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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VIII. Pedia Sapiens: A New Genesis Future

1. Mind Over Matter: Quantum, Atomic, Chemical Connectomics

Greco, Ralph, et al, eds. Nanoscale Technology in Biological Systems. Boca Raton: CRC Press, 2005. The latest advances with an emphasis on novel biomaterials and medical applications.

Gromski, Piotr, et al. How to Explore Chemical Space Using Algorithms and Automation. Nature Reviews Chemistry. 3/119, 2019. University of Glasgow computational chemists in coauthor Leroy Cronin’s lab explore the frontiers of novel material discovery, composition and enhanced utility.

Although extending the reactivity of a given class of molecules is relatively straightforward, the discovery of genuinely new reactivity and the molecules that result is a more challenging problem. Here, we describe how searching chemical space using automation and algorithms improves the probability of discovery. The former enables routine chemical tasks to be performed more quickly and consistently, while the latter uses algorithms to facilitate the searching of chemical knowledge databases. In order to find new chemical laws, we must seek to question current assumptions and biases. Accomplishing that involves algorithms to perform searches, and more general machine learning to predict the chemistry under investigation. (Abstract excerpt)

Gyongyosi, Laszlo and Sandor Imre. Multilayer Optimization for the Quantum Internet. Nature Scientific Reports. 8/12690, 2018. We enter this posting by University of Southampton and Budapest University of Technology systems physicists as a current example how quantum phenomena are being treated, availed, and creatively advanced in a similar manner to everywhere else.

We define a multilayer optimization method for the quantum Internet. Multilayer optimization integrates separate procedures for the optimization of the quantum layer and the classical layer of the quantum Internet. The multilayer optimization procedure defines advanced techniques for the optimization of the layers. The optimization of the quantum layer covers the minimization of total usage time of quantum memories in the quantum nodes, the maximization of the entanglement throughput over the entangled links, and the reduction of the number of entangled links between the arbitrary source and target quantum nodes. The objective of the optimization of the classical layer is the cost minimization of any auxiliary classical communications. The multilayer optimization framework provides a practically implementable tool for quantum network communications, or long-distance quantum communications. (Abstract)

Haba, Hiromitsu. A New Period in Superheavy Element Hunting. Nature Chemistry. 11/1, 2019. In a special issue for the 150th anniversary of the Periodic Table, a RIKEN Materials Research Group scientist considers how human ingenuity might proceed to expand nature’s iconic array of 118 elements via “islands of stability” all the way to atomic number 172. In regard, we emergent Earthlings seem to have reached some kind of “second singularity” whence cosmic material creation may pass to our respective human intention. See also Making the Heaviest Elements in the Universe: A Review of the Rapid Neutron Capture Process by John Cowen, et al at arXiv:1901.01410.

Halal, William. Technology’s Promise. New York: Palgrave Macmillan, 2008. The George Washington University futurist extrapolates a worldwide recreation of body, mind, society and nature, notably not without ethnic and ethical dilemmas, to be achieved via computer, medicine, energy, transport, and biopsychic enhancements.

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.

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)

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