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

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

Schmidt, Markus, et al, eds. Synthetic Biology: The Technoscience and its Societal Consequences. Dordrecht: Springer, 2009. A report on a European project to provide considerate guidance for an increasing human ability to “reengineer” the very molecular, genetic, and cellular basis of life. A companion 2010 volume might be Synthetic Biology: Building on Nature’s Inspiration from the National Academy of Sciences. From any historic, philosophical, or religious perspective this is a fantastic prospect in our midst, no less than the advent of a “new creation” as composite human inquiry and knowledge might take over, as seemingly intended, the cosmic evolutionary genesis.

Shang, Yorke, et al. A Semi-Synthetic Organism that Stores and Retrieves Increased Genetic Information. Nature. 551/644, 2017. This entry by nine Scripps Research Institute biochemists led by Floyd Romesberg (herein) has been cited as the forefront of advances into this sudden new phase of intentionally while ethically rescripting and recrafting life’s prior evolutionary biochemical, genomic, anatomic and physiological nature.

Since at least the last common ancestor of all life on Earth, genetic information has been stored in a four-letter alphabet that is propagated and retrieved by the formation of two base pairs. The central goal of synthetic biology is to create new life forms and functions, and the most general route to this goal is the creation of semi-synthetic organisms whose DNA harbours two additional letters that form a third, unnatural base pair. Here we report the in vivo transcription of DNA containing dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of natural or non-canonical amino acids into superfolder green fluorescent protein. The results demonstrate that interactions other than hydrogen bonding can contribute to every step of information storage and retrieval. The resulting semi-synthetic organism both encodes and retrieves increased information and should serve as a platform for the creation of new life forms and functions. (Abstract excerpt)

Singer, Emily. New Letters Added to the Genetic Alphabet. Quanta Magazine. July, 2015. Yes, another report about novel abilities to modify life’s genome endowment, in this case by biochemist Steven Benner’s Foundation for Applied Molecular Laboratory in Florida. But an auspicious difference, the advance involves “better blueprints for life” via additions of two synthetic nucleotides to evolution’s ATCG version. The technical reference is Structural Basis for a Six Nucleotide Genetic Alphabet by Millie Georgiadis, et al in the Journal of the American Chemical Society 137/6947, 2015. And the natural philosophy import is awesome. Collaborative human beings just now appear over a planetary surface whom are able to discern nature’s generative program. As a result, it can pass to their intentional rewrite, so as to take over and greatly enhance the organic material procreation of a genesis cosmos.

Sinha, Souvik, et al. Establishing the Fundamental Rules for Genetic Code Expansion. Nature Chemistry. July, 2023. UC Riverside biochemists scope out some ways by our which latest global acumen seems able to, incredibly, to begin to beneficially and carefully revise, edit, amend life;s genetic basis.

Genetic code expansion beyond α-amino acids by stitching together non-natural building blocks within the ribosome is a critical barrier is a latest frontier. Recently, molecular elements for the incorporation of non-natural amino acids into the ribosome has served to accelerate ribosomal synthesis. The reactivity of non-native substrates at the peptidyl transferase centre (PTC) of the ribosome, which catalyses the peptide bond formation, varies significantly and affects the reaction yield. Hence, it is of very vital to know the structural features that discriminate between reactive and non-reactive substrates at the PTC.

Sole, Ricard. Synthetic Transitions: Towards a New Synthesis. Sante Fe Institute Working Papers. 16-06-009, 2016. The Barcelona systems scientist avails the popular major evolutionary transitions scale to broach paths toward its intentional procreative continuance. The entry also appears as the lead article in a special Major Synthetic Evolutionary Transitions issue in the Philosophical Transactions of the Royal Society (371/20160175, 2016). A conceptual basis would then be a carry forth of intrinsic design principles which are being found to recur in kind at each prior stage. A modicum of “universal laws and traits,” along with an “algorithmic logic” is employed in its service. Various sections consider synthetic phases of prebiotic chemistry, replicators, genetics, cells, multicellularity, symbiosis, cognitive agents, languages, minds, and ecosystems, which are seen to readily iterate and emerge. Akin to Eric Smith and Harold Morowitz’s 2016 The Origin and Nature of Life on Earth (noted in reference 301) life’s natural development is best seen to proceed from physical realms by way of nested phase transitions. See also Synthetic Collective Intelligence by RS, et al in BioSystems (2016, search).

The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help defining a general framework to establish a theory of major transitions, both natural and artificial. Here we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics. (Abstract)

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)

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