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

1. Mind Over Matter and Energy: Quantum, Atomic, Chemical, Astronomic Realms

He, Xiaojin, et al. Exponential Growth and Selection in Self-Replicating Materials from DNA Origami Rafts. Nature Materials. 16/10, 2017. This entry by NYU Center for Soft Matter Research, and Tongji University, Shanghai, biochemists including Nadrian Seeman contributes to growing indications that this double helix nucleotide, broadly conceived, seem to have limitless innate qualities for our human co-creative curation going forward. The work merited a commentary Nanostructure Evolution by Friedrich Simmel in the same issue.

Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range. (Abstract excerpt)

Hia, Saw Wai. Atom-by-Atom Assembly. Reports on Progress in Physics. 77/056502, 2014. As another instance, an Argonne National Laboratory, Center for Nanoscale Materials, researcher extols the novel ability of our human phase to enter even into the realm of individual atoms. How fantastic is this – it seems we may be intentionally here so a natural evolutionary genesis can initiate and shift to a radical mode of our conscious new creation.

Atomic manipulation using a scanning tunneling microscope (STM) tip enables the construction of quantum structures on an atom-by-atom basis, as well as the investigation of the electronic and dynamical properties of individual atoms on a one-atom-at-a-time basis. An STM is not only an instrument that is used to 'see' individual atoms by means of imaging, but is also a tool that is used to 'touch' and 'take' the atoms, or to 'hear' their movements. Therefore, the STM can be considered as the 'eyes', 'hands' and 'ears' of the scientists, connecting our macroscopic world to the exciting atomic world. In this article, various STM atom manipulation schemes and their example applications are described. The future directions of atomic level assembly on surfaces using scanning probe tips are also discussed. (Abstract)

Hickinbotham, Simon, et al. Maximizing the Adjacent Possible in Automata Chemistries. Artificial Life. 22/1, 2016. In a paper which is a good example of biological and cosmic evolution in passage to our human intentional furtherance, York University, UK computer scientists including Susan Stepney consider algorithmic programs, broadly conceived, so as to design and advance novel, salutary materials and organisms.

Automata chemistries are good vehicles for experimentation in open-ended evolution, but they are by necessity complex systems whose low-level properties require careful design. To aid the process of designing automata chemistries, we develop an abstract model that classifies the features of a chemistry from a physical (bottom up) perspective and from a biological (top down) perspective. There are two levels: things that can evolve, and things that cannot. We equate the evolving level with biology and the non-evolving level with physics. We design our initial organisms in the biology, so they can evolve. We design the physics to facilitate evolvable biologies. This architecture leads to a set of design principles that should be observed when creating an instantiation of the architecture. (Abstract)

Hillis, Danny. The Enlightenment is Dead, Long Live the Entanglement. www.jods.mitpress.mit.edu. Reviewed more in Current Vistas, a 2016 manifesto for this epochal worldwide new age of organic genesis procreation.

Hirst, S. and L. Stapley. Parasitology: The Dawn of a New Millennium. Parasitology Today. 16/1, 2000. One medical example. From our worldwide perspective, once humankind’s collective, transcribed knowledge has emerged from the evolved, besieged human body and brain, it can be can fedback to cure and draw up these constituent members.

Hisata, Yusei, et al. Hisata, Yusei, et al. In-silico-assisted derivatization of triarylboranes for the catalytic reductive functionalization of aniline-derived amino acids and peptides with H. Nature Communications. 15/3708, 2024. We cite this entry by Osaka University computational chemists for its intentional recognition and inclusion of nature’s self-making propensities into a facile biochemistry.

Cheminformatics-based machine learning (ML) has helped identify optimal reaction conditions, including catalyst structures, in the field of synthetic chemistry. However, such ML strategies have remained used for catalytic molecular transformations using Lewis-acidic main-group elements. Here, the construction of a triarylborane library for the catalytic reductive alkylation of aniline-derived amino acids and C-terminal-protected peptides is reported. A combined theoretical and experimental approach identified the optimal borane which exhibits remarkable functional-group compatibility.

Holmes, Bob. Alive!. New Scientist. February 12,, 2005. A number of independent groups are attempting to “create a new form of living being from non-living chemicals in the lab.” One team associated with Los Alamos Laboratories cites four necessary steps: Containment – a form of bounded entity, Heredity – some mode of replication, Metabolism – processes that maintain viability, and Evolution – a capacity to grow and evolve. But a concluding observation by theologian John Haught is of special note. Although this research is often viewed as the human take over of life, incongruent to a religious persuasion, within an appropriate genesis cosmology, integral human persons are simply God’s method today of continuing and fostering life’s creation.

We are fully a part of nature, and as natural beings who are living and creating synthetic life, we are in a sense life creating more life, which is what’s been going on in evolution for 4 billion years now. And that does not in principle rule out that God would still be creating life using natural causes – namely us – which is the way in which theology understands God as always operating in the world. (Haught 33)

Huang, Yufeng, at al. Fractal Self-Organization of Bacteria-Inspired Agents. Chaos, Solitons, & Fractals. 20/2, 2012. From Marc-Olivier Coppens biochemical engineering laboratory at Rensselaer Polytechnic Institute, it is mathematically proposed, and experimentally supported, that microbial colonies, as exemplars of nonlinear viability, can inspire novel, palliative organic creations. Professor Coppens dedicates the article and project to his mentor and advisor Benoit Mandelbrot.

We develop an agent-based model as a preliminary theoretical basis to guide the synthesis of a new class of materials with dynamic properties similar to bacterial colonies. Each agent in the model is representative of an individual bacterium capable of: the uptake of chemicals (nutrients), which are metabolized; active movement (part viscous, part diffusive), consuming metabolic energy; and cellular division, when agents have doubled in size. The agents grow in number and self-organize into fractal structures, depending on the rules that define the actions of the agents and the parameter values. The environment of the agents includes chemicals responsible for their growth and is described by a diffusion-reaction equation with Michaelis-Menten kinetics. These rules are modeled mathematically by a set of equations with five dimensionless groups that are functions of physical parameters. Simulations are performed for different parameter values. The resulting structures are characterized by their fractal scaling regime, box-counting and mass-radius dimensions, and lacunarity. (Abstract)

Inosov, Dmytro. Quantum Magnetism in Minerals. Advances in Physics. 68/1, 2019. A Ukrainian solid state physicist presently at the Technical University of Dresden posts a 115 page, 750 reference, survey of these frontier realizations that quantum phenomena and condensed matter can be seamlessly unified. It’s sections go from Coupled spin dimers and Kagone systems to Quasi-2D lattices and Molecular magnets. As violent strife continues to rage across eastern Europe, human acumen can yet be able to learn all about and take over cosmic material creation, going forward.

The discovery of magnetism by the ancient Greeks was enabled by the natural occurrence of lodestone. Nowadays, minerals continue to inspire the search for novel magnetic materials with quantum-critical behavior or exotic ground states such as spin liquids. The recent interest in magnetic frustration and quantum magnetism was encouraged by crystalline structures of minerals realizing pyrochlore, kagome, or triangular arrangements of magnetic ions. In some cases, their structures are too complex to be synthesized artificially in a chemistry lab, especially in single-crystalline form, with unusual magnetic properties. The present review attempts to embrace this quickly emerging interdisciplinary field that bridges mineralogy with low-temperature condensed-matter physics and quantum chemistry. (Abstract excerpt)

Jha, Dipendra, et al. ElemNet: Deep Learning the Chemistry of Materials from only Elemental Composition. Nature Scientific Reports. 8/17593, 2018. We add this entry by Northwestern University and University of Chicago researchers as an example going forward of how materials science from physical compounds to complex biochemicals are being treated as due to a mathematical program (aka genotype). In regard, they are also becoming amenable to analysis and design by cerebral, multi-layer network processes.

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins. (Abstract)

Jin, Ren-Hua, et al. Biomimetic Synthesis of Shaped and Chiral Silica Entities Templated by Organic Objective Materials. Chemistry: A European Journal. 20/7198, 2014. This contribution by Kanagawa University, Japan, chemists, among thousands of its kind across the literature, applies biological topologies toward the creation of a new natural materiality. In regard, this frontier work could be seen as an intended passage to conscious human continuance for a new genesis future.

Organic molecules with accompanying self-organization have been a great subject in chemistry, material science and nanotechnology in the past two decades. One of the most important roles of organized organic molecules is the capability of templating complexly structured inorganic materials. The focus of this Minireview is on nanostructured silica with divergent morphologies and/or integrated chirality directed by organic templates of self-assembled polyamine/polypeptides/block copolymers, chiral organogels, self-organized chiral amphiphiles and chiral crystalline complexes, etc., by biomimetic silicification and conventional sol–gel reaction. Among them, biosilica (diatoms and sponges)-inspired biomimetic silicifications are particularly highlighted. (Abstract)

Johnson, George. A Shortcut Through Time: The Path to a Quantum Computer. New York: Knopf, 2003. A science writer narrates the players and their imaginations that portend an immense computational ability on an atomic scale.

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