VIII. Earth Earns: An Open CoCreative Earthropocene to Astropocene PediaVerse

2. Second Genesis: Sentient LifeKinder Transitions to a New Intentional, BioGenetic Questiny

Sole, Ricard. The Major Synthetic Evolutionary Transitions. Philosophical Transactions of the Royal Society B. 371/20160175, 2016. An introduction to an issue about this title subject which attests how much this view of life’s emergent, recurrent scale from replicative biochemicals to cells, organisms, brains, primates and onto linguistic cultures is an established paradigm. Ricard, an ICREA Complex Systems group leader at the Universitat Pompeu Fabra, Barcelona, is in pursuit of, with many colleagues (search RS), its salutary extension by way of natural biomimetic principles. His lead paper, Synthetic Transitions, is reviewed at length herein. A dozen authoritative entries follow such as Some Mechanistic Requirements for Major Transitions by Peter Schuster, Generating Minimal Living Systems from Non-Living Materials by Steen Rasmussen, et al, Biogeneric Developmental Processes: Drivers of Major Transitions in Animal Evolution by Stuart Newman, Agent-Based Models for the Emergence and Evolution of Grammar by Luc Steels (search), Energy and Time Determine Scaling in Biological and Computer Designs by Melanie Moses, et al, and Synthetic Consciousness by Paul Verschure. OK

Evolution is marked by well-defined events involving profound innovations that are known as ‘major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These ‘synthetic’ transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined. (Abstract)

Srinivas, Niranjan, et al. Enzyme-free Nucleic Acid Dynamical Systems. Science. 358/1401, 2018. We cite because CalTech, University of Washington, and UT Austin researchers including Erik Winfree advance understandings of the broad range of functional qualities that DNA nucleotide biomolecules innately seem to possess. These natural biochemicals are being found to have uniquely adaptable properties for all manner of structural formations, which our nascent human ingenuity can continue forth into a new biogenetic procreation.

Chemistries exhibiting complex dynamics—from inorganic oscillators to gene regulatory networks—have been long known but either cannot be reprogrammed at will or rely on the sophisticated enzyme chemistry underlying the central dogma. Can simpler molecular mechanisms, designed from scratch, exhibit the same range of behaviors? Abstract chemical reaction networks have been proposed as a programming language for complex dynamics, along with their systematic implementation using short synthetic DNA molecules. We developed this technology for dynamical systems by identifying critical design principles and codifying them into a compiler automating the design process. Using this approach, we built an oscillator containing only DNA components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chemical dynamics and that autonomous molecular systems can be designed via molecular programming languages. (Abstract)

The programmable nature of base-pairing interactions and the minimal requirements on the chemical environment make DNA a particularly attractive engineering material. Nucleic acids as chemical controllers naturally integrate with the ever-expanding range of molecular structures, machines, and devices developed in DNA nanotechnology and could eventually be embedded within complex synthetic organelles or artificial cells that sense, compute, and respond to their chemical and molecular environment. Besides addressing a technological challenge, we also answer a fundamental scientific question, showing that Watson-Crick base pairing alone suffices for complex temporal dynamics. (Conclusion)

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)

Stuart-Fox, Devi, et al. Challenges and Opportunities for Innovation in Bioinformed Sustainable Materials. Communications Materials. 4/80, 2023. This comprehensive, illustrated survey by twenty seven multidisciplinary researchers across Australia from Melbourne to New South Wales provides a thorough, consistent review of this creaturewise biomimicry endeavor. Within a wide evolutionary vista, an integral past to future turn and continuity is scoped out as our Earthuman acumen makes vital avail of natural guidance and begins a new intentional, sustainable cocreativity.

Nature provides a rich source of information for the design of novel materials; yet there remain many challenges so as to avail and advance their form, function, and sustainability of biological solutions. Here, we identify vital approaches in two main areas; the first relates to biological information for materials innovation, including key differences between biological and synthetic materials, and the relationship between structure and function. The second area relates to the design and manufacture of bioinformed materials, including the physical scale of material architectures and manufacturing scale up. (Excerpt)

Fig. 1. Materials and surfaces in nature are adaptive, biodegradable, multifunctional, self-assembling, self-cleaning, and self-repairing. The five images within the bioinformed cycle show examples of materials/surfaces exhibiting these feature) and describe bioinspired materials and technologies with these properties. Bioinformed materials should ideally exist within a circular lifecycle to achieve sustainability.

Bioinformed design approaches hold enormous promise for innovation to meet the challenges of a circular economy and sustainable world. We find the best design is one that resembles the process and outcome of biological evolution, insofar as the design process is refined to optimize multiple functions in a holistic way. We have outlined key challenges in harnessing biological knowledge for the design, manufacture, and uptake of such organic-like composition. Going forward, a multidisciplinary integration from the earliest stages which includes researchers, products plans, manufacturers, approval bodies, and end users is a vital requirement. (9)

Su, Manu and Javier Perez-Ramiriz.. Embracing data science in catalysis research. Nature Catalysis. 7/624, 2024.. Nature Catalysis. 7/624, 2024. We note this work by ETH Zurich scientists as an exemplary recognition of the natural presence and basic importance of nature’s self-making propensities and agencies as radical new phase of synthetic methods gets going forward.

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Accelerating catalyst discovery and development is vital to addressing global energy, sustainability and healthcare demands. The past decade has witnessed an application of computational concepts in catalysis research in this regard. Here we review how researchers have been to solve complex challenges across heterogeneous, homogeneous and enzymatic catalysis. We discuss the prevalence of catalytic tasks, model reactions and choice of algorithms along with frontiers in knowledge transfer opportunities among the catalysis subdisciplines. We advocate their adoption into routine experimental workflows to spur future research in digital catalysis. (Excerpt)

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)

Velasco-Garcia, Laura and Carla Casadevall. Bioinspired photocatalytic systems towards compartmentalized artificial photosynthesis. Communications Chemistry. 6/263, 2023. Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology describe initial proof of principle verifications that these nature-based approaches can facilitate viable ways to achieve this vital biological process going forward.

Artificial photosynthesis aims to produce fuels and chemicals from simpler versions using sunlight as an energy source. To achieve novel photocatalysis, this review turns to bioinspired artificial vesicles as a source. We discuss recent examples such as light harvesting, charge transfer, and fuel production. These studies cite the pivotal role of the membrane to increase the stability of reaction partners, a suitable local environment, and force proximity between electron donor and acceptor molecules. Overall, these findings pave the way for further bioinspired artificial photosynthesis projects. (Excerpt)

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)

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