EVOLUTION

Darwinism and the Fact of

Evolution
I. The Fact of Evolution
Evidence from biology and geology was contradictory to creationism
because it showed that species had changed through time and
descended with modification from common ancestors, instead of
each remaining unchanged since a special and independent origin.
We review three types of data. Taken together, they were
convincing enough to shake many scientists' belief in the Theory of
Special Creation.

Homology---literally, the study of likeness---was a key

concept in the new field of comparative anatomy.
Homologous structures in adults develop from the same
groups of cells in embryos. Therefore, homology is defined
as a similarity due to shared developmental pathways.
Nevertheless, why should some organisms share
developmental pathways? Darwin argued that descent from
a common ancestor was the most logical explanation. He
contended that the embryos in certain vertebrates (fish,
salamander, tortoise, chicken, pig, cow, human) are similar
because all vertebrates evolved from a common ancestor,
and because early developmental stages have remained
unchanged as fish, mammals, amphibians, and reptiles
diversified. Darwin's recognition of relationship through
shared descent was a conceptual breakthrough, and
extended to other phenomena other than homology.

Change Through Time

One of the central tenets of the Theory of Special Creation
was that species, once created, were immutable. Four lines
of evidence challenged this claim.

An early eighteenth-century palaeontologist named William

Clift was the first to publish an observation later confirmed
and expanded upon by Darwin (Eisely 1958). Fossil and
living mammals in the same geographic region are related
to each other, and distinctly different from faunas of other
areas. Clift worked on the extinct marsupial fauna of
Australia and noted its close relationship to forms alive
today; Darwin analyzed the armadillos of Argentina and their
relationship to the fossil glyptodonts he excavated there.
This general result, termed the Law of
Succession, provided strong documentation for evolution.

Darwin added another strong piece of evidence for change

through time: the presence of vestigial structures in a wide
variety of organisms. Some blind, cave-dwelling fish have
eye sockets but no eyes; flightless birds and insects have
reduced wings; humans have a non-functional appendix and
reduced tailbone. We also have muscles that make our body
hair stand on end when we are cold or excited. Erectile fur is
found in many mammals, and is important in signalling
alarm or aggressive intent. In humans, the result is
Goosebumps.

The Age of the Earth

By the time Darwin first began working on "the species
problem," data from the young science of geology had
challenged a factor of the Theory of Special Creation. Special
Creation stated that the earth was only about 6,000 years
old. Geologists were finding evidence that proved that the
earth was ancient; much older than 6,000 years.

James Hutton was the first to articulate a principle

called uniformitarianism: geological processes taking
place now operated similarly in the past. This assumption
led Hutton and Charles Lyell to infer that the geological time
scale was unimaginably long in human terms. Given the
measurements these early geologists made of ongoing rock-
forming processes like decomposition at beaches and river
deltas and the accumulation of marine shells (the precursors
of limestone), it was clear that vast stretches of time were
required to produce the immense rock formation they were
studying.

When Darwin began his work, Hutton and followers were

already in the midst of a 50-year effort to put the major rock
formations and fossil-bearing strata of Europe in a younger-
to-older sequence. Their technique, called, relative dating,
was based on the following:

• Younger rocks are deposited on top of older rocks

(principle of superposition)
• Lavas and sedimentary rocks were originally laid down
in a horizontal position, so that any tipping or bending
events occurred after deposition (principle of original
horizontality)
• Rocks that intrude into seams or as dikes are younger
than their host rocks (principle of cross-cutting
relationships)
• Boulders, cobbles, or other fragments found in a body
of rock are older than their host rock (principle of
inclusions)
• Earlier fossil life forms are simpler than more recent
forms, and more recent forms are most similar to
existing forms (principle of faunal succession)

Using these rules, geologists established the chronology

known as the geologic time scale and created the concept of
the geologic column. This is a history of the earth based on a
composite, older-to-younger sequence of rock strata. Taken
together with the principle of uniformitarianism, the geologic
time scale and the geologic column furnished impressive
evidence for an ancient earth.

II. Natural Selection: Darwin's 4

Postulates
Because homologies, extinction, and the law of succession
were widely recognized in Western Europe, the idea of
evolution had been in the air long before Darwin began his
work. Several writers, including Darwin's grandfather
Erasmus Darwin, had proposed that existing species are the
modified descendants of forms that existed previously.
However, no one had yet proposed a satisfactory
mechanism for how a population of organisms could change
through time. Darwin's solution is the theory of evolution by
natural selection. It can be stated concisely, as the logical
outcome of four postulates:

1. Individuals within species are variable.

2. Some of these variations are passed on to offspring.
3. In every generation, more offspring are produced than
can survive.
4. Survival and reproduction are not random: The
individuals that survive and go on to reproduce, or who
reproduce the most, are those with the most
favourable variations. They are naturally selected.

Evolutionary change is an outcome of the process described

by Darwin, which he called natural selection. The logic is
clear: If there is variation among individuals in a population
that can be passed on to offspring, and if there is differential
success among those individuals in surviving and/or
reproducing and thus is passing on those variations, then
the characteristics of the population will change slightly with
each succeeding generation.

III. The Nature of Natural Selection

Each generation is a product of selection by the
environmental conditions that prevailed in the generation
before. There is a common misconception, however, that
organisms can be adapted to future conditions, or that
selection can look ahead in the sense of anticipating
environmental changes during future generations. This is
impossible. Evolution is always a generation behind any
changes in the environment.

Natural selection can select only from the variations that

already exist in a population. Selection cannot, for example,
instantly create a new and optimal characteristic that was
not previously extant. Even though it only acts on existing
traits, natural selection can be a creative process that leads
to completely new characteristics. This seems paradoxical,
but novel features can evolve because selection is able to
"repurpose" existing behaviours, structures, or genes for
new functions.
Evolution by natural selection is sometimes characterized as
a random chance process, but nothing could be further from
the truth. Evolution is both directed and purposeful: it is
directed by the environment and purposeful in the sense of
increasing adaptation to that environment. Although
evolution has tended to increase the complexity, degree of
organization, and specialization of organisms through time,
it is not progressive in the everyday sense of leading toward
some predetermined goal. Evolution makes organisms
better only in the sense of increasing their adaptation to
their environment. There is no inexorable trend toward
higher forms of life.

One of the most pervasive misconceptions about natural

selection, especially selection on animal behaviour, is that
individual organisms will do things for the good of the
species. Self-sacrificing, or altruistic, acts do occur in nature:
Prairie dogs will give warning calls when predators approach,
and lionesses will nurse cubs that are not her own.

Mutation: The Origin of New

Genes and Alleles

I. Where New Alleles Come From

Most new alleles are derived from already existing alleles,
typically as a result of point mutation. Point mutations are
single-based substitutions cause by one of two processes:
random errors in DNA synthesis or random errors in the
repair of sites damaged by chemical mutagens or high-
energy radiation. DNA polymerase causes both types of
changes.

If during normal synthesis or repair synthesis, DNA

polymerase mistakenly substitutes a purine (Adenine or
Guanine) for another purine, or a pyrimidine (Thymine or
Cytosine) for another pyrimidine, the point mutation is called
a transition. If a purine is substituted for a pyrimidine, or
vice versa, then the mutation is called a transversion. Of the
two kinds of point mutations, transitions are far more
common, because they are easier mistakes for polymerase
to make and cause much less disruption in the DNA helix
during synthesis.

Mutation Rates
How often are new alleles formed? Many of our best data on
mutation rates are for loss-of-function mutations. In these
types of mutations, the lack of normal protein product leads
to an easily recognizable phenotype. The problem with this
method is that loss-of-function mutations result
from any process that inactivates a gene. Genes can be
knocked out by base-pair substitutions that produce a chain-
terminating codon or a dysfunctional amino acid sequence,
frameshifts (additions or deletions of one or two base pairs
that disrupt the reading sequence of codons), the insertion
of a mobile genetic element, chromosome rearrangements,
and so on. As a result, we have scant data on what is
perhaps the most interesting type of mutation rate for
evolutionary analyses: replacement substitutions per codon
per generation.

Mutation rates are very low on a per-gene basis, but there

are so many loci (approximately 100,000 in humans) that
almost 10% of all gametes carry a phenotypically detectable
mutation. It is probable that the majority of all offspring
carry at least one new allele somewhere in their genome.

II. Where New Genes Come From

As with new alleles, several kinds of mutations can create
new genes. Gene duplications are probably the most
important source of new genes. Duplications result from a
phenomenon known as unequal crossover. Unequal
crossover is a chance mistake caused by the proteins
involved in managing recombination (crossing over) during
meiosis. One of the products of unequal crossover is a
redundant stretch of DNA. The genome now has an extra
copy of the sequences located in the duplicated segment.
Because the parent copy still produces a normal product, the
redundant sequences are free to accumulate mutations
without consequences to the phenotype. The new sequence
may even change function over time, and become a new
locus. Because it creates additional DNA, gene duplication is
the first mechanism we have encountered that results in
entirely new possibilities for gene function. Duplicated genes
can (1) retain their original function and provide an
additional copy of the parent locus, (2) gain a new function
through mutation and selection, or (3) become functionless
pseudogenes.

In addition to duplication, other mechanisms can create new

genes or radically new functions for duplicated genes. One
example, called overprinting, results from point mutations
that produce new start codons and new reading frames for
translation. Evolution at the new locus is likely to be tightly
constrained, because any mutation that improves the
function of the overlapping protein would probably be
deleterious to the function of the replicate protein.
Overprinting has also been a common mechanism for
creating new genes during viral evolution.

III. Chromosome Alterations

A wide variety of changes can occur in the gross morphology
of chromosomes. Some of these mutations affect only gene
order and organization; others produce duplications or
deletions that affect the total amount of genetic material.
Chromosomal alterations can involve the entire DNA
molecule or just segments.

Inversions
Chromosome inversions involve much larger stretches of
DNA than other mutation types. They also produce very
different consequences. Inversions result from a multi-step
process that starts when ionizing radiation causes two
double-strand breaks in a chromosome. After breakage a
chromosome segment can detach, flip, and re-anneal in its
original location. Inversions affect a phenomenon known
as genetic linkage. Linkage is the tendency for alleles of
different genes to assort together at meiosis. Genes on the
same chromosome tends to more tightly linked than genes
on non-homologous chromosomes. The closer together
genes are on the same chromosome, the tighter the linkage.
Crossing over at meiosis, on the other hand, breaks up allele
combinations and reduces linkage.
The Origin of Life and
Precambrian Evolution
I. The Most Recent Common Ancestor of
All Living Things
The oldest fossils established as those of living organisms
are 3.465 billion years old. These fossils, which come from a
rock formation called the Apex chert in Western Australia,
show simple cells growing in short filaments. Their
discoverer, J. William Schopf (1993), believes these
organisms belonged to the cyanobacteria family. This
identification is tentative. The fossil record for times earlier
than 2.5 billion years ago is too spotty to allow
palaeontologists to trace lines of evolutionary descent from
present-day organisms back to the Apex chert fossils. As a
result, we have no way of knowing whether the organisms
recorded in the Apex chert represent extinct or living
branches of the tree of life. If we want to discover the
characteristics of the most recent common ancestor, we
must use methods other than examination of the fossil
record.

Finding the Common Ancestor without Fossils

If we knew the phylogeny, or evolutionary tree, of all living
things, we could use it to infer the characteristics of the
cenancestor. The first attempt to construct such a phylogeny
based on the morphologies of organisms (see reviews in
Woese 1991; Dolittle and Brown 1994). The morphological
approach was productive for biologists interested in the
branches of the tree of life that contain eukaryotes.
Morphology was the basis of the phylogeny of tetrapods. The
fact that monotremes, marsupials, and eutherians have hair,
for example, indicates that these mammal groups are more
closely related to each other than any of them related to any
other tetrapod.
When biologists developed methods for reading the
sequences of amino acids in proteins, and the sequences of
nucleotides in DNA and RNA, a new technique for estimating
phylogenies quickly became established (Zuckerkland and
Pauling, 1965). Imagine that we have a group of species, all
carrying their genomes in a particular gene. We can read the
sequence of nucleotides in this gene in each of the species,
and then compare the sequences. If the species are closely
related, their sequences will be familiar. If the species
occupy distant branches on the evolutionary tree, then their
sequences are less similar. As a result, we can use the
relative similarity of the sequences of the species to infer
their evolutionary relationships.

The Earliest Possible Date for the Cenancestor

If we assume that the cenancestor lived on Earth, then the
cenancestor could not have lived before the Earth existed
and was inhabitable. The Earth descended, along with the
sun and other planets, from an interstellar dust cloud
(Hughes 1989; Wetherill 1990). The cloud contained
hydrogen and helium left over from the big bang, plus
heavier elements ejected in the explosion of earlier
generations of stars. These heavy elements were vital: They
became major constituents of the Earth. As the spinning
interstellar dust cloud condensed under the force of gravity,
it formed countless small planetary bodies in orbit around a
central mass. The central mass became the sun; its
thermonuclear furnace ignited by heat generated during its
gravitational collapse. The orbiting planetesimals collided
with each other, forming the planets by gradual accretion.
The process of planetary accretion has slowed dramatically,
but it is not yet finished. Planetesimals---meteors---continue
to collide with the Earth and other planets. Radioisotope
dating of meteorites yields an estimated age for the solar
system, and hence the Earth, of 4.5 to 4.6 billion years
(Badash 1989).

The newborn Earth remained uninhabitable for at least a few

hundred million years. At first, it was simply much too hot.
The collisions of the plantesimials that formed the Earth
released enough heat to melt the entire planet (Wetherill
1990). Eventually the Earth's outer surface cooled and
solidified to form the crust, and water vapour released from
the planet's interior cooled and condensed to form the
oceans. We know that at least some solid crust existed by
about 4 billion years ago, because there are 3.96 billion-
year-old rocks in Arctic Canada (Bowring 1989), and 4.2 to
4.3 billion-year-old zircon crystals embedded in younger
sandstones in Australia (Myers and William 1985; Compston
and Pidgeon 1986). We know that surface water existed by
3.85 billion years ago, because there are sedimentary rocks
of that age at Akilia Island, Greenland, and sedimentary
rocks that are 3.8 billion years old at nearby Isua, Greenland
(Mojzsis 1996).

The oldest sedimentary rocks contain the oldest living

evidence suggesting the presence of life. The rocks are of a
type known as banded iron formations. Geological
processes have exposed the rocks to high temperatures and
pressures, which have compressed the rocks and
crystallized many of the minerals they contain. This
transformation would have destroyed any microfossils the
rocks might have originally harboured. The rocks do contain
apatite crystals, however. Apatite is calcium phosphate
minerals. Apatite is produced by many microorganisms, and
is the main component of bones and teeth in vertebrates.
Non-biological processes can also produce apatites.

Solid crust and oceans probably existed earlier than the 3.96
and 3.85 billion years ago demonstrated by the Canadian
and Akilia Island rocks, but erosion, plate tectonics, and
volcanic eruptions have obliterated all direct evidence. Even
if crust and oceans did exist earlier, however, continued
bombardment of the planet by large meteors probably would
have prevented life from establishment much earlier than
3.85 billion years ago. Large meteor impacts generate heat,
create sun-blocking dust, and produce a blanket of debris.
All of these effects, if intense enough, can kill organisms.
The mass extinction at the end of the Cretaceous that killed
off the non-avian dinosaurs may have been caused by a
large meteor impact. As time passed, and the Earth and
other planets swept up the largest planetesmials, the sizes
of the largest impacts decreased. It is estimated that the last
impact that had sufficient energy to vaporize the entire
global ocean, and thereby kill any moreover, all organisms
then alive, probably happened between 4.44 and 3.8 billion
years ago (Norman Sleep et. al. 1989).
Based on the Akilia sedimentary rocks, then, and on the
history of large impacts, we can estimate that the earliest
the cenancestor could possibly have lived was somewhere
between 3.85 and about 4.4 billion years ago.

The Latest Possible Date for the Cenancestor The

cenancestor could not have lived any more recently than the
occurrence of any of the branch points above it on the
universal phylogeny. The most definitive information about
branching times comes from fossils. The fossils useful in this
regard are those that can be confidently identified as
belonging to a particular group of organisms. If we can place
a fossil on the whole-life phylogeny, then we know that the
cenancestor is older than the fossil.

The oldest known fossils that are probably those of

eukaryotes are 2.1 billion years old. Found by Tsu-Ming Han
and Bruce Runnegar (1992) at the Empire Mine in Michigan,
these fossils show a spiral-shaped organism similar to a
more recent fossil named Grypania spiralis. G. spiralis is
known from fossils in Montana, China, and India that range
in age from 1.1 to 1.4 billion years old (Han and Runnegar
1992). Because of its large size and structural complexity,
palaeontologists believe that Grypania was a eukaryote,
probably an alga. Fossil cyanobacteria support a similar
conclusion (Schopf 1994a). In a testament to the length of
time that successful organisms can remain at least
superficially unchanged, many fossil cyanobacteria are
identifiable based on their structural similarity to extant
forms. The extant cyanobacteria occupy a limb of the
universal phylogeny that is, like those occupied by the
extant algae, several branch points above the last common
ancestor.

In summary, we can use the estimated universal phylogeny,

along with geological and paleontological data, to bracket
the time when the cenancestor could have lived. The earliest
possible date is between 4.4 and 3.85 billion years ago; the
most recent possible date is between 3.5 and 2 billion years
ago.

II. Origin of the Cenancestor

The most recent common ancestor of all extant organisms
was a descendant of the "one primordial form," the first self-
replicating entity that could evolve by natural selection. The
most compelling puzzles question what the primordial form
was, and how it was created by nonbiological processes. We
may never have direct fossil evidence of the nature of the
first living thing (Schopf 1994b). The oldest known rocks
from the inhabitable Earth contain evidence suggesting that
life was already established by the time the rocks were
formed. Even if we find rocks that date from the time of the
primordial form, it is unlikely that they will contain any
useful clues to the origin of life. The first self-replicating
entity was probably chemical, not cellular, meaning that it
had no cell walls to fossilize. Furthermore, the organic
molecules that likely made up the primordial form are far too
unstable to have remained preserved in rock for 4 billion
years.

We will assume that the primordial form originated on Earth.

We know that evolution before the cenancestor had to
progress from a collection of nonliving chemicals to the
primordial form to the cenancestor itself, and we know that
the cenancestor was essentially a modern organism.
Following the most widely accepted scenario, sometimes
referred to as the Oparin-Haldane Theory (Lazcano and
Miller 1996), we can break the spontaneous generation of
the primordial form into a series of steps that occurred
sequentially in the waters or moist clay of the young Earth:

1. Nonbiological processes synthesized organic

molecules, such as amino acids and nucleotides, that
would later serve as the building blocks of life. The
accumulation of these organic molecules in solution
created what is known as the pre-biotic soup.
2. The organic building blocks in the pre-biotic soup were
assembled into biological polymers, such as proteins
and nucleic acids.
3. Some combination of biological polymers was
assembled into a self-replicating organism that fed off
the organic molecules in the pre-biotic soup.

Once the first self-replicating organism appeared, its

descendants acquired cellular form and the metabolic ability
to synthesize their own organic building blocks. The actual
route of evolution may have been less direct than that, but
with this outline at least we have a starting point.
Nonbiological Synthesis of the Building Blocks of
Life The first step, the nonbiological synthesis of the
building blocks of life, is fairly easy, at least under the right
conditions. In 1953, Stanley L. Miller, then a graduate
student reported a simple and elegant experiment. He built
an apparatus that boiled water and circulated the hot vapor
through an atmosphere of methane (CH4), ammonia (NH3),
and hydrogen (H2), past an electric spark, and finally
through a cooling jacket that condensed the vapor and
directed it back into the bioling flask. Miller let the apparatus
run for a week; the water inside turned deep red and cloudy.
Using paper chromatography, Miller identified the cause of
the red color as a mixture of organic molecules, most
notably the amino acids glycine, alpha-alanine, and beta-
alanine. Since 1953, chemists working on the pre-biotic
synthesis of organic molecules have, in similar experiments,
documented the formation of a tremendous diversity of
organic molecules, includin amino acids, nucleotides, and
sugars. Miller used methane, ammonia, and hydrogen as his
atmosphere; at the time, this mixture was thought to model
the atmosphere of a young Earth. The implication of Miller's
result was that if lightning or UV radiation could have played
the role that the spark did in his experiment, then the young
Earth's oceans would have quickly become a rich pre-biotic
soup.

Many atmospheric chemists now believe that the early

atmosphere was dominated by carbon dioxide (CO2) rather
than methane, and molecular nitrogen (N2) rather than
ammonia (Kasting 1993). This conclusion is based on the
mixture of gases released by contemporary volcanoes, and
on improved knowledge of the chemical reactions that occur
in the upper atmosphere.

Even if the early atmosphere did not allow the synthesis of

organic molecules on Earth, there may have been another
mechanism for the accumulation of a pre-biotic soup. We
noted earlier that the young Earth experienced heavy
bombardment by meteors and comets. Carbonaceous
chondrite meteorites, believed to be fragments of asteroids,
contain an abundance of organic molecules (Chyba 1990;
Lazcano and Miller 1996). Thus, they very same
bombardment of the young Earth that made early conditions
uncomfortable for life may, ironically, have supplied the
ingredients for the construction of the primordial form.

The Cambrian Explosion

I. The Nature of the Fossil Record
How Organic Remains Fossilize A fossil is any trace left
by an organism that lived in the past. Fossils are enormously
diverse, but four general categories can be defined by
method of formation:

• Compression and impression fossils can result

when organic material is buried in water or wind-borne
sediment before it decomposes. Under the weight of
sand, mud, ash, or other particles deposited above, a
structure can leave an impression in the material
below. The resulting fossil is analogous to the record
left by footprints in mud or leaves in wet concrete. In
anoxic settings, the deposits can compress the cells
into a black, carbonaceous deposit on the substrate. If
the sediment is extremely fine-grained, compressions
often record details of external structure as fine as the
stomata and guard cells on plant leaves.
• Permineralized fossil can form when structures are
buried in sediments and dissolved minerals precipitate
in the cells. This process, which is analogous to the way
a microscopist embeds tissues with resin before
sectioning, can preserve details of internal structure.
• Casts and molds originate whern remains decay or
when shells dissolve after being buried in sediment.
Molds consist of unfilled spaces, while casts form when
new material infiltrates the space, fills it, and hardens
into rock. This process is analogous to the lost-wax
casting technique used by sculptors. Molds and casts
preserve information about external and internal
surfaces.
• Unaltered remains can be preserved in environments
that discourage loss from weathering, consumption by
scavenging animals, and decomposition by bacteria
and fungi. Organic material can remained preserved for
hundreds of millions of years.