Codes across (life)sciences.

The de novo design of artificial enzymes with customized catalytic functions represents a long-standing challenge in synthetic biology. Recent breakthroughs in deep learning, particularly the rise of Generative Artificial Intelligence (GAI), have transformed enzyme design from structure-centric strategies toward function-oriented paradigms. This review outlines the emerging computational frameworks that now span the entire design pipeline, including active site design, backbone generation, inverse folding, and virtual screening. Detailed description of active site, called a theozyme, is designed to stabilize transition states and can be guided by density functional theory (DFT) calculations that define the geometry of key catalytic components. Guided by the theozyme, GAI approaches such as diffusion and flow-matching models enable the generation of protein backbones pre-configured for catalysis. Inverse folding methods, exemplified by ProteinMPNN and LigandMPNN, further incorporate atomic-level constraints to optimize sequence–function compatibility. To assess and optimize catalytic performance, virtual screening platforms such as PLACER allow evaluation of protein–ligand conformational dynamics under catalytically relevant conditions. Through representative case studies, we illustrate how GAI-driven frameworks facilitate the rational creation of artificial enzymes with architectures distinct from natural homologs, thereby enabling catalytic activities not observed in nature. With the rapid progress and widespread adoption of GAI, we anticipate that de novo enzyme design with customized catalytic functions will soon evolve into a mature and broadly applicable methodology.

The last two decades have seen vigorous activity in synthetic biology research and the ever-increasing applications of these technologies. However, pedagogical research pertaining to teaching synthetic biology is scarce, especially when compared to other science and engineering disciplines. Within Canada, there are only three universities that offer synthetic biology programs, two of which are at the undergraduate level. Rather than taking place in formal academic settings, many Canadian undergraduate students are introduced to synthetic biology through participation in the annual International Genetically Engineered Machine (iGEM) competition. Although the iGEM competition has had a transformative impact on synthetic biology training in other nations, its impact in Canada has been relatively modest. Consequently, the iGEM competition remains a major setting for synthetic biology education in Canada. To promote further development of synthetic biology education, we surveyed undergraduate students from the Canadian iGEM design teams of 2019. We extracted insights from these data using qualitative analysis to provide recommendations for best teaching practices in synthetic biology undergraduate education, which we describe through our proposed Framework for Transdisciplinary Synthetic Biology Education (FTSBE).

Artificial Life Next Generation Perspectives: Echoes from the 2018 Conference in Tokyo.

EVA Copenhagen 2018 - Politics of the Machines - Art and After - Index

Synthetic biology is a new research field that comprises many different projects, approaches and definitions, which, at first glance, do not apparently have much in common. These approaches include the generation of bioengineered bacteria, artificial protocells or synthetic genomes, as well as pure in silico models of protocells or regulatory and metabolic pathways, all of which are products of synthetic biology. This Viewpoint tries to put together the various pieces by proposing five categories or subfields of synthetic biology and looking for their common denominators. The five categories are bioengineering, synthetic genomics, protocell synthetic biology, unnatural molecular biology and in silico approaches. For societal and ethical assessments of synthetic biology, it is important to consider both the differences and the similarities between the branches of synthetic biology in order to distinguish between questions that affect the field as a whole and those that are specific to individual categories. > Bioengineering, as part of synthetic biology, is the design of entirely new signalling pathways, including multiple genes and regulatory elements… The various definitions of synthetic biology shown in Sidebar A indicate that it is not a uniform discipline. Several commentators and scientists each have individual and varying definitions or classifications (Benner & Sismour, 2005; de Lorenzo et al , 2006; Forster & Church, 2007; O'Malley et al , 2008). The five categories proposed in this article take into consideration various aspects of these earlier classifications: in particular, the scientific disciplines from which the different branches of synthetic biology emerged, the stated goals and aims that researchers are striving for, and the techniques and strategies that they use to achieve these goals (Table 1). These categories should help to make societal assessments of synthetic biology more specific and precise by clarifying which issues concern which branches. ### Sidebar A | Definitions of synthetic biology 1. “Synthetic biology is (A) the design …

The evolution of genetic exploration tools, from laborious methods like radiationinduced mutations to the transformative CRISPR-Cas9 system, has fundamentally reshaped genetic research and gene editing capabilities. This journey, initiated by foundational techniques such as ZFNs and TALENs and culminating in the groundbreaking work of Doudna and Charpentier in 2012, has ushered in an era of precise DNA alteration and profound insights into gene functions. The CRISPR/Cas9 system uses the Cas9 enzyme and guides RNA (gRNA) to precisely target and cleave DNA, with subsequent repair via error-prone NHEJ or precise HDR, enabling versatile gene editing. Complementary computational tools like E-CRISP and Azimuth 2.0, alongside advanced deep learning models like DeepCRISPR, have significantly contributed to refining CRISPR experiments, optimizing gRNA efficiency, and predicting outcomes with greater precision. In clinical applications, CRISPR-Cas9 shows great promise for treating complex genetic disorders like sickle cell disease and β-thalassemia, but faces challenges such as off-target effects, immune responses to viral vectors, and ethical issues in germline editing. Overcoming these challenges requires meticulous experimentation and robust regulatory frameworks to ensure responsible and beneficial utilization of the CRISPR-Cas9 technology across diverse fields, including cancer treatment, genetic disease therapies, agriculture, and synthetic biology, while continually addressing ethical, safety, and legal considerations for its advancement and widespread adoption.

Reviewed by: Disciplining Reproduction: Modernity, American Life Sciences, and “the Problems of Sex.” Scott F. Gilbert Adele E. Clarke. Disciplining Reproduction: Modernity, American Life Sciences, and “the Problems of Sex.” Berkeley and Los Angeles: University of California Press, 1998. xvii + 421 pp. Ill. $45.00, £35.00. Disciplining Reproduction is a book about alliance politics, the construction of scientific boundaries, and how certain areas become amenable to scientific study. It lives up to its complex pun of a title in that it concerns both (a) how the social area of reproduction is disciplined (i.e., tamed); and (b) how the scientific concerns about reproduction become an academic discipline. Moreover, it is central to Clarke’s thesis that these two types of “disciplining” interact. The emotionally charged and personal worlds of reproduction must somehow have been made accessible to science, and existing scientific disciplines—such as biochemistry, embryology, pharmacology, endocrinology, and sexology—must somehow have been realigned so that their intersection set forms a new discipline: reproductive biology. If ever a field can be readily shown to be socially constructed, it is reproductive biology. Society has an enormous interest in reproduction—in who can do it with whom, when it can be done, and under what auspices. Reproduction has never been a strictly scientific or medical concern; rather, it has also been the focus of eugenicists, neo-Malthusians, feminists, agricultural reformers, politicians, and philanthropic organizations. Clarke views these actors as inhabiting different (and sometimes multiple) “social worlds.” She writes about how these different worlds have fought one another and/or formed alliances over the course of the past century, documenting how reproductive biology was forged in a context of British and American social movements. Reproductive biology and its accompanying technologies were financed by those interested in woman’s emancipation (such as Katherine McCormick, who funded Pincus’s contraceptive research) as well as by those interested in wielding scientific control over cultural practices [End Page 733] (such as the Rockefeller Foundation). Reproductive biology and its technologies of control were seen (especially by the eugenicists and the neo-Malthusians) as being at the heart of what constituted “the family.” The changing social topography caused different scientific worlds to meet and interact. Clarke describes reproductive biology as having been an “illegitimate” area of study until the alignment of the scientific disciplines enabled it to become a subject with its own textbooks and professors. But the scientific disciplines were, themselves, constrained by the specific practices of American and British cultures. Thus, Clarke details how certain areas of reproduction could be studied only in special contexts. She shows the critical importance of the agriculture schools, wherein animal husbandry research could lead to F. H. A. Marshall’s groundbreaking book The Physiology of Reproduction (1910). Similarly, she documents the struggle of endocrinology to take “problems of sex” from sexology into physiology (a battle whose fortunes are reflected in the funding from the Rockefeller Foundation), and she delineates how a volume such as Edgar Allen’s Sex and Internal Secretions functioned simultaneously as a textbook, a manifesto, a fund-raising document, and an organization builder. As it details the rise of reproductive biology from the realm of illegitimacy and the role of social factors in promoting its coalescence into a scientific discipline, Disciplining Reproduction also reflects the same processes in the history of science. The history of reproductive biology, like reproductive biology itself, had been an “illegitimate” discipline. Moreover, this history was made possible only when social forces—the rise of feminism in the Academy, and the prominence of reproductive biology in our contemporary culture—allowed people to study such things as the history of diaphragms or of in vitro fertilization. This is a rich and well-documented book. It is not a volume in which to find a detailed history of any of the scientists, reformers, techniques, or organizations involved in forming the field of reproductive biology. Rather, it is a set of contour maps in which to find how social movements, changes in scientific methodology, and changes in scientific knowledge permit certain areas of life to become studied. Scott F. Gilbert Swarthmore College Copyright © 1999 The Johns Hopkins University Press

As a highly promising interdisciplinary field in the life sciences, synthetic biology bridges such diverse disciplines as molecular biology, organic chemistry, IT, and engineering in order to create biological systems which do not exist in nature. As any emerging technology, synthetic biology is accompanied by many hopes and fears, amongst which the way in which it connects to medicine, and specifically how the biological body is viewed and treated, is equally rousing and provoking. The reality of the lab is one thing, another is the vision(s) of the future which synthetic biology inspires: equally fantastic and fundamentally human. Here we analyse several short films from the repository of the BIO·FICTION Science Art Film Festival, a festival which focuses on synthetic biology. The selected films engage with the human body and cover themes such as fantastical cross-species imaginations, the development of new organs, and future forms of geriatric care. Our analysis of these (semi)fictional films, which illustrate cultural reflections of the technological advances brought forth by synthetic biology, serves as a first exploration of how corporeality and the human body is imagined and displayed in these imaginary worlds, and what that might imply about how we view the human body in the present.

The article undertakes the problem of AGI (Artificial General Intelligence) research with reference to Nick Bostrom’s concept of existential risk and Ingmar Persson’s/Julian Savulescu’s proposal of bio­medical moral enhancement from a pedagogical-anthropological perspective. A major focus will be put on the absence of pedagogical paradigms within the techno-progressive discourse, which results in a very reduced idea of education and human development. In order to prevent future existential risks, the techno-progressive discourse should at least to some extent refer to the qualitative approaches of humanities. Especially pedagogical anthropology reflects the presupposed and therefore frequently unarticulated images of man within the various scientific disciplines and should hence be recognized as a challenge to the solely quantitative perspective of AGI researches and transhumanism. I will argue that instead of forcing man to adapt physically to artificial devices, as the techno-progressive discourses suggest, the most efficient way of avoiding future existential risks concerning the relationship between mankind and highly advanced technology would be—as John Gray Cox proposes—making AGIs adopt crucial human values, which would integrate their activity into the social interactions of the lifeworld ( Lebenswelt ).

This article introduces and elaborates the concept of rigorous creativity as an approach to working with artificial intelligence (AI) in artistic and cultural practice. Emerging from the collaborative initiative Electronic Life – a year-long, public-facing programme at Tate Britain – our approach positions AI not merely as a tool but as an encounter, a partner in thought and co-creation. Drawing on historical precedents (such as the New Tendencies movement and Harold Cohen’s AARON) and theoretical reflections (with reference to cognitive assemblages, extended mind theory, and the pharmakon), we argue for a situated, process-based mode of inquiry that is open-ended, critically alert, and participatory. As such, we critique prevailing modes of AI spectacle and techno-solutionism, calling instead for an interdisciplinary practice attuned to lifeworlds, institutional contexts, and emergent human – machine ecologies. Overall, we argue rigorous creativity allows for a renewed negotiation of authorship, aesthetic value, and collective agency vis-à-vis generative AI.

The emergence of synthetic biology holds the potential of a major breakthrough in the life sciences by transforming biology into a predictive science. The dual-use characteristics of similar breakthroughs during the twentieth century have led to the application of benignly intended research in e.g. virology, bacteriology and aerobiology in offensive biological weapons programmes. Against this background the article raises the question whether the precautionary governance of synthetic biology can aid in preventing this techno-science witnessing the same fate? In order to address this question, this paper proceeds in four steps: it firstly introduces the emerging techno-science of synthetic biology and presents some of its potential beneficial applications. It secondly analyses contributions to the bioethical discourse on synthetic biology as well as precautionary reasoning and its application to life science research in general and synthetic biology more specifically. The paper then identifies manifestations of a moderate precautionary principle in the emerging synthetic biology dual-use governance discourse. Using a dual-use governance matrix as heuristic device to analyse some of the proposed measures, it concludes that the identified measures can best be described as “patchwork precaution” and that a more systematic approach to construct a web of dual-use precaution for synthetic biology is needed in order to guard more effectively against the field’s future misuse for harmful applications.

When introducing new technologies, or dealing with uncertain situations in general, risk assessment is an established methodology to systematically and reliably consider whether intended benefits are gained or whether unwanted adverse effects are likely to occur. The German Advisory Council on Global Change (WBGU) distinguishes different risk categories according to the probability and extent of any possible damage. Building on that, the Gene-Risk Research Consortium elaborated a hierarchical risk assessment approach to analyze possible impact of the cultivation of genetically modified organisms (GMO). This approach is also adaptable to risks involved in the development of synthetic life forms. Since the use of GMO affects different levels of organization addressed by different scientific disciplines and stakeholders, the potential risks of GMO cultivation have to be denoted as being systemic and require interdisciplinary as well as transdisciplinary co-operation. Synthetic biology can build on risk management solutions which have been established for the use of GMO—at least to the extent that comparable risk dimensions have to be covered. For both technologies, risk assessment has to consider a wide spectrum of cause-and-effect chains and the potential impact over long time spans and large areas of space. It must also consider potential self-dispersal and subsequent evolutionary processes in the ecosphere after intended or accidental release into open ecosystems. A holistic risk assessment approach to GMO was settled upon by applying the concept of emergent properties structuring possible effects for different levels of organisation considering that interactions on lower levels (molecules, cells, organisms) in composition are supposed to bring up new interaction types on higher levels (populations, ecosystems, landscapes, biomes). In comparison with this structured approach, the current legal regulations, as established in the EU, can be improved in coherence and systematization by the proposed approach, in particular with regard to different ecological and economic implications of GMO (and in parallel potential releases of synthetic organisms). This is especially relevant on the landscape level; for instance, as a comprehensive systematization of region-specific adverse effects on non-target organisms, complex coexistence issues related to different production systems or some social ecological topics. In conclusion, human intervention involving self-reproducing entities by means of genetic engineering, as well as development of new synthetic life forms, should always evaluate the complete set of causal interactions on all levels of physical, biotic and social organisation in order to minimise the probability of unintended, undesirable and even harmful effects as far as feasible through anticipative assessment.KeywordsRisk AssessmentSynthetic BiologySystemic RiskEmergent PropertyGenetically Modify OrganismThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Biologists have used a reductionist approach to investigate the essence of life. In the last years, scientific disciplines have merged with the aim of studying life on a global scale in terms of molecules and their interactions. Based on high-throughput measurements, Systems Biology adopts mathematical modeling and computational simulation to reconstruct natural biological systems. Synthetic Biology seeks to engineer artificial biological systems starting from standard molecular compounds coding in DNA. Can Systems and Synthetic Biology be combined with the idea of creating a new science—‘SYS Biology’ that will not demarcate natural and artificial realities? What will this approach bring to medicine?

BiotecVisions 2012, April

The 30 years since the inception of Chemical Research in Toxicology, game-changing advances in chemical and molecular biology, the fundamental disciplines underpinning molecular toxicology, have been made. While these have led to important advances in the study of mechanisms by which chemicals damage cells and systems, there has been less focus on applying these advances to prediction, detection, and mitigation of toxicity. Over the last ∼15 years, synthetic biology, the repurposing of biological "parts" in systems engineered for useful ends, has been explored in other areas of the biomedical and life sciences, for such applications as detecting metabolites, drug discovery and delivery, investigating disease mechanisms, improving medical treatment, and producing useful chemicals. These examples provide models for the application of synthetic biology to toxicology, which, for the most part, has not yet benefited from such approaches. In this perspective, we review the synthetic biology approaches that have been applied to date and speculate on possible short to medium term and "blue sky" aspirations for synthetic biology, particularly in clinical and environmental toxicology. Finally, we point out key hurdles that must be overcome for the full potential of synthetic biology to be realized.