In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool. Evidence for common descent may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds have wings, even those that do not fly.
Today, there is debate over whether or not all organisms descended from a common ancestor, or a "last universal ancestor" (LUA), also called the "last universal common ancestor" (LUCA). The universality of genetic coding suggests common ancestry. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins, although exceptions to the basic twenty amino acids have been found. However, throughout history groupings based on appearance or function of species have sometimes been polyphyletic due to convergent evolution.
The "last universal ancestor" (LUA), or "last universal common ancestor" (LUCA), is the name given to the hypothetical single cellular organism or single cell that gave rise to all life on Earth 3.5 to 3.8 billion years ago[6]; however, this hypothesis has since been refuted on many grounds. For example, it was once thought that the genetic code was universal (see: universal genetic code), but many variations have been discovered[7] including various alternative mitochondrial codes.[8] Back in the early 1970s, evolutionary biologists thought that a given piece of DNA specified the same protein subunit in every living thing, and that the genetic code was thus universal. This was interpreted as evidence that every organism had inherited its genetic code from a single common ancestor, aka, an LUCA. In 1979, however, exceptions to the code were found in mitochondria, the tiny energy factories inside cells. Researchers studying human mitochondrial genes discovered that they used an alternative code, and many slight variants have been discovered since,[9] including various alternative mitochondrial codes,[10] as well as small variants such as Mycoplasma translating the codon UGA as tryptophan. Biologists subsequently found exceptions in bacteria and in the nuclei of algae and single-celled animals. For example, certain proteins may use alternative initiation (start) codons not normally used by that species.[11] In certain proteins, non-standard amino acids are substituted for standard stop codons, depending upon associated signal sequences in the messenger RNA: UGA can code for selenocysteine and UAG can code for pyrrolysine. Selenocysteine is now viewed as the 21st amino acid, and pyrrolysine is viewed as the 22nd. A detailed description of variations in the genetic code can be found at the NCBI web site.
It is now clear that the genetic code is not the same in all living things and this provides credence that all living things did not evolve on a firmly-rooted tree of life from a single LUCA. Further support that there is no LUCA has been provided over the years by horizontal/lateral gene transfer in both prokaryote and eukaryote single cell organisms. This is why phylogenetic trees cannot be rooted; why almost all phylogenetic trees have different branching structures, particularly near the base of the tree; and why many organisms have been found with codons and sections of their DNA sequence that are sometimes unrelated to other species.[12]
Information about the early development of life includes input from many different fields, including geology and planetary science. These sciences provide information about the history of the Earth and the changes produced by life. However, a great deal of information about the early Earth has been destroyed by geological processes over the course of time.
History of life
The chemical evolution from self-catalytic chemical reactions to life (see Origin of life) is not a part of biological evolution, but it is unclear at which point such increasingly complex sets of reactions became what we would consider, today, to be living organisms.
Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure and genetic code. Most scientists interpret this to mean all existing organisms share a common ancestor, which had already developed the most fundamental cellular processes, but there is no scientific consensus on the relationship of the three domains of life (Archaea, Bacteria, Eukaryota) or the origin of life. Attempts to shed light on the earliest history of life generally focus on the behavior of macromolecules, particularly RNA, and the behavior of complex systems.
The emergence of oxygenic photosynthesis (around 3 billion years ago) and the subsequent emergence of an oxygen-rich, non-reducing atmosphere can be traced through the formation of banded iron deposits, and later red beds of iron oxides. This was a necessary prerequisite for the development of aerobic cellular respiration, believed to have emerged around 2 billion years ago.
In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the Cambrian explosion (a period of unrivaled and remarkable, but brief, organismal diversity documented in the fossils found at the Burgess Shale) saw the creation of all the major body plans, or phyla, of modern animals. This event is now believed to have been triggered by the development of the Hox genes. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals, leading to the development of today's land ecosystems.
The evolutionary process may be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the history of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old. Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record.[13]. Such comparative studies however are invariably biased by disparities in the time scales over which evolutionary change is measured in the laboratory, field experiments, and the fossil record.
Horizontal gene transfer, and the history of life
The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly supplemented with phylogenetics - the reconstruction of phylogenies by the comparison of genetic (DNA) sequence.
"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."[14]
Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research", therefore "biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes."[15]
Future of life (cloning and synthetic organisms)
In modern terms, the category of organism cloning refers to the procedure of creating a new multicellular organism, genetically identical to another. However, cloning also has the potential of creating entirely new species of organisms. Organism cloning is the subject of much ethical debate (see Bioethics, Ethics of cloning, and Designer baby articles).
The J. Craig Venter Institute has recently assembled a synthetic yeast genome, Mycoplasma genitalium, by recombination of 25 overlapping DNA fragments in a single step. "The use of yeast recombination greatly simplifies the assembly of large DNA molecules from both synthetic and natural fragments."[16] Other companies, such as Synthetic Genomics, have already been formed to take advantage of the many commercial uses of custom designed genomes.
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