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

3. Supramolecular Systems Chemistry

McGregor, Simon, et al. Evolution of Associative Learning in Chemical Networks. PLoS Computational Biology. 8/11, 2012. By sophisticated experiments, McGregor and Phil Husbands, University of Sussex, Vera Vasas, Universitat Autònoma de Barcelona, and Christantha Fernando, University of London, bioinformation specialists find in these interactive chemistries an innate propensity to perform cognitive operations so as to enhance their viability. If this article is seen along with many similar reports across a quickening nature, at what point might we be able to imagine and realize a self-learning and self-discovering cosmic genesis?

Organisms that can learn about their environment and modify their behaviour appropriately during their lifetime are more likely to survive and reproduce than organisms that do not. While associative learning – the ability to detect correlated features of the environment – has been studied extensively in nervous systems, where the underlying mechanisms are reasonably well understood, mechanisms within single cells that could allow associative learning have received little attention. Here, using in silico evolution of chemical networks, we show that there exists a diversity of remarkably simple and plausible chemical solutions to the associative learning problem, the simplest of which uses only one core chemical reaction. We then asked to what extent a linear combination of chemical concentrations in the network could approximate the ideal Bayesian posterior of an environment given the stimulus history so far? This Bayesian analysis revealed the ‘memory traces’ of the chemical network. The implication of this paper is that there is little reason to believe that a lack of suitable phenotypic variation would prevent associative learning from evolving in cell signalling, metabolic, gene regulatory, or a mixture of these networks in cells. (Abstract)

Merindol, Remi and Andreas Walther. Materials Learning from Life: Concepts for Active, Adaptive and Autonomous Molecular Systems. Chemical Society Reviews. 46/5588, 2017. In a Chemical Systems Out of Equilibrium collection, Albert-Ludwigs University chemists well scope out the present state of science and art for condensed harder and softer matter studies into the 2010s. At once, nature’s chemical reactivity is seen to spring from vital thermodynamic complexities as it proceeds to structure and organize itself. As these inherent qualities become better quantified and understood, a radical new phase of intentional synthetic procreation is foreseen on the way to a better world.

Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed life provides the best demonstrations of complex and functional out-of-equilibrium systems: cells keep track of time, communicate, move, adapt, evolve and replicate continuously. Stirred by the understanding of biological principles, artificial out-of-equilibrium systems are emerging in many fields of soft matter science. Here we put in perspective the molecular mechanisms driving biological functions with the ones driving synthetic molecular systems. Focusing on principles that enable new levels of functionalities (temporal control, autonomous structures, motion and work generation, information processing) rather than on specific material classes, we outline key cross-disciplinary concepts that emerge in this challenging field. (Abstract)

Mikhailov, Alexander and Gerhard Ertl. Chemical Complexity: Self-Organization Processes in Molecular Systems. Switzerland: Springer Frontiers, 2017. A. Mikhailov and G. Ertl are senior physical chemists at the Fritz Haber Institute, Berlin. Ertl received the 2007 Nobel Prize in Chemistry for studies of catalytic self-organization processes in surface reactions. Typical chapters are Thermodynamics of Open Systems, Self-Assembly Phenomena, and Chemical Oscillations.

This book provides an outline of theoretical concepts and their experimental verification in studies of self-organization phenomena in chemical systems, as they emerged in the mid-20th century and have evolved since. Traditionally, physical chemistry has been concerned with interactions between atoms and molecules that produce a variety of equilibrium structures - or the 'dead' order - in a stationary state. But biological cells exhibit a different 'living' kind of order, prompting E. Schrödinger to pose his famous question “What is life?” in 1943. Through an unprecedented theoretical and experimental development, it was later revealed that biological self-organization phenomena are in complete agreement with the laws of physics, once they are applied to a special class of thermodynamically open systems and non-equilibrium states. This knowledge has in turn led to the design and synthesis of simple inorganic systems capable of self-organization effects.

Mueck, Leonie. Quantum Reform. Nature Chemistry. 7/5, 2015. An update survey of quantum systems chemistry which has become a field in its own right. In one more way this arcane realm is brought into the same natural fold, albeit with special features such as “quantum algorithms” for dynamic chemical processes. The International Congress of Quantum Chemistry is noted, Google for its large 2012 (Colorado) and 2015 (China) conferences.

Nicolaou, Zachery, et al.. Prevalence of Multistability and Nonstationarity in Driven Chemical Networks. Journal of Chemical Physics. June, 2023. ZN, University of Washington, Adilson Motter, Northwestern University and Jason Green, UMass Boston survey a spontaneous prebiotic liveliness which seems to presage animate varieties. Once again, an array of phenomenal propensities are seen altogether to lay down a path to evolution and maybe our curious Earthkinder.

External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, and alter their dynamical function. Here, we analyze changes giving rise to complex behavior in relatively random networks under external driving forces. When subject to an influx and outflux of chemical species, the steady state can undergo bifurcations and multistable oscillations. We then show that catalysis plays an important role in the emergence of animate complexity. Our results suggest that these innate conditions can be seen to engender biochemical processes and abiogenesis. (Abstract excerpt)

Nitschke, Jonathan. Molecular Networks Come of Age. Nature. 462/736, 2009. A Cambridge University chemist cites the work of Ludlow and Otto above, and a growing corpus to laud the novel thermodynamic and kinetic approaches being applied to material systems.

What is systems chemistry? It’s the study of complex systems, or networks, of molecules. Tools for analyzing complex networks are being developed and employed in fields as diverse as computer science and sociology. By applying these tools to systems of interacting molecules – molecules that might link together into larger superstructures, or catalyse one another’s formation – chemists can investigate how interactions between members propagate through networks, allowing complex behaviour to emerge. (736)

Pandoli, Omar and Gian Piero Spada. The Supramolecular Chemistry between Eastern Philosophy and the Complexity Theory. Journal of Inclusion Phenomena and Macrocyclic Chemistry. 65/1-2, 2009. A unique contribution in this important periodical that needs to be read in its entirety. Pandoli, University of Ferrera, presently Shanghai Jiao Tong University, and Spada, University of Bologna, achieve an extraordinary synthesis across the ages between an innately creative natural systems substance and the essences of holistic perennial wisdom, as especially its Taoist dynamics of Yin and Yang. Both of these disparate encounters report and reflect an informed matter that repeatedly organizes itself as it arises, grows, quickens, and personifies.

How supramolecular chemistry interplays between the eastern philosophy and the complexity theory relationship? From which point could we start to speak about the fundamental self-organization process that seems to be “the driving force that lead up to the evolution of the biological word from the inanimate matter”? We think the best way is to focus on the core, and move around a core concept: the self-processes in Nature are the starting point for the whole organic world. Taking suggestion from the old eastern philosophy and observing the recent western theory in this paper we will evidence some analogies between the two apparent different thoughts and show that both approaches want to know more about the emerging of life from inanimate matter. In this perspective we underline that Supramolecular Chemistry, investigating the emerging behaviour or properties of the whole complex system, has a central role to understand the spontaneous evolution of Nature. In this paper we introduce, first, some basic principles of the ancient eastern philosophy in synergy with the modern science of the complexity. Second, the theories dealing with autopoietic systems and dissipative structures, will be presented in order to compare biological and social mechanisms with the (organic) chemistry world. (205)

A complex adaptive system is also called “multi-agents system” in which the components of the system are considered a simple agent. In the first case the ignorant agent operates with spontaneous actions of trial and error to reach its own utility or goal. In this case, it acts without following an outline of rules of his wider environment. In the second case the selfish agent operates, at the beginning, locally without the cooperation of his neighborhood but, step by step his action changes something in the whole system with a global effect. This spontaneously global effect comes, or emerges, from a mutual adaptation of the simple agents that became a community of cooperative agents. (209)

The Journal of Inclusion Phenomena and Macrocyclic Chemistry is the premier publication reporting on original, interdisciplinary research on all aspects of host-guest systems. Specific areas of interest include the preparation and characterization of new hosts and new host-guest systems, especially those involving macrocyclic ligands; crystallographic, spectroscopic, thermodynamic and theoretical studies; applications in chromatography and inclusion polymerization; enzyme modelling; molecular recognition and catalysis by inclusion compounds; intercalates in biological and non-biological systems, cyclodextrin complexes and their applications in the agriculture, flavoring, food and pharmaceutical industries; synthesis, characterization and applications of zeolites.

Pross, Addy. Toward a General Theory of Evolution: Extending Darwinian Theory to Inanimate Matter. Journal of Systems Chemistry. 2/1, 2011. In this new online resource, the Ben Gurion University of the Negev chemist embellishes his deeper rootings of life through fertile chemical soils into its “physical” substrate. Six qualities of living systems in such regard are far-from-equilibrium, complexities, homochirality, teleonomic character, dynamic autocatalysis, and diverse adaptation. Although not ready to admit an implied organic cosmos, or genetic guise for these dynamics, (see Hillier) this epic morphing from old machine to phenomenal genesis grows in veracity.

Though Darwinian theory dramatically revolutionized biological understanding, its strictly biological focus has resulted in a widening conceptual gulf between the biological and physical sciences. In this paper we strive to extend and reformulate Darwinian theory in physicochemical terms so it can accommodate both animate and inanimate systems, thereby helping to bridge this scientific divide. The extended formulation is based on the recently proposed concept of dynamic kinetic stability and data from the newly emerging area of systems chemistry. The analysis leads us to conclude that abiogenesis and evolution, rather than manifesting two discrete stages in the emergence of complex life, actually constitute one single physicochemical process. (Abstract, 1)

2.1.2. Complexification at Both Chemical and Biological Levels. The above results, though still limited in scope, suggests that cooperative behavior can emerge and manifest itself at the molecular level, that the drive toward more complex replicating systems appears to underlie chemical, and not just biological, replicators. The implications of these preliminary findings appear to be far-reaching. They suggest that the biological drive toward greater complexity has its roots in chemistry, that the entire evolutionary process can be traced back to kinetic forces at the molecular level! (3-4)

Raucci, Umberto, et al. Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing, and Cloud Computing. Annual Review of Physical Chemistry. 74/313, 2023. National Accelerator Lab, Menlo Park, CA, and Stanford University scientists lay out tutorial research pathways with the aim of advancing beneficial chemical innovations by means of these novel title abilities. As a result, a new frontier opens as a new (second) substantial (re)creation.

Modern quantum chemistry algorithms are now able to quite enhance the prediction of nove molecular formulations and properties. Despite this progress, performing such calculations is not readily accessible since a domain expertise, programming skills, and powerful hardware is required. In this review, we discuss how to create practical platforms that can compute quantum chemistry properties such as artificial intelligence–driven input methods, and extended reality visualization. (Excerpt)

Reiher, Markus. Special Issue on Quantum Information in Chemistry. International Journal of Quantum Chemistry. 115/19, 2015. An ETH Zurich physical chemist and group leader introduces a cross-fertilization of quantum information processing methods with chemical research which is increasingly adopting a systems, network, and computational character. Some entries are Geometric Phases in Quantum Information, Orbital Entanglement in Quantum Chemistry, and The Radical Pair Mechanism and the Avian Chemical Compass.

Ruben, Mario, et al. Hierarchical Self-Assembly of Supramolecular Spintronic Modules into 1D- and 2D- Architectures with Emergence of Magnetic Properties. Chemistry: A European Journal. 11/1, 2005. Deep in the primary scientific literature a new universe is being uncovered whose matter is not a lumpen dross but which organizes itself in a progressive scale of complex, animate systems.

Ruiz-Mirazo, Kepa, et al. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chemical Reviews. 114/1, 2014. Ruiz-Mirazo, University of the Basque Country systems biophysicist and philosopher, Carlos Briones, Spanish National Research Council astrobiologist, and Andreas de la Escosura, Autonomous University of Madrid biochemist survey this historic project to reconstruct how living, evolving systems came to be. With 85 pages, 1,000 references, and a reach beyond biomolecules to chemical, thermodynamic and physical substrates and energies involved, it is a most comprehensive review to date. For starters, as now common, “life” is said to be represented by three main features – replication, metabolism, and compartments. In addition, conducive “prebiotic” conditions of complex biochemicals, autocatalysis, far-from-equilibrium states, morphogenesis, along with self-organizing and assembling dynamics from which life arose need to be included. Such emergent systems composed of “a great diversity of components with multiple interactions between them,” give rise to “global properties and dynamic behaviors.”

A more integral, expansive scenario is thus laid out, which quite implies an independent fertile nature able to do this. We also cite in Organic Universe and Origin of Life as a good example of the incipient cosmic revolution from insensate machine to organic genesis. But not yet, e.g., “metabolic machinery” is still used. While not the authors charge, the issue of what kind of overall reality must there be to inherently spawn living creatures, pregnant with people, does not enter. The contradiction of trying to explain and ground life, evolution and persons in a barren, hostile universe as the rarest accident must be soon resolved. However to add, might the whole 21st century project be equated with a further transition to a planetary progeny?

Although finding consensus about the nature and definition of life is a very difficult issue, and will remain as a subject of debate probably for a long time, there is nowadays relatively widespread agreement on which features should be shared by the simplest living systems. They must possess a genetic apparatus able to store and transmit information to their progeny, some sort of metabolism for gathering nutrients and energy from the environment, and a selectively permeable boundary that separates and distinguishes them from that environment. Hence, in order to explain how the first organisms might have appeared on Earth, or elsewhere, it is necessary to develop chemistries that enable the synthesis of information-bearing polymers, protometabolic networks, and protocellular compartments under compatible prebiotic conditions. Moreover, there is the need for finding thermodynamically and kinetically plausible pathways to integrate the three kinds of subsystems into far-from-equilibrium, autonomous agents with open-ended evolution capacities. (349)

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