In biology, evolution is a change in the traits of living organisms over generations. The common definition of the word in popular science includes the emergence of new species as a product of evolution as well. Since the development of modern genetics in the 1940s, evolution has been defined more specifically as a change in the frequency of alleles (alternative forms of the same gene) in a population from one generation to the next. In other fields evolution is used more generally to refer to any process of change over time.
One of the first coherent theories of biological evolution was proposed in the early 19th century by Jean-Baptiste Lamarck, though it did not meet with widespread approval. With the publication of Charles Darwin and Alfred Russel Wallace's joint paper in 1858 followed by Darwin's book Origin of Species in 1859, the theory of evolution by natural selection became firmly established within the scientific community and rapidly caught the public imagination. In the 1930s, work by a number of scientists combined Darwinian natural selection with the re-discovered theory of heredity proposed by Gregor Mendel to create the modern evolutionary synthesis. In the modern synthesis, "evolution" means a change in the frequency of an allele within a gene pool. This change may be caused by a number of different mechanisms: natural selection, genetic drift or changes in population structure (gene flow).
In common parlance the word "evolution" is often used as shorthand for the modern synthesis of evolution, including the theory that all extant species share a common ancestor. It also is often used to describe the mechanisms which act to change populations over time.
The theory underlying the modern synthesis has three major aspects:
- The common descent of all organisms from a single ancestor.
- The origin of novel traits in a lineage.
- The mechanisms that cause some traits to persist while others perish.
The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. In plain English, people use the word "theory" to signify "conjecture", "speculation", or "opinion". In contrast, a scientific theory is a model of the world (or some portion of it) from which falsifiable hypotheses can be generated and be verified through empirical observation. In this sense, "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship — for example, it is a "fact" that an apple dropped on earth will fall towards the center of the planet in a straight line, and the "theory" which explains it is the current theory of gravitation. Currently, the modern synthesis is the most powerful theory explaining variation and speciation, and within the science of biology, it has completely replaced earlier accepted explanations for the origin of species, including creationism and Lamarckism.
Ancestry of organisms
A group of organisms is said to have common descent if they have a common ancestor. 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 — even those which do not fly — have wings. Today, the theory of evolution has been strongly confirmed by the science of DNA genetics. For example, every living thing makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations) to translate nucleic acid sequences into proteins. Because the selection of these traits is somewhat arbitrary, their universality strongly suggests common ancestry.
In addition, abiogenesis — the generation of life from non-living matter — has never been observed, indicating that the origin of life from non-life is either extremely rare or only happens under conditions very unlike those of modern Earth. The 1953 Miller-Urey experiment suggests that conditions on the ancient earth may have permitted abiogenesis.
Since abiogenesis is rare or impossible under modern conditions and the evolutionary process is exceedingly slow, the diversity and complexity of modern life requires that the Earth be very old, on the order of billions of years. This is compatible with geological evidence that the Earth is approximately 4.6 billion years old. (See Timeline of evolution.)
Information about the early development of life includes input from the fields of geology and planetary science. These sciences provide information about the history of the Earth and the changes produced by life. A great deal of information about the early Earth has been destroyed by geological processes over the course of time.
Evidence of evolution
Fossils are important for estimating when various lineages developed. As fossilization is an uncommon occurrence, usually requiring hard parts (like bone) and death near a site where sediments are being deposited, the fossil record only provides sparse and intermittent information about the evolution of life. Fossil evidence of early life is sparse before the evolution of organisms with hard body parts, such as shell, bone, and teeth, but exists in the form of ancient microfossils and the fossilization of ancient burrows and a few soft-bodied organisms.
Nevertheless, fossil evidence of prehistoric organisms has been found all over the Earth. The age of fossils can often be deduced from the geologic context in which they are found; and their absolute age can be verified with radiometric dating. Some fossils bear a resemblance to organisms alive today, while others are radically different. Fossils have been used to determine at what time a lineage developed, and can be used to demonstrate the continuity between two different lineages through transitional fossils. Paleontologists investigate evolution largely through analysis of fossils.
Phylogeny, the study of the ancestry of species, has revealed that structures with similar internal organization may perform divergent functions. Vertebrate limbs are a common example of such homologous structures. A vestigial organ or structure may exist with little or no purpose in one organism, though they have a clear purpose in others. The human wisdom teeth and appendix are common examples.
Genetic sequence evidence
Comparison of the genetic sequence of organisms reveals that organisms that are phylogenetically close have a higher degree of sequence similarity than organisms that are phylogenetically distant. For example, neutral human DNA sequences are approximately 1.2% divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6% from gorillas , and 6.6% from baboons. Sequence comparison is considered such a robust measure that it is sometimes used to correct mistakes in the phylogenetic tree, in instances where other evidence is scarce.
Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA which are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration.
Since metabolic processes do not leave fossils, research into the evolution of the basic cellular processes is also done largely by comparison of existing organisms. Many lineages diverged at different stages of development, so it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor.
Origin of life
Not much is known about the earliest development of life. However, all existing organisms share certain traits, including the cellular structure, and the 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 (Archea, 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.
History of life
Though the origins of life are murky, other milestones in the evolutionary history of life are well-known. 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 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 land ecosystems with which we are familiar.
Emergence of novel traits
Mechanisms of inheritance
In Darwin's time, scientists did not share broad agreement on how traits were inherited. Today most inherited traits are traced to discrete, persistent entities called genes, encoded in linear molecules called DNA. Though by and large faithfully maintained, DNA is both variable across individuals and subject to a process of change or mutation (described below).
However, other non-DNA based forms of heritable variation exist. The processes that produce these variations leave the genetic information intact and are often reversible. This is called epigenetic inheritance and may include phenomena such as DNA methylation, prions, and structural inheritance. Investigations continue into whether these mechanisms allow for the production of specific beneficial heritable variation in response to environmental signals. If this is shown to be the case, then some instances of evolution would lie outside of the typically Darwinian framework, which avoided any connection between environmental signals and the production of heritable variation.
Darwin did not know the source of variations in individual organisms, but observed that it seemed to be by chance. Later work pinned much of this variation onto mutations. Mutations are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by "copying errors" in the genetic material during cell division and by exposure to radiation, chemicals, or viruses, or can occur deliberately under cellular control during processes such as meiosis or hypermutation. In multicellular organisms, mutations can be subdivided into germline mutations, which can be passed on to progeny and somatic mutations, which (when accidental) often lead to the malfunction or death of a cell and can cause cancer.
Mutations serve to introduce novel genetic variation, upon which selection may (or may not, see Neutral mutations) act. Neutral mutations do not affect the organism's chances of survival in its natural environment and can accumulate over time.
Differential survival of traits
While mutation can create new alleles, other factors influence the frequency of existing alleles. These factors mean that some characteristics will become more frequent while others diminish or are lost entirely. There are three known processes that affect the survival of a characteristic; or, more specifically, the frequency of an allele:
Natural selection is based on differential survival and reproduction rates as a result of the environment. Differential mortality is the survival rate of individuals before their reproductive age. If they survive, they are then selected further by differential fertility — that is, their total genetic contribution to the next generation. The central role of natural selection in evolutionary theory has given rise to a strong connection between that field and the study of ecology.
Natural selection can be subdivided into two categories:
- Ecological selection occurs when organisms which survive and reproduce increase the frequency of their genes in the gene pool over those which do not survive.
- Sexual selection occurs when organisms which are more attractive to the opposite sex because of their features reproduce more and thus increase the frequency of those features in the gene pool.
Natural selection also operates on mutations in several different ways:
- Purifying or background selection eliminates deleterious mutations from a population.
- Positive selection increases the frequency of a beneficial mutation.
- Balancing selection maintains variation within a population through a number of mechanisms, including:
Mutations that are not affected by natural selection are called neutral mutations. Their frequency in the population is governed entirely by genetic drift and gene flow. It is understood that an organism's DNA sequence, in the absence of selection, undergoes a steady accumulation of neutral mutations. The probable mutation effect is the proposition that a gene that is not under selection will be destroyed by accumulated mutations. This is an aspect of genome degradation.
- Selection of organisms for desirable characteristics, when done by humans, e.g. for agriculture or as pets, is called artificial selection.
- Baldwinian evolution refers to the way human beings, as cultured animals capable of symbolic (extrasomatic) learning, can change their environment, or the environment of any species, in such a way as to result in new selective forces.
Genetic drift describes changes in allele frequency from one generation to the next due to sampling variance. The frequency of an allele in the offspring generation will vary according to a probability distribution of the frequency of the allele in the parent generation.
Many aspects of genetic drift depend on the size of the population (generally abbreviated as N). This is especially important in small mating populations, where chance fluctuations from generation to generation can be large. Such fluctuations in allele frequency between successive generations may result in some alleles disappearing from the population. Two separate populations that begin with the same allele frequency might, therefore, "drift" by random fluctuation into two divergent populations with different allele sets (for example, alleles that are present in one have been lost in the other).
The relative importance of natural selection and genetic drift in determining the fate of new mutations also depends on the population size and the strength of selection: when N times s (population size times strength of selection) is small, genetic drift predominates. When N times s is large, selection predominates. Thus natural selection is 'more efficient' in large populations, or equivalently, genetic drift is stronger in small populations. Finally, the time for an allele to become fixed in the population by genetic drift (that is, for all individuals in the population to carry that allele) depends on population size, with smaller populations requiring a shorter time to fixation.
Gene flow (or gene admixture) is the only mechanism whereby populations can become closer genetically while building larger gene pools. Migration of one population into another area occupied by a second population can result in gene flow. Gene flow operates when geography and culture are not obstacles.
Through the process of natural selection, species become better adapted to their environments. Adaptation is any evolutionary process that increases the fitness of the individual, or sometimes the trait that confers increased fitness, e.g. a stronger prehensile tail or greater visual acuity. Note that adaptation is context-sensitive; a trait that increases fitness in one environment may decrease it in another.
Most biologists believe that adaptation occurs through the accumulation of many mutations of small effect. However, macromutation is an alternative process for adaptation which involves a single, very large scale mutation.
Speciation and extinction
Speciation is the creation of two or more species from one. There are various mechanisms by which this may take place. Allopatric speciation begins when subpopulations of a species become isolated geographically, for example by habitat fragmentation or migration. Sympatric speciation occurs when new species emerge in the same geographic area. Ernst Mayr's peripatric speciation is a type of speciation that exists in between the extremes of allopatry and sympatry. Peripatric speciation is a critical underpinning of the theory of punctuated equilibrium.
Extinction is the disappearance of species (i.e. gene pools). The moment of extinction is generally considered to be the death of the last individual of that species. Extinction is not an unusual event in geological time — species are created by speciation, and disappear through extinction.
Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time. Evolutionary biology is a kind of meta field because it includes scientists from many traditional taxonomically oriented disciplines. For example, it generally includes scientists who may have a specialist training in particular organisms such as mammalogy, ornithology, or herpetology but use those organisms as systems to answer general questions in evolution.
Evolutionary biology as an academic discipline in its own right emerged as a result of the modern evolutionary synthesis in the 1930s and 1940s. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term evolutionary biology in their titles.
Evolutionary developmental biology
Evolutionary developmental biology ("evo-devo") is an emergent subfield of evolutionary biology that looks at genes of related and unrelated organisms. By comparing the explicit nucleotide sequences of DNA/RNA, it is possible to experimentally determine and trace timelines of species development. For example, gene sequences support the conclusion that chimpanzees are the closest primate ancestor to humans, and that arthropods (e.g., insects) and vertebrates (e.g., humans) have a common biological ancestor.
History of evolutionary thought
The idea of biological evolution has existed since ancient times, notably among Hellenists such as Epicurus, but the modern theory was not established until the 18th and 19th centuries, by scientists such as Jean-Baptiste Lamarck and Charles Darwin. While transmutation of species was accepted by a sizeable number of scientists before 1859, it was the publication of Charles Darwin's The Origin of Species which provided the first cogent mechanism by which evolutionary change could persist: his theory of natural selection. Darwin was motivated to publish his work on evolution after receiving a letter from Alfred Russel Wallace, in which Wallace revealed his own discovery of natural selection. As such, Wallace is sometimes given shared credit for the theory of evolution.
Darwin's theory, though it succeeded in profoundly shaking scientific opinion regarding the development of life (and indeed resulted in a small social revolution), could not explain the source of variation in traits within a species, and Darwin's proposal of a hereditary mechanism (pangenesis) was not compelling to most biologists. It was not until the late 19th and early 20th centuries that these mechanisms were established.
When Gregor Mendel's work regarding the nature of inheritance in the late 19th century was "rediscovered" in 1900, it led to a storm of conflict between Mendelians (Charles Benedict Davenport) and biometricians (Walter Frank Raphael Weldon and Karl Pearson), who insisted that the great majority of traits important to evolution must show continuous variation that was not explainable by Mendelian analysis. Eventually, the two models were reconciled and merged, primarily through the work of the biologist and statistician R.A. Fisher. This combined approach, applying a rigorous statistical model to Mendel's theories of inheritance via genes, became known in the 1930s and 1940s as the modern evolutionary synthesis.
In the 1940s, following up on Griffith's experiment, Avery, McCleod and McCarty definitively identified deoxyribonucleic acid (DNA) as the "transforming principle" responsible for transmitting genetic information. In 1953, Francis Crick and James Watson published their famous paper on the structure of DNA, based on the research of Rosalind Franklin and Maurice Wilkins. These developments ignited the era of molecular biology and transformed the understanding of evolution into a molecular process: the mutation of segments of DNA (see molecular evolution).
George C. Williams' 1966 Adaptation and natural selection: A Critique of some Current Evolutionary Thought marked a departure from the idea of group selection towards the modern notion of the gene as the unit of selection.
Debates have continued within the field. One of the most prominent public debates was over the theory of punctuated equilibrium, a theory propounded by Niles Eldredge and Stephen Jay Gould to explain the paucity of transitional forms between phyla.
Impact of the theory of evolution
As the scientific explanation of life's diversity has developed, it has often displaced alternative, sometimes very widely held, explanations. Because the theory of evolution includes an explanation of humanity's origins, it has had a profound impact on human societies. Some have vigorously opposed acceptance of the scientific explanation due to its perceived religious implications (e.g., its implied rejection of the special creation of humans described in the Bible). In the United States this has led to a vigorous conflict between creation and evolution in public education, though this appears to be largely a local phenomenon.
Evolution and ethical systems
The theory of evolution by natural selection has also been adopted as a foundation for various ethical and social systems, such as social Darwinism, which holds that "the survival of the fittest" explains and justifies differences in wealth and success among societies and people. Eugenics is another ethical theory, which advocates the improvement of human hereditary qualities through means of social intervention including (but not limited to) birth control, selective breeding, genetic engineering and in some instances racial hygiene and even extermination. In the United States, the eugenics movement initially received broad popular, institutional, and scientific support, though not without criticism.  After the atrocities of the Holocaust became linked with eugenics, it greatly fell out of favor.
Today, Social Darwinism and eugenics are seldom met by anything but condemnation as scientific racism, though recent publications such as Herrnstein/Murray's The Bell Curve have led many to claim that this form of evolutionary interpretation continues to influence social thinkers.
The notion that humans share ancestors with other animals has also affected how some people view the relationship between humans and other species. Many proponents of animal rights hold that if animals and humans are of the same nature, then rights should not be restricted to humans. The theory has also been incorporated into other fields of knowledge, creating hybrids such as evolutionary psychology and sociobiology.
Evolution and religion
Before the serious study of geology as a science began, early in the 19th century, Abrahamic religions almost unanimously discounted or condemned any claims that life is the result of an evolutionary process, as did nearly all scientists. However, as geological evidence began to accumulate throughout the world, a number of scientists began to question whether a literal interpretation of the creation account in the Judeo-Christian Bible could be reconciled with their findings (and their implications). Certain religious geologists like Dean William Buckland in England, Edward Hitchcock in America and Hugh Miller in Scotland continued to explain the evidence in terms of a universal deluge, but after Charles Darwin published The Origin of Species in 1859, scientific opinion began to quickly swing away from literal interpretations of the Bible. This early debate about the literal validity of the Bible was not conducted behind closed doors and it unsettled educated opinion in both continents. Eventually it instigated a "counter-reformation" that took the form of a religious revival in both continents in 1857–1860.
Some groups, most prominently in the US, interpret Scripture to mean that a supreme being directly created humans and other animals as separate species. This view is commonly referred to as creationism, and continues to be defended by some religious groups, particularly among American Protestants.
In response to the wide scientific acceptance of the theory of evolution, many religions have formally or informally synthesized the scientific and religious viewpoints. Some religions have adopted a theistic evolution viewpoint, where the god provides a divine spark that ignited the process of evolution, and (or) where the god has guided the course of evolution.
For example, the Roman Catholic Church, beginning in 1950 with Pope Pius XII's encyclical Humani Generis, took up a neutral position with regard to evolution. "The Church does not forbid that...research and discussions, on the part of men experienced in both fields, take place with regard to the doctrine of evolution, in as far as it inquires into the origin of the human body as coming from pre-existent and living matter." . In an October 22, 1996, address to the Pontifical Academy of Science, Pope John Paul II updated the Church's position, recognizing that Evolution is "more than a hypothesis" . (For more see: evolution and the Roman Catholic Church).
On July 7, 2005, an op-ed essay by Cardinal Christoph Schönborn, archbishop of Vienna, claiming to clarify the position of the Roman Catholic Church on evolution, was published in the New York Times. In particular, the Cardinal appeared to minimize the significance of Pope John Paul II's oft-quoted remark that evolution is "more than a hypothesis." The late pope's comment was "rather vague and unimportant," said Schönborn , "Evolution in the sense of common ancestry might be true, but evolution in the neo-Darwinian sense—an unguided, unplanned process of random variation and natural selection—is not. Any system of thought that denies or seeks to explain away the overwhelming evidence for design in biology is ideology, not science." These comments from Schönborn have been interpreted by some to come indirectly from the new Pope Benedict, signalling the Catholic Church may be moving toward Intelligent Design. , 
The mythologies of some Eastern religions, on the other hand, bear striking resemblances to the theory of Evolution. Many claim that the ten avatars of Vishnu in Hinduism represent the evolution of life and of mankind. Matsya, the fish, represents life in water. Kurma, the tortoise, represents the next stage, amphibianism. The third animal, the boar Varaha, symbolizes life on land. Narasimha, the Man-Lion, symbolizes the commencement development of man. Vamana, the dwarf, symbolizes this incomplete development. Then, Parashurama, the forest-dweller, connotes completion of the basic development of humankind. The King Rama signals man's ability to govern nations. Krishna, an expert in the sixty-four fields of science and art according to Hinduism, indicates man's advancement to cultural concerns. Buddha, the Enlightened one, symbolizes the enlightenment and spiritual advancement of man. Note that the time of the avatars does not necessarily indicate much; kings ruled long before Rama and science was pursued long before Krishna. The avatars represent the order, and not the time, of these occurrences, according to certain Hindus.
- Darwin, Charles November 24 1859. On the Origin of Species by means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, Albemarle Street. 502 pages. Reprinted: Gramercy (May 22, 1995). ISBN 0517123207
- Zimmer, Carl. Evolution: The Triumph of an Idea. Perennial (October 1, 2002). ISBN 0060958502
- Larson, Edward J. Evolution: The Remarkable History of a Scientific Theory (Modern Library Chronicles). Modern Library (May 4, 2004). ISBN 0679642889
- Mayr, Ernst. What Evolution Is. Basic Books (October, 2002). ISBN 0465044263
- Gigerenzer, Gerd, et al., The empire of chance: how probability changed science and everyday life (New York: Cambridge University Press, 1989).
- Williams, G.C. (1966). Adaptation and Natural Selection: A Critique of some Current Evolutionary Thought. Princeton, N.J.: Princeton University Press.
- Sean B. Carroll, 2005, Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, W. W. Norton & Company. ISBN 0393060160
- Talk.Origins Archive — see also talk.origins
- National Academies Evolution Resources
- EvoWiki — A wiki whose goal is to promote general evolution education, and provide mainstream scientific responses to the arguments of antievolutionists.
- Evolution by Natural Selection — An introduction to the logic of the theory of evolution by natural selection
- Evolution — Provided by PBS.
- Howstuffworks.com — How Evolution Works
- Charles Darwin's writings
- Evolution News from Genome News Network (GNN)
- National Academy Press: Teaching About Evolution and the Nature of Science