自催化集合

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模板:Refimprove An autocatalytic set is a collection of entities, each of which can be created catalytically by other entities within the set, such that as a whole, the set is able to catalyze its own production. In this way the set as a whole is said to be autocatalytic. Autocatalytic sets were originally and most concretely defined in terms of molecular entities, but have more recently been metaphorically extended to the study of systems in sociology and economics.

An autocatalytic set is a collection of entities, each of which can be created catalytically by other entities within the set, such that as a whole, the set is able to catalyze its own production. In this way the set as a whole is said to be autocatalytic. Autocatalytic sets were originally and most concretely defined in terms of molecular entities, but have more recently been metaphorically extended to the study of systems in sociology and economics.

自催化集合是一组实体的集合，每一个实体都可以由集合内的其他实体催化而创造出来。这样一来，作为一个整体，该集合能够催化其自身的生成。以这种方式，该集合作为一个整体被称为是自催化的。自催化集合最初是用分子实体来定义的，这种定义也是最具体的，但最近被隐喻地扩展到社会学和经济学系统的研究。

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.

如果自催化集合被分裂成物理上分离的两个空间，它们仍有复制自身的能力。计算机模型表明，分裂来的每一半自催化集合都将重新自生成出初始集合中的所有反应，就像细胞有丝分裂一样。实际上，利用自催化的原理，一个小的代谢系统可以在几乎没有高水平组织的情况下自复制。这种性质解释了为什么自催化能作为复杂进化的基本机制。

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.

在沃森与克里克之前，生物学家认为自催化在原则上决定了代谢功能，即一种蛋白质帮助完成另一种蛋白质的合成等。在发现DNA双螺旋结构之后，中心法则被制定出来，即 DNA 转录成 RNA，再翻译成蛋白质。DNA 和 RNA 的分子结构以及维持它们复制的代谢，被认为过于复杂，不可能在化学汤中一步自发产生。

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 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。

= 定义 =

Given a set M of molecules, chemical reactions can be roughly defined as pairs r = (A, B) of subsets from M:

Given a set M of molecules, chemical reactions can be roughly defined as pairs r = (A, B) of subsets from M:

给定一组 m 分子，化学反应可以粗略地定义为 m 中子集的对 r = (a，b) :

 a1 + a2 + ... + ak → b1 + b2 + ... + bk

 a1 + a2 + ... + ak → b1 + b2 + ... + bk

 a1 + a2 + ... + ak → b1 + b2 + ... + bk

Let R be the set of allowable reactions. A pair (M, R) is a reaction system (RS).

Let R be the set of allowable reactions. A pair (M, R) is a reaction system (RS).

设 r 是允许反应的集合。一对(m，r)是一个反应体系(RS)。

Let C be the set of molecule-reaction pairs specifying which molecules can catalyze which reactions:

Let C be the set of molecule-reaction pairs specifying which molecules can catalyze which reactions:

设 c 为一组分子反应对，指定哪些分子可以催化哪些反应:

 C = {(m, r) | m ∈ M, r ∈ R}

 C = {(m, r) | m ∈ M, r ∈ R}

 C = {(m, r) | m ∈ M, r ∈ 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 Cl_R'(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 Cl_R'(F) is a minimal subset of M such that F ⊆ Cl_R'(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 something m 是一组食物(从环境中自由获得的少量分子) ，r ′ r 是反应的子集。我们定义了一个食物集合的闭合相对于这个反应子集 ClR’(f)作为包含食物集合的分子集合加上所有可以从食物集合中产生的分子，并且只使用这个反应子集合的反应。形式上，ClR’(f)是 m 的极小子集，使得 f something ClR’(f)和每个反应 r’(a，b) something r’:

 A ⊆ ClR'(F) ⇒ B ⊆ ClR'(F)

 A ⊆ ClR'(F) ⇒ B ⊆ ClR'(F)

 A ⊆ ClR'(F) ⇒ B ⊆ ClR'(F)

A reaction system (Cl_R'(F), R') is autocatalytic, if and only if for each reaction r'(A, B) ⊆ R':

1. there exists a molecule c ⊆ Cl_R'(F) such that (c, r') ⊆ C,
2. A ⊆ Cl_R'(F).

A reaction system (ClR'(F), R') is autocatalytic, if and only if for each reaction r'(A, B) ⊆ R':

1. there exists a molecule c ⊆ ClR'(F) such that (c, r') ⊆ C,
2. A ⊆ ClR'(F).

反应体系(ClR’(f) ，r’)是自催化的，当且仅当对于每个反应 r’(a，b) something r’: # 存在分子 c something ClR’(f)使得(c，r’) something c，# a something ClR’(f)。

= 实例 =

Let M = {a, b, c, d, f, g} and F = {a, b}. Let the set R contain the following reactions:

Let M = {a, b, c, d, f, g} and F = {a, b}. Let the set R contain the following reactions:

设 m = { a，b，c，d，f，g }和 f = { a，b }。设 r 包含以下反应:

 a + b  → c + d, catalyzed by g
 a + f  → c + b, catalyzed by d
 c + b  → g + a, catalyzed by d or f

 a + b  → c + d, catalyzed by g
 a + f  → c + b, catalyzed by d
 c + b  → g + a, catalyzed by d or f

A + b → c + d，g a + f → c + b，d c + b → g + a，d 或 f 催化

From the F = {a, b} we can produce {c, d} and then from {c, b} we can produce {g, a} so the closure is equal to:

From the F = {a, b} we can produce {c, d} and then from {c, b} we can produce {g, a} so the closure is equal to:

从 f = { a，b }我们可以产生{ c，d } ，然后从{ c，b }我们可以产生{ g，a } ，所以闭包等于:

 ClR'(F) = {a, b, c, d, g}

 ClR'(F) = {a, b, c, d, g}

ClR’(f) = { a，b，c，d，g }

According to the definition the maximal autocatalytic subset R' will consist of two reactions:

According to the definition the maximal autocatalytic subset R' will consist of two reactions:

根据定义，最大自催化子集 r’包括两个反应:

 a + b  → c + d, catalyzed by g
 c + b  → g + a, catalyzed by d

 a + b  → c + d, catalyzed by g
 c + b  → g + a, catalyzed by d

A + b → c + d，g c + b → g + a，d 催化

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，自催化体系中(c + b)的反应只能用 d 催化，而不能用 f 催化。

= 一个随机集是自动催化的概率 =

Studies of the above model show that random RS can be autocatalytic with high probability under some assumptions. This comes from the fact that with a growing number of molecules, the number of possible reactions and catalysations grows even larger if the molecules grow in complexity, producing stochastically enough reactions and catalysations to make a part of the RS self-supported. An autocatalytic set then extends very quickly with growing number of molecules for the same reason. These theoretical results make autocatalytic sets attractive for scientific explanation of the very early origin of life.

Studies of the above model show that random RS can be autocatalytic with high probability under some assumptions. This comes from the fact that with a growing number of molecules, the number of possible reactions and catalysations grows even larger if the molecules grow in complexity, producing stochastically enough reactions and catalysations to make a part of the RS self-supported. An autocatalytic set then extends very quickly with growing number of molecules for the same reason. These theoretical results make autocatalytic sets attractive for scientific explanation of the very early origin of life.

对上述模型的研究表明，在一定的假设条件下，随机遥感具有很高的自催化概率。这是因为随着分子数量的增加，如果分子的复杂性增加，可能的反应和催化作用的数量会变得更大，随机产生足够的反应和催化作用，使遥感系统的一部分得到自我支持。由于同样的原因，一个自催化装置随着分子数量的增加而迅速扩展。这些理论结果使得自动催化集对于科学解释早期生命起源具有吸引力。

= 形式限制 =

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.

从形式上讲，除了非结构化的实体以外，很难把分子看作任何东西，因为一系列可能的反应(和分子)将变得无穷无尽。因此，根据模拟 DNA、 RNA 或蛋白质所需的任意长度的聚合物是不可能的。对 RNA 世界的研究也遇到了同样的问题。

= 语言学方面 =

Contrary to the above definition, which applies to the field of Artificial chemistry, no agreed-upon notion of autocatalytic sets exists today.

Contrary to the above definition, which applies to the field of Artificial chemistry, no agreed-upon notion of autocatalytic sets exists today.

与适用于人工化学领域的上述定义相反，目前还没有一致认可的自动催化集的概念。

While above, the notion of catalyst is secondary insofar that only the set as a whole has to catalyse its own production, it is primary in other definitions, giving the term "Autocatalytic Set" a different emphasis. There, every reaction (or function, transformation) has to be mediated by a catalyst. As a consequence, while mediating its respective reaction, every catalyst denotes its reaction, too, resulting in a self denoting system, which is interesting for two reasons. First, real metabolism is structured in this manner. Second, self denoting systems can be considered as an intermediate step towards self describing systems.

While above, the notion of catalyst is secondary insofar that only the set as a whole has to catalyse its own production, it is primary in other definitions, giving the term "Autocatalytic Set" a different emphasis. There, every reaction (or function, transformation) has to be mediated by a catalyst. As a consequence, while mediating its respective reaction, every catalyst denotes its reaction, too, resulting in a self denoting system, which is interesting for two reasons. First, real metabolism is structured in this manner. Second, self denoting systems can be considered as an intermediate step 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。

From both a structural and a natural historical point of view, one can identify the ACS as seized in the formal definition the more original concept, while in the second, the reflection of the system in itself is already brought to an explicit presentation, since catalysts represent the reaction induced by them. In ACS literature, both concept are present, but differently emphasised.

From both a structural and a natural historical point of view, one can identify the ACS as seized in the formal definition the more original concept, while in the second, the reflection of the system in itself is already brought to an explicit presentation, since catalysts represent the reaction induced by them. In ACS literature, both concept are present, but differently emphasised.

从结构和自然历史的观点来看，可以认为正式定义中的加勒比国家联盟是更原始的概念，而在第二个定义中，已经明确表述了这一制度本身的反映，因为催化剂代表了由它们引起的反应。在 ACS 的文献中，这两个概念都存在，但是强调方式不同。

To complete the classification from the other side, generalised self reproducing systems move beyond self-denotation. There, no unstructured entities carry the transformations anymore, but structured, described ones. Formally, a generalised self reproducing system consists of two function, u and c, together with their descriptions Desc(u) and Desc(c) along following definition:

To complete the classification from the other side, generalised self reproducing systems move beyond self-denotation. There, no unstructured entities carry the transformations anymore, but structured, described ones. Formally, a generalised self reproducing system consists of two function, u and c, together with their descriptions Desc(u) and 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:

    u : Desc(X) -> X
    c : Desc(X) -> Desc(X)

    u : Desc(X) -> X
    c : Desc(X) -> Desc(X)

    u : Desc(X) -> X
    c : Desc(X) -> Desc(X)

where the function 'u' is the "universal" constructor, that constructs everything in its domain from appropriate descriptions, while 'c' is a copy function for any description. Practically, 'u' and 'c' can fall apart into many subfunctions or catalysts.

where the function 'u' is the "universal" constructor, that constructs everything in its domain from appropriate descriptions, while 'c' is a copy function for any description. Practically, 'u' and 'c' can fall apart into many subfunctions or catalysts.

其中函数‘ u’是“通用”构造函数，它根据适当的描述构造域中的所有内容，而‘ c’是任何描述的复制函数。实际上，“ u”和“ c”可以分解为许多子功能或催化剂。

Note that the (trivial) copy function 'c' is necessary because though the universal constructor 'u' would be able to construct any description, too, the description it would base on, would in general be longer than the result, rendering full self replication impossible.

Note that the (trivial) copy function 'c' is necessary because though the universal constructor 'u' would be able to construct any description, too, the description it would base on, would in 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。

This last concept can be attributed to von Neumann's work on self reproducing automata, where he holds a self description necessary for any nontrivial (generalised) self reproducing system to avoid interferences. Von Neumann planned to design such a system for a model chemistry, too.

This last concept can be attributed to von Neumann's work on self reproducing automata, where he holds a self description necessary for any nontrivial (generalised) self reproducing system to avoid interferences. Von Neumann planned to design 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。

= = 非自主的自动催化装置 =

Virtually all articles on autocatalytic sets leave open whether the sets are to be considered autonomous or not. Often, autonomy of the sets is silently assumed.

Virtually all articles on autocatalytic sets leave open whether the sets are to be considered autonomous or not. Often, autonomy of the sets is silently assumed.

几乎所有关于自动催化装置的条款都没有明确规定，无论这些装置是否被认为是自动的。通常，集合的自治性是默认的。

Likely, the above context has a strong emphasis on autonomous self replication and early origin of life. But the concept of autocatalytic sets is really more general and in practical use in various technical areas, e.g. where self-sustaining tool chains are handled. Clearly, such sets are not autonomous and are objects of human agency.

Likely, the above context has a strong emphasis on autonomous self replication and early origin of life. But the concept of autocatalytic sets is really more general and in practical use in various technical areas, e.g. where self-sustaining tool chains are handled. Clearly, such sets are not autonomous and are objects of human agency.

很可能，上面的内容强调了自主的自我复制和早期生命起源。但是自动催化集的概念实际上更为普遍，在各种技术领域都有实际应用。处理自我维持的工具链。显然，这样的集合是不自治的，是人类行为的对象。

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.

非自治自动催化装置的实际重要性的例子可以找到，例如。在编译器构造领域和操作系统中，明确讨论了各自构造的自引用性质，通常称为自举。

= 与其他生命理论的比较 =

Autocatalytic sets constitute just one of several current theories of life, including the chemoton of Tibor Gánti, the hypercycle of Manfred Eigen and Peter Schuster, 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.

Autocatalytic sets constitute just one of several current theories of life, including the chemoton of Tibor Gánti, the hypercycle of Manfred Eigen and Peter Schuster,

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。

= 最后一个通用共同祖先(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.

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.

一些作者将生命起源的模型与露卡相提并论，露卡是所有现存生命的最后一个共同祖先。这是一个严重的错误，因为没有认识到 l 指的是最后的共同祖先，而不是更古老的第一个祖先: 大量的进化发生在露卡出现之前。

Gill and Forterre expressed the essential point as follows:

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."

Gill and Forterre expressed the essential point as follows:

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”

References

Category:Origin of life Category:Artificial life

类别: 生命起源类别: 人工生命

This page was moved from wikipedia:en:Autocatalytic set. Its edit history can be viewed at 自催化集合/edithistory