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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Recent Additions

II. Pedia Sapiens: A Planetary Progeny Comes to Her/His Own Actual Factual Knowledge

B. The Spiral of Science: Manican to American to Earthicana Phases

    This graphic cover of Indiana University information scientist Katy Borner's 2010 Atlas of Science: Visualizing What We Know can illustrate the centuries and course of scientific progress. The author and her collagues are at the forefront of its present shift to worldwide phase of instant collaborations. This emergent global genius may then take on the guise of a sapient noosphere as it cerebrally scales and organizes itself. As this website seeks to convey, a grand consequence would be a realization that our composite humankinder is actually coming to its own natural knowledge and guidance, which the world so desparately needs.


In the middle and Renaissance ages a realization slowly dawned that our aware human sapience could learn about an extant world which seems to possess discernible properties that can be investigated, written, codified, and accumulated. Thus an incipient, eclectic scientific project by exploration, theory and experiment began. This endeavor went forth from the 15th to the 20th centuries to collect, name, count, measure, test and arrange an ever wider presence of atomic depth, celestial breadth and contingent evolutionary duration. It was an arduous, fraught chronicle as readers well know. But with each expansion from creature to cosmos, human seekers vanished into insignificance.

This agenda led to consequences quie opposed to the original initiative and promise. As nature was taken apart and reduced piecemeal, the world came to be more like a machine than an organism. A material, mechanical scheme took over devoid of sense or value, mind and spirit removed from matter. A first scientific revolution by way of natural philosophy and theology gave way to a second stage into the 19th century as it split into separate fields and a thousand sub-specialties. By this parcellation the living realm was disassembled, dissected and embalmed.

A reintegration began in the later 20th century when quantum physics and relativity theory began to imagine a seamless, interrelated unity. This conceptual shift is still working itself out and percolates into biological and social realms. For most of its tenure science was concerned with infinitesimal particles and infinite sidereal reaches. By means of networked computers and graphic visualizations, a “third infinity” of an oriented, recurrent, dynamic complexity and consciousness can now be perceived. The section is called The Spiral of Science because our phenomenal homo to anthropo reconstruction proceeds from individual (male) investigators to a collegial, cumulative dialogue and onto a worldwide, interdisciplinary community, noted next in Mindkind.

We also wish to cite a distinction between the two cultures of scientific method and natural philosophy since they are actually two different modes and phases. This lapse has led to confusion and a public dislike and distrust of science and medical information. Experimental findings such as gravity waves, biomolecules and weather patterns are the result of arduous trial, iterate, retest, rethink and so on. Evolutionary biology has indeed found that bird wings and human arms are related forms and how whales evolved from mammals who returned to seas. But a surmise since the late 19th century that life’s developmental emergence yet has no innate code cause, oriented direction or teleologic goal has become a vested, quite erroneous conclusion.

2020: By this year an awesome array of online eprint sites and myriad journals post thousands of papers each day. A cumulative repository builds on its own agency as researchers scan, read, fill in, modify and contribute further work. Website entries across the sections have come to perceive this endeavor as a self-organizing complex network system. A worldwise collective intelligence now seems in emergent effect whereof any ecosmic breadth and atomic depth has become cognitively accessible.

On the physics arXiv.org site one can find, e.g., Primordial Black Holes as Dark Matter (2006.02838) and Quantum Critical Spin-Density Waves (2006.05680). A preprint server for biology at bioRxiv.org has postings from Animal Behavior to COVID studies to Zoology. As a rule entries can have numerous, often international co-authors. By this view, our global genius seems engaged in a phenomenal task of observant universal self-quantification, written description, which altogether may be fed back to inform and achieve our KinderMind continuance.

Circa 2022, a further emergent spiral turn to a planetary Earthropo phase enhanced by AI advances is getting underway, which entries herein will report. Some examples are On Scientific Understanding with Artificial Intelligence (M. Krenn), and “Machine Scientists” Distill the Laws of Physics from Raw Data, and How to Make the Universe Think Like Us, both by Charlie Wood. Our PediaPedia 2023 entry will record more editions to this turning.

Bauer, Amanda, et al. Petabytes to Science. arXiv:1905.05116.

Berger, Bonnie. How to Succeed as a Computation Biologist in Today’s Research Climate. Cell Systems. 13/10, 2022.

Dworkin, Jordan, et al. The Emergent Integrated Network Structure of Scientific Research. PLoS One. 14/4, 2019.

Gebhart, Thomas and Russell Funk. The Emergence of Higher-Order Structure in Scientific and Technological Knowledge Networks. arXiv:2009.13620.

Gomez-Vargas, Isidro, et al. Neural Networks Optimized by Genetic Algorithms in Cosmology. arXiv:2209.02685.

Ju, Harang, et al. The Network Structure of Scientific Revolutions. arXiv:2010.08381.

Kitano, Hiroaki. Nobel Turing Challenge: Creating the Engine for Scientific Discovery. NPJ Systems Biology. 7/29, 2021.

Krenn, Mario, et al. Predicting the Future of AI with AI: A Knowledge Network. arXiv.2210.00881.

Lavin, Alexander, et al. Simulation Intelligence: Towards a New Generation of Scientific Methods. arXiv:2112.03235.

Marshall, Stuart, et al. Formalizing the Pathways to Life using Assembly Spaces. Entropy. 24/7, 2022.

Ntampaka, Michele and Alexey Vikhlinin. Toward an Understandable Machine Learning Encoder for Galaxy Cluster Cosmology. arXiv:2112.05768.

Schutt, Kristof, et al, eds. Machine Learning Meets Quantum Physics. International: Springer, 2020.

Tinetti, Giovanni, et al. Ariel: Enabling Planetary Science Across Light-Years. arXiv:2104.04824.

Renn, Jurgen. The Evolution of Knowledge: Rethinking Science for the Anthropocene Princeton: Princeton University Press, 2020.

Seif, Alireza, et al. Machine Learning the Thermodynamic Arrow of Time. Nature Physics. 17/1, 2022.


Astro2020: Decadal Survey on Astronomy and Astrophysics. sites.nationalacademies.org/SSB/CurrentProjects/SSB_185159. his is the main website for the National Academies of Sciences, Engineering and Medicine, Space Studies Board request for wide-ranging cosmological projects across the next 10 years. In regard, from January to May 2019 over 300 proposals were posted on the arXiv e-print site, just search Astro2020. As a small sample, we note The Next Decade of Astroinformatics, Toward Finding Earth 2.0, The Super Earth Opportunity, Stellar Characterization for Holistic Planetary Habitability, Tracing the Origin of Seed Black Holes, Quantum Chemistry for Exoplanetary Science, Cosmic Dawn and Reionization, Mapping Galactic Clusters, and every other astro-aspect as humankinder begins to carry out a genesis universe’s way of necessarily quantifying itself. The entries are often from a nominal group of 10 to 50 co-authors. Altogether a good example of nascent global science going on via its own many agent self-organization.

Dark Energy Survey Collaboration. www.darkenergysurvey.org/collaboration-and-sponsors. A composite website for studies of Galaxy Clusters, Supernovae, Weak Lensing, Theory, Milky Way, Large Structure, Redshifts, and much more as an example of the 21st century shift and advance to collective worldwise scientific endeavors.

DES is an international project with over 400 scientists from 25 institutions in 7 countries, who have come together to carry out the survey. Our team comprises university faculty and researchers, laboratory and observatory staff scientists, post-doctoral researchers, and graduate and undergraduate students. The support staff are also a critical part of the team: they make it possible for our scientists to travel to Chile to observe for the survey and to travel to conferences and collaboration meetings to discuss the latest results. (Website)

Frontiers Journals. www.frontiersin.org. An online publishing venture begun in 2007 by neuroscientists to free their field from the time and space constraints and inhibitions of paper versions. The endeavor experienced such success that it has expanded into dozens of specialized Frontiers web journals for many other scientific areas. Some examples are Frontiers in Fractal Physiology (search Werner) and Frontiers in Neuroinformatics (search Kaiser), realms that might not gain a presence otherwise. An “Unbiased, Fair, Real-Time, and Interactive” peer process is in place, with dual anonymous and an editorial reviewers. The full text of all papers are available via Open Access. We quote from the mission statement of a typical journal.

Frontiers in Bioinformatics and Computational Biology, a Specialty Section of Frontiers in Genetics, aims to publish research findings, methodology, opinion and hypothesis articles on all aspects of quantitative biology, with the emphasis on the molecular, cellular, organismal, population and phylogenetic levels; studies involving quantitative analysis at the ecosystem and biosphere levels will be considered until a better home for them emerges among the Frontiers journals. Specifically, Frontiers in Bioinformatics and Computational Biology welcomes papers that discuss i) analysis of amino acid and nucleotide sequences and structures; ii) analysis of large multidimensional numeric datasets, including gene expression readouts, gene and protein interaction data, metabolite and small molecule profiling, etc. iii) quantitative analysis of biological images; iv) phylogenetic approaches to biological questions; v) computational analysis of evolution of all life forms; vi) synthetic biology and biochemical engineering; vii) fundamental questions in the Origin of Life; ix) mathematical or statistical modeling of all of the above; and x) new or improved algorithms, software systems and online services dealing with all of the above. We welcome genome-scale and system-wide approaches.

Mozilla Science Lab. https://science.mozilla.org. A fledgling site by the Mozilla group to help facilitate researcher, developer, and librarian collaborations to Maximize access to papers, data, code and materials so anyone can read and contribute. Its emphasis is on worldwide openness and inclusion. Anyone can become a Fellow (I would add a Mellow), participate in an event such as Global Sprint 2017 in June, either online or in person, or join a Study/Learning Group. Three women, Stephanie Wright, Zannah Marsh, and Aurelian Moser, with luminous creative credits guide the effort.

Transforming Science: Mozilla Science Lab is a community of researchers, developers, and librarians making research open and accessible. We’re empowering open science leaders through fellowships, mentorship, and project-based learning.

Mozilla: is a free-software community created in 1998 by members of Netscape. The Mozilla community uses, develops, spreads and supports Mozilla products, thereby promoting exclusively free software and open standards.

Nature Scientific Reports. www.nature.com/srep/index. This is an online journal begun June 2011 with some 1100 articles by late January 2013, which span the physical, biological, medical, neural, and human sciences from cosmology to social networks. In our day of instant electronic publication and access everywhere, a true worldwide collaboration seems to be achieving its own cumulative knowledge and discovery. Our interest is to notice how many reports employ self-organizing, complex network systems by way of agents, nodes, entities in constant interactivity, which are then found to apply, almost word for word, in every stratified realm from galaxies to genomes, brains, and civilizations. In regard, typical papers about cosmic de Sitter spacetime, science dynamics, neural criticality, insect swarms (search Dmitri Krioukov, Xiaoling Sun, Jiangbo Pu, Douglas Kelley, in turn) and so on note that a pervasive presence of these related nonlinear features seems to implicate, indeed require, a universal, independent mathematical source. Many more periodicals such as Europhysics Letters EPL, Physica A, and Physical Review E publish akin work, often citing a statistical physics basis to report both exemplary and universal aspects.

Online and open access, Scientific Reports is a primary research publication from the publishers of Nature, covering all areas of the natural sciences. Hosted on nature.com — the home of over 80 journals published by Nature Publishing Group and the destination for millions of scientists globally every month — Scientific Reports is open to all, publishing technically sound, original research papers of interest to specialists within their field, without barriers to access. With the support of an external Editorial Board and a streamlined peer-review system, all papers are rapidly and fairly peer reviewed to ensure they are technically sound. An internal publishing team works with the board, and accepted authors, to ensure manuscripts are processed for publication as quickly as possible.

Alexeev, Yuri, et al. Quantum Computer Systems for Scientific Discovery. arXiv:1812.07577. Twenty five select researchers from across the USA including John Preskill and Seth Lloyd (23 men and 1 woman Shelby Kimmel) report on a late 2019 meeting about how this analytic and computational frontier capability might be coordinated with megadata projects, studies and explorations from astrocosmic to social, climate and medical areas going forward. One might note that as such collaborative, planet scale projects advance (still sans asking whom and why, does a discovery await), human beings might well seem as the universe’s way of achieving its own consciously perceived self-description which it vitally needs to read, understand and select itself.

The great promise of quantum computers comes with the dual challenges of building them and finding useful applications. We argue that these aspects should be considered together by co-designing full-stack systems along with their intended use so to hasten development and potential for scientific discovery. In this context, we identify scientific and community needs, opportunities, case studies, and issues for the development of quantum computers for science. This document is written by a community of university, national laboratory, and industrial researchers in the field of Quantum Information Science and Technology, and is based on a NSF workshop on held in October 2019 in Alexandria, VA. (Abstract)

Amato, Ivan. Super Vision: A New View of Nature. New York: Harry N. Abrams, 2003. From Galileo’s telescope and van Leeuwenhoek’s microscope to an international collaboration today, through human endeavor the universe has gained the ability of sight. Striking, colorful images along with narrative reveal this achievement from subatomic particle tracts to molecules, diatoms, frozen lightning, landscapes and on to galactic networks which look like neural networks in a brain.

Aung, Tin, et al. Genetic Association Study of Exfoliation Syndrome Identifies a Protective Rare Variant at LOXL1 and Five New Susceptibility Loci. Nature Genetics. 49/7, 2017. We note this paper about medical research findings to cure glaucoma and build a “disease biology” more for its almost 300 co-authors spread across every continent. With main bases in New York City and Singapore, a long list of credits such as King Saud University, Saudi Arabia, Shinjo Eye Clinic, Japan, and the University of Tasmania, Australia, a truly global network of visionary advances, fills two pages. Here is luminous evidence of a scientific ascent to a worldwide sapiensphere now learning on its bicameral own, which still remains unbeknownst to individual researchers.

Baaquie, Belal and Frederick Willeboordse. Exploring Integrated Science. Boca Raton: CRC Press, 2010. A large, illustrated volume by National University of Singapore physicists wherein 24 chapters – Universe, Numbers, Energy, Atoms, Molecules, Fluids, Materials, Polymers, Electricity, Odor, Sound, Photosynthesis, Vision, Biopolymers, Proteins RNA, DNA, Information, Nano, Complexity, Evolution, Relativity, QM I, QM II –each pose a question to engage the reader. For example ‘Information’ asks how do children come to resemble their parents. And notably as a contribution from a non-Western milieu, an inherent self-organization is tacitly allowed which impels and informs an emergent cosmic vitality.

Rather that the number of genes of an organism, it is the nonlinear manner is which genes interact that gives rise to how complex the organism is. (459)

Bainbridge, William Sims. The Evolution of Semantic Systems. Roco, Mihail and Carlo Montemagno, eds. The Coevolution of Human Potential and Converging Technologies. Annals of the New York Academy of Sciences, 2004. A Director of Information and Intelligent Systems at the National Science Foundation discusses the formation of a “cultural genetics” as a way to understand knowledge concepts and relationships in an evolutionary context.

Today, however, we have the research tools and analytical concepts necessary for a broad reorganization of science as a comprehensive model of reality based on a single set of principles. Fundamental to this vision are the unity of nature, the behavior of matter at the nanoscale, and the evolution of meaningful patterns in complex, self-organizing systems. (151)

Ball, Philip. Triumph of the Medieval Mind. Nature. 452/17, 2008. Drawing upon his new book Universe of Stone: Chartres Cathedral and the Triumph of the Medieval Mind, (London: Bodley Head) the British science writer contends that the historic intellectual revolution of natural philosophy, whence the extant world can be understood as reliably comprehensible, a valid object of study sans capricious divine intervention, occurred firstly in the early 12th century, much before the Renaissance. Thus began the contentious dichotomy between faith and reason, given revelation and found phenomena, still unresolved to this day.

Banzhaf, Wolf and Nelishia Pillay. Why Complex Systems Engineering Needs Biological Development. Complexity. 13/2, 2007. Computer scientists from the Memorial University of Newfoundland, and the University of KwaZulu-Natal, South Africa, contend that a more effective approach than prior top-down control and design is to draw upon natural evolutionary phenomena such as nonlinearity, self-organization, and adaptation which focus more on dynamically emergent processes than fixed, preconceived states.

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