Genesis: The Scientific Quest for Life's Origin Read online

  gen•e•sis

  gen•e•sis

  THE SCIENTIFIC QUEST FOR LIFE'S ORIGIN

  Robert M. Hazen

  Joseph Henry Press

  Washington, DC

  Joseph Henry Press 500 Fifth Street, NW Washington, DC 20001

  The Joseph Henry Press, an imprint of the National Academies Press, was created with the goal of making books on science, technology, and health more widely available to professionals and the public. Joseph Henry was one of the founders of the National Academy of Sciences and a leader in early American science.

  Any opinions, findings, conclusions, or recommendations expressed in this volume are those of the author and do not necessarily reflect the views of the National Academy of Sciences or its affiliated institutions.

  Library of Congress Cataloging-in-Publication Data

  Hazen, Robert M., 1948-

  Genesis : the scientific quest for life's origin / by Robert M. Hazen.

  p. cm.

  Includes bibliographical references and index.

  ISBN 0-309-13346-7 e-pub ISBN

  ISBN 0-309-09432-1

  1. Life—Origin. I. Title.

  QH325.H39 2005

  576.8'3—dc22

  2005012839

  Cover design by Michele de la Menardiere.

  Cover photo of microscopic vesicles courtesy of Robert M. Hazen and David W. Deamer. A key step in life's origin may have been the spontaneous assembly of these cell-like spheres of molecules.

  Illustrations on pages 18, 145, 153, 159, 195, and 226-227 by Matthew Frey, Wood Ronsaville Harlin, Inc., Annapolis, Maryland. Copyright Wood Ronsaville Harlin, Inc.

  Copyright 2005 by Robert M. Hazen. All rights reserved.

  Printed in the United States of America.

  For Glenn, Steve, and Hat

  Contents

  Prologue

  PART I EMERGENCE AND THE ORIGIN OF LIFE

  1 The Missing Law

  2 What Is Life?

  3 Looking for Life

  4 Earth's Smallest Fossils

  5 Idiosyncrasies

  Interlude—God in the Gaps

  PART II THE EMERGENCE OF BIOMOLECULES

  6 Stanley Miller's Spark of Genius

  7 Heaven or Hell?

  8 Under Pressure

  9 Productive Environments

  Interlude—Mythos Versus Logos

  PART III THE EMERGENCE OF MACROMOLECULES

  10 The Macromolecules of Life

  11 Isolation

  12 Minerals to the Rescue

  13 Left and Right

  Interlude—Where Are the Women?

  PART IV THE EMERGENCE OF SELF-REPLICATING SYSTEMS

  14 Wheels Within Wheels

  15 The Iron–Sulfur World

  16 The RNA World

  17 The Pre-RNA World

  18 The Emergence of Competition

  19 Three Scenarios for the Origin of Life

  Epilogue—The Journey Ahead

  Notes

  Bibliography

  Index

  Foreword

  A central theme of this book is the concept of emergence. What do we mean when we say that something emerges? In common usage, a shadowy figure emerges from the dark, a submarine emerges from the sea, a plot emerges in a novel. But emergence has come to have a different meaning in scientific terminology. Researchers are increasingly beginning to use emergence to describe processes by which more complex systems arise from simpler systems, often in unpredictable fashion.

  This use of the word “emergence” is in a sense the opposite of reductionism, the view that any phenomenon can be explained by understanding the parts of that system. Because reductionism has been such a powerful tool in the sciences, some scientists shy away from the concept of emergence, thinking it to be slightly weird. But there can be little doubt that the word itself is useful in referring to some of the most remarkable phenomena we observe in both nature and in the laboratory.

  An example is the way that orderly arrangements of molecules can appear spontaneously. For instance, if we add soap molecules to water, at first there is nothing present but the expected clear solution of individual molecules dissolved in the water. But at a certain concentration, additional molecules no longer dissolve but instead begin to associate into small aggregates called vesicles. And as the concentration increases, the vesicles begin to grow into membranous layers of soap molecules that cloud the originally clear solution. Finally, if we blow air through a straw into the solution, much larger structures—soap bubbles—appear at the surface.

  Such emergent phenomena—phenomena that exhibit self-organization—are common in our everyday experience. The laws of chemistry and physics permit certain kinds of molecules to self-assemble into aggregates that have surprising structures and properties. Sometimes the process is spontaneous, as in the formation of vesicles, but in other instances an input of energy is required to drive self-assembly. If we did not know by observation that soap molecules can self-assemble, we could not have predicted that vesicles would suddenly appear if we simply increased the concentration of soap molecules in solution. And even though we know that vesicles form, there is still no equation that can predict exactly what concentration of soap is required to form them.

  Life on Earth arose through a sequence of many such emergent phenomena, which define the subject of this book. Imagine that we could somehow travel back in time to the prebiotic Earth, some 4 billion years ago. It is very hot—hotter than the hottest desert today. Asteroid-sized objects bombard the surface. Comets crash through the atmosphere—no oxygen yet, just a mixture of carbon dioxide and nitrogen—and add more water to a globe-spanning ocean. Landmasses are present, but they are volcanic islands resembling Hawaii or Iceland, rather than continents.

  Imagine that we are standing on one such island, on a beach composed of black lava rocks, with tide pools containing clear seawater. We can scrutinize that water with a microscope, but there is nothing living to be seen in it, only a dilute solution of organic compounds and salts. If we could examine the mineral surfaces of the lava rocks, we would see that some of the organic compounds have formed a film adhering to the surface, while others have assembled into aggregates that disperse into the seawater.

  Now imagine that we return 100 million years later. Not much has changed. The landmasses are still volcanic islands, meteorite impacts have dwindled, and it might be a little less hot. But, when we look at the tide pools, we see a cloudiness that was not apparent earlier, and the mineral surfaces are coated with a thin film of slime. When we examine the water and lava with our microscope, we discover immense numbers of bacteria swarming in multiple layers. Life has begun.

  What happened in 100 million years that led to the origin of life? This is a fundamental question of biology, and the answer will surely change the way we think about ourselves as well as our place in the universe, because if life could begin on Earth, it could begin by similar processes on Earth-like planets circling other stars throughout the universe. The origin of life is the most extraordinary example of an emergent phenomenon, and the process by which life began must involve the same kinds of intermolecular forces and self-assembly processes that cause soap to form membranous vesicles. The origin of life must also have in some way incorporated the reactions and products that occur when energy flows through a molecular system and drives it toward ever more complex systems with emergent properties.

  This book explores the concept of emergence and the origin of life in a way that has never before been attempted. Science has thousands of investigators who pry away at highly focused aspects of the great questions, hardly awar
e of the vast unexplored problems spreading around them to the horizon. But each science has a few explorers—rare personalities willing to step back from the microscopic details, look toward the horizon, and gamble that patterns will emerge from their broader perspective. Robert Hazen is such an explorer, and this book is a journal of his explorations.

  Genesis: The Scientific Quest for Life's Origin is a pretty amazing book. Many authors of popular science books are teachers and professors, and it is only natural that their books come across that way: as lectures—factual, conceptual, theoretical. Occasionally, an author is able to assemble facts, concepts, and theory in a creative way to produce a book that introduces a significant new paradigm. Darwin did that, and more recently E. O. Wilson and Stephen Jay Gould.

  Hazen has taken a different approach, and a different set of words describes this book: It is personal, even intimate, filled with passion for the scientific enterprise. You will find facts, concepts, and theories here, too—but beyond that you will discover glimpses of scientists in action, chasing ideas in the lab and the field. You will find people struggling with experimental results, with interpretations, and with each other. You will find drama, which exists in the sciences as much as in any other human endeavor. And you will find cliffhangers: Will a future experiment show that Nick Platts' idea about primitive genetic polymers is correct? Or will it dash his hopes? Will new evidence permit a choice between the conflicting claims of Bill Schopf and Martin Brasier about the Apex Chert fossils?

  Like Wilson and Gould, Hazen is a working scientist—a mineralogist who has broadened his field of research in order to tackle, with his colleagues at the Carnegie Institution's Geophysical Laboratory, some of the deepest problems of biology. Where did organic compounds come from to kick-start the life process on the early Earth? How did life become chiral (that is, “handed”), starting with mixtures of molecules that differ only in whether their structures rotate polarized light to the left or to the right? How did metabolic pathways arise from the interaction of organic molecules and mineral surfaces? A convincing answer to any one of these questions would be a capstone to a remarkable life in science. In this book you will learn how Hazen and other explorers are struggling to find those answers.

  David Deamer

  Santa Cruz, California

  May 2005

  Preface

  And God said, “Let the waters bring forth swarms of living creatures.”

  Genesis 1:20

  How did life arise? Why are we here? For thousands of years humans have longed for answers to these deeply resonant questions.

  The Biblical account in the first chapter of Genesis, though rich in poetic metaphor, hardly puts the origin question to rest. Barring divine intervention, life must have emerged by a natural process—one fully consistent with the laws of chemistry and physics. Scientists believe in a universe ordered by natural laws; they resort to the power of observations, experiments, and theoretical reasoning to discover those laws. The methods of science are unsuited to address the “why” of our existence, but many of us feel driven to understand the nitty-gritty chemical details of how life began.

  Scientists surmise that life arose on the blasted, primitive Earth from the most basic of raw materials: air, water, and rock. Life emerged nearly 4 billion years ago by natural processes completely in accord with the laws of chemistry and physics, yet details of that transforming origin event pose mysteries as deep as any facing science. How did nonliving chemicals become alive?

  It is possible, of course, that life arose through an improbable sequence of many chemical reactions. If so, then living worlds will be rare in the universe and laboratory attempts to understand the origin process will be doomed to frustration. An unlikely sequence of unknown steps cannot be reproduced in any plausible experimental program.

  Alternatively, the universe may be organized in such a way that life emerges as an inevitable consequence of chemistry, given an appropriate environment and sufficient time. Starting with water, organic molecules, and a suitably protected energy-rich environment, life may be very likely to emerge from nonlife on any hospitable planet or moon. This scenario allows for fruitful systematic scientific study. If life is likely to arise whenever and wherever appropriate conditions occur, then scientists can hope to study life's origins in the lab through experiments that simulate those conducive conditions. Not surprisingly, most origin-of-life investigators favor the view that life is a cosmic imperative and that it is only a matter of time before we figure out how it happened. In this scenario, genesis occurs throughout the universe all the time.

  Genesis: The Scientific Quest for Life's Origin attempts to portray this great adventure—the effort to deduce how life began on the ancient Earth. The epic history of life's chemical origins is woefully incomplete. Daunting gaps exist in our knowledge, and much of what we have learned is hotly debated and subject to conflicting interpretations. Consequently, this book is as much about the process of defining what we do not know as it is about recounting well-established data and concepts. One objective of the book is to describe our present, imperfect state of understanding—and to offer a conceptually simple scenario for life's chemical origins. This theory synthesizes two fundamental frontier efforts: the mind-expanding theoretical field of emergence and the astonishing experimental discoveries in prebiotic chemistry.

  The science of emergence seeks to understand complex systems—systems that display novel collective behaviors that arise from the interactions of many simple components. From gravitational interactions of individual stars emerge the glorious sweeping arms of spiral galaxies. From the chemical interactions of individual ants emerge the extraordinarily complex social behavior of ant colonies. From the electrical interactions of individual neurons in your brain emerge thought and self-awareness. Emergence is nature's most powerful tool for making the universe a complex, patterned, entertaining place to live.

  Life itself is arguably the most remarkable of all emergent systems. Many origin-of-life experts adopt the view that life began as an inexorable sequence of emergent events, each of which was an inevitable consequence of interactions among versatile carbon-based molecules. Each emergent episode added layers of chemical and structural complexity to the existing environment. Intensive experiments at laboratories around the world reveal, step-by-step, the essential life-triggering reactions that must occur throughout the cosmos. First came the carbon-containing biomolecules, synthesized in unfathomable abundance on comets and asteroids, in the black near-vacuum of space, on the surface of the young Earth, and deep within our planet's restless crust. Then came the emergence of larger molecular structures—the selection, concentration, and assembly of life's membranes, proteins, and genetic molecules, built in part on a scaffolding of rocks and minerals. Eventually, these biomolecular structures formed self-replicating cycles—chemical systems that copied themselves and competed for a finite and dwindling supply of resources. Ultimately, competition between different self-replicating cycles triggered evolution by natural selection, and life was on its way.

  Part I introduces the theory of emergence, which provides a conceptual framework for understanding the immensely complex path from nonlife to the first living cell. Parts II, III, and IV explore experimental and theoretical attempts to understand, step by step, the specific emergent processes: the emergence of diverse biomolecules, the emergence of larger structures composed of many molecules, and finally the emergence of self-replicating collections of molecules. Be warned. Not all of these attempts are success stories: Scientific progress demands time-consuming, often tedious effort; most experiments end in failure; we spend much of our scientific lives making mistakes as fast as we can and desperately trying not to make the same mistake twice.

  The narrative focuses on the chemical transition from a prebiotic Earth rich in organic molecules to the so-called RNA World of self-replicating genetic molecules. I do not examine the important subsequent transition from the RNA World to the present wor
ld in which life is governed and sustained by DNA and proteins, nor do I examine the rich subject of life's evolution following the appearance of the first cell—both are complex topics requiring their own books.

  As in any scientific field, much of the richness of origin-of-life research lies in the details and not the overview. Thus I provide an extensive section of notes and a bibliography that directs readers to primary literature and more detailed discussions of many issues. The notes include comments and corrections from numerous experts who reviewed drafts of this book; in many instances these remarks highlight current uncertainties and controversies among scientists, including disagreements about my interpretations. Nonetheless, this book is not encyclopedic and only begins to address a vast and rapidly expanding literature. I apologize to those scientists whose important studies are not detailed.

  Why should an earth scientist, trained in the fields of mineralogy and crystallography, write such a book? By the mid-1990s, my research career at the Carnegie Institution of Washington's Geophysical Laboratory had reached a respectable plateau, achieved through two decades of solid, serviceable work in the specialized field of high-pressure crystal chemistry. With secure federal funding and a steady stream of publications, scientific life was good, at least on an immediate level; but something, I felt, was missing. The essence of science is the unmatched joy in seeking and finding answers to questions about the natural world, yet by the mid-1980s we had grasped the central principles of how crystals compress. The crystallographic questions I asked seemed increasingly narrow, while the answers provided few surprises. I was ready to try something new.