JohnScalesAvery 2012 3MOLECULARBIOLOGYANDE InformationTheoryAndE

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Chapter 3
MOLECULAR BIOLOGY AND

EVOLUTION
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Classical genetics
Charles Darwin postulated that natural selection acts on small inheritable
variations in the individual members of a species. His opponents objected
that these slight variations would be averaged away by interbreeding. Dar-
win groped after an answer to this objection, but he did not have one.
However, unknown to Darwin, the answer had been uncovered several years
earlier by an obscure Augustinian monk, Gregor Mendel, who was born in
Silesia in 1822, and who died in Bohemia in 1884.
Mendel loved both botany and mathematics, and he combined these two
interests in his hobby of breeding peas in the monastery garden. Mendel
carefully self-pollinated his pea plants, and then wrapped the flowers to
prevent pollination by insects. He kept records of the characteristics of
the plants and their offspring, and he found that dwarf peas always breed
true — they invariably produce other dwarf plants. The tall variety of pea
plants, pollinated with themselves, did not always breed true, but Mendel
succeeded in isolating a strain of true-breeding tall plants which he inbred
over many generations.
Next he crossed his true-breeding tall plants with the dwarf variety
and produced a generation of hybrids. All of the hybrids produced in this
way were tall. Finally Mendel self-pollinated the hybrids and recorded the
characteristics of the next generation. Roughly one quarter of the plants in
this new generation were true-breeding tall plants, one quarter were true-
breeding dwarfs, and one half were tall but not true-breeding.
Gregor Mendel had in fact discovered the existence of dominant and
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recessive genes. In peas, dwarfism is a recessive characteristic, while tallness

is dominant. Each plant has two sets of genes, one from each parent.
Whenever the gene for tallness is present, the plant is tall, regardless of
39
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40 INFORMATION THEORY AND EVOLUTION
whether it also has a gene for dwarfism. When Mendel crossed the pure-
breeding dwarf plants with pure-breeding tall ones, the hybrids received
one type of gene from each parent. Each hybrid had a tall gene and a
dwarf gene; but the tall gene was dominant, and therefore all the hybrids
were tall. When the hybrids were self-pollinated or crossed with each other,
a genetic lottery took place. In the next generation, through the laws of
chance, a quarter of the plants had two dwarf genes, a quarter had two tall
genes, and half had one of each kind.
Mendel published his results in the Transactions of the Brünn Natural
History Society in 1865, and no one noticed his paper1 . At that time,
Austria was being overrun by the Prussians, and people had other things
to think about. Mendel was elected Abbot of his monastery; he grew too
old and fat to bend over and cultivate his pea plants; his work on heredity
was completely forgotten, and he died never knowing that he would one
day be considered to be the founder of modern genetics.
In 1900 the Dutch botanist named Hugo de Vries, working on evening
primroses, independently rediscovered Mendel’s laws. Before publishing, he
looked through the literature to see whether anyone else had worked on the
subject, and to his amazement he found that Mendel had anticipated his
great discovery by 35 years. De Vries could easily have published his own
work without mentioning Mendel, but his honesty was such that he gave
Mendel full credit and mentioned his own work only as a confirmation of
Mendel’s laws. Astonishingly, the same story was twice repeated elsewhere
in Europe during the same year. In 1900, two other botanists (Correns
in Berlin and Tschermak in Vienna) independently rediscovered Mendel’s
laws, looked through the literature, found Mendel’s 1865 paper, and gave
him full credit for the discovery.
Besides rediscovering the Mendelian laws for the inheritance of domi-
nant and recessive characteristics, de Vries made another very important
discovery: He discovered genetic mutations — sudden unexplained changes
of form which can be inherited by subsequent generations. In growing
evening primroses, de Vries found that sometimes, but very rarely, a com-
pletely new variety would suddenly appear, and he found that the variation
could be propagated to the following generations. Actually, mutations had
been observed before the time of de Vries. For example, a short-legged
mutant sheep had suddenly appeared during the 18th century; and stock-
breeders had taken advantage of this mutation to breed sheep that could
1Mendel sent a copy of his paper to Darwin; but Darwin, whose German was weak,
seems not to have read it.
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MOLECULAR BIOLOGY AND EVOLUTION 41
not jump over walls. However, de Vries was the first scientist to study and
describe mutations. He noticed that most mutations are harmful, but that
a very few are beneficial, and those few tend in nature to be propagated to
future generations.
After the rediscovery of Mendel’s work by de Vries, many scientists
began to suspect that chromosomes might be the carriers of genetic in-
formation. The word “chromosome” had been invented by the German
physiologist, Walther Flemming, to describe the long, threadlike bodies
which could be seen when cells were stained and examined through, the
microscope during the process of division. It had been found that when an
ordinary cell divides, the chromosomes also divide, so that each daughter
cell has a full set of chromosomes.
The Belgian cytologist, Edouard van Benedin, had shown that in the
formation of sperm and egg cells, the sperm and egg receive only half of
the full number of chromosomes. It had been found that when the sperm
of the father combines with the egg of the mother in sexual reproduction,
the fertilized egg again has a full set of chromosomes, half coming from
the mother and half from the father. This was so consistent with the
genetic lottery studied by Mendel, de Vries and others, that it seemed
almost certain that chromosomes were the carriers of genetic information.
The number of chromosomes was observed to be small (for example, each
normal cell of a human has 46 chromosomes); and this made it obvious that
each chromosome must contain thousands of genes. It seemed likely that
all of the genes on a particular chromosome would stay together as they
passed through the genetic lottery; and therefore certain characteristics
should always be inherited together.
This problem had been taken up by Thomas Hunt Morgan, a professor
of experimental zoology working at Colombia University. He found it con-
venient to work with fruit flies, since they breed with lightning-like speed
and since they have only four pairs of chromosomes.
Morgan found that he could raise enormous numbers of these tiny insects
with almost no effort by keeping them in gauze-covered glass milk bottles,
in the bottom of which he placed mashed bananas. In 1910, Morgan found
a mutant white-eyed male fly in one of his milk-bottle incubators. He bred
this fly with a normal red-eyed female, and produced hundreds of red-eyed
hybrids. When he crossed the red-eyed hybrids with each other, half of
the next generation were red-eyed females, a quarter were red-eyed males,
and a quarter were white-eyed males. There was not one single white-eyed
female! This indicated that the mutant gene for white eyes was on the same
chromosome as the gene for the male sex.

As Morgan continued his studies of genetic linkages, however, it became
clear that the linkages were not absolute. There was a tendency for all
the genes on the same chromosome to be inherited together; but on rare
occasions there were “crosses”, where apparently a pair of chromosomes
broke at some point and exchanged segments. By studying these crosses
statistically, Morgan and his “fly squad” were able to find the relative
positions of genes on the chromosomes. They reasoned that the probability
for a cross to separate two genes should be proportional to the distance
between the two genes on the chromosome. In this way, after 17 years of
work and millions of fruit flies, Thomas Hunt Morgan and his coworkers
were able to make maps of the fruit fly chromosomes showing the positions
of the genes.
This work had been taken a step further by Hermann J. Muller, a mem-
ber of Morgan’s “fly squad”, who exposed hundreds of fruit flies to X-rays.
The result was a spectacular outbreak of man-made mutations in the next
generation.
“They were a motley throng”, recalled Muller. Some of the mutant flies
had almost no wings, others bulging eyes, and still others brown, yellow
or purple eyes; some had no bristles, and others curly bristles. Muller’s
experiments indicated that mutations can be produced by radiation-induced
physical damage; and he guessed that such damage alters the chemical
structure of genes.
In spite of the brilliant work by Morgan and his collaborators, no one
had any idea of what a gene really was.
The structure of DNA

Until 1944, most scientists had guessed that the genetic message was car-
ried by the proteins of the chromosome. In 1944, however, O.T. Avery and
his co-workers at the laboratory of the Rockefeller Institute in New York
performed a critical experiment, which proved that the material which car-
ries genetic information is not protein, but deoxyribonucleic acid (DNA) —
a giant chainlike molecule which had been isolated from cell nuclei by the
Swiss chemist, Friedrich Miescher.
Avery had been studying two different strains of pneumococci, the bac-
teria which cause pneumonia. One of these strains, the S-type, had a
smooth coat, while the other strain, the R-type, lacked an enzyme needed
for the manufacture of a smooth carbohydrate coat. Hence, R-type pneu-
mococci had a rough appearance under the microscope. Avery and his
co-workers were able to show that an extract from heat-killed S-type pneu-
mococci could convert the living R-type species permanently into S-type;
and they also showed that this extract consisted of pure DNA.
In 1947, the Austrian-American biochemist, Erwin Chargaff, began to
study the long, chainlike DNA molecules. It had already been shown by
Levine and Todd that chains of DNA are built up of four bases: adenine
(A), thymine (T), guanine (G) and cytosine (C), held together by a sugar-
phosphate backbone. Chargaff discovered that in DNA from the nuclei
of living cells, the amount of A always equals the amount of T; and the
amount of G always equals the amount of C.
When Chargaff made this discovery, neither he nor anyone else under-
stood its meaning. However, in 1953, the mystery was completely solved by
Rosalind Franklin and Maurice Wilkins at Kings College, London, together
with James Watson and Francis Crick at Cambridge University. By means
of X-ray diffraction techniques, Wilkins and Franklin obtained crystallo-
graphic information about the structure of DNA. Using this information,
together with Linus Pauling’s model-building methods, Crick and Watson
proposed a detailed structure for the giant DNA molecule.
The discovery of the molecular structure of DNA was an event of enor-
mous importance for genetics, and for biology in general. The structure was
a revelation! The giant, helical DNA molecule was like a twisted ladder:
Two long, twisted sugar-phosphate backbones formed the outside of the
ladder, while the rungs were formed by the base pairs, A, T, G and C. The
base adenine (A) could only be paired with thymine (T), while guanine (G)
fit only with cytosine (C). Each base pair was weakly joined in the center
by hydrogen bonds — in other words, there was a weak point in the center
of each rung of the ladder — but the bases were strongly attached to the
sugar-phosphate backbone. In their 1953 paper, Crick and Watson wrote:
”It has not escaped our notice that the specific pairing we have postu-
lated suggests a possible copying mechanism for genetic material”. Indeed,
a sudden blaze of understanding illuminated the inner workings of heredity,
and of life itself.
If the weak hydrogen bonds in the center of each rung were broken, the
ladderlike DNA macromolecule could split down the center and divide into
two single strands. Each single strand would then become a template for
the formation of a new double-stranded molecule.
Because of the specific pairing of the bases in the Watson-Crick model
of DNA, the two strands had to be complementary. T had to be paired
with A, and G with C. Therefore, if the sequence of bases on one strand

was (for example) TTTGCTAAAGGTGAACCA... , then the other strand
necessarily had to have the sequence AAACGATTTCCACTTGGT... The
Watson-Crick model of DNA made it seem certain that all the genetic
information needed for producing a new individual is coded into the long,
thin, double-stranded DNA molecule of the cell nucleus, written in a four-
letter language whose letters are the bases, adenine, thymine, guanine and
cytosine.
The solution of the DNA structure in 1953 initiated a new kind of
biology — molecular biology. This new discipline made use of recently-
discovered physical techniques — X-ray diffraction, electron microscopy,
electrophoresis, chromatography, ultracentrifugation, radioactive tracer
techniques, autoradiography, electron spin resonance, nuclear magnetic res-
onance and ultraviolet spectroscopy. In the 1960’s and 1970’s, molecular
biology became the most exciting and rapidly-growing branch of science.
Protein structure
In England, J.D. Bernal and Dorothy Crowfoot Hodgkin pioneered the ap-
plication of X-ray diffraction methods to the study of complex biological
molecules. In 1949, Hodgkin determined the structure of penicillin; and in
1955, she followed this with the structure of vitamin B12. In 1960, Max
Perutz and John C. Kendrew obtained the structures of the blood pro-
teins myoglobin and hemoglobin. This was an impressive achievement for
the Cambridge crystallographers, since the hemoglobin molecule contains
roughly 12,000 atoms.
The structure obtained by Perutz and Kendrew showed that hemoglobin
is a long chain of amino acids, folded into a globular shape, like a small,
crumpled ball of yarn. They found that the amino acids with an affinity for
water were on the outside of the globular molecule; while the amino acids for
which contact with water was energetically unfavorable were hidden on the
inside. Perutz and Kendrew deduced that the conformation of the protein
— the way in which the chain of amino acids folded into a 3-dimensional
structure — was determined by the sequence of amino acids in the chain.
In 1966, D.C. Phillips and his co-workers at the Royal Institution in
London found the crystallographic structure of the enzyme lysozyme (an
egg-white protein which breaks down the cell walls of certain bacteria).
Again, the structure showed a long chain of amino acids, folded into a
roughly globular shape. The amino acids with hydrophilic groups were on
the outside, in contact with water, while those with hydrophobic groups
were on the inside. The structure of lysozyme exhibited clearly an active
site, where sugar molecules of bacterial cell walls were drawn into a mouth-
like opening and stressed by electrostatic forces, so that bonds between the
sugars could easily be broken.
Meanwhile, at Cambridge University, Frederick Sanger developed meth-
ods for finding the exact sequence of amino acids in a protein chain. In 1945,
he discovered a compound (2,4-dinitrofluorobenzene) which attaches itself
preferentially to one end of a chain of amino acids. Sanger then broke down
the chain into individual amino acids, and determined which of them was
connected to his reagent. By applying this procedure many times to frag-
ments of larger chains, Sanger was able to deduce the sequence of amino
acids in complex proteins. In 1953, he published the sequence of insulin.
This led, in 1964, to the synthesis of insulin.
The biological role and structure of proteins which began to emerge was
as follows: A mammalian cell produces roughly 10,000 different proteins.
All enzymes are proteins; and the majority of proteins are enzymes — that
is, they catalyze reactions involving other biological molecules. All pro-
teins are built from chainlike polymers, whose monomeric sub-units are the
following twenty amino acids: glycine, aniline, valine, isoleucine, leucine,
serine, threonine, proline, aspartic acid, glutamic acid, lysine, arginine,
asparagine, glutamine, cysteine, methionine, tryptophan, phenylalanine,
tyrosine and histidine. These individual amino acid monomers may be con-
nected together into a polymer (called a polypeptide) in any order — hence
the great number of possibilities. In such a polypeptide, the backbone is a
chain of carbon and nitrogen atoms showing the pattern ...-C-C-N-C-C-N-
C-C-N-...and so on. The -C-C-N- repeating unit is common to all amino
acids. Their individuality is derived from differences in the side groups
which are attached to the universal -C-C-N- group.
Some proteins, like hemoglobin, contain metal atoms, which may be
oxidized or reduced as the protein performs its biological function. Other
proteins, like lysozyme, contain no metal atoms, but instead owe their bio-
logical activity to an active site on the surface of the protein molecule. In
1909, the English physician, Archibald Garrod, had proposed a one-gene-
one-protein hypothesis. He believed that hereditary diseases are due to
the absence of specific enzymes. According to Garrod’s hypothesis, dam-
age suffered by a gene results in the faulty synthesis of the corresponding
enzyme, and loss of the enzyme ultimately results in the symptoms of the
hereditary disease.
In the 1940’s, Garrod’s hypothesis was confirmed by experiments on

the mold, Neurospora, performed at Stanford University by George Beadle
and Edward Tatum. They demonstrated that mutant strains of the mold
would grow normally, provided that specific extra nutrients were added to
their diets. The need for these dietary supplements could in every case
be traced to the lack of a specific enzyme in the mutant strains. Linus
Pauling later extended these ideas to human genetics by showing that the
hereditary disease, sickle-cell anemia, is due to a defect in the biosynthesis
of hemoglobin.
RNA and ribosomes
Since DNA was known to carry the genetic message, coded into the sequence
of the four nucleotide bases, A, T, G and C, and since proteins were known
to be composed of specific sequences of the twenty amino acids, it was logical
to suppose that the amino acid sequence in a protein was determined by
the base sequence of DNA. The information somehow had to be read from
the DNA and used in the biosynthesis of the protein.
It was known that, in addition to DNA, cells also contain a similar,
but not quite identical, polynucleotide called ribonucleic acid (RNA). The
sugar-phosphate backbone of RNA was known to differ slightly from that of
DNA; and in RNA, the nucleotide thymine (T) was replaced by a chemically
similar nucleotide, uracil (U). Furthermore, while DNA was found only in
cell nuclei, RNA was found both in cell nuclei and in the cytoplasm of cells,
where protein synthesis takes place. Evidence accumulated indicating that
genetic information is first transcribed from DNA to RNA, and afterwards
translated from RNA into the amino acid sequence of proteins.
At first, it was thought that RNA might act as a direct template, to
which successive amino acids were attached. However, the appropriate
chemical complementarity could not be found; and therefore, in 1955, Fran-
cis Crick proposed that amino acids are first bound to an adaptor molecule,
which is afterward bound to RNA.
In 1956, George Emil Palade of the Rockefeller Institute used electron
microscopy to study subcellular particles rich in RNA (ribosomes). Ribo-
somes were found to consist of two subunits — a smaller subunit, with a
molecular weight one million times the weight of a hydrogen atom, and a
larger subunit with twice this weight.
It was shown by means of radioactive tracers that a newly synthesized
protein molecule is attached temporarily to a ribosome, but neither of the

two subunits of the ribosome seemed to act as a template for protein syn-
thesis. Instead, Palade and his coworkers found that genetic information is
carried from DNA to the ribosome by a messenger RNA molecule (mRNA).
Electron microscopy revealed that mRNA passes through the ribosome like
a punched computer tape passing through a tape-reader. It was found that
the adapter molecules, whose existence Crick had postulated, were smaller
molecules of RNA; and these were given the name “transfer RNA” (tRNA).
It was shown that, as an mRNA molecule passes through a ribosome, amino
acids attached to complementary tRNA adaptor molecules are added to the
growing protein chain.
The relationship between DNA, RNA, the proteins and the smaller
molecules of a cell was thus seen to be hierarchical: The cell’s DNA con-
trolled its proteins (through the agency of RNA); and the proteins con-
trolled the synthesis and metabolism of the smaller molecules.
The genetic code

In 1955, Severo Ochoa, at New York University, isolated a bacterial enzyme
(RNA polymerase) which was able join the nucleotides A, G, U and C so
that they became an RNA strand. One year later, this feat was repeated
for DNA by Arthur Kornberg.
With the help of Ochoa’s enzyme, it was possible to make synthetic RNA
molecules containing only a single nucleotide — for example, one could
join uracil molecules into the ribonucleic acid chain, ...U-U-U-U-U-U-... In
1961, Marshall Nirenberg and Heinrich Matthaei used synthetic poly-U as
messenger RNA in protein synthesis; and they found that only polypheny-
lalanine was synthesized. In the same year, Sydney Brenner and Francis
Crick reported a series of experiments on mutant strains of the bacterio-
phage, T4. The experiments of Brenner and Crick showed that whenever
a mutation added or deleted either one or two base pairs, the proteins pro-
duced by the mutants were highly abnormal and non-functional. However,
when the mutation added or subtracted three base pairs, the proteins often
were functional. Brenner and Crick concluded that the genetic language
has three-letter words (codons). With four different “letters”, A, T, G and
C, this gives sixty-four possible codons — more than enough to specify the
twenty different amino acids.
In the light of the phage experiments of Brenner and Crick, Nirenberg
and Matthaei concluded that the genetic code for phenylalanine is UUU
Fig. 3.1 Information coded on DNA molecules in the cell nucleus is transcribed to
mRNA molecules. The messenger RNA molecules in turn provide information for the
amino acid sequence in protein synthesis.
in RNA and TTT in DNA. The remaining words in the genetic code were
worked out by H. Gobind Khorana of the University of Wisconsin, who
used other mRNA sequences (such as GUGUGU..., AAGAAGAAG... and
GUUGUUGUU...) in protein synthesis. By 1966, the complete genetic
code, specifying amino acids in terms of three-base sequences, was known.
The code was found to be the same for all species studied, no matter how
widely separated they were in form; and this showed that all life on earth
belongs to the same family, as postulated by Darwin.
Fig. 3.2 mRNA passes through the ribosome like a punched computer tape passing
through a tape-reader.
Genetic engineering
In 1970, Hamilton Smith of Johns Hopkins University observed that when
the bacterium Haemophilus influenzae is attacked by a bacteriophage (a
virus parasitic on bacteria), it can defend itself by breaking down the DNA
of the phage. Following up this observation, he introduced DNA from the
bacterium E. coli into H. influenzae. Again the foreign DNA was broken
down.
Smith had, in fact, discovered the first of a class of bacterial enzymes
which came to be called “restriction enzymes” or “restriction nucleases”.
Fig. 3.3 This figure shows aspartic acid, whose residue (R) is hydrophilic, contrasted
with alanine, whose residue is hydrophobic.
Almost a hundred other restriction enzymes were subsequently discovered,

and each was found to cut DNA at a specific base sequence. Smith’s col-
league, Daniel Nathans, used the restriction enzymes Hin dll and Hin dill
to produce the first “restriction map” of the DNA in a virus.
In 1971 and 1972, Paul Berg, and his co-workers Peter Lobban, Dale
Kaiser and David Jackson at Stanford University, developed methods for
adding cohesive ends to DNA fragments. Berg and his group used the
calf thymus enzyme, terminal transferase, to add short, single-stranded
polynucleotide segments to DNA fragments. For example, if they added
the single-stranded segment AAAA to one fragment, and TTTT to another,
Table 3.1: The genetic code
TTT=Phe TCT=Ser TAT=Tyr TGT=Cys

TTC=Phe TCC=Ser TAC=Tyr TGC=Cys
TTA=Leu TCA=Ser TAA=Ter TGA=Ter
TTG=Leu TGC=Ser TAG=Ter TGG=Trp
CTT=Leu CCT=Pro CAT=His CGT=Arg
CTC=Leu CCC=Pro CAC=His CGC=Arg
CTA=Leu CCA=Pro CAA=Gln CGA=Arg
CTG=Leu CGC=Pro CAG=Gln CGG=Arg
ATT=Ile ACT=Thr AAT=Asn AGT=Ser
ATC=Ile ACC=Thr AAC=Asn AGC=Ser
ATA=Ile ACA=Thr AAA=Lys AGA=Arg
ATG=Met AGC=Thr AAG=Lys AGG=Arg
GTT=Val GCT=Ala GAT=Asp GGT=Gly
GTC=Val GCC=Ala GAC=Asp GGC=Gly
GTA=Val GCA=Ala GAA=Glu GGA=Gly
GTG=Val GGC=Ala GAG=Glu GGG=Gly
then the two ends joined spontaneously when the fragments were incubated
together. In this way, Paul Berg and his group made the first recombinant
DNA molecules.
The restriction enzyme Eco RI, isolated from the bacterium E. coli,
was found to recognize the pattern, GAATTC, in one strand of a DNA
molecule, and the complementary pattern, CTTAAG, in the other strand.
Instead of cutting both strands in the middle of the six-base sequence, Eco
RI was observed to cut both strands between G and A. Thus, each side of
the cut was left with a “sticky end” — a five-base single-stranded segment,
attached to the remainder of the double-stranded DNA molecule.
In 1972, Janet Mertz and Ron Davis, working at Stanford University,
demonstrated that DNA strands cut with Eco RI could be rejoined by
means of another enzyme — a DNA ligase. More importantly, when DNA
strands from two different sources were cut with Eco RI, the sticky end of
one fragment could form a spontaneous temporary bond with the sticky end
of the other fragment. The bond could be made permanent by the addition
of DNA ligase, even when the fragments came from different sources. Thus,
DNA fragments from different organisms could be joined together.
Bacteria belong to a class of organisms (prokaryotes) whose cells do not
have a nucleus. Instead, the DNA of the bacterial chromosome is arranged

in a large loop. In the early 1950’s, Joshua Lederberg had discovered that
bacteria can exchange genetic information. He found that a frequently-
exchanged gene, the F-factor (which conferred fertility), was not linked to
other bacterial genes; and he deduced that the DNA of the F-factor was
not physically a part of the main bacterial chromosome. In 1952, Lederberg
coined the word “plasmid” to denote any extrachromosomal genetic system.
In 1959, it was discovered in Japan that genes for resistance to antibiotics
can be exchanged between bacteria; and the name “R-factors” was given
to these genes. Like the F-factors, the R-factors did not seem to be part of
the main loop of bacterial DNA.
Because of the medical implications of this discovery, much attention
was focused on the R-factors. It was found that they are plasmids, small
loops of DNA existing inside the bacterial cell but not attached to the
bacterial chromosome. Further study showed that, in general, between one
percent and three percent of bacterial genetic information is carried by
plasmids, which can be exchanged freely even between different species of
bacteria.
In the words of the microbiologist, Richard Novick, “Appreciation of
the role of plasmids has produced a rather dramatic shift in biologists’
thinking about genetics. The traditional view was that the genetic makeup
of a species was about the same from one cell to another, and was constant
over long periods of time. Now a significant proportion of genetic traits are
known to be variable (present in some individual cells or strains, absent in
others), labile (subject to frequent loss or gain) and mobile — all because
those traits are associated with plasmids or other atypical genetic systems”.
In 1973, Herbert Boyer, Stanley Cohen and their co-workers at Stan-
ford University and the University of California carried out experiments in
which they inserted foreign DNA segments, cut with Eco RI, into plasmids
(also cut with Eco RI). They then resealed the plasmid loops with DNA
ligase. Finally, bacteria were infected with the gene-spliced plasmids. The
result was a new strain of bacteria, capable of producing an additional pro-
tein coded by the foreign DNA segment which had been spliced into the
plasmids.
Cohen and Boyer used plasmids containing a gene for resistance to an
antibiotic, so that a few gene-spliced bacteria could be selected from a
large population by treating the culture with the antibiotic. The selected
bacteria, containing both the antibiotic-resistance marker and the foreign
DNA, could then be cloned on a large scale; and in this way a foreign gene
could be “cloned”. The gene-spliced bacteria were chimeras, containing

genes from two different species.
The new recombinant DNA techniques of Berg, Cohen and Boyer had
revolutionary implications: It became possible to produce many copies of a
given DNA segment, so that its base sequence could be determined. With
the help of direct DNA-sequencing methods developed by Frederick Sanger
and Walter Gilbert, the new cloning techniques could be used for mapping
and sequencing genes.
Since new bacterial strains could be created, containing genes from other
species, it became possible to produce any protein by cloning the corre-
sponding gene. Proteins of medical importance could be produced on a
large scale. Thus, the way was open for the production of human insulin,
interferon, serum albumin, clotting factors, vaccines, and protein hormones
such as ACTH, human growth factor and leuteinizing hormone.
It also became possible to produce enzymes of industrial and agricul-
tural importance by cloning gene-spliced bacteria. Since enzymes catalyze
reactions involving smaller molecules, the production of these substrate
molecules through gene-splicing also became possible.
It was soon discovered that the possibility of producing new, transgenic
organisms was not limited to bacteria. Gene-splicing was also carried out
on higher plants and animals as well as on fungi. It was found that the bac-
terium Agrobacterium tumefaciens contains a tumor-inducing (Ti) plasmid
capable of entering plant cells and producing a crown gall. Genes spliced
into the Ti plasmid quite frequently became incorporated in the plant chro-
mosome, and afterwards were inherited in a stable, Mendelian fashion.
Transgenic animals were produced by introducing foreign DNA into
embryo-derived stem cells (ES cells). The gene-spliced ES cells were then
selected, cultured and introduced into a blastocyst, which afterwards was
implanted in a foster-mother. The resulting chimeric animals were bred,
and stable transgenic lines selected.
Thus, for the first time, humans had achieved direct control over the
process of evolution. Selective breeding to produce new plant and animal
varieties was not new — it is one of the oldest techniques of civilization.
However, the degree, precision, and speed of intervention which recombi-
nant DNA made possible was entirely new. In the 1970’s it became possible
to mix the genetic repertoires of different species: The genes of mice and
men could be spliced together into new, man-made forms of life!
The Polymerase Chain Reaction

One day in the early 1980’s, an American molecular biologist, Kary Mullis,
was driving to his mountain cabin with his girl friend. The journey was
a long one, and to pass the time, Kary Mullis turned over and over in his
mind a problem which had been bothering him: He worked for a California
biotechnology firm, and like many other molecular biologists he had been
struggling to analyze very small quantities of DNA. Mullis realized that
it would be desirable have a highly sensitive way of replicating a given
DNA segment — a method much more sensitive than cloning. As he drove
through the California mountains, he considered many ways of doing this,
rejecting one method after the other as impracticable. Finally a solution
came to him; and it seemed so simple that he could hardly believe that he
was the first to think of it. He was so excited that he immediately pulled
over to the side of the road and woke his sleeping girlfriend to tell her
about his idea. Although his girlfriend was not entirely enthusiastic about
being wakened from a comfortable sleep to be presented with a lecture
on biochemistry, Kary Mullis had in fact invented a technique which was
destined to revolutionize DNA technology: the Polymerase Chain Reaction
(PCR)2 .
The technique was as follows: Begin with a small sample of the ge-
nomic DNA to be analyzed. (The sample may be extremely small — only
a few molecules.) Heat the sample to 95 ◦ C to separate the double-stranded
DNA molecule into single strands. Suppose that on the long DNA molecule
there is a target segment which one wishes to amplify. If the target seg-
ment begins with a known sequence of bases on one strand, and ends with
a known sequence on the complementary strand, then synthetic “primer”
oligonucleotides3 with these known beginning ending sequences are added
in excess. The temperature is then lowered to 50-60 ◦ C, and at the lowered
temperature, the “start” primer attaches itself to one DNA strand at the
beginning of the target segment, while the “stop” primer becomes attached
to the complementary strand at the other end of the target segment. Poly-
merase (an enzyme which aids the formation of double-stranded DNA) is
then added, together with a supply of nucleotides. On each of the original
pieces of single-stranded DNA, a new complementary strand is generated
with the help of the polymerase. Then the temperature is again raised to
2 The flash of insight didn’t take long, but at least six months of hard work were needed
before Mullis and his colleagues could convert the idea to reality.
3 Short segments of single-stranded DNA.
95 ◦ C, so that the double-stranded DNA separates into single strands, and

the cycle is repeated.
In the early versions of the PCR technique, the polymerase was de-
stroyed by the high temperature, and new polymerase had to be added
for each cycle. However, it was discovered that polymerase from the bac-
terium Thermus aquaticus would withstand the high temperature. (Ther-
mus aquaticus lives in hot springs.) This discovery greatly simplified the
PCR technique. The temperature could merely be cycled between the high
and low temperatures, and with each cycle, the population of the target seg-
ment doubled, concentrations of primers, deoxynucleotides and polymerase
being continuously present.
After a few cycles of the PCR reaction, copies of copies begin to predom-
inate over copies of the original genomic DNA. These copies of copies have
a standard length, always beginning on one strand with the start primer,
and ending on that strand with the complement of the stop primer.
Two main variants of the PCR technique are possible, depending on
the length of the oligonucleotide primers: If, for example, trinucleotides are
used as start and stop primers, they can be expected to match the genomic
DNA at many points. In that case, after a number of PCR cycles, popu-
lations of many different segments will develop. Within each population,
however, the length of the replicated segment will be standardized because
of the predominance of copies of copies. When the resulting solution is
placed on a damp piece of paper or a gel and subjected to the effects of
an electric current (electrophoresis), the populations of different molecu-
lar weights become separated, each population appearing as a band. The
bands are profiles of the original genomic DNA; and this variant of the PCR
technique can be used in evolutionary studies to determine the degree of
similarity of the genomic DNA of two species.
On the other hand, if the oligonucleotide primers contain as many as 20
nucleotides, they will be highly specific and will bind only to a particular
target sequence of the genomic DNA. The result of the PCR reaction will
then be a single population, containing only the chosen target segment.
The PCR reaction can be thought of as autocatalytic, and as we shall see
in the next section, autocatylitic systems play an important role in modern
theories of the origin of life.
Theories of chemical evolution towards the origin of life

The possibility of an era of chemical evolution prior to the origin of life
entered the thoughts of Charles Darwin, but he considered the idea to be
much too speculative to be included in his published papers and books.
However, in February 1871, he wrote a letter to his close friend Sir Joseph
Hooker containing the following words:
“It is often said that all the conditions for the first production of a
living organism are now present, which could ever have been present. But
if (and oh what a big if) we could conceive in some warm little pond with all
sorts of ammonia and phosphoric salts, light, heat, electricity etc. present,
that a protein compound was chemically formed, ready to undergo still
more complex changes, at the present day such matter would be instantly
devoured, or absorbed, which would not have been the case before living
creatures were formed”.
The last letter which Darwin is known to have dictated and signed be-
fore his death in 1882 also shows that he was thinking about this problem:
“You have expressed quite correctly my views”, Darwin wrote, “where you
said that I had intentionally left the question of the Origin of Life uncan-
vassed as being altogether ultra vires in the present state of our knowledge,
and that I dealt only with the manner of succession. I have met with no ev-
idence that seems in the least trustworthy, in favor of so-called Spontaneous
Generation. (However) I believe that I have somewhere said (but cannot
find the passage) that the principle of continuity renders it probable that
the principle of life will hereafter be shown to be a part, or consequence, of
some general law...”
Modern researchers, picking up the problem where Darwin left it, have
begun to throw a little light on the problem of chemical evolution towards
the origin of life. In the 1930’s, J.B.S. Haldane in England and A.I. Oparin
in Russia put forward theories of an era of chemical evolution prior to the
appearance of living organisms.
In 1924, Oparin published a pamphlet on the origin of life. An expanded
version of this pamphlet was translated into English and appeared in 1936
as a book entitled The Origin of Life on Earth. In this book, Oparin
pointed out that at the time when life originated, conditions on earth were
probably considerably different than they are at present: The atmosphere
probably contained very little free oxygen, since free oxygen is produced
by photosynthesis which did not yet exist. On the other hand, he argued,
there were probably large amounts of methane and ammonia in the earth’s
primitive atmosphere4 . Thus, before the origin of life, the earth probably
had a reducing atmosphere rather than an oxidizing one. Oparin believed
that energy-rich molecules could have been formed very slowly by the action
of light from the sun. On the present-day earth, bacteria quickly consume
energy-rich molecules, but before the origin of life, such molecules could
have accumulated, since there were no living organisms to consume them.
(This observation is similar to the remark made by Darwin in his 1871 letter
to Hooker.)
The first experimental work in this field took place in 1950 in the lab-
oratory of Melvin Calvin at the University of California, Berkeley. Calvin
and his co-workers wished to determine experimentally whether the prim-
itive atmosphere of the earth could have been converted into some of the
molecules which are the building-blocks of living organisms. The energy
needed to perform these conversions they imagined to be supplied by vol-
canism, radioactive decay, ultraviolet radiation, meteoric impacts, or by
lightning strokes.
The earth is thought to be approximately 4.6 billion years old. At the
time when Calvin and his co-workers were performing their experiments,
the earth’s primitive atmosphere was believed to have consisted primarily
of hydrogen, water, ammonia, methane, and carbon monoxide, with a little
carbon dioxide. A large quantity of hydrogen was believed to have been
initially present in the primitive atmosphere, but it was thought to have
been lost gradually over a period of time because the earth’s gravitational
attraction is too weak to effectively hold such a light and rapidly-moving
molecule. However, Calvin and his group assumed sufficient hydrogen to be
present to act as a reducing agent. In their 1950 experiments they subjected
a mixture of hydrogen and carbon dioxide, with a catalytic amount of
Fe2+ , to bombardment by fast particles from the Berkeley cyclotron. Their
experiments resulted in a good yield of formic acid and a moderate yield
of formaldehyde. (The fast particles from the cyclotron were designed to
simulate an energy input from radioactive decay on the primitive earth.)
Two years later, Stanley Miller, working in the laboratory of Harold
Urey at the University of Chicago, performed a much more refined exper-
iment of the same type. In Miller’s experiment, a mixture of the gases
methane, ammonia, water and hydrogen was subjected to an energy input
from an electric spark. Miller’s apparatus was designed so that the gases
were continuously circulated, passing first through the spark chamber, then
4It is now believed that the main constituents of the primordial atmosphere were
carbon dioxide, water, nitrogen, and a little methane.
Fig. 3.4 Miller’s apparatus.
through a water trap which removed the non-volatile water soluble prod-
ucts, and then back again through the spark chamber, and so on. The
resulting products are shown as a function of time in Figure 3.5.
The Miller-Urey experiment produced many of the building-blocks of
living organisms, including glycine, glycolic acid, sarcosine, alanine, lac-
tic acid, N-methylalanine, β-alanine, succinic acid, aspartic acid, glutamic
acid, iminodiacetic acid, iminoacetic-propionic acid, formic acid, acetic
Fig. 3.5 Products as a function of time in the Miller-Urey experiment.
acid, propionic acid, urea and N-methyl urea5 . Another major product
was hydrogen cyanide, whose importance as an energy source in chemical
evolution was later emphasized by Calvin.
The Miller-Urey experiment was repeated and extended by the
Ceylonese-American biochemist Cyril Ponnamperuma and by the Amer-
ican expert in planetary atmospheres, Carl Sagan. They showed that when
phosphorus is made available, then in addition to amino acids, the Miller-
Urey experiment produces not only nucleic acids of the type that join to-
gether to form DNA, but also the energy-rich molecule ATP (adenosine
triphosphate). ATP is extremely important in biochemistry, since it is a
5 The chemical reaction that led to the formation of the amino acids that Miller
observed was undoubtedly the Strecker synthesis: HCN + NH3 + RC=O + H2 O →

RC(NH2 )COOH.
universal fuel which drives chemical reactions inside present-day living or-
ganisms.
Further variations on the Miller-Urey experiment were performed by
Sydney Fox and his co-workers at the University of Miami. Fox and his
group showed that amino acids can be synthesized from a primitive atmo-
sphere by means of a thermal energy input, and that in the presence of
phosphate esters, the amino acids can be thermally joined together to form
polypeptides. However, some of the peptides produced in this way were
cross linked, and hence not of biological interest.
In 1969, Melvin Calvin published an important book entitled Chemical
Evolution; Molecular Evolution Towards the Origin of Living Systems on
Earth and Elsewhere. In this book, Calvin reviewed the work of geochemists
showing the presence in extremely ancient rock formations of molecules
which we usually think of as being produced only by living organisms. He
then discussed experiments of the Miller-Urey type — experiments simulat-
ing the first step in chemical evolution. According to Calvin, not only amino
acids but also the bases adenine, thymine, guanine, cytosine and uracil, as
well as various sugars, were probably present in the primitive ocean in
moderate concentrations, produced from the primitive atmosphere by the
available energy inputs, and not broken down because no organisms were
present.
The next steps visualized by Calvin were dehydration reactions in which
the building blocks were linked together into peptides, polynucleotides,
lipids and porphyrins. Such dehydration reactions are in a thermody-
namically uphill direction. In modern organisms, they are driven by a
universally-used energy source, the high-energy phosphate bond of adeno-
sine triphosphate (ATP). Searching for a substance present in the primitive
ocean which could have driven the dehydrations, Calvin and his coworkers
experimented with hydrogen cyanide (HC≡N), and from the results of these
experiments they concluded that the energy stored in the carbon-nitrogen
triple bond of HC≡N could indeed have driven the dehydration reactions
necessary for polymerization of the fundamental building blocks. However,
later work made it seem improbable that peptides could be produced from
cyanide mixtures.
In Chemical Evolution, Calvin introduced the concept of autocataly-
sis as a mechanism for molecular selection, closely analogous to natural
selection in biological evolution. Calvin proposed that there were a few
molecules in the ancient oceans which could catalyze the breakdown of the
energy-rich molecules present into simpler products. According to Calvin’s
hypothesis, in a very few of these reactions, the reaction itself produced

more of the catalyst. In other words, in certain cases the catalyst not only
broke down the energy-rich molecules into simpler products but also cat-
alyzed their own synthesis. These autocatalysts, according to Calvin, were
the first systems which might possibly be regarded as living organisms.
They not only “ate” the energy-rich molecules but they also reproduced,
i.e. they catalyzed the synthesis of molecules identical with themselves.
Autocatalysis leads to a sort of molecular natural selection, in which the
precursor molecules and the energy-rich molecules play the role of “food”,
and the autocatalytic systems compete with each other for the food supply.
In Calvin’s picture of molecular evolution, the most efficient autocatalytic
systems won this competition in a completely Darwinian way. These more
efficient autocatalysts reproduced faster and competed more successfully
for precursors and for energy-rich molecules. Any random change in the
direction of greater efficiency was propagated by natural selection.
What were these early autocatalytic systems, the forerunners of life?
Calvin proposed several independent lines of chemical evolution, which
later, he argued, joined forces. He visualized the polynucleotides, the
polypeptides, and the metallo-porphyrins as originally having independent
lines of chemical evolution. Later, he argued, an accidental union of these
independent autocatalysts showed itself to be a still more efficient autocat-
alytic system. He pointed out in his book that “autocatalysis” is perhaps
too strong a word. One should perhaps speak instead of “reflexive cataly-
sis” , where a molecule does not necessarily catalyze the synthesis of itself,
but perhaps only the synthesis of a precursor. Like autocatalysis, reflexive
catalysis is capable of exhibiting Darwinian selectivity.
The theoretical biologist, Stuart Kauffman, working at the Santa Fe
Institute, has constructed computer models for the way in which the com-
ponents of complex systems of reflexive catalysts may have been linked
together. Kauffman’s models exhibit a surprising tendency to produce or-
derly behavior even when the links are randomly programmed.
In 1967 and 1968, C. Woese, F.H.C. Crick and L.E. Orgel proposed that
there may have been a period of chemical evolution involving RNA alone,
prior to the era when DNA, RNA and proteins joined together to form
complex self-reproducing systems. In the early 1980’s, this picture of an
“RNA world” was strengthened by the discovery (by Thomas R. Cech and
Sydney Altman) of RNA molecules which have catalytic activity.
Today experiments aimed at throwing light on chemical evolution to-
wards the origin of life are being performed in the laboratory of the Nobel
Laureate geneticist Jack Sjostak at Harvard Medical School. The labora-

tory is trying to build a synthetic cellular system that undergoes Darwinian
evolution.
In connection with autocatalytic systems, it is interesting to think of the
polymerase chain reaction, which we discussed above. The target segment
of DNA and the polymerase together form an autocatalytic system. The
“food” molecules are the individual nucleotides in the solution. In the PCR
system, a segment of DNA reproduces itself with an extremely high degree
of fidelity. One can perhaps ask whether systems like the PCR system can
have been among the forerunners of living organisms. The cyclic changes of
temperature needed for the process could have been supplied by the cycling
of water through a hydrothermal system. There is indeed evidence that hot
springs and undersea hydrothermal vents may have played an important
role in chemical evolution towards the origin of life. We will discuss this
evidence in the next section.
Throughout this discussion of theories of chemical evolution, and the
experiments which have been done to support these theories, energy has
played a central role. None of the transformations discussed above could
have taken place without an energy source, or to be more precise, they
could not have taken place without a source of free energy. In Chapter 4
we will discuss in detail the reason why free energy plays a central role,
not only in the origin of life but also in life’s continuation. We will see
that there is a connection between free energy and information, and that
information-containing free energy is needed to produce the high degree of
order which is characteristic of life.
Molecular evidence establishing family trees in evolution

Starting in the 1970’s, the powerful sequencing techniques developed by
Sanger and others began to be used to establish evolutionary trees. The
evolutionary closeness or distance of two organisms could be estimated from
the degree of similarity of the amino acid sequences of their proteins, and
also by comparing the base sequences of their DNA and RNA. One of the
first studies of this kind was made by R.E. Dickerson and his coworkers,
who studied the amino acid sequences in Cytochrome C, a protein of very
ancient origin which is involved in the “electron transfer chain” of respira-
tory metabolism. Some of the results of Dickerson’s studies are shown in
Figure 3.6.
Comparison of the base sequences of RNA and DNA from various species
Fig. 3.6 Evolutionary relationships established by Dickerson and coworkers by com-

paring the amino acid sequences of Cytochrome C from various species.
proved to be even more powerful tool for establishing evolutionary relation-

ships. Figure 3.7 shows the universal phylogenetic tree established in this
way by Iwabe, Woese and their coworkers.6 In Figure 3.7, all presently
6 “Phylogeny” means ”the evolutionary development of a species”. ”Ontogeny” means
“the growth and development an individual, through various stages, for example, from
fertilized egg to embryo, and so on”. Ernst Haeckel, a 19th century follower of Darwin,
Fig. 3.7 This figure shows the universal phylogenetic tree, established by the work of
Woese, Iwabe et al. Hyperthermophiles are indicated by bold lines and by bold type.
living organisms are divided into three main kingdoms, Eukaryotes, Eubac-
teria, and Archaebacteria. Carl Woese, who proposed this classification on
the basis of comparative sequencing, wished to call the three kingdoms “Eu-
carya, Bacteria and Archaea”. However, the most widely accepted terms
observed that, in many cases, “ontogeny recapitulates phylogeny”.
are the ones shown in capital letters on the figure. Before the comparative
RNA sequencing work, which was performed on the ribosomes of various
species, it had not been realized that there are two types of bacteria, so
markedly different from each other that they must be classified as belonging
to separate kingdoms. One example of the difference between archaebac-
teria and eubacteria is that the former have cell membranes which contain
ether lipids, while the latter have ester lipids in their cell membranes. Of
the three kingdoms, the eubacteria and the archaebacteria are “prokary-
otes”, that is to say, they are unicellular organisms having no cell nucleus.
Most of the eukaryotes, whose cells contain a nucleus, are also unicellular,
the exceptions being plants, fungi and animals.
One of the most interesting features of the phylogenetic tree shown
in Figure 3.7 is that the deepest branches — the organisms with short-
est pedigrees — are all hyperthermophiles, i.e. they live in extremely hot
environments such as hot springs or undersea hydrothermal vents. The
shortest branches represent the most extreme hyperthermophiles. The
group of archaebacteria indicated by (1) in the figure includes Ther-
mofilum, Thermoproteus, Pyrobaculum, Pyrodictium, Desulfuro-
coccus, and Sulfolobus — all hypothermophiles7 . Among the eubacteria,
the two shortest branches, Aquifex and Thermatoga are both hyperther-
mophiles8
The phylogenetic evidence for the existence of hyperthermophiles at a
very early stage of evolution lends support to a proposal put forward in
1988 by the German biochemist Günter Wächterhäuser. He proposed that
the reaction for pyrite formation,
F eS + H2 S → F eS2 + 2H + +2e−
which takes place spontaneously at high temperatures, supplied the energy

needed to drive the first stages of chemical evolution towards the origin
of life. Wächterhäuser pointed out that the surface of the mineral pyrite
(FeS2 ) is positively charged, and he proposed that, since the immediate
products of carbon-dioxide fixation are negatively charged, they would be
attracted to the pyrite surface. Thus, in Wächterhäuser’s model, pyrite
formation not only supplied the reducing agent needed for carbon-dioxide
7 Group (2) in Figure 3.7 includes Methanothermus, which is hyperthermophilic,
and Methanobacterium, which is not. Group (3) includes Archaeoglobus, which is

hyperthermophilic, and Halococcus, Halobacterium, Methanoplanus, Methanospirilum,
and Methanosarcina, which are not.
8 Thermophiles are a subset of the larger group of extremophiles.
fixation, but also the pyrite surface aided the process. Wächterhäuser fur-
ther proposed an archaic autocatylitic carbon-dioxide fixation cycle, which
he visualized as resembling the reductive citric acid cycle found in present-
day organisms, but with all reducing agents replaced by FeS + H2 S, with
thioester activation replaced by thioacid activation, and carbonyl groups
replaced by thioenol groups. The interested reader can find the details of
Wächterhäuser’s proposals in his papers, which are listed at the end of this
chapter.
A similar picture of the origin of life was proposed by Michael J. Russell
and Alan J. Hall in 1997. In this picture “...(i) life emerged as hot, reduced,
alkaline, sulphide-bearing submarine seepage waters interfaced with colder,
more oxidized, more acid, Fe2+ >>Fe3+ -bearing water at deep (ca. 4km)
floors of the Hadean ocean ca. 4 Gyr ago; (ii) the difference in acidity,
temperature and redox potential provided a gradient of pH (ca. 4 units),
temperature (ca. 60◦ C) and redox potential (ca. 500 mV) at the interface
of those waters that was sustainable over geological time-scales, providing
the continuity of conditions conducive to organic chemical reactions needed
for the origin of life...” 9 . Russell, Hall and their coworkers also emphasize
the role that may have been played by spontaneously-formed 3-dimensional
mineral chambers (bubbles). They visualize these as having prevented the
reacting molecules from diffusing away, thus maintaining high concentra-
tions.
Table 3.2 shows the energy-yielding reactions which drive the
metabolisms of some organisms which are of very ancient evolutionary ori-
gin. All the reactions shown in the table make use of H2 , which could have
been supplied by pyrite formation at the time when the organisms evolved.
All these organisms are lithoautotrophic, a word which requires some expla-
nation: A heterotrophic organism is one which lives by ingesting energy-rich
organic molecules which are present in its environment. By contrast, an au-
totrophic organism ingests only inorganic molecules. The lithoautotrophs
use energy from these inorganic molecules, while the metabolisms of pho-
toautotrophs are driven by energy from sunlight.
Evidence from layered rock formations called “stromatolites”, produced
by colonies of photosynthetic bacteria, show that photoautotrophs (or pho-
totrophs) appeared on earth at least 3.5 billion years ago. The geological
9 SeeW. Martin and M.J. Russell, On the origins of cells: a hypothesis for the evo-
lutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and
from prokaryotes to nucleated cells, Philos. Trans. R. Soc. Lond. B Biol. Sci., 358,
59-85, (2003).
Table 3.2: Energy-yielding reactions of some lithoautotrophic

hyperthermophiles. (After K.O. Setter)
Energy-yielding reaction Genera
4H2 +CO2 → CH4 +2H2 O Methanopyrus, Methanothermus,

Methanococcus
H2 +S◦ → H2 S Pyrodictium, Thermoproteus,

Pyrobaculum, Acidianus,
Stygiolobus
4H2 +H2 SO4 → H2 S+4H2 O Archaeoglobus
record also supplies approximate dates for other events in evolution. For
example, the date at which molecular oxygen started to become abundant
in the earth’s atmosphere is believed to have been 2.0 billion years ago, with
equilibrium finally being established 1.5 billion years in the past. Multi-
cellular organisms appeared very late on the evolutionary and geological
time-scale — only 600 million years ago. By collecting such evidence, the
Belgian cytologist Christian de Duve has constructed the phylogenetic tree
shown in Figure 3.8, showing branching as a function of time. One very
interesting feature of this tree is the arrow indicating the transfer of “en-
dosymbionts” from the eubacteria to the eukaryotes. In the next section,
we will look in more detail at this important event, which took place about
1.8 billion years ago.
Symbiosis
The word “symbiosis” is derived from Greek roots meaning “living to-
gether”. It was coined in 1877 by the German botanist Albert Bernard
Frank. By that date, it had become clear that lichens are composite organ-
isms involving a fungus and an alga; but there was controversy concerning
whether the relationship was a parasitic one. Was the alga held captive and
exploited by the fungus? Or did the alga and the fungus help each other,
Fig. 3.8 Branching of the universal phylogenetic tree as a function of time. “Protists”
are unicellular eukaryotes.
the former performing photosynthesis, and the latter leeching minerals from
the lichen’s environment? In introducing the word “symbiosis” (in German,
“Symbiotismus”), Frank remarked that “We must bring all the cases where
two different species live on or in one another under a comprehensive con-
cept which does not consider the role which the two individuals play but
is based on the mere coexistence, and for which the term symbiosis is to
be recommended”. Thus the concept of symbiosis, as defined by Frank,
included all intimate relationships between two or more species, including
parasitism at one extreme and “mutualism” at the other. However, as the
word is used today, it usually refers to relationships which are mutually

beneficial.
Charles Darwin himself had been acutely aware of close and mutually
beneficial relationships between organisms of different species. For example,
in his work on the fertilization of flowers, he had demonstrated the way in
which insects and plants can become exquisitely adapted to each other’s
needs. However, T.H. Huxley, “Darwin’s bulldog”, emphasized competition
as the predominant force in evolution. “The animal world is on about the
same level as a gladiator’s show”, Huxley wrote in 1888, “The creatures are
fairly well treated and set to fight — whereby the strongest, the swiftest
and the cunningest live to fight another day. The spectator has no need to
turn his thumbs down, as no quarter is given”. The view of nature as a sort
of ”gladiator’s contest” dominated the mainstream of evolutionary thought
far into the 20th century; but there was also a growing body of opinion
which held that symbiosis could be an extremely important mechanism for
the generation of new species.
Among the examples of symbiosis studied by Frank were the nitrogen-
fixing bacteria living in nodules on the roots of legumes, and the mycorrhizal
fungi which live on the roots of forest trees such as oaks, beech and conifers.
Frank believed that the mycorrhizal fungi aid in the absorption of nutrients.
He distinguished between “ectotrophic” fungi, which form sheaths around
the root fibers, and “endotrophic” fungi, which penetrate the root cells.
Other examples of symbiosis studied in the 19th century included borderline
cases between plants and animals, for example, paramecia, sponges, hydra,
planarian worms and sea anemones, all of which frequently contain green
bodies capable of performing photosynthesis.
Writing in 1897, the American lichenologist Albert Schneider prophe-
sied that “future studies may demonstrate that.., plasmic bodies (within
the eukaryote cell), such as chlorophyll granules, leucoplastids, chromo-
plastids, chromosomes, centrosomes, nucleoli, etc., are perhaps symbionts
comparable to those in less highly specialized symbiosis. Reinke expresses
the opinion that it is not wholly unreasonable to suppose that some highly
skilled scientist of the future may succeed in cultivating chlorophyll-bodies
in artificial media”.
Nineteenth century cytologists such as Robert Altman, Andreas Schim-
per and A. Benda focused attention on the chlorophyll-bodies of plants,
which Schimper named chloroplasts, and on another type of subcellular
granule, present in large numbers in all plant and animal cells, which
Benda named mitochondria, deriving the name from the Greek roots mitos
(thread) and chrondos (granule). They observed that these bodies seemed
to reproduce themselves within the cell in very much the manner that might
be expected if they were independent organisms. Schimper suggested that
chloroplasts are symbionts, and that green plants owe their origin to a union
of a colorless unicellular organism with a smaller chlorophyll-containing
species.
The role of symbiosis in evolution continued to be debated in the 20th
century. Mitochondria were shown to be centers of respiratory metabolism;
and it was discovered that both mitochondria and chloroplasts contain their
own DNA. However, opponents of their symbiotic origin pointed out that
mitochondria alone cannot synthesize all their own proteins: Some mi-
tochondrial proteins require information from nuclear DNA. The debate
was finally settled in the 1970’s, when comparative sequencing of ribosomal
RNA in the laboratories of Carl Woese, W. Ford Doolittle and Michael Gray
showed conclusively that both chloroplasts and mitochondria were origi-
nally endosymbionts. The ribosomal RNA sequences showed that chloro-
plasts had their evolutionary root in the cyanobacteria, a species of eubac-
teria, while mitochondria were traced to a group of eubacteria called the
alpha-proteobacteria. Thus the evolutionary arrow leading from the eubac-
teria to the eukaryotes can today be drawn with confidence, as in Figure
3.8.
Cyanobacteria are bluish photosynthetic bacteria which often become
linked to one another so as to form long chains. They can be found to-
day growing in large colonies on seacoasts in many parts of the world, for
example in Baja California on the Mexican coast. The top layer of such
colonies consists of the phototrophic cyanobacteria, while the organisms in
underlying layers are heterotrophs living off the decaying remains of the
cyanobacteria. In the course of time, these layered colonies can become
fossilized, and they are the source of the layered rock formations called
stromatolites (discussed above). Geological dating of ancient stromatolites
has shown that cyanobacteria must have originated at least 3.5 billion years
ago.
Cyanobacteria contain two photosystems, each making use of a different
type of chlorophyll. Photosystem I, which is thought to have evolved first,
uses the energy of light to draw electrons from inorganic compounds, and
sometimes also from organic compounds (but never from water). Photosys-
tem II, which evolved later, draws electrons from water. Hydrogen derived
from the water is used to produce organic compounds from carbon diox-
ide, and molecular oxygen is released into the atmosphere. Photosystem II
never appears alone. In all organisms which possess it, Photosystem II is

coupled to Photosystem I, and together the two systems raise electrons to
energy levels that are high enough to drive all the processes of metabolism.
Dating of ancient stromatolites makes it probable that cyanobacteria began
to release molecular oxygen into the earth’s atmosphere at least 3.5 billion
years ago; yet from other geological evidence we know that it was only 2
billion years ago that the concentration of molecular oxygen began to rise,
equilibrium being reached 1.5 billion years ago. It is believed that ferrous
iron, which at one time was very abundant, initially absorbed the photo-
synthetically produced oxygen. This resulted in the time-lag, as well as the
ferrous-ferric mixture of iron which is found in the mineral magnetite.
When the concentrations of molecular oxygen began to rise in earnest,
most of the unicellular microorganisms living at the time found themselves
in deep trouble, faced with extinction, because for them, oxygen was a
deadly poison; and very many species undoubtedly perished. However,
some of the archaebacteria retreated to isolated anaerobic niches where
we find them today, while others found ways of detoxifying the poisonous
oxygen. Among the eubacteria, the ancestors of the alpha-proteobacteria
were particularly good at dealing with oxygen and even turning it to ad-
vantage: They developed the biochemical machinery needed for respiratory
metabolism.
Meanwhile, during the period between 3.5 and 2.0 billion years before
the present, an extremely important evolutionary development had taken
place: Branching from the archaebacteria, a line of large10 heterotrophic
unicellular organisms had evolved. They lacked rigid cell walls, and they
could surround smaller organisms with their flexible outer membrane, draw-
ing the victims into their interiors to be digested. These new heterotrophs
were the ancestors of present-day eukaryotes, and thus they were the an-
cestors of all multicellular organisms.
Not only are the cells of present-day eukaryotes very much larger than
the cells of archaebacteria and eubacteria; their complexity is also astonish-
ing. Every eukaryote cell contains numerous intricate structures: a nucleus,
cytoskeleton, Golgi apparatus, endoplasmic reticulum, mitochondria, per-
oxisomes, chromosomes, the complex structures needed for mitotic cell divi-
sion, and so on. Furthermore, the genomes of eukaryotes contain very much
more information than those of prokaryotes. How did this huge and rela-
tively sudden increase in complexity and information content take place?
10 Not large in an absolute sense, but large in relation to the prokaryotes.
According to a growing body of opinion, symbiosis played an important

role in this development.
The ancestors of the eukaryotes were in the habit of drawing the smaller
prokaryotes into their interiors to be digested. It seems likely that in a few
cases the swallowed prokaryotes resisted digestion, multiplied within the
host, were transmitted to future generations when the host divided, and
conferred an evolutionary advantage, so that the result was a symbiotic
relationship. In particular, both mitochondria and chloroplasts have def-
initely been proved to have originated as endosymbionts. It is easy to
understand how the photosynthetic abilities of the chloroplasts (derived
from cyanobacteria) could have conferred an advantage to their hosts, and
how mitochondria (derived from alpha-proteobacteria) could have helped
their hosts to survive the oxygen crisis. The symbiotic origin of other sub-
cellular organelles is less well understood and is currently under intense
investigation.
If we stretch the definition of symbiosis a little, we can make the concept
include cooperative relationships between organisms of the same species.
For example, cyanobacteria join together to form long chains, and they live
together in large colonies which later turn into stromatolites. Also, some
eubacteria have a mechanism for sensing how many of their species are
present, so that they know, like a wolf pack, when it is prudent to attack
a larger organism. This mechanism, called “quorum sensing”, has recently
attracted much attention among medical researchers.
The cooperative behavior of a genus of unicellular eukaryotes called
slime molds is particularly interesting because it gives us a glimpse of how
multicellular organisms may have originated. The name of the slime molds
is misleading, since they are not fungi, but heterotrophic protists similar to
amoebae. Under ordinary circumstances, the individual cells wander about
independently searching for food, which they draw into their interiors and
digest, a process called “phagocytosis”. However, when food is scarce,
they send out a chemical signal of distress. Researchers have analyzed the
molecule which expresses slime mold unhappiness, and they have found it
to be cyclic adenosine monophosphate (cAMP). At this signal, the cells
congregate and the mass of cells begins to crawl, leaving a slimy trail.
At it crawls, the community of cells gradually develops into a tall stalk,
surmounted by a sphere — the “fruiting body”. Inside the sphere, spores
are produced by a sexual process. If a small animal, for example a mouse,
passes by, the spores may adhere to its coat; and in this way they may be
transported to another part of the forest where food is more plentiful.
Thus slime molds represent a sort of missing link between unicellular

and multicellular or organisms. Normally the cells behave as individualists,
wandering about independently, but when challenged by a shortage of food,
the slime mold cells join together into an entity which closely resembles a
multicellular organism. The cells even seem to exhibit altruism, since those
forming the stalk have little chance of survival, and yet they are willing to
perform their duty, holding up the sphere at the top so that the spores will
survive and carry the genes of the community into the future. We should
especially notice the fact that the cooperative behavior of the slime mold
cells is coordinated by chemical signals.
Sponges are also close to the borderline which separates unicellular eu-
karyotes (protists) from multicellular organisms, but they are just on the
other side of the border. Normally the sponge cells live together in a mul-
ticellular community, filtering food from water. However, if a living sponge
is forced through a very fine cloth, it is possible to separate the cells from
each other. The sponge cells can live independently for some time; but if
many of them are left near to one another, they gradually join together
and form themselves into a new sponge, guided by chemical signals. In a
refinement of this experiment, one can take two living sponges of differ-
ent species, separate the cells by passing the sponges through a fine cloth,
and afterwards mix all the separated cells together. What happens next
is amazing: The two types of sponge cells sort themselves out and become
organized once more into two sponges — one of each species.
Slime molds and sponges hint at the genesis of multicellular organisms,
whose evolution began approximately 600 million years ago. Looking at the
slime molds and sponges, we can imagine how it happened. Some unicellular
organisms must have experienced an enhanced probability of survival when
they lived as colonies. Cooperative behavior and division of labor within the
colonies were rewarded by the forces of natural selection, with the selective
force acting on the entire colony of cells, rather than on the individual
cell. This resulted in the formation of cellular societies and the evolution
of mechanisms for cell differentiation. The division of labor within cellular
societies (i.e., differentiation) came to be coordinated by chemical signals
which affected the transcription of genetic information and the synthesis
of proteins. Each cell within a society of cells possessed the entire genome
characteristic of the colony, but once a cell had been assigned its specific
role in the economy of the society, part of the information became blocked
— that is, it was not expressed in the function of that particular cell.
As multicellular organisms evolved, the chemical language of intercellular
communication became very much more complex and refined. We will

discuss the language of intercellular communication in more detail in a
later section.
Geneticists have become increasingly aware that symbiosis has probably
played a major role in the evolution of multicellular organisms. We men-
tioned above that, by means of genetic engineering techniques, transgenic
plants and animals can be produced. In these chimeras, genetic material
from a foreign species is incorporated into the chromosomes, so that it is
inherited in a stable, Mendelian fashion. J.A. Shapiro, one of whose arti-
cles is referenced at the end of this chapter, believes that this process also
occurs in nature, so that the conventional picture of evolutionary family
trees needs to be corrected. Shapiro believes that instead of evolutionary
trees, we should perhaps think of webs or networks.
For example, it is tempting to guess that symbiosis may have played
a role in the development of the visual system of vertebrates. One of
the archaebacteria, the purple halobacterium halobium (recently renamed
halobacterium salinarum), is able to perform photosynthesis by means
of a protein called bacterial rhodopsin, which transports hydrogen ions
across the bacterial membrane. This protein is a near chemical relative of
rhodopsin, which combines with a carotinoid to form the “visual purple”
used in the vertebrate eye. It is tempting to think that the close simi-
larity of the two molecules is not just a coincidence, and that vertebrate
vision originated in a symbiotic relationship between the photosynthetic
halobacterium and an aquatic ancestor of the vertebrates, the host being
able to sense when the halobacterium was exposed to light and therefore
transporting hydrogen ions across its cell membrane.
In this chapter, we have looked at the flow of energy and information
in the origin and evolution of life on earth. We have seen how energy-rich
molecules were needed to drive the first steps in the origin of life, and how
during the evolutionary process, information was preserved, transmitted,
and shared between increasingly complex organisms, the whole process be-
ing driven by an input of energy. In the next chapter, we will look closely
at the relationships between energy and information.
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MOLECULAR BIOLOGY AND

recessive genes. In peas, dwarfism is a recessive characteristic, while tallness

40 INFORMATION THEORY AND EVOLUTION

MOLECULAR BIOLOGY AND EVOLUTION 41

42 INFORMATION THEORY AND EVOLUTION

chromosome as the gene for the male sex.

The structure of DNA

MOLECULAR BIOLOGY AND EVOLUTION 43

44 INFORMATION THEORY AND EVOLUTION

with A, and G with C. Therefore, if the sequence of bases on one strand

MOLECULAR BIOLOGY AND EVOLUTION 45

46 INFORMATION THEORY AND EVOLUTION

In the 1940’s, Garrod’s hypothesis was confirmed by experiments on

RNA and ribosomes

MOLECULAR BIOLOGY AND EVOLUTION 47

protein molecule is attached temporarily to a ribosome, but neither of the

The genetic code

48 INFORMATION THEORY AND EVOLUTION

MOLECULAR BIOLOGY AND EVOLUTION 49

50 INFORMATION THEORY AND EVOLUTION

Almost a hundred other restriction enzymes were subsequently discovered,

MOLECULAR BIOLOGY AND EVOLUTION 51

Table 3.1: The genetic code

TTT=Phe TCT=Ser TAT=Tyr TGT=Cys

52 INFORMATION THEORY AND EVOLUTION

have a nucleus. Instead, the DNA of the bacterial chromosome is arranged

MOLECULAR BIOLOGY AND EVOLUTION 53

could be “cloned”. The gene-spliced bacteria were chimeras, containing

54 INFORMATION THEORY AND EVOLUTION

The Polymerase Chain Reaction

MOLECULAR BIOLOGY AND EVOLUTION 55

95 ◦ C, so that the double-stranded DNA separates into single strands, and

56 INFORMATION THEORY AND EVOLUTION

Theories of chemical evolution towards the origin of life

MOLECULAR BIOLOGY AND EVOLUTION 57

58 INFORMATION THEORY AND EVOLUTION

Fig. 3.4 Miller’s apparatus.

MOLECULAR BIOLOGY AND EVOLUTION 59

Fig. 3.5 Products as a function of time in the Miller-Urey experiment.

observed was undoubtedly the Strecker synthesis: HCN + NH3 + RC=O + H2 O →

60 INFORMATION THEORY AND EVOLUTION

MOLECULAR BIOLOGY AND EVOLUTION 61

hypothesis, in a very few of these reactions, the reaction itself produced

62 INFORMATION THEORY AND EVOLUTION

Laureate geneticist Jack Sjostak at Harvard Medical School. The labora-

Molecular evidence establishing family trees in evolution

MOLECULAR BIOLOGY AND EVOLUTION 63

Fig. 3.6 Evolutionary relationships established by Dickerson and coworkers by com-

proved to be even more powerful tool for establishing evolutionary relation-

64 INFORMATION THEORY AND EVOLUTION

MOLECULAR BIOLOGY AND EVOLUTION 65

which takes place spontaneously at high temperatures, supplied the energy

and Methanobacterium, which is not. Group (3) includes Archaeoglobus, which is

66 INFORMATION THEORY AND EVOLUTION

MOLECULAR BIOLOGY AND EVOLUTION 67

Table 3.2: Energy-yielding reactions of some lithoautotrophic

Energy-yielding reaction Genera

4H2 +CO2 → CH4 +2H2 O Methanopyrus, Methanothermus,

H2 +S◦ → H2 S Pyrodictium, Thermoproteus,