VIII. Earth Earns: An Open CoCreative Earthropocene to Astropocene PediaVerse

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

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)

Loman, Nick. The Sequencing Singularity. nanoporetech.com/resource-centre/videos/sequencing-singularity. A half hour 2016 YouTube presentation by the University of Birmingham genetic bioinformatics researcher, which is also available on the Oxford Nanopore site. The phrase was first cited in a 2015 Nature Reviews Microbiology article above to express how novel human abilities are beginning to curate, edit, and author anew life’s informative code.

Sequencing is poised to disrupt clinical practice. Whole swathes of diagnostic tests may eventually be replaced with a single assay - sequencing - as we reach the "sequencing singularity". I will review recent advances in the use of nanopore sequencing for clinical microbiology and human genetics, including our collaborations on viral and bacterial diagnostic sequencing, real-time surveillance, direct RNA and human whole-genome sequencing, and discuss the opportunities and barriers around moving to sequencing as a routine test in the clinic.

Nick works as Professor of Microbial Genomics and Bioinformatics in the Institute for Microbiology and Infection at the University of Birmingham. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. Nick has so far used high-throughput sequencing to investigate outbreaks of important Gram-negative multi-drug resistant pathogens, and recently helped establish real-time genomic surveillance of Ebola in Guinea. His current work focuses on the development of novel sequencing and bioinformatics methods to aid the interpretation of genome and metagenome scale data generated in clinical and public health microbiology. (NL website)

Maharbiz, Michel. Synthetic Multicellularity. Trends in Cell Biology. 22/12, 2012. A University of California, Berkeley, computer engineer considers early explorations of how complex systems biology might be availed to commence the respectful creation of utile multicellular organisms. The motivation and standard of behavior for such endeavors would be their service toward a better, sustainable world for life and people. See also in this dedicated issue “Directed Cytoskeleton Self-Organization” by Timothee Vignaud, et al, which alludes to independent principles of organic form and vitality.

Concluding Remarks That this has profound ethical and societal consequences cannot be overstated. There is – perhaps controversially – an ultimately ecological rationale for this vision. For the most part, the technological base created by the industrial revolution communicates poorly with the underlying organic technology of the planet. The rapid expansion of man-made, acellular, resource-consuming, and waste-producing constructs is in large part responsible for the ecological and climactic mess we are in. Mindful of the vast ethical and societal questions raised, it is worth considering a future wherein our homes, our factories, and our consumer gadgets can ‘understand’ the language of organic systems around them and form part of a related or hybrid framework of information and material exchange. This notion – that our societal artifacts should be mindful of their natural surroundings – has long and deep roots in many cultures and has modern reflections in, for example, the natural building movements. It is my contention that the development of synthetic multicellular – and likely hybrid- systems is a step down this transformative road. (621-622)

The cytoskeleton architecture supports many cellular functions. Cytoskeleton networks form complex intracellular structures that vary during the cell cycle and between different cell types according to their physiological role. These structures result…, from the interplay between intrinsic self-organization properties and the conditions imposed by spatial boundaries. Along these boundaries, cytoskeleton filaments are anchored, repulsed, aligned, or reoriented. Such local effects can propagate alterations throughout the network and guide cytoskeleton assembly over relatively large distances. The experimental manipulation of spatial boundaries using microfabrication methods has revealed the underlying physical processes directing cytoskeleton self-organization. Here we review, step-by-step, from molecules to tissues, how the rules that govern assembly have been identified. We describe how complementary approaches, all based on controlling geometric conditions, from in vitro reconstruction to in vivo observation, shed new light on these fundamental organizing principles. (Vignaud Abstract)

Majumder, Sagardip and Allen Liu. Bottom-Up Synthetic Biology: Modular Design for Making Artificial Platelets. Physical Biology. 15/1, 2018. An article by University of Michigan bioengineers for a dedicated issue with the first title, edited. We quote the issue summary, which also applies to this paper. One could then reflect that in a cosmic genesis its natural evolutionary methods seem meant to pass to and be enhanced by our humankinder evolitionary phase.

Spatially organized cellular processes arise from the interactions of nanometer building blocks. These emergent behaviors cannot be understood by knowing the parts alone, but rather how they interact. A central challenge in cell biology is thus to understand how cellular processes are organized spatiotemporally from the component parts. One powerful approach in such quest is bottom-up cellular reconstitution as an attempt to recreate the complexity of cellular life. Many examples of bottom-up reconstitution have come from various cytoskeletal, molecular motors, and membrane trafficking systems and provide vivid demonstrations of large-scale biomimetic behaviors. In addition, the use of cell-free extracts provides an experimental platform for connecting genetic information to modifying component parts. This special issue highlights both current cellular reconstitution efforts from purified proteins as well as cell-free systems of DNA-programmed behaviors in artificial cells.

Maniscalco, Sabrina, et al. Quantum Network Medicine. arXiv:2206.12405. With a Rethinking Medicine with Network Science and Quantum Algorithms subtitle, seventeen University of Helsinki, Finnish Quantum Institute physicists, provide a thorough study of how these universe to human, original and manifest realms, could inform and integrate so as to form a palliative synthesis. See also Translational Quantum Machine Intelligence for Tumor Dynamics in Oncology at (2202.10919). A planatural philoSophia might trace an overall evolution whence an accumulated medical/health corpus is meant to be fed back to the fraught beings from whom it arose. Thus a self-cocreative genesis which heals, medicates, cures itself comes into view.

The emerging field of network medicine views ways to investigate disease pathogenesis, integrating information from relevant Omics databases, including protein-protein interaction, correlation-based, gene regulatory, and Bayesian networks. However, this requires analysing large amounts of data with an urgent need for powerful computation methods. At the microscopic level, drug-target chemistry simulation becomes a quantum problem, which needs a quantum solution. As we will discuss, quantum computing may be a key ingredient in enabling the full potential of network medicine. We propose to combine network medicine and quantum algorithms in a novel research field for a new era of disease prevention and drug design. (Excerpt)

Matuszyńska,, Anna, et al. A New Era of Synthetic Biology: Microbial Community Design. Synthetic Biology. 9/1, 2024. As this accessible scientific frontier opens far and wide, in this Oxford journal RWTH Aachen University, Heinrich Heine University, Düsseldorf and Michigan State University computational bioresearchers can scope out careful project plans based upon latest realizations that no bacteria live alone. In fact they form filmy islands with a dynamic responsiveness to environments. As our knowledge grows about these lifestyles, better methods of disease mitigation, novel applications and more can proceed. See also Building Synthetic Cells from the Technology Infrastructure to Cellular Entities by Lynn Rothschild, et al in ACS Synthetic Biology (13/4, 2024).

Synthetic biology conceptualizes biological complexity as network systems with functionalities. With novel abilities to synthesize and transfer any DNA and RNA across organisms, the scope of synthetic biology is expanding to a level where artificial communities of synthetic organisms can be constructed. Here, we describe recent advances in computer-aided design of microbial communities. We argue for a shift from single organism approaches to their various contributions within the community. This approach aligns with synthetic biology strategies and presents exciting possibilities for the design of artificial communities. (Excerpt)

Mu, Wenjing, et al. Superstructural ordering in self-sorting coacervate-based protocell networks. Nature Chemistry. February, 2024. Chinese Academy of Sciences, Beijing, Beijing University of Chemical Technology, and Centre for Protolife Research School of Chemistry, University of Bristol (Stephen Mann) researchers post initial array of approaches and techniques by which various synthetic organisms may be brought into being. But at this early stage of intentional procreation, any foray as this must have serious ethical, philosophic and commom guidance before going further.

Bottom-up assembly of higher-order cyto-mimetic systems capable of coordinated physical behaviours, collective chemical signalling and spatially integrated processing is a pathway toward an artificial multicellularity. Here we develop coacervate microdroplets that self-sort into protocell networks. The protocell superstructures exhibit macromolecular spatial enzyme/ribozyme biocatalysis and molecular translocation. These methodologies are a step towards the spontaneous orchestration of protocell models into artificial tissues and colonies with ordered architectures and collective functions. (Abstract)

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)

Previous   1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10  Next  [More Pages]