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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VIII. Earth Earns: An Open Participatory Earthropocene to Astropocene CoCreative Future

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

Knox, Margaret. The Genie Gene. Scientific American. December, 2014. A popular report on the discovery by Jennifer Doudna, UC Berkeley and Emmanuelle Carpentier, Umea University, Sweden of a revolutionary way to easily alter and edit genetic material. Known as CRISPR for “clustered, regularly interspaced, short palindromic repeats,” it mimics how bacteria employ immune defenses. The innovative research has won prizes, large grants, and is seen as a breakthrough medical advance.

Kösoglu-Kind,, Busra, et al.. A biological sequence comparison algorithm using quantum computers. arXiv:2303.13608. This entry by University of Applied Sciences in Economics and Management, Dusseldorf, IBM, Armonk, USA, European Organization for Nuclear Research (CERN), Geneva and IBM, I München, Germany computer scientists is an example of the latest frontiers of our Earthuman endeavors to provide rapid, whole scale genome sequences, and to gain new, beneficial abilities going forward.

Genetic information is encoded in a linear sequence of nucleotides, where mutations refer to changes in the DNA or RNA nucleotide sequence. Thus careful monitoring of virulence-enhancing mutations is essential. However, vast classical computing power is required to analyze large genetic sequences. Inspired by human perception of vision and pixel perception of images on quantum computers, we leverage these techniques to implement a pairwise sequence analysis. We present a method to display and analyze the similarity between two genome sequences on a quantum computer where a similarity score is calculated to determine the similarity between nucleotides. (Excerpt)

Krane, Dan and Michael Raymer. Fundamental Concepts of Bioinformatics. San Francisco: Benjamin Cummings, 2003. A general introductory text for this merger of computers and biology.

Lajoie, Marc, et al. Overcoming Challenges in Engineering the Genetic Code. Journal of Molecular Biology. 428/5B, 2016. Harvard Medical School and Yale University systems geneticists including George Church consider issues and concerns such as do we really know what we are doing, how and why to carefully proceed, and so on. And as someone who had a day job for decades as an engineer, this term is quite inapt for such genomic, biological, organismic mediations going forward. What better word might serve our own “evolutionary” narrative so as to begin, as we are meant to do, a new genesis recreation?

Withstanding 3.5 billion years of genetic drift, the canonical genetic code remains such a fundamental foundation for the complexity of life that it is highly conserved across all three phylogenetic domains. Genome engineering technologies are now making it possible to rationally change the genetic code, offering resistance to viruses, genetic isolation from horizontal gene transfer, and prevention of environmental escape by genetically modified organisms. We discuss the biochemical, genetic, and technological challenges that must be overcome in order to engineer the genetic code. (Abstract)

Lale, Rahmi, et al. A Universal Approach to Gene Expression Engineering. Synthetic Biology. 7/1, 2022. Twelve Norwegian University of Science and Technology, Trondheim and Bielefeld University Germany biochemists come up with a versatile method to parse genomic processes, as they gain a wider influence, so to better analyze and enhance. Thus a global intellect proceeds apace to intentionally continue and advance life’s grand genesis.

In this study, we provide a universal approach to Gene Expression Engineering (GeneEE) for creating artificial expression systems which creates artificial 5ʹ regulatory sequences (ARES). The ARES recruit RNA polymerase, related sigma factors and ribosomal proteins that result in a wide range of expression levels. To showcase the universality of the approach, we demonstrate that 200-nucleotide (nt)-long DNA with random composition can be used to generate functional expression systems in six bacterial species. (Abstract excerpt)

We demonstrate that using the GeneEE approach, artificial gene expression systems can be created in all seven investigated microbes utilizing six markers/reporters. The GeneEE approach relies on nature’s ability to detect functional sequences among a set of DNA with random DNA composition. In this aspect, the approach can be applied in any HoI, making it a universal and versatile strategy for creating artificial gene expres-sion systems capable of functionally expressing a wide range of CDSs in a variety of host microorganisms. (11)

Lau, Yu Heng, et al. Large-Scale Recoding of a Bacterial Genome by Iterative Recombineering of Synthetic DNA. Nucleic Acids Research. 45/11, 2017. As the quote notes, a 13 person team from colleges and companies including Jeffrey Way, Pamela Silver, and Elena Schafer, move beyond gene sequencing onto initial surveys of how to edit, reconceive, and expand the generative capacities of nucleotide systems. But “engineering” is an inappropriate, off-putting term. Rather as humankinder altogether begins to engage, decipher, and modify evolution’s original genetic literacy, as it seems we are meant to do, a better image might be as creative co-authors and curators as we learn to read and write this natural language.

The ability to rewrite large stretches of genomic DNA enables the creation of new organisms with customized functions. However, few methods currently exist for accumulating such widespread genomic changes in a single organism. In this study, we demonstrate a rapid approach for rewriting bacterial genomes with modified synthetic DNA. (Abstract) The next widely anticipated breakthrough in genetic engineering is the ability to rapidly rewrite the genomes of industrially relevant microbes, plants, and animals. Rewriting entire genomes will deepen our understanding of the genetic code and dramatically transform human health, food and energy production, and our environment. A major challenge identified by the Genome Project-Write consortium is the efficiency of building and testing large modified genomes. (1)

Lawson, Christopher, et al. Common Principles and Best Practices for Engineering Microbiomes. Nature Reviews Microbiology. 17/725, 2019. In a Tractability and Translation section, a thirteen member team from the Universities of Wisconsin, Montana, Tennessee, Minnesota, Purdue, UC Santa Barbara, Michigan, Delft, and Lawrence Berkeley Labs scope out procedures as our composite human intellect begins to manage and make anew our microbial inhabitants. Some are symbiotic, but others are viral invasive. Thus, an historic phase of palliative and beneficial apply, with all due respects, is in commencement. See also Scientists’ Warning to Humanity: Microorganisms and Climate Change by Ricardo Cavicchioli, et al in this journal (June 18, 2019).

In a Tractability and Translation section, a thirteen member team from the Universities of Wisconsin, Montana, Tennessee, Minnesota, Purdue, UC Santa Barbara, Michigan, Delft, and Lawrence Berkeley Labs scope out procedures as our composite human intellect begins to manage and make anew our microbial inhabitants. Some are symbiotic, but others are viral invasive. Thus, an historic phase of palliative and beneficial apply, with all due respects, is in commencement. See also Scientists’ Warning to Humanity: Microorganisms and Climate Change by Ricardo Cavicchioli, et al in this journal (June 18, 2019).

Ledford, Heidi. CRISPR, the Disruptor. Nature. 522/21, 2015. We note this survey article within a topical section to report this breakthrough fast, low cost, easy and effective method of genetic editing and regulation to add, delete, or change specific gene sequences. CRISPR means “clustered regularly interspaced short palindromic repeats.” Among many reports, see also Editing Humanity in the August 22, 2015 issue of The Economist. One wonders what kind of self-sequencing uniVerse this might be, whence a human phenomenon can learn to read, curate and intentionally begin a new genesis creation.

Lepora, Nathan, et al. The State of the Art in Biomimetics. Bioinspiration & Biomimetics. 8/013001, 2013. Since evolutionary Nature has a billion years experience, we would be well advised and inspired to “mimic,” and intentionally continue on such biological design principles for better, more truly viable, organic societies. In this 21st century dedicated journal, University of Sheffield, UK, and Universitat Pompeu Fabra, Synthetic Perceptive, Emotive and Cognitive Systems, Spain imagineers provide a succinct survey of past art and future promise for this imperative project.

Biomimetics is a research field that is achieving particular prominence through an explosion of new discoveries in biology and engineering. The field concerns novel technologies developed through the transfer of function from biological systems. To analyze the impact of this field within engineering and related sciences, we compiled an extensive database of publications for study with network-based information analysis techniques. Criteria included publications by year and journal or conference, and subject areas judged by popular and common terms in titles. Our results reveal that this research area has expanded rapidly from less than 100 papers per year in the 1990s to several thousand papers per year in the first decade of this century. Moreover, this research is having impact across a variety of research themes, spanning robotics, computer science and bioengineering. In consequence, biomimetics is becoming a leading paradigm for the development of new technologies that will potentially lead to significant scientific, societal and economic impact in the near future. (Abstract)

Li, Heng and Richard Durbin. Genome assembly in the telomere-to-telomere era. arXiv:2308.07877. Dana Farber Cancer Institute, Boston biomedical to informatic researchers provide a detailed survey of this latest frontier as collaborative human acumen begins to parse, edit and read/write anew as a beneficial second genesis procreativity. And we cite the quote line that this work would not be possible a few years ago to note how fast science is advancing, which this Earthica intends to document.

De novo assembly is the process of reconstructing the genome sequence of an organism. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics. Until recently, genomes were composed of fragments with a few megabases but now long-reads enable near complete chromosome-level assembly, also known as telomere-to-telomerey. Here we review recent progress and how to derive near telomere-to-telomere assemblies and discuss potential future developments. (Abstract)

Thanks to the availability of PacBio HiFi reads and ONT ultra-long reads, the quality of de novo
assembly has improved dramatically in the past two years. Now a fully automated assembler
can phase and assemble some chromosomes from telomere to telomere for diploid mammals
and other species with large genomes. This was unthinkable in mid 2020. (11)

It is important to note that a complete assembly only sets a start for downstream biological
discoveries. While genome assembly has progressed rapidly, genome alignment and annotation tools have lagged far behind. We hope to see continued development of these tools in the future to realize the full power of (near) complete assembly. (12)

Li, yang, et al. Cooperativity Principles in Self-Assembled Nanomedicine. Chemical Reviews. Online April, 2018. UT Southwestern Medical Center and Peking University pharmaceutical biophysicists write a 24 page illustrated tutorial to these frontiers of “supramolecular self-assembly” as human intellect begins to take over for palliative and procreative benefit. By this view, biochemical such as enzymes similarly appear to cooperate with each other as they induce vital phase transitions. Nucleic acids are particularly amenable at they form many structures via cooperative aggregations beyond the double helix.

Nanomedicine is a discipline that applies nanoscience and nanotechnology principles to the prevention, diagnosis, and treatment of human diseases. Self-assembly of molecular components is becoming a common strategy in the design and syntheses of nanomaterials for biomedical applications. In both natural and synthetic self-assembled nanostructures, molecular cooperativity is emerging as an important hallmark. In many cases, interplay of many types of noncovalent interactions leads to dynamic nanosystems with emergent properties where the whole is bigger than the sum of the parts. In this review, we provide a comprehensive analysis of the cooperativity principles in multiple self-assembled nanostructures. In selected systems, we describe the examples on how to leverage molecular cooperativity to design nanomedicine with improved diagnostic precision and therapeutic efficacy in medicine. (Abstract)

Loman, Nicholas and Mark Pallen. Twenty Years of Bacterial Genome Sequencing. Nature Reviews Microbiology. 13/12, 2015. University of Birmingham and Warwick Medical School microbiologists proffer a cogent retrospect of progress from mid 1990s techniques through their iterative and revolutionary sophistication to today’s hyper-automation and computation. The British company Oxford Nanopore (search herein), which the lead author is affiliated with, is given as an instance of the latest methods. From their website under Publications, a YouTube talk by Loman with A Sequencing Singularity title can be accessed.

Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond. (Abstract)

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