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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. -
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). -
Phd Projects at the Institute of Origins
PhD projects at the Institute of Origins. A list of possible PhD projects at the Institute of Origins appear in the following pages. If you have any questions regarding any projects please contact the individual supervisors. Also if you have other suggestions for a project please contact us as well. The chemical composition of star forming regions near and far .................................... 3 ! Modelling the solubilities of organic solids in hydrocarbon liquids: application to the geology and astrobiology of Titan. .................................................................................... 4! Modeling turbulent flows in solar quiescent prominences ...............................................5! The zoo of exo-planets..................................................................................................8! Understanding the formation of heavy negative ions at Titan and Enceladus................9! Mapping anthropogenic versus natural sources of atmospheric CO2 ............................11! Probing Large Scale Structure with High Energy Neutrinos.........................................13! Future Moon Missions and High Energy Neutrinos ......................................................15! Measuring Cosmic Particles and the Upper Atmosphere with LOFAR.........................17! Mimicking planetary environments for assessing the survivability of bacterial organisms within an artificial environmental chamber. A combined planetary atmosphere and microbiological study for exploring panspermia................................ -
Origins of Life: a Problem for Physics
Origins of Life: A Problem for Physics Sara Imari Walker School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe AZ USA; Blue Marble Space Institute of Science, Seattle WA USA E-mail: [email protected] Abstract. The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the origin of life for those new to the origin of life field, with a forward look towards considering what it might take for a physical theory that universally explains the phenomenon of life to arise from the seemingly disconnected array of ideas proposed thus far. The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins. arXiv:1705.08073v1 [q-bio.PE] 23 May 2017 CONTENTS 2 Contents 1 Introduction 2 2 Knowns and unknowns in solving the origin of life 4 2.1 One planet, one sample: The significance of anthropic bias . .5 2.2 Two paths to a solution . -
Carl Sagan 1934–1996
Carl Sagan 1934–1996 A Biographical Memoir by David Morrison ©2014 National Academy of Sciences. Any opinions expressed in this memoir are those of the author and do not necessarily reflect the views of the National Academy of Sciences. CARL SAGAN November 9, 1934–December 20, 1996 Awarded 1994 NAS Pubic Welfare Medal Carl Edward Sagan was a founder of the modern disci- plines of planetary science and exobiology (which studies the potential habitability of extraterrestrial environments for living things), and he was a brilliant educator who was able to inspire public interest in science. A visionary and a committed defender of rational scientific thinking, he transcended the usual categories of academia to become one of the world’s best-known scientists and a true celebrity. NASA Photo Courtesy of Sagan was propelled in his careers by a wealth of talent, By David Morrison a large share of good luck, and an intensely focused drive to succeed. His lifelong quests were to understand our plane- tary system, to search for life beyond Earth, and to communicate the thrill of scientific discovery to others. As an advisor to the National Aeronautics and Space Administration (NASA) and a member of the science teams for the Mariner, Viking, Voyager, and Galileo missions, he was a major player in the scientific exploration of the solar system. He was also a highly popular teacher, but his influence reached far beyond the classroom through his vivid popular writing and his mastery of the medium of television. The early years Born in 1934, Sagan grew up in a workingclass Jewish neighborhood of Brooklyn, New York, and attended public schools there and in Rahway, New Jersey. -
An Evolving Astrobiology Glossary
Bioastronomy 2007: Molecules, Microbes, and Extraterrestrial Life ASP Conference Series, Vol. 420, 2009 K. J. Meech, J. V. Keane, M. J. Mumma, J. L. Siefert, and D. J. Werthimer, eds. An Evolving Astrobiology Glossary K. J. Meech1 and W. W. Dolci2 1Institute for Astronomy, 2680 Woodlawn Drive, Honolulu, HI 96822 2NASA Astrobiology Institute, NASA Ames Research Center, MS 247-6, Moffett Field, CA 94035 Abstract. One of the resources that evolved from the Bioastronomy 2007 meeting was an online interdisciplinary glossary of terms that might not be uni- versally familiar to researchers in all sub-disciplines feeding into astrobiology. In order to facilitate comprehension of the presentations during the meeting, a database driven web tool for online glossary definitions was developed and participants were invited to contribute prior to the meeting. The glossary was downloaded and included in the conference registration materials for use at the meeting. The glossary web tool is has now been delivered to the NASA Astro- biology Institute so that it can continue to grow as an evolving resource for the astrobiology community. 1. Introduction Interdisciplinary research does not come about simply by facilitating occasions for scientists of various disciplines to come together at meetings, or work in close proximity. Interdisciplinarity is achieved when the total of the research expe- rience is greater than the sum of its parts, when new research insights evolve because of questions that are driven by new perspectives. Interdisciplinary re- search foci often attack broad, paradigm-changing questions that can only be answered with the combined approaches from a number of disciplines. -
Isoprene Rule Revisited 242:2 R9–R22 Endocrinology REVIEW Terpenes, Hormones and Life: Isoprene Rule Revisited
242 2 Journal of S G Hillier and R Lathe Isoprene rule revisited 242:2 R9–R22 Endocrinology REVIEW Terpenes, hormones and life: isoprene rule revisited Stephen G Hillier1 and Richard Lathe2 1Medical Research Council Centre for Reproductive Health, University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh, UK 2Division of Infection and Pathway Medicine, University of Edinburgh Medical School, Edinburgh, UK Correspondence should be addressed to S G Hillier or R Lathe: [email protected] or [email protected] Abstract The year 2019 marks the 80th anniversary of the 1939 Nobel Prize in Chemistry awarded Key Words to Leopold Ruzicka (1887–1976) for work on higher terpene molecular structures, including f isoprene the first chemical synthesis of male sex hormones. Arguably his crowning achievement f terpene was the ‘biogenetic isoprene rule’, which helped to unravel the complexities of terpenoid f steroid biosynthesis. The rule declares terpenoids to be enzymatically cyclized products of f evolution substrate alkene chains containing a characteristic number of linear, head-to-tail f great oxidation event condensed, C5 isoprene units. The number of repeat isoprene units dictates the type of f Ruzicka terpene produced (i.e., 2, monoterpene; 3, sesquiterpene; 4, diterpene, etc.). In the case of triterpenes, six C5 isoprene units combine into C30 squalene, which is cyclized into one of the signature carbon skeletons from which myriad downstream triterpenoid structures are derived, including sterols and steroids. Ruzicka also had a keen interest in the origin of life, but the pivotal role of terpenoids has generally been overshadowed by nucleobases, amino acids, and sugars. -
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.