All known extant (surviving) organisms are based on the same biochemical processes: genetic information encoded as nucleic acid (DNA, or RNA for viruses), transcribed into RNA, then translated into proteins (that is, polymers of amino acids) by highly conserved ribosomes. Perhaps most tellingly, the Genetic Code (the "translation table" between DNA and amino acids) is the same for almost every organism, meaning that a piece of DNA in a bacterium codes for the same amino acid as in a human cell. ATP is used as energy currency by all extant life. A deeper understanding of developmental biology shows that common morphology is, in fact, the product of shared genetic elements. For example, although camera-like eyes are believed to have evolved independently on many separate occasions, they share a common set of light-sensing proteins (opsins), suggesting a common point of origin for all sighted creatures. Another noteworthy example is the familiar vertebrate body plan, whose structure is controlled by the homeobox (Hox) family of genes.
There is also a large body of molecular evidence for a number of different mechanisms for large evolutionary changes, among them: genome and gene duplication, which facilitates rapid evolution by providing substantial quantities of genetic material under weak or no selective constraints; horizontal gene transfer, the process of transferring genetic material to another cell that is not an organism's offspring, allowing for species to acquire beneficial genes from each other; and recombination, capable of reassorting large numbers of different alleles and of establishing reproductive isolation. The Endosymbiotic theory explains the origin of mitochondria and plastids (e.g. chloroplasts), which are organelles of eukaryotic cells, as the incorporation of an ancient prokaryotic cell into ancient eukaryotic cell. Rather than evolving eukaryotic organelles slowly, this theory offers a mechanism for a sudden evolutionary leap by incorporating the genetic material and biochemical composition of a separate species. Evidence supporting this mechanism has been found in the protist Hatena: as a predator it engulfs a green algae cell, which subsequently behaves as an endosymbiont, nourishing Hatena, which in turn loses its feeding apparatus and behaves as an autotroph.
Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged when new metabolic processes appeared, and it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor or by detecting their physical manifestations. As an example, the appearance of oxygen in the earth's atmosphere is linked to the evolution of photosynthesis.
Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis (2nd ed.). Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.. ISBN 0-87969-608-7.
Douglas J. Futuyma (1998). Evolutionary Biology (3rd ed.). Sinauer Associates Inc.. pp. 108–110. ISBN 0-87893-189-9.
Haszprunar (1995). "The mollusca: Coelomate turbellarians or mesenchymate annelids?". In Taylor. Origin and evolutionary radiation of the Mollusca : centenary symposium of the Malacological Society of London. Oxford: Oxford Univ. Press. ISBN 0-19-854980-6.
Kozmik, Z; Daube, M; Frei, E; Norman, B; Kos, L; Dishaw, LJ; Noll, M; Piatigorsky, J (2003). "Role of Pax genes in eye evolution: A cnidarian PaxB gene uniting Pax2 and Pax6 functions". Developmental cell 5 (5): 773–85. doi:10.1016/S1534-5807(03)00325-3. PMID 14602077.
Kozmik, Z; Daube, Michael; Frei, Erich; Norman, Barbara; Kos, Lidia; Dishaw, Larry J.; Noll, Markus; Piatigorsky, Joram (2003). "Role of Pax Genes in Eye Evolution A Cnidarian PaxB Gene Uniting Pax2 and Pax6 Functions". Developmental Cell 5 (5): 773–785. doi:10.1016/S1534-5807(03)00325-3. PMID 14602077.
Land, M.F. and Nilsson, D.-E., Animal Eyes, Oxford University Press, Oxford (2002) ISBN 0-19-850968-5.
Chen FC, Li WH (2001). "Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees". Am J Hum Genet. 68 (2): 444–56. doi:10.1086/318206. PMC 1235277. PMID 11170892.
Okamoto N, Inouye I (2005). "A secondary symbiosis in progress". Science 310 (5746): 287. doi:10.1126/science.1116125. PMID 16224014.
Okamoto N, Inouye I (2006). "Hatena arenicola gen. et sp. nov., a katablepharid undergoing probable plastid acquisition". Protist 157 (4): 401–19. doi:10.1016/j.protis.2006.05.011