III. Ecosmos: A Procreative Organic Habitable UniVerse
2. An Autocatalytic, Bootstrap EcosmoVerse
Hunding, Alex, et al. Compositional Complementarity and Prebiotic Ecology in the Origin of Life. BioEssays. 28/4, 2006. An international group coordinated by Robert Root-Bernstein moves beyond the gene or metabolism first version to propose that life arose not by a single entity or event but via conducive pre-biotic ecosystems. Biochemical precursors that complement each other fuse into networks and systems of increasing viable complexity. These diverse, interactive molecular communities then bootstrap a Darwinian evolution impelled by dynamic self-assembly.
In sum, self-organization, reproduction and inheritable variations emerge from composomal systems when they are kept away from equilibrium by coupling their assembly, chemistry and fission-fusion processes to an external free energy source in such a way as to evolve compartmentalization and autocatalysis. (405) The theme of this paper is that the co-evolution of populations of molecularly diverse aggregates (composomes) selected on the basis of molecular complementarity and the emergence of modular functionality forms a basis for addressing some of the issues raised by the origin of life….In this picture, life emerged as a functioning ecological system through a process of integration from diverse components, not as a single entity that subsequently evolved by an as-yet-unknown process into an ecologically diverse system. Rather, we have described a continuous process by which increasingly complex, integrated, self-replicating, autocatalytic, modular systems evolve new properties in tandem with their environments. (409-410)
Jee, Ah-Young, et al. Catalytic Enzymes are Active Matter. Proceedings of the National Academy of Sciences. 115/E10812, 2018. Center for Soft and Living Matter, Institute for Basic Science, South Korea researchers including Tsvi Tlusty cite theoretical and experimental reasons why this biological substance can well exhibit spontaneous activity.
Using a microscopic theory to analyze experiments, we demonstrate that enzymes are active matter. Superresolution fluorescence measurements—performed across four orders of magnitude of substrate concentration—show that catalysis boosts the motion of enzymes to be superdiffusive for a few microseconds, enhancing their effective diffusivity over longer timescales. Occurring at the catalytic turnover rate, these fast ballistic leaps maintain direction over a duration limited by rotational diffusion, driving enzymes to execute wormlike trajectories by piconewton forces. These findings violate the classical paradigm that chemical reaction and motility are distinct processes, and suggest reaction–motion coupling as a general principle of catalysis. (Abstract excerpt)
Kamimura, Atsushi and Kunihiko Kaneko. Molecular Diversity and Network Complexity in Growing Protocells. arXiv:1904.08094. University of Tokyo, Universal Biology Institute researchers continue their project (search KK) to explain how life gained its cellular vitalities by here adding an important presence of catalytic activities.
A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. We then study how the molecule species diversify and complex catalytic reaction networks develop through the evolutionary course. It is shown that molecule species first appear, at some generations, as parasitic ones that do not contribute to replication of other molecules. With this successive increase of host species, a complex joint network evolves. The present study sheds new light on the origin of molecular diversity and complex reaction network at the primitive stage of a cell. (Abstract excerpt)
Lancet, Doron. Systems Protobiology: Origin of Life by Mutually Catalytic Networks. Life. Online July, 2018. A Special Issue proposal by the Weizmann Institute of Science geneticist, which is open for papers until February 2019. Its intent is to be a space for extensive reviews and integrations of the equal presence and importance at life’s onset of active network phenomena along with biochemical, nucleotide molecules. We cite an edited write up, from which one might surmise that the particulate, nodal RNA mode and their metabolic, linked interconnections arose in tandem as archetypal complements. See Hordijk, et al above for an initial paper.
NASA’s definition of minimal life asserts that “Life is a self-sustaining chemical system capable of Darwinian evolution.” A majority opinion (RNA first) contends that self-sustaining and replicating capacities can only be attained via templating biopolymers, which copy sequence information. An alternative approach (metabolism first) claims that life began with mutually-catalytic networks, endowed with self-sustaining and reproduction capabilities, via network structures. RNA first implies that a single type of molecule with high internal complexity could jump-start life, later recruiting metabolism and enclosure. Metabolism first takes the stand that life was a multi-component network of diverse interacting molecules right from the beginning. In published research it is shown that such networks constitute not only a catalysis-based metabolism, but also compartmental and replication traits. This scenario is obviously much more life-like, and is analyzable by tools of the newly emerging disciplines of Systems Biology and Systems Chemistry. This special issue proposes a “Systems Protobiology”, as a composite merger for research to define and understand early protocellular life forms. (Proposal edits)
Liu, Yu and David Sumpter. Spontaneous Emergence of Self-Replication in Chemical Reaction Systems. arXiv:1801.05872. Uppsala University mathematicians contribute theoretical explanations about innate originations of living systems by way of an array of multi-catalytic agencies and processes. Cosmic material nature thus appears to be graced with such fertile, life-bearing propensities from universe to us, we peoples whom may reconstruct in wonderment.
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? We set up a general model for chemical reaction systems that properly accounts for energetics, kinetics and the conservation law. We find that (1) some systems are collectively-catalytic where reactants are transformed into end products with the assistance of intermediates, while some others are self-replicating where different parts replicate each other and the system self-replicates as a whole; (2) many alternative chemical universes often contain one or more such systems; (3) it is possible to construct a self-replicating system where the entropy of some parts spontaneously decreases, in a manner similar to that discussed by Schrodinger; (4) complex self-replicating molecules can emerge spontaneously and relatively easily from simple chemical reaction systems through a sequence of transitions. (Abstract)
Lockwood, Michael. The Labyrinth of Time: Introducing the Universe. Cambridge: Cambridge University Press, 2007. Amongst a standard review of quantum and relativity physics and cosmology is a chapter on the surprising occurrence, in this frame, of life’s autocatalytic, corporeal complex systems and sapient knowledge. Such an incongruity is then seen to be of sufficient import as to presage a transformative paradigm shift in our understanding of universe and human. A good example of the juxtaposition of waning and waxing cosmologies.
The emergence of order is far from being unique to the living world. Indeed, we have already, …encountered a non-biological illustration of the general principle that we are exploring here: the formation, by way of gravitational clumping, of galaxies, stars, and planetary systems. Suppose we separate off the universe’s gravitational degrees of freedom, thereby treating the ambient gravitational field as the ‘environment’ in which matter and (non-gravitational) radiation act out their parts in the cosmic play. Then the way in which the rich structures that comprise the subject matter of astronomy come into existence and maintain themselves in being. Even at a cosmic scale, the universe reveals itself as a self-organizing system. (260)
Nghe, Philippe, et al. Prebiotic Network Evolution. Molecular BioSystems. 11/3206, 2015. Reviewed in Origin of Life, in a Royal Society of Chemistry journal, after decades of origin of life studies to identify many relevant components, this premier paper with eight authors including Stuart Kauffman, Sara Walker, Wim Hordijk, and Niles Lehman can now aver an equally important presence of interconnective dynamics which altogether initiate the cellular ascent of organisms. “Collective autocatalytic sets” as an independent source prior to biochemistry, composed of characteristic “entity nodes and relational edges,” are seen to empower a “self-sustaining” vital organization.
Palyi, Gyula, et al, eds. Advances in Asymmetric Autocatalysis. Cambridge, MA: Academic Press, 2017. University of Modena, Italy and University of Pannonia, Hungary editors gather chapters about life’s deep propensity to catalyze, activate, organize itself by way of intrinsic, recurrent drives, structures and processes all the way from universe to us. A typical chapter is The Importance of Parachirality in Life Science by Noriko Fujii, et al.
Asymmetric autocatalysis is a chemical reaction which leads from achiral starting materials to chiral products, and in which the product accelerates its own formation reaction (conventional catalysis) and promotes the prevalence of its own chiral configuration (asymmetric induction). The book contains expert-contributed chapters that describe the most exciting recent developments in the field of the Soai reaction and in related topics, ranging from mechanistic studies and theoretical research, to practical problems in chiral syntheses and products.
Peng, Peng, Zhen, et al. An Ecological Framework for the Analysis of Prebiotic Chemical Reaction Networks. Journal of Theoretical Biology. Vol. 507, 2020. Wisconsin Institute for Discovery investigators including David Baum describe detailed experimental results that advance the vital role played by primordial autocatalytic chemicals and reactions so that biocomplex systems could come together on their way to life’s evolutionary development. See also Universal Motifs and the Diversity of Autocatalytic Systems by Alex Blokhuis, et al in PNAS (41/25230, 2020) for another strong endorsement.
It is becoming widely accepted that very early in life’s origin, even before the emergence of genetic encoding, reaction networks of diverse chemicals might have manifested key properties of life, namely self-propagation and adaptive evolution. To explore this, we study the dynamics of chemical reaction networks within the framework of chemical ecosystem ecology. We show that seeding an autocatalytic cycle with tiny amounts of its member chemicals results in logistic growth of all member chemicals in the cycle. This finding leads to an instructive analogy between an autocatalytic cycle and a biological species. We extend this finding to show that pairs of autocatalytic cycles can exhibit competitive, predator-prey, or mutualistic associations just like biological species. The basic model developed here helps explain the onset of adaptive evolution in prebiotic chemical reaction networks. (Abstract excerpt)
Piotto, Stefano, et al. Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions. Life. Online April 4, 2019. For a special collection about The Origin and Early Evolution of Life, University of Salerno biochemists deftly discern the evident presence of such self-initiating bootstrap processes which served to get vitality and development on its long ascent to our present retro-quantification.
The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible pathway for life emergence, and is by no means be a demonstration of how life really emerged. The best we can hope for is to indicate plausible chemical–physical conditions and mechanisms that might lead to self-organizing and autopoietic systems. Here we present a stochastic simulation, based on chemical reactions already observed in prebiotic environments, that might help in the design of new experiments. We will show how the definition of simple rules for the synthesis of random peptides may lead to the appearance of networks of autocatalytic cycles and the emergence of memory. (Abstract)
Pratt, Andrew. Prebiological Evolution and the Metabolic Origins of Life. Artificial Life. 17/3, 2011. See also Origin of Life, in this extensive paper, a University of Canterbury biochemist cites Tibor Ganti’s chemoton to propose an early rudimentary phase driven by complex, self-organizing, autocatalytic networks. From this basis, key components such as phosphates, iron and sulfur and the “RNA-first” approach can be linked through a sorting out of when each chemical came into play.
Preiner, Martina, et al. Catalysts, Autocatalysis and the Origin of Metabolism. Interface Focus. October, 2019. In an 80th birthday festschrift for the NASA astrobiologist Michael Russell, Heinrich Heine University, Dusseldorf and University College London bioscientists including John F. Allen describe the presence and contribution of these innate self-activating, combining, and emergent processes as they bring life to conducive matter. Circa autumn 2019, one could surmise that an animate ecosmos is engaged in some manner of auto-creative, autopoietic, self-making enterprise. How then might we sapient beings aspire to be the selves, aka cosmic catalysts, to take up and continue?
If life on Earth started out in geochemical environments like hydrothermal vents, then it started from gases like CO2, N2 and H2. Anaerobic autotrophs still live from these gases today, and inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and in biotic systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key aspects. The H2–CO2 redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that en route to nitrogenous organic compounds and autocatalytic networks will be an important step towards understanding prebiotic chemistry. (Abstract)