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on the interpretation of the Bible). As of 2020, neo-creationism underlies the intelligent-design movement, which has a "big tent" strategy making it inclusive of many Young-Earth creationists (such as Paul Nelson and Percival Davis) and some sympathetic Old-Earth creationists. === Neo-creationism and fundamentalist cladists === As of the 2010s, religious fundamentalist cladists that deny speciation and chronospecies have become more common, following similar lines of thought as creationists, usually replacing religious teachings about deities with religious philosophy. In addition to general denial of biological evolution, common talking points of such cladist creationists are denial of botany and ichthyology along with conflation of herpetology and ornithology along with ignorance of mutation rates and paraphyletic groups. Only a small amount of the general population thus far noticed the creeping spread of such religious cladists, as very few people even have the education to separate the use of the tool from the religious group, as the graph itself does not necessarily assume evolution. === Theistic evolution === Theistic evolution takes the general view that, instead of faith being in opposition to biological evolution, some or all classical religious teachings about God and creation are compatible with some or all of modern scientific theory, including, specifically, evolution. It generally views evolution as a tool used by a creator god, who is both the first cause and immanent sustainer/upholder of the universe; it is therefore well-accepted by people of strong theistic (as opposed to deistic) convictions. Theistic evolution can synthesize with the day-age interpretation of the Genesis creation myth; most adherents consider that the first chapters of Genesis should not be interpreted as a "literal" description, but rather as a literary framework or allegory. This position generally accepts the viewpoint of methodological naturalism, a long-standing convention of the scientific method in science. Many mainline/liberal denominations
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have long accepted evolution, and it is increasingly finding acceptance among evangelical Christians, who strive to keep traditional Christian theology intact. Theistic evolutionists have frequently been prominent in opposing creationism (including intelligent design). Notable examples have included biologist Kenneth R. Miller and theologian John F. Haught, who testified for the plaintiffs in Kitzmiller v. Dover Area School District in 2005. Another example is the Clergy Letter Project, which has compiled and maintains statements - signed by American Christian and non-Christian clergy of different denominations - rejecting creationism, with specific reference to points raised by intelligent-design proponents. Theistic evolutionists have also been active in Citizens Alliances for Science that oppose the introduction of creationism into public-school science classes (one example being evangelical Christian geologist Keith B. Miller, who is a prominent board member of Kansas Citizens for Science). === Agnostic evolution === Agnostic evolution is the position of acceptance of biological evolution, combined with the belief that it is not important whether God is, was, or will have been involved. === Materialistic evolution === Materialistic evolution is the acceptance of biological evolution, combined with the position that if the supernatural exists, it has little to no influence on the material world (a position common to philosophical naturalists, humanists and atheists). The New Atheists champion this view; they argue strongly that the creationist viewpoint is not only dangerous, but is completely rejected by science. == Arguments relating to the definition and limits of science == Critiques such as those based on the distinction between theory and fact are often leveled against unifying concepts within scientific disciplines. Principles such as uniformitarianism, Occam's razor or parsimony, and the Copernican principle are claimed to be the result of a bias within science toward philosophical naturalism, which is equated by many creationists with atheism. In countering
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this claim, philosophers of science use the term methodological naturalism to refer to the long-standing convention in science of the scientific method. The methodological assumption is that observable events in nature are explained only by natural causes, without assuming the existence or non-existence of the supernatural, and therefore supernatural explanations for such events are outside the realm of science. Creationists claim that supernatural explanations should not be excluded and that scientific work is paradigmatically close-minded. Because modern science tries to rely on the minimization of a priori assumptions, error, and subjectivity, as well as on avoidance of Baconian idols, it remains neutral on subjects such as religion or morality. Mainstream proponents accuse the creationists of conflating the two in a form of pseudoscience. === Theory vs fact === The argument that evolution is a theory, not a fact, has often been made against the exclusive teaching of evolution. The argument is related to a common misconception about the technical meaning of "theory" that is used by scientists. In common usage, "theory" often refers to conjectures, hypotheses, and unproven assumptions. In science, "theory" usually means "a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses." For comparison, the National Academy of Sciences defines a fact as "an observation that has been repeatedly confirmed and for all practical purposes is accepted as 'true'." It notes, however, that "truth in science ... is never final, and what is accepted as a fact today may be modified or even discarded tomorrow." Exploring this issue, paleontologist Stephen Jay Gould wrote: Evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain
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and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from ape-like ancestors whether they did so by Darwin's proposed mechanism or by some other yet to be discovered. Marston has argued that, although the creationism argument (that because evolution is "merely" a theory, it therefore cannot also be a fact) reflects a fundamental misunderstanding of the concepts, the scientific countering of the creationist position by the simple stipulation that evolution is a fact may be counterproductive; a better approach, according to Marston, is for scientists to present evolution not as a stipulated fact but as the "best explanation" for the development of life on Earth. This approach, Marston argues, is less likely to end discussion of the topic and is more readily and effectively defended, in part by reducing the burden of proof standards required for assertions of "fact" and by shifting the burden of proof to those who claim that creationism is a better explanation. === Falsifiability === Philosopher of science Karl R. Popper set out the concept of falsifiability as a way to distinguish science and pseudoscience: testable theories are scientific, but those that are untestable are not. In Unended Quest, Popper declared "I have come to the conclusion that Darwinism is not a testable scientific theory but a metaphysical research programme, a possible framework for testable scientific theories," while pointing out it had "scientific character." In what one sociologist derisively called "Popper-chopping," opponents of evolution seized upon Popper's definition to claim evolution was not a science, and claimed creationism was an equally valid metaphysical research program. For example, Duane Gish, a leading Creationist proponent, wrote in a letter to Discover
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magazine (July 1981): "Stephen Jay Gould states that creationists claim creation is a scientific theory. This is a false accusation. Creationists have repeatedly stated that neither creation nor evolution is a scientific theory (and each is equally religious)." Popper responded to news that his conclusions were being used by anti-evolutionary forces by affirming that evolutionary theories regarding the origins of life on Earth were scientific because "their hypotheses can in many cases be tested." Creationists claimed that a key evolutionary concept, that all life on Earth is descended from a single common ancestor, was not mentioned as testable by Popper, and claimed it never would be. In fact, Popper wrote admiringly of the value of Darwin's theory. Only a few years later, Popper wrote, "I have in the past described the theory as 'almost tautological' ... I still believe that natural selection works in this way as a research programme. Nevertheless, I have changed my mind about the testability and logical status of the theory of natural selection; and I am glad to have an opportunity to make a recantation." His conclusion, later in the article is "The theory of natural selection may be so formulated that it is far from tautological. In this case it is not only testable, but it turns out to be not strictly universally true." Debate among some scientists and philosophers of science on the applicability of falsifiability in science continues. Simple falsifiability tests for common descent have been offered by some scientists: for instance, biologist and prominent critic of creationism Richard Dawkins and J. B. S. Haldane both pointed out that if fossil rabbits were found in the Precambrian era, a time before most similarly complex lifeforms had evolved, "that would completely blow evolution out of the water." Falsifiability has caused problems for creationists:
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in his 1982 decision McLean v. Arkansas Board of Education, Judge William R. Overton used falsifiability as one basis for his ruling against the teaching of creation science in the public schools, ultimately declaring it "simply not science." === Conflation of science and religion === Creationists commonly argue against evolution on the grounds that "evolution is a religion; it is not a science," in order to undermine the higher ground biologists claim in debating creationists, and to reframe the debate from being between science (evolution) and religion (creationism) to being between two equally religious beliefs—or even to argue that evolution is religious while intelligent design is not. Those that oppose evolution frequently refer to those who accept evolution as "evolutionists" or "Darwinists." This is generally argued by analogy, by arguing that evolution and religion have one or more things in common, and that therefore evolution is a religion. Examples of claims made in such arguments are statements that evolution is based on faith, that supporters of evolution revere Darwin as a prophet and dogmatically reject alternative suggestions out-of-hand. These claims have become more popular in recent years as the neocreationist movement has sought to distance itself from religion, thus giving it more reason to make use of a seemingly anti-religious analogy. In biology, no scientist's claims, including Darwin's, are treated as sacrosanct, as shown by the aspects of Darwin's theory that have been rejected or revised by scientists over the years, to form first neo-Darwinism and later the modern evolutionary synthesis. === Appeal to consequences === A number of creationists have blurred the boundaries between their disputes over the truth of the underlying facts, and explanatory theories, of evolution, with their purported philosophical and moral consequences. This type of argument is known as an appeal to consequences, and is a
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logical fallacy. Examples of these arguments include those of prominent creationists such as Ken Ham and Henry M. Morris. == Disputes relating to science == Many creationists strongly oppose certain scientific theories in a number of ways, including opposition to specific applications of scientific processes, accusations of bias within the scientific community, and claims that discussions within the scientific community reveal or imply a crisis. In response to perceived crises in modern science, creationists claim to have an alternative, typically based on faith, creation science, or intelligent design. The scientific community has responded by pointing out that their conversations are frequently misrepresented (e.g. by quote mining) in order to create the impression of a deeper controversy or crisis, and that the creationists' alternatives are generally pseudoscientific. === Biology === Disputes relating to evolutionary biology are central to the controversy between creationists and the scientific community. The aspects of evolutionary biology disputed include common descent (and particularly human evolution from common ancestors with other members of the great apes), macroevolution, and the existence of transitional fossils. ==== Common descent ==== [The] Discovery [Institute] presents common descent as controversial exclusively within the animal kingdom, as it focuses on embryology, anatomy, and the fossil record to raise questions about them. In the real world of science, common descent of animals is completely noncontroversial; any controversy resides in the microbial world. There, researchers argued over a variety of topics, starting with the very beginning, namely the relationship among the three main branches of life. A group of organisms is said to have common descent if they have a common ancestor. A theory of universal common descent based on evolutionary principles was proposed by Charles Darwin and is now generally accepted by biologists. The most recent common ancestor of all living organisms is believed to
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have appeared about 3.9 billion years ago. With a few exceptions (e.g. Michael Behe) the vast majority of creationists rejected this theory in favor of the belief that a common design suggests a common designer (God). Many of these same creationists through the beginning of the 21st century also held that modern species were perpetually fixed from creation. However, now a large amount of creationists allow evolution of species, in the face of undeniable evidence for speciation. They contend, however, that it was specific "kinds" or baramin that were created initially, from which all present-day species arose. Thus all bear species may have developed from a common ancestor that was separately created to establish a bear-like baramin, by this type of creationism. This type of creationism often acknowledges the existence of evolutionary processes but denies that they demonstrate common ancestry or that evolutionary processes would have produced the diversity of contemporary life. Evidence of common descent includes evidence from genetics, fossil records, comparative anatomy, geographical distribution of species, comparative physiology and comparative biochemistry. ===== Human evolution ===== Human evolution is the study of the biological evolution of humans as a distinct species from its common ancestors with other animals. Analysis of fossil evidence and genetic distance are two of the means by which scientists understand this evolutionary history. Fossil evidence suggests that humans' earliest hominid ancestors may have split from other primates as early as the late Oligocene, circa 26 to 24 Ma, and that by the early Miocene, the adaptive radiation of many different hominoid forms was well underway. Evidence from the molecular dating of genetic differences indicates that the gibbon lineage (family Hylobatidae) diverged between 18 and 12 Ma, and the orangutan lineage (subfamily Ponginae) diverged about 12 Ma. While there is no fossil evidence thus far clearly
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documenting the early ancestry of gibbons, fossil proto-orangutans may be represented by Sivapithecus from India and Griphopithecus from Turkey, dated to around 10 Ma. Molecular evidence further suggests that between 8 and 4 Ma, first the gorillas, and then the chimpanzee (genus Pan) split from the line leading to the humans. We have no fossil record of this divergence, but distinctively hominid fossils have been found dating to 3.2 Ma (see Lucy) and possibly even earlier, at 6 or 7 Ma (see Toumaï). Comparisons of DNA show that 99.4 percent of the coding regions are identical in chimpanzees and humans (95–96% overall), which is taken as strong evidence of recent common ancestry. Today, only one distinct human species survives, but many earlier species have been found in the fossil record, including Homo erectus, Homo habilis, and Homo neanderthalensis. Creationists dispute there is evidence of shared ancestry in the fossil evidence, and argue either that these are misassigned ape fossils (e.g. that Java Man was a gibbon) or too similar to modern humans to designate them as distinct or transitional forms. Creationists frequently disagree where the dividing lines would be. Creation myths (such as the Book of Genesis) frequently posit a first man (Adam, in the case of Genesis), which has been advocated by creationists as underlying an alternative viewpoint to the scientific account. All these claims and objections are subsequently refuted. Creationists also dispute the scientific community's interpretation of genetic evidence in the study of human evolution. They argue that it is a "dubious assumption" that genetic similarities between various animals imply a common ancestral relationship, and that scientists are coming to this interpretation only because they have preconceived notions that such shared relationships exist. Creationists also argue that genetic mutations are strong evidence against evolutionary theory because, they assert,
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the mutations required for major changes to occur would almost certainly be detrimental. However, most mutations are neutral, and the minority of mutations which are beneficial or harmful are often situational; a mutation that is harmful in one environment may be helpful in another. ==== Macroevolution ==== In biology, macroevolution refers to evolution at and above the species level, including most of fossil history and much of systematics. Microevolution refers to the process in evolution within populations, including adaptive and neutral evolution. However, there is no fundamental distinction between these processes; small changes compound over time and eventually lead to speciation. Creationists argue that a finite number of discrete kinds were created, as described in the Book of Genesis, and these kinds determine the limits of variation. Early Creationists equated kinds with species, but most now accept that speciation can occur: not only is the evidence overwhelming for speciation, but the millions of species now in existence could not have fit in Noah's Ark, as depicted in Genesis. Created kinds identified by creationists are more generally on the level of the family (for example, Canidae), but the genus Homo is a separate kind. A Creationist systematics called Baraminology builds on the idea of created kind, calling it a baramin. While evolutionary systematics is used to explore relationships between organisms by descent, baraminology attempts to find discontinuities between groups of organisms. It employs many of the tools of evolutionary systematics, but Biblical criteria for taxonomy take precedence over all other criteria. This undermines their claim to objectivity: they accept evidence for the common ancestry of cats or dogs but not analogous evidence for the common ancestry of apes and humans. Recent arguments against macroevolution (in the Creationist sense) include the intelligent design (ID) arguments of irreducible complexity and specified complexity. Neither
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argument has been accepted for publication in a peer-reviewed scientific journal, and both arguments have been rejected by the scientific community as pseudoscience. When taken to court in an attempt to introduce ID into the classroom, the judge wrote "The overwhelming evidence at trial established that ID is a religious view, a mere re-labeling of creationism, and not a scientific theory." ==== Transitional fossils ==== It is commonly stated by critics of evolution that there are no known transitional fossils. This position is based on a misunderstanding of the nature of what represents a transitional feature. A common creationist argument is that no fossils are found with partially functional features. It is plausible that a complex feature with one function can adapt a different function through evolution. The precursor to, for example, a wing, might originally have only been used for gliding, trapping flying prey, or mating display. Today, wings can still have all of these functions, but they are also used in active flight. As another example, Alan Hayward stated in Creation and Evolution (1985) that "Darwinists rarely mention the whale because it presents them with one of their most insoluble problems. They believe that somehow a whale must have evolved from an ordinary land-dwelling animal, which took to the sea and lost its legs ... A land mammal that was in the process of becoming a whale would fall between two stools—it would not be fitted for life on land or at sea, and would have no hope for survival." The evolution of whales has been documented in considerable detail, with Ambulocetus, described as looking like a three-metre long mammalian crocodile, as one of the transitional fossils. The hippopotamus, the whale's closest living ancestor, exemplifies how an animal might be well-suited for both land and water. Although transitional
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fossils elucidate the evolutionary transition of one life-form to another, they only exemplify snapshots of this process. Due to the special circumstances required for preservation of living beings, only a very small percentage of all life-forms that ever have existed can be expected to be discovered. Thus, the transition itself can only be illustrated and corroborated by transitional fossils, but it will never be known in detail. Progressing research and discovery managed to fill in several gaps and continues to do so. Critics of evolution often cite this argument as being a convenient way to explain off the lack of 'snapshot' fossils that show crucial steps between species. The theory of punctuated equilibrium developed by Stephen Jay Gould and Niles Eldredge is often mistakenly drawn into the discussion of transitional fossils. This theory pertains only to well-documented transitions within taxa or between closely related taxa over a geologically short period. These transitions, usually traceable in the same geological outcrop, often show small jumps in morphology between periods of morphological stability. To explain these jumps, Gould and Eldredge envisaged comparatively long periods of genetic stability separated by periods of rapid evolution. For example, the change from a creature the size of a mouse, to one the size of an elephant, could be accomplished over 60,000 years, with a rate of change too small to be noticed over any human lifetime. 60,000 years is too small a gap to be identified or identifiable in the fossil record. Experts in evolutionary theory have pointed out that even if it were possible for enough fossils to survive to show a close transitional change critics will never be satisfied, as the discovery of one "missing link" itself creates two more so-called "missing links" on either side of the discovery. Richard Dawkins says that the reason
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for this "losing battle" is that many of these critics are theists who "simply don't want to see the truth." === Geology === Many believers in Young Earth creationism—a position held by the majority of proponents of 'flood geology'—accept biblical chronogenealogies (such as the Ussher chronology, which in turn is based on the Masoretic version of the Genealogies of Genesis). They believe that God created the universe approximately 6,000 years ago, in the space of six days. Much of creation geology is devoted to debunking the dating methods used in anthropology, geology, and planetary science that give ages in conflict with the young Earth idea. In particular, creationists dispute the reliability of radiometric dating and isochron analysis, both of which are central to mainstream geological theories of the age of the Earth. They usually dispute these methods based on uncertainties concerning initial concentrations of individually considered species and the associated measurement uncertainties caused by diffusion of the parent and daughter isotopes. A full critique of the entire parameter-fitting analysis, which relies on dozens of radionuclei parent and daughter pairs and gives essentially identical or near identical readings, has not been done by creationists hoping to cast doubt on the technique. The consensus of professional scientific organizations worldwide is that no scientific evidence contradicts the age of approximately 4.5 billion years. Young Earth creationists reject these ages on the grounds of what they regard as being tenuous and untestable assumptions in the methodology. They have often quoted apparently inconsistent radiometric dates to cast doubt on the utility and accuracy of the method. Mainstream proponents who get involved in this debate point out that dating methods only rely on the assumptions that the physical laws governing radioactive decay have not been violated since the sample was formed (harking back to Lyell's doctrine
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of uniformitarianism). They also point out that the "problems" that creationists publicly mentioned can be shown to either not be problems at all, are issues with known contamination, or simply the result of incorrectly evaluating legitimate data. === Other sciences === ==== Cosmology ==== While Young Earth creationists believe that the Universe was created by the Judeo-Christian-Islamic God approximately 6000 years ago, the current scientific consensus is that the Universe as we know it emerged from the Big Bang 13.8 billion years ago. The recent science of nucleocosmochronology is extending the approaches used for carbon-14 and other radiometric dating to the dating of astronomical features. For example, based upon this emerging science, the Galactic thin disk of the Milky Way galaxy is estimated to have been formed 8.3 ± 1.8 billion years ago. ==== Nuclear physics ==== Creationists point to experiments they have performed, which they claim demonstrate that 1.5 billion years of nuclear decay took place over a short period, from which they infer that "billion-fold speed-ups of nuclear decay" have occurred, a massive violation of the principle that radioisotope decay rates are constant, a core principle underlying nuclear physics generally, and radiometric dating in particular. The scientific community points to numerous flaws in these experiments, to the fact that their results have not been accepted for publication by any peer-reviewed scientific journal, and to the fact that the creationist scientists conducting them were untrained in experimental geochronology. In refutation of Young Earth claims of inconstant decay-rates affecting the reliability of radiometric dating, Roger C. Wiens, a physicist specializing in isotope dating states: There are only three quite technical instances where a half-life changes, and these do not affect the dating methods [under discussion]": Only one technical exception occurs under terrestrial conditions, and this is not for an isotope
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used for dating.... The artificially-produced isotope, beryllium-7 has been shown to change by up to 1.5%, depending on its chemical environment. ... [H]eavier atoms are even less subject to these minute changes, so the dates of rocks made by electron-capture decays would only be off by at most a few hundredths of a percent. ... Another case is material inside of stars, which is in a plasma state where electrons are not bound to atoms. In the extremely hot stellar environment, a completely different kind of decay can occur. 'Bound-state beta decay' occurs when the nucleus emits an electron into a bound electronic state close to the nucleus.... All normal matter, such as everything on Earth, the Moon, meteorites, etc. has electrons in normal positions, so these instances never apply to rocks, or anything colder than several hundred thousand degrees.... The last case also involves very fast-moving matter. It has been demonstrated by atomic clocks in very fast spacecraft. These atomic clocks slow down very slightly (only a second or so per year) as predicted by Einstein's theory of relativity. No rocks in our solar system are going fast enough to make a noticeable change in their dates.... === Misrepresentations of the scientific community === The Discovery Institute has a "formal declaration" titled "A Scientific Dissent From Darwinism" which has many evangelicals, people from fields irrelevant to biology and geology and few biologists. Many of the biologists who signed have fields not directly related to evolution. In response, there has been an analogous declaration humorously upholding the consensus, Project Steve, which emphasizes the large amount of scientists supporting the consensus. ==== Quote mining ==== As a means to criticize mainstream science, creationists sometimes quote scientists who ostensibly support the mainstream theories, but appear to acknowledge criticisms similar to those of
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creationists. These have very often been shown to be quote mines that do not accurately reflect the evidence for evolution or the mainstream scientific community's opinion of it, or are highly out-of-date. Many of the same quotes used by creationists have appeared so frequently in Internet discussions due to the availability of cut and paste functions, that the TalkOrigins Archive has created "The Quote Mine Project" for quick reference to the original context of these quotations. Creationists often quote mine Darwin, especially with regard to the seeming improbability of the evolution of the eye, to give support to their views. == Public policy issues == The creation–evolution controversy has grown in importance in recent years, interfacing with other contemporary political issues, primarily those in the United States that involve the Christian right. === Science education === Creationists promoted the idea that evolution is a theory in crisis with scientists criticizing evolution and claim that fairness and equal time requires educating students about the alleged scientific controversy. Opponents, being the overwhelming majority of the scientific community and science education organizations, See: List of scientific societies explicitly rejecting intelligent design Kitzmiller v. Dover Area School District, 04 cv 2688 (M.D. Pa. December 20, 2005). Whether ID Is Science, p. 83. The Discovery Institute's A Scientific Dissent From Darwinism petition begun in 2001 has been signed by "over 700 scientists" as of August 20, 2006. The four-day A Scientific Support for Darwinism petition gained 7,733 signatories from scientists opposing ID. AAAS 2002. The American Association for the Advancement of Science (AAAS), the largest association of scientists in the U.S., has 120,000 members, and firmly rejects ID. More than 70,000 Australian scientists "...urge all Australian governments and educators not to permit the teaching or promulgation of ID as science." National Center for Science Education]:
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List of statements from scientific professional organizations on the status intelligent design and other forms of creationism in the sciences. reply that there is no scientific controversy and that the controversy exists solely in terms of religion and politics. George Mason University Biology Department introduced a course on the creation/evolution controversy, and apparently as students learn more about biology, they find objections to evolution less convincing, suggesting that "teaching the controversy" rightly as a separate elective course on philosophy or history of science, or "politics of science and religion," would undermine creationists' criticisms, and that the scientific community's resistance to this approach was bad public relations. === Freedom of speech === Creationists have claimed that preventing them from teaching creationism violates their right of freedom of speech. Court cases (such as Webster v. New Lenox School District (1990) and Bishop v. Aronov (1991)) have upheld school districts' and universities' right to restrict teaching to a specified curriculum. == Issues relating to religion == === Religion and historical scientists === Creationists often argue that Christianity and literal belief in the Bible are either foundationally significant or directly responsible for scientific progress. To that end, Institute for Creation Research founder Henry M. Morris has enumerated scientists such as astronomer and philosopher Galileo Galilei, mathematician and theoretical physicist James Clerk Maxwell, mathematician and philosopher Blaise Pascal, geneticist monk Gregor Mendel, and Isaac Newton as believers in a biblical creation narrative. This argument usually involves scientists who were no longer alive when evolution was proposed or whose field of study did not include evolution. The argument is generally rejected as specious by those who oppose creationism. Many of the scientists in question did some early work on the mechanisms of evolution, e.g., the modern evolutionary synthesis combines Darwin's theory of evolution with Mendel's theories
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of inheritance and genetics. Though biological evolution of some sort had become the primary mode of discussing speciation within science by the late-19th century, it was not until the mid-20th century that evolutionary theories stabilized into the modern synthesis. Geneticist and evolutionary biologist Theodosius Dobzhansky, called the Father of the Modern Synthesis, argued that "Nothing in biology makes sense except in the light of evolution," and saw no conflict between evolutionary and his religious beliefs. Nevertheless, some of the historical scientists marshalled by creationists were dealing with quite different issues than any are engaged with today: Louis Pasteur, for example, opposed the theory of spontaneous generation with biogenesis, an advocacy some creationists describe as a critique on chemical evolution and abiogenesis. Pasteur accepted that some form of evolution had occurred and that the Earth was millions of years old. The relationship between religion and science was not portrayed in antagonistic terms until the late-19th century, and even then there have been many examples of the two being reconcilable for evolutionary scientists. Many historical scientists wrote books explaining how pursuit of science was seen by them as fulfillment of spiritual duty in line with their religious beliefs. Even so, such professions of faith were not insurance against dogmatic opposition by certain religious people. == Forums == === Debates === Many creationists and scientists engage in frequent public debates regarding the origin of human life, hosted by a variety of institutions. However, some scientists disagree with this tactic, arguing that by openly debating supporters of supernatural origin explanations (creationism and intelligent design), scientists are lending credibility and unwarranted publicity to creationists, which could foster an inaccurate public perception and obscure the factual merits of the debate. For example, in May 2004 Michael Shermer debated creationist Kent Hovind in front of a predominantly
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creationist audience. In Shermer's online reflection while he was explaining that he won the debate with intellectual and scientific evidence he felt it was "not an intellectual exercise," but rather it was "an emotional drama," with scientists arguing from "an impregnable fortress of evidence that converges to an unmistakable conclusion," while for creationists it is "a spiritual war." While receiving positive responses from creationist observers, Shermer concluded "Unless there is a subject that is truly debatable (evolution v. creation is not), with a format that is fair, in a forum that is balanced, it only serves to belittle both the magisterium of science and the magisterium of religion." (see Non-overlapping magisteria). Others, like evolutionary biologist Massimo Pigliucci, have debated Hovind, and have expressed surprise to hear Hovind try "to convince the audience that evolutionists believe humans came from rocks" and at Hovind's assertion that biologists believe humans "evolved from bananas." In September 2012, educator and television personality Bill Nye of Bill Nye the Science Guy fame spoke with the Associated Press and aired his fears about acceptance of creationist theory, believing that teaching children that creationism is the only true answer and without letting them understand the way science works will prevent any future innovation in the world of science. In February 2014, Nye defended evolution in the classroom in a debate with creationist Ken Ham on the topic of whether creation is a viable model of origins in today's modern, scientific era. Eugenie Scott of the National Center for Science Education, a nonprofit organization dedicated to defending the teaching of evolution in the public schools, claimed debates are not the sort of arena to promote science to creationists. Scott says that "Evolution is not on trial in the world of science," and "the topic of the discussion should not
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be the scientific legitimacy of evolution" but rather should be on the lack of evidence in creationism. Stephen Jay Gould adopted a similar position, explaining: Debate is an art form. It is about the winning of arguments. It is not about the discovery of truth. There are certain rules and procedures to debate that really have nothing to do with establishing fact—which [creationists] are very good at. Some of those rules are: never say anything positive about your own position because it can be attacked, but chip away at what appear to be the weaknesses in your opponent's position. They are good at that. I don't think I could beat the creationists at debate. I can tie them. But in courtrooms they are terrible, because in courtrooms you cannot give speeches. In a courtroom you have to answer direct questions about the positive status of your belief. === Political lobbying === On both sides of the controversy a wide range of organizations are involved at a number of levels in lobbying in an attempt to influence political decisions relating to the teaching of evolution. These include the Discovery Institute, the National Center for Science Education, the National Science Teachers Association, state Citizens Alliances for Science, and numerous national science associations and state academies of science. === Media coverage === The controversy has been discussed in numerous newspaper articles, reports, op-eds and letters to the editor, as well as a number of radio and television programmes (including the PBS series, Evolution (2001) and Coral Ridge Ministries' Darwin's Deadly Legacy (2006)). This has led some commentators to express a concern at what they see as a highly inaccurate and biased understanding of evolution among the general public. Edward Humes states: There are really two theories of evolution. There is the genuine scientific
|
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"page_id": 1115768,
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theory and there is the talk-radio pretend version, designed not to enlighten but to deceive and enrage. The talk-radio version had a packed town hall up in arms at the Why Evolution Is Stupid lecture. In this version of the theory, scientists supposedly believe that all life is accidental, a random crash of molecules that magically produced flowers, horses and humans—a scenario as unlikely as a tornado in a junkyard assembling a 747. Humans come from monkeys in this theory, just popping into existence one day. The evidence against Darwin is overwhelming, the purveyors of talk-radio evolution rail, yet scientists embrace his ideas because they want to promote atheism. == Outside the United States == While the controversy has been prominent in the United States, it has flared up in other countries as well. === Europe === Europeans have often regarded the creation–evolution controversy as an American matter. In recent years the conflict has become an issue in other countries including Germany, the United Kingdom, Italy, the Netherlands, Poland, Turkey and Serbia. On September 17, 2007, the Committee on Culture, Science and Education of the Parliamentary Assembly of the Council of Europe (PACE) issued a report on the attempt by American-inspired creationists to promote creationism in European schools. It concludes "If we are not careful, creationism could become a threat to human rights which are a key concern of the Council of Europe... The war on the theory of evolution and on its proponents most often originates in forms of religious extremism which are closely allied to extreme right-wing political movements... some advocates of strict creationism are out to replace democracy by theocracy." The Council of Europe firmly rejected creationism. === Australia === Under the former Queensland state government of Joh Bjelke-Petersen, in the 1980s Queensland allowed the teaching of
|
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"page_id": 1115768,
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"title": "Rejection of evolution by religious groups"
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creationism in secondary schools. In 2010, the Queensland state government introduced the topic of creationism into school classes within the "ancient history" subject where its origins and nature are discussed as a significant controversy. Public lectures have been given in rented rooms at universities, by visiting American speakers. One of the most acrimonious aspects of the Australian debate was featured on the science television program Quantum, about a long-running and ultimately unsuccessful court case by Ian Plimer, Professor of Geology at the University of Melbourne, against an ordained minister, Allen Roberts, who had claimed that there were remnants of Noah's Ark in eastern Turkey. Although the court found that Roberts had made false and misleading claims, they were not made in the course of trade or commerce, so the case failed. === Islamic countries === In recent times, the controversy over evolution has spread into several Islamic countries. In Egypt, evolution is currently taught in schools, but Saudi Arabia and Sudan have both banned the teaching of evolution in schools. Creation science has also been heavily promoted in Turkey, primarily by creationists like Harun Yahya. In Iran, the traditional practice of Shia Islam isn't preoccupied with Qur'anic literalism as in case of Saudi Wahhabism but ijtihad; many influential Iranian Shi'ite scholars, including several who were closely involved in Iranian Revolution, are not opposed to evolutionary ideas in general, disagreeing that evolution necessarily conflicts with the Muslim mainstream. Iranian pupils since 5th grade of elementary school learn only about evolution, thus portraying geologists and scientists in general as an authoritative voice of scientific knowledge. === Asia === ==== South Korea ==== In South Korea, most opposition to teaching evolution comes from the local evangelical community. As part of these efforts, the Korean Association for Creation Research (KACR) was established in 1981
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{
"page_id": 1115768,
"source": null,
"title": "Rejection of evolution by religious groups"
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by evangelical pastors Kim Yŏnggil and Ch'oe Yŏngsang. In South Korea, according to a 2009 survey, about 30 percent of the population believe in creation science while opposing the teaching of evolution. == See also == == Notes == == Citations == == References == == Further reading == == External links == "Ten Major Court Cases about Evolution and Creationism" – by Molleen Matsumura and Louise Mead, National Center for Science Education
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"page_id": 1115768,
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"title": "Rejection of evolution by religious groups"
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In general relativity, an absolute horizon is a boundary in spacetime, defined with respect to the external universe, inside which events cannot affect an external observer. Light emitted inside the horizon can never reach the observer, and anything that passes through the horizon from the observer's side is never seen again by the observer. An absolute horizon is thought of as the boundary of a black hole. In the context of black holes, the absolute horizon is generally referred to as an event horizon, though this is often used as a more general term for all types of horizons. The absolute horizon is just one type of horizon. For example, important distinctions must be made between absolute horizons and apparent horizons; the notion of a horizon in general relativity is subtle, and depends on fine distinctions. == Definition == An absolute horizon is only defined in an asymptotically flat spacetime – a spacetime which approaches flat space as one moves far away from any massive bodies. Examples of asymptotically flat spacetimes include Schwarzschild and Kerr black holes. The FRW universe – which is believed to be a good model for our universe – is generally not asymptotically flat. Nonetheless, we can think of an isolated object in an FRW universe as being nearly an isolated object in an asymptotically flat universe. The particular feature of asymptotic flatness which is needed is a notion of "future null infinity". This is the set of points which are approached asymptotically by null rays (light rays, for example) which can escape to infinity. This is the technical meaning of "external universe". These points are only defined in an asymptotically flat universe. An absolute horizon is defined as the past null cone of future null infinity. == Nature of the absolute horizon == The definition
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{
"page_id": 6817401,
"source": null,
"title": "Absolute horizon"
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of an absolute horizon is sometimes referred to as teleological, meaning that it cannot be known where the absolute horizon is without knowing the entire evolution of the universe, including the future. This is both an advantage and a disadvantage. The advantage is that this notion of a horizon is mathematically convenient and does not depend on the observer, unlike apparent horizons, for example. The disadvantage is that it requires the full history (all the way into the future) of the spacetime to be known, thus making event horizons unsuitable for empirical tests. In the case of numerical relativity, where a spacetime is simply being evolved into the future, only a finite portion of the spacetime can be known. == See also == Causal structure Cauchy horizon Cosmological horizon Ergosphere Killing horizon Naked singularity Particle horizon Photon sphere Reissner–Nordström solution Schwarzschild metric == References == == Further reading == Kip Thorne (1994). Black Holes and Time Warps. W. W. Norton. This is a popular book, aimed at the lay reader, containing good discussion of horizons and black holes.
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{
"page_id": 6817401,
"source": null,
"title": "Absolute horizon"
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Photoreceptor proteins are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Some examples are rhodopsin in the photoreceptor cells of the vertebrate retina, phytochrome in plants, and bacteriorhodopsin and bacteriophytochromes in some bacteria. They mediate light responses as varied as visual perception, phototropism and phototaxis, as well as responses to light-dark cycles such as circadian rhythm and other photoperiodisms including control of flowering times in plants and mating seasons in animals. == Structure == Photoreceptor proteins typically consist of a protein attached to a non-protein chromophore (sometimes referred as photopigment, even so photopigment may also refer to the photoreceptor as a whole). The chromophore reacts to light via photoisomerization or photoreduction, thus initiating a change of the receptor protein which triggers a signal transduction cascade. Chromophores found in photoreceptors include retinal (retinylidene proteins, for example rhodopsin in animals), flavin (flavoproteins, for example cryptochrome in plants and animals) and bilin (biliproteins, for example phytochrome in plants). The plant protein UVR8 is exceptional amongst photoreceptors in that it contains no external chromophore. Instead, UVR8 absorbs light through tryptophan residues within its protein coding sequence. == Photoreceptors in animals == Melanopsin: in vertebrate retina, mediates pupillary reflex, involved in regulation of circadian rhythms Photopsin: reception of various colors of light in the cone cells of vertebrate retina Rhodopsin: green-blue light reception in the rod cells of vertebrate retina Protein Kinase C: mediates photoreceptor deactivation, and retinal degeneration OPN5: sensitive to UV-light == Photoreceptors in plants == UVR8: UV-B light reception Cryptochrome: blue and UV-A light reception Phototropin: blue and UV-A light perception (to mediate phototropism and chloroplast movement) Zeitlupe: blue light entrainment of the circadian clock Phytochrome: red and far-red light reception All the photoreceptors listed above allow plants to sense light with wavelengths range from
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"page_id": 10094209,
"source": null,
"title": "Photoreceptor protein"
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280 nm (UV-B) to 750 nm (far-red light). Plants use light of different wavelengths as environmental cues to both alter their position and to trigger important developmental transitions. The most prominent wavelength responsible for plant mechanisms is blue light, which can trigger cell elongation, plant orientation, and flowering. One of the most important processes regulated by photoreceptors is known as photomorphogenesis. When a seed germinates underground in the absence of light, its stem rapidly elongates upwards. When it breaks through the surface of the soil, photoreceptors perceive light. The activated photoreceptors cause a change in developmental program; the plant starts producing chlorophyll and switches to photosynthetic growth. == Photoreceptors in phototactic flagellates == (Also see: Eyespot apparatus) Channelrhodopsin: in unicellular algae, mediates phototaxis Chlamyopsin and volvoxopsin Flavoproteins == Photoreceptors in archaea and bacteria == Bacteriophytochrome sensory bacteriorhodopsin Halorhodopsin Proteorhodopsin Cyanobacteriochrome == Photoreception and signal transduction == Visual cycle Visual phototransduction == Responses to photoreception == Visual perception Phototropism Phototaxis Circadian rhythm (body clock) Photoperiodism == See also == Biliproteins Photomolecular biology == References ==
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{
"page_id": 10094209,
"source": null,
"title": "Photoreceptor protein"
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Sir John Cunningham McLennan, (October 14, 1867 – October 9, 1935) was a Canadian physicist. Born in Ingersoll, Ontario, the son of David McLennan and Barbara Cunningham, he was the director of the physics laboratory at the University of Toronto from 1906 until 1932. McLennan was elected a Fellow of the Royal Society in 1915. McLennan delivered the Guthrie lecture to the Physical Society in 1918. With his graduate student, Gordon Merritt Shrum, he built a helium liquefier at the University of Toronto. In 1923, they became the second group of physicists in the world to successfully produce liquid helium, 15 years after Heike Kammerlingh Onnes. In 1926, McLennan was awarded the Royal Society of Canada's Flavelle Medal and in 1927 a Royal Medal. He died in 1935 near Abbeville in France on a train from Paris to London of a heart attack. He is buried beside his wife in Stow of Wedale, Scotland. == References == == Further reading == University of Toronto biography John Cunningham McLennan at The Canadian Encyclopedia John Cunningham McLennan archival papers held at the University of Toronto Archives and Records Management Services
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"page_id": 2492040,
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"title": "John Cunningham McLennan"
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Physical Review Accelerators and Beams is a monthly peer-reviewed open-access scientific journal, published by the American Physical Society. The journal focuses on accelerator physics and engineering. Its lead editor is Frank Zimmermann (CERN). The journal was established in 1998 as Physical Review Special Topics – Accelerators and Beams, obtaining its current title in 2016. The journal does not require article processing charges, being sponsored by academic and industrial institutions. == Abstracting and indexing == The journal is abstracted and indexed in: Current Contents/Physical, Chemical & Earth Sciences Inspec Science Citation Index Expanded Scopus According to the Journal Citation Reports, the journal has a 2021 impact factor of 1.879. == References == == External links == Official website
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"page_id": 49022601,
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"title": "Physical Review Accelerators and Beams"
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In atomic physics and quantum chemistry, the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals. For example, the electron configuration of the neon atom is 1s2 2s2 2p6, meaning that the 1s, 2s, and 2p subshells are occupied by two, two, and six electrons, respectively. Electronic configurations describe each electron as moving independently in an orbital, in an average field created by the nuclei and all the other electrons. Mathematically, configurations are described by Slater determinants or configuration state functions. According to the laws of quantum mechanics, a level of energy is associated with each electron configuration. In certain conditions, electrons are able to move from one configuration to another by the emission or absorption of a quantum of energy, in the form of a photon. Knowledge of the electron configuration of different atoms is useful in understanding the structure of the periodic table of elements, for describing the chemical bonds that hold atoms together, and in understanding the chemical formulas of compounds and the geometries of molecules. In bulk materials, this same idea helps explain the peculiar properties of lasers and semiconductors. == Shells and subshells == Electron configuration was first conceived under the Bohr model of the atom, and it is still common to speak of shells and subshells despite the advances in understanding of the quantum-mechanical nature of electrons. An electron shell is the set of allowed states that share the same principal quantum number, n, that electrons may occupy. In each term of an electron configuration, n is the positive integer that precedes each orbital letter (helium's electron configuration is 1s2, therefore n = 1, and the orbital contains two electrons). An atom's nth electron shell can accommodate 2n2 electrons. For example, the
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first shell can accommodate two electrons, the second shell eight electrons, the third shell eighteen, and so on. The factor of two arises because the number of allowed states doubles with each successive shell due to electron spin—each atomic orbital admits up to two otherwise identical electrons with opposite spin, one with a spin +1⁄2 (usually denoted by an up-arrow) and one with a spin of −1⁄2 (with a down-arrow). A subshell is the set of states defined by a common azimuthal quantum number, l, within a shell. The value of l is in the range from 0 to n − 1. The values l = 0, 1, 2, 3 correspond to the s, p, d, and f labels, respectively. For example, the 3d subshell has n = 3 and l = 2. The maximum number of electrons that can be placed in a subshell is given by 2(2l + 1). This gives two electrons in an s subshell, six electrons in a p subshell, ten electrons in a d subshell and fourteen electrons in an f subshell. The numbers of electrons that can occupy each shell and each subshell arise from the equations of quantum mechanics, in particular the Pauli exclusion principle, which states that no two electrons in the same atom can have the same values of the four quantum numbers. Exhaustive technical details about the complete quantum mechanical theory of atomic spectra and structure can be found and studied in the basic book of Robert D. Cowan. == Notation == Physicists and chemists use a standard notation to indicate the electron configurations of atoms and molecules. For atoms, the notation consists of a sequence of atomic subshell labels (e.g. for phosphorus the sequence 1s, 2s, 2p, 3s, 3p) with the number of electrons assigned to each subshell
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placed as a superscript. For example, hydrogen has one electron in the s-orbital of the first shell, so its configuration is written 1s1. Lithium has two electrons in the 1s-subshell and one in the (higher-energy) 2s-subshell, so its configuration is written 1s2 2s1 (pronounced "one-s-two, two-s-one"). Phosphorus (atomic number 15) is as follows: 1s2 2s2 2p6 3s2 3p3. For atoms with many electrons, this notation can become lengthy and so an abbreviated notation is used. The electron configuration can be visualized as the core electrons, equivalent to the noble gas of the preceding period, and the valence electrons: each element in a period differs only by the last few subshells. Phosphorus, for instance, is in the third period. It differs from the second-period neon, whose configuration is 1s2 2s2 2p6, only by the presence of a third shell. The portion of its configuration that is equivalent to neon is abbreviated as [Ne], allowing the configuration of phosphorus to be written as [Ne] 3s2 3p3 rather than writing out the details of the configuration of neon explicitly. This convention is useful as it is the electrons in the outermost shell that most determine the chemistry of the element. For a given configuration, the order of writing the orbitals is not completely fixed since only the orbital occupancies have physical significance. For example, the electron configuration of the titanium ground state can be written as either [Ar] 4s2 3d2 or [Ar] 3d2 4s2. The first notation follows the order based on the Madelung rule for the configurations of neutral atoms; 4s is filled before 3d in the sequence Ar, K, Ca, Sc, Ti. The second notation groups all orbitals with the same value of n together, corresponding to the "spectroscopic" order of orbital energies that is the reverse of the order in
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which electrons are removed from a given atom to form positive ions; 3d is filled before 4s in the sequence Ti4+, Ti3+, Ti2+, Ti+, Ti. The superscript 1 for a singly occupied subshell is not compulsory; for example aluminium may be written as either [Ne] 3s2 3p1 or [Ne] 3s2 3p. In atoms where a subshell is unoccupied despite higher subshells being occupied (as is the case in some ions, as well as certain neutral atoms shown to deviate from the Madelung rule), the empty subshell is either denoted with a superscript 0 or left out altogether. For example, neutral palladium may be written as either [Kr] 4d10 5s0 or simply [Kr] 4d10, and the lanthanum(III) ion may be written as either [Xe] 4f0 or simply [Xe]. It is quite common to see the letters of the orbital labels (s, p, d, f) written in an italic or slanting typeface, although the International Union of Pure and Applied Chemistry (IUPAC) recommends a normal typeface (as used here). The choice of letters originates from a now-obsolete system of categorizing spectral lines as "sharp", "principal", "diffuse" and "fundamental" (or "fine"), based on their observed fine structure: their modern usage indicates orbitals with an azimuthal quantum number, l, of 0, 1, 2 or 3 respectively. After f, the sequence continues alphabetically g, h, i... (l = 4, 5, 6...), skipping j, although orbitals of these types are rarely required. The electron configurations of molecules are written in a similar way, except that molecular orbital labels are used instead of atomic orbital labels (see below). == Energy of ground state and excited states == The energy associated to an electron is that of its orbital. The energy of a configuration is often approximated as the sum of the energy of each electron, neglecting the
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"page_id": 67211,
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electron-electron interactions. The configuration that corresponds to the lowest electronic energy is called the ground state. Any other configuration is an excited state. As an example, the ground state configuration of the sodium atom is 1s2 2s2 2p6 3s1, as deduced from the Aufbau principle (see below). The first excited state is obtained by promoting a 3s electron to the 3p subshell, to obtain the 1s2 2s2 2p6 3p1 configuration, abbreviated as the 3p level. Atoms can move from one configuration to another by absorbing or emitting energy. In a sodium-vapor lamp for example, sodium atoms are excited to the 3p level by an electrical discharge, and return to the ground state by emitting yellow light of wavelength 589 nm. Usually, the excitation of valence electrons (such as 3s for sodium) involves energies corresponding to photons of visible or ultraviolet light. The excitation of core electrons is possible, but requires much higher energies, generally corresponding to X-ray photons. This would be the case for example to excite a 2p electron of sodium to the 3s level and form the excited 1s2 2s2 2p5 3s2 configuration. The remainder of this article deals only with the ground-state configuration, often referred to as "the" configuration of an atom or molecule. == History == Irving Langmuir was the first to propose in his 1919 article "The Arrangement of Electrons in Atoms and Molecules" in which, building on Gilbert N. Lewis's cubical atom theory and Walther Kossel's chemical bonding theory, he outlined his "concentric theory of atomic structure". Langmuir had developed his work on electron atomic structure from other chemists as is shown in the development of the History of the periodic table and the Octet rule. Niels Bohr (1923) incorporated Langmuir's model that the periodicity in the properties of the elements might be explained
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{
"page_id": 67211,
"source": null,
"title": "Electron configuration"
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by the electronic structure of the atom. His proposals were based on the then current Bohr model of the atom, in which the electron shells were orbits at a fixed distance from the nucleus. Bohr's original configurations would seem strange to a present-day chemist: sulfur was given as 2.4.4.6 instead of 1s2 2s2 2p6 3s2 3p4 (2.8.6). Bohr used 4 and 6 following Alfred Werner's 1893 paper. In fact, the chemists accepted the concept of atoms long before the physicists. Langmuir began his paper referenced above by saying,«…The problem of the structure of atoms has been attacked mainly by physicists who have given little consideration to the chemical properties which must ultimately be explained by a theory of atomic structure. The vast store of knowledge of chemical properties and relationships, such as is summarized by the Periodic Table, should serve as a better foundation for a theory of atomic structure than the relatively meager experimental data along purely physical lines... These electrons arrange themselves in a series of concentric shells, the first shell containing two electrons, while all other shells tend to hold eight.…»The valence electrons in the atom were described by Richard Abegg in 1904. In 1924, E. C. Stoner incorporated Sommerfeld's third quantum number into the description of electron shells, and correctly predicted the shell structure of sulfur to be 2.8.6. However neither Bohr's system nor Stoner's could correctly describe the changes in atomic spectra in a magnetic field (the Zeeman effect). Bohr was well aware of this shortcoming (and others), and had written to his friend Wolfgang Pauli in 1923 to ask for his help in saving quantum theory (the system now known as "old quantum theory"). Pauli hypothesized successfully that the Zeeman effect can be explained as depending only on the response of the outermost (i.e.,
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{
"page_id": 67211,
"source": null,
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valence) electrons of the atom. Pauli was able to reproduce Stoner's shell structure, but with the correct structure of subshells, by his inclusion of a fourth quantum number and his exclusion principle (1925): It should be forbidden for more than one electron with the same value of the main quantum number n to have the same value for the other three quantum numbers k [l], j [ml] and m [ms]. The Schrödinger equation, published in 1926, gave three of the four quantum numbers as a direct consequence of its solution for the hydrogen atom: this solution yields the atomic orbitals that are shown today in textbooks of chemistry (and above). The examination of atomic spectra allowed the electron configurations of atoms to be determined experimentally, and led to an empirical rule (known as Madelung's rule (1936), see below) for the order in which atomic orbitals are filled with electrons. == Atoms: Aufbau principle and Madelung rule == The aufbau principle (from the German Aufbau, "building up, construction") was an important part of Bohr's original concept of electron configuration. It may be stated as: a maximum of two electrons are put into orbitals in the order of increasing orbital energy: the lowest-energy subshells are filled before electrons are placed in higher-energy orbitals. The principle works very well (for the ground states of the atoms) for the known 118 elements, although it is sometimes slightly wrong. The modern form of the aufbau principle describes an order of orbital energies given by Madelung's rule (or Klechkowski's rule). This rule was first stated by Charles Janet in 1929, rediscovered by Erwin Madelung in 1936, and later given a theoretical justification by V. M. Klechkowski: Subshells are filled in the order of increasing n + l. Where two subshells have the same value of n
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"page_id": 67211,
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+ l, they are filled in order of increasing n. This gives the following order for filling the orbitals: 1s, 2s, 2p, 3s, 3p, 4s, 3d, 4p, 5s, 4d, 5p, 6s, 4f, 5d, 6p, 7s, 5f, 6d, 7p, (8s, 5g, 6f, 7d, 8p, and 9s) In this list the subshells in parentheses are not occupied in the ground state of the heaviest atom now known (Og, Z = 118). The aufbau principle can be applied, in a modified form, to the protons and neutrons in the atomic nucleus, as in the shell model of nuclear physics and nuclear chemistry. === Periodic table === The form of the periodic table is closely related to the atomic electron configuration for each element. For example, all the elements of group 2 (the table's second column) have an electron configuration of [E] ns2 (where [E] is a noble gas configuration), and have notable similarities in their chemical properties. The periodicity of the periodic table in terms of periodic table blocks is due to the number of electrons (2, 6, 10, and 14) needed to fill s, p, d, and f subshells. These blocks appear as the rectangular sections of the periodic table. The single exception is helium, which despite being an s-block atom is conventionally placed with the other noble gasses in the p-block due to its chemical inertness, a consequence of its full outer shell (though there is discussion in the contemporary literature on whether this exception should be retained). The electrons in the valence (outermost) shell largely determine each element's chemical properties. The similarities in the chemical properties were remarked on more than a century before the idea of electron configuration. === Shortcomings of the aufbau principle === The aufbau principle rests on a fundamental postulate that the order of orbital energies
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"page_id": 67211,
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is fixed, both for a given element and between different elements; in both cases this is only approximately true. It considers atomic orbitals as "boxes" of fixed energy into which can be placed two electrons and no more. However, the energy of an electron "in" an atomic orbital depends on the energies of all the other electrons of the atom (or ion, or molecule, etc.). There are no "one-electron solutions" for systems of more than one electron, only a set of many-electron solutions that cannot be calculated exactly (although there are mathematical approximations available, such as the Hartree–Fock method). The fact that the aufbau principle is based on an approximation can be seen from the fact that there is an almost-fixed filling order at all, that, within a given shell, the s-orbital is always filled before the p-orbitals. In a hydrogen-like atom, which only has one electron, the s-orbital and the p-orbitals of the same shell have exactly the same energy, to a very good approximation in the absence of external electromagnetic fields. (However, in a real hydrogen atom, the energy levels are slightly split by the magnetic field of the nucleus, and by the quantum electrodynamic effects of the Lamb shift.) === Ionization of the transition metals === The naïve application of the aufbau principle leads to a well-known paradox (or apparent paradox) in the basic chemistry of the transition metals. Potassium and calcium appear in the periodic table before the transition metals, and have electron configurations [Ar] 4s1 and [Ar] 4s2 respectively, i.e. the 4s-orbital is filled before the 3d-orbital. This is in line with Madelung's rule, as the 4s-orbital has n + l = 4 (n = 4, l = 0) while the 3d-orbital has n + l = 5 (n = 3, l = 2). After
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calcium, most neutral atoms in the first series of transition metals (scandium through zinc) have configurations with two 4s electrons, but there are two exceptions. Chromium and copper have electron configurations [Ar] 3d5 4s1 and [Ar] 3d10 4s1 respectively, i.e. one electron has passed from the 4s-orbital to a 3d-orbital to generate a half-filled or filled subshell. In this case, the usual explanation is that "half-filled or completely filled subshells are particularly stable arrangements of electrons". However, this is not supported by the facts, as tungsten (W) has a Madelung-following d4 s2 configuration and not d5 s1, and niobium (Nb) has an anomalous d4 s1 configuration that does not give it a half-filled or completely filled subshell. The apparent paradox arises when electrons are removed from the transition metal atoms to form ions. The first electrons to be ionized come not from the 3d-orbital, as one would expect if it were "higher in energy", but from the 4s-orbital. This interchange of electrons between 4s and 3d is found for all atoms of the first series of transition metals. The configurations of the neutral atoms (K, Ca, Sc, Ti, V, Cr, ...) usually follow the order 1s, 2s, 2p, 3s, 3p, 4s, 3d, ...; however the successive stages of ionization of a given atom (such as Fe4+, Fe3+, Fe2+, Fe+, Fe) usually follow the order 1s, 2s, 2p, 3s, 3p, 3d, 4s, ... This phenomenon is only paradoxical if it is assumed that the energy order of atomic orbitals is fixed and unaffected by the nuclear charge or by the presence of electrons in other orbitals. If that were the case, the 3d-orbital would have the same energy as the 3p-orbital, as it does in hydrogen, yet it clearly does not. There is no special reason why the Fe2+ ion should
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have the same electron configuration as the chromium atom, given that iron has two more protons in its nucleus than chromium, and that the chemistry of the two species is very different. Melrose and Eric Scerri have analyzed the changes of orbital energy with orbital occupations in terms of the two-electron repulsion integrals of the Hartree–Fock method of atomic structure calculation. More recently Scerri has argued that contrary to what is stated in the vast majority of sources including the title of his previous article on the subject, 3d orbitals rather than 4s are in fact preferentially occupied. In chemical environments, configurations can change even more: Th3+ as a bare ion has a configuration of [Rn] 5f1, yet in most ThIII compounds the thorium atom has a 6d1 configuration instead. Mostly, what is present is rather a superposition of various configurations. For instance, copper metal is poorly described by either an [Ar] 3d10 4s1 or an [Ar] 3d9 4s2 configuration, but is rather well described as a 90% contribution of the first and a 10% contribution of the second. Indeed, visible light is already enough to excite electrons in most transition metals, and they often continuously "flow" through different configurations when that happens (copper and its group are an exception). Similar ion-like 3dx 4s0 configurations occur in transition metal complexes as described by the simple crystal field theory, even if the metal has oxidation state 0. For example, chromium hexacarbonyl can be described as a chromium atom (not ion) surrounded by six carbon monoxide ligands. The electron configuration of the central chromium atom is described as 3d6 with the six electrons filling the three lower-energy d orbitals between the ligands. The other two d orbitals are at higher energy due to the crystal field of the ligands. This picture is
|
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consistent with the experimental fact that the complex is diamagnetic, meaning that it has no unpaired electrons. However, in a more accurate description using molecular orbital theory, the d-like orbitals occupied by the six electrons are no longer identical with the d orbitals of the free atom. === Other exceptions to Madelung's rule === There are several more exceptions to Madelung's rule among the heavier elements, and as atomic number increases it becomes more and more difficult to find simple explanations such as the stability of half-filled subshells. It is possible to predict most of the exceptions by Hartree–Fock calculations, which are an approximate method for taking account of the effect of the other electrons on orbital energies. Qualitatively, for example, the 4d elements have the greatest concentration of Madelung anomalies, because the 4d–5s gap is larger than the 3d–4s and 5d–6s gaps. For the heavier elements, it is also necessary to take account of the effects of special relativity on the energies of the atomic orbitals, as the inner-shell electrons are moving at speeds approaching the speed of light. In general, these relativistic effects tend to decrease the energy of the s-orbitals in relation to the other atomic orbitals. This is the reason why the 6d elements are predicted to have no Madelung anomalies apart from lawrencium (for which relativistic effects stabilise the p1/2 orbital as well and cause its occupancy in the ground state), as relativity intervenes to make the 7s orbitals lower in energy than the 6d ones. The table below shows the configurations of the f-block (green) and d-block (blue) atoms. It shows the ground state configuration in terms of orbital occupancy, but it does not show the ground state in terms of the sequence of orbital energies as determined spectroscopically. For example, in the transition
|
{
"page_id": 67211,
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metals, the 4s orbital is of a higher energy than the 3d orbitals; and in the lanthanides, the 6s is higher than the 4f and 5d. The ground states can be seen in the Electron configurations of the elements (data page). However this also depends on the charge: a calcium atom has 4s lower in energy than 3d, but a Ca2+ cation has 3d lower in energy than 4s. In practice the configurations predicted by the Madelung rule are at least close to the ground state even in these anomalous cases. The empty f orbitals in lanthanum, actinium, and thorium contribute to chemical bonding, as do the empty p orbitals in transition metals. Vacant s, d, and f orbitals have been shown explicitly, as is occasionally done, to emphasise the filling order and to clarify that even orbitals unoccupied in the ground state (e.g. lanthanum 4f or palladium 5s) may be occupied and bonding in chemical compounds. (The same is also true for the p-orbitals, which are not explicitly shown because they are only actually occupied for lawrencium in gas-phase ground states.) The various anomalies describe the free atoms and do not necessarily predict chemical behavior. Thus for example neodymium typically forms the +3 oxidation state, despite its configuration [Xe] 4f4 5d0 6s2 that if interpreted naïvely would suggest a more stable +2 oxidation state corresponding to losing only the 6s electrons. Contrariwise, uranium as [Rn] 5f3 6d1 7s2 is not very stable in the +3 oxidation state either, preferring +4 and +6. The electron-shell configuration of elements beyond hassium has not yet been empirically verified, but they are expected to follow Madelung's rule without exceptions until element 120. Element 121 should have the anomalous configuration [Og] 8s2 5g0 6f0 7d0 8p1, having a p rather than a g electron.
|
{
"page_id": 67211,
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Electron configurations beyond this are tentative and predictions differ between models, but Madelung's rule is expected to break down due to the closeness in energy of the 5g, 6f, 7d, and 8p1/2 orbitals. That said, the filling sequence 8s, 5g, 6f, 7d, 8p is predicted to hold approximately, with perturbations due to the huge spin-orbit splitting of the 8p and 9p shells, and the huge relativistic stabilisation of the 9s shell. == Open and closed shells == In the context of atomic orbitals, an open shell is a valence shell which is not completely filled with electrons or that has not given all of its valence electrons through chemical bonds with other atoms or molecules during a chemical reaction. Conversely a closed shell is obtained with a completely filled valence shell. This configuration is very stable. For molecules, "open shell" signifies that there are unpaired electrons. In molecular orbital theory, this leads to molecular orbitals that are singly occupied. In computational chemistry implementations of molecular orbital theory, open-shell molecules have to be handled by either the restricted open-shell Hartree–Fock method or the unrestricted Hartree–Fock method. Conversely a closed-shell configuration corresponds to a state where all molecular orbitals are either doubly occupied or empty (a singlet state). Open shell molecules are more difficult to study computationally. == Noble gas configuration == Noble gas configuration is the electron configuration of noble gases. The basis of all chemical reactions is the tendency of chemical elements to acquire stability. Main-group atoms generally obey the octet rule, while transition metals generally obey the 18-electron rule. The noble gases (He, Ne, Ar, Kr, Xe, Rn) are less reactive than other elements because they already have a noble gas configuration. Oganesson is predicted to be more reactive due to relativistic effects for heavy atoms. Every system has
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{
"page_id": 67211,
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"title": "Electron configuration"
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the tendency to acquire the state of stability or a state of minimum energy, and so chemical elements take part in chemical reactions to acquire a stable electronic configuration similar to that of its nearest noble gas. An example of this tendency is two hydrogen (H) atoms reacting with one oxygen (O) atom to form water (H2O). Neutral atomic hydrogen has one electron in its valence shell, and on formation of water it acquires a share of a second electron coming from oxygen, so that its configuration is similar to that of its nearest noble gas helium (He) with two electrons in its valence shell. Similarly, neutral atomic oxygen has six electrons in its valence shell, and acquires a share of two electrons from the two hydrogen atoms, so that its configuration is similar to that of its nearest noble gas neon with eight electrons in its valence shell. == Electron configuration in molecules == Electron configuration in molecules is more complex than the electron configuration of atoms, as each molecule has a different orbital structure. The molecular orbitals are labelled according to their symmetry, rather than the atomic orbital labels used for atoms and monatomic ions; hence, the electron configuration of the dioxygen molecule, O2, is written 1σg2 1σu2 2σg2 2σu2 3σg2 1πu4 1πg2, or equivalently 1σg2 1σu2 2σg2 2σu2 1πu4 3σg2 1πg2. The term 1πg2 represents the two electrons in the two degenerate π*-orbitals (antibonding). From Hund's rules, these electrons have parallel spins in the ground state, and so dioxygen has a net magnetic moment (it is paramagnetic). The explanation of the paramagnetism of dioxygen was a major success for molecular orbital theory. The electronic configuration of polyatomic molecules can change without absorption or emission of a photon through vibronic couplings. === Electron configuration in solids === In
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{
"page_id": 67211,
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"title": "Electron configuration"
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a solid, the electron states become very numerous. They cease to be discrete, and effectively blend into continuous ranges of possible states (an electron band). The notion of electron configuration ceases to be relevant, and yields to band theory. == Applications == The most widespread application of electron configurations is in the rationalization of chemical properties, in both inorganic and organic chemistry. In effect, electron configurations, along with some simplified forms of molecular orbital theory, have become the modern equivalent of the valence concept, describing the number and type of chemical bonds that an atom can be expected to form. This approach is taken further in computational chemistry, which typically attempts to make quantitative estimates of chemical properties. For many years, most such calculations relied upon the "linear combination of atomic orbitals" (LCAO) approximation, using an ever-larger and more complex basis set of atomic orbitals as the starting point. The last step in such a calculation is the assignment of electrons among the molecular orbitals according to the aufbau principle. Not all methods in computational chemistry rely on electron configuration: density functional theory (DFT) is an important example of a method that discards the model. For atoms or molecules with more than one electron, the motion of electrons are correlated and such a picture is no longer exact. A very large number of electronic configurations are needed to exactly describe any multi-electron system, and no energy can be associated with one single configuration. However, the electronic wave function is usually dominated by a very small number of configurations and therefore the notion of electronic configuration remains essential for multi-electron systems. A fundamental application of electron configurations is in the interpretation of atomic spectra. In this case, it is necessary to supplement the electron configuration with one or more term symbols,
|
{
"page_id": 67211,
"source": null,
"title": "Electron configuration"
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|
which describe the different energy levels available to an atom. Term symbols can be calculated for any electron configuration, not just the ground-state configuration listed in tables, although not all the energy levels are observed in practice. It is through the analysis of atomic spectra that the ground-state electron configurations of the elements were experimentally determined. == See also == Born–Oppenheimer approximation d electron count Electron configurations of the elements (data page) Extended periodic table – discusses the limits of the periodic table Group (periodic table) HOMO/LUMO Molecular term symbol Octet rule Periodic table (electron configurations) Spherical harmonics Unpaired electron Valence shell == Notes == == References == == External links == What does an atom look like? Configuration in 3D
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{
"page_id": 67211,
"source": null,
"title": "Electron configuration"
}
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D-Mycosamine is an amino sugar found in several polyene antimycotics. Structural analogs of these agents lacking this monosaccharide component do not exhibit substantial antifungal activity. == References == Biosynthesis: [1]
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{
"page_id": 69666444,
"source": null,
"title": "Mycosamine"
}
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S-matrix theory was a proposal for replacing local quantum field theory as the basic principle of elementary particle physics. It avoided the notion of space and time by replacing it with abstract mathematical properties of the S-matrix. In S-matrix theory, the S-matrix relates the infinite past to the infinite future in one step, without being decomposable into intermediate steps corresponding to time-slices. This program was very influential in the 1960s, because it was a plausible substitute for quantum field theory, which was plagued with the zero interaction phenomenon at strong coupling. Applied to the strong interaction, it led to the development of string theory. S-matrix theory was largely abandoned by physicists in the 1970s, as quantum chromodynamics was recognized to solve the problems of strong interactions within the framework of field theory. But in the guise of string theory, S-matrix theory is still a popular approach to the problem of quantum gravity. The S-matrix theory is related to the holographic principle and the AdS/CFT correspondence by a flat space limit. The analog of the S-matrix relations in AdS space is the boundary conformal theory. The most lasting legacy of the theory is string theory. Other notable achievements are the Froissart bound, and the prediction of the pomeron. == History == S-matrix theory was proposed as a principle of particle interactions by Werner Heisenberg in 1943, following John Archibald Wheeler's 1937 introduction of the S-matrix. It was developed heavily by Geoffrey Chew, Steven Frautschi, Stanley Mandelstam, Vladimir Gribov, and Tullio Regge. Some aspects of the theory were promoted by Lev Landau in the Soviet Union, and by Murray Gell-Mann in the United States. == Basic principles == The basic principles are: Relativity: The S-matrix is a representation of the Poincaré group; Unitarity: S S † = 1 {\displaystyle SS^{\dagger }=1} ;
|
{
"page_id": 14026380,
"source": null,
"title": "S-matrix theory"
}
|
Analyticity: integral relations and singularity conditions. The basic analyticity principles were also called analyticity of the first kind, and they were never fully enumerated, but they include Crossing: The amplitudes for antiparticle scattering are the analytic continuation of particle scattering amplitudes. Dispersion relations: the values of the S-matrix can be calculated by integrals over internal energy variables of the imaginary part of the same values. Causality conditions: the singularities of the S-matrix can only occur in ways that don't allow the future to influence the past (motivated by Kramers–Kronig relations) Landau principle: Any singularity of the S-matrix corresponds to production thresholds of physical particles. These principles were to replace the notion of microscopic causality in field theory, the idea that field operators exist at each spacetime point, and that spacelike separated operators commute with one another. == Bootstrap models == The basic principles were too general to apply directly, because they are satisfied automatically by any field theory. So to apply to the real world, additional principles were added. The phenomenological way in which this was done was by taking experimental data and using the dispersion relations to compute new limits. This led to the discovery of some particles, and to successful parameterizations of the interactions of pions and nucleons. This path was mostly abandoned because the resulting equations, devoid of any space-time interpretation, were very difficult to understand and solve. == Regge theory == The principle behind the Regge theory hypothesis (also called analyticity of the second kind or the bootstrap principle) is that all strongly interacting particles lie on Regge trajectories. This was considered the definitive sign that all the hadrons are composite particles, but within S-matrix theory, they are not thought of as being made up of elementary constituents. The Regge theory hypothesis allowed for the construction
|
{
"page_id": 14026380,
"source": null,
"title": "S-matrix theory"
}
|
of string theories, based on bootstrap principles. The additional assumption was the narrow resonance approximation, which started with stable particles on Regge trajectories, and added interaction loop by loop in a perturbation series. String theory was given a Feynman path-integral interpretation a little while later. The path integral in this case is the analog of a sum over particle paths, not of a sum over field configurations. Feynman's original path integral formulation of field theory also had little need for local fields, since Feynman derived the propagators and interaction rules largely using Lorentz invariance and unitarity. == See also == Landau pole Regge trajectory Bootstrap model Pomeron Dual resonance model History of string theory == Notes == == References == Steven Frautschi, Regge Poles and S-matrix Theory, New York: W. A. Benjamin, Inc., 1963.
|
{
"page_id": 14026380,
"source": null,
"title": "S-matrix theory"
}
|
The IEEE Journal of Solid-State Circuits is a monthly peer-reviewed scientific journal on new developments and research in solid-state circuits, published by the Institute of Electrical and Electronics Engineers (IEEE) in New York City. The journal serves as a companion venue for expanding on work presented at the International Solid-State Circuits Conference, the Symposia on VLSI Technology and Circuits, and the Custom Integrated Circuits Conference. The journal has an impact factor of 6.12 and is edited by Dennis Sylvester (University of Michigan). == References == == External links == Official website
|
{
"page_id": 52037261,
"source": null,
"title": "IEEE Journal of Solid-State Circuits"
}
|
In human biology, the testosterone–cortisol ratio describes the ratio between testosterone, the primary male sex hormone and an anabolic steroid, and cortisol, another steroid hormone, in the human body. The ratio is often used as a biomarker of physiological stress in athletes during training, during athletic performance, and during recovery, and has been explored as a predictor of performance. At least among weight-lifters, the ratio tracks linearly with increases in training volume over the first year of training but the relationship breaks down after that. A lower ratio in weight-lifters just prior to performance appears to predict better performance. The ratio has been studied as a possible biomarker for criminal aggression, but as of 2009 its usefulness was uncertain. == References ==
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{
"page_id": 52889231,
"source": null,
"title": "Testosterone–cortisol ratio"
}
|
In the anatomy of the human ear, the perilymphatic duct is where the perilymphatic space (vestibule of the ear) is connected to the subarachnoid space. This works as a type of shunt to eliminate excess perilymph fluid from the perilymphatic space around the cochlea of the ear. Perilymph is continuous with cerebrospinal fluid (CSF) in the subarachnoid space. CSF pressure abnormalities do not generally have clinical impact on the inner ear which is explained physically by the bore diameter and length of the perilymphatic duct. This duct goes through the skull and is parallel with but not directly associated with the endolymphatic duct. The duct is lined by an epithelium. == References ==
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{
"page_id": 25101970,
"source": null,
"title": "Perilymphatic duct"
}
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The manipulation of atoms using optical fields is a vital and fundamental area of research within the field of atomic physics. This research revolves around leveraging the distinct characteristics of laser light and coherent optical fields to achieve precise control over various aspects of atomic systems. These aspects encompass regulating atomic motion, positioning atoms, manipulating internal states, and facilitating intricate interactions with neighboring atoms and photons. The utilization of optical fields provides a powerful toolset for exploring and understanding the quantum behavior of atoms and opens up promising avenues for applications in atomic, molecular, and optical physics. == Techniques == === Optical tweezers === Optical tweezers are a powerful and versatile tool used in atomic physics. Developed in the 1970s by Arthur Ashkin, optical tweezers have revolutionized research in various fields, enabling scientists to study the behavior of individual particles and explore fundamental phenomena. The development of optical tweezers resulted in Ashkin receiving the Nobel Prize in Physics in 2018. The underlying principle of optical tweezers relies on the transfer of momentum from the photons in the laser beam to the trapped particle. When a tightly focused laser beam interacts with a small particle, the variation in the intensity of the laser light creates an attractive force towards the region of highest intensity. This force effectively traps the particle at the focal point of the laser beam. The trapping force generated by the optical tweezers depends on several factors, including the intensity of the laser beam, the refractive index of the particle and the surrounding medium, and the size and shape of the particle. By adjusting these parameters, researchers can control the strength and stability of the trapping potential. === Optical molasses === Steven Chu, along with Claude Cohen-Tannoudji and William D. Phillips, were awarded the Nobel Prize in Physics
|
{
"page_id": 15795860,
"source": null,
"title": "Optical manipulation of atoms"
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in 1997 for their groundbreaking contributions to the development of methods to laser cool and trap atoms with laser light. Chu and his colleagues developed a technique called "optical molasses", which involved using carefully tuned laser beams to slow down and cool atoms in three dimensions. This process was akin to slowing down the atoms and confining them using an "optical trap". Optical molasses relies on the interaction between atoms and laser light to slow down the atoms' movement. This process takes advantage of the fact that atoms can absorb and emit photons when they are exposed to laser light of specific frequencies. The basic idea is to use laser beams that are red-detuned from an atomic transition. Red-detuned means that the frequency of the laser light is lower than the natural resonance frequency of the atoms. When atoms encounter such red-detuned laser light, they experience a "light shift", which creates a spatially dependent potential energy landscape. In the context of optical molasses, the term "molasses" refers to the slowing down of atoms, analogous to how molasses slows down the movement of objects moving through it. The molasses effect in laser cooling arises from the spatially varying light shift created by the red-detuned laser beams. When an atom moves in the presence of the laser beams, it experiences a varying light shift due to the intensity gradient of the laser light. This variation in the light shift creates an optical force that opposes the atom's motion, causing it to slow down. Atoms moving in the direction opposite to the laser beams experience the largest light shifts, leading to effective cooling. === Magneto-optical trap === A magneto-optical trap (MOT) confines and manipulates atoms using the combined action of magnetic fields and laser light. This innovative approach has paved the way for
|
{
"page_id": 15795860,
"source": null,
"title": "Optical manipulation of atoms"
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significant advancements in quantum optics, quantum information processing, and precision measurements. The first step in the operation of a MOT involves the cooling of atoms using beams in an Optical Molasses configuration (discussed in the section above). However, Optical Molasses only creates a velocity-dependent damping force. To truly trap atoms, a position-dependent restorative force must be established. This is accomplished through magnetic fields are employed in conjunction with the laser cooling mechanism. A quadrupolar magnetic field is created (typically by an Anti-Helmholtz Coil). Quadrupolar magnetic fields vary approximately linearly in space near their zero. This creates a position-dependent energy shift through Zeeman Splitting. Tuning the laser polarization to drive only the lower energy transition, (see Selection rules for more information) atoms moving away from the magnetic field zero will absorb a lower energy photon in a collision, absorbing the photon's momentum and being pushed towards the magnetic field zero. The atom is now in an excited state and will emit a photon and recoil, but in random directions, thus leading to an average force on the atom of zero. Thus a restorative force is created and the atoms will be trapped. === Optical lattice === An Optical lattice is a periodic potential formed by the interference of counter-propagating laser beams, creating a standing wave pattern of light that can trap neutral atoms at the antinodes or nodes of the field via the dipole force. First demonstrated in the late 1980s and 1990s, optical lattices have become a key tool in atomic, molecular, and optical physics. Their development was driven by the need to study quantum gases and simulate condensed matter systems in a highly controlled environment. The principle of an optical lattice relies on the AC Stark effect: atoms experience a spatially varying potential proportional to the intensity of the
|
{
"page_id": 15795860,
"source": null,
"title": "Optical manipulation of atoms"
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light field. By adjusting the laser wavelength, polarization, and geometry, researchers can tailor the dimensionality (1D, 2D, or 3D) and depth of the lattice potential. Lattices are typically categorized as red-detuned (atoms trapped at intensity maxima) or blue-detuned (trapped at minima), and can be extended to more complex geometries such as spin-dependent lattices or superlattices. Optical lattices continue to be a powerful platform for exploring quantum phase transitions, high-precision metrology, and fundamental tests of quantum mechanics. == Applications == === Laser cooling === Optical manipulation techniques are essential to laser cooling because precise control of light frequency, polarization, and intensity enables targeted interaction with atomic transitions. Laser cooling is broadly divided into Doppler cooling, in which atomic samples are limited by the recoil limit associated with the minimum kinetic after having emitted a photon; sub-Doppler cooling (such as polarization gradient cooling), which can achieve temperatures well below the Doppler limit. These methods form the basis for many advanced applications, including atomic clocks, Bose–Einstein condensation, and quantum information processing. Doppler cooling involves using laser light that is red-detuned from an atomic transition, which means the laser frequency is higher than the natural resonance frequency of the atoms. When atoms move towards the laser beam, they experience a higher frequency light shift, resulting in an optical force that slows them down. Doppler cooling is effective for cooling atoms along one direction but fails to cool atoms in all three dimensions. Optical molasses overcomes this limitation by employing multiple laser beams with different propagation directions and polarizations. The combined effect of the different beams allows cooling in all three dimensions, effectively trapping the atoms in the regions of lowest light intensity. === Quantum computation === Atoms can be used as qubits in quantum computing. The precise control offered by optical manipulation allows scientists
|
{
"page_id": 15795860,
"source": null,
"title": "Optical manipulation of atoms"
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to encode and manipulate quantum information in the quantum states of individual atoms. Laser beams and optical fields can coherently control the quantum states of atoms, enabling the creation of reliable qubits. Precision laser pulses are used to manipulate individual quantum bits, enabling operations such as single-qubit rotations and two-qubit entangling gates. For example, in trapped ion quantum computers, laser-driven transitions between internal states of ions allow for the realization of fundamental quantum logic gates, including high-fidelity entangling operations like the Mølmer–Sørensen gate. Optical manipulation techniques, such as laser cooling, can lead to long coherence times for atoms. Coherence time refers to the time during which a quantum system can maintain its quantum superposition state before decoherence occurs. Long coherence times are essential for performing quantum operations and minimizing errors in quantum computations. Quantum computing relies heavily on the phenomenon of entanglement, where qubits become deeply interconnected and share correlations that are impossible to reproduce classically. Optical manipulation can create and control entangled states of atoms, enabling the implementation of quantum algorithms and computational speedup. Optical manipulation techniques can be readily scaled to control larger numbers of atoms, paving the way for building scalable quantum computers. The ability to trap and manipulate arrays of atoms using optical lattices allows for the creation of larger and more complex quantum circuits. An example of controlling larger numbers of atoms can be seen in the manipulation of a BEC using counter propagating waves. === Atomic clocks === Optical manipulation involves laser cooling and trapping of atoms, reducing their kinetic energy to extremely low temperatures. This process allows scientists to create ultracold atomic ensembles with minimal thermal motion, leading to narrow linewidths in atomic transitions. Narrow linewidths are essential for achieving high precision in atomic clocks. Laser cooling and optical manipulation can also extend
|
{
"page_id": 15795860,
"source": null,
"title": "Optical manipulation of atoms"
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|
the coherence time of atomic states, reducing the sensitivity of atomic clocks to external disturbances. Longer coherence times translate into increased clock stability, allowing atomic clocks to maintain their precision over longer intervals. Furthermore, lasers are used for state preparation and measurement: optical pumping initializes qubits into well-defined states, while state-dependent fluorescence enables high-contrast readout. In more complex protocols, such as quantum logic spectroscopy, laser fields couple different species of ions via shared motional modes, allowing precise manipulation and indirect measurements. === Manipulation of a Bose–Einstein condensate (BEC) using a standing light wave === The manipulation of a Bose–Einstein condensate (BEC) using a standing light wave is an important technique in the field of atomic physics. A Bose-Einstein condensate is a state of matter that emerges when a group of atoms is cooled to extremely low temperatures, approaching absolute zero. Within this state, all the atoms composing the condensate converge into a single quantum state with macroscopic quantum coherence and behave as a unified, wave-like entity. One way to manipulate a BEC is by subjecting it to a standing light wave, which is formed by two counter-propagating laser beams. The frequency of these lasers is carefully chosen to match the energy difference between specific atomic energy levels, creating resonant interactions with the atoms in the condensate. The key phenomenon at play here is the two-photon recoil process. When a cold atom in the BEC absorbs a photon from one of the laser beams, it gains energy and gets excited to a higher energy level. Almost instantaneously, the atom emits a photon in the opposite direction, in the other laser beam, and returns to its initial state. As a result of this two-photon process, the atom receives a net momentum kick with a magnitude of 2ħk (where ħ is the reduced
|
{
"page_id": 15795860,
"source": null,
"title": "Optical manipulation of atoms"
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Planck constant and k is the magnitude of the wave vector of the laser) in the direction of the absorbed photon. Due to this momentum kick, the BEC cloud, which initially sits at the center of a trap, is split into two identical clouds. These two clouds then travel in opposite directions with a velocity proportional to the momentum kick they receive from the absorbed photons. This manipulation of a BEC using a standing light wave is significant for several reasons: It allows precise control of the position and motion of the BEC cloud Splitting the BEC into two identical clouds is useful for studying quantum interference and coherence effects. This technique is crucial for investigating quantum phenomena and understanding the behavior of quantum gases at ultra-cold temperatures. The controlled manipulation of BECs using optical fields has promising applications in quantum information processing, precision measurements, and quantum simulation. This leads to the creation of extremely narrow and well-defined atomic resonances. These narrow resonances enable more precise measurement of atomic transitions, resulting in more accurate frequency references for atomic clocks. == References == Lett, P. D.; Phillips, W. D.; Rolston, S. L.; Tanner, C. E.; Watts, R. N.; Westbrook, C. I. (17 September 2007). "Precise manipulation of a Bose-Einstein condensate using an optical standing wave". Phys. Rev. A. 76 (035601). Hughes, K. J.; Deissler, B.; Burke, J. H. T.; Sackett, C. A. "Optical molasses". J. Opt. Soc. Am. B. 6 (2084–2107). Foot, C.J. (2005). Atomic Physics. Oxford University Press. ISBN 978-0-19-850696-6.
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{
"page_id": 15795860,
"source": null,
"title": "Optical manipulation of atoms"
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Neuropeptides are chemical messengers made up of small chains of amino acids that are synthesized and released by neurons. Neuropeptides typically bind to G protein-coupled receptors (GPCRs) to modulate neural activity and other tissues like the gut, muscles, and heart. Neuropeptides are synthesized from large precursor proteins which are cleaved and post-translationally processed then packaged into large dense core vesicles. Neuropeptides are often co-released with other neuropeptides and neurotransmitters in a single neuron, yielding a multitude of effects. Once released, neuropeptides can diffuse widely to affect a broad range of targets. Neuropeptides are extremely ancient and highly diverse chemical messengers. Placozoans such as Trichoplax, extremely basal animals which do not possess neurons, use peptides for cell-to-cell communication in a way similar to the neuropeptides of higher animals. == Examples == Peptide signals play a role in information processing that is different from that of conventional neurotransmitters, and many appear to be particularly associated with specific behaviours. For example, in mammals oxytocin and vasopressin have striking and specific effects on social behaviours, including maternal behaviour and pair bonding. In invertibrates, CCAP has several functions including regulating heart rate, allatostatin and proctolin regulate food intake and growth, and bursicon controls tanning of the cuticle. == Synthesis == Neuropeptides are synthesized from inactive precursor proteins called prepropeptides. Prepropeptides contain sequences for a family of distinct peptides and often contain duplicated copies of the same peptides, depending on the organism. In addition to the precursor peptide sequences, prepropeptides also contain a signal peptide, spacer peptides, and cleavage sites. The signal peptide sequence guides the protein to the secretory pathway, starting at the endoplasmic reticulum. The signal peptide sequence is removed in the endoplasmic reticulum, yielding a propeptide. The propeptide travels to the Golgi apparatus where it is proteolytically cleaved and processed into multiple peptides.
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{
"page_id": 984726,
"source": null,
"title": "Neuropeptide"
}
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Peptides are packaged into dense core vesicles, where further cleaving and processing, such as C-terminal amidation, can occur. Dense core vesicles are transported throughout the neuron and can release peptides at the synaptic cleft, cell body, and along the axon. A single animal may use hundreds of different neuropeptides. In C. elegans, for example, 120 genes specify more than 250 neuropeptides. == Mechanism == Neuropeptides are released by dense core vesicles after depolarization of the cell. Compared to classical neurotransmitter signaling, neuropeptide signaling is more sensitive. Neuropeptide receptor affinity is in the nanomolar to micromolar range while neurotransmitter affinity is in the micromolar to millimolar range. Additionally, dense core vesicles contain a small amount of neuropeptide (3 - 10mM) compared to synaptic vesicles containing neurotransmitters (e.g. 100mM for acetylcholine). Evidence shows that neuropeptides are released after high-frequency firing or bursts, distinguishing dense core vesicle from synaptic vesicle release. Neuropeptides utilize volume transmission and are not reuptaken quickly, allowing diffusion across broad areas (nm to mm) to reach targets. Almost all neuropeptides bind to G protein-coupled receptors (GPCRs), inducing second messenger cascades to modulate neural activity on long time-scales. Expression of neuropeptides in the nervous system is diverse. Neuropeptides are often co-released with other neuropeptides and neurotransmitters, yielding a diversity of effects depending on the combination of release. For example, vasoactive intestinal peptide is typically co-released with acetylcholine. Neuropeptide release can also be specific. In Drosophila larvae, for example, eclosion hormone is expressed in just two neurons. === Co-release === Neuropeptides are often co-released with other neurotransmitters and neuropeptides to modulate synaptic activity. Synaptic vesicles and dense core vesicles can have differential activation properties for release, resulting in context-dependent co-release combinations. For example, insect motor neurons are glutamatergic and some contain dense core vesicles with proctolin. At low frequency activation, only
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"page_id": 984726,
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"title": "Neuropeptide"
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glutamate is released, yielding fast and rapid excitation of the muscle. At high frequency activation however, dense core vesicles release proctolin, inducing prolonged contractions. Thus, neuropeptide release can be fine-tuned to modulate synaptic activity in certain contexts. Some regions of the nervous system are specialized to release distinctive sets of peptides. For example, the hypothalamus and the pituitary gland release peptides (e.g. TRH, GnRH, CRH, SST) that act as hormones In one subpoplation of the arcuate nucleus of the hypothalamus, three anorectic peptides are co-expressed: α-melanocyte-stimulating hormone (α-MSH), galanin-like peptide, and cocaine-and-amphetamine-regulated transcript (CART), and in another subpopulation two orexigenic peptides are co-expressed, neuropeptide Y and agouti-related peptide (AGRP). These peptides are all released in different combinations to signal hunger and satiation cues. The following is a list of neuroactive peptides co-released with other neurotransmitters. Transmitter names are shown in bold. Norepinephrine (noradrenaline). In neurons of the A2 cell group in the nucleus of the solitary tract), norepinephrine co-exists with: Galanin Enkephalin Neuropeptide Y GABA Somatostatin (in the hippocampus) Cholecystokinin Neuropeptide Y (in the arcuate nucleus) Acetylcholine VIP Substance P Dopamine Cholecystokinin Neurotensin Glucagon-like peptide-1 (in the nucleus accumbens) Epinephrine (adrenaline) Neuropeptide Y Neurotensin Serotonin (5-HT) Substance P TRH Enkephalin Some neurons make several different peptides. For instance, vasopressin co-exists with dynorphin and galanin in magnocellular neurons of the supraoptic nucleus and paraventricular nucleus, and with CRF (in parvocellular neurons of the paraventricular nucleus) Oxytocin in the supraoptic nucleus co-exists with enkephalin, dynorphin, cocaine-and amphetamine regulated transcript (CART) and cholecystokinin. == Receptor targets == Most neuropeptides act on G-protein coupled receptors (GPCRs). Neuropeptide-GPCRs fall into two families: rhodopsin-like and the secretin class. Most peptides activate a single GPCR, while some activate multiple GPCRs (e.g. AstA, AstC, DTK). Peptide-GPCR binding relationships are highly conserved across animals. Aside from conserved structural relationships,
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{
"page_id": 984726,
"source": null,
"title": "Neuropeptide"
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some peptide-GPCR functions are also conserved across the animal kingdom. For example, neuropeptide F/neuropeptide Y signaling is structurally and functionally conserved between insects and mammals. Although peptides mostly target metabotropic receptors, there is some evidence that neuropeptides bind to other receptor targets. Peptide-gated ion channels (FMRFamide-gated sodium channels) have been found in snails and Hydra. Other examples of non-GPCR targets include: insulin-like peptides and tyrosine-kinase receptors in Drosophila and atrial natriuretic peptide and eclosion hormone with membrane-bound guanylyl cyclase receptors in mammals and insects. == Actions == Due to their modulatory and diffusive nature, neuropeptides can act on multiple time and spatial scales. A nearly complete map of these interactions is known for at least one small animal, C. elegans. For many other animals, at least some neuropeptide actions are known, as shown in the Examples section above. == Evolution of Neuropeptide Signaling == Peptides are ancient signaling systems that are found in almost all animals on Earth. Genome sequencing reveals evidence of neuropeptide genes in Cnidaria, Ctenophora, and Placozoa, some of oldest living animals with nervous systems or neural-like tissues. Recent studies also show genomic evidence of neuropeptide processing machinery in metazoans and choanoflagellates, suggesting that neuropeptide signaling may predate the development of nervous tissues. Additionally, Ctenophore and Placozoa neural signaling is entirely peptidergic and lacks the major amine neurotransmitters such as acetylcholine, dopamine, and serotonin. This also suggests that neuropeptide signaling developed before amine neurotransmitters. == Applications == Neuropeptides and antagonists that bind to their receptors can be used as insecticides. These include both naturally occurring neuropeptides and synthetic compounds designed to block their receptors. In humans, neuropeptides have been implicated in several human diseases. Antagonists to the related receptors may have clinical application. == Research history == In the early 1900s, chemical messengers were crudely extracted from
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{
"page_id": 984726,
"source": null,
"title": "Neuropeptide"
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|
whole animal brains and tissues and studied for their physiological effects. In 1931, von Euler and Gaddum, used a similar method to try and isolate acetylcholine but instead discovered a peptide substance that induced physiological changes including muscle contractions and depressed blood pressure. These effects were not abolished using atropine, ruling out the substance as acetylcholine. In insects, proctolin was the first neuropeptide to be isolated and sequenced. In 1975, Alvin Starratt and Brian Brown extracted the peptide from hindgut muscles of the cockroach and found that its application enhanced muscle contractions. While Starratt and Brown initially thought of proctolin as an excitatory neurotransmitter, proctolin was later confirmed as a neuromodulatory peptide. David de Wied first used the term "neuropeptide" in the 1970s to delineate peptides derived from the nervous system. == References == == External links == Neuropeptides Journal Neuropeptides reference website (a comprehensive neuropeptide database) NeuroPep 2.0: an updated database dedicated to neuropeptide and its receptor annotations A comprehensive review on neuropeptides: databases and computational tools Neuropeptides eBook series Neuropeptide chapter in the C. elegans Wormbook excellent, and very accessible, discussion of neuropeptide biology in C. elegans
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{
"page_id": 984726,
"source": null,
"title": "Neuropeptide"
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Are Quanta Real?: A Galilean Dialogue (1973) is a book by Swiss-American physicist J.M. Jauch, in which the three main characters meet over the period of several days to discuss various interpretations and philosophical consequences of quantum mechanics. Are Quanta Real? was inspired by and written in the style of Galileo's Dialogue Concerning the Two Chief World Systems. In the book, Jauch "resurrects" Galileo's three characters, Salviati, Sagredo, and Simplicio, centuries after their deaths to resume their previous dialogue in light of new developments in natural philosophy, specifically, quantum mechanics. The three characters engage in a series of debates and dialectic discussions to better their understanding of quantum phenomena using a series of thought experiments. In a foreword to the 1989 edition, Douglas Hofstadter explains how the book initially "electrified" him and offered a sense of encouragement while he was in the initial stages of writing Gödel, Escher, Bach: an Eternal Golden Braid. Are Quanta Real? received positive reviews from scientific journals and popular science magazines, has inspired essays on philosophy and science and was a finalist for a National Book Award. == References ==
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{
"page_id": 42993306,
"source": null,
"title": "Are Quanta Real?"
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In statistical mechanics the Percus–Yevick approximation is a closure relation to solve the Ornstein–Zernike equation. It is also referred to as the Percus–Yevick equation. It is commonly used in fluid theory to obtain e.g. expressions for the radial distribution function. The approximation is named after Jerome K. Percus and George J. Yevick. == Derivation == The direct correlation function represents the direct correlation between two particles in a system containing N − 2 other particles. It can be represented by c ( r ) = g t o t a l ( r ) − g i n d i r e c t ( r ) {\displaystyle c(r)=g_{\rm {total}}(r)-g_{\rm {indirect}}(r)\,} where g t o t a l ( r ) {\displaystyle g_{\rm {total}}(r)} is the radial distribution function, i.e. g ( r ) = exp [ − β w ( r ) ] {\displaystyle g(r)=\exp[-\beta w(r)]} (with w(r) the potential of mean force) and g i n d i r e c t ( r ) {\displaystyle g_{\rm {indirect}}(r)} is the radial distribution function without the direct interaction between pairs u ( r ) {\displaystyle u(r)} included; i.e. we write g i n d i r e c t ( r ) = exp [ − β ( w ( r ) − u ( r ) ) ] {\displaystyle g_{\rm {indirect}}(r)=\exp[-\beta (w(r)-u(r))]} . Thus we approximate c(r) by c ( r ) = e − β w ( r ) − e − β [ w ( r ) − u ( r ) ] . {\displaystyle c(r)=e^{-\beta w(r)}-e^{-\beta [w(r)-u(r)]}.\,} If we introduce the function y ( r ) = e β u ( r ) g ( r ) {\displaystyle y(r)=e^{\beta u(r)}g(r)} into the approximation for c(r) one obtains c ( r ) = g
|
{
"page_id": 10159772,
"source": null,
"title": "Percus–Yevick approximation"
}
|
( r ) − y ( r ) = e − β u y ( r ) − y ( r ) = f ( r ) y ( r ) . {\displaystyle c(r)=g(r)-y(r)=e^{-\beta u}y(r)-y(r)=f(r)y(r).\,} This is the essence of the Percus–Yevick approximation for if we substitute this result in the Ornstein–Zernike equation, one obtains the Percus–Yevick equation: y ( r 12 ) = 1 + ρ ∫ f ( r 13 ) y ( r 13 ) h ( r 23 ) d r 3 . {\displaystyle y(r_{12})=1+\rho \int f(r_{13})y(r_{13})h(r_{23})d\mathbf {r_{3}} .\,} The approximation was defined by Percus and Yevick in 1958. == Hard spheres == For hard spheres, the potential u(r) is either zero or infinite, and therefore the Boltzmann factor e − u / k B T {\displaystyle {\text{e}}^{-u/k_{\text{B}}T}} is either one or zero, regardless of temperature T. Therefore structure of a hard-spheres fluid is temperature independent. This leaves just two parameters: the hard-core radius R (which can be eliminated by rescaling distances or wavenumbers), and the packing fraction η (which has a maximum value of 0.64 for random close packing). Under these conditions, the Percus–Yevick equation has an analytical solution, obtained by Wertheim in 1963. === Solution as C code === The static structure factor of the hard-spheres fluid in Percus–Yevick approximation can be computed using the following C function: == Hard spheres in shear flow == For hard spheres in shear flow, the function u(r) arises from the solution to the steady-state two-body Smoluchowski convection–diffusion equation or two-body Smoluchowski equation with shear flow. An approximate analytical solution to the Smoluchowski convection-diffusion equation was found using the method of matched asymptotic expansions by Banetta and Zaccone in Ref. This analytical solution can then be used together with the Percus–Yevick approximation in the Ornstein-Zernike equation. Approximate solutions
|
{
"page_id": 10159772,
"source": null,
"title": "Percus–Yevick approximation"
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|
for the pair distribution function in the extensional and compressional sectors of shear flow and hence the angular-averaged radial distribution function can be obtained, as shown in Ref., which are in good parameter-free agreement with numerical data up to packing fractions η ≈ 0.5 {\displaystyle \eta \approx 0.5} . == See also == Hypernetted-chain equation – another closure relation Ornstein–Zernike equation == References ==
|
{
"page_id": 10159772,
"source": null,
"title": "Percus–Yevick approximation"
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AFM-IR (atomic force microscope-infrared spectroscopy) or infrared nanospectroscopy is one of a family of techniques that are derived from a combination of two parent instrumental techniques. AFM-IR combines the chemical analysis power of infrared spectroscopy and the high-spatial resolution of scanning probe microscopy (SPM). The term was first used to denote a method that combined a tuneable free electron laser with an atomic force microscope (AFM, a type of SPM) equipped with a sharp probe that measured the local absorption of infrared light by a sample with nanoscale spatial resolution. Originally the technique required the sample to be deposited on an infrared-transparent prism and be less than 1μm thick. This early setup improved the spatial resolution and sensitivity of photothermal AFM-based techniques from microns to circa 100 nm. Then, the use of modern pulsed optical parametric oscillators and quantum cascade lasers, in combination with top-illumination, have enabled to investigate samples on any substrate and with increase sensitivity and spatial resolution. As most recent advances, AFM-IR has been proved capable to acquire chemical maps and nanoscale resolved spectra at the single-molecule scale from macromolecular self-assemblies and biomolecules with circa 10 nm diameter, as well as to overcome limitations of IR spectroscopy and measure in aqueous liquid environments. Recording the amount of infrared absorption as a function of wavelength or wavenumber, AFM-IR creates an infrared absorption spectra that can be used to chemically characterize and even identify unknown samples. Recording the infrared absorption as a function of position can be used to create chemical composition maps that show the spatial distribution of different chemical components. Novel extensions of the original AFM-IR technique and earlier techniques have enabled the development of bench-top devices capable of nanometer spatial resolution, that do not require a prism and can work with thicker samples, and thereby greatly
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"page_id": 44893854,
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"title": "Infrared Nanospectroscopy (AFM-IR)"
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improving ease of use and expanding the range of samples that can be analysed. AFM-IR has achieved lateral spatial resolutions of ca. 10 nm, with a sensitivity down to the scale of molecular monolayer and single protein molecules with molecular weight down to 400-600 kDa. AFM-IR is related to techniques such as tip-enhanced Raman spectroscopy (TERS), scanning near-field optical microscopy (SNOM), nano-FTIR and other methods of vibrational analysis with scanning probe microscopy. == History == === Early history === The earliest measurements combining AFM with infrared spectroscopy were performed in 1999 by Hammiche et al. at the University of Lancaster in the United Kingdom, in an EPSRC-funded project led by M Reading and H M Pollock. Separately, Anderson at the Jet Propulsion Laboratory in the United States made a related measurement in 2000. Both groups used a conventional Fourier transform infrared spectrometer (FTIR) equipped with a broadband thermal source, the radiation was focused near the tip of a probe that was in contact with a sample. The Lancaster group obtained spectra by detecting the absorption of infrared radiation using a temperature sensitive thermal probe. Anderson took the different approach of using a conventional AFM probe to detect the thermal expansion. He reported an interferogram but not a spectrum; the first infrared spectrum obtained in this way was reported by Hammiche et al. in 2004: this represented the first proof that spectral information about a sample could be obtained using this approach. Both of these early experiments used a broadband source in conjunction with an interferometer; these techniques could, therefore, be referred to as AFM-FTIR although Hammiche et al. coined the more general term photothermal microspectroscopy or PTMS in their first paper. PTMS has various subgroups; including techniques that measure temperature measure thermal expansion use broadband sources. use lasers excite the
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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sample using evanescent waves, illuminate the sample directly from above etc. and different combinations of these. Fundamentally, they all exploit the photothermal effect. Different combinations of sources, methods, methods of detection and methods of illumination have benefits for different applications. Care should be taken to ensure that it is clear which form of PTMS is being used in each case. Currently there is no universally accepted nomenclature. The original technique dubbed AFM-IR that induced resonant motion in the probe using a Free Electron Laser has developed by exploiting the foregoing permutations so that it has evolved into various forms. The pioneering experiments of Hammiche et al and Anderson had limited spatial resolution due to thermal diffusion - the spreading of heat away from the region where the infrared light was absorbed. The thermal diffusion length (the distance the heat spreads) is inversely proportional to the root of the modulation frequency. Consequently, the spatial resolution achieved by the early AFM-IR approaches was around one micron or more, due to the low modulation frequencies of the incident radiation created by the movement of the mirror in the interferometer. Also, the first thermal probes were Wollaston wire devices that were developed originally for Microthermal analysis (in fact PTMS was originally considered to be one of a family of microthermal techniques). The comparatively large size of these probes also limited spatial resolution. Bozec et al. and Reading et al. used thermal probes with nanoscale dimensions and demonstrated higher spatial resolution. Ye et al described a MEM-type thermal probe giving sub-100 nm spatial resolution, which they used for nanothermal analysis. The process of exploring laser sources began in 2001 by Hammiche et al when they acquired the first spectrum using a tuneable laser (see Resolution improvement with pulsed laser source). A significant development was the
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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creation by Reading et al. in 2001 of a custom interface that allowed measurements to be made while illuminating the sample from above; this interface focused the infrared beam to a spot of circa 500μm diameter, close to the theoretical maximum. The use of top-down or top-side illumination has the important benefit that samples of arbitrary thickness can be studied on arbitrary substrates. In many cases this can be done without any sample preparation. All subsequent experiments by Hammiche, Pollock, Reading and their co-workers were made using this type of interface including the instrument constructed by Hill et al. for nanoscale imaging using a pulsed laser. The work of the University of Lancaster group in collaboration with workers from the University of East Anglia led to the formation of a company, Anasys Instruments, to exploit this and related technologies (see Commercialization). === Spatial resolution improvement with pulsed laser sources === In the first paper on AFM-based infrared by Hammiche et al., the relevant well-established theoretical considerations were outlined that predict that high spatial resolution can be achieved using rapid modulation frequencies because of the consequent reduction in the thermal diffusion length. They estimated that spatial resolutions in the range of 20 nm-30 nm should be achievable. The most readily available sources that can achieve high modulation frequencies are pulsed lasers: even when the rapidity of the pulses is not high, the square wave form of a pulse contains very high modulation frequencies in Fourier space. In 2001, Hammiche et al. used a type of bench-top tuneable, pulsed infrared laser known as an optical parametric oscillator or OPO and obtained the first probe-based infrared spectrum with a pulsed laser, however, they did not report any images. Nanoscale spatial resolution AFM-IR imaging using a pulsed laser was first demonstrated by Dazzi et
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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al at the University of Paris-Sud, France. Dazzi and his colleagues used a wavelength-tuneable, free electron laser at the CLIO facility in Orsay, France to provide an infrared source with short pulses. Like earlier workers, they used a conventional AFM probe to measure thermal expansion but introduced a novel optical configuration: the sample was mounted on an IR-transparent prism so that it could be excited by an evanescent wave. Absorption of short infrared laser pulses by the sample caused rapid thermal expansion that created a force impulse at the tip of the AFM cantilever. The thermal expansion pulse induced transient resonant oscillations of the AFM cantilever probe. This has led to the technique being dubbed Photo-Thermal Induced Resonance (PTIR), by some workers in the field. Some prefer the terms PTIR or PTMS to AFM-IR as the technique is not necessarily restricted to infrared wavelengths. The amplitude of the cantilever oscillation is directly related to the amount of infrared radiation absorbed by the sample. By measuring the cantilever oscillation amplitude as a function of wavenumber, Dazzi's group was able to obtain absorption spectra from nanoscale regions of the sample. Compared to earlier work, this approach improved spatial resolution because the use of short laser pulses reduced the duration of the thermal expansion pulse to the point that the thermal diffusion lengths can be on the scale of nanometres rather than microns. A key advantage of the use of a tuneable laser source, with a narrow wavelength range, is the ability to rapidly map the locations of specific chemical components on the sample surface. To achieve this, Dazzi's group tuned their free electron laser source to a wavelength corresponding to the molecular vibration of the chemical of interest, then mapped the cantilever oscillation amplitude as function of position across the sample. They
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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demonstrated the ability to map chemical composition in E. coli bacteria. They could also visualize polyhydroxybutyrate (PHB) vesicles inside Rhodobacter capsulatus cells and monitor the efficiency of PHB production by the cells. At the University of East Anglia in the UK, as part of an EPSRC-funded project led by M. Reading and S. Meech, Hill and his co-workers followed the earlier work of Reading et al. and Hammiche et al. and measured thermal expansion using an optical configuration that illuminated the sample from above in contrast to Dazzi et al. who excited the sample with an evanescent wave from below. Hill also made use of an optical parametric oscillator as the infrared source in the manner of Hammiche et al. This novel combination of topside illumination, OPO source and measuring thermal expansion proved capable of nanoscale spatial resolution for infrared imaging and spectroscopy (the figures show a schematic of the UEA apparatus and results obtained with it). The use by Hill and co-workers of illumination from above allowed a substantially wider range of samples to be studied than was possible using Dazzi's technique. By introducing the use of a bench top IR source and topdown illumination, the work of Hammiche, Hill and their coworkers made possible the first commercially viable SPM-based infrared instrument (see Commercialization). === Broadband pulsed laser sources === Reading et al. have explored the use of a broadband QCL combined with thermal expansion measurements. Above, the inability of thermal broadband sources to achieve high spatial resolution is discussed (see history). In this case the frequency of modulation is limited by the mirror speed of the interferometer which, in turn, limits the lateral spatial resolution that can be achieved. When using a broadband QCL the resolution is limited not by the mirror speed but by the modulation frequency
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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of the laser pulses (or other waveforms). The benefit of using a broadband source is that an image can be acquired that comprises an entire spectrum or part of a spectrum for each pixel. This is much more powerful than acquiring images bases on a single wavelength. The preliminary results of Reading et al. show that directing a broadband QCL though an interferometer can give an easily detectable response from a conventional AFM probe measuring thermal expansion. === Commercialization === The AFM-IR technique based on a pulsed infrared laser source was commercialized by Anasys Instruments, a company founded by Reading, Hammiche and Pollock in the United Kingdom in 2004; a sister, United States corporation was founded a year later. Anasys Instruments developed its product with support from the National Institute of Standards and Technology and the National Science Foundation. Since free electron lasers are rare and available only at select institutions, a key to enabling a commercial AFM-IR was to replace them with a more compact type of infrared source. Following the lead given by Hammiche et al in 2001 and Hill et al in 2008, Anasys Instruments introduced an AFM-IR product in early 2010, using a tabletop laser source based on a nanosecond optical parametric oscillator. The OPO source enabled nanoscale infrared spectroscopy over a tuning range of roughly 1000–4000 cm−1 or 2.5-10 μm. The initial product required samples to be mounted on infrared-transparent prisms, with the infrared light being directed from below in the manner of Dazzi et al. For best operation, this illumination scheme required thin samples, with optimal thickness of less than 1 μm, prepared on the surface of the prism. In 2013, Anasys released an AFM-IR instrument based on the work of Hill et al. that supported top-side illumination. "By eliminating the need to prepare
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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samples on infrared-transparent prisms and relaxing the restriction on sample thickness, the range of samples that could be studied was greatly expanded. The CEO of Anasys Instruments recognised this achievement by calling it " an exciting major advance" in a letter written to the university and included in the final report of EPSRC project EP/C007751/1. The UEA technique went on to become Anasys Instruments' flagship product. === Comparison to related photothermal techniques === It is worth noting that the first infrared spectrum obtained by measuring thermal expansion using an AFM was obtained by Hammiche and co-workers without inducing resonant motions in the probe cantilever. In this early example the modulation frequency was too low to achieve high spatial resolution but there is nothing, in principle, preventing the measurement of thermal expansion at higher frequencies without analysing or inducing resonant behaviour. Possible options for measuring the displacement of the tip rather than the subsequent propagation of waves along the cantilever include; interferometry focused at the end of the cantilever where the tip is located, a torsional motion resulting from an offset probe (it would only be influenced by the motions of the cantilever as a second order effect) and exploiting the fact that the signal from a heated thermal probe is strongly influenced by the position of the tip relative to the surface thus this could provide a measurement of thermal expansion that wasn't strongly influenced by or dependent upon resonance. The advantages of a non-resonant method of detection is that any frequency of light modulation could be used thus depth information could be obtained in a controlled way (see below) whereas methods that rely on resonance are limited to harmonics. The thermal-probe based method of Hammiche et al. has found a significant number of applications. A unique application made possible
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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by the top-down illumination combined with a thermal probe is localized depth profiling, this is not possible using either using the Dazzi et al. configuration of AFM-IR or that of Hill et al. despite the fact the latter uses top-down illumination. Obtaining linescans and images with thermal probes has been shown to be possible, sub-diffraction limit spatial resolution can be achieved and the resolution for delineating boundaries can be enhanced using chemometric techniques. In all of these examples a spectrum is acquired that spans the entire mid-IR range for each pixel, this is considerably more powerful than measuring the absorption of a single wavelength as is the case for AFM-IR when using either the method of Dazzi et al. or Hill et al. Reading and his group demonstrated how, because thermal probes can be heated, localized thermal analysis can be combined with photothermal infrared spectroscopy using a single probe. In this way local chemical information could be complemented with local physical properties such melting and glass transition temperatures. This in turn led to the concept of thermally assisted nanosampling, where the heated tip performs a local thermal analysis experiment then the probe is retracted taking with it down to femtograms of softened material that adhere to the tip. This material can then be manipulated and/or analysed by photothermal infrared spectroscopy or other techniques. This considerably increases the analytical power of this type of SPM-based infrared instrument beyond anything that can be achieved with conventional AFM probes such as those used in AFM-IR when using either the Dazzi et al. or the Hill et al. version. Thermal probe techniques have still not achieved the nanoscale spatial resolution that thermal expansion methods have attained though this is theoretically possible. For this, a robust thermal probe and a high intensity source is needed.
|
{
"page_id": 44893854,
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"title": "Infrared Nanospectroscopy (AFM-IR)"
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Recently, the first images using a QCL and a thermal probe have been obtained by Reading et al. A good signal to noise ratio enabled rapid imaging but sub-micron spatial resolution was not clearly demonstrated. Theory predicts improvements in spatial resolution could be achieved by confining data analysis to the early part of the thermal response to a step change increase in the intensity of the incident radiation. In this way pollution of the measurement from adjacent regions would be avoided, i.e. the measurement window could be confined to a suitable fraction of the time of flight of the thermal wave (using a Fourier analysis of the response could provide a similar outcome by using the high frequency components). This could be achieved by tapping the probe in synchrony with the laser. Similarly, lasers that provide very rapid modulations could further reduce thermal diffusion lengths. Although most effort to date has been focused on thermal expansion measurements, this might change. Truly robust thermal probes have recently become available, as have affordable compact QCL's that are tuneable over a broad frequency range. Consequently, it may soon be the case that thermal probe techniques will become as widely used as those based on thermal expansion. Ultimately, instruments that can easily switch between modes and even combine them using a single probe will certainly become available, for example, a single probe will eventually be able to measure both temperature and thermal expansion. == Recent improvements and single-molecule sensitivity == The original commercial AFM-IR instruments required most samples to be thicker than 50 nm to achieve sufficient sensitivity. Sensitivity improvements were achieved using specialized cantilever probes with an internal resonator and by wavelet based signal processing techniques. Sensitivity was further improved by Lu et al. by using quantum cascade laser (QCL) sources. The high
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
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repetition rate of the QCL allows absorbed infrared light to continuously excite the AFM tip at a "contact resonance" of the AFM cantilever. This resonance-enhanced AFM-IR, in combination with electric field enhancement from metallic tips and substrates led to the demonstration of AFM-IR spectroscopy and compositional imaging of films as thin as single self-assembled monolayers. AFM-IR has also been integrated with other sources including a picosecond OPO offering a tuning range 1.55 μm to 16 μm (from 6450 cm−1 to 625 cm−1). In its initial development, with samples deposited on transparent prisms and using OPO laser sources, the sensitivity of AFM-IR was limited to a minimal thickness of the sample of circa 50-100 nm as mentioned above. The advent of quantum cascade lasers (QCL) and the use of the electromagnetic field enhancement between metallic probes and substrates have improved the sensitivity and spatial resolution of AFM-IR down to the measurement of large (>0.3 μm) and flat (~2–10 nm) self-assembled monolayers, where still hundreds of molecules are present. Ruggeri et al. have recently developed off-resonance, low power and short pulse AFM-IR (ORS-nanoIR) to prove the acquisition of infrared absorption spectra and chemical maps at the single molecule level, in the case of macromolecular assemblies and large protein molecules with a spatial resolution of ca. 10 nm. == Nanoscale chemical imaging and mapping == === Nanoscale resolved chemical maps and spectra === AFM-IR enables nanoscale infrared spectroscopy, i.e. the ability to obtain infrared absorption spectra from nanoscale regions of a sample. Chemical compositional mapping AFM-IR can also be used to perform chemical imaging or compositional mapping with spatial resolution down to ~10-20 nm, limited only by the radius of the AFM tip. In this case, the tuneable infrared source emits a single wavelength, corresponding to a specific molecular resonance, i.e. a specific
|
{
"page_id": 44893854,
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"title": "Infrared Nanospectroscopy (AFM-IR)"
}
|
infrared absorption band. By mapping the AFM cantilever oscillation amplitude as a function of position, it is possible to map out the distribution of specific chemical components. Compositional maps can be made at different absorption bands to reveal the distribution of difference chemical species. === Complementary morphological and mechanical mapping === The AFM-IR technique can simultaneously provide complementary measurements of the mechanical stiffness and dissipation of a sample surface. When infrared light is absorbed by the sample the resulting rapid thermal expansion excites a "contact resonance" of the AFM cantilever, i.e. a coupled resonance resulting from the properties of both the cantilever and the stiffness and damping of the sample surface. Specifically, the resonance frequency shifts to higher frequencies for stiffer materials and to lower frequencies for softer material. Additionally, the resonance becomes broader for materials with larger dissipation. These contact resonances have been studied extensively by the AFM community (see, for example, atomic force acoustic microscopy). Traditional contact resonance AFM requires an external actuator to excite the cantilever contact resonances. In AFM-IR these contact resonances are automatically excited every time an infrared pulse is absorbed by the sample. So the AFM-IR technique can measure the infrared absorption by the amplitude of the cantilever oscillation response and the mechanical properties of the sample via the contact resonance frequency and quality factor. == Applications == Applications of AFM-IR have include the characterisation of protein, polymers composites, bacteria, cells, biominerals, pharmaceutical sciences, photonics/nanoantennas, fuel cells, fibers, skin, hair, metal organic frameworks, microdroplets, self-assembled monolayers, nanocrystals, and semiconductors. === Polymers === Polymers blends, composites, multilayer films and fibers AFM-IR has been used to identify and map polymer components in blends, characterize interfaces in composites, and even reverse engineer multilayer films Additionally AFM-IR has been used to study chemical composition in Poly(3][4-ethylenedioxythiophene) (PEDOT) conducting
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
}
|
polymers. and vapor infiltration into polyethylene terephthalate PET fibers. === Protein science === The chemical and structural properties of protein determine their interactions, and thus their functions, in a wide variety of biochemical processes. Since Ruggeri et al. pioneering work on the aggregation pathways of the Josephin domain of ataxin-3, responsible for type-3 spinocerebellar ataxia, an inheritable protein-misfolding disease, AFM-IR was used to characterize molecular conformations in a wide spectrum of applications in protein and life sciences. This approach has delivered new mechanistic insights into the behaviour of disease-related proteins and peptides, such as Aβ42, huntingtin and FUS, which are involved in the onset of Alzheimer's, Huntington's and Amyotrophic lateral sclerosis (ALS). Similarly AFM-IR has been applied to study studying protein based functional biomaterials. === Life sciences === AFM-IR has been used to characterise spectroscopically in detail chromosomes, bacteria and cells with nanoscale resolution. For example, in the case of infection of bacteria by viruses (Bacteriophages), and also the production of polyhydroxybutyrate (PHB) vesicles inside Rhodobacter capsulatus cells and triglycerides in Streptomyces bacteria (for biofuel applications). AFM-IR has also been used to evaluate and map mineral content, crystallinity, collagen maturity and acid phosphate content via ratiometric analysis of various absorption bands in bone. AFM-IR has also been used to perform spectroscopy and chemical mapping of structural lipids in human skin, cells and hair === Fuel cells === AFM-IR has been used to study hydrated Nafion membranes used as separators in fuel cells. The measurements revealed the distribution of free and ionically bound water on the Nafion surface. === Photonic nanoantennas === AFM-IR has been used to study the surface plasmon resonance in heavily silicon-doped indium arsenide microparticles. Gold split ring resonators have been studied for use with Surface-Enhanced Infrared Absorption Spectroscopy. In this case AFM-IR was used to measure the
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
}
|
local field enhancement of the plasmonics structures (~30X) at 100 nm spatial resolution. === Pharmaceutical sciences === AFM-IR has been used to study miscibility and phase separation in drug polymer blends, the chemical analysis of nanocrystalline drug particles as small 90 nm across, the interaction of chromosomes with chemotherapeutics drugs, and of amyloids with pharmacological approaches to contrast neurodegeneration. == Notes == == References == == External links == Infrared Imaging beyond the Diffraction Limit (NIST Andrea Centrone Group) Sub-wavelength resolution microspectroscopy (University of Texas Mikhail Belkin group) Nanoscale Microscopy and Spectroscopy Group (Wageningen University, Ruggeri group)
|
{
"page_id": 44893854,
"source": null,
"title": "Infrared Nanospectroscopy (AFM-IR)"
}
|
Termitophiles are macro-organisms adapted to live in association with termites or their nests. They include vertebrates, invertebrates and fungi and can either be obligate termitophiles (those that cannot live without the termites) or non-obligate termitophiles (those that can live independently and make use of the termite nests facultatively or opportunistically). Termitophiles may spend a just a part or the whole of their lifecycle inside a termite nest. The term termitariophily has been suggested as a term to describe the situation where a foreign organism merely uses the termite nest. Termites live in colonies and construct nests whose environments are controlled. The temperature, humidity, and other conditions inside the nests may be more favourable than the outdoor environment for the termitophiles while potentially also making use of the food resources within the nest, including the fungi grown by the colony or the eggs or larvae being reared. Termitophilous insects avoid the defenses of the termite colony through one or more of a number of adaptations including having a rounded and smooth body, having bristles (often yellow) on their body surface, masking their odor to avoid detection, exuding chemicals from their body that the termites find pleasing, or by appearing like inanimate objects or mimicking termites. == Insects == A number of species of staphylinid beetles are known to be termitophiles. Cretotrichopsenius burmiticus has been described from 99 million year old Burmese amber and shows termitophilous adaptations. Some like Trichopsenius frosti and Xenistusa hexagonalis are known to follow the trail pheromones of their termite host Reticulitermes virginicus. Trichopsenius frosti also has a cuticular hydrocarbon profile closely matching that of its host. Staphylinid termitophiles mostly in the subfamily Aleocharinae curl their abdomen over their body. The abdomen may also show enlargement of physogastry and in a few species there are protruding appendages that
|
{
"page_id": 77268639,
"source": null,
"title": "Termitophile"
}
|
mimic the body structure of a termite. The Australian species Austrospirachtha mimetes and Austrospirachtha carrijoi have abdomen resembling termites. Similar adaptations are seen in the South American Thyreoxenus alakazam and the African Coatonachthodes ovambolandicus. A subfamily of scarab beetles, the Termitotroginae, are small, blind, and with reduced antennae. The genus Termitotrox (includes Aphodiocopris) is known from the fungus combs of termites in India and Africa. They are thought to be obligate termitophiles. Some flies in the family Phoridae are termitophilous and grow as larvae within the termite nests. Some species have larvae that feed on the fungus comb while others are termite endoparasites or predators. == Fungi == Termite nest specific fungi include the Basidiobolus, Antennopsis, and some species of Xylaria. Several species of Termitomyces are grown intentionally as food by termites within their comb. == See also == Myrmecophiles Symphiles Inquiline == References ==
|
{
"page_id": 77268639,
"source": null,
"title": "Termitophile"
}
|
Citronellal or rhodinal (C10H18O) is a monoterpenoid aldehyde, the main component in the mixture of terpenoid chemical compounds that give citronella oil its distinctive lemon scent. Citronellal is a main isolate in distilled oils from the plants Cymbopogon (excepting C. citratus, culinary lemongrass), lemon-scented gum, and lemon-scented teatree. The (S)-(−)-enantiomer of citronellal makes up to 80% of the oil from kaffir lime leaves and is the compound responsible for its characteristic aroma. Citronellal has insect repellent properties, and research shows high repellent effectiveness against mosquitoes. Another research shows that citronellal has strong antifungal qualities. == Compendial status == British Pharmacopoeia == See also == Citral Citronellol Citronella oil Hydroxycitronellal Perfume allergy == References ==
|
{
"page_id": 1771169,
"source": null,
"title": "Citronellal"
}
|
Helix–coil transition models are formalized techniques in statistical mechanics developed to describe conformations of linear polymers in solution. The models are usually but not exclusively applied to polypeptides as a measure of the relative fraction of the molecule in an alpha helix conformation versus turn or random coil. The main attraction in investigating alpha helix formation is that one encounters many of the features of protein folding but in their simplest version. Most of the helix–coil models contain parameters for the likelihood of helix nucleation from a coil region, and helix propagation along the sequence once nucleated; because polypeptides are directional and have distinct N-terminal and C-terminal ends, propagation parameters may differ in each direction. The two states are helix state: characterized by a common rotating pattern kept together by hydrogen bonds, (see alpha-helix). coil state: conglomerate of randomly ordered sequence of atoms (see random coil). Common transition models include the Zimm–Bragg model and the Lifson–Roig model, and their extensions and variations. Energy of host poly-alanine helix in aqueous solution: Δ G folding = ( m − 2 ) Δ H α − m T Δ S {\displaystyle \Delta G_{\text{folding}}=(m-2)\Delta H_{\alpha }-mT\Delta S} where m is number of residues in the helix. == References ==
|
{
"page_id": 8914599,
"source": null,
"title": "Helix–coil transition model"
}
|
The genetic influences of post-traumatic stress disorder (PTSD) are not understood well due to the limitations of any genetic study of mental illness; in that, it cannot be ethically induced in selected groups. Because of this, all studies must use naturally occurring groups with genetic similarities and differences, thus the amount of data is limited. Still, genetics play some role in the development of PTSD. == Research and potential influences == Approximately 30% of the variance in PTSD is caused by genetics alone. For twins exposed to combat in the Vietnam War, a monozygotic (identical) twin with PTSD was associated with an increased risk of the co-twin having PTSD, as compared to dizygotic (non-identical) twins; additionally, assaultive trauma (compared to non-assaultive trauma) was more likely to exacerbate these effects. There is also evidence that those with a genetically smaller hippocampus are more likely to develop PTSD following a traumatic event. Research has also found that PTSD shares many genetic influences common to other psychiatric disorders. Panic and generalized anxiety disorders and PTSD share 60% of the same genetic variance. Alcohol, nicotine, and drug dependence share greater than 40% genetic similarities. Additional disorders—such as depression, schizophrenia, and bipolar disorder—share the same fundamental genetic phenotypes as PTSD. === Nature vs. nurture === An individual's potential for onset of many psychological disorders is heavily affected by genetic phenotypes, yet this is not the only contributing factor. Environment plays an important role as well, especially for trauma-based disorders such as PTSD, considering that certain life experiences can trigger the activation of an underlying genetic phenotype which might have been previously dormant. This can be further understood by examining the diathesis-stress model for the onset of psychological disorders, which explains that certain individuals, due to their genetic phenotypes, are more susceptible to psychological disorders when
|
{
"page_id": 44631723,
"source": null,
"title": "Genetics of post-traumatic stress disorder"
}
|
encountering the same stressful life situations or stimuli as other individuals without these same underlying genetic phenotypes. === Effects of neurotransmitters and hormones === Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the brain. A 2009 study reported a significant interaction between three single nucleotide polymorphisms (SNP) in the GABA alpha-2 receptor gene and the severity of childhood trauma in predicting PTSD in adults. Another study found an association between a specific SNP of the RGS2 gene and PTSD symptoms in adults who experienced high environmental stress (hurricane exposure) and low social support. Studies in 2008 found that several SNPs in the FKBP5 (FK506 binding protein 5) gene interact with childhood trauma to predict severity of adult PTSD. These findings suggest that individuals with these SNPs who are abused as children are more susceptible to PTSD as adults. This is particularly important given that FKBP5 SNPs have previously been associated with peritraumatic dissociation in medically injured children (that is, dissociation at the time of the childhood trauma), which has itself been shown to be predictive of PTSD. Furthermore, FKBP5 may be less expressed in those with current PTSD. In 2011, another study found that a single SNP in a putative estrogen response element on the ADCYAP1R1 gene predicts PTSD diagnosis and symptoms in females. Incidentally, this SNP is also associated with fear discrimination. The study suggests that perturbations in the PACAP/PAC1 pathway are involved in abnormal stress responses underlying PTSD. === Environmental influences === PTSD is a psychiatric disorder that requires an environmental event that individuals may variously respond to. Because of this, gene-environment studies tend to be the most indicative of their effect on the probability of PTSD than studies of the main effect of the gene. Studies have demonstrated the interaction between the FKBP5 gene and childhood
|
{
"page_id": 44631723,
"source": null,
"title": "Genetics of post-traumatic stress disorder"
}
|
environment to predict the severity of PTSD. Polymorphisms in FKBP5 have been associated with peritraumatic dissociation in mentally ill children. A 2008 study of highly traumatized, inner city African Americans demonstrated that four polymorphisms of the FKBP5 gene interacted with severity of childhood abuse to predict severity of adult PTSD symptoms. This finding was partially replicated in a 2010 study, which reported that within the African American population, the TT genotype of the FKBP5 gene is associated with the highest risk of PTSD among those having experienced childhood adversity, while those with this genotype that experienced no childhood adversity had the lowest risk of PTSD. In addition, alcohol dependence interacts with the FKBP5 polymorphisms and childhood adversity to increase the risk of PTSD in these populations. A 2005 study found that FKPB5 mRNA was differentially expressed in emergency room trauma patients who were later diagnosed with PTSD. However, a 2009 study found FKPB5 mRNA expression was reduced in 9/11 survivors diagnosed with PTSD. === Genetic influences === Catechol-O-methyl transferase (COMT) is an enzyme that catalyzes the extraneuronal breakdown of catecholamines. The gene that codes for COMT has a functional polymorphism in which a valine has been replaced with a methionine at codon 158. This polymorphism has lower enzyme activity and has been tied to a slower breakdown of the catecholamines. A study of Rwandan genocide survivors indicated that carriers of the Val allele demonstrated the expected response relationship between the higher number of lifetime traumatic events and a lifetime diagnosis of PTSD. However, those with homozygotes for the Met/Met genotype demonstrated a high risk of lifetime PTSD independent of the number of traumatic experiences. Those with Met/Met genotype also demonstrated a reduced extinction of conditioned fear responses which may account for the high risk for PTSD experienced by this genotype.
|
{
"page_id": 44631723,
"source": null,
"title": "Genetics of post-traumatic stress disorder"
}
|
Many genes impact the limbic-frontal neurocircuitry as a result of its complexity. The main effect of the D2A1 allele of the dopamine receptor D2 (DRD2) gene has a strong association with the diagnosis of PTSD. The D2A1 allele has also shown a significant association to PTSD in those having engaged in harmful drinking. In addition, a polymorphism in the dopamine transporter SLC6A3 gene has a significant association with chronic PTSD. A polymorphism of the serotonin receptor 2A gene has been associated with PTSD in Korean women. The short allele of the promoter region of the serotonin transporter (5-HTTLPR) has been shown to be less efficient than the long allele and is associated with the amygdala response for the extinction of fear conditioning. However, the short allele is associated with a decreased risk of PTSD in a low-risk environment, but a high risk of PTSD in a high-risk environment. The s/s genotype demonstrated a high risk for the development of PTSD even in response to a small number of traumatic events, but those with the l allele demonstrate increased rates of PTSD with increasing traumatic experiences. A genome-wide association study (GWAS) offers an opportunity to identify novel risk variants for PTSD that will in turn inform our understanding of the etiology of the disorder. Early results indicate the feasibility and potential power of GWAS to identify biomarkers for anxiety-related behaviors that suggest a future of PTSD. These studies will lead to the discovery of novel loci for the susceptibility and symptomatology of anxiety disorders including PTSD. == Epigenetics == Epigenetic modification is an environmentally induced change in DNA that alters a gene's function rather than its structure. Its biological mechanism typically involves the methylation of cytosine within a gene, which leads to decreased transcription and thus reduced expression of the gene.
|
{
"page_id": 44631723,
"source": null,
"title": "Genetics of post-traumatic stress disorder"
}
|
Epigenetic modification can offer insight into the importance of developmental timing of stressor exposure in producing the phenotypic changes associated with PTSD. Neuroendocrine alterations seen in animal models parallel those of PTSD in humans, where low basal cortisol and enhanced suppression of cortisol in response to synthetic glucocorticoid becomes hereditary. Lower levels of glucocorticoid receptor (GR) mRNA have been demonstrated in the hippocampus of suicide victims with histories of childhood abuse. Although it has not been possible to monitor the state of methylation over time, the interpretation is that early developmental methylation changes are long-lasting and enduring. It is hypothesized that epigenetic-mediated changes in the HPA axis could be associated with an increased vulnerability to PTSD following traumatic events. These findings support the mechanism in which early life trauma strongly validates as a risk factor for PTSD development in adulthood by recalibrating the set point and stress-responsivity of the HPA axis. Epigenetic mechanisms may also be relevant to the intrauterine environment. Pregnant mothers who developed PTSD from the 9/11 attacks produced infants with lower salivary cortisol levels, but only if the traumatic exposure occurred during the third trimester of gestation. These changes occur via transmission of hormonal responses to the fetus, leading to a reprogramming of the glucocorticoid responsivity in the offspring. Separate studies have reported an increased risk for PTSD and low cortisol levels in the offspring of female Holocaust survivors with PTSD. == Evolutionary psychology == Evolutionary psychology interprets fear responses as adaptations that may have been useful in the ancestral environment to avoid or cope with various threats. In general, mammals display several defensive behaviors roughly dependent on how close the threat is: avoidance, vigilant immobility, withdrawal, aggressive defense, appeasement, and finally complete frozen immobility (the last possibly to confuse a predator's attack reflex or to simulate
|
{
"page_id": 44631723,
"source": null,
"title": "Genetics of post-traumatic stress disorder"
}
|
a dead and contaminated body). PTSD may correspond to and be caused by overactivation of such fear circuits. Thus, PTSD avoidance behaviors may correspond to mammal avoidance of and withdrawal from threats. Heightened memory of past threats may increase avoidance of similar situations in the future as well as be a prerequisite for analyzing the past threat and develop better defensive behaviors if the threat should recur. PTSD hyperarousal may correspond to vigilant immobility and aggressive defense. Complex post-traumatic stress disorder (and phenomena such as the Stockholm syndrome) may in part correspond to the appeasement stage and possibly the frozen immobility stage. There may be evolutionary explanations for differences in resilience to traumatic events. For instance, PTSD is five to ten times less common following traumatic fires than physical abuse or combat. This may be explained by events such as forest fires long being part of the evolutionary history of mammals. In contrast, PTSD is much more common following modern warfare, perhaps because prolonged modern combat is an evolutionarily new development and very unlike the quick inter-group raids that are argued to have characterized the Paleolithic. == Notes == == References ==
|
{
"page_id": 44631723,
"source": null,
"title": "Genetics of post-traumatic stress disorder"
}
|
In ecology, a niche is the match of a species to a specific environmental condition. It describes how an organism or population responds to the distribution of resources and competitors (for example, by growing when resources are abundant, and when predators, parasites and pathogens are scarce) and how it in turn alters those same factors (for example, limiting access to resources by other organisms, acting as a food source for predators and a consumer of prey). "The type and number of variables comprising the dimensions of an environmental niche vary from one species to another [and] the relative importance of particular environmental variables for a species may vary according to the geographic and biotic contexts". A Grinnellian niche is determined by the habitat in which a species lives and its accompanying behavioral adaptations. An Eltonian niche emphasizes that a species not only grows in and responds to an environment, it may also change the environment and its behavior as it grows. The Hutchinsonian niche uses mathematics and statistics to try to explain how species coexist within a given community. The concept of ecological niche is central to ecological biogeography, which focuses on spatial patterns of ecological communities. "Species distributions and their dynamics over time result from properties of the species, environmental variation..., and interactions between the two—in particular the abilities of some species, especially our own, to modify their environments and alter the range dynamics of many other species." Alteration of an ecological niche by its inhabitants is the topic of niche construction. The majority of species exist in a standard ecological niche, sharing behaviors, adaptations, and functional traits similar to the other closely related species within the same broad taxonomic class, but there are exceptions. A premier example of a non-standard niche filling species is the flightless, ground-dwelling kiwi
|
{
"page_id": 67244,
"source": null,
"title": "Ecological niche"
}
|
bird of New Zealand, which feeds on worms and other ground creatures, and lives its life in a mammal-like niche. Island biogeography can help explain island species and associated unfilled niches. == Grinnellian niche == The ecological meaning of niche comes from the meaning of niche as a recess in a wall for a statue, which itself is probably derived from the Middle French word nicher, meaning to nest. The term was coined by the naturalist Roswell Hill Johnson but Joseph Grinnell was probably the first to use it in a research program in 1917, in his paper "The niche relationships of the California Thrasher". The Grinnellian niche concept embodies the idea that the niche of a species is determined by the habitat in which it lives and its accompanying behavioral adaptations. In other words, the niche is the sum of the habitat requirements and behaviors that allow a species to persist and produce offspring. For example, the behavior of the California thrasher is consistent with the chaparral habitat it lives in—it breeds and feeds in the underbrush and escapes from its predators by shuffling from underbrush to underbrush. Its 'niche' is defined by the felicitous complementing of the thrasher's behavior and physical traits (camouflaging color, short wings, strong legs) with this habitat. Grinnellian niches can be defined by non-interactive (abiotic) variables and environmental conditions on broad scales. Variables of interest in this niche class include average temperature, precipitation, solar radiation, and terrain aspect which have become increasingly accessible across spatial scales. Most literature has focused on Grinnellian niche constructs, often from a climatic perspective, to explain distribution and abundance. Current predictions on species responses to climate change strongly rely on projecting altered environmental conditions on species distributions. However, it is increasingly acknowledged that climate change also influences species interactions
|
{
"page_id": 67244,
"source": null,
"title": "Ecological niche"
}
|
and an Eltonian perspective may be advantageous in explaining these processes. This perspective of niche allows for the existence of both ecological equivalents and empty niches. An ecological equivalent to an organism is an organism from a different taxonomic group exhibiting similar adaptations in a similar habitat, an example being the different succulents found in American and African deserts, cactus and euphorbia, respectively. As another example, the anole lizards of the Greater Antilles are a rare example of convergent evolution, adaptive radiation, and the existence of ecological equivalents: the anole lizards evolved in similar microhabitats independently of each other and resulted in the same ecomorphs across all four islands. == Eltonian niche == In 1927 Charles Sutherland Elton, a British ecologist, defined a niche as follows: "The 'niche' of an animal means its place in the biotic environment, its relations to food and enemies." Elton classified niches according to foraging activities ("food habits"): For instance there is the niche that is filled by birds of prey which eat small animals such as shrews and mice. In an oak wood this niche is filled by tawny owls, while in the open grassland it is occupied by kestrels. The existence of this carnivore niche is dependent on the further fact that mice form a definite herbivore niche in many different associations, although the actual species of mice may be quite different. Conceptually, the Eltonian niche introduces the idea of a species' response to and effect on the environment. Unlike other niche concepts, it emphasizes that a species not only grows in and responds to an environment based on available resources, predators, and climatic conditions, but also changes the availability and behavior of those factors as it grows. In an extreme example, beavers require certain resources in order to survive and reproduce, but
|
{
"page_id": 67244,
"source": null,
"title": "Ecological niche"
}
|
also construct dams that alter water flow in the river where the beaver lives. Thus, the beaver affects the biotic and abiotic conditions of other species that live in and near the watershed. In a more subtle case, competitors that consume resources at different rates can lead to cycles in resource density that differ between species. Not only do species grow differently with respect to resource density, but their own population growth can affect resource density over time. Eltonian niches focus on biotic interactions and consumer–resource dynamics (biotic variables) on local scales. Because of the narrow extent of focus, data sets characterizing Eltonian niches typically are in the form of detailed field studies of specific individual phenomena, as the dynamics of this class of niche are difficult to measure at a broad geographic scale. However, the Eltonian niche may be useful in the explanation of a species' endurance of global change. Because adjustments in biotic interactions inevitably change abiotic factors, Eltonian niches can be useful in describing the overall response of a species to new environments. == Hutchinsonian niche == The Hutchinsonian niche is an "n-dimensional hypervolume", where the dimensions are environmental conditions and resources, that define the requirements of an individual or a species to practice its way of life, more particularly, for its population to persist. The "hypervolume" defines the multi-dimensional space of resources (e.g., light, nutrients, structure, etc.) available to (and specifically used by) organisms, and "all species other than those under consideration are regarded as part of the coordinate system." The niche concept was popularized by the zoologist G. Evelyn Hutchinson in 1957. Hutchinson inquired into the question of why there are so many types of organisms in any one habitat. His work inspired many others to develop models to explain how many and how similar
|
{
"page_id": 67244,
"source": null,
"title": "Ecological niche"
}
|
coexisting species could be within a given community, and led to the concepts of 'niche breadth' (the variety of resources or habitats used by a given species), 'niche partitioning' (resource differentiation by coexisting species), and 'niche overlap' (overlap of resource use by different species). Statistics were introduced into the Hutchinson niche by Robert MacArthur and Richard Levins using the 'resource-utilization' niche employing histograms to describe the 'frequency of occurrence' as a function of a Hutchinson coordinate. So, for instance, a Gaussian might describe the frequency with which a species ate prey of a certain size, giving a more detailed niche description than simply specifying some median or average prey size. For such a bell-shaped distribution, the position, width and form of the niche correspond to the mean, standard deviation and the actual distribution itself. One advantage in using statistics is illustrated in the figure, where it is clear that for the narrower distributions (top) there is no competition for prey between the extreme left and extreme right species, while for the broader distribution (bottom), niche overlap indicates competition can occur between all species. The resource-utilization approach postulates that not only can competition occur, but that it does occur, and that overlap in resource utilization directly enables the estimation of the competition coefficients. This postulate, however, can be misguided, as it ignores the impacts that the resources of each category have on the organism and the impacts that the organism has on the resources of each category. For instance, the resource in the overlap region can be non-limiting, in which case there is no competition for this resource despite niche overlap. An organism free of interference from other species could use the full range of conditions (biotic and abiotic) and resources in which it could survive and reproduce which is called
|
{
"page_id": 67244,
"source": null,
"title": "Ecological niche"
}
|
its fundamental niche. However, as a result of pressure from, and interactions with, other organisms (i.e. inter-specific competition) species are usually forced to occupy a niche that is narrower than this, and to which they are mostly highly adapted; this is termed the realized niche. Hutchinson used the idea of competition for resources as the primary mechanism driving ecology, but overemphasis upon this focus has proved to be a handicap for the niche concept. In particular, overemphasis upon a species' dependence upon resources has led to too little emphasis upon the effects of organisms on their environment, for instance, colonization and invasions. The term "adaptive zone" was coined by the paleontologist George Gaylord Simpson to explain how a population could jump from one niche to another that suited it, jump to an 'adaptive zone', made available by virtue of some modification, or possibly a change in the food chain, that made the adaptive zone available to it without a discontinuity in its way of life because the group was 'pre-adapted' to the new ecological opportunity. Hutchinson's "niche" (a description of the ecological space occupied by a species) is subtly different from the "niche" as defined by Grinnell (an ecological role, that may or may not be actually filled by a species—see vacant niches). A niche is a very specific segment of ecospace occupied by a single species. On the presumption that no two species are identical in all respects (called Hardin's 'axiom of inequality') and the competitive exclusion principle, some resource or adaptive dimension will provide a niche specific to each species. Species can however share a 'mode of life' or 'autecological strategy' which are broader definitions of ecospace. For example, Australian grasslands species, though different from those of the Great Plains grasslands, exhibit similar modes of life. Once a
|
{
"page_id": 67244,
"source": null,
"title": "Ecological niche"
}
|
niche is left vacant, other organisms can fill that position. For example, the niche that was left vacant by the extinction of the tarpan has been filled by other animals (in particular a small horse breed, the konik). Also, when plants and animals are introduced into a new environment, they have the potential to occupy or invade the niche or niches of native organisms, often outcompeting the indigenous species. Introduction of non-indigenous species to non-native habitats by humans often results in biological pollution by the exotic or invasive species. The mathematical representation of a species' fundamental niche in ecological space, and its subsequent projection back into geographic space, is the domain of niche modelling. == Contemporary niche theory == Contemporary niche theory (also called "classic niche theory" in some contexts) is a framework that was originally designed to reconcile different definitions of niches (see Grinnellian, Eltonian, and Hutchinsonian definitions above), and to help explain the underlying processes that affect Lotka–Volterra relationships within an ecosystem. The framework centers around "consumer-resource models" which largely split a given ecosystem into resources (e.g. sunlight or available water in soil) and consumers (e.g. any living thing, including plants and animals), and attempts to define the scope of possible relationships that could exist between the two groups. In contemporary niche theory, the "impact niche" is defined as the combination of effects that a given consumer has on both a). the resources that it uses, and b). the other consumers in the ecosystem. Therefore, the impact niche is equivalent to the Eltonian niche since both concepts are defined by the impact of a given species on its environment. The range of environmental conditions where a species can successfully survive and reproduce (i.e. the Hutchinsonian definition of a realized niche) is also encompassed under contemporary niche theory, termed
|
{
"page_id": 67244,
"source": null,
"title": "Ecological niche"
}
|
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