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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Recent Additions

VIII. Earth Earns: An Open Participatory Earthropocene to Ecosmocene CoCreativity

2. Second Genesis: Emergent LifeKinder Proceeds to an Aware BioGenetic Phase

Doursat, Rene, et al. Morphogenetic Engineering: Toward Programmable Complex Systems. Berlin: Springer, 2013. Rene Doursat, CNRS and Ecole Polytechnique, Paris, with Olivier Michel, Universite Paris, and Hiroki Sayama, Binghamton SUNY, and colleagues gather a volume to propose both novel understandings of life’s self-organizing evolutionary embryogenesis, so as to then intentionally apply these natural principles for recreating a better, more livable world. In regard, organic aspects such as nanomaterial, medical, agricultural, urban system domains receive specific treatment. The editor’s introductory chapter is “Morphogenetic Engineering: Reconciling Self-Organization and Architecture,” Other contributions are “Programming Self-Assembling Systems via Physically Encoded Information” by Navneet Bhalla and Peter Bentley and “Embryomorphic Engineering: Emergent Innovation Through Evolutionary Development” by Rene Doursat, et al. As the Abstracts next convey, it is worth notice that an inherent generative spontaneity is seen at work in life’s nonlinear emergence, which is evidentially traced to and rooted in conducive physical and chemical substrates.

Generally, phenomena of spontaneous pattern formation are random and repetitive, whereas elaborate devices are the deterministic product of human design. Yet, biological organisms and collective insect constructions are exceptional examples of complex systems that are both architectured and self-organized. Can we understand their precise self-formation capabilities and integrate them with technological planning? Can physical systems be endowed with information, or informational systems be embedded in physics, to create autonomous morphologies and functions? This book is the first initiative of its kind toward establishing a new field of research, Morphogenetic Engineering, to explore the modeling and implementation of “self-architecturing” systems. Particular emphasis is set on the programmability and computational abilities of self-organization, properties that are often underappreciated in complex systems science—while, conversely, the benefits of self-organization are often underappreciated in engineering methodologies. (Introduction Abstract)

Throughout nature, in both the inorganic and organic realms, complex entities emerge as a result of self-assembly from decentralised components governed by simple rules. Natural self-assembly is dictated by the morphology of the components and the environmental conditions they are subjected to, as well as the physical and chemical properties of their components and environments—their information. Components, their environment, and the interactions among them form a system, which can be described as a set of simple rules. The process of self-assembly is equivalent to a physical computation, through the interaction and transformation of physically and chemically encoded information. (Bhalla, Bentley Abstract)

Embryomorphic Engineering, a particular instance of Morphogenetic Engineering, takes its inspiration directly from biological development to create new robotic, software or network architectures by decentralized self-assembly of elementary agents. At its core, it combines three key principles of multicellular embryogenesis: chemical gradient diffusion (providing positional information to the agents), gene regulatory networks (triggering their differentiation into types, thus patterning), and cell division or aggregation (creating structural constraints, thus reshaping). In all cases, the specific genotype shared by all the agents makes the phenotype’s complex architecture and function modular, programmable and reproducible. (Doursat, et al, Abstract)

Draxler, Breanna. Life as We Grow It. Discover Magazine. October, 2013. An extensive report upon the potentials and perils of “Synthetic Biology,” as auspicious abilities to make over everything and everyone burst upon us. To get a handle and march on it, the magazine convened in July at UC Berkeley, aided by the Synberc consortium, scientists and ethicists George Church, Douglas Densmore, Drew Endy, Steve Evans, Jay Keasling, Christina Smolke, Virginia Ursin, Christopher Voigt, and Laurie Zoloth, along with futurist Juan Enriquez. Topical sections are Evolution by Design, Biology Reimagined, Designing Living Solutions, Programming Life, Replacing Petroleum, Promises and Implications, for which we need a tandem advance of monitored research with respectful considerations. But may one wonder what kind of an unfinished cosmos, by virtue of an emergent collective knowledge, then proceeds to cure, heal, correct, remake, improve, immortalize, the contingent fish on feet persons from which it arose?

Dyson, Freeman. Our Biotech Future. New York Review of Books. July 19, 2007. Our octogenarian Renaissance person surveys the entirety of past, present and future genetic evolution. Drawing on the biological wisdom of Carl Woese, who avers that life is not a machine but graced by dynamic organization, three phases can now be seen. When replicating molecules first appeared in ancient protocells, gene transfer was ‘horizontal’ in kind taking place readily across these prokaryotic vesicles. As nucleated cells and multicellular organisms arose, the Darwinian mode of ‘vertical’ asexual and sexual transfer proceeded until this day. With the advent of potent biotechnological capacities, a third phase is dawning which might again take to the sideways course. Dyson contends that much palliative benefit could result from its careful, sustainable implementation. An example cited is a recovery of village agriculture via appropriately modified crops in many lands of Africa and the Asian subcontinent, which would help reverse the flight to fetid mega-cities.

Egbert, Robert and Eric Klavins. Fine-Tuning Gene Networks using Simple Sequence Repeats. Proceedings of the National Academy of Sciences. 109/16817, 2012. University of Washington bioengineers develop effective methods for tweaking gene expression or harmony by way of “variable-length repeating DNA spacers.” In the same issue is a review “Making Gene Circuits Sing” by Arthur Prindle and Jeff Hasty. Who are we peoples to lately appear and be able to take up such editing and orchestrating of nature’s procreative genotype code?

The parameters in a complex synthetic gene network must be extensively tuned before the network functions as designed. Here, we introduce a simple and general approach to rapidly tune gene networks in Escherichia coli using hypermutable simple sequence repeats embedded in the spacer region of the ribosome binding site. By varying repeat length, we generated expression libraries that incrementally and predictably sample gene expression levels over a 1,000-fold range. We demonstrate the utility of the approach by creating a bistable switch library that programmatically samples the expression space to balance the two states of the switch, and we illustrate the need for tuning by showing that the switch’s behavior is sensitive to host context. Further, we show that mutation rates of the repeats are controllable in vivo for stability or for targeted mutagenesis—suggesting a new approach to optimizing gene networks via directed evolution. This tuning methodology should accelerate the process of engineering functionally complex gene networks. (Abstract)

Emani, Prashant, et al. Quantum Computing at the Frontiers of Biological Sciences. arXiv:1911.07127. Eighteen system geneticists from across the USA and onto the UK, including Marc Gerstein and Alan Aspuru-Guzik, scope out how the latest informational processing abilities by the unique properties of this physical realm can foster a new speedy phase of decipherment, discovery and biocreativity. Case examples are then drawn from an organismic span of genomes (GWAS) to cells, organic systems, brains, consequent behaviors and onto integrations across disciplines.

The search for meaningful structure in biological data is aided by advances in computational technology and data science. However, challenges arise as we push the limits of scale and complexity in biological problems. Classical computing hardware and algorithms continue to progress, but new paradigms to circumvent current barriers to processing speed are needed. Here we seek to innovate quantum computation and quantum information methods with polynomial and exponential speedups by way of machine learning. In regard, we explore the potential for quantum computing to aid in the merging of insights from genetics, genomics, neuroimaging and behavioral phenotyping. We highlight the need for a common language between biological data analysis and quantum computing algorithms across the biological sciences. (Abstract excerpt)

Erlich, Yaniv and Dina Zielinski. DNA Fountain Enables a Robust and Efficient Storage Architecture. Science. 355/950, 2017. New York Genome Center, Columbia University, bioinformatic geneticists achieve a novel method by which to better access the extraordinary ability of nucleotide molecules to store vast amounts of digital data.

DNA has the potential to provide large-capacity information storage. However, current methods have only been able to use a fraction of the theoretical maximum. Erlich and Zielinski present a method, DNA Fountain, which approaches the theoretical maximum for information stored per nucleotide. They demonstrated efficient encoding of information—including a full computer operating system—into DNA that could be retrieved at scale after multiple rounds of polymerase chain reaction. (Editor)

Falk, Johannes , et al. Context in Synthetic Biology. Journal of Chemical Physics. 180/024106, 2019. Technical University of Dormstadt biophysicists including Barbara Drossel scope out ways to intentionally carry forth the latest complexity theories so we can proceed to make Earth life better. It might also be noted that a 2001 paper, Biological Evolution and Statistical Physics, by B. Drossel in Advances in Physics (50/2) was one of the first of its integrative kind in a physics journal (second quote) which can show how far and fast this global project has grown and advanced.

Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its dynamics is therefore affected by potentially unknown interactions with the environment. It is well-known that the presence of the environment not only causes extrinsic noise but also memory effects, which means that the dynamics of the subnetwork is affected by its past states via a memory function that is characteristic of the environment. We study several generic scenarios for the coupling between a small module and a larger environment, with the environment consisting of a chain of mono-molecular reactions. By mapping the dynamics of this coupled system onto random walks, we are able to give exact analytical expressions for the arising memory functions. Hence, our results give insights into the possible types of memory functions and thereby help to better predict subnetwork dynamics. (Falk Abstract)

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. (Drossel 2001 Abstract)

Feldman, Aaron and Floyd Romesberg. Expansion of the Genetic Alphabet: A Chemist’s Approach to Synthetic Biology. Accounts of Chemical Research. Online December, 2017. In a breakthrough paper which achieved much press coverage, senior Scripps Research Institute chemists describe capabilities by which to commence an edit and rewrite of nature’s original four letter code. And if to wax about it , over some 13.8 billion cosmic years and 4 billion Earth years, life’s evolutionary emergence just now reaches our moment of intentional humankinder continuance for all futures. In regard, human beings may gain an apparent identity, which we need realize by ourselves, in some way as procreative bigender genomes. What am I trying to say – here is an example of a salutary discovery and destiny for human and universe in our midst for the asking and witness.

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)

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.

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