Monthly Archives: June 2016

Evolution – Wikipedia, the free encyclopedia

Posted: June 19, 2016 at 2:36 pm

Evolution is change in the heritable traits of biological populations over successive generations.[1][2] Evolutionary processes give rise to diversity at every level of biological organisation, including the levels of species, individual organisms, and molecules.[3]

All life on Earth shares a common ancestor known as the last universal ancestor,[4][5][6] which lived approximately 3.53.8 billion years ago,[7] although a study in 2015 found "remains of biotic life" from 4.1 billion years ago in ancient rocks in Western Australia.[8][9]

Repeated formation of new species (speciation), change within species (anagenesis), and loss of species (extinction) throughout the evolutionary history of life on Earth are demonstrated by shared sets of morphological and biochemical traits, including shared DNA sequences.[10] These shared traits are more similar among species that share a more recent common ancestor, and can be used to reconstruct a biological "tree of life" based on evolutionary relationships (phylogenetics), using both existing species and fossils. The fossil record includes a progression from early biogenic graphite,[11] to microbial mat fossils,[12][13][14] to fossilized multicellular organisms. Existing patterns of biodiversity have been shaped both by speciation and by extinction.[15] More than 99 percent of all species that ever lived on Earth are estimated to be extinct.[16][17] Estimates of Earth's current species range from 10 to 14 million,[18] of which about 1.2 million have been documented.[19]

In the mid-19th century, Charles Darwin formulated the scientific theory of evolution by natural selection, published in his book On the Origin of Species (1859). Evolution by natural selection is a process demonstrated by the observation that more offspring are produced than can possibly survive, along with three facts about populations: 1) traits vary among individuals with respect to morphology, physiology, and behaviour (phenotypic variation), 2) different traits confer different rates of survival and reproduction (differential fitness), and 3) traits can be passed from generation to generation (heritability of fitness).[20] Thus, in successive generations members of a population are replaced by progeny of parents better adapted to survive and reproduce in the biophysical environment in which natural selection takes place. This teleonomy is the quality whereby the process of natural selection creates and preserves traits that are seemingly fitted for the functional roles they perform.[21] Natural selection is the only known cause of adaptation but not the only known cause of evolution. Other, nonadaptive causes of microevolution include mutation and genetic drift.[22]

In the early 20th century the modern evolutionary synthesis integrated classical genetics with Darwin's theory of evolution by natural selection through the discipline of population genetics. The importance of natural selection as a cause of evolution was accepted into other branches of biology. Moreover, previously held notions about evolution, such as orthogenesis, evolutionism, and other beliefs about innate "progress" within the largest-scale trends in evolution, became obsolete scientific theories.[23] Scientists continue to study various aspects of evolutionary biology by forming and testing hypotheses, constructing mathematical models of theoretical biology and biological theories, using observational data, and performing experiments in both the field and the laboratory.

In terms of practical application, an understanding of evolution has been instrumental to developments in numerous scientific and industrial fields, including agriculture, human and veterinary medicine, and the life sciences in general.[24][25][26] Discoveries in evolutionary biology have made a significant impact not just in the traditional branches of biology but also in other academic disciplines, including biological anthropology, and evolutionary psychology.[27][28]Evolutionary Computation, a sub-field of Artificial Intelligence, is the result of the application of Darwinian principles to problems in Computer Science.

The proposal that one type of organism could descend from another type goes back to some of the first pre-Socratic Greek philosophers, such as Anaximander and Empedocles.[30] Such proposals survived into Roman times. The poet and philosopher Lucretius followed Empedocles in his masterwork De rerum natura (On the Nature of Things).[31][32] In contrast to these materialistic views, Aristotle understood all natural things, not only living things, as being imperfect actualisations of different fixed natural possibilities, known as "forms," "ideas," or (in Latin translations) "species."[33][34] This was part of his teleological understanding of nature in which all things have an intended role to play in a divine cosmic order. Variations of this idea became the standard understanding of the Middle Ages and were integrated into Christian learning, but Aristotle did not demand that real types of organisms always correspond one-for-one with exact metaphysical forms and specifically gave examples of how new types of living things could come to be.[35]

In the 17th century, the new method of modern science rejected Aristotle's approach. It sought explanations of natural phenomena in terms of physical laws that were the same for all visible things and that did not require the existence of any fixed natural categories or divine cosmic order. However, this new approach was slow to take root in the biological sciences, the last bastion of the concept of fixed natural types. John Ray applied one of the previously more general terms for fixed natural types, "species," to plant and animal types, but he strictly identified each type of living thing as a species and proposed that each species could be defined by the features that perpetuated themselves generation after generation.[36] These species were designed by God, but showed differences caused by local conditions. The biological classification introduced by Carl Linnaeus in 1735 explicitly recognized the hierarchical nature of species relationships, but still viewed species as fixed according to a divine plan.[37]

Other naturalists of this time speculated on the evolutionary change of species over time according to natural laws. In 1751, Pierre Louis Maupertuis wrote of natural modifications occurring during reproduction and accumulating over many generations to produce new species.[38]Georges-Louis Leclerc, Comte de Buffon suggested that species could degenerate into different organisms, and Erasmus Darwin proposed that all warm-blooded animals could have descended from a single microorganism (or "filament").[39] The first full-fledged evolutionary scheme was Jean-Baptiste Lamarck's "transmutation" theory of 1809,[40] which envisaged spontaneous generation continually producing simple forms of life that developed greater complexity in parallel lineages with an inherent progressive tendency, and postulated that on a local level these lineages adapted to the environment by inheriting changes caused by their use or disuse in parents.[41][42] (The latter process was later called Lamarckism.)[41][43][44][45] These ideas were condemned by established naturalists as speculation lacking empirical support. In particular, Georges Cuvier insisted that species were unrelated and fixed, their similarities reflecting divine design for functional needs. In the meantime, Ray's ideas of benevolent design had been developed by William Paley into the Natural Theology or Evidences of the Existence and Attributes of the Deity (1802)
, which proposed complex adaptations as evidence of divine design and which was admired by Charles Darwin.[46][47][48]

The crucial break from the concept of constant typological classes or types in biology came with the theory of evolution through natural selection, which was formulated by Charles Darwin in terms of variable populations. Partly influenced by An Essay on the Principle of Population (1798) by Thomas Robert Malthus, Darwin noted that population growth would lead to a "struggle for existence" in which favorable variations prevailed as others perished. In each generation, many offspring fail to survive to an age of reproduction because of limited resources. This could explain the diversity of plants and animals from a common ancestry through the working of natural laws in the same way for all types of organism.[49][50][51][52] Darwin developed his theory of "natural selection" from 1838 onwards and was writing up his "big book" on the subject when Alfred Russel Wallace sent him a version of virtually the same theory in 1858. Their separate papers were presented together at a 1858 meeting of the Linnean Society of London.[53] At the end of 1859, Darwin's publication of his "abstract" as On the Origin of Species explained natural selection in detail and in a way that led to an increasingly wide acceptance of concepts of evolution. Thomas Henry Huxley applied Darwin's ideas to humans, using paleontology and comparative anatomy to provide strong evidence that humans and apes shared a common ancestry. Some were disturbed by this since it implied that humans did not have a special place in the universe.[54]

Precise mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of pangenesis.[55] In 1865, Gregor Mendel reported that traits were inherited in a predictable manner through the independent assortment and segregation of elements (later known as genes). Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory.[56]August Weismann made the important distinction between germ cells that give rise to gametes (such as sperm and egg cells) and the somatic cells of the body, demonstrating that heredity passes through the germ line only. Hugo de Vries connected Darwin's pangenesis theory to Weismann's germ/soma cell distinction and proposed that Darwin's pangenes were concentrated in the cell nucleus and when expressed they could move into the cytoplasm to change the cells structure. De Vries was also one of the researchers who made Mendel's work well-known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline.[57] To explain how new variants originate, de Vries developed a mutation theory that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries.[42][58][59] In the 1930s, pioneers in the field of population genetics, such as Ronald Fisher, Sewall Wright and J. B. S. Haldane set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin's theory, genetic mutations, and Mendelian inheritance was thus reconciled.[60]

In the 1920s and 1930s a modern evolutionary synthesis connected natural selection, mutation theory, and Mendelian inheritance into a unified theory that applied generally to any branch of biology. The modern synthesis was able to explain patterns observed across species in populations, through fossil transitions in palaeontology, and even complex cellular mechanisms in developmental biology.[42][61] The publication of the structure of DNA by James Watson and Francis Crick in 1953 demonstrated a physical mechanism for inheritance.[62]Molecular biology improved our understanding of the relationship between genotype and phenotype. Advancements were also made in phylogenetic systematics, mapping the transition of traits into a comparative and testable framework through the publication and use of evolutionary trees.[63][64] In 1973, evolutionary biologist Theodosius Dobzhansky penned that "nothing in biology makes sense except in the light of evolution," because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent explanatory body of knowledge that describes and predicts many observable facts about life on this planet.[65]

Since then, the modern synthesis has been further extended to explain biological phenomena across the full and integrative scale of the biological hierarchy, from genes to species. This extension, known as evolutionary developmental biology and informally called "evo-devo," emphasises how changes between generations (evolution) acts on patterns of change within individual organisms (development).[66][67][68]

Evolution in organisms occurs through changes in heritable traitsthe inherited characteristics of an organism. In humans, for example, eye colour is an inherited characteristic and an individual might inherit the "brown-eye trait" from one of their parents.[69] Inherited traits are controlled by genes and the complete set of genes within an organism's genome (genetic material) is called its genotype.[70]

The complete set of observable traits that make up the structure and behaviour of an organism is called its phenotype. These traits come from the interaction of its genotype with the environment.[71] As a result, many aspects of an organism's phenotype are not inherited. For example, suntanned skin comes from the interaction between a person's genotype and sunlight; thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in genotypic variation; a striking example are people with the inherited trait of albinism, who do not tan at all and are very sensitive to sunburn.[72]

Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information.[70] DNA is a long biopolymer composed of four types of bases. The sequence of bases along a particular DNA molecule specify the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism.[73] However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by quantitative trait loci (multiple interacting genes).[74][75]

Recent findings have confirmed important examples of heritable changes that cannot be explained by changes to the sequence of nucleotides in the DNA. These phenomena are classed as epigenetic inheritance systems.[76]DNA methylation marking chromatin, self-sustaining metabolic loops, gene silencing by RNA interference and the three-dimensional conformation of proteins (such as prions) are areas where epigenetic inheritance systems have been discovered at the organismic level.[77][78] De
velopmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlay some of the mechanics in developmental plasticity and canalisation.[79] Heritability may also occur at even larger scales. For example, ecological inheritance through the process of niche construction is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effects that modify and feed back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors.[80] Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and symbiogenesis.[81][82]

An individual organism's phenotype results from both its genotype and the influence from the environment it has lived in. A substantial part of the phenotypic variation in a population is caused by genotypic variation.[75] The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of fixationwhen it either disappears from the population or replaces the ancestral allele entirely.[83]

Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural selection implausible. The HardyWeinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. The frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift.[84]

Variation comes from mutations in the genome, reshuffling of genes through sexual reproduction and migration between populations (gene flow). Despite the constant introduction of new variation through mutation and gene flow, most of the genome of a species is identical in all individuals of that species.[85] However, even relatively small differences in genotype can lead to dramatic differences in phenotype: for example, chimpanzees and humans differ in only about 5% of their genomes.[86]

Mutations are changes in the DNA sequence of a cell's genome. When mutations occur, they may alter the product of a gene, or prevent the gene from functioning, or have no effect. Based on studies in the fly Drosophila melanogaster, it has been suggested that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70% of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.[87]

Mutations can involve large sections of a chromosome becoming duplicated (usually by genetic recombination), which can introduce extra copies of a gene into a genome.[88] Extra copies of genes are a major source of the raw material needed for new genes to evolve.[89] This is important because most new genes evolve within gene families from pre-existing genes that share common ancestors.[90] For example, the human eye uses four genes to make structures that sense light: three for colour vision and one for night vision; all four are descended from a single ancestral gene.[91]

New genes can be generated from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the redundancy of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function.[92][93] Other types of mutations can even generate entirely new genes from previously noncoding DNA.[94][95]

The generation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions.[96][97] When new genes are assembled from shuffling pre-existing parts, domains act as modules with simple independent functions, which can be mixed together to produce new combinations with new and complex functions.[98] For example, polyketide synthases are large enzymes that make antibiotics; they contain up to one hundred independent domains that each catalyse one step in the overall process, like a step in an assembly line.[99]

In asexual organisms, genes are inherited together, or linked, as they cannot mix with genes of other organisms during reproduction. In contrast, the offspring of sexual organisms contain random mixtures of their parents' chromosomes that are produced through independent assortment. In a related process called homologous recombination, sexual organisms exchange DNA between two matching chromosomes.[100] Recombination and reassortment do not alter allele frequencies, but instead change which alleles are associated with each other, producing offspring with new combinations of alleles.[101] Sex usually increases genetic variation and may increase the rate of evolution.[102][103]

The two-fold cost of sex was first described by John Maynard Smith.[104] The first cost is that only one of the two sexes can bear young.[clarification needed] (This cost does not apply to hermaphroditic species, like most plants and many invertebrates.) The second cost is that any individual who reproduces sexually can only pass on 50% of its genes to any individual offspring, with even less passed on as each new generation passes.[105] (Again, this applies mostly to the evolution of sexual dimorphism, which occurred long after the evolution of sex itself.) Yet sexual reproduction is the more common means of reproduction among eukaryotes and multicellular organisms (although more common than sexual dimorphism). The Red Queen hypothesis has been used to explain the significance of sexual reproduction as a means to enable continual evolution and adaptation in response to coevolution with other species in an ever-changing environment.[105][106][107][108]

Gene flow is the exchange of genes between populations and between species.[109] It can therefore be a source of variation that is new to a population or to a species. Gene flow can be caused by the movement of individuals between separate populations of organisms, as might be caused by the movement of mice between inland and coastal populations, or the movement of pollen between heavy metal tolerant and heavy metal sensitive populations of grasses.

Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria.[110] In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species.[111] Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean weevil Callosobruchus chinensis has occurred.[112][113] An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which have received a range of genes from bacteria, fungi and plants.[114]Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains.[115]

Large-scale gene transfer has also occurred between the ancestors of eu
karyotic cells and bacteria, during the acquisition of chloroplasts and mitochondria. It is possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and archaea.[116]

From a Neo-Darwinian perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms.[84] For example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, genetic hitchhiking, mutation and gene flow.

Evolution by means of natural selection is the process by which traits that enhance survival and reproduction become more common in successive generations of a population. It has often been called a "self-evident" mechanism because it necessarily follows from three simple facts:[20]

More offspring are produced than can possibly survive, and these conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors are more likely to pass on their traits to the next generation than those with traits that do not confer an advantage.[117]

The central concept of natural selection is the evolutionary fitness of an organism.[118] Fitness is measured by an organism's ability to survive and reproduce, which determines the size of its genetic contribution to the next generation.[118] However, fitness is not the same as the total number of offspring: instead fitness is indicated by the proportion of subsequent generations that carry an organism's genes.[119] For example, if an organism could survive well and reproduce rapidly, but its offspring were all too small and weak to survive, this organism would make little genetic contribution to future generations and would thus have low fitness.[118]

If an allele increases fitness more than the other alleles of that gene, then with each generation this allele will become more common within the population. These traits are said to be "selected for." Examples of traits that can increase fitness are enhanced survival and increased fecundity. Conversely, the lower fitness caused by having a less beneficial or deleterious allele results in this allele becoming rarerthey are "selected against."[120] Importantly, the fitness of an allele is not a fixed characteristic; if the environment changes, previously neutral or harmful traits may become beneficial and previously beneficial traits become harmful.[73] However, even if the direction of selection does reverse in this way, traits that were lost in the past may not re-evolve in an identical form (see Dollo's law).[121][122]

Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorised into three different types. The first is directional selection, which is a shift in the average value of a trait over timefor example, organisms slowly getting taller.[123] Secondly, disruptive selection is selection for extreme trait values and often results in two different values becoming most common, with selection against the average value. This would be when either short or tall organisms had an advantage, but not those of medium height. Finally, in stabilising selection there is selection against extreme trait values on both ends, which causes a decrease in variance around the average value and less diversity.[117][124] This would, for example, cause organisms to slowly become all the same height.

A special case of natural selection is sexual selection, which is selection for any trait that increases mating success by increasing the attractiveness of an organism to potential mates.[125] Traits that evolved through sexual selection are particularly prominent among males of several animal species. Although sexually favoured, traits such as cumbersome antlers, mating calls, large body size and bright colours often attract predation, which compromises the survival of individual males.[126][127] This survival disadvantage is balanced by higher reproductive success in males that show these hard-to-fake, sexually selected traits.[128]

Natural selection most generally makes nature the measure against which individuals and individual traits, are more or less likely to survive. "Nature" in this sense refers to an ecosystem, that is, a system in which organisms interact with every other element, physical as well as biological, in their local environment. Eugene Odum, a founder of ecology, defined an ecosystem as: "Any unit that includes all of the organisms...in a given area interacting with the physical environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity and material cycles (ie: exchange of materials between living and nonliving parts) within the system."[129] Each population within an ecosystem occupies a distinct niche, or position, with distinct relationships to other parts of the system. These relationships involve the life history of the organism, its position in the food chain and its geographic range. This broad understanding of nature enables scientists to delineate specific forces which, together, comprise natural selection.

Natural selection can act at different levels of organisation, such as genes, cells, individual organisms, groups of organisms and species.[130][131][132] Selection can act at multiple levels simultaneously.[133] An example of selection occurring below the level of the individual organism are genes called transposons, which can replicate and spread throughout a genome.[134] Selection at a level above the individual, such as group selection, may allow the evolution of cooperation, as discussed below.[135]

In addition to being a major source of variation, mutation may also function as a mechanism of evolution when there are different probabilities at the molecular level for different mutations to occur, a process known as mutation bias.[136] If two genotypes, for example one with the nucleotide G and another with the nucleotide A in the same position, have the same fitness, but mutation from G to A happens more often than mutation from A to G, then genotypes with A will tend to evolve.[137] Different insertion vs. deletion mutation biases in different taxa can lead to the evolution of different genome sizes.[138][139] Developmental or mutational biases have also been observed in morphological evolution.[140][141] For example, according to the phenotype-first theory of evolution, mutations can eventually cause the genetic assimilation of traits that were previously induced by the environment.[142][143]

Mutation bias effects are superimposed on other processes. If selection would favor either one out of two mutations, but there is no extra advantage to having both, then the mutation that occurs the most frequently is the one that is most likely to become fixed in a population.[144][145] Mutations leading to the loss of function of a gene are much more common than mutations that produce a new, fully functional gene. Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution.[146] For example, pigments are no longer useful when animals live in the darkness of caves, and tend to be lost.[147] This kind of loss of function can occur because of mutation bias, and/or because the function had a cost, and once the benefit of the function disappeared, natural selection leads to the loss. Loss of sporulation ability in Bacillus subtilis during laboratory evolution appears to have been caused by
mutation bias, rather than natural selection against the cost of maintaining sporulation ability.[148] When there is no selection for loss of function, the speed at which loss evolves depends more on the mutation rate than it does on the effective population size,[149] indicating that it is driven more by mutation bias than by genetic drift. In parasitic organisms, mutation bias leads to selection pressures as seen in Ehrlichia. Mutations are biased towards antigenic variants in outer-membrane proteins.

Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles are subject to sampling error.[150] As a result, when selective forces are absent or relatively weak, allele frequencies tend to "drift" upward or downward randomly (in a random walk). This drift halts when an allele eventually becomes fixed, either by disappearing from the population, or replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations that began with the same genetic structure to drift apart into two divergent populations with different sets of alleles.[151]

It is usually difficult to measure the relative importance of selection and neutral processes, including drift.[152] The comparative importance of adaptive and non-adaptive forces in driving evolutionary change is an area of current research.[153]

The neutral theory of molecular evolution proposed that most evolutionary changes are the result of the fixation of neutral mutations by genetic drift.[22] Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift.[154] This form of the neutral theory is now largely abandoned, since it does not seem to fit the genetic variation seen in nature.[155][156] However, a more recent and better-supported version of this model is the nearly neutral theory, where a mutation that would be effectively neutral in a small population is not necessarily neutral in a large population.[117] Other alternative theories propose that genetic drift is dwarfed by other stochastic forces in evolution, such as genetic hitchhiking, also known as genetic draft.[150][157][158]

The time for a neutral allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations.[159] The number of individuals in a population is not critical, but instead a measure known as the effective population size.[160] The effective population is usually smaller than the total population since it takes into account factors such as the level of inbreeding and the stage of the lifecycle in which the population is the smallest.[160] The effective population size may not be the same for every gene in the same population.[161]

Recombination allows alleles on the same strand of DNA to become separated. However, the rate of recombination is low (approximately two events per chromosome per generation). As a result, genes close together on a chromosome may not always be shuffled away from each other and genes that are close together tend to be inherited together, a phenomenon known as linkage.[162] This tendency is measured by finding how often two alleles occur together on a single chromosome compared to expectations, which is called their linkage disequilibrium. A set of alleles that is usually inherited in a group is called a haplotype. This can be important when one allele in a particular haplotype is strongly beneficial: natural selection can drive a selective sweep that will also cause the other alleles in the haplotype to become more common in the population; this effect is called genetic hitchhiking or genetic draft.[163] Genetic draft caused by the fact that some neutral genes are genetically linked to others that are under selection can be partially captured by an appropriate effective population size.[157]

Gene flow involves the exchange of genes between populations and between species.[109] The presence or absence of gene flow fundamentally changes the course of evolution. Due to the complexity of organisms, any two completely isolated populations will eventually evolve genetic incompatibilities through neutral processes, as in the Bateson-Dobzhansky-Muller model, even if both populations remain essentially identical in terms of their adaptation to the environment.

If genetic differentiation between populations develops, gene flow between populations can introduce traits or alleles which are disadvantageous in the local population and this may lead to organisms within these populations evolving mechanisms that prevent mating with genetically distant populations, eventually resulting in the appearance of new species. Thus, exchange of genetic information between individuals is fundamentally important for the development of the biological species concept.

During the development of the modern synthesis, Sewall Wright developed his shifting balance theory, which regarded gene flow between partially isolated populations as an important aspect of adaptive evolution.[164] However, recently there has been substantial criticism of the importance of the shifting balance theory.[165]

Evolution influences every aspect of the form and behaviour of organisms. Most prominent are the specific behavioural and physical adaptations that are the outcome of natural selection. These adaptations increase fitness by aiding activities such as finding food, avoiding predators or attracting mates. Organisms can also respond to selection by cooperating with each other, usually by aiding their relatives or engaging in mutually beneficial symbiosis. In the longer term, evolution produces new species through splitting ancestral populations of organisms into new groups that cannot or will not interbreed.

These outcomes of evolution are distinguished based on time scale as macroevolution versus microevolution. Macroevolution refers to evolution that occurs at or above the level of species, in particular speciation and extinction; whereas microevolution refers to smaller evolutionary changes within a species or population, in particular shifts in gene frequency and adaptation.[166] In general, macroevolution is regarded as the outcome of long periods of microevolution.[167] Thus, the distinction between micro- and macroevolution is not a fundamental onethe difference is simply the time involved.[168] However, in macroevolution, the traits of the entire species may be important. For instance, a large amount of variation among individuals allows a species to rapidly adapt to new habitats, lessening the chance of it going extinct, while a wide geographic range increases the chance of speciation, by making it more likely that part of the population will become isolated. In this sense, microevolution and macroevolution might involve selection at different levelswith microevolution acting on genes and organisms, versus macroevolutionary processes such as species selection acting on entire species and affecting their rates of speciation and extinction.[170][171]

A common misconception is that evolution has goals, long-term plans, or an innate tendency for "progress," as expressed in beliefs such as orthogenesis and evolutionism; realistically however, evolution has no long-term goal and does not necessarily produce greater complexity.[172][173][174] Although complex species have evolved, they occur as a side effect of the overall number of organisms increasing and simple forms of life still remain more common in the
biosphere.[175] For example, the overwhelming majority of species are microscopic prokaryotes, which form about half the world's biomass despite their small size,[176] and constitute the vast majority of Earth's biodiversity.[177] Simple organisms have therefore been the dominant form of life on Earth throughout its history and continue to be the main form of life up to the present day, with complex life only appearing more diverse because it is more noticeable.[178] Indeed, the evolution of microorganisms is particularly important to modern evolutionary research, since their rapid reproduction allows the study of experimental evolution and the observation of evolution and adaptation in real time.[179][180]

Adaptation is the process that makes organisms better suited to their habitat.[181][182] Also, the term adaptation may refer to a trait that is important for an organism's survival. For example, the adaptation of horses' teeth to the grinding of grass. By using the term adaptation for the evolutionary process and adaptive trait for the product (the bodily part or function), the two senses of the word may be distinguished. Adaptations are produced by natural selection.[183] The following definitions are due to Theodosius Dobzhansky:

Adaptation may cause either the gain of a new feature, or the loss of an ancestral feature. An example that shows both types of change is bacterial adaptation to antibiotic selection, with genetic changes causing antibiotic resistance by both modifying the target of the drug, or increasing the activity of transporters that pump the drug out of the cell.[187] Other striking examples are the bacteria Escherichia coli evolving the ability to use citric acid as a nutrient in a long-term laboratory experiment,[188]Flavobacterium evolving a novel enzyme that allows these bacteria to grow on the by-products of nylon manufacturing,[189][190] and the soil bacterium Sphingobium evolving an entirely new metabolic pathway that degrades the synthetic pesticide pentachlorophenol.[191][192] An interesting but still controversial idea is that some adaptations might increase the ability of organisms to generate genetic diversity and adapt by natural selection (increasing organisms' evolvability).[193][194][195][196][197]

Adaptation occurs through the gradual modification of existing structures. Consequently, structures with similar internal organisation may have different functions in related organisms. This is the result of a single ancestral structure being adapted to function in different ways. The bones within bat wings, for example, are very similar to those in mice feet and primate hands, due to the descent of all these structures from a common mammalian ancestor.[199] However, since all living organisms are related to some extent,[200] even organs that appear to have little or no structural similarity, such as arthropod, squid and vertebrate eyes, or the limbs and wings of arthropods and vertebrates, can depend on a common set of homologous genes that control their assembly and function; this is called deep homology.[201][202]

During evolution, some structures may lose their original function and become vestigial structures.[203] Such structures may have little or no function in a current species, yet have a clear function in ancestral species, or other closely related species. Examples include pseudogenes,[204] the non-functional remains of eyes in blind cave-dwelling fish,[205] wings in flightless birds,[206] the presence of hip bones in whales and snakes,[198] and sexual traits in organisms that reproduce via asexual reproduction.[207] Examples of vestigial structures in humans include wisdom teeth,[208] the coccyx,[203] the vermiform appendix,[203] and other behavioural vestiges such as goose bumps[209][210] and primitive reflexes.[211][212][213]

However, many traits that appear to be simple adaptations are in fact exaptations: structures originally adapted for one function, but which coincidentally became somewhat useful for some other function in the process. One example is the African lizard Holaspis guentheri, which developed an extremely flat head for hiding in crevices, as can be seen by looking at its near relatives. However, in this species, the head has become so flattened that it assists in gliding from tree to treean exaptation. Within cells, molecular machines such as the bacterial flagella[215] and protein sorting machinery[216] evolved by the recruitment of several pre-existing proteins that previously had different functions.[166] Another example is the recruitment of enzymes from glycolysis and xenobiotic metabolism to serve as structural proteins called crystallins within the lenses of organisms' eyes.[217][218]

An area of current investigation in evolutionary developmental biology is the developmental basis of adaptations and exaptations.[219] This research addresses the origin and evolution of embryonic development and how modifications of development and developmental processes produce novel features.[220] These studies have shown that evolution can alter development to produce new structures, such as embryonic bone structures that develop into the jaw in other animals instead forming part of the middle ear in mammals.[221] It is also possible for structures that have been lost in evolution to reappear due to changes in developmental genes, such as a mutation in chickens causing embryos to grow teeth similar to those of crocodiles.[222] It is now becoming clear that most alterations in the form of organisms are due to changes in a small set of conserved genes.[223]

Interactions between organisms can produce both conflict and cooperation. When the interaction is between pairs of species, such as a pathogen and a host, or a predator and its prey, these species can develop matched sets of adaptations. Here, the evolution of one species causes adaptations in a second species. These changes in the second species then, in turn, cause new adaptations in the first species. This cycle of selection and response is called coevolution.[224] An example is the production of tetrodotoxin in the rough-skinned newt and the evolution of tetrodotoxin resistance in its predator, the common garter snake. In this predator-prey pair, an evolutionary arms race has produced high levels of toxin in the newt and correspondingly high levels of toxin resistance in the snake.[225]

Not all co-evolved interactions between species involve conflict.[226] Many cases of mutually beneficial interactions have evolved. For instance, an extreme cooperation exists between plants and the mycorrhizal fungi that grow on their roots and aid the plant in absorbing nutrients from the soil.[227] This is a reciprocal relationship as the plants provide the fungi with sugars from photosynthesis. Here, the fungi actually grow inside plant cells, allowing them to exchange nutrients with their hosts, while sending signals that suppress the plant immune system.[228]

Coalitions between organisms of the same species have also evolved. An extreme case is the eusociality found in social insects, such as bees, termites and ants, where sterile insects feed and guard the small number of organisms in a colony that are able to reproduce. On an even smaller scale, the somatic cells that make up the body of an animal limit their reproduction so they can maintain a stable organism, which then supports a small number of the animal's germ cells to produce offspring. Here, somatic cells respond to specific signals that instruct them whether to grow, remain as they are, or die. If cells ignore these signals and multiply inappropriately, their uncontrolled growth
causes cancer.[229]

Such cooperation within species may have evolved through the process of kin selection, which is where one organism acts to help raise a relative's offspring.[230] This activity is selected for because if the helping individual contains alleles which promote the helping activity, it is likely that its kin will also contain these alleles and thus those alleles will be passed on.[231] Other processes that may promote cooperation include group selection, where cooperation provides benefits to a group of organisms.[232]

Speciation is the process where a species diverges into two or more descendant species.[233]

There are multiple ways to define the concept of "species." The choice of definition is dependent on the particularities of the species concerned.[234] For example, some species concepts apply more readily toward sexually reproducing organisms while others lend themselves better toward asexual organisms. Despite the diversity of various species concepts, these various concepts can be placed into one of three broad philosophical approaches: interbreeding, ecological and phylogenetic.[235] The Biological Species Concept (BSC) is a classic example of the interbreeding approach. Defined by Ernst Mayr in 1942, the BSC states that "species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups."[236] Despite its wide and long-term use, the BSC like others is not without controversy, for example because these concepts cannot be applied to prokaryotes,[237] and this is called the species problem.[234] Some researchers have attempted a unifying monistic definition of species, while others adopt a pluralistic approach and suggest that there may be different ways to logically interpret the definition of a species.[234][235]

Barriers to reproduction between two diverging sexual populations are required for the populations to become new species. Gene flow may slow this process by spreading the new genetic variants also to the other populations. Depending on how far two species have diverged since their most recent common ancestor, it may still be possible for them to produce offspring, as with horses and donkeys mating to produce mules.[238] Such hybrids are generally infertile. In this case, closely related species may regularly interbreed, but hybrids will be selected against and the species will remain distinct. However, viable hybrids are occasionally formed and these new species can either have properties intermediate between their parent species, or possess a totally new phenotype.[239] The importance of hybridisation in producing new species of animals is unclear, although cases have been seen in many types of animals,[240] with the gray tree frog being a particularly well-studied example.[241]

Speciation has been observed multiple times under both controlled laboratory conditions and in nature.[242] In sexually reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four mechanisms for speciation. The most common in animals is allopatric speciation, which occurs in populations initially isolated geographically, such as by habitat fragmentation or migration. Selection under these conditions can produce very rapid changes in the appearance and behaviour of organisms.[243][244] As selection and drift act independently on populations isolated from the rest of their species, separation may eventually produce organisms that cannot interbreed.[245]

The second mechanism of speciation is peripatric speciation, which occurs when small populations of organisms become isolated in a new environment. This differs from allopatric speciation in that the isolated populations are numerically much smaller than the parental population. Here, the founder effect causes rapid speciation after an increase in inbreeding increases selection on homozygotes, leading to rapid genetic change.[246]

The third mechanism of speciation is parapatric speciation. This is similar to peripatric speciation in that a small population enters a new habitat, but differs in that there is no physical separation between these two populations. Instead, speciation results from the evolution of mechanisms that reduce gene flow between the two populations.[233] Generally this occurs when there has been a drastic change in the environment within the parental species' habitat. One example is the grass Anthoxanthum odoratum, which can undergo parapatric speciation in response to localised metal pollution from mines.[247] Here, plants evolve that have resistance to high levels of metals in the soil. Selection against interbreeding with the metal-sensitive parental population produced a gradual change in the flowering time of the metal-resistant plants, which eventually produced complete reproductive isolation. Selection against hybrids between the two populations may cause reinforcement, which is the evolution of traits that promote mating within a species, as well as character displacement, which is when two species become more distinct in appearance.[248]

Finally, in sympatric speciation species diverge without geographic isolation or changes in habitat. This form is rare since even a small amount of gene flow may remove genetic differences between parts of a population.[249] Generally, sympatric speciation in animals requires the evolution of both genetic differences and non-random mating, to allow reproductive isolation to evolve.[250]

One type of sympatric speciation involves crossbreeding of two related species to produce a new hybrid species. This is not common in animals as animal hybrids are usually sterile. This is because during meiosis the homologous chromosomes from each parent are from different species and cannot successfully pair. However, it is more common in plants because plants often double their number of chromosomes, to form polyploids.[251] This allows the chromosomes from each parental species to form matching pairs during meiosis, since each parent's chromosomes are represented by a pair already.[252] An example of such a speciation event is when the plant species Arabidopsis thaliana and Arabidopsis arenosa crossbred to give the new species Arabidopsis suecica.[253] This happened about 20,000 years ago,[254] and the speciation process has been repeated in the laboratory, which allows the study of the genetic mechanisms involved in this process.[255] Indeed, chromosome doubling within a species may be a common cause of reproductive isolation, as half the doubled chromosomes will be unmatched when breeding with undoubled organisms.[256]

Speciation events are important in the theory of punctuated equilibrium, which accounts for the pattern in the fossil record of short "bursts" of evolution interspersed with relatively long periods of stasis, where species remain relatively unchanged.[257] In this theory, speciation and rapid evolution are linked, with natural selection and genetic drift acting most strongly on organisms undergoing speciation in novel habitats or small populations. As a result, the periods of stasis in the fossil record correspond to the parental population and the organisms undergoing speciation and rapid evolution are found in small populations or geographically restricted habitats and therefore rarely being preserved as fossils.[170]

Extinction is the disappearance of an entire species. Extinction is not an unusual event, as species regularly appear through speciation and disappear through extinction.[258] Nearly all animal and plant species that have lived on Earth are now extinct,[259] and extinction appear
s to be the ultimate fate of all species.[260] These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass extinction events.[261] The CretaceousPaleogene extinction event, during which the non-avian dinosaurs became extinct, is the most well-known, but the earlier PermianTriassic extinction event was even more severe, with approximately 96% of all marine species driven to extinction.[261] The Holocene extinction event is an ongoing mass extinction associated with humanity's expansion across the globe over the past few thousand years. Present-day extinction rates are 1001000 times greater than the background rate and up to 30% of current species may be extinct by the mid 21st century.[262] Human activities are now the primary cause of the ongoing extinction event;[263]global warming may further accelerate it in the future.[264]

The role of extinction in evolution is not very well understood and may depend on which type of extinction is considered.[261] The causes of the continuous "low-level" extinction events, which form the majority of extinctions, may be the result of competition between species for limited resources (the competitive exclusion principle).[66] If one species can out-compete another, this could produce species selection, with the fitter species surviving and the other species being driven to extinction.[131] The intermittent mass extinctions are also important, but instead of acting as a selective force, they drastically reduce diversity in a nonspecific manner and promote bursts of rapid evolution and speciation in survivors.[265]

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The Earth is about 4.54 billion years old.[266][267][268] The earliest undisputed evidence of life on Earth dates from at least 3.5 billion years ago,[7][269] during the Eoarchean Era after a geological crust started to solidify following the earlier molten Hadean Eon. Microbial mat fossils have been found in 3.48 billion-year-old sandstone in Western Australia.[12][13][14] Other early physical evidence of a biogenic substance is graphite in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland[11] as well as "remains of biotic life" found in 4.1 billion-year-old rocks in Western Australia.[8][9] According to one of the researchers, "If life arose relatively quickly on Earth then it could be common in the universe."[8]

More than 99 percent of all species, amounting to over five billion species,[270] that ever lived on Earth are estimated to be extinct.[16][17] Estimates on the number of Earth's current species range from 10 million to 14 million,[18] of which about 1.2 million have been documented and over 86 percent have not yet been described.[19]

Highly energetic chemistry is thought to have produced a self-replicating molecule around 4 billion years ago, and half a billion years later the last common ancestor of all life existed.[5] The current scientific consensus is that the complex biochemistry that makes up life came from simpler chemical reactions.[271] The beginning of life may have included self-replicating molecules such as RNA[272] and the assembly of simple cells.[273]

All organisms on Earth are descended from a common ancestor or ancestral gene pool.[200][274] Current species are a stage in the process of evolution, with their diversity the product of a long series of speciation and extinction events.[275] The common descent of organisms was first deduced from four simple facts about organisms: First, they have geographic distributions that cannot be explained by local adaptation. Second, the diversity of life is not a set of completely unique organisms, but organisms that share morphological similarities. Third, vestigial traits with no clear purpose resemble functional ancestral traits and finally, that organisms can be classified using these similarities into a hierarchy of nested groupssimilar to a family tree.[276] However, modern research has suggested that, due to horizontal gene transfer, this "tree of life" may be more complicated than a simple branching tree since some genes have spread independently between distantly related species.[277][278]

Past species have also left records of their evolutionary history. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record.[279] By comparing the anatomies of both modern and extinct species, paleontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Further, as prokaryotes such as bacteria and archaea share a limited set of common morphologies, their fossils do not provide information on their ancestry.

More recently, evidence for common descent has come from the study of biochemical similarities between organisms. For example, all living cells use the same basic set of nucleotides and amino acids.[280] The development of molecular genetics has revealed the record of evolution left in organisms' genomes: dating when species diverged through the molecular clock produced by mutations.[281] For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 98% of their genomes and analysing the few areas where they differ helps shed light on when the common ancestor of these species existed.[282]

Prokaryotes inhabited the Earth from approximately 34 billion years ago.[284][285] No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years.[286] The eukaryotic cells emerged between 1.62.7 billion years ago. The next major change in cell structure came when bacteria were engulfed by eukaryotic cells, in a cooperative association called endosymbiosis.[287][288] The engulfed bacteria and the host cell then underwent coevolution, with the bacteria evolving into either mitochondria or hydrogenosomes.[289] Another engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants.[290]

The history of life was that of the unicellular eukaryotes, prokaryotes and archaea until about 610 million years ago when multicellular organisms began to appear in the oceans in the Ediacaran period.[284][291] The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria.[292] In January 2016, scientists reported that, about 800 million years ago, a minor genetic change in a single molecule called GK-PID may have allowed organisms to go from a single cell organism to one of many cells.[293]

Soon after the emergence of these first multicellular organisms, a remarkable amount of biological diversity appeared over approximately 10 million years, in an event called the Cambrian explosion. Here, the majority of types of modern animals appeared in the fossil record, as well as unique lineages that subsequently became extinct.[294] Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis.[295]

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Neo-Darwinism : The Current Paradigm. by Brig Klyce

Posted: at 2:36 pm

Will mutations produce wings like in angels, in a human being? If you wanted to develop a race of angels, would it be possible to select for a pair of wings? TheodosiusDobzhansky I could try! PeterMedawar (1) Charles Darwin championed the theory of common descent and evolution by natural selection among descendants with slight variations on the ancestors' features. The concept of natural selection springs from artificial selection, a procedure breeders use to enhance desired characteristics such as stamina, color, size, yield, and so forth, in animals and plants. Darwin thought that a similar process happens in nature. There is nothing to disagree with here. Natural selection can bring about evolution in a fashion similar to artificial selection. But animal breeders and plant breeders have always known that artificial selection has limits. Wholly new characteristics never emerge from artificial selection; they will never breed a dog with antlers. The same kind of limit applies to all natural selection operating on the available genetic material. Genetics Neo-Darwinism is an attempt to reconcile Mendelian genetics, which says that organisms do not change with time, with Darwinism, which claims they do. Lynn Margulis (2) Darwin actually knew very little about genetics. The great pioneer of that field was Gregor Mendel, whose work was contemporary with Darwin's. Now the theory of evolution incorporates Mendel's genetics into Darwin's framework; the combined theory was called "neo-Darwinism." (Recently, that cumbersome term is being replaced by the simpler "Darwinism".)

According to this paradigm, evolution is driven by chance. Chance mutations affect one or a few nucleotides of DNA per occurrence. Bigger changes come from recombination, a genetic process in which longer strands of DNA are swapped, transferred, or doubled. These two processes, mutation and recombination, create new meaning in DNA by lucky accidents. According to the prevailing paradigm, this is the mechanism behind evolution.

One problem with this story is that it is implausible. It is analogous to saying that a great work of literature such as Moby Dick could emerge from lesser preexisting books, if there were enough typos and swapping of paragraphs along the way. The trouble is, when this process is actually attempted with text, it never succeeds. Only with guidance can random processes lead to meaningful sentences or paragraphs. But plausibility in the current paradigm of evolution is apparently unnecessary. We are told by Richard Dawkins, "The general lesson we should learn is never to use human judgment in assessing such matters" (3).

Ordinary people are under the impression that there are examples in nature which prove that chance mutation and recombination can create new meaning in genetic code new genes. Yet the alleged examples of the phenomenon do not actually exemplify it. Consider the ability of bacteria to become resistant to antibiotics. Salvador Luria and Max Delbrck proved in 1943 that the resistant bacteria descended from preexisting strains; the genes for the resistance were already available in the gene pool. Although some have disputed this interpretation of their experiments, it is now well established. And today we know that bacteria often acquire whole new genes conferring resistance to antibiotics; the genes are imported on "resistance plasmids" (3.5).

Another example of similar "evolution" in eukaryotic cells is described in Renato Dulbecco's The Design of Life. This time the genes for the new characteristic are already present in the organism (4):

The study of this phenomenon has uncovered an amazing organization in the parasite's DNA. Radioactive probes ... have revealed that a hundred or more genes are devoted to coat variation, each gene specifying one kind of coat molecule.... Only one is active at a time.

The moth that has evolved to blend in with the sooty walls and treetrunks of modern industrial cities is another example of evolution in our time. Again, the genes for darker coloring in the moth were already available in the gene pool. Yes, there are a few documented examples in which a simple mutation in a bacterium brings about antibiotic resistance, but in these cases it does so by reducing or eliminating the affected gene's function, not by creating a new function. Among viruses, mutations can even alter a coating protein and thereby temporarily disguise the virus (4.5). But again, no new function is created. Such mutations could not drive the evolutionary progress we observe in the fossil record.

Of course, there are many examples of genes that have mutated slightly in the course of evolution without losing their original functions. And other examples, fewer in number, apparently indicate that genes may mutate slightly and acquire different but closely related functions. The globin family of genes are in this category. And in a third category, a handful of examples may indicate that a gene mutates slightly and acquires a wholly new function. These finally seem to be examples in which mutations create new meaning, but we are not sure this third account is accurate. The number of changed essential nucleotides in new genes that supposedly arose this way is still in the dozens at least, whereas the number of possible genes that would differ from a given average-size gene by only half-a-dozen essential nucleotides is enormous, on the order of 10^14. Blindly traversing even this short distance in sequence space so large requires incredible luck.

(Genetics and Fitness Landscapes) Epistasis and the Structure of Fitness Landscapes... by Franois Blanquart and Thomas Bataillon, doi:10.1534/genetics.115.182691, Genetics, 01 Jun 2016. Fisher's model was ...often unable to explain the full structure of fitness landscapes. 01 Jun 2016: ...The mutation event giving rise to industrial melanism in Britain was the insertion of a ...transposable element.... Toward a prospective molecular evolution by Xionglei He, Li Liu, doi:10.1126/science.aaf7543, Science, 13 May 2016. Two studies ...characterize the in vivo fitness landscape of two RNA genes. ...Although the number of mutants they examined is still a small fraction of all possible variants of the genes, most of the possible genotypes that differ from the wild-type by one or two point mutations were characterized. Thus, a high-quality local fitness landscape of a gene has been constructed. The fitness landscape of a tRNA gene by Chuan Li et al., doi:10.1126/science.aae0568, Science, online 14 Apr 2016. Approximately 1% of single point mutations in the gene are beneficial, while 42% are deleterious. 4 Sep 2015: ...Thousands of transcripts ...which are likely to have originated de novo.... 4 Jan 2016. Catarina Gadelha et al., "Membrane domains and flag
ellar pocket boundaries are influenced by the cytoskeleton in African trypanosomes" [abstract], doi:10.1073/pnas.0909289106, p17425-17430 v106, Proc. Natl. Acad. Sci. USA, 13 Oct 2009. Parasite breaks its own DNA to avoid detection, The Rockefeller University, 15 Apr 2009. 28 Aug 2007: Varying environments can speed up evolution. [mentions Fitness Landscapes.] Thanat Chookajorn et al., "Epigenetic memory at malaria virulence genes" [abstract], 10.1073/pnas.0609084103, Proc. Natl. Acad. Sci. USA, online 5 Jan 2007. "The malaria parasite Plasmodium falciparum can switch its variant surface proteins ...to evade the host immune response. ...The gene family is enormous with a virtually unlimited number of members. ...Control of var gene transcription and antigenic variation is associated with a chromatin memory...." 26 Sep 2005: Common bacteria share an infinite gene pool?! 16 Feb 2005: Fitness Landscapes. 2003, May 11: Computer model evolves complex functions? [mentions Fitness Landscapes.] 2003, March 25: Here Be Dragons, by David W. Koerner and Simon Levay. [mentions Fitness Landscapes.] ...African trypanosome source of scientific insight, The Rockefeller University, 25 Nov 2002.

The April 15, 1997 issue of Proc. Natl. Acad. Sci. USA contains a report with strong evidence sequence similarities linking two genes with different functions in a common Antarctic fish. One gene codes for trypsinogen, an enzyme produced in the pancreas. The other codes for a protein called antifreeze glycoprotein (AFGP) that keeps the fish's blood from freezing.

The related sequences are so similar that the biologists, from the University of Illinois, Urbana, date the divergence of the sequences as only five to 14 million years ago. This timing coincides with the independently estimated time when the Antarctic Ocean was frozen. "Selective pressure" would have favored the creation of an antifreeze gene then. The report makes a strong case that the antifreeze gene evolved from the trypsinogen gene by a series of steps including whole gene duplication; the deletion, insertion, duplication, and amplification of smaller sequences; and a frameshift mutation.

It is possible to estimate the likelihood of creating a new gene this way. One could estimate the actual rate at which the steps listed above occur in the fish germline cells and the fish population at the time when the Antarctic Ocean was freezing. From there one could straightforwardly calculate the approximate number of trials of new genes that could have occurred, during a reasonable time window, to produce an antifreeze protein gene in the fish. One could also estimate the number of different actual genes that would code for antifreeze proteins. Other work by the same authors in the same issue (8) makes this estimation seem possible. Finally, a mathematician could, with little trouble, count the number of possible different genes that could be created from the trypsinogen gene and other possible precursor genes by the steps listed above. These estimates would enable one to calculate the probability that an antifreeze gene would be found by trial and error in the time available.

The last estimate, however, turns out to be lethal to our chances. The number of possible different genes that could be created by only a handful of steps from the list above is enormous. For example, consider a gene of 2,500 nucleotides, allowing a 75% error rate (625 essential nucleotides.) The number of possible different genes that could be created by deleting a single essential nucleotide and inserting it elsewhere in the same gene, five successive times, is 10^28. When sequences for insertion into the target gene can be any length, and can come from any of thousands of other genes, the possibilities quickly approach the theoretical maximum in this example 4^625 or about 10^370. So the proposed mechanism does not increase the probability of arriving at a wholly new gene by chance. It's still monkeys writing Shakespeare, only now they have word processors with "cut and paste" functions.

The authors are aware of this problem and postulate other roles for genetic intermediates between the two genes. However, they seem to realize that this speculation is inadequate, because they conclude [the second article] by saying, "The selection of an appropriate permutation of three codons... was likely shaped by the structural specificity required for antifreeze ice interaction to take place." This sounds like teleology.

After the careful analysis by Chen et al., one might understand if a neo-Darwinists lost patience at this point in the discussion and simply asserted that it must have happened as they describe. Any reasonable person would admit that genetic sequences may gradually diverge over time, as in the antifreeze gene example. Cosmic Ancestry does not dispute that genetic sequences can gradually diverge over time, and that genetic recombination occurs. But for the discovery of lengthy new sequences with new meaning, the math in the example still doesn't work. And a model for this process in text, without guidance, will not succeed.

If the antifreeze gene was composed by the process Chen et al. describe, perhaps antifreeze activity is so non-specific that "almost any gene will do," as considered above. But if the precise antifreeze sequence was required (allowing only normal error tolerance), the composition process would have to have been guided somehow. Neo-Darwinism allows guidance by a chain of hypothetical intermediate steps (but not by teleology). Cosmic Ancestry would explain such guidance only by other instructions already in the genome; however, this concept is undeveloped.

(Antifreeze Protein Genes) Thomas J. Neara et al., "Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes" [abstract], doi:10.1073/pnas.111516910, Proc. Natl. Acad. Sci. USA, online 13 Feb 2012. Cheng Deng et al., "Evolution of an antifreeze protein by neofunctionalization under escape from adaptive conflict" [abstract], doi:10.1073/pnas.1007883107, Proc. Natl. Acad. Sci. USA, online 29 Nov 2010. "We found that an SAS gene, having both sialic acid synthase and rudimentary ice-binding activities, became duplicated." 12 Nov 2006: The Making of the Fittest, by geneticist Sean B. Carroll, W. W. Norton, 2006. Evolutionary Scrap-heap Challenge..., a Reply forwarded by Stan Franklin, 17 Apr 2006. 7 May 2004: Ultraconserved elements. 2003, November 20: In mammals, CNGs are more numerous and better conserved than genes a hint of possible other instructions already in the genome. 1999, October 21: A blood protein arose from a digestive enzyme.

Evidence from fossi
ls does not bear out Darwin's theory of gradual change. Instead, species remain relatively unchanged for long periods, and then suddenly, new kinds arise. Many bacteria today have apparently changed very little since they first appeared. Some archaebacterial species appear to be as old as life on Earth; they haven't evolved very far in almost four billion years. We know that bacteria were the only inhabitants of the earth until about 1.7 billion years ago. Apparently, no major evolutionary developments (multicellularity, cell specialization, etc.) happened among the bacteria for the first two billion years of life more than half of the time life has existed on Earth.

By contrast, the entire Cambrian Explosion of about 570 million years ago took only five to nine million years (11). All kinds of multicelled creatures, in astonishing variety, seemed to come at once out of nowhere (12). On the cover of Time we read this synopsis of the Cambrian Explosion: "New discoveries show that life as we know it began in an amazing biological frenzy that changed the planet almost overnight" (13).

Similar discontinuities can be seen on a finer scale in the individual histories of species. In fact, the sudden appearance of new kinds of creatures, without evidence of intermediate kinds, is more the rule than the exception. Examples of intermediate kinds, such as the dog-sized Mesohippus that preceded the horse are actually quite rare. Stephen Jay Gould calls this discrepancy between the theory (gradualism) and the evidence (big steps) the paleontologists' "trade secret."

Today there is still considerable discord over punctuated equilibrium. How real is stasis (the period without appreciable change), how gradual is punctuation, and how can neo-Darwinists account for them? One proposal is "species sorting" or "species selection." In general, the new idea is that big evolutionary steps occur gradually in small, isolated populations. When the evolutionary steps are complete, the small population with its new advantage quickly expands and replaces the bigger population. Thus, in the geological record the change looks instantaneous. This solution has some appeal, but it offers little more by way of explanation than that gradual evolution always takes place somewhere out of sight. In 1931, J.B.S. Haldane foresaw this problem. "The paleontologist can always postulate a slow evolution in some area hitherto unexplored geologically, followed by migration into known areas" (14). Perhaps punctuated equilibrium is a clue that the genetic mechanism underlying evolutionary progress is altogether different from the one currently in favor.

(Punctuated Equilibrium) Can Population Genetics Adapt to Rapid Evolution? by Philipp W. Messer, Stephen P. Ellner and Nelson G. Hairston Jr., doi:10.1016/j.tig.2016.04.005, Trends in Genetics, online 13 May 2016. The time-rate scaling of phenotypic evolution suggests that selection on phenotypes is often fluctuting in direction, allowing phenotypes to respond rapidly to environmental fluctuations while remaining within relatively constant bounds over longer periods. What sparked the Cambrian explosion? by Douglas Fox, doi:10.1038/530268a, Nature, 18 Feb 2016. J. William Schopf et al., "Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution's null hypothesis" [abstract], doi:10.1073/pnas.1419241112, PNAS, online 2 Feb 2015; and commentary: Scientists discover organism that hasnt evolved in more than 2 billion years, by Stuart Wolpert, UCLA Newsroom, 2 Feb 2015. M. Paul Smith and David A. T. Harper, "Causes of the Cambrian Explosion" [summary], doi:10.1126/science.1239450, p 355-1356 v 341, Science, 20 Sep 2013. Erik A. Sperling et al., "Oxygen, ecology, and the Cambrian radiation of animals" [abstract], doi:10.1073/pnas.1312778110, p13446-13451 v110, Proc. Natl. Acad. Sci. USA, 13 Aug 2013. "...Providing an integrated explanation for both the pattern and timing of Cambrian animal radiation." Josef C. Uyeda et al., "The million-year wait for macroevolutionary bursts" [abstract], doi:10.1073/pnas.1014503108, Proc. Natl. Acad. Sci. USA, online 23 Aug 2011. "The best-fitting model to explain this pattern is a model that combines rare but substantial bursts of phenotypic change with bounded fluctuations on shorter timescales." 18 Apr 2011: There is no gradualism in the fossil record Lynn Margulis 7 Jan 2009: Latent evolutionary potential was realized soon after environmental limitations were removed. 15 Jan 2008: Did meteors cause the Great Ordovician Biodiversification Event? 4 Jan 2008: A sudden diversification of life..., if confirmed,... reinforces the idea that major evolutionary innovations occurred in bursts. Gene Hunt, "The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages" [abstract], doi:10.1073/pnas.0704088104, p18404-18408 v104, Proc. Natl. Acad. Sci. USA, 20 Nov (online 14 Nov) 2007. "The rarity with which directional evolution was observed in this study corroborates a key claim of punctuated equilibria...." Antonis Rokas et al., "Animal Evolution and the Molecular Signature of Radiations Compressed in Time" [abstract], 10.1126/science.1116759, p 1933-1938 v 310, Science, 23 Dec 2006. "The differences ...suggest that the early history of metazoans was a radiation compressed in time, a finding that is in agreement with paleontological inferences." Ancient crustacean raises new questions, by Ivan Noble, BBC News Online, 19 July 2001: 511 million-year-old fossil supports Cambrian expolsion. Carol Kaesuk Yoon, "Fossil Findings May Force Revisions in the History of Life" [text], The New York Times, 22 May 2001. "The real peak of life's diversity may have come and gone more than 400 million years ago." 1999, November 3: Fossils of primitive fish have been found in the Lower Cambrian.

Richard Dawkins writes that the eye could evolve easily, by chance, in tiny steps. In an article entitled "The Eye in a Twinkling," he discusses how improvements of only one percent each could lead, in only some 400,000 generations, to the eye of a fish (15). He says eyes could have evolved many times, as they must have, because there are about 40 different kinds of eyes.

If eyes have evolved as Dawkins describes, by chance, then the genetic program to coordinate all the embryological steps in the growth of an eye (of each type) would evolve only after the genes for the steps themselves had evolved. Yet recently, scientists learned that the same gene coordinating the embryological steps in eye-making works in wasps and mice! The coordinating gene must have come first. "The observation that mammals and insects, which have evolved
separately for more than 500 million years, share the same master control gene for eye morphogenesis indicates that the genetic control mechanisms for development are much more universal than anticipated" (16). In March, 1997, a group of scientists at the National Eye Institute in Bethesda, Maryland and the University of Basel in Switzerland reported that a gene controlling eye development is shared by fruitflies, mice, and squid (17). These startling developments have made theorists reconsider how eyes evolved (18).

A coordinating gene that works the same way in very different animals is not confined to the eye. Homeotic genes in Drosophila (the fruitflies often used to study genetics) are known to control the expression of at least twenty of the fly's genes. Homeotic genes can be identified by the presence in them of a sequence 180 nucleotides long called a homeobox. "The big surprise concerning homeoboxes came in 1984 with the discovery of a homeobox, very similar to the Drosophila ones in a vertebrate, the toad Xenopus laevis. Soon afterwards the first mammalian homeoboxes were located..." (19). Coordinating genes appear to be standardized across a broad range of multicelled animals. And in March, 1997, biologists from the John Innes Centre for Plant Science Research in Norwich, England and Caltech found impressive similarities between homeotic genes in the fruitfly and a flowering plant (20).

It is difficult for neo-Darwinism to explain the appearance of embryological coordinating genes before the appearance of the embryological steps they coordinate. It's as if the blueprints for assembly-line manufacturing plants were on hand before the invention of assembly-line manufacturing.

(Coordinating Genes) 26 Aug 2009: "The Origin of Life on Earth" in a Scientific American Special Issue: "Understanding Origins". Wayne L. Davies et al., "Into the blue: Gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii" [abstract], doi:10.1101/gr.084509.108, p 415-426 v 19, Genome Research, Mar (online 4 Feb) 2009. 25 Jun 2008: Vertebrate and jellyfish eyes use similar genes. 21 May 2005: The key to early eye evolution? A highly conserved mechanism ...points to a common evolutionary origin of animal eyes. "The mechanisms used to control nerve cell formation in the zebrafish and fruitfly eyes thus appear to be exact copies of each other." Carl Neumann, Max Planck Institute for Developmental Biology, Tuebingen, 22 September 2000.

"Convergent evolution" has been observed since the time of Darwin. It is the name given to apparent coincidences in evolution, such as the physical similarity between sharks (fish) and dolphins (mammals), or the parallelism in the cochlea of birds and mammals. A striking example is the resemblance between the Tasmanian wolf, which is an Australian marsupial "dog," and mammalian dogs common on other continents. Although the two would be very far apart on a phylogenetic tree, it takes a skilled zoologist to distinguish them by anatomical features like the skeleton. And examples of convergence also appear at the molecular level, as in similar antibody proteins carried by camels and nurse sharks. As The New York Times observes, "The more scientists look, the more examples of convergence they find" (21).

Neo-Darwinism accounts for the phenomenon by supposing that evolutionary options are often severely restricted by circumstances. "Convergences keep happening because organisms keep wanting to do similar things, and there are only so many ways of doing them," says molecular biologist Rudolf A. Raff of Indiana University (22). So the phenomenon has been named "the principle of convergence" or "convergent evolution." But naming the problem doesn't mean it has been explained. The renowned Harvard biologist Stephen Jay Gould believes that slight differences in the course of evolution should lead to totally different outcomes. If so, convergence is baffling. A discerning witness is justified in wondering if neo-Darwinism adequately explains convergence, or if another theory might account for it better.

(Convergent Evolution) Sishuo Wang et al., "Long-Lasting Gene Conversion Shapes the Convergent Evolution of the Critical Methanogenesis Genes," doi:10.1534/g3.115.020180, G3, online 16 Sep 2015. M. Sabrina Pankey et al., "Predictable transcriptome evolution in the convergent and complex bioluminescent organs of squid" [abstract], doi:10.1073/pnas.1416574111, Proc. Natl. Acad. Sci. USA, online 4 Nov 2014. "Unless there are strong constraints, the probability of complex organs originating multiple times through similar trajectories should be vanishingly small." 27 Jun 2014: The same genes were recruited within the different species to make evolutionarily new structures that function similarly. Sylvain Aubry, Steven Kelly et al., "Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis" [html], doi:10.1371/journal.pgen.1004365, 10(6): e1004365, PLoS Genet, online 5 Jun 2014. Joe Parker et al., "Genome-wide signatures of convergent evolution in echolocating mammals" [html], doi:10.1038/nature12511, Nature, online 4 Sep 2013; and commentary: Queen Mary scientists uncover genetic similarities between bats and dolphins, Queen Mary University of London, 4 Sep 2013. Nicols Frankel et al., "Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolution" [abstract], doi:10.1073/pnas.1207715109, Proc. Natl. Acad. Sci. USA, online 29 Nov 2012. Mario Ventura et al., "Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee" [abstract], doi:10.1101/gr.124461.111, p1640-1649 v21, Genome Research, Oct 2011. Flajnik MF, Deschacht N, Muyldermans S, "A Case Of Convergence: Why Did a Simple Alternative to Canonical Antibodies Arise in Sharks and Camels?" [html], doi:10.1371/journal.pbio.1001120, 9(8): e1001120, PLoS Biol, online 2 Aug 2011. S. Hollis Woodard, Brielle J. Fischman et al., "Genes involved in convergent evolution of eusociality in bees" [abstract], doi:10.1073/pnas.1103457108, Proc. Natl. Acad. Sci. USA, online 11 Apr 2011. And commentary: The genes that make a bee sociable by Ewen Callaway, Nature.com, 11 Apr 2011. "Now, a genomic study of different bee species suggests that even when insects evolve eusociality independently, they often use the same genes and molecular pathways." Naomi J. Brown et al., "Independent and Parallel Recruitment of Preexisting Mechanisms Underlying C4 Photosynthesis" [abstract], doi:10.1126/science.1201248, p1436-1439 v331, Science, 18 Mar 2011. David B
. Wake et al., "Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution" [abstract], doi:10.1126/science.1188545, p1032-1035 v331, Science, 25 Feb 2011. "Common developmental genetic mechanisms have been shown to underlie features that long were considered classic examples of convergent evolution." Homoplasy: A Good Thread to Pull to Understand the Evolutionary Ball of Yarn, Press Release 11-041, National Science Foundation, 24 Feb 2011. "...The evolution of eyes, which evolved many times in different groups of organisms--from invertebrates to mammals--all of which share an identical genetic code for their eyes." John J. Wiens, "Re-evolution of lost mandibular teeth in frogs after more than 200 million years, and re-evaluating Dollo's law" [abstract], doi:10.1111/j.1558-5646.2011.01221.x, Evolution, online 27 Jan 2011. ...Re-Evolution Of Lost Teeth In Frogs After More Than 200 Million Years, Stony Brook University, 7 Feb 2011. 18 Jan 2011: Many features appear to have originated more than once in the history of life on Earth. Julius Lukes et al., "Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates" [abstract], doi:10.1073/pnas.0901004106, p 9963-9970 v 106, Proc. Natl. Acad. Sci. USA, 16 Jun 2009. Todd A. Castoe et al., "Evidence for an ancient adaptive episode of convergent molecular evolution" [abstract], doi:10.1073/pnas.0900233106, Proc. Natl. Acad. Sci. USA, online 28 Apr 2009. Bastien Boussau et al., "Parallel adaptations to high temperatures in the Archaean eon" [abstract], doi:10.1038/nature07393, p 942-946 v 456, Nature, 18-25 Dec 2008. Juan C. Opazo et al., "Genomic evidence for independent origins of -like globin genes in monotremes and therian mammals" [abstract], doi:10.1073/pnas.0710531105, p 1590-1595 v 105, Proc. Natl. Acad. Sci. USA, 23 Jan 2008. 28 Jan 2006: Important aspects of the history of life are replicable and predictable. 16 Mar 2005: Life's Solution, by Simon Conway Morris. Spider webs untangle evolution "...The concept that chance reigns supreme may ring less true when it comes to complex behaviours." Roxanne Khamsi, News@Nature.com, 1 Nov 2004. Juan Carlos Santos et al., "Multiple, recurring origins of aposematism and diet specialization in poison frogs" [abstract], doi:10.1073/pnas.2133521100, p 12792-12797 v 100, Proc. Natl. Acad. Sci. USA, 28 Oct 2003. Moya Meredith Smith and Zerina Johanson, "Separate Evolutionary Origins of Teeth from Evidence in Fossil Jawed Vertebrates" [abstract], doi:10.1126/science.1079623, p 1235-1236 v 299, Science, 21 Feb 2003. 23 Jan 2003: Wingless stick insects have re-evolved wings, perhaps many times. Poles apart, molars together "The teeth that might have allowed mammals to develop ...into today's relative giants arose twice on different continents." Juliette Shackleton, Nature Science Update, 4 January 2001.

Ernst Mayr's 1988 classic, Toward a New Philosophy of Biology, asks the question, "Does Microevolution Explain Macroevolution?" (24). The issue came into sharper focus after Niles Eldredge and Stephen Jay Gould introduced the concept of "punctuated equilibrium" into the discussion of evolution. Microevolution would occur during stasis, and macroevolution at the punctuation points. This scenario is inconsistent with neo-Darwinian gradualism, according to which macroevolution is simply cumulative microevolution over long periods of time. The question challenges standard neo-Darwinism at its heart.

In our opinion, neo-Darwinism adequately accounts for microevolution. Changes in existing allele frequencies are already known to cause microevolution such as the darkening of the English moth's wings. A single nucleotide substitution can alter a virus's protein coat into one that the host's immune system doesn't recognize. The insertion or deletion of a single nucleotide causes a nonsense mutation that would disable, for example, a promoter or repressor sequence, thereby switching other whole genetic programs off or on.

Macroevolutionary progress such as the evolution of photosynthesis, on the other hand, requires wholly new genes with lengthy new instruction sequences. Whereas a new gene can be activated by a single point mutation, as mentioned above, there is scant evidence that new genes can be composed by Darwinian random point mutations and recombination events. Examples supporting this composition method are very few and weak.

Notice the term "progress" in the preceding paragraph. Any significant advance in evolution requires new genes. But loss of function, of course, can occur without new genes. So, macroevolutionary loss of function is not hard to explain. The real question is, "Does microevolutionary progress explain macroevolutionary progress?"

An excellent example of microevolutionary progress was discovered in 1999, by geneticists and ophthalmologists at University College London. From sequences of opsin genes they have deduced a plausible way for trichromatic vision in the howler monkey to have evolved from dichromatic vision by neo-Darwinian gene duplication followed by nucleotide substitutions in one copy. Their analysis of the control regions of the genes, which are upstream of the coding regions, confirms the duplication. Interestingly, of the approximately 80 nucleotides from the coding region of the two genes that were compared, only one nucleotide was not identical. This plausible mutation causes a single amino acid substitution in the second howler opsin that changes its color sensitivity. The changed gene makes 3-color vision possible (25). In a recently discovered closely related example only two amino acid substitutions account for the blue-shifted vision of coelacanths (26).

The howler monkeys' acquisition of trichromatic vision represents evolutionary progress, unquestionably. But the same neo-Darwinian microevolutionary mechanism has not been shown to be capable of manufacturing the wholly new genes necessary for macroevolutionary progress. We believe that another source for these new genes is necessary.

(Microevolution & Macroevolution) Chris M Rands et al., "Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence" [html], doi:10.1186/1471-2164-14-95, n95 v14, BMC Genomics, 12 Feb 2013. Hiroshi Akashi et al., "Weak Selection and Protein Evolution" [abstract], doi:10.1534/genetics.112.140178, p15-31 v192, Genetics, 1 Sep 2012. 23 Feb 2012: Experimenters with a virus and its bacterial host in a quarantined system report a breakthrough. Tomohide Hiwatashi et al., "Gene conversion and purifying selection shape nucleotide
variation in gibbon L/M opsin genes" [abstract], doi:10.1186/1471-2148-11-312, v11 n312, BMC Evolutionary Biology, 22 Oct 2011. Takashi Tada et al., "Evolutionary replacement of UV vision by violet vision in fish" [abstract], doi:10.1073/pnas.0903839106, p17457-17462 v106, Proc. Natl. Acad. Sci. USA, 13 Oct 2009. "Mutagenesis experiments and ...computations show that the violet-sensitivity was achieved by the deletion of Phe-86...." 20 Sep 2008: Woodstock of evolution? Gerald H. Jacobs et al., "Emergence of Novel Color Vision in Mice Engineered to Express a Human Cone Photopigment" [abstract], 10.1126/science.1138838, p 1723-1725 v 315, Science, 23 Mar 2007. And commentary by Patrick Goymer, "Evolution: Colour vision for mice" [abstract], 10.1038/nrg2106, p 324-325 v 8, Nature Reviews Genetics, May 2007. 12 Nov 2006: The Making of the Fittest, by geneticist Sean B. Carroll, W. W. Norton, 2006. 23 Sep 2005: Today's protein families have been fine-tuned from ancient templates. Shozo Yokoyama and Naomi Takenaka, "The Molecular Basis of Adaptive Evolution of Squirrelfish Rhodopsins" [abstract], p 2071-2078 v 21 n 11, Molecular Biology and Evolution, Nov 2004: well-documented microevolution. 15 Jan 2004: Are normal microevolutionary processes sufficient to account for human origins? Uwe Stolz et al., "Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle" [abstract], Proc. Natl. Acad. Sci. USA, online 17 Nov 2003: typical example of microevolution. 2003, April 7: Stephen Jay Gould's account of macroevolution, in a new Encyclopedia of Evolution.... Macroevolutionary Progress Redefined..., a new webpage, posted 4 Sep 2002.

Artificial selection never produces wholly new characteristics. Without the input of new genes, there is no evidence that natural selection does either. The notion that mutation and recombination can compose new genes is implausible. There is scant evidence that mutation and recombination can compose functional new genes that differ from any known predecessor by more than, say, a dozen essential nucleotides. The evolution of antifreeze glycoproteins in Antarctic cod presents problems for both Darwinism and Cosmic Ancestry. Evolution does not appear to be gradual, contrary to Darwin's firm prediction. The standard theory cannot explain why the coordinating genes that control the development of embryos and major features are often very similar across totally different species. Convergent evolution is a surprise not well-explained by neo-Darwinism. Macroevolutionary progress is not accounted for by neo-Darwinian microevolution.

Does the "Extended Synthesis" Replace or not Replace Neo-Darwinism?... by Suzan Mazur, Huffington Post, 30 Apr 2016. Evolution of stickleback in 50 years on earthquake-uplifted islands by Emily A. Lescak et al., doi:10.1073/pnas.1512020112, PNAS, 14 Dec 2015. If the findings from stickleback are generalizable to other systems, then rapid evolution in the wild may be more common than previously documented. When Fruit Flies Get Sick, Their Offspring Become More Diverse, North Carolina State University, (+Newswise), 13 Aug 2015. Kevin N. Laland et al., "The extended evolutionary synthesis: its structure, assumptions and predictions" [html | pdf], doi:10.1098/rspb.2015.1019, Proc. R. Soc. B, 22 Aug 2015. "...It is vital that the conceptual frameworks themselves evolve in response to new data, theories and methodologies. This is not always straightforward, as habits of thought and practice are often deeply entrenched." We wish the new conceptual framework included this question: Is open-ended evolutionary innovation possible in a quarantined system? Aashiq H. Kachroo et al., "Systematic humanization of yeast genes reveals conserved functions and genetic modularity" [abstract], doi:10.1126/science.aaa0769, p 921-925 v 348, Science, 22 May 2015. 16 Jul 2015: ...Neo-Darwinism isn't falsifiable.... Peter Saunders 28 Apr 2015: Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Beyond genetics: illuminating the epigenome by Merlin Crossley, The Conversation, 20 Feb 2015. Sindhuja Devanapally et al., "Double-stranded RNA made in C. elegans neurons can enter the germline and cause transgenerational gene silencing" [abstract], doi:10.1073/pnas.1423333112, Proc. Natl. Acad. Sci. USA, online 2 Feb 2015. 15 Oct 2014: Does evolutionary theory need a rethink? New Genetic 'Operating System' Facilitated Evolution of 'Bilateral' Animals, UC San Diego News Center (+PhysOrg.com), 30 Sep 2014. "They found that TRF2 is present in bilateral animals, and is absent in animals that lack bilateral symmetry, such as jellyfish, sea anemones and sponges." Bolhuis JJ, Tattersall I, Chomsky N, Berwick RC, "How Could Language Have Evolved?" [html], doi:10.1371/journal.pbio.1001934, 12(8): e1001934, PLoS Biol., 26 Aug 2014. "...The relatively sudden origin of language poses difficulties that may be called 'Darwin's problem.'" Anton S. Petrov et al., "Evolution of the ribosome at atomic resolution" [abstract], doi:10.1073/pnas.1407205111, Proc. Natl. Acad. Sci. USA, online 30 Jun 2014. Evolution depends on rare chance events, "molecular time travel" experiments show, The University of Chicago Medicine (+Newswise), 19 Jun 2014. 7 Mar 2014: "Traditional evolutionary biology began in the 1930s...." Woltering JM, Noordermeer D, Leleu M, Duboule D, "Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits" [html], doi:10.1371/journal.pbio.1001773, 12(1): e1001773, PLoS Biol, 21 Jan 2014; and commentary: Mary Hoff, "A Footnote to the Evolution of Digits" [html], doi:10.1371/journal.pbio.1001774, 12(1): e1001774, PLoS Biol, 21 Jan 2014. "...Biologists should consider thinking in terms of regulatory circuitries rather than expression patterns when considering whether traits have arisen from a common ancestral characteristic." 20 Dec 2013: Eugene V. Koonin's book, The Logic of Chance Joana Projecto-Garcia, Chandrasekhar Natarajan et al., "Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds" [abstract], doi:10.1073/pnas.1315456110, p 20669-20674 v 110, Proc. Natl. Acad. Sci. USA, 17 Dec (online 2 Dec ) 2013. "These results demonstrate that repeated changes in biochemical phenotype involve parallelism at the molecular level...." Marc Kirschner, "Interview: Beyond Darwin: evolvability and the generation of novelty
" [html], doi:1186/1741-7007-11-110, n 110 v 11, BMC Biology, 7 Nov 2013. Darwinian evolution is clearly a good mechanism for improving things - but it is not necessarily a good mechanism for generating novelty. ...If you have processes that are already present but under suppression, then under stress you might see some of them emerge, and if you have fortuitous selection at the same time you can very quickly evolve. Evolution of new species requires few genetic changes, The University of Chicago Medicine (+Newswise), 31 Oct 2013. 2 Sep 2013: Metabolic systems ...contain a latent potential for evolutionary innovations with non-adaptive origins. 11 May 2013: ...TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage.... 30 Apr 2013: We don't fully understand how evolution works at the molecular level. Philip Ball Daniel W. McShea and Wim Hordijk, "Complexity by Subtraction" [abstract], doi:10.1007/s11692-013-9227-6, Evolutionary Biology, Apr 2013; and commentary: Study proposes alternative way to explain life's complexity, PhysOrg.com, 12 Apr 2013. Do plants 'veto' bad genes? by Heidi Ledford, Nature News, 8 Feb 2013. 20 Dec 2012: Evolution: A View from the 21st Century by James A. Shapiro Michael Lynch, "Evolutionary layering and the limits to cellular perfection" [abstract], doi:10.1073/pnas.1216130109, p18851-18856 v109 Proc. Natl. Acad. Sci. USA, 13 Nov (online 30 Oct) 2012. A New Theory of Early Animal Evolution, Astrobiology Magazine, 14 Oct 2012. Bruce Stillman, David Stewart and Jan Witkowski, eds., Evolution: The Molecular Landscape (Cold Spring Harbor Symposia on Quantitative Biology LXXIV), Cold Spring Harbor Laboratory Press, 2009. Science Study Shows 'Promiscuous' Enzymes Still Prevalent in Metabolism, UC San Diego (also Newswise), 30 Aug 2012. Giving Ancient Life Another Chance to Evolve, Georgia Institute of Technology, 11 Jul 2012. ...Hypothesis May be Game Changer for Evolutionary Theory by Whitney Heins, The University of Tennessee, 4 Apr 2012. Evolution: This View of Life, "an online general interest magazine in which all of the content is from an evolutionary perspective. It includes content aggregated from the internet, following the example set by the Huffington Post, as well as new content generated by our staff of editors and contributing authors in eleven subject areas: biology, culture, health, arts, technology, religion, politics, mind, economy, environment, and education," Binghamton University, NY, launched Feb 2012. Ed Yong, "Yeast suggests speedy start for multicellular life" [html], doi:10.1038/nature.2012.9810, Nature, 16 Jan 2012. 10 Jan 2012: The mechanisms for this increase in complexity are incredibly simple, common occurrences Geneticist Joe Thornton Acquired Traits Can Be Inherited Via Small RNAs, Newswise, 5 Dec 2011. Cells may stray from 'central dogma' by Erika Check Hayden, doi:10.1038/news.2011.304, NatureNews, online 19 May 2011. Eric J. Hayden et al., "Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme" [abstract], doi:10.1038/nature10083, p92-95 v474, Nature, 2 Jun 2011. Jeremy A. Draghi and Joshua B. Plotkin, "Molecular evolution: Hidden diversity sparks adaptation" [html], doi:10.1038/474045a, p45-46 v474, Nature, 2 Jun 2011. 18 Apr 2011: Natural selection eliminates and maybe maintains, but it doesn't create Lynn Margulis 11 Jan 2011: Anomalies in mainstream evolutionary theory have prompted a major amendment to darwinism. Michael W. Gray et al., "Irremediable Complexity?" [summary], doi:10.1126/science.1198594, p920-921 v330, Science, 12 Nov 2010. "Much of the bewildering intricacy of cells could consist of originally fortuitous molecular interactions that have become more or less fixed by constructive neutral evolution." 13 Jun 2010: What Darwin Got Wrong by Jerry Fodor and Massimo Piattelli-Palmarini [book review]. 12 Apr 2010: Stan Franklin forwards Michael Ruse's book review and we reply. Bob Grant, "Should Evolutionary Theory Evolve?" [link: registration required], p24 v24, TheScientist, 01 Jan 2010. Hubertus J. E. Beaumont et al., "Experimental evolution of bet hedging" [abstract], doi:10.1038/nature08504, p90-93 v462, Nature, 5 Nov 2009. Ratchet-like genetic mutations make evolution irreversible, University of Oregon, 23 Sep 2009. 14 Sep 2009: If we didn't know about life we wouldn't believe it Richard Dawkins. After dinosaurs, mammals rise but their genomes get smaller, Indiana University News Room, 27 Jul 2009. 25 Jul 2009: Spermatozoa of all species can take up exogenous DNA or RNA molecules and internalize them into nuclei. 23 Jul 2009: Primate-specific genes were inserted de novo, not generated by gradual divergence from non-primate genes. The Deep Metazoan Phylogeny Project Joram Piatigorsky, Gene Sharing and Evolution: The Diversity of Protein Functions, Harvard University Press, 2007. 16 Mar 2009: ...gene transfers of various types... and other forms of acquisition of 'foreign genomes' ...are more important.... Lynn Margulis Henry Gee, Rory Howlett and Philip Campbell, "15 Evolutionary Gems" [17-page PDF], doi:10.1038/nature07740, Nature.com, online Jan 2009. Sergey Kryazhimskiy and Joshua B. Plotkin, "The Population Genetics of dN/dS" [article], doi:10.1371/journal.pgen.1000304, 4(12): e1000304, PLoS Genetics, online 12 Dec 2008. Daniel G. Gibson et al., "One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome" [Open Access abstract], doi:10.1073/pnas.0811011106, p 20404-20409 v 105, Proc. Natl. Acad. Sci. USA, 23 Dec (online 10 Dec) 2008. 27 Nov 2008: The discovery answers an age-old question that has puzzled biologists since the time of Darwin.... Andrew L. Hufton et al., "Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement" [abstract], doi:10.1101/gr.080119.108, p 1582-1591 v 18, Genome Research, online 17 Sep 2008. Elizabeth Pennisi, "Deciphering the Genetics of Evolution" [link], doi:10.1126/science.321.5890.760, p 760-763 v 321, Science, 8 Aug 2008. "Powerful personalities lock horns over how the genome changes to set the stage for evolution." Ben-Yang Liao and Jianzhi Zhang, "Null mutations in human and mouse orthologs frequently result in different phenotypes" [abstract], doi:10.1073/pnas.0800387105, p 6987-6992 v 105, Proc. Natl. Acad. Sci. USA, 13 May (online 5 May) 2008. "...We find that >20% of human essential genes have nonessenti
al mouse orthologs." Todd A. Sangster et al., "HSP90-buffered genetic variation is common in Arabidopsis thaliana" [abstract], doi:10.1073/pnas.0712210105, Proc. Natl. Acad. Sci. USA, online 19 Feb 2008. "...HSP90 is likely to occupy a central position in the translation of genotypic variation into phenotypic differences." Todd A. Sangster et al., "HSP90 affects the expression of genetic variation and developmental stability in quantitative traits" [abstract], doi:10.1073/pnas.0712200105, Proc. Natl. Acad. Sci. USA, online 19 Feb 2008. Shocking Evolution Into Action, by Nicole Giese, Whitehead Institute for Biomedical Research, 18 Feb 2008 | also on Newswise.com. "The abundance of naturally occurring genetic variation that is affected by Hsp90 was remarkable." Inheritance via RNA is the subject of a Reply from Stan Franklin, 4 Jan 2008. Committee on Revising Science and Creationism, Science, Evolution, and Creationism [link], ISBN: 0-309-10587-0, National Academies Press, 2008. 19 Dec 2007: The ancestor of earthly life was molecularly complex. Anthony Poole and David Penny, "Eukaryote evolution: Engulfed by speculation" [text], 10.1038/447913a, p 913 v 447, Nature, 21 Jun 2007. "The onus is on proponents, not sceptics, to find evidence for their theories." Exploring the Dark Matter of the Genome, Physorg.com, 15 Jun 2007. Rajkumar Sasidharan and Cyrus Chothia, "The selection of acceptable protein mutations" [abstract], 10.1073/pnas.0703737104, Proc. Natl. Acad. Sci. USA, online 31 May 2007. "This work implies that commonly allowed mutations are selected by a set of general constraints that are well defined and whose nature varies with divergence." Jicheng Wang et al., "Evidence for mutation showers" [abstract], 10.1073/pnas.0610902104, Proc. Natl. Acad. Sci. USA, online 7 May 2007. Suzanne Estes and Stevan J. Arnold, "Resolving the Paradox of Stasis: Models with Stabilizing Selection Explain Evolutionary Divergence on All Timescales" [abstract | 18-page PDF], doi:10.1086/510633, p 227-244 v 169, The American Naturalist, Feb (online 4 Jan) 2007. Also see commentary: Andrew Hendry, "The Elvis paradox" [PDF], doi:10.1038/446147a, p 147-149 v 446, Nature, 8 Mar 2007. Jun Gojobori et al., "Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution" [abstract], 10.1073/pnas.0605565104, Proc. Natl. Acad. Sci. USA, online 26 Feb 2007. No Missing Link? Evolutionary Changes Occur Suddenly, Professor Says, ScienceDaily.com, 12 Feb 2007. Scientists Discover Parallel Codes In Genes, ScienceDaily.com, 9 Feb 2007. Genetic information: Codes and enigmas, doi:10.1038/444259a, by Helen Pearson, News@Nature.com, online 15 Nov 2006. Christopher D Herring, Anu Raghunathan, Christiane Honisch et al., "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale" [abstract], 10.1038/ng1906, Nature Genetics, online 5 Nov 2006. "We obtained proof that the observed spontaneous mutations were responsible for improved fitness by creating single, double and triple site-directed mutants...." Orkun S. Soyer and Sebastian Bonhoeffer, "Evolution of complexity in signaling pathways" [abstract], 10.1073/pnas.0604449103, Proc. Natl. Acad. Sci. USA, online 23 Oct 2006. "...Pathways could be driven toward complexity via simple evolutionary mechanisms...." 3 Oct 2006: Can plants overwrite unhealthy genes? P M Brakefield and V French, "Evo-devo focus issue: Editorial" [text], 10.1038/sj.hdy.6800878, p 137-138 v 97, Heredity, Sep 2006. "...The basic mechanisms of embryonic development are extremely ancient and have been highly conserved.... Evo-devo... should continue to reveal how genetic change in the processes of development can lead to the abundant diversity in form that we observe in nature." 7 Jun 2006: Blowflies were preadapted for the rapid evolution of insecticide resistance. Daniel M. Weinreich et al., "Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins" [abstract], p 111-114 v 312, Science, 7 Apr 2006. About optimization: 5 certain a-a substitutions could theoretically be reached 5!=120 ways, but only 10 of them are likely to be permitted by natural selection. T. Martin Embley1 and William Martin, "Eukaryotic evolution, changes and challenges" [abstract], p 623-630 v 440, Nature, 30 Mar 2006. 19 Feb 2006: Why has there has been so little change in major body plans since the Early Cambrian? 14 Feb 2006: Researchers evolve a complex genetic trait in the laboratory? 5 Jan 2006: "Evolution in Action" was the number one "Breakthrough of the Year" according to Science. 31 Oct 2005: The Plausibility of Life: Resolving Darwin's Dilemma, by Marc W. Kirschner and John C. Gerhart, Yale University Press, 2005. 30 Sep 2005: The chimp genome has been sequenced. At least seventeen human genes contain exons missing in chimps. Could evo-devo account for genetic novelty? Stan Franklin wonders, 25 Jul 2005. 14 Jul 2005: The World Summit on Evolution in the Galapagos Islands, 8-12 June 2005. University of Chicago study overturns conventional theory in evolution, by Catherine Gianaro, EurekAlert!, 7 Jun 2005. Alarm pheromone causes aphids to sprout wings, by Lynne Miller, EurekAlert!, 18 May 2005. Tohru Sugawara et al., "Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi" [abstract], p 5448-5453 v 102, Proc. Natl. Acad. Sci. USA, 12 Apr 2005. "...The number of genetic changes underlying the appearance of similar traits in cichlid diversification may be fewer than previously expected." 24 Mar 2005: Plants can overwrite unhealthy genes. 15 Mar 2005: "Biology today is no more fully understood in principle than physics was a century or so ago." Andrew P. Hendry, "The power of natural selection," p 694-695 v 433, Nature, 17 Feb 2005. "We are only deluding ourselves that we have a good handle on the typical power of selection in nature." 16 Feb 2005: Fitness Landscapes. I King Jordan et al., "A universal trend of amino acid gain and loss in protein evolution" [abstract], doi:10.1038/nature03306, p 633-638 v 433, Nature, 10 Feb 2005. 4 Feb 2005: Ernst Mayr died yesterday at 100 years of age. H. Allen Orr, "The Genetic Theory of Adaptation: A Brief History" [open access], doi:10.1038/nrg1523, p 119-127 v 6, Nature Reviews Genetics, Feb 2005. Our comment adaptation has a very short reach. Rachel B. Brem and Leonid Kruglyak, "The landscape of genetic complexity across 5,700 gene expression traits in yeast" [abstract], 10.1073/pnas.040870910
2, Proc. Natl. Acad. Sci. USA, online 19 Jan 2005. "Most detected QTLs (quantitative trait loci) have weak effects." Kenneth M. Weiss and Anne V. Buchanan, Genetics and the Logic of Evolution, ISBN: 0471238058, Wiley-Liss (John Wiley and Sons, Inc.), 9 Jan 2004. 21 Nov 2004: Vertebrate photoreceptor cells in a primitive invertebrate. 14 Nov 2004: The birth of a new gene unique to apes and humans.... Sinad Collins and Graham Bell, "Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga," p 566 - 569 v 431 Nature, 30 Sep 2004. "...Selection lines of the unicellular green alga Chlamydomonas failed to evolve specific adaptation to a CO2 concentration of 1,050 parts per million." Emma Marris, "Tibetans show 'evolution in action'" [story], 10.1038/news040913-20, News@nature.com, 16 Sep 2004. "A gene for well oxygenated blood is spreading in the Himalayas." (Once a gene is available, natural selection works on it.) Flies with inner ears? by David Secko, The Scientist, 13 Sep 2004. "...The gene could direct the development of an organ it does not even possess." 25 Jul 2004: 100 years old, Ernst Mayr reviews the development evolutionary thought in Science. David J. Amor et al., "Human centromere repositioning 'in progress'" [abstract], p 6542-6547 v 101, Proc. Natl. Acad. Sci. USA, 27 Apr 2004. The Most Natural Selection, by Steven Kotler, LA Weekly, 18 Apr 2004. If evolution rewards only reproductive success, why does homosexuality persist? 16 Apr 2004: The rat genome has been sequenced. 14 Apr 2004: "Can we ever hope to pin down the genetic changes that underlie the big steps in evolution?" 24 Feb 2004: Evolution caught in the act? Erik R. Zinser et al., "Bacterial Evolution Through the Selective Loss of Beneficial Genes: Trade-Offs in Expression Involving Two Loci" [abstract], p 1271-1277 v 164, Genetics, August 2003. Adaptation by gene loss can happen a third way. 2003, August 29: "...We must conclude that there are no detailed Darwinian accounts..." (Franklin M. Harold, 2001). Redundant Evolution, by Leslie Mullen, Astrobiology Magazine, 28 Apr 2003. 2003, April 16: Point mutations are less important than rearrangements of longer DNA strands in evolution.... A new branch on the tree of life, by Lynn Yarris, ScienceBeat, 4 Apr 2003. "Nature, it seems, found two different ways to evolve six legs." 2003, March 25: Here Be Dragons, by David W. Koerner and Simon Levay. 2003, March 3: What Evolution Is, by Ernst Mayr. Testing Darwinism versus Cosmic Ancestry a new CA webpage, 24 Nov 2002. Steve Olson, "Seeking the Signs of Selection" [summary], p 1324-1325 v 298, Science, 15 Nov 2002. Fossil protein breakthrough will probe evolution, by Fred Pearce, NewScientist.com, 13 Nov 2002. "...Osteocalcin can survive ...long enough to look back ...to the last common ancestor of humans and chimpanzees." Paul Raeburn, "'Of Moths and Men': The Moth That Failed" (book review) [text], The New York Times, 25 Aug 2001. Fossils Help Determine When Humans, Apes Diverged, nationalgeographic.com, 23 Aug 2002. "The gene,... was mutated (knocked out) in humans in comparison with the normal, intact gene in apes." 2002, July 14: Mouse vs Human 2002, Jul 7: Acquiring Genomes. Science Mimicking, Perhaps Even Predicting, Evolution about basic research that supports Darwinism, by Jonathan Sherwood, UniSci.com, 21 Mar 2002. 2002, Mar 2: Correction. 2002, Feb 8: Biologists demonstrate macroevolution and thus answer a major challenge to darwinism by creationists. 2001, December 21: A gene needed for multcellularity is present in a single-celled organism. Squirrels 'genetically altered' by forest. Actually they were altered by genes acquired from other squirrels. BBCNews, 21 Sep 2001. Donald R. Forsdyke, The Origin of Species, Revisited [contents, publisher's promo], McGill-Queen's University Press, 2001. 2001, May 28: Eukaryote-to-prokaryote evolution in 15 days?! 2000, December 26: An email to Massimo Pigliucci recaps the argument against Darwinism. 2000, December 15: Mutation appears to double lifespan of flies. 2000, November 23: Monad to Man, by Michael Ruse, about evolutionary progress. 2000, September 27: Prions can turn on genetic programs. 1999, July 15: A recent issue of Science features evolution. 1999, June 3: Example of microevolution. 1998, August 25: We owe the repertoire of our immune system to one transposon insertion, which occurred 450 million years ago in the ancestor of the jawed fishes. Was Darwin Wrong? The critics of evolution. Links to even-handed book reviews by Gert Korthof. The reviews have further links. The Tree of Life: an excellent growing illustrated resource on the classifications of life. Enter Evolution: Theory and History. Evolutionary scientists before Darwin, from UC Berkeley. Evolution, Science, and Society: a "white paper" on behalf of the field of evolutionary biology [Executive Summary] by Douglas J. Futuyma et al., revised Mar 1997.

1. Francisco J. Ayala and Theodosius Dobzhansky, eds. Studies in the Philosophy of Biology: Reduction and Related Problems. University of California Press 1974. p 364. 2. Lynn Margulis, [interviewed in] The Third Culture by John Brockman, Simon and Schuster, 1995. p 133. 3. Richard Dawkins, River Out of Eden, BasicBooks, 1995. p 70. 3.5. Michael T. Madigan, John M. Martinko and Jack Parker, Brock Biology of Microorganisms, eighth edition, Prentice Hall, 1997. p 332. 4. Renato Dulbecco, The Design of Life, Yale University Press, 1987. p 122. 4.5. Walter M. Fitch, Robin M. Bush, Catherine A. Bender and Nancy J. Cox, "Long term trends in the evolution of H(3) HA1 human influenza type A," p 7712-7718 v 94, Proc. Natl. Acad. Sci. USA, July 1997. 5. Manfred Eigen, "New Concepts for Dealing with the Evolution of Nucleic Acids," p 307-320, Cold Spring Harbor Symposia on Quantitative Biology, Volume LII: Evolution of Catalytic Function, Cold Spring Harbor Laboratory, 1987. 6. Liangbiao Chen, Arthur L. DeVries and Chi-Hing C. Cheng. "Evolution of antifreeze protein from a trypsinogen gene in Antarctic notothenioid fish" [abstract], p 3811-3816 v 94, Proc. Natl. Acad. Sci. USA, April 1997. 7. John M. Logsdon, Jr., and W. Ford Doolittle. "Origin of antifreeze protein genes: A cool tale in molecular evolution" [text], p 3485-3487 v 94, Proc. Natl. Acad. Sci. USA, April 1997. 8. Liangbiao Chen, Arthur L. DeVries and Chi-Hing C. Cheng, "Convergent evolution of antifreeze glysoproteins in Anta
rctic notothenioid fish and Arctic Cod" [abstract], p 3817-3822 v 94, Proc. Natl. Acad. Sci. USA, April 1997. 9. Paul Feyerabend, Against Method. London: Verso Publishing, 1978. p 60. 10. Charles Darwin, The Origin of Species, 6th edition, 1872; Down, England: Senate, 1994. p 146. The text of the first edition is available on the Internet: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, Albemarle Street, 1859. 11. Samuel A. Bowring, John P. Grotzinger, Clark E. Isachsen, Andrew H. Knoll, Shane M. Pelechaty and Peter Kolosov, "Calibrating Rates of Early Cambrian Evolution," p 1293-1298 v 261, Science, 3 September 1993. 12. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History, W.W. Norton and Company, 1989. 13. Madeleine J. Nash, "When Life Exploded," p 66-74, Time, 4 December 1995. 14. J.B.S. Haldane, On Being the Right Size and other essays, John Maynard Smith, ed., Oxford University Press, 1987. Includes the essay, "The Origin of Life," 1928. p 12. 15. Richard Dawkins, "The eye in a twinkling" p 690-691 v 368, Nature, 21 April 1994. 16. Georg Halder, Patrick Callaerts and Walter J. Gehring, "Induction of Ectopic Eyes by Targeted Expression of the eyeless Gene in Drosophila" [abstract], p 1788-1792 v 267, Science, 24 March 1995. 17. Constance Holden, "On the Path of the Primordial Eye" [html], p 1885 v 275, Science, 28 March 1997. 18. John Travis, "Eye-opening Gene: How many times did eyes arise?" in ScienceNewsOnline. 10 May 1997. 19. T.A. Brown, Genetics: A Molecular Approach, 2nd edition, Chapman and Hall, 1992. p 171. 20. Justin Goodrich, Preeya Puangsomlee, Marta Martin, Deborah Long, Elliot M. Meyerowitz and George Coupland, "A Polycomb-group gene regulates homeotic gene expression in Arabidosis," p 44-51 v 386, Nature, 6 March 1997. 20.5. Robert Macchiarelli "The whole tooth" [interview], p 349 v 425, Nature, 25 Sep 2003. 21. Natalie Angie, "When Evolution Creates the Same Design Again and Again," The New York Times, December 15, 1998. 22. Natalie Angie, "When Evolution Creates the Same Design Again and Again," The New York Times, December 15, 1998. 23. Neil A. Campbell, Biology, 3rd Edition, The Benjamin/Cummings Publishing Company, Inc., 1993. p G17-G18. 24. Ernst Mayr, Toward a New Philosophy of Biology: Observations of an Evolutionist, Harvard University Press, 1988. p 402. 25. KS Dulai, M von Dornum, JD Mollon and DM Hunt, "The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates," p 629-638 v 9 n 7, Genome Research, July 1999. 26. Shozo Yokoyama, Huan Zhang, F. Bernhard Radlwimmer and Nathan S. Blow, "Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae)" [abstract], p 6279-6284 v 96, Proc Natl Acad Sci USA, 25 May 1999. Also duscussed in "What'sNEW," 3 June 1999. 27. Karl R. Popper, "Two Faces of Common Sense..." p 32-105, Objective Knowledge: An Evolutionary Approach, Oxford University Press, 1972. p 69. 28. Robert Rosen, Life Itself: A Comprehensive Inquiry Into the Nature, Origin and Fabrication of Life, Columbia University Press, 1991. p 255. 29. Steve Fuller, Science, ISBN: 0-8166-3125-5, University of Minnesota Press, 1997. p 18.

RIA – Robotics Online – Industrial Robot Automation

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Robeye All In One (RAIO)

RAIO is a sensor for 3D Robotic Guidance designed for high industrial reliability. Driven by powerful visual recognition and guidance software, RAIO gives robots human sight delivering XYZRxRyRz.

Albany RapidProtect 2000

The machine protection door of choice for Automotive Line Builders for decades.

Worlds Most Cost-Effective Robots

Why do DENSO robots have such a low cost of ownership? DENSO's own manufacturing needs demand it.

More Reach, More PayloadMore EPSON

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KINGSTAR Soft Motion

Replace Your Motion Control Hardware with Quality, Precision Performance Software at Half the Cost.

Robotic Integration Capabilities

Intelligrated robotic systems offer speed, accuracy and reliability to meet strict requirements.

Multi-Axis Force/Torque Sensors

Gives robots a tactile sense of touch by sending feedback to control the robot's positioning.

High-Speed Palletizing Robots

Kawasakis CP Series robots are capable of industry leading palletizing rates of 2,050 cycles per hour!

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RIA - Robotics Online - Industrial Robot Automation

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Robotics News & Articles – IEEE Spectrum

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Robotics News & Articles - IEEE Spectrum

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Complementary and Alternative Medicine Guide | University …

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A.D.A.M., Inc. is accredited by URAC, also known as the American Accreditation HealthCare Commission (www.urac.org). URAC's accreditation program is an independent audit to verify that A.D.A.M. follows rigorous standards of quality and accountability. A.D.A.M. is among the first to achieve this important distinction for online health information and services. Learn more about A.D.A.M.'s editorial policy, editorial process and privacy policy. A.D.A.M. is also a founding member of Hi-Ethics and subscribes to the principles of the Health on the Net Foundation (www.hon.ch)

The information provided herein should not be used during any medical emergency or for the diagnosis or treatment of any medical condition. A licensed medical professional should be consulted for diagnosis and treatment of any and all medical conditions. Call 911 for all medical emergencies. Links to other sites are provided for information only -- they do not constitute endorsements of those other sites. 1997-2013 A.D.A.M., Inc. Any duplication or distribution of the information contained herein is strictly prohibited.

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About Life Extension: Anti-Aging, Health Supplements …

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Established in 1980, the Life Extension Foundation is a nonprofit organization, whose long-range goal is to radically extend the healthy human lifespan by discovering scientific methods to control aging and eradicate disease. One of the largest organizations of its kind in the world, the Life Extension Foundation has always been at the forefront of discovering new scientific breakthroughs for use in developing novel disease prevention and treatment protocols to improve the quality and length of human life. Through its private funding of research programs aimed at identifying and developing new therapies to slow and even reverse the aging process, the Life Extension Foundation seeks to reduce, and ultimately eliminate, such age-related killers as heart disease, stroke, cancer and Alzheimers disease.

The Life Extension Foundation is a nonprofit organization whose goal is to extend the healthy human lifespan by discovering scientific methods to control aging and eradicate disease. continue >>

Since its inception in 1980, the Life Extension Foundation has continued its dedication to finding new scientific methods for eradicating old age, disease and death. continue >>

The Life Extension Foundation has been a world leader in uncovering pioneering approaches for preventing and treating diseases. continue >>

Long-time members are keenly aware of the scientific research that Life Extension Foundation funds to develop validated methods to slow and reverse the aging process. continue >>

Life Extension Foundation Federal Income Tax information is now available to download in Adobe PDF format. continue >>

About Life Extension: Anti-Aging, Health Supplements ...

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Zeitgeist Information

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The Zeitgeist-Info (shortened to ZInfo), website is a resource of useful Zeitgeist Movement related posts, aimed at existing Zeitgeist Movement members. It was created to inform ZM members of advanced concepts and useful news and information.

New to the Zeitgeist Movement or don't even know what it is?

The term Zeitgeist refers to theintellectual, cultural and moral Spirit of the Times and we want to change that for the betterment of all humanity. Currently people define success by how much financial wealth, power, control or fame they have acquired. However we want to change it so we value people by how much they've contributed to humanity and the environment.

Check out the TEDx talk below for a quick introduction, or watch Zeitgeist Moving Forward, the 2.5 hour documentary/movie.

An Introduction to a Resource-Based Economy [ TEDx - Peter Joseph ]

Once you have watched the TED talk orZeitgeist Moving Forward then find and join your local ZM chapter. Don't forget to come back here for the latest in ZM information and concepts.

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The 6 short animations cover the basics of critical thinking including logic and faulty arguments. Well worth watching for anyone especially those who do lots of debating.

Original source :http://bridge8.wordpress.com/2012/01/30/critical-thinking-animations/

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Download the latest issue:

Spirit Of The Times #3 Transition to a Resource Based Economy

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In consolidating the Zeitgeist Info site, the Resources page has been converted into a Video Wall and updated with a few new resources.

Video Wall

If you are new to the movement then that page should be your first point of call for a great selection of videos.

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This is a repost from the Australian Atrium (Project Management) website and is aimed at Australian ZM members.

This is a proposal regarding the Beyond Zero Emissions renewable energy proposal. Beyond Zero Emissions is a group of engineers and scientists who have created a proposal to convert Australia's energy supply to 100% renewable energy within 10 years. It is primarily done using a mixture of wind power and concentrated solar thermal.

The Beyond Zero Emissions cause is very much in line with the Zeitgeist Movements aims and principals. We will need their help to prevent humanity from facing environmental and energy crises, whilst they need our help in order for the proposal to get traction.

We are interested in helping promote and champion the BZE emissions scheme.

In order to help us develop new project ideas we are working on a output centric approach.

1. You start off by writing the press release you would like to see. 2. You then write the FAQ. 3. If it's particularly complex you can even write a help manual. Only after you've gone through the above steps do you work backwards to find out what needs to be done/created and how.

Solar Concentrator Array

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Zeitgeist Movement chapters need to balance activity in at least 3 main areas, which include Activism, Learning and Relations. These activities can take the form of various types of projects and meetings, and ways in which to allocate time and resources.

Activism - Zeitgeist Movement chapters generally have two forms of activism, helping with the mindset change and physical activism/labour. The mindset activism is usually in the form of handing out DVDs, running film screenings, and town hall meetings. It is also one of the more important processes for gathering new members and affecting the culture and community around the chapter(s). The main mindset change happens when people understand the different values, definition of success and change in the defaults that we want to achieve. Many of the newer ZM members get annoyed at the lack of physical activism. As a movement we are only just starting to reach the point at which creating tangible change is an option. Some great examples would be converting existing people's lawn area into gardens, creating eco-village style setups which run on renewable energy and are progressively automated to the point they are creating an abundance of produce. An important requirement for the price of zero transition.

Learning - Furthering our understanding of the ZM but also the world around us. From the latest in science, to the history of economics, to current news. It also covers research and analysis, particularly with regard to how to do things more efficiently and effectively or in other ways. Learning is divided into two main sections: personal learning and chapter learning. Personal learning is particularly focused on reaching an understanding of how the world works, the issues with the current system, and the solutions (the RBE). This is usually done through watching movies, being a part of a mailing list, reading articles, creating newsletters, and attending or giving presentations.

Relations - This is about internal chapter relationships and relations with other organisations. A very important motivator for continuous membership is the social aspect of being surrounded by other people who care about and understand them. This sense of community is fostered by holding social meetups, like BBQs, or casually meeting up at a bar. The relations between chapters and with other organisations are also very important. The potential for the Zeitgeist Movement to foster a transition to a Resource Based Economy is facilitated by creating strong ties with other RBE advocating groups and organisations such as Beyond Zero Emissions (in Australia).

A basic outline of the sub-points is below

As an example, the table below lists of some projects being undertaken or planned in Australian ZM chapters. Some projects are listed twice as they have pronounced secondary effects, which arecoloured in grey.

On top of the three different buckets that need to be balanced is the almost constant review and admin work.

The regular review process could for example involve reading your posts, emails, and behaviour for the last week and allow you to both fix up mistakes and give you feedback regarding how to do thing better next time. A group review process should also be on the agenda of the next ZM meetup after an event (e.g Zday, ZMedia Festival).

The admin work involves general organisation work and maintenance. From maintaining mailing lists and websites to doing checks and balances, etc...

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I thought I knew a decent amount about energy and renewables, but still learnt a lot from this.

Energy Knowledge

It's only 19mins long and well worth watching.

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Survival of the Fittest

This is a great video which explains the true meaning of 'Survival of the Fittest'. It also does a great job of explaining some of the issues between Tournament and Pair Bonding Species.

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This is a MUST WATCH video of Derrick Jensen talking about the premises of our Civilisation and why it is
not sustainable.

In the talk he does a great job of explaining the premises, although if you enjoyed the video, or if you didn't fully understand it then you should probably read the book. (NB : ZInfo is not associated with Derrick and does not receive any money for any form of advertising, in any way).

Premises :

There are some points that I think could be debated or slightly tweaked. Especially premise 6. I agree that whilst civilisation won't go voluntarily, you don't have to have a Price of Infinity (enviro, energy, economic) collapse. We can guide civilisation through a Price of Zero collapse (using abundance, sustainability, automation and education).

As you'll see in the next post (about changing the value system), I think that point 8 needs to be pointed out to people. They know it, but don't realise that the economic system is given priority over nature, life, and human wellbeing. The Sydney, Australia chapter is currently editing some vox-pop/street interviews which show this mentality in action.

Regarding point 9. It's possible that if we were to be efficient and effective with the natural resources, we would likely be able to keep similar numbers of people or even raise the population whilst maintaining a stable equilibrium with the environment. But we would need to be net positive not net destructive to the environment. Humanity would also expand in numbers as we colonise other planets. But would shouldn't and likely won't do such a thing under the current culture and system. If we did it wouldn't be pretty for anything that got in our way.

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This is a quick announcement of the creation of the Transition Ideas Team (TIT) a new ZM team that Scott Wrampler and Michael Kubler are currently helping kick start.

For those who are interested here's a recent Blog Talk Radio show regarding the team which talks about the organisational structure and some of the initial teams. It's only 30mins long.

The team will be split into 3 main groups :

The Admin staff will be a small group who run the website, organise the tools and help co-ordinate the other two groups.

The Transition Proposals group will be a collection of people who, working alone or together, come up with various transition models then propose them.

The Proposal Analysts are those who are knowledgeable within their field and as a group can analyse the proposal and undertake useful critical analysis and highlight potential issues and also make suggestions or reccomendations.

The process of submitting, analysing and refining a proposal will itself need to be developed and refined over time. One of the hardest parts of the process will be removing human bias, especially those which are predictable. An example may be that proposals are to be madeanonymousbefore being presented to the proposal analysts. Once the analysts have provided feedback and the proposal refined the proposal can then be presented on the website for further analysis and discussions with the wider public.

It's possible that the team may itself change from being about transition ideas, to be a TransitionImplementationteam (or more likely, a group of teams).

If you have any transition ideas or suggestions then feel free to comment or email transition@zeitgeist-info.com

Thank you

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wage slave – Why Work

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What is a wage slave?

So what exactly IS a wage slave, anyway? It's doubtful that you'd be exploring this web site if you didn't have some idea at least, but for the sake of ease, we'll clarify further.

Here are some brief and incomplete definitions from CLAWS members:

"Wage slavery is the state where you are unable to perceive choices and create courses of action different from the grind of the job."

"Wage slave: A wage earner whose livelihood is completely dependent on the wages earned."

The point here, of course, is that we don't have a single agreed-upon definition of wage slavery. Many of us prefer to focus on wage slavery as a state of mind, while others prefer to focus on the external aspects of wage slavery such as the wage economy. But overall, we seem to sense something rotten at the core of what we've been taught about "making a living", and that's the place to begin our questioning.

Have you ever noticed how many of us seem to live "lives of quiet desperation", as Henry David Thoreau puts it? We feel trapped by forces beyond our control, trapped in a mindless job, for the sake of money, status or recognition. We complain that we never seem to have the time for what's really important to us, because our jobs take so much energy and focus that we hardly have anything left over. We plod along day to day; sometimes we even dread getting out of bed in the morning.

We see the futility of the standard, socially approved path in America. It goes something like this: Go to school, get good grades, so you can get a "good" job, make lots of money, get a mortgage and a car and a spouse, keep up with the Joneses, and be "successful". We know it's not the path for us; we want to define success for ourselves. But we don't know how to forge a new path for ourselves, because, well, what would we do for money if we quit? How would we support ourselves? Sometimes there's a glazed look in our eyes; it's as if some part of us has died. We are just doing time, working hard and hoping for the next promotion, waiting for the day when we can throw off our shackles, quit our dull jobs, and finally live life. Everything gets put on hold until we have more time, or more money. Meanwhile, life is passing us by.

Perhaps you are one of these people. If so, CLAWS was created for your benefit. We have news for you: You do not have to live your life that way. CLAWS is here to inspire you to greater fulfillment, and to help you figure out how to get out of the endless cycle of living paycheck to paycheck and feeling chained to a job you don't care about.

We have other news, too: It won't necessarily be the easiest thing you've ever done. You have a choice, but you may have to re-examine your way of thinking very thoroughly. The pull of the socially accepted way of doing things is amazingly strong, and trips up the best of us despite our good intentions. It takes a certain kind of independent thinker to be "job-free". We use that term rather than "unemployed", in an effort to convey to people that we're proud, not ashamed, of not having regular jobs. We also make an important distinction between jobs and work. All of us do some kind of work, though not necessarily for monetary compensation.

Another thing you'll need if you decide to rethink your beliefs about jobs and money is the willingness to challenge conventional wisdom. It will take perseverence, and a commitment to throw out the limiting beliefs you may have unwittingly adopted. This is not the path for everyone. If your priority is comfort or social approval, or if you're the sort of person who doesn't rock the boat, CLAWS probably won't meet your needs.

If you embark on this path, it's important to know what it will ask of you. It may require you to disassemble, dissect, and tear apart your old beliefs, let go of some mighty persistent and tempting illusions, and build a new foundation for your thinking, sometimes from scratch. Are you prepared to do this? If so, you're in the right place.

Even if you have seen through the false sense of "security" a normal job offers you, and already questioned that approach to life, you may not really believe you can do it. You may still have questions about how to bridge the gap from the old way of life to a new one that you envision. That's where we can help, dear reader. CLAWS would like to see you devote yourself to the life you've dreamed of, the life your heart desires. We don't want to see you waste your precious days any longer. Life is short, and the time to pursue your dreams is NOW.

In the words of Norman Cousins:

"Death is not the greatest loss in life. The greatest loss is what dies inside us while we live."

"The debt and work cycle is an ingenious tool of subjugation. Make people think they need all these things, then they must have a job, and they give up control of their lives. It's as simple as that. We live in one of the most free countries in the world, but we fix it so we are not free at all. " - Larry Roth

"Capitalism only supports certain kinds of groups, the nuclear family for example, or 'the people I know at my job', because such groups are already self-alienated & hooked into the Work/Consume/Die structure." - Hakim Bey

"Supposing we suddenly imagine a world in which nearly everybody is doing what they want. Then we don't need to be paid in order to work and the whole issue of how money circulates, how we get things done, suddenly alters." - Robert Theobald

"When survival or mere subsistence is at stake, a society can focus only on the overwhelming needs of the moment, and questions of meaningful work and leisure are considered purely academic. But we believe that the world has enough wealth to move all of humanity above survival and subsistence." - Alfonso Montuori & Isabella Conti, From Power to Partnership: Creating the Future of Love, Work, and Community

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wage slave - Why Work

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Wage-Slavery and Republican Liberty | Jacobin

Posted: at 2:33 pm

Generations of workers critiqued wage-labor in the name of republican liberty.

In a recent interview, historian Quentin Skinner had the following to say about Karl Marx and the republican theory of liberty. The republican or neo-Roman theory says that we are unfree when we are subject to another persons will:

I am very struck by the extent to which Marx deploys, in his own way, a neo-Roman political vocabulary. He talks about wage slaves, and he talks about the dictatorship of the proletariat. He insists that, if you are free only to sell your labour, then you are not free at all. He stigmatises capitalism as a form of servitude. These are all recognizably neo-Roman moral commitments.

Skinner also says that this is a question which would bear a great deal more investigation than it has received.

I have been engaging in some of this investigation. It is not just Marx or even primarily Marx who believed that the neo-roman theory of freedom leads directly to a critique of wage-slavery. As early as the late 1820s, urban workers seized on the inherited republicanism of the American Revolution and applied it to the wage-labor relationship. They organized themselves city-by-city into the first self-conscious political parties of labor and their main campaign was against wage-slavery.

They argued that the wealthy keep us in a state of humble dependence through their monopoly control of the means of production. As Thomas Skidmore, founder of the Workingmens Party of New York, put it:

thousands of our people of the present day in deep distress and poverty, dependent for their daily subsistence upon a few among us whom the unnatural operation of our own free and republican institutions, as we are pleased to call them, has thus arbitrarily and barbarously made enormously rich.

Their humble dependence meant that they had no choice but to sell their labor to some employer or another. Their only chance of leading a decent life was if some employer would give them a job. Though formally free, these workers were nonetheless economically dependent and thus unfree. That is why they saw themselves as denied their rightful republican liberty, and why wage-labor merited the name slavery. Skidmore made the comparison with classical slavery the most explicit:

For he, in all countries is a slave, who must work more for another than that other must work for him. It does not matter how this state of things is brought about; whether the sword of victory hew down the liberty of the captive, and thus compel him to labor for his conqueror, or whether the sword of want extort our consent, as it were, to a voluntary slavery, through a denial to us of the materials of nature

The critique of wage-slavery in the name of republican liberty could hardly be clearer.

Given their analysis of wage-labor, these artisan republicans were inexorably led to radical conclusions about the conditions that could restore workers their full independence. Every leading figure of these early workingmens parties made some form of the argument that the principles of equal distribution [of property be] everywhere adopted or that it was necessary to equalize property. Here, the property to be equally distributed was clearly means of production. And it was to be distributed not just in the form of land, but cooperative control over factories and other implements.

For instance, the major report articulating the principles of the Workingmens Party of New York included the demand for AN EQUAL AMOUNT OF PROPERTY ON ARRIVING AT THE AGE OF MATURITY. Only with control over this kind of property could workers structural dependence on owners be eliminated. For these Workies following out the logic of the republican theory led not to a nostalgic, agrarian idealism, but to the view that each persons independence depended upon everyone possessing equal and collective control of productive resources. Even more striking, they argued that the only way to achieve this condition of independence was through the joint political efforts of the dependent or enslaved class.

As Langdon Byllesby, one of the earliest of these worker republicans, wrote, history does not furnish an instance wherein the depository of power voluntarily abrogated its prerogative, or the oppressor relinquished his advantages in favour of the oppressed. It was up to the dependent classes, through the agency of their workingmens parties, to realize a cooperative commonwealth.

There is an important historical connection between these radical artisans and Marx. As Maximilen Rubel and Lewis Feuer have shown, just at the time that Marx turned from Hegelian philosophy to political economy, in 18412, he began to read comparative political history. He was particularly interested in the American republic, and read three main sources: Beaumont, Tocqueville, and a less well-known Englishman, Thomas Hamilton. Hamilton was a former colonel who wrote his own, very popular observation of his time traveling in the United States called Men and Manners in America, published in 1833. For Marx, Hamilton was the best source of the three because Hamilton, unlike the Frenchmen, actually met with and spoke to leaders of the Workingmans Party of New York. That section of Hamiltons travelogue includes ominous references to the Extreme Gauche of the Workies who wish to introduce an AGRARIAN LAW, and a periodical division of property, and includes gloomy reflections on the coming anarchy and despoliation. It is these very sections of Hamilton that Marx copied into his notebooks during this period of preparatory study.

Unbeknown to Marx, he was copying a copy. In those sections of Men and Manners Hamilton had essentially transcribed parts of Thomas Skidmores report to the Workingmens Party of New York, which were a distillation of the ideas that could be found in Skidmores lengthy The Rights of Man to Property! Skidmores book included the argument that property rights were invalid if they were used to make the poor economically dependent, allowing owners to live in idleness, partial or total, thus supporting himself, more or less, on the labors of others.

If property rights were illegitimate the minute they were used to make some dependent on others then it was clear all freedom-loving citizens were justified in transforming property relations in the name of republican liberty. This was why Skidmore proposed the radical demand that the workers APPROPRIATE ALSO, in the same way, THE COTTON FACTORIES, THE WOOLEN FACTORIES, THE IRON FOUNDERIES, THE ROLLING MILLS, HOUSES, CHURCHES, SHIPS, GOODS, STEAM-BOATS, FIELDS OF AGRICULTURE, &c. &c. &c. in manner as proposed in this work, AND AS IS THEIR RIGHT. The manner proposed for this expropriation of the expropriators was not violent revolution but a state constitutional convention in which all property would be nationalized and then redistributed in shares of equal value to be used to form cooperatives or buy land.

Marx never knew these labor republicans by name, nor any of their primary writings, but it is clear from his notebooks that their ideas and political self-organization contributed to his early thinking, especially at the moment at which he was formulating his view of workers as the universal class. Indeed, in On the Jewish Question, Beaumont, Tocqueville and the Englishman Hamiltons accounts of the United States feature heavily in Marxs discussion of America. It is there that Marx makes the famous distinction between political and human emancipation, arguing that the American republic shows us mos
t clearly the distinction between the two. This was almost exactly the same distinction that the Workies made when saying, as Philadelphian Samuel Simpson did, the consequence now is, that while the government is republican, society in its general features, is as regal as it is in England. A republican theory of wage-slavery was developed well before Marx (see here for evidence of similar developments in France that were also very likely to have influenced Marx).

In the United States, the republican critique of wage-labor went into abeyance for a time after the 1840s, or more appropriately, it was absorbed into the agrarian socialism of the National Reform Association a tale masterfully told by the historian Mark Lause in Young America: Land, Labor and Republican Community. But labor republicanism exploded back onto the political scene in the United States after the Civil War, especially with leading figures around the Knights of Labor and the eight-hour movement. The Knights were for a time one of the most powerful organizations in the country, organized skilled and unskilled labor together, and at their peak included more than 700,000official members, probably representing more than 1 million participating workers. The Knights used the republican concept of liberty to assert the universal interests of labor and to argue for the transformation of American society. George McNeill, a leading Knight, wrote that There is an inevitable and irresistible conflict between the wage-system of labor and the republican system of government. Ira Steward, most famous as an eight-hour campaigner, demanded a a republicanization of labor, as well as a republicanization of government.

These turns of phrase were more than rhetorical gestures. They were self-conscious appeals to the republican theory. Indeed the Journal of United Labor even reproduced a famous passage on slavery from Algernon Sidneys Discourses on Government in order to articulate why wage-labor was a form of servitude. The passage goes:

Slavery. The weight of chains, number of stripes, hardness of labor, and other effects of a masters cruelty, may make one servitude more miserable than another; but he is a slave who serves the gentlest man in the world, as well as he who serves the worst; and he does serve him if he must obey his commands and depend upon his will.

This passage, and Sidneys writings, have played a major role in contemporary scholarship on early modern republicanism, and here it is deployed to critique not the political enslavement to a monarch but wage-slavery.

In fact, the labor republicans not only drew on the republican theory but further developed it in light of the new dynamics of industrial capitalism. They noted that there were two interconnected forms of dependence. One was the general or structural dependence of the wage-laborer on employers, defined by the fact that the monopoly of control over productive property by some left the rest dependent upon those owners for their livelihoods. This, as George McNeil put it, meant that workers assent but they do not consent, they submit but do not agree.

The voluntaristic language here was meant to capture how, thought the workers were not literally slaves, they were nonetheless compelled to work for others. As Skinner has shown in his book on Hobbes, it is precisely this conflation of voluntaristic action and freedom that modern republicans have always rejected, and which their enemies, like Hobbes, have regularly defended. Though here, the workers dependence was not a feature so much of being the legal property of another as it was being forced, by economic need, to sell his labor:

when a man is placed in a position where he is compelled to give the benefit of his labor to another, he is in a condition of slavery, whether the slave is held in chattel bondage or in wages bondage, he is equally a slave.

Emancipation may have eliminated chattel slavery, but, as eight-hour campaigner Ira Steward once put it, the creation of this new form of economic dependence meant something of slavery still remainssomething of freedom is yet to come.

According to labor republicans, the structural dependence of the wage-laborer was translated, through the labor contract, to a more personal form of servitude to the employer. After all, the contract was an agreement of obedience in exchange for wages. It was an agreement to alienate control over ones own activity in exchange for the privilege of having enough money to buy necessities, and perhaps a few luxuries. Indeed, even if the wages were fairly high, the point of the contract was to become subject to the will of a specific owner or his manager. As one anonymous author put it, in the Journal of United Labor, Is there a workshop where obedience is not demanded not to the difficulties or qualities of the labor to be performed but to the caprice of he who pays the wages of his servants? As nearly every scholar of republican thought has noted, the language of being subject to the caprice of another is one of the most enduring rhetorical tropes of the neo-Roman theory of freedom. It is no accident that it would feature so heavily in labor republican arguments about domination in the workplace.

It was for this reason that the Knights of Labor believed that the only way to republicanize labor was to abolish as rapidly as possible, the wage system, substituting co-operation therefore. The point about a cooperative system was that property was collectively owned and work cooperatively managed. Only when the class differences between owners and workers were removed could republican liberty be truly universalized. It would, at once, remove the structural and personal dependence of workers.

As William H. Silvis, one of the earliest of these figures, argued, cooperation renders the workman independent of necessities which often compel him to submit to hectoring, domineering, and insults of every kind. What clearer statement could there be of the connection between the republican theory of liberty, economic dependence, and the modern wage-system? Here was a series of arguments that flowed naturally from the principles of the American Revolution.

To demand that there is to be a people in industry, as in government was simply to argue that the cooperative commonwealth was nothing more than the culmination and completion of the American Revolutions republican aspirations.

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Wage-Slavery and Republican Liberty | Jacobin

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Talk:Transhumanism/Archive 2 – Wikipedia, the free …

Posted: at 2:32 pm

Split long article

Might this longish entry be better presented as a series of pages? JasonS 03:34 Jan 13, 2003 (UTC)

Dnagod 20:56, 9 Feb 2005 (UTC)

In the interest of ensuring transhuman is NPOV: Who decides what the definition of transhumanism is?

This element of humanism, is that from huxley or someone else?

Does the man who invented the word, Julian Huxley decide the definition of Transhumanism, does one in modern times who publically states the definition decide or does the World Transhumanism Association decide?

I would like clarity as to who ultimately determines what transhumanism means because the definition used by the WTA and other groups differs. More importantly, what gives one authority or the command to be able to define in an undisputed what transhumanism is, so that other POV's can be excluded?

For instance I have reviewed the entire transtopia.org, euvolution.com/prometheism-transhumanism-posthumanism and cosmotheism.net site, and I can't seem to figure out how you could label it as disputed in the links section?

What is to say the world transhumanism association isnt disputed?

I can see how one might label cosmotheism as white racial separatist, but euvolution.com/prometheism-transhumanism-posthumanism and transtopia.org I would like more discussion as to why it is disputed as a transhumanism group. And why is Cosmotheism a disputed offshoot? Cosmotheism was developed in the 1960's and 1970's which came before extropy and WTA, so why is it an offshoot? I thought offshoot meant, that something existed and a branch or seed came off that plant. Can you please define offshoot and explain who decides what is or is not transhumanism?

More on this humanism element of Transhumanism, is that from huxley or someone else? Thanks.

Why does the link to cosmotheism keep getting deleted? Just because that article had a banned user associated w it doesn't make it any less relevent. Sam [Spade] 20:56, 4 Aug 2004 (UTC)

I'd like to incorporate a mention of the Human Cognome Project into this article, as it is relevent to human brain augmentation and AI research. Any suggestions? -- Dave User:Sydhart

Why is transtopia.org, euvolution.com/prometheism-transhumanism-posthumanism and cosmotheism.net labelled pseudotranshuman organizations? To me that represents bias as to why those web sites would be labelled pseudo, what makes a web site pseudo?

On the front page of euvolution.com/prometheism-transhumanism-posthumanism it states the following

(Prometheism is) The First Sovereign Transtopian & Neo-Eugenic Libertarian Religious-State.

In the principles sections of prometheism it states

Our Promethean Species embraces Conscious Evolution

Our immediate aim is to create a neo-eugenically enhanced race that will eventually become a new, superior species with whatever scientific means are available at the present time. In the short-term, this will be achieved via neo-eugenics, ie. voluntary positive eugenics, human cloning, germ-line engineering, gene therapy and genetic engineering.

In the long-term, when the science becomes available we intend to utilize transhuman technologies: nanotechnology, mind uploading, A/I and other variations of ultra exo-tech.

Our goal is to enable total and unlimited self-transformation, consciousness and expansion across the universe of our species.

It also states note the key words - Transhuman Technologies... and the embracing of transhumanism and extropy.

We Define neo-eugenics as conscious evolution (these words are interchangeable). Purposefully directed evolution via voluntary positive neo-eugenics (including voluntary selective breeding), cloning, genetic engineering and ultimately any and all transhuman technologies. Neo-Eugenics means harnessing all science, technology and knowledge available now or in the future, guiding it with spirituality, ethical considerations and higher consciousness, ultimately towards achieving total and unlimited self transformation. The term Neo-Eugenics embodies the sciences and philosophies involved in Biotechnology, Extropy and Transhumanism all merged in a philosophy of spiritual Conscious Evolution.

http://euvolution.com/prometheism-transhumanism-posthumanism/principles.htm

I believe removing prometheism from this page, will be cause to bring this issue to arbitration to confirm that the individual who keeps removing it obviously is biased and lacks an understanding of what transhumanism. NPOV. thats your problem brian NPOV and blatant bias.

Dnagod 22:22, 7 Feb 2005 (UTC)

Extropy and a lot of the other sites listed under manifestos are linked else where in the article, so I felt it important to also include these manifestos

Please do not revert to childish insults, and a biased personal agenda removing these links, they belong their and represent Principles which I dare say are some of the most interesting, fascinating and creative principles.

Don't abuse your privileges here and force your agenda on this topic of transhumanism, all perspectives are welcome here whether you like it or not.

Dnagod 17:26, 8 Feb 2005 (UTC)

What makes you think transtopianism (transtopia.org) is not secular?

STOP removing these links, you are biased, emotional, unfair, unbalanced and lacking in neutrality.

These links are to stay, and you have no right to remove them. They are valid and legit links, Do not abuse your privileges on this project or you will be revoked.

Dnagod 02:55, 9 Feb 2005 (UTC)

The man who invented the word Transhumanism (Huxley), was an open, avid and published advocate of state sponsored coercive eugenics, selective breeding, and elitist eugenic communities. Therefore you are wrong, and thus the specific issue of VOLUNTARY eugenics does NOT violate in anyway, shape or form, being part of transhumanism. You are wrong, biased, unfair, unbalanced, and lacking in neutrality. Transtopia.org and euvolution.com/prometheism-transhumanism-posthumanism DO NOT SUPPORT COERCIVE EUGENICS in their PRINCIPLES, THEY SUPPORT VOLUNTARY - EUGENICS - READ VOLUNTARY. Forgive the capitalization, but I do that for emphasis, not to scream.

please stop removing these links, you are biased, emotional, unfair, unbalanced and lacking in neutrality. These are not personal attacks, these are stated facts that you have not read the euvolution.com/prometheism-transhumanism-posthumanism web site.

These links are to stay, and you have no right to remove them. They are valid and legit links, Do not abuse your privileges on this project.

I ask you to bring arbitration and discussion on this fact. Your censorship, bias and personal agenda will not win. Go to euvolution.com/prometheism-transhumanism-posthumanism right now and find one place on this site that says prometheism supports COERCIVE EUGENICS. you will not find it anywhere. Prometheism.net clearly states that it only supports voluntary eugenics. Read the sworn oath on euvolution.com/prometheism-transhumanism-posthumanism

The Sworn Oath of Prometheism (front page of euvolution.com/prometheism-transhumanism-posthumanism)

We Prometheans are voluntarily coming together to purposefully direct the creation of a new post-human species. A species with higher intellect, creativity, consciousness and love of ones people. A communion of intellect and beauty, for the simple reason that it can be done. This creation is what gives us purpose and meaning. No other justification is required for this program to advance our Promethean species.

Next I want you to read the Principles of prometheism https://www.euvolution.com/prometheism-transhumanism-posthumanism/principles.htm

2. Our Promethean Species embraces Conscious Evolution

Our immediate aim is to create a neo-eugenically enhanced race that will eventually become a new, superior species with
whatever scientific means are available at the present time. In the short-term, this will be achieved via neo-eugenics, ie. voluntary positive eugenics, human cloning, germ-line engineering, gene therapy and genetic engineering.

5. Total Freedom, Liberty and Self-Determination

Our Libertarian religious nation is founded on the principles of total freedom of speech (including offensive language and language which hurts peoples feelings), freedom of thought, the right to bear arms, liberty, progress, productivity and the pursuit of individual happiness.

nation is VOLUNTARY ONLY. We REJECT all totalitarianism and believe COERCIVE neo-eugenics is counter to the ideal of individual freedom. The promethean governments sole purpose is to protect the rights of the individual. We DO NOT wish to STERILIZE anyone or FORCE anyone to practice neo-eugenics.

DNA or genetic capital is the most valuable commodity in the universe. Our primary goal is to promote positive and voluntary neo-eugenics by channeling national resources to the best, brightest and most creative.

This is from the principles of euvolution.com/prometheism-transhumanism-posthumanism Last Updated: 3/13/03 this means that prometheism is NOT FRINGE, it does not support the fringe philosophy of FORCED COERCIVE EUGENICS. Again the capitalization is not screaming, its meant to provide emphasis. Also my comments about you not being very knowledgeable about euvolution.com/prometheism-transhumanism-posthumanism and transtopia.org are not meant as personal insults or personal attacks, but as an observation.

Dnagod 20:06, 9 Feb 2005 (UTC)

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