Precambrian/Life origins

Welcome to the Wikiversity learning project for Life Origins. Participants in this project explore key originating steps in the evolution of life including the abiotic origin of life, the endosymbiotic origin of eukaryotes, the origin of action potentials and brains, the origin of the human species and the origin of human language.

Organization of this learning project
At least initially, there are page sections with short introductions and a list of suggested reading. Participants should feel free to learn by editing, in particular, feel free to start subsections for questions and discussion.

Origin of life
Early speculations about the origin of life were very limited due to the difficulty in revealing details of the chemical basis of life. Naturalists like Darwin could express vague suspicions about the boundary between non-living chemical systems and life, but it was not clear what constituted the most simple forms of life. Experimentalists such as Pasteur began to test how easy it is to make the transition from non-living chemical systems to microbial life, but they had no understanding of the likely differences between environmental conditions in the current biosphere of Earth and conditions when life first arose.
 * Darwin - Darwin (1809-1882) was reluctant to speculate about the origin of life, but in private he speculated that chemical reactions alone, "in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity," might have been the origin of life.
 * Louis Pasteur (1822–1895) and the debate of spontaneous generation. When natural selection first became known as a mechanism for change in living systems, very little was known about life at the microscopic level. It was not clear if transition from non-living chemistry to living cells was something that might easily take place at any time. Pouchet (1800-1872) claimed that boiled water and hay provided suitable conditions for the generation of new microbes. Pasteur showed that Pouchet's methods allowed living microbes back into the boiled hay after cooling. After heat sterilization, if care is taken to prevent contamination by living microbes, sterilized materials remain sterile. See: Louis Pasteur. Achievements and disappointments, 1861 by J. R. Porter (1961), starting on page 394.

Modern era
In the early 1900s biochemistry continued to mature, genetics began as a science and viruses began to be appreciated as very small biologically active agents near the boundary between non-living chemical systems and living cells. It became widely recognized that free oxygen on Earth is of biological origin, with profound implications for the abiotic production of organic molecules.
 * viruses and the boundary between replication chemicals and living organisms: The origin of life (1927) Viruses as non-living chemical systems that can replicate their genetic material by "taking over" living cells: viruses begin to provide a good model of the boundary between life and non-life.
 * Alexander Oparin (1894–1980) - idea that Earth's atmosphere did not have free oxygen when life began. In thinking about the transition from non-living chemical systems to life, it is important to take into account the actual chemical environment of the early Earth.
 * An example of early concerns about the evolvability of complex metabolic pathways: On the Evolution of Biochemical Syntheses (1945) by N. H. Horowitz
 * On the Early Chemical History of the Earth and the Origin of Life (1952) by Harold Urey (1893–1981)
 * Miller-Urey experiment. "Organic compound synthesis on the primitive earth" in Science (1959) Volume 130, pages 245-251.
 * The origin of self-replicating systems of macro-molecules. On the Origin of Macromolecular Sequences by Howard H. Pattee in Biophys J. (1961) Volume 1, pages 683–710. Leading up to the existence of a genetic code, can there be processes of "molecular selection" acting on the formation, survival, and eventually, self-replication of polymers?
 * Hydrogen cyanide dimer and chemical evolution by Robert M. Kliss and Clifford N. Matthews (1962). Speculation about abiotic formation of polymers with C-C-N backbones. What polymers might have been the first to form under abiotic conditions? See also:
 * Prebiological protein synthesis by C. N. Matthews and R. E. Moser (1966).
 * Synthesis of biologically pertinent peptides under possible primordial conditions by G. Steinman and M. N. Cole (1967).
 * The condensation of the adenylates of the amino acids common to protein by Gottfried Krampitz and Sidney W. Fox (1969).
 * An approach to the evolution of metabolism by Robert E. Eakin (1963). Early speculation about possible abiotic metabolism with high-energy phosphate-containing molecules. What types of catalysis would have predominated before enzymes existed?
 * The origins of life (1964) by George Wald (1906–1997). Discussion of issues such as why carbon is used in living organisms, not silicon.

Although biologists and biochemists have constructed their ideas about the origin of life upon the tenet of the "reducing atmosphere" (i.e. containing no free-oxygen), geologists have never been unanimous. /The Ecopoesis model/ is a recent proposal for a new approach to the issue.

Enzymes vs genes
The "classical" period of molecular biology revealed the capacity of nucleic acid molecules to function as genetic molecules. Proteins were thought of as the critically important biological catalysts in control of the chemistry of life. All life on Earth depends on a complex process by which genetic information stored in nucleic acid sequences is converted into the structure of proteins.

Francis Crick speculated about possible stages by which an initially simple translation system with a few amino acid types might have evolved into the more complex code used by existing organisms. At that time, everyone thought of proteins as the only kind of enzymes and ribozymes had not yet been found. However, even this speculation about an initially simplified genetic code did not generate much enthusiasm for the idea that a translation system depending on many proteins could evolve from a pre-biological "organic soup". The origin of translation appeared to be an impossible chicken-or-egg problem. Faced with this conceptually baffling problem, Crick and Orgel speculated about the possibility that the original production of living systems might be a very rare event, but once it had happened once it might be spread by intelligent life forms using space travel, a process they called "Directed Panspermia".

Related resource: Origin of translation

Ribozyme era
The conceptual log-jam in origin of life research was broken by a new fundamental biological discovery made in the 1980s: enzymatically-active RNA.

In a retrospective article, Crick and Orgel noted that they had been overly pessimistic about the chances of abiogenesis on Earth when they had assumed that some kind of self-replicating protein-based system was the molecular origin of life. With the discovery of ribozymes it became possible to imagine an RNA world and the origin of life in the form of possibly a single self-replicating polymer that could function as both a genetic molecule and as a source of enzymatic activities. See also: the RNA World learning resource at Wikiversity.

The fact that RNA is not a particularly stable molecule immediately raises thoughts about the possibility of some other polymer that was more stable than RNA serving as the first genetic molecule. Also, some interest began to shift from the problem of abiotic synthesis of polymers to the related problem of stabilizing useful polymers once they were created.

Another conceptual change from about the same time as the discovery of ribozymes was recognition that many microbes are not dependent on sunlight for energy. New knowledge of microbes that harvest chemical energy in deep sea and deep ground environments, including a diverse collection of extremophiles, has broadened thinking about the possibilities for early chemical systems that might have made the transition to a living state. Reviewed by Ronald F. Fox (1993). Stuart Kauffman - Wikipedia article.
 * A model for the RNA-catalyzed replication of RNA by T. R. Cech (1986).
 * Selection by differential molecular survival: a possible mechanism of early chemical evolution by Christian de Duve (1987).
 * An all-purine precursor of nucleic acids by G. Wächtershäuser (1988).
 * Before enzymes and templates: theory of surface metabolism by G. Wächtershäuser (1988).
 * Two-dimensional life? Christian de Duve and Stanley L. Miller (1991).
 * Evolution of the first metabolic cycles by G. Wächtershäuser (1990).
 * The deep, hot biosphere by T. Gold (1992).
 * Impact melting of frozen oceans on the early Earth: Implications for the origin of life by J. L. Bada, C. Bigham and Stanley L. Miller (1994). Snowball Earth - at Wikipedia.
 * Geomicrobiology of the Ocean Crust: A Role for Chemoautotrophic Fe-Bacteria by Katrina J. Edwards, Wolfgang Bach and Daniel R. Rogers (2003).
 * Review of Stuart Kauffman, The Origins of Order: Self-Organization and Selection in Evolution

Life: Classification and Origins
What are the evolutionary origins of Earth's major forms of life?

Thomas Cavalier-Smith reviewed the issue of life form origins in Deep phylogeny, ancestral groups and the four ages of life. In his Figure 1 (image shown to the right), the origin of Eukaryotes is emphasized.

It has been proposed that early eukaryotic cells had an endomembrane system and membrane-delineated nucleus. Around 850,000,000 years ago, mitochondria originated as endocytosed bacteria.

Figure 1 shows three kinds of photosynthetic life forms (green), categorized as chromista, plants and photosynthetic bacteria. The two types of photosynthetic eukaryotes originated by endocytosis of cyanobacteria. Microfossil evidence indicates that bacteria were the earliest form of life on Earth. Cavalier-Smith's Figure 3 (image shown to the right) divides the bacteria into two major forms, negibacteria, with two distinct lipid bilayer membranes, and the unimembrana. Cavalier-Smith further divides the unimembrana into Posibacteria and Archaebacteria.

Related resource: Bacterial fossil structure and preservation.

Cavalier-Smith has suggested that enough oxygenic photosynthesis took place approximately 2,500,000,000 years ago to cause removal of methane from the atmosphere, resulting in a Palaeoproterozoic global freeze.

Anaerobic photosynthetic bacteria similar to extant Chloroflexi probably existed prior to the evolution of Photosystem II. Stromatolites have been reported that date to over 3,000,000,000 years old.

Related resources

 * RNA World - was RNA the primordial macromolecule of life?
 * Human Genetic Uniqueness Project - what is unique about humans?
 * The concept of irreducible complexity - is translation an irreducibly complex biological process?
 * Theoretical model protocell that should be realizable in the lab
 * Evolution of life