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

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

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)

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, Boya,et al. Parallel molecular computation on digital data stored in DNA.. PNAS Nexus. September 5, 2023. We note this work by five UT Austin biochemists to record how nature’s nucleotide seems to have a wealth of further capacities as an informational repository. An additional interest is the author’s novel avail of implicate multicomputational methods, see Stephen Wolfram 2020-2023 work herein and on the arXiv preprint site.

The exponential accumulation of digital data is expected to outstrip magnetic and optical storage media. DNA’s higher information density makes it an attractive alternative. Here, we develop a dynamic DNA storage of general programmable computation “in chemistry” which provides for greater scalability. (Significance)
We show programs for binary counting and Turing universal cellular automaton (Wolfram) Rule 110. Our work thus merges DNA storage and computing as entirely molecular algorithms for the parallel manipulation of digital informationas preserved in DNA. (Abstract)

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)

Whitesides, George. Bioinspiration: Something for Everyone. Interface Focus. 5/4, 2015. In an issue on Bioinspiration of New Technologies, the Harvard University polychemist leads with a copious, procreative survey. At the outset, the concept and approach of drawing upon guidance from the natural wisdom of living systems to intentionally carry forward for a better world is extolled. The paper goes on about soft matter, self-assembly, mesoscale structures, information and energy, reaction networks, covalent synthesis, and so on, much from his own laboratory

Bioinspiration — using phenomena in biology to stimulate research in non-biological science and technology—is a strategy that suggests new areas for research. Beyond its potential to nucleate new ideas, bioinspiration has two other interesting characteristics. It can suggest subjects in research that are relatively simple technically; it can also lead to areas in which results can lead to useful function more directly than some of the more familiar areas now fashionable in chemistry. Bioinspired research thus has the potential to be accessible to laboratories that have limited resources, to offer routes to new and useful function, and to bridge differences in technical and cultural interactions of different geographical regions. (Abstract)

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