Evolution

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For criticism see Criticism of Evolution

The phylogenetic tree of life, based on rRNA gene data, showing the separation of the three domains.

The dictionary definition of the word "evolution" is any process of growth, change, or development. The word stems from the Latin evolutio (1622) meaning to unfold or to unroll. Prior to the late 1800s and the publications of Charles Darwin (1859) (1872), the word was in frequent use with respect to ideas and societies. One can also speak of stellar evolution, chemical evolution, or the evolution of ideas. More recently there are evolutionary algorithyms that model the processes of biolgical evolution on the computer.

In the 19th century, the word "evolution" was identified with improvement. Darwin, in keeping with his culture's facination with "The Theory of Progress", initially used the the words improvement and progress. Subsequently the idea of continual progress was refuted, and Darwin and other writers on evolution were careful to refer to an increase in complexity. However there was frequent confusion in the popular mind about the connection between evolution and progress.

Similarly, there is popular confusion about references to "Darwin's Theory of Evolution". In everyday language, theory is taken to be speculative, or unproven, and there are millions of people who do not know or understand the massive amount of evidence that supports the validity of biological evolution. Pehaps it is too late or impractical to drop the unfortunate use of that word in this context, but it probably should follow the idea of continuous progress into obsolesence. The remainder of this article addresses bilogical evolution, particularly the early work of Charles Darwin.

Biological Evolution I

Biological evolution consists of trillions of interactive processes acting over billions of years down to the present. As a result, it literally defies definition in a brief ,concise statement. This article presents the recognition and proof of these processes by following the thoughts of Charles Darwin as recorded in his 1859 publication On The Origin of Species by Means Of Natural Selection.

Darwin (b 1809) was born to be a naturalist. He spent his early youth observing and making notes of nature in the woods , fields , and streams around his home. He rejected the family traditional vocations of medicine, and the ministry at Cambridge University, and was encouraged to study natural history by Professsor John Henslow. Later when there was competition for the position of naturalist on the voyage of the Beagle, the recommendation of Hensow was instrumental in Darwin?s successful application. The voyage of the Beagle from 1831 to 1836 is well documented.Upon his return he had a sufficient inheritance for him and his family to live comfortably without other work.. He devoted his life to collecting immense amounts of data from his own efforts, from other naturalists, making observations, writing, reworking his notes, and discussing them at length with a few friends, while developing the concepts that we now call biological evolution.

Darwin did not have to start from scratch. Evolution, as an idea,had been around for a long time. He had at least three models of other kinds of evolution: Linnaeus, a Swedish botanist had made an influential classification of the then known plants and animals by 1753; Sir William Jones had recognized and described the common origin and diverging descent of the Indo-European languages by the late 1780s; Sir Charles Lyell had published his ?Principles of Geology? in 1830-1833 describing the evolution of geological formations over an estimated millions of years. Darwin carried volume 1 of that book aboard the Beagle.

"An Historical Sketch of the Progress of Opinion on the Origin of Species, Previoulsly to the Publication of the First Edition of This Work" was prepared by Charles Darwin for a later edition. In this piece,Darwin gives extensive credit to no less than twenty-one other scientists. He begins with Jean Baptiste Lamarck who published in 1801 and 1809 work in which he upholds the doctrine that all species,including man, are descended from other species. He then proceeds to name, give a description of the work, and the dates and titles of significant publications of many of the well-known scientists of the period. He ends with noting the 1958 presentation by Alfred Russel Wallace and himself at the Linnaean Society and publication in the Journal of that Society.

Variation Under Domestication

The Origin of the Species is not a casual read. Chapter One is a meticulous, detailed, comprehensive list of the variations in individual domestic plants and animals and how these variations have been manipulated by humans to increase features favored by the owners. In turn, the variations and features not favored by the humans may be decreased by appropriate manipulations. The features increased or decreased may have nothing to do with the well being of the animal. Many of the most strongly marked domestic animals could not live in the wild state. "The key is man?s power of accumulative selection: nature gives variations; man adds them up in certain directions useful to him. Breeders habitually speak of an animal?s organization as something plastic, which they can model as they please.?

Variation Under Nature

In Chapter II, Darwin addresses the variation in nature, which though more difficult to study and to follow over time, also occur in individuals, as well as in groups that live in close approximation to one another, or in geographical isolation, or in different climates as well as in different countries. Insects, small animals such as snails, plants, and trees lend themselves to more comprehensive study. The problem of differentiation of varieties and species becomes soon apparent. Mr Wallace?s study of butterflies (Lepidoptera) on the islands of the Malaysian archipelago can serve as an example.They may be classified under four headings: as variable forms;as local forms; as geographical forms or sub-species; and as representative species. The variable forms vary much on the same island. The local forms are more constant and distinct by island. The subspecies are local forms that seem to be constant and distinct. The representative species fill the same role as the others in the natural economy of each island, but are more distinct from each other than are the other types, and are clearly ranked as true species.

Darwin, while on the Beagle, was first struck by the difficulty in distinguishing between species and varieties by comparing the birds of the Galapagos Islands with each other as well as the birds of the (South)American mainland. Darwin cites the work of scientists from around the world, working with a wide variety of plants and animals. They all report the problem of distinguishing between varieties and species. The species that are the most numerous and the most widely distributed in any country give rise to the greater number of varieties that can be classified as sub-species or even separate species.[6]

Struggle For Existence

"A struggle for existence inevitably follows from the high rate at which all organic beings tend to increase.. Every being , which during its natural lifetime produces several eggs or seeds , must suffer destruction during some period of its life,...otherwise,on the principle of geometrical increase,its numbers would.. ..become so inordinately great that no country could support the product....It is the doctrine of Malthus applied...to the whole animal and vegetable kingdoms."[7]

Natural Selection ; Or Survival Of The Fittest

1.All of the plants and animals present individual differences in almost every part of their structure;
2.Owing to the geometrical rate of increase demonstrated by every organism, there is a severe struggle for life among all individuals and groups ;
3.All organisms live in states of infinite complexity of relationships with each other, and under the specific environmental conditions of space and time.
4.Some of the variations in structure, constitution, or habit that occur are advantageous to them.
5.Variations that are useful to the organic being will have the best chance of being preserved in the struggle for life.
6.The principle of inheritance will produce offspring similarly possessing these advantageous characteristics.
7. This principle of preservation,or the survival of the fittest,Darwin calls Natural Selection.[8]

"It is truly a wonderful fact that all animals and all plants throughout all time and space should be related to each other in groups, subordinate to groups, in the manner which we everywhere behold?.namely, varieties of the same species most closely related, species of the same genus less closely and unequally related, forming sections and sub-genera, species of distinct genera?much less closely related, and genera related in different degrees, forming sub-families, families, orders, sub-classes, and classes. ...The affinities of all the beings in the same class have sometimes been represented by a great tree."

Laws of Variation, and Difficulties: Chapters IV to XV

Thus in four succint, but impressively dense chapters Charles Darwin lays out the principles of Biological Evolution. These principles are as valid now as they were almost one hundred and fifty years ago. Even more impressive are the next eleven chapters where Darwin analyzes,dissects,and often refutes the difficulties,and problems that he, himself, recognizes as well as the hundreds of objections made by scientific colleagues throughout the world. Impossible to summarize here, it can be noted that topics as far removed as the color and stripes in horses, to the wings of nonflying and flying birds and other animals like bats and insects, to the transition of swim bladders of some fish into the lungs of vertebrates are covered and argued in meticulous detail. Three chapters are spent on "The Imperfections of the Geological Record"; on "The Geological Succession of Organic Beings"; and on "Geographical Distribution".[11]

Devoid of the narrative descriptions and arguments, an inadequate rendition of Darwin?s discussion of the eye may be provided by simply listing the different representative levels of the eye that Darwin had collected or had received from reputable scientists. Darwin first admits that on the surface it would seem absurd to think that any organ as complex as the eye could be formed by natural selection. However in providing a convincing argument to the contrary, he lists the following morphological details as levels of developing vision, that is, an eye:

1. Aggregates of pigment cells, without any nerves, apparently serving to distinguish light from dark..
2.The simplest eye consists of an optic nerve, surrounded by pigment cells and covered by translucent skin, but without any lens .
3.In certain star-fishes, small depressions in the layer of pigment which surrounds the nerve are filled with transparent gelatinous matter, projecting with a convex surface (similar to the cornea in animals).
4.In the great class of the Articulata (invertebrates like insects and crustacea), one also starts from an optic nerve coated with pigment.
5.But the numerous facets of their great compound eyes form true lenses and that the cones include modified nervous filaments.
6.The diversity of organs of vision in the Articulata were at that time classified into three major classes and seven subivisions.
7.In the Vertebrata, the lancelet has the simplest eye of a little sack of transparent skin, with a nerve, and lined with pigment.
8.In man according to Virchow, the beautiful crystalline lens is formed in the embryo by an accumulation of epidermic cells,lying in a sack?like fold of skin;and the vitreous body is formed from embryonic subcutaneous tissue.[12]

In summary , Darwin concludes with the following : "It is interesting to contemplate a tangled (stream) bank, clothed with plants of many kinds, with birds singing?., insects flitting about, ?with worms crawling?and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other?have all been produced by laws acting around us. These laws?being Growth with Reproduction; Inheritance ...; Variability from the direct and indirect conditions of life, and from use and disuse: A Ratio of Life so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less improved forms."[13]

References

1.Darwin, Charles, On The Origin of The Species By Means of Natural Selection New York:The Heritage Press 1963 pp470 (a reprint of the 6th ed.)
2.Kroeber,A.L., Evolution,History,and Culture in The Evolution of Maned.by Sol Tax, University of Chicago Press 1960 p1-16
3.Darwin, Charles G, (New) Preface to Charles Darwin loc.cit.p v-xxi
4.Darwin, Charles. "An Historical Sketch....." loc.cit. p xiii - xxi
5.Darwin, C. loc.cit. p 19
6.Darwin, C. loc.cit. p 30-49
7.Darwin, C. loc.cit. p 47
8.Darwin, C. loc.cit. p 103
9.Darwin, C. loc.cit. p 104
10.ibid.
11.Darwin, C. loc.cit. p272-375
12.Darwin, C. loc.cit. p 146-149
13.Darwin, C. loc.cit. p 445

Biological Evolution II

Gregor Mendel's work on the nature of inheritance in the late 19th century was "rediscovered" in 1900, but soon gave way to the classical genetics of Thomas Hunt Morgan 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.

The process of evolution has left numerous records which reveal the history of different species. While the best-known of these are the fossil record, fossils are only a small part of the overall physical record of evolution. Fossils, taken together with the comparative anatomy of present-day plants and animals, constitute the morphological, or anatomical, record. By comparing the anatomies of both modern and extinct species, biologists can reconstruct the lineages of those species with some accuracy. 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.

Fossils are important tools for estimating when various lineages developed. Since fossilization of an organism is an uncommon occurrence, usually requiring hard parts (like teeth, bone or pollen), the fossil record only provides sparse and intermittent information about the evolution of life. Fossil evidence of organisms without hard body parts is rare, but exists in the form of ancient microfossils and the fossilization of ancient burrows (trace fossils).

Evidence from studies of complex iteration

"It has taken more than five decades, but the electronic computer is now powerful enough to simulate evolution" 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.

"Computer simulations of the evolution of linear sequences have demonstrated the importance of recombination of blocks of sequence rather than point mutagenesis alone. 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).

Hawthorn fly

A clear case of evolution as an ongoing, observable fact involves the hawthorn fly, Rhagoletis pomonella. Different populations of hawthorn fly feed on different fruits. A new population spontaneously emerged in North America in the 19th century some time after apples, a non-native species, were introduced. The apple feeding population normally feeds only on apples and not on the historically preferred fruit of hawthorns. Likewise the current hawthorn feeding population does not normally feed on apples.

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

The Cambrian Explosion

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 followed by arthropods and other animals, leading to the development of land ecosystems with which we are familiar.The evolutionary process is exceedingly slow. Fossil evidence indicates that the diversity and complexity of life has developed over the history of the earth. Geological evidence indicates that the Earth is approximately 4.6 billion years old. The mechanisms of evolution include mutation, linkage, heterozygosity, recombination, gene flow, population structure, drift, natural selection, and adaptation.

Mutation

The ultimate source of all genetic variation is mutations. They are , transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can represent "copying errors" during cell division, and by exposure to chemicals,or viruses, or gamma rays.The frequency of so-called neutral mutations in the population is governed entirely by genetic drift and gene flow. A simple point mutation alters the function or expression of existing genes. Gene duplications, are a major mechanism for the alteration of genes; most genes belong to larger "families" of genes derived from a common ancestral gene.

Linkage and heterozygosity

Genetic variation cannot move perfectly freely through the population from one generation to the next. Deviations from a random distribution of alleles (a population where alleles are truly independently assorted and gametes randomly joined) may appear in the form of decreased heterozygosity - that is, the fraction of the population which has one copy of each allele. Low heterozygosity may result from inbreeding. High heterozygosity is usually a product of the introduction of a new population. A second significant restraint on alleles appears in the form of genetic linkage, where alleles that are nearby on a chromosome tend to be propagated together. This tendency is measured by comparing the co-occurrence of two alleles. A set of alleles that are often co-propagated is called a haplotype. Strong haplotype blocks can be a product of strong positive selection or rapid demographic changes.

Recombination

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. When alleles cannot be separated by recombination (for example in mammalian Y chromosomes).

Gene flow

Gene flow ) is introduction of variation into a population from an outside population. It is the only mechanism whereby two populations can become closer genetically while increasing their variation. Migration of one population into an area occupied by a second population can result in gene flow. Gene flow operates when geography and culture are not obstacles.

An important facet of evolution occurs through changes in population structure. The movement of populations and changes in their sizes have profound impacts on evolution by altering extant selection pressures or patterns of drift. For example, migration can result in admixture, leading to the introduction of new genetic variation, or it may result in geographic isolation which may in turn lead to reproductive isolation or speciation. Populations may also shrink or grow over time, producing "bottlenecks" or "explosions" respectively. Since population size has a profound effect on the relative strengths of genetic drift and natural selection. The free movement of alleles through a population may also be impeded by population structure.

An example of the effect of population structure is the so-called founder effect, resulting from a migration and population bottleneck. In this case, a single, rare allele may suddenly increase very rapidly in frequency 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.

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" - . 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. Many aspects of genetic drift depend on the size of the population This is especially important in small mating populations, where chance fluctuations from generation to generation can be large. Thus, natural selection is 'more efficient' in large populations, or equivalently, genetic drift is stronger in small populations.

Selection and adaptation

Natural selection comes from differences in survival and reproduction as a result of the environment. Differential mortality is the survival rate of individuals to their reproductive age. Differential fertility is the total genetic contribution to the next generation. Note that, whereas mutations and genetic drift are random, natural selection is not, as it preferentially selects for different mutations based on differential fitnes. Natural selection also operates on mutations in several different ways:

Positive or selection] increases the frequency of a beneficial mutation, *Stabilizing selection drives a population towards common traits. The stabilized population has relatively little genetic diversity. Turtles and sharks are a good example of stabilizing selection. Their form and traits have remained virtually identical over a long period of time.
Artificial selection refers to purposeful breeding of a species to produce desired traits. Humans have directed artificial selection in the breeding of both animals and plants,

External links and further reading

"A Teacher on the Front Line as Faith and Science Clash" article by Amy Harmon in The New York Times August 23, 2008
Evolution in Action a news summary ed. by Elizabeth Culotta,and Elizabeth Pennisi, in Science vol 310 p1878-1879, 23 December 2005
Goldsmith, Timothy H.,What Birds See in THE SCIENTIFIC AMERICAN, July,2006 p68-75

Adapted from the Wikipedia article, "Evolution" http://en.wikipedia.org/wiki/Evolution, used under the GNU Free Documentation License.
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