Origins of Life
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Building Blocks That Fall from the Sky
Building blocks that fall from the sky How did life on Earth begin? Scientists from the “Heidelberg Initiative for the Origin of Life” have set about answering this truly existential question. Indeed, they are going one step further and examining the conditions under which life can emerge. The initiative was founded by Thomas Henning, Director at the Max Planck Institute for Astronomy in Heidelberg, and brings together researchers from chemistry, physics and the geological and biological sciences. 18 MaxPlanckResearch 3 | 18 FOCUS_The Origin of Life TEXT THOMAS BUEHRKE he great questions of our exis- However, recent developments are The initiative was triggered by the dis- tence are the ones that fasci- forcing researchers to break down this covery of an ever greater number of nate us the most: how did the specialization and combine different rocky planets orbiting around stars oth- universe evolve, and how did disciplines. “That’s what we’re trying er than the Sun. “We now know that Earth form and life begin? to do with the Heidelberg Initiative terrestrial planets of this kind are more DoesT life exist anywhere else, or are we for the Origins of Life, which was commonplace than the Jupiter-like gas alone in the vastness of space? By ap- founded three years ago,” says Thom- giants we identified initially,” says Hen- proaching these puzzles from various as Henning. HIFOL, as the initiative’s ning. Accordingly, our Milky Way alone angles, scientists can answer different as- name is abbreviated, not only incor- is home to billions of rocky planets, pects of this question. -
Prebiological Evolution and the Metabolic Origins of Life
Prebiological Evolution and the Andrew J. Pratt* Metabolic Origins of Life University of Canterbury Keywords Abiogenesis, origin of life, metabolism, hydrothermal, iron Abstract The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. The initial protometabolism was based on positive feedback loops associated with in situ carbon fixation in which the initial protometabolites modified the catalytic capacity and mobility of metal-based catalysts, especially iron-sulfur centers. A number of selection mechanisms, including catalytic efficiency and specificity, hydrolytic stability, and selective solubilization, are proposed as key determinants for autocatalytic reproduction exploited in protometabolic evolution. This evolutionary process led from autocatalytic networks within preexisting compartments to discrete, reproducing, mobile vesicular protocells with the capacity to use soluble sugar phosphates and hence the opportunity to develop nucleic acids. Fidelity of information transfer in the reproduction of these increasingly complex autocatalytic networks is a key selection pressure in prebiological evolution that eventually leads to the selection of nucleic acids as a digital information subsystem and hence the emergence of fully functional chemotons capable of Darwinian evolution. 1 Introduction: Chemoton Subsystems and Evolutionary Pathways Living cells are autocatalytic entities that harness redox energy via the selective catalysis of biochemical transformations. -
The Place of RNA in the Origin and Early Evolution of the Genetic Machinery
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: The Place of RNA in the Origin and Early Evolution of the Genetic Machinery Günter Wächtershäuser Life 2014, 4, 1050-1091, doi:10.3390/4041050 Reviewer 1: Anonymous Reviewer 2: Wolfgang Buckel Editor: Niles Lehman (Guest editor of Special Issue “The Origins and Early Evolution of RNA”) Received: 24 October 2014 First Revision Received: 2 December 2014 Accepted: 9 December 2014 Published: 19 December 2014 First Round of Evaluation Round 1: Reviewer 1 Report and Author Response In this massive and dense manuscript, Günter Wächtershäuser furthers his views and opinions on the origin and evolution of life. He reviews some of his previous work and presents an alternative to the dominant ‘Ancient RNA world’ hypothesis. The alternative views he previously generated are much expanded in this manuscript. In light of recent research developments and argumentation (some of it reviewed), his views should be considered a welcome addition to the many ideas that populate the “origin of life” field of inquiry that counter the dominant paradigm. I have however a number of quibbles that if addressed could increase the accuracy, value and impact of the manuscript. I must note that a careful evaluation of all facets requires expertise in a multitude of disciplines (from prebiotic chemistry and structural biology to evolutionary bioinformatics and biochemistry) and considerable time, none of which I possess. Therefore, my comments will be slanted by my own expertise and will only serve the author as a partial devil’s advocate effort General commentary Section 1. The place of RNA in LUCA (page 2): In search of features that are more conserved (carrying deep phylogenetic memory) than the sequence of genes, Wächtershäuser focuses on a paper of his in Systematic and Applied Microbiology (1998) that uses gene content and order of microbial genomes to make inferences about the last universal common ancestor (LUCA) of cellular life. -
The Difficult Case of an RNA-Only Origin of Life
Emerging Topics in Life Sciences (2019) 3 469–475 https://doi.org/10.1042/ETLS20190024 Perspective The difficult case of an RNA-only origin of life Kristian Le Vay and Hannes Mutschler Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Downloaded from https://portlandpress.com/emergtoplifesci/article-pdf/3/5/469/859756/etls-2019-0024c.pdf by Max-Planck-Institut fur Biochemie user on 28 November 2019 Correspondence: Hannes Mutschler ([email protected]) The RNA world hypothesis is probably the most extensively studied model for the emergence of life on Earth. Despite a large body of evidence supporting the idea that RNA is capable of kick-starting autocatalytic self-replication and thus initiating the emergence of life, seemingly insurmountable weaknesses in the theory have also been highlighted. These problems could be overcome by novel experimental approaches, including out-of- equilibrium environments, and the exploration of an early co-evolution of RNA and other key biomolecules such as peptides and DNA, which might be necessary to mitigate the shortcomings of RNA-only systems. The conjecture that life on Earth evolved from an ‘RNA World’ remains one of the most popular hypotheses for abiogenesis, even 60 years after Alex Rich first put the idea forward [1]. For some, evi- dence based upon ubiquitous molecular fossils and the elegance of the idea that RNA once had a dual role as information carrier and prebiotic catalyst provide overwhelming support for the theory. Nevertheless, doubts remain surrounding the chemical evolution of an RNA world, whose classical scenario is based on a temporal sequence of nucleotide formation, enzyme-free polymerisation/replica- tion, recombination, encapsulation in lipid vesicles (or other compartments), evolution of ribozymes and finally the innovation of the genetic code and its translation (Figure 1)[2,3]. -
Chemical Evolution Theory of Life's Origins the Lattimer, AST 248, Lecture 13 – P.2/20 Organics
Chemical Evolution Theory of Life's Origins 1. the synthesis and accumulation of small organic molecules, or monomers, such as amino acids and nucleotides. • Production of glycine (an amino acid) energy 3HCN+2H2O −→ C2H5O2N+CN2H2. • Production of adenine (a base): 5 HCN → C5H5N5, • Production of ribose (a sugar): 5H2CO → C5H10O5. 2. the joining of these monomers into polymers, including proteins and nucleic acids. Bernal showed that clay-like materials could serve as sites for polymerization. 3. the concentration of these molecules into droplets, called protobionts, that had chemical characteristics different from their surroundings. This relies heavily on the formation of a semi-permeable membrane, one that allows only certain materials to flow one way or the other through it. Droplet formation requires a liquid with a large surface tension, such as water. Membrane formation naturally occurs if phospholipids are present. 4. The origin of heredity, or a means of relatively error-free reproduction. It is widely, but not universally, believed that RNA-like molecules were the first self-replicators — the RNA world hypothesis. They may have been preceded by inorganic self-replicators. Lattimer, AST 248, Lecture 13 – p.1/20 Acquisition of Organic Material and Water • In the standard model of the formatio of the solar system, volatile materials are concentrated in the outer solar system. Although there is as much carbon as nearly all other heavy elements combined in the Sun and the bulk of the solar nebula, the high temperatures in the inner solar system have lead to fractional amounts of C of 10−3 of the average. -
GENOME BIOLOGY and EVOLUTION (Online ISSN 1759-6653)
GENOME BIOLOGY AND EVOLUTION (Online ISSN 1759-6653) Founding Editor: Takashi Gojobori Editor-in-Chief: William Martin Editorial Assistant: Alison Bentley Editorial Board Names and full contact details for members of the editorial board are available at: www.oxfordjournals.org/our_journals/gbe/editorial_board.html. Information for Authors Information on preparing and submitting manuscripts and a Manuscript Submission Checklist are available at www.oxfordjournals.org/our_journals/gbe/for_authors/. SOCIETY FOR MOLECULAR BIOLOGY AND EVOLUTION www.smbe.org COUNCIL Michael Lynch, President Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405 USA. E-mail: [email protected]. Jody Hey, President-Elect Department of Genetics, Rutgers University, 604 Allison Road, Piscataway, NJ 08854 USA. E-mail: [email protected]. Paul Sharp, Past President Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT UK. E-mail: [email protected]. Jianzhi George Zhang, Secretary Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Kraus Natural Science Building, 830 N. University, Ann Arbor, MI 48109-1048 USA. E-mail: [email protected]. John Archibald, Treasurer Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5 Canada. E-mail: [email protected]. Laura Landweber, Councillor (2007–2009) Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1003 USA. E-mail: lfl@princeton.edu. Ziheng Yang, Councillor (2008–2010) Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK. E-mail: [email protected]. Dan Graur, Councillor (2009–2011) Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001 USA. -
The Origins of the RNA World
The Origins of the RNA World Michael P. Robertson and Gerald F. Joyce Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 Correspondence: [email protected] SUMMARY The general notion of an “RNA World” is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the compo- nents of RNA were available in some prebiotic pool, and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macro- molecules. A thorough consideration of this “RNA-first” view of the origin of life must recon- cile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving mole- cule, just as DNA and proteins were preceded by RNA. Outline 1 Introduction 4 Concluding remarks 2 An “RNA-first” view of the origin of life References 3 An “RNA-later” view of the origin of life Editors: John F. -
The Lamarckian Chicken and the Darwinian Egg Yitzhak Pilpel1* and Oded Rechavi2*
Pilpel and Rechavi Biology Direct (2015) 10:34 DOI 10.1186/s13062-015-0062-9 COMMENT Open Access The Lamarckian chicken and the Darwinian egg Yitzhak Pilpel1* and Oded Rechavi2* Abstract: “Which came first, the Chicken or the Egg?” We suggest this question is not a paradox. The Modern Synthesis envisions speciation through genetic changes in germ cells via random mutations, an “Egg first” scenario, but perhaps epigenetic inheritance mechanisms can transmit adaptive changes initiated in the soma (“Chicken first”). Reviewers: The article was reviewed by Dr. Eugene Koonin, Dr. Itai Yanai, Dr. Laura Landweber. Keywords: Evolution, Darwinian Evolution, Lamarckian Evolution, Modern Synthesis, Weismann Barrier, Epigenetic Inheritance, Transgenerational RNA Interference Background solution. Nevertheless, it is important to discuss why this In this commentary paper we wish to use the well- question is perceived as being paradoxical, and to exam- known “Chicken and Egg” paradox as a gateway for ine the true mystery that it holds; at the base of this discussing different processes of evolution. While in the dilemma stands an extremely important and unsolved biological sense this is not a paradox at all, the metaphor biological question: “Can the phenotype affect the is still useful because it allows examining of the distinc- genotype”? or put differently, “Can epigenetics translate tion between Lamarckian and Darwinian evolution, and into genetics”? specifically, since it enables us to raise an important and Asking the question in this manner allows mapping of unsolved question: “Can the phenotype affect the geno- the “Egg first” vs. the “Chicken first” options onto the type?” or in other words, “can epigenetics translate into distinction between Darwinian and Lamarckian evolu- genetics”? tion. -
Report for the Academic Year 1999
l'gEgasag^a3;•*a^oggMaBgaBK>ry^vg^.g^._--r^J3^JBgig^^gqt«a»J^:^^^^^ Institute /or ADVANCED STUDY REPORT FOR THE ACADEMIC YEAR 1998-99 PRINCETON • NEW JERSEY HISTORICAL STUDIES^SOCIAl SC^JCE LIBRARY INSTITUTE FOR ADVANCED STUDY PRINCETON, NEW JERSEY 08540 Institute /or ADVANCED STUDY REPORT FOR THE ACADEMIC YEAR 1 998 - 99 OLDEN LANE PRINCETON • NEW JERSEY • 08540-0631 609-734-8000 609-924-8399 (Fax) http://www.ias.edu Extract from the letter addressed by the Institute's Founders, Louis Bamberger and Mrs. FeUx Fuld, to the Board of Trustees, dated June 4, 1930. Newark, New Jersey. It is fundamental m our purpose, and our express desire, that in the appointments to the staff and faculty, as well as in the admission of workers and students, no account shall be taken, directly or indirectly, of race, religion, or sex. We feel strongly that the spirit characteristic of America at its noblest, above all the pursuit of higher learning, cannot admit of any conditions as to personnel other than those designed to promote the objects for which this institution is established, and particularly with no regard whatever to accidents of race, creed, or sex. ni' TABLE OF CONTENTS 4 • BACKGROUND AND PURPOSE 7 • FOUNDERS, TRUSTEES AND OFFICERS OF THE BOARD AND OF THE CORPORATION 10 • ADMINISTRATION 12 • PRESENT AND PAST DIRECTORS AND FACULTY 15 REPORT OF THE CHAIRMAN 18 • REPORT OF THE DIRECTOR 22 • OFFICE OF THE DIRECTOR - RECORD OF EVENTS 27 ACKNOWLEDGMENTS 41 • REPORT OF THE SCHOOL OF HISTORICAL STUDIES FACULTY ACADEMIC ACTIVITIES MEMBERS, VISITORS, -
The Emergence of Nucleic Acids in an Iron-Sulphur World
Cardiff University School of Earth, Ocean and Planetary Sciences THE EMERGENCE OF NUCLEIC ACIDS IN AN IRON-SULPHUR WORLD By Bryan Hatton Thesis submitted for the Degree of Philosophiae Doctor September 2007 UMI Number: U585139 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. Dissertation Publishing UMI U585139 Published by ProQuest LLC 2013. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 DECLARATION This work has not previously been accepted in substance for any degree and is not concurrently submitted in candidature for any degree. Signed . { 3 3 ...................(candidate) Date STATEMENT 1 This U ^j^s^being submitted in partial fulfillment of the requirements for the degree of Signed (3. r. 3 3 3 ^ 3 ^ ..............(candidate) STATEMENT 2 This thesis is the result of my own independent work/investigation, except where otherwise stated. Other sources are acknowledged by explicit references. Signed 33. (candidate) D a te <3? STATEMENT 3 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. -
EMT Biocomputing Workshop Report
FINAL WORKSHOP REPORT Sponsor: 004102 : Computing Research Association Award Number: AGMT dtd 7-2-08 Title: NSF Workshop on Emerging Models and Technologies in Computing: Bio-Inspired Computing and the Biology and Computer Science Interface. Report Prepared by: Professor Ron Weiss Departments of Electrical Engineering and Molecular Biology Princeton University Professor Laura Landweber Departments of Ecology and Evolutionary Biology and Molecular Biology Princeton University Other Members of the Organizing Committee Include: Professor Mona Singh Departments of Computer Science and Molecular Biology Princeton University Professor Erik Winfree Department of Computer Science California Institute of Technology Professor Mitra Basu Department of Computer Science Johns Hopkins University and the United States Naval Academy Workshop Website: https://www.ee.princeton.edu/Events/emt/ Draft: 09/07/2008 Table of Contents I. Executive Summary 1. Workshop Objectives 2. Summary of the Workshop Methodology and Findings 3. Recommendations II. Grand Challenges III. Breakout Group Presentations Appendices A1. Agenda A2. Participant List A3. Abstracts of Invited Presentations A4. Presentations Draft: 09/07/2008 I. Executive Summary I.1 Workshop Goals The National Science Foundation, Division of Computer and Information Science and Engineering (CISE), Computing and Communications Foundations (CCF) sponsored a Workshop on Emerging Models and Technologies in Computing (EMT): Bio- Inspired Computing. This workshop brought together distinguished leaders in the fields of synthetic biology, bio-computing, systems biology, and protein and nucleic acid engineering to share their vision for science and research and to learn about the research projects that EMT has funded. The goal was to explore and to drive the growing interface between Biology and Computer Science. -
The RNA World” Mean to “The Origin of Life”?
life Concept Paper What Does “the RNA World” Mean to “the Origin of Life”? Wentao Ma Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; [email protected] Received: 30 September 2017; Accepted: 24 November 2017; Published: 29 November 2017 Abstract: Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a relevant system that is “defined” by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution—provided that the genetic molecules can “simply” code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life.