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Organism

2007 Schools Wikipedia Selection. Related subjects: General Biology

   A crab is an example of an organism.
   Enlarge
   A crab is an example of an organism.

   In biology and ecology, an organism (in Greek organon = instrument) is
   a living complex adaptive system of organs that influence each other in
   such a way that they function in some way as a stable whole.

   The origin of life on earth and the relationships between its major
   lineages are controversial. Two main grades may be distinguished, the
   prokaryotes and eukaryotes. The prokaryotes are generally considered to
   represent two separate domains, called the Bacteria and Archaea, which
   are not closer to one another than to the eukaryotes. The gap between
   prokaryotes and eukaryotes is widely considered a major missing link in
   evolutionary history. Two eukaryotic organelles, namely mitochondria
   and chloroplasts, are generally considered to be derived from
   endosymbiotic bacteria.

   The phrase complex organism describes any organism with more than one
   cell.

Semantics

   The word "organism" may broadly be defined as an assembly of molecules
   that influence each other in such a way that they function as a more or
   less stable whole and have properties of life. However, many sources,
   lexical and scientific, add conditions that are problematic to defining
   the word.

   The Oxford English Dictionary defines an organism as "[an] individual
   animal, plant, or single-celled life form" This definition
   problematically excludes non-animal and plant multi-cellular life forms
   such as some fungi and protista. Less controversially, perhaps, it
   excludes viruses and theoretically-possible man-made non-organic life
   forms.
   A polypores mushroom has symbiotic relationship with this Birch Tree
   Enlarge
   A polypores mushroom has symbiotic relationship with this Birch Tree

   Chambers Online Reference provides a much broader definition: "any
   living structure, such as a plant, animal, fungus or bacterium, capable
   of growth and reproduction". The definition emphasises life; it allows
   for any life form, organic or otherwise, to be considered an organism.
   This does encompass all cellular life, as well as possible synthetic
   life. This definition does lack the anything approximating to the word
   "individual" which would exclude viruses.
   An ericoid mycorrhizal fungus
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   An ericoid mycorrhizal fungus

   The word "organism" usually describes an independent collections of
   systems (for example circulatory system, digestive system, reproductive
   system, themselves collections of organs; these are, in turn,
   collections of tissues, which are themselves made of cells. The concept
   of an organism can be challenged on grounds that organisms themselves
   are never truly independent of an ecosystem; groups or populations of
   organisms function in an ecosystem in a manner not unlike the function
   of multicellular tissues in an organism; when organisms enter into
   strict symbiosis, they are not independent in any sense that could not
   also be conferred upon an organ or a tissue. Symbiotic plant and algae
   relationships do consist of radically different DNA structures between
   contrasting groups of tissues, sufficient to recognize their
   reproductive independence. However, in a similar way, an organ within
   an "organism" (say, a stomach) can have an independent and complex
   interdependent relationship to separate whole organisms, or groups of
   organisms (a population of viruses, or bacteria), without which the
   organ's stable function would transform or cease. Other organs within
   that system (say, the ribcage) might be affected only indirectly by
   such an arrangement, much the same way species' affect one another
   indirectly in an ecosystem. Thus, the boundaries of the organism are
   nearly always disputable, and all living matter exists within larger
   heterarchical systems of life, made of wide varieties of transient
   living and dead tissues, and functioning in complex and dynamic
   relationships to one another.

Viruses

   Viruses are not typically considered to be organisms because they are
   not capable of independent reproduction or metabolism. This controversy
   is problematic, though, since some parasites and endosymbionts are
   incapable of independent life either. Although viruses do have enzymes
   and molecules characteristic of living organisms, they are incapable of
   surviving outside a host cell and most of their metabolic processes
   require a host and its 'genetic machinery'.

Superorganism

   A superorganism is an organism consisting of many organisms. This is
   usually meant to be a social unit of eusocial animals, where division
   of labour is highly specialised and where individuals are not able to
   survive by themselves for extended periods of time. Ants are the most
   well known example of such a superorganism. Thermoregulation, a feature
   usually exhibited by individual organisms, does not occur in
   individuals or small groups of honeybees of the species Apis mellifera.
   When these bees pack together in clusters of between 5000 and 40000,
   the colony can thermoregulate. James Lovelock, with his " Gaia Theory"
   has paralleled the work of Vladimir Vernadsky, who suggested the whole
   of the biosphere in some respects can be considered as a superorganism.
   A sea sponge is a very simple type of multicellular organism
   Enlarge
   A sea sponge is a very simple type of multicellular organism

   The concept of superorganism is under dispute, as many biologists
   maintain that in order for a social unit to be considered an organism
   by itself, the individuals should be in permanent physical connection
   to each other, and its evolution should be governed by selection to the
   whole society instead of individuals. While it's generally accepted
   that the society of eusocial animals is a unit of natural selection to
   at least some extent, most evolutionists claim that the individuals are
   still the primary units of selection.

   The question remains "What is to be considered the individual?".
   Darwinians like Richard Dawkins suggest that the individual selected is
   the " Selfish Gene". Others believe it is the whole genome of an
   organism. E.O. Wilson has shown that with ant-colonies and other social
   insects it is the breeding entity of the colony that is selected, and
   not its individual members. This could apply to the bacterial members
   of a stromatolite, which, because of genetic sharing, in some way
   comprise a single gene pool. Gaian theorists like Lynn Margulis would
   argue this applies equally to the symbiogenesis of the bacterial
   underpinnings of the whole of the Earth.

   It would appear, from computer simulations like Daisyworld that
   biological selection occurs at multiple levels simultaneously.

   It is also argued that humans are actually a superorganism that
   includes microorganisms such as bacteria. It is estimated that "the
   human intestinal microbiota is composed of 10^13 to 10^14
   microorganisms whose collective genome (" microbiome") contains at
   least 100 times as many genes as our own[...] Our microbiome has
   significantly enriched metabolism of glycans, amino acids, and
   xenobiotics; methanogenesis; and 2-methyl-D-erythritol 4-phosphate
   pathway–mediated biosynthesis of vitamins and isoprenoids. Thus, humans
   are superorganisms whose metabolism represents an amalgamation of
   microbial and human attributes." .

Organizational terminology

   All organisms are classified by the science of alpha taxonomy into
   either taxa or clades.

   Taxa are ranked groups of organisms which run from the general (
   domain) to the specific ( species). A broad scheme of ranks in
   hierarchical order is:
     * Domain
     * Kingdom
     * Phylum
     * Class
     * Order
     * Family
     * Genus
     * Species

   To give an example, Homo sapiens is the Latin binomial equating to
   modern humans. All members of the species sapiens are, at least in
   theory, genetically able to interbreed. Several species may belong to a
   genus, but the members of different species within a genus are unable
   to interbreed to produce fertile offspring. Homo, however, only has one
   surviving species (sapiens); Homo erectus, Homo neanderthalensis, &c.
   having become extinct thousands of years ago. Several genera belong to
   the same family and so on up the hierarchy. Eventually, the relevant
   kingdom (Animalia, in the case of humans) is placed into one of the
   three domains depending upon certain genetic and structural
   characteristics.

   All living organisms known to science are given classification by this
   system such that the species within a particular family are more
   closely related and genetically similar than the species within a
   particular phylum.

Chemistry

   Organisms are complex chemical reactions, organized in ways that
   promote reproduction and some measure of sustainability or survival.
   The molecular phenomena of chemistry are fundamental in understanding
   organisms, but it is a philosophical error (reductionism) to reduce
   organismal biology to mere chemistry. It is generally the phenomena of
   entire organisms that determine their fitness to an environment and
   therefore the survivability of their DNA based genes.

   Organisms clearly owe their origin, metabolism, and many other internal
   functions to the phenomena at the level of chemistry, especially the
   chemistry of large organic molecules. Organisms are complex systems of
   chemical compounds which, through interaction with each other and the
   environment, play a wide variety of roles.

   Organisms are semi-closed chemical systems. Although they are
   individual units of life (as the definition requires) they are not
   closed to the environment around them. To operate they constantly take
   in and release energy. Autotrophs produce usable energy (in the form of
   organic compounds) using light from the sun or inorganic compounds
   while heterotrophs take in organic compounds from the environment.

   The primary chemical element in these compounds is carbon. The physical
   properties of this element such as its great affinity for bonding with
   other small atoms, including other carbon atoms, and its small size
   makes it capable of forming multiple bonds, make it ideal as the basis
   of organic life. It is able to form small compounds containing three
   atoms (such as carbon dioxide) as well as large chains of many
   thousands of atoms which are able to store data ( nucleic acids), hold
   cells together and transmit information (protein).

   Some branches of biology, especially ecology, do not gain significant
   benefit from reduction to chemical reactions.

Macromolecules

   The compounds which make up organisms may be divided into
   macromolecules and other, smaller molecules. The four groups of
   macromolecule are nucleic acids, proteins, carbohydrates and lipids.
   Nucleic acids (specifically deoxyribonucleic acid, or DNA) store
   genetic data as a sequence of nucleotides. The particular sequence of
   the four different types of nucleotides ( adenine, cytosine, guanine,
   and thymine) dictate the many characteristics which constitute the
   organism. The sequence is divided up into codons, each of which is a
   particular sequence of three nucleotides and corresponds to a
   particular amino acid. Thus a a sequence of DNA codes for a particular
   protein which, due to the chemical properties of the amino acids of
   which it is made, folds in a particular manner and so performs a
   particular function.

   The following functions of protein have been recognized:
    1. Enzymes, which catalyze all of the reactions of metabolism;
    2. Structural proteins, such as tubulin, or collagen;
    3. Regulatory proteins, such as transcription factors or cyclins that
       regulate the cell cycle;
    4. Signalling molecules or their receptors such as some hormones and
       their receptors;
    5. Defensive proteins, which can include everything from antibodies of
       the immune system, to toxins (e.g., dendrotoxins of snakes), to
       proteins that include unusual amino acids like canavanine.

   Lipids make up the membrane of cells which constitutes a barrier,
   containing everything within the cell and preventing compounds from
   freely passing into, and out of, the cell. In some multi-cellular
   organisms they serve to store energy and mediate communication between
   cells. Carbohydrates also store and transport energy in some organisms,
   but are more easily broken down than lipids.

Structure

   All organisms consist of monomeric units called cells; some contain a
   single cell ( unicellular) and others contain many units (
   multicellular). Multicellular organisms are able to specialise cells to
   perform specific functions, a group of such cells is tissue the four
   basic types of which are epithelium, nervous tissue, muscle tissue and
   connective tissue. Several types of tissue work together in the form of
   an organ to produce a particular function (such as the pumping of the
   blood by the heart, or as a barrier to the environment as the skin).
   This pattern continues to a higher level with several organs
   functioning as an organ system to allow for reproduction, digestion,
   &c. Many multicelled organisms comprise of several organ systems which
   coordinate to allow for life.

The cell

   The cell theory, first developed in 1839 by Schleiden and Schwann,
   states that all organisms are composed of one or more cells; all cells
   come from preexisting cells; all vital functions of an organism occur
   within cells, and cells contain the hereditary information necessary
   for regulating cell functions and for transmitting information to the
   next generation of cells.

   There are two types of cells, eukaryotic and prokaryotic. Prokaryotic
   cells are usually singletons, while eukaryotic cells are usually found
   in multi-cellular organisms. Prokaryotic cells lack a nuclear membrane
   so DNA is unbound within the cell, eukaryotic cells have nuclear
   membranes.

   All cells, whether prokaryotic or eukaryotic, have a membrane, which
   envelopes the cell, separates its interior from its environment,
   regulates what moves in and out, and maintains the electric potential
   of the cell. Inside the membrane, a salty cytoplasm takes up most of
   the cell volume. All cells possess DNA, the hereditary material of
   genes, and RNA, containing the information necessary to build various
   proteins such as enzymes, the cell's primary machinery. There are also
   other kinds of biomolecules in cells.

   All cells share several abilities:
     * Reproduction by cell division ( binary fission, mitosis or
       meiosis).
     * Use of enzymes and other proteins coded for by DNA genes and made
       via messenger RNA intermediates and ribosomes.
     * Metabolism, including taking in raw materials, building cell
       components, converting energy, molecules and releasing by-products.
       The functioning of a cell depends upon its ability to extract and
       use chemical energy stored in organic molecules. This energy is
       derived from metabolic pathways.
     * Response to external and internal stimuli such as changes in
       temperature, pH or nutrient levels.
     * Cell contents are contained within a cell surface membrane that
       contains proteins and a lipid bilayera.

Life span

   One of the basic parameters of organism is its life span. Some animals
   live as short as one day, while some plants can live thousands of
   years. Aging is important when determining life span of most organisms,
   bacterium, a virus or even a prion.

Evolution

   A hypothetical phylogenetic tree of all extant organisms, based on 16S
   rRNA gene sequence data, showing the evolutionary history of the three
   domains of life, bacteria, archaea and eukaryotes. Originally proposed
   by Carl Woese.
   Enlarge
   A hypothetical phylogenetic tree of all extant organisms, based on 16S
   rRNA gene sequence data, showing the evolutionary history of the three
   domains of life, bacteria, archaea and eukaryotes. Originally proposed
   by Carl Woese.

   In biology, the theory of universal common descent proposes that all
   organisms on Earth are descended from a common ancestor or ancestral
   gene pool.

   Evidence for common descent may be found in traits shared between all
   living organisms. In Darwin's day, the evidence of shared traits was
   based solely on visible observation of morphologic similarities, such
   as the fact that all birds have wings, even those which do not fly.
   Today, there is strong evidence from genetics that all organisms have a
   common ancestor. For example, every living cell makes use of nucleic
   acids as its genetic material, and uses the same twenty amino acids as
   the building blocks for proteins. All organisms use the same genetic
   code (with some extremely rare and minor deviations) to translate
   nucleic acid sequences into proteins. The universality of these traits
   strongly suggests common ancestry, because the selection of many of
   these traits seems arbitrary.

   Information about the early development of life includes input from the
   fields of geology and planetary science. These sciences provide
   information about the history of the Earth and the changes produced by
   life. However, a great deal of information about the early Earth has
   been destroyed by geological processes over the course of time.

History of life

   The chemical evolution from self-catalytic chemical reactions to life
   (see Origin of life) is not a part of biological evolution, but it is
   unclear at which point such increasingly complex sets of reactions
   became what we would consider, today, to be living organisms.
   Precambrian stromatolites in the Siyeh Formation, Glacier National
   Park. In 2002, William Schopf of UCLA published a controversial paper
   in the journal Nature arguing that formations such as this possess 3.5
   billion year old fossilized algae microbes. If true, they would be the
   earliest known life on earth.
   Enlarge
   Precambrian stromatolites in the Siyeh Formation, Glacier National
   Park. In 2002, William Schopf of UCLA published a controversial paper
   in the journal Nature arguing that formations such as this possess 3.5
   billion year old fossilized algae microbes. If true, they would be the
   earliest known life on earth.

   Not much is known about the earliest developments in life. However, all
   existing organisms share certain traits, including cellular structure
   and genetic code. Most scientists interpret this to mean all existing
   organisms share a common ancestor, which had already developed the most
   fundamental cellular processes, but there is no scientific consensus on
   the relationship of the three domains of life ( Archaea, Bacteria,
   Eukaryota) or the origin of life. Attempts to shed light on the
   earliest history of life generally focus on the behaviour of
   macromolecules, particularly RNA, and the behaviour of complex systems.

   The emergence of oxygenic photosynthesis (around 3 billion years ago)
   and the subsequent emergence of an oxygen-rich, non-reducing atmosphere
   can be traced through the formation of banded iron deposits, and later
   red beds of iron oxides. This was a necessary prerequisite for the
   development of aerobic cellular respiration, believed to have emerged
   around 2 billion years ago.

   In the last billion years, simple multicellular plants and animals
   began to appear in the oceans. Soon after the emergence of the first
   animals, the Cambrian explosion (a period of unrivaled and remarkable,
   but brief, organismal diversity documented in the fossils found at the
   Burgess Shale) saw the creation of all the major body plans, or phyla,
   of modern animals. This event is now believed to have been triggered by
   the development of the Hox genes. About 500 million years ago, plants
   and fungi colonized the land, and were soon followed by arthropods and
   other animals, leading to the development of land ecosystems with which
   we are familiar.

   The evolutionary process may be exceedingly slow. Fossil evidence
   indicates that the diversity and complexity of modern life has
   developed over much of the history of the earth. Geological evidence
   indicates that the Earth is approximately 4.6 billion years old.
   Studies on guppies by David Reznick at the University of California,
   Riverside, however, have shown that the rate of evolution through
   natural selection can proceed 10 thousand to 10 million times faster
   than what is indicated in the fossil record.. Such comparative studies
   however are invariably biased by disparities in the time scales over
   which evolutionary change is measured in the laboratory, field
   experiments, and the fossil record.

Horizontal gene transfer, and the history of life

   The ancestry of living organisms has traditionally been reconstructed
   from morphology, but is increasingly supplemented with phylogenetics -
   the reconstructiion of phylogenies by the comparison of genetic
   (usually DNA) sequence.

   "Sequence comparisons suggest recent horizontal transfer of many genes
   among diverse species including across the boundaries of phylogenetic
   'domains'. Thus determining the phylogenetic history of a species can
   not be done conclusively by determining evolutionary trees for single
   genes."

   Biologist Gogarten suggests "the original metaphor of a tree no longer
   fits the data from recent genome research" therefore "biologists
   [should] use the metaphor of a mosaic to describe the different
   histories combined in individual genomes and use [the] metaphor of a
   net to visualize the rich exchange and cooperative effects of HGT among
   microbes."

Ecology

The ecosystem concept

   The first principle of ecology is that each living organism has an
   ongoing and continual relationship with every other element that makes
   up its environment. An ecosystem can be defined as any situation where
   there is interaction between organisms and their environment.

   The ecosystem is composed of two entities, the entirety of life, the
   biocoenosis and the medium that life exists in the biotope. Within the
   ecosystem, species are connected and dependent upon one another in the
   food chain, and exchange energy and matter between themselves and with
   their environment.

   The concept of an ecosystem can apply to units of variable size, such
   as a pond, a field, or a piece of deadwood. A unit of smaller size is
   called a microecosystem. For example, an ecosystem can be a stone and
   all the life under it. A mesoecosystem could be a forest, and a
   macroecosystem a whole ecoregion, with its drainage basin.

   The main questions when studying an ecosystem are:
     * Whether the colonization of a barren area could be carried out
     * Investigation the ecosystem's dynamics and changes
     * The methods of which an ecosystem interacts at local, regional and
       global scale
     * Whether the current state is stable
     * Investigating the value of an ecosystem and the ways and means that
       interaction of ecological systems provide benefit to humans,
       especially in the provision of healthy water.

   Ecosystems are often classified by reference to the biotopes concerned.
   The following ecosystems may be defined:
     * As continental ecosystems, such as forest ecosystems, meadow
       ecosystems such as steppes or savannas), or agro-ecosystems
     * As ecosystems of inland waters, such as lentic ecosystems such as
       lakes or ponds; or lotic ecosystems such as rivers
     * As oceanic ecosystems.

   Another classification can be done by reference to its communities,
   such as in the case of an human ecosystem.

Spatial relationships and subdivisions of land

   Ecosystems are not isolated from each other, but are interrelated. For
   example, water may circulate between ecosystems by the means of a river
   or ocean current. Water itself, as a liquid medium, even defines
   ecosystems. Some species, such as salmon or freshwater eels move
   between marine systems and fresh-water systems. These relationships
   between the ecosystems lead to the concept of a biome.

   A biome is a homogeneous ecological formation that exists over a large
   region as tundra or steppes. The biosphere comprises all of the Earth's
   biomes -- the entirety of places where life is possible -- from the
   highest mountains to the depths of the oceans.

   Biomes correspond rather well to subdivisions distributed along the
   latitudes, from the equator towards the poles, with differences based
   on to the physical environment (for example, oceans or mountain ranges)
   and to the climate. Their variation is generally related to the
   distribution of species according to their ability to tolerate
   temperature and/or dryness. For example, one may find photosynthetic
   algae only in the photic part of the ocean (where light penetrates),
   while conifers are mostly found in mountains.

   Though this is a simplification of more complicated scheme, latitude
   and altitude approximate a good representation of the distribution of
   biodiversity within the biosphere. Very generally, the richness of
   biodiversity (as well for animal than plant species) is decreasing most
   rapidly near the equator (as in Brazil) and less rapidly as one
   approaches the poles.

   The biosphere may also be divided into ecozone, which are very well
   defined today and primarily follow the continental borders. The
   ecozones are themselves divided into ecoregions, though there is not
   agreement on their limits.

Ecosystem productivity

   In an ecosystem, the connections between species are generally related
   to food and their role in the food chain. There are three categories of
   organisms:
     * Producers -- usually plants which are capable of photosynthesis but
       could be other organisms such as bacteria around ocean vents that
       are capable of chemosynthesis.
     * Consumers -- animals, which can be primary consumers (
       herbivorous), or secondary or tertiary consumers ( carnivorous).
     * Decomposers -- bacteria, mushrooms which degrade organic matter of
       all categories, and restore minerals to the environment.

   These relations form sequences, in which each individual consumes the
   preceding one and is consumed by the one following, in what are called
   food chains or food network. In a food network, there will be fewer
   organisms at each level as one follows the links of the network up the
   chain.

   These concepts lead to the idea of biomass (the total living matter in
   a given place), of primary productivity (the increase in the mass of
   plants during a given time) and of secondary productivity (the living
   matter produced by consumers and the decomposers in a given time).

   These two last ideas are key, since they make it possible to evaluate
   the load capacity -- the number of organisms which can be supported by
   a given ecosystem. In any food network, the energy contained in the
   level of the producers is not completely transferred to the consumers.
   And the higher one goes up the chain, the more energy and resources is
   lost and consumed. Thus, from an energy—and environmental—point of
   view, it is more efficient for humans to be primary consumers (to
   subsist from vegetables, grains, legumes, fruit, cotton, etc.) than as
   secondary consumers (from eating herbivores, omnivores, or their
   products, such as milk, chickens, cattle, sheep, etc.) and still more
   so than as a tertiary consumer (from consuming carnivores, omnivores,
   or their products, such as fur, pigs, snakes, alligators, etc.). An
   ecosystem(s) is unstable when the load capacity is overrun and is
   especially unstable when a population doesn't have an ecological niche
   and overconsumers.

   The productivity of ecosystems is sometimes estimated by comparing
   three types of land-based ecosystems and the total of aquatic
   ecosystems:
     * The forests (1/3 of the Earth's land area) contain dense biomasses
       and are very productive. The total production of the world's
       forests corresponds to half of the primary production.
     * Savannas, meadows, and marshes (1/3 of the Earth's land area)
       contain less dense biomasses, but are productive. These ecosystems
       represent the major part of what humans depend on for food.
     * Extreme ecosystems in the areas with more extreme climates --
       deserts and semi-deserts, tundra, alpine meadows, and steppes --
       (1/3 of the Earth's land area) have very sparse biomasses and low
       productivity
     * Finally, the marine and fresh water ecosystems (3/4 of Earth's
       surface) contain very sparse biomasses (apart from the coastal
       zones).

   Humanity's actions over the last few centuries have seriously reduced
   the amount of the Earth covered by forests ( deforestation), and have
   increased agro-ecosystems (agriculture). In recent decades, an increase
   in the areas occupied by extreme ecosystems has occurred (
   desertification).
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