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. An organism is in a non-equilibrium thermodynamic state, maintaining a homeostatic internal environment, and needs a continuous input of energy to maintain this state.

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

A complex organism is any organism with more than one cell.

Semantics

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, many sources add further conditions. For the Oxford English Dictionary, an organism is "[an] individual animal, plant, or single-celled life form." This excludes non-animal and plant multi-cellular life forms such as some fungi and protista, as well as viruses and theoretically-possible man-made non-organic life forms. 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.

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, 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.

Viruses

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

Superorganism

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 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.

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?" 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 comprises a single gene pool.

It is also 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. .

Organizational terminology

All organisms are classified by the science of 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 in hierarchical order is:

• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

For example, Homo sapiens is the Latin binomial equating to modern humans. All members of the species sapiens are, 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 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 within a particular family are more closely related and genetically similar than the species within a particular phylum.

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, 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 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, 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

See also: Common descent

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.

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.

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 around 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 period of 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 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

A principle of ecology is that each organism has an ongoing relationship with every other element in its environment. An ecosystem is any situation where there is interaction between organisms and their environment, and is composed of the entirety of life, the biocoenosis and the medium that life exists in the biotope. Within the ecosystem, species are connected and depend 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. 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 food chains with fewer organisms at each higher level of 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).

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 as the baseline dataset for studies of global biodiversity.
• 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 8500 years.
• The Tree of Life.