In biology, the concept of evolution applies to a natural process whereby a distinct population of living systems, a biological species, for example, changes in its biological characteristics over generations, often with many new and diverse types of living systems emerging in the process. That application of the word 'evolution' to living systems does not exhaust the biological systems the word applies to; it includes transgenerational molecular evolution and language evolution, for example.
In his 1998 edition of Evolutionary Biology, evolutionary biologist Douglas Futuyma defined 'evolution' thus:
"In its broadest sense, evolution simply means "change"...Usually..we don't apply the term to the changes an individual entity undergoes during its lifetime [i.e., its 'ontogeny']. Rather, an evolving system is ordinarily one in which there is descent of entities [viz., populations of similar entities], one generation from another, over time, and in which characteristics of the entities differ across generations. Thus evolution in a broad sense is descent with modification, and often with diversification."
Expanding in his 2009 edition of Evolution, he writes:
"It [‘evolution’] is sometimes used to describe changes in individual objects such as stars. Biological' (or organic) evolution, however, is change in the properties of groups of organisms over the course of generations. The development, or ONTOGENY, of an individual organism is not consid¬ered evolution: individual organisms do not evolve. Groups of organisms, which we may call populations, undergo descent with modification. Populations may become subdivided, so that several populations are derived from a common ancestral population. If different changes transpire in the several populations, the populations diverge.”
In one of the specific forms the process of evolution unrolls, a closely related group of organisms, referred to as a 'population', undergoes modifications of its characteristics—traits, or so-called phenotypes—over a period of generations in a manner that subdivides a parent population into distinctly differing descendant populations, a process in which a common ancestral population gives rise to diverse populations—the process of change referred to as 'descent with modification'.
- 1 Brief history of the idea of evolution
- 2 Mechanisms that mediate evolution
- 3 Current research
- 4 Common misunderstandings about evolutionary theory
- 5 Social and religious controversies
- 6 References
During the 1800s, before mid-century, two factors in combination had made biological evolution plausible and likely to open-minded leading scientists, such as the eminent geologist, Charles Lyell, and biologist Alfred Russel Wallace. The first: Evidence from strategraphic geology suggested a much older age of the earth than the approximately 4,000 years biblical scholars had determined for the Christian orthodox view, important evidence because of a constraining power of Christianity on the acceptance of scientific ideas that contradicted accepted interpretation of the Christian bible. No less important, the much older age of the earth would have extended greatly a time for biological evolution to occur. The second: Evidence from paleontology indicated the existence of unfamiliar species from the time of the old earth, in the old geographic strata, now extinct.
Thus, biological evolution was plausible and considered likely in science by the mid-1800s because the earth appeared very old and because species existed in the old earth, but not the contemporary species, extinct forms from which contemporary species might have descended by transformation. By mid-century the time was ripe for theories to explain how a descendant evolution might occur, and for a few, ripe for strictly naturalistic theories.
The word 'evolution' derives from the Latin word evolvere, which translates to 'to unfold', or 'to unroll', as if to unroll an ancient scroll and display the intellectual potentialities hidden within, or to unfold the map of time-development of biological diversity. Before the word 'evolution' was introduced in biology to refer to the process of transgenerational changes in species, the process was referred to as 'transmutation', or 'transformation', the concepts, 'transmutationism' and 'transformationism'.
As mentioned above, 'evolution' applies not only to biological evolution, the topic of the present article, but also to other domains of nature that change in a descendant way similar to that of biological evolution, such as the evolution of the universe itself.
Among the many ways biologists recognize the explanatory power of the concept of evolution, they can account for the vast biodiversity of living systems on Earth, including the many extinct species attested in the fossil record. An evolutionary perspective can lead to insights for preventing, diagnosing and treating human diseases.
Most biologists endorse the proposition of the 20th century's pioneering evolutionary biologist, Theodosius Dobzhansky, videlicet: "Nothing in biology makes sense except in the light of evolution." For evolutionary biologists, not surprisingly, evolution takes center stage, in particular as "the unifying theory of biology". 
Biologists distinguish between the factuality of evolution and theories of its mechanism.
Although there is overwhelming scientific consensus supporting the reality of biological evolution, because of its potential implications for the origins of humankind, evolutionary theory has been at the center of many social and religious controversies since its inception.
Brief history of the idea of evolution
The concept that plants and animals change form over generations has existed since ancient times, notably among Greek philosophers such as Anaximander and Epicurus  and Indian philosophers such as Patañjali.
Evolution is not so much a modern discovery as some of its advocates would have us believe. It made its appearance early in Greek philosophy, and maintained its position more or less, with the most diverse modifications, and frequently confused with the idea of emanation, until the close of ancient thought. The Greeks had, it is true, no term exactly equivalent to ” evolution”; but when Thales asserts that all things originated from water; when Anaximenes calls air the principle of all things, regarding the subsequent process as a thinning or thickening, they must have considered individual beings and the phenomenal world as, a result of evolution, even if they did not carry the process out in detail. Anaximander is often regarded as a precursor of the modem theory of development. He deduces living beings, in a gradual development, from moisture under the influence of warmth, and suggests the view that men originated from animals of another sort, since if they had come into existence as human beings, needing fostering care for a long time, they would not have been able to maintain their existence. In Empedocles, as in Epicurus and Lucretius, who follow in Hs [sic] footsteps, there are rudimentary suggestions of the Darwinian theory in its broader sense; and here too, as with Darwin, the mechanical principle comes in; the process is adapted to a certain end by a sort of natural selection, without regarding nature as deliberately forming its results for these ends. 
The ancient Greeks started the naturalists and devotees of natural history, as well as the world of science known as natural philosophy, on the path of thinking about change in the animate and inanimate world and the implications of those thoughts on the changes in the recent past and on future change. By the mid-1400s ideas of evolution began fast growing in abundance. Them concept of evolution responded to the fuel of expanding knowledge of fossilized living things, and the recognition of Earth's history, its long time of existence, coming up with the idea that the available time favored evolution of present living things from ancestors that looked different in their fossilized remains.
Mechanisms that mediate evolution
Jean-Baptiste Lamarck theorized that living things passed on their traits to offspring, but his theories differed from modern evolutionary theory in that he believed that acquired traits were passed on. Thus, Lamarckian evolution posits that the giraffe acquired its long neck from stretching to reach higher foliage. An individual giraffes lengthened its neck from a lifetime of stretching, and passed on the longer neck to its offspring, which themselves stretched to reach even-higher branches, creating a cycle that concluded with the long necks of today's giraffes.
The transmutation of species was accepted by many scientists before 1859, but Charles Darwin's On The Origin of Species by Means of Natural Selection provided the first convincing exposition of a mechanism by which evolutionary change could occur: natural selection. After many years of working in private on his theory, Darwin was motivated to publish his work on evolution when he received a letter from Alfred Russell Wallace in which Wallace revealed his own, independent discovery of natural selection. Accordingly, Wallace is usually given shared credit for originating the theory.
Darwin's book sparked a great deal of scientific and social debate. Darwin's work relied on many different fields of scientific inquiry for its evidence, and debates over the theory took place in many different arenas. Although the occurrence of biological evolution was generally accepted by scientists, Darwin's specific ideas about evolution—that it occurred gradually, through natural selection—were contested. Additionally, while Darwin was able to observe variation, and infer natural selection and thereby adaptation, he was unable to explain how variation might arise, or be altered over generations. Darwin's proposal of a hereditary mechanism (pangenesis) lacked evidence and was ultimately rejected, being replaced by genetics.
From the end of the 19th century through the early 20th century, forms of neo-Lamarckism, "progressive" evolution (orthogenesis), and an evolution which worked by "jumps" (saltationism, as opposed to gradualism) became popular, although a form of neo-Darwinism, led by August Weismann, also enjoyed some minor success. The biometric school of evolutionary theory, resulting from the work of Darwin's cousin, Francis Galton, emerged as well, using statistical approaches to biology which emphasized gradualism and some aspects of natural selection.
Mendel's work was "rediscovered" in 1901. Debates over various aspects of how evolution occurs have continued. One prominent debate was over the theory of punctuated equilibrium, proposed in 1972 by paleontologists Niles Eldredge and Stephen Jay Gould to explain the paucity of gradual transitions between species in the fossil record, as well as the absence of change or stasis that is observed over significant intervals of time.
Evolutionary biology is concerned with the origin and descent of species, as well as their changes over time. It is an interdisciplinary field including scientists from many traditional taxonomically-oriented disciplines, including scientists with specialist training in particular organisms, such as mammalogy, ornithology, or herpetology, but who use those organisms 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.
Evolutionary developmental biology (informally, evo-devo) is a field of biology that compares the developmental processes of different animals in an attempt to determine the ancestral relationship between organisms and how developmental processes evolved. The discovery of genes regulating development in model organisms allowed for comparisons to be made with genes and genetic networks of related organisms.
Physical anthropology emerged in the late 19th century 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 specific 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 the object of study of, physical anthropologists. In addition to studying skeletal remains, they began to study genetic variation among human populations (population genetics); thus, some physical anthropologists began calling themselves biological anthropologists.
Fossils are critical evidence for estimating when various lineages originated. Since fossilization of an organism is an uncommon occurrence, usually requiring hard parts (like teeth, bone or pollen), the fossil record is traditionally thought to provide only sparse and intermittent information about ancestral lineages. Fossilization of organisms without hard body parts is rare, but does happen under unusual circumstance; very rapid burial, and both low oxygen environment and sparse microbial action.
The fossil record contains the earliest known examples of life itself, as well as the earliest occurrences of individual lineages. The first complex animals date from the early Cambrian period, approximately 520 million years ago. The records of individual species yield information regarding the patterns and rates of evolution, showing for example if species evolve into new species (speciation) gradually and incrementally, or in relatively brief intervals of geologic time. The fossil record is a document of large scale patterns and events in the history of life, many of which have influenced the evolutionary history of numerous lineages. Mass extinctions frequently resulted in the loss of entire groups of species, such as the non-avian dinosaurs, while leaving others relatively unscathed. Recently, molecular biologists have used the time since divergence of related lineages to calibrate the rate at which mutations accumulate, and at which the genomes of different lineages evolve.
Phylogenetics, 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. The appendages on bat wings, for example, are very structurally similar to human hands, and may constitute a vestigial structure. Other examples include the presence of hip bones in whales and snakes. Such structures may exist with little or no function in a more current organism, yet have a clear function in an ancestral species of the same. Examples of vestigial structures in humans include wisdom teeth, the coccyx and the vermiform appendix.
Comparison of DNA sequences allows organisms to be grouped by sequence similarity, and the resulting phylogenetic trees are typically congruent with traditional taxonomy, and are often used to strengthen or correct taxonomic classifications. 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. 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. Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes. The sequence of the 16S rRNA gene, a vital gene encoding a part of the ribosome, was used to find the broad phylogenetic relationships between all extant life. The analysis, originally done by Carl Woese, resulted in the three-domain system, arguing for two major splits in the early evolution of life. The first split led to modern Bacteria and the subsequent split led to modern Archaea and Eukaryote.
The proteomic evidence also supports the universal ancestry of life. Vital proteins, such as the ribosome, DNA polymerase, and RNA polymerase are found in the most primitive bacteria to the most complex mammals. The core part of the protein is conserved across all lineages of life, serving similar functions. Higher organisms have evolved additional protein subunits, largely affecting the regulation and protein-protein interaction of the core. Other overarching similarities between all lineages of extant organisms, such as DNA, RNA, amino acids, and the lipid bilayer, give support to the theory of common descent. The chirality of DNA, RNA, and amino acids is conserved across all known life. As there is no functional advantage to right or left handed molecular chirality, the simplest hypothesis is that the choice was made randomly in the early beginnings of life and passed on to all extant life through common descent.
Molecular evidence also offers a mechanism for large evolutionary leaps and macroevolution. Horizontal gene transfer, the process in which an organism transfers genetic material (i.e. DNA) to another cell that is not its offspring, allows for large sudden evolutionary leaps in a species by incorporating beneficial genes evolved in another species. The Endosymbiotic theory explains the origin of mitochondria and plastids (e.g. chloroplasts), which are organelles of eukaryotic cells, as the incorporation of an ancient prokaryotic cell into ancient eukaryotic cell. Rather than evolving eukaryotic organelles slowly, this theory offers a mechanism for a sudden evolutionary leap by incorporating the genetic material and biochemical composition of a separate species. This evolutionary mechanism has been observed. Heneta, a protist, is an extant organism that is undergoing endosymbiotic evolution.
What accounts for genetic variation? Mutations are permanent, transmissible changes to the genetic material of a cell. These changes can be caused by: "copying errors" in the genetic material during cell division. (Explain frame shift) Exposure to radiation, certain chemicals, and some viruses can destabilize these genetic molecules and cause biochemical changes that are permanent. When mutations are made in the genes of a cell they ordinarily will be passed on to daughter cells when the cell divides. In multicellular organisms, the mutations will be passed on to progeny if germline mutations, that is- if the genes in the gametes are changed. Mutations that are not affected by natural selection are called neutral mutations. Their frequency in the population is governed by mutation rate, genetic drift and selective pressure on linked alleles. It is understood that most of a species' genome, in the absence of selection, undergoes a steady accumulation of neutral mutations.
Mobile elements, transposons, make up a major fraction of the genomes of plants and animals and appear to have played a significant role in the evolution of genomes. These mobile insertional elements can jump within a genome and alter existing genes and gene networks to produce evolutionary change and diversity.
Selection and adaptation
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 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:
- Positive or directional selection increases the frequency of a beneficial mutation, or pushes the mean in either direction.
- Purifying or stabilizing selection maintains a common trait in the population by decreasing the frequency of harmful mutations and weeding them out of the population. "Living fossils" are arguably the product of stabilizing selection, as their form and traits have remained virtually identical over a long period of time. It is argued that stabilizing selection is the most common form of natural selection.
- Artificial selection refers to purposeful breeding of a species to produce a more desirable and “perfect” breed. Humans have directed artificial selection in the breeding of both animals and plants, with examples ranging from agriculture (crops and livestock) to pets and horticulture. However, because humans are only part of the environment, the fractions of change in a species due to natural or artificial means can be difficult to determine. Artificial selection within human populations is a controversial enterprise known as eugenics.
- Balancing selection maintains variation within a population through a number of mechanisms, including:
- Heterozygote advantage or overdominance, where the heterozygote is more fit than either of the homozygous forms (exemplified by human sickle cell anemia conferring resistance to malaria)
- Frequency-dependent selection, where rare variants either have increased fitness or decreased fitness, because of their rarity.
- Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.
- Selective sweeps describe the affect of selection acting on linked alleles. It comes in two forms:
- Background selection occurs when a deleterious mutation is selected against, and linked mutations are eliminated along with the deleterious variant, resulting in lower genetic polymorphism in the surrounding region.
- Genetic hitchhiking occurs when a beneficial allele is selected for, and linked alleles, which can be neutral or beneficial, are pushed towards fixation along with the beneficial allele.
Most biologists believe that adaptation occurs through the accumulation of many mutations of small effect. However, macromutation is an alternative process for adaptation that involves a single, very large scale mutation.
In asexual organisms, variants in genes on the same chromosome will always be inherited together - they are linked, by virtue of being on the same DNA molecule. However, sexual organisms, in the production of gametes, shuffle linked alleles on homologous chromosomes inherited from the parents via meiotic recombination. This shuffling allows independent assortment of alleles (mutations) in genes to be propagated in the population independently. This allows bad mutations to be purged and beneficial mutations to be retained more efficiently than in asexual populations.
However, the meitoic recombination rate is not very high - on the order of one crossover (recombination event between homomolgous chromosomes) per chromosome arm per generation. Therefore, linked alleles are not perfectly shuffled away from each other, but tend to be inherited together. This tendency may be measured by comparing the co-occurrence of two alleles, usually quantified as linkage disequilibrium (LD). A set of alleles that are often co-propagated is called a haplotype. Strong haplotype blocks can be a product of strong positive selection.
Gene flow and population structure
Gene flow (also called gene admixture or simply migration) is the exchange of genetic variation between populations, when geography and culture are not obstacles. Ernst Mayr thought that gene flow is likely to be homogenising, and therefore counteract selective adaptation. Where there are obstacles to gene flow, the situation is termed reproductive isolation and is considered to be necessary for speciation.
The free movement of alleles through a population may also be impeded by population structure. For example, most real-world populations are not actually fully interbreeding; geographic proximity has a strong influence on the movement of alleles within the population.
An example of the effect of population structure is the so-called founder effect, resulting from a migration or population bottleneck, in which a population temporarily has very few individuals, and therefore loses a lot of genetic variation. In this case, a single, rare allele may suddenly increase very rapidly in frequency within a specific population if it happened to be prevalent in a small number of "founder" individuals. The frequency of the allele in the resulting population can be much higher than otherwise expected, especially for deleterious, disease-causing alleles. Since population size has a profound effect on the relative strengths of genetic drift and natural selection, changes in population size can alter the dynamics of these processes considerably.
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. Thus, over time even in the absence of selection upon the alleles, allele frequencies will tend to "drift" upward or downward, eventually becoming "fixed" - that is, going to 0% or 100% frequency. Thus, fluctuations in allele frequency between successive generations may result in some alleles disappearing from the population due to chance alone. Two separate populations that begin with the same allele frequencies therefore might drift apart by random fluctuation into two divergent populations with different allele sets (for example, alleles present in one population could be absent in the other, or vice versa).
The impact of genetic drift depends strongly on the size of the population (generally abbreviated as N): drift is important in small mating populations (see Founder effect and Population bottleneck), where chance fluctuations from generation to generation can be large. 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 predominant 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.
Speciation and extinction
Speciation is the process by which new biological species arise. This may take place by various mechanisms. Allopatric speciation occurs in populations that become isolated geographically, such as 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. An example of rapid sympatric speciation can be eloquently represented in the triangle of U; where new species of Brassica sp. have been made by the fusing of separate genomes from related plants.
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 — species are created by speciation, and disappear through extinction. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 90% of all marine species and 70% of terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event many forms of life perished (including approximately 50% of all genera), the most often mentioned among them being the extinction of the non-avian dinosaurs.
Evolution is still an active field of research in the scientific community. Improvements in sequencing methods have resulted in a large increase of sequenced genomes, allowing for the testing and refining of the theory of evolution with respect to whole genome data. Advances in computational hardware and software have allowed for the testing and extrapolation of increasingly advanced evolutionary models. Discoveries in biotechnology have produced methods for the ‘’de novo’’ synthesis of proteins and, potentially, entire genomes, driving evolutionary studies at the molecular level.
Common misunderstandings about evolutionary theory
Progressiveness, complexity, and evolution
|Evolutionary processes and, in general, scientific explanations of the world are often in contrast with the immediate and simple explanations that our brain gives of reality (e.g. the sun seems to turn around the earth, the earth seems to be flat), and are influenced by what Francis Bacon called "idola"[] (false notions or tendencies which distort the truth []).|
One of the most common misunderstandings of evolution is that one species can be "more highly evolved" than another, that evolution is necessarily progressive and/or leads to greater "complexity", or that its converse is "devolution". Evolution provides no assurance that later generations are more intelligent or complex than earlier generations. The claim that evolution results in progress is not part of modern evolutionary theory; it derives from earlier belief systems which were held around the time Darwin devised his theory of evolution.
Evolution has involved "progression" towards more complexity, since all of the earliest lifeforms were extremely simple and there was nowhere to go but up. However, there is no guarantee that any particular organism existing today will become more intelligent, more complex, bigger, or stronger in the future. In fact, natural selection will only favor this kind of "progression" if it has a variant to act upon that increases chance of survival, i.e. the ability to live long enough to raise offspring to sexual maturity. The same mechanism can actually favor lower intelligence, lower complexity, and so on if those traits become a selective advantage in the organism's environment.
One way of understanding the apparent "progression" of lifeforms over time is to remember that the earliest life began as components of cells. Evolution caused life to become more complex, since becoming simpler wasn't advantageous. Once individual lineages have attained sufficient complexity, simplifications (specialization) become more likely.
It is sometimes claimed that speciation – the origin of new species – has never been directly observed, and thus evolution cannot be called sound science. This is a misunderstanding of both science and evolution. First, scientific discovery does not occur solely through reproducible experiments; the principle of uniformitarianism allows natural scientists to infer causes through their empirical effects. Moreover, since the publication of On the Origin of Species scientists have confirmed Darwin's hypothesis by data gathered from sources that did not exist in his day, such as DNA similarity among species and new fossil discoveries. Finally, speciation has actually been directly observed. (See the hawthorn fly example.)
A variation of this assertion that microevolution has been observed and macroevolution has not been observed is subject to the same counterarguments. While there is debate over the details of how evolution happened, it is generally accepted that macroevolution uses the same mechanisms of change as those already observed in microevolution.
Purposiveness and evoluton
Peter Bowler, eminent historian of science, in his 3rd edition of his widely cited Evolution: History of an Idea, writes:
The antagonism of the creationists should not blind us to the fact that science and religion have sometimes been able to work in harmony. The history of evolutionism reveals many attempts to see the development of life on earth as the unfolding of a divine plan. There have certainly been some scientists who would adopt a more militant posture, arguing that humanity simply has to come to terms with the unpleasant fact that it is the product of a purposeless sequence of natural events.
Yes, we humans may have resulted from “a purposeless sequence of natural events”, but the fact of that happening to us I do not find “unpleasant”. The purposelessness of the sequence of natural events in evolution, even considering biological evolution only, does not necessarily exclude, in a lineage of entities, that new kinds of evolvable entities might emerge that could impose purpose on evolutionary change. Indeed, human culture emerged, in part from new entities called ‘memes’ or ‘culturgens’, whose evolvable complex associations create knowledge and ideas. The eugenics movement early exemplified the potentiality for the lineage culminating in Homo sapiens to purposefully order the sequence of natural events.
Social and religious controversies
Starting with the publication of The Origin of Species in 1859, the modern science of evolution has been a source of nearly constant controversy. In general, controversy has centered on the philosophical, cosmological, social, and religious implications of evolution, not on the science of evolution itself. The proposition that biological evolution occurs through the mechanism of natural selection has been almost completely uncontested within the scientific community for much of the 20th century.
As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its applicability to human beings. The idea that all diversity in life, including human beings, arose through natural processes without a need for supernatural intervention poses difficulties for the belief in purpose inherent in most religious faiths — and especially for the Abrahamic religions. Many religious people are able to reconcile the science of evolution with their faith, or see no real conflict Judaism and Catholicism are notable as major faith traditions whose adherents generally see no conflict between evolutionary theory and religious belief. The idea that faith and evolution are compatible has been called theistic evolution. Another group of religious people, generally referred to as creationists, consider evolutionary origin beliefs to be incompatible with their faith, their religious texts and their perception of design in nature, and so cannot accept what they call "unguided evolution".
One particularly contentious topic evoked by evolution is the biological status of humanity. Whereas the classical religious view can broadly be characterized as a belief in the great chain of being (in which people are "above" the animals but slightly "below" the angels), the science of evolution is clear both that humans are animals and that they share common ancestry with chimpanzees, gibbons, gorillas, and orangutans. Some people find the idea of common ancestry repellent, as, in their opinion, it "degrades" humankind. A related conflict arises when critics combine the religious view of people's superior status with the mistaken notion that evolution is necessarily "progressive". If human beings are superior to animals yet evolved from them, these critics claim, "inferior" animals would not still exist. Because animals that are (in their view) "inferior" creatures do demonstrably exist, those criticising evolution sometimes incorrectly take this as supporting their claim that evolution is false.
In some countries — notably the USA — these and other tensions between religion and science have fueled what has been called the creation-evolution controversy, which, among other things, has generated struggles over the teaching curriculum. While many other fields of science, such as cosmology and earth science, also conflict with a literal interpretation of many religious texts, evolutionary studies have borne the brunt of these debates.
Evolution has been used to support philosophical and ethical choices which most modern scientists argue are neither mandated by evolution nor supported by science. For example, the eugenic ideas of Francis Galton were developed into arguments that the human gene pool should be improved by selective breeding policies, including incentives for reproduction for those of "good stock" and disincentives, such as compulsory sterilization, "euthanasia", and later, prenatal testing, birth control, and genetic engineering, for those of "bad". Another example of an extension of evolutionary theory that is widely regarded as unwarranted is "Social Darwinism"; a term given to the 19th century Whig Malthusian theory developed by Herbert Spencer into ideas about "survival of the fittest" in commerce and human societies as a whole, and by others into claims that social inequality, racism, and imperialism were justified.
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- In the years after Darwin's publication, numerous "predecessors" to natural selection were discovered, such as William Charles Wells and Patrick Matthew, who had published unelaborated and undeveloped versions of similar theories earlier to little or no attention. Darwin was the first to develop the theory rigorously and developed it independently. On Matthew, one historian of evolution has written that he "did suggest a basic idea of selection, but he did nothing to develop it; and he published it in the appendix to a book on the raising of trees for shipbuilding. No one took him seriously, and he played no role in the emergence of Darwinism. Simple priority is not enough to earn a thinker a place in the history of science: one has to develop the idea and convince others of its value to make a real contribution. Darwin's notebooks confirm that he drew no inspiration from Matthew or any of the other alleged precursors." Bowler, PJ (2003). Evolution: The History of an Idea. Berkeley: University of California Press, 158.
- Bowler,P.J. (2003) Evolution: The History of an Idea. 3rd ed., completely rev. and expanded. Berkeley: University of California Press. ISBN 052236939. | Google Books preview. $From chapter 1: "Much can be gained from the lessons of history, especially an awareness of the dangers of oversimplification. Before we can undertake such a study, however, we must establish a framework for understanding the rise of modern evolutionism. We must identify the full range of issues over which evolutionism has challenged the traditional worldview. We must appreciate how aspects of the old view can be modernized to fit in with certain kinds of evolutionary thought. The basic idea of evolution can be developed in many different ways, each with its own broader implications. We must also look more closely at the problems facing the historian who has to seek a balance between the conventional image of science as the objective evaluation of factual data and the suspicion of many critics that scientific theories are value-laden contributions to philosophical and ideological debates."
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- Schweitzer M.H. et al (2005). "Soft-tissue vessels and cellular preservation in Tyrannosaurus rex". Science 307 (5717): 1952-1955.
- Two sources: 'Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees'. and 'Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes' " "
- The picture labeled "Human Chromosome 2 and its analogs in the apes" in the article Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry is literally a picture of a link in humans that links two separate chromosomes in the nonhuman apes creating a single chromosome in humans. It is considered a missing link, and the ape-human connection is of particular interest. Also, while the term originally referred to fossil evidence, this too is a trace from the past corresponding to some living beings which when alive were the physical embodiment of this link.
- The New York Times report Still Evolving, Human Genes Tell New Story, based on A Map of Recent Positive Selection in the Human Genome, states the International HapMap Project is "providing the strongest evidence yet that humans are still evolving" and details some of that evidence.
- Okamoto N, Inouye I. (2005). "A secondary symbiosis in progress". Science 310 (5746): 287.
- Okamoto N, Inouye I (2006). "Hatena arenicola gen. et sp. nov., a Katablepharid Undergoing Probable Plastid Acquisition.". Protist.
- Pseudogene evolution and natural selection for a compact genome. ""
- Hoskin et al (Oct 2005). "Reinforcement drives rapid allopatric speciation". Nature 437: 1353-1356.
- Savolainen et al (May 2006). "Sympatric speciation in palms on an oceanic island". Nature 441: 210-213.
- Barluenga et al (February 2006). "Sympatric speciation in Nicaraguan crater lake cichlid fish". Nature 439: 719-723.
- Hall MP. The Four Idols of Francis Bacon: The New Instrument of Knowledge.
- "In the Novum Organum (the new instrumentality for the acquisition of knowledge) Francis Bacon classified the intellectual fallacies of his time under four headings which he called idols. He distinguished them as idols of the Tribe, idols of the Cave, idols of the Marketplace and idols of the Theater…An idol is an image, in this case held in the mind, which receives veneration but is without substance in itself. Bacon did not regard idols as symbols, but rather as fixations."
- Fantini F. (2005) Didattica dell'evoluzione. In Evoluzione tra ricerca e didattica, XIV – Special number Edited by: Associazione Nazionale Insegnanti di Scienze Naturali. Agnano Pisano: Stamperia Editoriale Pisana; 2005:203-209.
- Guidetti R, Baraldi L, Calzolai C, Pini L, Veronesi P, Pederzoli A. (2007) Fantastic animals as an experimental model to teach animal adaptation. BMC Evolutionary Biology 7(Suppl 2):S13 doi: 10.1186/1471-2148-7-S2-S13.
- talkorigins Claim CB932: Evolution of degenerate forms
- Boxhorn, Joseph. Observed Instances of Speciation. Talk Origins Archive.
- An overview of the philosophical, religious, and cosmological controversies by a philosopher who strongly supports evolution is: Daniel Dennett, Darwin's Dangerous Idea: Evolution and the Meanings of Life (New York: Simon & Schuster, 1995). On the scientific and social reception of evolution in the 19th and early 20th centuries, see: Peter J. Bowler, Evolution: The History of an Idea, 3rd. rev. edn. (Berkeley: University of California Press, 2003).
- The Rabbinical Council of America notes that significant Jewish authorities have maintained that evolutionary theory, properly understood, is not incompatible with belief in a Divine Creator, nor with the first 2 chapters of Genesis. 
- The High Council of B'nei Noah a body of non-Jews guided by the Beit Din of B'nei Noah a sub-court of the developing Sanhedrin: Science and Religion: A proper perspective through an understanding of Hebrew sources
- Aish HaTorah According to a possible reading of ancient commentators' description of God and nature, the world may be simultaneously young and old.
- On the history of eugenics and evolution, see Daniel Kevles, In the Name of Eugenics: Genetics and the Uses of Human Heredity (New York: Knopf, 1985).