VII. Pedia Sapiens: A Genesis Future on Earth and in the Heavens

2. A Second Genesis: Life Begins Anew via an EarthWise Respectful Creativity

Mukai, Takahito, et al. Rewriting the Genetic Code. Annual Review of Microbiology. 71/557, 2017. Biochemists Mukai, Markus Englert, and Dieter Soll, Yale University and Marc Lajoie, University of Washington broach how the latest techniques can facilitate and commence an epochal moment whence human acumen can begin anew to modify life’s evolutionary genomic script. Some article sections are Natural Expansion of the Genetic Code, Orthogonal Translation Systems, Codon Reassessment, and Preparing for Radically Altered Genetic Codes.

The genetic code—the language used by cells to translate their genomes into proteins that perform many cellular functions—is highly conserved throughout natural life. Rewriting the genetic code could lead to new biological functions such as expanding protein chemistries with noncanonical amino acids (ncAAs) and genetically isolating synthetic organisms from natural organisms and viruses. It has long been possible to transiently produce proteins bearing ncAAs, but stabilizing an expanded genetic code for sustained function in vivo requires an integrated approach: creating recoded genomes and introducing new translation machinery that function together without compromising viability or clashing with endogenous pathways. In this review, we discuss design considerations and technologies for expanding the genetic code. The knowledge obtained by rewriting the genetic code will deepen our understanding of how genomes are designed and how the canonical genetic code evolved. (Abstract)

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.

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.

Rabinowitch, Ithai. What Would a Synthetic Connectome Look Like? Physics of Life Reviews. Online July 2, 2019. A Hebrew University of Jerusalem senior medical neurobiologist broaches an initial consideration of how collective human programs might carry forth the formative principles of our own brains, as we have just learned, into new, and improved cerebral procreations. The essay ranges from neural and genetic bases to ethical issues, within a sense that this endemic inter-relational quality is a distinctive feature.

A major challenge of contemporary neuroscience is to unravel the structure of the connectome, the ensemble of neural connections between different functional units of the brain, and to reveal how this structure relates to brain function. The synthetic biology approach comprises the assembly of new biological systems out of elementary biological parts, which is dubbed forward-engineering. The rationale is that building a system can be a good way to gain understandings of how that system works. As the fields of connectomics and synthetic biology are independently growing, I propose to beneficially combine them to create synthetic connectomics. This union could be a unifying platform for unraveling the complexities of brain operation and could provide an opportunity for empirically exploring theoretical predictions about network function. (Abstract excerpt)

Rampioni, Giordano, et al. A Synthetic Biology Approach to Bio-Chem-ICT: First Moves Towards Chemical Communication Between Synthetic and Natural Cells. Natural Computing. Online May, 2014. We select this paper among many as an example that theories and projects to commence a second nature via informed human intention might help explain how life began and arose in the first place. Italian systems biologists including Luisa Damaino go on to convey, as common today, how biology and evolution is better understood from substantial matter to cellular beings, universe to us, in terms of informational-computational phenomena and programs. This course is said to reflect every organism’s innate autopoietic autonomy, which we scientists might now respectfully appreciate, continue and enhance.

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