Evolution Genetics Population Genetics HLA MHC Inf & Imm Genetic Epidemiology Epidemiology Glossary Homepage
A Brief History of Life
M.Tevfik Dorak, M.D., Ph.D.
It is believed that
formation of the solar system started 4.6 billion years ago and life was
probably present on earth 4 billion years ago. The main source of energy was
heat (originated from accretion, radioactive decay and meteorite impacts). This
heat must have caused partial melting within the Earth resulting in separation
of molten metal core and silicate mantle and subsequently release of heat and
associated gases from the Earth’s interior (outgassing). The lack of oxygen
would have meant the lack of ozone layer. Thus, short wave solar UV light would
not have been absorbed. It is more likely that late outgassing occurred
producing a slightly more reducing than today’s atmosphere dominated by carbon
monoxide (CO) and nitrogen as N2 but also included sulphur dioxide (SO2), hydrogen (H2),
ammonia (NH3) and methane (CH4). There is little doubt that the Earth possessed a
hydrosphere (early oceans) 3.8 billion years ago. The evidence for this comes
from the ancient rocks at Isua in Greenland. This anoxic ocean would be rich in
soluble reduced (ferrous) iron. It is possible that in solutions containing
reduced iron, CO2 can be reduced to formaldehyde (HCHO) by
irradiation with UV light. This implies that reduced iron may have played an
important role as a source of reducing power in prebiotic chemistry. The primitive
atmosphere contained a lot of CO2, which is a
well-known greenhouse gas. In short, the environmental conditions under which
life arose on the primitive Earth were very different from those of today.
Among the theories on the
origin of life (App.1), the chemical theory originally proposed by Oparin and
Haldane and subsequently modified in 1980s is the most plausible one. Any
theory that is put forward should offer an explanation to the creation of the
basics of life: replication and metabolism. Evidence from extraterrestrial
environments, interstellar molecules and from other planets of the solar system
show that chemical evolution is able to produce organic molecules. It is
conceivable that the building blocks of life, amino acids and nucleic acid bases,
can be formed from the normal chemistry of carbon, hydrogen, oxygen, nitrogen
and sulphur. The pre-biotic chemistry would get enough energy to catalyse the
reactions from the Sun (short-wave UV light), electric discharges, and heat
(decay of radioactive elements, meteorite impacts and volcanic activity).
The essence of the
chemical theory is that life arose on Earth from organic molecules produced
abiogenically. It is believed that the appearance of life followed a period of
anaerobic chemical evolution and first protocells, organized replicating
systems and finally true cells evolved. This is the Oparin-Haldane theory first
proposed in 1920s. According to this scenario, organic molecules accumulated in
the oceans (primeval soup) and protocells and primitive cells obtained energy
using these chemicals (i.e., they were anaerobic heterotrophs). Once the most
likely substrates for prebiotic chemistry, hydrogen cyanide (HCN) and
formaldehyde (HCHO), were formed they would have to be concentrated to react further.
It has been proposed that clay particles provided surfaces where HCN, HCHO and
other molecules could be adsorbed and concentrated. If the chemicals are
available in enough quantities, more complex molecules can be produced from HCN
and HCHO in the presence of energy. For example HCHO can proceed to form sugars
(including riboses of nucleic acids DNA and RNA) from glycoaldehyde using UV
light or electrical discharges (formose reaction). Similarly, HCN can form
amino acids under mildly reducing conditions using the same energy sources.
Heating and cooling of these amino acids would generate protein-like
protenoids. Despite these advances made to explain the pre-biotic chemistry of
proteins, it has not yet been possible to come up with an idea to explain the
formation of nucleic acids in the primitive Earth.
An alternative theory
assumes that it was not the nucleic acids as in modern life forms but something
else in primitive life that acted as the replicating system. Cairns-Smith
proposed that electrically charged surfaces of clay particles might have been
the primitive replicating templates. It is thought that the distribution of
electrical charges on the clay surface acted as the genetic information and
ionic interactions with newly formed surface layers were the basis of
transmission of the information. The emergence of this idea coincided with
other evidence suggesting that the first type of metabolism that arose was
autotrophic. The energy may have been provided by the oxidation of ferrous iron
in iron-rich clays. It was also suggested that a primitive kind of
photosynthesis arose when iron-rich clays were exposed to UV radiation. The
most recent and comprehensive theory holds that the primitive ocean was too
dilute for all these reactions to occur and it must have all happened in the
atmosphere. There is no experimental support for this theory yet.
The common ancestor of
all life probably used RNA (ribosyme) as its genetic material. RNA can have
catalytic activity similar to that of protein enzymes so RNA can combine both a
genetic (informational) role and a functional (enzymatic) role. RNA is the
precursor of DNA and plays a role in several key cellular processes, including
DNA synthesis, translation and protein synthesis. The general idea is that RNA
was once the genetic material of early cells or protocells and DNA evolved
later. How RNA first arose is still a mystery. Reverse transcription, whereby
DNA is formed from RNA is an obvious route by which DNA could have arisen
eventually to replace RNA. Translation of RNA into proteins must have evolved
before switching to the DNA. Several theories have been put forward to explain
the evolution of translation.
Whatever may have happened before its emergence, the first organisms
that have left living descendants were simple unicellular prokaryotes. These
cells lack a true nucleus (eu-karyon), mitochondria or chloroplasts. They
probably first emerged 4 billion years ago and dominated the Earth for the next
2 billion years (the age of prokaryotes). The universal ancestor cell followed
three distinct pathways:
1. Evolution of Archaebacteria (prokaryotes; thermophilic Sulphobacteria
/ sulfobacteria, methanobacteria, halophilic bacteria)
2. Evolution of Eubacteria (prokaryotes; ordinary bacteria and Cyanobacteria
-blue-green algae-)
3. Evolution of nuclear line to form Eukaryotes (and eventually
protists, fungi, plants, animals) (nearly all are aerobic)
The great majority of modern eukaryotes arose through the association of
two or more different prokaryotes (a host anaerobic prokaryote engulfing an
aerobic one as its mitochondria or chloroplast). Molecular phylogenetic studies
using the rRNA sequencing data (since it has a very slow evolutionary rate it
is suitable for the analysis of organisms with a long evolutionary history)
showed that Sulphobacteria evolved least from the universal ancestor cell.
Archaebacteria as a whole group diverged less than either Eukaryotes or
Eubacteria from the universal ancestor and remain closest to it. There are also
other features of cells that suggest the same, for example, their membrane
lipids are ether-linked whereas eubacteria and eukaryotes have ester-linked
membrane lipids. There is no evidence to suggest that Archaebacteria are the
ancestor of Eubacteria and Eukaryotes, therefore, it is generally believed that
the ancestral life form gave rise to three groups.
One great transformation
in the evolution of early life forms was the shift from anoxic to
oxygen-containing atmosphere resulted from the oxygen released by
photosynthetic Cyanobacteria. Therefore, Cyanobacteria are photo-autotrophs
(see App.2). They use light as a source of energy, and CO2 as a source of carbon (photosynthesis). Heterotrophs,
on the other hand, use organic molecules synthesized outside their body as a
source of energy and carbon (aerobic respiration). In all life forms, energy is
obtained from high energy electrons during cyclic or non-cyclic electric
transport schemes during which the energy is transferred to and stored into the
universal energy currency ATP and low energy electrons are released at the end.
An exception to this general scheme is the fermenters who store their energy in
the form of proton motive force (PMF) as well as ATP. In some photo-autotrophs,
electrons are energised thorough the absorption of light by a special
light-sensitive pigment (bacteriorhodopsin) and then transferred to other
electron carriers.
In chemo-autotrophs, high
energy electrons are obtained from an external, inorganic substance.
Sulphobacteria use hydrogen sulfide (H2S) as the energy source and
the electron acceptor for the low energy electrons is oxygen, which is reduced
to water. Hydrothermalism, particularly in deep sea vents, maintains the
bacterial life of sulphobacteria and/or methanobacteria. Some species use
substances such as nitrate and reduce it to nitrite. Autotrophs can also
assimilate carbon from a simple inorganic molecule into complex organic
molecules. The most widespread way of doing this is the Calvin cycle that fixes
C from simple molecules like CO2 into their organic molecules. The Calvin
cycle is found in many photosynthetic Eubacteria and all green Eukaryotes.
Heterotrophs have
variation in the terminal electron acceptor. It is oxygen in aerobic
respiration and sulphate or nitrate in anaerobic respiration. When there is no
electron acceptor, fermentation under anaerobic conditions occurs resulting in
formation of lactic acid. This may be the only system in some prokaryotes and
is an emergency system in others.
The main feature of
Archaebacteria is that they live in extreme conditions. Sulphobacteria live in
extreme heat and in environments rich in sulphur including deep-sea
hydrothermal vents and coastal mud flats. Sulphobacteria are anaerobic
chemo-autotrophs (the genome of one of them, Sulfolobus
solfataricus, has been sequenced; see She
et al, 2001). If the hot spring scenario is correct, the Sulphobacteria
should closely resemble the ancestral prokaryotes. Methanogens are obligate
anaerobes, and Halobacteria
grow in very salty environments (usually aerobic heterotrophs). The Calvin
cycle is generally absent in Archaebacteria.
Eubacteria are more
diverged than Archaebacteria. They use several types of energy metabolism. In
this group, purple bacteria and Gram(+) bacteria are chemo-autotrophs and
Cyanobacteria are oxygenic photo-autotroph, many are heterotrophic with either
anaerobic or aerobic respiration. Chlamydia have no energy metabolism at all.
They depend on their hosts as parasites for eukaryotic cells. By evolving
oxygen respiration 3.5 billion years ago, Cyanobacteria enabled the eukaryotic
lineage to become aerobic (not immediately though. The atmosphere became rich
in oxygen only 2 billion years ago as iron acted as oxygen sink). When oxygen
was plentiful in the atmosphere, it was difficult for anaerobic cells to
survive. Some retreated to inhospitable and relatively anaerobic environments
and some acquired aerobic bacteria as endosymbionts (see below). The
phylogenetic relationships suggest that aerobic heterotrophs (like all aerobic
animals) and chemo-autotrophs (gram+ bacteria) evolved from early
photo-autotrophs. This implies that using light as an energy source may be just
as ancient as fermenting organic compounds. As an oxygenic photo-autotroph,
Cyanobacteria use two molecules of water as the electron donor and oxidize it
to oxygen while releasing four electrons. By releasing oxygen, they changed the
environmental conditions (ozone formation) and enabled the evolution of aerobic
respiration.
The autotrophic nature of
early life on Earth has been suggested by stromatolite (characteristic
structures formed by Cyanobacteria) fossils on Precambrian rocks and carbon
isotope ratios confirming that autotrophs fixing carbon via the Calvin cycle
must have existed for 3.5 billion years. Bacteria are the only life forms found
in the rocks for a long time (3.5 to 2.1 billion years ago). Eukaryotes were
numerous 1.9 to 2.1 billion years ago and fungi-like things appeared about 0.9
billion years ago.
Evolution of eukaryotes
from a presumed bacteria-like ancestor is one of the major events in
evolutionary history. They have a distinct nucleus, organelles involved in
energy metabolism (mitochondria and chloroplast), extensive internal membranes
and a cytoskeleton of protein fibers and flaments. Chloroplasts
(photosynthesis) in green plants and algae originated as free living bacteria
related to the cyanobacteria [the chloroplastic DNA is more similar to
free-living Cyanobacteria DNA than to sequences from the plants the
chloroplasts reside in]. The eukaryotic mitochondria (ATP synthesis) are
endosymbionts like chloroplasts. Mitochondria were acquired when aerobic Eubacteria
were engulfed by anaerobic host cells. As they conferred useful functions like
aerobic respiration and photosynthesis (chloroplasts), they were retained as
endosymbionts. This must have happened after the nucleus was acquired by the
eukaryotic lineage. The origin of eukaryotic nucleus is almost certainly
autogenous and not a result of endosymbiosis. Mitochondria are believed to have
originated from an ancestor of the present-day purple photosynthetic bacteria
that had lost its capacity for photosynthesis (chloroplasts from an ancestral
Cyanobacterium).
Animals start appearing
prior to the Cambrian, about 600 million years ago. The earliest known animals
occur in the widespread late Precambrian Ediacaran fauna (c. 620-550 Ma). The
Cambrian explosion (radiation), one of the most important events in the history
of life, began about 540 Ma at the start of the Cambrian period. This is the
largest radiation ever recorded. All the phyla of animals (except the subphylum
vertebrates) appeared around the Cambrian. This explosion may be due to the
availability of oxygen in large amounts enabling large animals to evolve. The
oldest known vertebrates (armored-jawless fish) appeared first in Ordovician
(510-439 Ma). The second part of Carboniferous saw the evolution of the first
reptiles, a group that evolved from amphibians and lived entirely on land.
About 380 million years ago, during the Devonian period, a group of fishes
evolved limbs and began to leave the water. All tetrapods (amphibians,
reptiles, birds and mammals) evolved as a result of this move. During the
Permian period (290-245 Ma), the Earth’s land areas became welded into a single
landmass (Pangaea). Many forms of marine animals disappeared and the reptiles
spread rapidly. The land was first colonized by lung-bearing fish about 250 Ma
and then by amphibians. The Mesozoic era is known as the age of reptiles from
which mammals and later birds evolved. The first mammals appeared in the
beginning of Mesozoic, during Triassic. Mammals had an adaptive radiation in
Paleocene following the mass extinction at late Cretaceous. First anhtropoid
appeared in Miocene about 20 Ma. The Pliocene epoch is the climax of the age of
mammals. The Pleistocene is marked by an abundance of large mammals.
All land plants evolved
from the green algae or Chlorophyta. In the period before the Permian (the
Carboniferous), the landscape was dominated by seedless ferns and their
relatives. Vascular plants first appeared in Silurian (439-409 Mya). After the
Permian extinction, gymnosperms became more abundant. They evolved seeds and
pollens (encased sperm). The angiosperms evolved from the gymnosperms during
the early Cretaceous about 140-125 Mya. They further diversified and dispersed
during the late Cretaceous (97.5-66.5 Mya). Currently, over three fourths of
all living plants are angiosperms. The angiosperms developed a close contact
with insects which promoted cross-pollination and resulted in more vigorous
offspring. Their generation time to reproduce is short, and their seeds can be
dispersed by animals. For these reasons, the angiosperms were able to travel
and disperse all around the world. The important events in the evolution of the
angiosperms were the evolution of showy flowers (to attract insects and birds),
the evolution of bilaterally symmetrical flowers (adaptation for specialized
pollinators), and the evolution of larger and more mobile animals (to disperse
fruits and seeds).
Appendix 1. Theories on the origin of life:
1. Divine creation
2. Spontaneous generation
3. Extraterrestrial theories (panspermia)
4. Chemical theory
Appendix 2. Metabolism in prokaryotes:
1. Autotrophs
a. photo-autotrophs (photosynthetic)
i. anoxygenic
ii. oxygenic (only in Cyanobacteria) (see Lecture
Note on Photosynthesis)
b. chemo-autotroph (Sulphobacteria)
2. Heterotrophs (they
make their food by oxidation of nitrogen, sulphur or other elements; they are
uncommon)
a. aerobic respiration (most Halobacteria)
b. anaerobic respiration (Methanogens)
Appendix 3. Possibilities on the first living cell:
1. Photo-autotroph: As an
anaerobic but oxygenic photosynthetic prokaryote Cyanobacteria is the strongest
candidate. It makes its own food and this is fueled by light. The fossil
evidence (stromatolite and oncolite) for their existence and carbon isotope
ratio suggesting oxygenic photosynthesis took place by 3.5 billion years ago
supports this idea.
or
2. Chemo-autotroph (chemosynthetic): If the hot-spring scenario is
correct, it would have to be Sulphobacteria. This anaerobic thermophilic
bacteria use H2S as electron donor (see Sulfur Cycle).
It does not use the Calvin cycle.
Whatever it was, the first living cell replicated by a mechanism not
based on nucleic acids. There is not enough evidence to support the suggestions
that either heterotrophs or fermenters may have been the first living cells.
see also http://www.ucmp.berkeley.edu/alllife/threedomains.html
Lecture Note on the Origin of Life
Zimmer C: How and Where Did Life on Earth Arise? Science
2005 (July 1)
M.Tevfik
Dorak, MD, PhD
Last updated 23 January
2007
Evolution Genetics Population Genetics HLA MHC Inf & Imm Genetic Epidemiology Epidemiology Glossary Homepage