Organism: Difference between revisions

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{{Short description|Individual living life form}}

{{redirect|Life on Earth|the TV series|Life on Earth (documentary)}}

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[[Image:EscherichiaColi NIAID.jpg|thumb|200 px|These ''[[Escherichia coli]]'' cells provide an example of a [[Microorganism]]]]

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{{Use dmy dates|date=July 2019}}

{{use British English|date=April 2024}}

{{redirect|Living creatures|the class of heavenly beings in Jewish mythology|living creatures (Bible)}}

An '''organism''' is any [[life|living]] thing that functions as an [[individual]].<ref name="Mosby-2017">{{Cite book |title=Mosby's Dictionary of Medicine, Nursing and Health Professions |publisher=[[Elsevier]] |year=2017 |isbn=978-0-3232-2205-1 |edition=10th |___location=St. Louis, Missouri |pages=1281}}</ref> Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Several criteria, few of which are widely accepted, have been proposed to define what constitutes an organism. Among the most common is that an organism has autonomous [[reproduction]], [[Cell growth|growth]], and [[metabolism]]. This would exclude [[virus]]es, even though they [[evolution|evolve]] like organisms.

Other problematic cases include [[colonial organism]]s; a colony of [[eusocial insect]]s is organised adaptively, and has [[Germ-Soma Differentiation|germ-soma specialisation]], with some insects reproducing, others not, like cells in an animal's body. The body of a [[siphonophore]], a jelly-like marine animal, is composed of organism-like [[zooid]]s, but the whole structure looks and functions much like an animal such as a [[jellyfish]], the parts collaborating to provide the functions of the colonial organism.

In [[biology]] and [[ecology]], an '''organism''' (in [[Greek language|Greek]] ''organon'' = instrument) is a [[life|living]] [[complex adaptive system]] of [[organ (anatomy)|organ]]s that influence each other in such a way that they [[role|function]] in some way as a stable whole.

The evolutionary biologists [[David C. Queller|David Queller]] and [[Joan E. Strassmann|Joan Strassmann]] state that "organismality", the qualities or attributes that define an entity as an organism, has evolved socially as groups of simpler units (from cells upwards) came to cooperate without conflicts. They propose that cooperation should be used as the "defining trait" of an organism. This would treat many types of collaboration, including the [[fungus]]/[[Algae|alga]] partnership of different species in a [[lichen]], or the permanent sexual partnership of an [[anglerfish]], as an organism.

The [[origin of life|origin]] of '''life on Earth''' and the relationships between its major lineages are controversial. Two main grades may be distinguished, the [[prokaryote]]s and [[eukaryote]]s. The prokaryotes are generally considered to represent two separate [[Three-___domain system|domains]], called the [[Bacterium|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]] [[organelle]]s, namely [[mitochondria]] and [[chloroplast]]s, are generally considered to be derived from [[endosymbiotic theory|endosymbiotic]] bacteria. Fungi, animals and plants are examples of species that are eukaryote.

== Etymology ==

The phrase ''[[multicellular organism|complex organism]]'' describes any organism with more than one [[cell (biology)|cell]].

The term "organism" (from the [[Ancient Greek]] {{Wikt-lang|grc|ὀργανισμός}}, derived from {{grc-transl|ὄργανον}}, meaning {{gloss|instrument, implement, tool}}, {{gloss|organ of sense}}, or {{gloss|apprehension}})<ref name="Liddell">{{LSJ|o)/rganon|ὄργανον|ref}}</ref><ref name="Online-Etym-Dict"/> first appeared in the English language in the 1660s<!--this is what the cited source says!--> with the now-obsolete meaning of an organic structure or organization.<ref name="Online-Etym-Dict">{{cite web |title=organism (n.) |url=https://www.etymonline.com/word/organism |publisher=[[Online Etymology Dictionary]] |access-date=11 April 2024}}</ref> It is related to the verb "organize".<ref name="Online-Etym-Dict"/> In his 1790 ''[[Critique of Judgment]]'', [[Immanuel Kant]] defined an organism as "both an organized and a self-organizing being".<ref>{{cite book |last=Kant |first=Immanuel |author-link=Immanuel Kant |title=[[Critique of Judgment]] |year=1790 |publisher=Lagarde und Friederich |at=§65 5:374}}</ref><ref>{{cite journal |last=Huneman |first=Philippe |title=Kant's Concept of Organism Revisited: A Framework for a Possible Synthesis between Developmentalism and Adaptationism? |journal=[[The Monist]] |volume=100 |issue=3 |year=2017 |pages=373–390 |doi=10.1093/monist/onx016 |jstor=26370801}}</ref>

== [[Semantics]] ==

== Whether criteria exist, or are needed ==

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.

[[File:Basilikumwurzling.jpg|thumb|upright|One criterion proposes that an organism cannot be divided without losing functionality.<ref name="Rosen-1958"/> This [[basil]] plant [[Cutting (plant)|cutting]] is however developing new adventitious roots from a small bit of [[Plant stem|stem]], forming a new plant.]]

The [[Oxford English Dictionary]] defines an organism as "[an] individual animal, plant, or single-celled life form"<ref name=OED>{{cite encyclopedia | encyclopedia=Oxford English Dictionary | edition=online | year=2004 | title=organism}}</ref> This definition problematically excludes non-animal and plant multi-cellular [[life form]]s such as some [[fungi]] and [[protista]]. Less controversially, perhaps, it excludes [[virus]]es and theoretically-possible man-made [[alternative biochemistry|non-organic life]] forms.

[[Image:Fungi_in_Borneo.jpg|thumb|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"<ref name=Chambers>{{cite encyclopedia | encyclopedia=Chambers 21st Century Dictionary | edition=online | year=1999 | title=organism}}</ref>. The definition emphasises [[life]]; it allows for any life form, [[biological matter|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.

[[Image:Ericoid mycorrhizal fungus.jpg|thumb|right|An ericoid mycorrhizal [[fungus]]]]

The word "organism" usually describes an independent collections of systems (for example [[circulatory system|circulatory]], [[digestive system|digestive]], or [[reproductive system|reproductive]]) themselves collections of [[organ (anatomy)|organ]]s; these are, in turn, collections of tissues, which are themselves made of [[cell (biology)|cell]]s. 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 [[heterarchy|heterarchical]] systems of life, made of wide varieties of transient living and dead tissues, and functioning in complex and dynamic relationships to one another.

Among the criteria that have been proposed for being an organism are:

=== Viruses ===

* autonomous [[reproduction]], [[Cell growth|growth]], and [[metabolism]]<ref name="Moreira-2009"/>

[[Virus|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 [[parasite]]s and [[endosymbiont]]s are also incapable of independent life. Although viruses have [[enzyme]]s and molecules characteristic of living organisms, they are incapable of reproducing outside a [[cell (biology)|host cell]] and most of their metabolic processes require a host and its 'genetic machinery.'

* noncompartmentability – structure cannot be divided without losing functionality.<ref name="Rosen-1958">{{Cite journal |last=Rosen |first=Robert |date=September 1958 |title=A relational theory of biological systems |url=http://link.springer.com/10.1007/BF02478302 |journal=The Bulletin of Mathematical Biophysics |volume=20 |issue=3 |pages=245–260 |doi=10.1007/BF02478302 |issn=0007-4985|url-access=subscription }}</ref> [[Richard Dawkins]] stated this as "the quality of being sufficiently heterogeneous in form to be rendered non-functional if cut in half".<ref name="Wilson-2000"/> However, many organisms <!--Hydra, currant bushes--> can be cut into pieces which then grow into whole organisms.<ref name="Wilson-2000"/>

* [[individuality]] – the entity has simultaneous holdings of genetic uniqueness, genetic homogeneity and [[autonomy]]<ref>{{Cite journal |last=Santelices |first=Bernabé |date=April 1999 |title=How many kinds of individual are there? |url=https://linkinghub.elsevier.com/retrieve/pii/S0169534798015195 |journal=[[Trends in Ecology & Evolution]] |volume=14 |issue=4 |pages=152–155 |doi=10.1016/S0169-5347(98)01519-5 |pmid=10322523 |url-access=subscription }}</ref>

* an [[immune response]], separating self from foreign<ref>{{cite journal |last=Pradeu |first=T. |title=What is an organism? An immunological answer |journal=[[History and Philosophy of the Life Sciences]] |volume=32 |issue=2–3 |pages=247–267 |year=2010 |pmid=21162370 }}</ref>

* "anti-[[entropy]]", the ability to maintain order, a concept first proposed by [[Erwin Schrödinger]];<ref name="Bailly-2009">{{cite journal |last1=Bailly |first1=Francis |last2=Longo |first2=Giuseppe |title=Biological Organization and Anti-entropy |journal=[[Journal of Biological Systems]] |volume=17 |issue=1 |date=2009 |issn=0218-3390 |doi=10.1142/S0218339009002715 |pages=63–96 |url=https://www.researchgate.net/publication/247697945}}</ref> or in another form, that [[Claude Shannon]]'s [[information theory]] can be used to identify organisms as capable of self-maintaining their information content<ref name="Piast-2019">{{Cite journal |last=Piast |first=Radosław W. |date=June 2019 |title=Shannon's information, Bernal's biopoiesis and Bernoulli distribution as pillars for building a definition of life |url=https://linkinghub.elsevier.com/retrieve/pii/S0022519319301109 |journal=[[Journal of Theoretical Biology]] |volume=470 |pages=101–107 |doi=10.1016/j.jtbi.2019.03.009 |pmid=30876803 |bibcode=2019JThBi.470..101P |s2cid=80625250 |url-access=subscription }}</ref>

Other scientists think that the concept of the organism is inadequate in biology;<ref>{{cite journal |last=Bateson |first=Patrick |title=The return of the whole organism |journal=Journal of Biosciences |volume=30 |issue=1 |pages=31–39 |date=February 2005 |pmid=15824439 |doi=10.1007/BF02705148 |s2cid=26656790 }}</ref>

=== Superorganism ===

that the concept of individuality is problematic;<ref name="Clarke-2010">{{Cite journal |last=Clarke |first=E. |title=The problem of biological individuality |journal=Biological Theory |volume=5 |issue=4 |pages=312–325 |year=2010 |doi=10.1162/BIOT_a_00068 |s2cid=28501709 }}</ref>

and from a philosophical point of view, question whether such a definition is necessary.<ref name="Pepper-2008">{{cite journal |last1=Pepper |first1=J.W. |last2=Herron |first2=M.D. |title=Does biology need an organism concept? |journal=Biological Reviews of the Cambridge Philosophical Society |volume=83 |issue=4 |pages=621–627 |date=November 2008 |pmid=18947335 |doi=10.1111/j.1469-185X.2008.00057.x |s2cid=4942890 }}</ref><ref name="Wilson-2007">{{Cite journal |last=Wilson |first=R. |title=The biological notion of individual |journal=[[Stanford Encyclopedia of Philosophy]] |date=2007}}</ref><ref name="Wilson-2000">{{Cite journal |pages=301–311 |last=Wilson |first=Jack A. |title=Ontological butchery: organism concepts and biological generalizations |journal=Philosophy of Science |date=2000 |jstor=188676 |volume=67 |doi=10.1086/392827 |s2cid=84168536 }}</ref>

Problematic cases include [[Colony (biology)|colonial organisms]]: for instance, a colony of [[eusocial insects]] fulfills criteria such as adaptive organisation and [[Germ-Soma Differentiation|germ-soma]] specialisation.<ref name="Folse-2010">{{cite journal |last1=Folse |first1=H.J., III |last2=Roughgarden |first2=J. |title=What is an individual organism? A multilevel selection perspective |journal=The Quarterly Review of Biology |volume=85 |issue=4 |pages=447–472 |date=December 2010 |pmid=21243964 |doi=10.1086/656905 |s2cid=19816447 }}</ref> If so, the same argument, or a criterion of high co-operation and low conflict, would include some [[Mutualism (biology)|mutualistic]] (e.g. lichens) and sexual partnerships (e.g. [[anglerfish]]) as organisms.<ref name="Queller-2009">{{cite journal |last1=Queller |first1=David C. |last2=Strassmann |first2=Joan E. |title=Beyond society: the evolution of organismality |journal=Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences |volume=364 |issue=1533 |pages=3143–3155 |date=November 2009 |pmid=19805423 |pmc=2781869 |doi=10.1098/rstb.2009.0095 }}</ref> If [[group selection]] occurs, then a group could be viewed as a [[superorganism]], optimized by group [[adaptation]].<ref>{{cite journal |last1=Gardner |first1=A. |last2=Grafen |first2=A. |title=Capturing the superorganism: a formal theory of group adaptation |journal=[[Journal of Evolutionary Biology]] |volume=22 |issue=4 |pages=659–671 |date=April 2009 |pmid=19210588 |doi=10.1111/j.1420-9101.2008.01681.x |s2cid=8413751 |doi-access=free }}</ref>

A superorganism is an organism consisting of many organisms. This is usually meant to be a social [[Units of measurement|unit]] of [[eusociality|eusocial]] animals, where [[division of labour]] is highly specialised and where individuals are not able to survive by themselves for extended periods of time. [[Ant]]s 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 [[honeybee]]s of the species ''[[Apis mellifera]]''. When these bees pack together in clusters of between 5000 and 40000, the colony can thermoregulate.<ref>{{cite journal

| last = Southwick

| first = Edward E.

| year = 1983

| title = The honey bee cluster as a homeothermic superorganism

| journal = Comparative Biochemistry and Physiology

| volume = 75A

| issue = 4

| pages = 741&ndash;745

| doi =10.1016/0300-9629(83)90434-6

| url =http://www.sciencedirect.com/science?_ob=MiamiImageURL&_imagekey=B6T2P-4867WXH-110-2&_cdi=4924&_user=4385511&_check=y&_orig=search&_coverDate=12%2F31%2F1983&_qd=1&view=c&wchp=dGLbVlz-zSkWW&md5=d23bd1cec870de7f5a44f8a2f367ed9c&ie=/sdarticle.pdf

| format = PDF

| accessdate = 2006-07-20

}}</ref> [[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.

[[Image:Elephant-ear-sponge.jpg|thumb|left|A [[sea sponge]] is a very simple type of [[multicellular organism]]]]

The concept of superorganism is under dispute, as many [[biology|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 [[evolutionist]]s claim that the individuals are still the [[primary]] units of selection.

Another view is that attributes like autonomy, genetic homogeneity and genetic uniqueness should be examined separately, rather than requiring that an organism possess all of them. On this view, there are multiple dimensions to biological individuality, resulting in several types of organism.<ref>{{cite journal |last=Santelices |first=B. |title=How many kinds of individual are there? |journal=[[Trends in Ecology & Evolution]] |volume=14 |issue=4 |pages=152–155 |date=April 1999 |pmid=10322523 |doi=10.1016/s0169-5347(98)01519-5 }}</ref>

The question remains "What is to be considered ''the [[individualism|individual]]''?". [[Darwinism|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.

== Organisms at differing levels of biological organisation ==

It would appear, from computer [[simulation|simulations]] like [[Daisyworld]] that biological [[natural selection|selection]] occurs at multiple levels simultaneously.

[[File:Lichen cross section – heteromeric thallus unlabelled.svg|thumb|upright=0.8|A [[lichen]] consists of a body formed mainly by [[fungi]], with unicellular [[algae]] or [[cyanobacteria]] (green) interspersed within the structure, and a bacterial [[microbiome]]. The [[species]] are mutually interdependent, like cells within a multicellular organism.<ref name="Lücking-2021"/>]]

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<sup>14<sup> microorganisms whose collective [[genome]] ("[[microbiome]]") contains at least 100 times as many genes as our own[...] Our microbiome has significantly enriched metabolism of [[glycan]]s, [[amino acid]]s, and [[xenobiotic]]s; [[methanogenesis]]; and 2-methyl-D-erythritol 4-phosphate pathway–mediated biosynthesis of vitamins and [[isoprenoid]]s. Thus, humans are superorganisms whose metabolism represents an amalgamation of microbial and human attributes." <ref>Gill S. R., et al. ''Science'', ''312'', 1355-1359 ('''2006'''). http://dx.doi.org/10.1126/science.1124234</ref>.

Differing levels of biological organisation give rise to potentially different understandings of the nature of organisms. A [[unicellular organism]] is a [[microorganism]] such as a [[protist]], [[bacterium]], or [[archaea]]n, composed of a single [[Cell (biology)|cell]], which may contain functional structures called [[organelle]]s.<ref name="Hine-2008">{{cite book |last=Hine |first=R.S. |title=A Dictionary of Biology |year=2008 |publisher=[[Oxford University Press]] |___location=Oxford |isbn=978-0-19-920462-5 |page=461 |edition=6th}}</ref> A [[multicellular organism]] such as an [[animal]], [[plant]], [[fungus]], or [[alga]] is composed of many cells, often specialised.<ref name="Hine-2008"/> A [[Colony (biology)|colonial organism]] such as a [[siphonophore]] is a being which functions as an individual but is composed of communicating individuals.<ref name="Wilson-2000"/> A [[superorganism]] is a colony, such as of [[ant]]s, consisting of many individuals working together as a single functional or [[Social group|social unit]].<ref name="Kelly-1994">{{cite book |last=Kelly |first=Kevin |title=Out of control: the new biology of machines, social systems and the economic world |publisher=[[Addison-Wesley]] |___location=Boston |year=1994 |pages=[https://archive.org/details/outofcontrolnewb00kell/page/98 98] |isbn=978-0-201-48340-6 |url-access=registration |url=https://archive.org/details/outofcontrolnewb00kell}}</ref><ref name="Folse-2010"/> A [[Mutualism (biology)|mutualism]] is a partnership of two or more [[species]] which each provide some of the needs of the other. A [[lichen]] consists of [[Fungus|fungi]] and [[algae]] or [[cyanobacteria]], with a bacterial [[microbiome]]; together, they are able to flourish as a kind of organism, the components having different functions, in habitats such as dry rocks where neither could grow alone.<ref name="Queller-2009"/><ref name="Lücking-2021">{{cite journal |last1=Lücking |first1=Robert |last2=Leavitt |first2=Steven D. |last3=Hawksworth |first3=David L. |title=Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics |journal=[[Fungal Diversity]] |volume=109 |issue=1 |date=2021 |doi=10.1007/s13225-021-00477-7 |pages=99–154|doi-access=free }}</ref> The evolutionary biologists [[David C. Queller|David Queller]] and [[Joan E. Strassmann|Joan Strassmann]] state that "organismality" has evolved socially, as groups of simpler units (from cells upwards) came to cooperate without conflicts. They propose that cooperation should be used as the "defining trait" of an organism.<ref name="Queller-2009"/>

== Organizational terminology ==

{|class="wikitable plainrowheaders" style="margin: 1em auto;"

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

|+ Queller and Strassmann's view of organisms as cooperating entities at differing levels of biological organisation<ref name="Queller-2009"/>

|-

! scope="col" | Level

! scope="col" | Example

! scope="col" | Composition

! scope="col" | Metabolism,<br/>growth,<br/>reproduction

! scope="col" | Co-operation

|-

! scope="row" | [[Virus]]

| [[Tobacco mosaic virus]] || [[Nucleic acid]], [[protein]] || No || No metabolism, so not living, not an organism, say many biologists;<ref name="Moreira-2009"/> but they evolve, their genes collaborating to manipulate the host<ref name="Queller-2009"/>

|-

! scope="row" | [[Unicellular organism]]

| ''[[Paramecium]]'' || One [[Cell (biology)|cell]], with [[organelle]]s e.g. [[Cilium|cilia]] for specific functions || Yes || Inter-cellular (inter-organismal) [[cell signaling|signalling]]<ref name="Hine-2008"/>

|-

! scope="row" | Swarming [[protist]]an

| ''[[Dictyostelium]]'' (cellular slime mould) || Unicellular [[amoeba]]e || Yes || Free-living unicellular amoebae for most of lifetime; swarm and aggregate to a multicellular slug, cells specialising to form a dead stalk and [[sorocarp|a fruiting body]]<ref name="Queller-2009"/>

|-

! scope="row" | [[Multicellular organism]]

| [[Mushroom]]-forming fungus || Cells, grouped into organs for specific functions (e.g. reproduction) || Yes || Cell specialisation, communication<ref name="Hine-2008"/>

|-

! scope="row" | Permanent sexual partnership

| [[Anglerfish]] || Male and female permanently fastened together || Yes || Male provides male [[gamete]]s; female provides all other functions<ref name="Queller-2009"/>

|-

! scope="row" | [[Mutualism (biology)|Mutualism]]

| [[Lichen]] || Organisms of different [[species]] || Yes || [[Fungus]] provides structure, absorbs water and minerals; [[Algae|alga]] photosynthesises<ref name="Queller-2009"/>

|-

! scope="row" | Joined [[Colony (biology)|colony]]

| [[Siphonophore]] || [[Zooid]]s joined together || Yes || Organism specialisation; inter-organism signalling<ref name="Wilson-2000"/>

|-

! scope="row" | [[Superorganism]]

| [[Ant]] colony || Individuals living together || Yes || Organism specialisation (many ants do not reproduce); [[Chemical communication in insects|inter-organism signalling]]<ref name="Kelly-1994"/>

|}

Samuel Díaz‐Muñoz and colleagues (2016) accept Queller and Strassmann's view that organismality can be measured wholly by degrees of cooperation and of conflict. They state that this situates organisms in evolutionary time, so that organismality is context dependent. They suggest that highly integrated life forms, which are not context dependent, may evolve through context-dependent stages towards complete unification.<ref name="Díaz-Muñoz-2016">{{cite journal |last1=Díaz-Muñoz |first1=Samuel L. |last2=Boddy |first2=Amy M. |last3=Dantas |first3=Gautam |last4=Waters |first4=Christopher M. |last5=Bronstein |first5=Judith L. |title=Contextual organismality: Beyond pattern to process in the emergence of organisms |journal=Evolution |volume=70 |issue=12 |year=2016 |issn=0014-3820 |pmid=27704542 |pmc=5132100 |doi=10.1111/evo.13078 |pages=2669–2677}}</ref>

Taxa are ranked groups of organisms which run from the general ([[___domain (biology)|___domain]]) to the specific ([[species]]). A broad scheme of ranks in hierarchical order is:

== Boundary cases ==

* [[Domain (biology)|Domain]]

* [[Kingdom (biology)|Kingdom]]

* [[Phylum]]

* [[Class (biology)|Class]]

* [[Order (biology)|Order]]

* [[Family (biology)|Family]]

* [[Genus]]

* [[Species]]

=== Viruses ===

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 (genus)|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.

{{main|Virus}}

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.

[[File:TMV structure simple.png|thumb|A virus such as [[tobacco mosaic virus]] is not a cell; it contains only its genetic material, and a protein coat.]]

[[Image:Blue crab on market in Piraeus - Callinectes sapidus Rathbun 20020819-317.jpg|thumb|200 px|A [[crab]] is an example of an organism.]]

== Chemistry ==

[[Virus]]es are not typically considered to be organisms, because they are incapable of autonomous [[reproduction]], [[Cell growth|growth]], [[metabolism]], or [[homeostasis]]. Although viruses have a few [[enzyme]]s and molecules like those in living organisms, they have no metabolism of their own; they cannot synthesize the organic compounds from which they are formed. In this sense, they are similar to inanimate matter.<ref name="Moreira-2009">{{cite journal |last1=Moreira |first1=D. |last2=López-García |first2=P.N. |title=Ten reasons to exclude viruses from the tree of life |journal=[[Nature Reviews Microbiology]] |volume=7 |issue=4 |pages=306–311 |date=April 2009 |pmid=19270719 |doi=10.1038/nrmicro2108 |s2cid=3907750 }}</ref> Viruses have their own [[gene]]s, and they [[evolution|evolve]]. Thus, an argument that viruses should be classed as living organisms is their ability to undergo evolution and replicate through self-assembly. However, some scientists argue that viruses neither evolve nor self-reproduce. Instead, viruses are evolved by their host cells, meaning that there was co-evolution of viruses and host cells. If host cells did not exist, viral evolution would be impossible. As for reproduction, viruses rely on hosts' machinery to replicate. The discovery of viruses with genes coding for energy metabolism and protein synthesis fuelled the debate about whether viruses are living organisms, but the genes have a cellular origin. Most likely, they were acquired through [[horizontal gene transfer]] from viral hosts.<ref name="Moreira-2009"/>

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.

{|class="wikitable plainrowheaders" style="margin: 1em auto;"

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 compound]]s which, through interaction with each other and the environment, play a wide variety of roles.

|+ Comparison of cellular organisms and viruses<ref name="Moreira-2009" />

|-

! scope="col" | Capability

! scope="col" | [[Cell (biology)|Cell]]ular organism

! scope="col" | [[Virus]]

|-

! scope="row" | [[Metabolism]]

| Yes

| No, rely entirely on host cell

|-

! scope="row" | [[Cell growth|Growth]]

| Yes

| No, just [[self-assembly]]

|-

! scope="row" | [[Reproduction]]

| Yes

| No, rely entirely on host cell

|-

! scope="row" | Store [[genetic information]] about themselves

| [[DNA]]

| DNA or [[RNA]]

|-

! scope="row" | Able to [[evolution|evolve]]

| [[Evolution|Yes]]: [[mutation]], [[Recombination (biology)|recombination]], [[natural selection]]

| [[Viral evolution|Yes]]: high mutation rate, natural selection

|}

===Evolutionary emergence of organisms===

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. [[Autotroph]]s produce usable energy (in the form of organic compounds) using light from the sun or inorganic compounds while [[heterotroph]]s take in organic compounds from the environment.

The [[RNA world]] is a hypothetical stage in the evolutionary history of life on Earth during which self-replicating RNA molecules reproduced before the evolution of DNA and proteins.<ref>Johnson, Mark (9 March 2024). "'Monumental' experiment suggests how life on Earth may have started". The Washington Post. Archived from the original on 9 March 2024. Retrieved 10 March 2024</ref> According to this hypothesis "organisms" emerged when RNA chains began to self-replicate, initiating the three mechanisms of Darwinian selection: [[heritability]], variation of type and differential reproductive output. The fitness of an RNA replicator (its per capita rate of increase) would presumably have been a function of its intrinsic adaptive capacities, determined by its [[nucleic acid sequence|nucleotide sequence]], and the availability of external resources.<ref name = Bernstein1983>Bernstein, H., Byerly, H. C., Hopf, F. A., Michod, R. A., & Vemulapalli, G. K. (1983). The Darwinian Dynamic. The Quarterly Review of Biology, 58(2), 185–207. http://www.jstor.org/stable/2828805</ref><ref name = Michod1999>Michod, R.E. Darwinian Dynamics: Evolutionary transitions in fitness and individuality. Copyright 1999 Princeton University Press, Princeton, New Jersey ISBN 0-691-02699-8</ref> The three primary adaptive capacities of these early "organisms" may have been: (1) replication with moderate fidelity, giving rise to both heritability while allowing variation of type, (2) resistance to decay, and (3) acquisition of and processing of resources<ref name = Bernstein1983/><ref name = Michod1999/> The capacities of these "organisms" would have functioned by means of the folded configurations of the RNA replicators resulting from their nucleotide sequences.

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 acid]]s), hold cells together and transmit information ([[protein]]).

=== Organism-like colonies ===

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

[[File:Apolemia sp.jpg|thumb|upright|''[[Apolemia]]'', a colonial [[Siphonophorae|siphonophore]] that functions as a single individual]]

=== Macromolecules ===

The philosopher Jack A. Wilson examines some boundary cases to demonstrate that the concept of organism is not sharply defined.<ref name="Wilson-2000"/> In his view, [[sponge]]s, [[lichen]]s, [[Siphonophorae|siphonophore]]s, [[Slime mold|slime mould]]s, and [[Eusociality|eusocial]] colonies such as those of [[ant]]s or [[Naked mole-rat|naked molerat]]s, all lie in the boundary zone between being definite colonies and definite organisms (or superorganisms).<ref name="Wilson-2000"/>

The compounds which make up organisms may be divided into [[macromolecule]]s and other, smaller molecules. The four groups of macromolecule are [[nucleic acid]]s, [[protein]]s, [[carbohydrate]]s and [[lipid]]s. Nucleic acids (specifically [[deoxyribonucleic acid]], or DNA) store genetic data as a sequence of [[nucleotide]]s. 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 [[codon]]s, 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, [[protein folding|folds]] in a particular manner and so performs a particular function.

{| class="wikitable plainrowheaders" style="margin: 1em auto;"

The following functions of protein have been recognized:

|+ Jack A. Wilson's analysis of the similar organism-like nature of siphonophores and jellyfish<ref name="Wilson-2000"/>

|-

! scope="col" | Function

! scope="col" | Colonial [[Siphonophorae|siphonophore]]

! scope="col" | [[Jellyfish]]

|-

! scope="row" | Buoyancy

| Top of [[Colony (biology)|colony]] is gas-filled || Jelly

|-

! scope="row" | Propulsion

| [[Nectophore]]s co-ordinate to pump water || Body pulsates to pump water

|-

! scope="row" | Feeding

| [[Palpon]]s and [[gastrozooid]]s ingest prey, feed other zooids || Tentacles trap prey, pass it to mouth

|-

! scope="row" | Functional structure

| Single functional individual || Single functional individual

|-

! scope="row" | Composition

| Many [[zooid]]s, possibly individuals || Many [[Cell (biology)|cell]]s

|}

{{Clear}}

=== Synthetic organisms ===

# [[Enzymes]], which catalyze all of the reactions of metabolism;

# Structural proteins, such as [[tubulin]], or [[collagen]];

# Regulatory proteins, such as [[transcription factors]] or cyclins that regulate the cell cycle;

# Signalling molecules or their receptors such as some [[hormones]] and their receptors;

# Defensive proteins, which can include everything from [[antibodies]] of the [[immune system]], to toxins (e.g., [[dendrotoxin]]s of snakes), to proteins that include unusual amino acids like [[canavanine]].

[[File:Insect cyborg.jpg|thumb|Insect [[cyborg]] ]]

Lipids make up the [[phospholipid membrane|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.

Scientists and bio-engineers are experimenting with different types of [[Synthetic biology|synthetic organism]], from [[Chimera (genetics)|chimaera]]s composed of cells from two or more species, [[cyborg]]s including [[electromechanics|electromechanical]] limbs, [[hybrot]]s containing both electronic and biological elements, and other combinations of systems that have variously evolved and been designed.<ref name="Clawson-2023">{{cite journal |last1=Clawson |first1=Wesley P. |last2=Levin |first2=Michael |title=Endless forms most beautiful 2.0: teleonomy and the bioengineering of chimaeric and synthetic organisms |journal=Biological Journal of the Linnean Society |volume=138 |issue=1 |date=2023-01-01 |issn=0024-4066 |doi=10.1093/biolinnean/blac116 |pages=141|doi-access=free }}</ref>

== Structure ==

An evolved organism takes its form by the partially understood mechanisms of [[evolutionary developmental biology]], in which the [[genome]] directs an elaborated series of interactions to produce successively more elaborate structures. The existence of chimaeras and hybrids demonstrates that these mechanisms are "intelligently" robust in the face of radically altered circumstances at all levels from molecular to organismal.<ref name="Clawson-2023"/>

All organisms consist of monomeric units called [[cell (biology)|cell]]s; 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 [[biological tissue|tissue]] the four basic types of which are [[epithelium]], [[nervous tissue]], [[muscle|muscle tissue]] and [[connective tissue]]. Several types of tissue work together in the form of an [[organ (anatomy)|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 [[reproductive system|reproduction]], [[digestive system|digestion]], &c. Many multicelled organisms comprise of several organ systems which coordinate to allow for life.

Synthetic organisms already take diverse forms, and their diversity will increase. What they all have in common is a [[Teleonomy|teleonomic]] or goal-seeking behaviour that enables them to correct errors of many kinds so as to achieve whatever result they are designed for. Such behaviour is reminiscent of intelligent action by organisms; intelligence is seen as an embodied form of [[cognition]].<ref name="Clawson-2023"/>

=== The cell ===

The [[cell theory]], first developed in 1839 by [[Matthias Jakob Schleiden|Schleiden]] and [[Theodor Schwann|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 [[genetics|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 [[cell membrane|membrane]], which envelopes the cell, separates its interior from its environment, regulates what moves in and out, and maintains the [[cell potential|electric potential of the cell]]. Inside the membrane, a [[salt]]y [[cytoplasm]] takes up most of the cell volume. All cells possess [[DNA]], the hereditary material of [[gene]]s, and [[RNA]], containing the information necessary to [[gene expression|build]] various [[protein]]s such as [[enzyme]]s, the cell's primary machinery. There are also other kinds of [[biomolecule]]s in cells.

All cells share several abilities<ref name="AlbertsCh1">[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=books&doptcmdl=GenBookHL&term=%22all+cells%22+AND+mboc4%5Bbook%5D+AND+372023%5Buid%5D&rid=mboc4.section.4#23 The Universal Features of Cells on Earth] in Chapter 1 of ''[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=books&doptcmdl=GenBookHL&term=cell+biology+AND+mboc4%5Bbook%5D+AND+373693%5Buid%5D&rid=mboc4 Molecular Biology of the Cell]'' fourth edition, edited by Bruce Alberts (2002) published by Garland Science.</ref>:

* Reproduction by [[cell division]] ([[binary fission]], [[mitosis]] or [[meiosis]]).

* Use of [[enzyme]]s and other [[protein]]s [[genetic code|coded for]] by [[DNA]] [[gene]]s and made via [[messenger RNA]] intermediates and [[ribosome]]s.

* [[Cell metabolism|Metabolism]], including taking in raw materials, building cell components, converting [[energy]], [[molecule]]s and releasing [[by-product]]s. 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 pathway]]s.

* Response to external and internal [[Signal transduction|stimuli]] such as changes in temperature, [[pH]] or nutrient levels.

* Cell contents are contained within a [[Cell membrane|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. [[Senescence|Aging]] is important when determining life span of most organisms, bacterium, a virus or even a [[prion]].

== Evolution ==

{{seealso|Universal common descent|Origin of life}}

[[Image:Phylogenetic_tree.svg|thumb|350px|left|A hypothetical [[phylogenetic tree]] of all extant organisms, based on 16S [[non-coding RNA|rRNA]] [[gene]] sequence data, showing the evolutionary history of the [[Three-___domain system| three domains of life]], [[bacteria]], [[archaea]] and [[eukaryote]]s. 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 acid]]s as its genetic material, and uses the same twenty [[amino acid]]s as the building blocks for [[protein]]s. All organisms use the same [[genetic code]] (with some extremely rare and minor deviations) to [[translation (genetics)|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.

<br style="clear:both;">

=== History of life ===

<!-- for future reference, heh, here's a ref to stromatolite debate that I took out because it messed up formatting -

"Ancient microfossils from Western Australia are again the subject of heated scientific argument: are they the oldest sign of life on Earth, or just a flaw in the rock?" "[http://www.abc.net.au/science/news/space/SpaceRepublish_497964.htm]" -->

{{main|Timeline of evolution}}

The [[chemical evolution]] from [[Catalyst|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.

[[Image:Stromatolites.jpg|right|thumb|280px|[[Precambrian]] [[stromatolite]]s in the Siyeh Formation, [[Glacier National Park (US)|Glacier National Park]]. In 2002, William Schopf of [[University of California, Los Angeles|UCLA]] published a controversial paper in the journal ''[[Nature (journal)|Nature]]'' arguing that formations such as this possess 3.5 billion year old [[fossil]]ized [[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]], [[Bacterium|Bacteria]], [[Eukaryota]]) or the [[origin of life]]. Attempts to shed light on the earliest history of life generally focus on the behavior of [[macromolecule]]s, particularly [[RNA]], and the behavior of [[complex system]]s.

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 formation|banded iron]] deposits, and later [[red bed]]s of iron oxides. This was a necessary prerequisite for the development of [[aerobic respiration|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 [[phylum (biology)|phyla]], of modern animals. This event is now believed to have been triggered by the development of the [[Homeobox|Hox genes]]. About 500 million years ago, [[plant]]s and [[fungi]] colonized the land, and were soon followed by [[arthropod]]s and other animals, leading to the development of land [[ecosystem]]s 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 Earth|history of the earth]]. [[geology|Geological]] evidence indicates that the Earth is approximately [[Age of the Earth|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.<ref>Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata) "[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9072971&query_hl=2]"</ref>. 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 gene transfer|horizontal transfer]] of many [[gene]]s 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." <ref>Oklahoma State - [http://opbs.okstate.edu/~melcher/MG/MGW3/MG334.html Horizontal Gene Transfer]</ref>

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." <ref>[http://www.esalenctr.org/display/confpage.cfm?confid=10&pageid=105&pgtype=1 esalenctr.org]</ref>

== Ecology ==

=== The ecosystem concept ===

{{main|Ecosystem}}

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 [[continent]]al ecosystems, such as [[forest ecosystem]]s, [[meadow]] ecosystems such as [[steppe]]s or [[savanna]]s), or [[Agroecology|agro-ecosystem]]s

* As ecosystems of inland waters, such as [[lentic ecosystem]]s such as [[lake]]s or [[pond]]s; or [[lotic ecosystem]]s such as [[river]]s

* As [[ocean]]ic 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 ===

{{main|Biome|ecozone}}

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 [[eel]]s 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 [[steppe]]s. 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 [[geographical pole|pole]]s, 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 [[photosynthesis|photosynthetic]] [[algae]] only in the ''photic'' part of the ocean (where light penetrates), while [[conifer]]s 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 ===

[[Image:Conch shell 2.jpg|thumb|right|A sea shell is a good example of an organism that utilizes [[bioceramics]].]]

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'' -- [[bacterium|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 chain]]s or food network. In a food network, there will be fewer organisms at each level<!-- [[chains tropic]] --> as one follows the links of the network up the chain.

These concepts lead to the idea of [[biomass (ecology)|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]]).

== References ==

{{reflist}}

<div class="references-small">

<references/>

</div>

== External links ==

* {{cite web |work=Tree of Life Web Project |url=http://tolweb.org/tree/phylogeny.html |title=The Tree of Life }}

* {{cite web |url=http://www.species2000.org/ |work=Species 2000 |title=Indexing the world's known species }}

{{Nature nav}}

* [http://news.bbc.co.uk/1/hi/sci/tech/944790.stm 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...."

{{Composition (Biology)}}

** [http://www.spaceref.com/news/viewpr.html?pid=4742 SpaceRef.com, July 29, 1997: Scientists Discover Methane Ice Worms On Gulf Of Mexico Sea Floor]

{{Self-replicating organic structures}}

*** [http://www.science.psu.edu/iceworms/iceworms.html The Eberly College of Science: Methane Ice Worms discovered on Gulf of Mexico Sea Floor] download Publication quality photos

** [http://www.sb-roscoff.fr/Ecophy/PDF/00-Fisher-NatWis.pdf Artikel, 2000: Methane Ice Worms: Hesiocaeca methanicola. Colonizing Fossil Fuel Reserves]

** [http://www.spaceref.com/news/viewnews.html?id=339 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.

* [http://news.bbc.co.uk/1/hi/sci/tech/2585235.stm 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...."

* [http://news.bbc.co.uk/1/hi/sci/tech/3003946.stm 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,"..."

* [http://www.anselm.edu/homepage/jpitocch/genbios/bi04syllabsu03.html Interactive Syllabus for General Biology - BI 04, Saint Anselm College, Summer 2003]

* [http://www.personal.psu.edu/users/j/s/jsf165/Bio110.html Jacob Feldman: Stramenopila]

* [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Root NCBI Taxonomy entry: root] (rich)

* [http://www.anselm.edu/homepage/jpitocch/genbios/surveybi04.html Saint Anselm College: Survey of representatives of the major Kingdoms] Citat: "...Number of [[kingdom (biology)|kingdom]]s has not been resolved...Bacteria present a problem with their diversity...[[Protista]] present a problem with their diversity...",

* [http://www.species2000.org/ 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.

* [http://www.abc.net.au/science/news/enviro/EnviroRepublish_828525.htm 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.]

* [http://tolweb.org/tree/phylogeny.html The Tree of Life].

{{Authority control}}

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