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

1. Ecosmopoiesis: An Autocatalytic, Bootstrap, Self-Made UniVerse

Unterberger, Jeremie and Philippe Nghe. Stoechiometric and Dynamical Autocatalysis for Diluted Chemical Reaction Networks. arXiv:2109.01130. We cite this entry by University of Lorraine and University of Paris chemists as an example of novel appreciations of the widespread, diverse presence and importance of natural catalytic self-creativity. In regard, one might well view a human functional identity as “ecosmic catalysts” as we may begin to intentionally take up and continue life’s future genesis.

Autocatalysis in a variety of active forms is being found to underlie the ability of chemical and biochemical systems to replicate. Here we study a topological condition for autocatalysis, namely: restricting the reaction network to highly diluted species, and assume a strongly connected component with at least one reaction with multiple products. We find this condition to be necessary and sufficient for stoechiometric autocatalysis. (Abstract excerpt)

Our main result in a nutshell: The chemical mechanism that epitomizes the ability of living systems to reproduce themselves is autocatalysis, namely, catalysis brought about by one of the products of the reactions. Autocatalysis must have been present from the early stages of the origin of life, from primitive forms of metabolism to autocatalytic sets based on the first catalytic biopolymers and the emergence of sustained template-based replication of nucleic acids. Diverse artificial autocatalytic systems have been implemented in the laboratory, and remnants of ancestral autocatalytic networks may be found in extant metabolic network. (1)

Vinicius, Lucio. Modular Evolution. Cambridge: Cambridge University Press, 2010. Reviewed much more in Systems Evolution, a University of Cambridge, Leverhulme Centre for Human Evolutionary Studies, postdoctoral fellow joins the overdue project to revise quite inadequate theories of life’s sequential rise from microbe to artifice.

Finally, it is impossible to ignore an apparent analogy between the transition to human history and the origin of life itself. As seen earlier, life can be equated with the origin of the DNA World, which established a distinction between the first exclusive information carrier (DNA) and the first exclusively functional entities (proteins). Similarly to the autocatalytic ribozymes that transferred its information roles to DNA and functional roles to proteins in the DNA World, thus becoming the mediator and regulator between the two new molecular types, historical humans seem to have evolved into mediators between cultural information predominantly stored in extended information carriers on the one hand, and the production of cultural extended phenotypes on the other: those two processes could be seen as ‘education’ and ‘work’ respectively. (205)

Virgo, Nathaniel. The Necessity of Extended Autopoiesis. Adaptive Behavior. Online April 16, 2019. Amongst an ongoing discussion of how living organisms continue to vitalize and compose themselves, an Earth-Life Science Institute, Tokyo research professor defends a wider view, which the Abstract notes, which expands beyond just a bodily locus. The target article for this commentary is Are Living Beings Extended Autopoietic Systems? by Mario Villalobos and Pablo Razeto-Barry (online January).

The theory of autopoiesis holds that an organism can be defined as a network of processes. However, an organism also has a physical body. The relationship between these two things—network and body—has been raised in this issue of Adaptive Behaviour, with reference to an extended interpretation of autopoiesis. This perspective holds that the network and the body are distinct things, and that the network should be thought of as extending beyond the boundaries of the body. The relationship between body and network is subtle, and I revisit it here from the extended perspective. I conclude that from an organism = network perspective, the body is a biological solution to the problem of maintaining both the distinctness of an organism, separate from but engaged with its environment and other organisms, and its distinctiveness as a particular individual. (Abstract)

Virgo, Nathaniel, et al. Complex Autocatalysis in Simple Chemistries. Artificial Life. 22/2, 2016. Virgo, and Takashi Ikegami, University of Tokyo, and Simon McGregor, University of Sussex seem to be encountering a fertile material cosmos with a propensity to develop and organize itself into biomolecules innately fit for life’s evolution. By some license, might we imagine an Autocatalytic Cosmos, whereof we peoples might aspire to be Cosmic Catalysts so as to intentionally carry forth?

Life on Earth must originally have arisen from abiotic chemistry. Since the details of this chemistry are unknown, we wish to understand, in general, which types of chemistry can lead to complex, lifelike behavior. Here we show that even very simple chemistries in the thermodynamically reversible regime can self-organize to form complex autocatalytic cycles, with the catalytic effects emerging from the network structure. We demonstrate this with a very simple but thermodynamically reasonable artificial chemistry model. By suppressing the direct reaction from reactants to products, we obtain the simplest kind of autocatalytic cycle, resulting in exponential growth. When these simple first-order cycles are prevented from forming, the system achieves superexponential growth through more complex, higher-order autocatalytic cycles. This leads to nonlinear phenomena such as oscillations and bistability, the latter of which is of particular interest regarding the origins of life. (Abstract)

Wagner, Nathaniel, et al. Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior. Life. 9/2, 2019. Ben-Gurion University, Centro de Astrobiologia, Madrid, and Williams College, MA researchers including Gonen Ashkenasy advance understandings of how intrinsic network topologies played a prime generative role to faciliatate the comings together of biomolecules on their way to evolution and us.

We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems. (Abstract)

Walker, Sara Imari and Paul Davies. The Algorithmic Origins of Life. Journal of the Royal Society Interface. 10/Art.79, 2013. Reviewed much more in Origin of Life, a major theoretical articulation of something innately procreative going on by its own quickening Earthly and cosmic selves.

Wang, Qingpu and Oliver Steinbock. Materials Synthesis and Catalysis in Microfluidic Devices: Prebiotic Chemistry in Mineral Membranes. ChemCatChem. 12/1, 2020. In this ChemPubSoc Europe journal, Florida State University chemists (search OS) add further confirmation of auto-creative processes by which living systems bootstrapped themselves into biocomplex emergence. In this edition, “self-organized compositional gradients,” among other forces are seen in progressive evolutionary effect. See also in this journal Thermodynamically and Kinetically Controlled Reactions in Biocatalysis by Stefan Marsden, et al (12/2) and Nature is the Cure: Engineering Redox Cofactors for Biomimetic and Bioinspired Catalysts by Marine Desage El Murr (12/1).

The processes that led to the origins of life possibly occurred in the inorganic precipitate membranes of alkaline hydrothermal vents. These geochemical systems provide spatial confinement, cross‐membrane gradients, and catalytic surfaces. Their study is challenging due to the vast parameter space and the need to maintain nonequilibrium conditions for long times. Microfluidic approaches offer an efficient solution by allowing the formation of mineral membranes at the interface of flowing reactant solutions and the control of steep gradients. In this minireview, we summarize recent progress with this approach and discuss their catalytic properties in the context of prebiotic chemistry. (Abstract excerpt)

Weller-Davies, Oliver, et al. Combinatorial Results for Network-Based Models of Metabolic Origins. arXiv:1910.09051. Oxford University and University of Canterbury New Zealand (Mike Steel) researchers advance the case that autocatalytic phenomena, broadly conceived, played an important role as sustainable, complex living systems proceeded to boot themselves up and running.

Witzany, Guenther. Crucial Steps to Life: From Chemical Reactions to Code Using Agents. BioSystems. Online December, 2015. The Austrian natural philosopher (search) continues his endeavor to scope out and articulate a genesis evolutionary synthesis distinguished by 21st century appreciations of genetic phenomena. The 20th century DNA dogmas are set aside and surpassed by realizations, much due to geneticist James Shapiro, of self-reading and editing genomes and epigenomes which take on a language-like character. In this papers Witzany comes closer to recognizing an actual independent, universal cosmic genetic code.

Also, more recent approaches that identify the key players in the emergence of biological information such as polypeptides, RNA-like polymers, and lipids and the known parameters such as viable cores, connectivity kinetics, information control, scalability, resource availability, and compartmentalization which may guide the aggregate evolution of collectively autocatalytic sets remain on the molecular stage and cannot explain how the genetic code molecules emerged into a real natural code with three inherent levels of rules (syntax, pragmatics, semantics). Mathematical analyses of network formation cannot explain the rule-based real-life interactions of social groups that share genetic identities within historically grown ecospheres. (3)

The genetic code with its typical language-like features (characters adopt syntactic, semantic, pragmatic rules) take the stage of a real natural language with the interactional group building of various RNA stem loops. The interactional and group building cooperativity of the RNA stem loops constitute the genetic code as a real natural code, not its physico-chemical key characters alone. (9) The emergence of the genetic code is not the emergence of the nucleotides which constitute the code. The origin of the genetic code as a natural language occurs exclusively within cooperative interacting RNAs. So we can define life as an emergent property of social interacting RNAs. From this perspective life is coherent with the emergence of communication, i.e. interactions based on a natural code that underlies syntactic, pragmatic and semantic rules. (13)

Wolchover, Natalie. Cosmic Triangles Open a Window to the Origin of Time. Quanta. October 29, 2019. In this posting about the bootstrap universe revival, the physics journalist continues her report begun in Physicists Uncover Geometric “Theory Space” by NW in Quanta (February 23, 2017) and herein. This review covers new work by Nima Arkani-Hamed based on The Cosmological Bootstrap: Inflationary Correlators from Symmetries and Singularities at arXiv:1811.00024, A trio of young physicists David Baumann, Gui Pimentel, and Hayden Lee (search arXiv) are profiled next. See also The Hidden Pattern by Gabriel Popkin in New Scientist for February 18, 2017, and The Bootstrap: Building Nature from the Bottom Up by Lauren Greenspan (Google title, name).

The physicists employed a strategy known as the bootstrap, a term derived from the phrase “pick yourself up by your own bootstraps” (instead of pushing off of the ground). The approach infers the laws of nature by considering only the mathematical logic and self-consistency of the laws themselves, instead of building on empirical evidence. Using the bootstrap philosophy, the researchers derived and solved a concise mathematical equation that dictates the possible patterns of correlations in the sky that result from different primordial ingredients. (2)

Wolchover, Natalie. Physicists Uncover Geometric “Theory Space.”. Quanta. February 23, 2017. The science writer reviews the “bootstrap” concept, which was first proposed by Geoffrey Chew in the 1960s as a theory of a self-creative cosmic emergence. While respected, it was tabled until a 2010s burst of interest gave it a new currency. This entry is well paired with a 2019 update Cosmic Triangles Open a Window to the Origin of Time by NW (Quanta, October 29), also reviewed herein. An initial entry could be The Conformal Bootstrap by David Poland and David Simmons-Duffin in Nature Physics (12/535, 2016) about its latest insightful technicalities. The luminous work of Alexander Polyakov and Nima Arkani-Hamed, both now at IAS Princeton, is profiled next, again the unfolding advance is well posted on arXiv.

In the 1960s, the charismatic physicist Geoffrey Chew espoused a radical vision of the universe, and with it, a new way of doing physics. Theorists of the era were struggling to find order in an unruly zoo of newfound particles. They wanted to know which ones were the fundamental building blocks of nature and which were composites. But Chew, a professor at the University of California, Berkeley, argued against such a distinction. “Nature is as it is because this is the only possible nature consistent with itself,” he wrote at the time. He believed he could deduce nature’s laws solely from the demand that they be self-consistent. Particles, Chew said, “pull themselves up by their own bootstraps.” (1)

As the new generation of bootstrappers explores this abstract theory space, they seem to be verifying the vision that Chew, now 92 and long retired, laid out half a century ago — but they’re doing it in an unexpected way. Their findings indicate that the set of all quantum field theories forms a unique mathematical structure, one that does indeed pull itself up by its own bootstraps, which means it can be understood on its own terms. (2) As physicists use the bootstrap to explore the geometry of this theory space, they are pinpointing the roots of “universality,” a remarkable phenomenon in which identical behaviors emerge in materials as different as magnets and water. (2)

It’s far from clear whether our own universe holographically emerges from a conformal field theory in the way that AdS universes do, or if this is even the right way to think about it. The hope is that, by bootstrapping their way around the unifying geometric structure of possible physical realities, physicists will get a better sense of where our universe fits in the grand scheme of things — and what that grand scheme is. (5)

Xavier, Joana, et al. Autocatalytic Chemical Networks at the Origin of Metabolism. Proceedings of the Royal Society B. March, 2020. Early evolution theorists posted in Germany, Austria, the USA, New Zealand and Portugal including Stuart Kauffman continue to highlight the intrinsic significance of nature’s self-activation propensity to get life going. A graphic image of a global oxygen-independent prokaryotic metabolism displays many instances where biochemical catalysts are in effect. Might we at some point gain a wider appreciation of a autocatalytic ecosmos which organizes itself at each scale? Are we peoples now the intended selves as cosmic catalysts to begin its future genesis phase by our own initiative the next step by our own initiative?

Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How these self-sustaining networks arose at life's origin is an open question. Here we identify reflexively autocatalytic food-generated networks (RAFs) as self-sustaining networks that collectively catalyse all their reaction. Our studies suggest that RAFs identify attributes of biochemical origins conserved in metabolic networks. RAFs are consistent with an autotrophic origin of metabolism and indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life. (Abstract excerpt)

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