Organism

In biology, an organism (from Greek: ὀργανισμός, organismos) is any individual entity that propagates the properties of life. It is a synonym for "life form".

Organisms are classified by taxonomy into specified groups such as the multicellular animals, plants, and fungi; or unicellular microorganisms such as a protists, bacteria, and archaea.[1] All types of organisms are capable of reproduction, growth and development, maintenance, and some degree of response to stimuli. Humans are multicellular animals composed of many trillions of cells which differentiate during development into specialized tissues and organs.

An 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).[2] Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes.

Estimates on the number of Earth's current species range from 10 million to 14 million,[3] of which only about 1.2 million have been documented.[4] More than 99% of all species, amounting to over five billion species,[5] that ever lived are estimated to be extinct.[6][7] In 2016, a set of 355 genes from the last universal common ancestor (LUCA) of all organisms was identified.[8][9]

EscherichiaColi NIAID
Escherichia coli (E. coli) is a microscopic single-celled organism, and a prokaryote as well.
Amoeba (Amöbe) 01
Amoebae are single-celled eukaryotes
Fungi in Borneo
Polypore fungi and angiosperm trees are large many-celled eukaryotes.

Etymology

The term "organism" (from Greek ὀργανισμός, organismos, from ὄργανον, organon, i.e. "instrument, implement, tool, organ of sense or apprehension"[10][11]) 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.[12]

Definitions

An organism may be defined as an assembly of molecules 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".[13] Many definitions exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the biochemical machinery of a host cell for reproduction.[14] A superorganism is an organism consisting of many individuals working together as a single functional or social unit.[15]

There has been controversy about the best way to define the organism[16][17][18][19][20][21][22][23][24] and indeed about whether or not such a definition is necessary.[25][26] Several contributions[27] are responses to the suggestion that the category of "organism" may well not be adequate in biology.[28]

Non-cellular life

Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction, growth or metabolism. This controversy is problematic because some cellular organisms are also incapable of independent survival (but are capable of independent metabolism and procreation) and live as obligatory intracellular parasites. Although viruses have a few enzymes and molecules characteristic of living organisms, they have no metabolism of their own; 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 genes, and they do evolve by mechanisms similar to the evolutionary mechanisms of organisms.

The most common argument in support of viruses as living organisms is their ability to undergo evolution and replicate through self-assembly. Some scientists argue that viruses neither evolve nor self- reproduce. In fact, 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 the reproduction, viruses totally rely on hosts' machinery to replicate.[29] The discovery of viral metagenomes with genes coding for energy metabolism and protein synthesis fueled the debate about whether viruses belong in the tree of life. 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.[29]

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 survivability of their DNA-based genes.

Organisms clearly owe their origin, metabolism, and many other internal functions to chemical phenomena, especially the chemistry of large organic molecules. Organisms are complex systems of chemical compounds 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 acids), hold cells together, and transmit information (protein).

Macromolecules

Compounds that make up organisms may be divided into macromolecules and other, smaller molecules. The four groups of macromolecule are nucleic acids, proteins, carbohydrates and lipids. Nucleic acids (specifically deoxyribonucleic acid, or DNA) store genetic data as a sequence of nucleotides. The particular sequence of the four different types of nucleotides (adenine, cytosine, guanine, and thymine) dictate many characteristics that constitute the organism. The sequence is divided up into codons, each of which is a particular sequence of three nucleotides and corresponds to a particular amino acid. Thus a sequence of DNA codes for a particular protein 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:

  1. Enzymes, which catalyze all of the reactions of metabolism
  2. Structural proteins, such as tubulin, or collagen
  3. Regulatory proteins, such as transcription factors or cyclins that regulate the cell cycle
  4. Signaling molecules or their receptors such as some hormones and their receptors
  5. Defensive proteins, which can include everything from antibodies of the immune system, to toxins (e.g., dendrotoxins of snakes), to proteins that include unusual amino acids like canavanine

A bilayer of phospholipids makes up the membrane of cells that constitutes a barrier, containing everything within the cell and preventing compounds from freely passing into, and out of, the cell. Due to the selective permeability of the phospholipid membrane, only specific compounds can pass through it. In some multicellular organisms, they serve as a storage of energy and mediate communication between cells. Carbohydrates are more easily broken down than lipids and yield more energy to compare to lipids and proteins. In fact, carbohydrates are the number one source of energy for all living organisms.

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 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 similar characteristics of:[30]

Evolutionary history

Last universal common ancestor

Stromatolites
Precambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, a paper in the scientific journal Nature suggested that these 3.5 Gya (billion years old) geological formations contain fossilized cyanobacteria microbes. This suggests they are evidence of one of the earliest known life forms on Earth.

The last universal common ancestor (LUCA) is the most recent organism from which all organisms now living on Earth descend.[31] Thus it is the most recent common ancestor of all current life on Earth. The LUCA is estimated to have lived some 3.5 to 3.8 billion years ago (sometime in the Paleoarchean era).[32][33] The earliest evidence for life on Earth is graphite found to be biogenic in 3.7 billion-year-old metasedimentary rocks discovered in Western Greenland[34] and microbial mat fossils found in 3.48 billion-year-old sandstone discovered in Western Australia.[35][36] Although more than 99 percent of all species that ever lived on the planet are estimated to be extinct,[6][7] there are currently 10–14 million species of life on Earth.[3]

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 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. Horizontal gene transfer makes it more difficult to study the last universal ancestor.[37] However, the universal use of the same genetic code, same nucleotides, and same amino acids makes the existence of such an ancestor overwhelmingly likely.[38]

Location of the root

The most commonly accepted location of the root of the tree of life is between a monophyletic 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.[39][40][41][42][43][44] A very small minority of studies have concluded differently, namely that the root is in the domain Bacteria, either in the phylum Firmicutes[45] or that the phylum Chloroflexi is basal to a clade with Archaea and Eukaryotes and the rest of Bacteria as proposed by Thomas Cavalier-Smith.[46]

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, CO2-fixing, H2-dependent with a Wood–Ljungdahl pathway (the reductive 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, 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 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.[47] 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.[48]

Reproduction

Sexual reproduction is widespread among current eukaryotes, and was likely present in the last common ancestor.[49] 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.[50] and Malik et al.[51] 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.[52]

In prokaryotes, 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.[53] Transformation is a common mode of DNA transfer among prokaryotes.[54]

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 transfer of many genes 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.[55]

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."[56]

Future of life (cloning and synthetic organisms)

Modern biotechnology is challenging traditional concepts of organism 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 much ethical debate.

In 2008, the J. Craig Venter Institute assembled a synthetic 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.[57] Other companies, such as Synthetic Genomics, have already been formed to take advantage of the many commercial uses of custom designed genomes.

See also

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External links

Aerobic organism

An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. In contrast, an anaerobic organism (anaerobe) is any organism that does not require oxygen for growth. Some anaerobes react negatively or even die if oxygen is present.

Anaerobic organism

An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if free oxygen is present. In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenated environment. Anaerobes may be unicellular (e.g. protozoans, bacteria) or multicellular.

Anatomical terms of location

Standard anatomical terms of location deal unambiguously with the anatomy of animals, including humans.

All vertebrates (including humans) have the same basic body plan – they are strictly bilaterally symmetrical in early embryonic stages and largely bilaterally symmetrical in adulthood. That is, they have mirror-image left and right halves if divided down the middle. For these reasons, the basic directional terms can be considered to be those used in vertebrates. By extension, the same terms are used for many other (invertebrate) organisms as well.

While these terms are standardized within specific fields of biology, there are unavoidable, sometimes dramatic, differences between some disciplines. For example, differences in terminology remain a problem that, to some extent, still separates the terminology of human anatomy from that used in the study of various other zoological categories.

Aquatic animal

An aquatic animal is an animal, either vertebrate or invertebrate, which lives in the water for most or all of its lifetime. Many insects such as mosquitoes, mayflies, dragonflies and caddisflies have aquatic larvae, with winged adults. Aquatic animals may breathe air or extract oxygen that dissolved in water through specialised organs called gills, or directly through the skin. Natural environments and the animals that live in them can be categorized as aquatic (water) or terrestrial (land). This designation is paraphyletic.

Asexual reproduction

Asexual reproduction is a type of reproduction by which offspring arise from a single organism, and inherit the genes of that parent only; it does not involve the fusion of gametes, and almost never changes the number of chromosomes. Asexual reproduction is the primary form of reproduction for single-celled organisms such as archaea and bacteria. Many plants and fungi sometimes reproduce asexually. Some asexual cells die when they are very young.

While all prokaryotes reproduce without the formation and fusion of gametes, mechanisms for lateral gene transfer such as conjugation, transformation and transduction can be likened to sexual reproduction in the sense of genetic recombination in meiosis. A complete lack of sexual reproduction is relatively rare among multi-cellular organisms, particularly animals. It is not entirely understood why the ability to reproduce sexually is so common among them. Current hypotheses suggest that asexual reproduction may have short term benefits when rapid population growth is important or in stable environments, while sexual reproduction offers a net advantage by allowing more rapid generation of genetic diversity, allowing adaptation to changing environments. Developmental constraints may underlie why few animals have relinquished sexual reproduction completely in their life-cycles. Another constraint on switching from sexual to asexual reproduction would be the concomitant loss of meiosis and the protective recombinational repair of DNA damage afforded as one function of meiosis.

Colony (biology)

In biology, a colony is composed of two or more conspecific individuals living in close association with, or connected to, one another. This association is usually for mutual benefit such as stronger defense or the ability to attack bigger prey. It is a cluster of identical cells (clones) on the surface of (or within) a solid medium, usually derived from a single parent cell, as in bacterial colony. In contrast, a solitary organism is one in which all individuals live independently and have all of the functions needed to survive and reproduce.

Colonies, in the context of development, may be composed of two or more unitary (or solitary) organisms or be modular organisms. Unitary organisms have determinate development (set life stages) from zygote to adult form and individuals or groups of individuals (colonies) are visually distinct. Modular organisms have indeterminate growth forms (life stages not set) through repeated iteration of genetically identical modules (or individuals), and it can be difficult to distinguish between the colony as a whole and the modules within. In the latter case, modules may have specific functions within the colony.

Some organisms are primarily independent and form facultative colonies in reply to environmental conditions while others must live in a colony to survive (obligate). For example, some carpenter bees will form colonies when a dominant hierarchy is formed between two or more nest foundresses (facultative colony), while corals are animals that are physically connected by living tissue (the coenosarc) that contains a shared gastrovascular cavity.

Female

Female (♀) is the sex of an organism, or a part of an organism, that produces non-mobile ova (egg cells). Barring rare medical conditions, most female mammals, including female humans, have two X chromosomes. Female characteristics vary between different species with some species containing more well defined female characteristics. Both genetics and environment shape the prenatal development of a female.

Genetically modified organism

A genetically modified organism (GMO) is any organism whose genetic material has been altered using genetic engineering techniques. The exact definition of a genetically modified organism and what constitutes genetic engineering varies, with the most common being an organism altered in a way that "does not occur naturally by mating and/or natural recombination". A wide variety of organisms have been genetically modified (GM), from animals to plants and microorganisms. Genes have been transferred within the same species, across species (creating transgenic organisms) and even across kingdoms. New genes can be introduced, or endogenous genes can be enhanced, altered or knocked out.

Creating a genetically modified organism is a multi-step process. Genetic engineers must isolate the gene they wish to insert into the host organism and combine it with other genetic elements, including a promoter and terminator region and often a selectable marker. A number of techniques are available for inserting the isolated gene into the host genome. Recent advancements using genome editing techniques, notably CRISPR, have made the production of GMO's much simpler. Herbert Boyer and Stanley Cohen made the first genetically modified organism in 1973, a bacteria resistant to the antibiotic kanamycin. The first genetically modified animal, a mouse, was created in 1974 by Rudolf Jaenisch, and the first plant was produced in 1983. In 1994 the Flavr Savr tomato was released, the first commercialized genetically modified food. The first genetically modified animal to be commercialized was the GloFish (2003) and the first genetically modified animal to be approved for food use was the AquAdvantage salmon in 2015.

Bacteria are the easiest organisms to engineer and have been used for research, food production, industrial protein purification (including drugs), agriculture, and art. There is potential to use them for environmental, purposes or as medicine. Fungi have been engineered with much the same goals. Viruses play an important role as vectors for inserting genetic information into other organisms. This use is especially relevant to human gene therapy. There are proposals to remove the virulent genes from viruses to create vaccines. Plants have been engineered for scientific research, to create new colors in plants, deliver vaccines and to create enhanced crops. Genetically modified crops are publicly the most controversial GMOs. The majority are engineered for herbicide tolerance or insect resistance. Golden rice has been engineered with three genes that increase its nutritional value. Other prospects for GM crops are as bioreactors for the production of biopharmaceuticals, biofuels or medicines.

Animals are generally much harder to transform and the vast majority are still at the research stage. Mammals are the best model organisms for humans, making ones genetically engineered to resemble serious human diseases important to the discovery and development of treatments. Human proteins expressed in mammals are more likely to be similar to their natural counterparts than those expressed in plants or microorganisms. Livestock are modified with the intention of improving economically important traits such as growth-rate, quality of meat, milk composition, disease resistance and survival. Genetically modified fish are used for scientific research, as pets and as a food source. Genetic engineering has been proposed as a way to control mosquitos, a vector for many deadly diseases. Although human gene therapy is still relatively new, it has been used to treat genetic disorders such as severe combined immunodeficiency, and Leber's congenital amaurosis.

Many objections have been raised over the development of GMO's, particularly their commercialization. Many of these involve GM crops and whether food produced from them is safe and what impact growing them will have on the environment. Other concerns are the objectivity and rigor of regulatory authorities, contamination of non-genetically modified food, control of the food supply, patenting of life and the use of intellectual property rights. Although there is a scientific consensus that currently available food derived from GM crops poses no greater risk to human health than conventional food, GM food safety is a leading issue with critics. Gene flow, impact on non-target organisms and escape are the major environmental concerns. Countries have adopted regulatory measures to deal with these concerns. There are differences in the regulation for the release of GMOs between countries, with some of the most marked differences occurring between the US and Europe. One of the key issues concerning regulators is whether GM food should be labeled and the status of gene edited organisms.

Host (biology)

In biology and medicine, a host is an organism that harbours a parasitic, a mutualistic, or a commensalist guest (symbiont), the guest typically being provided with nourishment and shelter. Examples include animals playing host to parasitic worms (e.g. nematodes), cells harbouring pathogenic (disease-causing) viruses, a bean plant hosting mutualistic (helpful) nitrogen-fixing bacteria. More specifically in botany, a host plant supplies food resources to micropredators, which have an evolutionarily stable relationship with their hosts similar to ectoparasitism. The host range is the collection of hosts that an organism can use as a partner.

Introduced species

An introduced species, alien species, exotic species, foreign species, non-indigenous species, or non-native species is a species living outside its native distributional range, but which has arrived there by human activity, either deliberate or accidental. Non-native species can have various effects on the local ecosystem. Introduced species that become established and spread beyond the place of introduction are called invasive species.

The impact of introduced species is highly variable. Some have a negative effect on a local ecosystem, while other introduced species may have no negative effect or only minor impact. Some species have been introduced intentionally to combat pests. They are called biocontrols and may be regarded as beneficial as an alternative to pesticides in agriculture for example. In some instances the potential for being beneficial or detrimental in the long run remains unknown.The effects of introduced species on natural environments have gained much scrutiny from scientists, governments, farmers, and others.

Microorganism

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.

The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.

Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here.

They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. A December 2017 report stated that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

Model organism

A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Model organisms are widely used to research human disease when human experimentation would be unfeasible or unethical. This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution.Studying model organisms can be informative, but care must be taken when generalizing from one organism to another.In researching human disease, model organisms allow for better understanding the disease process without the added risk of harming an actual human. The species chosen will usually meet a determined taxonomic equivalency to humans, so as to react to disease or its treatment in a way that resembles human physiology as needed. Although biological activity in a model organism does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models. There are three main types of disease models: homologous, isomorphic and predictive. Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease. Isomorphic animals share the same symptoms and treatments. Predictive models are similar to a particular human disease in only a couple of aspects, but are useful in isolating and making predictions about mechanisms of a set of disease features.

Multicellular organism

Multicellular organisms are organisms that consist of more than one cell, in contrast to unicellular organisms.All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni- and partially multicellular, like slime molds and social amoebae such as the genus Dictyostelium.

Multicellular organisms arise in various ways, for example by cell division or by aggregation of many single cells. Colonial organisms are the result of many identical individuals joining together to form a colony. However, it can often be hard to separate colonial protists from true multicellular organisms, because the two concepts are not distinct; colonial protists have been dubbed "pluricellular" rather than "multicellular".

Pathogen

In biology, a pathogen (Greek: πάθος pathos "suffering, passion" and -γενής -genēs "producer of"), in the oldest and broadest sense, is anything that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.

The term pathogen came into use in the 1880s. Typically, the term is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as certain kinds of worms and insect larvae, can also produce disease. However, these animals are usually, in common parlance, referred to as parasites rather than pathogens. The scientific study of microscopic organisms, including microscopic pathogenic organisms, is called microbiology, while the study of disease that may include these pathogens is called pathology. Parasitology, meanwhile, is the scientific study of parasites and the organisms that host them.

There are several pathways through which pathogens can invade a host. The principal pathways have different episodic time frames, but soil has the longest or most persistent potential for harboring a pathogen. Diseases in humans that are caused by infectious agents are known as pathogenic diseases, though not all diseases are caused by pathogens. Some diseases, such as Huntington's disease, are caused by inheritance of abnormal genes.

Pest (organism)

A pest is any animal or plant detrimental to humans or human concerns, including crops, livestock, and forestry. The term is also used of organisms that cause a nuisance, such as in the home. An older usage is of a deadly epidemic disease, specifically plague. In its broadest sense, a pest is a competitor of humanity.

Reproduction

Reproduction (or procreation or breeding) is the biological process by which new individual organisms – "offspring" – are produced from their "parents". Reproduction is a fundamental feature of all known life; each individual organism exists as the result of reproduction. There are two forms of reproduction: asexual and sexual.

In asexual reproduction, an organism can reproduce without the involvement of another organism. Asexual reproduction is not limited to single-celled organisms. The cloning of an organism is a form of asexual reproduction. By asexual reproduction, an organism creates a genetically similar or identical copy of itself. The evolution of sexual reproduction is a major puzzle for biologists. The two-fold cost of sexual reproduction is that only 50% of organisms reproduce and organisms only pass on 50% of their genes.Sexual reproduction typically requires the sexual interaction of two specialized organisms, called gametes, which contain half the number of chromosomes of normal cells and are created by meiosis, with typically a male fertilizing a female of the same species to create a fertilized zygote. This produces offspring organisms whose genetic characteristics are derived from those of the two parental organisms.

Sex

Organisms of many species are specialized into male and female varieties, each known as a sex. Sexual reproduction involves the combining and mixing of genetic traits: specialized cells known as gametes combine to form offspring that inherit traits from each parent. The gametes produced by an organism define its sex: males produce small gametes (e.g. spermatozoa, or sperm, in animals; pollen in seed plants) while females produce large gametes (ova, or egg cells). Individual organisms which produce both male and female gametes are termed hermaphroditic. Gametes can be identical in form and function (known as isogamy), but, in many cases, an asymmetry has evolved such that two different types of gametes (heterogametes) exist (known as anisogamy).

Physical differences are often associated with the different sexes of an organism; these sexual dimorphisms can reflect the different reproductive pressures the sexes experience. For instance, mate choice and sexual selection can accelerate the evolution of physical differences between the sexes.

Among humans and other mammals, males typically carry an X and a Y chromosome (XY), whereas females typically carry two X chromosomes (XX), which are a part of the XY sex-determination system. Humans may also be intersex. Other animals have different sex-determination systems, such as the ZW system in birds, the X0 system in insects, and various environmental systems, for example in crustaceans. Fungi may also have more complex allelic mating systems, with sexes not accurately described as male, female, or hermaphroditic.

Unicellular organism

A unicellular organism, also known as a single-celled organism, is an organism that consists of only one cell, unlike a multicellular organism that consists of more than one cell. Unicellular organisms fall into two general categories: prokaryotic organisms and eukaryotic organisms. Prokaryotes include bacteria and archaea. Many eukaryotes are multicellular, but the group includes the protozoa, unicellular algae, and unicellular fungi. Unicellular organisms are thought to be the oldest form of life, with early protocells possibly emerging 3.8–4 billion years ago.Although some prokaryotes live in colonies, they are not specialised into cells with differing functions. These organisms live together, and each cell must carry out all life processes to survive. In contrast, even the simplest multicellular organisms have cells that depend on each other to survive.

Most multicellular organisms have a unicellular life-cycle stage. Gametes, for example, are reproductive unicells for multicellular organisms. Additionally, multicellularity appears to have evolved independently many times in the history of life.

Some organisms are partially unicellular, like Dictyostelium discoideum. Additionally, unicellular organisms can be multinucleate, like Myxogastria and Plasmodium.

Zygosity

Zygosity (the noun, zygote, is from the Greek zygotos "yoked," from zygon "yoke") () is the degree of similarity of the alleles for a trait in an organism.

Most eukaryotes have two matching sets of chromosomes; that is, they are diploid. Diploid organisms have the same loci on each of their two sets of homologous chromosomes except that the sequences at these loci may differ between the two chromosomes in a matching pair and that a few chromosomes may be mismatched as part of a chromosomal sex-determination system. If both alleles of a diploid organism are the same, the organism is homozygous at that locus. If they are different, the organism is heterozygous at that locus. If one allele is missing, it is hemizygous, and, if both alleles are missing, it is nullizygous.

The DNA sequence of a gene often varies from one individual to another. Those variations are called alleles. While some genes have only one allele because there is low variation, others have only one allele because deviation from that allele can be harmful or fatal. But most genes have two or more alleles. The frequency of different alleles varies throughout the population. Some genes may have two alleles with equal distribution. For other genes, one allele may be common, and another allele may be rare. Sometimes, one allele is a disease-causing variation while the other allele is healthy. Sometimes, the different variations in the alleles make no difference at all in the function of the organism.

In diploid organisms, one allele is inherited from the male parent and one from the female parent. Zygosity is a description of whether those two alleles have identical or different DNA sequences. In some cases the term "zygosity" is used in the context of a single chromosome.

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