Organism

In

biology

, an organism () is any organic,

living

system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular

animal

s,

plant

s, and

fungi

; or unicellular microorganisms such as protists,

bacteria

, and

archaea

. All types of organisms are capable of

reproduction

, growth and development, maintenance, and some degree of response to stimuli.

Beetle

s,

squid

s, tetrapods,

mushroom

s, and vascular plants are examples of multicellular organisms that differentiate specialized tissues and organs during development.

A unicellular organism may be either a prokaryote or a

eukaryote

. Prokaryotes are represented by two separate domains –

bacteria

and

archaea

. Eukaryotic organisms are characterized by the presence of a membrane-bound

cell nucleus

and contain additional membrane-bound compartments called organelles (such as

mitochondria

in animals and plants and plastids in plants and

algae

, all generally considered to be derived from

endosymbiotic

bacteria). Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes.

Estimates on the number of Earth's current

species

range from 2 million to 1 trillion, of which over 1.7 million have been documented. More than 99% of all species, amounting to over five billion species, that ever lived are estimated to be

extinct

.

In 2016, a set of 355

gene

s from the last universal common ancestor (LUCA) of all organisms was identified.

Etymology

The term "organism" (from Greek ὀργανισμός, ''organismos'', from ὄργανον, ''organon'', i.e. "instrument, implement, tool, organ of sense or apprehension") first appeared in the English language in 1703 and took on its current definition by 1834 (Oxford English Dictionary). It is directly related to the term "organization". There is a long tradition of defining organisms as self-organizing beings, going back at least to

Immanuel Kant

's 1790 ''Critique of Judgment''.

Definitions

An organism may be defined as an assembly of

molecule

s functioning as a more or less stable whole that exhibits the

properties of life

. Dictionary definitions can be broad, using phrases such as "any living structure, such as a plant, animal, fungus or bacterium, capable of growth and reproduction". Many definitions exclude

virus

es and possible man-made non-organic life forms, as viruses are dependent on the biochemical machinery of a host cell for reproduction. A superorganism is an organism consisting of many individuals working together as a single functional or social unit.

There has been controversy about the best way to define the organism and indeed about whether or not such a definition is necessary. Several contributions are responses to the suggestion that the category of "organism" may well not be adequate in biology.

Viruses

Virus

es are not typically considered to be organisms because they are incapable of autonomous

reproduction

, growth or

metabolism

. Although some organisms are also incapable of independent survival and live as obligatory intracellular

parasites

, they are capable of independent metabolism and procreation. Although viruses have a few

enzyme

s and molecules characteristic of living organisms, they have no metabolism of their own; they cannot synthesize and organize the organic compounds from which they are formed. Naturally, this rules out autonomous reproduction: 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 classified as organisms, they do have their own

gene

s, and they do

evolve

by mechanisms similar to the evolutionary mechanisms of organisms. 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. This is not true for cells. If viruses did not exist, the direction of cellular evolution could be different, but cells would nevertheless be able to evolve. As for reproduction, viruses totally 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. The presence of these genes suggested that viruses were once able to metabolize. However, it was found later that the genes coding for energy and protein metabolism have a cellular origin. Most likely, these genes were acquired through horizontal gene transfer from viral hosts.

Chemistry

Organisms are complex chemical systems, organized in ways that promote reproduction and some measure of sustainability or survival. The same laws that govern non-living chemistry govern

the chemical processes of life

. It is generally the phenomena of entire organisms that determine their fitness to an environment and therefore the survival 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 that, through interaction and 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 chemical properties of this element such as its great affinity for bonding with other small atoms, including other carbon atoms, and its small size making 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 acid

s), 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 acid

s,

protein

s, carbohydrates and lipids. 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 many characteristics that 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 sequence of DNA codes for a particular protein that, due to the chemical properties of the amino acids it is made from,

folds

in a particular manner and so performs a particular function.

These protein functions have been recognized:
#

Enzyme

s, which catalyze the reactions of metabolism
# Structural proteins, such as

tubulin

, or

collagen

# Regulatory proteins, such as transcription factors or cyclins that regulate the cell cycle
# Signaling molecules or their receptors such as some

hormone

s and their receptors
# 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

A bilayer of

phospholipid

s makes up the membrane of cells that constitutes a barrier, containing everything within a cell and preventing compounds from freely passing into, and out of, the cell. Due to the selective permeability of the phospholipid membrane, only specific compounds can pass through it.

Structure

All organisms consist of structural 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 a tissue, and in animals these occur as four basic types, namely 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 such as the reproductive system, and

digestive system

. Many multicellular organisms consist of several organ systems, which coordinate to allow for life.

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, 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 multicellular 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

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

build

various

protein

s such as

enzyme

s, the cell's primary machinery. There are also other kinds of biomolecules in cells.

All cells share several similar characteristics of: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.
* Reproduction by

cell division

(

binary fission

,

mitosis

or

meiosis

).
* Use of enzymes and other proteins

coded

by DNA genes and made via messenger RNA intermediates and

ribosome

s.
* Metabolism, including taking in raw materials, building cell components, converting energy,

molecule

s 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 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 bilayer.

Evolutionary history

Last universal common ancestor

The last universal common ancestor (LUCA) is the most recent organism from which all organisms now living on Earth Common descent, descend. Thus it is the most recent common ancestor of all current life on Earth. The LUCA is estimated to have lived some Timeline of evolution, 3.5 to 3.8 billion years ago (sometime in the Paleoarchean era). The earliest evidence for life, life on Earth is graphite found to be Biogenic substance, biogenic in 3.7 billion-year-old Metasediment, metasedimentary rocks discovered in Western Greenland and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia. Although more than 99 percent of all species that ever lived on the planet are estimated to be extinct, it is likely that more than a billion species of life exist on Earth currently, with the highest estimates and projections reaching one trillion species.

Information about the early development of life includes input from many different fields, including 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.

All organisms 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 that do not fly.

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. Horizontal gene transfer makes it more difficult to study the last universal ancestor. However, the universal use of the same genetic code, same nucleotides, and same amino acids makes the existence of such an ancestor overwhelmingly likely.

Phylogeny

Location of the root

The most commonly accepted location of the root of the Tree of life (biology), tree of life is between a monophyletic domain (biology), domain Bacteria and a clade formed by Archaea and Eukaryota of what is referred to as the "traditional tree of life" based on several molecular studies. A very small minority of studies have concluded differently, namely that the root is in the domain Bacteria, either in the phylum Firmicutes or that the phylum Chloroflexi (phylum), Chloroflexi is basal to a clade with Archaea and Eukaryotes and the rest of Bacteria as proposed by Thomas Cavalier-Smith.

Research published in 2016, by William F. Martin, by genetically analyzing 6.1 million protein-coding genes from sequenced prokaryotic genomes of various phylogenetic trees, identified 355 protein clusters from amongst 286,514 protein clusters that were probably common to the LUCA. The results "depict LUCA as anaerobic organism, anaerobic, CO₂-fixing, H₂-dependent with a Wood–Ljungdahl pathway (the reductive Acetyl-CoA, acetyl-coenzyme A pathway), N₂-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, Flavin mononucleotide, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations." The results depict methanogenic clostridium, clostria as a basal clade in the 355 lineages examined, and suggest that the LUCA inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H₂, CO₂, and iron. However, the identification of these genes as being present in LUCA was criticized, suggesting that many of the proteins assumed to be present in LUCA represent later horizontal gene transfers between archaea and bacteria.

Reproduction

Sexual reproduction is widespread among current eukaryotes, and was likely present in the last common ancestor. This is suggested by the finding of a core set of genes for meiosis in the descendants of lineages that diverged early from the eukaryotic evolutionary tree. and Malik et al. It is further supported by evidence that eukaryotes previously regarded as "ancient asexuals", such as ''Amoeba'', were likely sexual in the past, and that most present day asexual amoeboid lineages likely arose recently and independently.

In prokaryotes, Transformation (genetics)#Natural transformation, natural bacterial transformation involves the transfer of DNA from one bacterium to another and integration of the donor DNA into the recipient chromosome by recombination. Natural bacterial transformation is considered to be a primitive sexual process and occurs in both bacteria and archaea, although it has been studied mainly in bacteria. Transformation is clearly a bacterial adaptation and not an accidental occurrence, because it depends on numerous gene products that specifically interact with each other to enter a state of natural competence to perform this complex process. Transformation is a common mode of DNA transfer among prokaryotes.

Horizontal gene transfer

The ancestry of living organisms has traditionally been reconstructed from morphology, but is increasingly supplemented with phylogenetics – the reconstruction of phylogenies by the comparison of genetic (DNA) sequence.

Sequence comparisons suggest recent horizontal gene transfer, horizontal transfer of many genes among diverse

species

including across the boundaries of phylogenetics, phylogenetic "domains". Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes.

Biologist Peter 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."

Future of life (cloning and synthetic organisms)

Modern biotechnology is challenging traditional concepts of organisms and species. Cloning is the process of creating a new multicellular organism, genetically identical to another, with the potential of creating entirely new species of organisms. Cloning is the subject of ethics of cloning, much ethical debate.

In 2008, the J. Craig Venter Institute assembled a synthetic Bacterial genome size, bacterial genome, ''Mycoplasma genitalium'', by using recombination in yeast of 25 overlapping DNA fragments in a single step. The use of yeast recombination greatly simplifies the assembly of large DNA molecules from both synthetic and natural fragments. Other companies, such as Synthetic Genomics, have already been formed to take advantage of the many commercial uses of custom designed genomes.

See also

* Earliest known life forms

References

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"
*

*** [https://web.archive.org/web/20090601140743/http://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
*
Artikel, 2000: Methane Ice Worms: Hesiocaeca methanicola. Colonizing Fossil Fuel Reserves
*

''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"


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

NCBI Taxonomy entry: root


Citat: "Number of kingdoms has not been resolved...Bacteria present a problem with their diversity...Protista present a problem with their diversity...",

Species 2000 Indexing the world's known species
Species 2000 has the objective of enumerating all known species of plants, animals, fungi and microbes on Earth as the baseline dataset for studies of global biodiversity. It will also provide a simple access point enabling users to link from here to other data systems for all groups of organisms, using direct species-links.


* [http://tolweb.org/tree/phylogeny.html The Tree of Life]
* [https://www.scribd.com/doc/1016/Life-from-birth-to-death/ Frequent questions from kids about life and their answers]

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Organisms,

ceb:organismo