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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:
a. photo-autotrophs (photosynthetic)
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.
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 The Phylogeny of Life (Berkeley)
BBC Nature: History of Life on Earth
Zimmer C: How and Where Did Life on Earth Arise? Science 2005 (July 1)
M.Tevfik Dorak, MD, PhD
Last updated 2 February 2012
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