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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VII. Pedia Sapiens: A Genesis Future on Earth and in the Heavens

2. Second Genesis: Life Begins Again via Our Repectful Creativity

Mind Over Matter has reviewed awesome new abilities to fathom, encode, take up and recommence an animate physical creation. Second Genesis moves on to report and document similar palliative and positive genetic and biological capabilities. We also make note of ethical concerns, many more throughout this site, which need play a major, guiding role. As evolution may finally reach its emergent term of geonatal (and cosmonatal) self-cognizance, our collective, sapient knowledge can help mitigate, revise, and enhance life’s genotype source and phenotype biology. Life’s long, arduous contingency phase, as a cobbled, tinkered, brutal yet an oriented gestation, might at last reach its intended curative and creative resolve and fulfillment. A Second Genesis phrase is proffered as most distinguished by a successful passage of the parental cosmome bigender endowment to our kinderkind edification.

FLinT Center for Fundamental Living Technology. flint.sdu.dk. A University of Southern Denmark group led by Steen Rasmussen (search), Pierre-Alain Monnard (search), and Carsten Svaneborg. The Science Advisory Board is made up of Mark Bedau, David Deamer, John McCaskill, and Norman Packard, who are leading researchers in this fledgling endeavor of cosmic biomimetics.

Our scientific mission is to analyze and understand the creative forces in natural- as well as in human-made systems. This is mainly done through the study of self-organizing processes. Our main focus is to assemble the components of minimal living systems. In physico-chemical systems this means assembling protocells bottom up from inorganinc and organic materials. In hardware systems we investigate implementation of e.g. 3D printers able to print themselves, while in computational systems we study the emergence of replicators. Our long-term technological vision is to develop the foundation for a living technology characterized by robustness, autonomy, energy efficiency, sustainability, local intelligence, self-repair, adaptation, self-replication and evolution, all properties current technology lack, but living systems possess.

Genome Engineering: Cutting-Edge Research and Applications. www.faseb.org/src/micro/Site/GenEng/Home.aspx. A mid June 2016 international conference sponsored by the Federation of American Society for Experimental Biology FASEB at the Lisbon Marriott Hotel, Portugal. The main keynote speaker is Emmanuelle Charpentier, the co-conceiver with Jennifer Doudna of CRISPR genome editing, and now director of the MPI for Infection Biology. The array of sessions and talks are all about this plethora of novel, inviting technologies that have opened for human, social, and environmental avail. Typical papers are Programming the Third Genome through Mitochondrial DNA Editing by Stephen Ekker (Mayo Clinic), The Genome Engineering Revolution and Plant Agriculture by Dan Voytas (University of Minnesota), and Epigenome Editing with ZFP and CRISPR by Qingzhou (Millipore Sigma).

Genome engineering is a rapidly growing discipline that seeks to develop new technologies for the precise manipulation of genes and genomes in cellula and in vivo. In addition to its utility for advancing our understanding of basic biology, genome engineering has numerous real-world applications, ranging from correction of disease-causing mutations in humans to engineering plants that better provide fuel, food and industrial raw materials. The first clinical trials and patient treatments using genome engineering approaches are now a reality. The scope of this meeting is expansive, encompassing multiple approaches for modifying genomes – from transgenesis and gene targeting to the creation of synthetic genomes. The experimental models featured include bacteria, fungi, model organisms (e.g.—Drosophila, C. elegans, zebrafish, mice, rats), plants, humans, and animals including livestock. We anticipate that this diversity of approaches and experimental systems will create a stimulating meeting environment that will enable new insights and advance the field.

Oxford Nanopore Technologies Limited. nanoporetech.com. This is a British company in Oxford Science Park since 2005 at the frontiers of public, beneficial genetic capabilities. An article A Genome in the Hand in The Economist (Dec. 9, 2017) cites their MinION device as a low cost, useable way of personal DNA sequencing which, for example, now serves medics in rural Africa. A Publications icon connects with technical papers such as Efficient Generation of Complete Sequences of MDR-encoding Plasmids and Automated Eukaryotic Genome Annotation based on Long-Read cDNA Sequencing.

Aktipis, Athena et al. Cancer across the Tree of Life: Cooperation and Cheating in Multicellularity. Philosophical Transactions of the Royal Society B. 370/Issue 1673, 2015. A lead article by UC San Francisco, University of Kiel, University of Montpellier, and University of Maryland researchers about advances in the study and resolve of this disease by way of complex systems science and the major transitions paradigm. These evolutionary and life history expansions, not possible much earlier, achieve a novel mathematical theory and natural basis for this virulent cellular aberration. Some papers are Infection and Cancer in Multicellular Organisms by Paul and Holly Ewald, and Comparative Oncology: What Dogs and Other Species can Teach us about Humans with Cancer by Joshua Schiffman and Matthew Breen. In retrospect, a worldwide palliative knowledge emerges which can be fed back to succor and cure the fraught beings it arose from. What kind of a genesis cosmos can learn and proceed, via a human phenomenon, to cure itself so as take over its future creation?

Multicellularity is characterized by cooperation among cells for the development, maintenance and reproduction of the multicellular organism. Cancer can be viewed as cheating within this cooperative multicellular system. Complex multicellularity, and the cooperation underlying it, has evolved independently multiple times. We review the existing literature on cancer and cancer-like phenomena across life, not only focusing on complex multicellularity but also reviewing cancer-like phenomena across the tree of life more broadly. We find that cancer is characterized by a breakdown of the central features of cooperation that characterize multicellularity, including cheating in proliferation inhibition, cell death, division of labour, resource allocation and extracellular environment maintenance (which we term the five foundations of multicellularity). Cheating on division of labour, exhibited by a lack of differentiation and disorganized cell masses, has been observed in all forms of multicellularity. This suggests that deregulation of differentiation is a fundamental and universal aspect of carcinogenesis that may be underappreciated in cancer biology. Understanding cancer as a breakdown of multicellular cooperation provides novel insights into cancer hallmarks and suggests a set of assays and biomarkers that can be applied across species and characterize the fundamental requirements for generating a cancer. (Abstract)

Evolution, Synthetic Biology, Protein Engineering, Biocatalysis, Biofuels. www.che.caltech.edu/groups/fha. The website for the Frances H. Arnold (Chemical Engineering) Research Group at the California Institute of Technology. A good example of the use of evolutionary principles and algorithms to achieve novel biomolecular entities of service to society in many areas, as the title conveys. I have recently heard Prof. Arnold speak at Smith College, and upon reflection, one gets the impression of material and biological creation passing to conscious, intentional human facilitation. (If the URL does not work, just Google her name.)

Arranz-Gilbert, Pol, et al. Next-Generation Genetic Code Expansion. Current Opinion in Chemical Biology. 46/1, 2018. Yale University biogeneticists associated with Mark Gerstein and Gunter Wagner scope out new abilities to modify, edit, rewrite, and expand so to carefully finesse “Genomically Recoded Organisms” (GROs). In a Synthetic Biology section, see also Expansion of the Genetic Code via the Genetic Alphabet by Vivian Dien, et al, and Synthetic Darwinism and the Aperiodic Crystal Structure by Nilesh Karalkar and Steven Benner (below).

Engineering of the translation apparatus has permitted the site-specific incorporation of nonstandard amino acids (nsAAs) into proteins, thereby expanding the genetic code of organisms. Conventional approaches have focused on porting tRNAs and aminoacyl-tRNA synthetases (aaRS) from archaea into bacterial and eukaryotic systems where they have been engineered to site-specifically encode nsAAs. These advances, together with the advent of engineered ribosomes and new molecular evolution methods, enable multisite incorporation of nsAAs and nonstandard monomers (nsM) paving the way for the template-directed production of functionalized proteins, new classes of polymers, and genetically encoded materials. (Abstract)

Baker, Monya. The Next Step for the Synthetic Genome. Nature. 473/403, 2011. The technology editor reports upon a pregnant age of human potentials to make genetic and biological life all over again. What manner of cosmos then after billions of years evolves we such beings able to “read and write” their own DNA code so as to continue creation in a radically intentional way?

Bates, Maxwell, et al. Genetic Constructor: An Online DNA Design Platform. ACS Synthetic Biology. Online October 12, 2017. We cite this paper by a dozen researchers from Autodesk Life Sciences, San Francisco, University of Edinburgh, and Radiant Genomics, Emeryville, CA to notice and report the extent to which a global human intellect is advancing and expanding this broadly conceived naturome literacy as a basis for a new intentional procreation.

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community. (Abstract)

Bedau, Mark and Emily Parke, eds. The Ethics of Protocells. Cambridge: MIT Press, 2009. Reviewed more in The Origin of Life, what to do about this instant ability to bring about a new creation.

Bedau, Mark, et al. Introduction to Recent Developments in Living Technology. Artificial Life. 19/3-4, 2013. With John McCaskill, Norman Packard, Emily Parke and Steen Rasmussen, a special issue to update and expand this American and European project with a Santa Fe Institute – University of Southern Denmark nexus to intentionally re-imagine a humane abidance much more life, creature, socially, and environmentally healthy. In regard, throughout the writings a respectful sense of cultural and ethical implications abides. See for example “Living in Living Cities” by Carlos Gershenson, and “Bespoke Physics for Living Technology” by David Ackley.

In the physics of the natural world, basic tasks of life, such as homeostasis and reproduction, are extremely complex operations, requiring the coordination of billions of atoms even in simple cases. By contrast, artificial living organisms can be implemented in computers using relatively few bits, and copying a data structure is trivial. Of course, the physical overheads of the computers themselves are huge, but since their programmability allows digital “laws of physics” to be tailored like a custom suit, deploying living technology atop an engineered computational substrate might be as or more effective than building directly on the natural laws of physics, for a substantial range of desirable purposes. This article suggests basic criteria and metrics for bespoke physics computing architectures, describes one such architecture, and offers data and illustrations of custom living technology competing to reproduce while collaborating on an externally useful computation. (Ackley Abstract)

This article presents an overview of current and potential applications of living technology to some urban problems. Living technology can be described as technology that exhibits the core features of living systems. These features can be useful to solve dynamic problems. In particular, urban problems concerning mobility, logistics, telecommunications, governance, safety, sustainability, and society and culture are presented, and solutions involving living technology are reviewed. A methodology for developing living technology is mentioned, and supraoptimal public transportation systems are used as a case study to illustrate the benefits of urban living technology. Finally, the usefulness of describing cities as living systems is discussed. (Gershenson Abstract)

Bedau, Mark, et al. Living Technology. Artificial Life. 16/1, 2010. With co-authors John McCaskill, Norman Packard, and Steen Rasmussen, whose common link could be the European Center for Living Technology, an entry to leading edges of the mind takeover of matter so as to (re)create and carry forth a better, more organic and humane, civilization.

The concept of living technology—that is, technology that is based on the powerful core features of life—is explained and illustrated with examples from artificial life software, reconfigurable and evolvable hardware, autonomously self-reproducing robots, chemical protocells, and hybrid electronic-chemical systems. We define primary (secondary) living technology according as key material components and core systems are not (are) derived from living organisms. Primary living technology is currently emerging, distinctive, and potentially powerful, motivating this review. We trace living technology's connections with artificial life (soft, hard, and wet), synthetic biology (top-down and bottom-up), and the convergence of nano-, bio-, information, and cognitive (NBIC) technologies. We end with a brief look at the social and ethical questions generated by the prospect of living technology. (89)

Benner, Steven, et al. Alternative Watson-Crick Synthetic Genetic Systems. Cold Spring Harbor Perspectives in Biology. 8/11, 2016. A Foundation for Applied Molecular Evolution, Florida, research team proposes an “artificially expanded genetic information system” AEGIS to begin some 63 years later to wholly rewrite nature’s genome code. The project takes on the guise of preparing a much larger, broadly conceived, edition to inform our novel evolutionary recreation. See also The Need for Integrated Approaches in Metabolic Engineering by Anna Lechner, et al in the same issue (Abstract below).

In its “grand challenge” format in chemistry, “synthesis” as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work. (Benner Abstract)

This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must be considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the “system” that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes. (Lechner Abstract)

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