The new foundations of evolution : on the tree of life

T h e Ne w Foundation s o f

EVOLUTIO N

TRE E O F LIF E

J A N SAP P

T h e Ne w Foundation s

o f Evolutio n

On the Tree o f Lif e

OXPOR D

UNIVERSITY PRESS

2009

OXPOR D

UNIVERSITY PRESS

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Library of Congress Cataloging-in-Publication Data

Sapp, Jan.

The new foundations of evolution : on the tree'of life / Jan Sapp.

p. cm.

Includes bibliographical references and index.

ISBN 978-0-19-538849-7; 978-0-19-538850-3 (pbk.)

1. Microorganisms—Evolution. 2. Microbial genetics. 3. Evolution (Biology).

4. Biology—Classsification. I. Tide. ........

QR13.S27 2009

571.2'9—dc22 2008050915

9 8 7 6 5 4 3 2 1

Printed in the United States of America

on acid-free paper

In memory of my father, Melan P. Sapp

FOREWORD

THE WORD "UNIQUE" best describes the book The New Foundations of Evolution:

On the Tree of Life and its author, the historian Jan Sapp. Historians of biology

typically focus on evolution a la Darwin. Yet, there is much to be understood

about the evolutionary process that never met the Darwinian eye, and much

more work to be done and biological systems to visit before science can say it

"understands" evolution.

I have struggled long and hard to convince biologists that biology owes both

science and mankind a genuinely scientific study of the evolutionary process,

and that the place to start is not with the birds, beetles, and the bees all over

again, where conventional evolutionary language shackles your thoughts before

you begin. One starts with the microbial world; starts within the cell, not with￾out; focuses on the origin and evolution of the cell's universal molecular com￾ponentry, not the adaptive embellishments. And one does not stick the label

"made by natural selection" on anything. Here, in this new venue, is where we

can begin to trace organisms back to their roots and begin to talk about evolu￾tion in a new, non-anthropomorphic language.

And finally! Along comes a book with an eye-popping title—The New

Foundations of Evolution: On the Tree of Life, and it is about the microbial world.

It is a book I never thought I'd see written by a historian. It says to historian

and scientist alike: "Yes, there is evolution after Darwin; and here is what it's

going to look like!"

It is impossible to understand the microbial world in any depth with￾out considering the constant evolutionary current that flows through it. To

account for the intricate and fascinating molecular structure within micro￾bial cells or the organization of these cells into delicately fabricated microbial

communities—so intimately interlinked with their environments—is a weav￾ing of ecology, evolution, and organism, the likes of which are not seen in the

larger world "above."

Dr. Sapp's book recounts the story of a basically isolated scientific field

struggling to define its venue, find itself, and take its proper place among the

other biological disciplines. It is a story of how molecular evolutionists working

in the microbial world were able to discover the large-scale structure of the tree

of life, and in the process questioned some of the major evolutionarv under￾standings, such as the doctrine of common descent, the notion that evolution

occurs only in very small random steps, and the idea that the organisms cannot

"learn" from other organisms or share inventions with them. And it is a story

of the discovery that there are not two primary lineages of living organisms

on this planet, the eukaryotes (animals, plants, fungi, and "protists") and the

microscopic prokarvotes, as everyone thought there were, but actually three.

The so-called prokarvotes are not all related to one another, but comprise two

great classes of (micro)organisms, which are less related to each other than we

are to plants. These are the Archaea and the Bacteria, and between them they

comprise the bulk of the biomass on this planet and by far the greatest cellular

diversity.

Dr. Sapp is as unique among historians of biology as his work is among

theirs. His is not a recounting of biology and evolution past, of problems solved

and tucked away. His is a story of bringing evolution and biology together, of a

new science of biology in the making. Thus, he finds his history on the unpaved

trails ot contemporary scientific exploration rather than safely recording his

travels along the scientific superhighways of the past.

CarlR. Woese

Viii | FOREWORD

PREFACE

THIS BOOK is ABOUT the search for the foundations of evolution on this planet,

the primary lineages of life, and the most profound differences in life's forms,

represented in its highest taxa—the domains and kingdoms. It is a story about

a revolution in the way in which biologists explore life's long history on Earth,

understand its evolutionary processes, and portray its variety. It is about life's

smallest entities, deepest diversity, and largest cellular biomass: the microbio￾sphere. To come to grips with microbial evolution is to reconsider much of

classical biology's understanding of the processes of evolution, its imagery,

methods, and doctrines.

Evolution is typically described as "the origin of species," as first summa￾rized in Charles Darwin's legendary work of 150 years ago and articulated in

the twentieth century. The problems, protests, and confusions that had side￾lined Darwin's theory for many decades were resolved ecumenically in the

1930s and 1940s by what became known as the "modern synthesis"—a fusion

of Mendelian genetics, population thinking, and natural history with Darwin's

theory of natural selection. Gene mutation and recombination between indi￾viduals of a species were the fuel for evolution by natural selection.

The evolutionary synthesis of the last century was forged in terms of a two￾kingdom world of animals and plants, whose histories cover at most 25% of

the span of evolutionary time on Earth. Focused on the origin of species, that

perspective had no concern for the primary groupings of life, the all-embracing

kingdoms. In effect, it was a sterile conception of evolution—a world without

a microbial foundation.

Evolution is not primarily about the origin of species. That formulation of

the problem does not offer useful explanation for the evolution that occurred

before organisms as we know them appeared or for understanding the evolu￾tionary process at a deep level, problems such as how life as we know it emerged,

and how cellular organization evolved, the genetic code developed, and genomes

formed. The origin of species perspective does not really help to rationalize

much of the great genetic and biochemical diversity on Earth in the microbial

world, where three domains and most of the kingdoms of life are distinguished.

Bacterial evolution is not a study in the origin of "species," a doubtful concept

at best in that sphere.

Classical evolutionists did, of course, see animals and plants as having

evolved somehow from the loosely conceived "lower" or "primitive" organisms,

which microbes were taken to be. But that microbial world lay far beyond their

purview and interest. Microbiology was largely consigned to pathology, agricul￾ture, and industry before the Second World War, and when microbes emerged

at the center of biology afterward, only a very few of them were chosen for study

as laboratory domesticates, which were taken as representatives of all. Their

study was motivated by their utility for molecular biology and biochemistry.

The elucidation of the structure of DNA, how it is replicated, and how it

encodes the genetic information for the synthesis of proteins came to define

the biology of the twentieth century. Molecular biology moved with breakneck

technological speed and great promise for medicine and agriculture. To the

extent that molecular biology showed interest in evolution, it was in guiding the

process to the benefit of humans in the future. The interest was generally not

there when it came to studying evolution's past to try to understand the process

more deeply. Leading microbiologists declared, in effect, that the bulk of organ￾ismal evolution simply cannot be known. Leading molecular biologists agreed

that the same was true of the evolution of the cell and its parts.

The emergence of molecular phylogenetics, beginning with the comparative

study of the amino acid sequences of proteins in the 1960s, broadened to include

RNA and individual genes in the 1970s, and then finally whole genomes in

the 1990s. All this brought revolutionary change to biology. Startling new and

fundamental concepts began to enter evolutionary biology when sequencing

was developed for the ancient informational molecules, the "ultimate molecu￾lar chronometers" that formed the basis of the genetic system in all organisms.

Evolutionary "signatures" from the deep evolutionary past began to emerge

from the information encoded in the RNAs of ribosomes—those structures

responsible for translating the sequence in the DNA gene into that of its cor￾responding protein. The information in that ribosomal RNA was held to reveal

the universal relationships among all organisms.

There were two separate aspects to classical evolutionary biology. One

was concerned with processes of evolutionary change: studies of the change

in gene frequencies within populations over time and context. The other was

concerned with genealogy or phylogeny: the evolutionary history of a group as

it unfolded over time. The group may comprise one or a few species, or it may

encompass a larger number of forms, for example, the modern and ancient

horse. Organisms were classified and arranged in a hierarchy of groups within a

group. Phylogenetic relations were portrayed as a bifurcating tree. Comparative

X | PREFACE