Mapping the Emergence of Synthetic Biology

Addressing semantic ambiguity in biotechnology: Proposals from the European research infrastructure IBISBA

Driven by numerous scientific discoveries in biology in the second half of the last century, biotechnology is now set to play an important role as a driver for advanced manufacturing, leveraging the power of living organisms to produce a range of goods and services. Considering this prospect, it is vital that terminology surrounding biotechnology is sufficiently clear to provide a basis for efficient regulation and public buy-in. Despite the apparent clarity of the term biotechnology, its definition is the subject of a longstanding debate and liberal interpretations. Likewise, other more recent terms such as biomanufacturing, synthetic biology and engineering biology also lack consensual definitions despite their use in both scientific and secular circles. Additionally, new terms such as precision fermentation and cellular agriculture, recently introduced in the framework of business-to-business exchanges, appear to call upon imaginaries rather than scientific facts. Herein, we examine the lexical complexity of the biotechnology field and argue that, for the sake of efficient policymaking, it is vital to harmonise the definitions of some core terms, including biotechnology, biomanufacturing, engineering biology and synthetic biology. With this aim in mind, this discussion paper is intended to be useful to policymakers and science communicators, whether in the media or in professional settings.

A new symbiotic, holistic and gradualist model proposal for the concept of "living organism"

In biology, the concept of "living organism" has traditionally been based on the smallest level of organization comprising all the necessary and essential characteristics of life: the cell. Today, this concept is being challenged by the analysis of ambiguous biological entities, located both below and above the level of the living cell, which exhibit some of the characteristics of living organisms. This situation has given rise to an epistemological pluralism of the concepts of "organism", "individual" and "living", for which no clear and unanimous definition has yet been accepted. The aim of this manuscript is to explore new ideas and perspectives for defining the concept of "living organism", in order to eliminate a certain level of pluralism that could generate confusion, particularly in the pragmatic context of biological research. First, I expose the dualism of the concepts of "organism" and "individual" and suggest a fusion of these concepts in order to eliminate a certain level of pluralism. In doing so, I develop a symbiotic and holistic definition of the concept of "living organism", which includes different structural levels of the organism: molecular, cellular and ecosystems. Second, I present the epistemological problem of the concept of "living", which is closely related to the concepts of "organism" and "individual", by analyzing the list and gradational types of definition. In doing so, I propose a new symbiotic, holistic and gradualist model of the concept of "living organism", using a gradation of several properties of the living applied to the different structural levels of the organism developed previously (molecular, cellular, ecosystems).

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.

The advancement of artificial intelligence in biomedical research and health innovation: challenges and opportunities in emerging economies

The advancement of artificial intelligence (AI), algorithm optimization and high-throughput experiments has enabled scientists to accelerate the discovery of new chemicals and materials with unprecedented efficiency, resilience and precision. Over the recent years, the so-called autonomous experimentation (AE) systems are featured as key AI innovation to enhance and accelerate research and development (R&D). Also known as self-driving laboratories or materials acceleration platforms, AE systems are digital platforms capable of running a large number of experiments autonomously. Those systems are rapidly impacting biomedical research and clinical innovation, in areas such as drug discovery, nanomedicine, precision oncology, and others. As it is expected that AE will impact healthcare innovation from local to global levels, its implications for science and technology in emerging economies should be examined. By examining the increasing relevance of AE in contemporary R&D activities, this article aims to explore the advancement of artificial intelligence in biomedical research and health innovation, highlighting its implications, challenges and opportunities in emerging economies. AE presents an opportunity for stakeholders from emerging economies to co-produce the global knowledge landscape of AI in health. However, asymmetries in R&D capabilities should be acknowledged since emerging economies suffers from inadequacies and discontinuities in resources and funding. The establishment of decentralized AE infrastructures could support stakeholders to overcome local restrictions and opens venues for more culturally diverse, equitable, and trustworthy development of AI in health-related R&D through meaningful partnerships and engagement. Collaborations with innovators from emerging economies could facilitate anticipation of fiscal pressures in science and technology policies, obsolescence of knowledge infrastructures, ethical and regulatory policy lag, and other issues present in the Global South. Also, improving cultural and geographical representativeness of AE contributes to foster the diffusion and acceptance of AI in health-related R&D worldwide. Institutional preparedness is critical and could enable stakeholders to navigate opportunities of AI in biomedical research and health innovation in the coming years.

Polyelectrolytes for Environmental, Agricultural, and Medical Applications

In recent decades, polyelectrolytes (PELs) have attracted significant interest owing to a surge in research dedicated to the development of new technologies and applications at the biological level. Polyelectrolytes are macromolecules of which a substantial portion of the constituent units contains ionizable or ionic groups. These macromolecules demonstrate varied behaviors across different pH ranges, ionic strengths, and concentrations, making them fascinating subjects within the scientific community. The aim of this review is to present a comprehensive survey of the progress in the application studies of polyelectrolytes and their derivatives in various fields that are vital for the advancement, conservation, and technological progress of the planet, including agriculture, environmental science, and medicine. Through this bibliographic review, we seek to highlight the significance of these materials and their extensive range of applications in modern times.

Epistemology of synthetic biology: a new theoretical framework based on its potential objects and objectives

Synthetic biology is a new research field which attempts to understand, modify, and create new biological entities by adopting a modular and systemic conception of the living organisms. The development of synthetic biology has generated a pluralism of different approaches, bringing together a set of heterogeneous practices and conceptualizations from various disciplines, which can lead to confusion within the synthetic biology community as well as with other biological disciplines. I present in this manuscript an epistemological analysis of synthetic biology in order to better define this new discipline in terms of objects of study and specific objectives. First, I present and analyze the principal research projects developed at the foundation of synthetic biology, in order to establish an overview of the practices in this new emerging discipline. Then, I analyze an important scientometric study on synthetic biology to complete this overview. Afterwards, considering this analysis, I suggest a three-level classification of the object of study for synthetic biology (which are different kinds of living entities that can be built in the laboratory), based on three successive criteria: structural hierarchy, structural origin, functional origin. Finally, I propose three successively linked objectives in which synthetic biology can contribute (where the achievement of one objective led to the development of the other): interdisciplinarity collaboration (between natural, artificial, and theoretical sciences), knowledge of natural living entities (past, present, future, and alternative), pragmatic definition of the concept of "living" (that can be used by biologists in different contexts). Considering this new theoretical framework, based on its potential objects and objectives, I take the position that synthetic biology has not only the potential to develop its own new approach (which includes methods, objects, and objectives), distinct from other subdisciplines in biology, but also the ability to develop new knowledge on living entities.

Navigating the Frontier of Synthetic Biology: An AI-Driven Analytics Platform for Exploring Research Trends and Relationships

The field of synthetic biology has experienced rapid growth in recent years, leading to an overwhelming amount of literature that can make it difficult to comprehend the scope and trends of the discipline. In this study, we employ topic modeling to comprehensively map research topics within synthetic biology, revealing subtopics and their relationships, as well as trends over time. We utilize metadata to identify the most significant journals and countries in the field and discuss potential policy impact on the research output. In addition, we investigate co-authorship networks to analyze collaborations among authors, institutions, and countries. We believe that our findings could serve as a valuable resource for gaining a deeper understanding of synthetic biology and provide a foundation for analyzing other disciplines.

Improving Deproteinization in Colombian Latex from Hevea brasiliensis: A Bibliometric Approximation

Natural Rubber Field Latex (NRFL) allergens restrict its use in some markets due to health-threatening allergic reactions. These molecules are proteins that are related to asymptomatic sensitization and hypersensitivity mediated by immunoglobulin E (IgE). Although NRFL allergens have been investigated since the 1980s, there are still gaps in knowledge regarding the development of deproteinized natural rubber (DPNR). Therefore, in this study, the deproteinization of NRFL from the lower basin of the Cauca River, Antioquia-Colombia was evaluated using eight systems. The highest removal value was 84.4% and was obtained from the treatment containing SDS (Sodium dodecyl sulfate), Urea, and Ethanol. It was also possible to determine that at high concentrations of SDS, removal percentages higher than 70% are reached. On the other hand, all deproteinizing systems decreased NRFL Zeta potentials without self-coagulation, suggesting enhanced colloidal stability in DPNR latex. On the other hand, the bibliometric analysis presented technological advances in DPRN through different parameters and bibliometric networks. The analysis presented makes an important contribution from the bibliometric approach that could be positive for the development of research on DPNR.

Function-based classification of hazardous biological sequences: Demonstration of a new paradigm for biohazard assessments

Bioengineering applies analytical and engineering principles to identify functional biological building blocks for biotechnology applications. While these building blocks are leveraged to improve the human condition, the lack of simplistic, machine-readable definition of biohazards at the function level is creating a gap for biosafety practices. More specifically, traditional safety practices focus on the biohazards of known pathogens at the organism-level and may not accurately consider novel biodesigns with engineered functionalities at the genetic component-level. This gap is motivating the need for a paradigm shift from organism-centric procedures to function-centric biohazard identification and classification practices. To address this challenge, we present a novel methodology for classifying biohazards at the individual sequence level, which we then compiled to distinguish the biohazardous property of pathogenicity at the whole genome level. Our methodology is rooted in compilation of hazardous functions, defined as a set of sequences and associated metadata that describe coarse-level functions associated with pathogens (e.g., adherence, immune subversion). We demonstrate that the resulting database can be used to develop hazardous “fingerprints” based on the functional metadata categories. We verified that these hazardous functions are found at higher levels in pathogens compared to non-pathogens, and hierarchical clustering of the fingerprints can distinguish between these two groups. The methodology presented here defines the hazardous functions associated with bioengineering functional building blocks at the sequence level, which provide a foundational framework for classifying biological hazards at the organism level, thus leading to the improvement and standardization of current biosecurity and biosafety practices.

Synthetic Biology Knowledge System

The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub repository that includes text and data information that has been mined from papers published in ACS Synthetic Biology. This paper describes the SBKS curation framework that is being developed to construct the knowledge stored in this repository. The text mining pipeline performs automatic annotation of the articles using natural language processing techniques to identify salient content such as key terms, relationships between terms, and main topics. The data mining pipeline performs automatic annotation of the sequences extracted from the supplemental documents with the genetic parts used in them. Together these two pipelines link genetic parts to papers describing the context in which they are used. Ultimately, SBKS will reduce the time necessary for synthetic biologists to find the information necessary to complete their designs.

Responsible innovation in synthetic biology in response to COVID-19: the role of data positionality

Synthetic biology, as an engineering approach to biological systems, has the potential to disruptively innovate the development of vaccines, therapeutics, and diagnostics. Data accessibility and differences in data-usage capabilities are important factors in shaping this innovation landscape. In this paper, the data that underpin synthetic biology responses to the COVID-19 pandemic are analyzed as positional information goods-goods whose value depends on exclusivity. The positionality of biological data impacts the ability to guide innovations toward societally preferred goals. From both an ethical and economic point of view, positionality can lead to suboptimal as well as beneficial situations. When aiming for responsible innovation (i.e. embedding societal deliberation in the innovation process), it is important to consider hurdles and facilitators in data access and use. Central governance and knowledge commons provide routes to mitigate the negative effects of data positionality.

YouTube resources for synthetic biology education

Online video resources have increasingly become a common way to effectively share scientific research ideas and engage viewers at many levels of interest or expertise. While synthetic biology is a comparatively young field, it has accumulated online videos across a spectrum of content and technical depth. Such video content can be used to introduce viewers to synthetic biology, supplement college course content, teach new lab skills and entertain. Here, we compile online videos concerning synthetic biology into public YouTube playlists tailored for six different, though potentially overlapping, audiences: those wanting an introduction to synthetic biology, those wanting to get quick overviews of specific topics within synthetic biology, those wanting teaching or public lectures, those wanting more technical research lectures, those wanting to learn lab protocols and those interested in the International Genetically Engineered Machine competition.

Scientometric analysis of the term 'microbiota' in research publications (1999-2017): a second youth of a century-old concept

Great progress in microbiota research during last decades resulted in a growing corpus of publications mentioning the term 'microbiota'. Specifically, the human microbiota increasingly recognised nowadays as one of the most important health challenges is becoming an emerging research front. By examining over 28 000 microbiota-related papers from the Web of Science database, our study aims to characterise the evolution of publication patterns in this field between 1999 and 2017. The corpus is first analysed in terms of breakdown by journal subject categories, then an additional insight in the structuring of the microbiota research into different topics is provided by means of topic modelling. Our results demonstrate that over time (i) a substantial increase in the publications number is accompanied by a broad diversification of associated journal subject categories; (ii) the research focus moved outside from its primary research field showing successive shifts from dentistry and ecologically centred areas, through agri-food applied topics, towards the most recent clinical applications. The trends in thematic structure of the field presented from a historical perspective suggest that the current systemic approach to host-microbiota relationship inherited from the ecological background of the concept of microbiota has opened up a number of new research directions and perspectives.

Regulation of Synthetic Biology: Developments Under the Convention on Biological Diversity and Its Protocols

The primary international forum deliberating the regulation of "synthetic biology" is the Convention on Biological Diversity (CBD), along with its subsidiary agreements concerned with the biosafety of living modified organisms (LMOs; Cartagena Protocol on Biosafety to the CBD), and access and benefit sharing in relation to genetic resources (Nagoya Protocol to the CBD). This discussion has been underway for almost 10 years under the CBD agenda items of "synthetic biology" and "new and emerging issues relating to the conservation and sustainable use of biological diversity," and more recently within the scope of Cartagena Protocol topics including risk assessment and risk management, and "digital sequence information" jointly with the Nagoya Protocol. There is no internationally accepted definition of "synthetic biology," with it used as an umbrella term in this forum to capture "new" biotechnologies and "new" applications of established biotechnologies, whether actual or conceptual. The CBD debates are characterized by polarized views on the adequacy of existing regulatory mechanisms for "new" types of LMOs, including the scope of the current regulatory frameworks, and procedures and tools for risk assessment and risk mitigation and/or management. This paper provides an overview of international developments in biotechnology regulation, including the application of the Cartagena Protocol and relevant policy developments, and reviews the development of the synthetic biology debate under the CBD and its Protocols, including the major issues expected in the lead up to and during the 2020 Biodiversity Conference.

Developing synthetic biology in Argentina: the Latin American TECNOx community as an alternative way for growth of the field

Synthetic biology emerged in the USA and Europe twenty years ago and quickly developed innovative research and technology as a result of continued funding. Synthetic biology is also growing in many developing countries of Africa, Asia and Latin America, where it could have a large economic impact by helping its use of genetic biodiversity in order to boost existing industries. Starting in 2011, Argentine synthetic biology developed along an idiosyncratic path. In 2011-2012, the main focus was not exclusively research but also on community building through teaching and participation in iGEM, following the template of the early "MIT school" of synthetic biology. In 2013-2015, activities diversified and included society-centered projects, social science studies on synthetic biology and bioart. Standard research outputs such as articles and industrial applications helped consolidate several academic working groups. Since 2016, the lack of a critical mass of researchers and a funding crisis were partially compensated by establishing links with Latin American synthetic biologists and with other socially oriented open technology collectives. The TECNOx community is a central node in this growing research and technology network. The first four annual TECNOx meetings brought together synthetic biologists with other open science and engineering platforms and explored the relationship of Latin American technologies with entrepreneurship, open hardware, ethics and human rights. In sum, the socioeconomic context encouraged Latin American synthetic biology to develop in a meandering and diversifying manner. This revealed alternative ways for growth of the field that may be relevant to other developing countries.

Risk Assessment and Regulation of Plants Modified by Modern Biotechniques: Current Status and Future Challenges

This review describes the current status and future challenges of risk assessment and regulation of plants modified by modern biotechniques, namely genetic engineering and genome editing. It provides a general overview of the biosafety and regulation of genetically modified plants and details different regulatory frameworks with a focus on the European situation. The environmental risk and safety assessment of genetically modified plants is explained, and aspects of toxicological assessments are discussed, especially the controversial debate in Europe on the added scientific value of untargeted animal feeding studies. Because RNA interference (RNAi) is increasingly explored for commercial applications, the risk and safety assessment of RNAi-based genetically modified plants is also elucidated. The production, detection, and identification of genome-edited plants are described. Recent applications of modern biotechniques, namely synthetic biology and gene drives, are discussed, and a short outlook on the future follows.

Co-evolution of physical and social sciences in synthetic biology

Emerging technologies research often covers various perspectives in disciplines and research areas ranging from hard sciences, engineering, policymaking, and sociology. However, the interrelationship between these different disciplinary domains, particularly the physical and social sciences, often occurs many years after a technology has matured and moved towards commercialization. Synthetic biology may serve an exception to this idea, where, since 2000, the physical and the social sciences communities have increasingly framed their research in response to various perspectives in biological engineering, risk assessment needs, governance challenges, and the social implications that the technology may incur. This paper reviews a broad collection of synthetic biology literature from 2000-2016, and demonstrates how the co-development of physical and social science communities has grown throughout synthetic biology's earliest stages of development. Further, this paper indicates that future co-development of synthetic biology scholarship will assist with significant challenges of the technology's risk assessment, governance, and public engagement needs, where an interdisciplinary approach is necessary to foster sustainable, risk-informed, and societally beneficial technological advances moving forward.

Using Data Mining to Explore Calmodulin Bibliography

In this chapter, we present a strategy and the techniques to approach a scientific field from a set of articles gathered from the bibliographic database "Web of Science." The strategy is based on methods developed to analyze social networks. We illustrate its use in studying the calmodulin field. The method allows to structure a huge number of articles when writing a review, to detect the key opinion leaders in a given field, and to locate their own research topic in the landscape of themes deciphered by our own community.We show that the free software VOSviewer may be used without knowledge in computing science and with a short learning period.

Tracking the emergence of synthetic biology

Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years. This paper contributes to efforts to delineate this emerging domain by presenting a newly constructed bibliometric definition of synthetic biology. Our approach is dimensioned from a core set of papers in synthetic biology, using procedures to obtain benchmark synthetic biology publication records, extract keywords from these benchmark records, and refine the keywords, supplemented with articles published in dedicated synthetic biology journals. We compare our search strategy with other recent bibliometric approaches to define synthetic biology, using a common source of publication data for the period from 2000 to 2015. The paper details the rapid growth and international spread of research in synthetic biology in recent years, demonstrates that diverse research disciplines are contributing to the multidisciplinary development of synthetic biology research, and visualizes this by profiling synthetic biology research on the map of science. We further show the roles of a relatively concentrated set of research sponsors in funding the growth and trajectories of synthetic biology. In addition to discussing these analyses, the paper notes limitations and suggests lines for further work.

Semi-automated Tip Snip cloning of restriction fragments into and out of plasmid polylinkers

Synthetic biologists rely on semi-synthetic recombinant plasmids, but DNA synthesis is constrained by practical limits on length, accuracy, and sequence composition. Cloned DNA parts can be assembled into longer constructs via subcloning, but conventional methods are labor-intensive. One-pot recombination reactions are more convenient but harder to troubleshoot, and those that depend on PCR to create fragments with compatible ends necessitate re-sequencing. The Tip Snip protocol described here enables the subcloning of an insert from one plasmid polylinker into another without PCR or gel purification steps. Cohesive ends of unwanted restriction fragments are snipped off by additional restriction endonucleases. The resulting short fragments (snippets) are eliminated by hybridization to complementary oligonucleotides (anti-snippets) and subsequent size-selection spin-column chromatography. Unwanted linear donor vectors are ligated to double-stranded oligonucleotides (unlinkers) so that only the desired insert and recipient plasmid form circular DNA capable of transforming bacteria. This new method is compatible with high-throughput processing and automated liquid handling, and because no specialized vectors, reagents, selection schemes, or analytical techniques are required, the barriers to adoption are low.