Main Microcosmos: Four Billion Years of Microbial Evolution

Microcosmos: Four Billion Years of Microbial Evolution

,
Microcosmos brings together the remarkable discoveries of microbiology of the past two decades and the pioneering research of Dr. Margulis to create a vivid new picture of the world that is crucial to our understanding of the future of the planet. Addressed to general readers, the book provides a beautifully written view of evolution as a process based on interdependency and the interconnectedness of all life on the planet.
Year: 1997
Publisher: University of California Press
Language: english
Pages: 306
ISBN 13: 9780520210646
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LYNN

MARGULIS

DORION SAGAN

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MICROCOSMOS
FOUR BILLION YEARS OF MICROBIAL EVOLUTION

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Foreword by Lewis Thomas

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Microcosmos

MICROCOSMOS
Four Billion Years of Evolution
from Our Microbial Ancestors

Lynn Margulis and Dorion Sagan
Foreword by Lewis Thomas

UNIVERSITY OF CALIFORNIA

Berkeley

Los

Angeles

PRESS

London

University of Califomia Press
Berkeley and Los Angeles, Califomia
University of California Press, Ltd.
London, England
First Califomia Paperback Printing 1997

Copyright

@ 1,986by

Lynn Margulis and Dorion Sagan

All rights reserved
including the right of reproduction
in whole or in part in any form
Manufactured in the United States of America

10987654321
Library of Congress Cataloging-in-Publication data
Margulis, Lynn, 1938Microcosmos : four billion years of evolution from our microbial
ancestors / LyrnMargulis and Dorion Sagan : foreword by Dr' Lewis
Thomas.

P.cm.

Originally published : New York : Summit Books, O 1985. With rev'
pref.
Includes bibliographical references and index.
ISBN G'520-2106t1-5 (pbk. : alk. paper)
1..

Evolution (Biology).

Dorion,

2.

1959- . II. Title.

QH371.M28

Microorganisms-Evolution. I. Sagan,

1997

576.8-DC27

96-49685

CIP
The paper used in this publication meets the minimum requirements of
American National Standard for lnformation Sciences-Permanence of
Paper for Printed Library Materials, ANSI239.4&1984. e)

To the memory of Moruis Alexnnder
(D ecember 24, 1.909 -N oaember 3, L994),

father and granilfatlur,

andhis loae of life

CONTENTS

F oreroord by

kutis

Thomas (19 8 5)

9

Preface

13

Acknowledgments

25

lntro duction: The Mcrocosm

27

L.
2.
3.
4.
5.
6.
7.
8.
9.

Out of the Cosmos
The Animation of Matter
The Language of Nature
Entering the Microcosm

39

47
59
69

Sex and Worldwide Genetic Exchange

85

The Oxygen Holocaust

99

New Cells
LivingTogether
The Symbiotic Brain
10. The Ridd1e of Sex
11. Late Bloomers: Animals and Plants
1.2. Egocentric Man
13. The Future Supercosm

115

127
137
155
167

193
235

Nofes

277

lnilex

285

7

TABLES

1. Geological Time

4A

2. Human Classification

198

3. Acceleration in Food Production

245

4. Hierarchy Charl

247

Sizes

8

FOREWORD
by
Lewis Thomas, M.D. (19L3-L993), President Emeritus,
Memorial Sloan-Kett ering Cancer Center

!f is on occasion the function of a foreword to provide
I the reader with advance notice of what he or she may
be in for. In the case of this book, unless the reader has
been keeping in close touch with quite recent events in microbiology, paleontology and evolutionary biology, what he or
she is in for is one great sulprise after another, even possibly
one shock after another. This is a book about the inextricable
connectedness of all creatures on the planet, the beings now
alive and all the numberless ones that came before. Margulis
and Sagan propose here a new way of looking at the world,

different from the view we mostly shared a few decades
back. The new view is based on solid research, done for
different reasons by many scientists in laboratories all around
the earth. Brought together and linked, their findings lead
to the conclusion that separateness is out of the question
in Nature. The biosphere is all of a piece, an immense, integrated living system, an organism.
I remember attending a series of seminars on a university
9

FOREWORD

10

campus long ago, formally entitled "Man's Place in Nature."
Mostly, it had to do with how man can fix Nature up; improv-

it

so that the world's affairs might move along more
agreeably: how to extract more of the Earth's energy resources, how to preserve certain areas of wilderness for our
pleasure, how to avoid polluting the waterways, how to control the human population, things of that order. The general
sense was that Nature is a piece of property, an inheritance,
owned and operated by mankind, a sort of combination park,
zoo and kitchen garden.
This is still the easy way to look at the world, if you can
keep your mind from wandering. Surely, we have had the
appearance of a dominant species, running the place, for
almost the entire period of our occupancy. At the beginning,
perhaps,'we were fragile, fallible creatures, just down from
the trees with nothing to boast of beyond our apposable thumbs and our exaggerated frontal lobes, hiding in
caves and sfudying fire. But we took over, and now we
seem to be everywhere, running everything, pole to pole,
mountain peaks to deep sea trenches, colonizing the moon
and eyeing the solar system. The very brains of the Earth.
The pinnacle of evolution, the most stunning of biological
successes, here to stay forever.
But there is another way to look at us, and this book is
the guide for that look. In evolutionary terms, we have only
just arrived. There may be younger species than ours, here
and there, but none on our scale, surely none so early on
in their development. We cannot trace ourselves back more
than a few thousand years before losing sight of what we
think of as the real human article, language-speaking,
song-singing, tool-making, fire-warming, comfortable, warmaking mankind. As a species, we are juvenile, perhaps
just beginning to develop, still learning to be human, an

ing

Foraoord

11

immature child of a species. And vulnerable, error-prone
still, at risk of leaving only a thin layer of radioactive fossils.
One thing we need to shaighten out in aid of our perspective is our lineage. We used to believe that we arived de
notso, set in place by the Management, maybe not yet dressed
but ready anyway to name all the animals. Then, after
Darwin, we had to face up to the embarrassment of
having apes somewhere in the family tree, with chimps as
cousins.

painful period in early adoleswishing them to be different, more like the parents of families
down the street. There is nothing really shameful about having odd-looking hominids as parents, but still most of us
would prefer, given the choice, to track our species back to
pure lines of kings and queens, stopping there and looking
no further.
But now look at our dilemma. The first of us,. the very
first of our line, appeared sometime around 3.5 billion years
ago, a single bacterial cell, the Ur-ancestor of all the life to
come. We go back to it, of. all things.
Moreover, for all our elegance and eloquence as a species,
for all our massive frontal lobes, for all our music, we have
not progressed all that far from our microbial forebears. They
are still with us, part of us. Or, put it another way, we are
part of them.
Once faced up to, it is a grand story, a marvelous epic,
still nowhere near its end. It is nothing less than the saga
of the life of the planet.
Lynn Margulis has been spending most of her professional
life studying the details of the story and has added significant
details from her own scientific research. Now, she and Dorion
Sagan have put it all together, literally, in this extraordinary
Many children go through

a

cence when they are uncomfortable about their parents,

12

FOREWORD

book, which is unlike any treafrnent of evolution for a general
readership that I have encountered before. It is a fascinating
account of what is by far the longest stage in the evolution
of the biosphere, the 2.5 billion year stretch of time in which
our microbial ancestors, all by themselves, laid out most of
the rules and regulations for interliving, habits we humans
should be studying now for clues to our own survival.
Most popular accounts of evolution and its problems start
out just a few hundred million years ago, paying brief respects
to the earliest forms of multicellular organisms and then moving quickly to the triumphant invention of vertebrate forms,
making it seem as though all the time that went before was
occupied by "primitive" and "simple" cells doing nothing
but waiting around for the real show to begin. Margulis and
Sagan fix this misapprehension of the real facts of life, demonstrating that the earliest bacteria learned almost everything
there is to know about living in a system, and they are,
principally, what we know today.
Perhaps we have had a shared hunch about our real origrn
longer than we think. It is there like a linguistic fossil, buried
in the ancient root from which we take our species' name.
The word for earth, at the beginning of the lndoeuropean
language thousands of years ago (no one knows for sure
how long ago) was dhglwn. From this word, meaning simply
earth came our word humus, the handiwork of soil bacteria.
Also, to teach us the lesson, humble, human, and, humane.
There is the outline of a philological parable here; some of
the details are filled in by this book.

PREFACE

What is the relationship between humans and Nature? The
Linnaean, or scientific, name of our own species is Homo
*piens sapien*"Man, the wise, the wise." But, as a humble
proposal or wisecrack, we suggest that humanity be rechristened Homo insapien*"Man, the unwise, the tasteless." We
love to think we are Nafure's rulers-"Man is the measure
of all things," said Protagoras 2,M yeats ago-but we are
less regal than we imagine. Micrrcosmos: Four Billion Years
of Eaolution ftom Our Microbial Ancestors (first published
in 1985) strips away the gilded clothing that serves as
humanity's self-image to reveal that our self-aggrandizing
view of ourselves is no more than that of a planetary fool.
Humans have longbeen the planetary orbiospheric equivalent of Freud's ego, which "plays the ridiculous role of the
clown in the circus whose gestures are intended to persuade
the audience that all the changes on the stage are brought
about by his orders." We resemble such a clown except that,
unlike him, our egotism conceming our own importance for
13

14

PRE.FACE

Nature is often humorless. Freud continues, "But only the
youngest members of the audience are taken in by him."s
Perhaps human gullibility regarding planetary ecology is also
a function of our youth<ur collective immaturity as one
of many species sharing the Earth. But even if we are Nature's
brilliant child, we are not that scientific conceit, "the most
highly evolved species." The human "emperor," from the
revisionary perspective of. Micrbcosmos, and in the humble
opinion of its authors, is wearing no clothes.
A forum inHarper's Magazine, entitled "O.ly Man's Presence Can Save Nafure,"5 exemplifies humanity's typically
grandiose, almost solipsistic, view of itself. Atmospheric
chemist ]ames Lovelock speaks of the relationship between
humans and Nature as an impending "wa{'l ecofundamentalist Dave Foreman declares that, far from being the central
nervous system or brain of Gaia, we are a cancer eating
away at her; while University of Texas Professor of Arts and
Humanities Frederick Turner transcendentally assures us that
humanity is the living incarnation of Nature's billion-yearold desire. We would like to take all these views to task. In
medieval times an interesting prop of the jesting Fool, besides
glittering jeweled bauble and wooden knife, was the globe.
Picture this figure<apped and belled Fool, ear flaps a-dangling as he handles a mock Earth-for a more festive, if no
less true, summary of how things stand between Homo sapiens
and Nature.
Through Plato, Socrates speaks of the folly of inscribing
one's opinions: although your views may change, your words
as committed to paper remain. Socrates at least did not write,
and what he knew, first and foremost, was that he did not
know. We, however, did write. Reversing the usual inflated
view of humanity, we wrote of Homo sapiens as a kind of
latter-day permutation in the ancient and ongoing evolution

Preface

15

of the smallest, most ancient, and most chemically versatile
inhabitants of the Earth, namely bacteria. We wrote that the
physiological system of lile on Earth, Gaia, could easily survive the loss of humanity, whereas humanity would not survive apart from that lrte. Microcosmos received generally
favorable reviews, but was criticized on several scores, most
vehemently for our cavalier attifude toward our own species.
We outraged some with the implication that even nudear
war would not be a total apocalypse, since the hardy bacteria
underlying life on a planetary scale would doubtless survive
it. Unlike spoken words floating off noncommittally into the
fickle winds of opinion, our words as hard symbols on PaPer
sat, as here they sit<bstinately confronting us with dogma
and didacticism instead of what otherwise might have been
merely a provisional opinion. Happily, though, the occasion
of the paperback reprinting of Miirocosmos offirs us an oPPorfunity, if not to rewrite and revise, at least to reflect on the
book and its main concerns.
Much has occurred, in science and in the world, in the
half decade since the hardcover first appeared. In "The Symbiotic Brain" (Chapter 9) we detailed the speculation that the
sperm tails of men, which propel sperm to the eggs of women,
evolved through symbiosis. We claimed that sperm tails and
oviduct undulipodia (among other subvisible structures) derived from spirochete bacteria that became ancestral cell
"whips." In 1989 three Rockefeller University scientists pubIished an arcane report of a new special cell DNA. Although
not yet definitive,T their discovery of "centriole-kinetosome
DNA,' on its own chromosome and tightly packed at the
base of each cell whip (undulipodium), is the single most
important scientific advance for the symbiotic theory of cell
evolution since the 1.953 discovery of DNA Ltself . Microcosmos,
in contrast to the usual view of neo-Darwinian evolution as

16

PREFACE

an unmitigated conflict in which only the strong survive,
more than everencourages explorationof an essential alternative: a symbiotic, interactive view of the history of life on
Earth. And although we would be foolish to propose that
competitive power struggles for limited space and resources
play no role in evolution, we show how it is equally foolish
to overlook the crucial importance of physical association
between organisms of different species, symbioses, as a major
source of evolutionary novelty. And during the last half decade events and moods have tended to underscore the importance of symbiosis and association far beyond the microworld of evolving bacteria.
As symbolized by the deconstruction of the Berlin Wall
and the end of the Cold War, it is folly not to extend the
lessons of evolution and ecology to the human and political
realm. Life is not merely a murderous game in which cheating
and killing insure the injection of the rogue's genes into
the next generation, but it is also a symbiotic, cooperative
venture in which partners triumph. Indeed, despite the bglittling of humanity that naturally occurs when one looks at
"Homo npiens ilpiens" from a planetaryperspective of billions
of years of cell evolution, we can rescue for ourselves some
of our old evolutionary grandeur when we recognize our
species not as lords but as parbners: we are in mute, incontro.
vertible partnership with the photosynthetic organisms that
feed us, the gas producers that provide oxygen, and the
heterotrophic bacteria and fungi that remove and convert
our waste. No political will or technological advance can
dissolve that partnership.
Another sign of this distinct sort of deserved grandeur is
our involvement in a project that may well outlast our species
as we know iI the introduction of biospheress to other planets
and to outer space. These expanding activities resemble noth-

Preface

17

ing so much as the reproduction of the planetary living system-the truly physiologically behaving nexus of all life on
Earth. The expansion and reproduction of the biosphere,
the production of materially closed, energetically oPen ecosystems on the Moon, Mars, and beyond, depends uPon
humanity in its widest sense as a planetary-technological
phenomenon. David Abram, a philosopher at SUNY-Stony
Brook, has spoken of humanity "incubating" technology.
A selfish attitude and an exaggerated sense of our own importance may have spurred the augmentation of technology and
human population at the exPense of other organisms. Yet
now, after the "incubation phase," the Gaian meaning of
technology reveals itself: as a human-mediated but not a
human phenomenon, whose applications stand to expand
the influence of all life on Earth, not just humanity.

we retrace evolutionary history from the
novel perspective of the bacteria. Bacteria, single and multicellular, small in size and huge in environmental influence,
were'the sole inhabitants of Earth from the inception of life
nearly four billion years ago until the evolution of cells with
nuclei some two billion years later. The first bacteria were
anaerobes: they were poisoned by the very oxygen some of
them produced as waste. They breathed in an atmosphere
that contained energetic comPounds like hydrogen sulfide
and methane. From the microcosmic perspective, plant life
and animal life, including the evolution of humani$, are
recent, passing phenomena within a far older and more fundamental microbial world. Feeding, moving, mutating,
sexually recombining, photosynthesuing, reproducing,
overgrowing, predacious, and energy-exPending symbiotic
microorganisms preceded all animals and all plants by at
least two billion years.

ln

Microcosmos

18

PRBFACE

What is humanity? The Earth? The relationship of the two,
if in fact they are two? Microcosmos approaches these large
questions from the particular perspective of a planet whose
evolution has been largely a bacterial phenomenon. We believe this formerly slighted perspective is a highly useful,
even essential, compensation required to balance the traditional anthropocenhic view which flatters humanity in an
unthinking, inappropriate way. Ultimately we may have
overcompensated. In the philosophical practice known as

deconstruction, powerful hierarchical oppositions are
dismantled by a dual process ]acques Denida caricatures or
characterizes as "reversal and displacement." This process
is at work in Microcosnos.. humanity is deconstructed as the
traditional hierarchy-recently evolved humans on top, evolutionarily older "lowey'' organisms below-is reversed. Miuocosmos removes man from the summit, showing the
immense ecological and evolutionary importance of the lowest of the small organisms, bacteria. But from the view of
deconstructive practice, Miuocosmos, which reverses the hierarchical opposition, does not take the next step of displacement: man is taken off the top of Nature only to be put on
the bottom. What ultimately must be called into question is
not the position assumed by humans in the opposition Man/
Nature but the oppositional distortions imposed by the hierarchy itself. (A more parochial matter for deconstruction, apparenfly of interest to Derrida himself, is the hierarchy trumanityl
animality.) If we were to entirely rewrite Microcosmos, we
might try to redress the naivet6 of this inversion, whichlike turning the king into a fool-upsets our conventions,
but only in a preliminary fashion without truly dismantling
them. Nearly all our predecessors assumed that humans have
some immense importance, either material or transcendental.
We picture humanity as one among other microbial phenom-

Preface

19

ena, employrngHottu insapiens as a nickname to remind ourselves to stave off the recurring fantasy that people master
(or can master) Gaia. The microbial view is ultimately provisional; there is no absolute dichotomy between humans and
bacteria. Homo insapiens, our more humbling name, seems

more fitting, somehow more "Socratic." At least we know,
says, that we do not know.
The Harpq's debate presented a diversity of characterizations of the relationship between "Man" and "Nafure." And
despite the title, "Only Man's Presence Can Save Nature,"
the editors dutifully informed us that one of the most significant contributions to the debate on hurnanit5/s status is that
"Nature has ended." lnMicrocosmoswe take a stance against
the division of humans beings from the rest of "Nature."
People are neither fundamentally in conflictwith nor essential
to the global ecosystem. Even if we accomplish the extraterrestrial expansion of life, it will not be to the credit of humanity
as humanity. Rather it will be to the credit of humanity as a
symbiotically evolving, globally interconnected, technologically enhanced, microbially based system. Given time, raccoons might also manufacture and launch their ecosystems
as space biospheres, establishing their bandit faces on other
planets as the avant-garde of Gaia's strange and seedlike
brood. Maybe not black-and-white raccoons, but diaphanous
nervous-system fragments of humanity, evolved beyond recognition as the organic components of reproducing machines,
might survive beyond the inevitable explosion and death of
the sun. Our microcosmic portrayal of. Homo *piens sapiens
as a kind of glorified sludge has the merit of reminding us
of our bacterial ancestry and our connections to a still largely
bacterial biosphere.
An old metaphysical preiudice, a thinly disguised axiom
of western philosophy, is that human beings are radically

it

20

PREFACE

separate from all other organisms. Descartes held that nonhuman animals lacked souls. For centuries scientists have suggested that thought, language, tool use, cultural evolution,
writing, technology-something, anything-unequivocally
distinguishes people from "lowe/' life forms. As recently
as 1.990 nafure writer William McKibben wrote, "In our modern minds nafure and human society are separate things
. . this separate nature . . . is quite real. It is fine to argue,
as certain poets and biologists have, that we must learn to
fit in with nature, to recognize that we are but one species
amongmany. . . . Butnoneofus, ontheinside, quitebelieve
it."e Perhaps this anthropocentric self-glorificati-on spurred
our ancestors on, gave them the confidence to be "fruitful
and multiplt''-to rush to the very brink we are on now of
a punctuated change in global climate, accompanied by mass
extinctions and a shift in the Gaian "geophysiology."
It is usually thought that Darwin, by presenting evidence
for the theory of evolution by natural selection, dramatically
knocked the pedestal out from under the feet of humanity,
undermining the case for God, leaving us uncomfortably in
the company of otheranimals bybroadcastingthe taboo secret
of our apish origins. The Darwinian revolution has often
been compared to that of Copernicus, who showed that the
- Earth is not the center of the Universe but merely a dust
speck in the corner of our galactic Milky Way cobweb. From
a philosophical point of view, however, far from the Darwinian revolution destroying our special relationship as the
unlquq life form, as a chosen species made in God's image
and with connections to saints and angels, what seems to
have happened in the wake of the Darwinian revolution is
that we, Homo sapiens sapien*man, the wise, the wis+
have come to replace God. No longer are we junior partners,
second in command. Darwinism may have destroyed the

Preface

2l

anthropomorphic deity of traditional religion, but instead
of humbling us into alvareness of the protoctists and all other
sibling life forms (the plants, fung1. bacteria, and other animals), it rendered us greedy to assume God's former place.
We put ourselves in the self-assumed position of divine rulers
over life on Earth, ambitiously devising planet-scale technologies and, in short, engineering the world.
Somewhat surprisingly to those not versed in the ways
of feedback, this self-serving attitude of human glorification
at the expense of other species no longer serves us. Our
extreme self-centeredness and hyperpopulation of the planet
have brought on wholesale ecological carnage, the greatest
threat of which is to ourselves. The haditional religious perspective-kept alive, as lve have seen, even inside secular
Darwinism-is that human beings are separate, unique, better. This is the attitude of ecological arrogance. The PersPective of Miuocosmos differs in that it is a deep-ecolory, a
particular variety of "green" perspective. Referring now to
Lewis Thomas's tracing of the early word human in the Foreword, Microcosmos tries to develop an attitude of ecological
humility. Retelling the story of life from the vantage point
of microbes, Microcosmos diametrically inverts the usual hierarchy: indeed, by claiming that the planetary system of life
has no essential need for man, that humanity is a temporary
pointillist epiphenomenon of the essential and anciently recombining microorganisms, we may have overstated, exaggerated the case. The problem with the reversal that places
microbes on top and people underneath is that dichotomization-important versus unimportant, essential versus unessential-remains. Woody Allen once said that he always put
his wife under a pedestal. Confronting our ecological arro'
gance does not solve the problem of the pedestal: it is still
assumed that one organism is better, higher, or "more

22

PREFACE

evolved" than the other. To deconstruct our destructive attitude of ecological arrogance, it is necessary to put ourselves
down. Once we recognize our energetic and chemical intercourse with other species, however, and the nonnegotiability
of our connections with them, we must remove the pedestal
altogether.

In tandem with its attempt to carry to the limits Darwin,s
"Copernican" revoluti on, Microcostnos stresses the symbiotic
history of life. Since the publication of the hardcover, more
striking evidence has accumulated to show that symbiosis,
theliving togetherand sometimes merging of different species
of organisms, has been cmcial to the evolution of life forms
on Earth. The most important examples of symbiosis-the
chloroplasts (of all plants) and the mitochondria (of all plants
and all animals), both of which were formerly independent
bacteria-are well detailed inMicrocosmos. But symbiosis now
appears to be particularly good as an explanation of "jumps"
in evolution that have momentous ecological importance.
Submarine fishes, luminously spotlighting the blackest of
waters, may have evolved into myriads of kinds, spurred
on by eye-patch, esophageal, or anal light organs harboring
glowing symbiotic bacteria.lo Different symbioses of fish and
beetles with glow-in-the-dark bacteria abound.
Another example of recent symbiosis research suggests
that the green algal transition to land plants resulted from
a merging of the genomes (genetic material) of a fungus
with some aquatic green alga ancestor. Lichens are wellknown products of symbioses. All lichens are fungi symbiotic
with cyanobacteria or fungi symbiotic with geen algae. The
two types of lif+photosynthesizer and consumer-intertwine to form a novel green low-lying plantlike organism
with remarkable longevity-the lichen. The amazing capacity
of lichens to proliferate on the bare face of rocks depends

Preface

23

on the symbiosis, the equally combined fungal and photosyn-

thetic partners that comprise the lichen entity. The newest
twist is that vascular plants-including herbs and shrubs
and all trees-may originally have been "inside-out lichens."
Their evolution may have involved a new partnership between widely differing species from different kingdoms of
life. If Professor Peter Atsatfs theory11 is correct, then the
interactive venfure between two kinds of organisms, fungi
and protoctistan green algae, accounted not for the appearance of some minor entity in the backwoods of evolution
but for the momentous evolution of the Kingdom Plantae,
the woods themselves.
The illusion of the independence of humans from Nature
is dangerous ignorance. An unbroken continuum of life exists
now as it has since life's inception-through Darwinian time
(four billion years) and Vernadskian space (a twenty-five kilometer ring, extending ten kilometers down to the abyss
and fifteen to the top of the troposphere).12Inside this living
system we are all embedded: to escaPe it is tantamount to
death. Emily Dickinson, noting "what mystery pervades a
well," charmingly described us and Nature. It is fifting to
cite her prior to the descent into the microcosm:
But nature is a stranger Yet;
The ones that cite her most
Have never passed her haunted house,
Nor simplified her ghost.
To pity those that know her not
Is helped by the regret
That those who know her,

know her less
The nearer her they

8et.13

-Dorion

Sagan and Lynn Margulis

]anuary 1997/1997

ACKNOWLEDCMENTS

In 1980 the colorful literary agent )ohn Brockman, dressing
like a fashion-conscious ltalian gangster, came from New
York to Boston to solicit a book from Lynn Margulis. Without
that initial visit, and his continual encouragement, this book
would never have been written. We are equally indebted
to his partner, Katinka Matson, who has been nothing but
helpful for the decade this book was in gestation. We would
like to thank Laszlo Meszoly who, at short notice, stippled
the evocative scenes of life's evolution through time. We express appreciation to the late biology-watcher Lewis Thomas
for writing the foreword and being an inspiration, worldtraveler David Abram for sharing his insights into nature,
and the late Theodore Sturgeon, whose science fiction story
"Microcosmic God" is paraphrased within these pages. We
also are deeply grateful to our friends, family, editors, publishers, and colleagues David Bermudes, Robert Bo5mton,
]ack Corliss, Geoff Cowley, Eileen Crist, W. Ford Doolittle,
Ann Druyan, Betsey Dexter Dyeq, Stephen ]ay Gould, Bruce
?5

26

AC KNOW L EDGM ENTS

Gregory Ricardo Guerrero, ]ames Hallgring, Stephanie Hiebert, Donald lohansory Geraldine Kline, Edmond LeBlanc,
]ames Lovelock, David Lyons, Lorraine Olendzenski, ]ennifer Margulis, Zachtary Margulis, Kelly McKinney, Philip
and Phylis Morrison, Elaine Pagels, |ohn Platt Carl Sagan,
]eremy Sagan, Mariorie Maclean, Arthur Samuelson,
Nathan Shafner, ]ames Silberman, William Solomon, |ohn
Stolz, William Irwin Thompson, Paul Trachtman, and peggy
Tsukahira.
We are sorry that our colleagues and friends Elso S.
Barghoorn and Heinz A. Lowenstam, who helped us with
this book, did not live to see the published paperback.
Most of the scientific research on which some of this text
is based has been supported by the planetary biology program of NASA, the Boston University and University of
Massachusetts, Amherst graduate schools. We are also
grateful to The Lounsbery Foundation for continuing support of this work. Most of the conclusions we have drawn
are based on research and discussion available in the scientific literature. Of course we owe a major debt to the many
unmentioned authors and scientists whose work provides a
basis for our narrative.
Lynn Margulis and Dorion Sagan
February 7997
Amherst, Massachusetts

INTRODUCTION:
THE MICROCOSM

\ A /UEN people look at life on Earth, it is easy to think
V V *" ,rp."*". The power of consciousr,ess, of our
"r"

society and our technical inventions, has made us think we
are the most advanced form of life on the planet. Even the
great blackness of space seen does not humble us. We view
space as a no man's land to penetrate and conquer as we

believe we have conquered the Earth.
Life on Earth has traditionally been studied as a prologue
to humans: "lower" forms of life lacking intelligence preceded
us and we now stand at the pinnacle of evolution. lndeed,
so godlike do we consider ourselves that we may think we
are taking evolution into our own hands by manipulating
DNA, the mainspring of life, according to our own design.
We study the microcosm-the age-old world of miooorganisms-to discover life's secret mechanisms so that we can
take better control, perhaps even "perfecf' ourselves and
the other living things on the Earth.
But during the past three decades, a revolution has taken
27

28

INTRODUCTION: THE MICROCOSM

place in the life sciences. Fossil evidence of primeval microbial life, the decoding of DNA, and discoveries about the composition of our own cells have exploded established ideas

about the origins of life and the dynamics of evolution on
Earth.

First, they have shown the folly of considering people as
special, apart and supreme. The microscope has gradually
exposed the vastness of the microcosm and is now giving
us a startling view of our true place in nature. It now appears
that microbes-also called microorganisms, gerns, bugs, protozoans, and bacteria, depending on the context-are not
only the building blocks of life, but occupy and are indispensable to every known living structure on the Earth today. From
the paramecium to the human race, all life forms are meticulously organized, sophisticated aggregates of evolving microbial life. Far from leaving microorganisms behind on an
evolutionary "ladder," we are both surrounded by them and
composed of them. Having survived in an unbroken line
from the beginnings of life, all organisms today are equally
evolved.
This realization sharply shows up the conceit and presumption of attempting to measure evolution by a linear progression from the simple-so-called lower-to the more complex
(with humans as the absolute "highest" forms at the top of
the hierarchy). As we shall see, the simplest and most ancient organisms are not only the forebears and the
present substrate of the Earth's biota, but they are ready
to expand and alter themselves and the rest of life, should
we "higher" organisms, be so foolish as to annihilate ourselves.

Next, the view of evolution as chronic bloody competition
among individuals and species, a popular distortion of Darwin's notion of "suryival of the fittest," dissolves before a

lntroiluction: The Microcosm

29

new view of continual cooperation, strong interaction, and
life forms. Life did not take
mutual dependence
"-or,g
over the globe by combat, but by networking. Life forms multiplied and complexified by co-opting others, not just by killing
them.
Because we cannot see the microcosm with the unaided
eye, we tend to discount its significance. Yet of the threeand-a-half billion years that life has existed on Earth, the
entire history of human beings from the cave to the condominium represents far less than one percent. Not only did life
originate on earth very early in its history as a planet, but
for the first full two billion years, Earth was inhabited solely
by bacteria.
ln fact, so significant are bacteria and their evolution that
the fundamental dMsion in forrrs of life on Earth is not
that between plants and animals, as is commonly assumed,
but between prokaryotes<rganis-ms composed of cells with
no nucleus, that is, bacteria-and eukaryotes-all the other
life forms.l In their first two billion years on Earth, prokaryotes continuously hansformed the Earth's surface and atmosphere. They invented all of life's essential, miniaturized
chemical systems-achievements that so far humanity has
not approached. This ancient high biotechnolory led to
the development of fermentation, photosynthesis, oxygen breathing, and the removal of nitrogen gas from the air.
It also led to worldwide crises of starvation, pollution,
and extinction long before the dawn of larger forms of
life.
These staggering events early in life's history came about
by the interaction of at least three recently discovered dynamics of evolution. The first is the remarkable orchestrating
abilities of DNA. Identified as the heredity-transmitting substance in l9M by Oswald T. Avery, Colin Macleod, and

30

INTRODUCTION: THE MICROCOSM

Maclyn McCarty, DNA's code was cracked in the 1.960s after
its method of replication was revealed by James Watson and
Francis Crick in 1.953. Governed by DNA, the living cell can
make a copy of itself, defying death and maintaining its identity by reproducing. Yet by also being susceptible to mutation,
which randomly tinkers with identig, the cell has the potential to survive change.
A second evolutionary dynamic is a sort of natural genetic
engineering. Evidence for it has long been accumulating in
the field of bacteriology. Over the past fifty years or so,
scientists have observed that prokaryotes routinely and rapidly transfer different bits of genetic material to other individuals. Each bacterium at any glven time has the use of accessory
genes, visiting from sometimes very different strains, which
perform functions that its own DNA may not cover. Some
of the genetic bits are recombined with the cell's native genes;
others are passed on again. Some visiting genetic bits can
readily move into the genetic apparatus of eukaryotic cells
(such as our own) as well.
These exchanges are a standard part of the prokaryotic
repertoire. Yet even today, many bacteriologists do not
grasp their full significance: that as a result of this ability,
all the world's bacteria essentially have access to a single
gene pool and hence to the adaptive mechanisms of the
entire bacterial kingdom. The speed of recombination over
that of mutation is superior: it could take eukaryotic organisms a million years to adjust to a change on a worldwide
scale that bacteria can accommodate in a few years. By
constantly and rapidly adapting to environmental conditions, the organisms of the microcosm support the entire
biota, their global exchange network ultimately affecting
every liri.g plant and animal. Human beings are just learning these technigues in the science of genetic engineering,

lntroduction: The Microcosm

31

whereby biochemicals are produced by introducing foreign
genes into reproducing cells. But prokaryotes have been
using these "new" techniques for billions of years. The
result is a planet made fertile and inhabitable for larger
forms of life by a communicating and cooperating worldwide superorganism of bacteria.
Far-reaching as they are, mutation and bacterial genetic
transfer alone do not account for the evolution of all the
life forms on the earth today. In one of the most exciting
discoveries of modern microbiology, clues to a third avenue
of change appeared in the observation of mitochondriatiny membrane-wrapped inclusions in the cells of animals,
plants, fungi, and protists alike. Although they lie outside
the nucleus in modern cells, mitochondria have their own
genes composed of DNA. Unlike the cells in which they
reside, mitochondria reproduce by simple division. Mtochondria reproduce at different times from the rest of the
cell. Without mitochondria, the nucleated cell, and hence
the plant or animal, cannot utilize oxygen and thus cannot
live.
Subsequent speculation brought biologists to a striking
scenario: The descendants of the bacteria that swam in primeval seas breathing oxyten three billion years ago exiJt now
in our bodies as mitochondria. At one 6me, the ancient
bacteria had combined with other microorganisms. Th"y
took up residence inside, providing waste disposal and oxygen-derived energy in return for food and shelter. The
merged organisms went on to evolve into more complex
oxygen-breathing forms of life. Here, then, was an evolutionary mechanism more sudden than mutation: a symbiotic
alliance that becomes pernanent. By creating organisms that
are not simply the sum of their symbiotic parts-but something more like the sum of all the possible combinations of

32

INTRODUCTION: THE MICROCOSM

their parts-such alliances Push developing beings into uncharted realms. Symbiosis, the merging of organisms into
new collectives, Proves to be a maior Power of change on
Earth.2

As we examine ourselves as products of symbiosis over
billions of years, the supporting evidence for our multimicrobe ancestry becomes overwhelming. Our bodies contain
a veritable history of life on Earth. Our cells maintain an
envfuonment that is carbon- and hydrogen-rich, like that of
the Earth when life began. They live in a medium of
water and palts like the composition of the early seas. We
became

*tB *"

are by the coming together of bacterial part-

ners in a watery environment. Although the evolutionary
dynamics of DNA, genetic transfer, and symbiosis were not
discovered until almost a century after Charles Darwin's
death in L882, he had the shrewdness to write, "We cannot
fathom the marvellous complexity of an organic being; but
on the hypothesis here advanced this complexity is much
increased. Each living creature must be looked at as a microcosm-a little universe, formed of a host of self-propagating
organisms, inconceivably minute and as numerous as the
stars in heaven."3 The strange nature of this little universe
is what this book is about.
The detailed structure of our cells betrays the secrets of
their ancestors. Electron microscopic images of nerve cells
from all animals reveal numerous conspicuous "microtubules." The waving cilia in the lining of our throats and
the whipping tail of the human sPenn cell both have the
same unusual "telephone dial" arrangement of microtubules
as do the cilia of ciliates, a group of successful microbes
including more than eight thousand different species. These
same microtubules appear in all cells of plants, animals, and
fungi each time the cells divide. Enigmatically, the microtu-

lntroduction: The Misocosm

33

bules of dividing cells are made of proteins nearly identical
to some found in brain cells; and these proteins resemble
those found in certain fast-moving bacteria we hypothesize
were among our ancestors.
These and other living relics of once-separate individuals,
detected in a variety of species, make it increasingly certain
that all visible organisms evolved through symbiosis, the
coming together that leads to physical interdependence and
the permanent sharing of cells and bodies. Although, as we
shall see, some details of the bacterial origin of microtubules,
mitochondria, and other cell parts are hard to explain, the
general outline of how evolution can work by symbigsis is
agreed upon by those scientists who are familiar with the
lifestyles of the microcosm.
The symbiotic process goes on unceasingly. We organisms
of the masocosm continue to interact with and depend
upon the microcosm, as well as upon each other. Certain
families of plants (such as the pea family, including peas,
beans, and their relatives such as clover and vetch) cannot
live in nitrogen-poor soil without the nitrogen-fixing bacteria in their root nodules, and we cannot live without the
nitrogen that comes from such plants. Neither cows nor
termites can digest the cellulose of grass and wood without
communities of microbes in their guts. Fully ten percent
of our own dry body weight consists of bacteria, some of
which, although they are not a congenital part of our bodies,
we can't live without. No mere quirk of nature, such coexistence is the stuff of evolution itself. Let evolution continue
a few million years more, for example, and those microorganisms producing vitamin B12in our intestines may become
parts of our own cells. An aggregate of specialized cells
may become an organ. The union of once-lethal bacteria
with amoebae, creating over time a new species of hybrid

t
u

INTRODUCTION: THE MICROCOSM

amoeba, has even been witnessed in the laboratory.
This revolution in the study of the microcosm brings before

us a breathtaking view. It is not preposterous to postulate
that the very consciousness that enables us to probe the
workings of our cells may have been born of the concerted
capacities of millions of microbes that evolved symbiotically
to become the human brain. Now, this consciousness has
led us to tinker with DNA and we have begun to tap in to
the ancient process of bacterial genetic transfer. Our ability
to make new kinds of life can be seen as the newest way
in which organic memory-life's recall and activation of the
past in the present-becomes more acute. In one of life's
giant, self-referential loops, changing DNA has led to the
consciousness that enables us to change DNA. Our curiosity, our thirst to know, our enthusiasm to enter space and
spread ourselves and our probes to other planets and beyond
represents part of the cutting edge of life's strategies for
expansion that began in the microcosm some three-and-ahalf billion years ago. We are but reflections of an ancient
trend.
From the first primordial bacteria to the present, myriads
of symbiotically formed organisms have lived and died. But
the microbial common denominator remains essentially unchanged. Our DNA is derived in an unbroken sequence from
the same molecules in the earliest cells that formed at the
edges of the first warm, shallow oceans. Our bodies, like
those of all life, preserve the environment of an earlier Earth.
We coexist with present-day microbes and harbor remnants
of others, symbiotically subsumed within our cells. [n this
way, the microcosm lives on in us and we in it.
Some people may find this notion disturbing, unsettling.
Besides popping the overblown balloon that is our presumption of human sovereignty over the rest of nature, it chal-

lntroduction: The

Microcosm

35

lenges our ideas of individuality, of uniqueness and independence. It even violates our view of ourselves as discrete physi-

cal beings separated from the rest of nature. To think of
ourselves and our environment as an evolutionary mosaic
of microscopic life evokes imagery of being taken over, dissolved, annihilated. Still more disturbing is the philosophical
conclusion we will reach later, that the possible rybernetic
control of the Earth's surface by unintelligent organisms calls
into question the alleged uniqueness of human intelligent
consciousness.

Paradoxically, as we magnify the microcosm to find our
origins, we appreciate sharply both the triumph and the insignificance of the individual. The smallest unit of life-a single
bacterial cell-is a monument of pattern and process unrivaled in the universe as we know it. Each individual that
grows, doubles its size, and reproduces is a great success
story. Yet just as the individual's success is subsumed in
that of its species, so is the species subsumed in the global
network of all lif+a success of an even greater order of
magnitude.
It is tempting, even for scientists, to get carried away by
success stories. From the disciples of Darwin to today's genetic engineers, science has popularized the view that humans are at the top rung of Earth's evolutionary "laddey''
and thatwith technologywe have stepped outside the framework of evolution. Some eminent and sophisticated scientists,
such as Francis Crick in his book, Life ltself , write that life
in general and human consciousness in particular are so miraculous that they couldn't be earthly at all, but must have
originated elsewhere in the universe.4 Others still believe
that humans are a product of a fatherly "higher intelligence"-the children of a divine patriarch.
This book was written to show that these views underes-

36

INTRODUCTION: THE MICROCOSM

timate the Earth and the ways of nature. There is no evidence that human beings are the supreme stewards of life
on Earth, nor the lesser offspring of a superintelligent extraterrestrial source. But there is evidence to show that we are
recombined from powerful bacterial communities with a multibillion-year-old history. We are a part of an inhicate network
that comes from the original bacterial takeover of the Earth.
Our powers of intelligence and technology do not belong
specifically to us but to all life. Since useful attributes are
rarely discarded in evolution it is likely that our Powers,
derived from the microcosm, will endure in the microcosm.
Intelligence and technology, incubated by humankind, are
really the property of the microcosm. They may well survive
our species in forms of the future that lie beyond our limited
imaginations.

Microcosmos

ego

4 bllllon yeera
Hailan Eot
Mioororstttos begins frut debris S supnooa erplniofl ,

Chapter

t

Out of the Cosmos

ROM the moment we consider origins on a cosmic scale,

F the view of ourselves as a part-a miniscule part-of the
universe is thrust upon us. For the very atoms that compose
our bodies were created not, of course, when we were conceived, but shortly after the birth of the universe itself.
It is a known astrophysical fact that most stars in the sky
are shooting away from each other at tremendous speeds.
lf we reverse this trend in our minds we come up with the
so-called Big Bang, the hypothetical release of all the energy,
matter, and antimatter in existence. Like any other look into
what Shakespeare called "the dim backward and abysm of
time," we must not mistake our best guesses or relatively
straight-line extrapolations of present conditions into the past
for the literal truth. Slight alterations in the most minor assumptions can lead to major distortions when magnified over
the 15,000 million year time span that is the purported age
of the present universe. Nonetheless, such extrapolations
yield the best picture we have of the cosmos which preceded
39

MI

40

C

ROC OSMOS

TABI.E 1
GEOTOGICAT TIME SCALE*
(in millions of years ago)
When
eon

began

Eons

Epochs

Periods

Eras

4,500
Hadean

3,900
Prephanerozoic

Archean

beginning and ending dates

for periods and epochs (in
millions of years ago)

2,500
Proterozoic

Cambrian

580

Ordovician
Paleozoic

580-24s

Silurian

Devonian

580-500
500--440

44HOO
400-345

Carboniferous 345-290
Phanerozoic
Mesozoic
24s--66
Cenozoic

66-0

Permian

290-245

Triassic

245-195

lurassic
cretaceous

1

Paleogene

Neogene
0
+

95-1 38

138-66

66-26

2A

Paleocene
Eocene

66-54
s4-38

Oligocene

38_26

Miocene 26-7
Pleiocene 7-2

Pleistocene 24.1

Recent

0.1-Now

Not to scale and simplified

the evolution of life in the microcosm, as well as of the microcosm and its relentless exPansion.
Over the first million years of expansion after the Big Bang,
the universe cooled from 100 billion degrees Kelvin, as estimated by physicist Steven Weinberg, to about 3000 degrees

4l

Out of the Cosmos

K, the point at which a single electron and proton could
join to create hydrogen, the simplest and most abundant
element in the universe.la Hydrogen coalesced into supemovaHnorrnous clouds that over billions of years contracted
from cosmic to submicrocosmic densities. Under the sheer
force of gravity, the cores of the supernovae became so hot
that thermonuclear reactions were fired, creating from hydrogen and various disparate subatomic particles all the heavier
elements in the universe that we know today. The richness
of hydrogen is in our bodies still-we contain more hydrogen
atoms than any other kind-primarily in water. Our bodies
of hydrogen mirror a universe of hydrogen.
The newly created elements spewed off into space as the
dust and gas that compose the galactic nebulae. Within the
nebulae, more stars and sometimes their satellite planets were
born, again as particles of dust and gas gravitated toward
each other, falling in and concentrating until nuclear reactions
were generated. Before the first matter that could be called
the Earth gathered within our solar nebula at an outer arm
of the Milky Way, five to fifteen billion years and billions of
coalescing events forming the stars of the universe had already
occurred.
In the cloud of Bases destined to become Earth were hydrogen, helium, carbon, nitrogen, oxygen, iron, aluminum, gold,
uranium, sulfur, phosphorus, and silicon. The other planets
in our solar system began as similar clumps of gas and dust
particles. But all would have cooled and floated about as
the aimless detritus of lifeless space were it not for the huge
star that formed from the center of the nebula, pulling the
hardening smaller bodies into orbit and igniting into a stable,
long-lasting burn that bathed its satellites in continuous emanations of light, gas, and energy.
At this point, about 4,500 million years ago, the Earth mass
.

42

MrcRo cosM os

was already in circumstances that were to suit it for the emergence of life. First, it was near a source of energ'y: the sun.
Second, of the nine major planets orbiting the sun, the earth
mass was not close enough so that its elements were all blown
away as gases or all liquefied as molten rock. Nor was it far

enough away for its gases to be frozen as ice, ammonia,
and methane as they are today on Titan, the largest moon
of Saturn. Water is liquid on Earth but not on Mercury where
it has all evaporated into space or on Jupiter where it is ice.
Finally, the Earth was large enough to hold an atmosphere,
enabling the fluid cycling of elements, yet not so large that
its gravity held an atmosphere too dense to admit light from
the sun.
When the sun ignited, an explosive blast of radiation swept
through the nascent solar system, stirring up the early atmospheres of the earth and other inner planets. Hydrogen, too
light a gas to be held by the earth's gravity, either floated
into space or combined with other elements, producing ingredients in the recipe for life. Of the hydrogen that was left,
some combined with carbon to make methane (CHa), some
with orygen to make water (HzO), some with nitrogen to
make ammonia (H3N), and some with sulfur to make hydrogen sulfide (HzS).
These gases, rearranged and recombined into long-chained
compounds, make practically every component of our bodies.
They are still retained as gases in the atmospheres of the
massive outer planets, )upiter, Safurn, Uranus, and Neptune,
or as solids frozen into their iry surfaces. On the smaller,
new, and molten Earth, however, phenomena more complex
than gravity began to involve these gases in cyclical processes
that would keep them here to the present day.
The fury and heat in which the early Earth was formed
was such that during these first years of the Hadean Eon

Out of the

Cosmos

43

(4,50G3,900 million years ago) there was no solid ground,
no oceans or lakes, perhaps not even the snow and sleet of
northern winters. The planet was a molten lava fireball, burning with heSt from the decay of radioactive uranium, thorium,
and potassium in its core. The water of the Earth, shooting in
steam geysers from the planet's interior, was so hot that it
never fell to the surface as rain but remained high in the
atmosphere, an uncondensable vapor. The atmosphere was
thicl with poisonous cyanide and formaldehyde. There was
no breathable orygen, nor any organisms capable of breathing
it.
No Earth-rocks have survived this hellish primeval chaos.
The Hadean Eon is dated from meteorites and from rocks
taken by Apollo astronauts from the airless moon, which began to cool4,600 million years ago while the Earth was still
molten. By about 3,900 million years ago, the Earth's surface
had cooled enough to form a thin cmst that lay uneasily on
the still-molten mantle, the structure below it. The crust was
punctured from below and impacted from above. Volcanoes
erupted at cracks and rifts, violently spilling their molten
glass. Meteorites-some as huge as mountains and more explosive than the combined nuclear warheads of both superpowers-made violent crash landings. They cratered the
chaotic terrain, sending up vast plumes of dust which were
rich in extraterrestrial materials. The dark dust clouds, swept
by vicious winds, swirled around the globe for months before
finally settling down. Meanwhile, tremendous frictional activity caused widespread thunderclaps and electrical lightning
storms.

Then, 3,900 million years ago, the Archean Eon began. It
was to last for one-and-a-third billion years, and was to see
everything from the orign of life to its spread as soft, colorful,
pu{ple and green mats and hard, rounded domes of bacteria.
The immense amounts of rock that 3,000 million years later

M

M IC ROC

OSMOS

would become the American, African, and Eurasian land
masses floated about the globe in the unfamiliar shapes of
ancient continents. The recognizable continents appeared in
their present positions in only the last tenth of a percent of
our planetary history.
Heat and radioactivity still brewing in the Earth's core sent
lava boiling up through cracks in the iust-cooling crust. Much
of the lava contained molten magnetic iron whose molecules
oriented themselves to the Earth's magnetic pole as it froze
into rock. In the early 1950s, studies of these ancient magnetic
orientations confirmed what earlier eyes had observed from
the shapes of continents and the correspondence of rock layers
and fossil wildlife at their edges: the several "plates" into
which the Earth's cmst is split move about on the molten
mantle, separating from some and crashing into others as
they shift. Moving up to centimeters a year, a continental
plate can cover a hundred miles in a million years. Two hundred million years ago, lor example, India was attached to
Antarctica, far from the rest of Asia. Drifting nearly two inches
a year, India moved northward over 4,000 miles, joining the
Asian continent only about sixty million years ago.
The seams between the plates host violent activity. Where
the plates are separating and magma boils up to fill the widening rifts, new land or ocean floor is created. Where they
collide, earthquakes and volcanoes abound and the Earth is
thrown up into mountains. The slow but violent confrontation
between the Indian and Asian plates thrust Mount Everest
and the Himalayas to the peak of the world.
Today the quakes and tremors along the San Andreas fault
in California signal the inexorable progress of the huge Pacific
plate, moving northwest as it collides against the northwardmoving plate from which the North American continent sticks
up. And in North Africa, the Zambezi River in Mozambique

Out of tlu Cosmos

45

in the earth's armor-the Great African riftthat is cracking the continent of Africa apart. Toward the
south, huge amounts of water fill the cracks as soon as they
traces a split

form; great volumes of rock are caving in. Toward the north,
at Afar in Ethiopia, water has not yet obscured the view.
Molten rock oozes toward the surface and freezes into "pillow
basalts" to form the floor of a new Pan-African ocean. The
floor of this future ocean is still largely dry. And the panoramic
view of the Afar valley is iust what you would see if the
water of the Atlantic Ocean were drained and you could
watch the formation of new sea floor along a rift zone.
The San Andreas fault, the African rift, the Mid-Aflantic
rift, the East Pacific rise, and the volcanic islands of Hawaii
are rare sites of earth-building activity on a largely placid
planet today. But during the Archean Eon, the Earth's surface
was riddled by such tectonic activities. Huge quantities of
steam shot out of blow holes and splitting seams. The Earth
lay covered in a darkening fog of carbon gases and sulfurous
fumes. Showers of iry comets and carbonaceous meteorites
bombarded the planet, burning through the atmosphere to
the weak and unstable surface, further rupturing the cmst.
Carbon and water came with them from space in sufficient
quantities to add to the Earth's own supplies of what were
later to become the staples of life.
As the Earth's surface continued to cool, the clouds of
steam filling the atmosphere could finally condense. Torrential
rains fell for perhaps a hundred thousand years without cease,
creating hot, shallow oceans. Submerged plate boundaries,
rich in chemicals and energy, steadily vented hydrogen-rich
gases into the seas. Water hitting the boiling lava in rifts
and volcanoes evaporated, condensed, and rained down
again. The waters began to erode the rocky landscape,
smoothing out the pockmarks and wounds made by the con-

M

M IC ROC OSMO

S

stant belching of volcanoes and powerful impacting of meteor-

ites. The waters rounded off the mountains as they were
created, washing minerals and salts into the oceans and land
pools. Meanwhile, in an event sometimes called the Big Belch,
tectonic activity released gases trapped in the Earth's interior
to form a new atmosphere of water vapor, nitrogen, argon,
neon, and carbon dioxide. By this time much of the ammonia,
methane, and other hydrogen-rich gases of the primary atmosphere had been lost into space. Lightning struck. The sun
continued to beam heat and ultraviolet light into the Earth's
thickening atmosphere, as the fast-spinning planet spun in
cycles of five-hour days and five-hour nights. The moon too
had condensed from the sun's nebula. Since some 15 percent
of the moon is material of Earth origin, the best recent model
suggests that the moon arose when a planetoid crashed into
the Earth's surface but could not completely escape Earthly
gravity, going into orbit. Our faithful natural satellite, rather
large for a puny inner planet like the Earth, from the beglnning
pulled rhythmically on the great bodies of water, creating
tides.

It is from this Archean Eon, from 3,900 to 2,500 million
years ago, that we have found the first traces of life.

3

bllllonyeara

ego

ArchunEon

Gtowing micmba trap miamls,form layers of rockin

Chapter

z

slullw

ocearc.

The Animation of Matter

quests are so magical as that for the origins of life.
Et*
I Scientists, alert for any due, have amassed a telling body

of data. A new underwater world, relevant to our thinking
about the origins of life, was discovered in 1973. Oceanographer Jack Corliss, a professor at Oregon State University,
saw for the first time undersea continental plate seams where
magma, steam, and gases still mingle with salty water as
they did everywhere in Archean times. Except for an occasional deep-sea fish and the tenacious films of the hardiest
microorganisms, the pitch-black, cold (4' centigrade) floor
of today's ocean is nearly everywhere barren. Yet along the
seams of the earth's great plates where sulfide spews up
from the hot mantle below, there are peculiar communities
of underwater creatures. At such sites near the Galapagos
Islands on the equator, off the shores of Baja California in
Mexico, and J,4gtg meters beneath the water in the Gulf of
Mexico a few hours west of St. Petersburg, Florida, oceanogri-

phers have found giant red tubeworms of the genus Riftia.
47

48

MI

C

ROC OSMO

S

So called because the rifts in the ocean floor are the only
place they have ever been found , Riftia-as well as various
fish, giant clams, other worms, and an occasional octopussurround the crevices and cracks. None of these animals of
the abyss feeds on plants. Plants, algae, any photosynthetic
life forms, need light, but no light penehates to the bottom
of the sea. Instead, the rift animals feed on shingy bacteria
that derive their energy from the sulfide and other hydrogenrich gases emanating from the Earth's hot-water vents.
The chemistry of which all life, including our own flesh,
is composed is that of reduced carbon compounds-that is,
carbon atoms surrounded by hydrogen atoms. |ack Corliss
believes that life could have begun at the ancient plate boundaries in the shallow, warm waters of the Archean Earth, where
hydrogen-rich gases from the Earth's interior reacted with
the carbon-rich.gases of the atmosphere. (Indeed, 90 percent of the carbon of our own bodies is estimated to have
passed at one time or another through such plate seams and
vents.)
The flexibility of carbon is one of the secrets of life on
Earth. In their highly agitated states during the hot, wet,
and molten Archean conditions, carbon atoms combined rapidly with hydrogen, nitrogen, oxygen, phosphorus, and sulfur
to generate a vast diversity of substances. This collection of
carbon-containing molecules has continued to exist, interact,
and evolve. Those six elements are now the chemical common denominator of all life, accounting tor 99 percent of the
dry weight of every living thiog. Moreover, the percentage of
each of these elements, the proportion of amino acids and
genetic components, and the distribution of long protein
and DNA macromolecules in the cells are similar in all
forms of life, from bacteria to the human body.ls Like Darwin's
recognition of the essential similarities of apes and humans,

The Animation of

Matter

49

these chemical similarities point to a common ancestor for
all life, and furthermore, to the sorts of conditions that must
have existed on the early Earth when there was little chemical
difference between living cells and their immediate environment.

In L953, a celebrated series of experiments at the University
of Chicago launched a new field of laboratory science, variously referred to as "prebiotic chemistry," "primitive Earthmodel experiments," or "experimental chemical evolution."
Stanley L. Miller, a graduate student of the Nobel Priz+
winning chemist, Harold C. Urey, bombarded a mock-up of
the primary atmosphere (a mixture of ammonia, water vapor,
hydrogen, and methane) with a lightninglike electrical discharge for a week. He was rewarded with the Production
of the two amino acids alanine and glycine as well as many
other organic substances thought before then only to be produced by living cells. (Small molecules of fewer than a dozen
or so carbon, nitrogen, hydrogen, and oxygen atoms, amino
acids are the components of all proteins.)
Since the Miller-Urey experiments, almost every simple
component of the complex molecules of cells has been produced in the laboratory by subjecting various mixtures of
simple gases and mineral solutions to different energy
sources.+lectric spark, silent electric discharge, ultraviolet
radiation, and heat. Satisfyingly enough, the four rnost abundant amino acids in the proteins of all organisms are the
most easily formed. The indispensable compound adenosine
triphosphate (ATP), a molecule that stores energy inside all
cells, and other triphosphate precursors to the nucleotides
(the structural bases of genes) also can be formed in these
sorts of experiments. In some of the most recent studies, all
five of the nucleotide parts that compose DNA and its partner

50

MICROCOSMOS

molecule RNA-adenine, cytosine, guanine, thymine, and
uracil--<ould be found in mixtures after methane, nitrogen,
hydrogen, and water gases had been bombarded with electric
sparks. RNA (ribonucleic acid), like DNA, is a long molecule
needed for the functioning and reproducing of every single
cell of every liri.g being. RNA too carries information and
is made of nucleotide bases, sugars, phosphoric acid-all molecules that could have formed by solar radiation on the Hadean earth.
Like the early Earth's environment, these experimental concoctions yield all sorts of other suggestive organiccompounds.
Their identity and possible function are often a mystery to
the human investigators-but not at all to passing microbes.
If not protected under sterile conditions, and as long as they
are in water solution, the most complex lab-synthesized chemical compounds are quickly gobbled up by modern airborne
bacteria and fungi. The microbes, which are nearly everywhere, simply land in the water for a quick meal.
Although no cells have yet crawled out of a test tube, chemist Leslie Orgel of the Salk hrstitute discovered in the 1980s
a 50-nucleotide-long, DNA-like molecule that formed spontaneously from simple carbon compounds and lead salts in
the total absence of living cells or complex compounds.
Professor Manfred Eigen and his coworkers at the Gottingen
Institute in Germany have made short RNA molecules that
have replicated by themselves in the total absence of living
cells. The late Sol Spiegelman and his colleague Donald Mills
of Columbia University synthesized in the test tube infective
viruses of the RNA variety that are fully capable of continued
replication inside their bacterial hosts. (Unable to create all
the components needed to be a true living system, viruses
are little more than a stretch of DNA or RNA coated with
protein.) Although Spiegelman used only an enzyme (a reusable biochemical that accelerates chemical reactions), a nu-

The Animation of

Matt*

51

cleic acid (RNA in this case), and the small molecular precursors of nucleic acids called nudeotides, he employed a form

of energy that did not exist on the early Earth: human effort
and dollars.
Such experiments have popularized thebelief among scientists and lay persons alike that one or a few lightning bolts
striking the rich, chemical "soup" of the Archean oceans could
have just happened to fuse carbon and hydrogen atoms together with other elements in the right combinations to produce life. One common concept is that life appeared suddenly
and almost instantaneously from the prebiotic soup. Other
scientists argue that the odds against such instant life are
beyond the astronomical-more unlikely than the assembly
of a Boeing 707 by a hurricane in a junkyard. But there is
no credible way to assess the probability of life's spontaneous
generation from nonlife. As origins-of-life expert Leslie Orgel
quipped, "We don't even know within a factor of LGoif other
soups are viable." All we know is that life did arise. Some
theorists feel forced to postulate that the Earth must have
been beeded by meteorites carrying the finished molecules
of life. They point to the fact that compounds related to the
five different kinds of nucleotides as well as amino acids
have been found in meteorites.
Yet the conclusions of both "instant life" and "life'from
meteorites" veer away from the cmcial point: that the proper
milieu for the slow brewing of early life from nonlife was
the early Earth. There was sufficient time and energy available
for life's molecular combinations to arise from chemical alliances encouraged by the ryclically changing, energy-charged
environment. Besides, chemicals do not combine randomly,
but in ordered, pattemed ways. There is no need to postulate
the unlikely when evidence for the likely abounds. The presence of organic compounds in meteorites only seems to confirm that a hydrogen-rich environment exposed to energy

52

MICROCOSMOS

in the presence of carbon<onditions that certainly existed
throughout our solar system, if not the universe-will, by
the rules of chemistry, produce the building blocks of life.
It is the many other unique qualities of the Earth, including
its wetness, balmy temperatures, and gravitational properties,
that made it a better environment for these molecules than
the other planets. The Earth's conditions favored certain
chemical combinations more than others, and over time a
direction was set.
The ponds, lakes, and warm, shallow seas of the early Earth,

exposed as they were to cycles of heat and cold, ultraviolet

light and darkness, evaporation and rain, harbored their
chemical ingredients through the gamut of energy states.
Combinations of .molecules formed, broke up, and reformed,
their molecular links forged by the constant energy input of
sunlight. As the Earth's various microenvironments settled
into more stable states, more complex molecule chains formed,
and remained intact for longer periods. By connecting to itself
five times, for example, hydrogen cyanide (HCN), a molecule
created in interstellar space and a deadly poison to modern
oxygen-breathing life, becomes adenine (HsCsNs), the main
part of one of the universal nucleotides which make up DNA,
RNA, and ATP.
With no oxygen in the atmosphere to react with and destroy
them, amino acids, nucleotides, and simple sugars could form
and remain in solution together. Even ATP, a molecule used
by all living cells without exception as a carrier for energy,
could form from the union of adenine with ribose (a sugar
with five carbon atoms) and three phosphate groups.
Some molecules turned out to be catalysts: they made it
easier and faster for other molecules to join or split without
themselves being destroyed. Catalysts were important before

Tlu Animation of

Matter

53

life because they worked against randomness to produce order
and pattern in chemical processes. Gradually, they and the
reactions they facilitated proliferated rnore than other combinations. Although increasingly complex, these processes had
lasting power. They endured in the waters of the early Earth.
Today, certain groups of molecules can self-catalyze a series
of surprisingly intricate and orderly or cyclical reactions, each
change bringing about another in the molecular chain. Some
of these "dead" autocatalytic reactions form patterns whose

increasing complexity over time is reminiscent of life.
From both theoretical calculations and laboratory evidence,
it has been sqggested that an interaction of two or more
autocatalytic cycles could have produced a "hypercycle."
Some scientists theorize that such catalyzing compounds
"competed" for elements in the environments, thus automatically limiting their existence. But the basic idea of the hyperrycle is quite the opposite. Far from destroylng each other in
a fight for chemical survival, self-organizing compounds complemented each other to produce lifelike, ultimately replicating, structures. These cyclical processes formed the basis not
only of the first cells but of all the myriad structures based
on cells and their products that followed. Cyclical processes
are very important to life. They allow life to preserve key
elements of its past despite the fluctuations and tendenry
toward disorder of the larger environment.
The more protected and concentrated the chemicals were,
the longer and more complex and self-reinforcing their activities could become. Some may have been shielded inside bubbles or held on the regular surfaces of clays and crystals.
Nature's fuchean experiments with long hydrocarbon chains
were yielding compounds that could encapsulate a droplet
of the surrounding water and its contents yet allow movement
of other chemicals in and out of the enclosure. This was the

54

MIC ROCOS MOS

semipenneable membrane, a sort of soft door that permitted
the entry of some chemicals while prohibiting that of others.
The chemical components came together to form membranes

and, in the business of making life anyway, membranes are
marvels of simplicity. Indeed, the events that led up to their
formation have been duplicated in the laboratory under conditions of temperature, acidity, and rycles of wetness and
evaporation that are common on the Earth.
A hydrocarton chain linked to a group of phosphorus and
oxygen atoms manifestsan electrical charge on the endbearing
the phosphate group and no charge on the other end. The
chemical as a whole attracts water on its charged end and
repels it on the noncharged end. Such chemicals, called phospholipids, tend to line up side by side with each other, the
noncharged ends pointing away from the water while the
charged ends point down into it. (This is essentially what
happens when a drop of oil enters water, instantly forming
a film.) These and other types of lipids tend spontaneously
to fold into drops, secluding materials on the inside from
those on the outside. They have also been shown to form
double layers when waves bring two water surfaces, filmed
with lipids, together. When this happens, the charged ends
of the sheet of lipid molecules point toward each other, sandwiched between the noncharged ends. In this way, the first
membranes were formed-the first semipermeable boundaries between "inside" and "outside"; the first distinction
between self and nonself.
The membranes of today's organisms are composed of several different kinds of lipids, proteins, and carbohydrates,
their functions so complex and precisely calibrated that we
are far from fully understanding them all. But the first phospholipid membrane, unlike various other encapsulating structures that can also form in nafure's crucible, could, by virtue

The Animation of

Matter

55

of its chemical properties alone, concentrate a solution of
other carbon chemicals. It could keep potentially interacting
components in close proximity; permitting "nutrients" to enter while preventing water from escaping. The membrane
makes possible that discrete unit of the microcosm, the bacterial cell. Most scientists feel that lipids combined with proteins
to make translucent packages of lifelike matter before the
beginning of life itself. No life without a membrane of some
kind is known.
There is still a missing link between the most complex
concoctions of the working scientist and the simplest viable
cell, both in theory and in the laboratory. The gap between
small organic chemicals, such as amino acids and nucleotides,
and larger biochemicals, such as RNA and protein, is enormous. But a few hundred million years of molecular activity
is a long, long time. Scientists have been working only a
few decades to provide conditions conducive to the origrn
of laboratory life, and have come very far. It is not inconceivable that before the turn of the twentieth century a live cell
will be spontaneously generated in the laboratory. Given millions of years, the chances of spontaneously forming hypercycles were immensely gpeater than those available to research
workers, who must substitute planning for the blind perseverance of time if they are ever to recreate life.
Probably not once, but several times, amino acids, nucleotides, simple sugars, phosphates, and their derivatives formed
and complexified with energy from the sun within the protection of a lipid bubble, absorbing ATP and other carbonnitrogen compounds from the outside as "food." Fairly
complex structures have formed spontaneously from lipid
mixfures in the laboratory. For example, David Deamer at
the University of California at Davis has observed that some
nucleotides are taken up and surrounded by spheres of lipid

56

MICROCOSMOS

if the proper ingredients are mixed under appropriate conditions. Bubbles of lipids split in two at first simply from the
strain of surface tension, each half carrying on its internal
activity. Later, the catalyzing molecules within may have begun to actively maintain the lipid membranes. Perhaps when
the supply of available component elements in their tiny local
niche was exhausted, the protocells simply broke down and
disappeared, while others formed in some other tidal pool,
each with a slightly different modus operandi.
To be alive, an entity must first be autopoiefic-that is, it
must actively maintain itself against the mischief of the
world.16 Life responds to disturbance, using matter and energy to stay intact. An organism constantly exchanges its
parts, replacing its component chemicals without ever losing
its identity. This modulating, "holistic" phenomenon of autopoiesis, of active self-maintenance, is at the basis of all known
life; all cells react to external perturbations in order to preserve
key aspects of their identity within their boundaries. tf the
external threats are major, normal cyclical processes may be
disrupted and schismogenesis may result. Schismogenesis, a
word coined by the biologist and philosopher Gregory Bateson, refers to rycles in living systems that oscillate unconkollably. Bateson believed that schizophrenia could be traced to
a special kind of schismogenesis, in this case an overabundance of feedback in the brain leading to mental disintegration. But this is only one highly specific example of the failure
of normal ryclical processes. In organisms such as plants and
animals, we recognize autopoiesis generally as "health."
Schismogenesis is its opposite. But even the predecessors
to cells must have had some sort of autopoiesis, the ability
to maintain their structural and biochemical integrity in the
face of environmental threats.
Once able to stay itself, a structure on its way to becoming
liri.g must reproduce itself. Before cells,life and nonlife may

The Animation of

Matter

57

have been indistinguishable. The first cell-like systems were
what the Belgian Nobel Prizewinning physicist Ilya Prigogine
has termed "dissipative structures"<bjects or Processes that
organize themselves and spontaneously change their form.
With an influx of energy, dissipative structures may become
more instead of less ordered. The sort of information theory
that has been so useful in communication technology applies
solely to information which consists almost entirely of confirmation. In dissipative structures, information begins to organize itself; pockets of elaboration arise.
From dissipative structures and hyperrycles emerged the
chain of nucleotides, ribose, and phosphate that can both
replicate itseU and catalyze chemical reactions. This chain is
ribonucleic acid, or RNA, the first sentence in the language
of nature. Not yet autopoietic, but highly structured, early
RNA in spheres surrounded by strings of lipids accumulated
in warm, organically rich waters on a benign Earth. With
no predators and plenty of energy, complexification followed.
On the Hadean Earth before the dawn of life two chemical
trends took hold: self-reference and autocatalysis. Chemicals
reacted ryclically, producing versions and variations of themselves that tended to.create an environment favorable to the
repetition of the original reactions. Autopoietic structures took
organization a step further: they used energy to actively and
successfully maintain themselves in the face of serious external
perturbations. Their boundaries became distinct. This gave
them both identity and memory. Today; although all of the
chemicals in our bodies are continually replaced, we do not
change our names or think of ourselves as different because
of it. Our organization is preserved, or rather it preserves
itself. From dissipative skuctures to RNA hypercycles to autopoietic systems to the first cnrdely replicating beings, we
begin to see the winding road that self-organizing structures
traveled on their iourney toward the living cell.

ago

2billionyeare
Early Protemzoic Eo'n
Hazanlous oxygm accwnulates ifl atuosphere as ruult of bacterial plutosyntlusis.

Chapter

ICCOnDING

I \

s

The Language of Nature

to the B ook of Genesis, God halted construction

of a majestically high tower in Shinar by introducing
many languages. The Tower of Babel never reached heaven
because its builders, stripped of their common tongue, became
confused. This parable shows the importance of a universal
language. While people still speak in many languages (though
fewer as time goes by), the genetic cod+the translation of
genes into proteins-is everywhere the same.
Learning the now universal RNA/DNA-based genetic language that emerged from the babel of Archean chemicals
made the new science of molecular biology thrilling indeed
in the past two decades. The genetic code is a unique phenomenon. The DNA or RNA molecule can replicate itself exactly;
but it can also cause the uniform assembly of those other
long biochemicals, proteins. This was the central insight of
the molecular biological revolution that began when James
Watson and Francis Crick discovered the structure of DNA

in

1953.

59

60

MI CROC OSM OS

As miraculous as it seems, replication is, on a moleculeto-molecule basis, a shockingly shaightforward chemical process. A complementary chemical strucfure prescribes the
shape and properties of replicating molecules: DNA and RNA
are one lengthwise half of a single long molecule. Like the
matching teeth of a zipper, in the presence of the right ingredients, the components of the missing half simply line up and
fit.
RNA is a particularly versatile sort of half-molecule. It can
match up another long RNA like itself, or it can match up
short bits of nucleotides with amino acids attached-producing all the proteins that give organisms their varied shape
and forms. RNA's components are the four different nucleotides, the bases adenine, guanine, cytosine, and uracil, each
of which holds onto a phosphate group (composed of phosphorus and oxygen) and ribose, a kind of sugar. Taken in
groups of three, the sequence of nucleotides in one type of
RNA can be a signal for a second type of matching RNA to
attach to amino acids in its environment. As the amino acids
link up, one after another, a protein is formed, and this protein
can, in fum, accelerate the further matching of the RNA molecule, thereby producing more RNA.
The first membrane-enclosed autopoietic bodies were probably governed only by RNA. They could replicate themselves
by making proteins that made more RNA. The development of the double-stranded, far longer and less accidentprone DNA molecule probably came later, gradually taking
on the function of a mold or template for the copying of
RNA.

DNA, too, is made of only four nucleotides, each with a
sugar, and a phosphate gIoup. DNA has thymine instead
of RNA's uracil and its sugar is deoxyribose instead of ribose.
The two intertwined DNA and RNA strands fit together with

The lnnguage of

Nature

67

adenine always linking with thymine and guanine always
with cytosine, again because of their chemical structure. The
smallest bacterium has hundreds of thousands of these paired
parts, the so-called base pairs; animal and plant cells many
millions. All cells today have both DNA and RNA. The lineup of nucleotides leads to the line-up of proteins, which makes
more nucleotides and makes them line up. This arrangement
of chemicals is not only dissipative and autopoietit, it is the
reproducing ancestor of every life form on Earth.
Proteins make an organism what it is. The line-up of nucleotides specifies the composition and quantity of proteins. Organisms differ largely because the sequence of spiraling
nucleotides in DNA molecules differs. Variations in the order
and number of nucleotide pairs lead to the fabrication of
different proteins. At least several thousand different proteins
in each cell determine how the organism looks, how it moves,
how its metabolism runs. Every cell needs proteins to speed
up chemical reactions. Without certain proteins, many essential biological reactions would take place very slowly or grind
to a halt. Chaos and ordinary chemistry would reign.
The common denominator of life extends further. Only
about twenty different amino acids, linked in chains of a
few dozen to several hundred, make up the proteins in all
known organisms on Earth. The amino acid sequence, primarily, determines the protein's shape, and the shape determines
its function. The code for translating the sequence of nucleotides in DNA to a sequence of amino acids in a protein is
nearly universal. In almost all cases, a given nucleotide sequence will translate into the same amino acid sequence.
In all organisms, each triplet of nucleotides on the coding
nucleic acid<alled a codon-specifies one amino acid. But
there are signs that two-nucleotide codons may have constituted an early version of this system. For example, the third

62

MIC ROC OSMOS

nucleotide in a codon is often redundant: uracil, adenine,
cytosine, or guanine could each be the third after a cytosineguanine doublet to form a triplet on messenger RNA. In any
of the four cases the amino acid arginine would be coded
for. Additionally, the middle nucleotide often determines the
simplest and most common amino acids. The early genetic
code was no doubt simpler and less faithful than it is today.
A living language, it still carries evidence of its etymological
roots.

Like words, too, the elements of the code can be tampered

with, rearranged, changed, and passed down in an altered
form. Mutations are heritable changes in the quantity or sequence of DNA bases. A mutation occurs when something
in the environment-radiation, say---€ither breaks a chemical
bond or forges an uncalled-for one, and the resulting change
in the DNA sequence, which confers new abilities or disabilities, is copied and passed down through the cell's descendants
or causes the cell's demise. Like the difference of an "s"
between the words laughter and slnughter, small changes or
additions can have synergetic effects.
In the excitement following the discovery of DNA's and
RNA's vital role, the lion's share of responsibility for life's
diversity was attributed to minute, base-pair mutations in
these molecules. But at an estimated rate of one base-pair
mutation per group of a million to a billion cells in each
generation, even base-pair mutations seem inadequate to explain life's grand variety of organisms.
In language, the swiftest and most telling changes come
about through usage. Sheet argot and slang, produced by
usage at its most basic, everyday level, constantly filter into
the mainstream of language and eventually find their way
into official dictionaries. As we shall discover in the next
chapter, the "street" where the genetic message undergoes
continual and rapid changes is the microcosm.

The Ianguage of

Nature

63

The reading and copying of the genetic message can happen

in an incredibly short time. In seconds to minutes, proteins
Although isolated DNA cannot replicate, if placed in a test tube with proteins (catalysts),
nucleotides (food), and an energy supply fiust the chemical
energy in the nudeotides), DNA can make a copy of itself
within seconds. To the great possible benefit of future medicine, it can even do so after having been frozen in solutions
in glass vials for several years. Although not capable, as are
whole organisms, of self-maintenance, DNA in the proper
chemical milieu can replicate.
ln 1977, Sir Frederick Sanger and his fellow researchers
at a medical research laboratory in Cambridge, England, decoded the first complete genetic message and uncovered a
new twist in the language. The DNA of a virus called ixl74
is only 5,375 nucleotides long, which would account for approximately 1,792 arrlrino acids-good for about five proteinsyet it codes for nine different kinds of protein, which require
about 3,200 amino acids. Sanger's group discovered that using
the same DNA one stretch of nucleic acid determines more
than a single protein, depending on where the messagereading begins. This seems a startling molecular "irlvention."
Yet, once again considering that life keeps itself together at
all costs, using nudeotide messages to specify proteins, it
doesn't seem so unlikely that the genetic code should have
developed double entendres. Indeed, a single length of nucleotide is read for different meanings in several kinds of
cells and in some mitochondria as well. There is ambiguity
in the universal language of life.
are assembled from amino acids.

In the study of complex animals and plants, traits such
as lungs or eyes or flowers that require the interaction of
many genetic factors are called semes. First life, too, evolved
because of conditions favoring not individual traits-this en-

a

M

ICROC OSMOS

zyme or that nucleotide base

pair-but

semes, chains of chemical reactions that yielded food or movement or some other
critical aptitude. In microbes semes tended to be metabolic.
Forinstance, microbes that made the metabolites they needed
by using carbon dioxide from the air starved far less often
than those unable to feed from carbon in the air. The biochemical steps allowing the use of atmospheric carbon dioxide is
an example of a microbial seme.
It seems silly to postulate a single dramatic moment of
magical lightning when DNA and RNA spontaneously formed
a cell and life began. Many dissipative structures, long chains
of different chemical reactions, must have evolved, reacted,
and broken down before the elegant double helix of our ultimate ancestor formed and replicated with high fidelity. In-

on totally different types of
replicating molecules may have arisen and developed for a
while before disappearing altogether. But because they are
the common denominator of all life todap it is clear that at
some point lipid membranes containingRNAand DNAbegan
to flourish. The numbers of these tiny bacterial spheres increased and diminished in a process of ebb and flow. To
borrow |ulian Huxley's simile, the waves break and go back
on themselves, yet the tide rises iust the same. At some point
some time before 3,500 million years ago, the evolutionary
tide reached the level of life as we know iil that of the membrane-bounded, 5,000-protein, RNA-messaged, DNA-governed cell. Once autopoiesis ensured its existence and
reproduction guaranteed its expansion, evolution was under
way. The Earth's microcosm, the Age of Bacteria, had begun.
deed, living forms based

The tiny Archean sacs of DNA and RNA carried out their
activities prodigiously. With sleep unknown to them they
gr€w, consumed energy and organic chemicals, and divided

The

langwge of

Nature

65

incessantly. Their colonies and fibers interconnected and covered the sterile globe in a spotty film. The dimensions of
this film have expanded into a patina of life, or biosphere,
the place where life exists. Today the biosphere surrounds
the Earth from a little deeper than six miles into the ocean to
over seven miles up, above the mountain tops at the top of
the lower atmosphere, called the troposphere. Bacteria first expanded in the waters, where they modified the liquid and
produced gases. They then expanded to the surfaces of the
sediments, where they still survive. None lived its complete
life in the atmosphere, nor can any being do so today. Nonetheless, mostly in the form of dormant particles (such as seeds,
spores, and eggs), some organisms can be found spending
some time in the atmosphere. The biota-all life on Earthbecomes tenuous at its exhemes several miles up and down.
The core of life on earth, the dense, thti',ri.g center of the
biota has been and still is within a few meters of the Earth's
surface. Dr. Sherwood Chang of NASA Ames Research Center
has suggested that life probably began at the interface of
liquid, solid, and gaseous surfaces where there is an energy
flux and dissipative structures can easily form. Today life
still thrives where water meets the land and air. The biota,
the sum of all life, primarily as the microbiota, the sum of
all microbial life, is ancient, extending through the vast biosphere. Over time it has spread out. Yet from the point of
view of chemical and metabolic innovation, the biota at its
core has not significantly changed. Composed of all reproducing beings, continuous through time, the planetary patina
has a life. of its own. The biota cycles inorganic substances,
such as roc.ks, muds, and gases, modulating and controlling
itself. Cells collectively preserve the water-, carbon-, and hydrogen-rich conditions of their origrn. The biosphere retains
in its midst gases such as hydrogen and methane that other-

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MIC ROC OSMOS

wise would long ago have been lost from the Earth by cosmic
processes. It is a souvenir of itself.
In a sense, the essence of living is a sort of memory, the
physical preservation of the past in the present. By reproducing, life forms bind the past and record messages for the

future. The oxygen-shunning bacteria of today tell us about
the oxygenless world in which they arose. Fossil fish tell us
of open bodies of water in continuous existence for a hundred
million years. Seeds that require freezing temperatures to
germinate tell us of frozen winters. Our own human embryos
represent phases of animal history in their stages of development.
Put another way, life is extremely conservative. On whatever level-the individual organism, the species, the biota as
a whol+life expends energy such that it preserves its past,
even if, paradoxically, various threats force it to innovate.
Since autopoiesis is an imperative of the biota as a whole,
life will expend huge quantities of energy to preserve itself.
It will change in order to stay the same.
There is Iittle doubt that the planetary patina-including
ourselver-is autopoietic. Life at the surface of the Earth seems
to regulate itself in the face of external perturbation, and
does so without regard for the individuals and species that
compose it. More than 99.99 percent of the species that have
ever efsted have become extintt, but the planetary patina,
with its army of cells, has continued for more than three
billion years. And the basis of the patina, past, present, and
future, is the microcosm-trillions of communicating, evolving microbes. The visible world is a late-arriving, overgrown
portion of the microcosm, and it functions only because of
its well-developed connection with the microcosm's activities.
Microbes by themselves are thought to have maintained the
mean temperature of the early Earth so that it was hospitable

The l-anguage of

Nature

6?

for life, despite the much cooler "start-up" sun that astronomers believe existed then. During Archean times "stupid"
microbes also continually modified the chemical comPosition
of the atmosphere so that it did not become prohibitive to
life as a whole. We know from the continuous fossil record
of life that the temperature and afinosphere of the planet
never destroyed all life. Barring divine intervention and luck,
only life itself seems powerful enough to have promoted the
conditions favoring its own prolonged survival in the face
of environmental adversity.
Grasping as best we can the formidable powers of the biosphere in which we live out our lives, it is difficult to retain
the delusion that without our help nature is helpless. As
important as all our activities seem to us, our own role in
evolution is transient and expendable in the context of the
rich layer of interliving beings forming the planet's surface.
We may pollute the air and waters for our grandchildren
and hasten our own demise, but this will exert no effect on
the continuation of the microcosm. Our own bodies are composed of one thousand billion (1012) animal cells and another
fen thousand billion (1013) bacterial cells. We have no natural
"enemies" that eat us. But after we die we return to our
forgotten stomping ground. The life forms that recycle the
substances of our bodies are primarily bacteria. The microcosm
is still evolving around us and within us. You could even
say, as we shall see, that the microcosm is evolving 4s us.

ago

Prctemmic Eon
1.3 btlllon yearr
Bacteria mctge, sptztrl to lit ul as @rtryite orgaainns

Chapter

4 Entering the Microcosm

I N tfZZ on the periphery of a tiny South African mountain

I

town called Fig Tree, Elso S. Barghoorn, a paleontologist
at Harvard University, hacked out pieces of flintlike rock from
the side of a worn mountain in the Barberton Mountain Land
and collected samples. Back in Cambridge, Massachusetts,
he cut the rock into slices so thin that light could be seen
through them. He placed the thin rock samples under a microscope.

Water loaded with minerals from nearby volcanoes had
formed the black chert, which Barghoorn knew from experience is the kind of rock most likely to contain fossils. More
than three billion years ago at this place, silica-rich lava repeatedly poured into thick black mud, hardening it into chert.
The restless volcanoes sPewed ash into the air, which fell
in immense piles on the mud and into the water of a nowvanished Swaziland sea that for millions of years covered
most of what is now southern Africa. The years of volcanism
and erosion, of transPort of rubble and stones, piled uP many
69

70

MI CROCOSMOS

complex layers of rocks. Over vast periods of time these layers

covered the shores and lined the floor of the ancient sea.
Today records of the bygone scene extend as hills and rock
ledges for hundreds of miles in South Africa and the country
of Swaziland. In some places the complex layers of Swaziland
rock are more than ten miles thick.
The Swartkoppie zone of this fossil ocean is laced by seams
of coal-like carbon deposits several hundred meters thick that
might be mistaken for the remains of a tropical swamp of
trees, seed ferns, and club mosses, like the ones that produced
coal in Pennsylvania 300 million years ago. Such carbon-rich
deposits in the earth have always meant photosynthetic life.
But these Swaziland rocks were laid down 3,400 million years
agetheyare more than ten times as old as the swamp forests.
(The very first fbssil land plants are about 450 million years
old.)
P:ofessor Barghoorn had been seeking the antiquity of life.
After much study of the thin sections of African cherts in
collaboration with his students, Barghoorn discovered hundreds of round objects, most of them simple spheres. But
one or two dumbbell shapes caught Barghoorn,s attention.
Were these life itself-<aught in the act of dividing? In other
samples from the nearby Kromberg Formation of rocks, thin
microscopic filaments were found similar to today's cyanobacteria (blue-green algae). Here were the oldest fossils on
the planet-hard evidence that bacteria, already accomplished
in photosynthesis, thrived on the Earth only 500 million years
after the earth's first rocks had formed.l7
Barghoorn's South African find was the fruit of a conscious
search. More than twenty years earlier, at the University of
Wisconsin, the geologist Stanley Tyler had showed him rocks
from the northem shores of Lake Superior. The 2,000 millionyear-old rocks were full of strange objects that had looked
like fossils of microscopic life to Barghoorn. Since 1954 then,

Entering the Microcosm

7l

Barghoorn had been on the lookout for early life. Barghoorn's

dogged persistence to find the oldest fossils in ordinarylooking rocks led to a thirty-year burst of microfossil research
that is still under way.
Until the 1950s it was thought that life began shortly before
570 million years ago, since an explosion of hard-shelled animal fossils, often called the Cambrian explosion, appears in
rocks of that age all over the Earth. No clear-cut examples
of skeletalized animal fossils in older rocks had ever been
found. Forgetting that simpler, softer-bodied animals might
not have been preserved, some scientists had assumed a rather
sudden appearance not only of all animals but even of life
itself.
lt turned out that the rocks of England and Wales which
held some of the best-studied early animal fossil deposits
were missing their late pre-Cambrian layers. When more continuous rock formations were found in China, South Australia,
Siberia, and elsewhere, they revealed many excellent sandstone impressions of recognizable, soft-bodied marine animals. More recently the pre-Cambrian has been carefully
combed by Barghoorn and others to reveal its nonobvious
fossils, and new evidence has pushed backward the probable
origln of life on the earth.
All the good evidence for early life is not in fossils of the
bodies of the organisms themselves