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

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

Naguleswaran, Sanjeev. Machine Learning and Quantum Intelligence for Health Data Scenarios. arXiv:2410.21339. We cite this entry by a QSPectral Systems, University of Adelaide AI scientist among many as an example of how Earthuman collective sapience can enter an epochal phase when our worldwise knowledge repository can both be retrospectively fed back to cure, heal, mitigate, and prevent prior evolutionary maladies and fed forward to begin a new intentional, evolitionary enhancement of body, mind, spirit and gaiable communities.

The advent of quantum computing offers unique capabilities to address complex, data-intensive problems such as medical analytics. Quantum Machine Learning leverages novel properties such as superposition and entanglement to enhance pattern recognition and classification, surpassing classical approaches. This paper explores QML's application in healthcare, focusing on kernel methods and hybrid quantum-classical networks for heart disease prediction and COVID-19 detection, assessing their feasibility and performance.

Nicolaou, K. C. Organic Synthesis: The Art and Science of Replicating the Molecules of Living Nature and Creating Others like Them in the Laboratory. Proceedings of the Royal Society A. Online January, 2014. The renowned Rice University biochemist surveys the unlimited horizons for “synthetic and medicinal chemistry” to both heal the past creature phase, and begin a new material nature of immense benefit. Of course all respectful ethics have to be considered beforehand. And may one add that such activities which seem so open and inviting to us imply a real role as cosmic chemists and catalysts.

Synthetic organic chemists have the power to replicate some of the most intriguing molecules of living nature in the laboratory and apply their developed synthetic strategies and technologies to construct variations of them. Such molecules facilitate biology and medicine, as they often find uses as biological tools and drug candidates for clinical development. In addition, by employing sophisticated catalytic reactions and appropriately designed synthetic processes, they can synthesize not only the molecules of nature and their analogues, but also myriad other organic molecules for potential applications in many areas of science, technology and everyday life. After a short historical introduction, this article focuses on recent advances in the field of organic synthesis with demonstrative examples of total synthesis of complex bioactive molecules, natural or designed, from the author’s laboratories, and their impact on chemistry, biology and medicine. (Abstract)

Nielsen, Peter. A New Molecule of Life? Scientific American. December, 2008. The director of the Center for Biomolecular Recognition at the University of Copenhagen describes a synthetic hybrid of protein and DNA called peptide nucleic acid or PNA that combines genetic information storage with a protein-like stability.

Noshay, Jaclyn, et al. Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering. Nucleic Acids Research. 51/19, 2023. Eleven computational biologists at Oak Ridge National Laboratory and the University of Tennessee explain a novel synthesis of these genetic editing abilities with quantum physical (organic) principles.

CRISPR-Cas9 tools have transformed genetic manipulation capabilities. While empirical rules have been developed for a range of model organisms, the basis for sgRNA efficiency remains poorly understood. Here we enter a novel feature set and a new public resource by way of quantum chemical tensors. We use the iterative AI model known as Random Forest (iRF) to encode attributes of position-specific sequences for Escherichia coli sgRNAs and identify traits for sgRNA design in bacterial species. We believe that these encodings can enhance our understanding of the quantum biological processes involved in the CRISPR-Cas9 machinery. (Abstract)

Ostrov, Nili, et al. Synthetic Genomes with Altered Genetic Codes. Current Opinion in Systems Biology. October, 2020. With sections such as Genetic codes that use unnatural codons, Altering the canonical triplet code, and more, Harvard Medical School geneticists including George Church post a latest survey about this epochal shift whence collective human intellect, with respectful observance, can begin a second ecosmic procreation. See also Technological Challenges and Milestones for Writing Genomes by Nili Ostrov, et al in Science (366/310, 2019).

The genetic code is the set of rules that define how information encoded in DNA is interpreted into amino acids to make proteins. Recently, technological advances in DNA synthesis, sequencing and genome engineering are enabling the development of synthetic genomes with altered genetic codes. Such comprehensive genome modifications endow these organisms with capabilities such as genetic isolation, virus resistance, and production of new functional proteins. (Abstract)

Whole genome recoding is an emerging field with great potential for elucidation of fundamental biological phenomena as well as generating novel enabling biotechnologies. Deeper understanding of genome structure and function is critical to succeed in these efforts, as well as development of robust computational and synthetic biology methods. While challenging, synthetic genomes with altered genetic codes offer an exciting opportunity to explore the rules of life. (8)

Parrington, John. Redesigning Life: How Genome Editing Will Transform the World. Oxford: Oxford University Press, 2016. An Oxford University pharmacologist and author describes many auspicious potentials by which to begin a epochal recreation by way of informed human intention to make everything anew. If to gloss, people can have roles as editors, curators, indeed writers of nature’s genomic script, CRISPR plus, as it may now pass our ethical continuance.

Pascalie, Jonathan, et al. Developmental Design of Synthetic Bacterial Architectures by Morphogenetic Engineering. ACS Synthetic Biology. Online May, 2016. A French theorist team including Rene Doursat continues their project to commence not only a genomics revolution, but a second genesis of an organismic anatomy and physiology so as to facilitate and develop improved, healthy, enhanced, intentional creaturely beings liberated from contingent evolutionary tinkering.

Peccoud, Jean. Synthetic Biology: Fostering the Cyber-Biological Revolution. Synthetic Biology. 1/1, 2016. This is an introductory article for this new online Oxford University Press journal by its Editor, the Colorado State University professor of chemical and Biological Engineering.

Since the description, in 2000, of two artificial gene networks, synthetic biology has emerged as a new engineering discipline that catalyzes a change of culture in the life sciences. Recombinant DNA can now be fabricated rather than cloned. Instead of focusing on the development of ad-hoc assembly strategies, molecular biologists can outsource the fabrication of synthetic DNA molecules to a network of DNA foundries. Model-driven product development cycles that clearly identify design, build, and test phases are becoming as common in the life sciences as they have been in other engineering fields. A movement of citizen scientists with roots in community labs throughout the world is trying to democratize genetic engineering. It challenges the life science establishment just like visionaries in the 70s advocated that computing should be personal at a time when access to computers was mostly the privilege of government scientists. Synthetic biology is a cultural revolution that will have far reaching implications for the biotechnology industry. The work of synthetic biologists today prefigures a new generation of cyber-biological systems that may to lead to the 5th industrial revolution. (Abstract)

Polka, Jessica, et al. Building Spatial Synthetic Biology with Compartments, Scaffolds, and Communities. Cold Spring Harbor Perspectives in Biology. 8/8, 2016. Harvard Medical School systems biologists Polka, Stephanie Hays, and Pamela Silver advance nature’s intentional recreation by novel inclusions of these consistent, organizational formations.

Traditional views of synthetic biology often treat the cell as an unstructured container in which biological reactions proceed uniformly. In reality, the organization of biological molecules has profound effects on cellular function: not only metabolic, but also physical and mechanical. Here, we discuss a variety of perturbations available to biologists in controlling protein, nucleotide, and membrane localization. These range from simple tags, fusions, and scaffolds to heterologous expression of compartments and other structures that confer unique physical properties to cells. Next, we relate these principles to those guiding the spatial environments outside of cells such as the extracellular matrix. Finally, we discuss new directions in building intercellular organizations to create novel symbioses. (Abstract)

Symbiotic consortia appeal to engineers for two reasons: (1) division of labor lends itself well to modularity, and (2) it is widely believed that consortia are more stable than mono-
cultures. In this vein, synthetic biologists have engineered consortia made up of different
strains of the same organism, as well as symbioses involving multiple species. (11)

Porcar, Manuel. The Hidden Charm of Life. Life. 9/1, 2019. An entry by a University of Valencia, Spain integrative biologist for a Synthetic Biology from Living Computers to Terraformation issue, see Jamie Davies herein for more. It begins by noting a present metaphor mix of machine and organic analogies and metaphors that it would do well going forward. As an example, “factory” is often applied to cellular metabolism. See also Is Research on Synthetic Cells Moving to the Next Level? by Pasquale Stano in this issue for another take.

Synthetic biology is an engineering view on biotechnology, which has revolutionized genetic engineering. The field has seen a constant development of metaphors that tend to highlight the similarities of cells with machines. I argue here that living organisms, particularly bacterial cells, are not machine-like, engineerable entities, but, instead, factory-like complex systems shaped by evolution. A change of the comparative paradigm in synthetic biology from machines to factories, from hardware to software, and from informatics to economy is discussed. (Abstract)

Porcar, Manuel and Jorge Pereto. Nature versus Design: Synthetic Biology or How to Build a Biological Non-Machine. Integrative Biology. 8/451, 2016. We note this contribution by University of Valencia, Spain, systems biologists because it emphasizes that organisms are not machines. Life has internal causes and purposes aided by resilient modules and redundancies, it is not made or moved by external ways. In regard, this novel field ought not tend to make organic forms and ways more mechanical, rather it should proceed toward a more life-like artificial environment, broadly conceived. See also in this issue A Morphospace for Synthetic Organs and Organoids by Aina Olli-Vila, et al (8/485) and Build to Understand: Synthetic Approaches to Biology by Le-Zhi Wang, et al (8/394). OK

Porcar, Manuel, et al. The Ten Grand Challenges of Synthetic Life. Systems and Synthetic Biology. 5/1-2, 2011. In this new journal for the most major evolutionary transition, as vast possibilities open, senior researchers and proponents including Antoine Danchin, Steen Rasmussen, Andres Moya, and others, from Spain, France, Germany, England, and Denmark to Santa Fe, New Mexico, scope out various lineaments at this early advent so as to better guide, focus, communicate, and safely, respectfully, avail.

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