Evolution: A View from the 21st Century. Fortified.

By James A. Shapiro

IT IS TIME FOR A NEW THEORY OF EVOLUTION BASED ON GENOMICS, NOT GUESSES

 

In 2011, James A. Shapiro's Evolution: A View from the 21st Century proposed a revolutionary paradigm for understanding biological evolution: natural genetic engineering, not random accidents, produce genome change. In the 21st-century view, organisms are active participants in the evolutionary process.

 

Since then, climate change and multiple crises in infectious disease have given new urgency to understanding evolution. In this expanded 2nd Edition, Shapiro shares new evidence that living cells re-engineer their genomes in response to environmental challenges and disruptions to cellular reproduction.

 

From the classroom to the laboratory, conventional wisdom still paints evolution as the passive result of mutational accidents and natural selection. A modern vision of evolution recognizes that all living beings, from the simplest organisms to humans, actively modify their read-write (RW) genomes as they evolve.

 

In an unpredictable world, the ability to evolve actively is essential to survival. Today, understanding evolution is equally critical to our shared future.

 

Read this book to learn:

• How interactions with other species, cells, and viruses shape an organism's evolution
• How better understanding evolution can help protect our health, food supply, and planet
• How to apply lessons from molecular genetics and genomics wisely to benefit society

 

Written for both general and academic readers, the 2nd Edition includes:

• Discussions of the latest thinking on evolutionary processes
• Published scientific papers sharing key research from the past decade
• The full text of the 2011 edition with appendices

 

• Language: English
• Publisher: Cognition Press
• Release date: Mar 3, 2022
• ISBN: 9781737498711

James A. Shapiro

James A. Shapiro is Professor of Microbiology in the Department of Biochemistry and Molecular Biology at the University of Chicago. He is the author of several pioneering books on mobile genetic elements, natural genetic engineering, bacterial multicellularity, and read-write genome evolution.

Book preview

EVOLUTION: A VIEW FROM THE 21ST CENTURY. FORTIFIED.

Why Evolution Works As Well As It Does

JAMES A. SHAPIRO

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Chicago, IL

Copyright ©2022 James A. Shapiro

All rights reserved. No part of this publication may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, without the prior written permission of the publisher, except in the case of brief quotations embodied in critical reviews and certain other noncommercial uses permitted by copyright law.

Cognition Press

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Project Management by Marla Markman, MarlaMarkman.com

Book Design by JETLAUNCH, JETLAUNCH.net

Lemur Moth Cover Photo by Michael Melford

Publisher’s Cataloging-in-Publication Data:

Names: Shapiro, James Alan, 1943-, author.

Title: Evolution : a view from the 21st century .

Fortified . 2nd Edition , why evolution works as well as it does / James A. Shapiro.

Description: Includes bibliographical references and index. |

Chicago, IL: Cognition Press, 2022.

Identifiers: LCCN: 2021917136 | ISBN: 978-1-7374987-0-4 (paperback) | 978-1-7374987-0-4 (ebook)

Subjects: LCSH Evolution. | Evolution (Biology)--History. | Evolutionary genetics. | Genomics. | Genomes. | Genetic engineering. | Molecular genetics. | BISAC SCIENCE / Life Sciences / Evolution | SCIENCE / Life Sciences / Genetics & Genomics |

SCIENCE / Life Sciences / Biology

Classification: LCC QH447 .S53 2021 | DDC 576.8--dc23

Printed in the United States of America

This book is dedicated to Felix, Gus, and Esme.

May their generation share nature’s deep wisdom

in adapting life to its home on Earth.

CONTENTS

ACKNOWLEDGEMENTS FOR THE 2nd EDITION

INTRODUCTION TO THE 2nd EDITION: HOW EVOLUTION REALLY WORKS AND WHY IT MATTERS TO OUR HEALTH AND FUTURE

The Surprising and Overwhelming Way Bacteria Evolved Widespread Multiple Antibiotic Resistances

Cancer Occurs When Injury Triggers Macroevolution and Turns Our Own Cells Against Us

What Bacteria Taught Me About Their Unsuspected Ability to Mobilize DNA

The Importance of Correctly Understanding Evolution Beyond Cancer and Antibiotic Resistance

Articulating and Updating a 21st-Century View of Evolution: Recognizing That Living Organisms Can Re-engineer Their RW Genomes

Genomes Contain More Than Genes and Encode More Than Proteins

Our Lives Constantly Depend on Targeted Controlled NGE, and Evolution Created This Capability More Than Once

What the 2nd Edition Aims to Do for Nonacademic Readers

What the 2nd Edition Aims to Do for the Academic Reader

The Final Take-Home Message: Active Evolvability Is Essential for Maintaining Life

PART I: BLOG POSTS ARTICULATING THE NEED FOR A NEW WAY OF THINKING ABOUT EVOLUTION IN THE 21st CENTURY

Does Natural Selection Really Explain What Makes Evolution Succeed?

Cell Mergers and the Evolution of New Life Forms: Symbiogenesis Rather Than Selection

What Is the Key to a Realistic Theory of Evolution?

More Evidence on the Real Nature of Evolutionary DNA Change (A Bit Wonky)

What Natural Genetic Engineering Does and Does Not Mean

In Memoriam: Carl Woese (1928-2012), the Most Important Evolutionary Biologist of the 20th Century

Interspecific Hybridization and Introgression in Animal Evolution

What Is the Best Way to Deal with Supernaturalists in Science and Evolution?

PART II: BLOG POSTS COVERING SPECIFIC TOPICS ABOUT EVOLUTION

II.A: Bacterial Antibiotic Resistance

Evolutionary Lessons from Superbugs

The Distinct Roles of Selection, Horizontal Transfer, and Natural Genetic Engineering in Dangerous Superbug Evolution

II.B: Active Biologically Mediated Genome Change

Barbara McClintock, X-rays, and Self-Aware, Self-Healing Cells

Barbara McClintock, Genome Self-Repair, and Cell Cognition: A Revolutionary Vision for the Future of Biology

Evelyn Witkin, Jean Weigle, the SOS Response, and How E. coli Generates Mutations in Response to UV Irradiation

How Natural Genetic Engineering Solves Problems in Protein Evolution

The Evolutionary Importance of Horizontal DNA Transfer into Animal Germlines

Interkingdom Horizontal DNA Transfer in All Directions: Infectious Bacteria Evolve by Acquiring Protein Domains from Eukaryotic Hosts

Take 2: Why Genetic Recombination Is Not Random and How Cells Take Advantage of Nonrandomness

Can Cells Bias Natural Genetic Engineering Toward Useful Evolutionary Outcomes?

Experimental Evolution I: How Can We Watch Natural Genetic Engineering in Real Time?

Experimental Evolution II: More Ways to Watch Natural Genetic Engineering in Real Time

II.C: Immune System–Targeted Genetic Engineering

Purposeful, Targeted Genetic Engineering in Immune System Evolution (Part I)

Your Life Depends on Immune Cells Doing the Impossible: Purposeful, Targeted DNA Engineering (Part II)

II.D: Natural Genetic Engineering of Cellular and Genomic Networks

Network Evolution: How Natural Genetic Engineering Builds Circuits in the Genome

Bob Dylan, ENCODE, and Evolutionary Theory: The Times They Are A-Changin’

Further Thoughts on the ENCODE/Junk DNA Debates

Mobile DNA Repeats and Transcriptional Formatting of the Mammalian Genome in Evolution

Why the Gene Concept Holds Back Evolutionary Thinking

II.E. Cell Cognition in Regulating Genome Functioning and Engineering

Cell Cognition and Cell Decision-Making

Living Cells, Complex Systems, and the Economy

DNA as Poetry: Multiple Messages in a Single Sequence

PART III: EVOLUTION: A VIEW FROM THE 21st CENTURY (1st EDITION)

PART IV: ARTICLES PUBLISHED IN THE SCIENTIFIC LITERATURE THAT FURTHER UPDATE THE 1st EDITION

Shapiro, J.A. (2013). How life changes itself: the Read-Write (RW) genome.

Phys Life Rev 10(3): 287-323. http://www.ncbi.nlm.nih.gov/pubmed/23876611.

Shapiro, J.A., Living Organisms Author Their Read-Write Genomes in Evolution. Biology (Basel), 2017. 6(4). https://pubmed.ncbi.nlm.nih.gov/29211049/

Shapiro, J.A., No genome is an island: toward a 21st century agenda for evolution. Ann N Y Acad Sci, 2019. 1447(1): p. 21-52.

https://pubmed.ncbi.nlm.nih.gov/30900279/

Shapiro, J.A., All living cells are cognitive. Biochem Biophys Res Commun, 2020. https://pubmed.ncbi.nlm.nih.gov/32972747/

GLOSSARY

ABOUT THE AUTHOR

LIST OF ILLUSTRATIONS

A major source for our modern ideas about biological diversity and evolutionary processes came initially from the study of fossils and how they changed over time. Accordingly, Richard Sheppard’s drawings based on photos of various real fossils have been commissioned for the pages separating different sections of the text. The drawings show a tiny fraction of the diversity of life forms and illustrate how some animal types changed over a few geological epochs. I hope these drawings will provide a refreshing counterpoint to the molecular details in the text.

Page iv: Redlichiida, such as this Paradoxides, may represent large ancestral trilobites found throughout the world during the Middle Cambrian period (509-497 MYA).

Page xii: Trilobite Fossil, Early Cambrian—Late Permian (521-252 MYA).

Page xiv: Cheirurus sp. Volkhov River Russia, a complex trilobite from the Ordovician age between the end of the Cambrian (485 MYA) and the start of the Silurian (444 MYA).

Page xxxiv: Eurypterus remipes, a Late Silurian sea scorpion arthropod from New York (432-418 MYA).

Page 20: Encrinus, an extinct genus of crinoids (filter-feeding sea bottom animals) that lived during the Late Silurian to Late Triassic (428-216 MYA).

Page 62: Adelophthalmus mansfieldi, from an extinct group of aquatic eurypterid arthropods leaving fossils from the Early Devonian to the Early Permian (408-283 MYA).

Page 84: Walliserops trifurcatus, a highly evolved trilobite from Morocco, lower to middle Devonian (419-359 Mya).

Page 86: Tiktaalik a single-species genus of extinct sarcopterygian (lobe-finned fish having many features related to tetrapod land animals), late Devonian (~375 MYA).

Page 114: Walchia piniformis, a fossil cypress-like conifer, lower Permian of the Saar-Nahe basin in Germany (310-290 MYA).

Page 166: Specimen of Annularia stellate, an extinct plant from Permian/Carboniferous (360-300 MYA).

Page 196: Pentremites godoni, a blastoid sea bud, an extinct type of stemmed echinoderm that used tentacles for filter-feeding, lower Carboniferous of Illinois (359-299 MYA).

Page 212: Agaricocrinus americanus, a fossil crinoid filter feeder from the Carboniferous/Permian of Indiana (359-299 MYA).

Page 278: Crinoid filter feeder from Iowa (330 MYA).

Page 283: Actinocrinus, filter-feeding crinoid from Indiana (330 MYA).

Page 284: Diplacaulus, an extinct genus of amphibians, late Carboniferous to Permian in Africa and North America (306-255 MYA).

Page 287: Captorhinus aguti, an extinct genus of reptiles, Permian (~280-271 MYA).

Page 288: Hupehsuchus, an extinct early Triassic genus of small marine reptiles found in China (~250 MYA).

Page 291: Ichthyosaurus communis lizard fish reptile from late Triassic and early Jurassic (~200 MYA). Some fossils still had baby specimens inside them, indicating that Ichthyosaurus was viviparous.

Page 292: Spiriferina rostrata, a Jurassic brachiopod with the lophophore digestive system support intact (205-171 MYA). Brachiopods have hard valve (shells) on the upper and lower surfaces, unlike the left-right arrangement in mollusc bivalves.

Page 311: Seirocrinus subsingularis, a crinoid suspension feeder from the early Jurassic Holzmaden Black Shale Formation, Germany (~183-180 MYA).

Page 312: Fossil Crinoid filter feeder from Germany showing the stem, calyx, and arms with pinnules (undated).

Page 314: Pleuroceridas solare, lower Jurassic carnivorous snail-like mollusc from Bavaria (190-183 MYA).

Page 380: Platysuchus (flat crocodile), an extinct genus of crocodyliform reptiles from early Jurassic Germany (183-176 MYA).

Page 446: Rhomaleosaurus cramptoni, an extinct genus of early Jurassic crocodile-like marine reptiles, North-East England (~183 to 175 MYA).

Page 488: Pleurosaurus, an extinct aquatic lizard-like reptile from Europe, late Triassic-late Jurassic (201-145 MYA).

Page 540: Lichnomesopsyche daohugouensis, extinct mesopsychid scorpionfly insects from the late Jurassic of China (~145 MYA).

Page 564: Coelacanth from the late Jurassic Solnhofen Limestone in Germany (~145 MYA).

Page 584: Eryon, a decapod crustacean from the Late Jurassic of Germany (~145 MYA).

Page 627: Mamenchisaurus sinocanadorum from the Middle-Late Jurassic of China, a dinosaur genus known for their remarkably long necks (161-114 MYA).

Page 628: Rhamphorhynchus muensteri, long-tailed winged flying dinosaur, late Jurrasic period (151-148 MYA).

Page 630: Didymoceras stevensoni, extinct genus of heteromorph ammonite cephalopod (squid-like) mollusc, late Cretaceous (~76 MYA).

ACKNOWLEDGEMENTS FOR THE 2nd EDITION

First of all, I want to thank all my colleagues in The Third Way of Evolution group (https://www.thethirdwayofevolution.com/) who have constantly championed the view that the book of evolution is more open than closed. I am deeply indebted to Denis Noble (https://www.denisnoble.com/), Henry Heng (http://genetics.wayne.edu/faculty/henry-heng), Perry Marshall (https://evo2.org/evolution/), Azra Raza (https://azraraza.com/), and Frank Laukien (https://www.bruker.com/about-us/d-frank-h-laukien-biography.html) with whom I organized the virtual October 14-16, 2020, Cancer and Evolution Symposium (http://www.evolutioncancer.org/) that taught me so much I did not know about eukaryotic and somatic evolution. Other people who were not recognized in the Acknowledgements to the 1st edition of this book and who influenced or stimulated my thinking in important ways are Peter and Rosemary Grant of Princeton (and the Galapagos, where they have witnessed real-time evolution in action), Robert Austin (physicist turned cell biologist) also from Princeton, Eugene Koonin from the National Institutes of Health (master bioinformatician), Eviatar Nevo from Haifa (pioneer in ecologically triggered evolution), Guenther Witzany from Salzburg (master organizer of barrier-defying evolution symposia), Pamela Lyon from Flinders University Adelaide, Australia (early bio-cognition champion), Nathalie Gontier from the University of Lisbon (explorer of epistemologies underpinning diverse theories of evolution), Wendell Read from Redondo Beach, California (innovative and searching evolution enthusiast), and Chaim Rosenblatt from Jerusalem (educator dedicated to bringing his students the latest in modern evolution science). In one way or another, all have challenged me to expand my thinking about how life changes itself. I owe two special thank yous: one to the fiction author Michael Fain, whose recommendations prompted me to make more proactive use of my blog posts to render the book more readable for nonscientists, and another to Perry Marshall who suggested that I publish this 2nd edition on my own. Further thanks are due to Ruth Kaufman and Joanne Sprott for proofreading the manuscript, to Richard Sheppard for his wonderful illustrations, to Karen Axelton for the back-cover description, and to Marla Markman for skillfully orchestrating the many steps that went into making this 2nd edition a reality.

Cheirurus sp.

INTRODUCTION TO THE 2nd EDITION:

HOW EVOLUTION REALLY WORKS AND WHY IT MATTERS TO OUR HEALTH AND FUTURE

We can now trace evolution by its historical record written in the DNA of all living organisms. So, it is time to recapitulate some of the lessons we have learned from genome sequences. Understanding the evolutionary process is central to the biological and social sciences as well as agriculture, health, and the environment. Despite massive genomic evidence to the contrary, the philosophy of evolution by random processes, the neo-Darwinian Modern Synthesis, still reigns supreme in the public mind, in the classroom, and in the minds of many scientists and clinicians as well. I learned early in my career that this conceptual dominance by an outdated theory is far more important than simply being an academic atavism.

The Surprising and Overwhelming Way Bacteria Evolved Widespread Multiple Antibiotic Resistances

In the past couple of years, both the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) have published serious warnings that society is rapidly becoming unable to combat disease caused by infectious bacteria [1, 2]. The reason is a very important lesson in evolutionary microbiology. Following World War II, mankind embarked on its largest real-world evolution experiment with the widespread application of antibiotics in the clinic and in agriculture. Society assumed, from the 1940s through the 1960s, that antibiotics had provided a permanent solution to infectious diseases caused by bacteria. This assumption was based upon theoretical population biology models of resistance emergence by chance mutations that would otherwise reduce bacterial fitness, and these models could be validated in the laboratory. However, as I learned in the final year of my PhD research (1966-1967) with Prof. William Hayes at Hammersmith Hospital in London, the bacteria in the clinics came up with forms of resistance totally unexpected by the Modern Synthesis.

Bacteria evolved mechanisms that could inactivate, block, or excrete various antibiotics. Moreover, bacteria transferred genetic determinants for these resistances between species and aggregated different resistances together on transmissible DNA elements known as resistance plasmids or R factors. In the microbial genetics research unit where I worked with Bill Hayes, Naomi Datta and Eleanor Meynell ran one of the main United Kingdom (UK) laboratories for studying these R factors. The research of Naomi, Eleanor, and other bacterial geneticists around the world opened up a rich treasure trove of active processes these small cells possess for mobilizing and rearranging their DNA to construct transmissible multidrug resistance arrays. The ultimate clinical result of our misunderestimating bacteria’s collective evolutionary capabilities is the major threat we now face from multidrug-resistant superbugs insensitive to currently available antibiotic therapies.

Cancer Occurs When Injury Triggers Macroevolution and Turns Our Own Cells Against Us

Fifty-three years later, I encountered almost the same set of scientific blinders in another medical field. Like many biologists, I had become interested in cancer development as a very thoroughly documented example of somatic evolution triggered by outside agents (carcinogens, radiation, viruses, bacteria, and even physical trauma) [3]. What most caught my attention was the speed with which tumor cells can generate large-scale genome restructuring. This seemed to me an indisputable example of non-Darwinian punctuated evolutionary change. As I came to appreciate from Henry Heng’s wonderful 2019 book, Genome Chaos: Rethinking Genetics, Evolution, and Molecular Medicine [4], cancer development was frequently an example of macroevolutionary change. Macroevolution, which restructures genomes to generate new species and other taxa, is quite distinct from microevolution, or the gradual accumulation of small mutations as described by Darwin in the first edition of Origin of Species in 1859. The macroevolution/microevolution distinction was first extensively described in Richard Goldschmidt’s long-neglected 1940 book, The Material Basis of Evolution. Unfortunately, Goldschmidt rarely figures in popular accounts of evolution science, and even when he does, he is almost invariably cited for his unjustly disparaged ideas about hopeful monsters (organisms with new embryonic forms and adult morphologies). Today, of course, hopeful monsters are seen as basic to the evolution of developmental patterns, the subject of blossoming new field called EvoDevo.

To make the macroevolutionary perspective on cancer more widely known and to point out its practical utility, I partnered with Henry Heng and three other nonorthodox evolutionists (Frank Laukien, Denis Noble, and Perry Marshall) plus an eloquent oncologist (Azra Raza) to organize a virtual cancer and evolution symposium, which was held quite successfully from October 14 to 16, 2020 (recorded in its entirety and available on YouTube and at www.cancerevolution.org). At the symposium, a highly respected oncologist informed us that research grant proposals to the National Cancer Institute (NCI) are not considered seriously if they do not accept the fundamental premises of the Modern Synthesis, namely that genomic changes in tumor evolution result from the action of accidental mutations and natural selection. The preferences of the NCI review panels notwithstanding, the rapidly growing body of evidence from cancer genomics tells quite a different and far more interesting story. It turns out that tumor cells, often when they become most dangerous, use deeply evolved DNA damage responses shared by plants and animals to create radically new genome structures, enabling them to grow unceasingly, metastasize to new tissues in the body, and resist chemotherapy.¹

Contrary to what conventional evolutionary wisdom teaches about the long periods of time needed for major hereditary changes to accumulate, these complex genome modification responses in cancer obviously occur within the span of a single human lifetime—and often within a few cell division cycles in laboratory experiments [5]. Moreover, it is becoming clear that certain highly toxic chemotherapies can trigger the very macroevolutionary changes that convert tolerable tumors into unstoppable lethal malignancies [6]. In other words, taking a 21st century view of somatic tumor macroevolution may lead us to extending life expectancies of patients with cancer by understanding better the genomic consequences of the therapies we apply to treat the disease and moderating their use to avoid triggering a fatal macroevolutionary cascade.

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¹ (https://pubmed.ncbi.nlm.nih.gov/33930405/)

What Bacteria Taught Me About Their Unsuspected Ability to Mobilize DNA

These two learning experiences at either end of my scientific career fit with my own research discoveries on the nature of genetic change by cell activities rather than by accidents or mistakes in genome replication. As a graduate student at Cambridge University in the UK, I characterized a series of spontaneous mutations affecting Escherichia coli bacterial sugar metabolism. Spontaneous means that no chemical or radiation treatments were used to induce the mutations. As I studied these mutations, they did not follow the rules established by molecular geneticists in the mid-1960s. They were neither nucleotide changes, substituting one base-pairing specificity for another, nor the recently discovered frameshift mutations, which either deleted or inserted one or two nucleotides of the DNA coding strands. Moreover, these mutations had extremely strong effects on expression of nearby unmutated coding sequences.

Eventually, I hypothesized (correctly, as it turned out) that these mutations resulted from the insertion of extra DNA into the target sequence on the bacterial chromosome. In other words, my E. coli bacteria were telling me that they could modify their genomes in totally unexpected ways [7]. As I and many other bacterial geneticists investigated these DNA insertion mutations over the next decade, it became clear that we had rediscovered the phenomenon of mobile DNA transposable elements, which could jump (that is, transpose) to new locations in the genome and alter the expression patterns of nearby sequences, much as Barbara McClintock had described in maize plants 20 years earlier [8]. Together with the lessons from transmissible antibiotic resistance, this experience alerted me to the simple fact that we can never assume that our knowledge is complete about the tools living organisms possess to modify their genomes.

The Importance of Correctly Understanding Evolution Beyond Cancer and Antibiotic Resistance

Antibiotic resistance and cancer are far from the only cases where a proper realistic understanding of the evolutionary process is of practical importance. For example, the intense campaigns by agrichemical firms to market genetically engineered, pesticide-resistant crops have had and are still having negative impacts on our food supply and the future of the planet. These homogeneous bioengineered genetically modified organism (GMO) crops crowd out natural varieties without consideration for the many advantages of biological diversity. Moreover, as with cancer, global hard-sell campaigns ignore the true evolutionary potential that plant and insect target pests possess for developing resistance, and they have done so reliably over the past half century of pesticide use [9].¹

In addition, we know today, from genomic data, that horizontal transfer of DNA encoding individual traits across taxonomic barriers is universal in evolutionary history. Bacterial and fungal sequences end up in plant and animal genomes, while bacteria use eukaryotic sequences to carry out pathogenesis [10]. Both microbes and larger organisms pick up new sequences from the ubiquitous viruses that fill the biosphere. This biological fact of life has not yet entered public consciousness, and its potential to produce negative outcomes is perilous to ignore. Every time a GMO is planted widely across the planet, there is a very real possibility that the plants themselves or herbivorous insects, fungi, bacteria, or viruses that prey on them may spread the bioengineered DNA encoding resistance to other, less desirable species. Needless to repeat, horizontal DNA transfer has largely been ignored by conventional evolutionary thinking and is not even mentioned in the most popular recent book on neo-Darwinian ideas [11].

The emergence of herbicide resistance in weed plants is now a well-established phenomenon (Leon, R. G., J. C. Dunne, and F. Gould, 2021, The role of population and quantitative genetics and modern sequencing technologies to understand evolved herbicide resistance and weed fitness. Pest Management Science 77(1): 12-21). As with bacteria, although by different genetic changes, the undesirable plants have managed to evolve resistance to multiple different agents at once (Tranel, P. J. 2017, Herbicide-resistance mechanisms: gene amplification is not just for glyphosate. Pest Management Science 73(11): 2225-2226).

Rather than the passive role in generating hereditary change that Modern Synthesis assigns to the evolving organism, we have to recognize that all organisms possess powerful biochemical and cellular tools for reshaping their heredity. Using these tools, living beings play a decidedly active role in the evolutionary process. Furthermore, genomic change does not arise uniquely in the siloed species genomes of classical theory. Many important evolutionary changes result from interactions between different kinds of cells, species, and infectious agents (both microbial and viral). In this time of a deadly pandemic caused by an RNA coronavirus, it is essential to recognize that even viruses do not simply change by replacing individual nucleotides in their genome sequences, as is so far the case with COVID-19 variants that challenge our vaccination strategies. DNA and RNA viruses also change by recombination, genome rearrangements, and incorporation of sequences from phylogenetically unrelated sources, including their human hosts [12]. Ecological change stimulates genome restructuring by stressing individual organisms (e.g., lack of food, exposure to adverse environments, absence of suitable mating partners) and also by increasing novel encounters between different inhabitants of the biosphere. I think it is likely that we will increasingly have an opportunity to witness some of these evolutionary processes at work in real time as climate change alters the planet and further impacts the living world.

Another area where updated evolutionary thinking is critical is in determining how we, as a society, utilize the powerful genome-modification technologies acquired from microorganisms. These new technologies give us the ability to target alterations in the heredity of virtually any life form, including human beings [13]. They have demonstrated their utility in correcting a limited number of hereditary defects in human somatic tissues, and over 5,000 articles in the National Institutes of Health (NIH) PubMed database appear in response to a search for CRISPR therapy.² The notion of biohacking has become popular in certain circles. Sports watchdogs wonder if athletes will secretly replace drug doping with modifying their own DNA to gain a competitive edge [14]. Genetic engineers are pondering a response to pandemics by inserting CRISPR targeting into our immune systems as an alternative to vaccines [15]. The promise of using genetic engineering to reverse aging has become a widely discussed topic [16] and has even led to the establishment of biotech companies promising to accomplish significantly extended and improved life expectancies (e.g., BioViva USA, https://bioviva-science.com/). In evaluating whether such grandiose promises are realistic and determining the regulations society needs to impose over genomic interventions in other species and in the human genome, it appears self-evident that we must integrate the lessons modern molecular genetics and genomics have taught us about how evolution really works.³

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¹ A recent article in the August 22, 2021, New York Times Magazine on the appearance of superweeds resistant to multiple herbicides brings this point home (Brown, H. C. (2021). Attack of the Superweeds. The New York Times Magazine (August 22): 26-33. https://www.nytimes.com/2021/08/18/magazine/superweeds-monsanto.html). Just like the bacteria, these weeds have managed their genomes and provide a broad defense against the limited chemical tools we use to eliminate them, and in so doing have become a menace to contemporary agriculture.

² Clustered regularly interspersed palindromic repeats," the DNA signature of a bacterial system adapted for targeted genetic engineering.

³ The subtitle of Walter Isaacson’s new book on 2020’s Nobel Laureate, Jennifer Doudna, sums it up nicely: The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race.

Articulating and Updating a 21st-Century View of Evolution: Recognizing That Living Organisms Can Re-engineer Their RW Genomes

In 2010, I took advantage of an invitation from a publisher (FT Press Science) to write a book explaining the molecular basis of active organic evolution. I called the book Evolution: A View from the 21st Century, and I tried to encompass all the molecular mechanisms utilized for genome restructuring under the umbrella term of natural genetic engineering (NGE). The print version was followed by an e-book and an audiobook version. Unfortunately, the original hardcover and paperback books are out of print, and for unknown reasons, the e-book is also no longer available. The audiobook is still available as of this writing, but I do not recommend it because the publisher did not consult me, and the narrator clearly did not understand the scientific material he was trying to articulate.

Ten years later, it is necessary to make the out-of-print text of the original 2011 book available again to the public and to expand the contents to reflect how the intervening decade has reinforced the accumulated empirical evidence in support of the arguments about active organismal and genome evolution I made in 2011. Evolution: A View from the 21st Century, Fortified. is thus the 2nd edition of Evolution: A View from the 21st Century from 2011. Over the last 10 years, mostly through extensive genome sequencing, we have seen more and more well-documented examples that show evolutionary change to be an active biological process rather than the passive consequence of mutational accidents and natural selection described by the conventional wisdom taught in our classrooms.

One feature of the 1st edition that I particularly appreciated revisiting is the focus on adaptive innovation rather than selection as the principle issue in evolutionary change. Genomics and experimentation have repeatedly provided answers to fundamental questions that have proven difficult to answer with random mutations and natural selection. For example:

Where do novel DNA sequences encoding new proteins and their constituent domains come from? Today we know of several different processes by which genomes acquire new protein and protein domain coding sequences. Examples include horizontal transfer across virtually all taxonomic boundaries from an unrelated organism or virus [17],¹ reverse transcription of a processed or recombinant RNA into so-called retrogenes [18, 19], or conversion of noncoding repetitive mobile DNA sequences into protein-coding sequences (exonization) [20].²³

How do cells establish coordinately regulated genomic networks for complex phenotypes? The process of generating and controlling genomic networks frequently involves one or both of two active processes: (i) whole-genome duplication (often following interspecific hybridization to generate spare coding regions for adaptation of organismal proteins to participate in cellular networks encoding novel phenotypic traits and functionalities [21] or (ii) distribution of repetitive mobile sequences to multiple genomic locations to serve as regulatory signals for networked expression of the dispersed genetic loci involved in determining a complex new character [22].⁴⁵

How do organisms determine when genome innovation for new adaptations becomes necessary? As mentioned previously, a growing body of research links stress conditions to the activation of genome restructuring functionalities capable of generating organisms with complex novel phenotypes. This process occurs prominently following interspecific hybridization (itself a response to reduced population size) and can be followed in real time in biological systems as diverse as Galapagos finches and cancer progression discussed later in Section IV. Conventional evolution theoreticians completely exclude any connection of genome change to lifetime experiences as a first principle of their theory. Nonetheless, today we have ample experimental evidence for such connections and even, in many cases, understanding of the molecular mechanisms that execute the linkages between experiences and NGE activities.⁶

I believe the main points of the original 2011 book have stood the test of time quite well. These include the following arguments:

Organisms actively restructure their genomes in the course of evolution using a set of biochemical and cellular NGE tools to rewrite their DNA. This means in informatic terms that the genome is a RW (read-write) data storage system, not an ROM (read-only memory) system that changes only by copying errors.

As outlined previously, NGE makes it possible to understand how adaptive complex cellular and developmental systems can evolve rapidly, involving changes at many genomic sites in a coordinated fashion, often by the insertion of repetitive mobile DNA elements that format transcriptional and epigenetic regulatory networks. NGE also provides several molecular mechanisms for domain shuffling and sharing among network proteins.

Genome change is not a blind process but involves sensing and control circuits that both activate NGE functions in response to ecological distress and bias the nature of the modifications that result.

The time has come to view RW genome evolution from an informatic smart systems perspective rather than from the more conventional and atomistic view as a collection of independently and randomly evolving gene units [23, 24].

The reasons for many of the differences between the neo-Darwinian vision of hereditary variation by random mutations and the view presented here of ecologically-responsive molecular rewriting of genomic DNA lies as much in philosophical predispositions as it does to technological advances in reading genome sequences. Darwin, and even more so his Modern Synthesis followers, wanted to ascribe the determination of evolutionary direction exclusively to the action of Natural Selection. This was a reaction to Lamarck’s suggestion that there is an internal pouvoir de la vie which pushes evolution towards ever more complex life forms. The neo-Darwnists were determined to expunge any hint of organismal volition or function in genome change. Natural Selection requires no biological input other than the ability to reproduce more successfully than competitor organisms. To give Natural Selection deterministic power over the evolutionary process, it was necessary to assume that genetic changes were random, of small phenotypic effect, and generated significant adaptive differences by accumulating over long periods of time due to selective advantages they conferred. Although Darwin himself, in his 1874 6th edition of Origin of Species, recognized how this narrow view of change excluded real-world processes of hereditary variation that occurred independently of Natural Selection (Chapter XV, p. 395), his 20th Century followers insisted on gradualist evolution. Thus, neo-Darwinian evolutionary theory blinded itself to the importance of ecologically responsive saltatory modes of hereditary variation, even when they were documented in the DNA sequence data. Today, by contrast, we are in a position to appreciate the complex interplay in all organisms of genome transmission, repair and modification systems, cell regulatory circuits, and organismal sensory networks that control the several processes of hereditary variation at work in somatic, germline and microbial cells.

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¹ (https://shapiro.bsd.uchicago.edu/Examples_of_inter-phylum_adaptive_horizontal_DNA_transfers_based_on_genomic_data.html)

² (https://shapiro.bsd.uchicago.edu/Instances_of_Orphan_Coding_Sequences_%28%E2%

80%9CNew_genes%E2%80%9D_and_New_exons%29_Discovered_in_Sequenced_Genomes.html)

³ (https://shapiro.bsd.uchicago.edu/Origination_of_Novel_Exons_from_Mobile_DNA_Elements.html)

⁴ (https://shapiro.bsd.uchicago.edu/Genomic_consequences_of_experimental_interspecific_hybridization_in_plants_and_animals.html)

⁵ (https://shapiro.bsd.uchicago.edu/Distributed_genome_network_innovation_attributed_to_mobile_DNA_elements.html)

⁶ (https://shapiro.bsd.uchicago.edu/Ecological_Factors_that_Induce_Mutagenic_DNA_Repair_or_Modulate_NGE_Responses.html)

Genomes Contain More Than Genes and Encode More Than Proteins

A major development in our understanding of genome function since the 1st edition appeared in 2011 is the growing recognition that genomes contribute to cell and organismal phenotypes by more than the proteins they encode. A major shortcoming of the Modern Synthesis is that it was based on a gene-centric view, which assumed that the genome is basically a collection of genes that are both the protein-coding units of heredity and the major sites of heritable variation. This view failed to take the evolutionary importance of chromosome structure into account [4][25]. It also blinded evolutionary biologists to the importance of McClintock’s mid–20th-century discovery of mobile controlling elements [8]. The ideas of genetic transposition and control of gene expression by these noncoding mobile elements were heretical notions that did not fit within the narrow confines of the Modern Synthesis concepts of genome function and variation. Barbara McClintock told me how angry looks from her colleagues greeted her after the first presentation on controlling elements to a Cold Spring Harbor Symposium in the 1950s.

A further empirical assault on the limited Modern Synthesis conceptual framework came in the form of extensive noncoding DNA in many genomes. In the late 1960s, Britten and Kohne discovered that a major fraction of genomic DNA from complex eukaryotes consists of highly repetitive sequences rather than the unique coding sequences predicted by the Modern Synthesis to make up the hereditary material [26]. In order to apply selectionist thinking to explain the presence of so much noncoding DNA, evolutionary biologists called this unexpected portion of the genome junk DNA [27] or selfish DNA [28]. An extreme view of these selfish genes was used to erect a whole philosophy of strictly passive evolutionary gradualism [29]. Today we know that the human genome contains at least 30 times as much repetitive noncoding DNA as protein-coding DNA [30]. A 2013 plot of organismal complexity against protein-coding and noncoding DNA showed that coding DNA peaked at approximately 3 × 10⁷ base-pairs (bp), while the noncoding DNA increased linearly with growing complexity up to ~2-3 × 10¹⁰ bp [31]. In other words, noncoding DNA tracks organismal complexity better than the protein-coding genes. In 2012, the year after the 1st edition of this book appeared, the encyclopedia of DNA elements (ENCODE) project, which has largely abandoned the term gene, revealed that the majority of the so-called junk DNA is actively transcribed in a regulated manner, indicating that it is functional [32, 33].

Mobile repetitive DNA is the most variable portion of the genome in the evolution of complex multicellular organisms. Our current understanding of mobile and repetitive DNA element functionality falls into two categories relevant to evolutionary change.

The first functional category follows McClintock and also Britten and Davidson in recognizing that this noncoding fraction of the genome can format transcriptional and epigenetic regulatory networks by placing the same sequence at different locations in the genome [34-36]. Among the evolutionary innovations wired by these mobile repeats are C4 photosynthesis in plants and viviparous reproduction in mammals, which is essential to our own reproduction [37-40].

The second functional category comes from direct observations showing that repetitive DNA elements contribute to a sizeable fraction of genomic sequences transcribed into noncoding RNAs (ncRNAs) that are key to cellular differentiation, genome transcription, and epigenetic regulation (small interfering [si]RNAs). Long noncoding RNAs (lncRNAs), in particular, coordinate all kinds of phenotypes, such as fruit ripening in tomatoes, sex determination in Drosophila, and pluripotency in human stem cells.¹ We are still in the phase of discovery regarding the innumerable functions ncRNAs, especially lncRNAs, play in genome regulation and maintenance, cell biology, and multicellular development [41].

Clearly, none of the eminent scientists who wrote about junk or selfish DNA could possibly have imagined the wide range of functionalities that we know today are executed by mobile DNA elements and ncRNA molecules. In summary, the basic Modern Synthesis idea that a genome was just a collection of naturally selected protein-coding sequences has proved totally inadequate.

As one product of our October 2020, Cancer and Evolution Symposium, Denis Noble and I wrote a review of the growing repertoire of evolutionary, genomic, and organismal phenomena that do not fit into conventional accounts of evolution based on Modern Synthesis.² These phenomena include real-time observation of rapid speciation by interspecific hybridizations within a few generations by Darwin’s own favorite example, the Galapagos finches [42], the functional importance of supposedly selfish or junk DNA made up of repetitive non-protein-coding sequences [26, 31, 34] and evolution by the many impacts of microbes (including endogenized viruses) on large organisms that have come to be considered holobionts whose phenotypes are driven both by their genomes and their microbiomes [43-45].

The major conclusion Denis and I drew from this review is that evolution science has effectively turned itself upside down conceptually. What I mean by conceptual inversion is that the 20th Century Modern Synthesis considered the evolving organism to be the passive beneficiary of random mutations and natural selection, whereas the 21st century view recognizes that evolving organisms play active and very diverse roles as agents of their own genomic, phenotypic, and adaptive changes.

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¹ (https://shapiro.bsd.uchicago.edu/Regulatory_Functions_Reported_for_Long_Non-coding_lncRNA_molecules.html)

² (https://pubmed.ncbi.nlm.nih.gov/33933502/)

Our Lives Constantly Depend on Targeted Controlled NGE, and Evolution Created This Capability More Than Once

Conventional evolutionary theory teaches that targeting genome change is unnatural, a recent human invention. Nonetheless, vertebrates have been doing just exactly that for about 500 million years as they evolved the intricate adaptive immune system that protects us from infections and cancer [46]. Furthermore, last year’s Nobel Prize in chemistry went to two women who pioneered RNA-targeted genetic engineering methods based on sophisticated systems from supposedly primitive prokaryotic cells without nuclei [47]. Bacteria and archaea have probably been using the now famous CRISPRs to defend themselves longer than nucleated eukaryotic cells have existed on Earth [48, 49].

CRISPR stands for clustered regularly interspersed palindromic repeats and were first noted in the 1990s as a characteristic genome sequence pattern of unknown significance, found in at least 90% of archaeal and 40% of bacterial genomes. After noting that the spacers between the interspersed palindromes contain sequences from viral and other external sources in the early 2000s, experimentalists quickly demonstrated that these exotic structures served as DNA sequence databases to record past infections and provide RNA-guided defenses against reinfection, in other words, to act as an adaptive immune system [50]. The nature of the defense was typically simple DNA cleavage at the site recorded in the CRISPR sequence to inactivate the genome of an invading virus or other genetic element, but as more CRISPR systems have been analyzed, we have come to see that CRISPR sequence acquisition and targeting have been incorporated into multiple sensory and NGE tasks, including reading and processing RNA [51] and guiding mobile DNA insertions into bacterial genomes [52-54].

While we are still in the discovery phase with CRISPR systems, the vertebrate (and especially mammalian) adaptive immune systems have been subject to intense molecular and genomic investigation for almost 50 years since the demonstration of somatic rearrangement in antibody-coding DNA [55]. In that period, we have acquired a very detailed understanding of how that lymphocyte DNA is constantly engineered to (i) generate tremendous antibody diversity, (ii) refine the affinity of antibodies that have recognized alien cells or viruses within our bodies, and (iii) alter the structure of these refined antibodies and target them to the right issues where they can best combat the invaders.

I describe details of these exquisitely orchestrated examples of sequential natural genetic engineering in B lymphocytes at length later in this volume (Part II.C, Part III Appendix 2). Suffice it to state here that each of these DNA change operations is timed, triggered, and targeted by the kind of well-defined, highly nonrandom (yet also highly nondeterministic) cellular and molecular processes that conventional evolutionists would have us believe are inconceivable. Nonetheless, they happen continuously in our bodies and keep us safe from many of the biosphere perils that surround us.

Although the mammalian adaptive immune system is exceptional in the complexity and specificity of its multiple actions on the antibody-coding loci in our genomes, it is far from unique in using DNA manipulations to modify cell-cell interactions. Even the simplest of prokaryotic cells, not to mention more complex eukaryotic parasites like the ones that cause sleeping sickness and malaria, rearrange the DNA encoding their surface proteins to alter them so they can escape antibody-guided destruction [56-61]. The general name for such genome manipulations is antigenic variation. In other words, our immune system is in a constant NGE arms race with the microbes that try to take over our bodies for their own ends.

What the 2nd Edition Aims to Do for Nonacademic Readers

This 2nd edition expands the 1st edition in two different ways. For nonprofessional readers interested in contemporary debates about evolution science who found the 1st edition too technical to comprehend, I have included discussions of many topics in the form of Huffington Post blogs written after the book appeared. These and other blogs not included here are still available online in their original time sequence.¹ The blogs cover basic thinking about how evolution actually occurs and hopefully will serve as a more reader-friendly introduction to this 2nd edition. There is also blog commentary on some of the technical points made in the book. Placing the more accessible blogs before the reprinted 1st edition will hopefully make the technical content more accessible at the beginning and even further into more technical discussions to readers who are not molecular biologists or geneticists. It is my wish that some of the blog posts will make sense to people interested in an up-to-date view of evolution science but who may find the 1st edition and the scientific papers I have added here technically challenging.

A second wish I have for this new edition is that readers will find my use of the word fortified in the title to be appropriate. I have outlined previously how I believe the science has progressed in the past decade, and the added scientific articles in this edition document some of that progress in detail. As I see it, virtually all the major progress in using the most modern tools of genome analysis these last 10 years favors the idea of evolution as an active process of self-modification by organisms endowed with a toolbox of change processes totally inconceivable at the time DNA was identified as the molecular carrier of genetic information in 1953 [62]. And the discoveries continue unabated. When I was learning about cancer genomes for the cancer and evolution symposium, I entered a realm of ongoing research on topics like polyploid giant cells [63], the mutagenic consequences of micronucleus formation after mitotic errors [5], and remarkable multisite mutator functions like alternative end-joining (altEJ) and human DNA polymerase θ (Pol θ) [64-66]. Clearly, the end is not yet in sight for the evolution saga.

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¹ (https://shapiro.bsd.uchicago.edu/publications.shtml)

What the 2nd Edition Aims to Do for the Academic Reader

I have included 4 published articles from scientific journals, which expand on subjects discussed in the 1st edition. The papers amplify the massive supporting evidence for a fortified 21st century view of evolution that has appeared since the publication of the 1st edition. The first of these articles from 2013—How life changes itself: the Read-Write (RW) genome—presents a more detailed explanation of how NGE functions at the molecular level [67].¹ The second article from 2017—Living Organisms Author Their Read-Write Genomes in Evolution—is an attempt to point out the accumulating and overwhelming data showing how living organisms actively rewrite their genomes when they make evolutionary changes [68]. This article is, admittedly, something of a data dump and has about 700 references plus those included with additional referenced tables available online.² This extensive documentation was meant to make the point that there are very large numbers of published studies that illustrate how NGE functions have played major roles in all aspects of genome evolution; among these online reference collections is one on the actions of lncRNAs.³

The third article from 2019—No Genome Is an Island—explores the fact that evolution does not proceed within the isolated genome of a single species but virtually always involves interactions with other cellular and/or viral genomes from the biosphere [69]. The paper also applies that biosphere-wide insight to thinking about evolutionary theory and puts forward some ideas about more realistic experimental approaches to evolutionary processes in the years ahead. The last paper from 2020—All Living Cells Are Cognitive—summarizes the evidence that cognitive capabilities are found in even the simplest of living cells, particularly concerning how they treat their own genomic DNA or DNA that comes from the outside [70].

Including these papers together with the 2011 1st edition allows me to cover two particular subjects that were not adequately discussed 10 years ago: (1) proposing more sophisticated experimental microcosms for realistic evolution experiments to replace the woefully inadequate isolated pure culture approaches often used in conventional studies [69] and (2) discussing the cognitive aspects of how cells read and react to both genomic and incoming DNA so they can appropriately activate NGE systems in response [70]. Reprinting these papers also makes it possible for me to link various topics to online compilations of extra references on my web page that are simply too numerous to include in the published articles.⁴ One of my rationales for aggregating and posting these reference collections was to demonstrate how mainstream many of the topics in the published papers have become in the genomics and molecular genetics literature (but sadly not yet in the evolution literature).

At first glance, some readers may consider the final 2020 paper included in this 2nd edition (All Living Cells Are Cognitive) to be out of place in a book devoted to evolution [70]. However, I include it for two reasons. First, many of the examples of active cognition in prokaryotic cells involve sensing DNA, such as the presence of external DNA in the environment by bacteria competent for incorporating it into their genomes, detecting DNA damage in the cellular genome to activate and target repair functions, and identifying foreign DNA entering from viruses or other cells to determine whether it may pose a threat.

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¹ (https://en.wikipedia.org/wiki/Natural_genetic_engineering)

² (https://shapiro.bsd.uchicago.edu/Genome Writing by Natural Genetic Engineering.html)

³ (https://shapiro.bsd.uchicago.edu/Regulatory_Functions_Reported_for_Long_Non-coding_lncRNA_molecules.html)

⁴ (https://shapiro.bsd.uchicago.edu/)

The Final Take-Home Message: Active Evolvability Is Essential for Maintaining Life

Two recent excursions into novel scientific territory, in particular, have fortified my conviction that an evolved ability to rewrite the genome is a fundamental vital property of all living organisms. The first excursion was researching my 2020 paper on cellular cognition; I based my argument that cognition is universal in all living cells in part on the demonstration that cognitive activities are clearly documented for mycoplasmas, the most elemental living cells with the smallest naturally evolved cellular genomes [70]. Along with learning about Mycoplasma cognitive behaviors, I also learned that these microbes devote a significant portion of their limited genomes to NGE functions: repetitive DNA; several kinds of mobile DNA elements; site-specific, transpositional, and homologous recombination activities; CRISPRs; and a very active sex life resulting in an enormous capacity to transfer DNA between cells [71-76]. Evidently, even the simplest organisms have found it essential to mobilize and rearrange their genomes.

The other excursion out of my scientific comfort zone was in cancer genomics for the cancer and evolution symposium described previously. There I learned that human (and other mammalian) cells have two kinds of biochemical systems for repairing broken DNA molecules. The one that is used in normal tissues is called canonical nonhomologous end-joining (cNHEJ), and it makes very few changes in the DNA [77, 78]. But the backup system that is active in cells that already are or may become cancerous is called alternative end-joining (altEJ), and it uses a highly mutagenic DNA polymerase θ (Pol theta or Pol θ) as it connects the broken ends [65, 66].¹ Pol θ is a remarkable protein. It creates all kinds of new DNA sequences by jumping from one chromosome region to another as it lays down new DNA strands complementary to its different templates, generating chimeric sequences that may encode fusion proteins with different genomic sources for each part of the molecule, something often seen in cancer [79, 80]. And sometimes Pol θ even synthesizes completely novel DNA strands with no template at all [5, 64]. If altEJ existed just as a backup to the normal cNHEJ break repair system, there is no reason for it to perform all these prodigious DNA gymnastics. The reason for Pol θ’s creativity may well be that some failures causing chromosome breakage signal to the cell that drastic genome change is necessary. In other words, DNA Pol θ’s inherent mutator functions have evolved not just for DNA repair but also to carry out repair that quite literally makes a difference and leads, as it does in cancer, to significant genome change.

Active genome change is a cognition-based functionality throughout the biosphere [68, 70]. It is essential to maintaining life in the face of a dynamic and unpredictable ecology. As Barbara McClintock pointed out in her Nobel Prize address, the ability to sense danger and change the genome in response was a fundamental capability of the maize plants she studied [81]. We now have solid evidence that similar potential exists in all three kingdoms of life. Indeed, without the ability to evolve actively and adapt to new circumstances, life as we know it would almost certainly have become extinct long ago.

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