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Punctuated equilibrium. A common misconception about evolution is that the development of new species generally requires millions of years. Indeed, the gradualist view that speciation involved a slow, steady, progressive transformation of an ancestral population into a new species has dominated much of evolutionary thought from the time of Darwin. Such a transformation was commonly viewed as involving large numbers of individuals ("usually the entire ancestral population"), being "even and slow," and occurring "over all or a large part of the ancestral species' geographic range" (Eldredge & Gould 1972). This concept was applied to the development of a new species by either phyletic evolution (where the descendant species arises by the transformation of the entire ancestral population) or by speciation (where the descendant species branches off from the ancestral population).

However, paleontologists now recognize that the fossil record does not generally yield the expected sequence of slightly altered intermediary forms, but instead the sudden appearance of species, and long periods when species do not change much.

The theory of punctuated equilibrium ascribes that the fossil record accurately reflects evolutionary change. That is, it posits that macroevolutionary patterns of species are typically ones of morphological stability during their existence (stasis), and that most evolutionary change is concentrated in events of speciation-with the origin of a new species usually occurring during geologically short periods of time when the long-term stasis of a population is punctuated by this rare and rapid speciation event. The sudden transitions between species are sometimes measured on the order of hundreds or thousands of years relative to their millions of years of existence. Although the theory of punctuated equilibrium originally generated a lot of controversy, it is now viewed highly favorably in the scientific community, and has even become a part of recent textbook orthodoxy.

Note that the theory of punctuated equilibrium merely addresses the pattern of evolution and is not tied to any one mode of speciation. Although occurring in a brief period of time, the species formation can go through all the stages, or can proceed by leaps. It is even neutral with respect to natural selection.

Punctuated origin of new designs. According to the gradualist viewpoint, the origin of novel features, such as feathers in birds and jaws in fish, can be explained as having arisen from numerous, tiny, imperceptible steps, with each step being advantageous and developed by natural selection. Darwin's proposed such a resolution for the origin of the vertebrate eye.

However, there are some structures for which it is difficult to conceive how such structures could be useful in incipient stages, and thus have selective advantage. One way in which evolutionary theory has dealt with such criticisms is the concept of "preadaptation," proposing that the intermediate stage may perform useful functions different from the final stage. Incipient feathers may have been used for retaining body warmth or catching insects, for example, prior to the development of a fully functional wing.

Another solution for origin of new designs, which is gaining renewed attention among evolutionists, is that the full sequence of intermediate forms may not have existed at all, and instead key features may have developed by rapid transitions, discontinuously. This view of a punctuational origin of key features arose because of: (1) the persistent problem of the lack of fossil evidence for intermediate stages between major designs, with transitions between major groups being characteristically abrupt; and (2) the inability to conceive of functional intermediates in select cases. In the later case, prominent evolutionist Stephen Jay Gould (1980b) cites the fur-lined pouches of pocket gophers and the maxillary bone of the upper jaw of certain genera of boid snakes being split into front and rear halves: "How can a jawbone be half broken?… What good is an incipient groove or furrow on the outside? Did such hypothetical ancestors run about three-legged while holding a few scraps of food in an imperfect crease with their fourth leg?"

The concept of punctuational origin is not necessarily opposed to natural selection as the creative force. For example, the rapid transition could be the product of a very small genetic change, even one mutation occurring by chance in a key gene, which is then acted upon by natural selection. However, the concept of a punctuational origin of new designs (as with punctuational equilibrium), is also viewed favorably by those advocating divine creation, due to the alignment of this view with the concept of discontinuous variation being the product of divine input, with natural selection simply the weeding out of previous, less well-adapted forms.

Punctuational models of speciation. Punctuational models of speciation are being advanced in contrast with what is sometimes labeled the "allopatric orthodoxy" (Gould 1980a; Gould and Eldredge 1977). Allopatric orthodoxy is a process of species origin involving geographic isolation, whereby a population completely separates geographically from a large parental population and develops gradually into a new species by natural selection until their differences are so great that reproductive isolation ensues. Reproductive isolation is therefore a secondary byproduct of geographic isolation, with the process involving gradual allelic substitution. Contrasted with this view are recent punctuational models for speciation, which postulate that reproductive isolation can rise rapidly, not through gradual selection, but without selective significance. In such models, reproductive isolation originates before adaptive, phenotypic differences are acquired. Selection does not play a creative role in initiating speciation, nor in the definitive aspect of reproductive isolation, although it is usually postulated as the important factor in building subsequent adaptation. One example of this is polyploidy, where there is a multiplication of the number of chromosomes beyond the normal diploid number. Another model is chromosomal speciation, involving large changes in chromosomes due to various genetic accidents.

Darwinism and Neo-Darwinism

Main articles: Darwinism and Neo-Darwinism

Darwinism is a term generally synonymous with the theory of natural selection. Harvard evolutionist Stephen Jay Gould (1982) maintains: "Although 'Darwinism' has often been equated with evolution itself in popular literature, the term should be restricted to the body of thought allied with Darwin's own theory of mechanism natural selection.” Although the term has been used in various ways depending on who is using it and the time period (Mayr 1991), Gould nonetheless finds a general agreement in the scientific community that "Darwinism should be restricted to the world view encompassed by the theory of natural selection itself."

The term neo-Darwinism is a very different concept. It is considered synonymous with the term "modern synthesis" or "modern evolutionary synthesis." The modern synthesis is the most significant, overall development in evolutionary thought since the time of Darwin, and is the prevailing paradigm of evolutionary biology. The modern synthesis melded the two major theories of classical Darwinism (theory of descent with modification and the theory of natural selection) with the rediscovered Mendelian genetics, recasting Darwin's ideas in terms of changes in allele frequency.

In essence, advances in genetics pioneered by Gregor Mendel led to a sophisticated concept of the basis of variation and the mechanisms of inheritance. Gregor Mendel proposed a gene-based theory of inheritance, describing the elements responsible for heritable traits as the fundamental units now called genes and laying out a mathematical framework for the segregation and inheritance of variants of a gene, which are now referred to as alleles. Later research identified the molecule DNA as the genetic material through which traits are passed from parent to offspring, and identified genes as discrete elements within DNA. Though largely maintained within organisms, DNA is both variable across individuals and subject to a process of change or mutation.

According to the modern synthesis, the ultimate source of all genetic variation is mutations. They are permanent, transmissible changes to the genetic material (usually DNA or RNA) of a cell, and can be caused by "copying errors" in the genetic material during cell division and by exposure to radiation, chemicals, or viruses.

In addition to passing genetic material from parent to offspring, nearly all organisms employ sexual reproduction to exchange genetic material. This, combined with meiotic recombination, allows genetic variation to be propagated through an interbreeding population.

According to the modern synthesis, natural selection acts on the genes, through their expression (phenotypes). 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 that 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.

Through the process of natural selection, species become better adapted to their environments. Note that, whereas mutations (and genetic drift) are random, natural selection is not, as it preferentially selects for different mutations based on differential fitness.

In recent years, there have been many challenges to the modern synthesis, to the point where Bowler (1988), a historian of evolutionary thought, states; "In the last decade or so it has become obvious that there is no longer a universal consensus in favor of the synthetic theory even within the ranks of working biologists." Gould (1980a) likewise notes "that theory, as a general proposition is effectively dead." These challenges include models of punctuational change, the theory of “neutralism,” and selection at levels above the individual. What some historians and philosophers of evolutionary thought see as challenges to the modern synthesis, others see as either erroneous theories or as theories that can be included within the umbrella of the modern synthesis.

Evidences of evolution

Main article: Evidence of evolution

For the broad concept of evolution ("any heritable change in a population of organisms over time"), evidences of evolution are readily apparent. Evidences include observed changes in domestic crops (creating a variety of corn with greater resistance to disease), bacterial strains (development of strains with resistance to antibiotics), laboratory animals (structural changes in fruit flies), and flora and fauna in the wild (color change in particular populations of peppered moths and polyploidy in plants).

Generally, however, the "evidences of evolution" being presented by scientists or textbook authors are for either (1) the theory of descent with modification; or (2) a comprehensive concept including both the theory of descent with modification and the theory of natural selection. In actuality, most of these evidences that have been catalogued are for the theory of descent with modification.

Evidences for the Theory of Descent with Modification

In the Origin of Species, Darwin marshaled many evidences for the theory of descent with modification, within such areas as paleontology, biogeography, morphology, and embryology. Many of these areas continue to provide the most convincing proofs of descent with modification even today (Mayr 1982; Mayr 2001). Supplementing these areas, are molecular evidences.

It is noteworthy that some of the best support for the theory of descent with modification comes from the observation of imperfections of nature, rather than perfect adaptations. As noted by Gould (1983):

All of the classical arguments for evolution are fundamentally arguments for imperfections that reflect history. They fit the pattern of observing that the leg of Reptile B is not the best for walking, because it evolved from Fish A. In other words, why would a rat run, a bat fly, a porpoise swim and a man type all with the same structures utilizing the same bones unless inherited from a common ancestor?

Fossil record

Fossil evidence of prehistoric organisms has been found all over the Earth. Fossils are traces of once living organisms. Fossilization on an organism is an uncommon occurrence, usually requiring hard parts (like bone) and death where sediments or volcanic ash may be deposited. Fossil evidence of organisms without hard body parts, such as shell, bone, teeth, and wood stems, is sparse, but exists in the form of ancient microfossils and the fossilization of ancient burrows and a few soft-bodied organisms. Some insects have been preserved in resin. The age of fossils can often be deduced from the geologic context in which they are found (the strata); and their age also can be determined with radiometric dating.

The comparison of fossils of extinct organisms in older geological strata with fossils found in more recent strata or with living organisms is considered strong evidence of descent with modification. Fossils found in more recent strata are often very similar to, or indistinguishable from living species, whereas the older the fossils the more different they are from living organisms or recent fossils. In addition, fossil evidence reveals that species of greater complexity have appeared on the earth over time, beginning in the Precambrian era some 600 millions of years ago with the first eukaryotes. The fossil records support the view that there is orderly progression in which each stage emerges from, or builds upon, preceding stages.

One of the problems with fossil evidence is the general lack of gradually sequenced intermediary forms. There are some fossil lineages that appear quite well-represented, such as from therapsid reptiles to the mammals, and between what is considered land-living ancestors of the whales and their ocean-living descendants. The transition from an ancestral horse (Eohippus) and the modern horse (Equus) is also significant, and Archaeopteryx has been postulated as fitting the gap between reptiles and birds. But generally, paleontologists do not find a steady change from ancestral forms to descendant forms, but rather discontinuities, or gaps in most every phyletic series. This has been explained both by the incompleteness of the fossil record and by proposals of speciation that involve short periods of time, rather than millions of years. (Notably, there are also gaps between living organisms, with a lack of intermediaries between whales and terrestrial mammals, between reptiles and birds, and between flowering plants and their closest relatives.) Archaeopteryx has recently come under criticism as a transitional fossil between reptiles and birds (Wells 2000).

The fact that the fossil evidence supports the view that species tend to remain stable throughout their existence and that new species appear suddenly is not problematic for the theory of descent with modification, but only with Darwin's concept of gradualism.

Morphological evidence

The study of comparative anatomy also yields evidence for the theory of descent with modification. For one, there are structures in diverse species that have similar internal organization yet perform different functions. Vertebrate limbs are a common example of such homologous structures. Bat wings, for example, are very similar to human hands. Also similar are the forelimbs of the penguin, the porpoise, the rat, and the alligator. In addition, these features derive from the same structures in the embryo stage. As queried earlier, “why would a rat run, a bat fly, a porpoise swim and a man type” all with limbs using the same bone structure if not coming from a common ancestor, since these are surely not the most ideal structures for each use (Gould 1983).

Likewise, a structure may exist with little or no purpose in one organism, yet the same structure has a clear purpose in other species. These features are called vestigial organs or vestigial characters. The human wisdom teeth and appendix are common examples. Likewise, some snakes have pelvic bones and limb bones, and some blind salamanders and blind cave fish have eyes. Such features would be the prediction of the theory of descent with modification, suggesting that they share a common ancestry with organisms that have the same structure, but which is functional.

For the point of view of classification, it can be observed that various species exhibit a sense of "relatedness," such as various catlike mammals can be put in the same family (Felidae), dog-like mammals in the same family (Canidae), and bears in the same family (Ursidae), and so forth, and then these and other similar mammals can be combined into the same order (Carnivora). This sense of relatedness, from external features, fits the expectations of the theory of descent with modification.

Phylogeny, the study of the ancestry (pattern and history) of organisms, yields a phylogenetic tree to show such relatedness (or a cladogram in other taxonomic disciplines).

Embryology

A common evidence for evolution is the assertion that the embryos of related animals are often quite similar to each other, often much more similar than the adult forms. For example, it is held that the development of the human embryo is compatible to comparable stages of other kinds of vertebrates (fish, salamander, tortoise, chicken, pig, cow, and rabbit). Furthermore, mammals such as cows and rabbits are more similar in embryological development than with alligators. Often, the drawings of early vertebrate embryos by Ernst Haeckel are offered as proof.

It has further been asserted that features, such as the gill pouches in the mammalian embryo resemble those of fish, are most readily explained as being remnants from the ancestral fish, which were not eliminated because they are embryonic "organizers" for the next step of development.

Wells (2000) has criticized embryological evidence on several points. For one, it is now known that Ernst Haeckel exaggerated the similarities of vertebrate embryos at the midpoint of embryological development, and omitted the earlier embryological stages when differences were more pronounced. Also, embryological development in some frog species looks very similar to that of birds, rather than other frog species. Remarkably, even as revered an evolutionist as Ernst Mayr, in his 2001 text What Evolution Is, used Haeckel drawings from 1870, which he knew were faked, noting "Haeckel (sp.) had fraudulently substituted dog embryos for the human ones, but they were so similar to humans that these (if available) would have made the same point."

Biogeography

The geographic distribution of plants and animals offers another commonly cited evidence for evolution (common descent). The fauna on Australia, with its large marsupials, is very different from that of the other continents. The fauna on Africa and South America are very different, but the fauna of Europe and North America, which were connected more recently, are similar. There are few mammals on oceanic islands. These findings support the theory of descent with modification, which holds that the present distribution of flora and fauna would be related to their common origins and subsequent distribution. The longer the separation of continents, such as with Australia's long isolation, the greater the expected divergence is.

Renowned evolutionist Mayr (1982) contends that "the facts of biogeography posed some of the most insoluble dilemmas for the creationists and were eventually used by Darwin as his most convincing evidence in favor of evolution."

Molecular evidence

Evidence for common descent may be found in traits shared between all living organisms. In Darwin's day, the evidence of shared traits was based solely on visible observation of morphologic similarities, such as the fact that all birds-even those which do not fly-have wings. Today, the theory of common descent is supported by genetic similarities. For example, every living cell makes use of nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for proteins. All organisms use the same genetic code (with some extremely rare and minor deviations) to translate nucleic acid sequences into proteins. The universality of these traits strongly suggests common ancestry, because the selection of these traits seems somewhat arbitrary.

Similarly, the metabolism of very different organisms is based on the same biochemistry. For example, the protein cytochrome c, which is needed for aerobic respiration, is universally shared in aerobic organisms, suggesting a common ancestor that used this protein. There are also variations in the amino acid sequence of cytochrome c, with the more similar molecules found in organisms that appear more related (monkeys and cattle) than between those that seem less related (monkeys and fish). The cytochrome c of chimpanzees is the same as that of humans, but very different from bread mold. Similar results have been found with blood proteins.

Other uniformity is seen in the universality of mitosis in all cellular organisms, the similarity of meiosis in all sexually reproducing organisms, the use of ATP by all organisms for energy transfer, and the fact that almost all plants use the same chlorophyll molecule for photosynthesis.

The closer that organisms appear to be related, the more similar are their respective genetic sequences. That is, comparison of the genetic sequence of organisms reveals that phylogenetically close organisms have a higher degree of sequence similarity than organisms that are phylogenetically distant. For example, neutral human DNA sequences are approximately 1.2 percent divergent (based on substitutions) from those of their nearest genetic relative, the chimpanzee, 1.6 percent from gorillas, and 6.6 percent from baboons. Sequence comparison is considered a measure robust enough to be used to correct erroneous assumptions in the phylogenetic tree in instances where other evidence is scarce.

Comparative studies also show that some basic genes of higher organisms are shared with homologous genes in bacteria.

Evidences for the Theory of Natural Selection

Concrete evidence for the theory of modification by natural selection is limited to the microevolutionary level-that is, events and processes at or below the level of species. As examples of such evidences, plant and animal breeders use artificial selection to produce different varieties of plants and strains of fish. Natural selection is seen in the changes of the shade of gray of populations of peppered moths (Biston betularia) observed in England.

Another example 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 nineteenth century sometime 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 to 6 percent hybridization rate) suggests this possibility (see Berlocher and Bush 1982; Berlocher and Feder 2002; Bush 1969; McPheron, Smith, and Berlocher 1988; Prokopy, Diehl, and Cooley 1988; Smith 1988).

The evidence that natural selection directs the major transitions between species and originates new designs (macroevolution) involves extrapolation from these evidences on the microevolutionary level. That is, it is inferred that if moths can change their color in 50 years, then new designs or entire new genera can originate over millions of years. If geneticists see population changes for fruit flies in laboratory bottles, then given eons of time, birds can be built from reptiles and fish with jaws from jawless ancestors.

However, at question has always been the sufficiency of extrapolation to the macroevolutionary level. As Mayr (2001) notes, "from Darwin's day to the present, there has been a heated controversy over whether macroevolution is nothing but an unbroken continuation of microevolution, as Darwin and his followers have claimed, or rather is disconnected from microevolution."

Teaching of evidences

Textbook authors have often confused the dialogue on evolution by treating the term as if it signified one unified whole-not only descent with modification, but also the specific Darwinian and neo-Darwinian theories regarding natural selection, gradualism, speciation, and so forth. Certain textbook authors, in particular, have exacerbated this terminological confusion by lumping "evidences of evolution" into a section placed immediately after a comprehensive presentation on Darwin's overall theory-thereby creating the misleading impression that the evidences are supporting all components of Darwin's theory, including natural selection (Swarts et al. 1994). In reality, the confirming information is invariably limited to the phenomenon of evolution having occurred (descent from a common ancestor or change of gene frequencies in populations), or perhaps including evidence of natural selection within populations.

Evolution as "fact" and "theory"

"Evolution" has been referred to both as a "fact" and as a "theory."

In scientific terminology, a theory is a model of the world (or some portion of it) from which falsifiable hypotheses can be generated and tested through controlled experiments, or be verified through empirical observation. "Facts" are parts of the world, or claims about the world, that are real or true regardless of what people think. Facts, as data or things that are done or exist, are parts of theories-they are things, or relationships between things, that theories take for granted in order to make predictions, or that theories predict. For example, it is a "fact" that an apple dropped on earth will fall towards the center of the planet in a straight line, and the "theory" that explains it is the current theory of gravitation.

In common usage, people use the word "theory" to signify "conjecture," "speculation," or "opinion." In this popular sense, "theories" are opposed to "facts." Thus, it is not uncommon for those opposed to evolution to state that it is just a theory, not a fact, implying that it is mere speculation. But for scientists, "theory" and "fact" do not stand in opposition, but rather exist in a reciprocal relationship.

Scientists sometimes refer to evolution as both a "fact" and a "theory."

In the broader usage of the term, calling evolution a "fact" references the confidence that scientists have that populations of organisms can change over time. In this sense, evolution occurs whenever a new strain of bacterium evolves that is resistant to antibodies that had been lethal to prior strains. Many evolutionists also call evolution a "fact" when they are referring to the theory of descent with modification, because of the substantial evidences that they perceive as having been marshaled for this theory. In this later sense, Mayr (2001) opines: "It is now actually misleading to refer to evolution as a theory, considering the massive evidence that has been discovered over the past 140 years documenting its existence. Evolution is no longer a theory, it is simply a fact."

When "evolution" is referred to as a theory by evolutionists, the reference is generally to an explanation for why and how evolution occurs (such as a theory of speciation or the theory of natural selection).

Modern alternative mechanisms and views

Symbiogenesis

Symbiogenesis is evolutionary change initiated by a long-term symbiosis of dissimilar organisms. Margulis and Sagan (2002) hold that random mutation is greatly overemphasized as the source of hereditary variation in standard Neo-Darwinistic doctrine. Rather, they maintain, the major source of transmitted variation actually comes from the acquisition of genomes-in other words, entire sets of genes, in the form of whole organisms, are acquired and incorporated by other organisms. This long-term biological fusion of organisms, beginning as symbiosis, is held to be the agent of species evolution.

For example, lichens are a composite organism composed of a fungus and a photosynthetic partner (usually either green algae or cyanobacteria, but in some cases yellow-green algae, brown algae, or both green algae and cyanobacteria). These intertwined organisms act as a unit that is distinct from its component parts. Lichens are considered to have arisen by symbiogenesis, involving acquisitions of cyanobacterial or algal genomes.

Another example is the photosynthetic animals or plant-animal hybrids in the form of slugs (shell-less mollusks) that have green algae in their tissues (such as Elysia viridis). These slugs are always green, never need to eat throughout their adult life, and are "permanently and discontinuously different from their gray, algae-eating ancestors" (Margulis and Sagan 2002). This is held to be another example of a symbiosis that lead to symbiogenesis.

Yet another example is cattle, which are able to digest cellulose in grass because of microbial symbionts in their rumen. Cattle cannot survive without such an association. Other examples of evolution resulting through merger of dissimilar organisms include associations of modern (scleractinian) coral and dinomastigotes (such as Gymnodinium microadriaticum) and the formation of new species and genera of flowering plants when when the leaves of these plants integrated a bacterial genome.

The formation of eukaryotes is postulated to have occurred through a symbiotic relationship between prokaryotes, a theory called endosymbiosis. According to this theory, mitochondria, chloroplasts, flagella, and even the cell nucleus would have arisen from prokaryote bacteria that gave up their independence for the protective and nutritive environment within a host organism.

Margulis and Sagan (2002) state that the formation of new species by inheritance of acquired microbes is best documented in protists. They conclude that "details abound that support the concept that all visible organisms, plants, animals, and fungi evolved by "body fusion."

More complex tree of life

The conventional paradigm of the theory of descent with modification presumes that the history of life maps as the "tree of life," a tree beginning with the trunk as one universal common ancestor and then progressively branching, with modern species at the twig ends. However, that clean and simple pattern is being called into question due to discoveries being made by sequencing genomes of specific organisms. Instead of being simple at its base, the tree of life is looking considerably more complex. At the level of single cells, before the emergence of multicellular organisms, the genomic signs point not to a single line of development, but rather to a bush or a network as diverse microbes at times exchange their genetic material, especially through the process of lateral gene transfer.

Other complicating factors are proposed based on the relatively sudden appearance of phyla during the Cambrian explosion and on evidence that animals may have originated more than once and in different places at different times (Whittington 19

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