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

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

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)

Martinez, Carlos Flores. SETI in the Light of Cosmic Convergent Evolution. Acta Astronautica. Online August, 2014. In this well written and referenced essay, a University of Heidelberg graduate student bravely contends that an intrinsic natural biogenesis is now robustly evident, if one is so inclined. A glimpse is thus achieved of a Copernican revolution from an old mechanical model to an epic revision which is increasingly obvious and proven across unifying sciences and fractal galaxies. See also a later paper by the author online November 2014 in this journal that draws upon growing evidence for a convergent evolution as a guide to seeking and finding astrolife.

Here it will be argued that nothing in astrobiology makes sense except in the light of “Cosmic Convergent Evolution” (CCE). This view of life contends that natural selection is a universal force of nature that leads to the emergence of similarly adapted life forms in analogous planetary biospheres. Although SETI historically preceded the rise of astrobiology that we have witnessed in the recent decade, one of its main tenets from the beginning was the convergence of life on a cosmic scale toward intelligent behavior and subsequent communication via technological means. The question of cultural convergence in terms of symbolic exchange, language and scientific capabilities between advanced interstellar civilizations has been the subject of ongoing debate. However, at the core of the search for extraterrestrial intelligence lies in essence a biological problem since even post-biological extraterrestrial intelligences must have had an origin based on self-replicating biopolymers. Thus, SETI assumes a propensity of the Universe towards biogenesis in accordance with CCE, a new evolutionary concept which posits the multiple emergence of life across the Cosmos. (Abstract excerpt)

Matteucci, Francesca, et al. The Chemical Evolution of the Milky Way. arXiv:1705.09596. A paper by Universita di Trieste, Osservatoria Astronomico di Bologna and Pontificia Universidad Catolica de Chile researchers. presented at the 2016 Mondello (Sicily) Frontier Research in Astrophysics II workshop. To then reflect, an auspicious human propensity and significance seems robustly evident whence worldwide collaborations can proceed to reconstruct a “galactic astroarchaeology.” What kind of cosmos requires its own consciously perceived self-description? Whom are we individual and collective sapient beings to do this, for what purpose? The conference contents in to be published by the Proceedings of Science online.

We will discuss some highlights concerning the chemical evolution of our Galaxy, the Milky Way. First we will describe the main ingredients necessary to build a model for the chemical evolution of the Milky Way. Then we will illustrate some Milky Way models which includes detailed stellar nucleosynthesis and compute the evolution of a large number of chemical elements, including C, N, O, α-elements, Fe and heavier. The main observables and in particular the chemical abundances in stars and gas will be considered. A comparison theory-observations will follow and finally some conclusions from this astroarchaeological approach will be derived. (Abstract)

McCabe, Michael and Holly Lucas. On the Origin and Evolution of Life in the Galaxy. International Journal of Astrobiology. 9/4, 2010. University of Portsmouth, UK, mathematicians extrapolate the Major Evolutionary Transitions scale, whose seven stages are here seen as (critical) self-organization, biomolecules, RNA to DNA, endosymbiosis, sexuality, multicellularity, and language, on to expanded celestial realms. In a similar vein to Milan Cirkovic (2012) and others, still another effort is made to reconceive a genesis cosmos by way of these robust, oriented biological emergences.

A simple stochastic model for evolution, based upon the need to pass a sequence of n critical steps is applied to both terrestrial and extraterrestrial origins of life. In the former case, the time at which humans have emerged during the habitable period of Earth suggests a value of n=4. Progressively adding earlier evolutionary transitions gives an optimum fit when n=5, implying either that their initial transitions are not critical or that habitability began around 6 Ga ago. The origin of life on Mars or elsewhere within the Solar System is excluded by the latter case and the simple anthropic argument is that extraterrestrial life is scarce in the Universe because it does not have time to evolve. Alternatively, the timescale can be extended if the migration of basic progenotic material to Earth is possible. If extra transitions are included in the model to allow for Earth migration, then the start of habitability needs to be even earlier than 6 Ga ago. Our present understanding of Galactic habitability and dynamics does not exclude this possibility. We conclude that Galactic punctuated equilibrium, proposed as a way round the anthropic problem, is not the only way of making life more common in the Galaxy. (Abstract)

McFadden, Johnjoe. Quantum Evolution. New York: Norton, 2001. Explores the hypothesis that the deep roots of emergent, sentient life can be traced to quantum principles.

Meyer-Ortmanns, Hildegard and Stefan Thurner, eds. Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Berlin: Springer, 2011. Jacobs University, Bremen, and University of Vienna systems physicists edit a significant volume from a 2009 Darwin conference that ranges much beyond selection to admit and entertain a stratified self-organization from cosmos to civilizations. In so doing, scientists and scholars are learning to view life’s sequential passage from universe to human, physical to planetary, in true terms of recurrent, dynamic, complex adaptive systems. Indeed “universality” is often used, whence evolution appears as a progressive iteration, as if some kind of program running itself. Chapters by Thurner, Bartelmann, Dehmelt and Bastiaens, and Frey and Reichenbach are reviewed elsewhere. But the academic endeavor seems constrained by a vested reductive method, understandably betwixt the mechanist Ptolemaic and organicist Copernican revolution. A natural philosophy able to imagine a greater genesis creation as it manifestly springs from its parent to child genetic code still eludes.

With contributions from a team of leading experts, this volume provides a comprehensive survey of recent achievements in our scientific understanding of evolution. The questions it asks concern the beginnings of the universe, the origin of life and the chances of its arising at all, the role of contingency, and the search for universal features in the plethora of evolutionary phenomena. The tools employed stem from a range of disciplines including mathematics, physics, biochemistry and cell biology. Self-organization as an overarching concept is demonstrated in the most diverse areas: from galaxy formation in the universe to spindle and aster formation in the cell. Chemical master equations, population dynamics, and evolutionary game theory are presented as suitable frameworks for understanding the universal mechanisms and organizational principles observed in a wide range of living units, ranging from cells to societies. (Publisher)

Morowitz, Harold and Eric Smith. Energy Flow and the Organization of Life. Santa Fe Institute Working Paper. 06-08-029, 2006. A biochemist and a thermodynamicist propose how living entities can be understood as an “inevitable” consequence of cosmic energetic properties. This imperative is then expressed on earth by geological processes which "forced life into existence." By their hypothesis, a universal metabolic biogenesis is traced from life’s first earthly appearance to its recapitulation in each organism today.

A deterministic emergence of life would reflect an essential continuity between physics, chemistry, and biology. It would show that a part of the order we recognize as living is thermodynamic order inherent in the geosphere, and that some aspects of Darwinian selection are expressions of the likely simpler statistical mechanics of physical and chemical self-organization. (1)

Morowitz, Harold, et al. Ligand Field Theory and the Origin of Life as an Emergent Feature of the Periodic Table of Elements. Biological Bulletin. 219/1, 2010. With co-authors Vijayasarathy Srinivasan and Eric Smith, veteran George Mason University and Santa Fe Institute researchers move closer to quantify, qualify, and admit that material earthly and cosmic nature ought to be realized as intrinsically suitable for organic evolution and our reflective witness.

The underlying theme of this essay is to show that, following from ligand field theory of transition metals and the nature of ligands produced in prebiotic synthesis experiments, life— or at least network anabolism—becomes a plausible emergent feature of the periodic table of the elements. (1) What (George) Wald was attempting—an approach that we follow — was to map biochemistry onto the underlying quantum- mechanical logic of chemistry as exhibited in the periodic table of the elements. (2)

Morrison, Shaunna, et al. The Paleomineralogy of the Hadean Eon Revisited. Life. 8/4, 2018. This paper in a special issue Minerals and Origins of Life (Lambert herein) by SM, Simone Runyon and Robert Hazen of the Carnegie Institution for Science, Washington, DC continues Hazen’s decade long project (search) to prove that planetary and extraterrestrial materials are conducive substrates for life to originate. (The Hadean Era is some 4.6 – 4.0 billion years ago.) His work with colleagues goes on to imply that appropriate mineral formations evolve in reciprocal tandem with living systems. By these insight, a long list of prebiotic organic materials and mineral species can be identified. Redox gradients and other reactivities in the mix reveal a native inherency made and meant for life to appear and develop. See also, for example Titan Mineralogy: A Window on Organic Mineral Evolution in American Mineralogist (Vol. 103, 2018).

A preliminary list of plausible near-surface minerals present during Earth’s Hadean Eon (>4.0 Ga) should be expanded to include: (1) phases that might have formed by precipitation of organic crystals prior to the rise of predation by cellular life; (2) minerals associated with large bolide impacts, especially through the generation of hydrothermal systems in circumferential fracture zones; and (3) local formation of minerals with relatively oxidized transition metals through abiological redox processes, such as photo-oxidation. Additional mineral diversity arises from the occurrence of some mineral species that form more than one ‘natural kind’, each with distinct chemical and morphological characteristics that arise by different paragenetic processes. A rich variety of chemically reactive sites were thus available at the exposed surfaces of common Hadean rock-forming minerals. (Abstract)

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