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André Breton

André Robert Breton (19 February 1896 – 28 September 1966) was a French writer and poet, the co-founder, leader, and principal theorist of surrealism. His writings include the first Surrealist Manifesto (Manifeste du surréalisme) of 1924, in which he defined surrealism as "pure psychic automatism".

Along with his role as leader of the surrealist movement he is the author of celebrated books such as Nadja and L'Amour fou. Those activities, combined with his critical and theoretical work on writing and the plastic arts, made André Breton a major figure in twentieth-century French art and literature.

Biography
André Breton was the only son born to a family of modest means in Tinchebray (Orne) in Normandy, France. His father, Louis-Justin Breton, was a policeman and atheist, and his mother, Marguerite-Marie-Eugénie Le Gouguès, was a former seamstress. Breton attended medical school, where he developed a particular interest in mental illness. His education was interrupted when he was conscripted for World War I.

During World War I, he worked in a neurological ward in Nantes, where he met the Alfred Jarry devotee Jacques Vaché, whose anti-social attitude and disdain for established artistic tradition influenced Breton considerably. Vaché committed suicide when aged 23, and his war-time letters to Breton and others were published in a volume entitled Lettres de guerre (1919), for which Breton wrote four introductory essays.

Breton married his first wife, Simone Kahn, on 15 September 1921. The couple relocated to rue Fontaine No. 42 in Paris on 1 January 1922. The apartment on rue Fontaine (in the Pigalle district) became home to Breton's collection of more than 5,300 items: modern paintings, drawings, sculptures, photographs, books, art catalogs, journals, manuscripts, and works of popular and Oceanic art. Like his father, he was an atheist.

From Dada to Surrealism
Breton launched the review Littérature in 1919, with Louis Aragon and Philippe Soupault. He also associated with Dadaist Tristan Tzara.

In Les Champs Magnétiques (The Magnetic Fields), a collaboration with Soupault, he implemented the principle of automatic writing. With the publication of his Surrealist Manifesto in 1924 came the founding of the magazine La Révolution surréaliste and the Bureau of Surrealist Research. A group of writers became associated with him: Soupault, Louis Aragon, Paul Éluard, René Crevel, Michel Leiris, Benjamin Péret, Antonin Artaud, and Robert Desnos.

Eager to combine the themes of personal transformation found in the works of Arthur Rimbaud with the politics of Karl Marx, Breton and others joined the French Communist Party in 1927, from which he was expelled in 1933. Nadja, a novel about his imaginative encounter with a woman who later becomes mentally ill, was published in 1928. Due to the economic depression, he had to sell his art collection and rebuilt it later.

In December 1929, Breton published the Second manifeste du surréalisme (Second manifesto of surrealism), which contained an oft-quoted declaration for which many, including Albert Camus, reproached Breton: "The simplest surrealist act consists, with revolvers in hand, of descending into the street and shooting at random, as much as possible, into the crowd".

In reaction to the Second manifesto, writers and artists published in 1930 a collective collection of pamphlets against Breton, entitled (in allusion to an earlier title by Breton) Un Cadavre. The authors were members of the surrealist movement who were insulted by Breton or had otherwise opposed his leadership. The pamphlet criticized Breton's oversight and influence over the movement. It marked a divide amidst the early surrealists. Georges Limbour and Georges Ribemont-Dessaignes commented on the sentence where shooting at random in the crowd is described as the simplest surrealist act. Limbour saw in it an example of buffoonery and shamelessness and Ribemont-Dessaignes called Breton a hypocrite, a cop and a priest.

After the publication of this pamphlet against Breton, the Manifesto had a second edition, where Breton added in a note: "While I say that this act is the simplest, it is clear that my intention is not to recommend it to all merely by virtue of its simplicity; to quarrel with me on this subject is much like a bourgeois asking any non-conformist why he does not commit suicide, or asking a revolutionary why he hasn't moved to the USSR".

In 1935, there was a conflict between Breton and the Soviet writer and journalist Ilya Ehrenburg during the first International Congress of Writers for the Defense of Culture, which opened in Paris in June. Breton had been insulted by Ehrenburg — along with all fellow surrealists — in a pamphlet which said, among other things, that surrealists shunned work, favouring parasitism, and that they endorsed "onanism, pederasty, fetishism, exhibitionism, and even sodomy". Breton slapped Ehrenburg several times on the street, which resulted in surrealists being expelled from the Congress. René Crevel, who according to Salvador Dalí was "the only serious communist among surrealists", was isolated from Breton and other surrealists, who were unhappy with Crevel because of his bisexuality and annoyed with communists in general.

In 1938, Breton accepted a cultural commission from the French government to travel to Mexico. After a conference at the National Autonomous University of Mexico about surrealism, Breton stated after getting lost in Mexico City (as no one was waiting for him at the airport) "I don't know why I came here. Mexico is the most surrealist country in the world."

However, visiting Mexico provided the opportunity to meet Leon Trotsky. Breton and other surrealists traveled via a long boat ride from Patzcuaro to the town of Erongarícuaro. Diego Rivera and Frida Kahlo were among the visitors to the hidden community of intellectuals and artists. Together, Breton and Trotsky wrote the Manifesto for an Independent Revolutionary Art (published under the names of Breton and Diego Rivera) calling for "complete freedom of art", which was becoming increasingly difficult with the world situation of the time.

World War II and exile
Breton was again in the medical corps of the French Army at the start of World War II. The Vichy government banned his writings as "the very negation of the national revolution" and Breton escaped, with the help of the American Varian Fry and Hiram "Harry" Bingham IV, to the United States and the Caribbean during 1941. He emigrated to New York City and lived there for a few years. In 1942, Breton organized a groundbreaking surrealist exhibition at Yale University.

In 1942, Breton collaborated with artist Wifredo Lam on the publication of Breton's poem "Fata Morgana", which was illustrated by Lam.

Breton got to know Martinican writers Suzanne Césaire and Aimé Césaire, and later composed the introduction to the 1947 edition of Aimé Césaire's Cahier d'un retour au pays natal. During his exile in New York City he met Elisa Bindhoff, the Chilean woman who would become his third wife.

In 1944, he and Elisa traveled to the Gaspé Peninsula in Québec, where he wrote Arcane 17, a book which expresses his fears of World War II, describes the marvels of the Percé Rock and the extreme northeastern part of North America, and celebrates his new romance with Elisa.

During his visit to Haiti in 1945–46, he sought to connect surrealist politics and automatist practices with the legacies of the Haitian Revolution and the ritual practices of Vodou possession. Recent developments in Haitian painting were central to his efforts, as can be seen from a comment that Breton left in the visitors' book at the Centre d'Art in Port-au-Prince: "Haitian painting will drink the blood of the phoenix. And, with the epaulets of [Jean-Jacques] Dessalines, it will ventilate the world." Breton was specifically referring to the work of painter and Vodou priest Hector Hyppolite, whom he identified as the first artist to directly depict Vodou scenes and the lwa (Vodou deities), as opposed to hiding them in chromolithographs of Catholic saints or invoking them through impermanent vevé (abstracted forms drawn with powder during rituals). Breton's writings on Hyppolite were undeniably central to the artist's international status from the late 1940s on, but the surrealist readily admitted that his understanding of Hyppolite's art was inhibited by their lack of a common language. Returning to France with multiple paintings by Hyppolite, Breton integrated this artwork into the increased surrealist focus on the occult, myth, and magic.

Breton's sojourn in Haiti coincided with the overthrow of the country's president, Élie Lescot, by a radical protest movement. Breton's visit was warmly received by La Ruche, a youth journal of revolutionary art and politics, which in January 1946 published a talk given by Breton alongside a commentary which Breton described as having "an insurrectional tone". The issue concerned was suppressed by the government, sparking a student strike, and two days later, a general strike: Lescot was toppled a few days later. Among the figures associated with both La Ruche and the instigation of the revolt were the painter and photographer Gérald Bloncourt and the writers René Depestre and Jacques Stephen Alexis. In subsequent interviews Breton downplayed his personal role in the unrest, stressing that "the misery, and thus, the patience of the Haitian people, were at the breaking point" at the time and stating that "it would be absurd to say that I alone incited the fall of the government". Michael Löwy has argued that the lectures that Breton gave during his time in Haiti resonated with the youth associated with La Ruche and the student movement, resulting in them "plac(ing) them as a banner on their journal" and "t(aking) hold of them as they would a weapon". Löwy has identified three themes in Breton's talks which he believes would have struck a particular chord with the audience, namely surrealism's faith in youth, Haiti's revolutionary heritage, and a quote from Jacques Roumain extolling the revolutionary potential of the Haitian masses.

Later life
Breton returned to Paris in 1946, where he opposed French colonialism (for example as a signatory of the Manifesto of the 121 against the Algerian War) and continued, until his death, to foster a second group of surrealists in the form of expositions or reviews (La Brèche, 1961–65). In 1959, he organized an exhibit in Paris.

By the end of World War II, André Breton decided to embrace anarchism explicitly. In 1952, Breton wrote "It was in the black mirror of anarchism that surrealism first recognised itself." Breton consistently supported the francophone Anarchist Federation and he continued to offer his solidarity after the Platformists around founder and Secretary General Georges Fontenis transformed the FA into the Fédération communiste libertaire (FCL).

Like a small number of intellectuals during the time of the Algerian War, he continued to support the FCL when it was forced to go underground, even providing shelter to Fontenis, who was in hiding. He refused to take sides in the politically divided French anarchist movement, even though both he and Péret expressed solidarity to the new Anarchist Federation rebuilt by a group of synthesist anarchists. He also worked with the FA in the Anti-Fascist Committees in the 1960s.

André Breton died at the age of 70 in 1966, and was buried in the Cimetière des Batignolles in Paris.

Breton as a collector
Breton was an avid collector of art, ethnographic material, and unusual trinkets. He was particularly interested in materials from the northwest coast of North America. During a financial crisis he experienced in 1931, most of his collection (along with that of his friend Paul Éluard) was auctioned. He subsequently rebuilt the collection in his studio and home at 42 rue Fontaine. The collection grew to over 5,300 items: modern paintings, drawings, sculptures, photographs, books, art catalogs, journals, manuscripts, and works of popular and Oceanic art.

French anthropologist Claude Lévi-Strauss endorsed Breton's skill in authentication based on their time together in 1940s New York.

After Breton's death on 28 September 1966, his third wife, Elisa, and his daughter, Aube, allowed students and researchers access to his archive and collection. After thirty-six years, when attempts to establish a surrealist foundation to protect the collection were opposed, the collection was auctioned by Calmels Cohen at Drouot-Richelieu. A wall of the apartment is preserved at the Centre Georges Pompidou.

Nine previously partly unpublished manuscripts, including the Manifeste du surréalisme, were auctioned by Sotheby's in May 2008.

Personal life
Breton married three times:

 * from 1921 to 1931, to Simone Collinet, née Kahn (1897–1980);
 * from 1934 to 1943, to Jacqueline Lamba, with whom he had his only child, a daughter, ;
 * from 1945 to 1966 (his death), to Elisa Bindhoff Enet.

Works

 * 1919: Mont de piété ["Mount of piety"]
 * 1920: S'il vous plaît – Published in English as: If You Please
 * 1920: Les Champs magnétiques (with Philippe Soupault) – Published in English as: The Magnetic Fields
 * 1923: Clair de terre – Published in English as: Earthlight
 * 1924: Les Pas perdus – Published in English as: The Lost Steps
 * 1924: Manifeste du surréalisme – Published in English as: Surrealist Manifesto
 * 1924: Poisson soluble ["Soluble fish"]
 * 1924: Un cadavre ["A corpse"]
 * 1926: Légitime défense ["Legitimate defense"]
 * 1928: Le Surréalisme et la peinture (expanded editions in 1945 and 1965) – Published in English as: Surrealism and Painting
 * 1928: Nadja (expanded edition 1963) – Published in English as: Nadja
 * 1930: Ralentir travaux ["Slow down, men at work"] (with René Char and Paul Éluard)
 * 1930: Deuxième Manifeste du surréalisme – Published in English as: The Second Manifesto of Surrealism
 * 1930: L'Immaculée Conception (with Paul Éluard) – Published in English as: Immaculate Conception
 * 1931: L'Union libre ["Free union"]
 * 1932: Misère de la poésie ["Poetry's misery"]
 * 1932: Le Revolver à cheveux blancs ["The white-haired revolver"]
 * 1932: Les Vases communicants (expanded edition 1955) – Published in English as: Communicating Vessels
 * 1933: Le Message automatique – Published in English as: The Automatic Message
 * 1934: Qu'est-ce que le surréalisme? – Published in English as: What Is Surrealism?
 * 1934: Point du jour – Published in English as: Break of Day
 * 1934: L'Air de l'eau ["The air of the water"]
 * 1935: Position politique du surréalisme ["Political position of surrealism"]
 * 1936: Au lavoir noir ["At the black washtub"]
 * 1936: Notes sur la poésie ["Notes on poetry"] (with Paul Éluard)
 * 1937: Le Château étoilé ["The starry castle"]
 * 1937: L'Amour fou – Published in English as: Mad Love
 * 1938: Trajectoire du rêve ["Trajectory of dream"]
 * 1938: Dictionnaire abrégé du surréalisme ["Abridged dictionary of surrealism"] (with Paul Éluard)
 * 1938: Pour un art révolutionnaire indépendant ["For an independent revolutionary art"] (with Diego Rivera)
 * 1940: Anthologie de l'humour noir (expanded edition 1966) – Published in English as: Anthology of Black Humor
 * 1941: "Fata morgana" (A long poem included in subsequent anthologies)
 * 1943: Pleine marge ["Full margin"]
 * 1944: Arcane 17 – Published in English as: Arcanum 17
 * 1945: Situation du surréalisme entre les deux guerres ["Situation of surrealism between the two wars"]
 * 1946: Yves Tanguy (monograph on Yves Tanguy)
 * 1946: Les Manifestes du surréalisme (Expanded editions 1955 and 1962) – Published in English as: Manifestoes of Surrealism
 * 1946: Young Cherry Trees Secured Against Hares – Jeunes cerisiers garantis contre les lièvres [Bilingual edition of poems translated by Edouard Roditi]
 * 1947: Ode à Charles Fourier – Published in English as: Ode to Charles Fourier
 * 1948: Martinique, charmeuse de serpents (with André Masson) – Published in English as: Martinique: Snake Charmer
 * 1948: La Lampe dans l'horloge ["The lamp in the clock"]
 * 1948: Poèmes 1919–48 ["Poems 1919–48"]
 * 1949: Flagrant délit ["Red-handed"]
 * 1952: Entretiens – Published in English as: Conversations: The Autobiography of Surrealism
 * 1953: La Clé des champs – Published in English as: Free Rein
 * 1954: Farouche à quatre feuilles ["Four-leaf feral"] (with Lise Deharme, Julien Gracq, Jean Tardieu)
 * 1957: L'Art magique – Published in English as: Magical Art
 * 1959: Constellations (with Joan Miró) – Published in English as: Constellations
 * 1961: Le la ["The A"]
 * 1966: Clair de terre (Anthology of poems 1919–1936) – Published in English as: Earthlight
 * 1968: Signe ascendant (Anthology of poems 1935–1961) ["Ascendant sign"]
 * 1970: Perspective cavalière – [Literally: ''Cavalier perspective"]
 * 1988: Breton : Oeuvres complètes, tome 1 ["Breton: The Complete Works, tome 1"]
 * 1992: Breton : Oeuvres complètes, tome 2 ["Breton: The Complete Works, tome 2"]
 * 1999: Breton : Oeuvres complètes, tome 3 ["Breton: The Complete Works, tome 3"]

title: André Breton


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Corporal punishment

A corporal punishment or a physical punishment is a punishment which is intended to cause physical pain to a person. When it is inflicted on minors, especially in home and school settings, its methods may include spanking or paddling. When it is inflicted on adults, it may be inflicted on prisoners and slaves, and can involve methods such as whipping with a belt or a horsewhip.

Physical punishments for crimes or injuries, including floggings, brandings and even mutilations, were practised in most civilizations since ancient times. With the growth of humanitarian ideals since the Enlightenment, such punishments are increasingly viewed as inhumane in Western society. By the late 20th century, corporal punishment had been eliminated from the legal systems of most developed countries.

In the twenty-first century, the legality of corporal punishment in various settings differs by jurisdiction. Internationally, the late twentieth and early twenty-first centuries saw the application of human rights law to the question of corporal punishment in a number of contexts:
 * Corporal punishment in the home, the punishment of children by parents or other adult guardians, is legal in most of the world. As of 2023, 65 countries, mostly in Europe and Latin America, have banned the practice.
 * School corporal punishment, of students by teachers or school administrators, such as caning or paddling, has been banned in many countries, including Canada, Kenya, South Africa, New Zealand and all of Europe. It remains legal, if increasingly less common, in some states of the United States and in some countries in Africa and Southeast Asia.
 * Judicial corporal punishment, such as whipping or caning, as part of a criminal sentence ordered by a court of law, has long disappeared from most European countries. As of 2021, it remains lawful in parts of Africa, Asia, the Anglophone Caribbean and indigenous communities in several countries of South America.
 * Prison corporal punishment or disciplinary corporal punishment, ordered by prison authorities or carried out directly by correctional officers against the inmates for misconduct in custody, has long been common practice in penal institutions worldwide. It has officially been banned in most Western civilizations during the 20th century, but is still employed in many other countries today. Punishments such as paddling, foot whipping or different forms of flagellation have been commonplace methods of corporal punishment within prisons. This was also common practice in the Australian penal colonies and prison camps of the Nazi regime in Germany.
 * Military corporal punishment is or was allowed in some settings in a few jurisdictions.

In many Western countries, medical and human rights organizations oppose the corporal punishment of children. Campaigns against corporal punishment have aimed to bring about legal reforms in order to ban the use of corporal punishment against minors in homes and schools.

Prehistory
Author Jared Diamond writes that hunter-gatherer societies have tended to use little corporal punishment whereas agricultural and industrial societies tend to use progressively more of it. Diamond suggests this may be because hunter-gatherers tend to have few valuable physical possessions, and misbehavior of the child would not cause harm to others' property.

Researchers who have lived among the Parakanã and Ju/'hoansi people, as well as some Aboriginal Australians, have written about the absence of the physical punishment of children in those cultures.

Wilson writes:

"Probably the only generalization that can be made about the use of physical punishment among primitive tribes is that there was no common procedure [...] Pettit concludes that among primitive societies corporal punishment is rare, not because of the innate kindliness of these people but because it is contrary to developing the type of individual personality they set up as their ideal [...] An important point to be made here is that we cannot state that physical punishment as a motivational or corrective device is 'innate' to man."

Antiquity
In the Western world, the corporal punishment of children has traditionally been used by adults in authority roles. Beating one's son as a form of punishment is even recommended in the book of Proverbs:

"He that spareth the rod, hateth his son; but he that loveth him, chasteneth him betimes. (Proverbs 13:24) A fool's lips enter into contention, and his mouth calleth for strokes. (Proverbs 18:6)

Chasten thy son while there is hope, and let not thy soul spare for his crying. (Proverbs 19:18)

Foolishness is bound in the heart of a child; but the rod of correction shall drive it from him. (Proverbs 22:15)

Withhold not correction from the child; for if thou beatest him with a rod, thou shalt deliver his soul from hell. (Proverbs 23:13–14)"

(Note: it has been debated among scholars as to whether what is encouraged here is the corporeal punishment of a "child" or a "young man". The word translated "child" in most cases in the Bible refers to a young man rather than a child.)

Robert McCole Wilson argues that, "Probably this attitude comes, at least in part, from the desire in the patriarchal society for the elder to maintain his authority, where that authority was the main agent for social stability. But these are the words that not only justified the use of physical punishment on children for over a thousand years in Christian communities, but ordered it to be used. The words were accepted with but few exceptions; it is only in the last two hundred years that there has been a growing body of opinion that differed. Curiously, the gentleness of Christ towards children (Mark, X) was usually ignored".

Corporal punishment was practiced in Egypt, China, Greece, and Rome in order to maintain judicial and educational discipline. Disfigured Egyptian criminals were exiled to Tjaru and Rhinocorura on the Sinai border, a region whose name meant "cut-off noses." Corporal punishment was prescribed in ancient Israel, but it was limited to 40 lashes. In China, some criminals were also disfigured but other criminals were tattooed. Some states gained a reputation for their cruel use of such punishments; Sparta, in particular, used them as part of a disciplinary regime which was designed to increase willpower and physical strength. Although the Spartan example was extreme, corporal punishment was possibly the most frequent type of punishment. In the Roman Empire, the maximum penalty which a Roman citizen could receive under the law was 40 "lashes" or 40 "strokes" with a whip which was applied to the back and shoulders, or 40 lashes or strokes with the "fasces" (similar to a birch rod, but consisting of 8–10 lengths of willow rather than birch) which were applied to the buttocks. Such punishments could draw blood, and they were frequently inflicted in public.

Quintilian (c. 35 – c. 100) voiced some opposition to the use of corporal punishment. According to Wilson, "probably no more lucid indictment of it has been made in the succeeding two thousand years".

"By that boys should suffer corporal punishment, though it is received by custom, and Chrysippus makes no objection to it, I by no means approve; first, because it is a disgrace, and a punishment fit for slaves, and in reality (as will be evident if you imagine the age change) an affront; secondly, because, if a boy's disposition be so abject as not to be amended by reproof, he will be hardened, like the worst of slaves, even to stripes; and lastly, because, if one who regularly exacts his tasks be with him, there will not be the need of any chastisement (Quintilian, Institutes of Oratory, 1856 edition, I, III)."

Plutarch, also in the first century, writes:

"This also I assert, that children ought to be led to honourable practices by means of encouragement and reasoning, and most certainly not by blows or ill-treatment, for it surely is agreed that these are fitting rather for slaves than for the free-born; for so they grow numb and shudder at their tasks, partly from the pain of the blows, partly from the degradation."

Middle Ages
In Medieval Europe, the Byzantine Empire blinded and denosed some criminals and rival emperors. Their belief that the emperor should be physically ideal meant that such disfigurement notionally disqualified the recipient from office. (The second reign of Justinian the Slit-nosed was the notable exception.) Elsewhere, corporal punishment was encouraged by the attitudes of the Catholic church towards the human body, flagellation being a common means of self-discipline. This had an influence on the use of corporal punishment in schools, as educational establishments were closely attached to the church during this period. Nevertheless, corporal punishment was not used uncritically; as early as the 11th century Saint Anselm, Archbishop of Canterbury was speaking out against what he saw as the excessive use of corporal punishment in the treatment of children.

Modernity
From the 16th century onwards, new trends were seen in corporal punishment. Judicial punishments were increasingly turned into public spectacles, with public beatings of criminals intended as a deterrent to other would-be offenders. Meanwhile, early writers on education, such as Roger Ascham, complained of the arbitrary manner in which children were punished.

Peter Newell writes that perhaps the most influential writer on the subject was the English philosopher John Locke, whose Some Thoughts Concerning Education explicitly criticised the central role of corporal punishment in education. Locke's work was highly influential, and may have helped influence Polish legislators to ban corporal punishment from Poland's schools in 1783, the first country in the world to do so. A consequence of this mode of thinking was a reduction in the use of corporal punishment in the 19th century in Europe and North America. In some countries this was encouraged by scandals involving individuals seriously hurt during acts of corporal punishment. For instance, in Britain, popular opposition to punishment was encouraged by two significant cases, the death of Private Frederick John White, who died after a military flogging in 1846, and the death of Reginald Cancellor, killed by his schoolmaster in 1860. Events such as these mobilised public opinion and, by the late nineteenth century, the extent of corporal punishment's use in state schools was unpopular with many parents in England. Authorities in Britain and some other countries introduced more detailed rules for the infliction of corporal punishment in government institutions such as schools, prisons and reformatories. By the First World War, parents' complaints about disciplinary excesses in England had died down, and corporal punishment was established as an expected form of school discipline.

In the 1870s, courts in the United States overruled the common-law principle that a husband had the right to "physically chastise an errant wife". In the UK, the traditional right of a husband to inflict moderate corporal punishment on his wife in order to keep her "within the bounds of duty" was similarly removed in 1891. See Domestic violence for more information.

In the United Kingdom, the use of judicial corporal punishment declined during the first half of the twentieth century and it was abolished altogether in the Criminal Justice Act, 1948 (zi & z2 GEo. 6. CH. 58.), whereby whipping and flogging were outlawed except for use in very serious internal prison discipline cases, while most other European countries had abolished it earlier. Meanwhile, in many schools, the use of the cane, paddle or tawse remained commonplace in the UK and the United States until the 1980s. In rural areas of the Southern United States, and in several other countries, it still is: see School corporal punishment.

Human rights
Key developments related to corporal punishment occurred in the late 20th century. Years with particular significance to the prohibition of corporal punishment are emphasised.
 * 1950: European Convention of Human Rights, Council of Europe. Article 3 bans "inhuman or degrading treatment or punishment".
 * 1978: European Court of Human Rights, overseeing its implementation, rules that judicial birching of a juvenile breaches Article 3.
 * 1985: Standard Minimum Rules for the Administration of Juvenile Justice, or Beijing Rules, United Nations (UN). Rule 17.3: "Juveniles shall not be subject to corporal punishment."
 * 1990 Supplement: Rules for the Protection of Juveniles Deprived of their Liberty. Rule 67: "...all disciplinary measures constituting cruel, inhumane or degrading treatment shall be strictly prohibited, including corporal punishment..."
 * 1990: Guidelines for the Prevention of Juvenile Delinquency, the Riyadh Guidelines, UN. Paragraph 21(h): education systems should avoid "harsh disciplinary measures, particularly corporal punishment."
 * 1966: International Covenant on Civil and Political Rights, UN, with currently 167 parties, 74 signatories. Article 7: "No one shall be subjected to torture or to cruel, inhuman or degrading treatment or punishment..."
 * 1992: Human Rights Committee, overseeing its implementation, comments: "the prohibition must extend to corporal punishment . . . in this regard . . . article 7 protects, in particular, children, . . .."
 * 1984: Convention against Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment, UN, with currently 150 parties and 78 signatories.
 * 1996: Committee Against Torture, overseeing its implementation, condemns corporal punishment.
 * 1966: International Covenant on Economic, Social and Cultural Rights, UN, with currently 160 parties, and 70 signatories. Article 13(1): "education shall be directed to the full development of the human personality and the sense of its dignity..."
 * 1999: Committee on Economic, Social and Cultural Rights, overseeing its implementation, comments: "corporal punishment is inconsistent with the fundamental guiding principle of international human rights law . . . the dignity of the individual."
 * 1961: European Social Charter, Council of Europe.
 * 2001: European Committee of Social Rights, overseeing its implementation, concludes: it is not "acceptable that a society which prohibits any form of physical violence between adults would accept that adults subject children to physical violence."

Children's rights
The notion of children's rights in the Western world developed in the 20th century, but the issue of corporal punishment was not addressed generally before mid-century. Years with particular significance to the prohibition of corporal punishment of children are emphasised.
 * 1923: Children's Rights Proclamation by Save the Children founder. (5 articles).
 * 1924 Adopted as the World Child Welfare Charter, League of Nations (non-enforceable).
 * 1959: Declaration of the Rights of the Child, (UN) (10 articles; non-binding).
 * 1989: Convention on the Rights of the Child, UN (54 articles; binding treaty), with currently 193 parties and 140 signatories. Article 19.1: "States Parties shall take all appropriate legislative, administrative, social and educational measures to protect the child from all forms of physical or mental violence, injury or abuse, neglect or negligent treatment, maltreatment or exploitation . . . ."
 * 2006: Committee on the Rights of the Child, overseeing its implementation, comments: there is an "obligation of all States Party to move quickly to prohibit and eliminate all corporal punishment."
 * 2011: Optional Protocol on a Communications Procedure allowing individual children to submit complaints regarding specific violations of their rights.
 * 2006: Study on Violence against Children presented by Independent Expert for the Secretary-General to the UN General Assembly.
 * 2007: Post of Special Representative of the Secretary-General on violence against children established.

Legal status
66 countries, most of them in Europe and Latin America, have prohibited any corporal punishment of children.

The earliest recorded attempt to prohibit corporal punishment of children by a state dates back to Poland in 1783. However, its prohibition in all spheres of life – in homes, schools, the penal system and alternative care settings – occurred first in 1966 in Sweden. The 1979 Swedish Parental Code reads: "Children are entitled to care, security and a good upbringing. Children are to be treated with respect for their person and individuality and may not be subjected to corporal punishment or any other humiliating treatment."

, corporal punishment of children by parents (or other adults) is outlawed altogether in 63 nations (including the partially recognized Republic of Kosovo) and 3 constituent nations.

For a more detailed overview of the global use and prohibition of the corporal punishment of children, see the following table.

Corporal punishment in the home
Domestic corporal punishment (i.e. the punishment of children by their parents) is often referred to colloquially as "spanking", "smacking", or "slapping".

It has been outlawed in an increasing number of countries, starting with Sweden in 1979. In some other countries, corporal punishment is legal, but restricted (e.g. blows to the head are outlawed, implements may not be used, only children within a certain age range may be spanked).

In all states of the United States and most African and Asian nations, corporal punishment by parents is legal. It is also legal to use certain implements (e.g. a belt or a paddle).

In Canada, spanking by parents or legal guardians (but nobody else) is legal, with certain restrictions: the child must be between the ages of 2–12, and no implement other than an open, bare hand may be used (belts, paddles, etc. are prohibited). It is also illegal to strike the head when disciplining a child.

In the UK (except Scotland and Wales), spanking or smacking is legal, but it must not cause an injury amounting to actual bodily harm (any injury such as visible bruising, breaking of the whole skin, etc.). In addition, in Scotland, since October 2003, it has been illegal to use any implements or to strike the head when disciplining a child, and it is also prohibited to use corporal punishment towards children under the age of 3 years. In 2019, Scotland enacted a ban on corporal punishment, which went into effect in 2020. Wales also enacted a ban in 2020, which has gone into effect in 2022.

In Pakistan, Section 89 of Pakistan Penal Code allows corporal punishment.

In 2024, children's doctors urged ministers to ban smacking children in England and Northern Ireland as their report warned that children suffer physically and mentally after being hit in their home. However, the UK government stated there were no plans to change the law on smacking in England and said it would observe the impact of legal amendments in Scotland and Wales.

Corporal punishment in schools
Corporal punishment in schools has been outlawed in many countries. It often involves striking the student on the buttocks or the palm of the hand with an implement (e.g. a rattan cane or a spanking paddle).

In countries where corporal punishment is still allowed in schools, there may be restrictions; for example, school caning in Singapore and Malaysia is, in theory, permitted for boys only.

In India and many other countries, corporal punishment has technically been abolished by law. However, corporal punishment continues to be practiced on boys and girls in many schools around the world. Cultural perceptions of corporal punishment have rarely been studied and researched. One study carried out discusses how corporal punishment is perceived among parents and students in India.

Medical professionals have urged putting an end to the practice, noting the danger of injury to children's hands especially.

Judicial or quasi-judicial punishment
Around 33 countries in the world still retain judicial corporal punishment, including a number of former British territories such as Botswana, Malaysia, Singapore and Tanzania. In Singapore, for certain specified offences, males are routinely sentenced to caning in addition to a prison term. The Singaporean practice of caning became much discussed around the world in 1994 when American teenager Michael P. Fay received four strokes of the cane for vandalism. Judicial caning and whipping are also used in Aceh Province in Indonesia.

A number of other countries with an Islamic legal system, such as Saudi Arabia, UAE, Qatar, Iran, Brunei, Sudan, and some northern states in Nigeria, employ judicial whipping for a range of offences. In April 2020, the Saudi Supreme Court ended the flogging punishment from its court system, and replaced it with jail time or fines. , some regions of Pakistan are experiencing a breakdown of law and government, leading to a reintroduction of corporal punishment by ad hoc Islamicist courts. As well as corporal punishment, some Islamic countries such as Saudi Arabia and Iran use other kinds of physical penalties such as amputation or mutilation. However, the term "corporal punishment" has since the 19th century usually meant caning, flagellation or bastinado rather than those other types of physical penalty.

In some countries, foot whipping (bastinado) is still practiced on prisoners.

Effects
According to a study headed by Harvard researchers, corporal punishment like spanking could affect the brain development of children. These effects are similar to the more severe form of violence. Corporal punishment is associated with physical injury and abuse, it erodes parent-child relationships, reduces cognitive abilities and IQ scores, leads to mental health problems including depression and anxiety, and it increases adult aggression and anti-social behaviors.

Rituals
In parts of England, boys were once beaten under the old tradition of "Beating the Bounds" whereby a boy was paraded around the edge of a city or parish and spanked with a switch or cane to mark the boundary. One famous "Beating the Bounds" took place around the boundary of St Giles and the area where Tottenham Court Road now stands in central London. The actual stone that marked the boundary is now underneath the Centre Point office tower.

In the Czech Republic, Slovakia, and some parts of Hungary, a tradition for health and fertility is carried out on Easter Monday. Boys and young men will spank or whip girls and young women on the bottom with braided willow branches. After the man sings the verse, the young woman turns around and the man takes a few whacks at her backside with the whip.

In popular culture
Art
 *  The Flagellation, (c.1455–70), by Piero della Francesca. Christ is lashed while Pontius Pilate looks on.
 * The Whipping, (1941), by Horace Pippin. A figure tied to a whipping post is flogged.

Film and TV

See: List of films and TV containing corporal punishment scenes.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Corporal punishment


text:
Genomics

Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

The field also includes studies of intragenomic (within the genome) phenomena such as epistasis (effect of one gene on another), pleiotropy (one gene affecting more than one trait), heterosis (hybrid vigour), and other interactions between loci and alleles within the genome.

Etymology
From the Greek ΓΕΝ gen, "gene" (gamma, epsilon, nu, epsilon) meaning "become, create, creation, birth", and subsequent variants: genealogy, genesis, genetics, genic, genomere, genotype, genus etc. While the word genome (from the German Genom, attributed to Hans Winkler) was in use in English as early as 1926, the term genomics was coined by Tom Roderick, a geneticist at the Jackson Laboratory (Bar Harbor, Maine), over beers with Jim Womack, Tom Shows and Stephen O’Brien at a meeting held in Maryland on the mapping of the human genome in 1986. First as the name for a new journal and then as a whole new science discipline.

Early sequencing efforts
Following Rosalind Franklin's confirmation of the helical structure of DNA, James D. Watson and Francis Crick's publication of the structure of DNA in 1953 and Fred Sanger's publication of the Amino acid sequence of insulin in 1955, nucleic acid sequencing became a major target of early molecular biologists. In 1964, Robert W. Holley and colleagues published the first nucleic acid sequence ever determined, the ribonucleotide sequence of alanine transfer RNA. Extending this work, Marshall Nirenberg and Philip Leder revealed the triplet nature of the genetic code and were able to determine the sequences of 54 out of 64 codons in their experiments. In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent (Ghent, Belgium) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein. Fiers' group expanded on their MS2 coat protein work, determining the complete nucleotide-sequence of bacteriophage MS2-RNA (whose genome encodes just four genes in 3569 base pairs [bp]) and Simian virus 40 in 1976 and 1978, respectively.

DNA-sequencing technology developed
In addition to his seminal work on the amino acid sequence of insulin, Frederick Sanger and his colleagues played a key role in the development of DNA sequencing techniques that enabled the establishment of comprehensive genome sequencing projects. In 1975, he and Alan Coulson published a sequencing procedure using DNA polymerase with radiolabelled nucleotides that he called the Plus and Minus technique. This involved two closely related methods that generated short oligonucleotides with defined 3' termini. These could be fractionated by electrophoresis on a polyacrylamide gel (called polyacrylamide gel electrophoresis) and visualised using autoradiography. The procedure could sequence up to 80 nucleotides in one go and was a big improvement, but was still very laborious. Nevertheless, in 1977 his group was able to sequence most of the 5,386 nucleotides of the single-stranded bacteriophage φX174, completing the first fully sequenced DNA-based genome. The refinement of the Plus and Minus method resulted in the chain-termination, or Sanger method (see below), which formed the basis of the techniques of DNA sequencing, genome mapping, data storage, and bioinformatic analysis most widely used in the following quarter-century of research. In the same year Walter Gilbert and Allan Maxam of Harvard University independently developed the Maxam-Gilbert method (also known as the chemical method) of DNA sequencing, involving the preferential cleavage of DNA at known bases, a less efficient method. For their groundbreaking work in the sequencing of nucleic acids, Gilbert and Sanger shared half the 1980 Nobel Prize in chemistry with Paul Berg (recombinant DNA).

Complete genomes
The advent of these technologies resulted in a rapid intensification in the scope and speed of completion of genome sequencing projects. The first complete genome sequence of a eukaryotic organelle, the human mitochondrion (16,568 bp, about 16.6 kb [kilobase]), was reported in 1981, and the first chloroplast genomes followed in 1986. In 1992, the first eukaryotic chromosome, chromosome III of brewer's yeast Saccharomyces cerevisiae (315 kb) was sequenced. The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8 Mb [megabase]) in 1995. The following year a consortium of researchers from laboratories across North America, Europe, and Japan announced the completion of the first complete genome sequence of a eukaryote, S. cerevisiae (12.1 Mb), and since then genomes have continued being sequenced at an exponentially growing pace. , the complete sequences are available for: 2,719 viruses, 1,115 archaea and bacteria, and 36 eukaryotes, of which about half are fungi.

Most of the microorganisms whose genomes have been completely sequenced are problematic pathogens, such as Haemophilus influenzae, which has resulted in a pronounced bias in their phylogenetic distribution compared to the breadth of microbial diversity. Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models. Yeast (Saccharomyces cerevisiae) has long been an important model organism for the eukaryotic cell, while the fruit fly Drosophila melanogaster has been a very important tool (notably in early pre-molecular genetics). The worm Caenorhabditis elegans is an often used simple model for multicellular organisms. The zebrafish Brachydanio rerio is used for many developmental studies on the molecular level, and the plant Arabidopsis thaliana is a model organism for flowering plants. The Japanese pufferfish (Takifugu rubripes) and the spotted green pufferfish (Tetraodon nigroviridis) are interesting because of their small and compact genomes, which contain very little noncoding DNA compared to most species. The mammals dog (Canis familiaris), brown rat (Rattus norvegicus), mouse (Mus musculus), and chimpanzee (Pan troglodytes) are all important model animals in medical research.

A rough draft of the human genome was completed by the Human Genome Project in early 2001, creating much fanfare. This project, completed in 2003, sequenced the entire genome for one specific person, and by 2007 this sequence was declared "finished" (less than one error in 20,000 bases and all chromosomes assembled). In the years since then, the genomes of many other individuals have been sequenced, partly under the auspices of the 1000 Genomes Project, which announced the sequencing of 1,092 genomes in October 2012. Completion of this project was made possible by the development of dramatically more efficient sequencing technologies and required the commitment of significant bioinformatics resources from a large international collaboration. The continued analysis of human genomic data has profound political and social repercussions for human societies.

The "omics" revolution

The English-language neologism omics informally refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics. The related suffix -ome is used to address the objects of study of such fields, such as the genome, proteome, or metabolome (lipidome) respectively. The suffix -ome as used in molecular biology refers to a totality of some sort; similarly omics has come to refer generally to the study of large, comprehensive biological data sets. While the growth in the use of the term has led some scientists (Jonathan Eisen, among others ) to claim that it has been oversold, it reflects the change in orientation towards the quantitative analysis of complete or near-complete assortment of all the constituents of a system. In the study of symbioses, for example, researchers which were once limited to the study of a single gene product can now simultaneously compare the total complement of several types of biological molecules.

Genome analysis
After an organism has been selected, genome projects involve three components: the sequencing of DNA, the assembly of that sequence to create a representation of the original chromosome, and the annotation and analysis of that representation.

Sequencing
Historically, sequencing was done in sequencing centers, centralized facilities (ranging from large independent institutions such as Joint Genome Institute which sequence dozens of terabases a year, to local molecular biology core facilities) which contain research laboratories with the costly instrumentation and technical support necessary. As sequencing technology continues to improve, however, a new generation of effective fast turnaround benchtop sequencers has come within reach of the average academic laboratory. On the whole, genome sequencing approaches fall into two broad categories, shotgun and high-throughput (or next-generation) sequencing.

Shotgun sequencing

Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and including entire chromosomes. It is named by analogy with the rapidly expanding, quasi-random firing pattern of a shotgun. Since gel electrophoresis sequencing can only be used for fairly short sequences (100 to 1000 base pairs), longer DNA sequences must be broken into random small segments which are then sequenced to obtain reads. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing is a random sampling process, requiring over-sampling to ensure a given nucleotide is represented in the reconstructed sequence; the average number of reads by which a genome is over-sampled is referred to as coverage.

For much of its history, the technology underlying shotgun sequencing was the classical chain-termination method or 'Sanger method', which is based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. Recently, shotgun sequencing has been supplanted by high-throughput sequencing methods, especially for large-scale, automated genome analyses. However, the Sanger method remains in wide use, primarily for smaller-scale projects and for obtaining especially long contiguous DNA sequence reads (>500 nucleotides). Chain-termination methods require a single-stranded DNA template, a DNA primer, a DNA polymerase, normal deoxynucleosidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation. These chain-terminating nucleotides lack a 3'-OH group required for the formation of a phosphodiester bond between two nucleotides, causing DNA polymerase to cease extension of DNA when a ddNTP is incorporated. The ddNTPs may be radioactively or fluorescently labelled for detection in DNA sequencers. Typically, these machines can sequence up to 96 DNA samples in a single batch (run) in up to 48 runs a day.

High-throughput sequencing
The high demand for low-cost sequencing has driven the development of high-throughput sequencing technologies that parallelize the sequencing process, producing thousands or millions of sequences at once. High-throughput sequencing is intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods. In ultra-high-throughput sequencing, as many as 500,000 sequencing-by-synthesis operations may be run in parallel.

The Illumina dye sequencing method is based on reversible dye-terminators and was developed in 1996 at the Geneva Biomedical Research Institute, by Pascal Mayer and Laurent Farinelli. In this method, DNA molecules and primers are first attached on a slide and amplified with polymerase so that local clonal colonies, initially coined "DNA colonies", are formed. To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are washed away. Unlike pyrosequencing, the DNA chains are extended one nucleotide at a time and image acquisition can be performed at a delayed moment, allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera. Decoupling the enzymatic reaction and the image capture allows for optimal throughput and theoretically unlimited sequencing capacity; with an optimal configuration, the ultimate throughput of the instrument depends only on the A/D conversion rate of the camera. The camera takes images of the fluorescently labeled nucleotides, then the dye along with the terminal 3' blocker is chemically removed from the DNA, allowing the next cycle.

An alternative approach, ion semiconductor sequencing, is based on standard DNA replication chemistry. This technology measures the release of a hydrogen ion each time a base is incorporated. A microwell containing template DNA is flooded with a single nucleotide, if the nucleotide is complementary to the template strand it will be incorporated and a hydrogen ion will be released. This release triggers an ISFET ion sensor. If a homopolymer is present in the template sequence multiple nucleotides will be incorporated in a single flood cycle, and the detected electrical signal will be proportionally higher.

Assembly
Sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as current DNA sequencing technology cannot read whole genomes as a continuous sequence, but rather reads small pieces of between 20 and 1000 bases, depending on the technology used. Third generation sequencing technologies such as PacBio or Oxford Nanopore routinely generate sequencing reads >10 kb in length; however, they have a high error rate at approximately 15 percent. Typically the short fragments, called reads, result from shotgun sequencing genomic DNA, or gene transcripts (ESTs).

Assembly approaches
Assembly can be broadly categorized into two approaches: de novo assembly, for genomes which are not similar to any sequenced in the past, and comparative assembly, which uses the existing sequence of a closely related organism as a reference during assembly. Relative to comparative assembly, de novo assembly is computationally difficult (NP-hard), making it less favourable for short-read NGS technologies. Within the de novo assembly paradigm there are two primary strategies for assembly, Eulerian path strategies, and overlap-layout-consensus (OLC) strategies. OLC strategies ultimately try to create a Hamiltonian path through an overlap graph which is an NP-hard problem. Eulerian path strategies are computationally more tractable because they try to find a Eulerian path through a deBruijn graph.

Finishing
Finished genomes are defined as having a single contiguous sequence with no ambiguities representing each replicon.

Annotation
The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching biological information to sequences, and consists of three main steps: Automatic annotation tools try to perform these steps in silico, as opposed to manual annotation (a.k.a. curation) which involves human expertise and potential experimental verification. Ideally, these approaches co-exist and complement each other in the same annotation pipeline (also see below).
 * 1) identifying portions of the genome that do not code for proteins
 * 2) identifying elements on the genome, a process called gene prediction, and
 * 3) attaching biological information to these elements.

Traditionally, the basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on homologues. More recently, additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. Ensembl) rely on both curated data sources as well as a range of software tools in their automated genome annotation pipeline. Structural annotation consists of the identification of genomic elements, primarily ORFs and their localisation, or gene structure. Functional annotation consists of attaching biological information to genomic elements.

Sequencing pipelines and databases
The need for reproducibility and efficient management of the large amount of data associated with genome projects mean that computational pipelines have important applications in genomics.

Functional genomics
Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein) functions and interactions. Functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein–protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional "gene-by-gene" approach.

A major branch of genomics is still concerned with sequencing the genomes of various organisms, but the knowledge of full genomes has created the possibility for the field of functional genomics, mainly concerned with patterns of gene expression during various conditions. The most important tools here are microarrays and bioinformatics.

Structural genomics
Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large numbers of sequenced genomes and previously solved protein structures allow scientists to model protein structure on the structures of previously solved homologs. Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or structural homology to a protein of known structure or based on chemical and physical principles for a protein with no homology to any known structure. As opposed to traditional structural biology, the determination of a protein structure through a structural genomics effort often (but not always) comes before anything is known regarding the protein function. This raises new challenges in structural bioinformatics, i.e. determining protein function from its 3D structure.

Epigenomics
Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence (Russell 2010 p. 475). Two of the most characterized epigenetic modifications are DNA methylation and histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.

Metagenomics

Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use "shotgun" Sanger sequencing or massively parallel pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its power to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world.

Viruses and bacteriophages
Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology. Historically, they were used to define gene structure and gene regulation. Also the first genome to be sequenced was a bacteriophage. However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of prophage sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome: Overall, this method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes.

Cyanobacteria
At present there are 24 cyanobacteria for which a total genome sequence is available. 15 of these cyanobacteria come from the marine environment. These are six Prochlorococcus strains, seven marine Synechococcus strains, Trichodesmium erythraeum IMS101 and Crocosphaera watsonii WH8501. Several studies have demonstrated how these sequences could be used very successfully to infer important ecological and physiological characteristics of marine cyanobacteria. However, there are many more genome projects currently in progress, amongst those there are further Prochlorococcus and marine Synechococcus isolates, Acaryochloris and Prochloron, the N2-fixing filamentous cyanobacteria Nodularia spumigena, Lyngbya aestuarii and Lyngbya majuscula, as well as bacteriophages infecting marine cyanobaceria. Thus, the growing body of genome information can also be tapped in a more general way to address global problems by applying a comparative approach. Some new and exciting examples of progress in this field are the identification of genes for regulatory RNAs, insights into the evolutionary origin of photosynthesis, or estimation of the contribution of horizontal gene transfer to the genomes that have been analyzed.

Applications

Genomics has provided applications in many fields, including medicine, biotechnology, anthropology and other social sciences.

Genomic medicine
Next-generation genomic technologies allow clinicians and biomedical researchers to drastically increase the amount of genomic data collected on large study populations. When combined with new informatics approaches that integrate many kinds of data with genomic data in disease research, this allows researchers to better understand the genetic bases of drug response and disease. Early efforts to apply the genome to medicine included those by a Stanford team led by Euan Ashley who developed the first tools for the medical interpretation of a human genome. The Genomes2People research program at Brigham and Women’s Hospital, Broad Institute and Harvard Medical School was established in 2012 to conduct empirical research in translating genomics into health. Brigham and Women's Hospital opened a Preventive Genomics Clinic in August 2019, with Massachusetts General Hospital following a month later. The All of Us research program aims to collect genome sequence data from 1 million participants to become a critical component of the precision medicine research platform.

Synthetic biology and bioengineering
The growth of genomic knowledge has enabled increasingly sophisticated applications of synthetic biology. In 2010 researchers at the J. Craig Venter Institute announced the creation of a partially synthetic species of bacterium, Mycoplasma laboratorium, derived from the genome of Mycoplasma genitalium.

Population and conservation genomics
Population genomics has developed as a popular field of research, where genomic sequencing methods are used to conduct large-scale comparisons of DNA sequences among populations - beyond the limits of genetic markers such as short-range PCR products or microsatellites traditionally used in population genetics. Population genomics studies genome-wide effects to improve our understanding of microevolution so that we may learn the phylogenetic history and demography of a population. Population genomic methods are used for many different fields including evolutionary biology, ecology, biogeography, conservation biology and fisheries management. Similarly, landscape genomics has developed from landscape genetics to use genomic methods to identify relationships between patterns of environmental and genetic variation.

Conservationists can use the information gathered by genomic sequencing in order to better evaluate genetic factors key to species conservation, such as the genetic diversity of a population or whether an individual is heterozygous for a recessive inherited genetic disorder. By using genomic data to evaluate the effects of evolutionary processes and to detect patterns in variation throughout a given population, conservationists can formulate plans to aid a given species without as many variables left unknown as those unaddressed by standard genetic approaches.

title: Genomics