Evolution: A View from the 21st Century

273 Pages·2011·1.128 MB·English

by  James A. Shapiro

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Praise for
Evolution: A View from the 21st Century
“A novel description of evolution based on modern genetic analysis is presented in
detail. Shapiro has written a stimulating, innovative manuscript that surely Darwin
would have liked.”
—Sidney Altman, Yale University;
Nobel Laureate in Chemistry, 1989
“Based on a long and highly competent personal experience in science and his
novel insights into biological functions, the author has reached views of biological
evolution that can reveal to a wide, interested readership how the living world
co-evolves with the environment through its intrinsic powers.”
—Werner Arber, Professor Emeritus, University of Basel, Switzerland;
Nobel Laureate in Physiology/Medicine, 1978
“Professor Shapiro’s offering is the best book on basic modern biology I have ever
seen. As far as I can tell, the book is a game changer.”
—Carl Woese, University of Illinois; discoverer of Archaea, the third realm of life;
National Medal of Science 2000
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“This moving, clearly written, if complex, description of ‘natural genetic
engineering’ explains evolutionary processes that preceded people by at least 3,000
million years. Shapiro’s detailed account of ubiquitous genetic dynamism, DNA
machination, repair, and recombination in real life, bacterial to mammalian,
destroys myths. Genes, whatever they are, are not ‘eternal.’... Shapiro’s careful,
authoritative narrative...is entirely scientific and should interest all of us who care
about the evolution of genetic systems.”
—Lynn Margulis, University of Massachusetts, Amherst;
National Academy of Sciences, National Medal of Science 1999
“From revisiting the Central Dogma, to outlining a systems biological approach to
evolution, this book is a magnificent analysis of the key questions of the origin of
variation and, therefore, of evolutionary change. Starting from his early encounter
with the work and ideas of Barbara McClintock, through to his work on systems
engineering as the key to understanding organisms, Jim Shapiro has new insights on
all the central issues of evolutionary theory. The genome becomes a read-write
storage system rather than the sole determinant of heredity. After reading this book,
you will find it imperative to see biology as the 21st century is coming to see it. The
ambitious title of the book is fully justified.
This book gives solid biological evidence on the origin of variation and evolutionary
change. That evidence will surprise those who still think that variation is random.
Cells and organisms sense their environment and transmit that information to their
genomes. Brilliant.”
—Denis Noble, CBE FRS, Balliol College, Oxford;
author of The Music of Life
“Evolution, or constant change in nature, is the deepest of human ideas. It is the
core of all physical, biological, and social systems and sciences—linking energy,
matter, life, and consciousness. The dramatic genomic revolution unfolded new
informative horizons of constant combinatorial diversity, change, and emerging
innovation from simple to complex in biological evolution. Much of the
understanding of genome complex adaptive architecture, dynamic reorganization,
expression, and regulation—as well as the origin of life, cells, and biochemical
networks—is a future challenge. This book highlights the exciting challenges to
explore future nonconventional and nondogmatic vistas of evolutionary biology.
The explorative mysteries include roles in evolution of nonrandom adaptive
mutations, epigenetics, and repetitive DNA function and regulation. All contribute
to dynamic systems biology and engineering between the evolving genome, cell, and
environmental stresses and changes affecting the dynamic genome read-write
memory system underlying life’s evolution.”
—Eviatar Nevo, University of Haifa, U.S. National Academy of Sciences;
explorer of Evolution Canyon
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Evolution
A View from the 21st Century
James A. Shapiro
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Vice President, Publisher: Tim Moore
Associate Publisher and Director of Marketing: Amy Neidlinger
Acquisitions Editor: Kirk Jensen
Editorial Assistant: Pamela Boland
Development Editor: Russ Hall
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Cover Designer: Chuti Prasertsith
Managing Editor: Kristy Hart
Project Editor: Anne Goebel
Copy Editor: Gayle Johnson
Proofreader: Linda Seifert
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Senior Compositor: Gloria Schurick
Manufacturing Buyer: Dan Uhrig
©2011 by James A. Shapiro
Publishing as FT Press Science
Upper Saddle River, New Jersey 07458
FT Press Science offers excellent discounts on this book when ordered in quantity for bulk
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All rights reserved. No part of this book may be reproduced, in any form or by any means,
without permission in writing from the publisher.
Printed in the United States of America
First Printing June 2011
ISBN-10: 0-13-278093-3
ISBN-13: 978-0-13-278093-3
Pearson Education LTD.
Pearson Education Australia PTY, Limited
Pearson Education Singapore, Pte. Ltd.
Pearson Education Asia, Ltd.
Pearson Education Canada, Ltd.
Pearson Educación de Mexico, S.A. de C.V.
Pearson Education—Japan
Pearson Education Malaysia, Pte. Ltd.
Library of Congress Cataloging-in-Publication Data:
Shapiro, James Alan, 1943-
Evolution : a view from the 21st century / James A. Shapiro.
p. cm.
ISBN 978-0-13-278093-3 (hardback : alk. paper)
1. Evolution (Biology) 2. Genomics. 3. Molecular genetics. 4. Evolutionary genetics. I.
Title.
QH447.S53 2012
576.8—dc22
2011008338
This book is dedicated to Felix and Gus and
all future grandchildren.
May their generation share nature’s deep wisdom in
adapting life to its home on Earth.
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Contents
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . .xiii
About the Author . . . . . . . . . . . . . . . . . . . . . . . .xv
A Note on Reading This Book for Individuals
with Different Backgrounds . . . . . . . . . . . . . . . .xvii
Introduction: Taking a Fresh Look at the Basics
of Evolution in the New Century . . . . . . . . . . . . . .1
Part I Sensing,Signaling,and Decision-Making in
Cell Reproduction . . . . . . . . . . . . . . . . . . . . . . .7
HowE.Coli Chooses the Best Sugar to Eat . . . . . . . . . .8
Proofreading DNA Replication . . . . . . . . . . . . . . . . . .12
DNA Damage Repair and Mutagenesis . . . . . . . . . . . .14
Cell Cycle Checkpoints . . . . . . . . . . . . . . . . . . . . . . .18
Signaling from the Cell Surface to the Genome:
Pheromone Response in the Sexually Aroused
Yeast Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21 ptg
The Role of Intercellular Signals in the Cell Death
Decision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
Revisiting the Central Dogma of Molecular Biology . . .24
Part II The Genome as a Read-Write (RW) Storage
System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Genome Formatting for Proper Access to Stored
Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
Genome Compaction,Chromatin Formatting,
and Epigenetic Regulation . . . . . . . . . . . . . . . . . . .31
Genome Formatting for Replication,Localization,
and Transmission to Daughter Cells . . . . . . . . . . . .36
Distinct Classes of DNA in the Genome . . . . . . . . . . .39
The Molecular Mechanisms of Natural Genetic
Engineering . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
Natural Genetic Engineering as Part of the Normal
Life Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
Cellular Regulation of Natural Genetic Engineering . . .69
Targeting of Natural Genetic Engineering within the
Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .82
Reviewing What Cells Can Do to Rewrite Their
Genomes over Time . . . . . . . . . . . . . . . . . . . . . . .87
viii Evolution: A View from the 21st Century
Part III Evolutionary Lessons from Molecular Genetics
and Genome Sequencing . . . . . . . . . . . . . . . . .89
Antibiotic Resistance and Horizontal DNA Transfer . . .90
The Modular and Duplicative Nature of
Protein Evolution . . . . . . . . . . . . . . . . . . . . . . . . .95
Molecular Taxonomy and the Discovery of a
New Cell Type . . . . . . . . . . . . . . . . . . . . . . . . . . . .98
Symbiogenesis and the Origin of Eukaryotic Cells . . .100
Natural Genetic Engineering and Evolutionary
Genomic Innovation . . . . . . . . . . . . . . . . . . . . . .107
Use and Reuse of Evolutionary Inventions . . . . . . . .115
What Makes a Man Different from a Mouse? . . . . . .118
Whole Genome Doubling at Critical Stages of
Evolutionary Innovation and Divergence . . . . . . . .120
Reviewing What the DNA Record Reveals about
Cell Activities over Evolutionary Time . . . . . . . . . .124
Part IV A New Conceptual Basis for Evolutionary
Research in the 21st Century . . . . . . . . . . . . .127
A Systems Approach to Generating Functional
Novelties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
Reorganizing Established Functions to Generate
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Novelty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .130
Generation of Novel Components . . . . . . . . . . . . . .131
Retention,Duplication,and Diversification of
Evolutionary Inventions . . . . . . . . . . . . . . . . . . . .133
The Implications of Targeting Genome
Restructuring . . . . . . . . . . . . . . . . . . . . . . . . . . .134
Can Genomic Changes Be Linked to Ecological
Disruptions? . . . . . . . . . . . . . . . . . . . . . . . . . . .139
What Might a 21st Century Theory of Evolution
Look Like? . . . . . . . . . . . . . . . . . . . . . . . . . . . . .142
Where Does Evolution Fit in 21st Century Science? . . .145
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . .149
References . . . . . . . . . . . . . . . . . . . . . . . . . .175
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .241
Contents ix
The following material can be found online only
(www.ftpress.com/shapiro):
Appendixes to Part I and Part II of the Printed Book
Appendix I.1. Thelacoperon control circuit.
Appendix I.2. S.cerevisiae pheromone response signal
network (Sprague 1991).
Appendix II.1. Formatting the genome for
transcriptional control.
Appendix II.2. Natural genetic engineering in
B lymphocytes for the rapid evolution and maturation
of a virtually infinite diversity of antigenbinding
proteins.
References
Table References for Part II and Part III of the Printed Book
Table II.1 DNA content in higher eukaryotes
(Shapiro and Sternberg 2005)
Table II.2 Different classes of annotated repetitive
genome components (amplified from (Shapiro and
Sternberg 2005))
Table II.3 Generic Cell Operations That Facilitate DNA
Restructuring [30,61,392] Note:These references are
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listed in the printed book only.
Table II.4 Natural Genetic Engineering Systems [6-8]
Note:These references are listed in the printed book
only.
Table II.5 Control of bacterial protein synthesis
(phase variation) and modification of protein structure
(antigenic variation) by natural genetic engineering
(expanded from (Wisniewski-Dye and Vial 2008))
Table II.6 Applications of site-specific recombination
to different functions in bacterial cells (Hallet and
Sherratt 1997)
Table II.7 Various stimuli documented to activate
natural genetic engineering
Table II.8 Genomic responses to changes in ploidy
and interspecific hybridization in plants and animals
Table II.9 RNA-based defense against viruses and
plasmids in bacteria,archaea,fungi and plants
Table II.10 Life history events that alter the epigenome
(DNA methylation and chromatin formatting)
Table II.11 Examples of targeted natural genetic
engineering
Table III.1 Examples of intercellular and interkingdom
DNA transfer
Table III.2 Natural genetic engineering documented in
the evolution of sequenced genomes