History of evolutionary thought
Evolutionary thought, the idea that species change over time, has roots in antiquity, in ideas of the Greeks, Romans, Chinese and Muslims. However, until the 18th century, Western biological thinking was dominated by essentialism, the idea that living forms are unchanging. During the Enlightenment, evolutionary cosmology and the mechanical philosophy spread from the physical sciences to natural history. Naturalists began to focus on the variability of species and the emergence of paleontology with the concept of extinction undermined the static view of nature. In the early 19th century Jean-Baptiste Lamarck proposed his theory of the transmutation of species, which was the first fully formed scientific theory of evolution.
The evolutionary theory often referred to as Darwinism was first put forward by Charles Darwin and Alfred Russel Wallace and discussed in detail in Darwin's On the Origin of Species (1859). Unlike Lamarck's theory, Darwinism proposed common descent and a branching tree of life. It was based on the idea of natural selection, and it synthesized evidence from animal husbandry, biogeography, geology, morphology, and embryology.
Darwin's work led to the rapid acceptance of evolution, but the mechanism he proposed, natural selection, was not widely accepted until the 1940s. Most biologists argued that other factors drove evolution, such as inheritance of acquired characteristics (neo-Lamarckism), an innate drive for change (orthogenesis), or sudden large mutations (saltationism). The synthesis of natural selection with Mendelian genetics during the 1920s and 1930s, founded the new discipline of population genetics. Throughout the 1930s and 1940s, population genetics became integrated with other branches of biology, finally resulting in a unified theory of evolution - the modern evolutionary synthesis.
Following the establishment of evolutionary biology, studies of mutation and variation in natural populations, combined with biogeography and systematics, led to sophisticated mathematical and causal models of evolution.  Paleontology and comparative anatomy allowed more detailed reconstructions of the history of life. After the rise of molecular genetics in the 1950s, the field of molecular evolution developed, based on DNA, RNA, and protein sequences. The gene-centered view of evolution then rose to prominence in the 1960s, followed by the neutral theory of molecular evolution, sparking debates over adaptationism, the units of selection, and the importance of genetic drift. In the late 20th century, genetic sequencing led to a reorganization of the tree of life into the three-domain system, and the newly-recognized factors of symbiogenesis and horizontal gene transfer have introduced yet more complexity into evolutionary history.

# Antiquity

## Greek thought
Some Greek philosophers discussed ideas that involved forms of organic evolution. Anaximander claimed that life had originally developed in the sea and only later moved onto land, and Empedocles also discussed a non-supernatural origin for living things. Empedocles even suggested a form of natural selection, which Aristotle summarized as, "Wherever then all the parts came about  just what they would have been if they had come to be for an end, such things survived, being organized spontaneously in a fitting way; whereas those which grew otherwise perished and continue to perish..."
Plato (427/8347/8 BC) was, in the words of biologist and historian Ernst Mayr, "the great antihero of evolutionism," as he established the philosophy of essentialism, which he called the theory of forms. This theory holds that objects observed in the real world are only reflections of a limited number of essences (eide). Variation is merely the result of an imperfect reflection of these constant essences. In his Timaeus, Plato set forth the idea that God had created the cosmos and everything in it because He is good, and hence, "... free from jealousy, He desired that all things should be as like Himself as they could be." God created all conceivable forms of life, since "... without them the universe will be incomplete, for it will not contain every kind of animal which it ought to contain, if it is to be perfect." This idea, that all potential forms of life are essential to a perfect creation, is called the plenitude principle, and it greatly influenced Christian thought.
Aristotle, (384322 BC), one of the most influential of the Greek philosophers, is the earliest natural historian whose work has come down to us in any real detail. His writings on biology were the result of his research into natural history on the isle of Lesbos, and have survived in the form of four books, usually known by their Latin names, De anima (on the essence of life), Historia animalium (inquiries about animals), De generatione animalium (reproduction), and De partibus animalium (anatomy). These works contain some remarkably astute observations and interpretations by Aristotle, along with sundry myths and mistakes  reflecting the uneven state of knowledge during his time.  However, for Charles Singer, "Nothing is more remarkable than  efforts to  the relationships of living things as a scala natur". This scala natur, described in History of Animals, classified organisms in relation to a hierarchical "Ladder of Life" or "Chain of Being", placing them according to complexity of structure and function, with organisms that showed greater vitality and ability to move described as "higher organisms".

## Chinese thought
Ideas on evolution were expressed by ancient Chinese thinkers such as Zhuangzi (Chang Tzu). According to Joseph Needham, Taoism explicitly denied the fixity of biological species.

## Roman thought
Titus Lucretius Carus (d. 50 BC), the Roman Epicurean and atomist, wrote the poem On the Nature of Things (De rerum natura), describing the development of the living earth in stages: from atoms colliding in the void as swirls of dust to early plants and animals springing from the early earth's substance, then a succession of animals, including a series of progressively less brutish humans. Lucretius may be seen as the earliest believer in hard inheritance. He said "For if each organism had not its own genetic bodies, how could we with certainty assign each to its mother?". The essence of Lucretius' ideas was naturalism, and the avoidance of supernatural interventions or explanations.

# Middle Ages

## Christian thought and the great chain of being
During the so-called Dark Ages, Greek classical learning was all but lost to the West. However, contact with the Islamic world, where Greek manuscripts were preserved and elaborated on, soon led to a massive spate of Latin translations in the 12th century. Europeans were thus re-introduced to the works of Plato and Aristotle, as well as Islamic thought. Christian thinkers combined Aristotlean classification with Plato's ideas of the goodness of God, and of all potential life forms being present in a perfect creation, to organize all inanimate, animate, and spiritual beings, into a huge interconnected system: the Scala Natur, or great chain of being.
Within this system, everything that existed could be placed in order, from "lowest" to "highest", with Hell at the bottom and God at the top  below God, an angelic hierarchy marked by the orbits of the planets, mankind in an intermediate position, and worms the lowest of the animals. As the universe was ultimately perfect, the Great Chain was also perfect. There were no empty links in the chain, and no link was represented by more than one species. But this also implied that, since every link is occupied, and none can be occupied twice, then no species can ever move from one position to another. To do so would leave one level empty and put two species on another. Thus, in this Christianized version of Plato's perfect universe, species could never change, but must remain forever fixed, in accordance with the text of Genesis. For humans to forget their position was even seen as sinful, whether they behaved like lower animals or aspired to a higher station than was given them by their Creator.
Creatures on adjacent steps were expected to closely resemble each other, an idea expressed in a saying which Charles Darwin often quoted: natura non facit saltum ("nature does not make leaps"). This basic concept of the great chain of being greatly influenced the thinking of Western civilization for centuries (and still has an influence today). It also formed a part of the argument from design presented by natural theology. As a classification system, it became the major organizing principle and foundation of the emerging science of biology in the 17th and 18th centuries.

## Islamic thought and the struggle for existence
Whereas Greek and Roman evolutionary ideas more or less died out in Europe after the fall of the Roman Empire, they were not lost to Islamic scientists and philosophers. In the Islamic Golden Age, early theories on evolution were taught in Islamic schools. John William Draper, the 19th century scientist, philosopher and historian, discussed the 12th century writings of al-Khazini as part of what he called the "Mohammedan theory of evolution". He compared these early theories to the modern Darwinian theory of evolution of his time, arguing that the former were developed "... much farther than we are disposed to do, extending them even to inorganic or mineral things."
The first Muslim biologist and philosopher to put forth detailed speculations about evolution was the Afro-Arab writer al-Jahiz in the 9th century. He considered the effects of the environment on the likelihood of an animal to survive and evolve, and first described the struggle for existence. Ibn Miskawayh's al-Fawz al-Asghar and the Brethren of Purity's Encyclopedia of the Brethren of Purity (The Epistles of Ikhwan al-Safa) expressed ideas about how species appeared: from matter into vapor and thence to water, then minerals into plants and then animals, leading to apes and, finally, humans. The polymath Ibn al-Haytham wrote a book in which he argued for evolutionism (although not natural selection). Numerous other Islamic scholars and scientists, such as Abu Rayhan al-Biruni, Nasir al-Din Tusi, and Ibn Khaldun discussed and developed these ideas. Translated into Latin, these works began to appear in the West after the Renaissance and may have had an impact on Western science.

# Renaissance and enlightenment
Some evolutionist theories explored between 1650 and 1800 postulated that the universe, including life on earth, had developed mechanically, entirely without divine guidance. Around this time, the mechanical philosophy of Descartes began to encourage the machine-like view of the universe which would come to characterise the scientific revolution. However, most contemporary theories of evolution, such of those of Gottfried Leibniz and J. G. Herder, held that evolution was a fundamentally spiritual process.  In 1751, Pierre Louis Maupertuis veered toward more materialist ground. He wrote of natural modifications occurring during reproduction and accumulating over the course of many generations, producing races and even new species, and he anticipated in general terms the idea of natural selection. Later in the 18th century G. L. L. Buffon suggested that what most people referred to as species were really just well-marked varieties modified from an original form by environmental factors. For example he believed that Lions, Tigers, leopards and house cats might all have a common ancestor. He speculated that the 200 or so species of mammals then known might have descended from as few as 38 original forms. Buffons evolutionary ideas were strictly limited. He believed each of the original forms had arisen through spontaneous generation and that they were shaped by internal moulds that limited the amount of change. Between 1767 and 1792 James Burnett, Lord Monboddo included in his writings not only the concept that that man had descended from primates, but also that, in response to their environment, creatures had found methods of transforming their characteristics over long time intervals.  In 1796 Charles Darwins grandfather,  Erasmus Darwin, published Zoonomia, which suggested "that all warm-blooded animals have arisen from one living filament.  In his 1802 poem Temple of Nature, he described the rise of life from minute organisms living in the mud to its modern diversity. 

# 19th century before On the Origin of Species

## Paleontology and geology
In 1796, Georges Cuvier published his findings on the differences between living elephants and those found in the fossil record. His analysis demonstrated that mammoths and mastodons were distinct species different from any living animal, effectively ending a long-running debate over the possibility of the extinction of a species. William Smith began the process of ordering rock strata by examining fossils in the layers while he worked on his geologic map of England. Independently, in 1811, Georges Cuvier and Alexandre Brongniart published an influential study of the geologic history of the region around Paris, which was based on the stratigraphic succession of layers of rock. These works helped establish the antiquity of the earth. Cuvier advocated catastrophism to explain the patterns of extinction and faunal succession revealed by the fossil record.
Knowledge of the fossil record continued to advance rapidly during the first few decades of the 19th century. By the 1840s, the outlines of the geologic timescale were becoming clear, and in 1841 John Phillips named three major eras, based on their predominant fauna: the Paleozoic, dominated by marine invertebrates and fish, the Mesozoic, the age of reptiles, and the current Cenozoic age of mammals. This progressive picture of the history of life was accepted even by conservative English geologists like Adam Sedgwick and William Buckland; however, also like Cuvier, they attributed the progression to repeated catastrophic episodes of extinction followed by new episodes of creation. Unlike Cuvier, Buckland and some other advocates of natural theology among British geologists made efforts to explicitly link the last catastrophic episode to the biblical flood.
From 1830 to 1833, Charles Lyell published his multi-volume work Principles of Geology, which advocated a uniformitarian alternative to the catastrophic theory of geology. Lyell claimed that, rather than being the products of cataclysmic (and possibly supernatural) events, the geologic features of the earth are better explained as the result of the same gradual geologic forces observable in the present day  but acting over immensely long periods of time. Although Lyell opposed evolutionary ideas (even questioning the consensus that the fossil record demonstrates a true progression), his concept that the earth was shaped by forces working gradually over an extended period, and the immense age of the earth assumed by his theories, would strongly influence future evolutionary thinkers such as Charles Darwin.

## Transmutation of species
Jean-Baptiste Lamarck proposed in his Philosophie Zoologique of 1809 a theory of the transmutation of species. Lamarck did not believe that all living things shared a common ancestor. Rather he believed that simple forms of life were created continuously by spontaneous generation. He also believed that an innate life force drove species to become more complex over time, advancing up a linear ladder of complexity that was related to the great chain of being. Lamarck also recognized that species were adapted to their environment. He explained this by saying that the same innate force driving increasing complexity, also caused the organs of an animal (or a plant) to change based on the use or disuse of that organ, just as muscles are affected by exercise. He argued that these changes would be inherited by the next generation and produce slow adaptation to the environment. It was this secondary mechanism of adaptation through the inheritance of acquired characteristics that would become known as Lamarckism and would influence discussions of evolution into the 20th century.  A radical British school of comparative anatomy that included the  anatomist Robert Grant was closely in touch with Lamarck's school of French Transformationism, which contained scientists such as Etienne Geoffroy Saint-Hilaire. Grant developed Lamarck's and Erasmus Darwin's ideas of transmutation and evolutionism, investigating homology to prove common descent. As a young student Charles Darwin joined Grant in investigations of the life cycle of marine animals. In 1826 an anonymous paper, probably written by Robert Jameson, praised Lammarck for explaining how higher animals had evolved from the simplest worms, which was the first use of the word evolved in a modern sense. 
In 1844 the Scottish publisher Robert Chambers anonymously published an influential, and extremely controversial book of popular science entitled Vestiges of the Natural History of Creation. This book proposed an evolutionary scenario for the origins of the solar system and life on earth. It claimed that the fossil record showed a progressive ascent of animals with current animals being branches off a main line that lead progressively to humanity. It implied that the transmutations lead to the unfolding of a preordained plan that had been woven into the laws that governed the universe. In this sense it was less completely materialistic than the ideas of radicals like Robert Grant, but its implication that humans were just the last step in the ascent of animal life incensed many conservative thinkers. The high profile of the public debate over Vestiges, with its depiction of evolution as a progressive process, would greatly influence the perception of Darwin's theory a decade later.
Ideas about the transmutation of species were associated with the radical materialism of the enlightenment and were attacked by more conservative thinkers. Cuvier attacked the ideas of Lamarck and Geoffroy Saint-Hilaire, agreeing with Aristotle that species were immutable. Cuvier believed that the individual parts of an animal were too closely correlated with one another to allow for one part of the anatomy to change in isolation from the others, and argued that the fossil record showed patterns of catastrophic extinctions followed by re-population, rather than gradual change over time. He also noted that drawings of animals and animal mummies from Egypt, which were thousands of years old, showed no signs of change when compared with modern animals. The strength of Cuvier's arguments and his reputation as a leading scientist helped keep transmutational ideas out of the scientific mainstream for decades.
In Britain, where the philosophy of natural theology remained influential, William Paley wrote the book Natural Theology with its famous watchmaker analogy, at least in part as a response to the transmutational ideas of Erasmus Darwin. Geologists influenced by natural theology, such as Buckland and Sedgwick, made a regular practice of attacking the evolutionary ideas of Lamarck, Grant, and The Vestiges of the Natural History of Creation. Although the geologist Charles Lyell opposed scriptural geology he also believed in the immutability of species, and in his Principles of Geology (18301833), he criticized Lamarck's theories of development. Idealists such as Louis Agassiz and Richard Owen believed that each species was fixed and unchangeable because it represented an idea in the mind of the creator. They believed that relationships between species could be discerned from developmental patterns in embryology, as well as in the fossil record, but that these relationships represented an underlying pattern of divine thought, with progressive creation leading to increasing complexity and culminating in humanity. Owen developed the idea of "archetypes" in the Divine mind that would produce a sequence of species related by anatomical homologies, such as vertebrate limbs. Owen led a public campaign that successfully marginalized Robert Grant in the scientific community.  Darwin would make good use of the homologies analyzed by Owen in his own theory, but the harsh treatment of Grant, along with the controversy surrounding Vestiges, would be major factors in his decision to delay publishing his ideas.

## Anticipations of natural selection
Several writers anticipated aspects of Darwin's theory, and in the third edition of On the Origin of Species published in 1861 he named those he had learnt about in an introductory appendix, An Historical Sketch of the Recent Progress of Opinion on the Origin of Species, which he added to in later editions.
In 1813, William Charles Wells read before the Royal Society essays assuming that there had been evolution of humans, and recognising the principle of natural selection. Charles Darwin and Alfred Russel Wallace were unaware of this work when they jointly published the theory in 1858, but Darwin later acknowledged that Wells had recognised the principle before them, writing that the paper "An Account of a White Female, part of whose Skin resembles that of a Negro" was published in 1818, and "he distinctly recognises the principle of natural selection, and this is the first recognition which has been indicated; but he applies it only to the races of man, and to certain characters alone." When Darwin was developing his theory, he was influenced by Augustin de Candolle's natural system of classification, which laid emphasis on the war between competing species.
Patrick Matthew wrote in the obscure book Naval Timber & Arboriculture that was published in 1831 of "continual balancing of life to circumstance. ...  progeny of the same parents, under great differences of circumstance, might, in several generations, even become distinct species, incapable of co-reproduction." Charles Darwin discovered this work after the initial publication of the Origin. In the brief historical sketch that Darwin included in the 3rd addition he says "Unfortunately the view was given by Mr. Matthew very briefly in an Appendix to a work on a different subject ... He clearly saw, however, the full force of the principle of natural selection."
It is important to understand that it is possible to look through the history of biology from the ancient Greeks onwards and discover anticipations of almost all of Darwin's key ideas. However, there are a couple of major differences between Darwin and his predecessors. Perhaps the most important difference is that the vast majority of Darwin's predecessors seem to have failed to understand the implications of their own ideas. As an example, Matthew chose to relegate his idea on natural selection to the appendix of a work on an unrelated subject, and William Charles Wells seems to have made little or no attempts to publicise his ideas beyond reading them to the Royal Society. Secondly, despite having enunciated the basic idea of natural selection, precursors of Darwin either assumed that it was self-evidently true, or gave merely logical arguments for its importance and failed to provide any empirical data. In other words, the anticipations of Darwin were merely formal and verbal.
T. H. Huxley pointed out in his essay on the reception of the Origin of Species:
The suggestion that new species may result from the selective action of external conditions upon the variations from their specific type which individuals present and which we call spontaneous because we are ignorant of their causation is as wholly unknown to the historian of scientific ideas as it was to biological specialists before 1858. But that suggestion is the central idea of the Origin of Species, and contains the quintessence of Darwinism.

## Natural selection
The biogeographical patterns Charles Darwin observed in places such as the Galapagos islands during the voyage of the Beagle caused him to doubt the fixity of species, and in 1837 Darwin started the first of a series of secret notebooks on transmutation. Darwin's observations lead him to view transmutation as a process of divergence and branching, rather than the ladder-like progression envisioned by Lamarck and others. In 1838 he read the new 6th edition of An Essay on the Principle of Population, written in the late 1700s by Thomas Malthus. Malthus' idea of population growth leading to a struggle for survival combined with Darwin's knowledge on how breeders selected traits, led to the inception of Darwin's theory of natural selection. Concerned by the intense controversy raging over other transmutational ideas, Darwin would develop this idea in private for the next 20 years, sharing it only with a handful of friendly naturalists through correspondence.
Unlike Darwin, Alfred Russel Wallace, influenced by the book Vestiges of the Natural History of Creation, already believed that transmutation of species occurred when he began his career as a naturalist. By 1855 his biogeographical observations during his field work in South America and the Malay Archipelago made him confident enough in a branching pattern of evolution to publish a paper that stated that every species originated in close proximity to an already existing closely allied species. Once again it was consideration of how the ideas of Malthus might apply to animal populations that lead Wallace to conclusions very similar to the ones reached by Darwin about the role of natural selection. In February 1858 Wallace, unaware of Darwin's unpublished ideas, wrote up his thoughts into an essay and mailed them to Darwin, asking for his opinion. The result was the joint publication of Darwin's theory of natural selection with Wallace in July. Darwin also began work in earnest on The Origin of Species, which he would publish in 1859.

# 18591930s: Darwin and after Darwin
While transmutation of species was accepted by a sizable number of scientists before 1859, it was the publication of Charles Darwin's On the Origin of Species that fundamentally transformed the debate over biological origins. Darwin argued that his branching version of evolution explained a wealth of facts in biogeography, anatomy, embryology, and other fields of biology. He also provided the first cogent mechanism by which evolutionary change could persist: his theory of natural selection.
One of the first and most important naturalists to be convinced by Origin was the British anatomist Thomas Henry Huxley. Huxley recognized that unlike the earlier transmutational ideas of Lamarck and Vestiges, Darwin's theory provided a mechanism for evolution without supernatural involvement. Huxley would make advocacy of evolution a cornerstone of the program of the X-club to reform and professionalize science by displacing natural theology with methodological naturalism, ending the domination of British natural science by the clergy. By the early 1870s in English-speaking countries, thanks partly to these efforts, evolution had become the mainstream scientific explanation for the origin of species. In his campaign for public and scientific acceptance of Darwin's theory, Huxley made extensive use of new evidence for evolution from paleontology. This included evidence that birds had evolved from reptiles, including the discovery of Archaeopteryx in Europe, and a number of fossils of primitive birds with teeth found in North America. Another important line of evidence involved fossils that helped trace the evolution of the horse from its small five-toed ancestors. However, acceptance of evolution among scientists in non-English speaking nations such as France, and the countries of southern Europe and Latin America was slower. An exception to this was Germany, where both August Weismann and Ernst Haeckel championed this idea: with Haeckel using evolution to challenge the established tradition of metaphysical idealism in German biology, much as Huxley used it to challenge natural theology in Britain.
Darwin's theory succeeded in profoundly shaking scientific opinion regarding the development of life and resulted in a small social revolution. However, this theory could not explain several critical components of the evolutionary process. Namely, Darwin was unable to explain the source of variation in traits within a species, and could not identify a mechanism that could pass traits faithfully from one generation to the next. Darwin's hypothesis of pangenesis, while relying in part on the inheritance of acquired characteristics, proved to be useful for statistical models of evolution that were developed by his cousin Francis Galton and the "biometric" school of evolutionary thought. This idea was, however, of little use to biologists.

## Application of the theory to humans
Charles Darwin was aware of the severe reaction in some parts of the scientific community against the suggestion made in Vestiges of the Natural History of Creation that humans had arisen from animals by a process of transmutation. Therefore he almost completely ignored the topic of human evolution in The Origin of Species. Despite this precaution, the issue featured prominently in the debate that followed the book's publication. For most of the first half of the 19th century the scientific community believed that, although geology had shown that the earth and life were very old, human beings had appeared suddenly just a few thousand years before the present. However, a series of archaeological discoveries in the 1840s and 1850s showed stone tools associated with the remains of extinct animals. By the early 1860s, as summarized in Charles Lyell's 1863 book Geological Evidences of the Antiquity of Man, it had become widely accepted that humans had existed during a prehistoric period - which stretched many thousands of years before the start of written history. This new view of human history was more compatible than the older one with an evolutionary origin for humanity. On the other hand, there was no fossil evidence of human evolution that was known at the time. The only human fossils found before the discovery of Java man in the 1890s were either of anatomically modern humans, or of Neanderthals that were too close, especially in the critical characteristic of cranial capacity, to modern humans for them to be convincing intermediates between humans and other primates.
Therefore the debate that immediately followed the publication of The Origin of Species centered on the similarities and differences between humans and modern apes. Richard Owen vigorously defended the traditional classification, suggested by Carolus Linnaeus and Cuvier, that placed humans in a completely separate order from any of the other mammals. On the other hand, Huxley sought to demonstrate a close anatomical relationship between humans and apes. In one very famous incident, Huxley showed that Owen was mistaken in claiming that the brains of gorillas lacked a structure present in human brains. Huxley summarized his argument in his highly influential 1863 book Evidence as to Man's place in Nature. Another viewpoint was advocated by Charles Lyell and Alfred Russel Wallace. They agreed that humans shared a common ancestor with apes, but questioned whether any purely materialistic mechanism could account for some of the differences between humans and apes, especially some aspects of the human mind.
In 1871 Darwin published The Descent of Man, and Selection in Relation to Sex, which contained his views on human evolution. Darwin argued that the differences between the human mind and the minds of the higher animals were a matter of degree rather than of kind. For example, he viewed morality as a natural outgrowth of instincts that were beneficial to animals living in social groups. He believed that all the differences between humans and apes could be explained by a combination of the selective pressures resulting from our ancestors moving from the trees to the plains, and sexual selection. The debate over human origins, and over the degree of human uniqueness would continue well into the 20th century.

## Alternatives to natural selection
Evolution was widely accepted in scientific circles within a few years after the publication of Origin, but the acceptance of natural selection as its driving mechanism was much less widespread. The four major alternatives to natural selection in the late 19th century, were theistic evolution, neo-Lamarckism, orthogenesis, and saltationism. Theistic evolution was the idea that God intervened in the process of evolution to guide it in such a way that the living world could still be considered to be designed. However, this idea rapidly fell out of favor among scientists. They became more and more committed to the idea of methodological naturalism and came to believe that direct appeals to supernatural involvement were scientifically unproductive and a form of special pleading. By 1900 it had completely disappeared from mainstream scientific discussions.
In the late 19th century the term neo-Lamarckism came to be associated with the position of naturalists who viewed the inheritance of acquired characteristics as the most important evolutionary mechanism. Advocates of this position included the British writer and Darwin critic Samuel Butler, the German biologist Ernst Haeckel, and the American paleontologist Edward Drinker Cope. They considered Lamarckism to be philosophically superior to Darwin's idea of selection acting on random variation. Cope looked for, and thought he found, patterns of linear progression in the fossil record. Inheritance of acquired characteristics was part of Haeckel's recapitulation theory of evolution, which held that the embryological development of an organism repeats its evolutionary history. Critics of neo-Lamarckism, such as the German biologist August Weismann and Alfred Russel Wallace, pointed out that no one had ever produced solid evidence for the inheritance of acquired characteristics. Despite these criticisms, neo-Lamarckism remained the most popular alternative to natural selection at the end of the 19th century, and would remain the position of some naturalists well into the 20th century.
Orthogenesis was the hypothesis that life has an innate tendency to change, in a unilinear fashion, towards ever-greater perfection. It had a significant following in the 19th century, and its proponents included the Russian biologist Leo Berg, and the American paleontologist Henry Fairfield Osborn. Orthogenesis was popular among some paleontologists, who believed that the fossil record showed a gradual and constant unidirectional change. Saltationism was the idea that new species arise as a result of large mutations. It was seen as a much faster alternative to the Darwinian concept of a gradual process of small random variations being acted on by natural selection, and was popular with early geneticists such as Hugo DeVries, William Bateson, and early in his career, T. H. Morgan. It became the basis of the mutation theory of evolution.

## Mendelian genetics, biometrics, and mutation
The rediscovery of Gregor Mendel's laws of inheritance in 1900 ignited a fierce debate between two camps of biologists. In one camp were the Mendelians, who were focused on discrete variations and the laws of inheritance. They were led by William Bateson (who coined the word genetics) and Hugo de Vries (who coined the word mutation). Their opponents were the biometricians, who were interested in the continuous variation of characteristics within populations. Their leaders, Karl Pearson and Walter Frank Raphael Weldon, followed in the tradition of Francis Galton - who had focused on measurement and statistical analysis of variation within a population. The biometricians rejected Mendelian genetics because they felt that discrete units of heredity, such as genes, could not explain the continuous range of variation seen in wild populations. Weldon's work with crabs and snails provided evidence that selection pressure from environmental factors really could shift the range of variation in real world populations, but the Mendelians maintained that the variations measured by biometricians were too insignificant to account for the evolution of new species.
When T. H. Morgan began experimenting with breeding the fruit fly Drosophila melanogaster he was a saltationist who hoped to demonstrate that a new species could be created in the lab by mutation alone. Instead, the work at his lab between 1910 and 1915 reconfirmed Mendelian genetics and provided solid experimental evidence linking it to chromosomal inheritance. It also demonstrated that most mutations had relatively small effects (such as a change in eye color), and that rather than creating a new species in a single step, they served to increase variation within the existing population.

# 1920s1940s:

## Population genetics
Eventually, the Mendelian and biometrician models were reconciled and merged during the development of the discipline of population genetics. A key part of this development was the work of the British biologist and statistician R.A. Fisher. In a series of papers starting in 1918 and culminating in his 1930 book Genetical Theory of Natural Selection Fisher showed that the continuous variation measured by the biometricians could be produced by the combined action of many discrete genes, and that natural selection could change gene frequencies in a population, driving evolution. In a series of papers starting in 1924 another British geneticist, J.B.S. Haldane, applied statistical analysis to real-world examples of natural selection, such as the evolution of industrial melanism in peppered moths, and showed that natural selection worked at a faster rate than even Fisher had thought possible. The American biologist Sewall Wright, who had a background in animal breeding experiments, focused on combinations of interacting genes, and the effects of inbreeding on small relatively isolated populations that exhibited genetic drift. In 1932 Wright introduced the concept of an adaptive landscape and argued that genetic drift and inbreeding could drive a small isolated sub-populations away from an adaptive peak, allowing natural selection to drive it towards different adaptive peaks. The work of Fisher, Haldane, and Wright founded the discipline of population genetics, which integrated natural selection with Mendelian genetics.

## Modern evolutionary synthesis
In the first couple of decades of the 20th century most field naturalists continued to believe that Lamarckian and orthogenic mechanisms of evolution provided the best explanation for the complexity they observed in the living world. However, as the field of genetics continued to develop, those views became less tenable. Theodosius Dobzhansky had been a postdoctoral worker in T. H. Morgan's lab and had been influenced by the work on genetic diversity done by Russian geneticists such as Sergei Chetverikov. He would help to bridge the divide between the population geneticists and the field biologists with his 1937 book Genetics and the origin of species. Dobzhansky examined the genetic diversity of wild populations, and showed that contrary to the assumptions of the population geneticists, these populations had large amounts of genetic diversity with marked differences between sub-populations. The book also took the highly mathematical work of the population geneticists and put it into more accessible form. Ernst Mayr was influenced by the work of the German biologist Bernhard Rensch on how local environmental factors influenced the geographic distribution of sub-species and closely related species. Mayr followed up on Dobzhansky's work with the 1942 book Systematics and the Origin of Species, which emphasized the importance of allopatric speciation in the formation of new species. This form of speciation occurs when geographical isolation of a sub-population is followed by the development of mechanisms for reproductive isolation. Mayr also formulated the biological species concept that defined a species as a group of interbreeding or potentially interbreeding populations that were reproductively isolated from all other populations. In the 1944 book Mode and Tempo in Evolution George Gaylord Simpson showed that the fossil record was consistent with the irregular non-directional pattern predicted by the developing evolutionary synthesis, and that the linear trends that earlier paleontologists had claimed supported orthogenesis and neo-Lamarckism did not hold up to closer examination. In 1950 G. Ledyard Stebbins published Variation and Evolution in Plants, which helped integrate botany into the synthesis. The emerging cross-discipline consensus on how evolution worked would be known as the modern evolutionary synthesis. It received its name from the book Evolution: the modern synthesis by Julian Huxley.

# 1940s1960s: Molecular biology
In the 1940s, following up on Griffith's experiment on bacterial transformation, Avery, MacLeod and McCarty definitively identified deoxyribonucleic acid (DNA) as the transforming principle responsible for transmitting genetic information. In 1953, Francis Crick and James D. 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.
During this era of molecular biology, it also became clear that a major mechanism for variation within a population is mutations of DNA. 
In the mid-1970s, Motoo Kimura formulated the neutral theory of molecular evolution, firmly establishing the importance of genetic drift as a major mechanism of evolution. The theory sparked the "neutralist-selectionist" debate, partially solved by the development of Tomoko Ohta's nearly neutral theory of evolution.

# Since the 1960s:

## Gene centered view of evolution
In the mid-1960s, George C. Williams strongly critiqued verbal explanations of adaptations couched in terms of "survival of the species" (essentially group selection arguments).  Such explanations were largely replaced by a gene-centered view of evolution, epitomised by the kin selection arguments of W. D. Hamilton, George R. Price and John Maynard Smith. This viewpoint would be summarized and popularized in the  influential 1976 book The Selfish Gene by Richard Dawkins. Models of the period showed that group selection was severely limited in its strength, although these models have since been shown to be too limited and newer models do admit the possibility of significant multi-level selection.
In 1973 Leigh Van Valen proposed the term Red Queen, which he took from Through the Looking Glass by Lewis Carroll, to describe a scenario where a species involved in one or more evolutionary arms races would have to constantly change just to keep pace with the species it was co-evolving with. Hamilton, Williams and others suggested that this idea might help explain the evolution of sexual reproduction, because the increased genetic diversity caused by sexual reproduction would help maintain resistance against rapidly evolving parasites. They felt this might explain why sexual reproduction was so common despite the tremendous cost from the gene-centric point of view of a system where only half of an organism's genome is passed on during reproduction. The gene-centric view has also led to an increased interest in Darwin's old idea of sexual selection, and  more recently in topics such as sexual conflict and intragenomic conflict.

## Punctuated equilibrium
One of the most prominent debates arising during this time period was over the theory of punctuated equilibrium, a theory propounded by Niles Eldredge and Stephen Jay Gould to account for the pattern of fossil species persisting phenotypically unchanged for long periods (what they termed stasis), with relatively brief periods of phenotypic change during speciation.

## Sociobiology
W. D. Hamilton's work on kin selection also contributed to the emergence of the discipline of sociobiology. Altruism has been a difficult problem for evolutionary theorists going all the way back to Darwin.  Significant progress was made in 1964 when Hamilton formulated the inequality known as Hamilton's rule which showed how eusociality (sterile worker classes) in insects and many other examples of altruistic behavior could have evolved through kin selection. Other theories, some derived from game theory, such as reciprocal altruism followed. In 1975 E.O. Wilson published the influential and highly controversial book Sociobiology: The New Synthesis which claimed evolutionary theory could help explain many aspects of animal, including human, behavior. Critics of sociobiology, including Stephen Jay Gould, and Richard Lewontin, claimed that sociobiology greatly overstated the degree to which complex human behaviors could be determined by genetic factors. They also claimed that the theories of sociobiologists often reflected their own ideological biases. Despite these criticisms, work in sociobiology and the related discipline of evolutionary psychology, including work on other aspects of the altruism problem, has continued.

## Evolutionary paths and processes
Improvements in sequencing methods have resulted in a large increase of sequenced genomes, allowing the testing and refining of the theory of evolution using this huge amount of genome data. This research is providing insights into the molecular mechanisms of speciation and adaptation. Such genetic analysis has produced fundamental changes, such as Carl Woese's Three-domain system, in our understanding of the evolutionary history of life. Advances in computational hardware and software have allowed for the testing and extrapolation of increasingly advanced evolutionary models and the development of the field of systems biology.  Discoveries in biotechnology are now producing methods for the synthesis and modification of entire genomes, driving evolutionary studies to the level where future experiments may involve the creation of entirely synthetic organisms.

## Microbiology and horizontal gene transfer
Microbiology has just recently developed into an evolutionary discipline. It was originally ignored due to the paucity of morphological traits and the lack of a species concept in microbiology, particularly amongst prokaryotes. Now, evolutionary researchers are taking advantage their improved understanding of microbial physiology and ecology, produced by the comparative ease of microbial genomics, to explore the taxonomy and evolution of these organisms. These studies are revealing completely unanticipated levels of diversity amongst microbes, demonstrating that these organisms are the dominant form of life on Earth.
One particularly important outcome from studies on microbial evolution was the discovery in Japan of horizontal gene transfer in 1959. This transfer of genetic material between different species of bacteria has played a major role in the propagation of antibiotic resistance. More recently, as knowledge of genomes has continued to expand, it has been suggested that lateral transfer of genetic material has played an important role in the evolution of all organisms. Indeed, as part of the endosymbiotic theory for the origin of organelles, horizontal gene transfer has been a critical step in the evolution of eukaryotes such as fungi, plants, and animals.

## Evo-devo
In the 1980s and 1990s the tenets of the modern evolutionary synthesis came under increasing scrutiny.  There was a renewal of structuralist themes in evolutionary biology in the work of biologists such as Brian Goodwin and Stuart Kauffman, which incorporated ideas from cybernetics and systems theory, and emphasized the self-organizing processes of development as factors directing the course of evolution. The evolutionary biologist Stephen Jay Gould revived earlier ideas of heterochrony, alterations in the relative rates of developmental processes over the course of evolution, to account for the generation of novel forms, and, with the evolutionary biologist Richard Lewontin, wrote an influential paper in 1979 suggesting that a change in one biological structure could arise incidentally as an accidental result of selection on another structure, rather than through direct selection for that particular adaptation.
Molecular data regarding the mechanisms underlying development accumulated rapidly during the 1980s and '90s. For example, it became clear that the diversity of animal morphology was not the result of different sets of proteins regulating the development of different animals, but from changes in the deployment of a small set of proteins that were common to all animals. These proteins became known as the "developmental toolkit". These various perspectives came to inform the disciplines of phylogenetics, paleontology and comparative developmental biology, spawning the new discipline of "evo-devo."
More recent work in this field has emphasized phenotypic and developmental plasticity.  It has been hypothesized, for example, that the rapid emergence of basic metazoan body plans in the Cambrian Explosion was due in part to changes in the environment acting on inherent material properties of cell aggregates, such as differential cell adhesion and biochemical oscillation.  The resulting forms were later locked in by means of stabilizing natural selection.  Experimental and theoretical research on these and related ideas has been presented in the multi-authored volume Origination of Organismal Form.

## Computer sciences
Recent decades have seen a rising interest in evolution within the computer sciences. Evolutionary computation, specifically evolutionary algorithms have found many applications in science and engineering as a means to solve complex problems, called combinatorial optimization problems. These algorithms have underlying mathematical principles based on an analogy with evolution, sharing concepts such as populations, generations, selection and mutation. The performance of these algorithms, also compared to other, more traditional optimization methods, are seen as evidence by some in support of evolutionary biology and its validity.

# Unconventional evolutionary thought

## Gaia hypothesis
Pierre Teilhard de Chardin formulated theories describing the gradual development of the Universe from subatomic particles to human society, considered by Teilhard as the last stage (see Gaia theory), but his ideas were not accepted by the scientific community. However, this hypothesis was later developed in a more limited and rigorous form by James Lovelock, who proposed that the living and nonliving parts of Earth can be viewed as a complex interacting system with similarity to a single organism. This modified hypothesis postulates that all living things have a regulatory effect on the Earth's environment that promotes life overall. Although not fully accepted by the scientific community, this hypothesis has been a useful spur to further research and is a topic of current scientific debate.

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