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The Evolution of Biological Information
The Evolution of
Biological Information
HOW EVOLUTION CREATES COMPLEXITY,
FROM VIRUSES TO BRAINS
CHRISTOPH ADAMI
Preface ix
Acknowledgements xv
References 521
Index 551
P R E FA C E
While the theory of evolution by no means materialized out of the blue (as
I shall discuss) and while an assortment of naturalists and scientists formu-
lated ideas similar to the central tenets of Darwinism, only Darwin himself
wrote about them fully conscious of their world-shaking implications.1
1. In a January 11, 1844, letter to England’s most eminent botanist, J. D. Hooker, Darwin
reveals his apprehensions: “At last gleams of light have come, and I am almost convinced (quite
contrary to the opinion I started with) that species are not (it is like confessing a murder)
immutable.” (F. Darwin, 1887, p. 384)
ix
x preface
Among the celebrated theories that constitute the framework of our knowl-
edge about the world, Darwinism is unique in another way. At the time of its
inception, the theory of evolution was based solely on observation and logical
deduction, not on empirical facts obtained by experimentation. It is perhaps
not unreasonable to see Darwin as akin to a sleuthing detective, weighing the
evidence available to him while formulating and rejecting hypothesis after
hypothesis until hitting on the one explanation that is consistent with all
available facts. While evolutionary theory can be couched in abstract terms
just as any theory in the physical sciences, its predictions could (at the time)
not be submitted to experimental tests, not even after the molecular revolu-
tion that brought with it the discovery of the genetic code and the molecular
mechanisms giving rise to variation. This is because macroevolution (that is,
speciation, adaptation, and innovation) would have taken too long for the
meticulous experimental approach that characterizes progress in the physical
sciences. Macroevolutionary timescales are usually measured in the millions
of years, or in the hundreds at the very best.2
This weakness of evolution as a scientific theory must be recognized as one
of the two major elements that have prevented Darwinism from being fully
accepted by both scientists (most of whom accepted it almost instantly) and
the public alike. The other element that constantly gnaws at the foundations of
evolutionary theory is the controversy about the explanation (or nonexplana-
tion) of life’s complexity. The controversies are varied, battles are fought both
within the ranks of scientists that would not doubt for a second the validity of
the central tenets of Darwinism, and without, by an incredulous public and by
entrenched creationists.
Explaining how Darwinian evolution can account for the complexity of life
(biocomplexity) thus emerges as one of the last remaining major problems in
evolutionary biology.3 Whether or not complexity increases in evolution, and
if it did, what the mechanisms are that fuel this growth, is a thorny question
because complexity itself is historically a vague concept. If different scientists
understand complexity in different ways, it is no wonder that an agreement
over this issue has not been reached.
These two factors, which impede a full acceptance of evolutionary theory
as sufficient to explain all forms of life on Earth, are moreover related: If
experiments could be conducted in which complexity visibly evolves from
simplicity, the controversy would surely shift from “Does It?” to “How Does
It?” In this book I shall pull together two strands of research that meet head-on
the perceived vulnerabilities of evolution as a complete and satisfying theory
of organic origin, diversity, and complexity. The first strand is the field of
experimental evolution, a discipline that few could have imagined in Darwin’s
days, but that today has matured into a quantitative science with the power
of falsification (the hallmark of scientific theories) in the last twenty years.
The other is the theoretical development of a concept of complexity, rooted
in mathematics and the theory of information, but germane to biology. No
mathematical concept of complexity has hitherto satisfied both mathemati-
cians and biologists alike. Both scientists and nonscientists have an intuitive
notion of what constitutes complexity; we “know it when we see it.” The theo-
retical concept that I introduce in this book seems to satisfy our intuition every
time it is subjected to the test, which bodes well for its acceptance as a mea-
sure for biocomplexity. Moreover, it proves to be both practical and universal.
Practical, because it implies a recipe to attach a number to the complexity of
any class of organisms (allowing in principle a comparison between species),
and universal because it does not refer at all to nucleic acids or proteins, or
any other particular feature of this world and the forms of life that populate
it. Rather, it is based on the universal concepts of automata and information
theory, which are abstract.
A mathematical description of the mechanisms that are responsible for the
evolution and growth of complexity, and experimental evidence buttressing
such a description, should go a long way to eliminate those doubts that are
anchored around the startling complexity of life and the seeming inability of
scientific theory to account for it. I will try in this book to convince the reader
that it can be accounted for, both in abstract terms and mathematical formu-
lae, and that the mechanisms responsible for the growth of complexity can be
investigated experimentally and be tested and retested.
But information theory can do more for biology than just provide for a
measure of complexity. In hindsight, everything in biology uses information in
one form or another, be it for communication (between cells, or organisms)
or for prediction (via molecular as well as neural circuits). As a consequence,
we must think of information theory as the unifying framework that allows us
to understand complex adaptive systems far from equilibrium, with biological
life being the prime example.
From the preceding comments, it should be clear that this is not a conven-
tional book about evolution. It is not a “whodunnit” in which the complicated
relationship between adapted forms is revealed through elaborate genetic or
behavioral experiments and observation. Rather, it treats evolutionary theory
as an empirical science, in which abstract concepts, mathematical models, and
xii preface
dedicated experiments play the role they have been playing in the physical
sciences in the last few hundred years. While I try to keep the mathemati-
cal sophistication to a minimum, a reader who wants to make the most of
this book should be prepared to follow basic algebra. Indeed, the concept of
genomic complexity—its acquisition and evolution—is so firmly rooted in
the theory of information that it would be impossible to bypass an exposition
of the framework due to Shannon (1948). Furthermore, molecular evolution
theory (due to Eigen 1971, Eigen and Schuster 1979), the theory of self-
replicating macromolecules under mutation and selection, is a kinetic theory
in which the time-dependence of concentrations of molecules are key. Thus,
basic notions from calculus will be required to follow those sections. Yet, I have
strived to explain the concepts that are introduced mathematically also in
intuitive language, so that the dynamics of evolution, and the circumstances
surrounding the evolution of complexity, should appear more clearly to every
serious reader interested in biocomplexity.
Another somewhat less conventional feature of this book is its exten-
sive use of the methods of computation. Virtually all the physical sciences
have branches nowadays that are almost entirely computational in nature:
the power of modern computers to take initial data and, armed with a set
of equations that model the system under investigation, grind through to
the consequences has revolutionized every facet of modern science. Even
within biology, the computer has taken major inroads, in particular in the
analysis of bioinformatics data, and the modeling of cellular processes and
development. Genetic algorithms, a method to search for rare bit patterns that
encode solutions to complex problems (usually in engineering) are inspired
by the Darwinian idea of inheritance with variation coupled with selection of
the fittest. But this is not, by far, the limit of how computers can aid in the study
of the evolutionary process. Computational evolutionary biology involves
building models of worlds in which the Darwinian principles are explored.
A particular branch of computational evolutionary biology involves not only
creating such an artificial world, but implanting in it not a simulation of evo-
lution, but the actual process itself. Because it is possible to create a form of life
that can inhabit and thrive in an artificial world (Ray 1992; Adami 1998), it
has become possible to conduct dedicated experiments that can explore fun-
damental aspects of evolution as they affect an alien form of life (sometimes
called “digital life”) (Harvey 1999; Zimmer 2001; Lenski 2001). Because such
experiments can only study those aspects of the evolutionary process that are
independent of the form of life it affects, we cannot, of course, hope to gain
insight from these experiments about phenomena that are intimately tied to
the type of chemistry used by the organism. But the beauty of digital life exper-
iments lies in their ability to make predictions about evolutionary mechanisms
preface xiii
and phenomena affecting all forms of life anywhere in the universe. When design-
ing experiments to test evolutionary theory, then, we must judiciously choose
the experimental organism to use, weighing its advantages and idiosyncrasies
(there is, after all, no “universal” organism anywhere on this world and likely
others), from the gallery available to us: viruses, bacteria, yeast, or fruit flies
(to name but a few), or indeed digital ones.
The foundation laid by Darwin, and the edifice of modern evolutionary
theory constructed in the twentieth century, is not shaken by the experi-
mental, computational, and information-theoretic approach outlined here.
I imagine it strengthened in those quarters where the structure was perceived
to be weak or vulnerable, and its expanse increased, to an ever more dazzling,
towering achievement within humanity’s endeavor to understand the world
around us, and ourselves.
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accordingly went, was introduced into the minister’s study, and
commenced the conversation by saying, “I believe there is a small
dispute between you and me, sir, and I thought I would call this
morning and try to settle it.” “Ha!” said the clergyman, “what is it?”
“Why,” replied the wag, “you say that the wicked will go into
punishment, and I do not think that they will.” “Oh, if that is all,”
said the minister, “there is no dispute between you and me. If you
turn to Matt. xxv. 46, you will find that the dispute is between you
and the Lord Jesus Christ, and I advise you to go immediately and
settle it with him.”
Geography.
Geography is that science which describes the earth on which we
live; its lands and waters; its mountains and valleys; its hills and
plains; its towns, cities, countries, nations, and inhabitants.
The above picture is a representation of one half of the earth, or
what is called the Western Hemisphere. On this you see the
continent of America, the Atlantic Ocean, the Pacific ocean, the
Northern ocean, and the Southern ocean. About three fourths of the
surface of the Western hemisphere is covered with water.
The continent of America consists of North America and South
America. These are united by a narrow strip of land, called the
isthmus of Darien. In the narrowest part, this isthmus is but about
thirty-seven miles wide.
North America is separated from Asia at the north-west, by
Behring’s Straits, which are about thirty-nine miles wide. North
America is separated from Greenland, which is a great island, almost
always covered with snow and ice, near the north pole.
The continent of North America is about 9000 miles long, from
Cape Horn, to the Northern ocean. It has a vast range of mountains,
extending, in a bending line, nearly the whole length of it. This
range is the longest in the world. In South America, some of the
mountains are about five miles high, and are the loftiest in the
world, except the peaks of the Himmaleh mountains, in Asia. It is
supposed that there are two hundred volcanoes in America.
The largest river in the world is the Mississippi, which, including
the Missouri, properly one of its branches, is about 4000 miles long.
The river Amazon, in South America, though not quite as long,
spreads its branches wider than any other river in the world, and
carries more water to the sea than any other river.
The largest fresh water lake in the world, is that of Lake Superior,
in North America.
The Eastern Hemisphere.
The above picture represents the Eastern Hemisphere. It includes
the Eastern Continent, which is divided into Europe, Asia, and Africa.
Africa is the south-western portion, Europe the north-western
portion, and Asia the north-eastern portion. The eastern continent
contains about twice as much land as the western continent.
Between Europe, Africa and Asia, is the Mediterranean sea, which
is about 2000 miles long, from east to west. The Atlantic ocean lies
west of Europe and Africa; the Indian ocean lies south of Asia, and
south-east of Africa; the Pacific ocean lies east of Asia.
Between the Indian ocean and Pacific ocean, are many large
islands. The largest is New Holland, which is about as extensive as
all Europe. This island belongs to the British nation, who have
settlements here, occupied by English, Scotch, and Irish people.
There are many curious things upon this island. The natives are a
kind of negro, who live in a manner almost as rude and savage as
wild bears. Among the animals, are the kangaroo, which goes forty
feet at a leap, and the platypus, with fur like a beaver and a bill like
a duck; swans which are black, and a kind of bird with a tail shaped
like a harp.
Asia is the most populous part of the globe, and has more
inhabitants than Europe, Africa, and America, all together. China
alone has about three hundred and sixty millions of people.
In America there are only a few great cities, such as New York,
Boston, Philadelphia, Baltimore, and New Orleans, in the United
States; Havana, in the West Indies; Mexico, in the United States of
Mexico; Lima, Buenos Ayres, Valparaiso, and Rio Janeiro, in South
America.
In Europe there are many great cities, among which London and
Paris are the largest; in Asia, Constantinople and Pekin are the
largest; in Africa, Grand Cairo and Alexandria are the largest.
Asia was the first part of the globe inhabited by human beings;
Africa was next inhabited, Europe next, and America last. America
was not discovered by the Europeans, till about three hundred and
fifty years ago.
The Bob-o-link.
This is the familiar name of the Rice Bunting. He is about seven
inches and a half long, of a deep black color, with the feathers edged
with white and yellow. In Massachusetts, it is first seen in May,
among the fields and meadows, which at that period begin to ring
with its cheerful song. This is familiar to every school-boy, and is
composed of sounds which resemble the words Bob-o-lee, Bob-o-
linke. Mr. Nuttall, who has written several books about birds, says
that as the Bob-o-link rises and hovers on the wing, near his mate,
he seems to say—“Bob-o-link, Bob-o-link, Tom Denny, Tom Denny,
come, pay me the two and sixpence you’ve owed me more than a
year and a half ago! tshe, tshe, tsh, tsh, tshe!” He then dives down
into the grass, as if to avoid a reply.
This bird builds its nest on the ground; it is formed of loose
withered grass, and can scarcely be distinguished from the earth
around it. The eggs are five or six, of a light olive color, spotted with
brown. The male keeps up a continued song while his partner is
sitting, as if to cheer her in her confinement; but when the young
brood appear, this song is less frequent, and he joins his mate in the
task of feeding and rearing them.
In August, the whole brood, old and young, set off for the south,
where they spend the winter, gathering the wild rice of Delaware as
they proceed, and offering great sport to the gunner. They swarm in
the rice fields of Carolina and Georgia, and are much disliked by the
planters for their voracity. They are excellent eating, being so fat
when they reach the West Indies, as to be called Butter birds. Here
they spend the winter, but never fail to return in the spring to their
native meadows, where they feed on insects, worms, crickets,
beetles, and also on grass seeds.
Boys are very fond of catching the Bob-o-link, which they sell for
cages; but, although he is tolerably lively in captivity, yet no one
who has seen and heard him at liberty, can take any pleasure in his
deadened music and dulled plumage. In a state of nature all birds
moult, that is, change their plumage, and after a time generally
reappear in their former gay attire; but we have been told that the
Bob-o-link, in captivity, after moulting once, never resumes the dress
he wore in freedom; as if, absent from his mate, for whom alone he
sung and plumed himself, it were of no consequence what his
appearance might be. Let those of my little readers who have an
opportunity of observing, see if this story be true.
The White or Polar Bear.
This formidable animal is generally found within the polar circle. It
is a land animal, yet it depends upon the sea for its subsistence. It
preys principally upon seals, young walruses and whales, and upon
those foxes and wolves which sometimes seek their food among the
ice. Its size varies, being from eight to twelve feet long, and
weighing from 900 to 1600 pounds. His fur is thick and very long,
and, like the feathers of water birds, cannot be wet by almost any
exposure to water. He swims at the rate of three miles an hour. He
cannot climb trees like other bears, nor does he need so to do, as
his habitation is among the icebergs. He is a very formidable and
powerful animal, and when attacked, makes desperate resistance.
From the nature of their food, the flesh of the polar bear is rank
and fishy, though not unwholesome. The fat resembles tallow, and
melts into a transparent oil, which has no offensive smell. The skin is
very serviceable, as well as handsome, for a variety of domestic
purposes, and it is an article of considerable value to the people of
the cold northern regions. The Greenlanders pull it off whole, and
make a sack of it, into which they creep, and find a warm and
comfortable bed. The natives of Hudson’s Bay make very handsome
and pliable garments of these skins.
The Polar Bear may be considered as the most interesting of all
bears. Much is said of its great strength, and power of enduring
hunger and cold; of the peculiarity of its form and appearance; of
the perils and privations to which it must often be exposed; of its
great ferocity and daring when attacked, and of its strong
attachment to its young. Nothing but death can stop the attentions
of the female to her cubs. When they are wounded, she will fondle
them, turn them over, lick them, offer them food, and pay them
even more tender attentions than some human beings bestow upon
their offspring; and when she finds all her efforts unavailing, she
makes most piteous moans.
The White Bear is found in the polar regions of both continents.
The Boy and his Mittens.—I was going around the corner of Park
street church, in February, 1835. It was the morning of one of those
days when the thermometer was hovering about the chill point of
zero. I chanced to notice a small boy, standing with his back to the
basement wall of the church; his cheeks glistening in the keen wind,
the tears flowing down his face, and a kind of blubbering sound
issuing from his mouth. His little red hands were bare, but in one of
them he held a pair of mittens. He was the picture of distress and
imbecility. I went up to him, and asked him why he was crying. “My
fingers are cold,” said he. “But why don’t you put on your mittens?”
said I. “Oh, because my fingers are so cold!” said he. “But can’t you
put them on?” said I. “Oh yes, I can put them on,” said the boy, “but
it hurts.”
“The child is father of the man,” thought I. This boy, here, in a
matter of his fingers, is acting precisely as many men act in regard
to matters of the deepest importance. Rather than bear the slight
pain of putting on his mittens, he will run the risk of freezing his
fingers. And when I see a man spending his time in idleness, and
thus laying up a prospect of future poverty and distress, rather than
work and be industrious, I think of the boy and his mittens. When I
see a man indulging in a habit of tippling, or any other bad practice,
because it is hard to leave off, I think of the boy and his mittens.
While the pure contemplative mind thus almost envies what the
rude observer would treat unfeelingly, it naturally shrinks into itself,
on the thought that there may be, in the immense chain of beings,
many, though as invisible to us as we to the inhabitants of this little
flower whose organs are not made for comprehending objects larger
than a mite, or more distant than a straw’s breadth, to whom we
may appear as much below regard as these to us.
With what derision should we treat those little reasoners, could
we hear them arguing for the unlimited duration of the carnation,
destined for the extent of their knowledge, as well as their action.
And yet, among ourselves there are reasoners who argue, on no
better foundation, that the earth which we inhabit is eternal.
The Kildeer Plover.
This bird is so called from its cry, resembling the word kildeer, and
is well known in all parts of the United States. It builds its nest in
level pastures which afford pools of water, or on sandy downs near
the sea. Its nest is a mere hollow, lined with straw or weeds; the
eggs are four, cream-colored, and spotted with black. The bird is
about ten inches long, is of an olive-gray color, and has long legs,
which enable it to wade in the water, of which it is very fond.
While rearing its young, the kildeer makes an incessant noise, and
if any one approaches its nest, it flies around and over him, calling
kildeer, kildeer, te dit, te dit, te dit, seeming to evince the utmost
anxiety. If this clamor does not frighten away the intruder, it will run
along the ground, with hanging wings, pretending to be lame, in
order to draw off attention from the nest. It seems to be a sleepless
bird, for it may be heard very late at night, in the spring and fall.
The kildeer feeds on grasshoppers and insects which it finds in
fields and in pools of water, wading in search of them. It is very
erect, runs with great swiftness, and flies very high in the air. Toward
autumn, large flocks descend to the seashore, where they are more
silent and circumspect.