User:Thompsma/Sandbox

New Section on Phylogenetic/Evolutionary trees

One of the large concerns with this article is its length. I have suggested before the "great battle for the current lead" that the length itself is not the problem, it is the structure that leads to increased length. We need a way to structure this article better and what not a better way than to turn to the evolutionary tree. I propose that a new section on phylogenetics or evolutionary trees be added after the history section in an effort to reduce the length of this article, to offer a more cogent explanation of traits, characters, homology, cladogenesis, anagenesis, the transmutation of species, and evolutionary radiations. Introducing "tree-like thinking" earlier in the article could help to organize and then shorten the remainder of the article. The scientific evidence for common ancestry is overwhelmingly observed in the anatomy of organisms, genomes, the universal genetic code, the geographic distributions of species and their genes, behaviour, breeding experiments, during development, and in the fossil record. Evolutionary biologists frame, test, and illustrate evolutionary hypotheses about the history and genealogical affinity of different lineages by sampling and comparing the evidence from their phenotypic and genotypic traits. Traits are the features of biological entities, including molecular, behavioural, developmental, or anatomical differences. The full physical expression of an organisms traits is its phenotype and all the heritable information encoded at the molecular level is its genotype. Evolutionary traits that are transmitted through common descent, that are similar in form, similarly located positionally relative to other traits, and share similar biological functions are said to be homologous characters. From genes to morphology, evolutionary biologists test genealogical hypotheses in the form of an evolutionary or phylogenetic tree, which is illuminated by the meticulous, systematic, and comparative analysis of homologous characters and their varied states.

Building upon our previous success (if we have strong support!) I will take a first stab at the next few sentences. Paragraphs to follow can explain genetic drift, genotype, phenotype, and so on. Looking forward to the discussions to follow:

• "Evolution (or more specifically biological or organic evolution) is the change in any lineage that reproduces heritable traits into descendant populations. A lineage is a single ancestral-descendant sequence that extends through multiple generations within a biological hierarchy of molecules, cells, organisms, populations, and species. The study of modern evolution itself originated in the 19th century in the writings of Charles Darwin who explained that evolution of living organisms is driven by natural selection. Natural selection is formulated on three recurrent facts in biological populations, including 1) heritability, 2) variation, and 3) the overproduction or superfecundity of offspring. There are diverse kinds of evolutionary transitions over short and vast dimensions of space and time. From genes to morphology, the genealogical affinity among lineages is illuminated by comparative analysis of characters and their varied states among lineages. Character data is systematically analysed when framing, testing, and illustrating evolutionary hypotheses about genealogical relations. Biological characters (traits) are meticulously and systematically analysed when framing, testing, and illustrating evolutionary hypotheses about genealogical relations in the form of an evolutionary tree. This kind of evidence reveals that evolution is the cause of speciation, whereby a single ancestral species branches into different species lineages."Thompsma (talk) 22:15, 5 October 2011 (UTC)

I think it is too wordy, but it is a template that we can build on. I deleted and modified a couple of sentences that seemed out of place and too jargony.Thompsma (talk) 22:25, 5 October 2011 (UTC)

Adding heritability and homology and other changes (hope I'm not getting too far ahead):

• "Evolution (or more specifically biological or organic evolution) is the change in any lineage that reproduces heritable traits into descendant populations. A lineage is a single ancestral-descendant sequence that extends through multiple generations within a biological hierarchy of molecules, cells, organisms, populations, and species. The study of modern evolution itself originated in the 19th century in the writings of Charles Darwin who explained that evolution of living organisms is driven by natural selection. Natural selection is formulated on three recurrent facts in biological populations, including 1) heritability, 2) variation, and 3) the overproduction or superfecundity of offspring. Heritability is a measure of how reliably a trait is transmitted from parent to offspring. The full physical expression of a lineage's traits is its phenotype and all the heritable information encoded at the molecular level is its genotype. Genotypic or phenotypic characters that are transmitted through common descent, that are similar in form, similarly located positionally relative to other characters, and share similar biological functions are said to be homologous. Homologous characters have a central role in piecing evolutionary history together. From genes to morphology, the genealogical affinity among lineages is illuminated by the meticulous, systematic, and comparative analysed analysis of homologous characters and their varied states among lineages. Evolutionary biologists frame, test, and illustrate evolutionary hypotheses about such genealogical relations in the form of an evolutionary tree. This kind of evidence reveals that evolution is the cause of speciation, whereby a single ancestral species branches into different species lineages."Thompsma (talk) 23:17, 5 October 2011 (UTC)

New Evolution Article

NOTE TO READERS: This is a draft format, I am doing research on this and the text is more extensive than it will be in its final form. Please withhold comment and modification until I am at a point where I am comfortable with the text. Thanks.

Evolution (or more specifically biological or organic evolution) is change in the descent of lineages that form complex relations as they compete for existence, reproduce, and interact mutualistically. In his landmark scientific text on evolution, "On The Origin of Species", Charles Darwin refers to the "great tree of life", "a web of complex relations", and includes a single illustration of an evolutionary tree. The tree represents the common ancestry of lineages that branch and diversify into "endless forms most beautiful and most wonderful". Lineages form through recursive generations of biological reproduction for all individuals in the biological hierarchy, including genes, cells, organisms, and species.

A core theory of evolution proposed by Charles Darwin is natural selection. Natural selection is formulated on three recurrent facts, including 1) heritability, 2) variation, and 3) the overproduction or superfecundity of offspring from diverse lineages that interact, perish, and persist over space and time. Heritability is the faithful expression of certain characters from one generation to the next. Homologous characters play a central role in evolutionary theory. A homologous character is similar in form, similarly located anatomically or positionally relative to other characters, and they share similar biological functions. Homology is explained by a common line of heritable descent.

The outward physical expression of a lineage is its phenotype, whereas the heritable information encoded at the molecular level is its genotype. The genotype of an individual refers to all its genes that interact in a complex hierarchical network that develops into the phenotype. Evolutionary novelties originate by various means, including changes in behaviour, sexual recombination, developmentally, symbiogenetically, environmentally, or through genetic mutation. The genotype develops into the phenotype during the ontogeny of an individual. Phenotypic variation can result as a complex developmental response to different environments. There is rarely a one-to-one readout from the smallest heritable unit, the gene, to the emergent phenotypic pattern. Variation within a lineage may evolve by random chance or become adapted by means of natural selection. Genes and their mutations appear with regular frequency. In larger populations their minute effects may be of such little consequence that they drift through populations in a stochastic manner. Adaptations, however, are not random as features of certain characters may confer a slight advantage for reproductive output or evolutionary fitness.

Scientific evidence for common ancestry is overwhelmingly observed in the anatomy of organisms, during development, in genomes, in the universal genetic code, in the geographic distributions of species and their genes, in behaviour, in breeding experiments, and in the fossil record. Common descent stretches back over 3.5 billion years during which life has existed on earth. Evolution reveals diverse kinds of evolutionary transitions over short and vast dimensions of space and time. From genes to morphology, homologous characters are used to construct evolutionary trees or, more precisely, phylogenetic networks for positing, framing, testing, and illustrating evolutionary hypotheses about genealogical relations. The genealogical affinity among lineages is illuminated by comparative analysis on the measured form of characters, their presence, and their varied states among lineages. This kind of evidence clearly reveals that evolution is the cause of speciation, whereby a single ancestral species splits into two or more different species lineages.

The scientific study of evolution began in the mid-nineteenth century, when research into the fossil record and the diversity of living organisms convinced most scientists that species evolve. The mechanisms driving these changes remained unclear until the theory of natural selection was independently proposed by Charles Darwin and Alfred Wallace in 1858. In the early 20th century, Darwinian theories of evolution were combined with genetics, palaeontology and systematics, which culminated into a union of ideas known as the modern evolutionary synthesis. The synthesis became a major principle of biology as it provided a coherent and unifying explanation for the history and diversity of life on Earth.

Evolution is currently applied and studied in various areas within biology such as conservation biology, developmental biology, ecology, physiology, paleontology and medicine. Moreover, it has also made an impact on other disciplines such as agriculture, anthropology, philosophy and psychology. Evolutionary biologists document the fact that evolution occurs, and also develop and test theories that explain its causes.

Characters that are common to a lineage preserve the evidence of heritable and common ancestry, while those that vary are of a central concern to evolutionary biologists. Biologists use taxonomic methods to systematically organize the naming conventions of evolutionary lineages and their relations.

Mutations at the genetic level may be incorporated into a larger network of developmental traits that tend to be more conserved and preserved from history.

A mammalian bat wing is not homologous to an avian bird wing, for example, but skeletal features, such as the humerus bone attached to the glenoid cavity of the scapula, is faithfully expressed in the common fore limbs both organisms. Hence, bats and birds are independently evolved flying organisms, but they share a common ancestry as vertebrates.

Traits are measurable features that distinguish individuals from each other and include anatomical, biochemical and behavioural characteristics. Inherited traits, such as eye color, may have variable states (e.g., blue vs. brown eyes) that define the observed phenotype of an individual. Traits may enhance an individual's chances of survival through their adapted functions. Over time, environmental fluctuations alter the character or phenotype of biological form as only a few individuals can pass on their traits to descendant populations through the eternal struggle for existence.

At the molecular level, DNA forms complementary biochemical bonds as nucleotide strands replicate into daughter cells and preserve of genetic lineages.

History

Main article: History of evolutionary thought

Prior to the published works of Darwin, a theoretical synthesis threading what seemed at the time to be disjointed facts forestalled advancement in the life sciences. In 1973, evolutionary biologist Theodosius Dobzhansky penned that "nothing in biology makes sense except in the light of evolution". Evolutionary science synthesizes the disjointed facts of history into a coherent explanatory framework for many observable facts of nature. Darwin's testable predictions turned out to be true. The research tradition that informed Darwin in preparation of his evolutionary synthesis has extensive roots in natural history. Natural historians had the goal of describing, classifying, and discovering the mysterious products of life in their attempt explain what seemed to be an underlying order of nature. Knowing the history of evolutionary biology is essential for understanding this topic and how the ideas have been translated into the modern context. Charles Darwin only used the term evolution scarcely and prior to his user of the term it had a different meaning. The word evolution has itself evolved, but its origins stem from its Latin roots meaning an unrolling or unfolding of what was thought to be a pre-existing form of a miniature adult (homonculus). More than the term, however, theories about the origins of species and their place in the natural philosophies pre-dates Darwin. In this context, historians use a wide net on the term evolution "to denote any theory postulating a natural process for the development of life on earth."

Pre-Darwin

"It is argued that where all things happened as if they were made for some purpose, being aptly united by chance, these were preserved, but such as were not aptly made, these were lost and still perish..." - Aristotle (350 BCE)

Further information: History of evolutionary thought

Elements of evolutionary theory, rudimentary notions of adaptation and fitness, were first debated in ancient Greece by the likes of Aristotle and Empedocles. Some philosophers refer to specific quotes suggesting that Aristotle (and others of antiquity) held evolutionary views. However, prior to the 19th century, there was no palaeontological underpinning of species origins or history, species were believed to originate by means of spontaneous generation. Aristotle, for example, also wrote about individual peculiarities and hybridization in species, but he conceived of "species" in terms of essences or ideals that were immutable, eternal, and therefore, his concepts are not compatible with evolution.

Few advancements of evolutionary significance appeared until the renaissance when Greek philosophy was supplanted by natural theology. During the renaissance, natural theologians, such as John Ray, asked why organisms were adapted in form to their environment or to serve particular tasks. These adaptations were attributed to the work of an intelligent creator, which has manifested into the modern creationist views about intelligent design. Natural theology extending from John Ray’s (1691) book on "The Wisdom of God Manifested in the Works of the Creation" reached an apogee in the writings of William Paley. Paley's published works on natural theology were required reading at Cambridge University from 1787 to 1920 and was a great inspiration to Charles Darwin: "I do not think I hardly ever admired a book more than Paley’s Natural Theology: I could almost formerly have said it by heart" Paley is best known for his argument from design as evidence for the existence of God and had a great working knowledge of biology.

The renaissance brought a new inspiration to naturalists seeking answers to an apparent order of nature as evidence of God's handiwork. The father of the modern biological system of classification, Carl Linnaeus, for example, believed that he was sent by God to reveal His balanced and harmonious plan through the apparent order of nature. Not everyone subscribed to natural theology, however, as is evident in the works of Comte de Buffon who published an extensive and influential encyclopaedic account (36 volumes from 1749–1788) on the wonders of nature, where he saw order, harmony, and balance. Buffon is sometimes credited as an early pioneer in evolution as he did not subscribe to a creator, but rather subscribed to the notion of natural laws that could be discovered through investigation. While Buffon made a large impression, Pierre Louis Maupertuis made less of an impression despite forwarding ideas (of a crude sort) on natural selection, heredity, isolation of species, and anticipated many of the major theories of evolution.

Turn of 19th century

The first person to forward a wholly coherent theory of evolution was Jean-Baptiste Lamarck, although his work has traditionally been viewed as antithetical to Darwinian evolution. A modern re-appraisal of Lamarck's work has generated a line of research known as neo-Lamarckian theory. Lamarck and Charles Darwin's grandfather, Erasmus Darwin, posited that characters acquired during the life of an organism through use and disuse could be passed onto subsequent generations.The classical fable of Lamarckian evolution is that of a giraffe stretching its neck to reach leaves and through such action, those that achieved a greater height could pass on such traits to their offspring. This tale of Lamarck is a grand oversimplification of his evolutionary theories.

Lamarck

Natural historians have referred to chains, cords, ladders and stairways depicting life in a natural order ascending from simple, primitive, low to complex, advanced, and high since antiquity. From 1802 until 1822 Jean-Baptiste Lamarck published the first theory of evolution that allowed for infinite diversification of species ascending progressively from simple to complex. According to Lamarck, primitive life forms originate abiogenetically and evolve, over time, into complexly organized beings, humans being the most perfect. The environment was important in Lamarck's two-part teleological explanation for the inheritance of acquired traits: 1) change in bodily organs grew with use and atrophied with disuse, and 2) such change was faithfully preserved through reproduction if both sexes had adopted the same habits and thus acquired the same traits. Lamarck coined the term biology, but he died blind and penniless with many of his ideas subject to ridicule and rejected, and yet some of his broader concepts on evolutionary inheritance continue to influence even the modern sciences.

Charles Lyell was influenced by Lamarck and compa

August Weismann is best known for his rejection of Lamarcks thesis by dividing organisms into germ cells (reproductive egg and sperm) and somatic cells (tissues and organs) and brought heritability down to the nucleus of the cell in 1885. Although he has been commonly cited as rejecting the thesis of acquired characters, Weismann accepted the thesis of acquired characters from the environment acting directly on the germ plasm, but experimentally rejected the hypothesis that acquired changes from use and disuse of somatic tissues.[29][30][27][31]

Citations used to research this that can be added after editing:

Advancements in our understanding of evolution stem from the science of palaeontology and developmental biology. An early pioneer in this respect is Geoffroy Saint-Hilaire who accepted evolution and proposed in 1825 that gross abnormalities in organisms could provide viable mutants for sudden transformations. Saint-Hilaire was an admirer of Lamarck's evolutionary theories and helped to bridge the relationship between palaeontology, developmental biology, and evolution by reference to anatomical parts that could be related to one another if they were composed of the same elements and found in the same position in different organisms (fossil or otherwise). Georges Cuvier an anatomist and founder of palaeontology helped to link the present to the past. Cuvier showed that there were successive eras in the fossil record where entire fauna and species went extinct, but he remained opposed to the idea of evolution. One of Cuvier's disciples, Sir Richard Owen, was a morphologist, museum curator, and palaeontologist who laid out the distinction between analogy and homology and developed the concepts of serial homology and an evolutionary archetype. Owen became known as the anti-evolution villain as he opposed Darwin's evolutionism, but reappraisals of his work reveals great importance of his contributions to evolutionary science. Sir Owen and other biologists at this time (including Darwin) were greatly influenced by developmental biologists, including Karl Ernst von Baer and his laws of development (divergence and progression) versus the concepts advanced by Louis Agassiz (another of Cuvier's disciples) on the theory of recapitulation (that animals advanced through an exact correspondence of developmental stages matching primitive forms of animals).

Darwin and Wallace

There is a simple grandeur in the view of life with its powers of growth, assimilation and reproduction, being originally breathed into matter under one or a few forms, and that whilst this our planet has gone circling on according to fixed laws, and land an water, in a cycle of change, have gone on replacing one another, that from simple an origin, through the process of gradual selection of infinitesimal changes, endless forms most beautiful and most wonderful have been evolved. (Charles Darwin, 1842)

Charles Darwin began writing out what became On the Origin of Species in 1842.

Charles Darwin studied at Cambridge University and obtained his ordinary degree in the spring of 1831. During his studies Darwin learned the tools of natural history. John S. Henslow, a professor of botany who studied and lectured on the limits to variation in species of plants, taught and formed a relationship with Darwin. Darwin also learned about geology on field excursion to North Wales with Professor Adam Sedgwick in the summer of 1831. These

Armed with the knowledge of the natural historians before him, 

Darwin was a convinced evolutionist by 1837 and first sketched the basic theory of natural selection into his notebook 1939 after his epic voyage on the H.M.S. Beagle as ships naturalist. Charles Darwin's son, Francis Darwin published a copy of Darwin's foundations on the Origin of Species which was hidden in a cupboard under the stairs an discovered only after his mother passed away and the premises were vacated in 1896. The abstract foundations from 1842 was penned in 35 pages and expanded to 230 pages by 1844. Darwin shared his ideas openly amongst friends, family, and peers. The full publication of his ideas did not appear until 1859 with the first edition of his most influential book, titled "On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life." There are many questions surrounding Darwin's lengthy delay and many have suggested that he was concerned about or feared a public backlash. However, a lengthy analysis of Darwin's correspondence and journals shows that he was not afraid of public backlash nor did he delay publication, but it was a project that he continued to work on and labour over and had not put much thought into publishing until he was persuaded by his peers to do so. Alfred Russel Wallace and Charles Darwin corresponded occasionally, starting in late 1855 or early 1856 in response to Wallace's publication in the Annals and Magazine of Natural History entitled "On the law which has regulated the introduction of new species". While Wallace's publication in 1855 had obvious implications for evolution, he did not provide a mechanistic explanation. Darwin was later contacted in June of 1858 by Alfred Russel Wallace where he presented a strikingly similar evolutionary theory. The independent discovery of natural selection by Wallace is notable, but many researchers have noted how the two theories differ and suggested that Darwin offered a more complete and accurate account of the process. Wallace's thought evolution proceeded indefinitely and progressively by the tendency of varieties to survive and depart from the original type. Darwin's theory of natural selection did not think that evolution would necessarily progress or evolve, nor did view species as departing from a type in the way that Wallace did. Darwin's theory was original and he went on to develop the ideas further in other publications, such as "The Descent of Man".

At the end of 1859, Darwin's publication of On the Origin of Species explained natural selection in detail and presented evidence leading to increasingly wide acceptance of the occurrence of evolution. Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. This caused an uproar around the world since it implied that the creation myth in the Christian Bible was false and humans did not have a special place in the universe.

Debate about the mechanisms of evolution continued and Darwin could not explain the source of the heritable variations which would be acted on by natural selection. Like Jean-Baptiste Lamarck, he still thought that parents passed on adaptations acquired during their lifetimes, a theory which was subsequently dubbed Lamarckism. In the 1880s, August Weismann's experiments indicated that changes from use and disuse were not heritable and Lamarckism gradually fell from favour. More significantly, Darwin could not account for how traits were passed down from generation to generation. In 1865 Gregor Mendel found that traits were inherited in a predictable manner. When Mendel's work was rediscovered in the 1900s, disagreements over the rate of evolution predicted by early geneticists and biometricians led to a rift between the Mendelian and Darwinian models of evolution. While the concept of genes was originally part of an alternative mutation theory of evolution, the gene theory ultimately described variation, which is the main fuel used by natural selection to shape the wide variety of adaptive traits observed in organic life. Even though Hugo de Vries and other early geneticists rejected gradual natural selection, their rediscovery of and subsequent work on genetics eventually provided a solid basis on which the theory of evolution stood even more convincingly than when it was originally proposed.

Early 20th century

The apparent contradiction between Darwin's theory of evolution by natural selection and Mendel's work was reconciled in the 1920s and 1930s by evolutionary biologists such as J.B.S. Haldane, Sewall Wright and particularly Ronald Fisher, who set the foundations for the establishment of the field of population genetics. The end result was a combination of evolution by natural selection and Mendelian inheritance, the modern evolutionary synthesis. The publication of the structure of DNA by James Watson and Francis Crick in 1953 demonstrated the physical basis for inheritance. Since then, genetics and molecular biology have become core parts of evolutionary biology and have revolutionised the field of phylogenetics.

In its early history, evolutionary biology primarily drew in scientists from traditional taxonomically oriented disciplines, whose specialist training in particular organisms addressed general questions in evolution. As evolutionary biology expanded as an academic discipline, particularly after the development of the modern evolutionary synthesis, it began to draw more widely from the biological sciences. Currently the study of evolutionary biology involves scientists from fields as diverse as biochemistry, ecology, genetics and physiology and evolutionary concepts are used in even more distant disciplines such as psychology, medicine, philosophy and computer science.

In the 1960s, scientists such as W. D. Hamilton and George C. Williams extended the gene-centered view of evolution pioneered by the founders of theoretical population genetics, to explain co-operation using concepts such as kin selection. In 1975, E. O. Wilson's book Sociobiology established a significant place for evolutionary theory in psychology, giving rise to the field of evolutionary psychology. In the 21st century, evolutionary biology remains an active field of scientific research.

After the synthesis

The law of inheritance of acquired characters stirred much controversy in the history of biology and politics. In Stalinist Russia it became official political policy that scientists were to adopt Trofim Lysenko's theories, based loosely on Lamark's theories through Ivan Michurin; those who wrote in support of Darwin and Mendelian inheritance were persecuted and even executed.

History of evolutionary thought - Nov 2011

Further information: History of evolutionary thought

The proposal that one type of animal could descend from an animal of another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander and Empedocles. In contrast to these materialistic views, Aristotle understood all natural things, not only living things, as being imperfect actualizations of different fixed natural possibilities, known as "forms", "ideas", or (in Latin translations) "species". This was part of his teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. Variations of this idea became the standard understanding of the Middle Ages, and were integrated into Christian learning, but Aristotle did not demand that real types of animals corresponded one-for-one with exact metaphysical forms, and specifically gave examples of how new types of living things could come to be.

In the 17th century the new method of modern science rejected Aristotle's approach, and sought explanations of natural phenomena in terms of laws of nature which were the same for all visible things, and did not need to assume any fixed natural categories, nor any divine cosmic order. But this new approach was slow to take root in the biological sciences, which became the last bastion of the concept of fixed natural types. John Ray used one of the previously more general terms for fixed natural types, "species", to apply to animal and plant types, but unlike Aristotle he strictly identified each type of living thing as a species, and proposed that each species can be defined by the features that perpetuate themselves each generation. These species were designed by God, but showing differences caused by local conditions. The biological classification introduced by Carolus Linnaeus in 1735 also viewed species as fixed according to a divine plan.

Other naturalists of this time speculated on evolutionary change of species over time according to natural laws. Maupertuis wrote in 1751 of natural modifications occurring during reproduction and accumulating over many generations to produce new species. Buffon suggested that species could degenerate into different organisms, and Erasmus Darwin proposed that all warm-blooded animals could have descended from a single micro-organism (or "filament"). The first fully-fledged evolutionary scheme was Lamarck's "transmutation" theory of 1809 which envisaged spontaneous generation continually producing simple forms of life developed greater complexity in parallel lineages with an inherent progressive tendency, and that on a local level these lineages adapted to the environment by inheriting changes caused by use or disuse in parents. (The latter process was later called Lamarckism.) These ideas were condemned by establishment naturalists as speculation lacking empirical support. In particular Georges Cuvier insisted that species were unrelated and fixed, their similarities reflecting divine design for functional needs. In the meantime, Ray's ideas of benevolent design had been developed by William Paley into a natural theology which proposed complex adaptations as evidence of divine design, and was admired by Charles Darwin.

In 1842 Charles Darwin penned his first sketch of what became On the Origin of Species.

The critical break from the concept of fixed species in biology began with the theory of evolution by natural selection, which was formulated by Charles Darwin. Partly influenced by An Essay on the Principle of Population by Thomas Robert Malthus, Darwin noted that population growth would lead to a "struggle for existence" where favorable variations could prevail as others perished. Each generation, many offspring fail to survive to an age of reproduction because of limited resources. This could explain the diversity of animals and plants from a common ancestry through the working of natural laws working the same for all types of thing. Darwin was developing his theory of "natural selection" from 1838 onwards until Alfred Russel Wallace sent him a similar theory in 1858. Both men presented their separate papers to the Linnean Society of London. At the end of 1859, Darwin's publication of On the Origin of Species explained natural selection in detail and in a way that lead to an increasingly wide acceptance of Darwinian evolution. Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. Some were disturbed by this since it implied that humans did not have a special place in the universe.

Precise mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis. In 1865 Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory. August Weismann made the important distinction between germ cells (sperm and eggs) and somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin's pangenesis theory to Wiesman's germ/soma cell distinction and proposed that Darwin's pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cells structure. De Vries was also one of the researchers who made Mendel's work well-known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline. To explain how new variants originate, De Vries developed a mutation theory that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries. At the turn of the 20th century, pioneers in the field of population genetics, such as J.B.S. Haldane, Sewall Wright, and Ronald Fisher, set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin's theory, genetic mutations, and Mendelian inheritance was thus reconciled.

In the 1920s and 1930s a modern evolutionary synthesis connected natural selection, mutation theory, and Mendelian inheritance into a unified theory that applied generally to any branch of biology. The modern synthesis was able to explain patterns observed across species in populations, through fossil transitions in palaeontology, and even complex cellular mechanisms in developmental biology. The publication of the structure of DNA by James Watson and Francis Crick in 1953 demonstrated a physical basis for inheritance. Molecular biology improved our understanding of the relationship between genotype and phenotype. Advancements were also made in phylogenetic systematics, mapping the transition of traits into a comparative and testable framework through the publication and use of evolutionary trees. In 1973, evolutionary biologist Theodosius Dobzhansky penned that "nothing in biology makes sense except in the light of evolution", because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent explanatory body of knowledge that describes and predicts many observable facts about life on this planet.

Since then, the modern synthesis has been further extended to explain biological phenomena across the full and integrative scale of the biological hierarchy, from genes to species. This extension has been dubbed "eco-evo-devo".

Geological time line

Time scales showing the history of the universe, the Earth, life's primordial origins, and key evolutionary transitions.

The present universe is 13.7 billion years old. Nearly 10 billion years later, the Earth formed continents and become cool to support the origins and evolution of life. The age of the universe is determined by the rate expansion of the cosmos, whereas radiometric dating techniques, strata, fossils, molecular clocks, and other lines of geological evidence are used to piece together the sequence and timing of evolution and historical transitions on this planet. Geological layers known as strata form into the depths of the planet with older foundations buried under sediments or layers of volcanic rock. Strata provide a sequential record of the planets geological and evolutionary history, but often show signs of unconformity as geologic activity erodes and can lead to a break in the original sequence of deposition. Like pages in a book, an index or 'yardstick' of stratigraphic time has been developed using a standardized nomenclature by the International Commission on Stratigraphy (ICS). Unique assemblages of fossil species are embedded within and restricted to the boundaries of defined strata.

Debate continues on the exact timing of the origins of life and even if life originated on Earth (i.e., panspermia). Molecular building blocks for life, including amino acids, RNA nucleotides, and other complex structures have been recreated in lab experiments simulating early atmospheric conditions using only abiotic source material. Organic compounds, including purines, pyrimidines, amino acids, and solid phosphorus were also identified in the Murchison meteorite and chondrites. The Archean environment had less solar luminosity, lots of volcanic activity, and an anoxic atmosphere dominated by carbon dioxide, nitrogen gases and water vapour, with traces of hydrogen, methane, amonia, and sulfur gases. Evidence of a dynamic early Earth stems from moon craters showing signs of heavy impactors (100-km diameter) until 3.8 Gya. Rocks from the Archaean (3.9-2.5 Gya) have been greatly degraded. Much of the original material has been recycled with less than 10% surviving to present time, but geologists infer from sediments that a significant amount of water appeared toward the end of the heavy bombardment. There is direct fossil evidence of diverse microfossils and biogenic markers of life by 3 Gya and putative evidence of bacterial erosion at 3.5 Gya when life was likely widespread. Putative signs of life appear in stromatalite sediments of the Eoarchean (3.9-3.6 Gya) after the Earth's first continent, Vaalbara, started to take form. Early life is widely inferred through models of biochemistry and the molecular bio-mechanics of living organisms to have been initiated by replicating RNA molecules acting as both template and enzyme in what has been dubbed the RNA world hypothesis. Scientists have recently sparked interests in volcanic pumice rafts floating on the waters surface serving as the early reaction vessels that could have provided the kind of environments needed for the evolution of organic polymers during primordial abiogensis.

The establishment of the photosynthetic organelle (plastid) in eukaryotes and the diversification of algae and plants were landmark evolutionary events because these taxa form the base of the food chain for many ecosystems on our planet.

Geological deposits from this time contain large amounts of unoxidized iron and other indicators that would have been oxidized if oxygen were present. Primitive antecedants to modern cyanobacteria evolved in this time. The microfossil morphology is similar to modern cyanobacteria and they were capable of H2-based (anoxic) photosynthetic oxygen production and respiratory oxygen consumption. Oxygenic phototrophs and primitive eukaryotes started to colonize marine ecosystems by 2.7 Gya. The eukaryotic lineage evolved through an endosymbiotic union with prokaryotes some time before 1.558 Gya. These prokaryotic symbionts are the antecedants to the mitochondria in our cells.

http://www.pnas.org/content/101/43/15386.longhttp://en.wikipedia.org/wiki/Special:Watchlist

http://mbe.oxfordjournals.org/content/21/5/809.full http://geology.rutgers.edu/pdf/Falkowski.etal.%202004.pdf http://www1.ub.edu/fvd4/wq/wqc/DadesWQC/Annu-Rev-Genet-2007-Plasts-Origin.pdf

Revised lead to Evolution

Evolution (also known as biological or organic evolution) is change over time in one or more inherited traits within and among populations of individuals. Life evolves through descent with modification by means of reproduction, heritability, and variation of traits in populations of individuals; those means exemplify the core principles of natural selection. Traits are measurable features that distinguish individuals from each other and include anatomical, biochemical and behavioural characteristics. Inherited traits, such as eye color, may have variable states (e.g., blue vs. brown eyes) that define the observed phenotype of an individual. Traits may enhance an individual's chances of survival through their adapted functions. Over time, environmental fluctuations alter the character or phenotype of biological form as only a few individuals can pass on their traits to descendant populations through the eternal struggle for existence. Evolution has led to the diversification of all living beings from a common ancestor, a diversification described by Charles Darwin as "endless forms most beautiful and most wonderful".

Evolution applies not just to organisms, but to the entire biological hierarchy that evolved into the nested and integrated units of evolution that surround us. Stretching back over 3.5 billion years, before the dinosaurs and multi-celled organisms had evolved, the origins of life perpetuated an evolutionary lineage from a single common ancestor. Over the course of time, collections of genes worked together and became nested into individual cells. Likewise, collections of cells nested into individual organs, organisms, and species; at each evolutionary transition, smaller collectives nest into larger individuals. This, however, is a simplification of the complexity in the biological hierarchy. Some cells even became nested into larger cells through a process called endosymbiosis. Endosymbiosis explains the origins of mitochondria and chloroplasts, whereby primitive eukaryotic cells symbiotically internalized a prokaryotic cell. The endosymbiotic origins of eukaryotic cells is one of many major evolutionary transitions that explains how collectives become integrated into the hierarchy of life.

There are four common evolutionary mechanisms at the genetic level that help to explain how evolution operates generally across the biological hierarchy:

• Natural selection: differential survival in the multiplication or reproduction of different heritable varieties of functional genes. Heritable traits in genes are the orderly templates of DNA sequence that are preserved through copied lineages that stem from an original template.

• Genetic drift: random change in proportion or frequency of genetic traits (i.e., alleles) in populations. Genetic drift refers to lineages of selectively neutral genetic variants—alleles—that have an equal chance of replicating into subsequent generations when there is no clear relationship between their relative fitness and performance.

• Mutation: change in a DNA sequence either by single nucleotide substitution (e.g., A to C, or G to T) or by wholesale duplication of an entire gene within a genome.

• Gene flow: the migration of genes from one population into another.

Prior to the 19th century, it was commonly believed that species did not go extinct and did not change since their 'creation' in Earth's history. This idea of immutable species was hotly debated throughout the 19th century, but evidence from around the globe and into the fossil record would culminate into a different perspective. Notable scientific figures, including Charles Darwin's grandfather, Erasmus Darwin suggested that species changed over time. Without foreknowledge of the genotype of organisms, but with extensive and detailed knowledge on the biology and geography of species, Charles Darwin developed and debated his evolutionary theory. He first shared his ideas with his peers in a rough sketch he penned in 1839, but did not intend it for publication.[1] Darwin's proposal was debated, but as discoveries mounted the evidence was conclusive: some species had gone extinct, some descendant species had changed in form, and there was sufficient geological time in the age of the Earth (4.54 billion years) for things to have evolved according to Darwin's original theory. Prior to the formal publication of Darwin's theory, Alfred Wallace independently developed the same theory based on his scientific observations in the wild and was put into contact with Darwin. Shortly thereafter, Darwin and Wallace jointly presented an abbreviated version of their findings to the Linnaen Society in 1858 and in 1859 Darwin published his extended thesis titled: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

In the early 20th century, Darwinian theory established the facts of evolution that were advanced by the re-discovery of Gregor Mendel's laws of genetic inheritance. This stimulated research and much debate into the quantitative and qualitative aspects of evolutionary inheritance and in the late 1930's there was a merger of opinion and clarification on many misconceptions about evolution that culminated into a modern evolutionary synthesis. The synthesis unified biology in the way it provided a coherent explanation for the history and diversity of life on Earth. The modern evolutionary synthesis matured in the late 20th century into an extended synthesis integrating developmental and ecological fields with Darwinian principals under the heading of evo-devo or eco-evo-devo. In the extended synthesis, Darwinian principals explain and apply generally to any level in the biological hierarchy, from genes to species. At each level in the hierarchy of life, the units of evolution produce offspring in like manner, genes give rise to genes, cells give rise to other cells, colonies give rise to other colonies, and species give rise to other species. Reproduction at the species level, for example, is called speciation, whereby a single ancestral species splits into two or more different species. The evidence for speciation is visible in anatomical, genetic and other similarities between groups of organisms, geographical distribution of related species, the fossil record, and in the DNA sequences of living organisms. In 1973, evolutionary biologist Theodosius Dobzhansky penned that "nothing in biology makes sense except in the light of evolution". Dobzhansky's statement continues to resonate through the many advancements in knowledge that Darwin's evolutionary principals has enabled in diverse scientific fields, including: conservation biology, developmental biology, ecology, physiology, paleontology, medicine, agriculture, anthropology, sociology, economics, philosophy, psychology, and more.

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Jean-Baptiste Lamark was the first in 1809 to unequivocally suggest that species evolved. Georges Cuvier ('father' of paleontology) noted that geological strata, arranged with the oldest at the base and most recent formations at the top, corresponded to the ages of unique fossil assemblages identified within them. at that time it was estimated by Lord Kelvin to 20 million years.

Conditions for evolution by means of natural selection are satisfied at the genetic level, namely: variation in a population of genes, differences in reproductive output where some genes replicate more readily than others (i.e., fitness differences), and heritability through the mechanics of Watson-Crick base pairing. Genetic drift is also called neutral evolution, because the gene traits evolve by chance instead of being subject to or adapted to an environmental condition. The last mechanism (gene flow) is a prelude to the multi-levelled aspect to evolution. At one level, genes code the information for traits that develop within an organism. At another level, however, these genes are exchanged and selected amongst populations. Hence, evolutionary biologists may query the mechanics of genetic evolution in a developmental context of an organisms fitness, such as what genes and mutations lead to different developmental outcomes. Alternatively, an evolutionary biologist may query the mechanics of genetic evolution in a larger population context, such as what genes are extinguished or spread more readily from one population to another.

Ecology Further reading

Introductory

• Altieri, M. 2001. The ecological impacts of agricultural biotechnology. An ActionBioscience.org original article[2]
• Beman, J. 2010. Energy economics in ecosystems. Nature Education Knowledge 1(8):22[3]
• Bestelmeyer, B.T. 2006. Threshold concepts and their use in rangeland management and restoration: The good, the bad, and the insidious. Restoration Ecology, 14(3):325-329[4]
• Bryant, P. J. Biodiversity and Conservation. A Hypertext Book.[5]
• Callicott, J. B., & Mumford, K. 1997. Ecological sustainability as a conservation concept. Conservation Biology, 11(1), 32-40[6]
• Costanza, R., Cumberland, J.H., Daily, H., Goodland, R., & Norgaard, R.B. 1997. An Introduction to Ecological Economics (e-book). St. Lucie Press and International Society for Ecological Economics[7]
• Davic, R. D., & Welsh, H. H. 2004. On the ecological roles of salamanders. Annual Review of Ecology, Evolution, and Systematics, 35(1), 405-434[8]
• Ecological Society of America. 2000. Ecosystem Services: A Primer.[9]
• Farabee, M.J. 2006. The Online Biology Book. Hosted by Estrella Mountain Community College, Avondale, Arizona[10]
• Forman, R.T.T., & Alexander, L.E. 1998. Roads and their major ecological effects. Annual Review of Ecology and Systematics, 29(1):207-231[11]
• Forseth, I. 2010. Terrestrial Biomes. Nature Education Knowledge 1(8):12[12]
• Hanski, I. 2005. Landscape fragmentation, biodiversity loss and the societal response. The longterm consequences of our use of natural resources may be surprising and unpleasant. Embo reports 6(5), 388-392[13]
• Hanski, I. 2008. The world that became ruined. EMBO reports 9:S34-S36[14]
• Henkel, T. P. 2010. Coral reefs. Nature Education Knowledge 1(11):5[15]
• Howe, H. F., & Smallwood, J. 1982. Ecology of Seed Dispersal. Annual Review of Ecology and Systematics, 13(1):201-228[16]
• McCabe, D. J. 2010. Rivers and streams: Life in flowing water. Nature Education Knowledge 1(12):4[17]
• Murphy, P. G., & Lugo, A. E. 1986. Ecology of tropical dry forest. Annual Review of Ecology and Systematics, 17:67-88[18]
• Naiman, R. J., & Décamps, H. 1997. The ecology of interfaces: Riparian zones. Annual Review of Ecology and Systematics, 28(1):621-658[19]
• Odum, H. 1973. Energy, ecology, and economics. Ambio, 2(6): 220-227[20]
• Polis, G. A., Anderson, W. B., & Holt, R. D. 1997. Toward an integration of landscape and food web ecology:The dynamics of spatially subsidized food webs. Annual Review of Ecology and Systematics, 28(1):289-316[21]
• Stevens, A. 2010. Earth's varying climate. Nature Education Knowledge 1(8):45[22]
• Swartz W, Sala E, Tracey S, Watson R, Pauly D, 2010 The Spatial Expansion and Ecological Footprint of Fisheries (1950 to Present). PLoS ONE 5(12): e15143[23]
• Turner, M. G. 1989. Landscape Ecology: The Effect of Pattern on Process. Annual Review of Ecology and Systematics, 20(1):171-197[24]
• Vanni, M. J. 2002. Nutrient cycling by animals in freshwater ecosystems. Annual Review of Ecology and Systematics, 33(1):341-370[25]
• Vitousek, P.M., & Sanford, R.L. 1986. Nutrient Cycling in Moist Tropical Forest. Annual Review of Ecology and Systematics, 17(1):137-167[26]
• Wilson, E. O., & Peter, F. M. (Eds.) 1986. Biodiversity. National Academy of Sciences (U.S.), Smithsonian Institution[27]

Advanced

• Barrett, S. C. H., & Harder, L. D. 1996. Ecology and evolution of plant mating. Trends in Ecology & Evolution, 11(2):73-79[28]
• Brand, F. S., and K. Jax. 2007. Focusing the meaning(s) of resilience: resilience as a descriptive concept and a boundary object. Ecology and Society, 12(1):23[29]
• Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M., & West, G. B. 2004. Toward a metabolic theory of ecology. Ecology, 85(7):1771–1789[30]
• Carpenter, S. R., Mooney, H. A., Agard, J., Capistrano, D., DeFries, R. S., Díaz, S., Dietz, T., et al. 2009. Science for managing ecosystem services: Beyond the Millennium Ecosystem Assessment. Proceedings of the National Academy of Sciences, 106(5):1305-1312[31]
• Chapin, F.S. 1980. The mineral nutrition of wild plants. Annual Review of Ecology and Systematics, 11(1):233-260[32]
• Dunne, J.A., Williams, R.J., Martinez, N.D., Wood, R.A., & Erwin, D.H. 2008. Compilation and network analyses of Cambrian food webs. PLoS Biol 6(4):e102[33]
• Ettema, C.H., & Wardle, D.A. 2002. Spatial soil ecology. Trends in Ecology & Evolution, 17(4):177-183[34]
• Getz, W.M., 2009. Disease and the dynamics of food webs. PLoS Biol 7(9): e1000209[35]
• Gotelli, N.J., Ellison, A.M. 2006. Food-Web models predict species abundances in response to habitat change. PLoS Biol 4(10): e324[36]
• Green, J.L., Hastings, A., Arzberger, P., Ayala, F., Cottingham, K.L., Cuddington, K., Davis, F., Dunne, J.A., Fortin, M-J., Gerber, L., Neubert, M. 2005. Complexity in ecology and conservation: mathematical, statistical, and computational challenges. BioScience, 55:501-510[37]
• Hanski, I. 1994. A practical model of metapopulation dynamics. Journal of Animal Ecology 63:151-162[38]
• Hanski, I. 1998. Metapopulation dynamics. Nature 396:41-49[39]
• Heneghan, L., D. C. Coleman, X. Zou, D. A. Crossley, and B. L. Haines. 1999. Soil microarthropod contributions to decomposition dynamics: Tropical-temperate comparisons of a single substrate. Ecology 80:1873–1882[phttp://cwt33.ecology.uga.edu/publications/pubs_no_citations/heneghan_98_microarthropod.pdf]
• Laland, K. N., Odling-Smee, J., & Feldman, M. W. 2000. Niche construction, biological evolution, and cultural change. Behavioral and Brain Sciences, 23:131–175[40]
• Magurran, A. E., & Henderson, P. A. 2010. Temporal turnover and the maintenance of diversity in ecological assemblages. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1558):3611-3620[41]
• Moilanen, A. and M. Nieminen. 2002. Simple connectivity measures in spatial ecology. Ecology, 84:1131-1145[42]
• Nosil, P., Sandoval, C.P. 2008. Ecological niche dimensionality and the evolutionary diversification of stick insects. PLoS ONE, 3(4):e1907[43]
• Peltonen, A. & Hanski, I. 1991. Patterns of island occupancy explained by colonization and extinction rates in shrews. Ecology 72:1698-1708[44]
• Peterson, G., Allen, C. R., & Holling, C. S. 1998. Ecological resilience, biodiversity, and scale. Ecosystems, 1:6–18[45]
• Quinn, J. F., & Dunham, A. E. 1983. On hypothesis testing in ecology and evolution. The American Naturalist, 122(5):602-617[46]
• Saccheri, I. & Hanski, I. 2006. Natural selection and population dynamics. Trends in Ecology and Evolution, 21:341-347[47]
• Schwachtje, J., Kutschbach, S., Baldwin, I.T. 2008. Reverse genetics in ecological research. PLoS ONE, 3(2):e1543[48]
• Simberloff, D. S. 1974. Equilibrium theory of island biogeography and ecology. Annual Review of Ecology and Systematics, 5(1):161-182[49]
• Wiens, J. J., & Donoghue, M. J. 2004. Historical biogeography, ecology and species richness. Trends in Ecology & Evolution, 19(12):639-644[50]
• Woiwod, I.P. & Hanski, I. 1992. Patterns of density dependence in moths and aphids. Journal of Animal Ecology 61:619-629[51]
• Womack, A. M., Bohannan, B. J. M., & Green, J. L. 2010. Biodiversity and biogeography of the atmosphere. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1558):3645-3653[52]

Cultural Evolution

In the biological sciences, a more inclusive definition of culture is recognized that explains how social behaviors evolve by means that are under the influence of natural selection and genetic drift. The modern synthesis of evolutionary theory was largely centered on the concept of genetic inheritance systems. However, extensions to evolutionary theory since the 1980's have discovered other heritable systems acting upon the extended phenotype that can be decoupled from the influence of genes. Inheritance systems are found in genes, language, symbolic forms of communication and in social learning. In a broader sense of the definition, there are two types of inheritance systems including genetic inheritance, which is explained by the modern evolutionary synthesis, and epigenetic inheritance, which "...is the inheritance of developmental variations that do not stem from differences in the sequence of DNA or from persistent inducing signals in the present environment." In other words, epigenetic inheritance can cover things such as cell-to-cell transmission and cultural inheritance including language.

Culture is biological: meaning in culture can be approached as the outcome of mechanism-based causation, because culture stems from individual cognition, which has a biological basis.

Wilson and Lumsden

Extended evolutionary theory recognizes a multi-dimensional system of inheritance and is also known as multi-level selection theory. These extended dimensions of inheritance are encompassed under the concept of the ecological niche. The ecological niche is defined as "the sum of all the natural selection pressures to which the population is exposed." The ecological niche is heritable. For example, termites are born into a colony that already has an elaborate mound infrastructure with chimneys and tunnels that regulates a homeostasis of the internal environments. The termite does not only inherit genes from its parents, it inherits a legacy through the extended ecological niche within which the colony survives. The ecological niche is subject to natural selection and it also feeds back into the selection pressure placed upon the genes. Hence, there is a dual system in operation. These principals apply to human culture as well. We are born into a society or a cultural niche that was constructed before our time and this feeds back its influenced onto the evolution of our genes.

Culture is as much part of human biology as bipedal locomotion, and cultural and genetic influences on human behavior are thoroughly intertwined.

Boyd et al.

Cultural evolution involves two essential transmission pathways, genetic and cultural inheritance systems. These two biologically based inheritance systems are not necessarily independent of one another. Behaviors that evolve solely by genetic means are said to be innate, such as fixed action potentials. Examples of a fixed action potential are seen in the immediate reaction when a doctor taps your knee-cap, when a bull becomes infuriated upon seeing the color red, or when ants become threatened and release pheromones that induces a near instantaneous response and collective attack from the rest of the colony. These types of behaviors are explained by genetic inheritance systems through the modern synthesis. Cultural inheritance systems, however, are based on socially learned behaviors. Chimpanzees, for example, Cultural inheritance may occur in any form of life, including birds, mammals and even insects.

In biology, evolution is descent with modification. Evolution explains the origin of species by means of natural selection. Natural selection is a force that eliminates individuals and their associated traits from the population. Natural selection is a consequence of three universal observations, including: 1) the overproduction of offspring leading to an exponential increase in population size if not constrained, 2) differential rates or probability of survival within generations among different representative varieties, and 3) the heritability or stability of traits creating a resemblance between parents and their offspring. The first treatise on evolution was published in 1859 by Charles Darwin in a book entitled: "On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life". Darwin's founding principals remain an important resource in the modern scientific understanding of our biological origins. Darwin's original thesis has since been quantified, tested and analyzed extensively. The principals of natural selection explain observations in genetics, paleontological studies of the fossil record and in social studies on group dynamics. The premise of natural selection remains one of the solidifying foundations in biological studies. Scientists have yet to find a convincing alternative explanation in their studies of natural systems that would refute Darwin's theory.

Gregor Mendel, a contemporary of Charles Darwin and the father of genetics, disovered the laws of inheritance by performing a series of garden pea experiments. Darwin's theory of natural selection coupled with Mendels laws of inheritance gives a complete explanation for the non-random or adapted preservation of traits. Traits become adapted, suited to their environment and assist in the life functions for survival and existence. Genes, organisms and species have traits. Traits are features that can be observed and described about living things that are used to construct and test hypotheses about evolutionary relations, adaptations and the principals of natural selection. Traits that are similar by means of descent are said to be homologous. A homologous trait is an organ or gene that is found in a similar place performing similar functions in different organisms for reasons that are due to common ancestry. For example, a bats wing and a birds wing are not homologous, because a birds wing is an elongated arm with feathers whereas a bats wing is an elongated hand with a skin membrane and fur. As vertebrates, however, these animals share a distant but common ancestry which is identified by their many homologous parts including vertebrae, radius, ulna, femur, brains, hearts and large parts of their genome.

Evolutionary biologists study all levels of biological organization, from genes to the highest taxonomic levels in the Linnean hierarchical system. As members of the life sciences, evolution and ecology are highly integrated disciplines. Ecologists study populations, communities and biomes where the living and non-living context of the evolutionary process is sorted out. Like ecologists, evolutionary biologists study and gather data on the anatomy, morphology, geography, genetics and history of living things. Evolution is also applied and studied in the fields of psychology, paleontology, philosophy, medicine, agriculture and conservation biology. Recent advances in molecular genetics have also made evolution applicable to whole genome biology as scientists piece together the complex and dynamic history of life. Evolutionary biologists study the development of organisms, their traits and genes in great detail. The analytical methods for testing evolutionary relations has been developed by various philosophical, systematics and statistical approaches, including taxonomy, cladistics, and phylogenetics.

The next two paragraphs I originally had in the lead above, but it might be too much info

Every living thing has genes, which are coded bits of information biochemically stored in four letter alphabetic chains of nucleotides (A,G,C,T) that run complementary to one another (i.e., A's pair with T's and G's pair with C's). These nucleotides are bound by chemical bonds that twist into a double helical structure called DNA. The unique sequence of nucleotides that codes for a particular protein is the genetic trait of a particular gene. Genes build proteins that build cells, organs, bodies and societies. The outword expression of genes builds phenotypic traits, which are the factual parts that everyone can see, such as eye color, height, size and shape.

In the early part of the 20th century microscopic observations of the cell nucleus of plants and animals generated an independent understading of inheritance that physically paralleled Mendels laws. In other words, the physical units of inheritance could be seen passing along cell lines as divide and reproduce. When cells divide, they reduce in half the number of chromosomes that become distributed equally to the two new daughter cells. The genome is the complete set of chromosomes that are made of coiled strings of DNA and it is stored in the nucleus of plant and animal cells. There are two distinct cell lines called the somatic cell line and the gametic cell line. Somatic cells cotain two copies of each chromosome and split by mitosis. Gametes (sperm and egg) contain one copy of each chromosome are produced by meiosis. Genetic information is passed onto subsequent generation only through the sperm and egg or gametic cell lines. Molecular enzymes, proteins and RNA replicate precise copies of the genome as it is passed onto daughter cells. During any of these processes, mutations that alter the DNA sequences of nucleotides produce new varieties of cells that are subject to the forces of natural selection.

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During sexual ertilization period, when sperm fuses to egg. The spermatid releases its genome into egg.

Characteristics of homologous traits, such as a unique gene sequence or tables of anatomical descriptions, are used to test evolutionary hypotheses about relations and the history of life. Population genetics and phylogeography are two branches of The basis of evolution is the passing of genes from one generation to the next. Genes are what produce an organism's inherited traits. These vary within populations, with organisms showing heritable differences (variation) in their traits. Evolution is the product of two opposing forces: processes that constantly introduce variation, and processes that make those variants become either more common or rare. New variation arises in two main ways: either from mutations in genes, or from the transfer of genes between populations and between species. New combinations of genes are also produced by genetic recombination, which can increase variation between organisms.genetic drift, an independent process that produces random changes in the frequency of traits in a population. Genetic drift results from the role that chance plays in whether a given trait will be passed on as individuals survive and reproduce.

, but he had exposed an unpublished discussion paper on his concepts to his colleagues in 1839. Alfred Russell Wallace independently developed the same theory. Darwin and Wallace jointly presented their theories to the Linnean Society in 1858. Darwin's more expansive body of evidence is based on extensive observations and knowledge he had learned about the plants and animals that he had collected and studied over his lifetime. Rudimentary concepts of evolution had been proposed before Darwin and was independently discovered by Alfred Russel Wallace. Darwin and Wallace read and applied Thomas Malthus' (1803) principals of populations, all organisms produce more offspring than can survive to age of reproduction, to their observations of natural systems. Darwin organized the many varieties of species he collected During his global expeditions on board the HMS Beagle by applying Carl Linnaeus's principals of taxonomy. The Linnaean hierarchy (Kingdom, Order, Family, Genus, Species) is a systematic way of grouping organisms according to their shared and common features. Linnaeus' principals were used to catalog specimens at museums of Natural History where Darwin would submit his collections and the method is still applied to this day.

In the early 19th century Charles Darwin's grandfather, Erasmus Darwin, published speculative theories on evolution on the basis of the inheritance of acquired characteristics. Charles Darwin expanded upon the inferences of his grandfather that living beings evolved and that some individuals will succeed in producing offspring where others will not. Variation among individuals is a fundamental ingredient of natural selection where some organisms would have features better suited to survival in current environments. Darwin also recognized that populations differ in their accumulated traits that were passed on from parent to offspring.In times since Darwin, scientists have further observed that all levels of biological organization, from genes to species, change over time and are shaped by the forces of natural selection.

Organisms develop, survive and reproduce within ecological communities. From birth to death, the genome of an organism remains actively engaged with the environment and contains all the information needed to regulate the behavour and timing of development. As organisms develop the outward synthesis of genes to proteins builds an outward body expressing phenotypic traits. For example, a 4000 year old frozen Palaeo-Eskimo named Inuk is thought to have had a brown eyed phenotype because his ancient genotype reveals four characterstic mutations. These mutations characterize a gene, called the HERC2-OCA2 locus, that is strongly correlated with brown eyes among Asians. Mutuations arise by random means to alter the arrangement of the heritable pieces of DNA, which are the fundamental biochemical units of life that contain codes for synthesizing proteins. The chemical structure of DNA was published in 1953 by James Watson and Francis Crick. The molecule forms a double helix structure with complementary strands of nucleotides. The two opposing and complementary strands form duplicate copies of the information that codes for proteins. In other words, Watson and Crick had discovered the underlying natural mechanism for heritability that Darwin and Gregor Mendel had observed in the century prior. Gregor Mendel was a Darwin's contemporary who had worked out the laws of inheritance by means of the random assortment of genetic units called alleles.

As organisms develop their phenotype is malleable to the forces of nature. Traits that provide a functional utility toward the survival of an individual and shaped by the forces of natural selection are called adaptations. Some organisms have adaptations that

is based on three observations produce more offspring per generation than can survive to age of reproduction. change in the genetic material of a population of organisms through successive generations, and principals of natural selection applied to groups, species, and society.

Charles Darwin had learned the system to classify nature according to the principals that Carl Linnaeus had developed as he traveled around the world to collect flowers, insects, birds and mammals. Once organized according to the systematic principals of the natural history tradition, Darwin, like others before him, started to see new patterns in the geographic distributions and what seemed to be an anatomical transition in body form. Prior to Darwin's publication, the understanding of nature was that there were varieties of organisms, but species had not changed since creation. Every species was as it had always been. After years of careful observation and applying the systematic methods of natural historians before him, Darwin outlined an alternative scientific theory. Darwin proposed his theory of natural selection, in other words the observed varieties had been selected by a purely natural system of operation. The bare-bones formulation of the theory of natural selection is based on three proven facts of nature: 1) every organism has an overproduction of offspring, 2) there are varieties, and 3) there is heritability. Natural selection, like gravity, is a force of nature. The full title of Charles Darwin's evolutionary treatise captures the full set of terms that are needed to understand the theory of evolution, "On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life"; will be referred to simply as The Origin hereafter. Evolution is a scientific explanation for the diversity and the history of species on planet Eath. Darwin's theory of natural selection was supported by the evidence that he had collected during his travels. His theory is a scientific understanding of the world because other scientists are welcome to independently examine the evidence as a means of testing his theory of natural selection.

Although the changes produced in a single generation are normally small, the accumulation of these differences over time can cause substantial changes in a population, a process that can result in the emergence of new species. Similarities among species suggest that all known species descended from a common ancestor (or ancestral gene pool) through this process of gradual divergence.

The basis of evolution is the passing of genes from one generation to the next. Genes are what produce an organism's inherited traits. These vary within populations, with organisms showing heritable differences (variation) in their traits. Evolution is the product of two opposing forces: processes that constantly introduce variation, and processes that make those variants become either more common or rare. New variation arises in two main ways: either from mutations in genes, or from the transfer of genes between populations and between species. New combinations of genes are also produced by genetic recombination, which can increase variation between organisms.

Two major mechanisms determine if variants will become more common or rare in a population. One is natural selection, a process whereby helpful traits (those that increase the chance of survival and reproduction) become more common in a population while harmful traits become increasingly rare. This occurs because individuals with advantageous traits are more likely to survive and reproduce, resulting in more individuals of the next generation inheriting those traits. Adaptations occur over many generations through successive, small, random changes in traits combined with natural selection of those variants best-suited for their environment. The other major mechanism driving evolution is genetic drift, an independent process that produces random changes in the frequency of traits in a population. Genetic drift results from the role that chance plays in whether a given trait will be passed on as individuals survive and reproduce.

Evolutionary biologists document the fact that evolution occurs, and also develop and test theories that explain its causes. The study of evolutionary biology began in the mid-nineteenth century, when research into the fossil record and the diversity of living organisms convinced most scientists that species changed over time. However, the mechanism driving these changes remained unclear until the theories of natural selection were independently proposed by Charles Darwin and Alfred Wallace. In 1859, Darwin's seminal work On the Origin of Species brought the new theories of evolution by natural selection to a wide audience, leading to the overwhelming acceptance of evolution among scientists. In the 1930s, Darwinian natural selection was combined with Mendelian inheritance to form the modern evolutionary synthesis, which connected the units of evolution (genes) and the mechanism of evolution (natural selection). This powerful explanatory and predictive theory has become the central organizing principle of modern biology, directing research and providing a unifying explanation for the diversity of life on Earth.

This article gives an introduction to evolution. The core basics of natural selection are described as well as an expanded view of evolution as it is understood by science and society. This article uses studies performed at a high school level to identify where students are most conceptually challenged and often mistaken in their understanding of evolutionary theory. School teachers and authors writing about evolution at a level that can be understood by everyone are greatly challened by the complexity and scientific understanding of the evolutionary process. There are fundamentals to evolution, however, that can be easily understood at an introdutory level that this article provides.

Teaching and writing about evolution at an introdutory level is complicated at two levels. First, natural systems are inherently complex and hierarchical. Second, evolution is a highly popularized and controversial topic that means different things to society than it does to science. Societal views on evolution include an expanded set of beliefs, including alternative ideas or misconceptions, that go beyond those expressed and understood to be logically consistent within the philosophy of science and peer-reviewed scientific studies.

Scientists and educators have written many popular books on evolution that feed into the public and media's representation of the concepts more so than the peer-reviewed literature. Different author's suggest different ideas and stress different areas of importance, which makes it appear as though science is debating the factual basis of evolution. Biology textbooks contain many diagrams and illustrations about the evolutionary process that are confusing and may even stimulate further the number of misconceptions.Alternative conceptions and erroneous conclusions are found in studies that probe the conceptual understanding of natural selection among biology majors and even among professionals. This article makes use of the research into alternative conceptions and understandings about evolutionary facts, theory and discourse (for example, ) to assist in reaching a proper understanding of the subject matter in a way that is introductory. In surveys and studies of those who accept versus those who reject evolution as a way of understanding the world, researchers find that this social distinction hinges on a proper understanding of the subject matter. Those who accept the theory, understand the concepts. Those who reject the theory, hold misconceptions about the science or are resistent to learning about the subject matter for religious or other strongly held beliefs.

Darwin's original treatise on evolution through the origin of species by means of natural selection remains one of the most precient and greatest scientific works in biology.The core thesis of Darwin's proposition on the theory of natural selection is still yielding new insight into the way that life has and continues to evolve. However, in the time since Darwin there have been new inventions and ways of probing deeper into the genetics of life. Paleontoligical findings, methods of analysis and resolution into the history of life on this planet has improved greatly. The discoveries since Darwin have not put his theory to rest, but have expanded our understanding of natural selection and other evolutionary forces that operate across all levels of organization. Evolution is more than natural selection or survival of the fittest, because there are different competing forces operating at different levels of biological organization. The forces of evolutionary change at the genetic level, for example, are largely neutral and random. Evolutionary theory has implications for matters of social relevance, inclding psychology, leadership, crime, cooperation, war, governance, public health, medicine, conservation biology and just about any other issue related to the well-being and understanding of humanity.

Darwin's idea: evolution by natural selection

Further information: Common descent

From the smallest bacteria to the gravitational forces acting on planets, nature is in motion all around us. Prior to Charles Darwin, nature was studied, by naturalists, such as Carl Linneus, who wanted to understand the divine order of nature, otherwise known as the balance of nature. Naturalists collected, named and organized plants, animals and minerals according to a rational and systematic method of grouping of like things. Natural history is the forerunner of Charles Darwin's theory of evolution by means of natural selection. Linnaeus, who is best known for the Linnaean system of biological classification (kingdom, order, family, genus, species) equated the study of the of nature to the worship of God's creations and believed that God had given him the greatest insight 'greater than any has ever gained' into the order of nature.

Charles Darwin had learned the system to classify nature according to the principals that Carl Linnaeus had developed as he traveled around the world to collect flowers, insects, birds and mammals. Once organized according to the systematic principals of the natural history tradition, Darwin, like others before him, started to see new patterns in the geographic distributions and what seemed to be an anatomical transition in body form. Prior to Darwin's publication, the understanding of nature was that there were varieties of organisms, but species had not changed since creation. Every species was as it had always been. After years of careful observation and applying the systematic methods of natural historians before him, Darwin outlined an alternative scientific theory. Darwin proposed his theory of natural selection, in other words the observed varieties had been selected by a purely natural system of operation. The bare-bones formulation of the theory of natural selection is based on three proven facts of nature: 1) every organism has an overproduction of offspring, 2) there are varieties, and 3) there is heritability. Natural selection, like gravity, is a force of nature. The full title of Charles Darwin's evolutionary treatise captures the full set of terms that are needed to understand the theory of evolution, "On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life"; will be referred to simply as The Origin hereafter. Evolution is a scientific explanation for the diversity and the history of species on planet Eath. Darwin's theory of natural selection was supported by the evidence that he had collected during his travels. His theory is a scientific understanding of the world because other scientists are welcome to independently examine the evidence as a means of testing his theory of natural selection.

Evolution is part of the natural sciences, which means that observable facts are used to piece together natural explanations for the way that world operates. Scientists develop theories in the process of linking fact to explanation. The explanation is the hypothesis. A scientific test means that other scientists are able to collect independent observable facts, to formulate an alternative hypothesis and to use a system of logic, such as math or statistics, that would lead them to reject the null-hypothesis. The null-hypothesis is usually an explanation that requires the least amount of steps or effort to link fact to explanation. If the null-hypothesis is rejected, the alternative hypothesis is worthy of further inquiry in context of the known theoretical understanding of the system. When theory becomes so reliable that it illuminates new independent theories and finds predictable outcomes, then it becomes a fact. In this way, evolution has become both fact and theory. This form of scientific explanation in the natural sciences differs from supernatural explanations. 

Darwin's theory took notice of the anatomical features in the varieties of plants animals that he and others had collected from marked locations across the globe. Through these observations, Charles Darwin spent X years writing about and perfecting his ideas in silence. The theory of natural selection proposes that life is not static, but rather it has evolved over time. In other words, the varieties and forms of individuals and species that we see before us are unique to our time because they evolved or have changed in form, either slightly or significantly, from their ancestors.

Charles Darwin also understood the laws of population growth and the struggle for life as he worded it in the title of his monumental book. According to the laws of population growth it is not possible for every living thing to survive to an age of reproduction. For example, a pair of spiders might produce thousands of fertile eggs, but by the next generation roughly two spiders will have replaced their parents, either because the others had died through some natural means or had failed to attract a sexual partner. This natural process or the balance of nature ensures that population numbers remain fairly stable over time, such that the world does not overflow with spiders. Hence, there is a process of selection that determines which two shall survive to an age of reproduction. In the second part of The Origin, Darwin refers to the preservation of favoured races. This part of the theory proposes that the two spiders that lived to reproduce where the ones that had inherited from their parents the attributes that favoured their survival. This process would ensure a stability to the system over time, such that only slight variations in form from generation to generation could be witnessed amongst the surviving. The explanation fit with the observation of slight variations that Darwin had noted in the bodies of the plants and animals that he had collected from different parts of the world. Moreover, the variations he saw could be matched in pattern to the spatial geography of the land, such that a gradient of form could be observed across distances separating populations of the same species. When plants or animals were organized according to their place of orign, Darwin and others could see a clear pattern of transitional varieties that matched with the spatial geography. On the Galapogos Islands, for example, it was noticed that islands that were close in proximity shared common varieties of the same species but as the distance between islands increased, new varieties of the same species were evident and the pattern seemed transitional.

Based on these observations, Charles Darwin presented his theory of natural selection. The bare-bones formulation of the theory of natural selection is based on three undeniable facts, including: 1) every species has an overproduction of offspring, 2) there are varieties, and 3) there is heritability. These three facts of nature explain the origin of every species on the planet, including the human species. Since Darwin's publication in 1859, there has been a vast stimulation of research into this theory that has proven itself one of the most reliable explanations for the observed patterns of life in every corner of the planet that has been researched and studied to date. However, Darwin wrote other books, such as The Descent of Man, and Selection in Relation to Sex, where he had expanded the theory even further; refered to as The Descent hereafter. In The Origin, Darwin had primarily focused on the forces of natural selection operating on individual organisms. In The Descent, Darwin had proposed another evolutionary theory that explained the origins of morality. This second part to the theory had remained somewhat dormant in the 20th century, but this multi-level selection theory of evolution has been re-examined and is proving as scientifically reliable as the theories presented in The Origin. The multi-level selection theory of evolution suggests that the forces of natural selection also operate among groups, such that the behaviour of members belonging to one group will determine the success of that group. If all members of a group are cheaters, thieves and liers, then it will not survive in the struggle for existence against a group whoose members are cooperating, honest, and moral citizens. The extention of Darwin's principals of natural selection to other levels of organization beyond the individual organism is known as multi-level selection.

The first part of the title to The Origin speaks of varieties. During Darwin's time, the technology to examine the molecular details or genetics of living beings had not been invented. Hence, Darwin could only postulate what was giving rise to new and original varieties in the populations. Today we understand that the origin of varieties stems from a process of random mutation at the genetic level.

that formed an integrated pattern such that living transitional forms could be discovered.