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Evolution

Evolution

, based on rRNA gene data, showing the separation of the three domains, bacteria, archaea, and eukaryotes, as described initially by Carl Woese.]] 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 terms organic evolution or biological evolution are often used to distinguish this meaning from other usages. 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. Because of its potential implications for the origins of humankind, the theory has been at the center of many social and religious controversies since its first inception (see Creation-evolution controversy). 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. The basic mechanisms that produce these changes are natural selection, genetic drift, and genetic variation. The primary sources of genetic variation are mutation, sex, and gene flow.

Overview of evolution

Evidence of evolution

The process of evolution has left behind numerous records which reveal the history of species. While the best-known of these are the fossils, fossils are only a small part of the overall physical record of evolution. Fossils, taken together with the comparative anatomy of present-day plants and animals, constitute the morphological record. By comparing the anatomies of both modern and extinct species, biologists can reconstruct the lineages of those species with some accuracy. Using fossil evidence, for instance, the connection between dinosaurs and birds has been established by way of so-called "transitional" species such as Archaeopteryx. The development of genetics has allowed biologists to study the genetic record of evolution as well. Although we cannot obtain the DNA sequences of most extinct species, the degree of similarity and difference among modern species allows geneticists to reconstruct lineages with greater accuracy. It is from genetic comparisons that claims such as the 98-99% similarity between humans and chimpanzees come from, for instance. Other evidence used to demonstrate evolutionary lineages includes the geographical distribution of species. For instance, monotremes and most marsupials are found only in Australia, 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 the earth. For instance, paleoclimatology attests to periodic ice ages during which the climate was much cooler; and these are found to match up with the spread of species such as the woolly mammoth which are better-equipped to deal with cold.

Morphological evidence

Fossils are important for estimating when various lineages developed. As fossilization on an organism 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. 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. Bat wings, for example, are very similar to hands. A vestigial organ or structure may exist with little or no purpose in one organism, though they have a clear purpose in other species. 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, and 6.6% from baboons. Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce. 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. 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 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.

History of evolutionary thought

metabolic.]] 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 by Means of Natural Selection 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. pangenesis, proposed the theory of punctuated equilibrium in 1972.]] 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.

Social and religious controversies

Stephen Jay Gould from 1871 reflects part of the social controversy over whether humans and apes share a common lineage.]] There has been constant controversy surrounding the ideas presented by The Origin of Species since it was first printed in 1859. Since the early twentieth century, however, the idea that biological evolution of some form occurred and is responsible for speciation has been almost completely uncontested within the scientific community. Most controversy over the theory has come because of its philosophical, cosmological, and religious implications, and supporters as well as detractors have interpreted it as generally indicating that human beings are, like all animals, evolved, and that this account of the origins of humankind is squarely at odds with many religious interpretations. The idea that humans are "merely" animals, and are genetically very closely related to primates, have been independently argued as repellent notions by generations of detractors. Others also intepreted the truth of the theory to imply varying types of social changes — one prominent example is the idea of eugenics, formulated by Darwin's cousin Francis Galton, which argues for the improvement of human heredity by means of political policies. Others have found different political interpretations which have been used as arguments both for and against the theory. The questions raised about the relation of evolution to the origins of humans has made it an especially tenacious issue with religious traditions. It has prominently been seen as opposing a "literal" interpretation of the account of the origins of humankind as described in Genesis, the first book of the Bible. In many countries — notably in the United States — this has led to what has been called the Creation-evolution controversy, which has focused primarily on struggles over teaching curriculum.

Science of evolution

Science: fact and theory

The word "evolution" has been used to refer both to a fact and a theory, and it is important to understand both these different meanings of evolution, and the relationship between fact and theory in science.

Evolution as fact and theory

When "evolution" is used to describe a fact, it refers to the observations that populations of one species of organism do, over time change into new, or several new, species. In this sense, evolution occurs whenever a new strain of bacterium evolves that is resistant to antibodies that had been lethal to prior strains. Another clear case of evolution as fact involves the hawthorn fly, Rhagoletis pomonella. Different populations of hawthorn fly feed on different fruits. A new population spontaneously emerged in North America in the 19th century some time after apples, a non-native species, were introduced. The apple feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. Likewise the current hawthorn feeding population does not normally feed on apples. A current area of scientific research is the investigation of whether or not the apple feeding race may further evolve into a new species. Some evidence, such as the fact that six out of thirteen alozyme loci are different, that hawthorn flies mature later in the season, and take longer to mature, than apple flies, and that there is little evidence of interbreeding (researchers have documented a 4-6%hybridization rate) suggests that this is indeed ocurring. (see Berlocher and Bush 1982, Berlocher and Feder 2002, Bush 1969, McPheron et. al. 1988, Prokopy et. al. 1988, Smith 1988) When "evolution" is used to describe a theory, it refers to an explanation for why and how evolution (for example, in the sense of "speciation") occurs. An example of evolution as theory is the modern synthesis of Darwin and Wallace's theory of natural selection and Mendel's principles of genetics. This theory has three major aspects: # Common descent of all organisms from a single ancestor or ancestral gene pool. # Manifestation of novel traits in a lineage. # Mechanisms that cause some traits to persist while others perish. When people provide evidence for evolution, in some cases they are providing evidence that evolution occurs; in other cases they are providing evidence that a given theory is the best explanation yet as to why and how evolution occurs.

The meaning of, and relationship between, fact and theory in science

:Main article: Theory 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 scientific terminology however, a theory is a model of the world (or some portion of it) from which falsifiable hypotheses can be generated and tested through controlled experiments, or be verified through empirical observation. 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 every apple ever dropped on earth (under normal, controlled conditions) has been observed to fall towards the center of the planet in a straight line, and the "theory" which explains these observations is the current theory of gravitation. In this same sense evolution is a fact and modern synthesis is currently the most powerful theory explaining evolution, variation and speciation. Within the science of biology, modern synthesis has completely replaced earlier accepted explanations for the origin of species, including Lamarckism and creationism.
Who studies evolution?
Scholars in a number of academic disciplines and subdisciplines document the fact of evolution, and contribute to the theory of evolution.
Physical anthropology
Physical anthropology emerged in the late 1800s as the study of human osteology, and the fossilized skeletal remains of other hominids. At that time anthropologists debated whether their evidence supported Darwin's claims, because skeletal remains revelaed temporal and spacial variation among hominids, but Darwin had not offered an explanation of the mechanisms that produce variation. With the recognition of Mendelian genetics and the rise of the modern synthesis, however, evolution became both the fundamental conceptual framework for, and object of study of, physical anthropologists. In addition to studying skeletal remains, they began to study genetic variation among human populations (i.e. population genetics; thus, some physical anthropologists began calling themselves biological anthropologists.
Evolutionary biology
Evolutionary biology is a subfield of biology concerned with the origin and descent of species, as well as their change over time. At first it was an interdisciplinarity field including 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.
Ancestry of organisms
vertebrates 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 genetics. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations) to translate nucleic acid sequences into proteins. The universality of these traits strongly suggests common ancestry, because the selection of these traits seems somewhat arbitrary, . 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 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. 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.
History of life
planetary sciences in the Siyeh Formation, Glacier National Park. In 2002, William Schopf of UCLA published a controversial paper in the journal Nature arguing that formations such as this possess 3.5 billion year old fossilized algae microbes. If true, they would be the earliest known life on earth.]] The chemical evolution from self-catalytic chemicals to life (see Origin of life) is not a part of biological evolution. Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure, and genetic code. Most scientists interpret this to mean all existing organisms share a common ancestor, 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. 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 the 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.
The Modern Synthesis
The current understanding of the mechanistics of evolution differs considerably from the theory first outlined by Charles Darwin. Importantly, advances in genetics pioneered by Gregor Mendel led to a sophisticated understanding of the basis of variation and the mechanisms of inheritance. In addition natural selection has come to be seen as only one of a number of forces acting in evolution. A notable milestone in this regard was the formulation of the neutral theory of molecular evolution by Motoo Kimura.
Heredity
Gregor Mendel first proposed a gene-based theory of inheritance, discretizing the elements responsible for heritable traints into the fundamental units we now call genes, and laying out a mathematical framework for the segregation and inheritance of variants of a gene, which we now refer to as alleles. Later research identified the molecule DNA as the genetic material, through which traits are passed from parent to offspring, and identified genes as discrete elements within DNA. Though largely faithfully maintained within organisms, DNA is both variable across individuals and subject to a process of change or mutation. Non-DNA based forms of heritable variation exist, which may change the way in which genes are expressed or maintained. 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.
Sexual reproduction
In addition to passing genetic material from parent to offspring, nearly all organisms employ sex to exchange genetic material. This, combined with meiotic recombination, allows genetic variation to be propagated through an interbreeding population. These mechanisms allow individual variations to be propagated more or less independently, so that the population as a whole can retain beneficial variation and eliminate harmful variation (rather than both of these effects competing within a single asexual organism). However, these mechanisms are not perfect, and so some variation is co-propagated as a result of linkage, producing some odd effects (see Muller's ratchet).
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. There are three known processes that affect the survival of a characteristic (or, more specifically, the frequency of an allele):
- Natural selection
- Changes in population structure
- Genetic drift These basic 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
Variation
Without genetic variation, populations cannot evolve. The two principle sources of genetic variation are mutations and gene flow. Other forms of genetic variation due to gene transfer include horizontal gene transfer, antigenic shift, and reassortment. Viruses can transfer genes between species [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]. Bacteria can incorporate genes from other dead bacteria, exchange genes with living bacteria, and can have plasmids "set up residence seperate from the host's genome" [http://www2.nau.edu/~bah/BIO471/Reader/Pennisi_2003.pdf]. "Genes that move between species play by rules that microbial experts are just beginning to discern" [http://66.102.7.104/search?q=cache:gto6eXfbGIEJ:www.niagara.edu/eli/Science%252016%2520July%25202004.GeneSwap.doc+sex+evolution+%22Horizontal+gene+transfer%22+-human+Conjugation+RNA+DNA&hl=en].
Mutation
The ultimate source of all genetic variation is mutations. They are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by "copying errors" in the genetic material during cell division and by exposure to radiation, chemicals, or viruses. In multicellular organisms, mutations can be subdivided into germline mutations that occur in the gametes and thus can be passed on to progeny, and somatic mutations that often lead to the malfunction or death of a cell and can cause cancer. 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 a species' genome, 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. Not all mutations are created equal; simple point mutations (substitutions), which comprise the vast majority of genetic variation, usually can only alter the function or level of expression of existing genes. Gene duplications, which may occur via a number of mechanisms, are believed to be the major mechanism for the introduction of new genes; 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 "paralogs"). Finally, large chromosomal rearrangements (like the fusion of two chromosomes in the chimp/human common ancestor that produced human chromosome 2) almost invariably result in a speciation event.
Gene flow
Gene flow (or gene admixture) is introduction of variation into a population from an outside population. It is the only mechanism whereby two populations can become closer genetically while increasing their variation. Migration of one population into an area occupied by a second population can result in gene flow. Gene flow operates when geography and culture are not obstacles. When gene flow is impeded by non-geographic obstacles, the situation is termed reproductive isolation and is considered to be the hallmark of speciation.
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, allele frequencies will tend to "drift" upward or downward, eventually becoming "fixed" - that is, going to 0% or 100% frequency. 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 frequencies 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). 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. 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.
Population structure
An important facet of evolution occurs through changes in population structure. The movement of populations and changes in their size can have profound impacts on evolution over and above those governed by selection and drift. Migration can result in admixture leading to the introduction of new genetic variation, or it may result in geographic isolation which may in turn lead to reproductive isolation or speciation. Populations may also shrink or grow over time, producing "bottlenecks" or "explosions" respectively. 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. Such changes may also produce dramatic and dangerous crashes in the level of genetic variation in the population, or allow rapid increases in standing genetic variation. 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. Many models of evolution rely on simplifying assumptions of constant population size and fully interbreeding populations for mathematical convenience. An example of the effect of population structure is the so-called founder effect, resulting from a migration and population bottleneck. In this case, a single, rare allele may suddenly increase very rapidly in frequency 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.
Selection and adaptation

Natural selection
Natural selection comes from differences in 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. 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:
- 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.
- Directional selection increases the frequency of a beneficial mutation.
- Balancing selection maintains variation within a population through a number of mechanisms, including:
- Heterozygote advantage or overdominance, where the heterozygote is more fit than either of the homozygous forms (exemplified by human sickle cell anemia conferring resistance to malaria)
- Frequency-dependent selection, where rare variants have a higher fitness, because of thier rarity.
- Stabilizing selection favors average characteristics in a population, thus reducing gene variation but retaining the mean.
- Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.
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
macromutation 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. 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 (See Image 5).
See also

Notes and references
# "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]" # Understanding Evolution, from California's Berkeley University. "[http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_17] [http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_16] # Li WH, Saunders MA (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87. Britten RJ (2002) Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci U S A 99: 13633–13635. # 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' "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11170892] [http://www.genome.org/cgi/content/full/13/5/813]" # 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]" # Reference for emergence of new race of apple maggot flies http://www.nd.edu/~aforbes/ # 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]" # The use of evolutionary principles to guide disease diagnosis and drug development with respect to bird flu (i.e. H5N1 virus) [http://www.cdc.gov/ncidod/EID/vol11no10/05-0644.htm] # Understanding Evolution, from California's Berkeley University: "Sex can introduce new gene combinations into a population. This genetic shuffling is another important source of genetic variation."[http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_17]
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- 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
- McPheron, B. A., D. C. Smith and S. H. Berlocher. 1988. Genetic differentiation between host races of Rhagoletis pomonella. Nature. 336:64-66.
- Gigerenzer, Gerd, et al., The empire of chance: how probability changed science and everyday life (New York: Cambridge University Press, 1989).
- Smith, D. C. 1988. Heritable divergence of Rhagoletis pomonella host races by seasonal asynchrony. Nature. 336:66-67.
- 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
External links

- [http://www.talkorigins.org Talk.Origins Archive] — see also talk.origins
- [http://evolution.berkeley.edu/ Understanding Evolution] @ [http://berkeley.edu Berkeley]
- [http://nationalacademies.org/evolution/ National Academies Evolution Resources]
- [http://www.evowiki.org/index.php/Main_Page EvoWiki] — A wiki whose goal is to promote general evolution education, and provide mainstream scientific responses to the arguments of antievolutionists.
- [http://www.chains-of-reason.org/chains/evolution-by-natural-selection/introduction.htm Evolution by Natural Selection] — An introduction to the logic of the theory of evolution by natural selection
- [http://www.pbs.org/wgbh/evolution/index.html Evolution] — Provided by PBS.
- [http://www.newscientist.com/channel/life/evolution Everything you wanted to know about evolution] — Provided by New Scientist.
- [http://evol.allenpress.com/evolonline/?request=index-html International Journal of Organic Evolution]
- [http://science.howstuffworks.com/evolution.htm/printable Howstuffworks.com — How Evolution Works]
- [http://pages.britishlibrary.net/charles.darwin/ Charles Darwin's writings]
- [http://www.genomenewsnetwork.org/categories/index/genome/evolution.php Evolution News from Genome News Network (GNN)]
- [http://www.nap.edu/books/0309063647/html/ National Academy Press: Teaching About Evolution and the Nature of Science]
- [http://www.evolution.mbdojo.com/evolution-for-beginners.html Evolution for beginners]
- [http://www.rmcybernetics.com/science/cybernetics/ai.htm RMCybernetics - AI] Evolution can create emergent behavior in a computer program.
- [http://www.sciencefriday.com/pages/2005/Nov/hour2_111805.html NPR - Science Friday: links to museums, articles and books.]
Evolution Simulators

- [http://www.truthtree.com/evolve.shtml Isolated species evolves to interact more efficiently with its environment (java applet)]
- [http://obermuhlner.com/public/Projects/Applets/Blobs/index.html Evolution in a predator-prey relationship (java applet)] Category:Evolutionary biology Category:Theories ko:진화 ja:進化 th:วิวัฒนาการ

Non-coding RNA
A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. A commonly used synonym is small RNA (sRNA). Less-frequently used synonyms are non-messenger RNA (nmRNA), small non-messenger RNA (snmRNA), and functional RNA (fRNA). The DNA sequence from which a non-coding RNA is transcribed as the end product is often called an RNA gene or non-coding RNA gene (see gene). The most prominent examples of non-coding RNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation and gene expression. However, since the late 1990s, many new non-coding RNAs have been found, and thus non-coding RNAs may play a much more significant role than previously thought. Human mitochondrial genome contains 24 RNA genes: 2 for 23S and 16S rRNR subunits of mitochondrial ribosomes. Nuclear genome contains c.a. 3000 RNA genes (less than 10% of total gene number). To identify RNA genes in sequenced DNA is very difficult. In addition to the RNA genes there are many related pseudogene/gene fragments.
Types (families) of non-coding RNAs

Transfer RNA
Transfer RNA (tRNA) is RNA that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein biosynthesis during translation.
Ribosomal RNA
Ribosomal RNA (rRNA) is the primary constituent of ribosomes. Ribosomes are the protein-manufacturing organelles of cells and exist in the cytoplasm. rRNA is transcribed from DNA, like all RNA. Ribosomal proteins are transported into the nucleus and assembled together with rRNA before being transported through the nuclear membrane. This type of RNA makes up the vast majority of RNA found in a typical cell. While proteins are also present in the ribosomes, solely rRNA is able to form peptides. Therefore ribosome often is referred to as ribozyme. There are 2 mitochondrial (23S and 16S) molecules and 4 types of cytoplasmic rRNA (28S, 5.8S, 5S (large ribosome subunit) and 18S (small subunit)). 28S, 5.8S and 18S rRNAs are encoded by a single transcription unit organized into 5 clusters (each has 30-40 repeats) on the 13,14,15, 21 and 22 chromosomes. 5S occurs in tandem arrays (~200-300 true 5S genes and many dispersed pseudogenes), the largest one on the chromosome 1q41-42. Cytoplasmic rRNA genes are highly repetitive because of huge demand of ribosomes for protein synthesis (gene dosage) in the cell.
Untranslated regions of mRNAs
Many non-coding RNAs are structural elements in the untranslated regions of mRNAs (i.e. cis-regulatory RNAs), for example riboswitches and the SECIS element.
Small nuclear RNA
Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the nucleus of eukaryotic cells. They are involved in a variety of important processes such as RNA splicing (removal of introns from hnRNA) and maintaining the telomeres. They are always associated with specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP) or sometimes as snurps.
Small nucleolar RNA
Small nucleolar RNA (snoRNA) is a class of small RNA molecules that are involved in chemical modifications of ribosomal RNAs (rRNAs) and other RNA genes, for example by methylation. snoRNAs are a component in the small nucleolar ribonucleoprotein (snoRNP), which contains snoRNA and proteins. The snoRNA guides the snoRNP complex to the modification site of the target RNA gene via sequences in the snoRNA that hybridize to the target site. The proteins then catalyze modification of the RNA gene.
microRNA
microRNA (also miRNA) are RNA genes that are the reverse complement of another gene's mRNA transcript and inhibit the expression of the target gene. See miRNA.
gRNAs
gRNAs (for guide RNA) are RNA genes that function in RNA editing. Thus far, RNA editing has been found only in the mitochondria of kinetoplastids, in which mRNAs are edited by inserting or deleting stretches of uridylates (Us). The gRNA forms part of the editosome and contains sequences that hybridize to matching sequences in the mRNA, to guide the mRNA modifications. The term "guide RNA" is also sometimes used generically to mean any RNA gene that guides an RNA/protein complex via hybridization of matching sequences.
efference RNA
Efference RNA (eRNA) is derived from intron sequences of genes or from non-coding DNA. The function is assumed to be regulation of translational activity by interference with the transcription apparatus or target proteins of the translated peptide in question, or by providing a concentration-based measure of protein expression, basically introducing a fine-tuned analog element in gene regulation as opposed to the digital on-or-off regulation by promoters. Research into the role of eRNAs is in its infancy.
Signal recognition particle RNA
The signal recognition particle (SRP) is an RNA-protein complex present in the cytoplasm of cells that binds to the mRNA of proteins that are destined for secretion from the cell. The RNA component of the SRP in eukaryotes is called 4.5S RNA.
pRNA
At least one species of DNA-containing phages, phi-29, uses a complex of six identical short RNA sequences as mechanical components (utilizing ATP for energy) of its DNA packaging machinery. How common this phenomenon is has yet to be determined.
tmRNA
tmRNA has a complex structure with tRNA-like and mRNA-like regions. It has currently only been found in bacteria, but is ubiquitous in all bacteria. tmRNA recognizes ribosomes that have trouble translating or reading an mRNA and stall, leaving an unfinished protein that may be detrimental to the cell. tmRNA acts like a tRNA first, and then an mRNA that encodes a peptide tag. The ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein. This attached tag targets the protein for destruction or proteolysis. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10881189&query_hl=5 How tmRNA works]
External

- [http://www.sanger.ac.uk/Software/Rfam/ The Rfam Database] A curated list of hundreds of families of related ncRNAs. Each family includes a multiple alignment of known members, and predicted homologs in a large genome database. The definition of "family" is a pragmatic one, the goal being to lead to high-quality annotations. Thus, some families are quite broad (e.g. all tRNAs are in one family, as of 2004), while some families are quite narrow (e.g. there are many microRNA families, one for each type).
- [http://biobases.ibch.poznan.pl/ncRNA/ Non-coding RNA database] ja:ncRNA ko:RRNA Category:RNA Category:Molecular genetics

Gene

:For the musical band, see Gene (band) Gene (band) (right). Introns are regions often found in eukaryote genes which are removed in the splicing process: only the exons encode the protein. This diagram labels a region of only 40 or so bases as a gene. In reality many genes are much larger.]] Genes are regions of the DNA that parents pass to offspring during reproduction as chromosomes in nuclei of gametes. These entities encode information essential for the construction and regulation of proteins (such as enzymes) and other molecules that determine the growth and functioning of the organism. The word "gene" comes from the Greek genos ("origin") and is shared by many disciplines, including classical genetics, molecular genetics, evolutionary biology and population genetics. Because each discipline models the biology of life differently, the usage of the word gene varies between disciplines. It may refer to either material or conceptual entities. Following the discovery that DNA is the genetic material, and with the growth of biotechnology and the project to sequence the human genome, the common usage of the word "gene" has increasingly reflected its meaning in molecular biology. In the molecular-biological sense, genes are the segments of DNA which cells transcribe into RNA and translate, at least in part, into proteins. The [http://song.sourceforge.net/ Sequence Ontology] project defines a gene as: "A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions". In common speech, "gene" is often used to refer to the hereditary cause of a trait, disease or condition—as in "the gene for obesity." Speaking more precisely, a biologist might refer to an allele or a mutation that has been implicated in or is associated with obesity. This is because biologists know that many factors other than genes decide whether a person is obese or not: eating habits, exercise, prenatal environment, upbringing, culture and the availability of food, for example. Moreover, it is very unlikely that variations within a single gene—or single genetic locus—fully determine one's genetic predisposition for obesity. These aspects of inheritance—the interplay between genes and environment, the influence of many genes—appear to be the norm with regard to many and perhaps most ("complex" or "multi-factoral") traits. The term phenotype refers to the characteristics that result from this interplay (see genotype-phenotype distinction).

Overview

Properties of genes

In molecular biology, the DNA of a gene encodes the chemical structure of a protein. The genetic code determines the sequence of the amino acids that make up a protein. The coding of a three nucleotide DNA sequence to a specific amino acid is essentially the same for all known life, from bacteria to humans. Through the proteins they encode, genes govern the cells in which they reside. In multicellular organisms they control the development of the individual from the fertilized egg and the day-to-day functions of the cells that make up tissues and organs. The instrumental roles of their protein products range from mechanical support of the cell structure to the transportation and manufacture of other molecules and to the regulation of other proteins' activities. The genes that exist today are those that have reproduced successfully in the past. Often, many individual organisms share a gene; thus, the death of an individual need not mean the extinction of the gene. Indeed, if the sacrifice of one individual enhances the survivability of other individuals with the same gene, the death of an individual may enhance the overall survival of the gene. This is the basis of the selfish gene view, popularized by Richard Dawkins. He points out in his book, The Selfish Gene, that to be successful genes need have no other "purpose" than to propagate themselves, even at the expense of their host organism's welfare. A human that behaved in such a way would be described as "selfish," although ironically a selfish gene may promote altruistic behaviours. According to Dawkins, the possibly disappointing answer to the question "what is the meaning of life?" may be "the survival and perpetuation of ribonucleic acids and their associated proteins".

Types of genes

Due to rare, spontaneous errors (e.g. in DNA replication) mutations in the sequence of a gene may arise. Once propagated to the next generation, this mutation may lead to variations within a species' population. Variants of a single gene are known as alleles, and differences in alleles may give rise to differences in traits, for example eye colour. A gene's most common allele is called the wild type allele, and rare alleles are called mutants. Normally, RNA is an intermediate product in the translation of a molecular gene into a protein. However, for some gene sequences, RNA molecules are actually the functional products. For example, RNAs known as ribozymes are capable of enzymatic function, or small interfering RNAs have a regulatory role. The DNA sequences from which such RNAs are transcribed are known as non-coding RNA, or RNA genes. All living organisms carry their genes and transmit them to offspring as DNA, but some viruses carry only RNA. Because they use RNA, their cellular hosts may synthesize their proteins as soon as they are infected and without the delay in waiting for transcription. On the other hand, RNA retroviruses, such as AIDS, require the reverse transcription of their genome from RNA into DNA before their proteins can be synthesized.

Human gene nomenclature

For each known human gene the HUGO Gene Nomenclature Committee (HGNC) approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the [http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl HGNC Database]. Each symbol is unique and each gene is only given one approved gene symbol. It is necessary to provide a unique symbol for each gene so that people can talk about them. This also facilitates electronic data retrieval from publications. In preference each symbol maintains parallel construction in different members of a gene family and can be used in other species, especially the mouse.

Typical numbers of genes in an organism

The following table gives typical numbers of genes and genome size for some organisms. Estimates of the number of genes in an organism are somewhat controversial because they depend on the discovery of genes, and no techniques currently exist to prove that a DNA sequence contains no gene. (In early genetics, genes could be identified only if there were mutations, or alleles.) Nonetheless, estimates are made based on current knowledge.

Chemistry and function of genes

Chemical structure of a gene

Four kinds of sequentially linked nucleotides compose a DNA molecule or strand (more at DNA). These four nucleotides constitute the genetic alphabet. A sequence of three consecutive nucleotides, called a codon, is the protein-coding vocabulary. The sequence of codons in a gene specifies the amino-acid sequence of the protein it encodes. In most eukaryotic species, very little of the DNA in the genome encodes proteins, and the genes may be separated by vast sequences of so-called junk DNA. Moreover, the genes are often fragmented internally by non-coding sequences called introns, which can be many times longer than the genes themselves. Introns are removed on the heels of transcription by splicing. In the primary molecular sense, they represent parts of a gene, however. All the genes and intervening DNA together make up the genome of an organism, which in many species is divided among several chromosomes and typically present in two or more copies. The location (or locus) of a gene and the chromosome on which it is situated is in a sense arbitrary. Genes that appear together on the chromosomes of one species, such as humans, may appear on separate chromosomes in another species, such as mice. Two genes positioned near one another on a chromosome may encode proteins that figure in the same cellular process or in completely unrelated processes. As an example of the former, many of the genes involved in spermatogenesis reside together on the Y chromosome. Many species carry more than one copy of their genome within each of their somatic cells. These organisms are called diploid if they have two copies or polyploid if they have more than two copies. In such organisms, the copies are practically never identical. With respect to each gene, the copies that an individual possesses are liable to be distinct alleles, which may act synergistically or antagonistically to generate a trait or phenotype. The ways that gene copies interact are explained by chemical dominance relationships (more at genetics, allele).

Expression of molecular genes

For various reasons, the relationship between DNA strand and a phenotype trait is not direct. The same DNA strand in 2 different individuals may result in different traits because of the effect of other DNA strands or the environment.
- The DNA strand is expressed into a trait only if it is transcribed to RNA. Because the transcription starts from a specific base-pair sequence (a promoter) and stops at another (a terminator), our DNA strand needs to be correctly placed between the two. If not, it is considered as junk DNA, and is not expressed.
- Cells regulate the activity of genes in part by increasing or decreasing their rate of transcription. Over the short term, this regulation occurs through the binding or unbinding of proteins, known as transcription factors, to specific non-coding DNA sequences called regulatory elements. Therefore, to be expressed, our DNA strand needs to be properly regulated by other DNA strands.
- The DNA strand may also be silenced through DNA methylation or by chemical changes to the protein components of chromosomes (see histone). This is a permanent form of regulation of the transcription.
- The RNA is often edited before its translation into a protein. Eukaryotic cells splice the transcripts of a gene, by keeping the exons and removing the introns. Therefore, the DNA strand needs to be in an exon to be expressed. Because of the complexity of the splicing process, one transcribed RNA may be spliced in alternate ways to produce not one but a variety of proteins (alternative splicing) from one pre-mRNA. Prokaryotes produce a similar effect by shifting reading frames during translation.
- The translation of RNA into a protein also starts with a specific start and stop sequence.
- Once produced, the protein interacts with the many other proteins in the cell, according to the cell metabolism. This interaction finally produces the trait. This complex process helps explain the different meanings of "gene":
- a nucleotide sequence in a DNA strand;
- or the transcribed RNA, prior to splicing;
- or the transcribed RNA after splicing, i.e. without the introns The latter meaning of gene is the result of more "material entity" than the first one.

Mutations and evolution

Just as there are many factors influencing the expression of a particular DNA strand, there are many ways to have genetic mutations. For example, natural variations within regulatory sequences appear to underlie many of the heritable characteristics seen in organisms. The influence of such variations on the trajectory of evolution through natural selection may be as large as or larger than variation in sequences that encode proteins. Thus, though regulatory elements are often distinguished from genes in molecular biology, in effect they satisfy the shared and historical sense of the word. Indeed, a breeder or geneticist, in following the inheritance pattern of a trait, has no immediate way to know whether this pattern arises from coding sequences or regulatory sequences. Typically, he or she will simply attribute it to variations within a gene. Errors during DNA replication may lead to the duplication of a gene, which may diverge over time. Though the two sequences may remain the same, or be only slightly altered, they are typically regarded as separate genes (i.e. not as alleles of the same gene). The same is true when duplicate sequences appear in different species. Yet, though the alleles of a gene differ in sequence, nevertheless they are regarded as a single gene (occupying a single locus).

History

The existence of genes was first suggested by Gregor Mendel, who, in the 1860s, studied inheritance in pea plants and hypothesized a factor that conveys traits from parent to offspring. Although he did not use the term gene, he explained his results in terms of inherited characteristics. Mendel was also the first to hypothesize independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, and the difference between what would later be described as genotype and phenotype. Mendel's concept was finally named when Wilhelm Johannsen coined the word gene in 1909. In the early 1900s, Mendel's work received renewed attention from scientists. In 1910, Thomas Hunt Morgan showed that genes reside on specific chromosomes. He later showed that genes occupy specific locations on the chromosome. With this knowledge, Morgan and his students began the first chromosomal map of the fruit fly Drosophila. In 1928, Frederick Griffith showed that genes could be transferred. In what is now known as Griffith's experiment, injections into a mouse of a deadly strain of bacteria that had been heat-killed transferred genetic information to a safe strain of the same bacteria, killing the mouse. In 1941, George Wells Beadle and Edward Lawrie Tatum showed that mutations in genes caused errors in certain steps in metabolic pathways. This showed that specific genes code for specific proteins, leading to the "one gene, one enzyme" hypothesis. Oswald Avery, Collin Macleod, and Maclyn McCarty showed in 1944 that DNA holds the gene's information. In 1953, James D. Watson and Francis Crick demonstrated the molecular structure of DNA. Together, these discoveries established the central dogma of molecular biology, which states that proteins are translated from RNA which is transcribed from DNA. This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses.

Evolutionary concept of gene

George C. Williams first explicitly advocated the gene-centered view of evolution in his book Adaptation and Natural Selection. Also, he proposed an evolutionary concept of gene to be used when we are talking about natural selection favoring some gene. The definition is: ""that which segregates and recombines with appreciable frequency." Acording to this definition, even an asexual genome could be considered a gene, insofar it have an appreciable permanency through many generations. The difference is: the molecular gene transcribes as a unit, and the evolutionary gene inherits as a unit. Richard Dawkins' The Selfish Gene and The Extended Phenotype defended that the gene is the only replicator in livings systems. This means that only genes transmit their structure largely intact and are potentially immortal in the form of copies. So, genes should be the unit of selection.

References

[http://print.google.com/print?id=WkHO9HI7koEC Google print]

External links

- [http://www.gene.ucl.ac.uk/nomenclature HUGO Gene Nomenclature Committee, HGNC]
- [http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl the HGNC Database]
- [http://www.gene.ucl.ac.uk/hugo/ Human Genome Organisation, HUGO]
- [http://www.newscientist.com/news/news.jsp?id=ns99996561 Recount slashes number of human genes] (from New Scientist magazine)
- [http://www.genome.gov/12513430 National Human Genome Research Institute — News Release]
- [http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v431/n7011/full/nature03001_fs.html Nature - 21 October 2004 — Finishing the euchromatic sequence of the human genome]
- [http://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=10116&build=3&ver=1#contigs Rat Genome]
- [http://plato.stanford.edu/entries/gene/ Stanford Encyclopedia of Philosophy entry]
- [http://www.ihop-net.org/UniPub/iHOP/ iHOP - Information Hyperlinked over Proteins]
- [http://www.pir.uniprot.org/ UniProt] Category:Cloning Category:Genetics Category:Molecular biology ko:유전자 ja:遺伝子 simple:Gene th:หน่วยพันธุกรรม

Bacterium

Actinobacteria
Aquificae
Bacteroidetes/Chlorobi
Chlamydiae/Verrucomicrobia
Chloroflexi
Chrysiogenetes
Cyanobacteria
Deferribacteres
Deinococcus-Thermus
Dictyoglomi
Fibrobacteres/Acidobacteria
Firmicutes
Fusobacteria
Gemmatimonadetes
Nitrospirae
Planctomycetes
Proteobacteria
Spirochaetes
Thermodesulfobacteria
Thermomicrobia
Thermotogae Bacteria (singular: bacterium) are a major group of living organisms. Most are microscopic and unicellular, with a relatively simple cell structure lacking a cell nucleus, and organelles such as mitochondria and chloroplasts. Their cell structure is further described in the article about prokaryotes, because bacteria are prokaryotes, in contrast to organisms with more complex cells, called eukaryotes. The term "bacteria" has variously applied to all prokaryotes or to a major group of them, otherwise called the eubacteria, depending on ideas about their relationships. In Wikipedia, bacteria is used specifically to refer to the eubacteria. Bacteria are the most abundant of all organisms. They are ubiquitous in soil, water, and as symbionts of other organisms. Many pathogens are bacteria. Most are minute, usually only 0.5-5.0 μm in their longest dimension, although giant bacteria like Thiomargarita namibiensis and Epulopiscium fishelsoni may grow past 0.5 mm in size. They generally have cell walls, like plant and fungal cells, but with a very different composition (peptidoglycans). Many move around using flagella, which are different in structure from the flagella of other groups.

History and taxonomy

The first bacteria were observed by Antony van Leeuwenhoek in 1683 using a single-lens microscope of his own design. The name bacterium was introduced much later, by Ehrenberg in 1828, derived from the Greek word βακτηριον meaning "small stick". Louis Pasteur (1822-1895) and Robert Koch (1843-1910) described the role of bacteria as conveyors and causes of disease or pathogens.

Metabolism

Bacteria show a wide variety of different metabolisms and can accordingly be classified into primary nutritional groups. The most common division is between heterotrophs, which depend on an organic source of carbon, and autotrophs, which are able to synthesize organic compounds from carbon dioxide and water. Autotrophs that obtain energy by oxidizing chemical compounds are called chemotrophs, and those that obtain their energy from light, via photosynthesis, are called phototrophs. There are many variations on this terminology such as chemoautotrophs and photosynthetic autotrophs and so on. In addition, bacteria are distinguished based on the source of reducing equivalents they are using. Those using inorganic compounds (e. g. water, hydrogen, sulfide or ammonia) for this purpose are called lithotrophs and others needing organic compounds (e. g. sugars or organic acids) and are called organotrophs. The metabolic modes of energy metabolism (phototrophy or chemotrophy), reducing equivalent sources (lithotrophy or organotrophy) and carbon sources (autotrophy or heterotrophy) can be combined differently in any single microorganism, and even shifting between different modes frequently occurs in many species. Other nutritional requirements include nitrogen, sulfur, phosphorus, vitamins and metallic elements such as sodium, potassium, calcium, magnesium, manganese, iron, zinc, cobalt, copper and nickel for normal growth. For some species, additional trace elements such as selenium, tungsten, vanadium or boron are needed. Based on their response to oxygen, most bacteria can be placed into one of three groups: Some bacteria can grow only in the presence of oxygen and are called aerobes; others can grow only in the absence of oxygen and are called anaerobes; and some can grow in the presence or absence of oxygen and are called facultative anaerobes.

Movement

Motile bacteria can move about, either using flagella, bacterial gliding, or changes of buoyancy. A unique group of bacteria, the spirochaetes, have structures similar to flagella, called axial filaments, between two membranes in the periplasmic space. They have a distinctive helical body that twists about as it moves. Bacterial flagella are arranged in many different ways. Bacteria can have a single polar flagellum at one end of a cell, clusters of many flagella at one end or flagella scattered all over the cell, as with Peritrichous. Many bacteria (such as E.coli) have two distinct modes of movement: forward movement (swimming) and tumbling. The tumbling allows them to reorient and introduces an important element of randomness in their forward movement. (see external links below for link to videos). Motile bacteria are attracted or repelled by certain stimuli, behaviors called taxes - for instance, chemotaxis, phototaxis, mechanotaxis and magnetotaxis. In one peculiar group, the myxobacteria, individual bacteria attract to form swarms and may differentiate to form fruiting bodies. The myxobacteria move only when on solid surfaces, unlike E. coli which is motile in liquid or solid media.

Groups and identification

myxobacteria Bacteria come in a variety of different shapes. Most are rod-shaped, sphere-shaped, or helix-shaped; these are respectively referred to as bacilli, cocci, and spirilla. An additional group, vibrios, are comma-shaped. Shape is no longer considered a defining factor in the classification of bacteria, but many genera are named for their shape (e.g. Bacillus, Streptococcus, Staphylococcus) and it is an important part in their identification. Another important tool is Gram staining, named after Hans Christian Gram who developed the technique. This separates bacteria into two groups, based on the composition of their cell wall. The first formal grouping of bacteria into phyla was based largely on this test:
- Gracilicutes - bacteria with a second cell membrane containing lipids, giving them Gram-negative stains
- Firmicutes - bacteria with a single membrane and thick peptidoglycan wall, giving them Gram-positive stains
- Mollicutes - bacteria with no second membrane or wall, giving them Gram-negative stains The archeabacteria were originally included as the Mendosicutes. As given, these phyla are no longer believed to represent monophyletic groups. The Gracilicutes have been divided into many different phyla. Most gram-positive bacteria are placed in the phyla Firmicutes and Actinobacteria, which are closely related. However, the Firmicutes have been redefined to include the mycoplasmas (Mollicutes) and certain Gram-negative bacteria.

Benefits and dangers

Bacteria are both harmful and useful to the environment, and animals, including humans. The role of bacteria in disease and infection is important. Some bacteria act as pathogens and cause tetanus, typhoid fever, pneumonia, syphilis, cholera, foodborne illness and tuberculosis. Sepsis, a systemic infectious syndrome characterized by shock and massive vasodilation, or localized infection, can be caused by bacteria such as streptococcus, staphylococcus, or many gram-negative bacteria. Some bacterial infections can spread throughout the host's body and become systemic. In plants, bacteria cause leaf spot, fireblight, and wilts. The mode of infection includes contact, air, food, water, and insect-borne microorganisms. The hosts infected with the pathogens may be treated with antibiotics, which can be classified as bacteriocidal and bacteriostatic, which at concentrations that can be reached in bodily fluids either kill bacteria or hamper their growth, respectively. Antiseptic measures may be taken to prevent infection by bacteria, for example, prior to cutting the skin during surgery or swabbing skin with alcohol when piercing the skin with the needle of a syringe. Sterilization of surgical and dental instruments is done to make them sterile or pathogen-free to prevent contamination and infection by bacteria. Sanitizers and disinfectants are used to kill bacteria or other pathogens to prevent contamination and risk of infection. In soil, microorganisms help in the transformation of nitrogen to ammonia with enzymes secreted by these microbes, which reside in the rhizosphere (a zone that includes the root surface and the soil that adheres to the root after gentle shaking). Some bacteria are able to use molecular nitrogen as their source of nitrogen, converting it to nitrogenous compounds, a process known as nitrogen fixation. Many other bacteria are found as symbionts in humans and other organisms. For example, the presence of the gut flora in the large intestine can help prevent the growth of potentially harmful microbes. The ability of bacteria to degrade a variety of organic compounds is remarkable. Highly specialized groups of microorganisms play important roles in the mineralization of specific classes of organic compounds. For example, the decomposition of cellulose, which is one of the most abundant constituents of plant tissues, is mainly brought about by aerobic bacteria that belong to the genus Cytophaga. This ability has also been utilized by humans in industry, waste processing, and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Some beaches in Prince William Sound were fertilized in an attempt to facilitate the growth of such bacteria after the infamous 1989 Exxon Valdez oil spill. These efforts were effective on beaches that were not too thickly covered in oil. Bacteria, often in combination with yeasts and molds, are used in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut, vinegar, wine, and yogurt. Using biotechnology techniques, bacteria can be bioengineered for the production of therapeutic drugs, such as insulin, or for the bioremediation of toxic wastes.

Miscellaneous

Two organelles, mitochondria and chloroplasts, are generally believed to have been derived from endosymbiotic bacteria. Microorganisms are widely distributed and are most abundant where they have food, moisture, and the right temperature for their multiplication and growth. They can be carried by air currents from one place to another. The human body is home to billions of microorganisms; they can be found on skin surfaces, in the intestinal tract, in the mouth, nose, and other body openings. They are in the air one breathes, the water one drinks, and the food one eats. The great antiquity of the bacteria has enabled them to evolve a great deal of genetic diversity. They are far more diverse than, say, the mammals or insects. For instance, the genetic distance between E. coli and Thermus aquaticus is greater than the distance between humans and oak trees.

References

- Some text in this entry was merged with the Nupedia article entitled Bacteria, written by Nagina Parmar; reviewed and approved by the Biology group (editor: Gaytha Langlois, lead reviewer: Gaytha Langlois, lead copyeditors: Ruth Ifcher and Jan Hogle)
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External links

- [http://www.dsmz.de/bactnom/bactname.htm Bacterial Nomenclature Up-To-Date from DSMZ]
- [http://www.sciencenews.org/pages/sn_arc99/4_17_99/fob5.htm The largest bacteria]
- [http://tolweb.org/tree?group=Eubacteria&contgroup=Life_on_Earth Tree of Life]
- [http://www.rowland.harvard.edu/labs/bacteria/index_movies.html Videos] of bacteria swimming and tumbling, use of optical tweezers and other fine videos.
- Category:Bacteriology ko:세균 ja:真正細菌 th:แบคทีเรีย

Eukaryote

|- | style = "background: pink; padding: 4px;" | Animalia - Animals |- | style = "background: lightblue; padding: 4px;" | Fungi |- | style = "background: lightgreen; padding: 4px;" | Plantae - Plants |- | style = "background: khaki; padding: 4px;" | Protista A eukaryote (also spelled eucaryote) is an organism with complex cells, in which the genetic material is organized into membrane-bound nuclei. Eukaryotes comprise animals, plants, and fungi—which are mostly multicellular—as well as various other groups that are collectively classified as protists (many of which are unicellular). In contrast, other organisms, such as bacteria, lack nuclei and other complex cell structures; such organisms are called prokaryotes. The eukaryotes share a common origin, and are often treated formally as a superkingdom, empire, or domain. The name comes from the Greek eus (meaning true) and karyon (meaning nut, referring to the cell nucleus).

Structure

Eukaryotic cells are generally much larger than prokaryotes, typically a thousand times by volume. They have a variety of internal membranes and structures, called organelles, and a cytoskeleton composed of microtubules and microfilaments, which play an important role in defining the cell's organization. Eukaryotic DNA is divided into several bundles called chromosomes, which are separated by a microtubular spindle during nuclear division. In addition to asexual cell division, most eukaryotes have some process of sexual reproduction via cell fusion, which is not found among prokaryotes. sexual reproduction

Internal membranes

Eukaryotic cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system. Simple compartments, called vesicles or vacuoles, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. It is probable that most other membrane-bound organelles are ultimately derived from such vesicles. The nucleus is surrounded by a double membrane, with pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form what is called the endoplasmic reticulum or ER, which is involved in protein transport. It includes the Rough ER where ribosomes are attached, and the proteins they synthesize enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the Smooth ER. In most eukaryotes, the proteins may be further modified in stacks of flattened vesicles, called Golgi bodies or dictyosomes. Vesicles may be specialized for various purposes. For instance, lysosomes contain enzymes that break down the contents of food vacuoles, and peroxisomes are used to break down peroxide which is toxic otherwise. Many protozoa have contractile vacuoles, which collect and expel excess water, and extrusomes, which expel material used to deflect predators or capture prey. In multicellular organisms, hormones are often produced in vesicles. In higher plants, most of a cell's volume is taken up by a central vacuole or tonoplast, which maintains its osmotic pressure.

Mitochondria and plastids

Mitochondria are organelles found in nearly all eukaryotes. They are surrounded by double membranes, the inner of which is folded into invaginations called cristae, where aerobic respiration takes place. They contain their own DNA and are only formed by the fission of other mitochondria. They are now generally held to have developed from endosymbiotic prokaryotes, probably proteobacteria. The few protozoa that lack mitochondria have been found to contain mitochondrion-derived organelles, such as hydrogenosomes and mitosomes. Plants and various groups of algae also have plastids. Again, these have their own DNA and developed from endosymbiotes, in this case cyanobacteria. They usually take the form of chloroplasts, which like cyanobacteria contain chlorophyll and produce energy through photosynthesis. Others are involved in storing food. Although plastids likely had a single origin, not all plastid-containing groups are closely related. Instead, some euk

Evolution

Overview of evolution

Evidence of evolution

Morphological evidence

Genetic sequence evidence

History of evolutionary thought

Social and religious controversies

Science of evolution

Science: fact and theory

Evolution as fact and theory

The meaning of, and relationship between, fact and theory in science

Who studies evolution?

Physical anthropology

Evolutionary biology

Evolutionary developmental biology

Ancestry of organisms

History of life

The Modern Synthesis

Heredity

Sexual reproduction

Mechanisms of evolution

Variation

Mutation

Gene flow

Drift

Population structure

Selection and adaptation

Natural selection

Adaptation

Speciation and extinction

See also

Notes and references

External links

Evolution Simulators

Non-coding RNA

Types (families) of non-coding RNAs

Transfer RNA

Ribosomal RNA

Untranslated regions of mRNAs

Small nuclear RNA

Small nucleolar RNA

microRNA

gRNAs

efference RNA

Signal recognition particle RNA

pRNA

tmRNA

External

Gene

Overview

Properties of genes

Types of genes

Human gene nomenclature

Typical numbers of genes in an organism

Chemistry and function of genes

Chemical structure of a gene

Expression of molecular genes

Mutations and evolution

History

Evolutionary concept of gene

See also

References

External links

Bacterium

History and taxonomy

Metabolism

Movement

Groups and identification

Benefits and dangers

Miscellaneous

See also

References

Further reading

External links

Eukaryote

Structure

Internal membranes

Mitochondria and plastids