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)

This text answers the question, posed by the editor, on the philosophical and social issues resulting from the synthetic assembly of a modified bacterial genome that was introduced in an existing bacterial species (M.mycoides)and so it was claimed to represent the first ever kind of synthetic life produced by human manipulation.

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)

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)

It is a most commonly accepted hypothesis that life originated from inanimate matter, somehow being a synthetic product of organic aggregates, and as such, a result of some sort of prebiotic synthetic biology. In the past decades, the newly formed scientific discipline of synthetic biology has set ambitious goals by pursuing the complete design and production of genetic circuits, entire genomes or even whole organisms. In this paper, I argue that synthetic biology might also shed (...) some novel and interesting perspectives on the question of the origin of life, and that, in addition, it might challenge our most commonly accepted definitions of life, thereby changing the ways we might think about life and its origin. (shrink)

Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is “iconoclastic”, as Gaston Bachelard phrases it, scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the “Morse code” of life, the “barcode” of life and the “book” of life. This paper focuses (...) on a different type of metaphor, however, namely on the archetypal metaphor of the mandala as a symbol of restored unity and wholeness. Notably, mandala images emerge in textual materials related to one of the new “frontiers” of contemporary technoscience, namely the building of a synthetic cell: a laboratory artefact that functions like a cell and is even able to replicate itself. The mandala symbol suggests that, after living systems have been successfully reduced to the elementary building blocks and barcodes of life, the time has now come to put these fragments together again. We can only claim to understand life, synthetic cell experts argue, if we are able to technically reproduce a fully functioning cell. This holistic turn towards the cell as a meaningful whole also requires convergence at the “subject pole”: the building of a synthetic cell as a practice of the self, representing a turn towards integration, of multiple perspectives and various forms of expertise. (shrink)

To construct a synthetic cell we need to understand the rules that permit life. A central idea in modern biology is that in addition to the four entities making reality, matter, energy, space and time, a fifth one, information, plays a central role. As a consequence of this central importance of the management of information, the bacterial cell is organised as a Turing machine, where the machine, with its compartments defining an inside and an outside and its metabolism, reads (...) and expresses the genetic program carried by the genome. This highly abstract organisation is implemented using concrete objects and dynamics, and this is at the cost of repeated incompatibilities (frustration), which need to be sorted out by appropriate «patches». After describing the organisation of the genome into the paleome (sustaining and propagating life) and the cenome (permitting life in context), we describe some chemical hurdles that the cell as to cope with, ending with the specific case of the methionine salvage pathway. (shrink)

Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed entities is indispensable. Discrimination requires management of information, an authentic, yet abstract, cur- rency of reality. For example proteins age, sometimes very fast. The cell must identify, then get rid of old proteins without destroying young ones. Implementing discrimination in cells leads to (...) the second set of functions, usually ignored. Being abstract, information must nevertheless be embodied into material entities, with unavoidable idiosyncratic properties. This brings about novel unmet needs. Hence, the buildup of cells elicits specific but awkward material implementations, ‘kludges’ that become essential under particular settings, while difficult to identify. Finally, a third functional category char- acterizes the need for growth, with metabolic implementations allowing the cell to put together the growth of its cytoplasm, membranes, and genome, spanning different spatial dimensions. Solving this metabolic quandary, critical for engineering novel synthetic biology chassis, uncovered an unexpected role for CTP synthetase as the coordinator of nonhomothetic growth. Because a significant number of SynBio constructs aim at creating cell factories we expect that they will be attacked by viruses (it is not by chance that the function of the CRISPR system was identified in industrial settings). Substantiating the role of CTP, natural selection has dealt with this hurdle via synthesis of the antimetabolite 30-deoxy-30,40-didehydro- CTP, recruited for antiviral immunity in all domains of life. (shrink)

[ENGLISH] This article discusses the potential of synthetic biology to address fundamental questions in the philosophy of biology regarding the nature of life and biological functions. Synthetic biology aims to reduce living organisms to their simplest forms by identifying the minimal components of a cell and also to create novel life forms through genetic reprogramming, biobrick assembly, or novel proteins. However, the technical success of these endeavors does not guarantee their conceptual success in defining life. There is a (...) lack of consensus among researchers on how to define and classify the entities produced in the lab, whether they should be considered living or categorized differently. The criteria for minimal cells and minimal life are subject to arbitrary choices and varying interpretations. The concept of function, crucial to synthetic biology, is also difficult to define. The article highlights the need to consider the minimal set of functions that characterize life before determining the smallest genomes that code for those functions. The arbitrary nature of defining both life and function complicates the understanding and classification of these entities. The article suggests that the traditional dichotomy between the living and the non-living may no longer be valid and that the concept of life itself may not require precise scientific definition. As synthetic biology advances, the article emphasizes the importance of redefining or constructing new categories to encompass the expanding possibilities and creations in the field. The ability to create new life forms raises questions about recognition, identification, and ethical implications, requiring a conceptual and philosophical engagement beyond the technical achievements of synthetic biology. -/- [FRENCH] L'article aborde le potentiel de la biologie synthétique pour répondre à des questions fondamentales de la philosophie de la biologie concernant la nature de la vie et des fonctions biologiques. La biologie synthétique vise à réduire les organismes vivants à leurs formes les plus simples en identifiant les composants minimaux d'une cellule et à créer de nouvelles formes de vie grâce à la reprogrammation génétique, à l'assemblage de biobriques ou à des protéines nouvelles. Cependant, le succès technique de ces approches ne garantit pas leur réussite conceptuelle dans la définition de la vie. Il n'y a pas de consensus parmi les chercheurs sur la façon de définir et de classer les entités produites en laboratoire, qu'elles doivent être considérées comme vivantes ou catégorisées différemment. Les critères des cellules minimales et de la vie minimale sont soumis à des choix arbitraires et à des interprétations variables. La notion de fonction, essentielle en biologie synthétique, est également difficile à définir. L'article met en évidence la nécessité de prendre en compte l'ensemble minimal de fonctions qui caractérisent la vie avant de déterminer les plus petits génomes qui codent ces fonctions. La nature arbitraire de la définition de la vie et de la fonction complique la compréhension et la classification de ces entités. L'article suggère que la dichotomie traditionnelle entre le vivant et le non-vivant pourrait ne plus être valable et que le concept même de vie ne nécessite pas une définition scientifique précise. À mesure que la biologie synthétique progresse, l'article souligne l'importance de redéfinir ou de construire de nouvelles catégories pour englober les possibilités et créations croissantes dans le domaine. La capacité à créer de nouvelles formes de vie soulève des questions de reconnaissance, d'identification et d'implications éthiques, nécessitant une réflexion conceptuelle et philosophique au-delà des avancées techniques de la biologie synthétique. (shrink)

The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including (...) transporters and the ribosome construction machinery, behave as would behave a material implementation of the informationmanaging agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell’s demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers. (shrink)

Change is the fundamental idea of evolution. Explaining the extraordinary biological change we see written in the history of genomes and fossil beds is the primary occupation of the evolutionary biologist. Yet it is a surprising fact that for the majority of evolutionary research, we have rarely studied how evolution typically unfolds in nature, in changing ecological environments, over space and time. While ecology played a major role in the eventual acceptance of the population genetic viewpoint of evolution in (...) the synthetic era (circa 1918-1956), it held a lesser role in the development of evolutionary theory until the 1980s, when we began to systematically study the evolutionary dynamics of natural populations in space and time. As a result, early evolutionary theory was initially constructed in an abstract vacuum that was unrepresentative of evolution in nature. The subtle synthesis between ecology with evolutionary biology (eco-evo synthesis) over the past 40 years has progressed our knowledge of natural selection dynamics as they are found in nature, thus revealing how natural selection varies in strength, direction, form, and, more surprisingly, level of biological organization. Natural selection can no longer be reduced to lower levels of biological organization (i.e., individuals, selfish genes) over shorter timescales but should be expanded to include adaptation at higher levels and over longer timescales. Long-term and/or emergent evolutionary phenomena, such as multilevel selection or evolvability, have thus become tenable concepts within an evolutionary biology that embraces ecology and spatiotemporal change. Evolutionary biology is currently suspended at an intermediate stage of scientific progress that calls for the organization of all the recent knowledge revealed by the eco-evo synthesis into a coherent and unified theoretical framework. This is where philosophers of biology can be of particular use, acting as a bridge between the subdisciplines of biology and inventing new theoretical strategies to organize and accommodate the recent knowledge. Philosophers have recommended transitioning away from outdated philosophies that were originally derived from physics within the philosophical zeitgeist of logical positivism (i.e., monism, reductionism, and monocausation) and toward a distinct philosophy of biology that can capture the natural complexity of multifaceted biological systems within diverse ecosystems—one that embraces the emerging philosophies of pluralism, emergence, and multicausality. Therefore, I see recent advances in ecology, evolutionary biology, and the philosophy of biology as laying the groundwork for another major biological synthesis, what I refer to as the Second Synthesis because, in many respects, it is analogous to the aims and outcomes of the first major biological synthesis (but is notably distinct from the inorganic and contrived progressive movement known as the extended evolutionary synthesis). With the general development of a distinctive philosophy of science, biology has rightfully emerged as an autonomous science. Thus, while the first synthesis legitimized biology, the Second Synthesis autonomized biology and afforded biology its own philosophy, allowing biology to finally realize its full scientific potential. (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)

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)

The guiding thread of the paper is the diagnosis that the advanced division of cognitive labor (that is, intellectual specialization) engenders a set of perennial, political and epistemic challenges (Millgram 2015) that, simultaneously, also generate opportunities for philosophy. In this paper, I re-characterize the nature of synthetic philosophy as a means to advance and institutionalize philosophy. For my definition of synthetic philosophy see section 2. In section 1, I treat Plato’s Republic as offering two models to represent philosophy's (...) relationship to the other sciences within the advanced division of labor. I highlight that for Plato intellectual specialization is central not just to economic, but also to political life. And, yet, that the very dispersion of scientific expertise, and its esoteric nature, also generates non-trivial challenges to the recognition and political utilization of knowledge. From Plato we can infer that in imperfect circumstances, philosophy’s self-constitution is, in part, a response to these challenges in political epistemology. However, how philosophy is institutionalized differs through time. In section 2, I re-introduce my conceptualization of synthetic philosophy and restate it. This makes visible that synthetic philosophy is already widely practiced in the profession as philosophy of the special sciences, PPE, formal modelling, public philosophy, etc. I use recent work by Dorst (2023) to illustrate synthetic philosophy and to identify some of the processes that give rise to the need for it. In sections 2-3, I contrast my account with the evolving ways that Philip Kitcher has conceptualized synthetic philosophy in order to make more precise the version promoted here. I do so not just because Kitcher and I use the same term, ‘synthetic philosophy,’ but because the temptations inherent in Kitcher’s approach should be resisted. -/- . (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)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. (...) On the basis of distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

The recent publications reported in 2022 reveal the possibility of obtaining mouse embryos without the need for egg or sperm. These ‘artificial embryos’ can recapitulate some stages of development ex utero – from neurulation to organogenesis – without implantation. Synthetic mouse embryos might serve as a valuable model to gain further insights into early developmental stages. Indeed, it is expected for these models to be replicated by employing human cells. This promising research raises ethical issues and expands the horizon (...) of ethics in regard to the development of the human embryo. From this point of view, we state some of the new open venues for bioethical research. (shrink)

Here we will see that contrary to the party line, Hume’s notion of a relation should be understood, in all cases, as a peculiar non-necessary synthetic relation; unique, but similar in a certain constructive sense to what I characterize as a mathematical notion of synthesis. And, most controversially, I argue that this non-necessary synthetic notion of a relation includes Hume’s arithmetical relations, which have typically been interpreted as either “analytic,” necessary, or both. In this general respect, Hume anticipates (...) Quine’s attack on the analytic/synthetic distinction. (shrink)

Synthetic biologists aim to generate biological organisms according to rational design principles. Their work may have many beneficial applications, but it also raises potentially serious ethical concerns. In this article, we consider what attention the discipline demands from bioethicists. We argue that the most important issue for ethicists to examine is the risk that knowledge from synthetic biology will be misused, for example, in biological terrorism or warfare. To adequately address this concern, bioethics will need to broaden its (...) scope, contemplating not just the means by which scientific knowledge is produced, but also what kinds of knowledge should be sought and disseminated. (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)

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)

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 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)

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)

In a recent article in this journal [Phil. Math., II, v.4 (1989), n.2, pp.?- ?] J. Fang argues that we must not be fooled by A.J. Ayer (God rest his soul!) and his cohorts into believing that mathematical knowledge has an analytic a priori status. Even computers, he reminds us, take some amount of time to perform their calculations. The simplicity of Kant's infamous example of a mathematical proposition (7+5=12) is "partly to blame" for "mislead[ing] scholars in the direction of (...) neglecting the temporal element"; yet a brief instant of time is required to grasp even this simple truth. If Kant were alive today, "and if he had had a little more mathematical savvy", Fang explains, he could have used the latest example of the largest prime number (391,581 x 2 216,193 - 1) as a better example of the "synthetic a priori" character of mathematics. The reason Fang is so intent upon emphasizing the temporal character of mathematics is that he wishes to avoid "the uncritical mixing of ... a theology and a philosophy of mathematics." For "in the light of the Computer Age today: finitism is king!" Although Kant's aim was explicitly "to study the 'human' ... faculty", Fang claims that even he did not adequatley emphasize "the clearly and concretely distinguishable line of demarcation between the human and divine faculties.". (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)

If humans eventually attain the ability to create new life forms, how will it affect the value of life? This is one of several questions that can be sources of concern when discussing synthetic life, but is the concern justified? In an attempt to answer this question, I have analyzed some possible reasons why an ability to create synthetic life would threaten the value of life in general (that is, not just of the synthetic creations), to see (...) if they really give us reason to worry. The main conclusion is that it is unlikely that a future human ability to create life will really have a great negative impact on these characteristics of life. It therefore seems unlikely that the value of life will be negatively affected by the ability to create synthetic life, though it is possible that the properties in question will be less salient in the synthetic life and thus that the value of the synthetic life will be lower than that of existing life, which in turn can lead to a disturbing difference in value between different kinds of life. (shrink)

This is a contribution to the idea that some proofs in first-order logic are synthetic. Syntheticity is understood here in its classical geometrical sense. Starting from Jaakko Hintikka’s original idea and Allen Hazen’s insights, this paper develops a method to define the ‘graphical form’ of formulae in monadic and dyadic fraction of first-order logic. Then a synthetic inferential step in Natural Deduction is defined. A proof is defined as synthetic if it includes at least one synthetic (...) inferential step. Finally, it will be shown that the proposed definition is not sensitive to different ways of driving the same conclusion from the same assumptions. (shrink)

The recent discussion of fictional models has focused on imagination, implicitly considering fictions as something nonconcrete. We present two cases from synthetic biology that can be viewed as concrete fictions. Both minimal cells and alternative genetic systems are modal in nature: they, as well as their abstract cousins, can be used to study unactualized possibilia. We approach these synthetic constructs through Vaihinger’s notion of a semi-fiction and Goodman’s notion of semifactuality. Our study highlights the relative existence of such (...) concrete fictions. Before their realizations neither minimal cells nor alternative genetic systems were any well-defined objects, and the subsequent experimental work has given more content to these originally schematic imaginings. But it is as yet unclear whether individual members of these heterogeneous groups of somewhat functional synthetic constructs will eventually turn out to be fully realizable, remain only partially realizable, or prove outright impossible. (shrink)

This article focuses on the distinction between analytic truths and synthetic truths, and between a priori truths and a posteriori truths in philosophy, beginning with a brief historical survey of work on the two distinctions, their relationship to each other, and to the necessary/contingent distinction. Four important stops in the history are considered: two involving Kant and W. V. O. Quine, and two relating to logical positivism and semantic externalism. The article then examines questions that have been raised about (...) the analytic–synthetic and a priori–a posteriori distinctions, such as whether all distinctively philosophical truths fall on one side of the line and whether the distinction is relevant to philosophy. It also discusses the argument that there is a lot more a priori knowledge than we ever thought, and concludes by describing epistemological accounts of analyticity. (shrink)

This is a review article based on William Franke's book, A Philosophy of the Unsayable. After contrasting standard "analytic" logic with its paradoxical alternative, "synthetic" logic, this article introduces three basic laws of synthetic logic that can help to clarify how it is possible to talk about the so-called "unsayable". Keeping these laws in mind as one reads a book such as Franke's enables one to understand the range of strategies one can employ in the attempt to use (...) words to evoke an experience of the unsayable. This article together with several others responding to Franke's book, and Franke's replies to the whole set of articles. (shrink)

With the recent renewed interest in AI, the field has made substantial advancements, particularly in generative systems. Increased computational power and the availability of very large datasets has enabled systems such as ChatGPT to effectively replicate aspects of human social interactions, such as verbal communication, thus bringing about profound changes in society. In this paper, we explain that the arrival of generative AI systems marks a shift from ‘interacting through’ to ‘interacting with’ technologies and calls for a reconceptualization of socio-technical (...) systems as we currently understand them. We dub this new generation of socio-technical systems synthetic to signal the increased interactions between human and artificial agents, and, in the footsteps of philosophers of information, we cash out agency in terms of ‘poiêsis’. We close the paper with a discussion of the potential policy implications of synthetic socio-technical system. -/- . (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)

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)

Recently, Bechtel and Abrahamsen have argued that mathematical models study the dynamics of mechanisms by recomposing the components and their operations into an appropriately organized system. We will study this claim through the practice of combinational modeling in circadian clock research. In combinational modeling, experiments on model organisms and mathematical/computational models are combined with a new type of model—a synthetic model. We argue that the strategy of recomposition is more complicated than what Bechtel and Abrahamsen indicate. Moreover, synthetic (...) modeling as a kind of material recomposition strategy also points beyond the mechanistic paradigm. (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of Standard (...) Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

This paper analyses the technoscientific objective of building a synthetic cell from a Jungian perspective. After decades of fragmentation and specialisation, the synthetic cell symbolises a turn towards restored wholeness, both at the object pole and at the subject pole. From a Jungian perspective, it is no coincidence that visual representations of synthetic cells often reflect an archetypal, mandala-like structure. As a symbol of restored unity, the synthetic cell mandala compensates for technoscientific fragmentation via active imagination, (...) providing a visual aid for the technoscientific turn towards reintegration. Although the biotechnological desire to reconstruct life in vitro has been compared to alchemy before, a Jungian analysis allows us to make this comparison more specific and precise. The problem of archetypal images, however, is that alluring prospects of reintegration may underestimate and obfuscate the deficiencies and tensions at work in the current situation. As a projection of a future wholeness, it fosters optimism, but may also function as a misleading façade, covering up collisions and complexities. This can be averted by the conscious employment of the mandala as a symbolic scaffold fostering processes of individuation and working through. (shrink)

The arrival of synthetic organs may mean we need to reconsider principles of ownership of such items. One possible ownership criterion is the boundary between the organ’s being outside or inside the body. What is outside of my body, even if it is a natural organ made of my cells, may belong to a company or research institution. Yet when it is placed in me, it belongs to me. In the future, we should also keep an eye on how (...) the availability of synthetic organs may change our attitudes toward our own bodies. (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)

Synthetic cells spark intriguing questions about the nature of life. Projects such as BaSyC (‘Building a Synthetic Cell’) aim to build an entity that mimics how living cells work from basic components. But what kind of entity would a synthetic cell really be? I assess this question from a philosophical perspective, and show how early fictional narratives of artificial life – such as the laboratory scene in Goethe’s Faust – can help us to understand the challenges faced (...) by synthetic biology researchers. (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.

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)

Synthetic biology has a strong modal dimension that is part and parcel of its engineering agenda. In turning hypothetical biological designs into actual synthetic constructs, synthetic biologists reach towards potential biology instead of concentrating on naturally evolved organisms. We analyze synthetic biology’s goal of making biology easier to engineer through the combinatorial theory of possibility, which reduces possibility to combinations of individuals and their attributes in the actual world. While the last decades of synthetic biology (...) explorations have shown biology to be much more difficult to engineer than originally conceived, synthetic biology has not given up its combinatorial approach. (shrink)

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)

The aim of this article is to investigate the relevance and implications of synthetic models for the study of the interactive dimension of minimal life and cognition, by taking into consideration how the use of artificial systems may contribute to an understanding of the way in which interactions may affect or even contribute to shape biological identities. To do so, this article analyzes experimental work in synthetic biology on different types of interactions between artificial and natural systems, more (...) specifically: between protocells and between biological living cells and protocells. It discusses how concepts such as control, cognition, communication can be used to characterize these interactions from a theoretical point of view, which criteria of relevance and evaluation of synthetic models can be applied to these cases, and what are their limits. (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)

The purpose of this paper is to analyze the theoretical commitments of autopoietic enactivism in relation to Errol E Harris’s dialectical holism in the interest of establishing a common metaphysical ground. This will be undertaken in three stages. First, it is argued that Harris’s reasoning provides a means of developing enactivist ontology beyond discussions limited to cognitive science and into domains of metaphysics that have traditionally been avoided by phenomenologists. Here, I maintain enactivist commitments are consistent with Harris’s reasoning from (...) certain synthetic a priori first principles, to his derivation of a teleological anthropic principle, which asserts the necessity of consciousness within the cosmos. Second, it is proposed that Steven Rosen’s long-standing proposal for a topology of phenomenology may provide a common logical foundation for both Harris and enactivists regarding anthropic reasoning. Third, it is argued that a pragmatic approach to process ontology is the most rigorous way of responding to the realism/anti-realism concerns that inevitably follow. If successful, this work will update Harris’s arguments with contemporary scientific and philosophical terminology and extend enactivism from philosophy of mind, into a general phenomenological ontology. (shrink)

The concept of truth has many aims but only one source. The article describes the primary concept of truth, here called the synthetic concept of truth, according to which truth is the objective result of the synthesis of us and nature in the process of rational cognition. It is shown how various aspects of the concept of truth -- logical, scientific, and mathematical aspect -- arise from the synthetic concept of truth. Also, it is shown how the paradoxes (...) of truth arise. (shrink)

Synthetic biology aims to synthesize novel biological systems or redesign existing ones. The field has raised numerous philosophical questions, but most especially what is novel to this field. In this article I argue for a novel take, since the dominant ways to understand synthetic biology’s specificity each face problems. Inspired by the examination of the work of a number of chemists, I argue that synthetic biology differentiates itself by a new regime of articulation, i.e. a new way (...) of articulating the questions and phenomena it wants to address. Instead of describing actual existing biological systems, the field aims to describe biological possibilities. In the second part I corroborate this hypothesis through a comparison between early research in the field of the origins of life and contemporary synthetic biologists, who are not so much interested in the historical origin of life on Earth, but rather in a universal biology of the possible origins of any life whatsoever. (shrink)