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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

A. UniVerse Alive: An Organic, Self-Made, Encoded, Familial Procreativity

Lash, Scott. Life (Vitalism). Theory, Culture & Society. 23/2-3, 2006. In this issue on Problematizing Global Knowledge reviewed in the Mindkind section (Featherstone), an article that extols a “neo-vitalism” as implied by the universal self-organizing dynamics of living organisms.

Lehn, Jean-Marie. Chemistry: Retrospects and Prospects. www.youtube.com/watch?v=0psUuAo_F6Y. A September 2009, Technion, Israel, lecture by the 1987 Nobel laureate in Chemistry presents the full spectrum of a “Cosmic Self-Organization” from a big bang origin to prebiotic molecules, living, evolving matter, and onto thinking entities. This fertile materiality is then seen to be suffused with and propelled by an informational essence. “Supramolecular chemistry is a dynamic chemistry,” within an organism-like cosmos to civilization spontaneity.

A consequence, as the first quote from a slide conveys, is that human beings are the selves whom may carry this unfinished creativity forward to a better future. A recent article by Dr. Lehn, “Chemistry: The Science and Art of Matter” from the January-March 2011 issue of The Unesco Courier, similarly advances this noble vision of a quickening creation in which we persons are invited to play a co-creator role in its continuing genesis.

From divided matter to condensed matter, then organized, living and thinking matter, the unfurling Universe is nudging the evolution of matter towards increasing complexity through self organization, under the pressure of information. The task of chemistry is to reveal the pathways of self organization and to trace the paths leading from inert matter, via a purely chemical, prebiotic evolution, to the creation of life, and beyond, to living and then thinking matter. In this way, it offers the means to interrogate the past, to explore the present and to build bridges towards the future. (9)

The particularity of chemistry is not only to discover, but to invent and, above all, to create. The Book of Chemistry is not only to be read, but to be written. The score of Chemistry is not only to be played, but to be composed. (9)

Liao, Qinqli, et al. Density Functional Theory Calculations on the Interstellar Formation of Biomolecules. arXiv:2310.14488. Into October, a research report from the Laboratory form Guangxi University, China provides a good current illustrated proof of an apparent celestial precursor fertility which seeds itself with a complexifying sequence of the vital biochemicals on the way to life’s organic evolution. By now, as the quotes say, an inherent presence of such an array of metabolic compounds have been found to suffuse the astronomic reaches. Once more, circa 2023/2024, a grand, consummate discovery event by our planetary prodigy seems to indeed be forming in our midst/

The density functional theory (DFT) is the most versatile electronic structure method used in quantum chemical calculations, an d is increasingly applied in astrochemical research. This mini-review provides an overview of the applications of DFT calculations in understanding the chemistry that occurs in star-forming regions. We survey the formation of biologically-relevant compounds such as nucleobases in the interstellar medium, as well as biologically-relevant molecules such as sugars, and polycyclic aromatic hydrocarbons. We conclude by noting several research areas such as the formation pathways of chiral amino acids, complex sugars, and the role of environmental factors in the formation of interstellar biomolecules. (Excerpt)

In our perspective, future research avenues should encompass the exploration of complex purine base formation, the elucidation of chiral amino acid synthesis pathways, comprehension of intricate sugar and biomolecule production, examination of the influence of metal ions and hydrogen bonding in ISM chemical reactions, refinement of computational models, and assessment of the impact of temperature and environmental variables on interstellar biomolecule formation. (9)

Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. (Wikipedia)

Lin, Yi, et al. Systems Science. Boca Raton: CRC Press, 2012. Yi Lin is a scientist and philosopher with appointments across China and the USA, and several texts on nonlinear theories from an Asian perspective to his credit. Coauthor Xiaojun Duan, with a Chinese PhD in systems engineering, professes at the National University of Defense Technology, Changsha. This special work is which sees dynamic complexity theories as a 21st century verification across millennias of Taoist yin/yang dialectics is reviewed more in Cosmic Code.

Lloyd, Seth. A Quantum of Natural Selection. Nature Physics. 5/3, 2009. A contribution by the MIT scientist to an issue on “Darwin and Physics.” But as quantum theory avers, ‘digital‘ is also graced by complementary wave relations. What will it take to realize that everyone is trying to translate a cosmic genesis of genotype and phenotype from parent to child?

Quantum mechanics makes nature digital. It is this digital character of all things at their smallest scale that nature discovered and used to construct the genetic basis for life. (164) The discrete quality of quantum mechanics, together with the ability to string together many atoms in a molecule, implies that physical systems are naturally capable of registering a large number of bits of information. Perhaps the most explicit example of such natural information is DNA. (164) Nature took these quantum gifts of stability, countability, information, information processing, and randomness and ran with them. The Universe began with a bang, and immediately started processing information. (165)

Lobkovsky, Alexander, et al. Universal Distribution of Protein Evolution Rates as a Consequence of Protein Folding Physics. Proceedings of the National Academy of Sciences. 107/2983, 2010. Along with NIH co-authors Yuri Wolf and Eugene Koonin, a theory that a ubiquitous protein-folding robustness which paces all cellular life can be seen to arise from inherent natural principles and properties.

Luisi, Pier Luigi. Contributions of Synthetic Biology to the Field of the Origin of Life. Macagnano, Antonella, et al, eds. Advanced Topics in Cell Model Systems. New York: Nova Science, 2009. The author (search) is an emeritus ETH-Zurich, Institut fur Polymere, chemist and complex systems scientist. Within a volume about life’s origins revealed via a systems biology that augurs for a second creation, it is vital, argues Luisi, to state what kind of encompassing nature may, or may not, avail. In so doing, as the quotes convey, the Copernican/Ptolemaic dichotomy and intertwined tangle that confounds our day can be engaged.

But also the philosophical framework of the ladder leading to the first cellular forms is still a matter of debate. In particular, looking at the prebiotic molecular evolution that goes from simple organic molecules to the early living cells, two main theories are opposing each other: one says that the origin of life was an inescapable event, an outcome that had to be realized once given the prebiotic conditions. This is the view that assumes a kind of absolute determinism in the pathway leading to life, where each step is causally determined by the previous one and determines the next one, in a sequence which inescapably leads to the living cellular form. Christian de Duve, Harold Morowitz, Stuart Kauffman, and others appear to favor this view. (60)

The opposite front is kept by people like Stephen Jay Gould, and most of the contemporary students in the field, who, in the footstep of classic Jacques Monod, accept the view that contingency is the main factor, which led to life starting from the simple organic molecules and their basic interactions. Contingency is the modern and more fashionable version of old “chance,” and sees that a certain outcome is given by the concomitance of factors which are independent from one another. The Cambrian revolution, according to Gould, was due to a series of factors with no causal dependency to each other. Change only one of these factors, and the event would not have happened. (60)

Lumsden, Charles, et al, eds. Physical Theory in Biology. Singapore: World Scientific, 1997. Technical papers which are set in either the mechanical or organic paradigm attempt a theoretical unification of life and matter.

Lynn, David, et al. Origins of Chemical Evolution. Accounts of Chemical Research. 45/12, 2012. In this popular publication of the American Chemical Society, an editorial introduction for a special issue with twenty contributions about how primal cosmic and earthly material substrates are being realized as innately conducive for living systems to arise and evolve. This edition could be joined with Astrochemistry and Astrobiology (Springer, 2013) to document how these revolutionary vistas of a genesis universe are now being proven. And we ought to see this advance from both sides. While the roots and seeds of life are found to run deeper into native biochemical precursors, the condensed matter ground studied by statistical physics or mechanics (check journals by those titles) is becoming animated by way of its nonlinear, nonequilbrium, self-organizing propensities. Along with dedicated studies as “On the Origin of Single Chirality of Amino Acids and Sugars in Biogenesis” by Jason Hein and Donna Blackmond, a number of articles such as “From Prelife to Life: How Chemical Kinetics Become Evolutionary Dynamics” by Irene Chen and Martin Nowak present synoptic reviews. In regard, this paper, along with “Ocean-Atmosphere Interactions in the Emergence of Complexity in Simple Chemical Systems,” Elizabeth Griffith, et al, “Systems of Creation: The Emergence of Life from Nonliving Matter,” Stephen Mann, “Toward Self-Constructing Materials” by Nicolas Giuseppone, and “Digital and Analog Chemical Evolution” by Jay Goodwin, et al, are noted herein, search each name.

The origins of life on Earth, the remarkable result of chemical evolution through emerging self-assembly into ever-increasing hierarchical complexity in structure and function, remains one of the greatest research challenges of our time. These diverse approaches to deconvolution and reintegration of the origins of the cell, projected in collaboration through the lens of chemical evolution, suggest a remarkable degree of intrinsic molecular intelligence that guide the bottom-up emergence of living matter. (2023) Accordingly, this issue circumscribes the functional concepts, leveraging Nature's platforms for molecular information, using its existing chemical inventory or libraries, and, with selective and judicious tinkering along the way, elaborates the basic rules of bottom-up self-assembly guided by both digital and analog molecular recognition systems. (2024)

Mallory, Stewart, et al. An Active Approach to Colloidal Self-Assembly. Annual Review of Physical Chemistry. Online November, 2017. Columbia University and Complutense University of Madrid researchers provide a tutorial about how many crystalline, (bio)molecular materials appear to possess an intrinsic motive spontaniety as they constantly assemble into viable formations.

In this review, we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field, with a specific focus on dry active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. We then discuss the case of amphiphilic and dipolar Janus particles. Finally, we show how the geometry of the colloids and/or the directionality of their interactions can be used to control the physical properties of the assembled active aggregates, and we suggest possible strategies for how to exploit activity as a tunable driving force for self-assembly. (Abstract)

Colloids are a homogeneous, noncrystalline substance consisting of large molecules or ultramicroscopic particles of one substance dispersed through a second substance. Colloids include gels, sols, and emulsions; the particles do not settle and cannot be separated out by ordinary filtering or centrifuging like those in a suspension.

Mann, Stephen. New Paradigms at the Proto-life/Synthetic Biology Interface. http://wyss.harvard.edu/viewevent/181/new-paradigms-at-the-protolifesynthetic-biology-interface. A November 2011 presentation at a Harvard University Origins of Life Initiative Forum by the University of Bristol Director of the Centre for Organized Matter Chemistry. And as such work grows in number and reach, we seem to be closing on the discovery of an inherent rootedness of living systems and beings in a fertile “inorganic, physical” material nature. Check Mann’s website at www.inchm.bris.ac.uk/mann/webpage.htm for his diverse projects and publications.

The advent of life from pre-biotic origins remains a deep and possibly inexplicable scientific mystery. Nevertheless, the logic of living cells offers potential insights into an unknown proto-biological world that can be used to stimulate novel advances in living technologies, artificial life and systems chemistry. In this talk, I will review some recent studies undertaken in our laboratory that provide alternative paradigms at the interface between proto-life research and synthetic biology. Two themes will be addressed (somewhat obliquely!). Firstly, can proteins maintain their structure and function in the absence of water (or any other solvent) whilst retained in the liquid state? And secondly, can protocell models be constructed without an enclosing organic membrane?

Specifically, I will describe our current studies on the first known examples of solvent-less liquid proteins, including studies on the dioxygen binding and temperature-dependent chain unfolding properties of liquid myoglobin. Then I will discuss our recent investigations on artificial protocells that are derived from inorganic or membrane-free compartmentalization, and illustrate respectively how such structures can be used as bio-inorganic reactors for enzyme catalysis and in vitro gene expression, or as a plausible model of pre-biotic organization. (Abstract)

Supramolecular Templating of Organized Inorganic Matter. Organized-matter chemistry is concerned with the synthesis, characterization and application of complex materials that exhibit order on length scales from the molecular to macroscopic. This talk will present an overview of several recent strategies in which the synthesis of organized inorganic nanostructures is controlled by organic supramolecular structures. A key aspect of this approach is the integration of organic self-organization and inorganic assembly such that hybrid materials are constructed by direct or synergistic templating. This principle will be illustrated using several examples of our most recent work including the synthesis and assembly of mesostructured silica in lipid helicoids and tobacco mosaic virus liquid crystals, DNA-driven self assembly of gold nanorods, and the surfactant-mediated synthesis of linear chains of nanoparticles and nanofilament arrays in water-in-oil microemulsions. (Mann’s website)

Mann, Stephen. Systems of Creation: The Emergence of Life from Nonliving Matter. Accounts of Chemical Research. 45/12, 2012. The University of Bristol chemist and author introduces his project to vitalize past and future, as if a first and second genesis. This new article makes much of nature’s proclivity to form viable enclosed cellular entities, often nested in one another. Again the main features of life’s origin and evolution are Compartmentalization, Metabolism, and Replication, powered by flows of energy. Indeed, as do others, mechanical terms are used, along with material substrates as “nonliving” or inorganic. But in these many papers the active presence of nonlinear dynamics, often autopoietic in kind, is fully accepted and assumed, as if a worldwide cosmic Copernican revolution on the horizon.

Complex processes of compartmentalization, replication, metabolism, energization, and evolution provide the framework for a universal biology that penetrates deep into the history of life on the Earth. However, the advent of protolife systems was most likely coextensive with reduced grades of cellularity in the form of simpler compartmentalization modules with basic autonomy and abridged systems functionalities (cells focused on specific functions such as metabolism or replication). In this regard, we discuss recent advances in the design, chemical construction, and operation of protocell models based on self-assembled phospholipid or fatty acid vesicles, self-organized inorganic nanoparticles, or spontaneous microphase separation of peptide/nucleotide membrane-free droplets. These studies represent a first step towards addressing how the transition from nonliving to living matter might be achieved in the laboratory. They also evaluate plausible scenarios of the origin of cellular life on the early Earth. (Abstract)

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