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Friday, August 17, 2018

Utopia

From Wikipedia, the free encyclopedia

Nowa Huta in Kraków, Poland, serves as an unfinished example of a Utopian ideal city.

A utopia (/jˈtpiə/ yoo-TOH-pee-ə) is an imagined community or society that possesses highly desirable or nearly perfect qualities for its citizens. The opposite of a utopia is a dystopia. One could also say that utopia is a perfect "place" that has been designed so there are no problems.

Utopian ideals often place emphasis on egalitarian principles of equality in economics, government and justice, though by no means exclusively, with the method and structure of proposed implementation varying based on ideology.[2][3] According to Lyman Tower Sargent "there are socialist, capitalist, monarchical, democratic, anarchist, ecological, feminist, patriarchal, egalitarian, hierarchical, racist, left-wing, right-wing, reformist, Naturists/Nude Christians, free love, nuclear family, extended family, gay, lesbian, and many more utopias [...] Utopianism, many argue, is essential for the improvement of the human condition. But if used wrongly, it becomes dangerous. Utopia has an inherent contradictory nature here."[4] Sargent argues that utopia's nature is inherently contradictory, because societies are not homogenous, and have desires which conflict and therefore cannot simultaneously be satisfied. If any two desires cannot be simultaneously satisfied, true utopia cannot be attained because in utopia all desires are satisfied.

The term utopia was coined from Greek by Sir Thomas More for his 1516 book Utopia, describing a fictional island society in the south Atlantic Ocean off the coast of South America.

The word comes from Greek: οὐ ("not") and τόπος ("place") and means "no-place", and strictly describes any non-existent society 'described in considerable detail'. However, in standard usage, the word's meaning has narrowed and now usually describes a non-existent society that is intended to be viewed as considerably better than contemporary society.[5] Eutopia, derived from Greek εὖ ("good" or "well") and τόπος ("place"), means "good place", and is strictly speaking the correct term to describe a positive utopia. In English, eutopia and utopia are homophonous, which may have given rise to the change in meaning.[5][6]

Varieties

Left panel (The Earthly Paradise – Garden of Eden) from Hieronymus Bosch's The Garden of Earthly Delights.

Chronologically, the first recorded Utopian proposal is Plato's Republic.[7] Part conversation, part fictional depiction, and part policy proposal, Republic would categorize citizens into a rigid class structure of "golden," "silver," "bronze" and "iron" socioeconomic classes. The golden citizens are trained in a rigorous 50-year-long educational program to be benign oligarchs, the "philosopher-kings." Plato stressed this structure many times in statements, and in his published works, such as the Republic. The wisdom of these rulers will supposedly eliminate poverty and deprivation through fairly distributed resources, though the details on how to do this are unclear. The educational program for the rulers is the central notion of the proposal. It has few laws, no lawyers and rarely sends its citizens to war, but hires mercenaries from among its war-prone neighbors. These mercenaries were deliberately sent into dangerous situations in the hope that the more warlike populations of all surrounding countries will be weeded out, leaving peaceful peoples.

During the 16th century, Thomas More's book Utopia proposed an ideal society of the same name.[8] Readers, including Utopian socialists, have chosen to accept this imaginary society as the realistic blueprint for a working nation, while others have postulated that Thomas More intended nothing of the sort.[9] It is believed that More's Utopia functions only on the level of a satire, a work intended to reveal more about the England of his time than about an idealistic society.[10] This interpretation is bolstered by the title of the book and nation, and its apparent confusion between the Greek for "no place" and "good place": "utopia" is a compound of the syllable ou-, meaning "no", and topos, meaning place. But the homophonic prefix eu-, meaning "good," also resonates in the word, with the implication that the perfectly "good place" is really "no place."

Ecological

Ecological utopian society describes new ways in which society should relate to nature. These works perceive a widening gap between the modern Western way of living that destroys nature[11] and a more traditional way of living before industrialization[12]. Ecological utopias may advocate a society that is more sustainable. According to the Dutch philosopher Marius de Geus, ecological utopias could be inspirational sources for movements involving green politics.[13]

Economics

Particularly in the early 19th century, several utopian ideas arose, often in response to the belief that social disruption was created and caused by the development of commercialism and capitalism. These ideas are often grouped in a greater "utopian socialist" movement, due to their shared characteristics. A once common characteristic is an egalitarian distribution of goods, frequently with the total abolition of money. Citizens only do work which they enjoy and which is for the common good, leaving them with ample time for the cultivation of the arts and sciences. One classic example of such a utopia was Edward Bellamy's Looking Backward. Another socialist utopia is William Morris's News from Nowhere, written partially in response to the top-down (bureaucratic) nature of Bellamy's utopia, which Morris criticized. However, as the socialist movement developed, it moved away from utopianism; Marx in particular became a harsh critic of earlier socialism he described as utopian. (For more information, see the History of Socialism article.) In a materialist utopian society, the economy is perfect; there is no inflation, and only perfect social and financial equality exists.

In 1905, H.G. Wells published A Modern Utopia, which was widely read and admired and provoked much discussion. Also consider Eric Frank Russell's book The Great Explosion (1963) whose last section details an economic and social utopia. This forms the first mention of the idea of Local Exchange Trading Systems (LETS).

During the "Khrushchev Thaw" period,[14] the Soviet writer Ivan Efremov produced the science-fiction utopia Andromeda (1957) in which a major cultural thaw took place: humanity communicates with a galaxy-wide Great Circle and develops its technology and culture within a social framework characterized by vigorous competition between alternative philosophies.

The English political philosopher James Harrington, author of the utopian work The Commonwealth of Oceana, published in 1656, inspired English country party republicanism and was influential in the design of three American colonies. His theories ultimately contributed to the idealistic principles of the American Founders. The colonies of Carolina (founded in 1670), Pennsylvania (founded in 1681), and Georgia (founded in 1733) were the only three English colonies in America that were planned as utopian societies with an integrated physical, economic, and social design. At the heart of the plan for Georgia was a concept of “agrarian equality” in which land was allocated equally and additional land acquisition through purchase or inheritance was prohibited; the plan was an early step toward the yeoman republic later envisioned by Thomas Jefferson.

The communes of the 1960s in the United States were often an attempt to greatly improve the way humans live together in communities. The back-to-the-land movements and hippies inspired many to try to live in peace and harmony on farms, remote areas, and to set up new types of governance.[18] Communes like Kaliflower, which existed between 1967 and 1973, attempted to live outside of society's norms and create their own ideal communist based society.[19]

Intentional communities were organized and built all over the world with the hope of making a more perfect way of living together. While many of these new small communities failed, some are growing, such as the Twelve Tribes Communities that started in the United States. Since its start, it has now grown into many groups around the world.

Religious utopias

New Harmony, a Utopian attempt; depicted as proposed by Robert Owen.

Inter-religious utopias

The inter-religious utopia is similar to multiculturalism where real world cultures have successfully worked together to create a wider society based on shared values. A transparent ideology of God and religion used in inter-religious utopias is commonly stated by many people as their view of God manifesting within a community.[citation needed] In more extended theories, the formula goes up to the next level with different religious leaders setting aside their differences and accepting harmony, peace and understanding to unite all religions within one another. Other inter-religious utopias may go even further and describe a religion where humans become God or merge with a primal force that reigned before the birth of the universe. Religion and God could be used as a self-motivating factor for people to believe in and to raise themselves out of difficult situations.

Intra-religious utopias

In the United States and Europe, during the Second Great Awakening (ca. 1790–1840) and thereafter, many radical religious groups formed utopian societies in which faith could govern all aspects of members' lives. These utopian societies included the Shakers, who originated in England in the 18th century and arrived in America in 1774. A number of religious utopian societies from Europe came to the United States from the 18th century throughout the 19th century, including the Society of the Woman in the Wilderness (led by Johannes Kelpius (1667–1708)), the Ephrata Cloister (established in 1732), and the Harmony Society, among others. The Harmony Society was a Christian theosophy and pietist group founded in Iptingen, Germany, in 1785. Due to religious persecution by the Lutheran Church and the government in Württemberg,[20] the society moved to the United States on October 7, 1803, settled in Pennsylvania. On February 15, 1805, about 400 followers formally organized the Harmony Society, placing all their goods in common. The group lasted until 1905, making it one of the longest-running financially successful communes in American history. The Oneida Community, founded by John Humphrey Noyes in Oneida, New York, was a utopian religious commune that lasted from 1848 to 1881. Although this utopian experiment has become better known today for its manufacture of Oneida silverware, it was one of the longest-running communes in American history. The Amana Colonies were communal settlements in Iowa, started by radical German pietists, which lasted from 1855 to 1932. The Amana Corporation, manufacturer of refrigerators and household appliances, was originally started by the group. Other examples are Fountain Grove (founded in 1875), Riker's Holy City and other Californian utopian colonies between 1855 and 1955 (Hine), as well as Sointula[21] in British Columbia, Canada. The Amish and Hutterites can also be considered an attempt towards religious utopia. A wide variety of intentional communities with some type of faith-based ideas have also started across the world.

A new heaven and new earth[Rev 21:1], Mortier's Bible, Phillip Medhurst Collection

The Book of Revelation in the Christian Bible depicts an eschatological time with the defeat of Satan and of evil. The main difference compared to the Old Testament promises is that such a defeat also has an ontological value (Rev 21:1;4: "Then I saw 'a new heaven and a new earth,' for the first heaven and the first earth had passed away, and there was no longer any sea...'He will wipe every tear from their eyes. There will be no more death' or mourning or crying or pain, for the old order of things has passed away") and no longer just gnosiological (Isaiah 65:17: "See, I will create/new heavens and a new earth./The former things will not be remembered,/nor will they come to mind"). Narrow interpretation of the text depicts Heaven on Earth, or a Heaven brought to Earth without sin. Daily and mundane details of this new Earth, where God and Jesus rule, remain unclear, although it is implied to be similar to the biblical Garden of Eden. Some theological philosophers believe that heaven will not be a physical realm, but instead an incorporeal place for souls.[24]

Science and technology

Utopian flying machines, France, 1890-1900 (chromolithograph trading card).

Though Francis Bacon's New Atlantis is imbued with a scientific spirit, scientific and technological utopias tend to be based in the future, when it is believed that advanced science and technology will allow utopian living standards; for example, the absence of death and suffering; changes in human nature and the human condition. Technology has affected the way humans have lived to such an extent that normal functions, like sleep, eating or even reproduction, have been replaced by artificial means. Other examples include a society where humans have struck a balance with technology and it is merely used to enhance the human living condition (e.g. Star Trek). In place of the static perfection of a utopia, libertarian transhumanists envision an "extropia", an open, evolving society allowing individuals and voluntary groupings to form the institutions and social forms they prefer.

Mariah Utsawa presented a theoretical basis for technological utopianism and set out to develop a variety of technologies ranging from maps to designs for cars and houses which might lead to the development of such a utopia.

One notable example of a technological and libertarian socialist utopia is Scottish author Iain Banks' Culture.

Opposing this optimism is the prediction that advanced science and technology will, through deliberate misuse or accident, cause environmental damage or even humanity's extinction. Critics, such as Jacques Ellul and Timothy Mitchell advocate precautions against the premature embrace of new technologies. Both raise questions about changing responsibility and freedom brought by division of labour. Authors such as John Zerzan and Derrick Jensen consider that modern technology is progressively depriving humans of their autonomy, and advocate the collapse of the industrial civilization, in favor of small-scale organization, as a necessary path to avoid the threat of technology on human freedom and sustainability.

There are many examples of techno-dystopias portrayed in mainstream culture, such as the classics Brave New World and Nineteen Eighty-Four, often published as "1984", which have explored some of these topics.

Feminism

Utopias have been used to explore the ramifications of genders being either a societal construct, or a biologically "hard-wired" imperative, or some mix of the two.[25] Socialist and economic utopias have tended to take the "woman question" seriously, and often to offer some form of equality between the sexes as part and parcel of their vision, whether this be by addressing misogyny, reorganizing society along separatist lines, creating a certain kind of androgynous equality that ignores gender, or in some other manner. For example, Edward Bellamy's Looking Backward (1887) responded, progressively for his day, to the contemporary women's suffrage and women's rights movements. Bellamy supported these movements by incorporating the equality of women and men into his utopian world's structure, albeit by consigning women to a separate sphere of light industrial activity (due to women's lesser physical strength), and making various exceptions for them in order to make room for (and to praise) motherhood. One of the earlier feminist utopias that imagines complete separatism is Charlotte Perkins Gilman's Herland (1915).

In science fiction and technological speculation, gender can be challenged on the biological as well as the social level. Marge Piercy's Woman on the Edge of Time portrays equality between the genders and complete equality in sexuality (regardless of the gender of the lovers). Birth-giving, often felt as the divider that cannot be avoided in discussions of women's rights and roles, has been shifted onto elaborate biological machinery that functions to offer an enriched embryonic experience, When a child is born, it spends most of its time in the children's ward with peers. Three "mothers" per child are the norm, and they are chosen in a gender neutral way (men as well as women may become "mothers") on the basis of their experience and ability. Technological advances also make possible the freeing of women from childbearing in Shulamith Firestone's The Dialectic of Sex. The fictional aliens in Mary Gentle's Golden Witchbreed start out as gender-neutral children and do not develop into men and women until puberty, and gender has no bearing on social roles. In contrast, Doris Lessing's The Marriages Between Zones Three, Four and Five (1980) suggests that men's and women's values are inherent to the sexes and cannot be changed, making a compromise between them essential. In My Own Utopia (1961) by Elizabeth Mann Borghese, gender exists but is dependent upon age rather than sex — genderless children mature into women, some of whom eventually become men.[25] "William Marston's Wonder Woman comics of the 1940s featured Paradise Island, also known as Themyscira, a matriarchal all-female community of peace, loving submission, bondage, and giant space kangaroos."[26]

Utopian single-gender worlds or single-sex societies have long been one of the primary ways to explore implications of gender and gender-differences.[27] In speculative fiction, female-only worlds have been imagined to come about by the action of disease that wipes out men, along with the development of technological or mystical method that allow female parthenogenic reproduction. Charlotte Perkins Gilman's 1915 novel approaches this type of separate society. Many feminist utopias pondering separatism were written in the 1970s, as a response to the Lesbian separatist movement;[27][28][29] examples include Joanna Russ's The Female Man and Suzy McKee Charnas's Walk to the End of the World and Motherlines.[29] Utopias imagined by male authors have often included equality between sexes, rather than separation, although as noted Bellamy's strategy includes a certain amount of "separate but equal".[30] The use of female-only worlds allows the exploration of female independence and freedom from patriarchy. The societies may be lesbian, such as Daughters of a Coral Dawn by Katherine V. Forrest, or not, and may not be sexual at all — a famous early sexless example being Herland (1915) by Charlotte Perkins Gilman.[28] Charlene Ball writes in Women's Studies Encyclopedia that use of speculative fiction to explore gender roles in future societies has been more common in the United States compared to Europe and elsewhere,[25] although such efforts as Gerd Brantenberg's Egalia's Daughters and Christa Wolf's portrayal of the land of Colchis in her Medea: Voices are certainly as influential and famous as any of the American feminist utopias.

Utopianism


In many cultures, societies, and religions, there is some myth or memory of a distant past when humankind lived in a primitive and simple state, but at the same time one of perfect happiness and fulfillment. In those days, the various myths tell us, there was an instinctive harmony between humanity and nature. People's needs were few and their desires limited. Both were easily satisfied by the abundance provided by nature. Accordingly, there were no motives whatsoever for war or oppression. Nor was there any need for hard and painful work. Humans were simple and pious, and felt themselves close to their God or gods. According to one anthropological theory, hunter-gatherers were the original affluent society.

These mythical or religious archetypes are inscribed in many cultures, and resurge with special vitality when people are in difficult and critical times. However, in utopias, the projection of the myth does not take place towards the remote past, but either towards the future or towards distant and fictional places, imagining that at some time in the future, at some point in space, or beyond death, there must exist the possibility of living happily.

These myths of the earliest stage of humankind have been referred to by various cultures, societies, and religions:

Golden Age

The Greek poet Hesiod, around the 8th century BC, in his compilation of the mythological tradition (the poem Works and Days), explained that, prior to the present era, there were four other progressively more perfect ones, the oldest of which was the Golden Age.

Plutarch, the Greek historian and biographer of the 1st century, dealt with the blissful and mythic past of the humanity.

Arcadia

From Sir Philip Sidney's prose romance The Old Arcadia (1580), originally a region in the Peloponnesus, Arcadia became a synonym for any rural area that serves as a pastoral setting, a locus amoenus ("delightful place").

The Biblical Garden of Eden

The Biblical Garden of Eden as depicted in the Old Testament Bible's Book of Genesis 2 (Authorized Version of 1611):
"And the Lord God planted a garden eastward in Eden; and there he put the man whom he had formed. And out of the ground made the Lord God to grow every tree that is pleasant to the sight, and good for food; the tree of life also in the midst of the garden, and the tree of knowledge of good and evil. [...]


And the Lord God took the man, and put him into the garden of Eden to dress it and to keep it. And the Lord God commanded the man, saying, Of every tree of the garden thou mayest freely eat: but of the tree of the knowledge of good and evil, thou shalt not eat of it: for in the day that thou eatest thereof thou shalt surely die. [...]


And the Lord God said, It is not good that the man should be alone; [...] And the Lord God caused a deep sleep to fall upon Adam, and he slept: and he took one of his ribs, and closed up the flesh instead thereof; and the rib, which the Lord God had taken from man, made he a woman, and brought her unto the man."
According to the exegesis that the biblical theologian Herbert Haag proposes in the book Is original sin in Scripture?,[31] published soon after the Second Vatican Council, Genesis 2:25 would indicate that Adam and Eve were created from the beginning naked of the divine grace, an originary grace that, then, they would never have had and even less would have lost due to the subsequent events narrated. On the other hand, while supporting a continuity in the Bible about the absence of preternatural gifts (Latin: dona praeternaturalia)[32] with regard to the ophitic event, Haag never makes any reference to the discontinuity of the loss of access to the tree of life.

The Land of Cockaigne

The Land of Cockaigne (also Cockaygne, Cokaygne), was an imaginary land of idleness and luxury, famous in medieval stories, and the subject of several poems, one of which, an early translation of a 13th-century French work, is given in George Ellis' Specimens of Early English Poets. In this, "the houses were made of barley sugar and cakes, the streets were paved with pastry, and the shops supplied goods for nothing." London has been so called (see Cockney), but Boileau applies the same to Paris.[33]

The Peach Blossom Spring

The Peach Blossom Spring, a prose written by the Chinese writer Tao Yuanming (c. 220 - 589 CE), describes a utopian place.[34][35] The narrative goes that a fisherman from Wuling sailed upstream a river and came across a beautiful blossoming peach grove and lush green fields covered with blossom petals.[36] Entranced by the beauty, he continued upstream.[36] When he reached the end of the river, he stumbled onto a small grotto.[36] Though narrow at first, he was able to squeeze through the passage and discovered an ethereal utopia, where the people led an ideal existence in harmony with nature.[37] He saw a vast expanse of fertile lands, clear ponds, mulberry trees, bamboo groves, and the like with a community of people of all ages and houses in neat rows.[37] The people explained that their ancestors escaped to this place during the civil unrest of the Qin dynasty and they themselves had not left since or had contact with anyone from the outside.[38] They had not even heard of the later dynasties of bygone times or the then-current Jin dynasty.[38] In the story, the community was secluded and unaffected by the troubles of the outside world.[38] The sense of timelessness was also predominant in the story as a perfect utopian community remains unchanged, that is, it had no decline nor the need to improve.[38] Eventually, the Chinese term Peach Blossom Spring (桃花源) came to be synonymous for the concept of utopia.[39]

Datong

Datong is a traditional Chinese Utopia. The main description of it is found in the Chinese Classic of Rites, in the chapter called "Li Yun" (禮運). Later, Datong and its ideal of 'The World Belongs to Everyone/The World is Held in Common' 'Tianxia weigong/天下为公' 'influenced modern Chinese reformers and revolutionaries, such as Kang Youwei.

Schlaraffenland

Schlaraffenland is an analogous German tradition.

All these myths also express some hope that the idyllic state of affairs they describe is not irretrievably and irrevocably lost to mankind, that it can be regained in some way or other.

One way might be a quest for an "earthly paradise"—a place like Shangri-La, hidden in the Tibetan mountains and described by James Hilton in his utopian novel Lost Horizon (1933). Christopher Columbus followed directly in this tradition in his belief that he had found the Garden of Eden when, towards the end of the 15th century, he first encountered the New World and its indigenous inhabitants.

Utopian and dystopian fiction

From Wikipedia, the free encyclopedia

The utopia and its opposite, the dystopia, are genres of speculative fiction that explore social and political structures. Utopian fiction portrays a setting that agrees with the author's ethos, having various attributes of another reality intended to appeal to readers. Dystopian (or dystopic) fiction (sometimes combined with, but distinct from apocalyptic literature) is the opposite: the portrayal of a setting that completely disagrees with the author's ethos. Many novels combine both, often as a metaphor for the different directions humanity can take, depending on its choices, ending up with one of two possible futures. Both utopias and dystopias are commonly found in science fiction and other speculative fiction genres, and arguably are by definition a type of speculative fiction.

More than 400 utopian works were published prior to the year 1900 in the English language alone, with more than a thousand others during the twentieth century.[2]

Subgenres

Utopian fiction

The word utopia was first used in direct context by Sir Thomas More in his 1516 work Utopia. The word utopia resembles both the Greek words "no place", "outopos", and "good place", "eutopos". In his book, which was written in Latin, More sets out a vision of an ideal society. As the title suggests, the work presents an ambiguous and ironic projection of the ideal state. The whimsical nature of the text can be confirmed by the narrator of Utopia's second book, Raphael Hythloday. The Greek root of Hythloday suggests an 'expert in nonsense'. An earlier example of a Utopian work from classical antiquity is Plato's The Republic, in which he outlines what he sees as the ideal society and its political system. Later examples can be seen in Samuel Johnson's The History of Rasselas, Prince of Abissinia and Samuel Butler's Erewhon, which uses an anagram of "nowhere" as its title. This, like much of the utopian literature, can be seen as satire; Butler inverts illness and crime, with punishment for the former and treatment for the latter.

Dystopian fiction

A dystopia is a society characterized by a focus on that which is contrary to the author's ethos, such as mass poverty, public mistrust and suspicion, a police state or oppression.[1] Most authors of dystopian fiction explore at least one reason why things are that way, often as an analogy for similar issues in the real world. Dystopian literature is used to "provide fresh perspectives on problematic social and political practices that might otherwise be taken for granted or considered natural and inevitable".[3]

Some dystopias claim to be utopias. Samuel Butler's Erewhon can be seen as a dystopia because of the way sick people are punished as criminals while thieves are "cured" in hospitals, which the inhabitants of Erewhon see as natural and right, i.e. utopian (as mocked in Voltaire's Candide).

Dystopias usually extrapolate elements of contemporary society and thus can be read as political warnings. The 1921 novel We by Yevgeny Zamyatin predicts a post-apocalyptic future in which society is entirely based on logic and modeled after mechanical systems. George Orwell cited We as an influence on his Nineteen Eighty-Four, a novel about Oceania, a state at perpetual war, its population controlled through propaganda. Big Brother and the daily Two Minutes Hate set the tone for an all-pervasive self-censorship. Aldous Huxley's novel Brave New World started as a parody of utopian fiction, and projected into the year 2540 industrial and social changes he perceived in 1931, leading to industrial success by a coercively persuaded population divided into five castes; the World State kills everyone 60 years old or older.

Anthony Burgess's 1962 novel A Clockwork Orange is set in a future England that has a subculture of extreme youth violence, and details the protagonist's experiences with the state intent on changing his character at their whim. Margaret Atwood's The Handmaid's Tale describes a future United States governed by a totalitarian theocracy, where women have no rights. Examples of young adult dystopian fiction include The Hunger Games by Suzanne Collins, The House of the Scorpion by Nancy Farmer, Divergent, Insurgent by Veronica Roth, The Maze Runner by James Dashner, and Delirium by Lauren Oliver. Video games often include dystopias as well; notable examples include the Fallout series, BioShock, and the later games of the Half-Life series.

History of dystopian fiction

The history of dystopian literature can be traced back to the 19th century. Most experts in literature agree that the origins of dystopian fiction are rooted strongly in utopian fiction. Dystopian fiction emerged as a response to utopian fiction, a great example of which is Edward Bellamy’s 1888 best-selling novel Looking Backward, about a socialist utopia set in 2000.[4] Dystopian fiction usually has satirical elements interwoven in it. It is based on imagined scenarios rather than real ones, but they are incorporated into storylines that readers can relate to the present.

Coming to the historical background of dystopian fiction, it is almost impossible to talk about it without referring to the historical background of utopian fiction. Utopian texts often ‘made promises’, while dystopian texts ‘issued warnings' [5] Utopian writers based their writing on perfect patterns and organized societies; however, at the outset of the 19th century, writers began to recognise the impossibility of such utopic scenarios and an anti-utopic wave gripped literature. (insert in-text citation). The beginning of technological dystopian fiction can be traced back to E.M. Forster’s (1879-1970) "The Machine Stops". Forster is widely accepted as the 'pioneer of dystopian literature.'

After Forster's "The Machine Stops", more dystopian literature emerged, such as We and Brave New World. M Keith Booker states that these fictions are “the great defining texts of the genre of dystopian fiction, both in [the] vividness of their engagement with real-world social and political issues, and in the scope of their critique of the societies on which they focus.” [6]

Another very important figure in Dystopian Literature is H.G. Wells, whose work The Time Machine (1895) is also universally accepted[by whom?] as one of the best prototypes for dystopian literature. Post World War II, even more dystopian fiction was produced. These works of fiction were interwoven with political commentary: the end of World War II brought about fears of an impending Third World War and a consequent apocalypse, which began to be reflected in these works. There is a fine line between apocalyptic literature and dystopian literature, however the difference is mostly negligible. The most striking feature of Dystopian fiction is its dynamic and ever-changing character. This is primarily because different social and political situations around the world influenced different dystopic writers. This is why the entire body of dystopian fiction is incredibly diverse and heterogenous. Works of this genre spanning different times and different years are different as authors carefully observed what was going on around them and then wrote on the issues that concerned them deeply, often putting a different spin on things. Today, Dystopian fiction draws not only on several topics that older dystopic works talked about such as totalitarian governments and anarchism, but also on topics that are widely talked about in today’s society such as pollution, global warming, climate change, health, the economy and technology. Dystopian fiction has also found its way to the young adult (YA) genre of literature, as opposed to the more adult audience that it was originally meant for.

Combinations

Jonathan Swift's Gulliver's Travels is sometimes linked with utopian (and dystopian) literature, because it shares the general preoccupation with ideas of the good (and bad) society. Of the countries Lemuel Gulliver visits, Brobdingnag and Country of the Houyhnhnms approach a utopia; the others have significant dystopian aspects.

Many works combine elements of both utopias and dystopias. Typically, an observer from our world will journey to another place or time and see one society the author considers ideal, and another representing the worst possible outcome. The point is usually that the choices we make now may lead to a better or worse potential future world. Ursula K. Le Guin's Always Coming Home fulfils this model, as does Marge Piercy's Woman on the Edge of Time. In Starhawk's The Fifth Sacred Thing there is no time-travelling observer, but her ideal society is invaded by a neighbouring power embodying evil repression. In Aldous Huxley's Island, in many ways a counterpoint to his better-known Brave New World, the fusion of the best parts of Buddhist philosophy and Western technology is threatened by the "invasion" of oil companies. As another example, in the "Unwanteds" series by Lisa McMann, a paradox occurs where the outcasts from a complete dystopia are treated to absolute utopia, and therefore believe that those who were privileged in said dystopia were actually the unlucky ones.

In another literary model, the imagined society journeys between elements of utopia and dystopia over the course of the novel or film. At the beginning of The Giver by Lois Lowry, the world is described as a utopia, but as the book progresses, the world's dystopian aspects are revealed.

Ecotopian fiction

In ecotopian fiction, the author posits either a utopian or dystopian world revolving around environmental conservation or destruction. Danny Bloom coined the term "cli fi" in 2006, with a Twitter boost from Margaret Atwood in 2011, to cover climate change-related fiction,[7] but the theme has existed for decades. Novels dealing with overpopulation, such as Harry Harrison's Make Room! Make Room! (made into movie Soylent Green), were popular in the 1970s, reflecting the popular concern with the effects of overpopulation on the environment. The novel Nature's End by Whitley Strieber and James Kunetka (1986) posits a future in which overpopulation, pollution, climate change, and resulting superstorms, have led to a popular mass-suicide political movement. Some other examples of ecological dystopias are depictions of Earth in the films Wall-E and Avatar.

While eco-dystopias are more common, a small number of works depicting what might be called eco-utopia, or eco-utopian trends, have also been influential. These include Ernest Callenbach's Ecotopia, an important 20th century example of this genre. Kim Stanley Robinson has written a number of books dealing with environmental themes, including the Mars trilogy. Most notably, however, his Three Californias Trilogy contrasted an eco-dystopia with an eco-utopia, and a sort of middling-future. Robinson has also edited an anthology of short ecotopian fiction, called Future Primitive: The New Ecotopias.

There are a few dystopias that have an "anti-ecological" theme. These are often characterized by a government that is overprotective of nature or a society that has lost most modern technology and struggles for survival. A good example of this is the novel Riddley Walker.

Feminist utopias

Another subgenre is feminist utopias and the overlapping category of feminist science fiction. Writer Sally Miller Gearhart calls this sort of fiction political: it contrasts the present world with an idealized society, criticizes contemporary values and conditions, sees men or masculine systems as the major cause of social and political problems (e.g. war), and presents women as equal to men, having ownership over their reproductive functions.

Utopias have explored the ramification of gender being either a societal construct or a hard-wired imperative.[8] In Mary Gentle's Golden Witchbreed, gender is not chosen until maturity, and gender has no bearing on social roles. In contrast, Doris Lessing's The Marriages Between Zones Three, Four and Five (1980) suggests that men's and women's values are inherent to the sexes and cannot be changed, making a compromise between them essential. In My Own Utopia (1961) by Elisabeth Mann Borgese, gender exists but is dependent upon age rather than sex — genderless children mature into women, some of whom eventually become men.[8] Marge Piercy's novel Woman on the Edge of Time keeps human biology, but removes pregnancy and childbirth from the gender equation by resorting to assisted reproductive technology while allowing both women and men the nurturing experience of breastfeeding.

Utopic single-gender worlds or single-sex societies have long been one of the primary ways to explore implications of gender and gender-differences.[9] One solution to gender oppression or social issues in feminist utopian fiction is to remove men, either showing isolated all-female societies as in Charlotte Perkins Gilman's Herland, or societies where men have died out or been replaced, as in Joanna Russ's A Few Things I Know About Whileaway, where "the poisonous binary gender" has died off. In speculative fiction, female-only worlds have been imagined to come about by the action of disease that wipes out men, along with the development of technological or mystical method that allow female parthenogenetic reproduction. The resulting society is often shown to be utopian by feminist writers. Many influential feminist utopias of this sort were written in the 1970s; the most often studied examples include Joanna Russ's The Female Man, Suzy McKee Charnas's The Holdfast Chronicles.[11] Such worlds have been portrayed most often by lesbian or feminist authors; their use of female-only worlds allows the exploration of female independence and freedom from patriarchy. The societies may not necessarily be lesbian, or sexual at all — Herland (1915) by Charlotte Perkins Gilman is a famous early example of a sexless society.[10] Charlene Ball writes in Women's Studies Encyclopedia that use of speculative fiction to explore gender roles has been more common in the United States than in Europe and elsewhere.[8]

Utopias imagined by male authors have generally included equality between sexes, rather than separation.[12]

Feminist dystopias have become prevalent in young adult fiction, or YA, in recent years, focusing on the relationship between gender identity and the teenager. For instance, the Birthmarked trilogy by Caragh M. O'Brien focuses on a teenage midwife in a future post-apocalyptic world while the second novel in the series places the teenage heroine Gaia in a matriarchy.

Cultural impact

Étienne Cabet's work Travels in Icaria caused a group of followers to leave France in 1848 and travel to the United States to start a series of utopian settlements in Texas, Illinois, Iowa, California, and elsewhere. These groups lived in communal settings and lasted until 1898.

Central dogma of molecular biology

From Wikipedia, the free encyclopedia

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA and RNA makes protein," although this is not its original meaning. It was first stated by Francis Crick in 1958:


and re-stated in a Nature paper published in 1970:[3]

Information flow in biological systems
 

A second version of the central dogma is popular but incorrect. This is the simplistic DNA → RNA → protein pathway published by James Watson in the first edition of The Molecular Biology of the Gene (1965). Watson's version differs from Crick's because Watson describes the two-step (DNA → RNA and RNA → protein) pathway as the central dogma.[4] While the dogma, as originally stated by Crick, remains valid today, Watson's version does not.

The dogma is a framework for understanding the transfer of sequence information between information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3=9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: three general transfers (believed to occur normally in most cells), three special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and three unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation). The special transfers describe: RNA being copied from RNA (RNA replication), DNA being synthesised using an RNA template (reverse transcription), and proteins being synthesised directly from a DNA template without the use of mRNA. The unknown transfers describe: a protein being copied from a protein, synthesis of RNA using the primary structure of a protein as a template, and DNA synthesis using the primary structure of a protein as a template - these are not thought to naturally occur.[3]

Biological sequence information

The biopolymers that comprise DNA, RNA and (poly)peptides are linear polymers (i.e.: each monomer is connected to at most two other monomers). The sequence of their monomers effectively encodes information. The transfers of information described by the central dogma ideally are faithful, deterministic transfers, wherein one biopolymer's sequence is used as a template for the construction of another biopolymer with a sequence that is entirely dependent on the original biopolymer's sequence.

General transfers of biological sequential information

Cdmb.svg
Table of the three classes of information transfer suggested by the dogma
General Special Unknown
DNA → DNA RNA → DNA protein → DNA
DNA → RNA RNA → RNA protein → RNA
RNA → protein DNA → protein protein → protein

DNA replications

In the sense that DNA replication must occur if genetic material is to be provided for the progeny of any cell, whether somatic or reproductive, the copying from DNA to DNA arguably is the fundamental step in the central dogma. A complex group of proteins called the replisome performs the replication of the information from the parent strand to the complementary daughter strand.[5]
The replisome comprises:
This process typically takes place during S phase of the cell cycle.

Transcription

Central Dogma of Molecular Biochemistry with Enzymes.jpg

Transcription is the process by which the information contained in a section of DNA is replicated in the form of a newly assembled piece of messenger RNA (mRNA). Enzymes facilitating the process include RNA polymerase and transcription factors. In eukaryotic cells the primary transcript is pre-mRNA. Pre-mRNA must be processed for translation to proceed. Processing includes the addition of a 5' cap and a poly-A tail to the pre-mRNA chain, followed by splicing. Alternative splicing occurs when appropriate, increasing the diversity of the proteins that any single mRNA can produce. The product of the entire transcription process (that began with the production of the pre-mRNA chain) is a mature mRNA chain.

Translation

The mature mRNA finds its way to a ribosome, where it gets translated. In prokaryotic cells, which have no nuclear compartment, the processes of transcription and translation may be linked together without clear separation. In eukaryotic cells, the site of transcription (the cell nucleus) is usually separated from the site of translation (the cytoplasm), so the mRNA must be transported out of the nucleus into the cytoplasm, where it can be bound by ribosomes. The ribosome reads the mRNA triplet codons, usually beginning with an AUG (adenineuracilguanine), or initiator methionine codon downstream of the ribosome binding site. Complexes of initiation factors and elongation factors bring aminoacylated transfer RNAs (tRNAs) into the ribosome-mRNA complex, matching the codon in the mRNA to the anti-codon on the tRNA. Each tRNA bears the appropriate amino acid residue to add to the polypeptide chain being synthesised. As the amino acids get linked into the growing peptide chain, the chain begins folding into the correct conformation. Translation ends with a stop codon which may be a UAA, UGA, or UAG triplet.
The mRNA does not contain all the information for specifying the nature of the mature protein. The nascent polypeptide chain released from the ribosome commonly requires additional processing before the final product emerges. For one thing, the correct folding process is complex and vitally important. For most proteins it requires other chaperone proteins to control the form of the product. Some proteins then excise internal segments from their own peptide chains, splicing the free ends that border the gap; in such processes the inside "discarded" sections are called inteins. Other proteins must be split into multiple sections without splicing. Some polypeptide chains need to be cross-linked, and others must be attached to cofactors such as haem (heme) before they become functional.

Special transfers of biological sequential information

Reverse transcription

Unusual flows of information highlighted in green


Reverse transcription is the transfer of information from RNA to DNA (the reverse of normal transcription). This is known to occur in the case of retroviruses, such as HIV, as well as in eukaryotes, in the case of retrotransposons and telomere synthesis. It is the process by which genetic information from RNA gets transcribed into new DNA.

RNA replication

RNA replication is the copying of one RNA to another. Many viruses replicate this way. The enzymes that copy RNA to new RNA, called RNA-dependent RNA polymerases, are also found in many eukaryotes where they are involved in RNA silencing.[6]

RNA editing, in which an RNA sequence is altered by a complex of proteins and a "guide RNA", could also be seen as an RNA-to-RNA transfer.

Direct translation from DNA to protein

Direct translation from DNA to protein has been demonstrated in a cell-free system (i.e. in a test tube), using extracts from E. coli that contained ribosomes, but not intact cells. These cell fragments could synthesize proteins from single-stranded DNA templates isolated from other organisms (e,g., mouse or toad), and neomycin was found to enhance this effect. However, it was unclear whether this mechanism of translation corresponded specifically to the genetic code.[7][8]

Transfers of information not explicitly covered in the theory

Posttranslational modification

After protein amino acid sequences have been translated from nucleic acid chains, they can be edited by appropriate enzymes. Although this is a form of protein affecting protein sequence, not explicitly covered by the central dogma, there are not many clear examples where the associated concepts of the two fields have much to do with each other.

Inteins

An intein is a "parasitic" segment of a protein that is able to excise itself from the chain of amino acids as they emerge from the ribosome and rejoin the remaining portions with a peptide bond in such a manner that the main protein "backbone" does not fall apart. This is a case of a protein changing its own primary sequence from the sequence originally encoded by the DNA of a gene. Additionally, most inteins contain a homing endonuclease or HEG domain which is capable of finding a copy of the parent gene that does not include the intein nucleotide sequence. On contact with the intein-free copy, the HEG domain initiates the DNA double-stranded break repair mechanism. This process causes the intein sequence to be copied from the original source gene to the intein-free gene. This is an example of protein directly editing DNA sequence, as well as increasing the sequence's heritable propagation.

Methylation

Variation in methylation states of DNA can alter gene expression levels significantly. Methylation variation usually occurs through the action of DNA methylases. When the change is heritable, it is considered epigenetic. When the change in information status is not heritable, it would be a somatic epitype. The effective information content has been changed by means of the actions of a protein or proteins on DNA, but the primary DNA sequence is not altered.

Prions

Prions are proteins of particular amino acid sequences in particular conformations. They propagate themselves in host cells by making conformational changes in other molecules of protein with the same amino acid sequence, but with a different conformation that is functionally important or detrimental to the organism. Once the protein has been transconformed to the prion folding it changes function. In turn it can convey information into new cells and reconfigure more functional molecules of that sequence into the alternate prion form. In some types of prion in fungi this change is continuous and direct; the information flow is Protein → Protein.
Some scientists such as Alain E. Bussard and Eugene Koonin have argued that prion-mediated inheritance violates the central dogma of molecular biology.[9][10] However, Rosalind Ridley in Molecular Pathology of the Prions (2001) has written that "The prion hypothesis is not heretical to the central dogma of molecular biology—that the information necessary to manufacture proteins is encoded in the nucleotide sequence of nucleic acid—because it does not claim that proteins replicate. Rather, it claims that there is a source of information within protein molecules that contributes to their biological function, and that this information can be passed on to other molecules."[11]

Natural genetic engineering

James A. Shapiro argues that a superset of these examples should be classified as natural genetic engineering and are sufficient to falsify the central dogma. While Shapiro has received a respectful hearing for his view, his critics have not been convinced that his reading of the central dogma is in line with what Crick intended.[12][13]

Use of the term "dogma"

In his autobiography, What Mad Pursuit, Crick wrote about his choice of the word dogma and some of the problems it caused him:
"I called this idea the central dogma, for two reasons, I suspect. I had already used the obvious word hypothesis in the sequence hypothesis, and in addition I wanted to suggest that this new assumption was more central and more powerful. ... As it turned out, the use of the word dogma caused almost more trouble than it was worth. Many years later Jacques Monod pointed out to me that I did not appear to understand the correct use of the word dogma, which is a belief that cannot be doubted. I did apprehend this in a vague sort of way but since I thought that all religious beliefs were without foundation, I used the word the way I myself thought about it, not as most of the world does, and simply applied it to a grand hypothesis that, however plausible, had little direct experimental support."
Similarly, Horace Freeland Judson records in The Eighth Day of Creation:[14]
"My mind was, that a dogma was an idea for which there was no reasonable evidence. You see?!" And Crick gave a roar of delight. "I just didn't know what dogma meant. And I could just as well have called it the 'Central Hypothesis,' or — you know. Which is what I meant to say. Dogma was just a catch phrase."

Comparison with the Weismann barrier

In August Weismann's germ plasm theory, the hereditary material, the germ plasm, is confined to the gonads. Somatic cells (of the body) develop afresh in each generation from the germ plasm. Whatever may happen to those cells does not affect the next generation.

The Weismann barrier, proposed by August Weismann in 1892, distinguishes between the "immortal" germ cell lineages (the germ plasm) which produce gametes and the "disposable" somatic cells. Hereditary information moves only from germline cells to somatic cells (that is, somatic mutations are not inherited). This, before the discovery of the role or structure of DNA, does not predict the central dogma, but does anticipate its gene-centric view of life, albeit in non-molecular terms.

Xenobiology

From Wikipedia, the free encyclopedia

Xenobiology (XB) is a subfield of synthetic biology, the study of synthesizing and manipulating biological devices and systems. Xenobiology derives from the Greek word xenos, which means "stranger, guest". Xenobiology describes a form of biology that is not (yet) familiar to science and is not found in nature. In practice it describes novel biological systems and biochemistries that differ from the canonical DNA-RNA-20 amino acid system (see central dogma of molecular biology). For example, instead of DNA or RNA, XB explores nucleic acid analogues, termed Xeno Nucleic Acid (XNA) as information carriers. It also focuses on an expanded genetic code and the incorporation of non-proteinogenic amino acids into proteins.

Difference between xeno-, exo-, and astro-biology

"Astro" means "star" and "exo" means "outside". Both exo- and astrobiology deal with the search for naturally evolved life in the Universe, mostly on other planets in the circumstellar habitable zone. (These are also occasionally referred to as xenobiology.[4]) Whereas astrobiologists are concerned with the detection and analysis of (hypothetically) existing life elsewhere in the universe, xenobiology attempts to design forms of life with a different biochemistry or different genetic code than on planet Earth.[4]

Aims of xenobiology

  • Xenobiology has the potential to reveal fundamental knowledge about biology and the origin of life. In order to better understand the origin of life, it is necessary to know why life evolved seemingly via an early RNA world to the DNA-RNA-protein system and its nearly universal genetic code.[5] Was it an evolutionary "accident" or were there constraints that ruled out other types of chemistries? By testing alternative biochemical "primordial soups", it is expected to better understand the principles that gave rise to life as we know it.
  • Xenobiology is an approach to develop industrial production system with novel capabilities by means of enhanced biopolymer engineering and pathogen resistance. The genetic code encodes in all organisms 20 canonical amino acids that are used for protein biosynthesis. In rare cases, special amino acids such as selenocysteine, pyrrolysine or formylmethionine, can be incorporated by the translational apparatus in to proteins of some organisms.[6] By using additional amino acids from among the over 700 known to biochemistry, the capabilities of proteins may be altered to give rise to more efficient catalytical or material functions. The EC-funded project Metacode,[7] for example, aims to incorporate metathesis (a useful catalytical function so far not known in living organisms) into bacterial cells. Another reason why XB could improve production processes lies in the possibility to reduce the risk of virus or bacteriophage contamination in cultivations since XB cells would no longer provide suitable host cells, rendering them more resistant (an approach called semantic containment)
  • Xenobiology offers the option to design a "genetic firewall", a novel biocontainment system, which may help to strengthen and diversify current bio-containment approaches.[4] One concern with traditional genetic engineering and biotechnology is horizontal gene transfer to the environment and possible risks to human health. One major idea in XB is to design alternative genetic codes and biochemistries so that horizontal gene transfer is no longer possible.[8] Additionally alternative biochemistry also allows for new synthetic auxotrophies. The idea is to create an orthogonal biological system that would be incompatible with natural genetic systems.[9]

Scientific approach

In xenobiology, the aim is to design and construct biological systems that differ from their natural counterparts on one or more fundamental levels. Ideally these new-to-nature organisms would be different in every possible biochemical aspect exhibiting a very different genetic code.[10] The long-term goal is to construct a cell that would store its genetic information not in DNA but in an alternative informational polymer consisting of xeno nucleic acids (XNA), different base pairs, using non-canonical amino acids and an altered genetic code. So far cells have been constructed that incorporate only one or two of these features.

Xeno nucleic acids (XNA)

Originally this research on alternative forms of DNA was driven by the question of how life evolved on earth and why RNA and DNA were selected by (chemical) evolution over other possible nucleic acid structures.[11] Two hypotheses for the selection of RNA and DNA as life's backbone are either they are favored under life on Earth's conditions, or they were coincidentally present in pre-life chemistry and continue to be used now.[12] Systematic experimental studies aiming at the diversification of the chemical structure of nucleic acids have resulted in completely novel informational biopolymers. So far a number of XNAs with new chemical backbones or leaving group of the DNA have been synthesized,[1][13][14][15] e.g.: hexose nucleic acid (HNA); threose nucleic acid (TNA),[16] glycol nucleic acid (GNA) cyclohexenyl nucleic acid (CeNA).[17] The incorporation of XNA in a plasmid, involving 3 HNA codons, has been accomplished already in 2003.[18] This XNA is used in vivo (E coli) as template for DNA synthesis. This study, using a binary (G/T) genetic cassette and two non-DNA bases (Hx/U), was extended to CeNA, while GNA seems to be too alien at this moment for the natural biological system to be used as template for DNA synthesis.[19] Extended bases using a natural DNA backbone could, likewise, be transliterated into natural DNA, although to a more limited extent.[20]

Aside being used as extensions to template DNA strands, XNA activity has been tested for use as genetic catalysts. Although proteins are the most common components of cellular enzymatic activity, nucleic acids are also used in the cell to catalyze reactions. A 2015 study found several different kinds of XNA, most notably FANA (2'-fluoroarabino nucleic acids), as well as HNA, CeNA and ANA (arabino nucleic acids) could be used to cleave RNA during post-transcriptional RNA processing acting as XNA enzymes, hence the name XNAzymes. FANA XNAzymes also showed the ability to ligate DNA, RNA and XNA substrates.[12] Although XNAzyme studies are still preliminary, this study was a step in the direction of searching for synthetic circuit components that are more efficient than those containing DNA and RNA counterparts that can regulate DNA, RNA, and their own, XNA, substrates.

Expanding the genetic alphabet

While XNAs have modified backbones, other experiments target the replacement or enlargement of the genetic alphabet of DNA with unnatural base pairs. For example, DNA has been designed that has - instead of the four standard bases A, T, G, and C - six bases A, T, G, C, and the two new ones P and Z (where Z stands for 6-Amino-5-nitro3-(l'-p-D-2'-deoxyribofuranosyl)-2(1H)-pyridone, and P stands for 2-Amino-8-(1-beta-D-2'-deoxyribofuranosyl)imidazo[1,2-a]-1,3,5-triazin-4 (8H)). In a systematic study, Leconte et al. tested the viability of 60 candidate bases (yielding potentially 3600 base pairs) for possible incorporation in the DNA.[24]

In 2002, Hirao et al. developed an unnatural base pair between 2-amino-8-(2-thienyl)purine (s) and pyridine-2-one (y) that functions in vitro in transcription and translation toward a genetic code for protein synthesis containing a non-standard amino acid.[25] In 2006, they created 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) as a third base pair for replication and transcription,[26] and afterward, Ds and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (Px) was discovered as a high fidelity pair in PCR amplification.[27][28] In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic alphabet expansion significantly augment DNA aptamer affinities to target proteins.[29]

In May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA, alongside the four naturally occurring nucleotides, and by including individual artificial nucleotides in the culture media, were able to passage the bacteria 24 times; they did not create mRNA or proteins able to use the artificial nucleotides.[30][31][32]

Novel polymerases

Neither the XNA nor the unnatural bases are recognized by natural polymerases. One of the major challenges is to find or create novel types of polymerases that will be able to replicate these new-to-nature constructs. In one case a modified variant of the HIV-reverse transcriptase was found to be able to PCR-amplify an oligonucleotide containing a third type base pair.[33][34] Pinheiro et al. (2012) demonstrated that the method of polymerase evolution and design successfully led to the storage and recovery of genetic information (of less than 100bp length) from six alternative genetic polymers based on simple nucleic acid architectures not found in nature Xeno nucleic acids.[35]

Genetic code engineering

One of the goals of xenobiology is to rewrite the genetic code. The most promising approach to change the code is the reassignment of seldomly used or even unused codons.[36] In an ideal scenario, the genetic code is expanded by one codon, thus having been liberated from its old function and fully reassigned to a non-canonical amino acid (ncAA) (“code expansion”). As these methods are laborious to implement, and some short cuts can be applied (“code engineering”), for example in bacteria that are auxotrophic for specific amino acids and at some point in the experiment are fed isostructural analogues instead of the canonical amino acids for which they are auxotrophic. In that situation, the canonical amino acid residues in native proteins are substituted with the ncAAs. Even the insertion of multiple different ncAAs into the same protein is possible.[37] Finally, the repertoire of 20 canonical amino acids can not only be expanded, but also reduced to 19.[38] By reassigning transfer RNA (tRNA)/aminoacyl-tRNA synthetase pairs the codon specificity can be changed. Cells endowed with such aminoacyl-[tRNA synthetases] are thus able to read [mRNA] sequences that make no sense to the existing gene expression machinery.[39] Altering the codon: tRNA synthetases pairs may lead to the in vivo incorporation of the non-canonical amino acids into proteins.[40][41] In the past reassigning codons was mainly done on a limited scale. In 2013, however, Farren Isaacs and George Church at Harvard University reported the replacement of all 321 TAG stop codons present in the genome of E. coli with synonymous TAA codons, thereby demonstrating that massive substitutions can be combined into higher-order strains without lethal effects.[42] Following the success of this genome wide codon replacement, the authors continued and achieved the reprogramming of 13 codons throughout the genome, directly affecting 42 essential genes.[43]

An even more radical change in the genetic code is the change of a triplet codon to a quadruplet and even pentaplet codon pioneered by Sisido in cell-free systems [44] and by Schultz in bacteria.[45] Finally, non-natural base pairs can be used to introduce novel amino acid in proteins.[46]

Directed evolution

The goal of substituting DNA by XNA may also be reached by another route, namely by engineering the environment instead of the genetic modules. This approach has been successfully demonstrated by Marlière and Mutzel with the production of an E. coli strain whose DNA is composed of standard A, C and G nucleotides but has the synthetic thymine analogue 5-chlorouracil instead of thymine (T) in the corresponding positions of the sequence. These cells are then dependent on externally supplied 5-chlorouracil for growth, but otherwise they look and behave as normal E. coli. These cells, however, are currently not yet fully auxotrophic for the Xeno-base since they are still growing on thymine when this is supplied to the medium.[47]

Biosafety

Xenobiological systems are designed to convey orthogonality to natural biological systems. A (still hypothetical) organism that uses XNA,[48] different base pairs and polymerases and has an altered genetic code will hardly be able to interact with natural forms of life on the genetic level. Thus, these xenobiological organisms represent a genetic enclave that cannot exchange information with natural cells.[49] Altering the genetic machinery of the cell leads to semantic containment. In analogy to information processing in IT, this safety concept is termed a “genetic firewall”.[4][50] The concept of the genetic firewall seems to overcome a number of limitations of previous safety systems.[51][52] A first experimental evidence of the theoretical concept of the genetic firewall was achieved in 2013 with the construction of a genomically recoded organism (GRO). In this GRO all known UAG stop codons in E.coli were replaced by UAA codons, which allowed for the deletion of release factor 1 and reassignment of UAG translation function. The GRO exhibited increased resistance to T7 bacteriophage, thus showing that alternative genetic codes do reduce genetic compatibility.[53] This GRO, however, is still very similar to its natural “parent” and cannot be regarded as a genetic firewall. The possibility of reassigning the function of large number of triplets opens the perspective to have strains that combine XNA, novel base pairs, new genetic codes, etc. that cannot exchange any information with the natural biological world. Regardless of changes leading to a semantic containment mechanism in new organisms, any novel biochemical systems still has to undergo a toxicological screening. XNA, novel proteins, etc. might represent novel toxins, or have an allergic potential that needs to be assessed.[54][55]

Governance and regulatory issues

Xenobiology might challenge the regulatory framework, as currently laws and directives deal with genetically modified organisms and do not directly mention chemically or genomically modified organisms. Taking into account that real xenobiology organisms are not expected in the next few years, policy makers do have some time at hand to prepare themselves for an upcoming governance challenge. Since 2012, the following groups have picked up the topic as a developing governance issue: policy advisers in the US,[56] four National Biosafety Boards in Europe,[57] the European Molecular Biology Organisation,[58] and the European Commission's Scientific Committee on Emerging and Newly Identified Health Risks (SCENIHR) in three opinions (Definition,[59] Risk assessment methodologies and safety aspects,[60] and Risks to the environment and biodiversity related to synthetic biology and research priorities in the field of synthetic biology [61]).

Ocean temperature

From Wikipedia, the free encyclopedia https://en.wikipedia.org/wiki/Ocean_temperature Graph showing ocean tempe...