Semantics

The word "organism" may broadly be defined as an assembly of molecules that function as a more or less stable whole and has the properties of life. However, many sources propose definitions that exclude viruses and theoretically-possible man-made non-organic life forms.^[3] Viruses are dependent on the biochemical machinery of a host cell for reproduction.

Chambers Online Reference provides a broad definition: "any living structure, such as a plant, animal, fungus or bacterium, capable of growth and reproduction".^[4]

In multicellular life the word "organism" usually describes the whole hierarchical assemblage 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. In some plants and the nematode Caenorhabditis elegans, individual cells are totipotent.

A superorganism is an organism consisting of many individuals working together as a single functional or social unit.

Viruses

Viruses are not typically considered to be organisms because they are incapable of "independent" or autonomous reproduction or metabolism. This controversy is problematic because some cellular organisms also incapable of independent survival (but not of independent metabolism and procreation) and live as obligatory intracellular parasites. Although viruses have a few enzymes and molecules characteristic of living organisms, they have no metabolism of their own and cannot synthesize and organize the organic compounds that form them. Naturally, this rules out autonomous reproduction and they can only be passively replicated by the machinery of the host cell. In this sense they are similar to inanimate matter. While viruses sustain no independent metabolism, and thus are usually not accounted organisms, they do have their own genes and they do evolve by similar mechanisms by which organisms evolve.

Organizational terminology

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The hierarchy of biological classification's eight major taxonomic ranks. Intermediate minor rankings are not shown.

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 systems, 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 chemical phenomena, 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 three-atom compounds (such as carbon dioxide), as well as large chains of many thousands of atoms that can store data (nucleic acids), hold cells together, and transmit information (protein).

Macromolecules

Compounds that 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 that 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 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. Signaling 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 that constitutes a barrier, containing everything within the cell and preventing compounds from freely passing into, and out of, the cell. In some multicellular 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 specialize 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 consist 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 envelops 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, 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.

Life span

One of the basic parameters of organism is its life span. Some organisms 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.^{[citation needed]}