III. Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet, Incubator Lifescape

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

Kulikov, Vladislav, et al. Spontaneous Assembly of an Organic-Inorganic Nucleic Acid Z-DNA Double Helix Structure. Angewandte Chemie International Edition. 56/4, 2017. If one may translate this technical contribution by a nine member team based at coauthor Leroy Cronin’s University of Glasgow chemistry laboratory, its content strongly implies an abiding chemical nature with a fertile biological essence. Over cosmic and Earthly evolution, complex biochemicals and genetic nucleotide molecules innately form on their own due to endemic energies and material qualities. A note on Cronin’s website is also appended to further qualify. An Organic, Animate, Conducive Universe this gains a proven validity, and now awaits our phenomenal human recognition and continuance.

Herein, we report a hybrid polyoxometalate organic–inorganic compound, Na2[(HGMP)2Mo5O15]⋅7 H2O (1; where GMP=guanosine monophosphate), which spontaneously assembles into a structure with dimensions that are strikingly similar to those of the naturally occurring left-handed Z-form of DNA. The helical parameters in the crystal structure of the new compound, such as rise per turn and helical twist per dimer, are nearly identical to this DNA conformation, allowing a close comparison of the two structures. Solution circular dichroism studies show that compound 1 also forms extended secondary structures in solution. Gel electrophoresis studies demonstrate the formation of non-covalent adducts with natural plasmids. Thus we show a route by which simple hybrid inorganic–organic monomers, such as compound 1, can spontaneously assemble into a double helix without the need for a covalently connected linear sequence of nucleic acid base pairs. (Abstract)

Genetic material in the form of DNA and RNA is essential for life and evolution, but how did it first arise? This is a big mystery and poses a classic ‘chicken and egg’ conundrum: what type of molecule could have determined the sequence of the very molecule in which sequence is encoded? Researchers in the Cronin Group have reported an organic-inorganic compound whose structure closely resembles the naturally occurring Z-form of DNA which forms simply by mixing molybdate with GMP at low pH. It is hoped that the structure could open new avenues in the exploration of the transition between biologically inert matter and living systems. (http://www.chem.gla.ac.uk/cronin)

Lambert, Jean-Francois and Maguy Jaber. Minerals and Origins of Life. Life. Online, 2018. Sorbonne Universite and Institut Universitaire de France materials scientists explain and post this special open issue about realizations that nature’s cosmic materiality seems to be an inherently suitable substrate for the occasion and rise of living systems. See, e.g., How do Nucleotides Adsorb onto Clays? and especially The Paleomineralogy of the Hadean Eon (Morrison, Runyon and R. Hazen herein).

When life arose on our planet, a complex mineral world was already present and certainly interacted with the first biomolecules. How it channeled chemical evolution has been the subject of much speculation; specific roles for minerals have been invoked for the emergence of the three main distinguishing features of life: Information storage, metabolism, and compartmentalization. Mineral surfaces may have aided selectivity in adsorption and/or polymerization, thus forming a subset in the space of possible proteins and nucleic acids. A lot remains to be understood concerning the relevant molecular surfaces and their interactions with biomolecules.

As regards metabolic activity, mineral surfaces are well-known as catalysts, but they can act as reaction media offering thermochemical conditions and allow macroscopic gradients and cyclical variations to produce the molecular-level imbalances characteristic of life. This includes chemical energy in the form of molecular-scale concentration gradients, and the appearance of proto-metabolic cycles including reactions with mineral surfaces. Minerals may also have played a role in compartmentalization, to offset dilutions that would destroy emerging prebiotic systems. (Issue proposal excerpts)

Lambert, Neill, et al. Quantum Biology. Nature Physics. 9/1, 2013. As life is being found to root ever into material depths and evolutionary time, RIKEN Advanced Science Institute, Japan, National Cheng Kung University, Taiwan, National Taiwan University, and University of Michigan biophysicists note the many ways that organic phenomena such as photosynthesis, magnetoreception, olfaction, enzyme catalysis, and so on can be traced to and seen as a signature of fertile quantum foundations.

Before the twentieth century, biology and physics rarely crossed paths. Biological systems were often seen as too complex to be penetrable with mathematical methods. After all, how could a set of differential equations or physical principles shed light on something as complex as a living being? In the early twentieth century, with the advent of more powerful microscopes and techniques, researchers began to delve more deeply into possible physical and mathematical descriptions of microscopic biological systems1. Some famous examples (among many) include Turing patterns and morphogenesis, and Schrödinger’s lecture series and book ‘What is Life?,’ in which he predicted several of the functional features of DNA. The pace of progress in this field is now rapid, and many branches of physics and mathematics have found applications in biology; from the statistical methods used in bioinformatics, to the mechanical and factory-like properties observed at the microscale within cells. (10)

Lanza, Robert. Biocentrism: How Life and Consciousness are the Keys to Understanding the True Nature of the Universe. New York: BenBella Books, 2009. A book noted as another sign of a growing cosmic reconception in terms of animate, risen, mindful vitality. But alas, it is one person’s well intentioned effort based on some seven claims drawn from a take of quantum physics sans much evidence, at best based on J. A. Wheeler’s vision that sentient observers are necessary to bring physical matter into overt reality.

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.

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