Evolution

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Charles Darwin, father of the theory of evolution by natural selection.

In biology, evolution is the process by which populations of organisms acquire and pass on novel traits from generation to generation, affecting the overall makeup of the population and even leading to the emergence of new species.

The development of the modern theory of evolution began with the introduction of the concept of natural selection in a joint 1858 paper by Charles Darwin and Alfred Russel Wallace. This theory achieved a wider readership in Darwin's 1859 book, The Origin of Species. Darwin and Wallace proposed that evolution occurs because a heritable trait that increases an individual's chance of successfully reproducing will become more common, by inheritance, from one generation to the next, and likewise a heritable trait that decreases an individual's chance of reproducing will become rarer. This work was groundbreaking, and overturned other evolutionary theories, such as that advanced by Jean Baptiste Lamarck.

In the 1930s, scientists combined Darwinian natural selection with the re-discovered theory of Mendelian heredity to create the modern synthesis, now one of the fundamental scientific theories of biology. In the modern synthesis, "evolution" is defined as a change in the frequency of alleles within a population from one generation to the next. This change may be caused by different mechanisms, including natural selection, genetic drift, or changes in population structure (gene flow).

Scientific theory

The theory underlying the modern synthesis has three major aspects:

1. The common descent of all organisms from a single ancestor or ancestral gene pool.
2. The manifestation of novel traits in a lineage.
3. The mechanisms that cause some traits to persist while others perish.

The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. In plain English, people use the word "theory" to signify "conjecture", "speculation", or "opinion". In this popular sense, "theories" are opposed to "facts" — parts of the world, or claims about the world, that are real or true regardless of what people think. In contrast, a scientific theory is a model of the world (or some portion of it) from which falsifiable hypotheses can be generated and tested through controlled experiments, or be verified through empirical observation. In this scientific sense, "facts" are parts of theories — they are things, or relationships between things, that theories must take for granted in order to make predictions, or that theories predict. In other words, 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 dropped on earth will fall towards the center of the planet in a straight line, and the "theory" which explains it is the current theory of gravitation. Currently, the modern synthesis is the most powerful theory explaining variation and speciation, and within the science of biology it has completely replaced earlier accepted explanations for the origin of species, including Lamarckism and creationism.

Ancestry of organisms

Pre-Cambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, William Schopf of UCLA published a controversial paper in the journal Nature arguing that formations such as this possess 3.5 billion year old fossilized algae microbes. [1] If true, they would be the earliest known life on earth.

A phylogenetic tree of all living things, based on rRNA gene data, showing the separation of the three domains bacteria, archaea, and eukaryotes as described initially by Carl Woese. Trees constructed with other genes are generally similar, although they may place some early branching groups very differently, presumably owing to rapid rRNA evolution. The exact relationships of the three domains are still being debated.

Genetic testing has shown that humans and chimpanzees have most of their DNA in common. In a study of 90,000 base pairs, Wayne State University's Morris Goodman found humans and chimpanzees share 99.4% of their DNA.[2] [3].

This is a NASA recreation of the famous Miller-Urey experiment. In 1953, Stanley Miller and Harold Urey sealed the chemical precursors to life in a closed environment, and subjected them to conditions similar to primordial earth.

For more details on this topic, see 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 (which is called having "common descent").

Evidence for common descent may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds — even those which do not fly — have wings. Today, the theory of evolution has been strongly confirmed by the science of DNA genetics. For example, every living thing makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations) to translate nucleic acid sequences into proteins. Because the selection of these traits is somewhat arbitrary, their universality strongly suggests common ancestry.

In addition, abiogenesis — the generation of life from non-living matter — has never been observed, indicating that the origin of life from non-life is either extremely rare or only happens under conditions very unlike those of modern Earth. The 1953 Miller-Urey experiment suggests that conditions on the ancient earth may have permitted abiogenesis.

It should be noted that abiogenesis is its own standalone theory apart from evolution. Evolution deals with descent with modification from a common ancestor while abiogenesis deals with how that common ancestor came to be in the first place.

The evolutionary process can be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the age of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old. (See Timeline of evolution.)

Studies on guppies [4] by the National Science Foundation, however, have shown that evolutionary rates in the wild can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record.

Information about the early development of life includes input from the fields of geology and planetary science. These sciences provide information about the history of the Earth and the changes produced by life. A great deal of information about the early Earth has been destroyed by geological processes over the course of time.

Evidence of evolution

Main article: Evidence of evolution

Morphological evidence

Fossils are important for estimating when various lineages developed. As fossilization is an uncommon occurrence, usually requiring hard parts (like bone) and death near a site where sediments are being deposited, the fossil record only provides sparse and intermittent information about the evolution of life. Fossil evidence of organisms without hard body parts, such as shell, bone, and teeth, is sparse but exists in the form of ancient microfossils and the fossilization of ancient burrows and a few soft-bodied organisms.

Nevertheless, fossil evidence of prehistoric organisms has been found all over the Earth. The age of fossils can often be deduced from the geologic context in which they are found; and their absolute age can be verified with radiometric dating. Some fossils bear a resemblance to organisms alive today, while others are radically different. Fossils have been used to determine at what time a lineage developed, and transitional fossils can be used to demonstrate continuity between two different lineages. Paleontologists investigate evolution largely through analysis of fossils.

Phylogeny, the study of the ancestry of species, has revealed that structures with similar internal organization may perform divergent functions. Vertebrate limbs are a common example of such homologous structures. A vestigial organ or structure may exist with little or no purpose in one organism, though they have a clear purpose in others. The human wisdom teeth and appendix are common examples.

Genetic sequence evidence

Comparison of the genetic sequence of organisms reveals that phylogenetically close organisms have a higher degree of sequence similarity than organisms that are phylogenetically distant. For example, neutral human DNA sequences are approximately 1.2% divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6% from gorillas [5], and 6.6% from baboons[6]. Sequence comparison is considered a measure robust enough to be used to correct mistakes in the phylogenetic tree in instances where other evidence is scarce.

Further evidence for common descent comes from genetic detritus such as pseudogenes, regions of DNA which are orthologous to a gene in a related organism, but are no longer active and appear to be undergoing a steady process of degeneration[7].

Since 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 at different stages of development, so it is theoretically possible to determine when certain metabolic processes appeared by comparing the traits of the descendants of a common ancestor.

Origin of life

Main article: Origin of life

Not much is known about the earliest development of 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 (Archea, Bacteria, Eukaryota) or the origin of life. Attempts to shed light on the earliest history of life generally focus on the behavior of macromolecules, particularly RNA, and the behavior of complex systems.

History of life

Main article: Timeline of evolution

Though the origins of life are murky, other milestones in the evolutionary history of life are well known. The emergence of oxygenic photosynthesis (around 3 billion years ago) and the subsequent emergence of an oxygen-rich, non-reducing atmosphere can be traced through the formation of banded iron deposits, and later red beds of iron oxides. This was a necessary prerequisite for the development of aerobic cellular respiration, believed to have emerged around 2 billion years ago. In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after the emergence of the first animals, the Cambrian explosion (a period of unrivaled and remarkable, but brief, organismal diversity documented in the fossils found at the Burgess Shale) saw the creation of all the major body plans, or phyla, of modern animals. This event is now believed to have been triggered by the development of Hox genes. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals, leading to the development of land ecosystems with which we are familiar.

Emergence of novel traits

Mutation

Main article: Mutation

Darwin did not know the source of variations in individual organisms, but observed that it seemed to be by chance. Later work pinned much of this variation onto mutations. Mutations are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by "copying errors" in the genetic material during cell division and by exposure to radiation, chemicals, or viruses. In multicellular organisms, mutations can be subdivided into germline mutations, which can be passed on to progeny and somatic mutations, which (when accidental) often lead to the malfunction or death of a cell and can cause cancer.

Mutations serve to introduce novel genetic variation which may affect the fitness of the organism.

Survival of traits

Mechanisms of inheritance

In Darwin's time, scientists did not share broad agreement on how traits were inherited. Today most inherited traits are traced to discrete, persistent entities called genes, encoded in linear molecules called DNA. Though largely faithfully maintained, DNA is both variable across individuals and subject to a process of change or mutation (described above).

However, other non-DNA based forms of heritable variation exist. The processes that produce these variations leave the genetic information intact and are often reversible. This is called epigenetic inheritance and may include phenomena such as DNA methylation, prions, and structural inheritance. Investigations continue into whether these mechanisms allow for the production of specific beneficial heritable variation in response to environmental signals. If this 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.

There are factors that influence the frequency of existing alleles. These factors mean that some characteristics will become more frequent while others diminish or are lost entirely. There are three known processes that affect the survival of a characteristic (or, more specifically, the frequency of an allele):

• Natural selection
• Gene flow
• Genetic drift

Natural selection

Main article: Natural selection

Natural selection is survival and reproduction as a result of the environment. Differential mortality is the survival rate of individuals to their reproductive age. Differential fertility is the total genetic contribution to the next generation. The central role of natural selection in evolutionary theory has given rise to a strong connection between that field and the study of ecology.

Natural selection can be subdivided into two categories:

• Ecological selection occurs when organisms 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:

• Purifying or background selection eliminates deleterious mutations from a population.
• Positive selection increases the frequency of a beneficial mutation.
• Balancing selection maintains variation within a population through a number of mechanisms, including:
  • Overdominance or heterozygote advantage, where the heterozygote is more fit than either of the homozygous forms (exemplified by human sickle cell anemia conferring resistance to malaria)
  • Frequency-dependent selection, where the rare variants have a higher fitness.
• Stabilizing selection favors average characteristics in a population, thus reducing gene variation but retaining the mean.
• Directional selection favors one extreme of a characteristic; results in a shift in the mean in the direction of the extreme.
• Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.

Mutations that are not affected by natural selection are called neutral mutations. Their frequency in the population is governed entirely by genetic drift and gene flow. It is understood that an organism's DNA sequence, in the absence of selection, undergoes a steady accumulation of neutral mutations. The probable mutation effect is the proposition that a gene that is not under selection will be destroyed by accumulated mutations. This is an aspect of genome degradation.

• Baldwinian evolution refers to the way human beings, as cultured animals capable of symbolic (extrasomatic) learning, can change their environment, or the environment of any species, in such a way as to result in new selective forces.

Gene flow

Gene flow (or gene admixture) is the only mechanism whereby populations can become closer genetically while building larger gene pools. Migration of one population into another area occupied by a second population can result in gene flow. Gene flow operates when geography and culture are not obstacles.

Genetic drift

Main article: 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.

Many aspects of genetic drift depend on the size of the population (generally abbreviated as N). This is especially important in small mating populations, where chance fluctuations from generation to generation can be large. Such fluctuations in allele frequency between successive generations may result in some alleles disappearing from the population. Two separate populations that begin with the same allele frequency therefore might "drift" by random fluctuation into two divergent populations with different allele sets (for example, alleles that are present in one have been lost in the other).

The relative importance of natural selection and genetic drift in determining the fate of new mutations also depends on the population size and the strength of selection: when N times s (population size times strength of selection) is small, genetic drift predominates. When N times s is large, selection predominates. Thus, natural selection is 'more efficient' in large populations, or equivalently, genetic drift is stronger in small populations. Finally, the time for an allele to become fixed in the population by genetic drift (that is, for all individuals in the population to carry that allele) depends on population size, with smaller populations requiring a shorter time to fixation.

Adaptation

Through the process of natural selection, species become better adapted to their environments. Adaptation is any evolutionary process that increases the fitness of the individual, or sometimes the trait that confers increased fitness, e.g. a stronger prehensile tail or greater visual acuity. Note that adaptation is context-sensitive; a trait that increases fitness in one environment may decrease it in another.

Evolution does not act in a linear direction towards a pre-defined "goal" — it only responds to various types of adaptionary changes. The belief in a telelogical evolution of this sort is known as orthogenesis, and is not supported by the scientific theory of evolution. One example of this misconception is the erroneous belief humans will evolve more fingers in the future on account of their increased use of machines such as computers. 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.

Speciation and extinction

Speciation is the creation of two or more species from one. This may take place by various mechanisms. Allopatric speciation occurs in populations that become isolated geographically, such as by habitat fragmentation or migration. Sympatric speciation occurs when new species emerge in the same geographic area. Ernst Mayr's peripatric speciation is a type of speciation that exists in between the extremes of allopatry and sympatry. Peripatric speciation is a critical underpinning of the theory of punctuated equilibrium.

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.

Evolutionary biology

Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time. Evolutionary biology is a kind of meta field because it includes scientists from many traditional taxonomically oriented disciplines. For example, it generally includes scientists who may have a specialist training in particular organisms such as mammalogy, ornithology, or herpetology but use those organisms as systems to answer general questions in evolution.

Evolutionary biology as an academic discipline in its own right emerged as a result of the modern evolutionary synthesis in the 1930s and 1940s. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term evolutionary biology in their titles.

Evolutionary developmental biology

Evolutionary developmental biology is an emergent subfield of evolutionary biology that looks at genes of related and unrelated organisms. By comparing the explicit nucleotide sequences of DNA/RNA, it is possible to experimentally determine and trace timelines of species development. For example, gene sequences support the conclusion that chimpanzees are the closest primate ancestor to humans, and that arthropods (e.g., insects) and vertebrates (e.g., humans) have a common biological ancestor.

History of evolutionary thought

The 1859 edition of On the Origin of Species

Stephen Jay Gould, who, along with Niles Eldredge proposed the theory of punctuated equilibrium in 1972

Main article: History of evolutionary thought

The idea of biological evolution has existed since ancient times, notably among Hellenists such as Epicurus and Anaximander, but the modern theory was not established until the 18th and 19th centuries, by scientists such as Jean-Baptiste Lamarck and Charles Darwin. While transmutation of species was accepted by a sizeable number of scientists before 1859, it was the publication of Charles Darwin's The Origin of Species which provided the first cogent mechanism by which evolutionary change could occur: his theory of natural selection. Darwin was motivated to publish his work on evolution after receiving a letter from Alfred Russel Wallace, in which Wallace revealed his own discovery of natural selection. As such, Wallace is sometimes given shared credit for the theory of evolution.

Darwin's theory, though it succeeded in profoundly shaking scientific opinion regarding the development of life, could not explain the source of variation in traits within a species, and Darwin's proposal of a hereditary mechanism (pangenesis) was not compelling to most biologists. It was not until the late 19th and early 20th centuries that these mechanisms were established.

When Gregor Mendel's work regarding the nature of inheritance in the late 19th century was "rediscovered" in 1900, it led to a storm of conflict between Mendelians (Charles Benedict Davenport) and biometricians (Walter Frank Raphael Weldon and Karl Pearson), who insisted that the great majority of traits important to evolution must show continuous variation that was not explainable by Mendelian analysis. Eventually, the two models were reconciled and merged, primarily through the work of the biologist and statistician R.A. Fisher. This combined approach, applying a rigorous statistical model to Mendel's theories of inheritance via genes, became known in the 1930s and 1940s as the modern evolutionary synthesis.

In the 1940s, following up on Griffith's experiment, Avery, McCleod and McCarty definitively identified deoxyribonucleic acid (DNA) as the "transforming principle" responsible for transmitting genetic information. In 1953, Francis Crick and James Watson published their famous paper on the structure of DNA, based on the research of Rosalind Franklin and Maurice Wilkins. These developments ignited the era of molecular biology and transformed the understanding of evolution into a molecular process: the mutation of segments of DNA (see molecular evolution).

George C. Williams' 1966 Adaptation and natural selection: A Critique of some Current Evolutionary Thought marked a departure from the idea of group selection towards the modern notion of the gene as the unit of selection. In the mid-1970s, Motoo Kimura formulated the neutral theory of molecular evolution, firmly establishing the importance of genetic drift as a major mechanism of evolution.

Debates have continued within the field. One of the most prominent public debates was over the theory of punctuated equilibrium, proposed in 1972 by paleontologists Niles Eldredge and Stephen Jay Gould to explain the paucity of transitional forms between phyla in the fossil record.

Impact of theory

Main article: Social implications of the theory of evolution

Ever since Darwin's theory of evolution was first published it has never been out of print or out of controversy. Although rarely disputed scientifically, due to the emotive subject matter, it has caught the attention of a lot of people, and drawn condemnation from several religious groups. When it was first published, many of Darwin's peers were incredulous, and the concept was believed to be too radical.^{Citation needed} For instance, a now frequently cited cartoon depicts a human and a great ape side by side, both in disbelief that they were members of the same evolutionary "family." In 1860, over a thousand people attended a debate which degenerated into uproar when Bishop Samuel Wilberforce accused T.H. Huxley of claiming an attachment to apes (Bryson 2004). However the theory has since gained prestige, as it has been corroborated by all scientific evidence.

As the scientific explanation of life's diversity has developed, evolution has displaced alternative, sometimes very widely held, explanations, and it is now taught, almost exclusively, to students around the world.^{Citation needed} Particularly in the US, this has led to a vigorous conflict between creation and evolution in public education, and the creation evolution controversy in general.

See also

References

• Darwin, Charles November 24, 1859. On the Origin of Species by means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, Albemarle Street. 502 pages. Reprinted: Gramercy (May 22, 1995). ISBN 0517123207
• Zimmer, Carl. Evolution: The Triumph of an Idea. Perennial (October 1, 2002). ISBN 0060958502
• Larson, Edward J. Evolution: The Remarkable History of a Scientific Theory (Modern Library Chronicles). Modern Library (May 4, 2004). ISBN 0679642889
• Mayr, Ernst. What Evolution Is. Basic Books (October, 2002). ISBN 0465044263
• Gigerenzer, Gerd, et al., The empire of chance: how probability changed science and everyday life (New York: Cambridge University Press, 1989).
• Williams, G.C. (1966). Adaptation and Natural Selection: A Critique of some Current Evolutionary Thought . Princeton, N.J.: Princeton University Press.
• Sean B. Carroll, 2005, Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom, W. W. Norton & Company. ISBN 0393060160
• Bill Bryson, A Short History of Nearly Everything, Black Swan Books (2004), ISBN 0-552-99704-8

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• Talk.Origins Archive — see also talk.origins
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• EvoWiki — A wiki whose goal is to promote general evolution education, and provide mainstream scientific responses to the arguments of antievolutionists.
• Evolution by Natural Selection — An introduction to the logic of the theory of evolution by natural selection
• Evolution — Provided by PBS.
• Everything you wanted to know about evolution — Provided by New Scientist.
• International Journal of Organic Evolution
• Howstuffworks.com — How Evolution Works
• Charles Darwin's writings
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• National Academy Press: Teaching About Evolution and the Nature of Science
• Evolution for beginners
• RMCybernetics - AI Evolution can create emergent behavior in a computer program.