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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VII. Pedia Sapiens: A Genesis Future on Earth and in the Heavens

1. Mind Over Matter: A Quantum, Atomic, Chemical Materiality

Luisi, Pier Luigi and Cristiano Chiarabelli, eds. Chemical Synthetic Biology. New York: Wiley, 2011. A table of contents and sample first chapter are available on the publisher’s book webpage. Four parts cover Nucleic Acids, Peptides and Proteins, Complex Systems, and General Problems. Dr. Luisi introduces, and a typical chapter is “Synthetic Genetic Codes as the Basis of Synthetic Life” by J. Tze-Fei Wong and Hong Xue

Chemistry plays a very important role in the emerging field of synthetic biology. In particular, chemical synthetic biology is concerned with the synthesis of chemical structures, such as proteins, that do not exist in nature. With contributions from leading international experts, Chemical Synthetic Biology shows how chemistry underpins synthetic biology. The book is an essential guide to this fascinating new field, and will find a place on the bookshelves of researchers and students working in synthetic chemistry, synthetic and molecular biology, bioengineering, systems biology, computational genomics, and bioinformatics. (Publisher)

Marcovich, Anne and Terry Shinn. Toward a New Dimension: Exploring the Nanoscale. Oxford: Oxford University Press, 2014. An update introduction to these microscape frontiers of physical and biological co-creation. In a section entitled Life as a Dynamic Lego Game, in accord with a nature that “tinkers” by trying out many candidates, a program is proposed to include and balance both selective effects along with an intentional engineering design.

Marelli, Benedetto, et al. Programming Function into Mechanical Forms by Directed Assembly of Silk Bulk Materials. Proceedings of the National Academy of Sciences. 114/451, 2017. An eight member team of Tufts University biomedical, chemical, and electrical engineers quantify how these exemplary fabrics have been formed by nature, and then go on to discuss their novel, intentional advance and use. The work merited a report in the same issue as When Bottom-Up Meets Top Down by the Israeli chemists Zvi Shtein and Oded Shoseyov where this evolutionary passage of natural materiality onto humanly creative intention is given notice.

We report simple, water-based fabrication methods based on protein self-assembly to generate 3D silk fibroin bulk materials that can be easily hybridized with water-soluble molecules to obtain multiple solid formats with predesigned functions. Controlling self-assembly leads to robust, machinable formats that exhibit thermoplastic behavior consenting material reshaping at the nanoscale, microscale, and macroscale. We illustrate the versatility of the approach by realizing demonstrator devices where large silk monoliths can be generated, polished, and reshaped into functional mechanical components that can be nanopatterned, embed optical function, heated on demand in response to infrared light, or can visualize mechanical failure through colorimetric chemistries embedded in the assembled (bulk) protein matrix. Finally, we show an enzyme-loaded solid mechanical part, illustrating the ability to incorporate biological function within the bulk material with possible utility for sustained release in robust, programmably shapeable mechanical formats. (Abstract)

McCarthy, Wil. Hacking Matter. New York: Basic Books, 2003. A technology writer extols the seemingly unlimited potentials to redesign, create and “program” the subatomic basis of nature, by which endeavor humankind might take over the material creation of the universe.

Moeini, Samaneh and Tie Jun Cui. Reflective Metasurfaces: Fractal Coding Metamaterials. Annalen der Physik. 531/2, 2019. University of Aveiro, Portugal and Southeast University, Nanking, China informatic engineers (a global team posts in a German periodical) discern and deftly apply nature’s self-similar mathematics to create a novel realm of visionary surfaces.

Editor’s Note In article number 1800134, Samaneh Moeini and Tie Jun Cui propose a concept of fractal coding metamaterials, which can be used to design reflective metasurfaces with self‐similar pseudo‐random phase responses. The introduced coding strategy utilizes fractal interpolation functions. An analytical relation between the reflection phase distribution and the far‐field radiation pattern is derived.

Moore, Katharine, et al. Universal Characteristics of Chemical Synthesis and Property Optimization. Chemical Science. 2/417, 2011. As the Abstract conveys, in this Royal Society of Chemistry journal, Princeton University mathematical chemists including Alex Pechen and Jason Dominy press the frontiers of 2010s new material creations. See also Why is Chemical Synthesis and Property Optimization Easier than Expected? by this group in Physical Chemistry Chemical Physics (13/10048, 2011).

A common goal in chemistry is to optimize a synthesis yield or the properties of a synthesis product by searching over a suitable set of variables (e.g., reagents, solvents, reaction temperature, etc.). Synthesis and property optimizations are regularly performed, yet simple reasoning implies that meeting these goals should be exceedingly difficult due to the large numbers of possible variable combinations that may be tested. This paper resolves this conundrum by showing that the explanation lies in the inherent attractive topology of the fitness landscape specifying the synthesis yield or property value as a function of the variables. Under simple physical assumptions, the landscape is shown to contain no suboptimal local extrema that could act as traps on the way to the optimal outcome. The literature contains broad evidence supporting this “OptiChem” theory. OptiChem theory implies that increasing the number of variables employed should result in more efficient and effective optimization, contrary to intuition. (Abstract)

Naam, Ramez. The Infinite Resource: The Power of Ideas on a Finite Planet. Hanover, NH: University Press of New England, 2013. The Egyptian-American computer scientist and futurist tracks the course of history by an ever growing social, public information repository, good for survival and prosperity. The “Tragedy of the Commons” whence consumption out ran supplies is to be countered by a nascent “Knowledge Commons.” Into the 21st century, as megacities take on a guise as dynamic organisms, the locus of learning decisively shifts to a composite worldwide phase. Indeed, a vectorial learning capacity and acquisition could be seen to well define the arc of evolution and humanity as a grand endeavor of self-education, counter to wasteful entropies. As a result, if we might become mindful together, our future destinies will much depend on our own common, informed choice.


“It was the best of times, it was the worst of times.” The opening line of Charles Dickens’ 1859 masterpiece A Tale of Two Cities applies equally well to our present era. We live in unprecedented wealth and comfort, with capabilities undreamt of in previous ages. WE live in a world facing unprecedented global risks – risks to our continued prosperity, to our survival, and to the health of our planet itself. We might think of our current situation as A Tale of Two Earths. (Preface)

This is a story about these two conflicting realities of our present day. The core argument of this book is that the force that’s propelled us to our present well-being is also the most powerful resource we have to tackle our future challenges: innovation. If we tap into and direct that force correctly, we have the very real potential to lift global wealth and well-being while reducing our impact on the planet and even reversing the damage we’ve done. If we fail to tap into that force, we flirt with the very real prospect of disaster. (Preface)

The whole world is becoming a city now. The technology of the Internet, mobile phones, and a million spinoffs of that are networking us all together. We’re drawing more connections, exchanging more insights, innovations, and information, Minds are the source of wealth and innovation. But their production isn’t linear. It scales with the number and quality of connections. And so, the more minds we have – educated minds, empowered minds, interconnected minds – the more each produces. (291) Our planet is like a giant living brain. Each mind added to it is a neuron. Each connection between those minds is a synapse. As we grow larger, we grow denser in connections, and so we grow smarter, more able to innovate, at rates faster than we consume. (291)

The human mind is the ultimate source of all wealth. We stand poised on the brink of the largest-ever explosion of human mental power, a second Renaissance, more transformative, more far-reaching, and more inclusive that the first. If we make the right choices to empower humans minds and encourage innovation, to steer innovation toward the solutions for our planet’s problems, and to embrace the fruits that it offers, then the future will be one of almost unimaginable wealth, health, and well-being. (308)

Nguyen, Michael and Suriyanarayanan Vaikuntanathan. Design Principles for Nonequilibrium Self-Assembly. Proceedings of the National Academy of Sciences. 113/14231, 2016. While the specific medium for these University of Chicago chemists is nanoscale colloids, the article goes on to show how independent physical and thermal fgenerative forces can be intentionally applied so as to create new material solutions. In regard, we could be reflectively witnessing the phenomenal passage of nature’s creative propensities to our collaborative human furtherance.

Understanding the principles governing self-assembly remains an important problem in statistical mechanics. We find, surprisingly, that general design principles for this challenging problem can be obtained by applying ideas from the field of stochastic thermodynamics to nonequilibrium self-assembly problems. Our central results constrain the set of possible configurations achievable under a nonequilibrium drive. (Significance)

Nosengo, Nicola. The Material Code. Nature. 533/23, 2016. A news report on the historic revolution with regard to the formula and preparation of novel atomic, (bio)chemical, electronic, structural compositions. The articles draws on the work of Gerbrand Ceder and Kristin Persson (search) which we reported in 2013. A national and worldwide collaboration has since expanded their vision of treating natural materiality as genomic in kind, so as to apply similar computational, machine learning, and intelligent search approaches. In the USA, a NAS Materials Genome Initiative is underway, an Open Quantum Materials Database at Northwestern University, along with other projects. New journals such as NPJ: Computational Materials, Computational Materials Science, and Nature Reviews: Materials cover the latest advances. By a philosophical regard could be seen an epic takeover by human intellect of substantial matter from subatomic scales as we Earthlings may begin a new intentional creation. A further import would be to witness this endeavor as a matteromics effort, which deeply infers an organic cosmic genesis.

Oganessian, Yuri. Superheavy Elements. Physics World. July, 2004. The discovery – and novel creation - of transuranium elements now extends to “islands of stability” in atomic number ranges of 112 to 118. The former Soviet Union has long been a leader in this regard.

Oganessian, Yuri and Krzysztof Rykaczewski. A Beachhead on the Island of Stability. Physics Today. August, 2015. Joint Institute for Nuclear Research, Russia, and Oak Ridge National Laboratory senior researchers review recent progress to synthesize the heaviest transuranium elements. This work presages dramatic expansions of the Periodic Table first laid out by their countryman Dmitri Mendeleev in the 1870s. Again by a natural philosophy view, phenomenal human beings seem to be a genesis universe’s way of taking over and beginning a new atomic material creation.

Olson, G. Designing a New Material World. Science. 288/993, 2000. As science and technology increasingly articulates material dimensions it can further these substantial realms by “...the creation of materials from thought.”

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