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Ecology

Ecology is the natural science of the relationships among living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere levels. Ecology overlaps with the closely related sciences of biogeography, evolutionary biology, genetics, ethology, and natural history. Ecology is a branch of biology, and is the study of abundance, biomass, and distribution of organisms in the context of the environment. It encompasses life processes, interactions, and adaptations; movement of materials and energy through living communities; successional development of ecosystems; cooperation, competition, and predation within and between species; and patterns of biodiversity and its effect on ecosystem processes. Ecology has practical applications in conservation biology, wetland management, natural resource management (agroecology, agriculture, forestry, agroforestry, fisheries, mining, tourism), urban planning (urban ecology), community health, economics, basic and applied science, and human social interaction (human ecology). The word ecology was coined in 1866 by the German scientist Ernst Haeckel. The science of ecology as we know it today began with a group of American botanists in the 1890s. Evolutionary concepts relating to adaptation and natural selection are cornerstones of modern ecological theory. Ecosystems are dynamically interacting systems of organisms, the communities they make up, and the non-living (abiotic) components of their environment. Ecosystem processes, such as primary production, nutrient cycling, and niche construction, regulate the flux of energy and matter through an environment. Ecosystems have biophysical feedback mechanisms that moderate processes acting on living (biotic) and abiotic components of the planet. Ecosystems sustain life-supporting functions and provide ecosystem services like biomass production (food, fuel, fiber, and medicine), the regulation of climate, global biogeochemical cycles, water filtration, soil formation, erosion control, flood protection, and many other natural features of scientific, historical, economic, or intrinsic value. Levels, scope, and scale of organization The scope of ecology contains a wide array of interacting levels of organization spanning micro-level (e.g., cells) to a planetary scale (e.g., biosphere) phenomena. Ecosystems, for example, contain abiotic resources and interacting life forms (i.e., individual organisms that aggregate into populations which aggregate into distinct ecological communities). Because ecosystems are dynamic and do not necessarily follow a linear successional route, changes might occur quickly or slowly over thousands of years before specific forest successional stages are brought about by biological processes. An ecosystem's area can vary greatly, from tiny to vast. A single tree is of little consequence to the classification of a forest ecosystem, but is critically relevant to organisms living in and on it. Several generations of an aphid population can exist over the lifespan of a single leaf. Each of those aphids, in turn, supports diverse bacterial communities. The nature of connections in ecological communities cannot be explained by knowing the details of each species in isolation, because the emergent pattern is neither revealed nor predicted until the ecosystem is studied as an integrated whole. Some ecological principles, however, do exhibit collective properties where the sum of the components explain the properties of the whole, such as birth rates of a population being equal to the sum of individual births over a designated time frame. The main subdisciplines of ecology, population (or community) ecology and ecosystem ecology, exhibit a difference not only in scale but also in two contrasting paradigms in the field. The former focuses on organisms' distribution and abundance, while the latter focuses on materials and energy fluxes. Hierarchy The scale of ecological dynamics can operate like a closed system, such as aphids migrating on a single tree, while at the same time remaining open about broader scale influences, such as atmosphere or climate. Hence, ecologists classify ecosystems hierarchically by analyzing data collected from finer scale units, such as vegetation associations, climate, and soil types, and integrate this information to identify emergent patterns of uniform organization and processes that operate on local to regional, landscape, and chronological scales. To structure the study of ecology into a conceptually manageable framework, the biological world is organized into a nested hierarchy, ranging in scale from genes, to cells, to tissues, to organs, to organisms, to species, to populations, to guilds, to communities, to ecosystems, to biomes, and up to the level of the biosphere. This framework forms a panarchy and exhibits non-linear behaviors; this means that "effect and cause are disproportionate, so that small changes to critical variables, such as the number of nitrogen fixers, can lead to disproportionate, perhaps irreversible, changes in the system properties." Biodiversity Biodiversity (an abbreviation of "biological diversity") describes the diversity of life from genes to ecosystems and spans every level of biological organization. The term has several interpretations, and there are many ways to index, measure, characterize, and represent its complex organization. Biodiversity includes species diversity, ecosystem diversity, and genetic diversity and scientists are interested in the way that this diversity affects the complex ecological processes operating at and among these respective levels. Biodiversity plays an important role in ecosystem services which by definition maintain and improve human quality of life. Conservation priorities and management techniques require different approaches and considerations to address the full ecological scope of biodiversity. Natural capital that supports populations is critical for maintaining ecosystem services and species migration (e.g., riverine fish runs and avian insect control) has been implicated as one mechanism by which those service losses are experienced. An understanding of biodiversity has practical applications for species and ecosystem-level conservation planners as they make management recommendations to consulting firms, governments, and industry. Habitat The habitat of a species describes the environment over which a species is known to occur and the type of community that is formed as a result. More specifically, "habitats can be defined as regions in environmental space that are composed of multiple dimensions, each representing a biotic or abiotic environmental variable; that is, any component or characteristic of the environment related directly (e.g. forage biomass and quality) or indirectly (e.g. elevation) to the use of a location by the animal." For example, a habitat might be an aquatic or terrestrial environment that can be further categorized as a montane or alpine ecosystem. Habitat shifts provide important evidence of competition in nature where one population changes relative to the habitats that most other individuals of the species occupy. For example, one population of a species of tropical lizard (Tropidurus hispidus) has a flattened body relative to the main populations that live in open savanna. The population that lives in an isolated rock outcrop hides in crevasses where its flattened body offers a selective advantage. Habitat shifts also occur in the developmental life history of amphibians, and in insects that transition from aquatic to terrestrial habitats. Biotope and habitat are sometimes used interchangeably, but the former applies to a community's environment, whereas the latter applies to a species' environment. Niche Definitions of the niche date back to 1917, but G. Evelyn Hutchinson made conceptual advances in 1957 by introducing a widely adopted definition: "the set of biotic and abiotic conditions in which a species is able to persist and maintain stable population sizes." The ecological niche is a central concept in the ecology of organisms and is sub-divided into the fundamental and the realized niche. The fundamental niche is the set of environmental conditions under which a species is able to persist. The realized niche is the set of environmental plus ecological conditions under which a species persists. The Hutchinsonian niche is defined more technically as a "Euclidean hyperspace whose dimensions are defined as environmental variables and whose size is a function of the number of values that the environmental values may assume for which an organism has positive fitness." Biogeographical patterns and range distributions are explained or predicted through knowledge of a species' traits and niche requirements. Species have functional traits that are uniquely adapted to the ecological niche. A trait is a measurable property, phenotype, or characteristic of an organism that may influence its survival. Genes play an important role in the interplay of development and environmental expression of traits. Resident species evolve traits that are fitted to the selection pressures of their local environment. This tends to afford them a competitive advantage and discourages similarly adapted species from having an overlapping geographic range. The competitive exclusion principle states that two species cannot coexist indefinitely by living off the same limiting resource; one will always out-compete the other. When similarly adapted species overlap geographically, closer inspection reveals subtle ecological differences in their habitat or dietary requirements. Some models and empirical studies, however, suggest that disturbances can stabilize the co-evolution and shared niche occupancy of similar species inhabiting species-rich communities. The habitat plus the niche is called the ecotope, which is defined as the full range of environmental and biological variables affecting an entire species. Niche construction Organisms are subject to environmental pressures, but they also modify their habitats. The regulatory feedback between organisms and their environment can affect conditions from local (e.g., a beaver pond) to global scales, over time and even after death, such as decaying logs or silica skeleton deposits from marine organisms. The process and concept of ecosystem engineering are related to niche construction, but the former relates only to the physical modifications of the habitat whereas the latter also considers the evolutionary implications of physical changes to the environment and the feedback this causes on the process of natural selection. Ecosystem engineers are defined as: "organisms that directly or indirectly modulate the availability of resources to other species, by causing physical state changes in biotic or abiotic materials. In so doing they modify, maintain and create habitats." The ecosystem engineering concept has stimulated a new appreciation for the influence that organisms have on the ecosystem and evolutionary process. The term "niche construction" is more often used in reference to the under-appreciated feedback mechanisms of natural selection imparting forces on the abiotic niche. An example of natural selection through ecosystem engineering occurs in the nests of social insects, including ants, bees, wasps, and termites. There is an emergent homeostasis or homeorhesis in the structure of the nest that regulates, maintains and defends the physiology of the entire colony. Termite mounds, for example, maintain a constant internal temperature through the design of air-conditioning chimneys. The structure of the nests themselves is subject to the forces of natural selection. Moreover, a nest can survive over successive generations, so that progeny inherit both genetic material and a legacy niche that was constructed before their time. Biome Biomes are larger units of organization that categorize regions of the Earth's ecosystems, mainly according to the structure and composition of vegetation. There are different methods to define the continental boundaries of biomes dominated by different functional types of vegetative communities that are limited in distribution by climate, precipitation, weather, and other environmental variables. Biomes include tropical rainforest, temperate broadleaf and mixed forest, temperate deciduous forest, taiga, tundra, hot desert, and polar desert. Other researchers have recently categorized other biomes, such as the human and oceanic microbiomes. To a microbe, the human body is a habitat and a landscape. Microbiomes were discovered largely through advances in molecular genetics, which have revealed a hidden richness of microbial diversity on the planet. The oceanic microbiome plays a significant role in the ecological biogeochemistry of the planet's oceans. Biosphere The largest scale of ecological organization is the biosphere: the total sum of ecosystems on the planet. Ecological relationships regulate the flux of energy, nutrients, and climate all the way up to the planetary scale. For example, the dynamic history of the planetary atmosphere's CO2 and O2 composition has been affected by the biogenic flux of gases coming from respiration and photosynthesis, with levels fluctuating over time in relation to the ecology and evolution of plants and animals. Ecological theory has also been used to explain self-emergent regulatory phenomena at the planetary scale: for example, the Gaia hypothesis is an example of holism applied in ecological theory. The Gaia hypothesis states that there is an emergent feedback loop generated by the metabolism of living organisms that maintains the core temperature of the Earth and atmospheric conditions within a narrow self-regulating range of tolerance. Population ecology Population ecology studies the dynamics of species populations and how these populations interact with the wider environment. A population consists of individuals of the same species that live, interact, and migrate through the same niche and habitat. A primary law of population ecology is the Malthusian growth model which states, "a population will grow (or decline) exponentially as long as the environment experienced by all individuals in the population remains constant." Simplified population models usually starts with four variables: death, birth, immigration, and emigration. An example of an introductory population model describes a closed population, such as on an island, where immigration and emigration does not take place. Hypotheses are evaluated with reference to a null hypothesis which states that random processes create the observed data. In these island models, the rate of population change is described by: where N is the total number of individuals in the population, b and d are the per capita rates of birth and death respectively, and r is the per capita rate of population change. Using these modeling techniques, Malthus' population principle of growth was later transformed into a model known as the logistic equation by Pierre Verhulst: where N(t) is the number of individuals measured as biomass density as a function of time, t, r is the maximum per-capita rate of change commonly known as the intrinsic rate of growth, and is the crowding coefficient, which represents the reduction in population growth rate per individual added. The formula states that the rate of change in population size will grow to approach equilibrium, where, when the rates of increase and crowding are balanced, . A common, analogous model fixes the equilibrium, as K, which is known as the "carrying capacity." Population ecology builds upon these introductory models to further understand demographic processes in real study populations. Commonly used types of data include life history, fecundity, and survivorship, and these are analyzed using mathematical techniques such as matrix algebra. The information is used for managing wildlife stocks and setting harvest quotas. In cases where basic models are insufficient, ecologists may adopt different kinds of statistical methods, such as the Akaike information criterion, or use models that can become mathematically complex as "several competing hypotheses are simultaneously confronted with the data." Metapopulations and migration The concept of metapopulations was defined in 1969 as "a population of populations which go extinct locally and recolonize". Metapopulation ecology is another statistical approach that is often used in conservation research. Metapopulation models simplify the landscape into patches of varying levels of quality, and metapopulations are linked by the migratory behaviours of organisms. Animal migration is set apart from other kinds of movement because it involves the seasonal departure and return of individuals from a habitat. Migration is also a population-level phenomenon, as with the migration routes followed by plants as they occupied northern post-glacial environments. Plant ecologists use pollen records that accumulate and stratify in wetlands to reconstruct the timing of plant migration and dispersal relative to historic and contemporary climates. These migration routes involved an expansion of the range as plant populations expanded from one area to another. There is a larger taxonomy of movement, such as commuting, foraging, territorial behavior, stasis, and ranging. Dispersal is usually distinguished from migration because it involves the one-way permanent movement of individuals from their birth population into another population. In metapopulation terminology, migrating individuals are classed as emigrants (when they leave a region) or immigrants (when they enter a region), and sites are classed either as sources or sinks. A site is a generic term that refers to places where ecologists sample populations, such as ponds or defined sampling areas in a forest. Source patches are productive sites that generate a seasonal supply of juveniles that migrate to other patch locations. Sink patches are unproductive sites that only receive migrants; the population at the site will disappear unless rescued by an adjacent source patch or environmental conditions become more favorable. Metapopulation models examine patch dynamics over time to answer potential questions about spatial and demographic ecology. The ecology of metapopulations is a dynamic process of extinction and colonization. Small patches of lower quality (i.e., sinks) are maintained or rescued by a seasonal influx of new immigrants. A dynamic metapopulation structure evolves from year to year, where some patches are sinks in dry years and are sources when conditions are more favorable. Ecologists use a mixture of computer models and field studies to explain metapopulation structure. Community ecology Community ecology is the study of the interactions among a collection of species that inhabit the same geographic area. Community ecologists study the determinants of patterns and processes for two or more interacting species. Research in community ecology might measure species diversity in grasslands in relation to soil fertility. It might also include the analysis of predator-prey dynamics, competition among similar plant species, or mutualistic interactions between crabs and corals. Ecosystem ecology Ecosystems may be habitats within biomes that form an integrated whole and a dynamically responsive system having both physical and biological complexes. Ecosystem ecology is the science of determining the fluxes of materials (e.g. carbon, phosphorus) between different pools (e.g., tree biomass, soil organic material). Ecosystem ecologists attempt to determine the underlying causes of these fluxes. Research in ecosystem ecology might measure primary production (g C/m^2) in a wetland in relation to decomposition and consumption rates (g C/m^2/y). This requires an understanding of the community connections between plants (i.e., primary producers) and the decomposers (e.g., fungi and bacteria). The underlying concept of an ecosystem can be traced back to 1864 in the published work of George Perkins Marsh ("Man and Nature"). Within an ecosystem, organisms are linked to the physical and biological components of their environment to which they are adapted. Ecosystems are complex adaptive systems where the interaction of life processes form self-organizing patterns across different scales of time and space. Ecosystems are broadly categorized as terrestrial, freshwater, atmospheric, or marine. Differences stem from the nature of the unique physical environments that shapes the biodiversity within each. A more recent addition to ecosystem ecology are technoecosystems, which are affected by or primarily the result of human activity. Food webs A food web is the archetypal ecological network. Plants capture solar energy and use it to synthesize simple sugars during photosynthesis. As plants grow, they accumulate nutrients and are eaten by grazing herbivores, and the energy is transferred through a chain of organisms by consumption. The simplified linear feeding pathways that move from a basal trophic species to a top consumer is called the food chain. Food chains in an ecological community create a complex food web. Food webs are a type of concept map that is used to illustrate and study pathways of energy and material flows. Empirical measurements are generally restricted to a specific habitat, such as a cave or a pond, and principles gleaned from small-scale studies are extrapolated to larger systems. Feeding relations require extensive investigations, e.g. into the gut contents of organisms, which can be difficult to decipher, or stable isotopes can be used to trace the flow of nutrient diets and energy through a food web. Despite these limitations, food webs remain a valuable tool in understanding community ecosystems. Food webs illustrate important principles of ecology: some species have many weak feeding links (e.g., omnivores) while some are more specialized with fewer stronger feeding links (e.g., primary predators). Such linkages explain how ecological communities remain stable over time and eventually can illustrate a "complete" web of life. The disruption of food webs may have a dramatic impact on the ecology of individual species or whole ecosystems. For instance, the replacement of an ant species by another (invasive) ant species has been shown to affect how elephants reduce tree cover and thus the predation of lions on zebras. Trophic levels A trophic level (from Greek troph, τροφή, trophē, meaning "food" or "feeding") is "a group of organisms acquiring a considerable majority of its energy from the lower adjacent level (according to ecological pyramids) nearer the abiotic source." Links in food webs primarily connect feeding relations or trophism among species. Biodiversity within ecosystems can be organized into trophic pyramids, in which the vertical dimension represents feeding relations that become further removed from the base of the food chain up toward top predators, and the horizontal dimension represents the abundance or biomass at each level. When the relative abundance or biomass of each species is sorted into its respective trophic level, they naturally sort into a 'pyramid of numbers'. Species are broadly categorized as autotrophs (or primary producers), heterotrophs (or consumers), and Detritivores (or decomposers). Autotrophs are organisms that produce their own food (production is greater than respiration) by photosynthesis or chemosynthesis. Heterotrophs are organisms that must feed on others for nourishment and energy (respiration exceeds production). Heterotrophs can be further sub-divided into different functional groups, including primary consumers (strict herbivores), secondary consumers (carnivorous predators that feed exclusively on herbivores), and tertiary consumers (predators that feed on a mix of herbivores and predators). Omnivores do not fit neatly into a functional category because they eat both plant and animal tissues. It has been suggested that omnivores have a greater functional influence as predators because compared to herbivores, they are relatively inefficient at grazing. Trophic levels are part of the holistic or complex systems view of ecosystems. Each trophic level contains unrelated species that are grouped together because they share common ecological functions, giving a macroscopic view of the system. While the notion of trophic levels provides insight into energy flow and top-down control within food webs, it is troubled by the prevalence of omnivory in real ecosystems. This has led some ecologists to "reiterate that the notion that species clearly aggregate into discrete, homogeneous trophic levels is fiction." Nonetheless, recent studies have shown that real trophic levels do exist, but "above the herbivore trophic level, food webs are better characterized as a tangled web of omnivores." Keystone species A keystone species is a species that is connected to a disproportionately large number of other species in the food-web. Keystone species have lower levels of biomass in the trophic pyramid relative to the importance of their role. The many connections that a keystone species holds means that it maintains the organization and structure of entire communities. The loss of a keystone species results in a range of dramatic cascading effects (termed trophic cascades) that alters trophic dynamics, other food web connections, and can cause the extinction of other species. The term keystone species was coined by Robert Paine in 1969 and is a reference to the keystone architectural feature as the removal of a keystone species can result in a community collapse just as the removal of the keystone in an arch can result in the arch's loss of stability. Sea otters (Enhydra lutris) are commonly cited as an example of a keystone species because they limit the density of sea urchins that feed on kelp. If sea otters are removed from the system, the urchins graze until the kelp beds disappear, and this has a dramatic effect on community structure. Hunting of sea otters, for example, is thought to have led indirectly to the extinction of the Steller's sea cow (Hydrodamalis gigas). While the keystone species concept has been used extensively as a conservation tool, it has been criticized for being poorly defined from an operational stance. It is difficult to experimentally determine what species may hold a keystone role in each ecosystem. Furthermore, food web theory suggests that keystone species may not be common, so it is unclear how generally the keystone species model can be applied. Complexity Complexity is understood as a large computational effort needed to piece together numerous interacting parts exceeding the iterative memory capacity of the human mind. Global patterns of biological diversity are complex. This biocomplexity stems from the interplay among ecological processes that operate and influence patterns at different scales that grade into each other, such as transitional areas or ecotones spanning landscapes. Complexity stems from the interplay among levels of biological organization as energy, and matter is integrated into larger units that superimpose onto the smaller parts. "What were wholes on one level become parts on a higher one." Small scale patterns do not necessarily explain large scale phenomena, otherwise captured in the expression (coined by Aristotle) 'the sum is greater than the parts'. "Complexity in ecology is of at least six distinct types: spatial, temporal, structural, process, behavioral, and geometric." From these principles, ecologists have identified emergent and self-organizing phenomena that operate at different environmental scales of influence, ranging from molecular to planetary, and these require different explanations at each integrative level. Ecological complexity relates to the dynamic resilience of ecosystems that transition to multiple shifting steady-states directed by random fluctuations of history. Long-term ecological studies provide important track records to better understand the complexity and resilience of ecosystems over longer temporal and broader spatial scales. These studies are managed by the International Long Term Ecological Network (LTER). The longest experiment in existence is the Park Grass Experiment, which was initiated in 1856. Another example is the Hubbard Brook study, which has been in operation since 1960. Holism Holism remains a critical part of the theoretical foundation in contemporary ecological studies. Holism addresses the biological organization of life that self-organizes into layers of emergent whole systems that function according to non-reducible properties. This means that higher-order patterns of a whole functional system, such as an ecosystem, cannot be predicted or understood by a simple summation of the parts. "New properties emerge because the components interact, not because the basic nature of the components is changed." Ecological studies are necessarily holistic as opposed to reductionistic. Holism has three scientific meanings or uses that identify with ecology: 1) the mechanistic complexity of ecosystems, 2) the practical description of patterns in quantitative reductionist terms where correlations may be identified but nothing is understood about the causal relations without reference to the whole system, which leads to 3) a metaphysical hierarchy whereby the causal relations of larger systems are understood without reference to the smaller parts. Scientific holism differs from mysticism that has appropriated the same term. An example of metaphysical holism is identified in the trend of increased exterior thickness in shells of different species. The reason for a thickness increase can be understood through reference to principles of natural selection via predation without the need to reference or understand the biomolecular properties of the exterior shells. Relation to evolution Ecology and evolutionary biology are considered sister disciplines of the life sciences. Natural selection, life history, development, adaptation, populations, and inheritance are examples of concepts that thread equally into ecological and evolutionary theory. Morphological, behavioural, and genetic traits, for example, can be mapped onto evolutionary trees to study the historical development of a species in relation to their functions and roles in different ecological circumstances. In this framework, the analytical tools of ecologists and evolutionists overlap as they organize, classify, and investigate life through common systematic principles, such as phylogenetics or the Linnaean system of taxonomy. The two disciplines often appear together, such as in the title of the journal Trends in Ecology and Evolution. There is no sharp boundary separating ecology from evolution, and they differ more in their areas of applied focus. Both disciplines discover and explain emergent and unique properties and processes operating across different spatial or temporal scales of organization. While the boundary between ecology and evolution is not always clear, ecologists study the abiotic and biotic factors that influence evolutionary processes, and evolution can be rapid, occurring on ecological timescales as short as one generation. Behavioural ecology All organisms can exhibit behaviours. Even plants express complex behaviour, including memory and communication. Behavioural ecology is the study of an organism's behaviour in its environment and its ecological and evolutionary implications. Ethology is the study of observable movement or behaviour in animals. This could include investigations of motile sperm of plants, mobile phytoplankton, zooplankton swimming toward the female egg, the cultivation of fungi by weevils, the mating dance of a salamander, or social gatherings of amoeba. Adaptation is the central unifying concept in behavioural ecology. Behaviours can be recorded as traits and inherited in much the same way that eye and hair colour can. Behaviours can evolve by means of natural selection as adaptive traits conferring functional utilities that increases reproductive fitness. Predator-prey interactions are an introductory concept into food-web studies as well as behavioural ecology. Prey species can exhibit different kinds of behavioural adaptations to predators, such as avoid, flee, or defend. Many prey species are faced with multiple predators that differ in the degree of danger posed. To be adapted to their environment and face predatory threats, organisms must balance their energy budgets as they invest in different aspects of their life history, such as growth, feeding, mating, socializing, or modifying their habitat. Hypotheses posited in behavioural ecology are generally based on adaptive principles of conservation, optimization, or efficiency. For example, "[t]he threat-sensitive predator avoidance hypothesis predicts that prey should assess the degree of threat posed by different predators and match their behaviour according to current levels of risk" or "[t]he optimal flight initiation distance occurs where expected postencounter fitness is maximized, which depends on the prey's initial fitness, benefits obtainable by not fleeing, energetic escape costs, and expected fitness loss due to predation risk." Elaborate sexual displays and posturing are encountered in the behavioural ecology of animals. The birds-of-paradise, for example, sing and display elaborate ornaments during courtship. These displays serve a dual purpose of signalling healthy or well-adapted individuals and desirable genes. The displays are driven by sexual selection as an advertisement of quality of traits among suitors. Cognitive ecology Cognitive ecology integrates theory and observations from evolutionary ecology and neurobiology, primarily cognitive science, in order to understand the effect that animal interaction with their habitat has on their cognitive systems and how those systems restrict behavior within an ecological and evolutionary framework. "Until recently, however, cognitive scientists have not paid sufficient attention to the fundamental fact that cognitive traits evolved under particular natural settings. With consideration of the selection pressure on cognition, cognitive ecology can contribute intellectual coherence to the multidisciplinary study of cognition." As a study involving the 'coupling' or interactions between organism and environment, cognitive ecology is closely related to enactivism, a field based upon the view that "...we must see the organism and environment as bound together in reciprocal specification and selection...". Social ecology Social-ecological behaviours are notable in the social insects, slime moulds, social spiders, human society, and naked mole-rats where eusocialism has evolved. Social behaviours include reciprocally beneficial behaviours among kin and nest mates and evolve from kin and group selection. Kin selection explains altruism through genetic relationships, whereby an altruistic behaviour leading to death is rewarded by the survival of genetic copies distributed among surviving relatives. The social insects, including ants, bees, and wasps are most famously studied for this type of relationship because the male drones are clones that share the same genetic make-up as every other male in the colony. In contrast, group selectionists find examples of altruism among non-genetic relatives and explain this through selection acting on the group; whereby, it becomes selectively advantageous for groups if their members express altruistic behaviours to one another. Groups with predominantly altruistic members survive better than groups with predominantly selfish members. Coevolution Ecological interactions can be classified broadly into a host and an associate relationship. A host is any entity that harbours another that is called the associate. Relationships between species that are mutually or reciprocally beneficial are called mutualisms. Examples of mutualism include fungus-growing ants employing agricultural symbiosis, bacteria living in the guts of insects and other organisms, the fig wasp and yucca moth pollination complex, lichens with fungi and photosynthetic algae, and corals with photosynthetic algae. If there is a physical connection between host and associate, the relationship is called symbiosis. Approximately 60% of all plants, for example, have a symbiotic relationship with arbuscular mycorrhizal fungi living in their roots forming an exchange network of carbohydrates for mineral nutrients. Indirect mutualisms occur where the organisms live apart. For example, trees living in the equatorial regions of the planet supply oxygen into the atmosphere that sustains species living in distant polar regions of the planet. This relationship is called commensalism because many others receive the benefits of clean air at no cost or harm to trees supplying the oxygen. If the associate benefits while the host suffers, the relationship is called parasitism. Although parasites impose a cost to their host (e.g., via damage to their reproductive organs or propagules, denying the services of a beneficial partner), their net effect on host fitness is not necessarily negative and, thus, becomes difficult to forecast. Co-evolution is also driven by competition among species or among members of the same species under the banner of reciprocal antagonism, such as grasses competing for growth space. The Red Queen Hypothesis, for example, posits that parasites track down and specialize on the locally common genetic defense systems of its host that drives the evolution of sexual reproduction to diversify the genetic constituency of populations responding to the antagonistic pressure. Biogeography Biogeography (an amalgamation of biology and geography) is the comparative study of the geographic distribution of organisms and the corresponding evolution of their traits in space and time. The Journal of Biogeography was established in 1974. Biogeography and ecology share many of their disciplinary roots. For example, the theory of island biogeography, published by the Robert MacArthur and Edward O. Wilson in 1967 is considered one of the fundamentals of ecological theory. Biogeography has a long history in the natural sciences concerning the spatial distribution of plants and animals. Ecology and evolution provide the explanatory context for biogeographical studies. Biogeographical patterns result from ecological processes that influence range distributions, such as migration and dispersal. and from historical processes that split populations or species into different areas. The biogeographic processes that result in the natural splitting of species explain much of the modern distribution of the Earth's biota. The splitting of lineages in a species is called vicariance biogeography and it is a sub-discipline of biogeography. There are also practical applications in the field of biogeography concerning ecological systems and processes. For example, the range and distribution of biodiversity and invasive species responding to climate change is a serious concern and active area of research in the context of global warming. r/K selection theory A population ecology concept is r/K selection theory, one of the first predictive models in ecology used to explain life-history evolution. The premise behind the r/K selection model is that natural selection pressures change according to population density. For example, when an island is first colonized, density of individuals is low. The initial increase in population size is not limited by competition, leaving an abundance of available resources for rapid population growth. These early phases of population growth experience density-independent forces of natural selection, which is called r-selection. As the population becomes more crowded, it approaches the island's carrying capacity, thus forcing individuals to compete more heavily for fewer available resources. Under crowded conditions, the population experiences density-dependent forces of natural selection, called K-selection. In the r/K-selection model, the first variable r is the intrinsic rate of natural increase in population size and the second variable K is the carrying capacity of a population. Different species evolve different life-history strategies spanning a continuum between these two selective forces. An r-selected species is one that has high birth rates, low levels of parental investment, and high rates of mortality before individuals reach maturity. Evolution favours high rates of fecundity in r-selected species. Many kinds of insects and invasive species exhibit r-selected characteristics. In contrast, a K-selected species has low rates of fecundity, high levels of parental investment in the young, and low rates of mortality as individuals mature. Humans and elephants are examples of species exhibiting K-selected characteristics, including longevity and efficiency in the conversion of more resources into fewer offspring. Molecular ecology The important relationship between ecology and genetic inheritance predates modern techniques for molecular analysis. Molecular ecological research became more feasible with the development of rapid and accessible genetic technologies, such as the polymerase chain reaction (PCR). The rise of molecular technologies and the influx of research questions into this new ecological field resulted in the publication Molecular Ecology in 1992. Molecular ecology uses various analytical techniques to study genes in an evolutionary and ecological context. In 1994, John Avise also played a leading role in this area of science with the publication of his book, Molecular Markers, Natural History and Evolution. Newer technologies opened a wave of genetic analysis into organisms once difficult to study from an ecological or evolutionary standpoint, such as bacteria, fungi, and nematodes. Molecular ecology engendered a new research paradigm for investigating ecological questions considered otherwise intractable. Molecular investigations revealed previously obscured details in the tiny intricacies of nature and improved resolution into probing questions about behavioural and biogeographical ecology. For example, molecular ecology revealed promiscuous sexual behaviour and multiple male partners in tree swallows previously thought to be socially monogamous. In a biogeographical context, the marriage between genetics, ecology, and evolution resulted in a new sub-discipline called phylogeography. Human ecology Ecology is as much a biological science as it is a human science. Human ecology is an interdisciplinary investigation into the ecology of our species. "Human ecology may be defined: (1) from a bioecological standpoint as the study of man as the ecological dominant in plant and animal communities and systems; (2) from a bioecological standpoint as simply another animal affecting and being affected by his physical environment; and (3) as a human being, somehow different from animal life in general, interacting with physical and modified environments in a distinctive and creative way. A truly interdisciplinary human ecology will most likely address itself to all three." The term was formally introduced in 1921, but many sociologists, geographers, psychologists, and other disciplines were interested in human relations to natural systems centuries prior, especially in the late 19th century. The ecological complexities human beings are facing through the technological transformation of the planetary biome has brought on the Anthropocene. The unique set of circumstances has generated the need for a new unifying science called coupled human and natural systems that builds upon, but moves beyond the field of human ecology. Ecosystems tie into human societies through the critical and all-encompassing life-supporting functions they sustain. In recognition of these functions and the incapability of traditional economic valuation methods to see the value in ecosystems, there has been a surge of interest in social-natural capital, which provides the means to put a value on the stock and use of information and materials stemming from ecosystem goods and services. Ecosystems produce, regulate, maintain, and supply services of critical necessity and beneficial to human health (cognitive and physiological), economies, and they even provide an information or reference function as a living library giving opportunities for science and cognitive development in children engaged in the complexity of the natural world. Ecosystems relate importantly to human ecology as they are the ultimate base foundation of global economics as every commodity, and the capacity for exchange ultimately stems from the ecosystems on Earth. Restoration Ecology Ecology is an employed science of restoration, repairing disturbed sites through human intervention, in natural resource management, and in environmental impact assessments. Edward O. Wilson predicted in 1992 that the 21st century "will be the era of restoration in ecology". Ecological science has boomed in the industrial investment of restoring ecosystems and their processes in abandoned sites after disturbance. Natural resource managers, in forestry, for example, employ ecologists to develop, adapt, and implement ecosystem based methods into the planning, operation, and restoration phases of land-use. Another example of conservation is seen on the east coast of the United States in Boston, MA. The city of Boston implemented the Wetland Ordinance, improving the stability of their wetland environments by implementing soil amendments that will improve groundwater storage and flow, and trimming or removal of vegetation that could cause harm to water quality. Ecological science is used in the methods of sustainable harvesting, disease, and fire outbreak management, in fisheries stock management, for integrating land-use with protected areas and communities, and conservation in complex geo-political landscapes. Relation to the environment The environment of ecosystems includes both physical parameters and biotic attributes. It is dynamically interlinked and contains resources for organisms at any time throughout their life cycle. Like ecology, the term environment has different conceptual meanings and overlaps with the concept of nature. Environment "includes the physical world, the social world of human relations and the built world of human creation." The physical environment is external to the level of biological organization under investigation, including abiotic factors such as temperature, radiation, light, chemistry, climate and geology. The biotic environment includes genes, cells, organisms, members of the same species (conspecifics) and other species that share a habitat. The distinction between external and internal environments, however, is an abstraction parsing life and environment into units or facts that are inseparable in reality. There is an interpenetration of cause and effect between the environment and life. The laws of thermodynamics, for example, apply to ecology by means of its physical state. With an understanding of metabolic and thermodynamic principles, a complete accounting of energy and material flow can be traced through an ecosystem. In this way, the environmental and ecological relations are studied through reference to conceptually manageable and isolated material parts. After the effective environmental components are understood through reference to their causes; however, they conceptually link back together as an integrated whole, or holocoenotic system as it was once called. This is known as the dialectical approach to ecology. The dialectical approach examines the parts but integrates the organism and the environment into a dynamic whole (or umwelt). Change in one ecological or environmental factor can concurrently affect the dynamic state of an entire ecosystem. Disturbance and resilience A disturbance is any process that changes or removes biomass from a community, such as a fire, flood, drought, or predation. Disturbances are both the cause and product of natural fluctuations within an ecological community. Biodiversity can protect ecosystems from disturbances. The effect of a disturbance is often hard to predict, but there are numerous examples in which a single species can massively disturb an ecosystem. For example, a single-celled protozoan has been able to kill up to 100% of sea urchins in some coral reefs in the Red Sea and Western Indian Ocean. Sea urchins enable complex reef ecosystems to thrive by eating algae that would otherwise inhibit coral growth. Similarly, invasive species can wreak havoc on ecosystems. For instance, invasive Burmese pythons have caused a 98% decline of small mammals in the Everglades. Metabolism and the early atmosphere The Earth was formed approximately 4.5 billion years ago. As it cooled and a crust and oceans formed, its atmosphere transformed from being dominated by hydrogen to one composed mostly of methane and ammonia. Over the next billion years, the metabolic activity of life transformed the atmosphere into a mixture of carbon dioxide, nitrogen, and water vapor. These gases changed the way that light from the sun hit the Earth's surface and greenhouse effects trapped heat. There were untapped sources of free energy within the mixture of reducing and oxidizing gasses that set the stage for primitive ecosystems to evolve and, in turn, the atmosphere also evolved. Throughout history, the Earth's atmosphere and biogeochemical cycles have been in a dynamic equilibrium with planetary ecosystems. The history is characterized by periods of significant transformation followed by millions of years of stability. The evolution of the earliest organisms, likely anaerobic methanogen microbes, started the process by converting atmospheric hydrogen into methane (4H2 + CO2 → CH4 + 2H2O). Anoxygenic photosynthesis reduced hydrogen concentrations and increased atmospheric methane, by converting hydrogen sulfide into water or other sulfur compounds (for example, 2H2S + CO2 + hv → CH2O + H2O + 2S). Early forms of fermentation also increased levels of atmospheric methane. The transition to an oxygen-dominant atmosphere (the Great Oxidation) did not begin until approximately 2.4–2.3 billion years ago, but photosynthetic processes started 0.3 to 1 billion years prior. Radiation: heat, temperature and light The biology of life operates within a certain range of temperatures. Heat is a form of energy that regulates temperature. Heat affects growth rates, activity, behaviour, and primary production. Temperature is largely dependent on the incidence of solar radiation. The latitudinal and longitudinal spatial variation of temperature greatly affects climates and consequently the distribution of biodiversity and levels of primary production in different ecosystems or biomes across the planet. Heat and temperature relate importantly to metabolic activity. Poikilotherms, for example, have a body temperature that is largely regulated and dependent on the temperature of the external environment. In contrast, homeotherms regulate their internal body temperature by expending metabolic energy. There is a relationship between light, primary production, and ecological energy budgets. Sunlight is the primary input of energy into the planet's ecosystems. Light is composed of electromagnetic energy of different wavelengths. Radiant energy from the sun generates heat, provides photons of light measured as active energy in the chemical reactions of life, and also acts as a catalyst for genetic mutation. Plants, algae, and some bacteria absorb light and assimilate the energy through photosynthesis. Organisms capable of assimilating energy by photosynthesis or through inorganic fixation of H2S are autotrophs. Autotrophs—responsible for primary production—assimilate light energy which becomes metabolically stored as potential energy in the form of biochemical enthalpic bonds. Physical environments Water Diffusion of carbon dioxide and oxygen is approximately 10,000 times slower in water than in air. When soils are flooded, they quickly lose oxygen, becoming hypoxic (an environment with O2 concentration below 2 mg/liter) and eventually completely anoxic where anaerobic bacteria thrive among the roots. Water also influences the intensity and spectral composition of light as it reflects off the water surface and submerged particles. Aquatic plants exhibit a wide variety of morphological and physiological adaptations that allow them to survive, compete, and diversify in these environments. For example, their roots and stems contain large air spaces (aerenchyma) that regulate the efficient transportation of gases (for example, CO2 and O2) used in respiration and photosynthesis. Salt water plants (halophytes) have additional specialized adaptations, such as the development of special organs for shedding salt and osmoregulating their internal salt (NaCl) concentrations, to live in estuarine, brackish, or oceanic environments. Anaerobic soil microorganisms in aquatic environments use nitrate, manganese ions, ferric ions, sulfate, carbon dioxide, and some organic compounds; other microorganisms are facultative anaerobes and use oxygen during respiration when the soil becomes drier. The activity of soil microorganisms and the chemistry of the water reduces the oxidation-reduction potentials of the water. Carbon dioxide, for example, is reduced to methane (CH4) by methanogenic bacteria. The physiology of fish is also specially adapted to compensate for environmental salt levels through osmoregulation. Their gills form electrochemical gradients that mediate salt excretion in salt water and uptake in fresh water. Gravity The shape and energy of the land are significantly affected by gravitational forces. On a large scale, the distribution of gravitational forces on the earth is uneven and influences the shape and movement of tectonic plates as well as influencing geomorphic processes such as orogeny and erosion. These forces govern many of the geophysical properties and distributions of ecological biomes across the Earth. On the organismal scale, gravitational forces provide directional cues for plant and fungal growth (gravitropism), orientation cues for animal migrations, and influence the biomechanics and size of animals. Ecological traits, such as allocation of biomass in trees during growth are subject to mechanical failure as gravitational forces influence the position and structure of branches and leaves. The cardiovascular systems of animals are functionally adapted to overcome the pressure and gravitational forces that change according to the features of organisms (e.g., height, size, shape), their behaviour (e.g., diving, running, flying), and the habitat occupied (e.g., water, hot deserts, cold tundra). Pressure Climatic and osmotic pressure places physiological constraints on organisms, especially those that fly and respire at high altitudes, or dive to deep ocean depths. These constraints influence vertical limits of ecosystems in the biosphere, as organisms are physiologically sensitive and adapted to atmospheric and osmotic water pressure differences. For example, oxygen levels decrease with decreasing pressure and are a limiting factor for life at higher altitudes. Water transportation by plants is another important ecophysiological process affected by osmotic pressure gradients. Water pressure in the depths of oceans requires that organisms adapt to these conditions. For example, diving animals such as whales, dolphins, and seals are specially adapted to deal with changes in sound due to water pressure differences. Differences between hagfish species provide another example of adaptation to deep-sea pressure through specialized protein adaptations. Wind and turbulence Turbulent forces in air and water affect the environment and ecosystem distribution, form, and dynamics. On a planetary scale, ecosystems are affected by circulation patterns in the global trade winds. Wind power and the turbulent forces it creates can influence heat, nutrient, and biochemical profiles of ecosystems. For example, wind running over the surface of a lake creates turbulence, mixing the water column and influencing the environmental profile to create thermally layered zones, affecting how fish, algae, and other parts of the aquatic ecosystem are structured. Wind speed and turbulence also influence evapotranspiration rates and energy budgets in plants and animals. Wind speed, temperature and moisture content can vary as winds travel across different land features and elevations. For example, the westerlies come into contact with the coastal and interior mountains of western North America to produce a rain shadow on the leeward side of the mountain. The air expands and moisture condenses as the winds increase in elevation; this is called orographic lift and can cause precipitation. This environmental process produces spatial divisions in biodiversity, as species adapted to wetter conditions are range-restricted to the coastal mountain valleys and unable to migrate across the xeric ecosystems (e.g., of the Columbia Basin in western North America) to intermix with sister lineages that are segregated to the interior mountain systems. Fire Plants convert carbon dioxide into biomass and emit oxygen into the atmosphere. By approximately 350 million years ago (the end of the Devonian period), photosynthesis had brought the concentration of atmospheric oxygen above 17%, which allowed combustion to occur. Fire releases CO2 and converts fuel into ash and tar. Fire is a significant ecological parameter that raises many issues pertaining to its control and suppression. While the issue of fire in relation to ecology and plants has been recognized for a long time, Charles Cooper brought attention to the issue of forest fires in relation to the ecology of forest fire suppression and management in the 1960s. Native North Americans were among the first to influence fire regimes by controlling their spread near their homes or by lighting fires to stimulate the production of herbaceous foods and basketry materials. Fire creates a heterogeneous ecosystem age and canopy structure, and the altered soil nutrient supply and cleared canopy structure opens new ecological niches for seedling establishment. Most ecosystems are adapted to natural fire cycles. Plants, for example, are equipped with a variety of adaptations to deal with forest fires. Some species (e.g., Pinus halepensis) cannot germinate until after their seeds have lived through a fire or been exposed to certain compounds from smoke. Environmentally triggered germination of seeds is called serotiny. Fire plays a major role in the persistence and resilience of ecosystems. Soils Soil is the living top layer of mineral and organic dirt that covers the surface of the planet. It is the chief organizing centre of most ecosystem functions, and it is of critical importance in agricultural science and ecology. The decomposition of dead organic matter (for example, leaves on the forest floor), results in soils containing minerals and nutrients that feed into plant production. The whole of the planet's soil ecosystems is called the pedosphere where a large biomass of the Earth's biodiversity organizes into trophic levels. Invertebrates that feed and shred larger leaves, for example, create smaller bits for smaller organisms in the feeding chain. Collectively, these organisms are the detritivores that regulate soil formation. Tree roots, fungi, bacteria, worms, ants, beetles, centipedes, spiders, mammals, birds, reptiles, amphibians, and other less familiar creatures all work to create the trophic web of life in soil ecosystems. Soils form composite phenotypes where inorganic matter is enveloped into the physiology of a whole community. As organisms feed and migrate through soils they physically displace materials, an ecological process called bioturbation. This aerates soils and stimulates heterotrophic growth and production. Soil microorganisms are influenced by and are fed back into the trophic dynamics of the ecosystem. No single axis of causality can be discerned to segregate the biological from geomorphological systems in soils. Paleoecological studies of soils places the origin for bioturbation to a time before the Cambrian period. Other events, such as the evolution of trees and the colonization of land in the Devonian period played a significant role in the early development of ecological trophism in soils. Biogeochemistry and climate Ecologists study and measure nutrient budgets to understand how these materials are regulated, flow, and recycled through the environment. This research has led to an understanding that there is global feedback between ecosystems and the physical parameters of this planet, including minerals, soil, pH, ions, water, and atmospheric gases. Six major elements (hydrogen, carbon, nitrogen, oxygen, sulfur, and phosphorus; H, C, N, O, S, and P) form the constitution of all biological macromolecules and feed into the Earth's geochemical processes. From the smallest scale of biology, the combined effect of billions upon billions of ecological processes amplify and ultimately regulate the biogeochemical cycles of the Earth. Understanding the relations and cycles mediated between these elements and their ecological pathways has significant bearing toward understanding global biogeochemistry. The ecology of global carbon budgets gives one example of the linkage between biodiversity and biogeochemistry. It is estimated that the Earth's oceans hold 40,000 gigatonnes (Gt) of carbon, that vegetation and soil hold 2070 Gt, and that fossil fuel emissions are 6.3 Gt carbon per year. There have been major restructurings in these global carbon budgets during the Earth's history, regulated to a large extent by the ecology of the land. For example, through the early-mid Eocene volcanic outgassing, the oxidation of methane stored in wetlands, and seafloor gases increased atmospheric CO2 (carbon dioxide) concentrations to levels as high as 3500 ppm. In the Oligocene, from twenty-five to thirty-two million years ago, there was another significant restructuring of the global carbon cycle as grasses evolved a new mechanism of photosynthesis, C4 photosynthesis, and expanded their ranges. This new pathway evolved in response to the drop in atmospheric CO2 concentrations below 550 ppm. The relative abundance and distribution of biodiversity alters the dynamics between organisms and their environment such that ecosystems can be both cause and effect in relation to climate change. Human-driven modifications to the planet's ecosystems (e.g., disturbance, biodiversity loss, agriculture) contributes to rising atmospheric greenhouse gas levels. Transformation of the global carbon cycle in the next century is projected to raise planetary temperatures, lead to more extreme fluctuations in weather, alter species distributions, and increase extinction rates. The effect of global warming is already being registered in melting glaciers, melting mountain ice caps, and rising sea levels. Consequently, species distributions are changing along waterfronts and in continental areas where migration patterns and breeding grounds are tracking the prevailing shifts in climate. Large sections of permafrost are also melting to create a new mosaic of flooded areas having increased rates of soil decomposition activity that raises methane (CH4) emissions. There is concern over increases in atmospheric methane in the context of the global carbon cycle, because methane is a greenhouse gas that is 23 times more effective at absorbing long-wave radiation than CO2 on a 100-year time scale. Hence, there is a relationship between global warming, decomposition and respiration in soils and wetlands producing significant climate feedbacks and globally altered biogeochemical cycles. History Early beginnings Ecology has a complex origin, due in large part to its interdisciplinary nature. Ancient Greek philosophers such as Hippocrates and Aristotle were among the first to record observations on natural history. However, they viewed life in terms of essentialism, where species were conceptualized as static unchanging things while varieties were seen as aberrations of an idealized type. This contrasts against the modern understanding of ecological theory where varieties are viewed as the real phenomena of interest and having a role in the origins of adaptations by means of natural selection. Early conceptions of ecology, such as a balance and regulation in nature can be traced to Herodotus (died c. 425 BC), who described one of the earliest accounts of mutualism in his observation of "natural dentistry". Basking Nile crocodiles, he noted, would open their mouths to give sandpipers safe access to pluck leeches out, giving nutrition to the sandpiper and oral hygiene for the crocodile. Aristotle was an early influence on the philosophical development of ecology. He and his student Theophrastus made extensive observations on plant and animal migrations, biogeography, physiology, and their behavior, giving an early analogue to the modern concept of an ecological niche. Ernst Haeckel (left) and Eugenius Warming (right), two founders of ecology Ecological concepts such as food chains, population regulation, and productivity were first developed in the 1700s, through the published works of microscopist Antonie van Leeuwenhoek (1632–1723) and botanist Richard Bradley (1688?–1732). Biogeographer Alexander von Humboldt (1769–1859) was an early pioneer in ecological thinking and was among the first to recognize ecological gradients, where species are replaced or altered in form along environmental gradients, such as a cline forming along a rise in elevation. Humboldt drew inspiration from Isaac Newton, as he developed a form of "terrestrial physics". In Newtonian fashion, he brought a scientific exactitude for measurement into natural history and even alluded to concepts that are the foundation of a modern ecological law on species-to-area relationships. Natural historians, such as Humboldt, James Hutton, and Jean-Baptiste Lamarck (among others) laid the foundations of the modern ecological sciences. The term "ecology" was coined by Ernst Haeckel in his book Generelle Morphologie der Organismen (1866). Haeckel was a zoologist, artist, writer, and later in life a professor of comparative anatomy. Opinions differ on who was the founder of modern ecological theory. Some mark Haeckel's definition as the beginning; others say it was Eugenius Warming with the writing of Oecology of Plants: An Introduction to the Study of Plant Communities (1895), or Carl Linnaeus' principles on the economy of nature that matured in the early 18th century. Linnaeus founded an early branch of ecology that he called the economy of nature. His works influenced Charles Darwin, who adopted Linnaeus' phrase on the economy or polity of nature in The Origin of Species. Linnaeus was the first to frame the balance of nature as a testable hypothesis. Haeckel, who admired Darwin's work, defined ecology in reference to the economy of nature, which has led some to question whether ecology and the economy of nature are synonymous. From Aristotle until Darwin, the natural world was predominantly considered static and unchanging. Prior to The Origin of Species, there was little appreciation or understanding of the dynamic and reciprocal relations between organisms, their adaptations, and the environment. An exception is the 1789 publication Natural History of Selborne by Gilbert White (1720–1793), considered by some to be one of the earliest texts on ecology. While Charles Darwin is mainly noted for his treatise on evolution, he was one of the founders of soil ecology, and he made note of the first ecological experiment in The Origin of Species. Evolutionary theory changed the way that researchers approached the ecological sciences. Since 1900 Modern ecology is a young science that first attracted substantial scientific attention toward the end of the 19th century (around the same time that evolutionary studies were gaining scientific interest). The scientist Ellen Swallow Richards adopted the term "oekology" (which eventually morphed into home economics) in the U.S. as early as 1892. In the early 20th century, ecology transitioned from a more descriptive form of natural history to a more analytical form of scientific natural history. Frederic Clements published the first American ecology book in 1905, presenting the idea of plant communities as a superorganism. This publication launched a debate between ecological holism and individualism that lasted until the 1970s. Clements' superorganism concept proposed that ecosystems progress through regular and determined stages of seral development that are analogous to the developmental stages of an organism. The Clementsian paradigm was challenged by Henry Gleason, who stated that ecological communities develop from the unique and coincidental association of individual organisms. This perceptual shift placed the focus back onto the life histories of individual organisms and how this relates to the development of community associations. The Clementsian superorganism theory was an overextended application of an idealistic form of holism. The term "holism" was coined in 1926 by Jan Christiaan Smuts, a South African general and polarizing historical figure who was inspired by Clements' superorganism concept. Around the same time, Charles Elton pioneered the concept of food chains in his classical book Animal Ecology. Elton defined ecological relations using concepts of food chains, food cycles, and food size, and described numerical relations among different functional groups and their relative abundance. Elton's 'food cycle' was replaced by 'food web' in a subsequent ecological text. Alfred J. Lotka brought in many theoretical concepts applying thermodynamic principles to ecology. In 1942, Raymond Lindeman wrote a landmark paper on the trophic dynamics of ecology, which was published posthumously after initially being rejected for its theoretical emphasis. Trophic dynamics became the foundation for much of the work to follow on energy and material flow through ecosystems. Robert MacArthur advanced mathematical theory, predictions, and tests in ecology in the 1950s, which inspired a resurgent school of theoretical mathematical ecologists. Ecology also has developed through contributions from other nations, including Russia's Vladimir Vernadsky and his founding of the biosphere concept in the 1920s and Japan's Kinji Imanishi and his concepts of harmony in nature and habitat segregation in the 1950s. Scientific recognition of contributions to ecology from non-English-speaking cultures is hampered by language and translation barriers. Ecology surged in popular and scientific interest during the 1960–1970s environmental movement. There are strong historical and scientific ties between ecology, environmental management, and protection. The historical emphasis and poetic naturalistic writings advocating the protection of wild places by notable ecologists in the history of conservation biology, such as Aldo Leopold and Arthur Tansley, have been seen as far removed from urban centres where, it is claimed, the concentration of pollution and environmental degradation is located. Palamar (2008) notes an overshadowing by mainstream environmentalism of pioneering women in the early 1900s who fought for urban health ecology (then called euthenics) and brought about changes in environmental legislation. Women such as Ellen Swallow Richards and Julia Lathrop, among others, were precursors to the more popularized environmental movements after the 1950s. In 1962, marine biologist and ecologist Rachel Carson's book Silent Spring helped to mobilize the environmental movement by alerting the public to toxic pesticides, such as DDT, bioaccumulating in the environment. Carson used ecological science to link the release of environmental toxins to human and ecosystem health. Since then, ecologists have worked to bridge their understanding of the degradation of the planet's ecosystems with environmental politics, law, restoration, and natural resources management. See also Carrying capacity Chemical ecology Climate justice Circles of Sustainability Cultural ecology Dialectical naturalism Ecological death Ecological empathy Ecological overshoot Ecological psychology Ecology movement Ecosophy Ecopsychology Human ecology Industrial ecology Information ecology Landscape ecology Natural resource Normative science Philosophy of ecology Political ecology Theoretical ecology Sensory ecology Sexecology Spiritual ecology Sustainable development Lists Glossary of ecology Index of biology articles List of ecologists Outline of biology Terminology of ecology Notes References External links The Nature Education Knowledge Project: Ecology Biogeochemistry Emergence

Evolutionary biology

Evolutionary biology is the subfield of biology that studies the evolutionary processes (natural selection, common descent, speciation) that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes (physical characteristics) of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed on to their offspring. Some examples of evolution in species over many generations are the peppered moth and flightless birds. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology. The investigational range of current research has widened to encompass the genetic architecture of adaptation, molecular evolution, and the different forces that contribute to evolution, such as sexual selection, genetic drift, and biogeography. Moreover, the newer field of evolutionary developmental biology ("evo-devo") investigates how embryogenesis is controlled, thus yielding a wider synthesis that integrates developmental biology with the fields of study covered by the earlier evolutionary synthesis. Subfields Evolution is the central unifying concept in biology. Biology can be divided into various ways. One way is by the level of biological organization, from molecular to cell, organism to population. Another way is by perceived taxonomic group, with fields such as zoology, botany, and microbiology, reflecting what was once seen as the major divisions of life. A third way is by approaches, such as field biology, theoretical biology, experimental evolution, and paleontology. These alternative ways of dividing up the subject have been combined with evolutionary biology to create subfields like evolutionary ecology and evolutionary developmental biology. More recently, the merge between biological science and applied sciences gave birth to new fields that are extensions of evolutionary biology, including evolutionary robotics, engineering, algorithms, economics, and architecture. The basic mechanisms of evolution are applied directly or indirectly to come up with novel designs or solve problems that are difficult to solve otherwise. The research generated in these applied fields, contribute towards progress, especially from work on evolution in computer science and engineering fields such as mechanical engineering. Different types of evolution Adaptive evolution Adaptive evolution relates to evolutionary changes that happen due to the changes in the environment, this makes the organism suitable to its habitat. This change increases the chances of survival and reproduction of the organism (this can be referred to as an organism's fitness). For example, Darwin's Finches on Galapagos island developed different shaped beaks in order to survive for a long time. Adaptive evolution can also be convergent evolution if two distantly related species live in similar environments facing similar pressures. Convergent evolution Convergent evolution is the process in which related or distantly related organisms evolve similar characteristics independently. This type of evolution creates analogous structures which have a similar function, structure, or form between the two species. For example, sharks and dolphins look alike but they are not related. Likewise, birds, flying insects, and bats all have the ability to fly, but they are not related to each other. These similar traits tend to evolve from having similar environmental pressures. Divergent evolution Divergent evolution is the process of speciation. This can happen in several ways: Allopatric speciation is when species are separated by a physical barrier that separates the population into two groups. Evolutionary mechanisms such as genetic drift and natural selection can then act independently on each population. Peripatric speciation is a type of allopatric speciation that occurs when one of the new populations is considerably smaller than the other initial population. This leads to the founder's effect and the population can have different allele frequencies and phenotypes than the original population. These small populations are also more likely to see effects from genetic drift. Parapatric speciation is allopatric speciation but occurs when the species diverge without a physical barrier separating the population. This tends to occur when a population of a species is incredibly large and occupies a vast environment. Sympatric speciation is when a new species or subspecies sprouts from the original population while still occupying the same small environment, and without any physical barriers separating them from members of their original population. There is scientific debate as to whether sympatric speciation actually exists. Artificial speciation is when scientists purposefully cause new species to emerge to use in laboratory procedures. Coevolution The influence of two closely associated species is known as coevolution. When two or more species evolve in company with each other, one species adapts to changes in other species. This type of evolution often happens in species that have symbiotic relationships. For example, predator-prey coevolution, this is the most common type of co-evolution. In this, the predator must evolve to become a more effective hunter because there is a selective pressure on the prey to steer clear of capture. The prey in turn need to develop better survival strategies. The Red Queen hypothesis is an example of predator-prey interations. The relationship between pollinating insects like bees and flowering plants, herbivores and plants, are also some common examples of diffuse or guild coevolution. Mechanism: The process of evolution The mechanisms of evolution focus mainly on mutation, genetic drift, gene flow, non-random mating, and natural selection. Mutation: Mutation is a change in the DNA sequence inside a gene or a chromosome of an organism. Most mutations are deleterious, or neutral; i.e. they can neither harm nor benefit, but can also be beneficial sometimes. Genetic drift: Genetic drift is a variational process, it happens as a result of the sampling errors from one generation to another generation where a random event that happens by chance in nature changes or influences allele frequency within a population. It has a much stronger effect on small populations than large ones. Gene flow: Gene flow is the transfer of genetic material from the gene pool of one population to another. In a population, migration occurs from one species to another, resulting in the change of allele frequency. Natural selection: The survival and reproductive rate of a species depends on the adaptability of the species to their environment. This process is called natural selection. Some species with certain traits in a population have higher survival and reproductive rate than others (fitness), and they pass on these genetic features to their offsprings. Evolutionary developmental biology In evolutionary developmental biology, scientists look at how the different processes in development play a role in how a specific organism reaches its current body plan. The genetic regulation of ontogeny and the phylogenetic process is what allows for this kind of understanding of biology to be possible. By looking at different processes during development, and going through the evolutionary tree, one can determine at which point a specific structure came about. For example, the three germ layers can be observed to not be present in cnidarians and ctenophores, which instead present in worms, being more or less developed depending on the kind of worm itself. Other structures like the development of Hox genes and sensory organs such as eyes can also be traced with this practice. Phylogenetic Trees Phylogenetic Trees are representations of genetic lineage. They are figures that show how related species are to one another. They formed by analyzing the physical traits as well as the similarities of the DNA between species. Then by using a molecular clock scientists can estimate when the species diverged. An example of a phylogeny would be the tree of life. Homologs Genes that have shared ancestry are homologs. If a speciation event occurs and one gene ends up in two different species the genes are now orthologous. If a gene is duplicated within the a singular species then it is a paralog. A molecular clock can be used to estimate when these events occurred. History The idea of evolution by natural selection was proposed by Charles Darwin in 1859, but evolutionary biology, as an academic discipline in its own right, emerged during the period of the modern synthesis in the 1930s and 1940s. It was not until the 1980s that many universities had departments of evolutionary biology. In the United States, many universities have created departments of molecular and cell biology or ecology and evolutionary biology, in place of the older departments of botany and zoology. Palaeontology is often grouped with earth science. Microbiology too is becoming an evolutionary discipline now that microbial physiology and genomics are better understood. The quick generation time of bacteria and viruses such as bacteriophages makes it possible to explore evolutionary questions. Many biologists have contributed to shaping the modern discipline of evolutionary biology. Theodosius Dobzhansky and E. B. Ford established an empirical research programme. Ronald Fisher, Sewall Wright, and J. B. S. Haldane created a sound theoretical framework. Ernst Mayr in systematics, George Gaylord Simpson in paleontology and G. Ledyard Stebbins in botany helped to form the modern synthesis. James Crow, Richard Lewontin, Dan Hartl, Marcus Feldman, and Brian Charlesworth trained a generation of evolutionary biologists. Current research topics Current research in evolutionary biology covers diverse topics and incorporates ideas from diverse areas, such as molecular genetics and computer science. First, some fields of evolutionary research try to explain phenomena that were poorly accounted for in the modern evolutionary synthesis. These include speciation, the evolution of sexual reproduction, the evolution of cooperation, the evolution of ageing, and evolvability. Second, some evolutionary biologists ask the most straightforward evolutionary question: "what happened and when?". This includes fields such as paleobiology, where paleobiologists and evolutionary biologists, including Thomas Halliday and Anjali Goswami, studied the evolution of early mammals going far back in time during the Mesozoic and Cenozoic eras (between 299 million to 12,000 years ago). Other fields related to generic exploration of evolution ("what happened and when?" ) include systematics and phylogenetics. Third, the modern evolutionary synthesis was devised at a time when nobody understood the molecular basis of genes. Today, evolutionary biologists try to determine the genetic architecture of interesting evolutionary phenomena such as adaptation and speciation. They seek answers to questions such as how many genes are involved, how large are the effects of each gene, how interdependent are the effects of different genes, what do the genes do, and what changes happen to them (e.g., point mutations vs. gene duplication or even genome duplication). They try to reconcile the high heritability seen in twin studies with the difficulty in finding which genes are responsible for this heritability using genome-wide association studies. One challenge in studying genetic architecture is that the classical population genetics that catalysed the modern evolutionary synthesis must be updated to take into account modern molecular knowledge. This requires a great deal of mathematical development to relate DNA sequence data to evolutionary theory as part of a theory of molecular evolution. For example, biologists try to infer which genes have been under strong selection by detecting selective sweeps. Fourth, the modern evolutionary synthesis involved agreement about which forces contribute to evolution, but not about their relative importance. Current research seeks to determine this. Evolutionary forces include natural selection, sexual selection, genetic drift, genetic draft, developmental constraints, mutation bias and biogeography. This evolutionary approach is key to much current research in organismal biology and ecology, such as life history theory. Annotation of genes and their function relies heavily on comparative approaches. The field of evolutionary developmental biology ("evo-devo") investigates how developmental processes work, and compares them in different organisms to determine how they evolved. Many physicians do not have enough background in evolutionary biology, making it difficult to use it in modern medicine. However, there are efforts to gain a deeper understanding of disease through evolutionary medicine and to develop evolutionary therapies. Drug resistance today Evolution plays a role in resistance of drugs; for example, how HIV becomes resistant to medications and the body's immune system. The mutation of resistance of HIV is due to the natural selection of the survivors and their offspring. The few HIV that survive the immune system reproduced and had offspring that were also resistant to the immune system. Drug resistance also causes many problems for patients such as a worsening sickness or the sickness can mutate into something that can no longer be cured with medication. Without the proper medicine, a sickness can be the death of a patient. If their body has resistance to a certain number of drugs, then the right medicine will be harder and harder to find. Not completing the prescribed full course of antibiotic is also an example of resistance that will cause the bacteria against which the antibiotic is being taken to evolve and continue to spread in the body. When the full dosage of the medication does not enter the body and perform its proper job, the bacteria that survive the initial dosage will continue to reproduce. This can make for another bout of sickness later on that will be more difficult to cure because the bacteria involved will be resistant to the first medication used. Taking the full course of medicine that is prescribed is a vital step in avoiding antibiotic resistance. Individuals with chronic illnesses, especially those that can recur throughout a lifetime, are at greater risk of antibiotic resistance than others. This is because overuse of a drug or too high of a dosage can cause a patient's immune system to weaken and the illness will evolve and grow stronger. For example, cancer patients will need a stronger and stronger dosage of medication because of their low functioning immune system. Journals Some scientific journals specialise exclusively in evolutionary biology as a whole, including the journals Evolution, Journal of Evolutionary Biology, and BMC Evolutionary Biology. Some journals cover sub-specialties within evolutionary biology, such as the journals Systematic Biology, Molecular Biology and Evolution and its sister journal Genome Biology and Evolution, and Cladistics. Other journals combine aspects of evolutionary biology with other related fields. For example, Molecular Ecology, Proceedings of the Royal Society of London Series B, The American Naturalist and Theoretical Population Biology have overlap with ecology and other aspects of organismal biology. Overlap with ecology is also prominent in the review journals Trends in Ecology and Evolution and Annual Review of Ecology, Evolution, and Systematics. The journals Genetics and PLoS Genetics overlap with molecular genetics questions that are not obviously evolutionary in nature. See also Comparative anatomy Computational phylogenetics Evolutionary computation Evolutionary dynamics Evolutionary neuroscience Evolutionary physiology On the Origin of Species Macroevolution Phylogenetic comparative methods Quantitative genetics Selective breeding Taxonomy (biology) Speculative evolution References External links Evolution and Paleobotany at the Encyclopædia Britannica Philosophy of biology

Ecosystem ecology

Ecosystem ecology is the integrated study of living (biotic) and non-living (abiotic) components of ecosystems and their interactions within an ecosystem framework. This science examines how ecosystems work and relates this to their components such as chemicals, bedrock, soil, plants, and animals. Ecosystem ecology examines physical and biological structures and examines how these ecosystem characteristics interact with each other. Ultimately, this helps us understand how to maintain high quality water and economically viable commodity production. A major focus of ecosystem ecology is on functional processes, ecological mechanisms that maintain the structure and services produced by ecosystems. These include primary productivity (production of biomass), decomposition, and trophic interactions. Studies of ecosystem function have greatly improved human understanding of sustainable production of forage, fiber, fuel, and provision of water. Functional processes are mediated by regional-to-local level climate, disturbance, and management. Thus ecosystem ecology provides a powerful framework for identifying ecological mechanisms that interact with global environmental problems, especially global warming and degradation of surface water. This example demonstrates several important aspects of ecosystems: Ecosystem boundaries are often nebulous and may fluctuate in time Organisms within ecosystems are dependent on ecosystem level biological and physical processes Adjacent ecosystems closely interact and often are interdependent for maintenance of community structure and functional processes that maintain productivity and biodiversity These characteristics also introduce practical problems into natural resource management. Who will manage which ecosystem? Will timber cutting in the forest degrade recreational fishing in the stream? These questions are difficult for land managers to address while the boundary between ecosystems remains unclear; even though decisions in one ecosystem will affect the other. We need better understanding of the interactions and interdependencies of these ecosystems and the processes that maintain them before we can begin to address these questions. Ecosystem ecology is an inherently interdisciplinary field of study. An individual ecosystem is composed of populations of organisms, interacting within communities, and contributing to the cycling of nutrients and the flow of energy. The ecosystem is the principal unit of study in ecosystem ecology. Population, community, and physiological ecology provide many of the underlying biological mechanisms influencing ecosystems and the processes they maintain. Flowing of energy and cycling of matter at the ecosystem level are often examined in ecosystem ecology, but, as a whole, this science is defined more by subject matter than by scale. Ecosystem ecology approaches organisms and abiotic pools of energy and nutrients as an integrated system which distinguishes it from associated sciences such as biogeochemistry. Biogeochemistry and hydrology focus on several fundamental ecosystem processes such as biologically mediated chemical cycling of nutrients and physical-biological cycling of water. Ecosystem ecology forms the mechanistic basis for regional or global processes encompassed by landscape-to-regional hydrology, global biogeochemistry, and earth system science. History Ecosystem ecology is philosophically and historically rooted in terrestrial ecology. The ecosystem concept has evolved rapidly during the last 100 years with important ideas developed by Frederic Clements, a botanist who argued for specific definitions of ecosystems and that physiological processes were responsible for their development and persistence. Although most of Clements ecosystem definitions have been greatly revised, initially by Henry Gleason and Arthur Tansley, and later by contemporary ecologists, the idea that physiological processes are fundamental to ecosystem structure and function remains central to ecology. Later work by Eugene Odum and Howard T. Odum quantified flows of energy and matter at the ecosystem level, thus documenting the general ideas proposed by Clements and his contemporary Charles Elton. In this model, energy flows through the whole system were dependent on biotic and abiotic interactions of each individual component (species, inorganic pools of nutrients, etc.). Later work demonstrated that these interactions and flows applied to nutrient cycles, changed over the course of succession, and held powerful controls over ecosystem productivity. Transfers of energy and nutrients are innate to ecological systems regardless of whether they are aquatic or terrestrial. Thus, ecosystem ecology has emerged from important biological studies of plants, animals, terrestrial, aquatic, and marine ecosystems. Ecosystem services Ecosystem services are ecologically mediated functional processes essential to sustaining healthy human societies. Water provision and filtration, production of biomass in forestry, agriculture, and fisheries, and removal of greenhouse gases such as carbon dioxide (CO2) from the atmosphere are examples of ecosystem services essential to public health and economic opportunity. Nutrient cycling is a process fundamental to agricultural and forest production. However, like most ecosystem processes, nutrient cycling is not an ecosystem characteristic which can be “dialed” to the most desirable level. Maximizing production in degraded systems is an overly simplistic solution to the complex problems of hunger and economic security. For instance, intensive fertilizer use in the midwestern United States has resulted in degraded fisheries in the Gulf of Mexico. Regrettably, a “Green Revolution” of intensive chemical fertilization has been recommended for agriculture in developed and developing countries. These strategies risk alteration of ecosystem processes that may be difficult to restore, especially when applied at broad scales without adequate assessment of impacts. Ecosystem processes may take many years to recover from significant disturbance. For instance, large-scale forest clearance in the northeastern United States during the 18th and 19th centuries has altered soil texture, dominant vegetation, and nutrient cycling in ways that impact forest productivity in the present day. An appreciation of the importance of ecosystem function in maintenance of productivity, whether in agriculture or forestry, is needed in conjunction with plans for restoration of essential processes. Improved knowledge of ecosystem function will help to achieve long-term sustainability and stability in the poorest parts of the world. Operation Biomass productivity is one of the most apparent and economically important ecosystem functions. Biomass accumulation begins at the cellular level via photosynthesis. Photosynthesis requires water and consequently global patterns of annual biomass production are correlated with annual precipitation. Amounts of productivity are also dependent on the overall capacity of plants to capture sunlight which is directly correlated with plant leaf area and N content. Net primary productivity (NPP) is the primary measure of biomass accumulation within an ecosystem. Net primary productivity can be calculated by a simple formula where the total amount of productivity is adjusted for total productivity losses through maintenance of biological processes: NPP = GPP – Rproducer Where GPP is gross primary productivity and Rproducer is photosynthate (Carbon) lost via cellular respiration. NPP is difficult to measure but a new technique known as eddy co-variance has shed light on how natural ecosystems influence the atmosphere. Figure 4 shows seasonal and annual changes in CO2 concentration measured at Mauna Loa, Hawaii from 1987 to 1990. CO2 concentration steadily increased, but within-year variation has been greater than the annual increase since measurements began in 1957. These variations were thought to be due to seasonal uptake of CO2 during summer months. A newly developed technique for assessing ecosystem NPP has confirmed seasonal variation are driven by seasonal changes in CO2 uptake by vegetation. This has led many scientists and policy makers to speculate that ecosystems can be managed to ameliorate problems with global warming. This type of management may include reforesting or altering forest harvest schedules for many parts of the world. Decomposition and nutrient cycling Decomposition and nutrient cycling are fundamental to ecosystem biomass production. Most natural ecosystems are nitrogen (N) limited and biomass production is closely correlated with N turnover. Typically external input of nutrients is very low and efficient recycling of nutrients maintains productivity. Decomposition of plant litter accounts for the majority of nutrients recycled through ecosystems (Figure 3). Rates of plant litter decomposition are highly dependent on litter quality; high concentration of phenolic compounds, especially lignin, in plant litter has a retarding effect on litter decomposition. More complex C compounds are decomposed more slowly and may take many years to completely breakdown. Decomposition is typically described with exponential decay and has been related to the mineral concentrations, especially manganese, in the leaf litter. Globally, rates of decomposition are mediated by litter quality and climate. Ecosystems dominated by plants with low-lignin concentration often have rapid rates of decomposition and nutrient cycling (Chapin et al. 1982). Simple carbon (C) containing compounds are preferentially metabolized by decomposer microorganisms which results in rapid initial rates of decomposition, see Figure 5A, models that depend on constant rates of decay; so called “k” values, see Figure 5B. In addition to litter quality and climate, the activity of soil fauna is very important However, these models do not reflect simultaneous linear and non-linear decay processes which likely occur during decomposition. For instance, proteins, sugars and lipids decompose exponentially, but lignin decays at a more linear rate Thus, litter decay is inaccurately predicted by simplistic models. A simple alternative model presented in Figure 5C shows significantly more rapid decomposition that the standard model of figure 4B. Better understanding of decomposition models is an important research area of ecosystem ecology because this process is closely tied to nutrient supply and the overall capacity of ecosystems to sequester CO2 from the atmosphere. Trophic dynamics Trophic dynamics refers to process of energy and nutrient transfer between organisms. Trophic dynamics is an important part of the structure and function of ecosystems. Figure 3 shows energy transferred for an ecosystem at Silver Springs, Florida. Energy gained by primary producers (plants, P) is consumed by herbivores (H), which are consumed by carnivores (C), which are themselves consumed by “top- carnivores”(TC). One of the most obvious patterns in Figure 3 is that as one moves up to higher trophic levels (i.e. from plants to top-carnivores) the total amount of energy decreases. Plants exert a “bottom-up” control on the energy structure of ecosystems by determining the total amount of energy that enters the system. However, predators can also influence the structure of lower trophic levels from the top-down. These influences can dramatically shift dominant species in terrestrial and marine systems The interplay and relative strength of top-down vs. bottom-up controls on ecosystem structure and function is an important area of research in the greater field of ecology. Trophic dynamics can strongly influence rates of decomposition and nutrient cycling in time and in space. For example, herbivory can increase litter decomposition and nutrient cycling via direct changes in litter quality and altered dominant vegetation. Insect herbivory has been shown to increase rates of decomposition and nutrient turnover due to changes in litter quality and increased frass inputs. However, insect outbreak does not always increase nutrient cycling. Stadler showed that C rich honeydew produced during aphid outbreak can result in increased N immobilization by soil microbes thus slowing down nutrient cycling and potentially limiting biomass production. North atlantic marine ecosystems have been greatly altered by overfishing of cod. Cod stocks crashed in the 1990s which resulted in increases in their prey such as shrimp and snow crab Human intervention in ecosystems has resulted in dramatic changes to ecosystem structure and function. These changes are occurring rapidly and have unknown consequences for economic security and human well-being. Applications and importance Lessons from two Central American cities The biosphere has been greatly altered by the demands of human societies. Ecosystem ecology plays an important role in understanding and adapting to the most pressing current environmental problems. Restoration ecology and ecosystem management are closely associated with ecosystem ecology. Restoring highly degraded resources depends on integration of functional mechanisms of ecosystems. Without these functions intact, economic value of ecosystems is greatly reduced and potentially dangerous conditions may develop in the field. For example, areas within the mountainous western highlands of Guatemala are more susceptible to catastrophic landslides and crippling seasonal water shortages due to loss of forest resources. In contrast, cities such as Totonicapán that have preserved forests through strong social institutions have greater local economic stability and overall greater human well-being. This situation is striking considering that these areas are close to each other, the majority of inhabitants are of Mayan descent, and the topography and overall resources are similar. This is a case of two groups of people managing resources in fundamentally different ways. Ecosystem ecology provides the basic science needed to avoid degradation and to restore ecosystem processes that provide for basic human needs. See also Biogeochemistry Community ecology Earth system science Holon (philosophy) Landscape ecology Systems ecology MuSIASEM References Systems ecology Global natural environment Ecological processes Ecosystems

Physiology

Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a subdiscipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out chemical and physical functions in a living system. According to the classes of organisms, the field can be divided into medical physiology, animal physiology, plant physiology, cell physiology, and comparative physiology. Central to physiological functioning are biophysical and biochemical processes, homeostatic control mechanisms, and communication between cells. Physiological state is the condition of normal function. In contrast, pathological state refers to abnormal conditions, including human diseases. The Nobel Prize in Physiology or Medicine is awarded by the Royal Swedish Academy of Sciences for exceptional scientific achievements in physiology related to the field of medicine. Foundations Because physiology focuses on the functions and mechanisms of living organisms at all levels, from the molecular and cellular level to the level of whole organisms and populations, its foundations span a range of key disciplines: Anatomy is the study of the structure and organization of living organisms, from the microscopic level of cells and tissues to the macroscopic level of organs and systems. Anatomical knowledge is important in physiology because the structure and function of an organism are often dictated by one another. Biochemistry is the study of the chemical processes and substances that occur within living organisms. Knowledge of biochemistry provides the foundation for understanding cellular and molecular processes that are essential to the functioning of organisms. Biophysics is the study of the physical properties of living organisms and their interactions with their environment. It helps to explain how organisms sense and respond to different stimuli, such as light, sound, and temperature, and how they maintain homeostasis, or a stable internal environment. Genetics is the study of heredity and the variation of traits within and between populations. It provides insights into the genetic basis of physiological processes and the ways in which genes interact with the environment to influence an organism's phenotype. Evolutionary biology is the study of the processes that have led to the diversity of life on Earth. It helps to explain the origin and adaptive significance of physiological processes and the ways in which organisms have evolved to cope with their environment. Subdisciplines There are many ways to categorize the subdisciplines of physiology: based on the taxa studied: human physiology, animal physiology, plant physiology, microbial physiology, viral physiology based on the level of organization: cell physiology, molecular physiology, systems physiology, organismal physiology, ecological physiology, integrative physiology based on the process that causes physiological variation: developmental physiology, environmental physiology, evolutionary physiology based on the ultimate goals of the research: applied physiology (e.g., medical physiology), non-applied (e.g., comparative physiology) Subdisciplines by level of organisation Cell physiology Although there are differences between animal, plant, and microbial cells, the basic physiological functions of cells can be divided into the processes of cell division, cell signaling, cell growth, and cell metabolism. Subdisciplines by taxa Plant physiology Plant physiology is a subdiscipline of botany concerned with the functioning of plants. Closely related fields include plant morphology, plant ecology, phytochemistry, cell biology, genetics, biophysics, and molecular biology. Fundamental processes of plant physiology include photosynthesis, respiration, plant nutrition, tropisms, nastic movements, photoperiodism, photomorphogenesis, circadian rhythms, seed germination, dormancy, and stomata function and transpiration. Absorption of water by roots, production of food in the leaves, and growth of shoots towards light are examples of plant physiology. Animal physiology Human physiology Human physiology is the study of how the human body's systems and functions work together to maintain a stable internal environment. It includes the study of the nervous, endocrine, cardiovascular, respiratory, digestive, and urinary systems, as well as cellular and exercise physiology. Understanding human physiology is essential for diagnosing and treating health conditions and promoting overall wellbeing. It seeks to understand the mechanisms that work to keep the human body alive and functioning, through scientific enquiry into the nature of mechanical, physical, and biochemical functions of humans, their organs, and the cells of which they are composed. The principal level of focus of physiology is at the level of organs and systems within systems. The endocrine and nervous systems play major roles in the reception and transmission of signals that integrate function in animals. Homeostasis is a major aspect with regard to such interactions within plants as well as animals. The biological basis of the study of physiology, integration refers to the overlap of many functions of the systems of the human body, as well as its accompanied form. It is achieved through communication that occurs in a variety of ways, both electrical and chemical. Changes in physiology can impact the mental functions of individuals. Examples of this would be the effects of certain medications or toxic levels of substances. Change in behavior as a result of these substances is often used to assess the health of individuals. Much of the foundation of knowledge in human physiology was provided by animal experimentation. Due to the frequent connection between form and function, physiology and anatomy are intrinsically linked and are studied in tandem as part of a medical curriculum. Subdisciplines by research objective Comparative physiology Involving evolutionary physiology and environmental physiology, comparative physiology considers the diversity of functional characteristics across organisms. History The classical era The study of human physiology as a medical field originates in classical Greece, at the time of Hippocrates (late 5th century BC). Outside of Western tradition, early forms of physiology or anatomy can be reconstructed as having been present at around the same time in China, India and elsewhere. Hippocrates incorporated the theory of humorism, which consisted of four basic substances: earth, water, air and fire. Each substance is known for having a corresponding humor: black bile, phlegm, blood, and yellow bile, respectively. Hippocrates also noted some emotional connections to the four humors, on which Galen would later expand. The critical thinking of Aristotle and his emphasis on the relationship between structure and function marked the beginning of physiology in Ancient Greece. Like Hippocrates, Aristotle took to the humoral theory of disease, which also consisted of four primary qualities in life: hot, cold, wet and dry. Galen (–200 AD) was the first to use experiments to probe the functions of the body. Unlike Hippocrates, Galen argued that humoral imbalances can be located in specific organs, including the entire body. His modification of this theory better equipped doctors to make more precise diagnoses. Galen also played off of Hippocrates' idea that emotions were also tied to the humors, and added the notion of temperaments: sanguine corresponds with blood; phlegmatic is tied to phlegm; yellow bile is connected to choleric; and black bile corresponds with melancholy. Galen also saw the human body consisting of three connected systems: the brain and nerves, which are responsible for thoughts and sensations; the heart and arteries, which give life; and the liver and veins, which can be attributed to nutrition and growth. Galen was also the founder of experimental physiology. And for the next 1,400 years, Galenic physiology was a powerful and influential tool in medicine. Early modern period Jean Fernel (1497–1558), a French physician, introduced the term "physiology". Galen, Ibn al-Nafis, Michael Servetus, Realdo Colombo, Amato Lusitano and William Harvey, are credited as making important discoveries in the circulation of the blood. Santorio Santorio in 1610s was the first to use a device to measure the pulse rate (the pulsilogium), and a thermoscope to measure temperature. In 1791 Luigi Galvani described the role of electricity in the nerves of dissected frogs. In 1811, César Julien Jean Legallois studied respiration in animal dissection and lesions and found the center of respiration in the medulla oblongata. In the same year, Charles Bell finished work on what would later become known as the Bell–Magendie law, which compared functional differences between dorsal and ventral roots of the spinal cord. In 1824, François Magendie described the sensory roots and produced the first evidence of the cerebellum's role in equilibration to complete the Bell–Magendie law. In the 1820s, the French physiologist Henri Milne-Edwards introduced the notion of physiological division of labor, which allowed to "compare and study living things as if they were machines created by the industry of man." Inspired in the work of Adam Smith, Milne-Edwards wrote that the "body of all living beings, whether animal or plant, resembles a factory ... where the organs, comparable to workers, work incessantly to produce the phenomena that constitute the life of the individual." In more differentiated organisms, the functional labor could be apportioned between different instruments or systems (called by him as appareils). In 1858, Joseph Lister studied the cause of blood coagulation and inflammation that resulted after previous injuries and surgical wounds. He later discovered and implemented antiseptics in the operating room, and as a result, decreased the death rate from surgery by a substantial amount. The Physiological Society was founded in London in 1876 as a dining club. The American Physiological Society (APS) is a nonprofit organization that was founded in 1887. The Society is, "devoted to fostering education, scientific research, and dissemination of information in the physiological sciences." In 1891, Ivan Pavlov performed research on "conditional responses" that involved dogs' saliva production in response to a bell and visual stimuli. In the 19th century, physiological knowledge began to accumulate at a rapid rate, in particular with the 1838 appearance of the Cell theory of Matthias Schleiden and Theodor Schwann. It radically stated that organisms are made up of units called cells. Claude Bernard's (1813–1878) further discoveries ultimately led to his concept of milieu interieur (internal environment), which would later be taken up and championed as "homeostasis" by American physiologist Walter B. Cannon in 1929. By homeostasis, Cannon meant "the maintenance of steady states in the body and the physiological processes through which they are regulated." In other words, the body's ability to regulate its internal environment. William Beaumont was the first American to utilize the practical application of physiology. Nineteenth-century physiologists such as Michael Foster, Max Verworn, and Alfred Binet, based on Haeckel's ideas, elaborated what came to be called "general physiology", a unified science of life based on the cell actions, later renamed in the 20th century as cell biology. Late modern period In the 20th century, biologists became interested in how organisms other than human beings function, eventually spawning the fields of comparative physiology and ecophysiology. Major figures in these fields include Knut Schmidt-Nielsen and George Bartholomew. Most recently, evolutionary physiology has become a distinct subdiscipline. In 1920, August Krogh won the Nobel Prize for discovering how, in capillaries, blood flow is regulated. In 1954, Andrew Huxley and Hugh Huxley, alongside their research team, discovered the sliding filaments in skeletal muscle, known today as the sliding filament theory. Recently, there have been intense debates about the vitality of physiology as a discipline (Is it dead or alive?). If physiology is perhaps less visible nowadays than during the golden age of the 19th century, it is in large part because the field has given birth to some of the most active domains of today's biological sciences, such as neuroscience, endocrinology, and immunology. Furthermore, physiology is still often seen as an integrative discipline, which can put together into a coherent framework data coming from various different domains. Notable physiologists Women in physiology Initially, women were largely excluded from official involvement in any physiological society. The American Physiological Society, for example, was founded in 1887 and included only men in its ranks. In 1902, the American Physiological Society elected Ida Hyde as the first female member of the society. Hyde, a representative of the American Association of University Women and a global advocate for gender equality in education, attempted to promote gender equality in every aspect of science and medicine. Soon thereafter, in 1913, J.S. Haldane proposed that women be allowed to formally join The Physiological Society, which had been founded in 1876. On 3 July 1915, six women were officially admitted: Florence Buchanan, Winifred Cullis, Ruth Skelton, Sarah C. M. Sowton, Constance Leetham Terry, and Enid M. Tribe. The centenary of the election of women was celebrated in 2015 with the publication of the book "Women Physiologists: Centenary Celebrations And Beyond For The Physiological Society." Prominent women physiologists include: Bodil Schmidt-Nielsen, the first woman president of the American Physiological Society in 1975. Gerty Cori, along with her husband Carl Cori, received the Nobel Prize in Physiology or Medicine in 1947 for their discovery of the phosphate-containing form of glucose known as glycogen, as well as its function within eukaryotic metabolic mechanisms for energy production. Moreover, they discovered the Cori cycle, also known as the Lactic acid cycle, which describes how muscle tissue converts glycogen into lactic acid via lactic acid fermentation. Barbara McClintock was rewarded the 1983 Nobel Prize in Physiology or Medicine for the discovery of genetic transposition. McClintock is the only female recipient who has won an unshared Nobel Prize. Gertrude Elion, along with George Hitchings and Sir James Black, received the Nobel Prize for Physiology or Medicine in 1988 for their development of drugs employed in the treatment of several major diseases, such as leukemia, some autoimmune disorders, gout, malaria, and viral herpes. Linda B. Buck, along with Richard Axel, received the Nobel Prize in Physiology or Medicine in 2004 for their discovery of odorant receptors and the complex organization of the olfactory system. Françoise Barré-Sinoussi, along with Luc Montagnier, received the Nobel Prize in Physiology or Medicine in 2008 for their work on the identification of the Human Immunodeficiency Virus (HIV), the cause of Acquired Immunodeficiency Syndrome (AIDS). Elizabeth Blackburn, along with Carol W. Greider and Jack W. Szostak, was awarded the 2009 Nobel Prize for Physiology or Medicine for the discovery of the genetic composition and function of telomeres and the enzyme called telomerase. See also Outline of physiology Biochemistry Biophysics Cytoarchitecture Defense physiology Ecophysiology Exercise physiology Fish physiology Insect physiology Human body Molecular biology Metabolome Neurophysiology Pathophysiology Pharmacology Physiome American Physiological Society International Union of Physiological Sciences The Physiological Society Brazilian Society of Physiology References Bibliography Human physiology Widmaier, E.P., Raff, H., Strang, K.T. Vander's Human Physiology. 11th Edition, McGraw-Hill, 2009. Marieb, E.N. Essentials of Human Anatomy and Physiology. 10th Edition, Benjamin Cummings, 2012. Animal physiology Hill, R.W., Wyse, G.A., Anderson, M. Animal Physiology, 3rd ed. Sinauer Associates, Sunderland, 2012. Moyes, C.D., Schulte, P.M. Principles of Animal Physiology, second edition. Pearson/Benjamin Cummings. Boston, MA, 2008. Randall, D., Burggren, W., and French, K. Eckert Animal Physiology: Mechanism and Adaptation, 5th Edition. W.H. Freeman and Company, 2002. Schmidt-Nielsen, K. Animal Physiology: Adaptation and Environment. Cambridge & New York: Cambridge University Press, 1997. Withers, P.C. Comparative animal physiology. Saunders College Publishing, New York, 1992. Plant physiology Larcher, W. Physiological plant ecology (4th ed.). Springer, 2001. Salisbury, F.B, Ross, C.W. Plant physiology. Brooks/Cole Pub Co., 1992 Taiz, L., Zieger, E. Plant Physiology (5th ed.), Sunderland, Massachusetts: Sinauer, 2010. Fungal physiology Griffin, D.H. Fungal Physiology, Second Edition. Wiley-Liss, New York, 1994. Protistan physiology Levandowsky, M. Physiological Adaptations of Protists. In: Cell physiology sourcebook: essentials of membrane biophysics. Amsterdam; Boston: Elsevier/AP, 2012. Levandowski, M., Hutner, S.H. (eds). Biochemistry and physiology of protozoa. Volumes 1, 2, and 3. Academic Press: New York, NY, 1979; 2nd ed. Laybourn-Parry J. A Functional Biology of Free-Living Protozoa. Berkeley, California: University of California Press; 1984. Algal physiology Lobban, C.S., Harrison, P.J. Seaweed ecology and physiology. Cambridge University Press, 1997. Stewart, W. D. P. (ed.). Algal Physiology and Biochemistry. Blackwell Scientific Publications, Oxford, 1974. Bacterial physiology El-Sharoud, W. (ed.). Bacterial Physiology: A Molecular Approach. Springer-Verlag, Berlin-Heidelberg, 2008. Kim, B.H., Gadd, M.G. Bacterial Physiology and Metabolism. Cambridge, 2008. Moat, A.G., Foster, J.W., Spector, M.P. Microbial Physiology, 4th ed. Wiley-Liss, Inc. New York, NY, 2002. External links physiologyINFO.org – public information site sponsored by the American Physiological Society Branches of biology

Systematics

Systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees (synonyms: phylogenetic trees, phylogenies). Phylogenies have two components: branching order (showing group relationships, graphically represented in cladograms) and branch length (showing amount of evolution). Phylogenetic trees of species and higher taxa are used to study the evolution of traits (e.g., anatomical or molecular characteristics) and the distribution of organisms (biogeography). Systematics, in other words, is used to understand the evolutionary history of life on Earth. The word systematics is derived from the Latin word of Ancient Greek origin systema, which means systematic arrangement of organisms. Carl Linnaeus used 'Systema Naturae' as the title of his book. Branches and applications In the study of biological systematics, researchers use the different branches to further understand the relationships between differing organisms. These branches are used to determine the applications and uses for modern day systematics. Biological systematics classifies species by using three specific branches. Numerical systematics, or biometry, uses biological statistics to identify and classify animals. Biochemical systematics classifies and identifies animals based on the analysis of the material that makes up the living part of a cell—such as the nucleus, organelles, and cytoplasm. Experimental systematics identifies and classifies animals based on the evolutionary units that comprise a species, as well as their importance in evolution itself. Factors such as mutations, genetic divergence, and hybridization all are considered evolutionary units. With the specific branches, researchers are able to determine the applications and uses for modern-day systematics. These applications include: Studying the diversity of organisms and the differentiation between extinct and living creatures. Biologists study the well-understood relationships by making many different diagrams and "trees" (cladograms, phylogenetic trees, phylogenies, etc.). Including the scientific names of organisms, species descriptions and overviews, taxonomic orders, and classifications of evolutionary and organism histories. Explaining the biodiversity of the planet and its organisms. The systematic study is that of conservation. Manipulating and controlling the natural world. This includes the practice of 'biological control', the intentional introduction of natural predators and disease. Definition and relation with taxonomy John Lindley provided an early definition of systematics in 1830, although he wrote of "systematic botany" rather than using the term "systematics". In 1970 Michener et al. defined "systematic biology" and "taxonomy" (terms that are often confused and used interchangeably) in relationship to one another as follows: Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific names for organisms, (b) describes them, (c) preserves collections of them, (d) provides classifications for the organisms, keys for their identification, and data on their distributions, (e) investigates their evolutionary histories, and (f) considers their environmental adaptations. This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above. The term "taxonomy" was coined by Augustin Pyramus de Candolle while the term "systematic" was coined by Carl Linnaeus the father of taxonomy. Taxonomy, systematic biology, systematics, biosystematics, scientific classification, biological classification, phylogenetics: At various times in history, all these words have had overlapping, related meanings. However, in modern usage, they can all be considered synonyms of each other. For example, Webster's 9th New Collegiate Dictionary of 1987 treats "classification", "taxonomy", and "systematics" as synonyms. According to this work, the terms originated in 1790, c. 1828, and in 1888 respectively. Some claim systematics alone deals specifically with relationships through time, and that it can be synonymous with phylogenetics, broadly dealing with the inferred hierarchy of organisms. This means it would be a subset of taxonomy as it is sometimes regarded, but the inverse is claimed by others. Europeans tend to use the terms "systematics" and "biosystematics" for the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently. However, taxonomy, and in particular alpha taxonomy, is more specifically the identification, description, and naming (i.e. nomenclature) of organisms, while "classification" focuses on placing organisms within hierarchical groups that show their relationships to other organisms. All of these biological disciplines can deal with both extinct and extant organisms. Systematics uses taxonomy as a primary tool in understanding, as nothing about an organism's relationships with other living things can be understood without it first being properly studied and described in sufficient detail to identify and classify it correctly. Scientific classifications are aids in recording and reporting information to other scientists and to laymen. The systematist, a scientist who specializes in systematics, must, therefore, be able to use existing classification systems, or at least know them well enough to skilfully justify not using them. Phenetics was an attempt to determine the relationships of organisms through a measure of overall similarity, making no distinction between plesiomorphies (shared ancestral traits) and apomorphies (derived traits). From the late-20th century onwards, it was superseded by cladistics, which rejects plesiomorphies in attempting to resolve the phylogeny of Earth's various organisms through time. systematists generally make extensive use of molecular biology and of computer programs to study organisms. Taxonomic characters Taxonomic characters are the taxonomic attributes that can be used to provide the evidence from which relationships (the phylogeny) between taxa are inferred. Kinds of taxonomic characters include: Morphological characters General external morphology Special structures (e.g. genitalia) Internal morphology (anatomy) Embryology Karyology and other cytological factors Physiological characters Metabolic factors Body secretions Genic sterility factors Molecular characters Immunological distance Electrophoretic differences Amino acid sequences of proteins DNA hybridization DNA and RNA sequences Restriction endonuclease analyses Other molecular differences Behavioral characters Courtship and other ethological isolating mechanisms Other behavior patterns Ecological characters Habit and habitats Food Seasonal variations Parasites and hosts Geographic characters General biogeographic distribution patterns Sympatric-allopatric relationship of populations See also Cladistics – a methodology in systematics Evolutionary systematics – a school of systematics Global biodiversity Phenetics – a methodology in systematics that does not infer phylogeny Phylogeny – the historical relationships between lineages of organism 16S ribosomal RNA – an intensively studied nucleic acid that has been useful in phylogenetics Phylogenetic comparative methods – use of evolutionary trees in other studies, such as biodiversity, comparative biology. adaptation, or evolutionary mechanisms References Notes Further reading Brower, Andrew V. Z. and Randall T. Schuh. 2021. Biological Systematics: Principles and Applications, 3rd edn. Simpson, Michael G. 2005. Plant Systematics. Wiley, Edward O. and Bruce S. Lieberman. 2011. "Phylogenetics: Theory and Practice of Phylogenetic Systematics, 2nd edn." External links Society of Australian Systematic Biologists Society of Systematic Biologists The Willi Hennig Society Evolutionary biology Biological classification

Biophysics

Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology. The term biophysics was originally introduced by Karl Pearson in 1892. The term biophysics is also regularly used in academia to indicate the study of the physical quantities (e.g. electric current, temperature, stress, entropy) in biological systems. Other biological sciences also perform research on the biophysical properties of living organisms including molecular biology, cell biology, chemical biology, and biochemistry. Overview Molecular biophysics typically addresses biological questions similar to those in biochemistry and molecular biology, seeking to find the physical underpinnings of biomolecular phenomena. Scientists in this field conduct research concerned with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis, as well as how these interactions are regulated. A great variety of techniques are used to answer these questions. Fluorescent imaging techniques, as well as electron microscopy, x-ray crystallography, NMR spectroscopy, atomic force microscopy (AFM) and small-angle scattering (SAS) both with X-rays and neutrons (SAXS/SANS) are often used to visualize structures of biological significance. Protein dynamics can be observed by neutron spin echo spectroscopy. Conformational change in structure can be measured using techniques such as dual polarisation interferometry, circular dichroism, SAXS and SANS. Direct manipulation of molecules using optical tweezers or AFM, can also be used to monitor biological events where forces and distances are at the nanoscale. Molecular biophysicists often consider complex biological events as systems of interacting entities which can be understood e.g. through statistical mechanics, thermodynamics and chemical kinetics. By drawing knowledge and experimental techniques from a wide variety of disciplines, biophysicists are often able to directly observe, model or even manipulate the structures and interactions of individual molecules or complexes of molecules. In addition to traditional (i.e. molecular and cellular) biophysical topics like structural biology or enzyme kinetics, modern biophysics encompasses an extraordinarily broad range of research, from bioelectronics to quantum biology involving both experimental and theoretical tools. It is becoming increasingly common for biophysicists to apply the models and experimental techniques derived from physics, as well as mathematics and statistics, to larger systems such as tissues, organs, populations and ecosystems. Biophysical models are used extensively in the study of electrical conduction in single neurons, as well as neural circuit analysis in both tissue and whole brain. Medical physics, a branch of biophysics, is any application of physics to medicine or healthcare, ranging from radiology to microscopy and nanomedicine. For example, physicist Richard Feynman theorized about the future of nanomedicine. He wrote about the idea of a medical use for biological machines (see nanomachines). Feynman and Albert Hibbs suggested that certain repair machines might one day be reduced in size to the point that it would be possible to (as Feynman put it) "swallow the doctor". The idea was discussed in Feynman's 1959 essay There's Plenty of Room at the Bottom. History The studies of Luigi Galvani (1737–1798) laid groundwork for the later field of biophysics. Some of the earlier studies in biophysics were conducted in the 1840s by a group known as the Berlin school of physiologists. Among its members were pioneers such as Hermann von Helmholtz, Ernst Heinrich Weber, Carl F. W. Ludwig, and Johannes Peter Müller. William T. Bovie (1882–1958) is credited as a leader of the field's further development in the mid-20th century. He was a leader in developing electrosurgery. The popularity of the field rose when the book What Is Life?'' by Erwin Schrödinger was published. Since 1957, biophysicists have organized themselves into the Biophysical Society which now has about 9,000 members over the world. Some authors such as Robert Rosen criticize biophysics on the ground that the biophysical method does not take into account the specificity of biological phenomena. Focus as a subfield While some colleges and universities have dedicated departments of biophysics, usually at the graduate level, many do not have university-level biophysics departments, instead having groups in related departments such as biochemistry, cell biology, chemistry, computer science, engineering, mathematics, medicine, molecular biology, neuroscience, pharmacology, physics, and physiology. Depending on the strengths of a department at a university differing emphasis will be given to fields of biophysics. What follows is a list of examples of how each department applies its efforts toward the study of biophysics. This list is hardly all inclusive. Nor does each subject of study belong exclusively to any particular department. Each academic institution makes its own rules and there is much overlap between departments. Biology and molecular biology – Gene regulation, single protein dynamics, bioenergetics, patch clamping, biomechanics, virophysics. Structural biology – Ångstrom-resolution structures of proteins, nucleic acids, lipids, carbohydrates, and complexes thereof. Biochemistry and chemistry – biomolecular structure, siRNA, nucleic acid structure, structure-activity relationships. Computer science – Neural networks, biomolecular and drug databases. Computational chemistry – molecular dynamics simulation, molecular docking, quantum chemistry Bioinformatics – sequence alignment, structural alignment, protein structure prediction Mathematics – graph/network theory, population modeling, dynamical systems, phylogenetics. Medicine – biophysical research that emphasizes medicine. Medical biophysics is a field closely related to physiology. It explains various aspects and systems of the body from a physical and mathematical perspective. Examples are fluid dynamics of blood flow, gas physics of respiration, radiation in diagnostics/treatment and much more. Biophysics is taught as a preclinical subject in many medical schools, mainly in Europe. Neuroscience – studying neural networks experimentally (brain slicing) as well as theoretically (computer models), membrane permittivity. Pharmacology and physiology – channelomics, electrophysiology, biomolecular interactions, cellular membranes, polyketides. Physics – negentropy, stochastic processes, and the development of new physical techniques and instrumentation as well as their application. Quantum biology – The field of quantum biology applies quantum mechanics to biological objects and problems. Decohered isomers to yield time-dependent base substitutions. These studies imply applications in quantum computing. Agronomy and agriculture Many biophysical techniques are unique to this field. Research efforts in biophysics are often initiated by scientists who were biologists, chemists or physicists by training. See also Biophysical Society Index of biophysics articles List of publications in biology – Biophysics List of publications in physics – Biophysics List of biophysicists Outline of biophysics Biophysical chemistry European Biophysical Societies' Association Mathematical and theoretical biology Medical biophysics Membrane biophysics Molecular biophysics Neurophysics Physiomics Virophysics Single-particle trajectory References Sources External links Biophysical Society Journal of Physiology: 2012 virtual issue Biophysics and Beyond bio-physics-wiki Link archive of learning resources for students: biophysika.de (60% English, 40% German) Applied and interdisciplinary physics

Evolution

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