Evolution

This article is about evolution in the field of biology.
 Charles Darwin, father of the theory of evolution by natural selection.
Broadly defined, biological evolution is any heritable change in a population of organisms over time. Changes may be slight or large, but must be passed on to the next generation (or many generations) and must involve populations, not individuals.
Similarly, the term may be presented in terms of allele frequency (with an "allele" being an alternative form of a gene, such as different alleles code for different eye colors): "Evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next" (Curtis & Barnes 1989). Both a slight change (as in pesticide resistance in a strain of bacteria) and a large change (as in the development of major new designs such as feathered wings, or even the present diversity of life from simple prokaryotes) qualify as evolution.
However, "evolution" commonly is used more narrowly to refer to the specific theory that all organisms have descended from common ancestors, also known as the "theory of descent with modification," or to refer to one explanation for the process by which change occurs, the "theory of modification through natural selection." The term also is used with reference to a comprehensive theory that includes both the non-causal pattern of descent with modification and the causal mechanism of natural selection.
Evolution is a central concept in biology. Geneticist T. Dobzhansky (1973) has stated, "Nothing in biology makes sense, except in the light of evolution," and biologist Ernst Mayr (2001) has stated, "Evolution is the most profound and powerful idea to have been conceived in the last two centuries."
Nonetheless, the concepts of evolution have often engendered controversy during the past two centuries, particularly from Christians, whose traditional views have been challenged both by the long time period of evolution and by the purposeless, materialistic mechanism inherent in having natural selection be the creative force. Modern Christian viewpoints range from rejecting both descent with modification (the pattern) and the mechanism of natural selection (the process), to accepting descent with modification but not the theory of natural selection, to those claiming natural selection as God's way of creating things. (See evolution and religion below.)

Contents

1 Evolutionary theory

1.1 Theory of descent with modification
1.2 Theory of natural selection
1.3 Speciation and extinction
1.4 Rate of evolution


2 Darwinism and Neo-Darwinism
3 Evidences of evolution

3.1 Evidences for the Theory of Descent with Modification

3.1.1 Fossil record
3.1.2 Morphological evidence
3.1.3 Embryology
3.1.4 Biogeography
3.1.5 Molecular evidence


3.2 Evidences for the Theory of Natural Selection
3.3 Teaching of evidences


4 Evolution as "fact" and "theory"
5 Modern alternative mechanisms and views

5.1 Symbiogenesis
5.2 More complex tree of life
5.3 Non-random variation


6 History of Life
7 Evolution and religion
8 History of evolutionary thought
9 Disciplines in evolutionary studies

9.1 Physical anthropology
9.2 Evolutionary biology

9.2.1 Evolutionary developmental biology




10 References
11 Credits



The development of modern theories of evolution began with the introduction of the concept of natural selection in a joint 1858 paper by Charles Darwin and Alfred Russel Wallace, and the publication of Darwin's 1859 book, The Origin of Species. Darwin and Wallace proposed that evolution occurs because a heritable trait that increases an individual's chance of successfully reproducing will become more common, by inheritance, from one generation to the next, and likewise a heritable trait that decreases an individual's chance of reproducing will become rarer. In the 1930s, scientists combined Darwinian natural selection with the re-discovered theory of Mendelian heredity to create the modern synthesis, which is the prevailing paradigm of evolutionary theory.

Evolutionary theory
As broadly and commonly defined in the scientific community, the term evolution connotes heritable changes in populations of organisms over time, or changes in the frequencies of alleles over time. A popular definition along these lines is that offered by Douglas J. Futuyma (1986) in Evolutionary Biology: "Biological evolution…is change in the properties of populations of organisms that transcend the lifetime of a single individual…. The changes in populations that are considered evolutionary are those that are inheritable via the genetic material from one generation to another." In this sense, the term does not specify any overall pattern of change through the ages, nor the process whereby change occurs (although the term is also employed in such a manner).
However, there are two very important and popular evolutionary theories that address the pattern and process of evolution: "theory of descent with modification" and "theory of natural selection," respectively, as well as other concepts in evolutionary theory that deal with speciation and the rate of evolution.

Theory of descent with modification
The "theory of descent with modification" is the major kinematic theory that deals with the pattern of evolution—that is, it treats non-causal relations between ancestral and descendant species, orders, phyla, and so forth. The theory of descent with modification, also called the "theory of common descent," essentially postulates that all organisms have descended from common ancestors by a continuous process of branching. In other words, narrowly defined, all life evolved from one kind of organism or from a few simple kinds, and each species arose in a single geographic location from another species that preceded it in time. Each group of organisms shares a common ancestor. In the broadest sense of the terminology, the theory of descent with modification simply states that more recent forms result from modification of earlier forms.
One of the major contributions of Charles Darwin was to marshal substantial evidence for the theory of descent with modification, particularly in his book, Origin of Species. Among the evidences that evolutionists use to document the "pattern of evolution" are the fossil record, the distribution patterns of existing species, methods of dating fossils, and comparison of homologous structures. (See evidences of evolution below.)

Theory of natural selection
Main articles: Darwinism and Natural selection
The second major evolutionary theory is the "theory of modification through natural selection," also known as the "theory of natural selection." This is a dynamic theory that involves mechanisms and causal relationships. The theory of natural selection is one explanation offered for how evolution might have occurred; in other words, the "process" by which evolution took place to arrive at the pattern.
The term natural selection may be defined as the mechanism whereby biological individuals that are endowed with favorable or deleterious traits reproduce more or less than other individuals that do not possess such traits. Natural selection generally is defined independently of whether or not there is actually an effect on the gene-frequency of a population. That is, it is limited to the selection process itself, whereby individuals in a population experience differential survival and reproduction based on a particular phenotypic variation(s).
The theory of evolution by natural selection is the comprehensive proposal involving both heritable genetic variations in a population and the mechanism of natural selection that acts on these variations, such that individuals with greater fitness are more likely to contribute offspring to the next generation, while individuals with lesser fitness are more likely to die early or fail to reproduce. As a result, genotypes with greater fitness become more abundant in the next generation, while genotypes with a lesser fitness become rarer. This theory encompasses both minor changes in gene frequency in populations, brought about by the creative force of natural selection, and major evolutionary changes brought about through natural selection, such as the origin of new designs. For Darwin, however, the term natural selection generally was used synonymously with evolution by natural selection.
In the theory of natural selection as currently conceived, there is both a chance component and a non-random component. Genetic variation is seen as developing randomly, by chance, such as through mutations or genetic recombination. Mayr (2002) states that the production of genetic variation "is almost exclusively a chance phenomena." In every generation, new mutations and recombinations arise spontaneously, producing a new spectrum of phenotypes for natural selection—a non-random selective force (Mayr 2002)—to act upon. However, Mayr (2002) also notes that chance plays an important role even in "the process of the elimination of less fit individuals," and particularly during periods of mass extinction. Thus, chance (stochastic processes, randomness) also plays a major role in the theory of natural selection.
According to the theory of natural selection, natural selection is the directing or creative force of evolution. Natural selection is considered far more than just a minor force for weeding out unfit organisms. Even Paley and other natural theologians accepted natural selection, albeit as a mechanism for removing unfit organisms, rather than as a directive force for creating new species and new designs.
Concrete evidence for the theory of modification by natural selection is limited to microevolution—that is, evolution at or below the level of species. The evidence that natural selection directs changes on the macroevolutionary level—such as the major transitions between higher taxa and the origination of new designs—necessarily involves extrapolation from these evidences on the microevolutionary level. The validity of making such extrapolations has recently been challenged by some prominent evolutionists.
The theory of natural selection received a much more contentious response than did the theory of descent with modification. One of Darwin's chief purposes in publishing the Origin of Species was to show that natural selection had been the chief agent of the changes presented in the theory of descent with modification. While the theory of descent with modification was accepted by the scientific community soon after its introduction, the theory of natural selection took until the mid-1900s to be accepted. However, even today, this theory remains controversial, with detractors in both the scientific and religious communities.

Speciation and extinction
Main articles: Speciation and Species
The concepts of speciation and extinction are important to any understanding of evolutionary theory.
Speciation is the term that refers to creation of new and distinct biological species by branching off from the ancestral population. Various mechanisms have been presented whereby a single evolutionary lineage splits into two or more genetically independent lineages. For example, allopatric speciation is held to occur in populations that become isolated geographically, such as by habitat fragmentation or migration. Sympatric speciation is held to occur when new species emerge in the same geographic area. Ernst Mayr's peripatric speciation is a proposal for a type of speciation that exists in between the extremes of allopatry and sympatry, where zones of differentiating species abut but do not overlap.

 An allosaurus skeleton.
Extinction is the disappearance of species (i.e. gene pools). The moment of extinction generally occurs at the death of the last individual of that species. Extinction is not an unusual event in geological time. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 90 percent of all marine species and 70 percent of terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event, many forms of life perished (including approximately 50 percent of all genera), the most often mentioned among them being the extinction of the dinosaurs.
One of the unheralded laws of evolutionary theory is that macroevolutionary changes are irreversible—lineages do not return to their ancestral form, even when they return to the ancestral way of life.

Rate of evolution
Main article: Punctuated equilibrium
The concept of gradualism has often been linked with evolutionary thought. Gradualism is a view of descent with modification as proceeding by means of slow accumulation of very small changes, with the evolving population passing through all the intermediate stages—sort of a "march of frequency distributions" through time (Luria, Gould, and Singer 1981).
Darwin himself insisted that evolution was entirely gradual. Indeed, he stated in the Origin of Species:

"As natural selection acts solely by accumulating slight, successive, favourable variations, it can produce no great or sudden modifications; it can act only by very short and slow steps."
Nature "can never take a leap, but must advance by the shortest and slowest steps."
"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."
The Darwinian and Neo-Darwinian emphasis on gradualism has been subject to re-examination on several levels: the levels of major evolutionary trends, origin of new designs, and models of speciation.
Punctuated equilibrium. A common misconception about evolution is that the development of new species generally requires millions of years. Indeed, the gradualist view that speciation involved a slow, steady, progressive transformation of an ancestral population into a new species has dominated much of evolutionary thought from the time of Darwin. Such a transformation was commonly viewed as involving large numbers of individuals ("usually the entire ancestral population"), being "even and slow," and occurring "over all or a large part of the ancestral species' geographic range" (Eldredge & Gould 1972). This concept was applied to the development of a new species by either phyletic evolution (where the descendant species arises by the transformation of the entire ancestral population) or by speciation (where the descendant species branches off from the ancestral population).
However, paleontologists now recognize that the fossil record does not generally yield the expected sequence of slightly altered intermediary forms, but instead the sudden appearance of species, and long periods when species do not change much.
The theory of punctuated equilibrium ascribes that the fossil record accurately reflects evolutionary change. That is, it posits that macroevolutionary patterns of species are typically ones of morphological stability during their existence (stasis), and that most evolutionary change is concentrated in events of speciation—with the origin of a new species usually occurring during geologically short periods of time when the long-term stasis of a population is punctuated by this rare and rapid speciation event. The sudden transitions between species are sometimes measured on the order of hundreds or thousands of years relative to their millions of years of existence. Although the theory of punctuated equilibrium originally generated a lot of controversy, it is now viewed highly favorably in the scientific community, and has even become a part of recent textbook orthodoxy.
Note that the theory of punctuated equilibrium merely addresses the pattern of evolution and is not tied to any one mode of speciation. Although occurring in a brief period of time, the species formation can go through all the stages, or can proceed by leaps. It is even neutral with respect to natural selection.
Punctuated origin of new designs. According to the gradualist viewpoint, the origin of novel features, such as feathers in birds and jaws in fish, can be explained as having arisen from numerous, tiny, imperceptible steps, with each step being advantageous and developed by natural selection. Darwin's proposed such a resolution for the origin of the vertebrate eye.
However, there are some structures for which it is difficult to conceive how such structures could be useful in incipient stages, and thus have selective advantage. One way in which evolutionary theory has dealt with such criticisms is the concept of "preadaptation," proposing that the intermediate stage may perform useful functions different from the final stage. Incipient feathers may have been used for retaining body warmth or catching insects, for example, prior to the development of a fully functional wing.
Another solution for origin of new designs, which is gaining renewed attention among evolutionists, is that the full sequence of intermediate forms may not have existed at all, and instead key features may have developed by rapid transitions, discontinuously. This view of a punctuational origin of key features arose because of: (1) the persistent problem of the lack of fossil evidence for intermediate stages between major designs, with transitions between major groups being characteristically abrupt; and (2) the inability to conceive of functional intermediates in select cases. In the later case, prominent evolutionist Stephen Jay Gould (1980b) cites the fur-lined pouches of pocket gophers and the maxillary bone of the upper jaw of certain genera of boid snakes being split into front and rear halves:
"How can a jawbone be half broken?… What good is an incipient groove or furrow on the outside? Did such hypothetical ancestors run about three-legged while holding a few scraps of food in an imperfect crease with their fourth leg?"
The concept of punctuational origin is not necessarily opposed to natural selection as the creative force. For example, the rapid transition could be the product of a very small genetic change, even one mutation occurring by chance in a key gene, which is then acted upon by natural selection. However, the concept of a punctuational origin of new designs (as with punctuational equilibrium), is also viewed favorably by those advocating divine creation, due to the alignment of this view with the concept of discontinuous variation being the product of divine input, with natural selection simply the weeding out of previous, less well-adapted forms.
Punctuational models of speciation. Punctuational models of speciation are being advanced in contrast with what is sometimes labeled the "allopatric orthodoxy" (Gould 1980a; Gould and Eldredge 1977). Allopatric orthodoxy is a process of species origin involving geographic isolation, whereby a population completely separates geographically from a large parental population and develops gradually into a new species by natural selection until their differences are so great that reproductive isolation ensues. Reproductive isolation is therefore a secondary byproduct of geographic isolation, with the process involving gradual allelic substitution. Contrasted with this view are recent punctuational models for speciation, which postulate that reproductive isolation can rise rapidly, not through gradual selection, but without selective significance. In such models, reproductive isolation originates before adaptive, phenotypic differences are acquired. Selection does not play a creative role in initiating speciation, nor in the definitive aspect of reproductive isolation, although it is usually postulated as the important factor in building subsequent adaptation. One example of this is polyploidy, where there is a multiplication of the number of chromosomes beyond the normal diploid number. Another model is chromosomal speciation, involving large changes in chromosomes due to various genetic accidents.

Darwinism and Neo-Darwinism
Main articles: Darwinism and Neo-Darwinism
Darwinism is a term generally synonymous with the theory of natural selection. Harvard evolutionist Stephen Jay Gould (1982) maintains: "Although 'Darwinism' has often been equated with evolution itself in popular literature, the term should be restricted to the body of thought allied with Darwin's own theory of mechanism [natural selection].” Although the term has been used in various ways depending on who is using it and the time period (Mayr 1991), Gould nonetheless finds a general agreement in the scientific community that "Darwinism should be restricted to the world view encompassed by the theory of natural selection itself."
The term neo-Darwinism is a very different concept. It is considered synonymous with the term "modern synthesis" or "modern evolutionary synthesis." The modern synthesis is the most significant, overall development in evolutionary thought since the time of Darwin, and is the prevailing paradigm of evolutionary biology. The modern synthesis melded the two major theories of classical Darwinism (theory of descent with modification and the theory of natural selection) with the rediscovered Mendelian genetics, recasting Darwin's ideas in terms of changes in allele frequency.
In essence, advances in genetics pioneered by Gregor Mendel led to a sophisticated concept of the basis of variation and the mechanisms of inheritance. Gregor Mendel proposed a gene-based theory of inheritance, describing the elements responsible for heritable traits as the fundamental units now called genes and laying out a mathematical framework for the segregation and inheritance of variants of a gene, which are now referred to as alleles. Later research identified the molecule DNA as the genetic material through which traits are passed from parent to offspring, and identified genes as discrete elements within DNA. Though largely maintained within organisms, DNA is both variable across individuals and subject to a process of change or mutation.
According to the modern synthesis, the ultimate source of all genetic variation is mutations. They 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.
In addition to passing genetic material from parent to offspring, nearly all organisms employ sexual reproduction to exchange genetic material. This, combined with meiotic recombination, allows genetic variation to be propagated through an interbreeding population.
According to the modern synthesis, natural selection acts on the genes, through their expression (phenotypes). Natural selection can be subdivided into two categories:

Ecological selection occurs when organisms that survive and reproduce increase the frequency of their genes in the gene pool over those that do not survive.
Sexual selection occurs when organisms that 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.
Through the process of natural selection, species become better adapted to their environments. Note that, whereas mutations (and genetic drift) are random, natural selection is not, as it preferentially selects for different mutations based on differential fitness.
In recent years, there have been many challenges to the modern synthesis, to the point where Bowler (1988), a historian of evolutionary thought, states; "In the last decade or so it has become obvious that there is no longer a universal consensus in favor of the synthetic theory even within the ranks of working biologists." Gould (1980a) likewise notes "that theory, as a general proposition is effectively dead." These challenges include models of punctuational change, the theory of “neutralism,” and selection at levels above the individual. What some historians and philosophers of evolutionary thought see as challenges to the modern synthesis, others see as either erroneous theories or as theories that can be included within the umbrella of the modern synthesis.

Evidences of evolution
Main article: Evidence of evolution
For the broad concept of evolution ("any heritable change in a population of organisms over time"), evidences of evolution are readily apparent. Evidences include observed changes in domestic crops (creating a variety of corn with greater resistance to disease), bacterial strains (development of strains with resistance to antibiotics), laboratory animals (structural changes in fruit flies), and flora and fauna in the wild (color change in particular populations of peppered moths and polyploidy in plants).
Generally, however, the "evidences of evolution" being presented by scientists or textbook authors are for either (1) the theory of descent with modification; or (2) a comprehensive concept including both the theory of descent with modification and the theory of natural selection. In actuality, most of these evidences that have been catalogued are for the theory of descent with modification.

Evidences for the Theory of Descent with Modification
In the Origin of Species, Darwin marshaled many evidences for the theory of descent with modification, within such areas as paleontology, biogeography, morphology, and embryology. Many of these areas continue to provide the most convincing proofs of descent with modification even today (Mayr 1982; Mayr 2001). Supplementing these areas, are molecular evidences.
It is noteworthy that some of the best support for the theory of descent with modification comes from the observation of imperfections of nature, rather than perfect adaptations. As noted by Gould (1983):

All of the classical arguments for evolution are fundamentally arguments for imperfections that reflect history. They fit the pattern of observing that the leg of Reptile B is not the best for walking, because it evolved from Fish A. In other words, why would a rat run, a bat fly, a porpoise swim and a man type all with the same structures utilizing the same bones unless inherited from a common ancestor?
Fossil record
Fossil evidence of prehistoric organisms has been found all over the Earth. Fossils are traces of once living organisms. Fossilization on an organism is an uncommon occurrence, usually requiring hard parts (like bone) and death where sediments or volcanic ash may be deposited. Fossil evidence of organisms without hard body parts, such as shell, bone, teeth, and wood stems, is sparse, but exists in the form of ancient microfossils and the fossilization of ancient burrows and a few soft-bodied organisms. Some insects have been preserved in resin. The age of fossils can often be deduced from the geologic context in which they are found (the strata); and their age also can be determined with radiometric dating.
The comparison of fossils of extinct organisms in older geological strata with fossils found in more recent strata or with living organisms is considered strong evidence of descent with modification. Fossils found in more recent strata are often very similar to, or indistinguishable from living species, whereas the older the fossils the more different they are from living organisms or recent fossils. In addition, fossil evidence reveals that species of greater complexity have appeared on the earth over time, beginning in the Precambrian era some 600 millions of years ago with the first eukaryotes. The fossil records support the view that there is orderly progression in which each stage emerges from, or builds upon, preceding stages.
One of the problems with fossil evidence is the general lack of gradually sequenced intermediary forms. There are some fossil lineages that appear quite well-represented, such as from therapsid reptiles to the mammals, and between what is considered land-living ancestors of the whales and their ocean-living descendants. The transition from an ancestral horse (Eohippus) and the modern horse (Equus) is also significant, and Archaeopteryx has been postulated as fitting the gap between reptiles and birds. But generally, paleontologists do not find a steady change from ancestral forms to descendant forms, but rather discontinuities, or gaps in most every phyletic series. This has been explained both by the incompleteness of the fossil record and by proposals of speciation that involve short periods of time, rather than millions of years. (Notably, there are also gaps between living organisms, with a lack of intermediaries between whales and terrestrial mammals, between reptiles and birds, and between flowering plants and their closest relatives.) Archaeopteryx has recently come under criticism as a transitional fossil between reptiles and birds (Wells 2000).
The fact that the fossil evidence supports the view that species tend to remain stable throughout their existence and that new species appear suddenly is not problematic for the theory of descent with modification, but only with Darwin's concept of gradualism.

Morphological evidence
The study of comparative anatomy also yields evidence for the theory of descent with modification. For one, there are structures in diverse species that have similar internal organization yet perform different functions. Vertebrate limbs are a common example of such homologous structures. Bat wings, for example, are very similar to human hands. Also similar are the forelimbs of the penguin, the porpoise, the rat, and the alligator. In addition, these features derive from the same structures in the embryo stage. As queried earlier, “why would a rat run, a bat fly, a porpoise swim and a man type” all with limbs using the same bone structure if not coming from a common ancestor, since these are surely not the most ideal structures for each use (Gould 1983).
Likewise, a structure may exist with little or no purpose in one organism, yet the same structure has a clear purpose in other species. These features are called vestigial organs or vestigial characters. The human wisdom teeth and appendix are common examples. Likewise, some snakes have pelvic bones and limb bones, and some blind salamanders and blind cave fish have eyes. Such features would be the prediction of the theory of descent with modification, suggesting that they share a common ancestry with organisms that have the same structure, but which is functional.
For the point of view of classification, it can be observed that various species exhibit a sense of "relatedness," such as various catlike mammals can be put in the same family (Felidae), dog-like mammals in the same family (Canidae), and bears in the same family (Ursidae), and so forth, and then these and other similar mammals can be combined into the same order (Carnivora). This sense of relatedness, from external features, fits the expectations of the theory of descent with modification.
Phylogeny, the study of the ancestry (pattern and history) of organisms, yields a phylogenetic tree to show such relatedness (or a cladogram in other taxonomic disciplines).

Embryology
A common evidence for evolution is the assertion that the embryos of related animals are often quite similar to each other, often much more similar than the adult forms. For example, it is held that the development of the human embryo is compatible to comparable stages of other kinds of vertebrates (fish, salamander, tortoise, chicken, pig, cow, and rabbit). Furthermore, mammals such as cows and rabbits are more similar in embryological development than with alligators. Often, the drawings of early vertebrate embryos by Ernst Haeckel are offered as proof.
It has further been asserted that features, such as the gill pouches in the mammalian embryo resemble those of fish, are most readily explained as being remnants from the ancestral fish, which were not eliminated because they are embryonic "organizers" for the next step of development.
Wells (2000) has criticized embryological evidence on several points. For one, it is now known that Ernst Haeckel exaggerated the similarities of vertebrate embryos at the midpoint of embryological development, and omitted the earlier embryological stages when differences were more pronounced. Also, embryological development in some frog species looks very similar to that of birds, rather than other frog species. Remarkably, even as revered an evolutionist as Ernst Mayr, in his 2001 text What Evolution Is, used Haeckel drawings from 1870, which he knew were faked, noting "Haeckel (sp.) had fraudulently substituted dog embryos for the human ones, but they were so similar to humans that these (if available) would have made the same point."

Biogeography
The geographic distribution of plants and animals offers another commonly cited evidence for evolution (common descent). The fauna on Australia, with its large marsupials, is very different from that of the other continents. The fauna on Africa and South America are very different, but the fauna of Europe and North America, which were connected more recently, are similar. There are few mammals on oceanic islands. These findings support the theory of descent with modification, which holds that the present distribution of flora and fauna would be related to their common origins and subsequent distribution. The longer the separation of continents, such as with Australia's long isolation, the greater the expected divergence is.
Renowned evolutionist Mayr (1982) contends that "the facts of biogeography posed some of the most insoluble dilemmas for the creationists and were eventually used by Darwin as his most convincing evidence in favor of evolution."

Molecular evidence
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 common descent is supported by genetic similarities. 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. All organisms use the same genetic code (with some extremely rare and minor deviations) to translate nucleic acid sequences into proteins. The universality of these traits strongly suggests common ancestry, because the selection of these traits seems somewhat arbitrary.
Similarly, the metabolism of very different organisms is based on the same biochemistry. For example, the protein cytochrome c, which is needed for aerobic respiration, is universally shared in aerobic organisms, suggesting a common ancestor that used this protein. There are also variations in the amino acid sequence of cytochrome c, with the more similar molecules found in organisms that appear more related (monkeys and cattle) than between those that seem less related (monkeys and fish). The cytochrome c of chimpanzees is the same as that of humans, but very different from bread mold. Similar results have been found with blood proteins.
Other uniformity is seen in the universality of mitosis in all cellular organisms, the similarity of meiosis in all sexually reproducing organisms, the use of ATP by all organisms for energy transfer, and the fact that almost all plants use the same chlorophyll molecule for photosynthesis.
The closer that organisms appear to be related, the more similar are their respective genetic sequences. That is, comparison of the genetic sequence of organisms reveals that phylogenetically close organisms have a higher degree of sequence similarity than organisms that are phylogenetically distant. For example, neutral human DNA sequences are approximately 1.2 percent divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6 percent from gorillas, and 6.6 percent from baboons. Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce.
Comparative studies also show that some basic genes of higher organisms are shared with homologous genes in bacteria.

Evidences for the Theory of Natural Selection
Concrete evidence for the theory of modification by natural selection is limited to the microevolutionary level—that is, events and processes at or below the level of species. As examples of such evidences, plant and animal breeders use artificial selection to produce different varieties of plants and strains of fish. Natural selection is seen in the changes of the shade of gray of populations of peppered moths (Biston betularia) observed in England.
Another example involves the hawthorn fly, Rhagoletis pomonella. Different populations of hawthorn fly feed on different fruits. A new population spontaneously emerged in North America in the nineteenth century sometime after apples, a non-native species, were introduced. The apple-feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. Likewise the current hawthorn feeding population does not normally feed on apples. A current area of scientific research is the investigation of whether or not the apple-feeding race may further evolve into a new species. Some evidence, such as the fact that six out of thirteen alozyme loci are different, that hawthorn flies mature later in the season, and take longer to mature than apple flies, and that there is little evidence of interbreeding (researchers have documented a 4 to 6 percent hybridization rate) suggests this possibility (see Berlocher and Bush 1982; Berlocher and Feder 2002; Bush 1969; McPheron, Smith, and Berlocher 1988; Prokopy, Diehl, and Cooley 1988; Smith 1988).
The evidence that natural selection directs the major transitions between species and originates new designs (macroevolution) involves extrapolation from these evidences on the microevolutionary level. That is, it is inferred that if moths can change their color in 50 years, then new designs or entire new genera can originate over millions of years. If geneticists see population changes for fruit flies in laboratory bottles, then given eons of time, birds can be built from reptiles and fish with jaws from jawless ancestors.
However, at question has always been the sufficiency of extrapolation to the macroevolutionary level. As Mayr (2001) notes, "from Darwin's day to the present, there has been a heated controversy over whether macroevolution is nothing but an unbroken continuation of microevolution, as Darwin and his followers have claimed, or rather is disconnected from microevolution."

Teaching of evidences
Textbook authors have often confused the dialogue on evolution by treating the term as if it signified one unified whole—not only descent with modification, but also the specific Darwinian and neo-Darwinian theories regarding natural selection, gradualism, speciation, and so forth. Certain textbook authors, in particular, have exacerbated this terminological confusion by lumping "evidences of evolution" into a section placed immediately after a comprehensive presentation on Darwin's overall theory—thereby creating the misleading impression that the evidences are supporting all components of Darwin's theory, including natural selection (Swarts et al. 1994). In reality, the confirming information is invariably limited to the phenomenon of evolution having occurred (descent from a common ancestor or change of gene frequencies in populations), or perhaps including evidence of natural selection within populations.

Evolution as "fact" and "theory"
"Evolution" has been referred to both as a "fact" and as a "theory."
In scientific terminology, a theory is a model of the world (or some portion of it) from which falsifiable hypotheses can be generated and tested through controlled experiments, or be verified through empirical observation. "Facts" are parts of the world, or claims about the world, that are real or true regardless of what people think. Facts, as data or things that are done or exist, are parts of theories—they are things, or relationships between things, that theories take for granted in order to make predictions, or that theories predict. 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" that explains it is the current theory of gravitation.
In common usage, people use the word "theory" to signify "conjecture," "speculation," or "opinion." In this popular sense, "theories" are opposed to "facts." Thus, it is not uncommon for those opposed to evolution to state that it is just a theory, not a fact, implying that it is mere speculation. But for scientists, "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship.
Scientists sometimes refer to evolution as both a "fact" and a "theory."
In the broader usage of the term, calling evolution a "fact" references the confidence that scientists have that populations of organisms can change over time. In this sense, evolution occurs whenever a new strain of bacterium evolves that is resistant to antibodies that had been lethal to prior strains. Many evolutionists also call evolution a "fact" when they are referring to the theory of descent with modification, because of the substantial evidences that they perceive as having been marshaled for this theory. In this later sense, Mayr (2001) opines: "It is now actually misleading to refer to evolution as a theory, considering the massive evidence that has been discovered over the past 140 years documenting its existence. Evolution is no longer a theory, it is simply a fact."
When "evolution" is referred to as a theory by evolutionists, the reference is generally to an explanation for why and how evolution occurs (such as a theory of speciation or the theory of natural selection).

Modern alternative mechanisms and views
Symbiogenesis
Symbiogenesis is evolutionary change initiated by a long-term symbiosis of dissimilar organisms. Margulis and Sagan (2002) hold that random mutation is greatly overemphasized as the source of hereditary variation in standard Neo-Darwinistic doctrine. Rather, they maintain, the major source of transmitted variation actually comes from the acquisition of genomes—in other words, entire sets of genes, in the form of whole organisms, are acquired and incorporated by other organisms. This long-term biological fusion of organisms, beginning as symbiosis, is held to be the agent of species evolution.
For example, lichens are a composite organism composed of a fungus and a photosynthetic partner (usually either green algae or cyanobacteria, but in some cases yellow-green algae, brown algae, or both green algae and cyanobacteria). These intertwined organisms act as a unit that is distinct from its component parts. Lichens are considered to have arisen by symbiogenesis, involving acquisitions of cyanobacterial or algal genomes.
Another example is the photosynthetic animals or plant-animal hybrids in the form of slugs (shell-less mollusks) that have green algae in their tissues (such as Elysia viridis). These slugs are always green, never need to eat throughout their adult life, and are "permanently and discontinuously different from their gray, algae-eating ancestors" (Margulis and Sagan 2002). This is held to be another example of a symbiosis that lead to symbiogenesis.
Yet another example is cattle, which are able to digest cellulose in grass because of microbial symbionts in their rumen. Cattle cannot survive without such an association. Other examples of evolution resulting through merger of dissimilar organisms include associations of modern (scleractinian) coral and dinomastigotes (such as Gymnodinium microadriaticum) and the formation of new species and genera of flowering plants when when the leaves of these plants integrated a bacterial genome.
The formation of eukaryotes is postulated to have occurred through a symbiotic relationship between prokaryotes, a theory called endosymbiosis. According to this theory, mitochondria, chloroplasts, flagella, and even the cell nucleus would have arisen from prokaryote bacteria that gave up their independence for the protective and nutritive environment within a host organism.
Margulis and Sagan (2002) state that the formation of new species by inheritance of acquired microbes is best documented in protists. They conclude that "details abound that support the concept that all visible organisms, plants, animals, and fungi evolved by "body fusion."

More complex tree of life
The conventional paradigm of the theory of descent with modification presumes that the history of life maps as the "tree of life," a tree beginning with the trunk as one universal common ancestor and then progressively branching, with modern species at the twig ends. However, that clean and simple pattern is being called into question due to discoveries being made by sequencing genomes of specific organisms. Instead of being simple at its base, the tree of life is looking considerably more complex. At the level of single cells, before the emergence of multicellular organisms, the genomic signs point not to a single line of development, but rather to a bush or a network as diverse microbes at times exchange their genetic material, especially through the process of lateral gene transfer.
Other complicating factors are proposed based on the relatively sudden appearance of phyla during the Cambrian explosion and on evidence that animals may have originated more than once and in different places at different times (Whittington 1985; Gordon 1999; Woese 1998; Wells 2000).

Non-random variation
The current paradigm of the theory of natural selection is that the process has a major stochastic (random) element, with heritable variation arising through chance, and then being acted upon by the largely non-random force of natural selection made manifest as various species compete for limited resources. An alternative view is that the introduced variation is non-random.
In particular, various theistic perspectives see directed variation, from a Supreme Being, as the creative force of evolution. Natural selection, rather than being the creative force of evolution, may be variously viewed as a force for advancement of the new variation or may be considered largely inconsequential. Some role may also be accorded differential selection, such as mass extinctions. This view sees the evolutionary process as progressive, non-materialistic, and purposeful.
Neither of these contrasted worldviews—random variation and the purposeless, non-progressive role of natural selection, or purposeful, progressive variation—are conclusively proved or unproved by scientific methodology, and both are theoretically possible.

History of Life
 Pre-Cambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, William Schopf of UCLA published a controversial paper in the journal Nature arguing that formations such as this possess 3.5 billion-year-old fossilized algae microbes. If true, they would be the earliest known life on earth.
The appearance of life on earth (see origin of life) is not a part of biological evolution.
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 that had already developed the most fundamental cellular processes. There is no scientific consensus on the relationship of the three domains of life (Archea, Bacteria, Eukaryota) or the origin of life.
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. 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 the land ecosystems of today.
Utilizing the fossil record, scientists have constructed geological timetables, or geological time scales to offer a picture of the history of life on earth, organized by presenting the type of plant and animal life according to the time of appearance (often listed in terms of era, period, epoch, and years). This timetable, for example, locates the first bacteria and the first algae in the Precambrian era, over 1 billion years ago, the first marine invertebrates in the Cambrian period of the Paleozoic era (some 580 million years ago), early mammals in the Triassic period of the Mesozoic era, the first flowering plants in the Cretaceous period of the Mesozoic era, and the development of early hominids in the Pliocene epoch of the Tertiary period of the Cenozoic era, and so forth.
One of the great puzzles in biology is the sudden appearance of most body plans of animals during the early Cambrian period and why there have been no major new structural types in the subsequent 500 million years (Mayr 2001).
Scientists also strive to show lineages, from ancestral to descendant organisms. There are numerous evidences that are used in constructing this more defined history of life, with the best known being the fossil record, but also utilizing the comparative anatomy of present-day plants and animals. By comparing the anatomies of both modern and extinct species, biologists attempt to reconstruct the lineages of those species. Transitional fossils have been proposed to picture continuity between two different lineages. For instance, the connection between dinosaurs and birds has been proposed by way of so-called "transitional" species such as Archaeopteryx.
The development of genetics also has allowed biologists to investigate the genetic record of the history of life as well. Although we cannot obtain the DNA sequences of most extinct species, the degree of similarity and difference among modern species allows geneticists to reconstruct lineages. It is from genetic comparisons that claims such as the 98 to 99 percent similarity between humans and chimpanzees come from, for instance.
Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, monotremes and most marsupials are found only in Australia, postulating that their common ancestor with placental mammals lived before the submerging of the ancient land bridge between Australia and Asia.
Scientists correlate all of the above evidence—drawn from paleontology, anatomy, genetics, and geography—with other information about the history of the earth. For instance, paleoclimatology attests to periodic ice ages during which the climate was much cooler; and these are found to match up with the spread of species such as the woolly mammoth that are better equipped to deal with cold.

Evolution and religion
 A satirical image of Charles Darwin as an ape from 1871 reflects part of the social controversy over whether humans and apes share a common lineage.
Main article: Evolution and religion
Since the publication of the The Origin of Species in 1859, the concept of evolution has engendered controversy, particularly from religious leaders. Popular writings often tend to create an artificial dichotomy—either belief in a Creator is correct or evolution is correct: evolution and religion (specifically creation by a Supreme Being or God) are presented as if mutually exclusive alternatives. Thus, many religious adherents reject evolution out of hand, not wishing to reject God.
Nevertheless, religious viewpoints are varied with respect to evolution. Some faith communities, such as "young-earth creationists" stand in opposition to both the theory of descent with modification and the theory of natural selection. Holding strictly to the letter of Genesis, they hold that the Earth is only 6,000 years old, that God created all the plants and animals in the first week of creation, and that the fossil record is actually artifacts from before the Flood.
Other believers accept the pattern observed in nature (theory of descent with modification) but not the process (theory of natural selection). They hold that God as Creator had a hand in his creations at many stages along the way from bacterium to human, imparting his design and his image. This is what is classically called creationism, or more narrowly "old-earth creationism," since it accepts the scientific account of the gradual development of life on earth over four billion years. They critique the young earth position by citing the verse, "with the Lord one day is as a thousand years, and a thousand years as one day" (2 Peter 3:8).
Still others accept natural selection as the causal agent of large-scale change. This latter view fits that of evolutionary geneticist Theodosius Dobzhansky (1973): "It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist and an evolutionist. Evolution is God's or Nature's, method of creation." Theologically, this would be a Deist position, since once God set up natural selection, it would have carried on autonomously without any activity on God's part. It might be termed "theistic evolution" but certainly not "creation."
By itself, the theory of descent with modification poses little difficulty to most religious adherents, since it is neutral with respect to the process. The mechanism that gives rise to the pattern could occur by natural selection or it could occur by the directive force of a supreme being. In 1859, most scientists and laymen believed that the biotic world was constant. The massive evidence that Darwin presented was so convincing that within a few years every biologist became an evolutionist, believing that the world was the product of a continuing process of change. For most biologists today, the view that evolution takes place—that there is a systematic change in populations—is taken as fact.
Adherents of scientific creationism, and in particular young-earth creationists, do oppose the theory of descent with modification, but they represent only a small body of those individuals that do believe in a creation by a supreme being.
Classical creationists are likewise opposed to evolution, despite having a belief system that allows descent with modification and change in gene frequencies in populations. Mainly, they are opposed to the specific Darwinian theory of evolution by natural selection, which has three radical components that are particularly troublesome: (1) purposelessness, (2) philosophical materialism, and (3) lack of being progressive.
Natural selection is purposeless, requiring no input from a higher Power; it does not require God or God's purposes as an explanation for the seeming harmony in the world. Thus natural selection is opposed to creation as an active process by which God acts to mold life to his purposes. Religious believers who palpably experience God acting in their personal lives find it hard to accept that God also does not act to develop his creation.
Natural selection is materialistic, holding that matter is the main reality of existence and that mental and spiritual phenomena, including thought, will, and feeling, can be explained in terms of matter, as its byproducts. Many religious believers understand God to have created human beings for the expressed purpose of embodying reason and spirituality, by which they can know God and manifest a divine nature. A theory such as evolution, which holds that mind and spirit are mere byproducts of a materialistic process, cannot square with belief in the supremacy of mind and spirit as the highest aspects of creation.
Evolution by natural selection is not progressive from lower to higher, but just an adaptation to local environments; it could form a man with his superior brain or a parasite, but no one could say which is higher or lower. Humans are granted no special status. The view that human beings are evolved, not as a designed end-result but as if by accident, is squarely at odds with many religious interpretations.
Belief in creation by a higher power is linked with some notion of design. The designs of the creation begin in the mind of God, who forms creatures according to these designs. This is what the Gospel of John teaches by the statement: "In the beginning was the Word"—and Jewish, Muslim and Hindu scriptures have similar concepts. If there is an evolutionary process, there should be the input of God's design along the way, directing the process. In this view, protozoa cannot just evolve by a purposeless process into mammals. The creation of higher-order beings should require the investment of God's labor and thought. The development of sophisticated new designs via such a "purposeless" process as natural selection has been compared to having a hurricane assemble a 747 airplane from just the parts.
In recent years, the intelligent design (ID) movement has gained momentum in the United States. ID essentially holds that it is possible to infer from empirical evidence that some features of the natural world are best explained by an intelligent agent. This movement seeks to present in educational institutions a scientific critique of evolutionary theory and offer the possibility of living organisms being designed. Technically it is not considered a religious perspective according to many of its advocates, since it presents its views without reference to whom or what that designer may be.

History of evolutionary thought
The idea of biological evolution has existed since ancient times, notably among Hellenists such as Epicurus and Anaximander, but the modern theory was not established until the eighteenth and nineteenth 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 that provided the mechanism of natural selection as the means by which evolutionary change occurs. Darwin was motivated to publish his work after receiving a letter from Alfred Russel Wallace, in which Wallace revealed his own concept of natural selection.
Darwin's theory 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 nineteenth and early twentieth centuries that these mechanisms were established.
When Gregor Mendel's work regarding the nature of inheritance in the late nineteenth century was "rediscovered," 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, Oswald Avery, Colin McCleod, and Maclyn 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.
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. In the mid-1970s, Motoo Kimura formulated the neutral theory of molecular evolution, firmly establishing the importance of genetic drift as a major mechanism involved in evolution.

Disciplines in evolutionary studies
Scholars in a number of academic disciplines and subdisciplines are involved in evolutionary studies.

Physical anthropology
Physical anthropology emerged in the late 1800s as the study of human osteology, and the fossilized skeletal remains of other hominids. At that time, anthropologists debated whether their evidence supported Darwin's claims, because skeletal remains revealed temporal and spatial variation among hominids, but Darwin had not offered an explanation of the mechanisms that produce variation. With the recognition of Mendelian genetics and the rise of the modern synthesis, however, evolution became both the fundamental conceptual framework for, and object of study of, physical anthropologists. In addition to studying skeletal remains, they began to study genetic variation among human populations (i.e. population genetics; thus, some physical anthropologists began calling themselves biological anthropologists).

Evolutionary biology
Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time.
At first, it was an interdisciplinary field, including scientists from many traditional taxonomically oriented disciplines, but not a discipline in its own right. Scientists were involved who generally had specialist training in particular organisms or groups of organisms, such as mammalogy, ornithology, or herpetology, but used 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 is an emergent subfield of evolutionary biology that looks at genes of related and unrelated organisms. By comparing the nucleotide sequences of DNA/RNA, it is possible to experimentally develop proposals for timelines of species development. For example, gene sequences support the perspective that chimpanzees are the closest primate ancestor to humans, and that arthropods (e.g., insects) and vertebrates have a common biological ancestor.

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