Evolution: Difference between revisions

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The theory of evolution is attractive to scientists because it can account for the vast [[biodiversity]] on [[Earth]], including the many [[extinction|extinct]] species attested in the [[fossil record]].<ref name=Futuyma>{{cite book | last = Futuyma | first = Douglas J. | authorlink = Douglas J. Futuyma | year = 2005 | title = Evolution | publisher = Sinauer Associates, Inc | location = [[Sunderland, Massachusetts|Sunderland]], [[Massachusetts]] | id = ISBN 0-87893-187-2}}</ref><ref>{{cite book | last = Gould | first = Stephen J. | authorlink = Stephen Gould  | year = 2002 | title = The Structure of Evolutionary Theory | publisher = Belknap Press | id = ISBN 0-674-00613-5}}</ref>
The theory of evolution is attractive to scientists because it can account for the vast [[biodiversity]] on [[Earth]], including the many [[extinction|extinct]] species attested in the [[fossil record]].<ref name=Futuyma>{{cite book | last = Futuyma | first = Douglas J. | authorlink = Douglas J. Futuyma | year = 2005 | title = Evolution | publisher = Sinauer Associates, Inc | location = [[Sunderland, Massachusetts|Sunderland]], [[Massachusetts]] | id = ISBN 0-87893-187-2}}</ref><ref>{{cite book | last = Gould | first = Stephen J. | authorlink = Stephen Gould  | year = 2002 | title = The Structure of Evolutionary Theory | publisher = Belknap Press | id = ISBN 0-674-00613-5}}</ref>


The basic mechanisms that produce evolutionary change are [[natural selection]] (which includes [[ecological selection|ecological]], [[sexual selection|sexual]], and [[kin selection|kin]] selection) and [[genetic drift]]; these two mechanisms act on the genetic variation created by [[mutation]], [[genetic recombination]] and [[gene flow]]. Natural selection is the process by which individual organisms with favorable traits are more likely to survive and [[biological reproduction|reproduce]]. If those traits are heritable, they are passed to succeeding generations, with the result that beneficial heritable traits become more common in the next generation.<ref>{{cite journal | author = Lande, R. | coauthors = Arnold, S.J. | year = 1983 | title = The measurement of selection on correlated characters | journal = [[Evolution (journal)|Evolution]] | volume = 37 | pages = 1210&ndash;1226}}</ref><ref name=Futuyma/><ref>{{cite journal | author = Haldane, J.B.S. | year = 1953 | title = The measurement of natural selection | journal = Proceedings of the 9th International Congress of Genetics | volume = 1 | pages = 480&ndash;487}}</ref> Given enough time, this passive process can result in varied [[adaptation]]s to changing environmental conditions.<ref name="understandingevolution">{{cite web | url = http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_14 | title = Mechanisms: the processes of evolution | accessdate = 2006-07-14 | work = Understanding Evolution | publisher = [[University of California, Berkeley]]}}</ref>
The basic mechanisms that produce evolutionary change are [[natural selection]] and [[kin selection|kin]] selection) and [[genetic drift]].  Natural selection was first described in a joint 1858 paper by [[Charles Darwin]] and [[Alfred Russel Wallace]],  and then popularized in Darwin's 1859 book ''[[The Origin of Species]]''.
 
is the process by which individual organisms with favorable traits are more likely to survive and [[biological reproduction|reproduce]]. If those traits are heritable, they are passed to succeeding generations, with the result that beneficial heritable traits become more common in the next generation.<ref>{{cite journal | author = Lande, R. | coauthors = Arnold, S.J. | year = 1983 | title = The measurement of selection on correlated characters | journal = [[Evolution (journal)|Evolution]] | volume = 37 | pages = 1210&ndash;1226}}</ref><ref name=Futuyma/><ref>{{cite journal | author = Haldane, J.B.S. | year = 1953 | title = The measurement of natural selection | journal = Proceedings of the 9th International Congress of Genetics | volume = 1 | pages = 480&ndash;487}}</ref> Given enough time, this passive process can result in varied [[adaptation]]s to changing environmental conditions.<ref name="understandingevolution">{{cite web | url = http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_14 | title = Mechanisms: the processes of evolution | accessdate = 2006-07-14 | work = Understanding Evolution | publisher = [[University of California, Berkeley]]}}</ref>
The modern understanding of evolution is based on the theory of natural selection, which was first set out in a joint 1858 paper by [[Charles Darwin]] and [[Alfred Russel Wallace]] and popularized in Darwin's 1859 book ''[[The Origin of Species]]''. In the 1930s, Darwinian natural selection was combined with the theory of [[Gregor Mendel|Mendelian]] [[heredity]] to form the [[modern evolutionary synthesis]], also known as "Neo-[[Darwinism]]". The modern synthesis describes evolution as a change in the frequency of [[allele]]s within a population from one generation to the next.<ref name="understandingevolution"/> With its explanatory and [[predictive power]], this theory has become the central organizing principle of modern biology, relating directly to topics such as the origin of [[antibiotic resistance]] in bacteria, [[eusociality]] in insects, and the staggering [[biodiversity]] of Earth's [[ecosystem]].


Although there is overwhelming [[scientific consensus]] supporting the validity of evolution, because of its potential implications for the origins of humankind, evolutionary theory has been at the center of many [[creation-evolution controversy|social and religious controversies]] since its inception.  
Although there is overwhelming [[scientific consensus]] supporting the validity of evolution, because of its potential implications for the origins of humankind, evolutionary theory has been at the center of many [[creation-evolution controversy|social and religious controversies]] since its inception.  


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{{main|Evolutionary biology}}
{{main|Evolutionary biology}}


=== History of evolutionary thought ===
=== Brief history of evolutionary thought ===
{{main|History of evolutionary thought}}
{{main|History of evolutionary thought}}
[[Image:Charles Darwin.jpg|frame|left|[[Charles Darwin]] in 1854, five years before publishing ''[[The Origin of Species]]''.]]
[[Image:Charles Darwin.jpg|frame|left|[[Charles Darwin]] in 1854, five years before publishing ''[[The Origin of Species]]''.]]


The idea of biological evolution has existed since ancient times, notably among Greek philosophers such as [[Anaximander]] and [[Epicurus]] and Indian philosophers such as [[Patañjali]]. However, scientific theories of evolution were not proposed until the 18th and 19th centuries, by scientists such as [[Jean-Baptiste Lamarck]] and [[Charles Darwin]].
The general concept that plants and animals might change form over generations has existed since ancient times, notably among Greek philosophers such as [[Anaximander]] and [[Epicurus]] and Indian philosophers such as [[Patañjali]].
 
[[Jean-Baptiste Lamarck]] and [[Charles Darwin]].


The [[transmutation of species]] was accepted by many scientists before 1859, but Charles Darwin's ''[[The Origin of Species|On The Origin of Species by Means of Natural Selection]]'' provided the first convincing exposition<ref>In the years after Darwin's publication and fame, 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. Historians acknowledge that 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." {{cite book | last = Bowler | first = Peter J. | authorlink = Peter J. Bowler | year = 2003 | title = Evolution: The History of an Idea | publisher = University of California Press | location = Berkeley| pages =158}}</ref> 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 Russel Wallace in which Wallace revealed his own, independent discovery of natural selection. Accordingly, Wallace is sometimes given shared credit for originating the theory.<ref>{{cite book | last = Bowler | first = Peter J. | authorlink = Peter J. Bowler | year = 2003 | title = Evolution: The History of an Idea | publisher = University of California Press | location = Berkeley}}</ref>
The [[transmutation of species]] was accepted by many scientists before 1859, but Charles Darwin's ''[[The Origin of Species|On The Origin of Species by Means of Natural Selection]]'' provided the first convincing exposition<ref>In the years after Darwin's publication and fame, 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. Historians acknowledge that 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." {{cite book | last = Bowler | first = Peter J. | authorlink = Peter J. Bowler | year = 2003 | title = Evolution: The History of an Idea | publisher = University of California Press | location = Berkeley| pages =158}}</ref> 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 Russel Wallace in which Wallace revealed his own, independent discovery of natural selection. Accordingly, Wallace is sometimes given shared credit for originating the theory.<ref>{{cite book | last = Bowler | first = Peter J. | authorlink = Peter J. Bowler | year = 2003 | title = Evolution: The History of an Idea | publisher = University of California Press | location = Berkeley}}</ref>
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[[Image:Mendel.png|frame|right|[[Gregor Mendel]]'s work on the [[Mendelian inheritance|inheritance]] of traits in pea plants laid the foundation for [[genetics]].]]
[[Image:Mendel.png|frame|right|[[Gregor Mendel]]'s work on the [[Mendelian inheritance|inheritance]] of traits in pea plants laid the foundation for [[genetics]].]]


Darwin's lack of a hereditary mechanism is often seen today as a major stumbling block in the historical acceptance of his theory, but in his time it was not a pressing issue, as questions of the development of an organism were seen as more important than questions of the transmission of hereditary traits; Darwin and other biologists of his day thought that the answers to heredity would be found in [[embryology]] rather than in breeding experiments. Work on plant hybridity by a contemporary of Darwin's, an [[Augustinians|Augustinian]] monk in [[Bohemia]] named [[Gregor Mendel]], revealed that certain traits in [[pea]]s occurred in discrete forms (that is, they were either one distinct trait or another,  such as "round" or "wrinkled") and were inherited in a well-defined and predictable manner. Mendel's [[Mendelian inheritance#Mendel.27s law of segregation|Law of Segregation]] and [[Mendelian inheritance#Mendel.27s law of independent assortment|Law of Independent Assortment]] would eventually become key theories in the development of [[genetics]], but in Darwin's time their significance was not seen (even by Mendel himself).<ref name="mendelianrevolution"/>
Mendel's work was "rediscovered" in 1901, and  
 
When Mendel's work was "rediscovered" in 1901, it was initially interpreted as supporting an anti-Darwinian "jumping" form of evolution. The convinced Mendelians, such as [[William Bateson]] and [[Charles Benedict Davenport]], and biometricians, such as [[Walter Frank Raphael Weldon]] and [[Karl Pearson]], became embroiled in a bitter debate, with Mendelians charging that the biometricians did not understand biology, and biometricians arguing that most biological traits exhibited continuous variation rather than the "jumps" expected by the early Mendelian theory.<ref name="diftraits">It is now recognized that the Mendelians were investigating ''Mendelian traits'', those traits where existing variation is controlled by one gene and therefore is discrete, and the biometricians were investigating ''complex traits'', where those traits were controlled by multiple genes, and the variation is therefore continuous.</ref> However, the simple version of the theory of early Mendelians soon gave way to the [[classical genetics]] of [[Thomas Hunt Morgan]] and his school, which thoroughly grounded and articulated the applications of Mendelian laws to biology. Eventually, it was shown that a rigorous statistical approach to Mendelism was reconcilable with the data of the biometricians by the work of statistician and population geneticist [[Ronald Fisher|R.A. Fisher]] in the 1930s. Following this, the work of population geneticists&mdash;notably [[Sewall Wright]] and [[J. B. S. Haldane]]&mdash;and zoologists in the 1930s and 1940s synthesized Darwinian evolution with genetics, creating the [[modern evolutionary synthesis]].<ref name="mendelianrevolution"/> Genes were then still theoretical entities, and many paleontologists and embryologists were inclined to dismiss them as being of no, or minor, importance, but subsequent advancements have made genetics a key aspect of evolutionary biology.<ref>Resynthesizing evolutionary and developmental biology. Gilbert SF, Opitz JM, Raff RA. Developmental Biology 1996 Feb 1;173(2):357-72</ref>
 
The most significant recent developments in evolutionary biology have been the improved understanding of and advances in [[genetics]].<ref>{{cite news | author = Rincon, Paul | url = http://news.bbc.co.uk/1/hi/sci/tech/4552466.stm | title = Evolution takes science honours | publisher = [[BBC News]] | date = 2005 | accessdate = 2006-07-16}} According to the [[BBC]], [[Colin Norman]], news editor of [[Science (journal)|Science]], said "[S]cientists tend to take for granted that evolution underpins modern biology [...] Evolution is not just something that scientists study as an esoteric enterprise. It has very important implications for public health and for our understanding of who we are" and Dr. Mike Ritchie, of the school of biology at the University of St Andrews, UK said "The big recent development in evolutionary biology has obviously been the improved resolution in our understanding of genetics. Where people have found a gene they think is involved in speciation, I can now go and look how it has evolved in 12 different species of fly, because we've got the genomes of all these species available on the web."</ref> In the 1940s, following up on [[Griffith's experiment]], [[Oswald Avery|Avery]], [[Colin MacLeod|MacLeod]] and [[Maclyn McCarty|McCarty]] definitively identified [[DNA]] (deoxyribonucleic acid) 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 (see [[molecular evolution]]): the [[mutation]] of segments of DNA. [[George C. Williams]]' 1966 ''Adaptation and natural selection: A Critique of some Current Evolutionary Thought'' marked a departure from the idea of [[group selection]] towards the modern notion of the gene as the [[unit of selection]]. In the mid-1970s, [[Motoo Kimura]] formulated the [[neutral theory of molecular evolution]], firmly establishing the importance of [[genetic drift]] as a mechanism of evolution.


Debates over various aspects of how evolution occurs have continued. One prominent debate was over the theory of [[punctuated equilibrium]], proposed in 1972 by [[paleontology|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.
Debates over various aspects of how evolution occurs have continued. One prominent debate was over the theory of [[punctuated equilibrium]], proposed in 1972 by [[paleontology|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.


===Academic disciplines===
===Academic disciplines===
Scholars in a number of academic disciplines continue to document examples of the theory of evolution, contributing to a deeper understanding of its underlying mechanisms. Every subdiscipline within [[biology]] both informs and is informed by knowledge of the details of evolution, such as in [[ecological genetics]], [[human evolution]], [[molecular evolution]], and [[phylogenetics]]. Areas of mathematics (such as [[bioinformatics]]), physics, chemistry and other fields all make important foundational contributions to the theory of evolution. Even disciplines as far removed as [[geology]] and [[sociology]] play a part, since the process of biological evolution has coincided in time and space with the development of both the Earth and human civilization.


[[Evolutionary biology]] is a subdiscipline of biology concerned with the origin and descent of [[species]], as well as their changes over time. It was originally an [[interdisciplinarity|interdisciplinary]] field including scientists from many traditional [[alpha taxonomy|taxonomically]]-oriented disciplines. For example, it generally includes scientists who may have a specialist training in particular organisms, such as [[mammalogy]], [[ornithology]], or [[herpetology]], but 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. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term ''evolutionary biology'' in their titles.
[[Evolutionary biology]] is a subdiscipline of biology concerned with the origin and descent of [[species]], as well as their changes over time. It was originally an [[interdisciplinarity|interdisciplinary]] field including scientists from many traditional [[alpha taxonomy|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. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term ''evolutionary biology'' in their titles.


[[Evolutionary developmental biology]] (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 [[gene]]s regulating development in model organisms allowed for comparisons to be made with genes and genetic networks of related organisms.
[[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 [[gene]]s regulating development in model organisms allowed for comparisons to be made with genes and genetic networks of related organisms.
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[[Physical anthropology]] emerged in the late 19th century as the study of human [[osteology]], and the fossilized skeletal remains of other [[Hominidae|hominid]]s. 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.
[[Physical anthropology]] emerged in the late 19th century as the study of human [[osteology]], and the fossilized skeletal remains of other [[Hominidae|hominid]]s. 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.


==Evidence of evolution==
===Fossil Record===
{{main|Evidence of evolution}}
[[Image:Skelett vom Wal MK1888 ohne Text.gif|350px|thumb|Letter ''c'' in the picture indicates the undeveloped hind legs of a [[baleen whale]], [[vestigial structure|vestigial]] remnants of its terrestrial ancestors.]]
Evolution has left numerous records which reveal the history of different species. [[fossil record|Fossils]], together with the [[comparative anatomy]] of present-day plants and animals, constitute the morphological, or [[anatomy|anatomical]], record. By comparing the anatomies of both modern and extinct species, [[paleontology|paleontologists]] can infer the lineages of those species. Important fossil evidence includes the connection of distinct classes of organisms by so-called "[[transitional fossil|transitional]]" species, such as the [[Archaeopteryx]], which provided early evidence for the link between [[dinosaur]]s and [[bird]]s,<ref>{{cite book | author = Feduccia, Alan | year = 1996 | title = The Origin and Evolution of Birds | publisher = Yale University Press | location = New Haven | id = ISBN 0-300-06460-8}}</ref> and the recently-discovered [[Tiktaalik]], which clarifies the development from [[fish]] to [[tetrapod|animals with four limbs]].<ref>{{cite journal | author = Daeschler, Edward B., Shubin, Neil H., & Jenkins Jr, Farish A. | year = 2006 | month = April | title = A Devonian tetrapod-like fish and the evolution of the tetrapod body plan | journal = [[Nature (journal)|Nature]] | volume = 440 | pages = 757&ndash;763 | doi = 10.1038/nature04639 | url = http://www.nature.com/nature/journal/v440/n7085/abs/nature04639.html | accessdate = 2006-07-14}}</ref>
 
The development of [[genetics|molecular genetics]], and particularly of DNA sequencing, has allowed biologists to study the record of evolution left in the organisms' genetic structures. The degree of similarity and difference in the DNA sequences of modern species allows geneticists to reconstruct their lineages. It is from DNA sequence comparisons that figures such as the 95% similarity between humans and chimpanzees are obtained.<ref>{{cite journal | author = Chimpanzee Sequencing and Analysis Consortium | year = 2005 | title = Initial sequence of the chimpanzee genome and comparison with the human genome | journal = [[Nature (journal)|Nature]] | volume = 437 | pages = 69&ndash;87}}</ref><ref>{{cite journal | author = Britten, R.J. | year = 2002 | title = Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels | journal = Proc Natl Acad Sci U S A | volume = 99 | pages = 13633&ndash;13635}}</ref>
 
Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, [[monotreme]]s and most [[marsupial]]s are found only in [[Australia]], showing that their common ancestor with placental mammals lived before the submerging of the ancient [[land bridge]] between Australia and Asia.


Scientists correlate all of the above evidence, drawn from [[paleontology]], anatomy, genetics, and geography, with other information about the [[history of Earth]]. For instance, [[paleoclimatology]] attests to periodic [[ice age]]s during which the world's climate was much cooler, and these are often found to match up with the spread of species which are better-equipped to deal with the cold, such as the [[woolly mammoth]].
[[Fossil]]s are xxxx. 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<ref>{{cite journal| author =Schweitzer M.H. ''et al'' | year =2005| title = Soft-tissue vessels and cellular preservation in Tyrannosaurus rex| journal =Science | volume =307 | issue =5717 | pages =1952-1955}}</ref>.
 
===Morphological evidence===
[[Image:Skelett vom Wal MK1888 ohne Text.gif|350px|thumb|Letter ''c'' in the picture indicates the undeveloped hind legs of a [[baleen whale]], [[vestigial structure|vestigial]] remnants of its terrestrial ancestors.]]


[[Fossil]]s 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 happens under unusual circumstances, such as rapid burial, low oxygen environments, or microbial action<ref>{{cite journal| author =Schweitzer M.H. ''et al'' | year =2005| title = Soft-tissue vessels and cellular preservation in Tyrannosaurus rex| journal =Science | volume =307 | issue =5717 | pages =1952-1955}}</ref>.
The fossil record contains the earliest known examples of life itself, as well as the earliest occurrences of individual [[Lineage (evolution)|lineages]].  


The fossil record provides several types of data important to the study of evolution. First, the fossil record contains the earliest known examples of life itself, as well as the earliest occurrences of individual [[Lineage (evolution)|lineages]]. For example, the first complex animals date from the [[early Cambrian]] period, approximately 520 million years ago. Second, 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. Thirdly, 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 [[Lineage (evolution)|lineages]]. For example, [[Extinction event|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.
For example, the first complex animals date from the [[early Cambrian]] period, approximately 520 million years ago. Second, 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. Thirdly, 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 [[Lineage (evolution)|lineages]]. For example, [[Extinction event|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 [[homology (biology)|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]].
[[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 [[homology (biology)|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]].
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Further evidence for reconstructing ancestral lineages comes from [[junk DNA]] such as [[pseudogene]]s, ''i.e.'', 'dead' genes, which steadily accumulate mutations.<ref>Pseudogene evolution and natural selection for a compact genome. "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10833048]"</ref>
Further evidence for reconstructing ancestral lineages comes from [[junk DNA]] such as [[pseudogene]]s, ''i.e.'', 'dead' genes, which steadily accumulate mutations.<ref>Pseudogene evolution and natural selection for a compact genome. "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10833048]"</ref>


Since [[metabolism|metabolic]] processes do not leave fossils, research into the evolution of the basic cellular processes is done largely by comparison of existing organisms. Many lineages diverged when new metabolic processes appeared, and it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor or by detecting their physical manifestations.  As an example, the appearance of oxygen in the earth's atmosphere is linked to the evolution of photosynthesis.
===Evidence from studies of complex iteration===
<!--This section uses waaay too many lengthy quotations. Create a daughter article if you want that much level of detail for this section; otherwise, the section should just briefly explain the topic in a few paragraphs, with no more than a couple of brief quotations.-->
"It has taken more than five decades, but the electronic computer is now powerful enough to simulate evolution" assisting [[bioinformatics]] in its attempt to solve biological problems.<ref>[http://www.trnmag.com/Stories/2003/052103/Simulated_evolution_gets_complex_052103.html Simulated evolution gets complex]</ref> [[Computer science]] allows the [[iteration]] of self changing [[complex system]]s to be studied, allowing a mathematically exact understanding of the nature of the processes behind evolution and providing evidence for the hidden causes of known evolutionary events. The evolution of specific cellular mechanisms like [[spliceosome]]s that can turn the cell's genome into a vast workshop of billions of interchangeable parts can be studied for the first time in an exact way.
Christoph Adami et al., for example, make this point in ''Evolution of biological complexity'':
{{cquote|To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural "Maxwell Demon," within a fixed environment, genomic complexity is forced to increase.<ref>{{cite journal | author=Adami C, Ofria C, Collier TC | title=Evolution of biological complexity | journal=Proc Natl Acad Sci U S A | year=2000 | pages=4463-8 | volume=97 | issue=9 | id=PMID 10781045}}</ref&gt;}}
David J. Earl and Michael W. Deem also make this point in ''Evolvability is a selectable trait'':
{{cquote|Not only has life evolved, but life has evolved to evolve. That is, correlations within protein structure have evolved, and mechanisms to manipulate these correlations have evolved in tandem. The rates at which the various events within the hierarchy of evolutionary moves occur are not random or arbitrary but are selected by Darwinian evolution. Sensibly, rapid or extreme environmental change leads to selection for greater evolvability. This selection is not forbidden by causality and is strongest on the largest-scale moves within the mutational hierarchy. Many observations within evolutionary biology, heretofore considered evolutionary happenstance or accidents, are explained by selection for evolvability. For example, the vertebrate immune system shows that the variable environment of antigens has provided selective pressure for the use of adaptable codons and low-fidelity polymerases during somatic hypermutation. A similar driving force for biased codon usage as a result of productively high mutation rates is observed in the hemagglutinin protein of [[Influenzavirus A|influenza A]].<ref>{{cite journal | author=Earl DJ, Deem MW | title=Evolvability is a selectable trait | journal=Proc Natl Acad Sci U S A | year=2004 | pages=11531-6 | volume=101 | issue=32 | id=PMID 15289608}}</ref>}}
"Computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of sequence rather than point mutagenesis alone. Repeated cycles of point mutagenesis, recombination, and selection should allow in vitro molecular evolution of complex sequences, such as proteins."<ref>{{cite journal | author=Stemmer WP | title=DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution | journal=Proc Natl Acad Sci U S A | year=1994 | pages=10747-51 | volume=91 | issue=22 | id=PMID 7938023}}</ref> Evolutionary molecular engineering, also called "directed evolution" or "in vitro molecular evolution", involves the iterated cycle of mutation, multiplication with recombination, and selection of the fittest of individual molecules (proteins, DNA and RNA). The process of natural evolution can be reconstructed, showing possible paths from catalytic cycles based on proteins to ones based on RNA to ones based on DNA.<ref>[http://www.scripps.edu/newsandviews/e_20060327/evo.html scripps.edu]
[http://bio.kaist.ac.kr/~jsrhee/research03.html bio.kaist.ac.kr] [http://www.isgec.org/gecco-2005/free-tutorials.html#ivme free-tutorial] [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=45099 pubmedcentral.nih.gov]</ref>
==Ancestry of organisms==
{{seealso|Common descent}}
[[Image:Huxley - Mans Place in Nature.jpg|left|250px|thumbnail|Morphologic similarities in the [[Hominidae]] family is evidence of common descent.]]
In biology, the theory of universal [[common descent]] proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool.
Evidence for common descent is inferred from traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds, even those which do not fly, have wings. Today, there is strong evidence from genetics that all organisms have a common ancestor. For example, every living cell makes use of [[nucleic acid]]s as its genetic material, and uses the same twenty [[amino acid]]s as the building blocks for [[protein]]s. All organisms use the same [[genetic code]] (with some extremely rare and minor deviations) to [[translation (genetics)|translate]] nucleic acid sequences into proteins. The universality of these traits strongly suggests common ancestry, because the selection of many of these traits seems arbitrary.
Information about the early development of life includes input from the fields of geology and [[planetary science]]. These sciences provide information about the history of the Earth and the changes produced by life. However, a great deal of information about the early Earth has been destroyed by geological processes over the course of time.
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===History of life===
<!-- for future reference, heh, here's a ref to stromatolite debate that I took out because it messed up formatting -
"Ancient microfossils from Western Australia are again the subject of heated scientific argument: are they the oldest sign of life on Earth, or just a flaw in the rock?" "[http://www.abc.net.au/science/news/space/SpaceRepublish_497964.htm]" -->
{{main|Timeline of evolution}}
The [[chemical evolution]] from [[Catalyst|self-catalytic chemical reactions]] to [[life]] (see [[Origin of life]]) is not a part of biological evolution, but it is unclear at which point such increasingly complex sets of reactions became what we would consider, today, to be living organisms.
[[Image:Stromatolites.jpg|right|thumb|280px|[[Precambrian]] [[stromatolite]]s in the Siyeh Formation, [[Glacier National Park (US)|Glacier National Park]]. In 2002, William Schopf of [[University of California, Los Angeles|UCLA]] published a controversial paper in the journal ''[[Nature (journal)|Nature]]'' arguing that formations such as this possess 3.5 billion year old [[fossil]]ized [[alga]]e microbes. If true, they would be the earliest known life on earth.]]
Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure and [[genetic code]]. Most scientists interpret this to mean all existing organisms share a common ancestor, which had already developed the most fundamental cellular processes, but there is no [[scientific consensus]] on the relationship of the three domains of life ([[Archaea]], [[Bacterium|Bacteria]], [[Eukaryota]]) or the [[origin of life]]. Attempts to shed light on the earliest history of life generally focus on the behavior of [[macromolecule]]s, particularly [[RNA]], and the behavior of [[complex system]]s.
The emergence of oxygenic [[photosynthesis]] (around 3 billion years ago) and the subsequent emergence of an oxygen-rich, non-reducing atmosphere can be traced through the formation of [[Banded iron formation|banded iron]] deposits, and later [[red bed]]s of iron oxides. This was a necessary prerequisite for the development of [[aerobic respiration|aerobic]] [[cellular respiration]], believed to have emerged around 2 billion years ago.
In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the [[Cambrian explosion]] (a period of unrivaled and remarkable, but brief, organismal diversity documented in the fossils found at the [[Burgess Shale]]) saw the creation of all the major body plans, or [[phylum (biology)|phyla]], of modern animals. This event is now believed to have been triggered by the development of the [[Homeobox|Hox genes]]. About 500 million years ago, [[plant]]s and [[fungi]] colonized the land, and were soon followed by [[arthropod]]s and other animals, leading to the development of land [[ecosystem]]s with which we are familiar.
The evolutionary process may be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the [[history of Earth|history of the earth]]. [[geology|Geological]] evidence indicates that the Earth is approximately [[Age of the earth|4.6 billion years old]]. Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record.<ref>Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata) "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9072971&query_hl=2]"</ref>. Such comparative studies however are invariably biased by disparities in the time scales over which evolutionary change is measured in the laboratory, field experiments, and the fossil record.
The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly supplemented with phylogenetic&mdash;the reconstruction of phylogenies by the comparison of genetic (usually DNA) sequence.<ref>Oklahoma State - [http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html Horizontal Gene Transfer]: "Sequence comparisons suggest recent horizontal transfer of many [[gene]]s among diverse [[species]] including across the boundaries of [[phylogenetic]] 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."</ref> Biologist Gogarten suggests that "the original metaphor of a tree no longer fits the data from recent genome research", and that therefore "biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of [[horizontal gene transfer|HGT]] among microbes".<ref>[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1 esalenctr.org]</ref>
==Modern synthesis==
{{main|Modern evolutionary synthesis}}
Charles Darwin was able to observe variation, infer natural selection and thereby adaptation, but didn't know the basis of heritability.  He couldn't explain ''how'' organisms might change over generations. It also seemed that when two individuals were crossed, their traits must be ''blended'' in the progeny, so that eventually all variation would be lost.
The blending problem was solved when the population geneticists [[Ronald Fisher|R.A. Fisher]], [[Sewall Wright]], and [[J. B. S. Haldane]], married Darwinian evolutionary theory to population genetic theory, which was based on [[Gregor Mendel|Mendelian]] [[genetics]] (genes as ''discrete units'' of heredity).
The problem of what the mechanisms might be was solved in principle with the identification of DNA as the genetic material by [[Oswald Avery]] and colleagues, and the articulation of the double-helical structure of DNA by [[James Watson]] and [[Francis Crick]] provided a physical basis for the notion that genes were [[genetic code|encoded]] in DNA.
===Heredity===
[[Image:DNA123.png|thumb|left|125px|A section of a model of a DNA molecule.]]
Gregor Mendel's work provided the first firm basis to the idea that heredity occurred in discrete units. He noticed several traits in peas that occur in only one of two forms (e.g., the peas were either "round" or "wrinkled"), and was able to show that the traits were: heritable (passed from parent to offspring); discrete (i.e., if one parent had round peas and the other wrinkled, the progeny were not intermediate, but either round or wrinkled); and were distributed to progeny in a well-defined and predictable manner ([[Mendelian inheritance]]). His research laid the foundation for the concept of discrete heritable [[Trait (biology)|traits]], known today as [[gene]]s. After Mendel's work was "rediscovered" in 1900, it was discovered that the concepts could have wide applicability, and that most complex traits were polygenetic and not controlled by single unit characters.
Later research gave a physical basis to the notion of genes, and eventually identified [[DNA]] as the genetic material, and identified genes as discrete elements within DNA. DNA is not perfectly copied, and rare mistakes ([[mutation]]s) in genes can affect traits that the genes control (e.g., pea shape).
A gene can have modifications such as [[DNA methylation]], which do not change the nucleotide sequence of a gene, but do result in the [[epigenetic inheritance]] of a change in the expression of that gene in a trait.
Non-DNA based forms of heritable variation exist, such transmission of the secondary structures of [[prion]]s, and [[structural inheritance]] of patterns in the rows of cilia in protozoans such as ''Paramecium''<ref>
BEISSON, J. & SONNEBORN, T. M. (1965). Cytoplasmic inheritance of the organization of the cell cortex of Paramecium aurelia. Proc. natn. Acad Sci. U.S.A. 53, 275-282</ref> and [http://dev.biologists.org/cgi/reprint/105/3/447| ''Tetrahymena'']. Investigations continue into whether these mechanisms allow for the production of specific beneficial heritable variation in response to environmental signals. If this were shown to be the case, then some instances of evolution would lie outside of the typical Darwinian framework, which avoids any connection between environmental signals and the production of heritable variation. However, the processes that produce these variations leave the genetic information intact and are often reversible, and are rather rare.
===Variation===
Evolutionary changes are the product of evolutionary forces acting on [[genetic variation]]. In natural populations, there is a certain amount of [[phenotype|phenotypic]] variation (e.g., what makes you appear different from your neighbor). This phenotypic variation is the result of variants in gene sequences among the individuals of a population. There may be one or more functional variants of a gene or locus, and these variants are called [[allele]]s. Most sites in the [[genome]] (''i.e.'', complete DNA sequence) of a species are identical in all individuals in the population; sites with more than one allele are called [[polymorphic]] or segregating sites.
All genetic variation begins as a new mutation in a single individual; in subsequent generations the frequency of that variant may fluctuate in the population, becoming more or less prevalent relative to other alleles at the site. This change in allele frequency is the commonly accepted definition of evolution, and all evolutionary forces act by driving allele frequency in one direction or another. Variation disappears when it reaches the point of fixation - when it either reaches a frequency of zero and disappears from the population, or reaches a frequency of one and replaces the ancestral allele entirely.
===Mechanisms of evolution===
Evolution consists of two basic types of processes: those that introduce new genetic variation into a population, and those that affect the frequencies of existing variation. Paleontologist [[Stephen J. Gould]] once phrased this succinctly as "''variation proposes and selection disposes.''"<ref>{{cite web|url= http://www.nybooks.com/articles/1151 |title= Darwinian Fundamentalism  |accessdate=2006-08-01 |author= Stephen J. Gould |date=1997-06-12 |publisher=New York Review of Books}}</ref>
These mechanisms of evolution have all been observed in the present and in evidence of their existence in the past. Their study is being used to guide the development of new medicines and other health aids such as the current effort to prevent a [[H5N1]] (i.e. bird flu) pandemic.<ref>The use of evolutionary principles to guide disease diagnosis and drug development with respect to bird flu (i.e. H5N1 virus) is shown [http://www.cdc.gov/ncidod/EID/vol11no10/05-0644.htm here at CDC]. [http://www.nap.edu/books/0309095042/html/123.html#p2000c2099960123001 Here] is the "tree of life" showing the evolution by [[reassortment]] of [[H5N1]] that created the Z genotype in 2002 and [http://www.cdc.gov/ncidod/EID/vol11no10/05-0644-G1.htm here] is evolution by [[antigenic drift]] that created dozens of highly [[pathogenic]] varieties of the Z genotype of avian flu virus [[H5N1]], some of which are increasingly adopted to mammals. Evolution. Right before our eyes.</ref>


====Mutation====
====Mutation====
{{main|Mutation}}
{{main|Mutation}}
[[Image:dna-split.png|thumb|right|150px|Mutation occurs because of "copy errors" that occur during DNA replication.]]
[[Image:dna-split.png|thumb|right|150px|Mutation occurs because of "copy errors" that occur during DNA replication.]]
Genetic variation arises due to random mutations that occur at a certain rate in the [[genomes]] of all organisms. Mutations are permanent, transmissible changes to the [[genetic material]] (usually [[DNA]] or [[RNA]]) of a [[cell (biology)|cell]], and can be caused by: "copying errors" in the genetic material during [[cell division]]; by exposure to [[Radioactive decay|radiation]], chemicals, or [[virus (biology)|viruses]]. In multicellular organisms, mutations can be subdivided into ''germline mutations'' that occur in the [[gamete]]s and thus can be passed on to progeny, and ''somatic mutations'' that can lead to the malfunction or death of a cell and can cause [[cancer]].
Mutations that are not affected by natural selection are called [[Neutral theory of molecular evolution|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.


Individual [[genes]] can be affected by [[point mutation|point mutations]], also known as [[Single nucleotide polymorphism|SNPs]], in which a single [[base pair]] is altered. The substitution of a single base pair may or may not affect the function of the gene (see [[mutation]]) while deletions and insertions of a single or several base pairs usually results in a non-functional gene.<ref>Snustad, P. and Simmons, A. 2000. Principles of Genetics, 2nd edition. John Wiley and Sons, Inc. New-York, p.20</ref>
What accounts for genetic variation? Genes are made out of biochemicals, including DNA and RNA. Changes in the bonding of the nucleotides that make them up are one way that the genetic code can change.  Mutations are permanent, transmissible changes to the [[genetic material]] of a [[cell (biology)|cell]].  These changes can be caused by: "copying errors" in the genetic material during [[cell division]]. (Explain frame shift)
Exposure to [[Radioactive decay|radiation]], certain chemicals, and some [[virus (biology)|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 theory of molecular evolution|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.
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.
On the other hand, [[gene duplication]]s, which may occur via a number of mechanisms, are believed to be one major source of raw material for evolving new genes as tens to hundreds of genes are duplicated in animal genomes every million years.<ref>{{cite book| last = Carroll S.B,. Grenier J.K., Weatherbee S.D. | title = From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design.  Second Edition| publisher = Blackwell Publishing| date = 2005| location = Oxford | id = ISBN 1-4051-1950-0 }}</ref> Most genes belong to larger "families" of genes derived from a common ancestral gene (two genes from a species that are in the same family are dubbed "[[paralog]]s"). Another mechanism causing gene duplication is intergenic recombination, particularly '[http://www.pnas.org/cgi/content/full/94/15/7698| exon shuffling]', ''i.e.'', an abberant recombination that joins the 'upstream' part of one gene with the 'downstream' part of another.  [[Polyploidy|Genome duplications]] and chromosome duplications also appear to have served a significant role in evolution.  Genome duplication has been the driving force in the [[Teleostei]] genome evolution, where up to four genome duplications are thought to have happened, resulting in species with more than 250 chromosomes.
Large [[chromosomal]] rearrangements do not necessarily change gene function, but do generally result in reproductive isolation, and, by definition, [[speciation]] ([[species]] (in sexual organisms) are usually defined by the ability to interbreed).  An example of this mechanism is the fusion of two chromosomes in the [[homo genus]] that produced human chromosome 2; this fusion did not occur in the [[chimp]] [[Lineage (evolution)|lineage]], resulting in two separate chromosomes in extant chimps.


====Selection and adaptation====
====Selection and adaptation====
{{main|Natural selection|Adaptation}}
{{main|Natural selection|Adaptation}}
[[Image:Peacock.displaying.better.800pix.jpg|thumb|right|250px|A [[peacock]]'s tail is the canonical example of [[sexual selection]]]]
[[Image:Peacock.displaying.better.800pix.jpg|thumb|right|250px|A [[peacock]]'s tail is the canonical example of [[sexual selection]]]]
Natural selection comes from differences in survival and reproduction <!-- The environment is just one of the two major sources (ecological selection), the other is partners (sexual selection)-->. Differential mortality is the survival rate of individuals to their reproductive age. Differential fertility is the total genetic contribution to the next generation. Note that, whereas mutations and genetic drift are random, natural selection is not, as it preferentially selects for different mutations based on differential fitnesses. For example, rolling dice is random, but always picking the higher number on two rolled dice is not random. The central role of natural selection in evolutionary theory has given rise to a strong connection between that field and the study of [[ecology]].


Natural selection can be subdivided into two categories:
Natural selection can be subdivided into two categories:
Line 191: Line 98:
** [[Genetic hitchhiking]] occurs when a beneficial [[allele]] is selected for, and [[Genetic linkage|linked]] [[allele]]s, which can be neutral or beneficial, are pushed towards fixation along with the beneficial [[allele]].
** [[Genetic hitchhiking]] occurs when a beneficial [[allele]] is selected for, and [[Genetic linkage|linked]] [[allele]]s, which can be neutral or beneficial, are pushed towards fixation along with the beneficial [[allele]].


Through the process of natural selection, organisms become better adapted to their environments. [[Adaptation]] is any evolutionary process that increases the [[fitness (biology)|fitness]] of the individual, or sometimes the trait that confers increased fitness, e.g. a stronger prehensile tail or greater visual acuity. Note that adaptation is context-sensitive; a trait that increases fitness in one environment may decrease it in another.
Evolution does not act in a linear direction towards a pre-defined "goal" &mdash; it only responds to various types of adaptionary changes. The belief in a [[teleology|telelogical]] evolution of this sort is known as [[orthogenesis]], and is not supported by the scientific understanding of evolution. One example of this misconception is the erroneous belief humans will evolve [[polydactyly|more fingers]] in the future on account of their increased use of machines such as [[computer]]s. In reality, this would only occur if more fingers offered a significantly higher rate of reproductive success than those not having them, which seems very unlikely at the current time.


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.
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.
Line 226: Line 130:
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.
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.


====Horizontal gene transfer====
{{main|Horizontal gene transfer}}
[[Horizontal gene transfer]] (HGT) (or Lateral gene transfers) is any process in which an organism transfers [[genetic material]] (i.e. [[DNA]]) to another organism that is not its offspring.  This mechanism allows for the transfer of genetic material between unrelated organisms of the same [[species]] or of different species.
Many mechanisms for [[horizontal gene transfer]] have been observed, such as [[antigenic shift]], [[reassortment]], and [[hybrid]]ization. Viruses can transfer genes between species via [[Transduction (genetics)|transduction]],<ref>[http://66.102.7.104/search?q=cache:tpICVNWaTbgJ:non.fiction.org/lj/community/ref_courses/3484/enmicro.pdf+sex+evolution+%22Horizontal+gene+transfer%22+-human+Conjugation+RNA+DNA&hl=en enmicro.pdf]</ref>. Bacteria can incorporate genes from other dead bacteria or [[plasmids]] via [[Transformation (genetics)|transformation]], exchange genes with living bacteria via [[Bacterial conjugation|conjugation]], and can have [[plasmid]]s "set up residence separate from the host's genome".<ref>[http://www2.nau.edu/~bah/BIO471/Reader/Pennisi_2003.pdf Pennisi_2003.pdf]</ref> 
HGT has been shown to result in the spread of [[antibiotic resistance]] across [[bacterial]] populations.<ref>{{cite journal| last = Dzidic S, Bedekovic V.| title = Horizontal gene transfer-emerging multidrug resistance in hospital bacteria | journal = Acta pharmacologica Sinica| volume = 24| issue = 6 | pages = 519-526 | date = 2003}}</ref>  Furthermore, findings indicate that HGT has been a major mechanism for [[prokaryotic]] and [[eukaryotic]] evolution.<ref>{{cite journal| last = Andersson JO| title = Lateral gene transfer in eukaryotes | journal = Cellular and molecular life sciences| volume = 62| issue = 11 | pages = 1182-1197 | date = 2005}}</ref><ref>{{cite journal| last = Katz LA| title = Lateral gene transfers and the evolution of eukaryotes: theories and data | journal = International journal of systematic and evolutionary microbiology| volume = 52| issue = 5 | pages = 1893-1900 | date = 2002}}</ref>
HGT complicates the inference of the [[phylogeny]] of life, as the original metaphor of a tree of life no longer fits.  Rather, since genetic information is passed to other organisms and other species in addition to being passed from parent to offspring, ''"biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes."''<ref>[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1 Evolutionary Theory] by Peter Gogarten, Ph.D.</ref>


===Speciation and extinction===
===Speciation and extinction===

Revision as of 13:06, 20 November 2006

Template:Otheruses4 File:Great Image Needed.jpg In biology, the theory of evolution holds a central place. This theory was first proposed in the Nineteenth Century by Charles Darwin and others, includingxxxxx.

Technically, evolution involves change in the heritable traits of a population over successive generations, as determined by shifts in the allele frequencies of genes. Over time, this process can result in speciation, the development of new species from existing ones. A main assumption in evolutionary theory is that contemporary organisms are related to each other through common descent from a single, or small number, of distantly common ancestors - the first life forms on earth that succeeded in giving rise to viable offspring.

The theory of evolution is attractive to scientists because it can account for the vast biodiversity on Earth, including the many extinct species attested in the fossil record.[1][2]

The basic mechanisms that produce evolutionary change are natural selection and kin selection) and genetic drift. Natural selection was first described in a joint 1858 paper by Charles Darwin and Alfred Russel Wallace, and then popularized in Darwin's 1859 book The Origin of Species. is the process by which individual organisms with favorable traits are more likely to survive and reproduce. If those traits are heritable, they are passed to succeeding generations, with the result that beneficial heritable traits become more common in the next generation.[3][1][4] Given enough time, this passive process can result in varied adaptations to changing environmental conditions.[5]


Although there is overwhelming scientific consensus supporting the validity of 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.

Template:Evolution3

Study of evolution

For more information, see: Evolutionary biology.


Brief history of evolutionary thought

For more information, see: History of evolutionary thought.
Charles Darwin in 1854, five years before publishing The Origin of Species.

The general concept that plants and animals might change form over generations has existed since ancient times, notably among Greek philosophers such as Anaximander and Epicurus and Indian philosophers such as Patañjali.

Jean-Baptiste Lamarck and Charles Darwin.

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[6] 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 Russel Wallace in which Wallace revealed his own, independent discovery of natural selection. Accordingly, Wallace is sometimes given shared credit for originating the theory.[7]

The publication of 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 as a consequence debates over the theory took place in many different arenas. Although the occurrence of biological evolution of some sort came to be widely accepted by scientists, Darwin's specific ideas about evolution—that it occurred gradually, through natural selection—were actively attacked and 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,[8] 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.[9]

Gregor Mendel's work on the inheritance of traits in pea plants laid the foundation for genetics.

Mendel's work was "rediscovered" in 1901, and

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.

Academic disciplines

Evolutionary biology is a subdiscipline of biology concerned with the origin and descent of species, as well as their changes over time. It was originally 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. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term evolutionary biology in their titles.

Evolutionary developmental biology (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.

Fossil Record

File:Skelett vom Wal MK1888 ohne Text.gif
Letter c in the picture indicates the undeveloped hind legs of a baleen whale, vestigial remnants of its terrestrial ancestors.

Fossils are xxxx. 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[10].

The fossil record contains the earliest known examples of life itself, as well as the earliest occurrences of individual lineages.

For example, the first complex animals date from the early Cambrian period, approximately 520 million years ago. Second, 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. Thirdly, 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. For example, 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.

Molecular evidence

Comparison of the 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.[11] Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes.[12][13] 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.[14][15]

Further evidence for reconstructing ancestral lineages comes from junk DNA such as pseudogenes, i.e., 'dead' genes, which steadily accumulate mutations.[16]



Mutation

For more information, see: Mutation.
Mutation occurs because of "copy errors" that occur during DNA replication.

What accounts for genetic variation? Genes are made out of biochemicals, including DNA and RNA. Changes in the bonding of the nucleotides that make them up are one way that the genetic code can change. 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

For more information, see: Natural selection and Adaptation.
A peacock's tail is the canonical example of sexual selection

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:
  • 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.

Recombination

For more information, see: Genetic recombination.


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.

Recombination is mildly mutagenic, which is one of the proposed reasons why it occurs with limited frequency. Recombination also breaks up gene combinations that have been successful in previous generations, and hence should be opposed by selection. However, recombination could be favoured by negative frequency-dependent selection (this is when rare variants increase in frequency) because it leads to more individuals with new and rare gene combinations being produced.

When alleles cannot be separated by recombination (for example in mammalian Y chromosomes), we see a reduction in effective population size, known as the Hill Robertson effect, and the successive establishment of bad mutations, known as Muller's ratchet.

Gene flow and Population structure

Main article: Population genetics
Map of the world showing distribution of camelids. Solid black lines indicate possible migration routes.

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.

Drift

For more information, see: Genetic drift.


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

An Allosaurus skeleton.

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.[17]. Sympatric speciation occurs when new species emerge in the same geographic area[18][19] 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.

Current Research

See also: Ancestral Reconstruction, Human Genome Project, Bioinformatics, and Evo-devo

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.

Micro RNA's

Small RNA's or micro RNA's (miRNA) appear highly significant in regulation of gene expression during development. They support the RNA world hypothesis and serve a role in the evolution of plants and animals.[20][21][22] Micro RNA's contribution to evolution is considered an epigenetic mechanism in evolutionary developmental biology. Micro RNA's appear to constitute 1% of the human genome. Scientist are designing silencing interference micro RNA's in the hopes of shutting down genes involved in cancer, diseases, and the contribution of genes in developmental biology.

Misunderstandings about modern evolutionary biology

Although the modern synthesis is a central theory in science, many misunderstandings about specific facets of the modern synthesis are prevalent among the general population. These misunderstandings have had a negative impact on the acceptance of the modern synthesis,[23][24] most notably in the United States.[25] Some of the most common misunderstandings are examined in this section.

Distinctions between theory and fact

Further information: Scientific Theory
See also: Theory vs. Fact

Stephen Jay Gould explained that "evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered."[26]

The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. A theory is an attempt to identify and describe relationships between phenomena or things, and generates falsifiable predictions which can be tested through controlled experiments and empirical observation. Speculative or conjectural explanations tend to be called hypotheses, and well tested explanations, theories. Fact tends to mean a datum, an observation, i.e., a fact is obtained by a fairly direct observation. However, a fact does not mean absolute certainty; in science, fact can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent."[27] A theory is obtained by inference from a body of facts. Fact and theory denote the epistemological status of knowledge; how the knowledge was obtained, what sort of knowledge it is.

In this scientific sense, "facts" are what theories attempt to explain. So, for scientists "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship; for example, it is a "fact" that an apple will fall to the ground if it becomes dislodged from a branch and the "theory" which explains this is the current theory of gravitation. In the same way, heritable variation, natural selection, and response to selection (e.g. in domesticated plants and animals) are "facts", and the generalization or extrapolation beyond these phenomena, and the explanation for them, is the "theory of evolution".[28]

Evolution and devolution

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".[29] 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.

In many cases evolution does involve "progression" towards more complexity, since the earliest lifeforms were extremely simple compared to many of the species existing today, 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 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 maximally simple forms. Evolution caused life to become more complex, since becoming simpler wasn't advantageous. Once individual lineages have attained sufficient complexity, however, simplifications (specialization) are as likely as increased complexity. This can be seen in many parasite species, for example, which have evolved simpler forms from more complex ancestors.[30]

Speciation

For more information, see: Speciation.
The existence of several different, but related, finches on the Galápagos Islands is evidence of the occurrence of speciation.

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.[31] (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.

Self-organization and entropy

For more information, see: Self-organization.


It is claimed that evolution, by increasing complexity without supernatural intervention, violates the second law of thermodynamics. This law posits that in an idealised isolated system, entropy will tend to increase or stay the same. Entropy is a measure of the dispersal of energy in a physical system so that it is not available to do mechanical work.[32] The claim ignores the fact that biological systems are not isolated systems. Simple calculations[33] show that the Sun-Earth-space system does not violate the second law because the massive increase in entropy due to the Sun and Earth radiating into space dwarfs the small decrease in entropy caused by the evolution of life. In statistical thermodynamics entropy has been envisioned as a measure of the statistical "disorder" at a microstate level, leading to the mistaken idea that entropy implies increasing chaos.[32]

In fact, the flow of matter and energy through open systems allows self-organization enabling an increase in complexity without guidance or management. Examples include mineral crystals and snowflakes. Life inherently involves open systems, not isolated systems, as all organisms exchange energy and matter with their environment, and similarly the Earth receives energy from the Sun and emits energy back into space.

Information

Some assert that evolution cannot create information, or that information can only be created by an intelligence. Physical information exists regardless of the presence of an intelligence, and evolution allows for new information whenever a novel mutation or gene duplication occurs and is kept. It does not need to be beneficial or visually apparent to be "information." However, even if those were requirements they would be satisfied with the appearance of nylon-eating bacteria,[34] which required new enzymes to efficiently digest a material that never existed until the modern age.[35]

Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa strain POA, which initially had no enzymes capable of degrading nylon oligomers. This indicates that the ability of bacteria to digest nylon can evolve if proper artificial selection is applied.[36] Recently, the same group solved the high resolution X-ray crystal structure of the newly evolved nylon-digesting enzyme.[37] Using the structural results, the authors propose "that the amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the" nylon-digesting enzyme. This hypothesis still needs to be confirmed by detailed mutagenesis studies.

Social and religious controversies

For more information, see: Social effect of evolutionary theory and Creation-evolution controversy.


A satirical 1871 image of Charles Darwin as a quadrupedal ape reflects part of the social controversy over whether humans and other apes share a common lineage.

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.[38]

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[39]; Judaism and Catholicism are notable as major faith traditions whose adherents generally see no conflict between evolutionary theory and religious belief.[40][41][42] 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 United States — 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.[43]

References

  1. ↑ 1.0 1.1 Futuyma, Douglas J. (2005). Evolution. Sunderland, Massachusetts: Sinauer Associates, Inc. ISBN 0-87893-187-2. 
  2. ↑ Gould, Stephen J. (2002). The Structure of Evolutionary Theory. Belknap Press. ISBN 0-674-00613-5. 
  3. ↑ Lande, R.; Arnold, S.J. (1983). "The measurement of selection on correlated characters". Evolution 37: 1210–1226.
  4. ↑ Haldane, J.B.S. (1953). "The measurement of natural selection". Proceedings of the 9th International Congress of Genetics 1: 480–487.
  5. ↑ Mechanisms: the processes of evolution. Understanding Evolution. University of California, Berkeley. Retrieved on 2006-07-14.
  6. ↑ In the years after Darwin's publication and fame, 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. Historians acknowledge that 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, Peter J. (2003). Evolution: The History of an Idea. Berkeley: University of California Press, 158. 
  7. ↑ Bowler, Peter J. (2003). Evolution: The History of an Idea. Berkeley: University of California Press. 
  8. ↑ Darwin’s Theory of Pangenesis
  9. ↑ Bowler, Peter J. (1989). The Mendelian Revolution: The Emergence of Hereditarian Concepts in Modern Science and Society. Baltimore: John Hopkins University Press. 
  10. ↑ Schweitzer M.H. et al (2005). "Soft-tissue vessels and cellular preservation in Tyrannosaurus rex". Science 307 (5717): 1952-1955.
  11. ↑ 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' "[1] [2]"
  12. ↑ 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.
  13. ↑ 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.
  14. ↑ Okamoto N, Inouye I. (2005). "A secondary symbiosis in progress". Science 310 (5746): 287.
  15. ↑ Okamoto N, Inouye I. (2006). "Hatena arenicola gen. et sp. nov., a Katablepharid Undergoing Probable Plastid Acquisition.". Protist Article in Print.
  16. ↑ Pseudogene evolution and natural selection for a compact genome. "[3]"
  17. ↑ Hoskin et al (Oct 2005). "Reinforcement drives rapid allopatric speciation". Nature 437: 1353-1356.
  18. ↑ Savolainen et al (May 2006). "Sympatric speciation in palms on an oceanic island". Nature 441: 210-213.
  19. ↑ Barluenga et al (February 2006). "Sympatric speciation in Nicaraguan crater lake cichlid fish". Nature 439: 719-723.
  20. ↑ Sempere LF, Cole CN, McPeek MA, Peterson KJ. (2006). "The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint..". J Exp Zoolog B Mol Dev Evol (Jul 12). PMID 16838302.
  21. ↑ Massirer KB, Pasquinelli AE. (2006). "The evolving role of microRNAs in animal gene expression.journal = Bioessays." 28 (5): 449-52. PMID 16615087.
  22. ↑ Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA. (2006). "Conservation and divergence of plant microRNA genes.". Plant J. 46 (2): 243-59. PMID 16623887.
  23. ↑ BBC Report on Biology Education in North America "In a study of 1,200 college freshmen, Professor Alters found that 45% of those who doubted the theory of evolution had specific misunderstandings about some of the science that has been used to support it."
  24. ↑ Constance Holden (1998). "SCIENCE EDUCATION: Academy Rallies Teachers on Evolution". Science 280 (5361): 194.
  25. ↑ Miller JD,Scott EC, Okamoto S. (2006). "Science communication. Public acceptance of evolution.". Science 313 (5788): 765-766.
  26. ↑ Stephen Jay Gould, "Evolution as Fact and Theory" 1994
  27. ↑ Stephen Jay Gould, "Evolution as Fact and Theory" 1994
  28. ↑ Evolution is a Fact and a Theory
  29. ↑ talkorigins Claim CB932: Evolution of degenerate forms
  30. ↑ Scientific American; Biology: Is the human race evolving or devolving?
  31. ↑ Boxhorn, Joseph. Observed Instances of Speciation. Talk Origins Archive.
  32. ↑ 32.0 32.1 Disorder — A Cracked Crutch For Supporting Entropy Discussions
  33. ↑ Does Life On Earth Violate the Second Law of Thermodynamics?
  34. ↑ Evolution and Information: The Nylon Bug. New Mexicans for Science and Reason.
  35. ↑ It wasn't a highly competent design because the bacteria weren't extracting a lot of energy from the process, just enough to get by. And it was based on a simply frame shift reading of a gene that had other uses. But with a simple frame shift of a gene that was already there, it could now "eat" nylon. Future mutations, perhaps point mutations inside that gene, could conceivably heighten the energy gain of the nylon decomp process, and allow the bacteria to truly feast and reproduce faster and more plentifully on just nylon, thus leading perhaps in time to an irreducibly complex arrangement between bacteria who live solely on nylon and a man-made fiber produced only by man. Darwinism or Directed Mutations?
  36. ↑ Prijambada I.D. et al (1995). "Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution". Applied and Environmental Microbiology 61 (5): 2020–2022.
  37. ↑ Negoro S et al (2005). "X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme". The Journal of Biological Chemistry 280 (47): 39644-39652.
  38. ↑ 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).
  39. ↑ [4]
  40. ↑ 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. [5]
  41. ↑ 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
  42. ↑ Aish HaTorah According to a possible reading of ancient commentators' description of God and nature, the world may be simultaneously young and old.
  43. ↑ 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).

General references

  • Sean B. Carroll, 2005, Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, W. W. Norton & Company. ISBN 0-393-06016-0
  • Futuyma, D. (2005). Evolution. Sinauer Associates, Inc.. ISBN 0-87893-187-2. 
  • Natalia S. Gavrilova & Leonid A. Gavrilov, 2002, Evolution of Aging, In: David J. Ekerdt (ed.) Encyclopedia of Aging, New York, Macmillan Reference USA, 2002, vol.2, 458-467.ISBN 0-02-865472-2
  • Gigerenzer, Gerd, et al., The empire of chance: how probability changed science and everyday life (New York: Cambridge University Press, 1989).
  • Edward J. Larson, Evolution: The Remarkable History of a Scientific Theory (Modern Library Chronicles). Modern Library (May 4, 2004). ISBN 0-679-64288-9
  • Mayr, Ernst. What Evolution Is. Basic Books (October, 2002). ISBN 0-465-04426-3
  • Menand, Louis. 2001 The Metaphysical Club. New York: Farar, Straus and Giraux. ISBN 0-374-19963-9
  • Smith, D. C. (1988). "Heritable divergence of Rhagoletis pomonella host races by seasonal asynchrony". Nature 336 (6194): 66-67. DOI:10.1038/336066a0.

External links

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Evolution Simulators

See also

For a more comprehensive list of topics, see Category:Evolution and Category:Evolutionary biology

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