Organism

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Biologists readily recognize an organism (in Greek organon = instrument) as a living complex adaptive system of components that interrelate and interact in such a way that they function as a integrated stable unit, a separate distinct individual -- such as an amoeba, a beetle, a tree, a fish, a human -- that can sustain the activity of living, and reproduce progeny that resemble it. In other words, biologists can readily recognize some living systems as 'organisms', though they may have different perspectives on whether other living systems, such a colony of ants or a biofilm of bacteria, count as 'organisms'.

The simplest organism consists of just one cell, but there are many complex organisms that are multi-cellular. The distinctive features common to living organisms are fully discussed in the article Life.

Microscopic organisms, generally single-celled and invisible to the naked eye, are the most numerous and diverse organisms on Earth, but multicellular organisms such as plants, animals, fish and fungi are more prominent in the everyday world of unaided visual experience.

The origin of living organisms from prebiotic chemistry remains an unsolved scientific question. Of the three domains of organisms -- Bacteria, Archaea and Eukarya (eukaryotes) -- biologists recognize three distinct canonical patterns of biochemistry, exemplified by their protein synthesis machinery.

Majestic marine organisms - A Sawfish and other fish at the Georgia (USA) aquarium

## Contents

* 1 Definitions
* 1.1 Superorganism
* 2 Organizational terminology
* 3 Structure
* 3.1 The cell
* 4 Evolution
* 4.1 History of life
* 5 Ecology
* 6 References

## Definitions[edit]

As a living system, an organism can be viewed from several different biological perspectives:

* Living systems import free energy, energy-rich matter, order and information from their environment, and export waste in the form of degraded energy, unusable materials, and more disorder (entropy) than the order they generate within themselves. The downhill flow of free energy enables living systems to organize themselves and sustain that organization, and thus to delay (for their lifetime) the dictate of the Second Law of Thermodynamics, which states that organized systems ultimately degrade to a state of randomness;
* The basic building blocks and working units of all living systems are cells, separated from their surroundings by a boundary membrane that allows energy, material and information exchange with their surroundings;
* The basic (genetic) database that cells draw upon for self-organization comes as part of their starting materials. This source of information, in the form of nucleic acid macromolecules, encodes many different types of proteins that interact according to their natural physico-chemical properties to self-assemble an organization of hierarchically arranged subsystems that can import energy and export waste.
* Cells inherit genetic and other forms of heritable information from ‘parent’ cells, raising as yet unanswered questions: how did cells arise in the first place? and how did they acquire stores of information?;[1] (see Origin of life and Evolution of cells)
* The molecular interactions that self-assemble and sustain the living organization are governed by the universal laws of physics and chemistry; those laws, together with the inherited information, enable a self-organizing system that can work autonomously in its own behalf for persistence of the living state and for reproduction, and allow properties and physiological functions to emerge that could not be anticipated from those of the system's components alone.
* The activities of a living system have no 'master controller'; they need only a type of organization that maintains the system far-from-equilibrium, which can yield improbable self-organized structures and activities.
* Living things cannot escape from real-time changes in external conditions, so they must maintain homeostasis, exhibit robustness in their organization, and must be adaptable enough to reorganize to sustain their living state. Robustness and adaptability derive from the properties of a hierarchical network of subnetworks of molecular circuits;
* Living systems generate complexity and emergent properties as a hierarchy of emergent subsystems embedded in even more complex emergent systems, as in the case of an organism living in an environment of other organisms.
* Living systems produce enough reproductive variability to allow evolution through natural selection, which guides the continuation of a 3.5 billion year history of Earth’s living world. By evolution, living systems generate increasing varieties of living systems, occupy an extreme spectrum of environments, create their own environments,[2] and permit sufficient complexity to enable them to process information in a way that allows them to ‘experience’ themselves. See Life.

An 'organism' may 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, some sources add further conditions. For the Oxford English Dictionary, an organism is "[an] individual animal, plant, or single-celled life form." This glosses over the existence of non-animal and plant multi-cellular life forms such as some fungi and protists, as well as viruses.

Chambers Online Reference gives a 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, and encompasses all cellular life as well as possible synthetic life.

Viruses are often not considered to be organisms because they are not cells, and are incapable of independent reproduction, metabolism, and in particular, do not posses the machinery to make proteins. Some cellular parasites and endosymbionts are also incapable of independent life. Viruses are however able to evolve by natural selection and do posses genetic material, which can be either RNA or DNA.

Tibor Gánti's chemoton is an abstract model for a minimum living organism introduced in 1971. Its characteristics are separation, metabolism, replication, information-storage, and an autocathalytic subsystem.

The word 'organism' usually describes an independent collections of systems (for example circulatory system or digestive system) that are themselves collections of organs; these are, in turn, collections of tissues, made of cells. The concept of an organism can be challenged on grounds that organisms are never truly independent of an ecosystem; groups or populations of organisms function in an ecosystem in a manner not unlike multicellular tissues in an organism; when organisms enter into strict symbiosis, they are not independent. Symbiotic plant and algae relationships 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 as species affect one another indirectly in an ecosystem. Thus all living matter exists within larger heterarchical systems of life, made of wide varieties of transient living and dead tissues, and functioning in complex, dynamic relationships to one another.

### Superorganism[edit]

A superorganism is an organism that consists of many organisms. This is usually meant to be a social unit of eusocial animals, where division of labour is specialised and where individuals cannot survive by themselves for long. Ants are the best known example of 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.[3]

The concept of superorganism is disputed, as many biologists maintain that, 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 evolutionary biologists claim that the individuals are still the primary units of selection.

The question remains "What is to be considered the individual?" E.O. Wilson has shown that with ant-colonies and other social insects it is the breeding entity of the colony that is selected, not its individual members. This could apply to the bacterial members of a stromatolite, which, because of genetic sharing, comprises a single gene pool.

It can also be argued that humans are a superorganism that includes microorganisms such as bacteria. The human intestinal microbiota is composed of 1013 to 1014 microorganisms whose collective genome ('microbiome') contains at least 100 times as many genes as our own. Thus, humans are superorganisms whose metabolism is an amalgamation of microbial and human attributes. [4].

## Organizational terminology[edit]

All organisms are classified by alpha taxonomy into taxa or clades. Taxa are ranked groups of organisms which run from the general (domain) to the specific (species). A broad scheme of ranks is:

* Domain e.g. Eucaryota
* Kingdom Animalia
* Phylum chordata (subphylum, vertebrata)
* Class mammalia
* Order primates
* Family hominidae
* Genus homo
* Species sapiens

For example, Homo sapiens is the Latin binomial for modern humans. All members of the species sapiens can, in theory, interbreed. Several species may belong to a genus, but different species within a genus cannot interbreed to produce fertile offspring. Homo only has one surviving species (sapiens); Homo erectus, Homo neanderthalensis etc. having become extinct long 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 are classified by this system such that the species in a particular family are more genetically similar than the species within a particular phylum.

## Structure[edit]

All organisms consist of monomeric units called cells; some contain a single cell (unicellular), others contain many (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. This pattern continues to a higher level with several organs functioning as an organ system to allow for reproduction, digestion etc. Many multicelled organisms comprise of several organ systems which coordinate to allow for life.

### The cell[edit]

The cell theory, 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 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 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[5]:

* 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, assembling 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 bilayer.

## Evolution[edit]

See Evolution of cells
A hypothetical phylogenetic tree of life based on differences in rRNA, showing the diversity of Bacteria, Archaea, and Eukarya (eukaryotes). The nature of the root of this tree is currently a subject of hot scientific debate.

In biology, current theories of early evolution propose that organisms alive today are descended from a common ancestral gene pool. Evidence for common origins can be found in the traits that are common to all living organisms. In Darwin's day, the evidence of shared traits was based on observation of morphologic similarities, such as the fact that all birds have wings, even those which do not fly. Today, there is evidence from genetics that all organisms have a shared ancestry in ancient communities of microbes.

Early organisms may have shared their components more widely than existing organisms. Recent research indicates this early ancestry represents a stage in evolution in which representation of evolution as different organism lineages represented by branching (bifurcating) trees is misleading, and the earliest living communities may well have shared their genes extensively.

Every living cell uses nucleic acids as its genetic material, and uses the same twenty amino acids as the building blocks for its proteins. All organisms use the same genetic code (with some extremely rare and minor deviations)[6] to translate nucleic acid sequences into proteins. These features are thought to have been shared by the ancestral gene pool.[7]

### History of life[edit]

For more information, see: Evolution/Timelines.

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.

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 necessary for the development of aerobic cellular respiration, believed to have emerged about 2 billion years ago. In the last billion years, simple multicellular plants and animals began to appear in the oceans. Soon after, the Cambrian explosion (a brief period of remarkable 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 believed to have been triggered by the development of Hox genes. About 500 million years ago, plants and fungi colonized the land, soon followed by arthropods and other animals, leading to the development of land ecosystems.

## Ecology[edit]

A principle of ecology is that each organism has an ongoing relationship with every other element in its environment. These relationships occur within local, regional, global and temporal contexts. An ecological system (that is, ecosystem) is any situation where there is interaction among organisms and components of their environment. Such systems embody the entirety of life—the biocoenosis or biogeosphere—as well as the media that support life that exists in the biotope. Within the ecosystem, species are connected and depend upon one another (for example, within food webs, and exchange energy and matter among themselves and with their environment. The concept of an ecosystem can apply to such units of variable size as a pond, a field, or even a small piece of deadwood. A unit of smaller size (for example, the interior of a cell supporting a microbial parasite) may be called a microecosystem. Not surprisingly, an ecosystem can be a stone and all the life beneath it; a mesoecosystem could be a forest; and, a macroecosystem a whole ecoregion, with its drainage basin (that is, a watershed). In an ecosystem, the connections among species are generally related to their place in the food web. There are three categories of organisms:

* Producers \-- usually plants that are capable of photosynthesis but could be such other organisms such bacteria living around ocean vents that are capable of chemosynthesis.
* Consumers \-- animals, that can be primary consumers (herbivorous), or secondary or tertiary consumers (carnivorous).
* Decomposers \-- bacteria, mushrooms and other fungi that degrade organic matter of all categories, and restore minerals to the environment.

These relations form food webs with fewer organisms at each higher level of the web. 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).

## References[edit]

1. ↑ Note: We can arrive at a more-or-less empirically sound explanation of what constitutes living systems without having a good explanation for how they arose in the first place, because we can study the here-and-now and not the there-and-then.
2. ↑ Odling-Smee FJ, Laland KN, Feldman MW (2003) Niche Construction; The Neglected Process in Evolution. Princeton: Princeton University Press. ISBN 0691044384
3. ↑ Southwick, EE (1983). "The honey bee cluster as a homeothermic superorganism" (PDF). Comp Bioch Physiol 75A (4): 741-745\. DOI:10.1016/0300-9629(83)90434-6. Retrieved on 2006-07-20. Research Blogging.
4. ↑ Gill SR et al (2006)Science 312:1355-9 [1]
5. ↑ The Universal Features of Cells on Earth in Chapter 1 of Molecular Biology of the Cell fourth edition, edited by Bruce Alberts (2002) published by Garland Science.
6. ↑ Ambrogelly A, Palioura S, Soll D. (2007) Natural expansion of the genetic code. Nat Chem Biol 3:29-35 PMID 17173027
7. ↑ Woese C (2002) On the evolution of cells. Proc Natl Acad Sci USA 99:8742-7 PMID 12077305 This article shifts the emphasis in early phylogenic adaptation from vertical to horizontal gene transfer. (Open access.)
* Esser C et al. (2004) A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 21:1643-50 PMID 15155797
* Forterre P (2006) Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain. PNAS 103:3669-3674
* Rivera MC, Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-5 PMID 15356622
* Simonson AB et al. (2005) Decoding the genomic tree of life. Proc Natl Acad Sci USA 102 Suppl 1:6608-13 PMID 15851667