Evolution



There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Evolution refers to change in a biological population's inherited traits from generation to generation. All species on Earth originated by the mechanism of evolution, through descent from common ancestors. Evolution occurs as changes accumulate over generations. Charles Darwin recognized evolution by natural selection, also called "descent with modification", as the fundamental process underlying all of life, whether viewed at a large scale above the level of species (macroevolution — in terms of formation of new species, changes within lineages, and extinction), or at a small scale within a species (microevolution — in terms of change in gene frequency). In a nutshell, evolution by natural selection can be simplified to the following principles:


 * Variability: individuals in a population display differences in form, physiology, and behaviour.
 * Differential Fitness: differences between individuals confer different survival and reproduction rates.
 * Heredity: differences in fitness can pass on to subsequent generations.

In modern genetic terminology, variability of traits in a population is the expression (phenotype) of heritable traits (genes), which (at least on Earth) are stored in DNA (or sometimes in RNA or in proteins). Variability of traits ultimately originates from mutation, and new combinations of genes are continually produced via recombination as part of sexual reproduction. The result of natural selection is adaptation, like a "hand in glove" fit between organism and environment. Evolution, defined in population genetics as change in gene frequency in a population, can be influenced by other processes besides natural selection, including genetic drift (random changes, especially in small populations) and gene flow (wherein new genes come into a population from other populations). In a sense, mutation is an innovative process of expansion in which new possibilities come into existence (most of which don't work so well), and this is balanced by natural selection, a process of contraction that reduces the possibilities to those that work best in a particular environment.

Etymology
The word evolution (from the Latin e, meaning "from, out of," and volvo, "to roll," thus "to unroll [like a scroll]") was initially used in 1662, and was variously used, including with respect to physical movement, describing tactical wheeling maneuvers for realignment of troops or ships. In medicine, mathematics, and general writing early use of the term referred to growth and development within individuals. ; its first use in relation to biological change over generations came in 1762, when Charles Bonnet used it for his now outdated concept of "pre-formation", in which females carried a miniature form (homunculus) of all future generations. The term gradually gained more general meaning of progressive change. In 1832 Scottish geologist Charles Lyell referred to gradual change over long periods of time. Charles Darwin only used the word in print once, in the closing paragraph of The Origin of Species (1859), and rather favored the phrases "transmutation by means of natural selection" and "descent with modification". In the subsequent modern synthesis of evolution, Julian Huxley and others adopted the term, which thereby became the accepted technical term used by scientists. Although in contemporary usage the term "evolution" most commonly refers to biological evolution, usage has evolved, and the word also refers more generally to "accumulation of change", including in many disciplines besides biology.

Prehistory of evolution
The idea that life has evolved over time is not a recent one, and Charles Darwin did not, in fact, come up with the idea of evolution in general. For example, ancient Greek philosophers, like Aristotle, had ideas about biological development. Later, in Medieval times, Augustine used evolution as a basis for the philosophy of history.

Origins of the theory
The first significant step in the theory of evolution was made by Carl Linnaeus. His leading contribution to science was his creation of the binomial system of nomenclature &mdash; in lay terms, the two-part name given to species, such as Homo sapiens for humans. He, like other biologists of his time, believed in the fixity of the species, and in the scala naturae, or the scale of life. His ideas were consistent with the Judeo-Christian teachings of his time.

Erasmus Darwin, the grandfather of Charles Darwin, was the first scientist to whom credit can be given for something starting to approach modern concepts of evolution, as noted in his contributions to botany and zoology. His writings contained many comments (mostly in footnotes and side writings) that suggested his beliefs in common descent. He concluded that vestigial organs (such as the appendix in humans) are leftovers from previous generations. The elder Darwin, however, offered no mechanism by which he believed evolution could occur. He also believed in theistic evolution, claiming God began it.

Late eighteenth-century contributions
Georges Cuvier proposed a mechanism by which the fossil record could develop over time without evolution - which by now had come into usage as a term. His hypothesis, catastrophism, was that a series of disasters destroy all life within a limited area, and that living organisms move in to this newly opened area. This idea prefigures in some respects the 1970s hypothesis of 'punctuated equilibrium'.

Lamarck was the first scientist to whom credit can be given for a theory of evolution. His idea centered on use and disuse, the concept being that the more an organism used a particular part of its body, the more developed that organ became within a species. It is sound only for individuals (e.g. a weightlifter will develop larger muscles over time, but will not pass this trait on to any children.) Lamarckian inheritance of acquired traits was an essential part of the Lysenko-Michurin theory, which was favored by Stalin and dominated Soviet genetics from the 1930s until 1965. Nevertheless, modern research into suggests that parents can induce some traits into their offspring by non-genetic inheritance, and that Lamarck was therefore not completely wrong.

Natural selection


By the first half of the 19th century, scientists had gathered a great deal of information on species, and had inferred that life on Earth had existed for a very long time, and that some species had become extinct. Natural selection was the first theory to provide a mechanism to explain those observations. Prior to the theory of natural selection, the concept that species could change over time had been proposed, but without a satisfactory explanation. Alfred Russel Wallace and Charles Darwin came to the conclusion, independently, that competition for resources and the struggle for survival helped determine which changes became permanent and which traits were discarded.

The theory of evolution by natural selection, as we know it today, was published in a joint paper by Wallace and Darwin on 20 August, 1858, based on Wallace's observations in the Malay Archipelago and Darwin's observations over many years including those made during his voyage on HMS Beagle. Charles Lyell's Principles of Geology, which suggested slow changes over very long periods of time, also contributed to the nascent theory. Darwin drew heavily on his knowledge of human experience in breeding domestic animals (artificial selection), particularly the varieties produced by pigeon breeders (Darwin was one himself), for his understanding of how variations could develop within a population over time. However, before the discovery of mutations, biologists had no clue how heritable variation could originate in the first place. Darwin set out his theory (at the time, a hypothesis) of natural selection in his books On the Origin of Species and The Descent of Man.

Other mechanisms
For more information, see Non-Darwinian evolution.

Although natural selection was the first mechanism proposed in evolutionary theory (and remains the most common), other forms of selection play a part as well. The most notable of these is sexual selection, which occurs due to some heritable preference for a trait in breeding partners. Derivation of traits through this mechanism is driven by (usually) the female's choice in mating partner rather than direct impact on fitness. Sexual selection often leads to the rise of features which would likely not occur under natural selection, such as the tail of a peacock or the long necks of giraffes.

Sexual selection can be divided into two forms, distinguishable by who actually "makes" mating decisions. The first of these is intersexual selection, and in this form of selection the limiting sex (which is usually female) will choose a partner. The other form is intrasexual selection, or mate competition. In this form of selection, one sex (usually males) competes for "mating rights" to members of the other sex.

In addition to selection, other mechanisms have been proposed, most notably genetic drift. More controversial is the importance of symbiosis (which has been recognized in the case of the origins of eukaryotes). Universally rejected is Lamarckism or directed (rather than random) variations.

The eclipse of Darwinism
The eclipse of Darwinism is a phrase to describe the state of affairs prior to the modern synthesis when evolution was widely accepted in scientific circles but relatively few biologists believed that natural selection was its primary mechanism. Instead non-Darwinian mechanisms of evolution such as neo-Lamarckism, saltationism, or orthogenesis were advocated. These mechanisms were included in most textbooks until the 1930's but were rejected by the neo-Darwinian synthesis theorists in the 1940's as evidence had proven the role of natural selection in evolution.

Modern Synthesis
The modern evolutionary synthesis (or neo-Darwinism) brings together ideas from several biological specialties in an attempt to explain how biological evolution proceeds. Many scientists have accepted it. It is also referred to as the "new synthesis", the "evolutionary synthesis", the "neo-Darwinian synthesis" or the "synthetic theory of evolution". The synthesis evolved between 1936 and 1947 with the reconciliation of Mendelian genetics with natural selection into a gradual framework of evolution. The synthesis of Darwinian natural selection (1859) and Mendelian inheritance (1865) is the cornerstone of neo-Darwinism.

Julian Huxley (1887 – 1975) invented the term "modern synthesis" when he produced his book Evolution: The Modern Synthesis (1942). Other major contributors to the modern synthesis included R. A. Fisher (1890 - 1962), Theodosius Dobzhansky (1900 - 1975), Ernst Mayr (1904 - 2005), George Gaylord Simpson (1902 – 1984), and (1906 - 2000).

Extended Evolutionary Synthesis
Since the 1980s (approximately), new conceptions of evolutionary theory have emerged, grouped under the umbrella term of the "Extended Synthesis". Advocates aim to modify the existing Modern Synthesis. This proposed extended synthesis incorporates new possibilities for integration and expansion in evolutionary theory, such as evo-devo, and  Proponents include Massimo Pigliucci, Gerd Müller, and Eva Jablonka. In 2008 sixteen scientists met at the Konrad Lorenz Institute in Altenberg, Austria, to propose an extended synthesis.

The principles of evolution
Evolutionary theory has at its core three main tenets, observations of patterns within nature. These three patterns were observed by both Darwin and Wallace, and they eventually gave rise to the modern theory of evolution by natural selection.

Natural variability
Darwin and Wallace both noted that populations display natural variability in form, physiology, and behaviour (phenotypic variability). For example, within a population, some members may be very large, some may be very small, and most may be somewhere in the middle. This natural variability is the fundamental source upon which natural selection acts.

Differential fitness
Having observed that natural variability exists, early evolutionary biologists also noted that some of these variants endowed their possessor with some competitive edge over other members of the species, conferring greater survival or reproduction. Although at first the implications of this fact were unclear, the writings of Thomas Malthus spurred Darwin and Wallace to recognize that individuals that have traits that enhance their ability to survive and reproduce pass on these traits to subsequent generations. Differential fitness, also known as differential reproductive success, in essence, is the process by which traits that enhance survival and reproduction gain greater representation in subsequent generations.

Heritability
Only if variation is heritable, will it confer an advantage into future generations. Although early evolutionary scientists did not have the benefit of modern molecular tools, they surmised that the source of variation must in part have a heritable basis, in contrast with variation expressed solely in response to different environmental conditions. In fact, one of the first predictions made by evolutionary theory was the existence of a heritable factor, now known to be DNA!

Thus the combination of phenotypic variability, differential fitness, and heritability of fitness define evolution by natural selection. Darwin and Wallace independently came to the conclusion that those organisms best suited to their environment would survive to produce more offspring. Therefore, the heritable factor responsible would increase in frequency within the population.

Patterns in nature
Evolutionary biology seeks to explain the following three broad patterns observable in all life.

Diversity
Diversity is fundamental to life at all levels of organization: ecosystems, communities, species, populations, individuals, organs, and molecules.

According to the Genetic Variation Program arm of the National Human Genome Research Institute, about 99.5% of human DNA is the same from person to person. The other 0.5% accounts for a number of simple and complex traits we possess. There is tremendous genetic diversity within almost all species, including humans. No two individuals have an identical DNA sequence, with the exception of identical twins or clones. This genetic variation contributes to phenotypic variation - that is, diversity in the outward appearance and behavior of individuals of the same species.

Adaptation
Populations must adapt to their environment to survive.

Living organisms have morphological, biochemical, and behavioral features that make them well adapted for life in the environments in which they are usually found. For example, consider the hollow bones and feathers of birds that enable them to fly, or the cryptic coloration that allows many organisms to hide from their predators or prey. These features may give the superficial appearance that organisms were designed by a creator (or engineer) to live in a particular environment. Evolutionary biology has demonstrated that adaptations arise through selection acting on a population through genetic variation.

Divergence
Species evolved along different paths from a common ancestor.

All living species differ from one another. In some cases, these differences are subtle, while in other cases the differences are dramatic. Carl Linnaeus (1707-1778) proposed a classification that is still used today with slight changes. In the modern scheme, related species are grouped into genera, related genera into families, and so on. This hierarchical pattern of relationship produces a tree-like pattern, which implies a process of splitting and divergence from a common ancestor. While Linnaeus classified species using similar physical characteristics, modern evolutionary biologists also base classification on DNA analysis, which can distinguish between superficial resemblances between species and those which are due to common ancestry.

Mechanisms of evolution
Biological evolution results from changes over time in the genetic constitution of species. The accumulation of genetic variations often, but not always, produces noticeable changes in the appearance or behavior of organisms. Evolution requires both the production of variation and the spread of some variants that replace others.

Offspring with genetic mutations are different from their parents
Genetic variation arises through two processes, mutation and recombination. Mutation occurs when DNA is imperfectly copied during replication, or by changes in genetic material caused by such mutagens as radiation, leading to a difference between a parent's gene and that of its offspring. Some mutations affect only one bit in the DNA; others produce rearrangements of, or changes in, large blocks of DNA.

Genes can be shuffled between organisms
Recombination occurs when genes from two parents are shuffled to produce an offspring, as happens in every instance of sexual reproduction. Usually the two parents belong to the same species, but sometimes (especially in bacteria) genes move between more distantly related organisms.

Not all mutations become fixed in a population
The fate of any particular genetic variant depends on two processes, drift and selection. Drift refers to random fluctuations in gene frequency, and its effects are usually seen at the level of DNA. Ten flips of a coin do not always (or even usually) produce exactly five heads and five tails; drift refers to the same statistical issue applied to the transmission of genetic variants across generations. Genetic drift is inverse to population size; that is, genetic drift has a greater effect on small populations than larger ones. For example, if a small part of a population becomes geographically isolated its members will develop new traits faster.

Natural selection guarantees that the fittest are most likely to pass on their genes
The principle of natural selection was discovered by Charles Darwin (1809-1882), and it is the process by which organisms become adapted to their environments. Selection occurs when some individual organisms have genes that encode physical or behavioral features that allow them to better harvest resources, avoid predators, reproduce successfully, and so forth, relative to other individuals that do not carry those genes. The individuals that have more useful (adaptive) features will tend to leave more offspring than other individuals, so the responsible genes will become more common over time, leading the population as a whole to become better adapted.

Gene duplication allows for new genes to be added to a genome
Through a variety of mechanisms, gene duplication can occur which gives rise to two identical genes in the genome. Since only one of these genes is necessary, the other gene can undergo mutations without having an adverse effect on the original function of the gene. These duplicated genes called paralogs can give rise to protein families with similar yet distinctly different functions. For example, the olfactory protein family consists of around 900 different smell receptors that all arose via gene duplication followed by unimpeded mutation.

Distinct species diverge from one ancestor and can no longer interbreed
The process that many people find most confusing about evolution is speciation, which is not a separate mechanism at all, but rather a consequence of the preceding mechanisms played out in time and space. Speciation occurs when a population changes sufficiently over time that it becomes convenient to refer to the early and late forms by different names. Speciation also occurs when one population splits into two distinct forms that can no longer interbreed. Reproductive isolation does not generally happen in one generation; it may require many thousands of generations when, for example, one part of a population becomes geographically separated from the rest and adapts to a new environment. Given time, it is inevitable that two populations that live apart will diverge by mutation, drift, and selection until eventually their genes are no longer compatible for successful reproduction.

An example of speciation based on a 2008 DNA and protein analysis. Note how butterflies, moths, sawflies, wasps, ants, bees, caddisflies, fleas, scorpionflies, snow scorpionflies (not the same but related!), and true flies all have a common ancestor but through the process of millions of years a wide assortment of different species evolved.

Spatial evolution
Working alongside with natural selection (death and survival pressure), spatial evolution is caused by individuals with random variation that are selected nonrandomly by how fast they travel away from home populations. The faster the individuals, the faster the individual she or he mates with, leading to fast offspring. This is both behavioral and morphological. The individuals 'race' their way to become a distinct species. Examples of Spatial evolution are new. For example, Australian researchers have detailed a new mechanism of evolution that is not based on natural selection but rather on how populations of organisms, such as cane toads, move around.

Evidence for evolution


Common descent explains the many shared features (homologies) of the majority of the organisms on the planet. There is an enormous amount of evidence that suggests all living organisms derived from a common ancestor long ago. For instance, all vertebrate embryos have the same body plan and look very similar in early development. We have the genetic code, which is all but identical in every known organism, from bacteria to humans. We have the shared presence of in similar species. All simians, including us humans, have an inactive gene, L-gulonolactone oxidase, which was originally used to synthesize Vitamin C. Then, we have the evidence for convergence, which explains relationships for all species, from fungal slime you find in shower stalls to sequoia. The tree of life between simple anatomical similarities is strikingly similar to a tree constructed from genetic molecular similarities. Then, there are others, including cool stuff like chromosome fusion, retroviruses, Hox genes, and deep homology, oh my.

Considering all of this, evolution has the intricacy and the reality of quantum mechanics. But you don't see unqualified people running around and decrying quantum mechanics, do you? Well actually you do, but opposition to quantum mechanics is widely considered fringe kookery, while opposition to evolution is treated by many people as a reasonable position.

So yes, in other words, evolution is a theory.

Non-biological evolution
Researchers can also apply evolutionary concepts to non-biological processes, such as (for example) universe-formation, evolutionary algorithms in computer science, and the development of languages. The study of etymology is one component of analyzing how languages have evolved - linguistic evolution parallels biological evolution (for example) in the way a single language may diverge over time into two different languages when two populations that speak the same language become geographically isolated.

Another example of non-biological evolution is the evolution of technology and innovation, which, while being (mostly) intelligently-designed, is (mostly) not random, and tends to develop on the basis of existing tools and concepts. James Burke studied, authored books, and hosted television programmes on the evolution of technology through a historical context.

Researchers have devised models of cultural evolution (such as memetics) and applied them over the years with varying degrees of success. Evolutionary psychology studies some of the fall-out from the biological evolution of human brains.

Somewhat confusingly, some sciences use the word "evolution" in a way that has no relation to the biological concept whatsoever. When an astronomer speaks of "stellar evolution", (s)he is talking about the changes that happen to a star over very long periods of time, as it progresses from gas cloud to protostar to main-sequence star to post-main-sequence (super)giant to stellar remnant. When a cosmologist speaks of "cosmic evolution", (s)he is talking about the changes in the size/shape/nature of the Universe over time, sometimes on very long time-scales, and sometimes at very brief time-scales (such as fractions of a second after the Big Bang). Neither of these uses of the word "evolution" has anything to do with populations, heritable traits, selection criteria, descent, or any of the other hallmarks of "evolution" as the term is used in biology.

Creationists consequently confuse the biological and non-biological meanings of the word "evolution": they claim that the Theory of Evolution - catchily mis-summarized as "molecules-to-man" - includes the origin of the universe and the origin of life. The biological theory of evolution as proposed by Darwin and others has nothing to say about either the origin of the universe or the origin of life on Earth, though some biologists have extended the theory to the very beginning of life.

Broad anti-evolution arguments
We can allow satellites, planets, suns, [the] universe, nay whole systems of universes, to be governed by laws, but the smallest insect, we wish to be created at once by special act. There are a number of broad arguments creationists/anti-evolutionists make. Specific claims are examined at our common descent page. They're mostly arguments born of a lack of understanding what evolution by mutation and natural selection actually is, though they're rarely advanced by more savvy creationists as direct misrepresentations and distortions of the theory of evolution.

Appeal to improbability
Often creationists ask how likely it is that all this complex life could have come about by random chance. They suggest that since individual events, such as the abiogenetic formation of proteins, emergence of RNA, organization of unicellular into multicellular organisms, etc., are purportedly so highly improbable that the entire chain events culminating in the existence of even a single complex organism could not have happened as described. Therefore, God did it. As creationism is largely a program of negative apologetics (e.g. an attempt to show a claim that is viewed as contrary to Christian faith is internally inconsistent or irrational according to the Christian perspective), arguments such as this are in essence arguments from incredulity with the proponent denying a fact (in this case the statistical probability that such and such essential event will have occurred) in order to draw the unsupported conclusion that some other cause (the Christian God) was at work.

The implied argument that a god or "designer" was at work is itself fraught with more untenable problems. Putting aside that the illusion of design is itself problematic, and assuming for the sake of argument that "design" is even identifiable in biological systems, if "random chance" is inadequate to account for some outcome, one is simply making unsupported assertions to contend that it is more probable that a designer was at work. If the causes are "designers" about which nothing is known, if they are capable of doing anything, if it is not known how or why they act, if it is not known when they acted (or will act), or if it is not known what they did (or did not, or could, or would), the causes are not enough to account for the results. If so, "design" in this sense is indistinguishable from random chance.

Nonetheless, evolution by natural selection isn't a random process. While genetic mutations may appear randomly, the natural selection of specific traits to produce a statistically significant allele (gene variation) frequency in a discrete population of organisms is highly deterministic. If a gene aids survival with respect to any particular environmental stressor, then it is selected by means of the survival and reproduction of the individuals carrying that gene and perpetuates in the population of organisms. If the trait is detrimental to survival, it will leave organisms vulnerable to a particular environmental stressor and through attrition lower the frequency of the allele(s) contributing to that trait in the subject population.

Microevolution and macroevolution


Many creationists hold erroneous beliefs about evolution such as that which is expressed by the statement "I accept microevolution, but not macroevolution." (This is the position of YEC nincompoop Kent Hovind.) Microevolution is supposed to be evolution that doesn't result in a new species, and macroevolution is supposed to be evolution that does lead to a new species. This argument is akin to someone saying that while one believes that wind can sometimes erode rock, one doesn't believe it can change the rock's shape. Micro- and macroevolution describe the same process, but with a difference in operational time. If one accepts microevolution, they must also accept macroevolution, since the former inevitably leads to the latter if given a long enough time period and the separation of breeding isolates. One simply cannot (logically) accept one and not the other. In biology, macroevolution is a broad subject of which speciation is only one part. This argument against speciation may be an attempt by creationists to reserve the power to produce a species for God alone.

Some creationists have abandoned the attempt to deny that new species can appear (and disappear) by natural means, in favor of drawing a barrier, not between species, but between baramins (also known as "kinds"), some sort of collection larger than species. To date, there has not been given any indication of just what sort of a thing a baramin is, what is the nature of the barrier between baramins, or how one might detect the barrier (or suspect its non-existence) in any particular case, other than the uninformative "baramins are those things that present a barrier to evolution."

Irreducible complexity
Irreducible complexity is a fancy name for the "watchmaker" argument. In a nutshell, irreducible complexity describes an organ (or other facet of a living thing) which the ideology's supporters claim could not have evolved in small gradual steps. It is claimed to be so complex that it cannot be reduced into other parts. In fact, every example of irreducible complexity Behe and others have come up with has been shown to not be irreducibly complex (for example, the incremental stages towards the "irreducibly complex" human eye that are found in the sight organs of other living organisms).

Falsifiability
For any theory to be accepted as scientific it must be falsifiable. In other words, it must be capable of making statements which could theoretically be disproven. Evolution's opponents claim that the theory of evolution does not have this property, although this claim can be easily rejected. Theoretically, evolution could be falsified if scientists discovered an organism so complex and unique, with absolutely no explainable path as to how it could have evolved. Such an organism has not been found. Similarly—and ironically—there are the demands made by some creationists that they be shown, say, a dog giving birth to a cat before they'll accept evolution. Such an event, if it occurred, would falsify (or at least strongly challenge) evolution, since speciation doesn't happen in a single generation and modern animals don't evolve into other modern animals.

It's only a theory
Sometimes the phrase "evolution is only a theory" will be heard. This phrase rests on the common use of "theory" to mean what scientists call a "hypothesis," i.e., is something that is possible but not proven. Science, however, uses "theory" in a much different sense, namely as  a testable model of the manner of interaction of a set of natural phenomena, capable of predicting future occurrences or observations of the same kind, and capable of being tested through experiment or observation. This sets it at a significantly higher level of reasoning than "wild and unproven guess," which is what is implied when this argument is mentioned. Also unlike "wild guesses", scientific theory is among the best explanations for phenomena, and scientists who successfully create new theories will often be famous. As Sheldon Cooper once said, "Evolution isn't an opinion, it's fact." Note that creationists don't say that gravity is "only a theory." And if anyone says you can't directly observe evolution, send them to Professor Lenski.

Evolution is both a theory and a fact
Strictly speaking, evolution is something that happens in the world of life, and should be distinguished from a theory of evolution, which is (according to the above definition) a model of how evolution occurs. Thus evolution bears the same relationship with a theory of evolution as flight with a theory of flight, or sound with a theory of sound, or planetary motion with a theory of planetary motion. This is often expressed in the saying that "Evolution is both a theory and a fact", that is to say, the word "evolution" can refer not only to the process (the "something that happens"), but also to a fact that it is observed under such-and-such circumstances, and to a theory that is involved with the process ("how it happens", "what the consequences are of it happening").

Lack of scientific consensus
One creationist claim is that there is a lack of support for evolution among scientists. This claim has for example been articulated, "Interestingly, ever since Charles Darwin's book The Origin of Species was published in 1859, various aspects of the theory have been a matter of considerable disagreement even among top evolutionary scientists." To counter this claim one need only note that scientists' disagreements are about details over the way that evolution functions - and not about the historical fact of it.

Incompatibility with the Second Law of Thermodynamics
One counter-argument is that evolution is incompatible with the Second Law of Thermodynamics, which derives from an inaccurate, oversimplified statement of this law: "everything in the world becomes more disordered over time," and that evolution would involve an increase in order over time as species evolve. However, the precise statements given by Kelvin and Clausius consider isolated, closed systems in which neither energy nor matter are transferred in or out — the Earth is far from an isolated system as energy is radiated into the Earth system from the Sun, and the only true closed system in the universe is the universe.

Furthermore, the word "disorder" is used incorrectly as an analogy to the more difficult-to-understand concept of entropy, and misinterpreted to imply that "order" is equivalent to intricacy of species on Earth, making this a weak argument from analogy. Entropy, simply put, is how far a system is from equilibrium. For example the Sun is far from equilibrium with its surroundings, but as the Sun ages and more fuel is burned, the energy is radiated from the small volume (the Sun) to a large volume (the Solar System), bringing the Sun closer to equilibrium with its surroundings. The Second Law of Thermodynamics therefore holds true for the Earth-Sun system, and evolution of species on Earth is of no relevance to the universe obeying the Second Law of Thermodynamics.

Because the Second Law of Thermodynamics is based upon statistical physics, the universe does not even need to obey the Second Law of Thermodynamics, and therefore evolution would not need to obey or disobey the Second Law of Thermodynamics. The Second Law of Thermodynamics is an empirical law based on observations by scientists. The universe could, hypothetically, momentarily arrange itself in a state of slightly lower entropy than previously; however, the statistical chances of the universe doing this are, for all intents and purposes, nil. By analogy, shuffling a deck of cards and getting them in order or throwing a broken plate on the floor and returning it to pristine condition are both plausible, but the chances are so small as to be approximately zero.

Where entropy, understood correctly as randomness, comes in is in the origin of mutations. Mutations are indeed random, they cause random phenotypic impairments, and in this sense they increase entropy. They create "genetic garbage" that needs to be removed, and natural selection is the garbage man. In other words, people who carry too many mutations have to get sick and disabled enough to reduce their reproduction, so that population-level entropy can remain comfortably low. Evolutionary geneticists call this mutation-selection balance. Favourable mutations that can be positively selected are very rare, although they are the kind that in the aggregate can turn an ape into a human. Evolution by natural selection is not contradicted by the second law of thermodynamics, but it is the explanation why we can exist despite it.

What Evolution is not
Unfortunately, "evolution" is sometimes understood to encompass the whole of science and even ethics - and this tends to be a misunderstanding common among different types of creationists.

It should be clearly understood that evolution does not explain, makes no attempt to explain and is not designed to explain:


 * The origin of the universe. This lies under the domain of physics (specially cosmology), not biology. Nevertheless scientists are working on various models of Big Bang cosmology which attempt to explain the earliest moments of the universe.


 * The origin of life. While it is true that evolution accepts that all of life on Earth is based on a common ancestor, it does not explain how life arose in the first place. Studies into the the origin of life are called abiogenesis


 * Morality. The science of evolution makes no ethical claims.

Evolution explains the diversity of life in an existing universe and in which life exists - nothing more.

Evolution simulations
Many simulations of evolution (of digital creatures) towards some goal exist. Some of the best are documented here:

Cary Huang's "Evolution Simulator"
In which creatures made of nodes and muscles frantically try to run to the right. Code publicly available; run it online!

BoxCar2D
In which randomly generated octagons with wheels frantically try to drive to the right. Run it online! Code not publicly available; explanation available.

Clock Evolution
Or, "Evolution IS a Blind Watchmaker". Watch a bunch of gears, ratchets, clock hands, and springs frantically try to accurately tell time, and simultaneously disprove the watchmaker analogy. Code publicly available.

Pattern of disks evolves into to Mona Lisa in ~1 million generations
A computer-generated pattern made of disks, randomly mutated, with selective-breeding from patterns which best fit the Mona Lisa painting.

Historical writings

 * Contributions to the theory of natural selection. A series of essays by Alfred Russel Wallace
 * Darwinism (1889) by Alfred Russel Wallace
 * The Decent of Man by Charles Darwin
 * On the Origin of Species By Means of Natural Selection by Charles Darwin

Other sources

 * Wile, Jay L. Exploring Creation With General Science. Anderson: Apologia Educational Ministries, Inc. 2000