine and that it is the perpetual task of bioethics to bring concerns of justice to bear on medical practice. On such an account, justice is medicine's lifeblood, that by which it contributes to life as opposed to diminishing it. It is in this larger, historical, intersectional, critical, and ethically minded context that we must approach pressing questions facing (...) medicine, including the question of the import and role of genomic knowledge for human life. The second premise is that, at least in principle, the knowledge generated by genomics can be a gift or a weight, or both at the same time. That is to say that, on the one hand, genomic knowledge is a gift, creating novel insights into the genetic drivers of disease and into the geographical paths of our ancestors. And on the other hand, it is a weight, creating new obligations, new forms of social classification, and new forms of surveillance. Because it is in many ways the “common sense” of the day that genomic knowledge is a gift, this special report, which contains nine essays, concentrates on the ways in which such knowledge can be a weight, a weight that has the potential to thwart—and historically has thwarted—medicine from genuinely advancing justice . (shrink)

This paper addresses the cultural impact of genomics and the Human Genome Project on human self-understanding. Notably, it addresses the claim made by Francis Collins that the genome is the language of God and the claim made by Max Delbrück that Aristotle must be credited with having predicted DNA as the soul that organises bio-matter. From a continental philosophical perspective I will argue that human existence results from a dialectical interaction between two types of texts: the language of molecular (...) biology and the language of civilisation; the language of the genome and the language of our socio-cultural, symbolic ambiance. Whereas the former ultimately builds on the alphabets of genes and nucleotides, the latter is informed by primordial texts such as the Bible and the Quran. In applied bioethics deliberations on genomics, science is easily framed as liberating and progressive, religious world-views as conservative an... (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Abstract: This working paper focuses on the question whether there is a therapeutic imperative that, in specific situations, would oblige us to perform genome editing at the germline level in the context of assisted reproduction. The answer to this central question is discussed primarily with reference to specific scenarios where preimplantation genetic diagnosis (PGD) does not represent an acceptable alternative to germline genome editing based on either medical, or ethical, or – from the perspective of the potential parents – moral (...) or religious grounds. This article deals with four different types of case constellations that result from these possible reasons against PGD as well as from the necessity or dispensability of a subsequent “control PGD.” These cases are discussed based on hypotheses concerning contextual factors and theoretical assumptions. In conclusion, we point out that if our assumptions are correct, there is probably no therapeutic imperative for genome editing at the germline level. We draw this rationale from the fact that germline interventions are likely not person-affecting. However, we caution the reader that our result is preliminary and needs to be more carefully examined in future work in light of the bioethical debate and potential objections. -/- // Abstract: Im Zentrum dieses Working Papers steht die Frage, ob es einen therapeutischen Imperativ geben kann, der uns, in bestimmten Situationen, verpflichten würde, eine Genomeditierung (genome editing) auf Keimbahnebene im Rahmen der assistierten Befruchtung vorzunehmen. Die Antwort auf diese zentrale Frage wird insbesondere mit Bezug auf Fälle diskutiert, in denen das Verfahren der Präimplantationsdiagnostik (PID) keine aus entweder medizinischen oder ethischen oder – aus Sicht der potentiellen Eltern – moralischen bzw. religiösen Gründen akzeptable Alternative zu einem Keimbahneingriff darstellt. Die möglichen Gründe gegen die PID sowie die Erforderlichkeit oder Verzichtbarkeit einer nachfolgenden «Kontroll-PID» ergeben vier verschiedene Fallkonstellationen, denen sich der Beitrag zuwendet. Auf Grundlage von Hypothesen zu kontextuellen Faktoren und theoretischen Annahmen diskutieren wir diese Fälle. Im Ergebnis verweisen wir darauf, dass es, wenn unsere Annahmen zutreffen, vermutlich keinen therapeutischen Imperativ zum genome editing auf Keimbahnebene gibt. Dies begründet sich daraus, dass der Keimbahneingriff vermutlich nicht als personenbezogen (person-affecting) zu bezeichnen ist. Wir weisen jedoch darauf hin, dass unser Ergebnis vorläufig ist und unter Berücksichtigung der bioethischen Debatte und möglicher Einwände genauer geprüft werden muss. -/- // Résumé: Ce Working Paper se concentre sur la question de l’existence d’un impératif thérapeutique qui, dans des situations spécifiques, nous obligerait à réaliser une édition du génome au niveau de la lignée germinale dans le cadre de la procréation assistée. Afin de répondre à cette question centrale nous développons quatre scénarios spécifiques dans lesquels le diagnostic préimplantatoire (DPI) ne représente pas une alternative acceptable à l’édition du génome germinal pour des raisons médicales, éthiques ou – du point de vue des futurs parents – morales ou religieuses. Cet article traite de quatre constellations différentes de cas résultant des raisons mises en avant pour s'opposer au DPI ainsi que de la nécessité ou de l’inutilité d’un ultérieur « DPI de contrôle » Ces cas sont discutés sur la base d’hypothèses portant sur les facteurs contextuels et sur les présupposés théoriques. En conclusion, nous soulignons que si nos hypothèses sont correctes, il n’y a probablement aucun impératif thérapeutique justifiant l’édition du génome au niveau de la lignée germinale. Nous arrivons à cette conclusion parce qu’une intervention au niveau de la lignée germinale n’est probablement pas susceptible d’affecter la personne. Cependant, nous mettons en garde le lecteur sur le fait que notre conclusion est préliminaire et qu’elle doit être examinée avec soin dans des futurs travaux instruits par le débat bioéthique et par les éventuelles objections. (shrink)

Rohwer & Marris claim that “many conservation biologists” believe that there is a prima facie duty to preserve the genetic integrity of species. (A prima facie duty is a necessary pro tanto moral reason.) They describe three possible arguments for that belief and reject them all. They conclude that the biologists they cite are mistaken, and that there is no such duty: duties to preserve genetic integrity are merely instrumental: we ought act to preserve genetic integrity only because doing so (...) is required by some other duty, such as the duty to preserve taxonomic biodiversity, or the duty to preserve the reproductive fitness of existing species. In permitting for instance the introgression of cattle genes into the genome of Bison bison we therefore do not necessarily fail in any respect ethically. I criticize the paper on three fronts. (shrink)

Although legal personality has slowly begun to be granted to non-human entities that have a direct impact on the natural functioning of human societies (given their cultural significance), the same cannot be said for computer-based intelligence systems. While this notion has not had a significantly negative impact on humanity to this point in time that only remains the case because advanced computerised intelligence systems (ACIS) have not been acknowledged as reaching human-like levels. With the integration of ACIS in medical assistive (...) technologies such as companion robots and bionics, our legal treatment of ACIS must also adapt—least society faces legal challenges that may potentially lead to legally sanctioned discriminatory treatment. For this reason, this article exposes the complexity of normalizing definitions of “natural” human subjects, clarifies how current bioethical discourse has been unable to effectively guide ACIS integration into implanted and external artefacts, and argues for the establishment of legal delineations between various ACIS-human mergers in reference to legal protections and obligations internationally. (shrink)

In English, the Medieval philosophers on the genome. ISBN 978 84 686 6263 3 Bubok Publishing S.L., 2015.

On June 26, 2000, President Clinton, together with Francis Collins and Craig Venter, solemnly announced, from the East Room of the White House, that the grand effort to sequence the human genome, the Human Genome Project (HGP), was rapidly nearing its completion. Symbolism abounded. The event was framed as a crucial marker in the history of both humanity and knowledge by explicitly connecting the completion of the HGP with a number of already acknowledged and established scientific highlights. Tensions abounded as (...) well, however, notably between competing metaphors. In the course of the HGP, metaphors had become crucially important in framing and conveying what the HGP was really about. They had proved themselves to be of key importance when it came to defining and explaining the project’s significance for both science and society. Powerful images and metaphors had been deployed in order to secure unprecedented amounts of funding, on the one hand by comparing the HGP to other big technoscientific projects such as space travel, high energy physics, the atomic bomb and a territorial mapping exercise, and on the other hand through the suggestion that, once we have our “blueprint”, “code of codes”, “parts list”, etc. available, cancer genes will no longer have a place to hide. This article sets out to analyze this clash of metaphors, firmly embedded within the HGP but culminating at the press conference, arguing that the June 2000 event is even reminiscent of a somewhat similar event, depicted by a famous altarpiece, ‘The adoration of the Lamb’, on display in Ghent Cathedral and finished more than five centuries before. (shrink)

WHO in 2019 established the Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing, which has recently published a Draft Governance Framework on Human Genome Editing. Although the Draft Framework is a good point of departure, there are four areas of concern: first, it does not sufficiently address issues related to establishing safety and efficacy. Second, issues that are a source of tension between global standard setting and state sovereignty need to be addressed in a (...) more nuanced fashion. Third, it fails to meaningfully engage with the extent to which the conceptualisation of human dignity may justifiably vary between jurisdictions. Fourth, the meaning of harm to the interests of a future person requires clarity. Provided these four areas of concern can be addressed, the future of the global governance of human genome editing may hold promise. (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)

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)

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)

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)

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)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common (...) understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

A strong motivation for the human genome project was to relate biological features to the structure and function of small sets of genes, and ideally to individual genes. However, it is now increasingly realized that many problems require a "systems" approach emphasizing the interplay of large numbers of genes, and the involvement of complex networks of gene regulation. This implies a new emphasis on integrative, systems theoretical approaches. It may be called 'holistic' if the term is used without irrational overtones, (...) in the general sense of directing attention to integrated features of organs and organisms. In the history of biology, seemingly conflicting reductionist and holistic notions have alternated, with bottom-up as well as top-down approaches eventually contributing to the solutions of basic problems. By now, there is no doubt that biological features and phenomena are rooted in physico-chemical processes of the molecules involved; and yet, integrated systems aspects are becoming more and more relevant in developmental biology, brain and behavioural science, and socio-biology. -/- . (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)

The study of culture and cultural selection from a biological perspective has been hampered by the lack of any firm theoretical basis for how the information for cultural traits is stored and transmitted. In addition, the study of any living system with a decentralized or multi-level information structure has been somewhat restricted due to the focus in genetics on the gene and the particular hereditary structure of multicellular organisms. Here a different perspective is used, one which regards living systems as (...) self-constructing energy users that utilize their genome as a library of information, making the genetic system just another component that adds fitness to the overall integrated unit. In this framework, basic fitness is measured as the ability to gather energy for growth and reproduction, and the fitness of the genetic system is broken down into two aspects: first, the effectiveness in searching for new somatic functional information, and second, the effectiveness in searching for better structures to store and process information. With this more generalized perspective, major evolutionary transitions to higher levels of organization become competitions between different information structures; furthermore the functioning and fitness of cultural systems can be more easily described and compared with other modes of information storage within biological systems. Modern technological societies are self-constructing systems that rely on written (symbolic) information storage and very complex algorithms that effectively search for variation with a high probability of successful selection. These systems are currently competing with traditional organic systems, and this competition constitutes the latest major evolutionary transition. Upon comparison of the energy-gathering potential of symbolic-based systems with DNA-based life, it appears that symbolic systems have a tremendous fitness potential and the current shift to a higher level of selection may be as significant and far-reaching as any of the previous major evolutionary transitions. (shrink)