Untangling Molecular Biodiversity: Explaining Unity and Diversity Principles of Organization with Molecular Structure and Evolutionary Genomics

673 Pages·2020·76.547 MB·English

by  Gustavo Caetano-Anolles

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World Scientifi c
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Published by
World Scientific Publishing Co. Pte. Ltd.
5 Toh Tuck Link, Singapore 596224
USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601
UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE
Library of Congress Control Number: 2020041551
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library.
UNTANGLING MOLECULAR BIODIVERSITY
Explaining Unity and Diversity Principles of Organization with Molecular Structure and
Evolutionary Genomics
Copyright © 2021 by World Scientific Publishing Co. Pte. Ltd.
All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means,
electronic or mechanical, including photocopying, recording or any information storage and retrieval
system now known or to be invented, without written permission from the publisher.
For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance
Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy
is not required from the publisher.
ISBN 978-981-4656-61-0 (hardcover)
ISBN 978-981-4656-62-7 (ebook for institutions)
ISBN 978-981-4656-63-4 (ebook for individuals)
For any available supplementary material, please visit
https://www.worldscientific.com/worldscibooks/10.1142/9506#t=suppl
Typeset by Stallion Press
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Printed in Singapore
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s
Preface: Untangling molecular biodiversity vii
t
List of Contributors xi
Unity On unity in organisms and its evolution 1
n
Memory Retrodiction — Exploring the history
of parts and wholes in the biosystems
e of life 23
Linkage A “double tale” of module creation
t in evolving networks 91
Structure RNA structure and diversified life 169
nOrigins It takes a well rooted trunk to bear
a tree — reductionist models of
divergent evolution and further
o
aspects of reality 223
Language The language of biomolecular
C communication 283
Growth Molecular accretion, growth and
innovation 347
Persistence A model of lineage evolution based
on the persistence strategy hypothesis 395
Panspermia An early cellular origin of viruses 421
Complexity Some considerations towards a
predictive theory of life 453
v
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vi Untangling Molecular Biodiversity Explaining Unity and Diversity Principles
Power Life as a tendency to go beyond
itself — The struggle for power 491
Time Temporal parts and biological change 529
Foresight Empedocles’ On Nature, P. Strasb.
Gr. Inv. 1665–6, a theory of networks
and evolutionary growth ~2,400
years before Darwin 599
Index 649
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9”x6” b3969 Untangling Molecular Biodiversity Explaining Unity and Diversity Principles
eUntangling molecular biodiversity
The universe appears complex and diverse. These properties
cmaterialize for example in entities, processes, and dynamic
behaviors of different kinds. We, as humans, have developed
a deep capacity for analysis and manipulation of this com-
aplexity and diversity. At first, we learned to exploit the envi-
ronment for survival. The developed awareness accumulated
insights that favored persistence. Our inquisitive nature
fadvanced our Weltanschauung, our world view, when we
learned how to better control our existence. Our ingenuity
and the development of technological power transformed
e
mythologies into science, knowledge and action. This unique
capacity developed by the human mind is now massively
transforming our planet (perhaps the universe) despite viral
r
pandemics and global change instabilities. François Jacob
realized that our big and complex brain had an “in-built need
for order.” Indeed, our species dissects, tinkers and manipu-
P
lates. We dissect by examining how things work but often
dissect through classification. We classify everything, from
galaxies, stars and planets to molecules, genes, and organ-
isms. We count and measure, store and preserve. We build
libraries, museums, repositories, universities, and a world of data.
Remarkably, we also retrodict with memories, learning, experi-
ences, analysis and retrospections. We record history and learn from
our past. This helps predict future outcomes and become better
engineers. In doing so, we continue to embrace the impact of our
persistence.
Untangling Molecular Biodiversity presents a unique global frame-
work to explain molecular and organismal diversity at different
temporal scales and complexity levels. When exploring complexity
and diversity the concept of “level,” which has been applied to a
variety of doctrines, becomes apparent. Mario Bunge in his
vii
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viii Untangling Molecular Biodiversity Explaining Unity and Diversity Principles
“semantical preliminary” attempts its dissection for science and
ontology (Review of Metaphysics 13: 396–406, 1960). He finds
that levels can be described with nine different meanings: degree,
degree of complexity, degree of analytical depth, emergent whole,
poistem, rank, layer, rooted layer, and grade. When “level = degree
of any kind,” levels are considered grades in a static scale or are
considered stages in a process. Such is the case of the abundance
of a protein structural variant in a proteome (an extensive prop-
erty), the level of functionality of a system (a processual property),
or the level of abstraction or importance in a classification scheme
(a complexity property). When “level = emergent whole,” levels
become players of a parthood relationship that measures integra-
tion and diversity. This view is enhanced by interrelated qualities
(poistems), hierarchical views (ranks), stratigraphic arrangements
(layers) or tree emergences (rooted layers). Finally, levels can rep-
resent linear or non-linear grades of order that are part of an evo-
lutionary series and have emerged in time from lower or higher
pre-existing levels. This last “level = grade” instantiation appropri-
ately describes what biologists call “levels of organization,” which
is helpful for building ontological definitions and understanding
biological complexity.
The theoretical framework we here present is for the most part
grounded in evolutionary genomics and systems biology. This book
tackles important questions of origin and structure, such as the ori-
gin of life, the emergence of biochemistry, the origin of viruses, the
nature of the last universal common ancestor of diversified life, the
rationale for having three cellular superkingdoms, the role of infor-
mation and thermodynamics in evolution, and the centrality of
modules in biology. It also explores philosophical problems, such as
the search for truth in scientific inquiry, the difficulties of temporal
parts and retrodiction, Nietzsche’s Wille zur Macht driving force of
power, and the unity-and-diversity dichotomy of the living world
that was advanced by Empedocles. In fact, these paradigms are
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Untangling molecular biodiversity ix
made explicit through the looking-glass of macromolecules, the
component parts that carry the genetic and functional information
of life. Some principles that are discussed are general and could be
applied to selected aspects of our world and universe.
Untangling Molecular Biodiversity explores 13 general themes:
Unity, Memory, Linkage, Structure, Origins, Language, Growth,
Persistence, Panspermia, Complexity, Power, Time, and Foresight.
These themes are tightly linked and form a fully-connected concep-
tual network. The reader can therefore wander through themes by
choosing any chapter as starting point and then selecting other
chapters through pathways of interest across the thematic network.
One major emphasis of modern biology has been the survey of
organismal parts, their mechanisms, and their diversity in the living
world. In the post-genomic era, this survey has produced a “big
data” deluge, which must now be integrated to find meaningful
biological knowledge. The different themes address integrative
frameworks for biological organization, evolutionary patterns of
molecular biodiversity, links between molecular structure and evo-
lutionary genomics, persistence strategies that borrow from engi-
neering and systems biology, the structural diversity of the molecular
world, and explorations of the origin and evolution of cells and
viruses. Consequently, this book represents a very unique collection
of ideas that can attract the attention of a broad readership. I hope
the readers will find each and every theme exciting and thought
provoking.
I am grateful to all authors that contributed to this editorial project.
Their effort and ideas have helped integrate the many aspects of
inquiry that are presented in this exceptional compendium. I thank
them for their patience during the long time it took to assemble this
volume. I thank my son Derek for the artistic renditions of the book
cover and for the many figure illustrations of this book. I also thank
Jay Mittenthal for prompting the exploration of unity and diversity
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