更改

Autocatalytic sets also have the ability to replicate themselves if they are split apart into two physically separated spaces. Computer models illustrate that split autocatalytic sets will reproduce all of the reactions of the original set in each half, much like cellular mitosis. In effect, using the principles of autocatalysis, a small metabolism can replicate itself with very little high level organization. This property is why autocatalysis is a contender as the foundational mechanism for complex evolution.

Autocatalytic sets also have the ability to replicate themselves if they are split apart into two physically separated spaces. Computer models illustrate that split autocatalytic sets will reproduce all of the reactions of the original set in each half, much like cellular mitosis. In effect, using the principles of autocatalysis, a small metabolism can replicate itself with very little high level organization. This property is why autocatalysis is a contender as the foundational mechanism for complex evolution.

Prior to [[James D. Watson|Watson]] and [[Francis Crick|Crick]], biologists considered autocatalytic sets the way [[metabolism]] functions in principle, i.e. one [[protein]] helps to synthesize another protein and so on. After the discovery of the [[double helix]], the [[central dogma of molecular biology]] was formulated, which is that [[DNA]] is transcribed to [[RNA]] which is translated to protein. The molecular structure of DNA and RNA, as well as the metabolism that maintains their reproduction, are believed to be too complex to have arisen spontaneously in one step from a soup of chemistry.

Prior to [[James D. Watson|Watson]] and [[Francis Crick|Crick]], biologists considered autocatalytic sets the way [[metabolism]] functions in principle, i.e. one [[protein]] helps to synthesize another protein and so on. After the discovery of the [[double helix]], the [[central dogma of molecular biology]] was formulated, which is that [[DNA]] is transcribed to [[RNA]] which is translated to protein. The molecular structure of DNA and RNA, as well as the metabolism that maintains their reproduction, are believed to be too complex to have arisen spontaneously in one step from a soup of chemistry.

Prior to Watson and Crick, biologists considered autocatalytic sets the way metabolism functions in principle, i.e. one protein helps to synthesize another protein and so on. After the discovery of the double helix, the central dogma of molecular biology was formulated, which is that DNA is transcribed to RNA which is translated to protein. The molecular structure of DNA and RNA, as well as the metabolism that maintains their reproduction, are believed to be too complex to have arisen spontaneously in one step from a soup of chemistry.

Prior to Watson and Crick, biologists considered autocatalytic sets the way metabolism functions in principle, i.e. one protein helps to synthesize another protein and so on. After the discovery of the double helix, the central dogma of molecular biology was formulated, which is that DNA is transcribed to RNA which is translated to protein. The molecular structure of DNA and RNA, as well as the metabolism that maintains their reproduction, are believed to be too complex to have arisen spontaneously in one step from a soup of chemistry.

Several models of the [[origin of life]] are based on the notion that life may have arisen through the development of an initial molecular autocatalytic set which evolved over time.  Most of these models which have emerged from the studies of [[complex system]]s predict that life arose not from a molecule with any particular trait (such as self-replicating [[RNA World|RNA]]) but from an autocatalytic set. The first empirical support came from Lincoln and Joyce, who obtained autocatalytic sets in which "two [RNA] enzymes catalyze each other’s synthesis from a total of four component substrates."<ref>{{cite journal | author = Lincoln TA, Joyce GF | title = Self-sustained replication of an RNA enzyme | journal = Science | volume = 323 | issue = 5918 | pages = 1229–32 |date=February 2009 | pmid = 19131595 | pmc = 2652413 | doi = 10.1126/science.1167856 | bibcode = 2009Sci...323.1229L }}</ref> Furthermore, an evolutionary process that began with a population of these self-replicators yielded a population dominated by [[Genetic recombination|recombinant]] replicators.

Several models of the [[origin of life]] are based on the notion that life may have arisen through the development of an initial molecular autocatalytic set which evolved over time.  Most of these models which have emerged from the studies of [[complex system]]s predict that life arose not from a molecule with any particular trait (such as self-replicating [[RNA World|RNA]]) but from an autocatalytic set. The first empirical support came from Lincoln and Joyce, who obtained autocatalytic sets in which "two [RNA] enzymes catalyze each other’s synthesis from a total of four component substrates."<ref>{{cite journal | author = Lincoln TA, Joyce GF | title = Self-sustained replication of an RNA enzyme | journal = Science | volume = 323 | issue = 5918 | pages = 1229–32 |date=February 2009 | pmid = 19131595 | pmc = 2652413 | doi = 10.1126/science.1167856 | bibcode = 2009Sci...323.1229L }}</ref> Furthermore, an evolutionary process that began with a population of these self-replicators yielded a population dominated by [[Genetic recombination|recombinant]] replicators.

Several models of the origin of life are based on the notion that life may have arisen through the development of an initial molecular autocatalytic set which evolved over time.  Most of these models which have emerged from the studies of complex systems predict that life arose not from a molecule with any particular trait (such as self-replicating RNA) but from an autocatalytic set. The first empirical support came from Lincoln and Joyce, who obtained autocatalytic sets in which "two [RNA] enzymes catalyze each other’s synthesis from a total of four component substrates." Furthermore, an evolutionary process that began with a population of these self-replicators yielded a population dominated by recombinant replicators.

Several models of the origin of life are based on the notion that life may have arisen through the development of an initial molecular autocatalytic set which evolved over time.  Most of these models which have emerged from the studies of complex systems predict that life arose not from a molecule with any particular trait (such as self-replicating RNA) but from an autocatalytic set. The first empirical support came from Lincoln and Joyce, who obtained autocatalytic sets in which "two [RNA] enzymes catalyze each other’s synthesis from a total of four component substrates." Furthermore, an evolutionary process that began with a population of these self-replicators yielded a population dominated by recombinant replicators.

生命起源的几个模型都是基于这样一个理念，即生命可能是通过一个随着时间演化的原初分子自催化集合的发展而产生的。从复杂系统研究中产生的大多数模型都这样预测，生命并非起源于具有任何特定特征的分子(如能自复制的RNA) ，而是起源于一个自催化的集合。第一个经验性的支持来自林肯（Lincoln）和乔伊斯（Joyce），他们构造出了自催化集合（两种[RNA]酶通过四种底物组件互相催化对方的合成）。此外，一个始于这些自复制因子的群体通过进化产生了一个以重组复制因子占主导的群体。

生命起源的几个模型都是基于这样一个理念，即生命可能是通过一个随着时间演化的原初分子自催化集合的发展而产生的。从复杂系统研究中产生的大多数模型都如此预测，生命并非起源于具有任何特定特征的分子(如能自复制的RNA) ，而是起源于一个自催化的集合。首个实证性的证据来自林肯（Lincoln）和乔伊斯（Joyce），他们构造出了一个自催化集合（两种[RNA]酶通过四种底物组件互相催化对方的合成）。此外，一个始于这些自复制因子的群体通过进化产生了一个以重组复制因子占主导的群体。

Modern life has the traits of an autocatalytic set, since no particular molecule, nor any class of molecules, is able to replicate itself. There are several models based on autocatalytic sets, including those of [[Stuart Kauffman]]<ref>Kauffman, Stuart A. (2008) ''Reinventing the Sacred: A New View of Science, Reason, and Religion''.  [Basic Books],  {{ISBN|0-465-00300-1}}, chapter 5, especially pp. 59–71</ref> and others.

Modern life has the traits of an autocatalytic set, since no particular molecule, nor any class of molecules, is able to replicate itself. There are several models based on autocatalytic sets, including those of [[Stuart Kauffman]]<ref>Kauffman, Stuart A. (2008) ''Reinventing the Sacred: A New View of Science, Reason, and Religion''.  [Basic Books],  {{ISBN|0-465-00300-1}}, chapter 5, especially pp. 59–71</ref> and others.

Modern life has the traits of an autocatalytic set, since no particular molecule, nor any class of molecules, is able to replicate itself. There are several models based on autocatalytic sets, including those of Stuart KauffmanKauffman, Stuart A. (2008) Reinventing the Sacred: A New View of Science, Reason, and Religion.  [Basic Books],  , chapter 5, especially pp. 59–71 and others.

Modern life has the traits of an autocatalytic set, since no particular molecule, nor any class of molecules, is able to replicate itself. There are several models based on autocatalytic sets, including those of Stuart KauffmanKauffman, Stuart A. (2008) Reinventing the Sacred: A New View of Science, Reason, and Religion.  [Basic Books],  , chapter 5, especially pp. 59–71 and others.

现代生命具有自催化集合的特征，因为没有任何特定的分子或任何类型的分子，能够自复制。目前有几个基于自催化集合的模型，包括斯图尔特·考夫曼（Stuart Kauffman）和其他人的模型。

现代生命具有自催化集合的特征，显然任何特定的分子或任何类型的分子都不能自复制。目前已有几个基于自催化集合的模型，包括斯图尔特·考夫曼（Stuart Kauffman）和其他人的模型。

==Formal definition==

==Formal definition==

Let F ⊆ M be a set of food (small numbers of molecules freely available from the environment) and R' ⊆ R be some subset of reactions. We define a closure of the food set relative to this subset of reactions ClR'(F) as the set of molecules that contains the food set plus all molecules that can be produced starting from the food set and using only reactions from this subset of reactions. Formally ClR'(F) is a minimal subset of M such that F ⊆ ClR'(F) and for each reaction r'(A, B) ⊆ R':

Let F ⊆ M be a set of food (small numbers of molecules freely available from the environment) and R' ⊆ R be some subset of reactions. We define a closure of the food set relative to this subset of reactions ClR'(F) as the set of molecules that contains the food set plus all molecules that can be produced starting from the food set and using only reactions from this subset of reactions. Formally ClR'(F) is a minimal subset of M such that F ⊆ ClR'(F) and for each reaction r'(A, B) ⊆ R':

设F（F ⊆ M）是一组食物（可从环境中自由获得的少量分子) 的集合，并设R'（R' ⊆ R）是一些反应的子集。我们定义了一个食物集合相对于该反应子集 ClR'(F)的闭包，作为一个包含了食物集合加上所有可以从食物集合中产生的分子的集合，并且，只使用该反应子集中的反应。形式上， ClR'(F)是 M的最小子集，使得F ⊆ ClR'(F)以及每个反应r'(A, B) ⊆ R':

设F（F ⊆ M）是一组食物（即可从环境中自由获得的少量分子) 的集合，并设R'（R' ⊆ R）是一些反应的子集。我们定义了一个食物集合相对于该反应子集 ClR'(F)的闭包，作为一个包含了食物集合加上所有可以从食物集合中产生的分子的集合，并且，只使用该反应子集中的反应。形式上， ClR'(F)是M的最小子集，使得F ⊆ ClR'(F)以及每个反应r'(A, B) ⊆ R':

   A ⊆ Cl_R'(F) ⇒ B ⊆ Cl_R'(F)

   A ⊆ Cl_R'(F) ⇒ B ⊆ Cl_R'(F)

The reaction for (a + f) does not belong to R' because f does not belong to closure. Similarly the reaction for (c + b) in the autocatalytic set can only be catalyzed by d and not by f.

The reaction for (a + f) does not belong to R' because f does not belong to closure. Similarly the reaction for (c + b) in the autocatalytic set can only be catalyzed by d and not by f.

(a + f)的反应不属于 R'，因为f不属于闭包。同样，自催化集合中(c + b)的反应只能用d催化，而不能用f催化。

(a + f)的反应不属于R'，因为f不属于闭包。同样，自催化集合中(c + b)的反应只能用d催化，而不能用f催化。

==Probability that a random set is autocatalytic==

==Probability that a random set is autocatalytic==

for the same reason. These theoretical results make autocatalytic sets attractive for scientific explanation of the very early origin of life.

for the same reason. These theoretical results make autocatalytic sets attractive for scientific explanation of the very early origin of life.

==Formal limitations==

==Formal limitations==

Formally, it is difficult to treat molecules as anything but unstructured entities, since the set of possible reactions (and molecules) would become infinite. Therefore, a derivation of arbitrarily long polymers as needed to model DNA, RNA or proteins is not possible, yet. Studies of the RNA World suffer from the same problem.

Formally, it is difficult to treat molecules as anything but unstructured entities, since the set of possible reactions (and molecules) would become infinite. Therefore, a derivation of arbitrarily long polymers as needed to model DNA, RNA or proteins is not possible, yet. Studies of the RNA World suffer from the same problem.

==Linguistic aspects==

==Linguistic aspects==

no agreed-upon notion of autocatalytic sets exists today.

no agreed-upon notion of autocatalytic sets exists today.

While above, the notion of catalyst is secondary insofar that only the set as

While above, the notion of catalyst is secondary insofar that only the set as

towards self describing systems.

towards self describing systems.

尽管如此，只有整套催化剂才能促进其自身的生产，因此，催化剂的概念是次要的，但在其他定义中，它是主要的，因此”自动催化集”一词的重点有所不同。在那里，每一个反应(或功能，转变)都必须由催化剂调节。因此，在介导各自反应的同时，每一个催化剂也表示其反应，从而形成一个自指示体系，这是有趣的，原因有二。首先，真正的新陈代谢是以这种方式组织的。其次，自我表示系统可以被认为是通向自我描述系统的中间步骤。

尽管在上文中，催化剂的概念是次要的，因为只有一整套催化剂才能作为一个整体来催化其自身的生成。但在其他定义中，“自催化集合”一词的侧重点有所不同，其催化的概念是主要的。在那里，每一个反应(或功能、转化)都必须由催化剂介导。因此，在介导各自反应的同时，每一个催化剂也指向它自己的反应，从而形成一个自指系统。这是有趣的，原因有二。首先，真实的新陈代谢是以这种方式组织的。其次，自指系统可以被认为是通向自我描述系统的中间步骤。

From both a structural and a natural historical point of view, one can

From both a structural and a natural historical point of view, one can

but differently emphasised.

but differently emphasised.

To complete the classification from the other side, generalised self

To complete the classification from the other side, generalised self

Desc(c) along following definition:

Desc(c) along following definition:

为了从另一方面完成分类，一般化的自我复制系统超越了自我标志。在那里，不再有非结构化实体进行转换，而是结构化的、描述性的转换。形式上，一个广义的自复制系统由两个函数组成，u 和 c，以及它们的描述 Desc (u)和 Desc (c) ，定义如下:

为了从另一方面完成分类，广义的自复制系统超越了自指。在那里，不再有非结构化实体进行转化，而是结构化的、描述性的转换。形式上，一个广义的自复制系统由两个函数组成，u 和 c，以及它们的描述Desc(u)和Desc(c)，定义如下:

     u : Desc(X) -> X

     u : Desc(X) -> X

function for any description. Practically, 'u' and 'c' can fall apart into many subfunctions or catalysts.

function for any description. Practically, 'u' and 'c' can fall apart into many subfunctions or catalysts.

Note that the (trivial) copy function 'c' is necessary because though the universal constructor 'u'

Note that the (trivial) copy function 'c' is necessary because though the universal constructor 'u'

general be longer than the result, rendering full self replication impossible.

general be longer than the result, rendering full self replication impossible.

请注意，(琐碎的)复制函数‘ c’是必要的，因为尽管通用构造函数‘ u’也可以构造任何描述，但它所基于的描述通常会比结果长，使得完全自我复制成为不可能。

请注意，(平庸的)复制函数‘c’是必要的，因为尽管通用构造函数‘u’也可以构造任意描述，但它将要基于的描述通常会比结果更长，从而导致不可能完全自复制。

This last concept can be attributed to [[John von Neumann|von Neumann]]'s

This last concept can be attributed to [[John von Neumann|von Neumann]]'s

such a system for a model chemistry, too.

such a system for a model chemistry, too.

这最后一个概念可以归因于冯 · 诺依曼关于自复制自动机的工作，在这个工作中，他拥有任何非平凡的(广义的)自复制系统所必需的自我描述，以避免干扰。冯 · 诺依曼也计划为模型化学设计这样一个系统。

这最后一个概念可以归因于冯 · 诺依曼关于自复制自动机的工作。在这个自复制自动机中，他拥有任何非平凡的(广义)自复制系统所必需的自我描述，以避免干扰。冯 · 诺依曼也计划为模型化学设计这样一个系统。

==Non-autonomous autocatalytic sets==

==Non-autonomous autocatalytic sets==

==Non-autonomous autocatalytic sets==

==Non-autonomous autocatalytic sets==

= = = 非自主的自动催化装置 = =  

= = = 非自治的自催化集合 = =  

Virtually all articles on autocatalytic sets leave open whether the sets are

Virtually all articles on autocatalytic sets leave open whether the sets are

assumed.

assumed.

Likely, the above context has a strong emphasis on autonomous self replication

Likely, the above context has a strong emphasis on autonomous self replication

handled. Clearly, such sets are not autonomous and are objects of human agency.

handled. Clearly, such sets are not autonomous and are objects of human agency.

Examples of practical importance of non-autonomous autocatalytic sets can be found e.g. in the field of [[Bootstrapping (compilers)|compiler construction]] and in [[Self-hosting (compilers)|operating systems]], where the self-referential nature of the respective constructions is explicitly discussed, very often as [[bootstrapping]].

Examples of practical importance of non-autonomous autocatalytic sets can be found e.g. in the field of [[Bootstrapping (compilers)|compiler construction]] and in [[Self-hosting (compilers)|operating systems]], where the self-referential nature of the respective constructions is explicitly discussed, very often as [[bootstrapping]].

Examples of practical importance of non-autonomous autocatalytic sets can be found e.g. in the field of compiler construction and in operating systems, where the self-referential nature of the respective constructions is explicitly discussed, very often as bootstrapping.

Examples of practical importance of non-autonomous autocatalytic sets can be found e.g. in the field of compiler construction and in operating systems, where the self-referential nature of the respective constructions is explicitly discussed, very often as bootstrapping.

==Comparison with other theories of life==

==Comparison with other theories of life==

  the  (M,R) systems of Robert Rosen, and the autopoiesis (or self-building) of Humberto Maturana and Francisco Varela. All of these (including autocatalytic sets) found their original inspiration in Erwin Schrödinger's book What is Life? but at first they appear to have little in common with one another, largely because the authors did not communicate with one another, and none of them made any reference in their principal publications to any of the other theories.  Nonetheless, there are more similarities than may be obvious at first sight, for example between Gánti and Rosen. Until recently there have been almost no attempts to compare the different theories and discuss them together.

  the  (M,R) systems of Robert Rosen, and the autopoiesis (or self-building) of Humberto Maturana and Francisco Varela. All of these (including autocatalytic sets) found their original inspiration in Erwin Schrödinger's book What is Life? but at first they appear to have little in common with one another, largely because the authors did not communicate with one another, and none of them made any reference in their principal publications to any of the other theories.  Nonetheless, there are more similarities than may be obvious at first sight, for example between Gánti and Rosen. Until recently there have been almost no attempts to compare the different theories and discuss them together.

自催化集合只是当前几个生命理论中的一个，包括 Tibor Gánti 的 chemoton、 Manfred Eigen 和 Peter Schuster 的超循环、 Robert Rosen 的(m，r)系统以及 Humberto Maturana 和 Francisco Varela 的自创生理论。所有这些(包括自动催化装置)的灵感都来源于埃尔温·薛定谔的《什么是生命？但起初他们之间似乎没有什么共同点，主要是因为作者之间没有交流，他们在主要出版物中也没有提到任何其他理论。尽管如此，两者之间的相似之处比乍看之下可能显而易见的要多，例如 Gánti 和罗森大厦之间的相似之处。直到最近，几乎没有人试图比较不同的理论并一起讨论它们。

自催化集合只是当前几种生命理论之一，其包括提博尔·甘蒂（Tibor Gánti）的化学子（Chemoton）、 曼弗雷德·艾根（Manfred Eigen）和彼得·舒斯特（Peter Schuster）的超循环、罗伯特·罗森（Robert Rosen）的[[Robert Rosen (theoretical biologist)#Complexity and complex scientific models: (M,R) systems |(''M,R'')系统]]以及亨伯托·马图拉纳（Humberto Maturana）和弗朗西斯科·瓦雷拉（Francisco Varela）的自创生理论。所有这些（包括自催化集合）的灵感都来源于埃尔温·薛定谔（Erwin Schrödinger）的《生命是什么？》。但一开始，他们之间似乎没有什么共同之处，主要是因为作者之间没有交流，他们在主要出版物中也没有提到任何其他理论。尽管如此，它们之间的相似之处比乍看之下还要多，例如甘蒂和罗森之间的相似之处。直到最近，几乎没有人试图比较不同的理论并一起讨论它们。

==Last Universal Common Ancestor (LUCA)==

==Last Universal Common Ancestor (LUCA)==

==Last Universal Common Ancestor (LUCA)==

==Last Universal Common Ancestor (LUCA)==

= = 最后一个通用共同祖先(LUCA) = =  

= = 最后普遍的共同祖先(LUCA) = =  

Some authors equate models of the origin of life with LUCA, the '''L'''ast '''U'''niversal '''C'''ommon '''A'''ncestor of all extant life.<ref>{{cite journal | pmid=34575021 | doi= 10.3390/life11090872 |pmc=8467930 | title = The Way forward for the Origin of Life: Prions and Prion-Like Molecules First Hypothesis| last1 =Jheeta | first1 =S.| last2 = Chatzitheodoridis| first2 =E. | last3 = Devine| first3 =Kevin| last4 = Block| first4 = J.|journal = Life |date =2021| volume = 11|issue = 9 |pages = 872

Some authors equate models of the origin of life with LUCA, the '''L'''ast '''U'''niversal '''C'''ommon '''A'''ncestor of all extant life.<ref>{{cite journal | pmid=34575021 | doi= 10.3390/life11090872 |pmc=8467930 | title = The Way forward for the Origin of Life: Prions and Prion-Like Molecules First Hypothesis| last1 =Jheeta | first1 =S.| last2 = Chatzitheodoridis| first2 =E. | last3 = Devine| first3 =Kevin| last4 = Block| first4 = J.|journal = Life |date =2021| volume = 11|issue = 9 |pages = 872

Some authors equate models of the origin of life with LUCA, the Last Universal Common Ancestor of all extant life.  This is a serious error resulting from failure to recognize that L refers to the last common ancestor, not to the first ancestor, which is much older: a large amount of evolution occurred before the appearance of LUCA.

Some authors equate models of the origin of life with LUCA, the Last Universal Common Ancestor of all extant life.  This is a serious error resulting from failure to recognize that L refers to the last common ancestor, not to the first ancestor, which is much older: a large amount of evolution occurred before the appearance of LUCA.

Gill and Forterre expressed the essential point as follows:<ref>{{cite journal | doi= 10.1017/S1473550415000282 |title = Origin of life: LUCA and extracellular membrane vesicles (EMVs)|journal= Int. J. Astrobiol.|last1 = Gill| first1 =S. |last2 = Forterre| first2 =P. |volume =15|

Gill and Forterre expressed the essential point as follows:<ref>{{cite journal | doi= 10.1017/S1473550415000282 |title = Origin of life: LUCA and extracellular membrane vesicles (EMVs)|journal= Int. J. Astrobiol.|last1 = Gill| first1 =S. |last2 = Forterre| first2 =P. |volume =15|

  LUCA should not be confused with the first cell, but was the product of a long period of evolution. Being the "last" means that LUCA was preceded by a long succession of older "ancestors."

  LUCA should not be confused with the first cell, but was the product of a long period of evolution. Being the "last" means that LUCA was preceded by a long succession of older "ancestors."

吉尔和福特尔表达的基本观点如下: 露卡不应与第一个细胞混淆，而是长期进化的产物。作为“最后一个”意味着 LUCA 之前有一系列更古老的“祖先”

吉尔（Gill）和福特尔（Forterre）表达了以下基本观点: LUCA不应与第一个出现的细胞混淆，LUCA是长期进化的产物，作为“最后的”意味着LUCA之前有一系列更古老的“祖先”。

==References==

==References==