Origins of Life: a Problem for Physics
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Molecular Cooperation: a Self-Less Origin of Life N
XVIIIth Intl Conf on Origin of Life 2017 (LPI Contrib. No. 1967) 4122.pdf July 16-21, 2017 at UC San Diego, CA, USA Molecular Cooperation: A Self-less Origin of Life N. Lehman1 1Department of Chemistry, Portland State University * [email protected] Introduction: Molecular cooperation is the obligate dependence of multiple information- bearing molecules on the propagation of the system as a whole. In an RNA world, multiple types of such cooperation would have been possible [1], including simple reaction pathways with more than one informational reactant, polymer strands that interact to form a catalytic whole, cross- catalysis and cyclical-catalysis, a formal autocatalytic set, and perhaps even a hypercycle. I will discuss these various types of molecular cooperation and explore how they differ from “simple” chemistry that may have many reactants but no cooperative component. Reproduction, replication, and recombination: Living systems are characterized by the propagation and proliferation of informational units as a function of time. Szathmáry [2] intro- duced a distinction between replicators and reproducers. Here, I will expand on this difference, tie them into prebiotic chemistry, and emphazise that cooperation must have played a key role in the origins of life, rather than being a later evolutionary invention. Reproduction is the ability of one molecule to catalyze the production of other, similar molecules. Replication is a sub-set of reproduction whereby a template is used to augment the creation of a second molecule from the first, one monomer at a time. Recombination is the swapping of large blocks of genetic infor- mation, rather than a series of unit-by-unit replication events. -
Comment on “Tibor Gánti and Robert Rosen” by Athel Cornish-Bowden
Comment on \Tibor G´anti and Robert Rosen" by Athel Cornish-Bowden Wim Hordijk SmartAnalaytiX.com, Lausanne, Switzerland Mike Steel Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand 1. Introduction In a recent article published in this journal [1], a comparison is made between Tibor G´anti's chemoton model and Robert Rosen's (M; R) systems. This com- parison is very insightful indeed. As the author remarks, these models seem to be two contrasting approaches, but upon closer inspection have more in common than one would initially think. At the end of the article, the author also briefly mentions related models, such as autopoietic systems and autocatalytic sets. In particular, autocatalytic sets are presented as follows [1]: \Autocatalytic sets (Kauffman, 1986) are the most different, because all of the others incorporate, at least implicitly, the idea that a min- imal self-organizing system must be small, i.e. that it must have a minimum of components. Kauffman, in contrast, made no such condition, but instead imagined self-organization as a property that might arise spontaneously in a system with enough weakly interact- ing components. As he assumed (reasonably) that the probability that any given component might catalyse a particular condensation reaction would be very small, this inevitably leads to the conclusion that the total number of components must be very large (at least Preprint submitted to Journal of Theoretical Biology October 10, 2015 millions) in order to have certainty that every reaction will have a catalyst." However, work on autocatalytic networks over the past 15 years has clearly established a contrary conclusion: autocatalytic sets of small size are not only predicted, but observed in simulations and the laboratory. -
Topological and Thermodynamic Factors That Influence the Evolution of Small Networks of Catalytic RNA Species
Downloaded from rnajournal.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Topological and thermodynamic factors that influence the evolution of small networks of catalytic RNA species JESSICA A.M. YEATES,1 PHILIPPE NGHE,2 and NILES LEHMAN1 1Department of Chemistry, Portland State University, Portland, Oregon 97207, USA 2Laboratoire de Biochimie, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), PSL Research University, CNRS UMR 8231, 75231 Paris, France ABSTRACT An RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks could have been an important feature of the RNA world during the nascent evolution of life on the Earth. However, the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self-assemble via genotype-selfish and genotype-cooperative interactions into full-length ribozymes to investigate the dynamics of small (three- and four-membered) networks. We focused on the influence of a three-membered core network on the incorporation of additional nodes, and on the degree and direction of connectivity as single new nodes are added to this core. We confirmed experimentally the predictions that additional links to a core should enhance overall network growth rates, but that the directionality of the link (a “giver” or a “receiver”) impacts the growth of the core itself. -
MMM #278 Since December 1986 SEPTEMBER 2014 – P 1
MMM #278 Since December 1986 SEPTEMBER 2014 – p 1 Two worlds of the Inner Solar System that present enormous challenges for human visitors, explorers, and settlers Feature Articles: 2 In Focus: Venus & Mercury: Why Limit Human Frontiers to Moon and Mars? 3 Venus: The Sources of Radical Transformation are already “on Location” 5 Mercury: Discovery of a hidden Settlement Sweet Spot; “Location, Location, Location” 7 Moon Base Costs: Dave Dietzler Below: Previous Articles about Venus have focused on “Aerostat stations” high above the surface, where air pressure and temperatures are human-friendly Above left: a Venus aerostat station - right: at an altitude where temperatures and pressures are benign For past articles, Visit http://www.moonsociety.org/publications/mmm_classics/ or /mmm_themes/ MMM #278 Since December 1986 SEPTEMBER 2014 – p 2 About Moon Miners’ Manifesto - “The Moon - it’s not Earth, but it’s Earth’s!” • MMM’s VISION: “expanding the human economy through of-planet resources”; early heavy reliance on Lunar materials; early use of Mars system and asteroid resources; and permanent settlements supporting this economy. • MMM’s MISSION: to encourage “spin-up” entrepreneurial development of the novel technologies needed and promote the economic-environmental rationale of space and lunar settlement. • Moon Miners’ Manifesto CLASSICS: The non-time-sensitive articles and editorials of MMM’s first twenty years plus have been re-edited, reillustrated, and republished in 23 PDF format volumes, for free downloading from this location: http://www.MoonSociety.org/publications/mmm_classics/ • MMM THEME Issues: 14 collections of articles according to themes: ..../publications/mmm_themes/ • MMM Glossary: new terms, old terms/new meanings: www.moonsociety.org/publications/m3glossary.html • MMM retains its editorial independence and serves many groups, each with its own philosophy, agenda, and programs. -
First Life in Primordial-Planet Oceans: the Biological Big Bang Gibson/Wickramasinghe/Schild First Life in Primordial-Planet Oceans: the Biological Big Bang
Journal of Cosmology First life in primordial-planet oceans: the biological big bang Gibson/Wickramasinghe/Schild First life in primordial-planet oceans: the biological big bang Carl H. Gibson 1,2 1 University of California San Diego, La Jolla, CA 92093-0411, USA [email protected], http://sdcc3.ucsd.edu/~ir118 N. Chandra Wickramasinghe3,4 3Cardiff Centre for Astrobiology, 24 Llwynypia Road, Lisvane, Cardiff CF14 0SY [email protected] Rudolph E. Schild5,6 5 Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138, USA 6 [email protected] Abstract: A scenario is presented for the formation of first life in the universe based on hydro- gravitational-dynamics (HGD) cosmology. From HGD, the dark matter of galaxies is H-He gas dominated planets (primordial-fog-particle PFPs) in million solar mass clumps (protoglobularstar- cluster PGCs), which formed at the plasma to gas transition temperature 3000 K. Stars result from mergers of these hot-gas-planets. Over-accretion causes stars to explode as supernovae that scatter life-chemicals (C, N, O, P, S, Ca, Fe etc.) to other planets in PGC clumps and beyond. These chemicals were first collected gravitationally by merging PFPs to form H-saturated, high-pressure, dense oceans of critical-temperature 647 K water over iron-nickel cores at ~ 2 Myr. Stardust fertil- izes the formation of first life in a cosmic hot-ocean soup kitchen comprised of all planets and their moons in meteoric communication, > 10100 kg in total. Ocean freezing at 273 K slows this biologi- cal big bang at ~ 8 Myr. HGD cosmology confirms that the evolving seeds of life are scattered on intergalactic scales by Hoyle-Wickramasinghe cometary panspermia. -
Foldamer Hypothesis for the Growth and Sequence Differentiation of Prebiotic Polymers
Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers Elizaveta Gusevaa,b,c, Ronald N. Zuckermannd, and Ken A. Dilla,b,c,1 aLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794; bDepartment of Chemistry, Stony Brook University, Stony Brook, NY 11794; cDepartment of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794; and dMolecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Contributed by Ken A. Dill, July 10, 2017 (sent for review December 8, 2016; reviewed by Hue Sun Chan and Steve Harvey) It is not known how life originated. It is thought that prebiotic that autocatalytic chain elongation arises from template-assisted processes were able to synthesize short random polymers. How- ligation and random breakage (13). Autocatalytic templating ever, then, how do short-chain molecules spontaneously grow of the self-replication of peptides has also been shown (14, longer? Also, how would random chains grow more informational 15). These are models of the “preinformational” world before and become autocatalytic (i.e., increasing their own concentra- heteropolymers begin to encode biological sequence–structure tions)? We study the folding and binding of random sequences relationships. of hydrophobic (H) and polar (P) monomers in a computational Another class of models describes a “postinformational” het- model. We find that even short hydrophobic polar (HP) chains can eropolymer world, in which there is already some tendency of collapse into relatively compact structures, exposing hydrophobic chains to evolve. In one such model, it is assumed that polymers surfaces. In this way, they act as primitive versions of today’s pro- serve as their own templates because of the ability of certain het- tein catalysts, elongating other such HP polymers as ribosomes eropolymers to concentrate their own precursors (16–19). -
Primordial Planets, Comets and Moons Foster Life in the Cosmos
Primordial planets, comets and moons foster life in the cosmos Carl H. Gibsona*, N. Chandra Wickramasingheb and Rudolph E. Schildc a UCSD, La Jolla, CA, 92093-0411, USA; b Cardiff Univ., Cardiff, UK; c Harvard, Cambridge, MA, USA ABSTRACT A key result of hydrogravitational dynamics cosmology relevant to astrobiology is the early formation of vast numbers of hot primordial-gas planets in million-solar-mass clumps as the dark matter of galaxies and the hosts of first life. Photon viscous forces in the expanding universe of the turbulent big bang prevent fragmentations of the plasma for mass scales smaller than protogalaxies. At the plasma to gas transition 300,000 years after the big bang, the 107 decrease in kinematic viscosity ν explains why ~3x107 planets are observed to exist per star in typical galaxies like the Milky Way, not eight or nine. Stars form by a binary accretional cascade from Earth-mass primordial planets to progressively larger masses that collect and recycle the stardust chemicals of life produced when stars overeat and explode. The astonishing complexity of molecular biology observed on Earth is possible to explain only if enormous numbers of primordial planets and their fragments have hosted the formation and wide scattering of the seeds of life virtually from the beginning of time. Geochemical and biological evidence suggests that life on Earth appears at the earliest moment it can survive, in highly evolved forms with complexity requiring a time scale in excess of the age of the galaxy. This is quite impossible within standard cold-dark-matter cosmology where planets are relatively recent, rare and cold, completely lacking mechanisms for intergalactic transport of life forms. -
Exploring the Origins of Life with Autocatalytic Sets
Physical Sciences︱ The COOLscience Club Exploring the origins of life with autocatalytic sets How did we get here? ne of the most popular are still those in the fullerene family, This question has plagued theories about the beginnings which are strange, football-shaped philosophers, scientists and Oof our universe is the Big networks of carbon atoms, but even individuals alike for hundreds, Bang theory. This is the idea that the largest of these contains just the universe started as an infinitely 70 atoms. if not thousands of years. How did our complex chemistry evolve? The COOL Science Club explore questions around Evolved species, such as dense and warm point that suddenly the origin of life. humans, are incredibly complex violently expanded within just a few Fullerenes aren’t found everywhere. systems, even down to the fractions of a second. While the exact Many planets only have very simple microscopic cellular level, beginning of the universe, what molecules, composed of less than structures. Understanding how such in 1971. Later on, the theory was and understanding our own happened within the first trillionth of 10 atoms. So how did such simple sets work might not just give us a further developed by him and others, origins of life and how our Professor Stuart Kauffman and a trillionth of a second, still has many chemical building blocks come deeper understanding of the origins of with computational and experimental collaborators are working on the theory DNA came to be what we mysteries, scientists now have many together to create the complexity our life but pave the way to new living studies looking to investigate and of autocatalytic sets. -
Spontaneous Formation of Autocatalytic Sets with Self-Replicating Inorganic Metal Oxide Clusters
Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters Haralampos N. Mirasa, Cole Mathisa, Weimin Xuana, De-Liang Longa, Robert Powa, and Leroy Cronina,1 aSchool of Chemistry, University of Glasgow, G12 8QQ Glasgow, United Kingdom Edited by Thomas E. Mallouk, The Pennsylvania State University, University Park, PA, and approved March 25, 2020 (received for review December 10, 2019) Here we show how a simple inorganic salt can spontaneously form of any added ligands or reducing agents (14). When a reducing autocatalytic sets of replicating inorganic molecules that work via agent is used, it is possible to produce a family of reduced clusters ≡ 3– molecular recognition based on the {PMo12} [PMo12O40] Keggin where the nuclearity can increase up to a maximum of 368 and ≡ 22– ion, and {Mo36} [H3Mo57M6(NO)6O183(H2O)18] cluster. These diverse structures such as nanosized spheres {Mo132}, wheels 16– small clusters are able to catalyze their own formation via an autocat- {Mo154}, capped wheels {Mo248} ≡ [H16Mo248O720(H2O)128] ,and alytic network, which subsequently template the assembly of gigantic 48– “lemon”-shaped {Mo368} ≡ [H16Mo368O1032(H2O)240(SO4)48] ≡ 14– molybdenum-blue wheel {Mo154} [Mo154O462H14(H2O)70] ,{Mo132} clusters (Fig. 1). Even with a reducing agent less than 10 specific ≡ VI V 42– [Mo 72Mo 60O372(CH3COO)30(H2O)72] ball-shaped species contain- classes of large reduced molybdate clusters are known (Fig. 1) ing 154 and 132 molybdenum atoms, and a {PMo12}⊂{Mo124Ce4} ≡ VI V VI V 5– despite an incalculable number of possibilities, and the reactions [H16Mo 100Mo 24Ce4O376(H2O)56 (PMo 10Mo 2O40)(C6H12N2O4S2)4] that form the clusters are fast. -
Prebiotic Network Evolution: Six Key Parameters
Molecular BioSystems Prebiotic Network Evolution: Six Key Parameters Journal: Molecular BioSystems Manuscript ID MB-ART-09-2015-000593.R1 Article Type: Review Article Date Submitted by the Author: 02-Oct-2015 Complete List of Authors: Nghe, Philippe; CNRS ESPCI ParisTech, Laboratoire de Biochimie Hordijk, Wim; SmartAnalytiX.com, Kauffman, Stuart; Institute for Systems Biology, Walker, Sara; Arizona State University, School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science Schmidt, Francis; University of Missouri, Biochemistry Kemble, Harry; CNRS ESPCI ParisTech, Yeates, Jessica; Portland State University, Chemistry Lehman, Niles; Portland State University, Department of Chemistry Page 1 of 36 Molecular BioSystems Prebiotic Network Evolution: Six Key Parameters Philippe Nghe 1†, Wim Hordijk 2†, Stuart A. Kauffman 3, Sara I. Walker 4, Francis J. Schmidt 5, Harry Kemble 1, Jessica A.M. Yeates 6, and Niles Lehman 6* 1 Laboratoire de Biochimie, CNRS - ESPCI ParisTech, France 2 SmartAnalytiX.com, Lausanne, Switzerland 3 Institute for Systems Biology, Seattle, WA 98109 USA 4 School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287 USA 5 Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA 6 Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207 USA †These authors contributed equally to this work. *To whom correspondence should be addressed at: Niles Lehman Department of Chemistry Portland State University PO Box 751 Portland, OR 97207 +1-503-725-8769 [email protected] 1 Molecular BioSystems Page 2 of 36 Abstract The origins of life likely required the cooperation among a set of molecular species interacting in a network. -
Origin of Life Ashwini Kumar Lal Ministry of Statistics & Programme Implementation Government of India, New Delhi Abstract
1 Origin of Life by Ashwini Kumar Lal Ministry of Statistics & Programme Implementation Government of India, New Delhi Abstract The evolution of life has been a big enigma despite rapid advancements in the field of astrobiology, astrophysics and genetics in recent years. The answer to this puzzle has been as mindboggling as the riddle relating to evolution of Universe itself. Despite the fact that panspermia has gained considerable support as a viable explanation for origin of life on the Earth and elsewhere in the Universe, the issue however, remains far from a tangible solution. This paper examines the various prevailing hypotheses regarding origin of life like abiogenesis, RNA World, iron-sulphur world, panspermia, and concludes that delivery of life-bearing organic molecules by the comets in the early epoch of the Earth alone possibly was not responsible for kickstarting the process of evolution of life on our planet. Key words : Abiogenesis, Biopoiesis Panspermia, LUCA, Microbes, Thermophiles, Extremophiles, Cyanobacteria, RNA world, Miller-Urey Experiment, Iron - sulphur world, Comets 2 Introduction: The question of evolution of life on the Earth and elsewhere in the Universe has ever been as challenging as the question of evolution of the Universe itself. Science does not provide authentic explanation regarding the origin of the Universe in the controversial ‘Big Bang’ theory for evolution of the Universe (Arp et al. 1990), nor does it provide any satisfactory explanation regarding the origin of life despite considerable advancements -
Presentation
IRENA MAMAJANOV FROM MESSY CHEMISTRY TO THE ORIGINS OF LIFE Habitability: Producing Conditions Conducive to Life LPI “First Billion Years” Conference Series September 9 2019 PLANETARY HABITABILITY AS PERCEIVED BY A CHEMIST WHAT IS HABITABILITY ANYWAY? Planetary habitability is the measure of a planet's or a natural satellite's potential to develop and sustain life. EARTH-CENTRIC? DEFINITION OF LIFE LIFE IS A SELF-SUSTAINING SYSTEM CAPABLE OF DARWINIAN EVOLUTION NASA Working Definition HOW WE STUDY ORIGINS OF LIFE TWO APPROACHES IN THE BROADEST SENSE ▸ More Earth biology-centric ▸ Prebiotic synthesis of biological building blocks ▸ Setting biological processes in abiotic environments ▸ Evolution of biological structures ▸ More open-ended: Building a chemical system capable of Darwinian Evolution ▸ Selectivity ▸ Replication ▸ Heredity MORE EARTH BIOLOGY-CENTRIC: UNSATISFYING? TV PARADOX ? ? “MORE OPEN ENDED” APPROACH ▸ Looking at systems level processes. MESSY CHEMISTRY ▸ “Systems Chemistry” usually = small defined networks ▸ “Messy Chemistry” = the network chemistry of large, “intractable”, prebiotically plausible systems. ▸ Sloppy biological processes ▸ Processes resembling biological but inefficient Small fraction of the Organic Chemistry M. Kowalik, C.M. Gothard, A.M. Drews, N.A. Gothard, B.A. Grzybowski, K.J.M. Bishop, Parallel optimization of synthetic pathways within the network of organic chemistry. Angew. Network (~0.001%). Chem. Int. Ed. 51, 7928-7932 (2012). EVOLUTION OF THE CHEMOSPHERE AND BIOCHEMICAL NETWORKS Biomimetic Systems Systems approximating biological fUnction • Protoenzymes • Protocells Open-Ended Systems Systems having no predetermined limit or boundary • Autocatalytic systems M. Kowalik, C.M. Gothard, A.M. Drews, N.A. Gothard, B.A. Grzybowski, K.J.M. Bishop (2012) Angew. Chem. Int. Ed. 51:7928-7932 Small fraction of the Organic Chemistry Network (~0.001%).