Organism

These Escherichia coli cells provide an example of a Microorganism

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. Fungi, animals and plants are examples of species that are eukaryote.

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

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 anything approximating to the word "individual" which would exclude viruses.

An ericoid mycorrhizal fungus

The word "organism" usually describes an independent collections of systems (for example circulatory, digestive, or reproductive) 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 also incapable of independent life. Although viruses have enzymes and molecules characteristic of living organisms, they are incapable of reproducing 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

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 10¹³ 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.

A crab is an example of an organism.

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

See also: Universal common descent and Origin of life

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.

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 behavior of macromolecules, particularly RNA, and the behavior 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 (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).

External links

• BBCNews: 27 September, 2000, When slime is not so thick Citat: "...It means that some of the lowliest creatures in the plant and animal kingdoms, such as slime and amoeba, may not be as primitive as once thought...."
  • SpaceRef.com, July 29, 1997: Scientists Discover Methane Ice Worms On Gulf Of Mexico Sea Floor
    • The Eberly College of Science: Methane Ice Worms discovered on Gulf of Mexico Sea Floor download Publication quality photos
  • Artikel, 2000: Methane Ice Worms: Hesiocaeca methanicola. Colonizing Fossil Fuel Reserves
  • SpaceRef.com, May 04, 2001: Redefining "Life as We Know it" Hesiocaeca methanicola In 1997, Charles Fisher, professor of biology at Penn State, discovered this remarkable creature living on mounds of methane ice under half a mile of ocean on the floor of the Gulf of Mexico.
• BBCNews, 18 December, 2002, 'Space bugs' grown in lab Citat: "...Bacillus simplex and Staphylococcus pasteuri...Engyodontium album...The strains cultured by Dr Wainwright seemed to be resistant to the effects of UV - one quality required for survival in space...."
• BBCNews, 19 June, 2003, Ancient organism challenges cell evolution Citat: "..."It appears that this organelle has been conserved in evolution from prokaryotes to eukaryotes, since it is present in both,"..."
• Interactive Syllabus for General Biology - BI 04, Saint Anselm College, Summer 2003
• Jacob Feldman: Stramenopila
• NCBI Taxonomy entry: root (rich)
• Saint Anselm College: Survey of representatives of the major Kingdoms Citat: "...Number of kingdoms has not been resolved...Bacteria present a problem with their diversity...Protista present a problem with their diversity...",
• Species 2000 Indexing the world's known species. Species 2000 has the objective of enumerating all known species of plants, animals, fungi and microbes on Earth as the baseline dataset for studies of global biodiversity. It will also provide a simple access point enabling users to link from here to other data systems for all groups of organisms, using direct species-links.
• The largest organism in the world may be a fungus carpeting nearly 10 square kilometers of an Oregon forest, and may be as old as 10500 years.
• The Tree of Life.