lets get the debate started: creationism vs evolution?

Question

give me your POV and uphold your feeling whether based on documented fact or faith facts?-----people, I respect you all but get down to it.

Answer 1

In biology, evolution is the change in the heritable traits of a population over successive generations, as determined by the shifting allele frequencies of genes. Evolution is ultimately the source of the vast diversity of life: all contemporary organisms are related to each other through common descent, products of cumulative evolutionary changes over billions of years. Over time, new species evolve from existing species through speciation, and other species become extinct, resulting in the ever-changing biological world reflected in the fossil record.

The basic mechanisms that produce evolutionary change are natural selection (which includes ecological and sexual selection) and genetic drift acting on the genetic variation created by mutation, genetic recombination and gene flow. Natural selection is the process by which individual organisms with favorable traits are more likely to survive and reproduce. If those traits are heritability, they pass them to their offspring, with the result that beneficial heritable traits become more common in the next generation.[1][2][3] Given enough time, this passive process can result in varied adaptations to changing environmental conditions.[4]

The modern understanding of evolution is based on the theory of natural selection, which was first set out in a joint 1858 paper by Charles Darwin and Alfred Russel Wallace and popularized in Darwin's 1859 book The Origin of Species. In the 1930s, scientists combined Darwinian natural selection with the theory of Mendelian heredity to form the modern evolutionary synthesis, also known as "Neo-Darwinism". The modern synthesis describes evolution as a change in the frequency of alleles within a population from one generation to the next.[4] This theory has become the central organizing principle of modern biology, relating directly to topics such as the origin of antibiotic resistance in bacteria, eusociality in insects, and the staggering biodiversity of the living world.

Because of its potential implications for the origins of humankind, evolutionary theory has been at the center of many social and religious controversies since its inception.

History of evolutionary thought
Main article: History of evolutionary thought

Charles Darwin in 1854, five years before publishing The Origin of Species.The idea of biological evolution has existed since ancient times, notably among Greek philosophers such as Anaximanderand Epicurus and Indian philosophers such as Patanjali. However, scientific theories of evolution were not established until the 18th and 19th centuries, by scientists such as Jean-Baptiste Lamarck and Charles Darwin. The transmutation of species was accepted by many scientists before 1859, but Charles Darwin's On The Origin of Species by Means of Natural Selection provided the first cogent theory for a mechanism by which evolutionary change could occur: 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, independent discovery of natural selection. Accordingly, Wallace is sometimes given shared credit for originating the theory.[5]

Darwin's theory, although successful in profoundly shaking scientific opinion about 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 biologists. Although the occurrence of evolution of some sort became a widely-accepted view among scientists, Darwin's specific ideas about evolution; that it occurred gradually by natural and sexual selection; were actively attacked and rejected. From the end of the 19th century through the early 20th century, forms of neo-Lamarckism, "progressive" evolution (orthogenesis), and an evolution which worked by "jumps" (saltationism, as opposed to gradualism) became popular, although a form of neo-Darwinism, led by August Weismann, also enjoyed some minor success. The biometric school of evolutionary theory, resulting from the work of Darwin's cousin, Francis Galton, emerged as well, using statistical approaches to biology which emphasized gradualism and some aspects of natural selection.[6]


Gregor Mendel's work on the inheritance of traits in pea plants laid the foundation for genetics.When Gregor Mendel's work on the nature of inheritance in the late 19th century was "rediscovered" in 1900, it was interpreted as supporting an anti-Darwinian "jumping" form of evolution. The convinced Mendelians, such as William Bateson and Charles Benedict Davenport, and biometricians, such as Walter Frank Raphael Weldon and Karl Pearson, became embroiled in a bitter debate, with Mendelians charging that the biometricians did not understand biology, and biometricians arguing that most biological traits exhibited continuous variation rather than the "jumps" expected by the early Mendelian theory. However, the simple version of the theory of early Mendelians soon gave way to the classical genetics of Thomas Hunt Morgan and his school, which thoroughly grounded and articulated the applications of Mendelian laws to biology. Eventually, it was shown that a rigorous statistical approach to Mendelism was reconcilable with the data of the biometricians by the work of biologist and statistician R.A. Fisher in the 1930s. Following this, the work of population geneticists and zoologists in the 1930s and 1940s created a model of Darwinian evolution compatible with the science of genetics, which became known as the modern evolutionary synthesis.[6]

The most significant recent developments in evolutionary biology have been the improved understanding and advancement of genetics.[7] In the 1940s, following up on Griffith's experiment, Avery, McCleod and McCarty definitively identified DNA (deoxyribonucleic acid) as the "transforming principle" responsible for transmitting genetic information. In 1953, Francis Crick and James D. Watson published their famous paper on the structure of DNA, based on the research of Rosalind Franklin and Maurice Wilkins. These developments ignited the era of molecular biology and transformed the understanding of evolution into a molecular process: 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 mechanism of evolution.

Debates have continued within the field. One prominent public debate was over the theory of punctuated equilibrium, proposed in 1972 by paleontologists Niles Eldredge and Stephen Jay Gould to explain the paucity of gradual transitions between species in the fossil record, as well as the absence of change or stasis that is observed over significant intervals of time.


Science of evolution
The word Evolution has been used to refer both to a fact and a theory. The existence of these two distinct meanings, and confusion over the relationship between and definitions of fact and theory in science, have often caused misunderstandings among laypeople about the scientific status of evolution.

For example, evolution occurs whenever a new species of bacterium evolves a resistance to an antibiotic which previously was lethal to that bacterium. Evolution is the observation that biological organisms evolve. In other words, descendants are seen to have gone through a type of genetic modification process when compared to their ancestors. The modification is most often the result of natural genetic synthesis, and the differential traits manifested may be translated into changes in the genetic composition of the population. As the populations of organisms change over time, the organisms are often observed to be well suited to their environments, and many different species of organisms resembling each other closely, are indicative of evolution.

The goal of the modern scientific method is to formulate testable hypotheses. Meaning, ideas which can be tested directly by evidence and experimentation. When a hypothesis is found to be consistent, and holds up under extensive testing, it is then generally agreed that it represents a fundamental explanation of the observations of the original formulation. In this case, the hypothesis-turned-fundamental concept is elevated to the status of a theory. It is important to note that in no case is a scientific theory free from further testing and revision, nor is it necessarily considered a sufficient explanation of the observations to the exclusion of additional testable scientific hypotheses.

Charles Darwin presented the first hypothesis, explaining these observations of evolution, which have stood up to extensive and repeated testing. Darwin's theory is therefore properly termed a Theory of Evolution by Natural Selection. Evolution as explained by Natural Selection is the theory, not evolution itself. And as with all scientific ideas that have withstood testing, it is considered a theory.


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

Evolutionary biology is a subdiscipline of biology concerned with the origin and descent of species, as well as their changes over time. It was originally an interdisciplinary 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 who use those organisms to answer general questions in evolution. Evolutionary biology as an academic discipline in its own right emerged as a result of the modern evolutionary synthesis in the 1930s and 1940s. It was not until the 1970s and 1980s, however, that a significant number of universities had departments that specifically included the term evolutionary biology in their titles.

Evolutionary developmental biology is an emergent subfield of evolutionary biology which inspects the genes of related and unrelated organisms. By comparing the explicit nucleotide sequences of DNA and RNA, it is possible to trace and experimentally determine the timelines of species development. For example, gene sequences support the conclusion that chimpanzees are the closest non-extinct primate relative to humans, and that arthropods and vertebrates have a common biological ancestor.

Physical anthropology emerged in the late 19th century as the study of human osteology, and the fossilized skeletal remains of other hominids. At that time, anthropologists debated whether their evidence supported Darwin's claims, because skeletal remains revealed temporal and spatial variation among hominids, but Darwin had not offered an explanation of the specific mechanisms that produce variation. With the recognition of Mendelian genetics and the rise of the modern synthesis, however, evolution became both the fundamental conceptual framework for, and the object of study of, physical anthropologists. In addition to studying skeletal remains, they began to study genetic variation among human populations (population genetics); thus, some physical anthropologists began calling themselves biological anthropologists.


Evidence of evolution
Main article: Evidence of evolution
Evolution has left numerous records which reveal the history of different species. Fossils, together with the comparative anatomy of present-day plants and animals, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. Important fossil evidence includes the connection of distinct classes of organisms by so-called "transitional" species, such as the Archaeopteryx, which provided early evidence for the link between dinosaurs and birds, and the recently-discovered Tiktaalik, which clarifies the development from fish to animals with four limbs[8].

The development of molecular genetics, particularly DNA sequencing, has allowed biologists to study the record of evolution left in the DNA. The degree of similarity and difference in the DNA sequences of modern species allows geneticists to reconstruct their lineages. It is from DNA sequence comparisons that figures such as the 95% similarity between humans and chimpanzees come.[9]

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 world's climate was much cooler, and these are often found to match up with the spread of species which are better-equipped to deal with the cold, such as the woolly mammoth.


Morphological evidence

Fossil fish of the genus Knightia.Fossils are critical evidence for estimating when various lineages originated. Since fossilization of an organism is an uncommon occurrence, usually requiring hard parts (like teeth, bone or pollen), the fossil record is traditionally thought to provide only sparse and intermittent information about ancestral lineages. Fossilization of organisms without hard body parts is rare, but happens under unusual circumstances, such as rapid burial, low oxygen environments, or microbial action.

The fossil record provides several types of data important to the study of evolution. First, the fossil record contains the earliest known times of origination of life itself, as well as the earliest occurrences of individual lineages. For example, the first complex animals are known from the early Cambrian period, approximately 520 million years ago. Second, the records of individual species yield information regarding the patterns and rates of evolution, showing for example if species evolve into new species (speciation) gradually and incrementally, or in relatively brief intervals of geologic time. Thirdly, the fossil record is a document of large scale patterns and events in the history of life, many of which have influenced the evolutionary history of numerous lineages. For example, mass extinctions frequently resulted in the loss of entire groups of species, such as the non-avian dinosaurs, while leaving others relatively unscathed. Recently, many molecular biologists have used times of divergence of related lineages to calibrate the rate at which mutations accumulate, and at which the genomes of different lineages evolve.

Phylogenetics, the study of the ancestry of species, has revealed that structures with similar internal organization may perform divergent functions. Vertebrate limbs are a common example of such homologous structures. The appendages on bat wings, for example, are very structurally similar to human hands, and may constitute a vestigial structure. Other examples would include the presence of hip bones in whales and snakes. Such structures may exist with little or no purpose in a more current organism, yet have a clear purpose in an ancestral species of the same. Examples of vestigial structures in humans include wisdom teeth, the coccyx and the vermiform appendix.


Genetic sequence evidence
Comparison of the DNA sequences allows organisms to be grouped by sequence similarity, and the resulting phylogenetic trees are typically congruent with traditional taxonomy, and are often used to strengthen or correct taxonomic classifications. 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.[10] Genetic sequence evidence thus allows inference and quantification of genetic relatedness between humans and other apes.[11][12] 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 reconstructing ancestral lineages comes from junk DNA such as pseudogenes, i.e., 'dead' genes, which steadily accumulate mutations. [13]

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.


Evidence from studies of complex iteration
"It has taken more than five decades, but the electronic computer is now powerful enough to simulate evolution" assisting bioinformatics in its attempt to solve biological problems.[14] Computer science allows the iteration of self changing complex systems to be studied, allowing a mathematically exact understanding of the nature of the processes behind evolution and providing evidence for the hidden causes of known evolutionary events. The evolution of specific cellular mechanisms like spliceosomes that can turn the cell's genome into a vast workshop of billions of interchangeable parts can be studied for the first time in an exact way.

Christoph Adami et al., for example, make this point in Evolution of biological complexity:

To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural "Maxwell Demon," within a fixed environment, genomic complexity is forced to increase. [15]

David J. Earl and Michael W. Deem also make this point in Evolvability is a selectable trait:

Not only has life evolved, but life has evolved to evolve. That is, correlations within protein structure have evolved, and mechanisms to manipulate these correlations have evolved in tandem. The rates at which the various events within the hierarchy of evolutionary moves occur are not random or arbitrary but are selected by Darwinian evolution. Sensibly, rapid or extreme environmental change leads to selection for greater evolvability. This selection is not forbidden by causality and is strongest on the largest-scale moves within the mutational hierarchy. Many observations within evolutionary biology, heretofore considered evolutionary happenstance or accidents, are explained by selection for evolvability. For example, the vertebrate immune system shows that the variable environment of antigens has provided selective pressure for the use of adaptable codons and low-fidelity polymerases during somatic hypermutation. A similar driving force for biased codon usage as a result of productively high mutation rates is observed in the hemagglutinin protein of influenza A. [16]

"Computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of sequence rather than point mutagenesis alone. Repeated cycles of point mutagenesis, recombination, and selection should allow in vitro molecular evolution of complex sequences, such as proteins." [17] Evolutionary molecular engineering, also called "directed evolution" or "in vitro molecular evolution", involves the iterated cycle of mutation, multiplication with recombination, and selection of the fittest of individual molecules (proteins, DNA and RNA). The process of natural evolution can be reconstructed, showing possible paths from catalytic cycles based on proteins to ones based on RNA to ones based on DNA.[18]


Hawthorn fly
An interesting example of evolution at work is the case of the hawthorn fly, Rhagoletis pomonella. Different populations of hawthorn fly feed on different fruits. An appearance of a possibly 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 occurring. The emergence of the new hawthorn fly is an example of evolution in process.[19]


Ancestry of organisms
See also: Common descent

Morphologic similarities in the Hominidae family is evidence of common descent.In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool.

Evidence for common descent 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, there is strong evidence from genetics that all organisms have a common ancestor. 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 many of these traits seems arbitrary.

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



History of life
Main article: Timeline of evolution
The chemical evolution from self-catalytic chemical reactions to life (see Origin of life) is not a part of biological evolution, but it is unclear at which point such increasingly complex sets of reactions became what we would consider, today, to be living organisms.


Precambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, William Schopf of UCLA published a controversial paper in the journal Nature arguing that formations such as this possess 3.5 billion year old fossilized algae microbes. If true, they would be the earliest known life on earth.Not much is known about the earliest developments in life. However, all existing organisms share certain traits, including cellular structure and genetic code. Most scientists interpret this to mean all existing organisms share a common ancestor, which had already developed the most fundamental cellular processes, but there is no scientific consensus on the relationship of the three domains of life (Archaea, 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 evolutionary process may be exceedingly slow. Fossil evidence indicates that the diversity and complexity of modern life has developed over much of the history of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old. Studies on guppies by David Reznick at the University of California, Riverside, however, have shown that the rate of evolution through natural selection can proceed 10 thousand to 10 million times faster than what is indicated in the fossil record.[20]. Such comparative studies however are invariably biased by disparities in the time scales over which evolutionary change is measured in the laboratory, field experiments, and the fossil record.


Horizontal gene transfer, and the history of life
The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly supplemented with phylogenetics - the reconstructiion of phylogenies by the comparison of genetic (usually DNA) sequence.

"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes." [21]

Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research" therefore "biologists [should] use the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes." [22]


Modern synthesis
Main article: Modern evolutionary synthesis
Charles Darwin was able to observe variation, and infer natural selection and thereby adaptation, but didn't know the basis of heritability, and therefore couldn't explain how organisms might change over generations. It also seemed that when two individuals were crossed, their traits must be blended in the progeny, so that eventually all variation would be lost, much as if you mix a set of paints, you eventually end up with grey.

The blending problem was solved when the population geneticists R.A. Fisher, Sewall Wright and J. B. S. Haldane, married Darwinian evolutionary theory to population genetic theory, which was based on Mendelian genetics (genes as discrete units).

The problem of what the mechanisms might be was solved in principle with the identification of DNA as the genetic material by Oswald Avery and colleagues, and the solving of the crystal structure of DNA by Francis Crick and James Watson showed that genes must be encoded in DNA.


Heredity

A section of a model of a DNA molecule.Gregor Mendel first proposed that there are discrete units of heritability (which we now know as genes). He noticed several traits in peas that occur in only one of two forms (e.g., the peas were either round or wrinkled), and was able to show that the traits were: heritable (i.e., not controlled by the environment); discrete (i.e., if one parent had round peas and the other wrinkled, the progeny were not intermediate, but either round or wrinkled); and were distributed to progeny in a way that could be described by mathematical laws (mendelian inheritance). From these observations he was able to infer that those traits were controlled by discrete units, which we now know as genes.

Later research identified DNA as the genetic material, and identified genes as discrete elements within DNA. DNA is not perfectly copied, and rare mistakes (mutations) in genes can affect traits that the genes control (e.g., pea shape).

A gene can have modifications such as DNA methylation, which do not change the nucleotide sequence of a gene, but do result in the epigenetic inheritance of a change in the expression of that gene in a trait.

Non-DNA based forms of heritable variation exist, such transmission of the secondary structures of prions, and structural inheritance of patterns in the rows of cilia in protozoans such as Paramecium[23] and Tetrahymena. Investigations continue into whether these mechanisms allow for the production of specific beneficial heritable variation in response to environmental signals. If this were shown to be the case, then some instances of evolution would lie outside of the typical Darwinian framework, which avoids any connection between environmental signals and the production of heritable variation. However, the processes that produce these variations leave the genetic information intact and are often reversible, and are rather rare.


Variation
Evolutionary changes are the product of evolutionary forces acting on genetic variation. In natural populations, there is a certain amount of phenotypic variation (e.g., what makes you appear different from your neighbor). This phenopyic variation is the result of variants in gene sequences among the individuals of a population. There may be one or more functional variants of a gene or locus, and these variants are called alleles. Most sites in the genome (i.e., complete DNA sequence) of a species are identical in all individuals in the population; sites with more than one allele are called polymorphic or segregating sites.

All genetic variation begins as a new mutation in a single individual; in subsequent generations the frequency of that variant may fluctuate in the population, becoming more or less prevalent relative to other alleles at the site. This change in allele frequency is the commonly accepted definition of evolution, and all evolutionary forces act by driving allele frequency in one direction or another. Variation disappears when it reaches the point of fixation - when it either reaches a frequency of zero and disappears from the population, or reaches a frequency of one and replaces the ancestral allele entirely.


Mechanisms of evolution
Evolution consists of two basic types of processes: those that introduce new genetic variation into a population, and those that affect the frequencies of existing variation. "Variation proposes and selection disposes." [24]

These mechanisms of evolution have all been observed in the present and in evidence of their existence in the past. Their study is being used to guide the development of new medicines and other health aids such as the current effort to prevent a H5N1 (i.e. bird flu) pandemic. [25]


Mutation
Main article: Mutation

Mutation occurs because of a small number of errors that occur during DNA replication.Natural genetic variation arises as random mutations that inevitably occur at a certain rate in genes. Mutations are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by: "copying errors" in the genetic material during cell division; 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 by mutation rate, genetic drift and selective pressure on linked alleles. It is understood that a species' genome, in the absence of selection, undergoes a steady accumulation of neutral mutations.

Not all mutations are created equal; simple point mutations (substitutions) or SNPs (Single Nucleotide Polymorphisms), which comprise a major class of genetic variation, and insertions and deletions (indels) usually can only alter the function or regulation (spatial and temporal expression; levels of expression) of existing genes.

On the other hand, gene duplications, which may occur via a number of mechanisms, are believed to be one major source of raw material for evolving 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"). Another mechanism for is intergenic recombinatin, particularly 'exon shuffling', i.e., an abberant recombination that joins the 'upstream' part of one gene with the 'downstream' part of another.

Finally, large chromosomal rearrangements (like the fusion of two chromosomes in the chimp/human common ancestor that produced human chromosome 2) do not necessarily change gene function, but do generally result in reproductive isolation, and, by definition, speciation (since "species" (in sexual organisms) are usually defined by the ability to interbreed).


Recombination
Main article: Evolution of sex
In asexual organisms, variants in genes on the same chromosome will always be inherited together - they are linked, by virtue of being on the same DNA molecule. However, sexual organisms, in the production of gametes, shuffle linked alleles on homologous chromosomes inherited from the parents via meiotic recombination. This shuffling allows independent assortment of alleles (mutations) in genes to be propagated in the population independently. This allows bad mutations to be purged and beneficial mutations to be retained more efficiently than in asexual populations.

However, the meitoic recombination rate is not very high - on the order of one crossover (recombination event between homomolgous chromosomes) per chromosome arm per generation. Therefore, alleles in adjacent genes are not perfectly shuffled away from each other, but tend to be inherited together. This tendency may be measured by comparing the co-occurrence of two alleles, usually quantified as linkage disequilibrium (LD). A set of alleles that are often co-propagated is called a haplotype. Strong haplotype blocks can be a product of strong positive selection.

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

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


Gene flow and Population structure
Main article: Population genetics

Map of the world showing distribution of camelids. Solid black lines indicate possible migration routes.Gene flow (also called gene admixture or simply migration) is the exchange of genetic variation between populations, when geography and culture are not obstacles. Ernst Mayer thought that gene flow is likely to be homogenising, and therefore counteract selective adaptation. Where there are obstacles to gene flow, the situation is termed reproductive isolation and is considered to be necessary for speciation.

The free movement of alleles through a population may also be impeded by population structure. For example, most real-world populations are not actually fully interbreeding; geographic proximity has a strong influence on the movement of alleles within the population.

An example of the effect of population structure is the so-called founder effect, resulting from a migration or population bottleneck, in which a population temporarily has very few individuals, and therefore loses a lot of genetic variation. In this case, a single, rare allele may suddenly increase very rapidly in frequency within a specific population if it happened to be prevalent in a small number of "founder" individuals. The frequency of the allele in the resulting population can be much higher than otherwise expected, especially for deleterious, disease-causing alleles. Since population size has a profound effect on the relative strengths of genetic drift and natural selection, changes in population size can alter the dynamics of these processes considerably.


Drift
Main article: Genetic drift
Genetic drift describes changes in allele frequency from one generation to the next due to sampling variance. The frequency of an allele in the offspring generation will vary according to a probability distribution of the frequency of the allele in the parent generation. 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 present in one population could be absent in the other, or vice versa).

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.


Horizontal gene transfer
One source of genetic variation is horizontal gene transfer, the movement of genetic material across species boundaries, which can include horizontal gene transfer, antigenic shift, reassortment, and hybridization. Viruses can transfer genes between species [26]. Bacteria can incorporate genes from other dead bacteria, exchange genes with living bacteria, and can have plasmids "set up residence separate from the host's genome" [27].


Selection and adaptation
Main articles: Natural selection, Adaptation

A peacock's tail is the canonical example of sexual selectionNatural selection comes from differences in survival and reproduction . 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:

Positive or directional selection increases the frequency of a beneficial mutation, or pushes the mean in either direction.
Purifying or stabilizing selection maintains a common trait in the population by decreasing the frequency of harmful mutations and weeding them out of the population. "Living fossils" are arguably the product of stabilizing selection, as their form and traits have remained virtually identical over a long period of time. It is argued that stabilizing selection is the most common form of natural selection.
Artificial selection refers to purposeful breeding of a species to produce a more desirable and “perfect” breed. Humans have directed artificial selection in the breeding of both animals and plants, with examples ranging from agriculture (crops and livestock) to pets and horticulture. However, because humans are only part of the environment, the fractions of change in a species due to natural or artificial means can be difficult to determine. Artificial selection within human populations is a controversial enterprise known as eugenics.
Balancing selection maintains variation within a population through a number of mechanisms, including:
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 either have increased fitness or decreased fitness, because of their rarity.
Disruptive selection favors both extremes, and results in a bimodal distribution of gene frequency. The mean may or may not shift.
Selective sweeps describe the affect of selection acting on linked alleles. It comes in two forms:
Background selection occurs when a deleterious mutation is selected against, and linked mutations are eliminated along with the deleterious variant, resulting in lower genetic polymorphism in the surrounding region.
Genetic hitchhiking occurs when a positive mutation is selected for, and linked mutations are pushed towards fixation along with the positive variant.
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 understanding 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

An Allosaurus skeleton.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. An example of rapid sympatric speciation can be eloquently represented in the triangle of U; where new species of Brassica sp. have been made by the fusing of separate genomes from related plants.

Extinction is the disappearance of species (i.e. gene pools). The moment of extinction generally occurs at the death of the last individual of that species. Extinction is not an unusual event in geological time — species are created by speciation, and disappear through extinction. The Permian-Triassic extinction event was the Earth's most severe extinction event, rendering extinct 90% of all marine species and 70% of terrestrial vertebrate species. In the Cretaceous-Tertiary extinction event many forms of life perished (including approximately 50% of all genera), the most often mentioned among them being the extinction of the non-avian dinosaurs.



Current Research
Evolution is still an active field of research in the scientific community. Improvements in sequencing methods have resulted in a large increase of sequenced genomes, allowing for the testing and refining of the theory of evolution with respect to whole genome data. Advances in computational hardware and software have allowed for the testing and extrapolation of increasingly advanced evolutionary models. Discoveries in biotechnology have produced methods for the ‘’de novo’’ synthesis of proteins and, potentially, entire genomes, driving evolutionary studies at the molecular level.

This section encompasses summaries of recent and ongoing cited and peer-reviewed research in the field of evolution.


Ancestral Protein and DNA Reconstruction
Originally proposed by Pauling and Zuckerkandl in 1963[28] the reconstruction of ancient proteins and DNA sequences has only recently become a significant scientific endeavor. The developments of extensive genomic sequence databases in conjunction with advances in biotechnology and phylogenetic inference methods have made ancestral reconstruction cheap, fast, and scientifically practical.

Ancestral protein and DNA reconstruction allows for the recreation of protein and DNA evolution in the laboratory so that it can be studies directly[29]. With respect to proteins, this allows for the investigation of the evolution of present-day molecular structure and function. Additionally, ancestral protein reconstruction can lead to the discoveries of new biochemical functions that have been lost in modern proteins[30]. It also allows insights into the biology and ecology of extinct organisms[31]. Although the majority of ancestral reconstructions have dealt with proteins, it has also been used to test evolutionary mechanisms at the level of bacterial genomes[32] and primate gene sequences[33].

In summary, ancestral reconstruction allows for the study of evolutionary pathways, adaptive selection, and functional divergence of the evolutionary past. For a review of biological and computational techniques of ancestral reconstruction see Chang et al[34]. For criticism of ancestral reconstruction computation methods see Williams P.D. et al[35] and for criticism of the phylogenetic methods used in ancestral reconstruction see Lucena B. and Haussler D.[36]


Misunderstandings about modern evolutionary biology
Though the modern synthesis is almost universally accepted within the scientific community, many people find aspects of it counterintuitive. While from a scientific viewpoint one of the great strengths of evolution by natural selection is that it has no need for a supernatural intelligence or any intelligent designer, people often find that it introduces concepts which go against their perception of design, purpose, directive principle, or finality in nature, and so find difficult to accept. As Louis Menand has pointed out, "Darwin wanted to establish... that the species — including human beings — were created by, and evolve according to, processes that are entirely natural, chance-generated, and blind." [37] People can feel that such a theory robs life and the universe of any transcendental meaning.

In the resulting controversy, publicity is given to creationist arguments against evolution and natural selection, which generally involve misunderstandings or misconceptions about evolution or about science in general.[38] Some of the most common arguments are examined in this section. More are considered at An Index to Creationist Claims.


Distinctions Between Theory and Fact
Further information: Theory
The modern synthesis, like its Mendelian and Darwinian antecedents, is a scientific theory. When speaking casually, people use the word "theory" to signify "conjecture", "speculation", or "opinion", and the word "fact" to signify true, or verifiably true, statements [39] In this sense, "theories" are opposed to "facts". In a more strict sense, though, fact and theory denote the epistemological status of knowledge; how the knowledge was obtained, what sort of knowledge it is. In science, fact tends to mean a datum, an observation, i.e., a fact is obtained by a fairly direct observation. In contrast, a theory is obtained by inference from a body of facts.

A theory is an attempt to identify and describe relationships between phenomena or things, and generates falsifiable predictions which can be tested through controlled experiments, or empirical observation. Provisional theories tend to be called hypotheses, and well tested theories, theories.

In this scientific sense, "facts" are what theories attempt to explain. So, for scientists "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship; for example, it is a "fact" that an apple will fall to the ground if it becomes dislodged from a branch and the "theory" which explains this is the current theory of gravitation. In the same way, heritable variation, natural selection, and response to selection (e.g. in domesticated plants and animals) are "facts", and the generalization or extrapolation beyond these phenomena, and the explanation for them, is the "theory of evolution". [40]

Evolutionary theory is powerfully predictive, and biological research relies extensively on it. The Modern evolutionary synthesis has replaced earlier explanations for the origin of species, including Lamarckism, and is currently the most powerful theory explaining biology.


Evolution and devolution
One of the most common misunderstandings of evolution is that one species can be "more highly evolved" than another, that evolution is necessarily progressive and/or leads to greater "complexity", or that its converse is "devolution".[41] Evolution provides no assurance that later generations are more intelligent, complex, or morally worthy than earlier generations. The claim that evolution results in progress is not part of modern evolutionary theory; it derives from earlier belief systems which were held around the time Darwin devised his theory of evolution.

In many cases evolution does involve "progression" towards more complexity, since the earliest lifeforms were extremely simple compared to many of the species existing today, and there was nowhere to go but up. However, there is no guarantee that any particular organism existing today will become more intelligent, more complex, bigger, or stronger in the future. In fact, natural selection will only favor this kind of "progression" if it increases chance of survival, i.e. the ability to live long enough to raise offspring to sexual maturity. The same mechanism can actually favor lower intelligence, lower complexity, and so on if those traits become a selective advantage in the organism's environment. One way of understanding the apparent "progression" of lifeforms over time is to remember that the earliest life began as maximally simple forms. Evolution caused life to become more complex, since becoming simpler wasn't advantageous. Once individual lineages have attained sufficient complexity, however, simplifications (specialization) are as likely as increased complexity. This can be seen in many parasite species, for example, which have evolved simpler forms from more complex ancestors.[42]


Speciation
Main article: Speciation

The existence of several different, but related, finches on the Galápagos Islands convinced Darwin of the occurrence of speciation.It is sometimes claimed that speciation – the origin of new species – has never been directly observed, and thus evolution cannot be called sound science. (A variation of this assertion is that "microevolution" has been observed and "macroevolution" has not been observed. Some creationists redefine macroevolution as a change from one "kind" to another, though it is unclear what a "kind" in this context is intended to refer to.) This is a misunderstanding of both science and evolution. First, scientific discovery does not occur solely through reproducible experiments; the principle of uniformitarianism allows natural scientists to infer causes through their empirical effects. Moreover, since the publication of On the Origin of Species scientists have confirmed Darwin's hypothesis by data gathered from sources that did not exist in his day, such as DNA similarity among species and new fossil discoveries. Finally, speciation has been directly observed. [43] (See the hawthorn fly example, above.)


Self-organization and entropy
Main article: Self-organization
It is claimed that evolution, by increasing complexity without supernatural intervention, violates the second law of thermodynamics. This law posits that in an idealised isolated system, entropy will tend to increase or stay the same. Entropy is a measure of the amount of energy in a physical system which cannot be used to do mechanical work, and in statistical thermodynamics it is envisioned as a measure of the statistical "disorder" at a microstate level.

The claim ignores the fact that biological systems are not isolated systems. The Sun provides a large amount of energy to the Earth, and this flow of heat results in huge increases in entropy, when compared with decreases associated with decreasing the disorder of biological systems.

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


Information
Some assert that evolution cannot create information, or that information can only be created by an intelligence. Physical information exists regardless of the presence of an intelligence, and evolution allows for new information whenever a novel mutation or gene duplication occurs and is kept. It does not need to be beneficial or visually apparent to be "information." However, even if those were requirements they would be satisfied with the appearance of nylon-eating bacteria, [44] which required new enzymes to efficiently digest a material that never existed until the modern age.

"It wasn't a highly competent design because the bacteria weren't extracting a lot of energy from the process, just enough to get by. And it was based on a simply frame shift reading of a gene that had other uses. But with a simple frame shift of a gene that was already there, it could now "eat" nylon. Future mutations, perhaps point mutations inside that gene, could conceivably heighten the energy gain of the nylon decomp process, and allow the bacteria to truly feast and reproduce faster and more plentifully on just nylon, thus leading perhaps in time to an irreducibly complex arrangement between bacteria who live solely on nylon and a man-made fiber produced only by man." [45]
Japanese researchers demonstrated that nylon degrading ability can be obtained de novo in laboratory cultures of Pseudomonas aeruginosa strain POA, which initially had no enzymes capable of degrading nylon oligomers. This indicates that the ability of bacteria to digest nylon can evolve if proper artificial selection is applied.[46]. Recently, the same group solved the high resolution X-ray crystal structure of the of the newly evolved nylon-digesting enzyme[47]. Using the structural results, the authors propose "that the amino acid replacements in the catalytic cleft of a preexisting esterase with the beta-lactamase fold resulted in the evolution of the" nylon-digesting enzyme. This hypothesis still needs to be confirmed by detailed mutagenesis studies.


Social and religious controversies
Main articles: Social effect of evolutionary theory, Creation-evolution controversy

A satirical 1871 image of Charles Darwin as an ape reflects part of the social controversy over whether humans and apes share a common lineage.Starting with the publication of The Origin of Species in 1859, the modern science of evolution has been a source of nearly constant controversy. In general, controversy has centered on the philosophical, cosmological, social, and religious implications of evolution, not on the science of evolution itself. The proposition that biological evolution occurs through one method or another has been almost completely uncontested within the scientific community since the early 20th century.[48]

As Darwin recognized early on, perhaps the most controversial aspect of evolutionary thought is its applicability to human beings. The idea that all diversity in life, including human beings, arose through natural processes without a need for supernatural intervention poses difficulties for the belief in purpose inherent in most religious faiths — and especially for the Abrahamic religions. Many religious people are able to reconcile the science of evolution with their faith, or see no real conflict [49]; Judaism is notable as one of those faith traditions many of whose adherents see no conflict between evolutionary theory and their religious beliefs.[50] [51] [52] The idea that faith and evolution are compatible has been called theistic evolution. Another group of religious people, generally referred to as creationists, consider evolutionary origin beliefs to be incompatible with their faith, their religious texts and their perception of design in nature, and so cannot accept what they call "unguided evolution".

One particularly contentious topic evoked by evolution is the biological status of humanity. Whereas the classical religious view can be broadly characterized as a belief in the great chain of being (in which people are "above" the animals but slightly "below" the angels), the science of evolution is clear both that humans are animals and that they share common ancestry with chimpanzees, gorillas, and orangutans. Some people find the idea of common ancestry repellent, as, in their opinion, it "degrades" humankind. A related conflict arises when critics combine the religious view of people's superior status with the mistaken notion that evolution is necessarily "progressive". If human beings are superior to animals yet evolved from them, these critics claim, "inferior" animals would not still exist. Because animals that are (in their view) "inferior" creatures do demonstrably exist, those criticising evolution sometimes incorrectly take this as supporting their claim that evolution is false.

In some countries — notably the United States — these and other tensions between religion and science have fueled what has been called the creation-evolution controversy, which, among other things, has generated struggles over the teaching curriculum. While many other fields of science, such as cosmology and earth science, also conflict with a literal interpretation of religious texts, evolutionary studies have borne the brunt of these debates.

Evolution has been used to support philosophical and ethical choices which most modern scientists argue are neither mandated by evolution nor supported by science. For example, the eugenic ideas of Francis Galton were developed into arguments that the human gene pool should be improved by selective breeding policies, including incentives for reproduction for those of "good stock" and disincentives, such as compulsory sterilization, "euthanasia", and later, prenatal testing, birth control, and genetic engineering, for those of "bad". Another example of an extension of evolutionary theory that is widely regarded as unwarranted is "Social Darwinism"; a term given to the 19th century Whig Malthusian theory developed by Herbert Spencer into ideas about "survival of the fittest" in commerce and human societies as a whole, and by others into claims that social inequality, racism, and imperialism were justified.[53]



Notes
^ Lande R & Arnold SJ (1983) The measurement of selection on correlated characters. Evolution 37:1210-26
^ Futuyma DJ (2005) Evolution. Sinauer Associates, Inc., Sunderland, Massachusetts. ISBN 0878931872
^ Haldane, J.B.S. 1953. The measurement of natural selection. Proceedings of the 9th International Congress of Genetics. 1: 480-487
^ a b "Understanding Evolution", University of California, Berkeley, online at http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_17 and http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_16.
^ For the history of evolutionary thought from the eighteenth through the mid-20th centuries is Peter J. Bowler, Evolution: The History of an Idea, 3rd. rev. edn. (Berkeley: University of California Press, 2003).
^ a b For detailed discussion of the history of heredity, especially in relation to evolutionary thought, see Peter J. Bowler, The Mendelian Revolution: The Emergence of Hereditarian Concepts in Modern Science and Society (Baltimore: John Hopkins University Press, 1989).
^ According to the BBC: Colin Norman, news editor of Science, said "[S]cientists tend to take for granted that evolution underpins modern biology [...] Evolution is not just something that scientists study as an esoteric enterprise. It has very important implications for public health and for our understanding of who we are" and Dr. Mike Ritchie, of the school of biology at the University of St Andrews, UK said "The big recent development in evolutionary biology has obviously been the improved resolution in our understanding of genetics. Where people have found a gene they think is involved in speciation, I can now go and look how it has evolved in 12 different species of fly, because we've got the genomes of all these species available on the web." BBC News
^ Feduccia, A (1996). The Origin and Evolution of Birds. New Haven, Yale University Press. ISBN 0-30006460-8.
^ Chimpanzee Sequencing and Analysis Consortium (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' "[1] [2]"
^ The picture labeled "Human Chromosome 2 and its analogs in the apes" in the article Comparison of the Human and Great Ape Chromosomes as Evidence for Common Ancestry is literally a picture of a link in humans that links two separate chromosomes in the nonhuman apes creating a single chromosome in humans. It is considered a missing link, and the ape-human connection is of particular interest. Also, while the term originally referred to fossil evidence, this too is a trace from the past corresponding to some living beings which when alive were the physical embodiment of this link.
^ The New York Times report Still Evolving, Human Genes Tell New Story, based on A Map of Recent Positive Selection in the Human Genome, states the International HapMap Project is "providing the strongest evidence yet that humans are still evolving" and details some of that evidence.
^ Pseudogene evolution and natural selection for a compact genome. "[3]"
^ Simulated evolution gets complex
^ Adami C, Ofria C, Collier TC (2000). "Evolution of biological complexity". Proc Natl Acad Sci U S A 97 (9): 4463-8. PMID 10781045.
^ Earl DJ, Deem MW (2004). "Evolvability is a selectable trait". Proc Natl Acad Sci U S A 101 (32): 11531-6. PMID 15289608.
^ Stemmer WP (1994). "DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution". Proc Natl Acad Sci U S A 91 (22): 10747-51. PMID 7938023.
^ scripps.edu bio.kaist.ac.kr free-tutorial pubmedcentral.nih.gov
^ Berlocher, S.H. and G.L. Bush. 1982. An electrophoretic analysis of Rhagoletis (Diptera: Tephritidae) phylogeny. Systematic Zoology 31:136-155; Berlocher, S.H. and J.L. Feder. 2002. Sympatric speciation in phytophagous insects: moving beyond controversy? Annual Review of Entomology 47:773-815; Bush, G.L. 1969. Sympatric host race formation and speciation in frugivorous flies of the genus Rhagoletis (Diptera: Tephritidae). Evolution 23:237-251; Prokopy, R.J., S.R. Diehl and S.S. Cooley. 1988. Behavioral evidence for host races in Rhagoletis pomonella flies. Oecologia 76:138-147. Proc. Natl. Acad. Sci. USA - Vol. 94, pp. 11417-11421, October 1997 - Evolution article Selective maintenance of allozyme differences among sympatric host races of the apple maggot fly
^ Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata) "[4]"
^ Oklahoma State - Horizontal Gene Transfer
^ esalenctr.org
^ BEISSON, J. & SONNEBORN, T. M. (1965). Cytoplasmic inheritance of the organization of the cell cortex of Paramecium aurelia. Proc. natn. Acad Sci. U.S.A. 53, 275-282
^ NY Books
^ The use of evolutionary principles to guide disease diagnosis and drug development with respect to bird flu (i.e. H5N1 virus) is shown here at CDC. Here is the "tree of life" showing the evolution by reassortment of H5N1 that created the Z genotype in 2002 and here is evolution by antigenic drift that created dozens of highly pathogenic varieties of the Z genotype of avian flu virus H5N1, some of which are increasingly adopted to mammals. Evolution. Right before our eyes.
^ enmicro.pdf
^ Pennisi_2003.pdf
^ Pauling L. and Zuckerkandl E. (1963). "Chemical paleogenetics, molecular restoration studies of extinct forms of life". Acta chemica Scandinavica 17 (89): 9-16.
^ Chang S.W.; Ugalde J.A.; Matz M.V. (2005). "Applications of Ancestral Protein Reconstruction in Understanding Protein Function: GFP-Like Proteins". Methods in Enzymology 395: 652-670.
^ Jermann T. M. et al (1995). "Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily". Nature 374 (6517): 57-59.
^ Chang B.S. et al (2002). "Recreating a functional ancestral archosaur visual pigment". Molecular Biology and Evolution 19 (9): 1483-1489.
^ Zhang C. et al (2003). "Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations". Journal of Bacteriology 185 (18): 5573-5584.
^ Krishnan N.M. et al (2004). "Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference". Molecular Biology and Evolution 21 (10): 1871-1883.
^ Chang S.W.; Ugalde J.A.; Matz M.V. (2005). "Applications of Ancestral Protein Reconstruction in Understanding Protein Function: GFP-Like Proteins". Methods in Enzymology 395: 652-670.
^ Williams P.D. et al (2006). "Assessing the accuracy of ancestral protein reconstruction methods". PLoS Computational Biology 2 (6): e69.
^ Lucena B. and Haussler D. (2005). "Counterexample to a claim about the reconstruction of ancestral character states". Molecular Systems Biology 54 (4): 693-695.
^ (Menand 2001: 121)
^ 15 Answers to Creationist Nonsense Scientific American
^ [5]
^ Evolution is a Fact and a Theory
^ talkorigins Claim CB932: Evolution of degenerate forms
^ Scientific American; Biology: Is the human race evolving or devolving?
^ Boxhorn, Joseph. Observed Instances of Speciation. Talk Origins Archive.
^ Evolution and Information: The Nylon Bug. New Mexicans for Science and Reason.
^ Babinski, Edward T.. Darwinism or Directed Mutations?.
^ Prijambada I.D. et al (1995). "Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution". Applied and Environmental Microbiology 61 (5): 2020–2022.
^ Negoro S et al (2005). "X-ray crystallographic analysis of 6-aminohexanoate-dimer hydrolase: molecular basis for the birth of a nylon oligomer-degrading enzyme". The Journal of Biological Chemistry 280 (47): 39644-39652.
^ An overview of the philosophical, religious, and cosmological controversies by a philosopher who strongly supports evolution is: Daniel Dennett, Darwin's Dangerous Idea: Evolution and the Meanings of Life (New York: Simon & Schuster, 1995). On the scientific and social reception of evolution in the 19th and early 20th centuries, see: Peter J. Bowler, Evolution: The History of an Idea, 3rd. rev. edn. (Berkeley: University of California Press, 2003).
^ [6]
^ The Rabbinical Council of America notes that significant Jewish authorities have maintained that evolutionary theory, properly understood, is not incompatible with belief in a Divine Creator, nor with the first 2 chapters of Genesis. [7]
^ The High Council of B'nei Noah a body of non-Jews guided by the Beit Din of B'nei Noah a sub-court of the developing Sanhedrin: Science and Religion: A proper perspective through an understanding of Hebrew sources
^ Aish HaTorah According to a possible reading of ancient commentators' description of God and nature, the world may be simultaneously young and old.
^ On the history of eugenics and evolution, see Daniel Kevles, In the Name of Eugenics: Genetics and the Uses of Human Heredity (New York: Knopf, 1985).

I hopr this will answer your Q

Answer 2

1

Answer 3

"Get the debate started"???? This debate has been raging every since Darwin was created ... er, ever since Darwin began to evolve, ... er ever since we have had the option between two theories.

I hold to creationism, but I will admit that this is a "default" position for me. The possibility of evolution having occurred are simply too far-fetched to buy. First of all, while we have seen adaptation within species, I don't know that we have evidence of new species arising in this way. Second, when we do see additional chromosomes (as in Down's Syndrome), it is NOT advantageous.

Third, consider what has to happen for the advancement to occur. At one point, the most developed organism had 10 pairs of chromosomes. One of them has an offspring that happens to have a 21st chromosome. And (as noted above, where these mutations are usually NOT advantageous) we have to assume that this particular mutation was advantageous--even though we have never witnessed this happening. And we have to assume--here's the tricky part--that another member of the species had an offspring with the same sort of mutation (so that they could mate and carry on the new line) within the same time frame and location (so that they could meet to procreate) and of the opposite sex.

I think it takes less faith to believe in creation, myself. The mathematics of evolution simply do not add up.

At one time I though maybe believing both was the answer. I found that I was mistaken--it is just a fancy way of trying to ride the fence and not make a decision. If a person doesn't have a preference, that's fine--but I don't see any hope in seriously seeking to say that God created evolution.

So I'm a creationist, primarily because science has not convinced me that they have an explanation that really makes sense. Unless I see good evidence, I have no reason to change my way of thinking.

Answer 4

The best way to set up the essay would be to define both Creationism and Evolution (in their own paragraphs.) Expound upon those definitions and give it a little fluff without adding to it what you think or feel about the two. Then, you should put the two together, by saying something about how both disregard the other. You should mention that it is strange how Creationism would never bring up evolution and how evolution "scientifically" disproves creationism. Then, you should say something like: Perhaps they both have it incorrect; perhaps Creationism includes evolution and that is the logical way the "Creator" could make life possible....I'm not really saying that correctly, but you get the drift. I did an essay on this as well, and ended up getting a really good grade on it in university English. Good luck.

Answer 5

Why not both?

The notion that it can't be both basically is that the initial idea of creationism that is hundreds of years old is so stupid it boggles the mind.

(history lesson, the world is 6000 years old, created on Sunday 23rd of October, 4004BC at 9am. - all of the stuff today comes from this initial finding. 9am? if its 9am in New york, its 4pm in Athens, so what time zone is that? god has a time zone? god uses a human time system? i thought god was not bound from time?

The big bang created the world, maybe true, may not be. what caused the big bang? why was god not changing things in the world to bring about evolution? natural selection is just a theory.

I think this problem occurs for two reasons. Christians tend to belief that science is out to get them, not true. science is devoid of any religious, political or otherwise feeling.

people also tend to belief the bible is literally true. it was written by human people long after the death of Christ.

I don't think it is out of line to believe in both. I do not believe the world was created in the way outlined in the bible, it makes little sense, both in science and otherwise. But that does not change my religious beliefs.

I remember talking to a guy who was asked if i created the world, would i not want praise by the people who live on.
I did not respond but really wanted to say "if i created the world, and a race to live on it, i think i would be above the need for social acceptance"

I also remember a story told to me by an english teacher, which reminds me of the standard creationism theory.before the real advent of science when people thought "every moving thing makes a sound, the earth moves, why can't we hear it?" then they came up with a winning answer "god created the earth, god is perfect, the world is perfect, we can't hear it because we are not perfect"

I think someone said something about "god created it that way" is not a scientific answer to anything

Answer 6

Creationism is a valid thing to have faith in, but it is not scientific. In order to be scientific it must be able to be proven or disproven. Saying 'God made it that way' removes any ability to prove or disprove because God him/herself cannot be proven.

Evolution on the other hand has proof requirements, the key part of evolution, natural selection, has been proven again and again. The only problem is that not every aspect of evolution has been proven/understood 100%, but then gravity hasn't been proven/understood 100% either.

This is definately an oversimplification of the issue...

Answer 7

Evolution. Creationism has too many loopholes and contradictions. Never has been any hard, irrefutable, physical proof of a god. Science has proved quite a bit.

Answer 8

3

Answer 9

2