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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 Astropocene CoCreative Future

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

Freedens, Julius, et al. Total Synthesis of Escherichia coli with a Recoded Genome. Nature. Online May 15, 2019. This achievement by a 14 member Cambridge University, Medical Research Council Laboratory of Molecular Biology team led by Jason Chin (search) merited a New York Times May 16 review by Carl Zimmer with the title Scientists Created Bacteria with a Synthetic Genome. Is This Artificial Life? In much regard, the answer is yes for these microbe colonies do seem to thrive with DNA constructed from scratch by human ingenuity.

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, but many substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. (Abstract excerpt)

Fromenteze, Thomas. et al.. Morphogenetic metasurfaces: unlocking the potential of Turing patterns. Nature Communications.. 14/6249, 2023. University of Limoges, Queen’s University Belfast, and Duke University researchers describe an intentional continuance of life’s dynamic, vivifying systems as newly understood so as to introduce and conceive a novel geonomic, cocreative, beneficial animate materiality going forward.

We apply of the reaction-diffusion principle imagined by Alan Turing in an attempt to explain the structuring of living organisms for the procedural conception and synthesis of radiating metasurfaces. The adaptation of this biologic method guides the growth of anisotropic cellular patterns arranged to satisfy electromagnetic constraints so to facilitate radiation waves controlled in frequency, space, and polarization. Our use of morphogenesis-inspired models proves well suited for solving generative design problems and converting physical constraints into simulated chemical reactants which empower andenhance the emergence of self-organizing meta-atoms. (Excerpt)

This research occurs within a broader context of the development of artificial life. Identifying fundamental mechanisms exploited by living organisms, these advances open the way to the design of dynamic systems with complex interactions and a capacity for self-structuring the synthesis of actual forms and functions. In such a context, associative learning based on encoding environmental information and interaction rules open promising perspectives for more efficient and complex generative models, (6)

Galloway, Johanna, et al. Biomimetic Synthesis of Materials for Technology. Chemistry: A European Journal. 19/8710, 2013. We note as a good instance of phenomenal human beings who after gaining knowledge of a living universe, can intentionally, wisely apply it to continue a genesis creation. In this case University of Leeds “bionanoscientists” draw upon natural principles to conceive a better, more creature friendly, earth home environment.

In a world with ever decreasing natural reserves, researchers are striving to find sustainable methods of producing components for technology. Bioinspired, biokleptic and biomimetic materials can be used to form a wide range of technologically relevant materials under environmentally friendly conditions. Here we investigate a range of biotemplated and bioinspired materials that can be used to develop components for devices, such as optics, photonics, photovoltaics, circuits and data storage. (Abstract)

Gersbach, Charles. Genome Engineering: The Next Genomic Revolution. Nature Methods. 11/10, 2014. A Duke University biomedical professor advises that our editing of genome sequences seems similar to the way one edits computer code. A new “scientific paradigm” is said to be evident whence genomes appear as “infinitely editable pieces of software.”

Gibson, Daniel, et al, eds. Synthetic Biology: Tools for Engineering Biological Systems. Cold Spring Harbor, NY: CSH Laboratory Press, 2017. Craig Venter Institute geneticist editors gather a current volume on this active field and frontier. Some chapters are Minimal Cells – Real and Imagined, Alternative Watson-Crick Synthetic Genetic Systems (search Benner), Synthetic Morphogenesis, and Synthetic Botany. See also a companion volume Synthetic Biology: Parts, Devices and Applications from Wiley-Blackwell, 2018.

Synthetic biology involves the rational design and construction of biological components and systems from genetic elements and metabolic pathways to entirely new organisms. Progress in this field has been rapid, and it promises to significantly expand our capabilities in biotechnology, medicine, and agriculture. The collection examines the tools and techniques employed to develop new drugs, diagnostic approaches, food sources, and clean energy, and what synthetic biology has taught us about natural living systems. The contributors discuss advances in DNA synthesis and assembly, genome editing (e.g., CRISPR/Cas9), and artificial genetic systems. Progress in designing complex genetic switches and circuits, expanding the genetic code, modifying cellular organization, and producing proteins using cell-free systems, are also covered.

Gilbert, Charles and Tom Ellis. Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties. ACS Synthetic Biology. 8/1, 2019. As collective human ingenuity initiates a second intentional evolutionary co-creation, Imperial College London bioengineers scope out ways to join microbial, cellular, morphogenetic and more phases into novel, palliative, beneficial ways living systems.

Natural biological materials exhibit remarkable properties: self-assembly from simple raw materials, precise control of morphology, diverse physical and chemical properties, self-repair, and to sense-and-respond to environmental stimuli. But, could it be possible to genetically program microbes to create entirely new and useful biological materials? At the intersection of microbiology, material science, and synthetic biology, an emerging field of biological engineered living materials (ELMs) is underway. Here we review recent efforts to program cells to produce living materials with novel functional properties, focusing on microbial systems that can be engineered to grow materials and on new genetic circuits for pattern formation. (Abstract)

Gines, Guillaume, et al. Microscopic Agents Programmed by DNA Circuits. Nature Nanotechnology. 12/4, 2017. We cite this materials science contribution by University of Tokyo and CNRS, Paris researchers because it conveys how nucleotide molecules appear to possess many more constructive qualities beyond their genetic utility. An inherent prescriptive, textual feature then becomes evident, along a further array of advantages. See also a note Programmed Communication in the same issue. By extension, along with some deeply cerebral essence, nature’s materiality could be seen as wholly genomic in kind.

Information stored in synthetic nucleic acids sequences can be used in vitro to create complex reaction networks with precisely programmed chemical dynamics. Here, we scale up this approach to program networks of microscopic particles (agents) dispersed in an enzymatic solution. Agents may possess multiple stable states, thus maintaining a memory and communicate by emitting various orthogonal chemical signals, while also sensing the behaviour of neighbouring agents. Using this approach, we can produce collective behaviours involving thousands of agents, for example retrieving information over long distances or creating spatial patterns. Our systems recapitulate some fundamental mechanisms of distributed decision making and morphogenesis among living organisms and could find applications in cases where many individual clues need to be combined to reach a decision, for example in molecular diagnostics. (Abstract)

Goho, Alexandra. Life Made to Order. Technology Review. April, 2003. As emergent humankind begins to rewrite life’s program, a “biological literacy,” properly guided, that can create custom organisms for novel medicines and food supplies. This journal from MIT covers the occasion of such potential advances.

Hagen, Kristin, et al, eds. Ambivalences of Creating Life: Societal and Philosophical Dimensions of Synthetic Biology. Dordrecht: Springer, 2016. A collection from a 2014 interdisciplinary summer seminar about the book title, held in Berlin. We note so as to emphasize that this vast new venture ought to be respectfully oriented and thought through from its very beginnings. See also Synthetic Biology: Metaphors, Worldviews, Ethics and Law edited by Joachim Boldt (Springer, 2016).

"Synthetic biology" is the label of a new technoscientific field with many different facets and agendas. One common aim is to "create life", primarily by using engineering principles to design and modify biological systems for human use. In a wider context, the topic has become one of the big cases in the legitimization processes associated with the political agenda to solve global problems with the aid of (bio-) technological innovation. Conceptual-level and meta-level analyses are needed: we should sort out conceptual ambiguities to agree on what we talk about, and we need to spell out agendas to see the disagreements clearly. The book is based on the interdisciplinary summer school "Analyzing the societal dimensions of synthetic biology", which took place in Berlin in September 2014.

Haimovich, Adrian, et al. Genomes by Design. Nature Reviews Genetics. 16/501, 2015. Yale University systems biologists entertain a novel phase of not only “reading” nucleotide sequences, but of taking up their “writing” anew. We cite this frontier article as a sample among thousands across a proliferation of genetic, biological, informatics, journals and beyond. See also The Genome Project-Write by Jef Boeke, et al in Science (Online June 2016) about a consortium led by George Church, and Genotype Specification Language by Erin Wilson, et al in ACS Synthetic Biology (5/6, 2016).

Next-generation DNA sequencing has revealed the complete genome sequences of numerous organisms, establishing a fundamental and growing understanding of genetic variation and phenotypic diversity. Engineering at the gene, network and whole-genome scale aims to introduce targeted genetic changes both to explore emergent phenotypes and to introduce new functionalities. Expansion of these approaches into massively parallel platforms establishes the ability to generate targeted genome modifications, elucidating causal links between genotype and phenotype, as well as the ability to design and reprogramme organisms. In this Review, we explore techniques and applications in genome engineering, outlining key advances and defining challenges. (Abstract)

Hernandez-Espinosa, Nancy, et al. Stimulus-responsive Self-assembly of Protein-based Fractals by Computational Design. Nature Chemistry. 11/7, 2019. A team of nineteen Rutgers University biochemists provide a good example of an intentional avail of nature’s animate propensity to form fractional self-similarity topologies as its preferred topology. In addition to biomolecular compounds, these geometric features need be factored as a vital aspect of novel procreations. By way of late 2010s display graphics, fractal zooms are shown which course through many scalar dimensions.

Hoang, Tuan-Hao, et al. On Synergistic Interactions between Evolution, Development and Layered Learning. IEEE Transactions on Evolutionary Computation. 15/3, 2011. Computation theorists Hoang, Le Quy Don Technical University, Hanoi, with Robert McKay, Seoul National University, Daryl Essam, University of New South Wales, and Nquyen Xuan Hoai, Hanoi University, survey in retrospect life’s evolution as a developmental process distinguished by incremental learning stages. Since nature knows best, such principles and procedures ought to be applied to improve our civilizational problem solving abilities going forward. And again if to wonder, might worldwide projects of this kind represent a generative cosmos just now passing to a profound revolutionary phase as a “second genesis,” via our intentional new creation?

We investigate interactions between evolution, development and lifelong layered learning in a combination we call evolutionary developmental evaluation (EDE), using a specific implementation, developmental tree-adjoining grammar guided genetic programming (GP). The approach is consistent with the process of biological evolution and development in higher animals and plants, and is justifiable from the perspective of learning theory. In experiments, the combination is synergistic, outperforming algorithms using only some of these mechanisms. It is able to solve GP problems that lie well beyond the scaling capabilities of standard GP. The solutions it finds are simple, succinct, and highly structured. We conclude this paper with a number of proposals for further extension of EDE systems. (Abstract)

We concentrate on four aspects of evolutionary development in complex organisms: an underlying evolutionary mechanism, a developmental mechanism, multiple evaluations throughout development, and layered learn of increasingly complex problems. Implementing them in a genetic programming system, we investigate their performance, in particular investigating whether they interact synergistically to solve more complex problems than the individual components can handle. (287)

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