Universal grammar

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Universal_grammar

Universal grammar (UG), in modern linguistics, is the theory of the innate biological component of the language faculty, usually credited to Noam Chomsky. The basic postulate of UG is that there are innate constraints on what the grammar of a possible human language could be. When linguistic stimuli are received in the course of language acquisition, children then adopt specific syntactic rules that conform to UG. The advocates of this theory emphasize and partially rely on the poverty of the stimulus (POS) argument and the existence of some universal properties of natural human languages. However, the latter has not been firmly established.

Other linguists have opposed that notion, arguing that languages are so diverse that the postulated universality is rare. The theory of universal grammar remains a subject of debate among linguists.

Overview

The term "universal grammar" is placeholder for whichever domain-specific features of linguistic competence turn out to be innate. Within generative grammar, it is generally accepted that there must be some such features, and one of the goals of generative research is to formulate and test hypotheses about which aspects those are. In day-to-day generative research, the notion that universal grammar exists motivates analyses in terms of general principles. As much as possible, facts about particular languages are derived from these general principles rather than from language-specific stipulations.

Evidence

Further information: Poverty of the stimulus

The idea that at least some aspects are innate is motivated by poverty of the stimulus arguments. For example, one famous poverty of the stimulus argument concerns the acquisition of yes–no questions in English. This argument starts from the observation that children only make mistakes compatible with rules targeting hierarchical structure even though the examples which they encounter could have been generated by a simpler rule that targets linear order. In other words, children seem to ignore the possibility that the question rule is as simple as "switch the order of the first two words" and immediately jump to alternatives that rearrange constituents in tree structures. This is taken as evidence that children are born knowing that grammatical rules involve hierarchical structure, even though they have to figure out what those rules are.

History

Between 1100 and 1400, the theoretical work on matters of language significantly expanded in western Europe, its typical social context being the teaching of grammar, logic, or theology, producing a vast literature on aspects of linguistic theory, such as a 13th century theory of grammar known in modern times as modism, although no assertions were made in the texts about "a theory of language," as such. While not much work was done on the evolution of languages, Dante and Roger Bacon offered perceptive observations. Bacon had a complex notion of grammar, which ranged from the teaching of elementary Latin through what he termed "rational grammar", to research on the so-called languages of sacred wisdom, i.e. Latin and Greek. Professor of Latin literature Raf Van Rooy quotes Bacon's "notorious" dictum on grammar used to denote regional linguistic variation and notes Bacon's contention that Latin and Greek, although "one in substance," were each characterized by many idioms (idiomata: proprietates). Van Rooy speculates that Bacon's references to grammar concerned a "quasi-universal nature of grammatical categories," whereas his assertions on Greek and Latin were applications of his lingua/idioma distinction rather than a generalizing statements on the nature of grammar. Linguistics professor Margaret Thomas acknowledges that "intellectual commerce between ideas about Universal Grammar and [second language] acquisition is not a late-20th century invention," but rejects as "convenient" the interpretation of Bacon's dictum by generative grammarians as an assertion by the English polymath of the existence of universal grammar.

The concept of a generalized grammar was at the core of the 17th century projects for philosophical languages. An influential work in that time was Grammaire générale by Claude Lancelot and Antoine Arnauld. They describe a general grammar for languages, coming to the conclusion that grammar has to be universal. There is a Scottish school of universal grammarians from the 18th century that included James Beattie, Hugh Blair, James Burnett, James Harris, and Adam Smith, distinguished from the philosophical-language project.

The article on grammar in the first edition of the Encyclopædia Britannica (1771) contains an extensive section titled "Of Universal Grammar."

In the late 19th and early 20th century, Wilhelm Wundt and Otto Jespersen claimed that these earlier arguments were overly influenced by Latin and ignored the breadth of worldwide language real grammar", but reduced it to universal syntactic categories or super-categories, such as number, tenses, etc.

Behaviorists, after the rise of the eponymous theory, advanced the idea that language acquisition, like any other kind of learning, could be explained by a succession of trials, errors, and rewards for success. In other words, children, according to behaviorists, learn their mother tongue by simple imitation, i.e. through listening and repeating what adults say. For example, when a child says "milk" and the mother will smile and give milk to her child, then, as a result, the child will find this outcome rewarding, which enhances the child's language development.

Theories of universal grammar

Within generative grammar, there are a variety of theories about what universal grammar consists of. One notable hypothesis proposed by Hagit Borer holds that the fundamental syntactic operations are universal and that all variation arises from different feature-specifications in the lexicon. On the other hand, a strong hypothesis adopted in some variants of Optimality Theory holds that humans are born with a universal set of constraints, and that all variation arises from differences in how these constraints are ranked. In a 2002 paper, Noam Chomsky, Marc Hauser and W. Tecumseh Fitch proposed that universal grammar consists solely of the capacity for hierarchical phrase structure.

Main hypotheses

In an article entitled "The Faculty of Language: What Is It, Who Has It, and How Did It Evolve?" Hauser, Chomsky, and Fitch present the three leading hypotheses for how language evolved and brought humans to the point where they have a universal grammar.

The first hypothesis states that the faculty of language in the broad sense (FLb) is strictly homologous to animal communication. This means that homologous aspects of the faculty of language exist in non-human animals.

The second hypothesis states that the FLb is a derived and uniquely human adaptation for language. This hypothesis holds that individual traits were subject to natural selection and came to be specialized for humans.

The third hypothesis states that only the faculty of language in the narrow sense (FLn) is unique to humans. It holds that while mechanisms of the FLb are present in both human and non-human animals, the computational mechanism of recursion has evolved recently, and solely in humans.

Presence of creole languages

The presence of creole languages is sometimes cited as further support for this theory, especially by Bickerton's language bioprogram theory. Creole languages develop and form when disparate societies with no common language come together and are forced to devise a new system of communication. The system used by the original speakers is typically an inconsistent mix of vocabulary items, known as pidgin. As these speakers' children begin to acquire their first language, they use the pidgin input to effectively create their own original language, known as a creole language. Unlike pidgins, creole languages have native speakers (those with language acquisition from early childhood) and make use of a full, systematic grammar.

Bickerton claims the fact that certain features are shared by virtually all creole languages supports the notion of a universal grammar. For example, their default point of reference in time (expressed by bare verb stems) is not the present moment, but the past. Using pre-verbal auxiliaries, they uniformly express tense, aspect, and mood. Negative concord occurs, but it affects the verbal subject (as opposed to the object, as it does in languages like Spanish). Another similarity among creole languages can be identified in the fact that questions are created simply by changing the intonation of a declarative sentence; not its word order or content.

Opposing this notion, the work by Carla Hudson-Kam and Elissa Newport suggests that creole languages may not support a universal grammar at all. In a series of experiments, Hudson-Kam and Newport looked at how children and adults learn artificial grammars. They found that children tend to ignore minor variations in the input when those variations are infrequent, and reproduce only the most frequent forms. In doing so, the children tend to standardize the language they hear around them. Hudson-Kam and Newport hypothesize that in a pidgin-development situation (and in the real-life situation of a deaf child whose parents are or were disfluent signers), children systematize the language they hear, based on the probability and frequency of forms, and not that which has been suggested on the basis of a universal grammar. Further, they argue, it seems to follow that creole languages would share features with the languages from which they are derived, and thus look similar in terms of grammar.

Many researchers of universal grammar argue against the concept of relexification, i.e. that a language replaces its lexicon almost entirely with that of another. This, they argue, goes against the universalist notions of a universal grammar, which has an innate grammar.

Views and assessments

Recent research has used recurrent neural network architectures (RNNs). McCoy et al. (2018) focused on a strong version of the poverty-of-the-stimulus argument, which claims that language learners require a hierarchical constraint, although they report that a milder version, which only asserts that a hierarchical bias is necessary, is difficult to assess using RNNs because RNNs must possess some biases and the nature of these biases remains "currently poorly understood." They go on to acknowledge that while all the architectures they used had a bias toward linear order and the GRU-with-attention architecture was the only one that overcame this linear bias sufficiently to generalize hierarchically. "Humans certainly could have such an innate constraint."

The empirical basis of poverty-of-the-stimulus arguments has been challenged by Geoffrey Pullum and others, leading to a persistent back-and-forth debate in the language acquisition literature.

Language acquisition researcher Michael Ramscar has suggested that when children erroneously expect an ungrammatical form that then never occurs, the repeated failure of expectation serves as a form of implicit negative feedback that allows them to correct their errors over time, in the way that, for example, children correct grammar generalizations like goed to went through repetitive failure.

In addition, it has been suggested that people learn about probabilistic patterns of word distribution in their language, rather than hard and fast rules (see Distributional hypothesis). For example, in English, children overgeneralize the past tense marker "-ed" and conjugate irregular verbs as if they were regular, producing forms like goed and eated, and then correct this deviancy over time. It has also been hypothesized that the poverty of the stimulus problem can be largely avoided if it is assumed that children employ similarity-based generalization strategies in language learning, i.e. generalizing about the usage of new words from similar words they already know how to use.

Neurogeneticists Simon Fisher and Sonja Vernes observe that, with human language-skills being evidently unmatched elsewhere in the world's fauna, there have been several theories about one single mutation event occurring some time in the past in our nonspeaking ancestors, as argued by e.g. Chomsky (2011), i.e. some "lone spark that was sufficient to trigger the sudden appearance of language and culture." They characterize that notion as "romantic" and "inconsistent with the messy mappings between genetics and cognitive processes." According to Fisher & Vernes, the link between genes to grammar has not been consistently mapped by scientists. What has been established by research, they claim, relates primarily to speech pathologies. The arising lack of certainty, they conclude, has provided an audience for "unconstrained speculations" that have fed the "myth" of "so-called grammar genes".

Professor of Natural Language Computing Geoffrey Sampson maintains that universal grammar theories are not falsifiable and are therefore pseudoscientific. He argues that the grammatical "rules" linguists posit are simply post-hoc observations about existing languages, rather than predictions about what is possible in a language. Sampson claims that every one of the "poor" arguments used to justify the language-instinct claim is wrong. He writes that "either the logic is fallacious, or the factual data are incorrect (or, sometimes, both)," and the "evidence points the other way." Children are good at learning languages, because people are good at learning anything that life throws at us — not because we have fixed structures of knowledge built-in. Similarly, professor of cognitive science Jeffrey Elman argues that the unlearnability of languages ostensibly assumed by universal grammar is based on a too-strict, "worst-case" model of grammar, which is not in keeping with any actual grammar.

Linguist James Hurford, in his article "Nativist and Functional Explanations in Language Acquisition," offers the major differences between the glossogenetic and the phylogenetic mechanisms. He states that, "Deep aspects of the form of language are not likely to be readily identifiable with obvious specific uses, and one cannot suppose that it will be possible to attribute them directly to the recurring short-term needs of successive generations in a community. Here, nativist explanations for aspects of the form of language, appealing to an innate LAD, seem appropriate. But use or function can also be appealed to on the evolutionary timescale, to attempt to explain the structure of the LAD itself." For Hurford, biological mutations plus functional considerations constitute the explanans, while the LAD itself constitutes the explanandum. The LAD is part of the species' heredity, the result of mutations over a long period, he states. But, while he agrees with Chomsky that the mechanism of grammaticisation is located in "the Chomskyan LAD" and that Chomsky is "entirely right in emphasising that a language (E-language) is an artifact resulting from the interplay of many factors," he states that this artifact should be of great interest and systematic study, and can affect grammatical competence, i.e. "I-language."

Morten H. Christiansen, professor of Psychology, and Nick Chater, professor of Psychology and Language Sciences, have argued that "a biologically determined UG is not evolutionarily viable." As the processes of language change are much more rapid than processes of genetic change, they state, language constitutes a "moving target" both over time and across different human populations, and, hence, cannot provide a stable environment to which language genes could have adapted. In following Darwin, they view language as a complex and interdependent "organism," which evolves under selectional pressures from human learning and processing mechanisms, so that "apparently arbitrary aspects of linguistic structure may result from general learning and processing biases deriving from the structure of thought processes, perceptuo-motor factors, cognitive limitations, and pragmatics". Professor of linguistics Norbert Hornstein countered polemically that Christiansen and Chater appear "to have no idea what generative grammar [theory] is," and "especially, but not uniquely, about the Chomsky program." Hornstein points out that all "grammatically informed psycho-linguistic works done today or before" understand that generative/universal grammar capacities are but one factor among others needed to explain real-time acquisition." Christiansen and Chater's observation that "language use involves multiple interacting variables" [italics in the original] is, essentially, a truism. It is nothing new, he argues, to state that "much more than a competence theory will be required" to figure out how language is deployed, acquired, produced, or parsed. The position, he concludes, that universal grammar properties are just "probabilistic generalizations over available linguistic inputs" belongs to the "traditional" and "debunked" view held by associationists and structuralists many decades in the past.

In the same vein, professor of linguistics Nicholas Evans and professor of psycholinguistics Stephen C. Levinson observe^[40] that Chomsky's notion of a Universal Grammar has been mistaken for a set of substantial research findings about what all languages have in common, while, it is, "in fact," the programmatic label for "whatever it turns out to be that all children bring to learning a language." For substantial findings about universals across languages, they argue, one must turn to the field of linguistic typology, which bears a "bewildering range of diverse languages" and in which "generalizations are really quite hard to extract." Chomsky's actual views, combining, as they claim, philosophical and mathematical approaches to structure with claims about the innate endowment for language, have been "hugely influential in the cognitive sciences.

Wolfram Hinzen, in his work The philosophical significance of Universal Grammar seeks to re-establish the epistemological significance of grammar and addresses the three main current objections to Cartesian universal grammar, i.e. that it has no coherent formulation, it cannot have evolved by standard, accepted neo-Darwinian evolutionary principles, and it goes against the variation extant at all levels of linguistic organization, which lies at the heart of human faculty of language.

In the domain of field research, Daniel Everett has claimed that the Pirahã language is a counterexample to the basic tenets of universal grammar because it lacks clausal embedding. According to Everett, this trait results from Pirahã culture emphasizing present-moment concrete matters. Nevins et al. (2007) have responded that Pirahã does, in fact, have clausal embedding, and that, even if it did not, this would be irrelevant to current theories of universal grammar. They addressed each of Everett's claims and, using Everett's "rich material" data, claim to have found no evidence of a causal relation between culture and grammatical structure. Pirahã grammar, they concluded, presents no unusual challenge, much less the "severe" one claimed by Everett, to the notion of a universal grammar.

Developments

In 2017, Chomsky and Berwick co-wrote their book titled Why Only Us, where they defined both the minimalist program and the strong minimalist thesis and its implications, to update their approach to UG theory. According to Berwick and Chomsky, "the optimal situation would be that UG reduces to the simplest computational principles which operate in accord with conditions of computational efficiency. This conjecture is ... called the Strong Minimalist Thesis (SMT)."

The significance of SMT is to shift the previous emphasis on a universal grammar to the concept that Chomsky and Berwick now call "merge". "Merge" is defined there as follows:

Every computational system has embedded within it somewhere an operation that applies to two objects X and Y already formed, and constructs from them a new object Z. Call this operation Merge.

SMT dictates that "Merge will be as simple as possible: it will not modify X or Y or impose any arrangement on them; in particular, it will leave them unordered; an important fact. Merge is therefore just set formation: Merge of X and Y yields the set {X, Y}."

Ideology

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Ideology

An ideology is a set of beliefs or values attributed to a person or group of persons, especially those held for reasons that are not purely about belief in certain knowledge, in which "practical elements are as prominent as theoretical ones". Formerly applied primarily to economic, political, or religious theories and policies, in a tradition going back to Karl Marx and Friedrich Engels, more recent use treats the term as mainly condemnatory.

The term was coined by Antoine Destutt de Tracy, a French Enlightenment aristocrat and philosopher, who conceived it in 1796 as the "science of ideas" to develop a rational system of ideas to oppose the irrational impulses of the mob. In political science, the term is used in a descriptive sense to refer to political belief systems.

Etymology

Antoine Destutt de Tracy coined the term ideology.

The term ideology originates from French idéologie, itself coined from combining Greek: idéā (ἰδέα, 'notion, pattern'; close to the Lockean sense of idea) and -logíā (-λογῐ́ᾱ, 'the study of').

An ideologue is someone who strongly believes in an ideology. The term carries negative connotations, often referring to someone who is blindly partisan, zealous, or fanatical in their beliefs.

History

The term "ideology" and the system of ideas associated with it were developed in 1796 by Antoine Destutt de Tracy (1754–1836), who crystallised his ideas while in prison (November 1793 to October 1794) pending trial during the Reign of Terror of c. 1793 to July 1794. While imprisoned he read the works of Locke and Étienne Bonnot de Condillac.

Hoping to form a secure foundation for the moral and political sciences, Tracy devised the term for a "science of ideas", basing such upon two things: (1) the sensations that people experience as they interact with the material world; and (2) the ideas that form in their minds due to those sensations. Tracy conceived of ideology as a liberal philosophy that would defend individual liberty, property, free markets, and constitutional limits on state power. He argues that, among these aspects, ideology is the most generic term because the 'science of ideas' also contains the study of their expression and deduction. The coup d'état that overthrew Maximilien Robespierre in July 1794 allowed Tracy to pursue his work. Tracy reacted to the terroristic phase of the revolution (during the Napoleonic regime of 1799 to 1815 as part of the Napoleonic Wars) by trying to work out a rational system of ideas to oppose the irrational mob-impulses that had nearly destroyed him.

A subsequent early source for the near-original meaning of ideology is Hippolyte Taine's work on the Ancien Régime, Origins of Contemporary France (French: Les Origines de la France Contemporaine) volume I (1875). He describes ideology as rather like teaching philosophy via the Socratic method, though without extending the vocabulary beyond what the general reader already possessed, and without the examples from observation that practical science would require. Taine identifies it not just with Tracy but also with his milieu, and includes Condillac as one of its precursors.

Napoleon Bonaparte (1769–1821) came to view ideology as a term of abuse, which he often hurled against his liberal foes in Tracy's Institut national. According to Karl Mannheim's historical reconstruction of the shifts in the meaning of ideology, the modern meaning of the word was born when Napoleon used it to describe his opponents as "the ideologues". Tracy's major book, The Elements of Ideology (French: Élémens d'idéologie, published 1804–1815), was soon translated into major European languages.

In the century following Tracy's formulations, the term ideology moved back and forth between positive and negative connotations. When post-Napoleonic governments adopted a reactionary stance, the concept influenced the Italian, Spanish and Russian thinkers who had begun to describe themselves as liberals and who attempted to reignite revolutionary activity in the early 1820s, including the Carbonari societies in France and Italy and the Decembrists in Russia. Karl Marx (1818–1883) adopted Napoleon's negative sense of the term, using it in his writings, in which he once described Tracy as a fischblütige Bourgeoisdoktrinär (a "fish-blooded bourgeois doctrinaire"). The term has since dropped some of its pejorative sting (euphemism treadmill), and has become a neutral term in the analysis of differing political opinions and views of social groups. While Marx situated the term within class struggle and domination, others believed it was a necessary part of institutional functioning and social integration.

In parallel with post-Soviet Russian ideas about the mono-ideologies of (for example) monotheism, Walter Brueggemann (1933–2025) has examined "ideological extension" in historical religious/political contexts.

Definitions and analysis

There are many different kinds of ideologies, including political, social, epistemological, and ethical. Recent analysis tends to posit that ideology is a 'coherent system of ideas' that rely on a few basic assumptions about reality that may or may not have any factual basis. Through this system, ideas become coherent, repeated patterns through the subjective ongoing choices that people make. These ideas serve as the seed around which further thought grows. The belief in an ideology can range from passive acceptance up to fervent advocacy. Definitions, such as by Manfred Steger and Paul James, emphasize both the issue of patterning and contingent claims to truth. They wrote: "Ideologies are patterned clusters of normatively imbued ideas and concepts, including particular representations of power relations. These conceptual maps help people navigate the complexity of their political universe and carry claims to social truth."

Studies of the concept of ideology itself (rather than specific ideologies) have been carried out under the name of systematic ideology in the works of George Walford and Harold Walsby, who attempt to explore the relationships between ideology and social systems. David W. Minar describes six different ways the word ideology has been used:

1. As a collection of certain ideas with certain kinds of content, usually normative;
2. As the form or internal logical structure that ideas have within a set;
3. By the role ideas play in human-social interaction;
4. By the role ideas play in the structure of an organization;
5. As meaning, whose purpose is persuasion; and
6. As the locus of social interaction.

For Willard A. Mullins, an ideology should be contrasted with the related (but different) issues of utopia and historical myth. An ideology is composed of four basic characteristics:

1. it must have power over cognition;
2. it must be capable of guiding one's evaluations;
3. it must provide guidance towards action; and
4. it must be logically coherent.

Terry Eagleton outlines (more or less in no particular order) some definitions of ideology:

1. The process of production of meanings, signs and values in social life
2. A body of ideas characteristic of a particular social group or class
3. Ideas that help legitimate a dominant political power
4. False ideas that help legitimate a dominant political power
5. Systematically distorted communication
6. Ideas that offer a position for a subject
7. Forms of thought motivated by social interests
8. Identity thinking
9. Socially necessary illusion
10. The conjuncture of discourse and power
11. The medium in which conscious social actors make sense of their world
12. Action-oriented sets of beliefs
13. The confusion of linguistic and phenomenal reality
14. Semiotic closure
15. The indispensable medium in which individuals live out their relations to a social structure
16. The process that converts social life to a natural reality

German philosopher Christian Duncker called for a "critical reflection of the ideology concept". In his work, he strove to bring the concept of ideology into the foreground, as well as the closely connected concerns of epistemology and history, defining ideology in terms of a system of presentations that explicitly or implicitly lay claim to absolute truth.

Marxist interpretation

Karl Marx posits that a society's dominant ideology is integral to its superstructure.

Marx's analysis sees ideology as a system of false consciousness that arises from economic relationships, reflecting and perpetuating the interests of the dominant class.

In the Marxist base and superstructure model of society, base denotes the relations of production and modes of production, and superstructure denotes the dominant ideology (i.e. religious, legal, political systems). The economic base of production determines the political superstructure of a society. Ruling class-interests determine the superstructure and the nature of the justifying ideology—actions feasible because the ruling class control the means of production. For example, in a feudal mode of production, religious ideology is the most prominent aspect of the superstructure, while in capitalist formations, ideologies such as liberalism and social democracy dominate. Hence the great importance of ideology justifies a society and politically confuses the alienated groups of society via false consciousness. Some explanations have been presented. Antonio Gramsci uses cultural hegemony to explain why the working-class have a false ideological conception of what their best interests are. Marx argued: "The class which has the means of material production at its disposal has control at the same time over the means of mental production."

The Marxist formulation of "ideology as an instrument of social reproduction" is conceptually important to the sociology of knowledge, viz. Karl Mannheim, Daniel Bell, and Jürgen Habermas et al. Moreover, Mannheim has developed and progressed from the "total" but "special" Marxist conception of ideology to a "general" and "total" ideological conception acknowledging that all ideology (including Marxism) resulted from social life, an idea developed by the sociologist Pierre Bourdieu. Slavoj Žižek and the earlier Frankfurt School added to the "general theory" of ideology a psychoanalytic insight that ideologies do not include only conscious but also unconscious ideas.

Ideology and the commodity (Debord)

The French Marxist theorist Guy Debord, founding member of the Situationist International, argued that when the commodity becomes the "essential category" of society, i.e. when the process of commodification has been consummated to its fullest extent, the image of society propagated by the commodity (as it describes all of life as constituted by notions and objects deriving their value only as commodities tradeable in terms of exchange value), colonizes all of life and reduces society to a mere representation, The Society of the Spectacle.

Unifying agents (Hoffer)

The American philosopher Eric Hoffer identified several elements that unify followers of a particular ideology:

1. Hatred: "Mass movements can rise and spread without a God, but never without belief in a devil." The "ideal devil" is a foreigner.
2. Imitation: "The less satisfaction we derive from being ourselves, the greater is our desire to be like others…the more we mistrust our judgment and luck, the more are we ready to follow the example of others."
3. Persuasion: The proselytizing zeal of propagandists derives from "a passionate search for something not yet found more than a desire to bestow something we already have."
4. Coercion: Hoffer asserts that violence and fanaticism are interdependent. People forcibly converted to Islamic or communist beliefs become as fanatical as those who did the forcing. He says: "It takes fanatical faith to rationalize our cowardice."
5. Leadership: Without the leader, there is no movement. Often the leader must wait long in the wings until the time is ripe. He calls for sacrifices in the present, to justify his vision of a breathtaking future. The skills required include: audacity, brazenness, iron will, fanatical conviction; passionate hatred, cunning, a delight in symbols; ability to inspire blind faith in the masses; and a group of able lieutenants. Charlatanism is indispensable, and the leader often imitates both friend and foe, "a single-minded fashioning after a model." He will not lead followers towards the "promised land", but only "away from their unwanted selves".
6. Action: Original thoughts are suppressed, and unity encouraged, if the masses are kept occupied through great projects, marches, exploration and industry.
7. Suspicion: "There is prying and spying, tense watching and a tense awareness of being watched." This pathological mistrust goes unchallenged and encourages conformity, not dissent.

Ronald Inglehart

Ronald Inglehart of the University of Michigan is author of the World Values Survey, which, since 1980, has mapped social attitudes in 100 countries representing 90% of global population. Results indicate that where people live is likely to closely correlate with their ideological beliefs. In much of Africa, South Asia and the Middle East, people prefer traditional beliefs and are less tolerant of liberal values. Protestant Europe, at the other extreme, adheres more to secular beliefs and liberal values. Alone among high-income countries, the United States is exceptional in its adherence to traditional beliefs, in this case Christianity.

Political ideologies

See also: List of political ideologies

In political science, a political ideology is a certain ethical set of ideals, principles, doctrines, myths, or symbols of a social movement, institution, class, or large group that explains how society should work, offering some political and cultural blueprint for a certain social order. Political ideologies are concerned with many different aspects of a society, including but not limited to: the economy, the government, the environment, education, health care, labor law, criminal law, the justice system, social security and welfare, public policy and administration, foreign policy, rights, freedoms and duties, citizenship, immigration, culture and national identity, military administration, and religion.

Political ideologies have two dimensions:

1. Goals: how society should work; and
2. Methods: the most appropriate ways to achieve the ideal arrangement.

A political ideology largely concerns itself with how to allocate power and to what ends power should be used. Some parties follow a certain ideology very closely, while others may take broad inspiration from a group of related ideologies without specifically embracing any one of them. Each political ideology contains certain ideas on what it considers the best form of government (e.g., democracy, demagogy, theocracy, caliphate etc.), scope of government (e.g. authoritarianism, libertarianism, federalism, etc.) and the best economic system (e.g. capitalism, socialism, etc.). Sometimes the same word is used to identify both an ideology and one of its main ideas. For instance, socialism may refer to an economic system, or it may refer to an ideology that supports that economic system. Post 1991, many commentators claim that we are living in a post-ideological age, in which redemptive, all-encompassing ideologies have failed. This view is often associated with Francis Fukuyama's writings on the end of history. Contrastly, Nienhueser (2011) sees research (in the field of human resource management) as ongoingly "generating ideology".

There are many proposed methods for the classification of political ideologies. Ideologies can identify themselves by their position on the political spectrum (e.g. left, center, or right). They may also be distinguished by single issues around which they may be built (e.g. civil libertarianism, support or opposition to European integration, legalization of marijuana). They may also be distinguished by political strategies (e.g. populism, personalism). The classification of political ideology is difficult, however, due to cultural relativity in definitions. For example, "what Americans now call conservatism much of the world calls liberalism or neoliberalism"; a conservatism in Finland would be labeled socialism in the United States.

Philosopher Michael Oakeshott defines single-issue ideologies as "the formalized abridgment of the supposed sub-stratum of the rational truth contained in the tradition". Moreover, Charles Blattberg offers an account that distinguishes political ideologies from political philosophies.

Slavoj Žižek argues how the very notion of post-ideology can enable the deepest, blindest form of ideology. A sort of false consciousness or false cynicism, engaged in for the purpose of lending one's point of view the respect of being objective, pretending neutral cynicism, without truly being so. Rather than help avoiding ideology, this lapse only deepens the commitment to an existing one. Zizek calls this "a post-modernist trap". Peter Sloterdijk advanced the same idea already in 1988.

Studies have shown that political ideology is somewhat genetically heritable.

Ideology and state

Main article: Ideocracy

When a political ideology becomes a dominantly pervasive component within a government, one can speak of an ideocracy. Different forms of government use ideology in various ways, not always restricted to politics and society. Certain ideas and schools of thought become favored, or rejected, over others, depending on their compatibility with or use for the reigning social order.

In The Anatomy of Revolution, Crane Brinton said that new ideology spreads when there is discontent with an old regime. The may be repeated during revolutions itself; extremists such as Vladimir Lenin and Robespierre may thus overcome more moderate revolutionaries. This stage is soon followed by Thermidor, a reining back of revolutionary enthusiasm under pragmatists like Napoleon and Joseph Stalin, who bring "normalcy and equilibrium". Brinton's sequence ("men of ideas>fanatics>practical men of action") is reiterated by J. William Fulbright, while a similar form occurs in Eric Hoffer's The True Believer.

Epistemological ideologies

Even when the challenging of existing beliefs is encouraged, as in scientific theories, the dominant paradigm or mindset can prevent certain challenges, theories, or experiments from being advanced. A special case of science that has inspired ideology is ecology, which studies the relationships among living things on Earth. Perceptual psychologist James J. Gibson believed that human perception of ecological relationships was the basis of self-awareness and cognition itself. Linguist George Lakoff has proposed a cognitive science of mathematics wherein even the most fundamental ideas of arithmetic would be seen as consequences or products of human perception—which is itself necessarily evolved within an ecology.

Deep ecology and the modern ecology movement (and, to a lesser degree, Green parties) appear to have adopted ecological sciences as a positive ideology. Some notable economically based ideologies include neoliberalism, monetarism, mercantilism, mixed economy, social Darwinism, communism, laissez-faire economics, and free trade. There are also current theories of safe trade and fair trade that can be seen as ideologies.

Psychological explanations of ideology

A large amount of research in psychology is concerned with the causes, consequences and content of ideology, with humans being dubbed the "ideological animal" by Althusser. Many theories have tried to explain the existence of ideology in human societies.

Jost, Ledgerwood, and Hardin (2008) propose that ideologies may function as prepackaged units of interpretation that spread because of basic human motives to understand the world, avoid existential threat, and maintain valued interpersonal relationships. The authors conclude that such motives may lead disproportionately to the adoption of system-justifying worldviews. Psychologists generally agree that personality traits, individual difference variables, needs, and ideological beliefs seem to have something in common.

Just-world theory posits that people want to believe in a fair world for a sense of control and security and generate ideologies in order to maintain this belief, for example by justifiying inequality or unfortunate events. A critique of just world theory as a sole explanation of ideology is that it does not explain the differences between ideologies.

Terror management theory posits that ideology is used as a defence mechanism against threats to their worldview which in turn protect and individuals sense of self-esteem and reduce their awareness of mortality. Evidence shows that priming individuals with an awareness of mortality does not cause individuals to respond in ways underpinned by any particular ideology, but rather the ideology that they are currently aware of.

System justification theory posits that people tend to defend existing society, even at times against their interest, which in turn causes people to create ideological explanations to justify the status quo. Jost, Fitzimmons and Kay argue that the motivation to protect a preexisting system is due to a desire for cognitive consistency (being able to think in similar ways over time), reducing uncertainty and reducing effort, illusion of control and fear of equality. According to system justification theory, ideologies reflect (unconscious) motivational processes, as opposed to the view that political convictions always reflect independent and unbiased thinking.

Ideology and the social sciences

Semiotic theory

According to semiotician Bob Hodge:

[Ideology] identifies a unitary object that incorporates complex sets of meanings with the social agents and processes that produced them. No other term captures this object as well as 'ideology'. Foucault's 'episteme' is too narrow and abstract, not social enough. His 'discourse', popular because it covers some of ideology's terrain with less baggage, is too confined to verbal systems. 'Worldview' is too metaphysical, 'propaganda' too loaded. Despite or because of its contradictions, 'ideology' still plays a key role in semiotics oriented to social, political life.

Authors such as Michael Freeden have also recently incorporated a semantic analysis to the study of ideologies.

Sociology

Sociologists define ideology as "cultural beliefs that justify particular social arrangements, including patterns of inequality". Dominant groups use these sets of cultural beliefs and practices to justify the systems of inequality that maintain their group's social power over non-dominant groups. Ideologies use a society's symbol system to organize social relations in a hierarchy, with some social identities being superior to other social identities, which are considered inferior. The dominant ideology in a society is passed along through the society's major social institutions, such as the media, the family, education, and religion. As societies changed throughout history, so did the ideologies that justified systems of inequality.

Sociological examples of ideologies include racism, sexism, heterosexism, ableism, and ethnocentrism.

Quotations

"We do not need…to believe in an ideology. All that is necessary is for each of us to develop our good human qualities. The need for a sense of universal responsibility affects every aspect of modern life." — Dalai Lama

"The function of ideology is to stabilize and perpetuate dominance through masking or illusion." — Sally Haslanger

"[A]n ideology differs from a simple opinion in that it claims to possess either the key to history, or the solution for all the 'riddles of the universe,' or the intimate knowledge of the hidden universal laws, which are supposed to rule nature and man." — Hannah Arendt

Y chromosome

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Y_chromosome

 

Human Y chromosome
Human Y chromosome (after G-banding)
Y chromosome in human male karyogram
Features
Length (bp)	62,460,029 bp (CHM13)
No. of genes	693 (CCDS)
Type	Allosome
Centromere position	Acrocentric (10.4 Mbp)
Complete gene lists
CCDS	Gene list
HGNC	Gene list
UniProt	Gene list
NCBI	Gene list
External map viewers
Ensembl	Chromosome Y
Entrez	Chromosome Y
NCBI	Chromosome Y
UCSC	Chromosome Y
Full DNA sequences
RefSeq	NC_000024 (FASTA)
GenBank	CM000686 (FASTA)

The Y chromosome is one of two sex chromosomes in therian mammals and other organisms. Along with the X chromosome, it is part of the XY sex-determination system, in which the Y is used for sex-determining as the presence of the Y chromosome typically causes offspring produced in sexual reproduction to develop phenotypically male. In mammals, the Y chromosome contains the SRY gene, which usually triggers the differentiation of male gonads. The Y chromosome is typically only passed from male parents to male offspring.

Overview

Discovery

The Y chromosome was identified as a sex-determining chromosome by Nettie Stevens at Bryn Mawr College in 1905 during a study of the mealworm Tenebrio molitor. Edmund Beecher Wilson independently discovered the same mechanisms the same year, working with Hemiptera. Stevens proposed that chromosomes always existed in pairs and that the smaller chromosome (now labelled "Y") was the pair of the X chromosome discovered in 1890 by Hermann Henking. She realized that the previous idea of Clarence Erwin McClung, that the X chromosome determines sex, was wrong and that sex determination is, in fact, due to the presence or absence of the Y chromosome. In the early 1920s, Theophilus Painter determined that X and Y chromosomes determined sex in humans (and other mammals).

The chromosome was given the name "Y" simply to follow on from Henking's "X" alphabetically. The idea that the Y chromosome was named after its similarity in appearance to the letter "Y" is mistaken. All chromosomes normally appear as an amorphous blob under the microscope and only take on a well-defined shape during mitosis. This shape is vaguely X-shaped for all chromosomes. It is entirely coincidental that the Y chromosome, during mitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape.

Different variations

Most therian mammals have only one pair of sex chromosomes in each cell. Males usually have one Y chromosome and one X chromosome, while females usually have two X chromosomes. In mammals, the Y chromosome contains the SRY gene which triggers phenotypic male development. Differences in the Y chromosome are associated with both atypical sexual development and fertility conditions.

In humans, people with an extra X chromosome often develop Klinefelter syndrome, and people with an extra Y chromosome develop Jacob's Syndrome, as genes on the Y chromosome generally trigger the development of a male phenotype. Other chromosomal variations include three X chromosomes (or Trisomy X), and Monosomy X (or Turner Syndrome), where individuals only have one X chromosome and no Y chromosome. Some individuals with an XY karyotype, develop phenotypically female due to mutation in genes such as the SRY gene or MAP3K1.

Origins and evolution

Before Y chromosome

Many ectothermic vertebrates have no sex chromosomes. If these species have different sexes, sex is determined environmentally rather than genetically. For some species, especially reptiles, sex depends on the incubation temperature. Some vertebrates are hermaphrodites, though hermaphroditic species are most commonly sequential, meaning the organism switches sex, producing male or female gametes at different points in its life, but never producing both at the same time. This is opposed to simultaneous hermaphroditism, where the same organism produces male and female gametes at the same time. Most simultaneous hermaphrodite species are invertebrates, and among vertebrates, simultaneous hermaphroditism has only been discovered in a few orders of fish.

Origin

The X and Y chromosomes are thought to have evolved from a pair of identical chromosomes, termed autosomes, when an ancestral animal developed an allelic variation (a so-called "sex locus") and simply possessing this allele caused the organism to develop phenotypically male. Over time, the two chromosomes diverged into separate X and Y configurations, with the Y chromosome losing many of its original genes, and gaining only a few others specifically involved in sex differentiation.

Until recently, the X and Y chromosomes in mammals were thought to have diverged around 300 million years ago. However, research published in 2008 analyzing the platypus genome suggested that the XY sex-determination system would not have been present more than 166 million years ago, when monotremes split from other mammals. This re-estimation of the age of the therian XY system is based on the finding that sequences that are on the X chromosomes of marsupials and eutherian mammals are not present on the autosomes of platypus and birds. The older estimate was based on erroneous reports that the platypus X chromosomes contained these sequences.

Recombination inhibition

Most chromosomes recombine during meiosis. However, the X and Y pair in a shared region known as the pseudoautosomal region (PAR). The PAR undergoes frequent recombination between the X and Y chromosomes, but recombination is suppressed in other regions of the Y chromosome. These regions contain genes specifically involved in male sexual differentiation. Without regional suppression, the genes could be lost from the Y chromosome in recombination, causing developmental issues such as infertility.

The lack of recombination across the majority of the Y chromosome makes it a useful tool in studying human evolution, since recombination complicates the mathematical models used to trace ancestries.

Degeneration

By one estimate, the human Y chromosome has lost 1,393 of its 1,438 original genes throughout its existence, and linear extrapolation of this 1,393-gene loss over 300 million years gives a rate of genetic loss of 4.6 genes per million years. Continued loss of genes at this rate would result in a Y chromosome with no functional genes – that is the Y chromosome would lose complete function – within the next 10 million years, or half that time with the current age estimate of 160 million years. Comparative genomic analysis reveals that many mammalian species are experiencing a similar loss of function in their heterozygous sex chromosome. Degeneration may simply be the fate of all non-recombining sex chromosomes, due to three common evolutionary forces: high mutation rate, inefficient selection, and genetic drift.

With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the human genome. However, these changes have been limited to non-coding sequences and comparisons of the human and chimpanzee Y chromosomes (first published in 2005) show that the human Y chromosome has not lost any genes since the divergence of humans and chimpanzees between 6–7 million years ago. Additionally, a scientific report in 2012 stated that only one gene had been lost since humans diverged from the rhesus macaque 25 million years ago. These facts provide direct evidence that the linear extrapolation model is flawed and suggest that the current human Y chromosome is either no longer shrinking or is shrinking at a much slower rate than the 4.6 genes per million years estimated by the linear extrapolation model.

High mutation rate

The human Y chromosome is particularly exposed to high mutation rates due to the environment in which it is housed. The Y chromosome is passed exclusively through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a greater risk of mutation than the rest of the genome. The increased mutation opportunity for the Y chromosome is reported by Graves as a factor 4.8. However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.

The observation that the Y chromosome experiences little meiotic recombination and has an accelerated rate of mutation and degradative change compared to the rest of the genome suggests an evolutionary explanation for the adaptive function of meiosis concerning the main body of genetic information. Brandeis proposed that the basic function of meiosis (particularly meiotic recombination) is the conservation of the integrity of the genome, a proposal consistent with the idea that meiosis is an adaptation for repairing DNA damage.

Inefficient selection

Without the ability to recombine during meiosis, the Y chromosome is unable to expose individual alleles to natural selection. Deleterious alleles are allowed to "hitchhike" with beneficial neighbors, thus propagating maladapted alleles into the next generation. Conversely, advantageous alleles may be selected against if they are surrounded by harmful alleles (background selection). Due to this inability to sort through its gene content, the Y chromosome is particularly prone to the accumulation of non-coding DNA. Massive accumulations of retrotransposable elements are scattered throughout the Y. The random insertion of DNA segments often disrupts encoded gene sequences and renders them nonfunctional. However, the Y chromosome has no way of weeding out these "jumping genes". Without the ability to isolate alleles, selection cannot effectively act upon them.

A clear, quantitative indication of this inefficiency is the entropy rate of the Y chromosome. Whereas all other chromosomes in the human genome have entropy rates of 1.5–1.9 bits per nucleotide (compared to the theoretical maximum of exactly 2 for no redundancy), the Y chromosome's entropy rate is only 0.84. From the definition of entropy rate, the Y chromosome has a much lower information content relative to its overall length, and is more redundant.

Genetic drift

Even if a well-adapted Y chromosome manages to maintain genetic activity by avoiding mutation accumulation, there is no guarantee it will be passed down to the next generation. The population size of the Y chromosome is inherently limited to 1/4 that of autosomes: diploid organisms contain two copies of autosomal chromosomes, while only half the population contains 1 Y chromosome. Thus, genetic drift is an exceptionally strong force acting upon the Y chromosome. Through sheer random assortment, an adult male may never pass on his Y chromosome if he only has female offspring. Thus, although a male may have a well-adapted Y chromosome free of excessive mutation, it may never make it into the next gene pool. The repeat random loss of well-adapted Y chromosomes, coupled with the tendency of the Y chromosome to evolve to have more deleterious mutations rather than less for reasons described above, contributes to the species-wide degeneration of Y chromosomes through Muller's ratchet.

Gene conversion

As has already been mentioned, the Y chromosome is unable to recombine during meiosis like the other human chromosomes; however, in 2003, researchers from MIT discovered a process which may slow down the process of degradation. They found that human Y chromosome can "recombine" with itself, using palindrome base pair sequences. Such a "recombination" is called gene conversion.

In the case of the Y chromosomes, the palindromes are not noncoding DNA; these strings of nucleotides contain functioning genes important for male fertility. Most of the sequence pairs are greater than 99.97% identical. The extensive use of gene conversion may play a role in the ability of the Y chromosome to edit out genetic mistakes and maintain the integrity of the relatively few genes it carries. In other words, since the Y chromosome is single, it has duplicates of its genes on itself instead of having a second, homologous chromosome. When errors occur, it can use other parts of itself as a template to correct them.

Findings were confirmed by comparing similar regions of the Y chromosome in humans to the Y chromosomes of chimpanzees, bonobos and gorillas. The comparison demonstrated that the same phenomenon of gene conversion appeared to be at work more than 5 million years ago, when humans and the non-human primates diverged from each other.

Gene conversion tracts formed during meiosis are long, about 2,068 base pairs, and significantly biased towards the fixation of G or C nucleotides (GC biased). The recombination intermediates preceding gene conversion were found to rarely take the alternate route of crossover recombination. The Y-Y gene conversion rate in humans is about 1.52 x 10⁻⁵ conversions/base/year. These gene conversion events may reflect a basic function of meiosis, that of conserving the integrity of the genome.

Future evolution

According to some theories, in the terminal stages of the degeneration of the Y chromosome, other chromosomes may increasingly take over genes and functions formerly associated with it, and finally, within the framework of this theory, the Y chromosome disappears entirely, and a new sex-determining system arises.

Several species of rodent in the sister families Muridae and Cricetidae have reached a stage where the XY system has been modified, in the following ways:

• The Transcaucasian mole vole, Ellobius lutescens, the Zaisan mole vole, Ellobius tancrei, and the Japanese spinous country rats Tokudaia osimensis and Tokudaia tokunoshimensis, have lost the Y chromosome and SRY entirely. Tokudaia spp. have relocated some other genes ancestrally present on the Y chromosome to the X chromosome. Both sexes of Tokudaia spp. and Ellobius lutescens have an XO genotype (Turner syndrome), whereas all Ellobius tancrei possess an XX genotype. The new sex-determining system(s) for these rodents remains unclear.
• The wood lemming Myopus schisticolor, the Arctic lemming, Dicrostonyx torquatus, and multiple species in the grass mouse genus Akodon have evolved fertile females who possess the genotype generally coding for males, XY, in addition to the ancestral XX female, through a variety of modifications to the X and Y chromosomes.
• In the creeping vole, Microtus oregoni, the females, with just one X chromosome each, produce X gametes only, and the males, XY, produce Y gametes, or gametes devoid of any sex chromosome, through nondisjunction.

Outside of the rodents, the black muntjac, Muntiacus crinifrons, evolved new X and Y chromosomes through fusions of the ancestral sex chromosomes and autosomes.

Modern data casts doubt on the hypothesis that the Y-chromosome will disappear. This conclusion was reached by scientists who studied the Y chromosomes of rhesus monkeys. When genomically comparing the Y chromosome of rhesus monkeys and humans, scientists found very few differences, given that humans and rhesus monkeys diverged 30 million years ago.

Outside of mammals, some organisms have lost the Y chromosome, such as most species of nematodes. However, for the complete elimination of Y to occur, it was necessary to develop an alternative way of determining sex (for example, by determining sex by the ratio of the X chromosome to autosomes), and any genes necessary for male function had to be moved to other chromosomes. In the meantime, modern data demonstrate the complex mechanisms of Y chromosome evolution and the fact that the disappearance of the Y chromosome is not guaranteed.

1:1 sex ratio

Fisher's principle outlines why almost all species using sexual reproduction have a sex ratio of 1:1. W. D. Hamilton gave the following basic explanation in his 1967 paper on "Extraordinary sex ratios", given the condition that males and females cost equal amounts to produce:

1. Suppose male births are less common than female.
2. A newborn male then has better mating prospects than a newborn female, and therefore can expect to have more offspring.
3. Therefore, parents genetically disposed to produce males tend to have more than average numbers of grandchildren born to them.
4. Therefore, the genes for male-producing tendencies spread, and male births become more common.
5. As the 1:1 sex ratio is approached, the advantage associated with producing males dies away.
6. The same reasoning holds if females are substituted for males throughout. Therefore, 1:1 is the equilibrium ratio.

Non-therian Y chromosome

Many groups of organisms, in addition to therian mammals, have Y chromosomes, but these Y chromosomes do not share common ancestry with therian Y chromosomes. Such groups include monotremes, Drosophila, some other insects, some fish, some reptiles, and some plants. In Drosophila melanogaster, the Y chromosome does not trigger male development. Instead, sex is determined by the number of X chromosomes. The D. melanogaster Y chromosome does contain genes necessary for male fertility. So XXY D. melanogaster are female, and D. melanogaster with a single X (X0) are male but sterile. There are some species of Drosophila in which X0 males are both viable and fertile.

ZW chromosomes

Main article: ZW sex-determination system

Other organisms have mirror image sex chromosomes: where the homogeneous sex is the male, with two Z chromosomes, and the female is the heterogeneous sex with a Z chromosome and a W chromosome. For example, the ZW sex-determination system is found in birds, snakes, and butterflies; the females have ZW sex chromosomes, and males have ZZ sex chromosomes.

Non-inverted Y chromosome

There are some species, such as the Japanese rice fish, in which the XY system is still developing and crossover between the X and Y is still possible. Because the male-specific region is very small and contains no essential genes, it is even possible to artificially induce XX males and YY females with no ill effect.

Multiple XY pairs

Monotremes like platypuses possess four or five pairs of XY sex chromosomes, each pair consisting of sex chromosomes with homologous regions. The chromosomes of neighboring pairs are partially homologous, such that a chain is formed during mitosis. The first X chromosome in the chain is also partially homologous with the last Y chromosome, indicating that profound rearrangements, some adding new pieces from autosomes, have occurred in history.

Platypus sex chromosomes have strong sequence similarity with the avian Z chromosome, indicating close homology, and the SRY gene so central to sex-determination in most other mammals is apparently not involved in platypus sex-determination.

Human Y chromosome

The human Y chromosome is composed of about 57 million base pairs of DNA, making it similar in size to chromosome 19 and represents roughly 0.9% of the total DNA in a male cell. The human Y chromosome carries 693 genes, 106 of which are protein-coding. However, some genes are repeated, making the number of exclusive protein-coding genes just 42. The Consensus Coding Sequence (CCDS) Project only classifies 63 out of 107 genes.

All single-copy Y-linked genes are hemizygous (present on only one chromosome) except in cases of aneuploidy such as XYY syndrome or XXYY syndrome. Traits that are inherited via the Y chromosome are called Y-linked traits, or holandric traits (from Ancient Greek ὅλος hólos, "whole" + ἀνδρός andrós, "male").

Sequence of the human Y chromosome

At the end of the Human Genome Project (and after many updates) almost half of the Y chromosome remained un-sequenced even in 2021; a different Y chromosome from the HG002 (GM24385) genome was completely sequenced in January 2022 and is included in the new "complete genome" human reference genome sequence, CHM13. The complete sequencing of a human Y chromosome was shown to contain 62,460,029 base pairs and 41 additional genes. This added 30 million base pairs, but it was discovered that the Y chromosome can vary a lot in size between individuals, from 45.2 million to 84.9 million base pairs.

Since almost half of the human Y sequence was unknown before 2022, it could not be screened out as contamination in microbial sequencing projects. As a result, the NCBI RefSeq bacterial genome database mistakenly includes some Y chromosome data.

Structure

Cytogenetic band

G-banding ideograms of human Y chromosome

 

G-banding ideogram of human Y chromosome in resolution 850 bphs. Band length in this diagram is proportional to base-pair length. This type of ideogram is generally used in genome browsers (e.g., Ensembl, UCSC Genome Browser).

 

G-banding patterns of human Y chromosome in three different resolutions (400, 550 and 850). Band length in this diagram is based on the ideograms from ISCN (2013). This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.

 

G-bands of human Y chromosome in resolution 850 bphs

Chr.	Arm	Band	ISCN start	ISCN stop	Basepair start	Basepair stop	Stain	Density
Y	p	11.32	0	149	1	300,000	gneg
Y	p	11.31	149	298	300,001	600,000	gpos	50
Y	p	11.2	298	1043	600,001	10,300,000	gneg
Y	p	11.1	1043	1117	10,300,001	10,400,000	acen
Y	q	11.1	1117	1266	10,400,001	10,600,000	acen
Y	q	11.21	1266	1397	10,600,001	12,400,000	gneg
Y	q	11.221	1397	1713	12,400,001	17,100,000	gpos	50
Y	q	11.222	1713	1881	17,100,001	19,600,000	gneg
Y	q	11.223	1881	2160	19,600,001	23,800,000	gpos	50
Y	q	11.23	2160	2346	23,800,001	26,600,000	gneg
Y	q	12	2346	3650	26,600,001	57,227,415	gvar

Non-combining region of Y (NRY)

Further information: Human Y-chromosome DNA haplogroup

The human Y chromosome is normally unable to recombine with the X chromosome, except for small pieces of pseudoautosomal regions (PARs) at the telomeres (which comprise about 5% of the chromosome's length). These regions are relics of ancient homology between the X and Y chromosomes. The bulk of the Y chromosome, which does not recombine, is called the "NRY", or non-recombining region of the Y chromosome. Single-nucleotide polymorphisms (SNPs) in this region are used to trace direct paternal ancestral lines.

More specifically, PAR1 is at 0.1–2.7 Mb. PAR2 is at 56.9–57.2 Mb. The non-recombining region (NRY) or male-specific region (MSY) sits between. Their sizes are now known perfectly from CHM13: 2.77 Mb and 329.5 kb. Until CHM13 the data in PAR1 and PAR2 was just copied over from the X chromosome.

Sequence classes

Genes

Number of genes

Older gene count estimates of the human Y chromosome used only partial sequences. Only the T2T sequence (2023) was able to produce a complete sequence of the human Y chromosome.

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes	Source	Release date
CCDS	63	—	—		2016-09-08
HGNC	45	55	381		2017-05-12
Ensembl	63	109	392		2017-03-29
UniProt	47	—	—		2018-02-28
NCBI	73	122	400		2017-05-19
T2T	106	883 transcripts	—		2023-08-23

Gene list

See also: Category:Genes on human chromosome Y

In general, the human Y chromosome is extremely gene poor—it is one of the largest gene deserts in the human genome. Disregarding pseudoautosomal genes, genes encoded on the human Y chromosome include:

Genes on the non-recombining portion of the Y chromosome

Name	X paralog	Note
SRY	SOX3	Sex-determining region. This is the p arm [Yp].
ZFY	ZFX	Zinc finger.
RPS4Y1	RPS4X	Ribosomal protein S4.
AMELY	AMELX	Amelogenin.
TBL1Y	TBL1X
PCDH11Y	PDCH11X	X-transposed region (XTR) from Xq21, one of two genes. Once dubbed "PAR3"[76] but later refuted.
TGIF2LY	TGIF2LX	The other X-transposed gene.
TSPY1, TSPY2	TSPX	Testis-specific protein.
AZFa	(none)	Not a gene. First part of the AZF (Azoospermia factor) region on arm q. Contains the following four genes. X counterparts escape inactivation.
USP9Y	USP9X	Ubiquitin protease.
DDX3Y	DDX3X	Helicase.
UTY	UTX	Histone demethylase.
TB4Y	TB4X
AZFb	(none)	Second AZF region on arm q. Prone to NAHR [non-allelic homologous recombination] with AZFc. Overlaps with AZFc. Contains three single-copy gene regions and repeats.
CYorf15	CXorf15
RPS4Y2	RPS4X	Another copy of ribosomal protein S4.
EIF1AY	EIF4AX
KDM5D	KDM5C
XKRY	XK (protein)	Found in the "yellow" amplicon.
HSFY1, HSFY2	HSFX1, HSFX2	Found in the "blue" amplicon.
PRY, PRY2		Found in the "blue" amplicon. Identified by similarity to PTPN13 (Chr. 4).
RBMY1A1	RBMY	Large number of copies. Part of an RBM gene family of RNA recognition motif (RRM) proteins.
AZFc	(none)	Final (distal) part of the AZF. Multiple palindromes.
DAZ1, DAZ2, DAZ3, DAZ4		RRM genes in two palindromic clusters. BOLL and DAZLA are autosomal homologs.
CDY1, CDY2		CDY1 is actually two identical copies. CDY2 is two closely related copies in palindrome P5. Probably derived from autosomal CDYL.
VCY1, VCY2	VCX1 through 3	Three copies of VCX2 (BPY2). Part of the VCX/VCY family. The two copies of BPY1 are instead in Yq11.221/AZFa.

Y-chromosome-linked diseases

Diseases linked to the Y chromosome typically involve an aneuploidy, an atypical number of chromosomes.

Loss of Y chromosome

Males can lose the Y chromosome in a subset of cells, known as mosaic loss. Mosaic loss is strongly associated with age, and smoking is another important risk factor for mosaic loss.

Mosaic loss may be related to health outcomes, indicating that the Y chromosome plays important roles outside of sex determination. Males with a higher percentage of hematopoietic stem cells lacking the Y chromosome have a higher risk of certain cancers and have a shorter life expectancy. In many cases, a cause and effect relationship between the Y chromosome and health outcomes has not been determined, and some propose loss of the Y chromosome could be a "neutral karyotype related to normal aging". However, a 2022 study showed that mosaic loss of the Y chromosome causally contributes to fibrosis, heart risks, and mortality.

Further studies are needed to understand how mosaic Y chromosome loss may contribute to other sex differences in health outcomes, such as how male smokers have between 1.5 and 2 times the risk of non-respiratory cancers as female smokers. Potential countermeasures identified so far include not smoking or stopping smoking and at least one potential drug that "may help counteract the harmful effects of the chromosome loss" is under investigation.

Y chromosome microdeletion

Y chromosome microdeletion (YCM) is a family of genetic disorders caused by missing genes in the Y chromosome. Many affected men exhibit no symptoms and lead normal lives. However, YCM is also known to be present in a significant number of men with reduced fertility or reduced sperm count.

Defective Y chromosome

This can result in the person developing a female phenotype even though they possess an XY karyotype. This can result in both infertility and only partial sexual development.

An incomplete Y chromosome such as 45X, plus a fragment of Y, can result in incomplete genital differentiation, such that the infant may not have fully developed internal or external gonads. A full spectrum of variation can occur, especially if mosaicism is present. When the Y fragment is minimal and nonfunctional, the individual can develop phonetically female with features of Turner syndrome or mixed gonadal dysgenesis.

XXY

Main article: Klinefelter syndrome

Klinefelter syndrome (47, XXY) is not an aneuploidy of the Y chromosome, but a condition of having an extra X chromosome, which usually results in defective postnatal testicular function. The mechanism is not fully understood; it does not seem to be due to direct interference by the extra X with expression of Y genes.

XYY

Main article: XYY syndrome

47, XYY syndrome (simply known as XYY syndrome) is caused by the presence of a single extra copy of the Y chromosome in each of a male's cells. 47, XYY males have one X chromosome and two Y chromosomes, for a total of 47 chromosomes per cell. Researchers have found that an extra copy of the Y chromosome is associated with increased stature and an increased incidence of learning problems in some boys and men, but the effects are variable, often minimal, and the vast majority do not know their karyotype.

In 1965 and 1966, Patricia Jacobs and colleagues published a chromosome survey of 315 male patients at Scotland's only special security hospital for the developmentally disabled, finding a higher than expected number of patients to have an extra Y chromosome. The authors of this study wondered "whether an extra Y chromosome predisposes its carriers to unusually aggressive behaviour", and this conjecture "framed the next fifteen years of research on the human Y chromosome".

Through studies over the next decade, this conjecture was shown to be incorrect: the elevated crime rate of XYY males is due to lower median intelligence and not increased aggression, and increased height was the only characteristic that could be reliably associated with XYY males. The "criminal karyotype" concept is therefore inaccurate.

There are also XXXY syndrome and XXXXY syndrome.

Rare

The following Y-chromosome-linked diseases are rare, but notable because of their elucidation of the nature of the Y chromosome.

More than two Y chromosomes

Greater degrees of Y chromosome polysomy (having more than one extra copy of the Y chromosome in every cell, e.g., XYYY) are considerably rarer. The extra genetic material in these cases can lead to skeletal abnormalities, dental abnormalities, decreased IQ, delayed development, and respiratory issues, but the severity of these conditions is variable.

XX male syndrome

XX male syndrome occurs due to a genetic recombination in the formation of the male gametes, causing the SRY portion of the Y chromosome to move to the X chromosome. When such an X chromosome is present in a zygote, male gonads develop because of the SRY gene.

Genetic genealogy

Main articles: Human Y-chromosome DNA haplogroup and Y-chromosomal Adam

In human genetic genealogy (the application of genetics to traditional genealogy), use of the information contained in the Y chromosome is of particular interest because, unlike other chromosomes, the Y chromosome is passed exclusively from father to son, on the patrilineal line. Mitochondrial DNA, maternally inherited by both sons and daughters, is used in an analogous way to trace the matrilineal line.

Brain function

Research is currently investigating whether male-pattern neural development is a direct consequence of Y-chromosome-related gene expression or an indirect result of Y-chromosome-related androgenic hormone production.

Microchimerism

In 1974, male chromosomes were discovered in fetal cells in the blood circulation of women.

In 1996, it was found that male fetal progenitor cells could persist postpartum in the maternal bloodstream for as long as 27 years.

A 2004 study at the Fred Hutchinson Cancer Research Center, Seattle, investigated the origin of male chromosomes found in the peripheral blood of women who had not had male progeny. A total of 120 subjects (women who had never had sons) were investigated, and it was found that 21% of them had male DNA in their peripheral blood. The subjects were categorised into four groups based on their case histories:

• Group A (8%) had only female progeny.
• Patients in Group B (22%) had a history of one or more miscarriages.
• Patients Group C (57%) had their pregnancies medically terminated.
• Group D (10%) had never been pregnant before.

The study noted that 10% of the women had never been pregnant before, raising the question of where the Y chromosomes in their blood could have come from. The study suggests that possible reasons for the occurrence of male chromosome microchimerism could be one of the following:

• miscarriages,
• pregnancies,
• vanished male twin,
• possibly from sexual intercourse.

A 2012 study at the same institute has detected cells with the Y chromosome in multiple areas of the brains of deceased women.