Comp. by: AbdulMalik Stage: Proof Chapter No.: FrontMatter Title Name: MOORE Date:30/8/12 Time:11:02:10 Page Number: 1 FUNGAL BIOLOGY IN THE ORIGIN AND EMERGENCE OF LIFE The rhythm of life on Earth includes several strong themes contributed by Kingdom Fungi. So why are fungi ignored when theorists ponder the origin of life? Casting aside common theories that life originated in an oceanic primaeval soup, in a deep, hot place, or even a warm little pond, this is a mycological perspective on the emergence of life on Earth. The author traces the crucial role played by the first biofilms – products of aerosols, storms, volcanic plumes and rainout from a turbulent atmosphere – which formed in volcanic caves 4 billion years ago. Moore describes how these biofilms contributed to the formation of the first prokaryotic cells, and later, unicellular stem eukaryotes, highlighting the role of the fungal grade of organisation in the evolution of higher organisms. Based on the latest research, this is a unique account of the origin of life and its evolutionary diversity to the present day. david moore is an Honorary Reader in the Faculty of Life Sciences at the University of Manchester. Having recently retired after 43 years researching and teaching genetics and mycology, his ongoing research activities include computer programs simulating fungal growth and differentiation, and geno- mic data mining. In recent years he has created the educational websites www.fungi4schools.org (sponsored by the British Mycological Society) and www.davidmoore.org.uk. He is co-author of 21st Century Guidebook to Fungi (Cambridge, 2011). Comp. by: AbdulMalik Stage: Proof Chapter No.: FrontMatter Title Name: MOORE Date:30/8/12 Time:11:02:10 Page Number: 2 Comp. by: AbdulMalik Stage: Proof Chapter No.: FrontMatter Title Name: MOORE Date:30/8/12 Time:11:02:10 Page Number: 3 FUNGAL BIOLOGY IN THE ORIGIN AND EMERGENCE OF LIFE David Moore Faculty of Life Sciences, University of Manchester Comp. by: AbdulMalik Stage: Proof Chapter No.: FrontMatter Title Name: MOORE Date:30/8/12 Time:11:02:11 Page Number: 4 cambridge university press Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo, Delhi, Mexico City Cambridge University Press The Edinburgh Building, Cambridge CB28RU, UK Published in the United States of America by Cambridge University Press, New York www.cambridge.org Information on this title: www.cambridge.org/9781107652774 © Cambridge University Press 2013 This publication is in copyright. Subject to statutory exception and to the provisions of relevant collective licensing agreements, no reproduction of any part may take place without the written permission of Cambridge University Press. First published 2013 Printed in the United Kingdom at the University Press, Cambridge A catalogue record for this publication is available from the British Library Library of Congress Cataloging in Publication data ISBN 978-1-107-65277-4 Paperback Cambridge University Press has no responsibility for the persistence or accuracy of URLs for external or third-party internet websites referred to in this publication, and does not guarantee that any content on such websites is, or will remain, accurate or appropriate. Comp. by: AbdulMalik Stage: Proof Chapter No.: FrontMatter Title Name: MOORE Date:30/8/12 Time:11:02:11 Page Number: 5 CONTENTS 1 Learning from life on Earth in the present day page 1 2 Essentials of fungal cell biology 19 3 First, make a habitat 42 4 The building blocks of life 52 5 An extraterrestrial origin of life? 62 6 Endogenous synthesis of prebiotic organic compounds on the young Earth 70 7 Cooking the recipe for life 85 8 ‘It’s life, Jim ...’ 95 9 Coming alive: what happened and where? 109 10 My name is LUCA 123 11 Towards eukaryotes 142 v Comp. by: AbdulMalik Stage: Proof Chapter No.: FrontMatter Title Name: MOORE Date:30/8/12 Time:11:02:11 Page Number: 6 vi | CONTENTS 12 Rise of the fungi 157 13 Emergence of diversity 180 References 204 Index 219 Comp. by: AbdulMalik Stage: Proof Chapter No.: 1 Title Name: MOORE Date:30/8/12 Time:11:07:45 Page Number: 1 ONE LEARNING FROM LIFE ON EARTH IN THE PRESENT DAY The only known habitat for life is the planet we call Earth. The only place we know the life experiment has been carried out is this planet Earth. We do not know how life originated here, however. Nevertheless, we understand a great deal about the physical and chemical conditions, the environments, and some of the spontaneous (‘self-organising’) mechanisms that the physics and chemistry of this Universe make possible, so there is no difficulty in formulating reasonable models for the emergence and onward evolution of living things. One of the best existing books about this topic starts like this: The main assumption held by most scientists about the origin of life on Earth is that life originated from inanimate matter through a spontan- eous and gradual increase of molecular complexity. This view was given a well-known formulation by Alexander Oparin [Oparin, 1957a], a brilliant Russian chemist who was influenced both by Darwinian theor- ies and by dialectical materialism. A similar view coming from a quite different context was put forward by J. B. Haldane [Haldane, 1929]. By definition, this transition to life via prebiotic molecular evolution excludes panspermia (the idea that life on Earth comes from space) and divine intervention. (Luisi, 2006, chapter 1,p.1) Although I intend to discuss here the notion of panspermia (see Chapter 5, below), I will not discuss the other mechanism that Pier Luigi Luisi says is excluded by prebiotic molecular evolution in the quotation above, namely divine intervention. I choose not to include this because personally I see no 1 Comp. by: AbdulMalik Stage: Proof Chapter No.: 1 Title Name: MOORE Date:30/8/12 Time:11:07:46 Page Number: 2 2 | FUNGAL BIOLOGY IN THE ORIGIN AND EMERGENCE OF LIFE need to invoke divinely magical or mythological processes in the scientific story I wish to tell: basic physics and chemistry are enough. If you want to round out your reading on the topic then I suggest you start with chapter 1 in Luisi (2006) and chapter 6 of Lurquin (2003). For the real hard-core discus- sion you don’t need to go much further than Dawkins (1986, 2006) and Scott (2009). If you put the words ‘dawkins’ and ‘god’ together in Amazon’s search window, the software will display publications on both sides of the argument, and from the number of items offered you may get an inkling of why I decided not to venture into this part of the arena! Having indicated what I will not discuss let me indicate what I will describe here. This book examines the most likely mechanisms by which life arose and progressed on Earth as we understand it from the most recent research. In many ways this book is a tourist guide in which I will escort you, the reader/tourist, through more than 4 billion years of the historical journey experienced by this planet. Because the only known habitat for life is planet Earth, we will start by examining how the habitat that has cradled the life we know about was formed. Among others, we will visit the following intellec- tual places: The formation of the Earth, in context of the origin of the Solar System, and how the basic chemistry, physics and geology of the early Earth influence the search for the origins of life. From this argument I will advance the view that the origin of life may be a logical inevitability of chemical evolution in a wide range of environmen- tal conditions and I will account for the origin of biological building blocks on a prebiological world from a wide range of sources. Although it is most frequently argued that the primitive Earth’s ocean was the one and only location in which prebiological chemical evolution could have occurred, I will develop the notion that for very extensive periods of time, billions upon billions of aerosol droplets existed all over the proto- planet Earth within which billions upon billions of different chemical reactions might have taken place, forming molecules and reaction trains that might have contributed to the origin of life. This leads naturally to speculations about evolution of almost-living protocells of all sorts: those without a genetic apparatus, those comprised of autocatalytic chemical cycles, the RNA-world and protein-world pre- cursors of living things, and those exploiting advantages of existing within lipid envelopes –with all of these existing at the same time but in different aerosol droplets. Bring those aerosols down to earth in rain or spindrift and they will form slime upon the sterile solidified volcanic lava. Where that slime is pro- tected from hostile solar radiation by tephra or in lava bubble caves something like a prebiological biofilm will form, within which all Comp. by: AbdulMalik Stage: Proof Chapter No.: 1 Title Name: MOORE Date:30/8/12 Time:11:07:46 Page Number: 3 LEARNING FROM LIFE ON EARTH IN THE PRESENT DAY | 3 pathways were effective (if they could happen, they did happen) and where they coexisted and were coextensive they could work together, creating ever more integrated and interconnected chemical systems. Life emerged from non-enzymatic systems of autocatalytic chemical cycles which later acquired the capacity of enzymatically controlled metabolism. The characteristics expressed by the earliest living, or even pre-living, things (their ‘lifestyle’) were those that today would be categorised as being heterotrophic. The first chemical machines used readily available nutrients. As these were exhausted, selective advantage was gained by those chemical machines able to release chemical catalysts into the envir- onment to degrade the tars and other polymers accumulated by hundreds of millions of years of abiotic chemical reactions.