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Monday, April 17, 2017

Symbiosis

From Wikipedia, the free encyclopedia
 
In a symbiotic mutualistic relationship, the clownfish feeds on small invertebrates that otherwise have potential to harm the sea anemone, and the fecal matter from the clownfish provides nutrients to the sea anemone. The clownfish is additionally protected from predators by the anemone's stinging cells, to which the clownfish is immune. The clownfish also emits a high pitched sound that deters butterfly fish, which would otherwise eat the anemone.[1]

Symbiosis (from Greek συμβίωσις "living together", from σύν "together" and βίωσις "living")[2] is any type of a close and long-term biological interaction between two different species, be it mutualistic, commensalistic, or parasitic. In 1879, Heinrich Anton de Bary defined it as "the living together of unlike organisms."

Symbiosis can be obligatory, which means that one or both of the symbionts entirely depend on each other for survival, or facultative (optional) when they can generally live independently.

Symbiosis is also classified by physical attachment; symbiosis in which the organisms have bodily union is called conjunctive symbiosis, and symbiosis in which they are not in union is called disjunctive symbiosis.[3] When one organism lives on another such as mistletoe, it is called ectosymbiosis, or endosymbiosis when one partner lives inside the tissues of another, as in Symbiodinium in corals.[4][5]

Definition

In 1877, Albert Bernhard Frank used the term symbiosis which previously had been used to depict people living together in community to describe the mutualistic relationship in lichens.[6] In 1879, the German mycologist Heinrich Anton de Bary defined it as "the living together of unlike organisms."[7][8] The definition has varied among scientists with some advocating that it should only refer to persistent mutualisms, while others thought it should apply to any type of persistent biological interaction in other words mutualistic, commensalistic, or parasitic.[9]
After 130 years of debate,[10] current biology and ecology textbooks use the latter "de Bary" definition or an even broader definition where symbiosis means all species interactions, and the restrictive definition where symbiosis means only mutualism is no longer used.[11]

Obligate versus facultative

Symbiotic relationships can be obligate, meaning that one or both of the symbionts entirely depend on each other for survival. For example, in lichens, which consist of fungal and photosynthetic symbionts, the fungal partners cannot live on their own.[7][12][13][14] The algal or cyanobacterial symbionts in lichens, such as Trentepohlia, can generally live independently, and their symbiosis is, therefore, facultative (optional).[citation needed]

Physical interaction

Alder tree root nodule

Endosymbiosis is any symbiotic relationship in which one symbiont lives within the tissues of the other, either within the cells or extracellularly.[5][15] Examples include diverse microbiomes, rhizobia, nitrogen-fixing bacteria that live in root nodules on legume roots; actinomycete nitrogen-fixing bacteria called Frankia, which live in alder root nodules; single-celled algae inside reef-building corals; and bacterial endosymbionts that provide essential nutrients to about 10%–15% of insects.[citation needed]

Ectosymbiosis, also referred to as exosymbiosis, is any symbiotic relationship in which the symbiont lives on the body surface of the host, including the inner surface of the digestive tract or the ducts of exocrine glands.[5][16] Examples of this include ectoparasites such as lice, commensal ectosymbionts such as the barnacles which attach themselves to the jaw of baleen whales, and mutualist ectosymbionts such as cleaner fish.

Mutualism

Hermit crab, Calcinus laevimanus, with sea anemone.

Mutualism or interspecies reciprocal altruism is a relationship between individuals of different species where both individuals benefit.[17] In general, only lifelong interactions involving close physical and biochemical contact can properly be considered symbiotic. Mutualistic relationships may be either obligate for both species, obligate for one but facultative for the other, or facultative for both.
Bryoliths document a mutualistic symbiosis between a hermit crab and encrusting bryozoans; Banc d'Arguin, Mauritania

A large percentage of herbivores have mutualistic gut flora to help them digest plant matter, which is more difficult to digest than animal prey.[4] This gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores' intestines.[18] Coral reefs are the result of mutualisms between coral organisms and various types of algae which live inside them.[19] Most land plants and land ecosystems rely on mutualisms between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting water and minerals from the ground.[20]

An example of mutual symbiosis is the relationship between the ocellaris clownfish that dwell among the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clownfish from its predators. A special mucus on the clownfish protects it from the stinging tentacles.[21]

A further example is the goby fish, which sometimes lives together with a shrimp. The shrimp digs and cleans up a burrow in the sand in which both the shrimp and the goby fish live. The shrimp is almost blind, leaving it vulnerable to predators when outside its burrow. In case of danger the goby fish touches the shrimp with its tail to warn it. When that happens both the shrimp and goby fish quickly retreat into the burrow.[22] Different species of gobies (Elacatinus spp.) also exhibit mutualistic behavior through cleaning up ectoparasites in other fish.[23]

Another non-obligate symbiosis is known from encrusting bryozoans and hermit crabs. The bryozoan colony (Acanthodesia commensale) develops a cirumrotatory growth and offers the crab (Pseudopagurus granulimanus) a helicospiral-tubular extension of its living chamber that initially was situated within a gastropod shell.[24]

A spectacular examples of obligate mutualism is between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps. The worm has no digestive tract and is wholly reliant on its internal symbionts for nutrition. The bacteria oxidize either hydrogen sulfide or methane, which the host supplies to them. These worms were discovered in the late 1980s at the hydrothermal vents near the Galapagos Islands and have since been found at deep-sea hydrothermal vents and cold seeps in all of the world's oceans.[25]

There are many types of tropical and sub-tropical ants that have evolved very complex relationships with certain tree species.[26]

Mutualism and endosymbiosis

During mutualistic symbioses, the host cell lacks some of the nutrients which the endosymbiont provides. As a result, the host favors endosymbiont's growth processes within itself by producing some specialized cells. These cells affect the genetic composition of the host in order to regulate the increasing population of the endosymbionts and ensure that these genetic changes are passed onto the offspring via vertical transmission (heredity).[27]

As the endosymbiont adapts to the host's lifestyle the endosymbiont changes dramatically. There is a drastic reduction in its genome size, as many genes are lost during the process of metabolism, and DNA repair and recombination, while important genes participating in the DNA to RNA transcription, protein translation and DNA/RNA replication are retained. The decrease in genome size is due to loss of protein coding genes and not due to lessening of inter-genic regions or open reading frame (ORF) size. Species that are naturally evolving and contain reduced sizes of genes can be accounted for an increased number of noticeable differences between them, thereby leading to changes in their evolutionary rates. When endosymbiotic bacteria related with insects are passed on to the offspring strictly via vertical genetic transmission, intracellular bacteria go across many hurdles during the process, resulting in the decrease in effective population sizes, as compared to the free living bacteria. The incapability of the endosymbiotic bacteria to reinstate their wild type phenotype via a recombination process is called Muller's ratchet phenomenon. Muller's ratchet phenomenon together with less effective population sizes leads to an accretion of deleterious mutations in the non-essential genes of the intracellular bacteria.[28] This can be due to lack of selection mechanisms prevailing in the relatively "rich" host environment.[29][30]

Commensalism

Phoretic mites on a fly (Pseudolynchia canariensis).

Commensalism describes a relationship between two living organisms where one benefits and the other is not significantly harmed or helped. It is derived from the English word commensal, which is used of human social interaction. The word derives from the medieval Latin word, formed from com- and mensa, meaning "sharing a table."[17][31]

Commensal relationships may involve one organism using another for transportation (phoresy) or for housing (inquilinism), or it may also involve one organism using something another created, after its death (metabiosis). Examples of metabiosis are hermit crabs using gastropod shells to protect their bodies and spiders building their webs on plants.

Parasitism

Flea bites on a human is an example of parasitism.

A parasitic relationship is one in which one member of the association benefits while the other is harmed.[32] This is also known as antagonistic or antipathetic symbiosis.[3] Parasitic symbioses take many forms, from endoparasites that live within the host's body to ectoparasites that live on its surface. In addition, parasites may be necrotrophic, which is to say they kill their host, or biotrophic, meaning they rely on their host's surviving. Biotrophic parasitism is an extremely successful mode of life. Depending on the definition used, as many as half of all animals have at least one parasitic phase in their life cycles, and it is also frequent in plants and fungi. Moreover, almost all free-living animals are host to one or more parasite taxa. An example of a biotrophic relationship would be a tick feeding on the blood of its host.

Amensalism

Amensalism is the type of relationship that exists where one species is inhibited or completely obliterated and one is unaffected by the other. There are two types of amensalism, competition and antibiosis. Competition is where a larger or stronger organism deprives a smaller or weaker one from a resource. Antibiosis occurs when one organism is damaged or killed by another through a chemical secretion. An example of competition is a sapling growing under the shadow of a mature tree. The mature tree can rob the sapling of necessary sunlight and, if the mature tree is very large, it can take up rainwater and deplete soil nutrients. Throughout the process, the mature tree is unaffected by the sapling. Indeed, if the sapling dies, the mature tree gains nutrients from the decaying sapling. Note that these nutrients become available because of the sapling's decomposition, rather than from the living sapling, which would be a case of parasitism.[citation needed] An example of antibiosis is Juglans nigra (black walnut), secreting juglone, a substance which destroys many herbaceous plants within its root zone.[33]
Amensalism is an interaction where an organism inflicts harm to another organism without any costs or benefits to the perpetrator.[34] A clear case of amensalism is where sheep or cattle trample grass. Whilst the presence of the grass causes negligible detrimental effects to the animal's hoof, the grass suffers from being crushed. Amensalism is often used to describe strongly asymmetrical competitive interactions, such as has been observed between the Spanish ibex and weevils of the genus Timarcha which feed upon the same type of shrub. Whilst the presence of the weevil has almost no influence on food availability, the presence of ibex has an enormous detrimental effect on weevil numbers, as they consume significant quantities of plant matter and incidentally ingest the weevils upon it.[35]

Synnecrosis

Synnecrosis is a rare type of symbiosis in which the interaction between species is detrimental to both organisms involved.[3] It is a short-lived condition, as the interaction eventually causes death. Because of this, evolution selects against synnecrosis and it is uncommon in nature. An example of this is the relationship between some species of bees and victims of the bee sting. Species of bees who die after stinging their prey inflict pain on themselves (albeit to protect the hive) as well as on the victim. This term is rarely used.[36]

Evolution

Leafhoppers protected by meat ants

While historically, symbiosis has received less attention than other interactions such as predation or competition,[37] it is increasingly recognized as an important selective force behind evolution,[4][38] with many species having a long history of interdependent co-evolution.[39] In fact, the evolution of all eukaryotes (plants, animals, fungi, and protists) is believed under the endosymbiotic theory to have resulted from a symbiosis between various sorts of bacteria.[4][40][41] This theory is supported by certain organelles dividing independently of the cell, and the observation that some organelles seem to have their own nucleic acid.[42]

Vascular plants

About 80% of vascular plants worldwide form symbiotic relationships with fungi, for example, in arbuscular mycorrhizas.[43]

Symbiogenesis

The biologist Lynn Margulis, famous for her work on endosymbiosis, contends that symbiosis is a major driving force behind evolution. She considers Darwin's notion of evolution, driven by competition, to be incomplete and claims that evolution is strongly based on co-operation, interaction, and mutual dependence among organisms. According to Margulis and Dorion Sagan, "Life did not take over the globe by combat, but by networking."[44]

Co-evolution

Symbiosis played a major role in the co-evolution of flowering plants and the animals that pollinate them. Many plants that are pollinated by insects, bats, or birds have highly specialized flowers modified to promote pollination by a specific pollinator that is also correspondingly adapted. The first flowering plants in the fossil record had relatively simple flowers. Adaptive speciation quickly gave rise to many diverse groups of plants, and, at the same time, corresponding speciation occurred in certain insect groups. Some groups of plants developed nectar and large sticky pollen, while insects evolved more specialized morphologies to access and collect these rich food sources. In some taxa of plants and insects the relationship has become dependent,[45] where the plant species can only be pollinated by one species of insect.[46]

Sunday, April 16, 2017

Geological history of oxygen

From Wikipedia, the free encyclopedia
 
O2 build-up in the Earth's atmosphere. Red and green lines represent the range of the estimates while time is measured in billions of years ago (Ga).
Stage 1 (3.85–2.45 Ga): Practically no O2 in the atmosphere.
Stage 2 (2.45–1.85 Ga): O2 produced, but absorbed in oceans and seabed rock.
Stage 3 (1.85–0.85 Ga): O2 starts to gas out of the oceans, but is absorbed by land surfaces and formation of ozone layer.
Stages 4 and 5 (0.85 Ga–present): O2 sinks filled, the gas accumulates.[1]

Before photosynthesis evolved, Earth's atmosphere had no free oxygen (O2).[2] Photosynthetic prokaryotic organisms that produced O2 as a waste product lived long before the first build-up of free oxygen in the atmosphere,[3] perhaps as early as 3.5 billion years ago. The oxygen they produced would have been rapidly removed from the atmosphere by weathering of reducing minerals, most notably iron. This "mass rusting" led to the deposition of iron oxide on the ocean floor, forming banded iron formations. Oxygen only began to persist in the atmosphere in small quantities about 50 million years before the start of the Great Oxygenation Event.[4] This mass oxygenation of the atmosphere resulted in rapid buildup of free oxygen. At current rates of primary production, today's concentration of oxygen could be produced by photosynthetic organisms in 2,000 years.[5] In the absence of plants, the rate of oxygen production by photosynthesis was slower in the Precambrian, and the concentrations of O2 attained were less than 10% of today's and probably fluctuated greatly; oxygen may even have disappeared from the atmosphere again around 1.9 billion years ago.[6] These fluctuations in oxygen concentration had little direct effect on life,[citation needed] with mass extinctions not observed until the appearance of complex life around the start of the Cambrian period, 541 million years ago.[7] The presence of O
2
provided life with new opportunities. Aerobic metabolism is more efficient than anaerobic pathways, and the presence of oxygen undoubtedly created new possibilities for life to explore.[8]:214, 586[9] Since the start of the Cambrian period, atmospheric oxygen concentrations have fluctuated between 15% and 35% of atmospheric volume.[10] The maximum of 35% was reached towards the end of the Carboniferous period (about 300 million years ago), a peak which may have contributed to the large size of insects and amphibians at that time.[9] Whilst human activities, such as the burning of fossil fuels, affect relative carbon dioxide concentrations, their effect on the much larger concentration of oxygen is less significant.[11]

Effects on life

The concentration of oxygen in the atmosphere is often cited as a possible contributor to large-scale evolutionary phenomena, such as the origin of the multicellular Ediacara biota, the Cambrian explosion, trends in animal body size, and other extinction and diversification events.[9]

The large size of insects and amphibians in the Carboniferous period, when the oxygen concentration in the atmosphere reached 35%, has been attributed to the limiting role of diffusion in these organisms' metabolism.[citation needed] But Haldane's essay[12] points out that it would only apply to insects. However, the biological basis for this correlation is not firm, and many lines of evidence show that oxygen concentration is not size-limiting in modern insects.[9] There is no significant correlation between atmospheric oxygen and maximum body size elsewhere in the geological record.[9] Ecological constraints can better explain the diminutive size of post-Carboniferous dragonflies - for instance, the appearance of flying competitors such as pterosaurs, birds and bats.[9]

Rising oxygen concentrations have been cited as a driver for evolutionary diversification, although the physiological arguments behind such arguments are questionable, and a consistent pattern between oxygen concentrations and the rate of evolution is not clearly evident.[9] The most celebrated link between oxygen and evolution occurs at the end of the last of the Snowball glaciations, where complex multicellular life is first found in the fossil record. Under low oxygen concentrations and before the evolution of nitrogen fixation, biologically-available nitrogen compounds were in limited supply [13] and periodic "nitrogen crises" could render the ocean inhospitable to life.[9] Significant concentrations of oxygen were just one of the prerequisites for the evolution of complex life.[9] Models based on uniformitarian principles (i.e. extrapolating present-day ocean dynamics into deep time) suggest that such a concentration was only reached immediately before metazoa first appeared in the fossil record.[9] Further, anoxic or otherwise chemically "nasty" oceanic conditions that resemble those supposed to inhibit macroscopic life re-occur at intervals through the early Cambrian, and also in the late Cretaceous – with no apparent effect on lifeforms at these times.[9] This might suggest that the geochemical signatures found in ocean sediments reflect the atmosphere in a different way before the Cambrian - perhaps as a result of the fundamentally different mode of nutrient cycling in the absence of planktivory.[7][9]

Friday, April 14, 2017

Action at a distance

In physics, action at a distance is the concept that an object can be moved, changed, or otherwise affected without being physically touched (as in mechanical contact) by another object. That is, it is the nonlocal interaction of objects that are separated in space. Pioneering physicist Albert Einstein described the phenomenon as "spooky action at a distance".[1]

This term was used most often in the context of early theories of gravity and electromagnetism to describe how an object responds to the influence of distant objects. For example, Coulomb's law and the law of universal gravitation are such early theories.

More generally "action at a distance" describes the failure of early atomistic and mechanistic theories which sought to reduce all physical interaction to collision. The exploration and resolution of this problematic phenomenon led to significant developments in physics, from the concept of a field, to descriptions of quantum entanglement and the mediator particles of the Standard Model.[2]

Electricity and magnetism

Efforts to account for action at a distance in the theory of electromagnetism led to the development of the concept of a field which mediated interactions between currents and charges across empty space.

According to field theory we account for the Coulomb (electrostatic) interaction between charged particles through the fact that charges produce around themselves an electric field, which can be felt by other charges as a force. Maxwell directly addressed the subject of action-at-a-distance in chapter 23 of his A Treatise on Electricity and Magnetism in 1873.[3] He began by reviewing the explanation of Ampere's formula given by Gauss and Weber. On page 437 he indicates the physicists' disgust with action at a distance. In 1845 Gauss wrote to Weber desiring "action, not instantaneous, but propagated in time in a similar manner to that of light." This aspiration was developed by Maxwell with the theory of an electromagnetic field described by Maxwell's equations, which used the field to elegantly account for all electromagnetic interactions, as well as light (which, until then, had been seen as a completely unrelated phenomenon). In Maxwell's theory, the field is its own physical entity, carrying momenta and energy across space, and action-at-a-distance is only the apparent effect of local interactions of charges with their surrounding field.

Electrodynamics was later described without fields (in Minkowski space) as the direct interaction of particles with lightlike separation vectors[dubious ]. This resulted in the Fokker-Tetrode-Schwarzschild action integral. This kind of electrodynamic theory is often called "direct interaction" to distinguish it from field theories where action at a distance is mediated by a localized field (localized in the sense that its dynamics are determined by the nearby field parameters).[4] This description of electrodynamics, in contrast with Maxwell's theory, explains apparent action at a distance not by postulating a mediating entity (the field) but by appealing to the natural geometry of special relativity.

Direct interaction electrodynamics is explicitly symmetrical in time, and avoids the infinite energy predicted in the field immediately surrounding point particles. Feynman and Wheeler have shown that it can account for radiation and radiative damping (which had been considered strong evidence for the independent existence of the field). However various proofs, beginning with that of Dirac have shown that direct interaction theories (under reasonable assumptions) do not admit Lagrangian or Hamiltonian formulations (these are the so-called No Interaction Theorems). Also significant is the measurement and theoretical description of the Lamb shift which strongly suggests that charged particles interact with their own field. Fields, because of these and other difficulties, have been elevated to the fundamental operators in QFT and modern physics has thus largely abandoned direct interaction theory.

Gravity

Newton

Newton's theory of gravity offered no prospect of identifying any mediator of gravitational interaction. His theory assumed that gravitation acts instantaneously, regardless of distance. Kepler's observations gave strong evidence that in planetary motion angular momentum is conserved. (The mathematical proof is only valid in the case of a Euclidean geometry.) Gravity is also known as a force of attraction between two objects because of their mass.

From a Newtonian perspective, action at a distance can be regarded as: "a phenomenon in which a change in intrinsic properties of one system induces a change in the intrinsic properties of a distant system, independently of the influence of any other systems on the distant system, and without there being a process that carries this influence contiguously in space and time" (Berkovitz 2008).[5]

A related question, raised by Ernst Mach, was how rotating bodies know how much to bulge at the equator. This, it seems, requires an action-at-a-distance from distant matter, informing the rotating object about the state of the universe. Einstein coined the term Mach's principle for this question.
It is inconceivable that inanimate Matter should, without the Mediation of something else, which is not material, operate upon, and affect other matter without mutual Contact…That Gravity should be innate, inherent and essential to Matter, so that one body may act upon another at a distance thro' a Vacuum, without the Mediation of any thing else, by and through which their Action and Force may be conveyed from one to another, is to me so great an Absurdity that I believe no Man who has in philosophical Matters a competent Faculty of thinking can ever fall into it. Gravity must be caused by an Agent acting constantly according to certain laws; but whether this Agent be material or immaterial, I have left to the Consideration of my readers.[5]
— Isaac Newton, Letters to Bentley, 1692/3

Einstein

According to Albert Einstein's theory of special relativity, instantaneous action at a distance was seen to violate the relativistic upper limit on speed of propagation of information. If one of the interacting objects were to suddenly be displaced from its position, the other object would feel its influence instantaneously, meaning information had been transmitted faster than the speed of light.

One of the conditions that a relativistic theory of gravitation must meet is to be mediated with a speed that does not exceed c, the speed of light in a vacuum. It could be seen from the previous success of electrodynamics that the relativistic theory of gravitation would have to use the concept of a field or something similar.

This problem has been resolved by Einstein's theory of general relativity in which gravitational interaction is mediated by deformation of space-time geometry. Matter warps the geometry of space-time and these effects are, as with electric and magnetic fields, propagated at the speed of light. Thus, in the presence of matter, space-time becomes non-Euclidean, resolving the apparent conflict between Newton's proof of the conservation of angular momentum and Einstein's theory of special relativity. Mach's question regarding the bulging of rotating bodies is resolved because local space-time geometry is informing a rotating body about the rest of the universe. In Newton's theory of motion, space acts on objects, but is not acted upon. In Einstein's theory of motion, matter acts upon space-time geometry, deforming it, and space-time geometry acts upon matter, by affecting the behavior of geodesics.

Gravitational waves were first detected by the Advanced LIGO on 14 September 2015, finally giving scientific measurements to validate this 100-year old theory.[6]

Quantum mechanics

Since the early twentieth century, quantum mechanics has posed new challenges for the view that physical processes should obey locality. Whether quantum entanglement counts as action-at-a-distance hinges on the nature of the wave function and decoherence, issues over which there is still considerable debate among scientists and philosophers. One important line of debate originated with Einstein, who challenged the idea that quantum mechanics offers a complete description of reality, along with Boris Podolsky and Nathan Rosen. They proposed a thought experiment involving an entangled pair of observables with non-commuting operators (e.g. position and momentum).[7]
This thought experiment, which came to be known as the EPR paradox, hinges on the principle of locality. A common presentation of the paradox is as follows: two particles interact and fly off in opposite directions. Even when the particles are so far apart that any classical interaction would be impossible (see principle of locality), a measurement of one particle nonetheless determines the corresponding result of a measurement of the other.

After the EPR paper, several scientists such as de Broglie studied local hidden variables theories. In the 1960s John Bell derived an inequality that indicated a testable difference between the predictions of quantum mechanics and local hidden variables theories.[8] To date, all experiments testing Bell-type inequalities in situations analogous to the EPR thought experiment have results consistent with the predictions of quantum mechanics, suggesting that local hidden variables theories can be ruled out. Whether or not this is interpreted as evidence for nonlocality depends on one's interpretation of quantum mechanics.[5]

Non-standard interpretations of quantum mechanics vary in their response to the EPR-type experiments. The Bohm interpretation gives an explanation based on nonlocal hidden variables for the correlations seen in entanglement. Many advocates of the many-worlds interpretation argue that it can explain these correlations in a way that does not require a violation of locality,[9] by allowing measurements to have non-unique outcomes.