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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
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VIII. Pedia Sapiens: A New Genesis Future

2. Second Genesis: Life Begins Anew via an EarthWise CoCreativity

Bhasin, Devesh and Daniel McAdams. The Characterization of Biological Organization, Abstraction and Novelty in Biomimetic Design. Design. 2/4, 2018. In this new MDPI online journal, in a topical Advances in Biologically Inspired Design issue, Texas A&M University engineers at once review prior creativities and solutions of evolutionary nature, so as to intentionally avail and carry forth to a better futurity. See also the MDPI journal Biomimetics which emphasizes more specific examples.

Through a billion year evolution, a latent record of successful and detailed design practices has developed in nature. The endeavors to exploit this resource have resulted in successful products in various fields including, but not limited to, networking, propulsion, surface engineering, and robotics. In this work, a study of existing biomimetic designs has been carried out according to the biological organizational level, the abstraction level, and a novelty measure. Through this review and categorization, we recognize patterns in existing biomimetic and bio-inspired products by analyzing their cross-categorical distribution. Using the distribution, we identify the categories which yield novel bio-inspired designs. (Abstract excerpt)

Biologically-inspired design is a design philosophy that encourages us to learn from nature, and results in the discovery of non-conventional solutions to problems that are often more efficient, economic, and elegant. Taking inspiration from nature has made (and can make) valuable contributions to engineering. In the last few decades, there has been increased attention on the significant technical innovations that can result from biological inspiration. This Special Issue is focused on the techniques, approaches and theories that facilitate biologically inspired design for engineering applications. Manuscript submissions on original research and literature reviews in the areas mentioned as keywords below are highly encouraged. (Issue Proposal)

Biondi, Elisa and Steven Benner. Artificially Expanded Genetic Information Systems for New Aptamer Technologies. Biomedicines. 6/2, 2018. It is now known that life’s four letter G A T C code, while universally in effect and enough to get us here, is an arbitrary sufficiency. In this MDPI online journal, in an Engineering Aptamers for Biomedical Applications issue, Foundation for Applied Molecular Evolution, Florida bioresearchers (search SB) consider ways to read, expand, enhance and begin to rewrite anew. From our 2020 vista, it might seem that a family genesis ecosmos wants our homo to Anthropo sapience to move from an inefficient stochastic (tinkered) past to an intentional, respectfully guided procreation. See also Aptamer Cell-Based Selection by Silvia Catuogno and Carla Esposito in this issue. A popular review of this work, along with F. Romesberg below, is Life, Rewritten by James Crow in the New Scientist (December 8, 2018).

Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”

Aptamers are high affinity single-stranded DNA/RNA molecules, produced by a combinatorial procedure named SELEX (Systematic Evolution of Ligands by Exponential enrichment), that are emerging as promising diagnostic and therapeutic tools.

Blain, J. Craig and Jack Szostak. Progress Toward Synthetic Cells. Annual Review of Biochemistry. Online March, 2014. As the Abstract notes, Massachusetts General Hospital, Center for Computational and Integrative Biology, researchers now predict, after years of approaches and trials, that the intentional new creation of living systems from nucleotides, proteins, microbes, and so on, is now a matter of time and endeavor. This is notable since Szostak received the 2009 Nobel Prize in Chemistry.

The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that the synthesis of life is now a realistic goal. Protocell research, fueled by advances in the biophysics of primitive membranes and the chemistry of nucleic acid replication, is providing new insights into the origin of cellular life. Parallel efforts to construct more complex artificial cells, incorporating translational machinery and protein enzymes, are providing information about the requirements for protein-based life. We discuss recent advances and remaining challenges in the synthesis of artificial cells, the possibility of creating new forms of life distinct from existing biology, and the promise of this research for gaining a deeper understanding of the nature of living systems. (Abstract)

Bonomo, Melia and Michael Deem. The Physicist’s Guide to One of Biotechnology’s Hottest New Topics: CRISPR-Cas. arXiv:1712.09865. Rice University biophysicists (search MD) offer a 64 page perspective about adaptive topologies, immunity, genetic expression, interference, memories, and other relevant properties, which can be given a physical basis. An example is a notice of Markov mathematics in genomic phenomena. By their lights, a Lamarckian-type evolutionary process may then become apparent.

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. Here we review a large body of CRISPR-Cas research to explore themes of evolution and selection, population dynamics, horizontal gene transfer, specific and cross-reactive interactions, cost and regulation, as well as non-defensive CRISPR functions that boost host cell robustness. Physical understanding of the CRISPR-Cas system will advance applications, such as efficient and specific genetic engineering, cell labeling and information storage, and combating antibiotic resistance. (Abstract)

Cameron, Ewen, et al. A Brief History of Synthetic Biology. Natures Reviews Microbiology. 12/5, 2014. Researchers at Howard Hughes Medical Institute, Boston provide a succinct retrospective and timeline survey so as to orient current and future endeavors and advances.

The ability to rationally engineer microorganisms has been a long-envisioned goal dating back more than a half-century. With the genomics revolution and rise of systems biology in the 1990s came the development of a rigorous engineering discipline to create, control and programme cellular behaviour. The resulting field, known as synthetic biology, has undergone dramatic growth throughout the past decade and is poised to transform biotechnology and medicine. This Timeline article charts the technological and cultural lifetime of synthetic biology, with an emphasis on key breakthroughs and future challenges. (Abstract)

Cepelewicz, Jordana. Is a Bigger Genetic Code Better? Get Ready to Find Out. Quanta. Online January 2, 2018. A science writer surveys the current burst of capabilities and projects to begin, after some 13.8 billion cosmic years, to edit, alter, redesign, and radically expand nature’s past version of four letters for 20 amino acids. The article is based on interviews with and reports by leading edge researchers such as Steven Benner, Floyd Romesberg, George Church, Stephen Freeland and Jason Chin. While “nature’s head start” of a good enough but trial and error code brought life and people to this point, a second genesis horizon opens before us which invites our respectfully informed editorial and authorial continuance.

The ability to increase the number of base pairs or amino acids changes the rules of that game entirely. Because even a binary system of bases would have been incredibly efficient, many researchers posit that primitive cellular life began with a single pair of bases, and evolved a second pair only after cellular systems became more complex and sophisticated, and a higher information density in DNA became advantageous. But why stop at four? “Would upgrading to six or eight bases be augmenting this?” Freeland asked. “You’d get even more information per length of genetic segment. It would be very interesting to see the ramifications of that, to see if it would actually make something better and more efficient. (5, sample text)

Chari, Raj and George Church. Beyond Editing to Writing Large Genomes. Nature Reviews Genetics. Online September, 2017. Harvard Medical School geneticists press on at these frontiers of church work as it becomes evident that we collaborative persons have an unlimited capacity to do this, while in turn this genetic realm seems most amenable for us to proceed.

Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort. Finally, we describe the features of an ideal platform and provide a roadmap to facilitate the efficient writing of large genomes. (Abstract)

Cheng, Feng, et al. Directed Evolution 2.0: Improving and Deciphering Enzyme Properties. Chemical Communications. 51/9760, 2015. In an issue edited by Nicholas Turner and Frances Arnold on this title topic, RWTH Aachen University researchers Chen, Leilei Zhu, and Ulrich Schwaneberg review the fertile field of a mindful “engineering” of protein forms and metabolic dynamics for organism, community and environment, broadly conceived. Again we cite as an entry among many, see also, e.g., Constitutional Self-selection from Dynamic Combinatorial Libraries in Aqueous Solution through Supramolecular Interactions by Jordi Sola in this journal (50/4564, 2014).

Directed evolution has matured to a routinely applied algorithm to tailor enzyme properties to meet the demands in various applications. In order to free directed enzyme evolution from methodological restraints and to efficiently explore its potential, many different strategies have been used in directed evolution campaigns. Analysis of directed evolution campaigns reveals that traditional approaches, in which several iterative rounds of diversity generation and screening are performed, are gradually replaced by strategies which require less time, less screening efforts, and generate a molecular understanding of the targeted properties. In this review, conceptual advances in knowledge generating directed evolution strategies are summarized, compared to each other and to traditional directed evolution strategies. Finally, a ‘KnowVolution’ (knowledge gaining directed evolution) termed strategy is proposed. (Cheng Abstract)

We describe the predominant formation of a specific constitution arising from the combination of building blocks with different topologies through disulphide chemistry in a Dynamic Combinatorial Library (DCL). The supramolecular interactions established by a zwitterionic cysteine moiety are responsible for the self-selection of one product from all the virtual members of a large library. (Sola Abstract)

Chin, Jason. Expanding and Reprogramming the Genetic Code. Nature. 550/53, 2017. The MRC Laboratory of Molecular Biology, Cambridge University geneticist reports upon his Centre for Chemical and Synthetic Biology project of systematic genetic code reprogramming, which is here explained in graphic technical expertise. For reference see his earlier Expanding and Reprogramming the Genetic Code of Cells and Animals in the Annual Review of Biochemistry (83/379, 2017), both Abstracts below.

Nature uses a limited, conservative set of amino acids to synthesize proteins. The ability to genetically encode an expanded set of building blocks with new chemical and physical properties is transforming the study, manipulation and evolution of proteins, and is enabling diverse applications, including approaches to probe, image and control protein function, and to precisely engineer therapeutics. Underpinning this transformation are strategies to engineer and rewire translation. Emerging strategies aim to reprogram the genetic code so that noncanonical biopolymers can be synthesized and evolved, and to test the limits of our ability to engineer the translational machinery and systematically recode genomes. (2017 Abstract)

Genetic code expansion and reprogramming enable the site-specific incorporation of diverse designer amino acids into proteins produced in cells and animals. Recent advances are enhancing the efficiency of unnatural amino acid incorporation by creating and evolving orthogonal ribosomes and manipulating the genome. Increasing the number of distinct amino acids that can be site-specifically encoded has been facilitated by the evolution of orthogonal quadruplet decoding ribosomes and the discovery of mutually orthogonal synthetase/tRNA pairs. Rapid progress in moving genetic code expansion from bacteria to eukaryotic cells and animals (C. elegans and D. melanogaster) and the incorporation of useful unnatural amino acids has been aided by the development and application of the pyrrolysyl–transfer RNA (tRNA) synthetase/tRNA pair for unnatural amino acid incorporation. (2014 Abstract)

Church, George and Ed Regis. Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. New York: Basic Books, 2012. A renowned Harvard Medical School geneticist and a science writer achieve an informed, universe to us, manifesto going forward as regnant humans may now begin a new creation, a second intentional genesis. A Prologue is “From Bioplastics to H. Sapiens 2.0,” with degrees of high tech computerese. Ch. 2 is “-3,500 Myr Archean: Reading the Most Ancient Texts and the Future of Living Software.” Similar scintillations follow evolution’s course of “natural genome engineering” all the way to an Epigenetic Epilogue: “The End of the Beginning, Transhumanism and the Panspermia Era.” An innovative concept of emergent life as “replicated complexity” or “replexity” is introduced, as pervasive genetic programs run and iterate. Dr. Church believes these advances have the potential to fully heal our maladies and diseases of soma, psyche, and indeed the biosphere, while quite aware of necessities for strident controls.

A brief review does not do justice. For starters, one may note that almost everyone cited is a man. This auspicious past, present, and future scenario is traversed without wonderment as to whatever may be going on, what could it all be and mean. On the face of it, a 21st century recognition of a greater nature deeply textual in its generative essence is recorded, albeit algorithmic in kind, which we are summoned to decipher (sequence), translate and read. The final bold quote is a rare allusion to a universal genome, which this website tries to document and convey. George Church says he is a speaker at Ray Kurzweil’s Singularity University (search). Is evolution mechanically “random” or is something like a (maternal) developmental gestation going on? Are collectively intelligent persons, as if genes and neurons, the phenomenal way a genesis uniVerse tries to consciously read, and carry forth, its own genetic code?

Just as computers were universal machines in the sense that given the appropriate programming they could simulate the activities of any other machine, so biological organisms approached the condition of being universal constructors in the sense that with appropriate changes to their genetic programming, they could be made to produce practically any imaginable artifact. A living organism, after all, was a ready-made, prefabricated production system that, like a computer, was governed by a program, its genome. Synthetic biology and synthetic genomics, the large-scale remaking of a genome, were attempts to capitalize on the facts that by making small changes in their genetic software a bioengineer can effect changes in their output. (4)

The original ancient text is written in the genomic DNA of every being alive today. That text is as old as life itself, and over 1030copies of it are distributed around the earth, from 5 kilometers deep within the earth’s crust to the edge of our atmosphere, and in every drop of the ocean. For such a significant text, its translation into modern languages began only recently, in the 1970s. Other naturalistic, geological, and astronomical resources can also be considered ancient texts. We surmise that the ancients text written by humans, as well as the texts of natural data, are all transmitting profound truths that are not intrinsically contradictory. We try to align and weave these various threads to help us understand the past and the future. (38)

My gut feeling is that, despite limitations of space and time, we humans can suddenly start to evolve thousands of times faster than the impressive Cambrian era, and that we can direct this diversity toward our material needs instead of letting it occur randomly. (73) As a general goal I propose that, as a minimum, we ought to avoid the loss of all intelligent life in the universe. (244) The genome should become not the genome of one lonely being or one planet. It should become the genome of the Universe. (244)

Cobb, Ryan, et al. Directed Evolution: An Evolving and Enabling Synthetic Biology Tool. Current Opinion in Chemical Biology. 16/285, 2012. University of Illinois biomolecular engineers propose to join techniques which deal with parts and circuits into inclusive complex pathways and systems. By an emphasis on such interactions, a new mode of assisted evolutionary processes can better begin this second genesis phase of informed human ingenuity. In the same issue an editorial A Different Life? stresses the value of this research for its palliative benefit to beings and societies.

Synthetic biology, with its goal of designing biological entities for wide-ranging purposes, remains a field of intensive research interest. However, the vast complexity of biological systems has heretofore rendered rational design prohibitively difficult. As a result, directed evolution remains a valuable tool for synthetic biology, enabling the identification of desired functionalities from large libraries of variants. This review highlights the most recent advances in the use of directed evolution in synthetic biology, focusing on new techniques and applications at the pathway and genome scale. (Abstract)

Cussat-Blanc, Sylvain, et al. Artificial Gene Regulatory Networks. Artificial Life. 24/4, 2018. Computational biologists S C-B, University of Toulouse, Kyle Harrington, University of Idaho, and Walter Banzhaf, Michigan State University (search) review past theories, present appreciations and future utilities of this genomic feature which dynamically links diverse nucleotides into equally real, functional systems. Its wide range covers Gene Regulation in Nature, GRNs in Cellular Physiology, Development, Evolution, and Epigenetics, GRN Internal Dynamics, and onto Artificial GRNs in Embryogenesis, braced by some 150 references. In regard, a broad train is taken from earlier biomolecular components to their 21st century integrative connections. In the later 2010s going forward, new ventures can be scoped out with palliative and procreative horizons.

In nature, gene regulatory networks are a key mediator between the information stored in the DNA of living organisms (their genotype) and the structural and behavioral expression this finds in their bodies, surviving in the world (their phenotype). They integrate environmental signals, steer development, buffer stochasticity, and allow evolution to proceed. In engineering, modeling and implementations of artificial gene regulatory networks have been an expanding field of research and development over the past few decades. This review discusses the concept of gene regulation, describes the current state of the art in gene regulatory networks, including modeling and simulation, and reviews their use in artificial evolutionary settings. We provide evidence for the benefits of this concept in natural and the engineering domains. (Abstract)

In summary, gene regulation has emerged as a key player in translating the information provided by an organism's inherited DNA into the structure (via growth and development) and behavior of that organism. Time scales range from seconds (in the case of the regulation of metabolism in neurons to thousands of years (in the case of evolutionary processes). Gene regulatory networks have been compared to the compilers of computer languages that translate code into behavior of the underlying machine. However, there is much more to the computational modeling of gene regulation, and this brings us to our next topic. (301)

Possibilities opened by gene regulatory networks are numerous. Whereas biologists have made significant progress in understanding the inner mechanisms of gene regulation in living systems, much remains to be discovered and understood. These mechanisms produce extremely complex behaviors in living organisms, from embryogenesis to the regulation of everyday life. Computer science and more specifically artificial intelligence will benefit from these discoveries and, with gene regulatory networks, could produce more intelligent behaviors for artificial agents in the near future. (321)

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