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Thursday, February 19, 2015

Recapitulation theory


From Wikipedia, the free encyclopedia

The theory of recapitulation, also called the biogenetic law or embryological parallelism— often expressed in Ernst Haeckel's phrase "ontogeny recapitulates phylogeny"—is a largely discredited biological hypothesis that in developing from embryo to adult, animals go through stages resembling or representing successive stages in the evolution of their remote ancestors. While examples of embryonic stages show that molecular features of ancestral organisms exist, the theory of recapitulation itself has been viewed within the field of developmental biology as a historical side-note rather than as dogma.[1][2][3]

With different formulations, such ideas have been applied and extended to several fields and areas, including the origin of language, religion, biology, cognition and mental activities,[4] anthropology,[5] education theory[6] and developmental psychology.[7] Recapitulation theory is still considered plausible and is applied by some researchers in fields such as the study of the origin of language,[8] cognitive development,[9] behavioral development in animal species.[10]

Origins

The earliest recorded trace of a recapitulation theory is from the Egyptian Pharaoh Psamtik I (664 – 610 BCE), who used it as a hypothesis on the origin of language.[11][12] The concept of recapitulation was first formulated outside the field of biology. It was widely held among traditional theories of the origin of language (glottology), being assumed as a premise that children's use of language gives insights on its origin and evolution.[13]

The idea was reprised in 1720 by Giambattista Vico in his influential Scienza Nuova.[13][14][15] It was first formulated in biology in the 1790s among the German Natural philosophers,[16] after which, Marcel Danesi states, it soon gained the status of a supposed biogenetic law.[13]

The first formal formulation was proposed by Étienne Serres in 1824–26 as what became known as the "Meckel-Serres Law", it attempted to provide a link between comparative embryology and a "pattern of unification" in the organic world. It was supported by Étienne Geoffroy Saint-Hilaire and became a prominent part of his ideas which suggested that past transformations of life could have had environmental causes working on the embryo, rather than on the adult as in Lamarckism. These naturalistic ideas led to disagreements with Georges Cuvier. It was widely supported in the Edinburgh and London schools of higher anatomy around 1830, notably by Robert Edmond Grant, but was opposed by Karl Ernst von Baer's ideas of divergence, and attacked by Richard Owen in the 1830s.[17]

Haeckel


George Romanes's 1892 copy of Ernst Haeckel's controversial embryo drawings (this version of the figure is often attributed incorrectly to Haeckel).[18]

Ernst Haeckel attempted to synthesize the ideas of Lamarckism and Goethe's Naturphilosophie with Charles Darwin's concepts. While often seen as rejecting Darwin's theory of branching evolution for a more linear Lamarckian "biogenic law" of progressive evolution, this is not accurate: Haeckel used the Lamarckian picture to describe the ontogenetic and phylogenetic history of individual species, but agreed with Darwin about the branching of all species from one, or a few, original ancestors.[19]

Since early in the twentieth century, Haeckel's "biogenetic law" has been refuted on many fronts.[3]

Haeckel formulated his theory as "Ontogeny recapitulates phylogeny". The notion later became simply known as the recapitulation theory. Ontogeny is the growth (size change) and development (shape change) of an individual organism; phylogeny is the evolutionary history of a species. Haeckel claimed that the development of advanced species passes through stages represented by adult organisms of more primitive species.[3] Otherwise put, each successive stage in the development of an individual represents one of the adult forms that appeared in its evolutionary history.

For example, Haeckel proposed that the pharyngeal grooves between the pharyngeal arches in the neck of the human embryo not only roughly resembled gill slits of fish, but directly represented an adult "fishlike" developmental stage, signifying a fishlike ancestor. Embryonic pharyngeal slits, which form in many animals when the thin branchial plates separating pharyngeal pouches and pharyngeal grooves perforate, open the pharynx to the outside. Pharyngeal arches appear in all tetrapod embryos: in mammals, the first pharyngeal arch develops into the lower jaw (Meckel's cartilage), the malleus and the stapes. But these embryonic pharyngeal arches, grooves, pouches, and slits in human embryos can not at any stage carry out the same function as the gills of an adult fish.

Haeckel produced several embryo drawings that often overemphasized similarities between embryos of related species. The misinformation was propagated through many biology textbooks, and popular knowledge, even today. Modern biology rejects the literal and universal form of Haeckel's theory.[20]

Haeckel's drawings were disputed by Wilhelm His, who had developed a rival theory of embryology.[21] His developed a "causal-mechanical theory" of human embryonic development.[22]

Darwin's view, that early embryonic stages are similar to the same embryonic stage of related species but not to the adult stages of these species, has been confirmed by modern evolutionary developmental biology[citation needed].

Modern status

The Haeckelian form of recapitulation theory is considered defunct.[23] However, embryos do undergo a period where their morphology is strongly shaped by their phylogenetic position, rather than selective pressures.[24]
"Embryos do reflect the course of evolution, but that course is far more intricate and quirky than Haeckel claimed. Different parts of the same embryo can even evolve in different directions. As a result, the Biogenetic Law was abandoned, and its fall freed scientists to appreciate the full range of embryonic changes that evolution can produce—an appreciation that has yielded spectacular results in recent years as scientists have discovered some of the specific genes that control development."[25]

Influence

Cognitive development

Although Haeckel's specific form of recapitulation theory is now discredited among biologists, the strong influence it had on social and educational theories of the late 19th century still resonates in the 21st century. Research in the late 20th century confirmed that "both biological evolution and the stages in the child’s cognitive development follow much the same progression of evolutionary stages as that suggested in the archaeological record."[9]

English philosopher Herbert Spencer was one of the most energetic promoters of evolutionary ideas to explain many phenomena. He compactly expressed the basis for a cultural recapitulation theory of education in the following claim, published in 1861, five years before Haeckel first published on the subject:[6] G. Stanley Hall used Haeckel's theories as the basis for his theories of child development.
If there be an order in which the human race has mastered its various kinds of knowledge, there will arise in every child an aptitude to acquire these kinds of knowledge in the same order.... Education is a repetition of civilization in little.[26]
— Herbert Spencer
Developmental psychologist Jean Piaget favored a weaker version of the formula, according to which ontogeny parallels phylogeny because the two are subject to similar external constraints.[27]

The Austrian pioneer in psychoanalysis, Sigmund Freud, also favored Haeckel's doctrine. He was trained as a biologist under the influence of recapitulation theory at the time of its domination, and retained a Lamarckian outlook with justification from the recapitulation theory.[28] He also distinguished between physical and mental recapitulation, in which the differences would become an essential argument for his theory of neuroses.[28]

Art criticism

More recently, several art historians, most prominently musicologist Richard Taruskin, have applied the term "ontogeny becomes phylogeny" to the process of creating and recasting art history, often to assert a perspective or argument. For example, the peculiar development of the works by modernist composer Arnold Schoenberg (here an "ontogeny") is generalized in many histories into a "phylogeny" – a historical development ("evolution") of Western Music toward atonal styles of which Schoenberg is a representative. Such historiographies of the "collapse of traditional tonality" are faulted by art historians as asserting a rhetorical rather than historical point about tonality's "collapse".[29]

Taruskin also developed a variation of the motto into the pun "ontogeny recapitulates ontology" to refute the concept of "absolute music" advancing the socio-artistic theories of Carl Dalhaus. Ontology is the investigation of what exactly something is, and Taruskin asserts that an art object becomes that which society and succeeding generations made of it. For example, composer Johann Sebastian Bach's St. John Passion, composed in the 1720s, was appropriated by the Nazi regime in the 1930s for propaganda. Taruskin claims the historical development of the Passion (its ontogeny) as a work with an anti-Semitic message does, in fact, inform the work's identity (its ontology), even though that was an unlikely concern of the composer. Music or even an abstract visual artwork can not be truly autonomous ("absolute") because it is defined by its historical and social reception.[29]

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Modern evolutionary synthesis


From Wikipedia, the free encyclopedia

The modern evolutionary synthesis is a 20th century synthesis of ideas from several fields of biology which provides a widely accepted account of evolution. It is also referred to as the new synthesis, the modern synthesis, the evolutionary synthesis, millennium synthesis or the neo-Darwinian synthesis.

The synthesis, produced between 1936 and 1947, reflects the consensus about how evolution proceeds.[1] The previous development of nineteenth century evolutionary ideas by Charles Darwin, Gregor Mendel and others and the population genetics, between 1918 and 1932, was a stimulus, as it showed that Mendelian genetics was consistent with natural selection and gradual evolution. The synthesis is still, to a large extent, the current paradigm in evolutionary biology.[2]

The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century. At its heart was the question of whether Mendelian genetics could be reconciled with gradual evolution by means of natural selection. A second issue was whether the broad-scale changes (macroevolution) seen by palaeontologists could be explained by changes seen in local populations (microevolution).

The synthesis included evidence from biologists, trained in genetics, who studied populations in the field and in the laboratory. These studies were crucial to evolutionary theory. The synthesis drew together ideas from several branches of biology which had become separated, particularly genetics, cytology, systematics, botany, morphology, ecology and paleontology.

Julian Huxley invented the term, when he produced his book, Evolution: The Modern Synthesis (1942). Other major figures in the modern synthesis include R. A. Fisher, Theodosius Dobzhansky, J. B. S. Haldane, Sewall Wright, E. B. Ford, Ernst Mayr, Bernhard Rensch, Sergei Chetverikov, George Gaylord Simpson, and G. Ledyard Stebbins.

Summary of the modern synthesis

The modern synthesis bridged the gap between the work of experimental geneticists and naturalists, and paleontologists. It states that:[3][4][5]
  1. All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.
  2. Evolution is gradual: small genetic changes regulated by natural selection accumulate over long periods. Discontinuities amongst species (or other taxa) are explained as originating gradually through geographical separation and extinction. This theory contrast with the saltation theory of Bateson (1894).[6]
  3. Natural selection is by far the main mechanism of change; even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment.
  4. The role of genetic drift is equivocal. Though strongly supported initially by Dobzhansky, it was downgraded later as results from ecological genetics were obtained.
  5. Thinking in terms of populations, rather than individuals, is primary: the genetic diversity existing in natural populations is a key factor in evolution. The strength of natural selection in the wild is greater than previously expected; the effect of ecological factors such as niche occupation and the significance of barriers to gene flow are all important.
  6. In palaeontology, the ability to explain historical observations by extrapolation from microevolution to macroevolution is proposed. Historical contingency means explanations at different levels may exist. Gradualism does not mean constant rate of change.
The idea that speciation occurs after populations are reproductively isolated has been much debated.
In plants, polyploidy must be included in any view of speciation. Formulations such as 'evolution consists primarily of changes in the frequencies of alleles between one generation and another' were proposed rather later. The traditional view is that developmental biology ('evo-devo') played little part in the synthesis,[7] but an account of Gavin de Beer's work by Stephen J. Gould suggests he may be an exception.[8]

Developments leading up to the synthesis

1859–1899

Charles Darwin's On the Origin of Species was successful in convincing most biologists that evolution had occurred, but was less successful in convincing them that natural selection was its primary mechanism. In the 19th and early 20th centuries, variations of Lamarckism, orthogenesis ('progressive' evolution), and saltationism (evolution by jumps) were discussed as alternatives.[9]
Also, Darwin did not offer a precise explanation of how new species arise. As part of the disagreement about whether natural selection alone was sufficient to explain speciation, George Romanes coined the term neo-Darwinism to refer to the version of evolution advocated by Alfred Russel Wallace and August Weismann with its heavy dependence on natural selection.[10] Weismann and Wallace rejected the Lamarckian idea of inheritance of acquired characteristics, something that Darwin had not ruled out.[11]

Weismann's idea was that the relationship between the hereditary material, which he called the germ plasm (German, Keimplasma), and the rest of the body (the soma) was a one-way relationship: the germ-plasm formed the body, but the body did not influence the germ-plasm, except indirectly in its participation in a population subject to natural selection. Weismann was translated into English, and though he was influential, it took many years for the full significance of his work to be appreciated.[12] Later, after the completion of the modern synthesis, the term neo-Darwinism came to be associated with its core concept: evolution, driven by natural selection acting on variation produced by genetic mutation, and genetic recombination (chromosomal crossovers).[10]

1900–1915

Gregor Mendel's work was re-discovered by Hugo de Vries and Carl Correns in 1900. News of this reached William Bateson in England, who reported on the paper during a presentation to the Royal Horticultural Society in May 1900.[13] It showed that the contributions of each parent retained their integrity rather than blending with the contribution of the other parent. This reinforced a division of thought, which was already present in the 1890s.[14] The two schools were:
  • Saltationism (large mutations or jumps), favored by early Mendelians who viewed hard inheritance as incompatible with natural selection[15]
  • Biometric school: led by Karl Pearson and Walter Weldon, argued vigorously against it, saying that empirical evidence indicated that variation was continuous in most organisms, not discrete as Mendelism predicted.
The relevance of Mendelism to evolution was unclear and hotly debated, especially by Bateson, who opposed the biometric ideas of his former teacher Weldon. Many scientists believed the two theories substantially contradicted each other.[16] This debate between the biometricians and the Mendelians continued for some 20 years and was only solved by the development of population genetics.

T. H. Morgan began his career in genetics as a saltationist, and started out trying to demonstrate that mutations could produce new species in fruit flies. However, the experimental work at his lab with Drosophila melanogaster, which helped establish the link between Mendelian genetics and the chromosomal theory of inheritance, demonstrated that rather than creating new species in a single step, mutations increased the genetic variation in the population.[17]

The foundation of population genetics

The first step towards the synthesis was the development of population genetics. R.A. Fisher, J.B.S. Haldane, and Sewall Wright provided critical contributions. In 1918, Fisher produced the paper "The Correlation Between Relatives on the Supposition of Mendelian Inheritance",[18] which showed how the continuous variation measured by the biometricians could be the result of the action of many discrete genetic loci. In this and subsequent papers culminating in his 1930 book The Genetical Theory of Natural Selection, Fisher was able to show how Mendelian genetics was, contrary to the thinking of many early geneticists, completely consistent with the idea of evolution driven by natural selection.[19] During the 1920s, a series of papers by J.B.S. Haldane applied mathematical analysis to real world examples of natural selection such as the evolution of industrial melanism in peppered moths.[19] Haldane established that natural selection could work in the real world at a faster rate than even Fisher had assumed.[20]

Sewall Wright focused on combinations of genes that interacted as complexes, and the effects of inbreeding on small relatively isolated populations, which could exhibit genetic drift. In a 1932 paper he introduced the concept of an adaptive landscape in which phenomena such as cross breeding and genetic drift in small populations could push them away from adaptive peaks, which would in turn allow natural selection to push them towards new adaptive peaks.[19] Wright's model would appeal to field naturalists such as Theodosius Dobzhansky and Ernst Mayr who were becoming aware of the importance of geographical isolation in real world populations.[20] The work of Fisher, Haldane and Wright founded the discipline of population genetics. This is the precursor of the modern synthesis, which is an even broader coalition of ideas.[19][20][21] One limitation of the modern synthesis version of population genetics is that it treats one gene locus at a time, neglecting genetic linkage and resulting linkage disequilibrium between loci.

The modern synthesis

Theodosius Dobzhansky, a Ukrainian emigrant, who had been a postdoctoral worker in Morgan's fruit fly lab, was one of the first to apply genetics to natural populations. He worked mostly with Drosophila pseudoobscura. He says pointedly: "Russia has a variety of climates from the Arctic to sub-tropical... Exclusively laboratory workers who neither possess nor wish to have any knowledge of living beings in nature were and are in a minority."[22] Not surprisingly, there were other Russian geneticists with similar ideas, though for some time their work was known to only a few in the West.
His 1937 work Genetics and the Origin of Species was a key step in bridging the gap between population geneticists and field naturalists. It presented the conclusions reached by Fisher, Haldane, and especially Wright in their highly mathematical papers in a form that was easily accessible to others. It also emphasized that real world populations had far more genetic variability than the early population geneticists had assumed in their models, and that genetically distinct sub-populations were important. Dobzhansky argued that natural selection worked to maintain genetic diversity as well as driving change. Dobzhansky had been influenced by his exposure in the 1920s to the work of a Russian geneticist named Sergei Chetverikov who had looked at the role of recessive genes in maintaining a reservoir of genetic variability in a population before his work was shut down by the rise of Lysenkoism in the Soviet Union.[19][20]

Edmund Brisco Ford's work complemented that of Dobzhansky. It was as a result of Ford's work, as well as his own, that Dobzhansky changed the emphasis in the third edition of his famous text from drift to selection.[23] Ford was an experimental naturalist who wanted to test natural selection in nature. He virtually invented the field of research known as ecological genetics. His work on natural selection in wild populations of butterflies and moths was the first to show that predictions made by R.A. Fisher were correct. He was the first to describe and define genetic polymorphism, and to predict that human blood group polymorphisms might be maintained in the population by providing some protection against disease.[24]

Ernst Mayr's key contribution to the synthesis was Systematics and the Origin of Species, published in 1942. Mayr emphasized the importance of allopatric speciation, where geographically isolated sub-populations diverge so far that reproductive isolation occurs. He was skeptical of the reality of sympatric speciation believing that geographical isolation was a prerequisite for building up intrinsic (reproductive) isolating mechanisms. Mayr also introduced the biological species concept that defined a species as a group of interbreeding or potentially interbreeding populations that were reproductively isolated from all other populations.[19][20][25] Before he left Germany for the United States in 1930, Mayr had been influenced by the work of German biologist Bernhard Rensch. In the 1920s Rensch, who like Mayr did field work in Indonesia, analyzed the geographic distribution of polytypic species and complexes of closely related species paying particular attention to how variations between different populations correlated with local environmental factors such as differences in climate. In 1947, Rensch published Neuere Probleme der Abstammungslehre: die Transspezifische Evolution (English translation 1959: Evolution above the Species level). This looked at how the same evolutionary mechanisms involved in speciation might be extended to explain the origins of the differences between the higher level taxa. His writings contributed to the rapid acceptance of the synthesis in Germany.[26][27]

George Gaylord Simpson was responsible for showing that the modern synthesis was compatible with paleontology in his book Tempo and Mode in Evolution published in 1944. Simpson's work was crucial because so many paleontologists had disagreed, in some cases vigorously, with the idea that natural selection was the main mechanism of evolution. It showed that the trends of linear progression (in for example the evolution of the horse) that earlier paleontologists had used as support for neo-Lamarckism and orthogenesis did not hold up under careful examination. Instead the fossil record was consistent with the irregular, branching, and non-directional pattern predicted by the modern synthesis.[19][20]

The botanist G. Ledyard Stebbins was another major contributor to the synthesis. His major work, Variation and Evolution in Plants, was published in 1950. It extended the synthesis to encompass botany including the important effects of hybridization and polyploidy in some kinds of plants.[19]

Further advances

The modern evolutionary synthesis continued to be developed and refined after the initial establishment in the 1930s and 1940s. The work of W. D. Hamilton, George C. Williams, John Maynard Smith and others led to the development of a gene-centered view of evolution in the 1960s.
The synthesis as it exists now has extended the scope of the Darwinian idea of natural selection to include subsequent scientific discoveries and concepts unknown to Darwin, such as DNA and genetics, which allow rigorous, in many cases mathematical, analyses of phenomena such as kin selection, altruism, and speciation.

In The Selfish Gene, author Richard Dawkins asserts the gene is the only true unit of selection.[28] (Dawkins also attempts to apply evolutionary theory to non-biological entities, such as cultural memes, imagined to be subject to selective forces analogous to those affecting biological entities.)

Others, such as Stephen Jay Gould, reject the notion that genetic entities are subject to anything other than genetic or chemical forces, (as well as the idea evolution acts on "populations" per se), reasserting the centrality of the individual organism as the true unit of selection, whose specific phenotype is directly subject to evolutionary pressures.

In 1972, the notion of gradualism in evolution was challenged by a theory of "punctuated equilibrium" put forward by Gould and Niles Eldredge, proposing evolutionary changes could occur in relatively rapid spurts, when selective pressures were heightened, punctuating long periods of morphological stability, as well-adapted organisms coped successfully in their respective environments.

Discovery in the 1980s of Hox genes and regulators conserved across multiple phyletic divisions began the process of addressing basic theoretical problems relating to gradualism, incremental change, and sources of novelty in evolution. Suddenly, evolutionary theorists could answer the charge that spontaneous random mutations should result overwhelmingly in deleterious changes to a fragile, monolithic genome: Mutations in homeobox regulation could safely—yet dramatically—alter morphology at a high level, without damaging coding for specific organs or tissues.

This, in turn, provided the means to model hypothetical genomic changes expressed in the phenotypes of long-extinct species, like the recently discovered "fish with hands"' Tiktaalik.

As these recent discoveries suggest, the synthesis continues to undergo regular review, drawing on insights offered by both new biotechnologies and new paleontological discoveries.[29] (See also Current research in evolutionary biology).

After the synthesis


The structure of evolutionary biology.
The history and causes of evolution (center) are subject to various subdisciplines of evolutionary biology. The areas of segments give an impression of the contributions of subdisciplines to the literature of evolutionary biology.

There are a number of discoveries in earth sciences and biology which have arisen since the synthesis. Listed here are some of those topics which are relevant to the evolutionary synthesis, and which seem soundly based.

Understanding of Earth history

The Earth is the stage on which the evolutionary play is performed. Darwin studied evolution in the context of Charles Lyell's geology, but our present understanding of Earth history includes some critical advances made during the last half-century.
  • The identification of the first generally accepted fossils of microbial life was made by geologists. These rocks have been dated as about 3.465 billion years ago.[35] Walcott was the first geologist to identify pre-Cambrian fossil bacteria from microscopic examination of thin rock slices. He also thought stromatolites were organic in origin. His ideas were not accepted at the time, but may now be appreciated as great discoveries.[36]
  • Information about paleoclimates is increasingly available, and being used in paleontology. One example: the discovery of massive ice ages in the Proterozoic, following the great reduction of CO2 in the atmosphere. These ice ages were immensely long, and led to a crash in microflora.[37] 
Conclusion: Our present knowledge of earth history strongly suggests that large-scale geophysical events influenced macroevolution and megaevolution. These terms refer to evolution above the species level, including such events as mass extinctions, adaptive radiation, and the major transitions in evolution.[41][42]

Symbiotic origin of eukaryotic cell structures

Once symbiosis was discovered in lichen and in plant roots (rhizobia in root nodules) in the 19th century, the idea arose that the process might have occurred more widely, and might be important in evolution. Anton de Bary invented the concept of symbiosis;[43] several Russian biologists promoted the idea;[44] Edmund Beecher Wilson mentioned it in his text The Cell;[45] as did Ivan Emanuel Wallin in his Symbionticism and the origin of species;[46] and there was a brief mention by Julian Huxley in 1930;[47] all in vain because sufficient evidence was lacking. Symbiosis as a major evolutionary force was not discussed at all in the evolutionary synthesis.[48]
The role of symbiosis in cell evolution was revived partly by Joshua Lederberg,[49] and finally brought to light by Lynn Margulis in a series of papers and books.[50][51] Some organelles are recognized as being of microbial origin: mitochondria and chloroplasts definitely, cilia, flagella and centrioles possibly, and perhaps the nuclear membrane and much of the chromosome structure as well. What is now clear is that the evolution of eukaryote cells is either caused by, or at least profoundly influenced by, symbiosis with bacterial and archaean cells in the Proterozoic.

The origin of the eukaryote cell by symbiosis in several stages was not part of the evolutionary synthesis. It is, at least on first sight, an example of megaevolution by big jumps. However, what symbiosis provided was a copious supply of heritable variation from microorganisms, which was fine-tuned over a long period to produce the cell structure we see today. This part of the process is consistent with evolution by natural selection.[52]

Trees of life

The ability to analyse sequence in macromolecules (protein, DNA, RNA) provides evidence of descent, and permits us to work out genealogical trees covering the whole of life, since now there are data on every major group of living organisms. This project, begun in a tentative way in the 1960s, has become a search for the universal tree or the universal ancestor, a phrase of Carl Woese.[53][54] 
The tree that results has some unusual features, especially in its roots. There are two domains of prokaryotes: bacteria and archaea, both of which contributed genetic material to the eukaryotes, mainly by means of symbiosis. Also, since bacteria can pass genetic material to other bacteria, their relationships look more like a web than a tree. Once eukaryotes were established, their sexual reproduction produced the traditional branching tree-like pattern, the only diagram Darwin put in the Origin. The last universal ancestor (LUA) would be a prokaryotic cell before the split between the bacteria and archaea. LUA is defined as most recent organism from which all organisms now living on Earth descend (some 3.5 to 3.8 billion years ago, in the Archean era).[55]
This technique may be used to clarify relationships within any group of related organisms. It is now a standard procedure, and examples are published regularly. April 2009 sees the publication of a tree covering all the animal phyla, derived from sequences from 150 genes in 77 taxa.[56]

Early attempts to identify relationships between major groups were made in the 19th century by Ernst Haeckel, and by comparative anatomists such as Thomas Henry Huxley and E. Ray Lankester. Enthusiasm waned: it was often difficult to find evidence to adjudicate between different opinions. Perhaps for that reason, the evolutionary synthesis paid surprisingly little attention to this activity. It is certainly a lively field of research today.

Evolutionary developmental biology

What once was called embryology played a modest role in the evolutionary synthesis,[57] mostly about evolution by changes in developmental timing (allometry and heterochrony).[58] Man himself was, according to Bolk, a typical case of evolution by retention of juvenile characteristics (neoteny). He listed many characters where "Man, in his bodily development, is a primate foetus that has become sexually mature."[59] Unfortunately, his interpretation of these ideas was non-Darwinian, but his list of characters is both interesting and convincing.[60]
Evolutionary developmental biology (evo-devo) springs from clear proof that development is closely controlled by special genetic systems, and the hope that comparison of these systems will tell us much about the evolutionary history of different groups.[61][62] In a series of experiments with the fruit-fly Drosophila, Edward B. Lewis was able to identify a complex of genes whose proteins bind to the cis-regulatory regions of target genes. The latter then activate or repress systems of cellular processes that accomplish the final development of the organism.[63][64] Furthermore, the sequence of these control genes show co-linearity: the order of the loci in the chromosome parallels the order in which the loci are expressed along the anterior-posterior axis of the body. Not only that, but this cluster of master control genes programs the development of all higher organisms.[65][66] Each of the genes contains a homeobox, a remarkably conserved DNA sequence. This suggests the complex itself arose by gene duplication.[67][68][69] In his Nobel lecture, Lewis said "Ultimately, comparisons of the [control complexes] throughout the animal kingdom should provide a picture of how the organisms, as well as the [control genes] have evolved."

The term deep homology was coined to describe the common origin of genetic regulatory apparatus used to build morphologically and phylogenetically disparate animal features.[70] It applies when a complex genetic regulatory system is inherited from a common ancestor, as it is in the evolution of vertebrate and invertebrate eyes. The phenomenon is implicated in many cases of parallel evolution.[71]

A great deal of evolution may take place by changes in the control of development. This may be relevant to punctuated equilibrium theory, for in development a few changes to the control system could make a significant difference to the adult organism. An example is the giant panda, whose place in the Carnivora was long uncertain.[72] Apparently, the giant panda's evolution required the change of only a few genetic messages (5 or 6 perhaps), yet the phenotypic and lifestyle change from a standard bear is considerable.[73][74] The transition could therefore be effected relatively swiftly.

Fossil discoveries

In the past thirty or so years there have been excavations in parts of the world which had scarcely been investigated before. Also, there is fresh appreciation of fossils discovered in the 19th century, but then denied or deprecated: the classic example is the Ediacaran biota from the immediate pre-Cambrian, after the Cryogenian period. These soft-bodied fossils are the first record of multicellular life. The interpretation of this fauna is still in flux.

Many outstanding discoveries have been made, and some of these have implications for evolutionary theory. The discovery of feathered dinosaurs and early birds from the Lower Cretaceous of Liaoning, N.E. China have convinced most students that birds did evolve from coelurosaurian theropod dinosaurs. Less well known, but perhaps of equal evolutionary significance, are the studies on early insect flight, on stem tetrapods from the Upper Devonian,[75][76] and the early stages of whale evolution.[77]

Recent work has shed light on the evolution of flatfish (pleuronectiformes), such as plaice, sole, turbot and halibut. Flatfish are interesting because they are one of the few vertebrate groups with external asymmetry. Their young are perfectly symmetrical, but the head is remodelled during a metamorphosis, which entails the migration of one eye to the other side, close to the other eye. Some species have both eyes on the left (turbot), some on the right (halibut, sole); all living and fossil flatfish to date show an 'eyed' side and a 'blind' side.[78] The lack of an intermediate condition in living and fossil flatfish species had led to debate about the origin of such a striking adaptation. The case was considered by Lamark,[79] who thought flatfish precursors would have lived in shallow water for a long period, and by Darwin, who predicted a gradual migration of the eye, mirroring the metamorphosis of the living forms. Darwin's long-time critic St. George Mivart thought that the intermediate stages could have no selective value,[80] and in the 6th edition of the Origin, Darwin made a concession to the possibility of acquired traits.[81] Many years later the geneticist Richard Goldschmidt put the case forward as an example of evolution by saltation, bypassing intermediate forms.[82][83]

A recent examination of two fossil species from the Eocene has provided the first clear picture of flatfish evolution. The discovery of stem flatfish with incomplete orbital migration refutes Goldschmidt's ideas, and demonstrates that "the assembly of the flatfish bodyplan occurred in a gradual, stepwise fashion".[84] There are no grounds for thinking that incomplete orbital migration was maladaptive, because stem forms with this condition ranged over two geological stages, and are found in localities which also yield flatfish with the full cranial asymmetry. The evolution of flatfish falls squarely within the evolutionary synthesis.[78]

Horizontal gene transfer

Horizontal gene transfer (HGT) (or lateral gene transfer) is any process in which an organism gets genetic material from another organism without being the offspring of that organism.

Most thinking in genetics has focused on vertical transfer, but there is a growing awareness that horizontal gene transfer is a significant phenomenon. Amongst single-celled organisms it may be the dominant form of genetic transfer. Artificial horizontal gene transfer is a form of genetic engineering.

Richardson and Palmer (2007) state: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear."[85]

The bacterial means of HGT are:
  • Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA).
  • Transduction, the process in which bacterial DNA is moved from one bacterium to another by a bacterial virus (a bacteriophage, or 'phage').
  • Bacterial conjugation, a process in which a bacterial cell transfers genetic material to another cell by cell-to-cell contact.
  • Gene transfer agent (GTA) is a virus-like element which contains random pieces of the host chromosome. They are found in most members of the alphaproteobacteria order Rhodobacterales.[86] They are encoded by the host genome. GTAs transfer DNA so frequently that they may have an important role in evolution.[87]
    A 2010 report found that genes for antibiotic resistance could be transferred by engineering GTAs in the laboratory.[86]
Some examples of HGT in metazoa are now known. Genes in bdelloid rotifers have been found which appear to have originated in bacteria, fungi, and plants. This suggests they arrived by horizontal gene transfer. The capture and use of exogenous (~foreign) genes may represent an important force in bdelloid evolution.[88][89] The team led by Matthew S. Meselson at Harvard University has also shown that, despite the lack of sexual reproduction, bdelloid rotifers do engage in genetic (DNA) transfer within a species or clade. The method used is not known at present.

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Evolving a bigger brain with human DNA

Original link:  http://phys.org/news/2015-02-evolving-bigger-brain-human-dna.html

Evolving a bigger brain with human DNA 
The human version of a DNA sequence called HARE5 turns on a gene important for brain development (gene activity is stained blue), and causes a mouse embryo to grow a 12 percent larger brain by the end of pregnancy than an embryo injected with …more
The size of the human brain expanded dramatically during the course of evolution, imparting us with unique capabilities to use abstract language and do complex math. But how did the human brain get larger than that of our closest living relative, the chimpanzee, if almost all of our genes are the same?

Duke scientists have shown that it's possible to pick out key changes in the between chimpanzees and humans and then visualize their respective contributions to by using mouse embryos.

The team found that humans are equipped with tiny differences in a particular regulator of , dubbed HARE5, that when introduced into a , led to a 12% bigger than in the embryos treated with the HARE5 sequence from chimpanzees.

The findings, appearing online Feb. 19, 2015, in Current Biology, may lend insight into not only what makes the special but also why people get some diseases, such as autism and Alzheimer's disease, whereas chimpanzees don't.

"I think we've just scratched the surface, in terms of what we can gain from this sort of study," said Debra Silver, an assistant professor of molecular genetics and microbiology in the Duke University Medical School. "There are some other really compelling candidates that we found that may also lead us to a better understanding of the uniqueness of the human brain."

Every genome contains many thousands of short bits of DNA called 'enhancers,' whose role is to control the activity of genes. Some of these are unique to humans. Some are active in specific tissues. But none of the human-specific enhancers previously had been shown to influence brain anatomy directly.

In the new study, researchers mined databases of genomic data from humans and chimpanzees, to find enhancers expressed primarily in the brain tissue and early in development. They prioritized enhancers that differed markedly between the two species.

The group's initial screen turned up 106 candidates, six of them near genes that are believed to be involved in . The group named these 'human-accelerated regulatory enhancers,' HARE1 through HARE6.

The strongest candidate was HARE5 for its chromosomal location near a gene called Frizzled 8, which is part of a well-known molecular pathway implicated in brain development and disease. The group decided to focus on HARE5 and then showed that it was likely to be an enhancer for Frizzled8 because the two DNA sequences made physical contact in .

The human HARE5 and the chimpanzee HARE5 sequences differ by only 16 letters in their genetic code. Yet, in mouse embryos the researchers found that the human enhancer was active earlier in development and more active in general than the chimpanzee enhancer.

"What's really exciting about this was that the activity differences were detected at a critical time in brain development: when neural progenitor cells are proliferating and expanding in number, just prior to producing neurons," Silver said.

The researchers found that in the mouse embryos equipped with Frizzled8 under control of human HARE5, progenitor cells destined to become neurons proliferated faster compared with the chimp HARE5 mice, ultimately leading to more neurons.

As the mouse embryos neared the end of gestation, their brain size differences became noticeable to the naked eye. Graduate student Lomax Boyd started dissecting the brains and looking at them under a microscope.

"After he started taking pictures, we took a ruler to the monitor. Although we were blind to what the genotype was, we started noticing a trend," Silver said.

All told, human HARE5 mice had brains 12% larger in area compared with chimpanzee HARE5 mice. The neocortex, involved in higher-level function such as language and reasoning, was the region of the brain affected.

Producing a short list of strong candidates was in itself a feat, accomplished by applying the right filters to analysis of human and chimpanzee genomes, said co-author Gregory Wray, professor of biology and director of the Duke Center for Genomic and Computational Biology.

"Many others have tried this and failed," Wray said. "We've known other people who have looked at genes involved in brain size evolution, tested them out and done the same kinds of experiments we've done and come up dry."

The Duke team plans to study the human HARE5 and chimp HARE5 mice into adulthood, for possible differences in brain structure and behavior. The group also hopes to explore the role of the other HARE sequences in brain development.

"What we found is a piece of the genetic basis for why we have a bigger brain," Wray said. "It really shows in sharp relief just how complicated those changes must have been. This is probably only one piece—a little piece."

Explore further: Humans' big brains might be due in part to newly identified protein

More information: "Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex," J. Lomax Boyd, Stephanie L. Skove, Jeremy Rouanet, Louis-Jan Pilaz, Tristan Bepler, Raluca Gordan, Gregory A. Wray, Debra L. Silver. Current Biology, February 19, 2015. DOI: 10.1016/j.cub.2015.01.041
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Scientists announce anti-HIV agent so powerful it can work in a vaccine

HIV
Human immunodefieciency virus (HIV). Credit: C. Goldsmith/public domain
Original link:  http://medicalxpress.com/news/2015-02-scientists-anti-hiv-agent-powerful-vaccine.html

In a remarkable new advance against the virus that causes AIDS, scientists from the Jupiter, Florida campus of The Scripps Research Institute (TSRI) have announced the creation of a novel drug candidate that is so potent and universally effective, it might work as part of an unconventional vaccine.

The research, which involved scientists from more than a dozen research institutions, was published February 18 online ahead of print by the prestigious journal Nature.

The study shows that the new drug candidate blocks every strain of HIV-1, HIV-2 and SIV (simian immunodeficiency ) that has been isolated from humans or rhesus macaques, including the hardest-to-stop variants. It also protects against much-higher doses of virus than occur in most human transmission and does so for at least eight months after injection.

"Our compound is the broadest and most potent entry inhibitor described so far," said Michael Farzan, a TSRI professor who led the effort. "Unlike antibodies, which fail to neutralize a large fraction of HIV-1 strains, our protein has been effective against all strains tested, raising the possibility it could offer an effective HIV vaccine alternative."

Blocking a Second Site

When HIV infects a cell, it targets the CD4 lymphocyte, an integral part of the body's immune system. HIV fuses with the cell and inserts its own genetic material—in this case, single-stranded RNA—and transforms the host cell into a HIV manufacturing site.

The new study builds on previous discoveries by the Farzan laboratory, which show that a co-receptor called CCR5 contains unusual modifications in its critical HIV-binding region, and that proteins based on this region can be used to prevent infection.

With this knowledge, Farzan and his team developed the new drug candidate so that it binds to two sites on the surface of the virus simultaneously, preventing entry of HIV into the host cell.

"When antibodies try to mimic the receptor, they touch a lot of other parts of the viral envelope that HIV can change with ease," said TSRI Research Associate Matthew Gardner, the first author of the study with Lisa M. Kattenhorn of Harvard Medical School. "We've developed a direct mimic of the receptors without providing many avenues that the virus can use to escape, so we catch every virus thus far."

The team also leveraged preexisting technology in designing a delivery vehicle—an engineered adeno-associated virus, a small, relatively innocuous virus that causes no disease. Once injected into muscle tissue, like HIV itself, the vehicle turns those cells into "factories" that could produce enough of the new protective protein to last for years, perhaps decades, Farzan said.

Data from the new study showed the drug candidate binds to the envelope of HIV-1 more potently than the best against the virus. Also, when macaque models were inoculated with the , they were protected from multiple challenges by SIV.

"This is the culmination of more than a decade's worth of work on the biochemistry of how HIV enters cells," Farzan said. "When we did our original work on CCR5, people thought it was interesting, but no one saw the therapeutic potential. That potential is starting to be realized."

Explore further: Scientists discover HIV antibody that binds to novel target on virus

More information: Nature, DOI: 10.1038/nature14264

Journal reference: Nature search and more info website
 
Provided by The Scripps Research Institute search and more info
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