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

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

Qiu, Yuchi, et al. Cluster Learning-Assisted Directed Evolution. Nature Computational Science. December, 2021. We cite this entry by Michigan State University biochemists as an example among many similar endeavors as our worldwide intellect proceeds to revise and enhance life’s biological composition going forward. For another instance, see AI Revolutions in Biology by Anatassis Perrakis and Titia Sixma in EMBO Reports (22/e54046, 2021.)

A directed evolution as a strategy for protein engineering is presently difficult to do. Machine learning-assisted directed evolution (MLDE), which screens sequence properties in silico, can optimize and reduce the experimental burden. This work introduces an MLDE method along with cluster learning-assisted directed evolution (CLADE). By screening 480 sequences out of 160,000 in a four-site combinatorial library, CLADE achieves global maximal fitness hit rates of up to 91.0%.

Rabinowitch, Ithai. What Would a Synthetic Connectome Look Like? Physics of Life Reviews. Online July 2, 2019. A Hebrew University of Jerusalem senior medical neurobiologist broaches an initial consideration of how collective human programs might carry forth the formative principles of our own brains, as we have just learned, into new, and improved cerebral procreations. The essay ranges from neural and genetic bases to ethical issues, within a sense that this endemic inter-relational quality is a distinctive feature.

A major challenge of contemporary neuroscience is to unravel the structure of the connectome, the ensemble of neural connections between different functional units of the brain, and to reveal how this structure relates to brain function. The synthetic biology approach comprises the assembly of new biological systems out of elementary biological parts, which is dubbed forward-engineering. The rationale is that building a system can be a good way to gain understandings of how that system works. As the fields of connectomics and synthetic biology are independently growing, I propose to beneficially combine them to create synthetic connectomics. This union could be a unifying platform for unraveling the complexities of brain operation and could provide an opportunity for empirically exploring theoretical predictions about network function. (Abstract excerpt)

Rampioni, Giordano, et al. A Synthetic Biology Approach to Bio-Chem-ICT: First Moves Towards Chemical Communication Between Synthetic and Natural Cells. Natural Computing. Online May, 2014. We select this paper among many as an example that theories and projects to commence a second nature via informed human intention might help explain how life began and arose in the first place. Italian systems biologists including Luisa Damaino go on to convey, as common today, how biology and evolution is better understood from substantial matter to cellular beings, universe to us, in terms of informational-computational phenomena and programs. This course is said to reflect every organism’s innate autopoietic autonomy, which we scientists might now respectfully appreciate, continue and enhance.

Ravoo, Bart. Frontiers of Molecular Self-Assembly. Israel Journal of Chemistry. 59/868, 2019. An introduction to a special issue on this active global research endeavor to realize, and implement nature’s own deep propensity to organize, vivify and autocreate itself. Some papers are Self-Sorting in Supramolecular Assembly, Dissipative Self-Assembly of Peptides, and From Discrete Structures to Biomimetic Materials.

Renata, Hans, et al. Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution. Angewandte Chemie International Edition. 54/3351, 2015. California Institute of Technology chemical engineers Renate, Jane Wang, and Frances Arnold continue their project (see Arnold Lab publications) to learn how living systems became vitally complex so as to initiate a biomimetic palliative and sustainable phase. See also, for example, The Nature of Chemical Innovation: New Enzymes by Evolution by Frances Arnold in Quarterly Reviews of Biophysics (48/404, 2015).

High selectivity and exquisite control over the outcome of reactions entice chemists to use biocatalysts in organic synthesis. However, many useful reactions are not accessible because they are not in nature’s known repertoire. In this Review, we outline an evolutionary approach to engineering enzymes to catalyze reactions not found in nature. We begin with examples of how nature has discovered new catalytic functions and how such evolutionary progression has been recapitulated in the laboratory starting from extant enzymes. We then examine non-native enzyme activities that have been exploited for chemical synthesis, with an emphasis on reactions that do not have natural counterparts. Non-natural activities can be improved by directed evolution, thus mimicking the process used by nature to create new catalysts. Finally, we describe the discovery of non-native catalytic functions that may provide future opportunities for the expansion of the enzyme universe. (Abstract)

Enzyme: Any of numerous proteins produced in living cells that accelerate or catalyze the metabolic processes of an organism. a substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction.

Ronquist, Scott, et al. Algorithm for Cellular Reprogramming. Proceedings of the National Academy of Sciences. 114/11832, 2017. A ten person interdisciplinary team from the University of Michigan, University of Maryland, Harvard University and IXL Learning, Raleigh, NC provide a microcosm of the frontier abilities of genomic and biological research. As the quote cites, a radical new phase is respectfully beginning to take over living systems for all manner of curative benefits and enhancements. This capacity involves “a dynamic systems view of the genome” so as to achieve an intentional employ of nature’s independent, universal source code.

Reprogramming the human genome toward any desirable state is within reach; application of select transcription factors drives cell types toward different lineages in many settings. We introduce the concept of data-guided control in building a universal algorithm for directly reprogramming any human cell type into any other type. Our algorithm is based on time series genome transcription and architecture data and known regulatory activities of transcription factors, with natural dimension reduction using genome architectural features. Our algorithm predicts known reprogramming factors, top candidates for new settings, and ideal timing for application of transcription factors. This framework can be used to develop strategies for tissue regeneration, cancer cell reprogramming, and control of dynamical systems beyond cell biology. (Significance)

Rothschild, Lynn, et al. Building Synthetic Cells from the Technology Infrastructure to Cellular Entities. ACS Synthetic Biology.. 13/4, 2024. Seventeen scientists across the USA from NASA Ames Research Center to GeorgiaTech scope out a thorough project plan as these historic, mid-decade abilities increasingly invite and enable our second, singular commencement of a new biocreativity going forward.

Despite novel cellular technologies, a functioning cell “from scratch” has yet to be accomplished. The pursuit of this goal alone will yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have so far sought to reproduce living system features such as compartmentalization, metabolism, and replication and derived responsiveness to stimuli, directed movement and more. Here, we review these approaches, look ahead at work to be done and a “roadmap” with key milestones to achieve the vision of building cells from molecular parts. (Excerpt)

Rozhkova, Elena and Katsuhiko Ariga, eds. From Molecules to Materials: Pathways to Artificial Photosynthesis. Heidelberg: Springer, 2016. Elena Rozhkova is a Principal Investigator at the Center for Nanoscale Materials, Argonne National Laboratory, USA, and Katsuhike Ariga is the Director of the Supermolecules Unit, Research Center for Materials Nanoarchitectonics, National Institute for Materials Science, Japan. Typical chapters are Enzymes as Exploratory Catalysts in Artificial Photosynthesis, and From Molecular to Hybrid Nanoconstructs. Our interest is the phenomenal passage of life’s basic usage of solar light energy onto intentional, worldwide human avail and continuance.

This interdisciplinary book focuses on the various aspects transformation of the energy from sunlight into the chemical bonds of a fuel, known as the artificial photosynthesis, and addresses the emergent challenges connected with growing societal demands for clean and sustainable energy technologies. The editors assemble the research of world-recognized experts in the field of both molecular and materials artificial systems for energy production. Contributors cover the full scope of research on photosynthesis and related energy processes.

Scalise, Dominic and Rebecca Shulman. Controlling Matter at the Molecular Scale with DNA Circuits. Annual Review of Biomedical Engineering. 21/469, 2019. Johns Hopkins University biophysicists continue to advance (search) their studies of the many, seemingly unlimited, structural, computational and electronic capabilities of nucleotide biomolecules much beyond their genetic role. In regard, might these innate propensities imply a deep natural fertility which we cocreative peoples are meant to learn, avail to take forth anew?

In recent years, diverse mechanisms have been developed that allow DNA strands to sense information inputs so to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits which can act as chemical processors to program complex material behaviors. There are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as direct the self-assembly and dynamic reconfiguration of nanostructures, and manipulate DNA crystals, hydrogels, and vesicles. These interfaces can enable chemical circuits to exert algorithmic control over responsive materials so they can grow, heal, and interact with their environments. (Abstract)

Scheufele, Dietram, et al. What We Know about Effective Public Engagement on CRISPR and Beyond. Proceedings of the National Academy of Sciences. 118/22, 2021. In a NAS Colloquium on Life 2.0: The Promise and Challenge of a CRISPR Path to a Sustainable Planet (see below), University of Wisconsin and University of Vienna scholars scope out a wide-ranging advocacy of education programs, cultural factors, controversial issues and more so that these palliative, beneficial advances can be well accepted. (As I record in June, we see how many misunderstandings are hampering vaccine use.) Typical issue entries are Targeted DNA Insertion in Plants, Synthetic Threads through the Web of Life (Mary Power) and Toward the Correction of Muscular Dystrophy by Gene Editing.

Advances in gene editing technologies for human, plant, and animal applications have led to calls from bench and social scientists, as well as a wide variety of stakeholders, for broad public engagement in the decision-making about these new technologies. At present, there is limited understanding among the groups about 1) the goals of this engagement, 2) what we know from scientific evaluations about their effectiveness, and 3) how to societal decision or policy making. Here we systematize common goals, principles, and modalities of public engagement. Finally, we outline scientific and social pathways forward as we navigate the world of Life 2.0. (Abstract excerpt)

The NAS Colloquium on “Life 2.0: The Promise and Challenge of a CRISPR Path to a Sustainable Planet“ reviews the history of genome editing and explores various recent uses of CRISPR technology. The papers included in this special issue emerged from sessions describing the urgent need for CRISPR-based approaches; exploring agricultural genome editing in plants and animals, gene drives, and gene therapies; and addressing ethical issues associated with new, complex technologies and human genome editing.

Schindler, Daniel, et al. Synthetic Genomics: A New Venture to Dissect Genome Fundamentals and Engineer New Function. Current Opinion in Chemical Biology. 46/56, 2018. University of Manchester, Manchester Institute of Biotechnology, UK, and Chinese Academy of Sciences, Institute of Synthetic Biology researchers contribute to this open frontier going forward, as if a second, intentional genesis, to take up and continue life’s evolutionary genetic endowment by learning to (re)write palliative and beneficent editions. See also Recent Advances in DNA Nanotechnology in this journal (46/63). But as I long had a day job as an engineer, this word should rightly be replaced for it is inappropriate as often used. Might one suggest something like “engender” for this quite organic creativity?

Since the first synthetic gene was synthesized in 1970s, the efficiency and the capacity of made-to-order DNA sequence synthesis has increased by several orders of magnitude. Advances in DNA synthesis and assembly over the past years has resulted in a steep drop in price for custom made DNA. Similar effects were observed in DNA sequencing technologies which underpin DNA-reading projects. Today, synthetic DNA sequences with more than 10 000 bps and turn-around times of a few weeks are commercially available. This enables researchers to perform large-scale projects to write synthetic chromosomes and characterize their functionalities in vivo. Synthetic genomics opens up new paradigms to study the genome fundamentals and engineer novel biological functions. (Abstract)

Schmidt, Gregory. The Best Toys That Teach Kids How to Code. New York Times. December 19, 2017. In the week before Christmas, a delightful, illustrated feature about how companies are coming up with encoded building kits such as Think & Learn Code-a-Pillar (Fisher Price), LEGO Boost and FurReal Proto Max (Hasbro). Another source is Kodable who crafts programming experiences for elementary schools. A toy tester site named Wirecutter can be accessed which notes a learning center in San Francisco named the Makery. To scale up many levels, might we adults be able to learn and imagine a “Kodable Kosmos” by way of our human universe genome HUG project?

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