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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VIII. Earth Earns: An Open Participatory Earthropocene to Ecosmocene CoCreativity

2. Second Genesis: Emergent LifeKinder Proceeds to an Aware BioGenetic Phase

Srinvasarao, Mohan, et al. Biologically Inspired Far-from-Equilibrium Materials. MRS Bulletin. 44/2, 2019. In this international Materials Research Society main publication, systems chemists MS, Georgia Tech, Germano Iannacchione, Worcester PolyTech, and Atad Parikh, UC Davis introduce a special issue with this title. What is notable today is a fertile integration and avail of these life-like, thermodynamic energies and activities into this older inorganic, metallurgical field. See also herein, Bioinspired Nonequilibrium Search for Novel Materials by Arvind Murugan and Heinrich Jaeger, and Nature’s Functional Nanomaterials by Bodo Wilts, et al.

Traditional approaches to materials synthesis have largely relied on uniform, equilibrated phases leading to static “condensed-matter” structures. Departures from these modes of materials design are pervasive in biology. From the folding of proteins to the reorganization of self-regulating cytoskeletal networks, biological materials reflect a major shift in emphasis from equilibrium thermodynamics to out-of-equilibrium regimes. Here, highly structured dynamical states that are out of equilibrium facilitate the creation of new materials capable of performing life-like functions such as complex and cooperative processes, self-replication, and self-repair, ultimately biological principles of spatiotemporal modes of self-assembly. (Srinvasarao Abstract excerpts)

Searching for materials with improved or novel properties involves an iterative process to successively narrow the gap between some initial starting point and the desired design target. This can be viewed as an optimization problem in a high-dimensional space, often with dozens of material parameters that need to be tuned. To tackle this, the evolutionary process in biology has been a source of inspiration for effective search algorithms. Here, we go beyond black box algorithms and take a broader view of computational evolution strategies. We discuss recent strategies that exploit knowledge about the material configuration statistics and highlight advantages by way of time-varying environments. Throughout, we emphasize that the search strategies themselves can be viewed as a nonequilibrium dynamical process in design space. (Murugan Abstract)

Swiegers, Gerhard, ed.. Bioinspiration and Biomimicry in Chemistry. Boca Raton: CRC Press, 2012. An international authorship considers our novel capabilities to reinvent, foster, and continue the well-being of biosphere and its human members through an intentional, ethical apply of natural bioprinciples. With Forewords by Jean-Marie Lehn, Nobel laureate in Chemistry, and Janine Benyus, whose 1997 Biomimicry initiated the endeavor, chapters evoke self-assembly, functional hierarchies, cooperativity in biochemicals, bionanotechnology, biomineralization, catalysis and so on. A final chapter proposes we ought to make use of life’s complex system dynamics of emergence, autonomous agents, non-equilibrium processes, and more.

As recognition implies information, supramolecular chemistry has brought forward the concept that chemistry is also in information science, information being stored at the molecular level and processed at the supramolecular level. On this basis, supramolecular chemistry is actively exploring systems undergoing self-organization, that, systems capable of generating, spontaneously but in an information-controlled manner, well defined functional architectures by self-assembly from their components, thus behaving as programmed chemical systems. (Lehn, xvii-xviii)

Tack, Drew, et al. Evolving Bacterial Fitness with an Expanded Genetic Code. Nature Scientific Reports. 8/3288, 2018. National Institute for Science and Technology and UT Austin, Center for Systems and Synthetic Biology researchers broach another way that life’s billion year default genomic system can now and henceforth be modified, edited, rewritten by our collaborative worldwise capabilities. What an epochal, auspicious, singular moment this can be as a genesis cosmos begins a new procreative phase by way of our intentional, respectful agency.

Since the fixation of the genetic code, evolution has largely been confined to 20 proteinogenic amino acids. The development of orthogonal translations that allow for the codon-specific incorporation of noncanonical amino acids may provide a means to expand the code, but these translation systems cannot be superimposed on cells that have spent billions of years optimizing their genomes with the canonical code. We have therefore carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop. While the evolved lineages had not resolved the ambiguous coding of the amber codon, the improvements in fitness allowed new amber codons to populate protein coding sequences. (Abstract edits)

Overall, our method provides one of the first experiments investigating how a new genetic code is adopted by an organism, and evolved lineages may represent evolutionary intermediates to the adoption of a new amino acid. All lineages overcame the fitness burden associated with 3nY toxicity, but ncAA addiction was required to enforce an active OTS. Further experimentation using the method described here, or similar approaches, will provide insight into the recoding of the genetic code during evolution, and may allow the evolution of biochemically unique organisms. (9)

Toda, Satoshi, et al. Programming Self-Organizing Multicellular Structures with Synthetic Cell-Cell Signaling. Science. 361/156, 2018. UC San Francisco and Stanford University researchers begin to intentionally carry forth nature’s innate capacities to arrange, grow and evolve itself. To wit, a genesis procreation is initiated by this work and many other efforts to read, avail and apply of these dynamic encodings. See also a commentary on this paper, Living Shapes Engineered by Jesse Tordoff and Ron Weiss, in Nature (559/184, 2018).

A common theme in the self-organization of multicellular tissues is the use of cell-cell signaling networks to induce morphological changes. We used the modular synNotch juxtacrine signaling platform to engineer artificial genetic programs in which specific cell-cell contacts induced changes in cadherin cell adhesion. Despite their simplicity, these minimal intercellular programs were sufficient to yield assemblies with hallmarks of natural developmental systems: robust self-organization into multi-domain structures, well-choreographed sequential assembly, cell type divergence, symmetry breaking, and the capacity for regeneration upon injury. These results provide insights into the evolution of multi-cellularity and demonstrate the potential to engineer customized self-organizing tissues or materials. (Abstract)

Venetz, Jonathan, et al. Chemical Synthesis Rewriting of a Bacterial Genome to Achieve Design Flexibility and Biological Functionality. Proceedings of the National Academy of Science. 116/8070, 2019. Thirteen Institute of Molecular Systems Biology, ETH Zurich researchers scope out this epic revolution as ecosmic life, mind, and selves in collective concert are poised to begin a second, intentional, evolitionary cocreative phase.

The fundamental biological functions of a living cell are stored within the DNA sequence of its genome. Classical genetic approaches dissect the functioning of biological systems by analyzing individual genes, yet uncovering the essential gene set of an organism has remained very challenging. It is argued that the rewriting of entire genomes through the process of chemical synthesis provides a powerful and complementary research concept to understand how essential functions are programmed into genomes. (Significance)

Vibhute, Mahesh and Hannes Mutschler. A Primer on Building Life-Like Systems. ChemSystemsChem. December, 2022. Dortmund University, Germany biochemists offer a current review as scientific efforts readily proceed apace, so it seems, to begin a second intentional genesis. Their gist is to gather life’s prime features so to see how they interact and accord as a basic guide going forward. In regard four prime aspects are Evolution, Robustness, Replication and Autonomy, (which can defines a main identity and purpose, such as the new evolitional phase.

The quest to understand life and recreate it in vitro has been tried through many routes. These different approaches for experimental investigation of life aim to piece together the puzzle either by tracing life's origin or by synthesizing life-like systems from non-living components. Unlike efforts to define life, these experimental inquiries aim to recapture specific features of living cells, such as reproduction, self-organization or metabolic functions that operate far from thermodynamic equilibrium.. In this Perspective, we discuss properties whose realization would, in our view, allow the best possible experimental emulation of a minimal form of biological life. (Excerpt)

Vidiella, Blai, et al. Engineering Self-Organized Criticality in Living Cells. Nature Communications. 12/4415, 2021. Six Barcelona systems theorists including Ricard Sole not only add increasing evidence for the universal presence of this optimum poise between more or less order, but goes on to consider how novel cellular phenomena can be designed and facilitated to reside in this beneficial mode. See also Criticality and Adaptivity in Enzymatic Networks by Paul Steiner, et al in the Biophysical journal (111/1078, 2016) as a cited example.

Complex dynamical fluctuations, whether molecular noise within cells, collective intelligence, brain dynamics or computer traffic have been shown to display behaviors consistent with a critical state between order and disorder. Living close to the critical point can have a number of adaptive advantages and life’s evolution seems to select (and even tend to) these critical states. Is this the case of living cells? It is difficult to test this given the dimensionalities associated with gene and metabolic webs. In this paper we seek to engineer synthetic gene networks displaying self-organized criticalities in intracellular traffic. (Abstract excerpt)

Voegle, Kilian, et al. Genetically Encoded Membranes for Bottom-Up Biology. ChemSystemsChem. Online August, 2019. Technische Universitat Munchen biophysicists including Friedrich Simmel discuss ways to achieve synthetic self-assembled cellular compartments such as external feeding and fusion, chemical reactions, lipid metabolisms, peptide basal, and more. Graphic illustrations impress with how readily our human capabilities seem suited for such an intelligent, intentional take up and over, in a respectful Gaiaspheric manner, of life’s Earthly and cosmic evolutionary gestation.

The creation of self‐replicating cell‐mimicking systems – artificial cells – is one of the major goals of bottom‐up synthetic biology. An essential aspect is the presence of membranous compartments which can grow and divide in synchrony with the internal dynamics of the cells. In the context of autonomously self‐replicating systems, genetically encoded membranes are of particular interest. Herein, we discuss typical approaches taken for the creation of cell‐like microcompartments via self‐assembly of amphiphiles. We address some of the challenges associated with the generation of phospholipid or peptide‐based membranes via genetic and enzymatic processes. (Abstract)

Artificial living systems are often conceived as compartmentalized chemical systems that are able to grow and divide, replicate and pass on genetic information, which would convey the potential for Darwinian evolution. The creation of such systems necessarily involves the realization and study of out of equilibrium chemical reaction networks that control molecular self‐assembly and self‐organization processes. A key challenge in this context is the encapsulation of the systems and the coupling and coordination of their internal gene replication and metabolism with the dynamics of the compartment resulting in growth and division. (1)

Wang, Lei and Peter Schultz. Expanding the Genetic Code. Angewandte Chemie. 44/1, 2005. An international journal of chemistry and biology, wherein this extensive paper is listed as Protein Science. In a genesis perspective, this work is an example of life through its cerebral human phase beginning to intentionally recreate itself anew.

By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties. (35)

Wang, Yueqiang, et al. Genome Writing: Current Progress and Related Applications. Genomics, Proteomics & Bioinformatics. Online February, 2018. Genetic researchers based at the Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen and similar labs across China proceed with an especial emphasis on literary and editorial features as they come to distinguish our nascent abilities to embellish and continue life’s genetic narrative.

The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects. (Abstract)

Ward, Thomas. Artificial Enzymes Made to Order: Combination of Computational Design and Directed Evolution. Angewandte Chemie International. 47/7802, 2008. We note this work by a University of Basel chemist as one sample from myriad efforts (note the page number in just this journal) of the phenomenal human take up and over of materiality and its future organic enhancement. An approach employed is known as the “RosettaMatch computational algorithm.” But within our tacit scientific, philosophical, and religious Ptolemaic mindset that denies, indeed cannot even contain, such abilities and purpose, this remains mostly unbeknownst. (see also Winpenny herein)

wendell, A. Lim, et al. The emerging era of cell engineering: Harnessing the modularity of cells to program complex biological function. Science. 378/6622, 2022. As the Abstract notes, a UC San Francisco senior biochemist broadly introduces a special Cell Engineering issue which situates its novel approach and facilities at a cellular level. Two papers are Bacterial as Interactive Cancer Therapies and Scaling Up Complexity in Synthetic Developmental Biology.

A new era of biological engineering is emerging in which living cells are used to address therapeutic challenges. These efforts are distinct from older molecular methods that involve individual genes and proteins. Rather they use molecular components as modules to reprogram how cells decide and communicate to achieve higher-order physiological functions in vivo. This cell-centric approach is enabled by a growing tool kit that can synthetically control core cell-level functional outputs, such as where in the body a cell should go, what other cells it should interact with, and what messages it should transmit or receive. (Excerpt)

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