Synthetic organisms and living machines : Positioning the products of synthetic biology at the borderline between living and non-living matter

The view of synthetic biology in the field of ethics: a thematic systematic review

Synthetic biology is designing and creating biological tools and systems for useful purposes. It uses knowledge from biology, such as biotechnology, molecular biology, biophysics, biochemistry, bioinformatics, and other disciplines, such as engineering, mathematics, computer science, and electrical engineering. It is recognized as both a branch of science and technology. The scope of synthetic biology ranges from modifying existing organisms to gain new properties to creating a living organism from non-living components. Synthetic biology has many applications in important fields such as energy, chemistry, medicine, environment, agriculture, national security, and nanotechnology. The development of synthetic biology also raises ethical and social debates. This article aims to identify the place of ethics in synthetic biology. In this context, the theoretical ethical debates on synthetic biology from the 2000s to 2020, when the development of synthetic biology was relatively faster, were analyzed using the systematic review method. Based on the results of the analysis, the main ethical problems related to the field, problems that are likely to arise, and suggestions for solutions to these problems are included. The data collection phase of the study included a literature review conducted according to protocols, including planning, screening, selection and evaluation. The analysis and synthesis process was carried out in the next stage, and the main themes related to synthetic biology and ethics were identified. Searches were conducted in Web of Science, Scopus, PhilPapers and MEDLINE databases. Theoretical research articles and reviews published in peer-reviewed journals until the end of 2020 were included in the study. The language of publications was English. According to preliminary data, 1,453 publications were retrieved from the four databases. Considering the inclusion and exclusion criteria, 58 publications were analyzed in the study. Ethical debates on synthetic biology have been conducted on various issues. In this context, the ethical debates in this article were examined under five themes: the moral status of synthetic biology products, synthetic biology and the meaning of life, synthetic biology and metaphors, synthetic biology and knowledge, and expectations, concerns, and problem solving: risk versus caution.

A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things?

The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.

Implementing re-configurable biological computation with distributed multicellular consortia

The use of synthetic biological circuits to deal with numerous biological challenges has been proposed in several studies, but its implementation is still remote. A major problem encountered is the complexity of the cellular engineering needed to achieve complex biological circuits and the lack of general-purpose biological systems. The generation of re-programmable circuits can increase circuit flexibility and the scalability of complex cell-based computing devices. Here we present a new architecture to produce reprogrammable biological circuits that allow the development of a variety of different functions with minimal cell engineering. We demonstrate the feasibility of creating several circuits using only a small set of engineered cells, which can be externally reprogrammed to implement simple logics in response to specific inputs. In this regard, depending on the computation needs, a device composed of a number of defined cells can generate a variety of circuits without the need of further cell engineering or rearrangements. In addition, the inclusion of a memory module in the circuits strongly improved the digital response of the devices. The reprogrammability of biological circuits is an intrinsic capacity that is not provided in electronics and it may be used as a tool to solve complex biological problems.

Fake cells and the aura of life: A philosophical diagnostic of synthetic life

Synthetic biology is often seen as the engineering turn in biology. Philosophically speaking, entities created by synthetic biology, from synthetic cells to xenobots, challenge the ontological divide between the organic and inorganic, as well as between the natural and the artificial. Entities such as synthetic cells can be seen as hybrid or transitory objects, or neo-things. However, what has remained philosophically underexplored so far is the impact these hybrid neo-things will have on (our phenomenological experience of) the living world. By extrapolating from Walter Benjamin's account of how technological reproducibility affects the aura of art, we embark upon an exploratory inquiry that seeks to fathom how the technological reproducibility of life itself may influence our experience and understanding of the living. We conclude that, much as technologies that enabled reproduction corroded the aura of original artworks (as Benjamin argued), so too will the aura of life be under siege in the era of synthetic lifeforms. This article zooms in on a specific case study, namely the research project Building a Synthetic Cell (BaSyC) and its mission to create a synthetic cell-like entity, as autonomous as possible, focusing on the properties that differentiate organic from synthetic cells.

Some Characteristics and Arguments in Favor of a Science of Machine Behavior Analysis

Researchers and practitioners recognize four domains of behavior analysis: radical behaviorism, the experimental analysis of behavior, applied behavior analysis, and the practice of behavior analysis. Given the omnipresence of technology in every sphere of our lives, the purpose of this conceptual article is to describe and argue in favor of a fifth domain: machine behavior analysis. Machine behavior analysis is a science that examines how machines interact with and produce relevant changes in their external environment by relying on replicability, behavioral terminology, and the philosophical assumptions of behavior analysis (e.g., selectionism, determinism, parsimony) to study artificial behavior. Arguments in favor of a science of machine behavior include the omnipresence and impact of machines on human behavior, the inability of engineering alone to explain and control machine behavior, and the need to organize a verbal community of scientists around this common issue. Regardless of whether behavior analysts agree or disagree with this proposal, I argue that the field needs a debate on the topic. As such, the current article aims to encourage and contribute to this debate.

Carbon-Based Materials for Articular Tissue Engineering: From Innovative Scaffolding Materials toward Engineered Living Carbon

Carbon materials constitute a growing family of high-performance materials immersed in ongoing scientific technological revolutions. Their biochemical properties are interesting for a wide set of healthcare applications and their biomechanical performance, which can be modulated to mimic most human tissues, make them remarkable candidates for tissue repair and regeneration, especially for articular problems and osteochondral defects involving diverse tissues with very different morphologies and properties. However, more systematic approaches to the engineering design of carbon-based cell niches and scaffolds are needed and relevant challenges should still be overcome through extensive and collaborative research. In consequence, this study presents a comprehensive description of carbon materials and an explanation of their benefits for regenerative medicine, focusing on their rising impact in the area of osteochondral and articular repair and regeneration. Once the state-of-the-art is illustrated, innovative design and fabrication strategies for artificially recreating the cellular microenvironment within complex articular structures are discussed. Together with these modern design and fabrication approaches, current challenges, and research trends for reaching patients and creating social and economic impacts are examined. In a closing perspective, the engineering of living carbon materials is also presented for the first time and the related fundamental breakthroughs ahead are clarified.

Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology

The construction of artificial cells from inanimate molecular building blocks is one of the grand challenges of our time. In addition to being used as simplified cell models to decipher the rules of life, artificial cells have the potential to be designed as micromachines deployed in a host of clinical and industrial applications. The attractions of engineering artificial cells from scratch, as opposed to re-engineering living biological cells, are varied. However, it is clear that artificial cells cannot currently match the power and behavioural sophistication of their biological counterparts. Given this, many in the synthetic biology community have started to ask: is it possible to interface biological and artificial cells together to create hybrid living/synthetic systems that leverage the advantages of both? This article will discuss the motivation behind this cellular bionics approach, in which the boundaries between living and non-living matter are blurred by bridging top-down and bottom-up synthetic biology. It details the state of play of this nascent field and introduces three generalised hybridisation modes that have emerged.

Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology

The construction of artificial cells from inanimate molecular building blocks is one of the grand challenges of our time. In addition to being used as simplified cell models to decipher the rules of life, artificial cells have the potential to be designed as micromachines deployed in a host of clinical and industrial applications. The attractions of engineering artificial cells from scratch, as opposed to re-engineering living biological cells, are varied. However, it is clear that artificial cells cannot currently match the power and behavioural sophistication of their biological counterparts. Given this, many in the synthetic biology community have started to ask: is it possible to interface biological and artificial cells together to create hybrid living/synthetic systems that leverage the advantages of both? This article will discuss the motivation behind this cellular bionics approach, in which the boundaries between living and non-living matter are blurred by bridging top-down and bottom-up synthetic biology. It details the state of play of this nascent field and introduces three generalised hybridisation modes that have emerged.

The Conception of Synthetic Entities from a Personalist Perspective

Synthetic biology opens up the possibility of producing new entities not found in nature, whose classification as organisms or machines has been debated. In this paper we are focusing on the delimitation of the moral value of synthetic products, in order to establish the ethically right way to behave towards them. In order to do so, we use personalism as our ethical framework. First, we examine how we can distinguish between organisms and machines. Next, we discuss whether the products of synthetic biology can be considered organisms at all and assess what their moral value is and how should we behave towards them. Finally, we discuss the hypothetical case of synthetic humans.

Is Research on "Synthetic Cells" Moving to the Next Level?

"Synthetic cells" research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on "synthetic cells" moving to a next level?

Emergence of an enslaved phononic bandgap in a non-equilibrium pseudo-crystal

Material systems that reside far from thermodynamic equilibrium have the potential to exhibit dynamic properties and behaviours resembling those of living organisms. Here we realize a non-equilibrium material characterized by a bandgap whose edge is enslaved to the wavelength of an external coherent drive. The structure dynamically self-assembles into an unconventional pseudo-crystal geometry that equally distributes momentum across elements. The emergent bandgap is bestowed with lifelike properties, such as the ability to self-heal to perturbations and adapt to sudden changes in the drive. We derive an exact analytical solution for both the spatial organization and the bandgap features, revealing the mechanism for enslavement. This work presents a framework for conceiving lifelike non-equilibrium materials and emphasizes the potential for the dynamic imprinting of material properties through external degrees of freedom.

Prospective Technology Assessment of Synthetic Biology: Fundamental and Propaedeutic Reflections in Order to Enable an Early Assessment

Synthetic biology is regarded as one of the key technosciences of the future. The goal of this paper is to present some fundamental considerations to enable procedures of a technology assessment (TA) of synthetic biology. To accomplish such an early "upstream" assessment of a not yet fully developed technology, a special type of TA will be considered: Prospective TA (ProTA). At the center of ProTA are the analysis and the framing of "synthetic biology," including a characterization and assessment of the technological core. The thesis is that if there is any differentia specifica giving substance to the umbrella term "synthetic biology," it is the idea of harnessing self-organization for engineering purposes. To underline that we are likely experiencing an epochal break in the ontology of technoscientific systems, this new type of technology is called "late-modern technology." -I start this paper by analyzing the three most common visions of synthetic biology. Then I argue that one particular vision deserves more attention because it underlies the others: the vision of self-organization. I discuss the inherent limits of this new type of late-modern technology in the attempt to control and monitor possible risk issues. I refer to Hans Jonas' ethics and his early anticipation of the risks of a novel type of technology. I end by drawing conclusions for the approach of ProTA towards an early societal shaping of synthetic biology.

Low potency toxins reveal dense interaction networks in metabolism

BACKGROUND

The chemicals of metabolism are constructed of a small set of atoms and bonds. This may be because chemical structures outside the chemical space in which life operates are incompatible with biochemistry, or because mechanisms to make or utilize such excluded structures has not evolved. In this paper I address the extent to which biochemistry is restricted to a small fraction of the chemical space of possible chemicals, a restricted subset that I call Biochemical Space. I explore evidence that this restriction is at least in part due to selection again specific structures, and suggest a mechanism by which this occurs.

RESULTS

Chemicals that contain structures that our outside Biochemical Space (UnBiological groups) are more likely to be toxic to a wide range of organisms, even though they have no specifically toxic groups and no obvious mechanism of toxicity. This correlation of UnBiological with toxicity is stronger for low potency (millimolar) toxins. I relate this to the observation that most chemicals interact with many biological structures at low millimolar toxicity. I hypothesise that life has to select its components not only to have a specific set of functions but also to avoid interactions with all the other components of life that might degrade their function.

CONCLUSIONS

The chemistry of life has to form a dense, self-consistent network of chemical structures, and cannot easily be arbitrarily extended. The toxicity of arbitrary chemicals is a reflection of the disruption to that network occasioned by trying to insert a chemical into it without also selecting all the other components to tolerate that chemical. This suggests new ways to test for the toxicity of chemicals, and that engineering organisms to make high concentrations of materials such as chemical precursors or fuels may require more substantial engineering than just of the synthetic pathways involved.

Synthetic biology as red herring

It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice-agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy.

The mismeasure of machine: Synthetic biology and the trouble with engineering metaphors

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 functionality, 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 adaptations, 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 opportunistic 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 suggest. 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 implement 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 "engineering" 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 engineering 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.

Novel organisms: comparing invasive species, GMOs, and emerging pathogens

Invasive species, range-expanding species, genetically modified organisms (GMOs), synthetic organisms, and emerging pathogens increasingly affect the human environment. We propose a framework that allows comparison of consecutive stages that such novel organisms go through. The framework provides a common terminology for novel organisms, facilitating knowledge exchange among researchers, managers, and policy makers that work on, or have to make effective decisions about, novel organisms. The framework also indicates that knowledge about the causes and consequences of stage transitions for the better studied novel organisms, such as invasive species, can be transferred to more poorly studied ones, such as GMOs and emerging pathogens. Finally, the framework advances understanding of how climate change can affect the establishment, spread, and impacts of novel organisms, and how biodiversity affects, and is affected by, novel organisms.

Designing de novo: interdisciplinary debates in synthetic biology

Synthetic biology is often presented as a promissory field that ambitions to produce novelty by design. The ultimate promise is the production of living systems that will perform new and desired functions in predictable ways. Nevertheless, realizing promises of novelty has not proven to be a straightforward endeavour. This paper provides an overview of, and explores the existing debates on, the possibility of designing living systems de novo as they appear in interdisciplinary talks between engineering and biological views within the field of synthetic biology. To broaden such interdisciplinary debates, we include the views from the social sciences and the humanities and we point to some fundamental sources of disagreement within the field. Different views co-exist, sometimes as controversial tensions, but sometimes also pointing to integration in the form of intermediate positions. As the field is emerging, multiple choices are possible. They will inform alternative trajectories in synthetic biology and will certainly shape its future. What direction is best is to be decided in reflexive and socially robust ways.

The conception of life in synthetic biology

The phrase 'synthetic biology' is used to describe a set of different scientific and technological disciplines, which share the objective to design and produce new life forms. This essay addresses the following questions: What conception of life stands behind this ambitious objective? In what relation does this conception of life stand to that of traditional biology and biotechnology? And, could such a conception of life raise ethical concerns? Three different observations that provide useful indications for the conception of life in synthetic biology will be discussed in detail: 1. Synthetic biologists focus on different features of living organisms in order to design new life forms, 2. Synthetic biologists want to contribute to the understanding of life, and 3. Synthetic biologists want to modify life through a rational design, which implies the notions of utilising, minimising/optimising, varying and overcoming life. These observations indicate a tight connection between science and technology, a focus on selected aspects of life, a production-oriented approach to life, and a design-oriented understanding of life. It will be argued that through this conception of life synthetic biologists present life in a different light. This conception of life will be illustrated by the metaphor of a toolbox. According to the notion of life as a toolbox, the different features of living organisms are perceived as various rationally designed instruments that can be used for the production of the living organism itself or secondary products made by the organism. According to certain ethical positions this conception of life might raise ethical concerns related to the status of the organism, the motives of the scientists and the role of technology in our society.

Engineering and ethical perspectives in synthetic biology. Rigorous, robust and predictable designs, public engagement and a modern ethical framework are vital to the continued success of synthetic biology

The applications of synthetic biology will involve the release of artificial life forms into the environment. These organisms will present unique safety challenges that need to be addressed by researchers and regulators to win public engagement and support.

When does the co-evolution of technology and science overturn into technoscience?

In this paper, the relations between science and technology, intervention and representation, the natural and the artificial are analysed on the background of the formation of modern science in the sixteenth century. Due to the fact that technique has been essential for modern science from its early beginning, modern science is characterised by a hybridisation of knowledge and intervention. The manipulation of nature in order to measure its properties has steadily increased until artificial things have been produced, such as laser beams, chemical compounds, elementary particles. Furthermore, the structural bracing of natural science, technological development, and industrial exploitation of nature go also back to the foundation of modern science. In order to strengthen the debate on technoscience against this background, the specific characteristics of technoscientific objects have to be clarified as have the specific characteristics of the social organisation of technoscience and its performance.

Synthetic biology: an emerging research field in China

Synthetic biology is considered as an emerging research field that will bring new opportunities to biotechnology. There is an expectation that synthetic biology will not only enhance knowledge in basic science, but will also have great potential for practical applications. Synthetic biology is still in an early developmental stage in China. We provide here a review of current Chinese research activities in synthetic biology and its different subfields, such as research on genetic circuits, minimal genomes, chemical synthetic biology, protocells and DNA synthesis, using literature reviews and personal communications with Chinese researchers. To meet the increasing demand for a sustainable development, research on genetic circuits to harness biomass is the most pursed research within Chinese researchers. The environmental concerns are driven force of research on the genetic circuits for bioremediation. The research on minimal genomes is carried on identifying the smallest number of genomes needed for engineering minimal cell factories and research on chemical synthetic biology is focused on artificial proteins and expanded genetic code. The research on protocells is more in combination with the research on molecular-scale motors. The research on DNA synthesis and its commercialisation are also reviewed. As for the perspective on potential future Chinese R&D activities, it will be discussed based on the research capacity and governmental policy.

Synthetic toxicology: where engineering meets biology and toxicology

This article examines the implications of synthetic biology (SB) for toxicological sciences. Starting with a working definition of SB, we describe its current subfields, namely, DNA synthesis, the engineering of DNA-based biological circuits, minimal genome research, attempts to construct protocells and synthetic cells, and efforts to diversify the biochemistry of life through xenobiology. Based on the most important techniques, tools, and expected applications in SB, we describe the ramifications of SB for toxicology under the label of synthetic toxicology. We differentiate between cases where SB offers opportunities for toxicology and where SB poses challenges for toxicology. Among the opportunities, we identified the assistance of SB to construct novel toxicity testing platforms, define new toxicity-pathway assays, explore the potential of SB to improve in vivo biotransformation of toxins, present novel biosensors developed by SB for environmental toxicology, discuss cell-free protein synthesis of toxins, reflect on the contribution to toxic use reduction, and the democratization of toxicology through do-it-yourself biology. Among the identified challenges for toxicology, we identify synthetic toxins and novel xenobiotics, biosecurity and dual-use considerations, the potential bridging of toxic substances and infectious agents, and do-it-yourself toxin production.