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第1行： − 本词条由余凡尘初步翻译+ + + + + − 此词条暂由彩云小译翻译，翻译字数共1689，未经人工整理和审校，带来阅读不便，请见谅。 − − {{Refimprove|date=January 2011}} − An '''autocatalytic set''' is a collection of entities, each of which can be created [[catalysis|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 [[autocatalysis|autocatalytic]]. Autocatalytic sets were originally and most concretely defined in terms of [[molecular entity|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. − 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.+ − 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 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. − 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 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，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== − − = = 形式化定义 = = − − ===Definition=== − − ===Definition=== − − − − Given a set M of [[molecule]]s, [[chemical reaction]]s can be roughly defined as pairs r = (A, B) of subsets from M:<ref>{{cite journal | author = Hordijk W | title = Autocatalytic Sets: From the Origin of Life to the Economy | journal = BioScience | volume = 63 | issue = 11 | pages = 877–881| year = 2013 | doi = 10.1525/bio.2013.63.11.6 | doi-access = free }}</ref> − − Given a set M of molecules, chemical reactions can be roughly defined as pairs r = (A, B) of subsets from M: − − 给定一组分子的集合M，化学反应可以粗略地定义为M的子集对r = (A, B): − 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). − Let C be the set of molecule-reaction pairs specifying which molecules can [[catalyst|catalyze]] which reactions: − − Let C be the set of molecule-reaction pairs specifying which molecules can catalyze which reactions: 第73行：
第31行： − 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 (mathematics)|closure]] of the food set relative to this subset of reactions Cl<sub>R'</sub>(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<sub>R'</sub>(F) is a minimal subset of M such that F ⊆ Cl<sub>R'</sub>(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（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 ⊆ ClR'(F) ⇒ B ⊆ ClR'(F) − − A ⊆ ClR'(F) ⇒ B ⊆ ClR'(F) − − A reaction system (Cl<sub>R'</sub>(F), R') is ''autocatalytic'', if and only if for each reaction r'(A, B) ⊆ R': − # there exists a molecule c ⊆ Cl<sub>R'</sub>(F) such that (c, r') ⊆ C, − # A ⊆ Cl<sub>R'</sub>(F). − − A reaction system (ClR'(F), R') is autocatalytic, if and only if for each reaction r'(A, B) ⊆ R': − # there exists a molecule c ⊆ ClR'(F) such that (c, r') ⊆ C, − # A ⊆ ClR'(F). − − 反应系统(Cl<sub>R'</sub>(F), R')是自催化的，当且仅当对于每个反应r'(A, B) ⊆ R': − # 存在一个分子c ⊆ ClR'(F)使得(c, r') ⊆ C，+ − # A ⊆ ClR'(F).。 − ===Example===+ + − ===Example=== − − = = 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: + − − 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 第128行：
第52行： − 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: 第136行：
第57行： − 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: − 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 第156行：
第65行： − 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. − ==Probability that a random set is autocatalytic== − − ==Probability that a random set is autocatalytic== − − = = 一个随机集合是自催化的概率 = = − − 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.<ref>{{cite journal | author = Mossel E, Steel M. | title = Random biochemical networks and the probability of self-sustaining autocatalysis | journal = Journal of Theoretical Biology | volume = 233 | issue = 3 | pages = 327–336 | year = 2005 | pmid = 15652142| doi = 10.1016/j.jtbi.2004.10.011| bibcode = 2005JThBi.233..327M | citeseerx = 10.1.1.133.9352 }}</ref> 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，在某些假设条件下，随机集合RS有很高的概率是自催化的。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，从而随机产生出足够多的反应和催化作用，使得RS的一部分实现自供给。出于同样的原因，一个自催化集合会随着分子数的增加而迅速扩展。这些理论结果吸引了人们用自催化集合来科学地解释生命起源问题。 − − ==Formal limitations== − − ==Formal limitations== − − = = 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 [[polymer]]s 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== − − = = 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. + − 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. − 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，人们可以将形式化定义的ACS（'''autocatalytic set'''）视为更初始的概念，而在第二个定义中，系统本身的反映已经被明确地呈现出来，因为催化剂诱导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: 第259行：
第92行： − u : Desc(X) -> X − c : Desc(X) -> Desc(X) − − u : Desc(X) -> X − c : Desc(X) -> Desc(X) − − where the function 'u' is the [[Von Neumann universal constructor|"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定义域中的所有内容，而‘c’被用于任意描述的复制函数。实际上，“u”和“c”可以分解为许多的子功能或催化剂。 − − 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，(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+ − work on [[Self-replication|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==+ − = = = 非自治的自催化集合 = = − − 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. + − 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. − 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.+ − 展现非自治自催化集合的实际重要性的例子可以在编译器构造领域和操作系统中被找到，其中明确讨论了各自构造的自参考性质，通常称为自举（Bootstrapping）。 − + + + + − ==Comparison with other theories of life== − + + + − Autocatalytic sets constitute just one of several current theories of life, including the [[chemoton]]<ref name="gantibook">{{cite book| isbn= 9780198507260| title = The Principles of Life | last = Gánti | first = Tibor |publisher = Oxford University Press | date = 2003|editor1 = Eörs Száthmary | editor2 = James Griesemer}}</ref> of [[Tibor Gánti]], the [[Hypercycle (chemistry)|hypercycle]] of [[Manfred Eigen]] and [[Peter Schuster]],<ref>{{cite journal | doi= 10.11007/bf00450633|last1 = Eigen |first1 = M| last2 = Schuster |first2 =P | title = The hypercycle: a principle of natural self-organization. A: emergence of the hypercycle| journal= Naturwissenschaften|volume = 64|issue = 11|pages = 541–565}}</ref><ref>{{cite journal | doi= 10.1007/bf00420631|last1 = Eigen |first1 = M| last2 = Schuster |first2 =P | title = The hypercycle: a principle of natural self-organization. B: the abstract hypercycle| journal= Naturwissenschaften|volume = 65|issue = 1 |pages = 7–41}}</ref> − <ref>{{cite journal | doi= 10.1007/bf00420631|last1 = Eigen |first1 = M| last2 = Schuster |first2 =P | title = The hypercycle: a principle of natural self-organization. C: the realistic hypercycle| journal= Naturwissenschaften|volume = 65|issue = 7 |pages = 41–369}}</ref> the [[Robert Rosen (theoretical biologist)#Complexity and complex scientific models: (M,R) systems | (''M,R'') systems]]<ref>{{cite journal | doi= 10.1007/BF02477890 |last1 = Rosen | first1 = R.| date = 1958 |journal = Bull. Math. Biophys.| volume = 20|issue= 4|pages = 317–341|title = The representation of biological systems from the standpoint of the theory of categories}}</ref><ref>{{cite book| last1 = Rosen | first1 = R.| date = 1991| title = Life Itself: a comprehensive inquiry into the nature, origin, and fabrication of life| publisher = Columbia University Press| place= New York}}</ref> of [[Robert Rosen (theoretical biologist)|Robert Rosen]], and the [[autopoiesis]] (or ''self-building'')<ref>{{cite book| last1=Maturana |first1 = H. R.|last2 =Varela|first2 = F. |title = Autopoiesis and cognition: the realisation of the living|date=1980|publisher= D. Reidel Publishing Company| place = Dordrecht}}</ref> of [[Humberto Maturana]] and [[Francisco Varela]]. All of these (including autocatalytic sets) found their original inspiration in Erwin Schrödinger's book ''What is Life?''<ref>{{cite book| last1 = Schrödinger| first1 = Erwin|title = What is Life? |publisher = Cambridge University Press|date = 1944}}</ref> 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.<ref>{{cite journal | doi= 10.1016/j.jtbi.2015.05.015|title = Tibor Gánti and Robert Rosen: contrasting approaches to the same problem|last1 =Cornish-Bowden | first1 =A.|journal= J. Theor. Biol. |volume = 381|pages = 6–10|date=2015}}</ref> Until recently<ref>{{cite journal | doi= 10.1016/j.jtbi.2011.06.033 |title= From ''L’Homme Machine'' to metabolic closure: steps towards understanding life|last1 = Letelier|first1 = J C|last2=Cárdenas |first2 =M L|last3=Cornish-Bowden|first3 =A |journal=J. Theor. Biol. | date = 2011 | volume= 286|issue= 1 | pages= 100–113}}</ref><ref>{{cite journal | doi= 10.1016/j.biosystems.2014.03.002| title=Time rescaling and pattern formation in biological evolution| journal =BioSystems|volume=123 |pages= 19–26|date= 2014|last=Igamberdiev|first=A.U.}}</ref><ref>{{cite journal | doi= 10.1016/j.biosystems.2019.104063 − |last2=Cárdenas |first2 =M L|last1=Cornish-Bowden|first1 =A|title =Contrasting theories of life: historical context, current theories. In search of an ideal theory|journal=BioSystems|volume =188|pages=104063|date=2020}}</ref> 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)== − + − + − = = 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 − }}</ref> 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.<ref>{{cite journal | doi= 10.1016/j.jtbi.2017.05.023 | title = Life before LUCA |last2=Cárdenas |first2 =M L|last1=Cornish-Bowden|first1 =A| journal = J. Theor. Biol. | volume = 434 | pages=68–74}}</ref> − 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LUCA（the '''L'''ast '''U'''niversal '''C'''ommon '''A'''ncestor）等价。这是一个严重的错误，因为没有认识大量的进化发生在LUCA出现之前，LUCA只是指最后的共同祖先，而不是更古老的第一个祖先。 − 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|+ − issue= 1 |pages=7-15| date = 2016}}</ref>+ − <blockquote> 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."</blockquote> − 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（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”。 − + − {{Reflist}}+ − [[Category:Origin of life]] − [[Category:Artificial life]] − Category:Origin of life+ − Category:Artificial life+ − 类别: 生命起源类别: 人工生命 − <noinclude>+ + − <small>This page was moved from [[wikipedia:en:Autocatalytic set]]. Its edit history can be viewed at [[自催化集合/edithistory]]</small></noinclude> − + + +
无编辑摘要
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'''自催化集合 autocatalytic set''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。
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，分裂出的每一半自催化集合都会重新自生成出初始集合中的所有反应，就像细胞的有丝分裂一样。实际上，利用自催化的原理，一个小的代谢系统就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之一。
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，分裂出的每一半自催化集合都会重新自生成出初始集合中的所有反应，就像细胞的有丝分裂一样。实际上，利用自催化的原理，一个小的代谢系统就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之一。
在James D. Watson与Francis Crick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。
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Lincoln和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）。<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>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。
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·艾伦·考夫曼 Stuart Alan 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>和其他人的模型。
== 定义 ==
给定一组分子的集合M，化学反应可以粗略地定义为M的子集对r = (A, B):<ref>{{cite journal | author = Hordijk W | title = Autocatalytic Sets: From the Origin of Life to the Economy | journal = BioScience | volume = 63 | issue = 11 | pages = 877–881| year = 2013 | doi = 10.1525/bio.2013.63.11.6 | doi-access = free }}</ref>
= = 定义 = =
a<sub>1</sub> + a<sub>2</sub> + ... + a<sub>k</sub> → b<sub>1</sub> + b<sub>2</sub> + ... + b<sub>k</sub>
a<sub>1</sub> + a<sub>2</sub> + ... + a<sub>k</sub> → b<sub>1</sub> + b<sub>2</sub> + ... + b<sub>k</sub>
设R是可发生的反应的集合。一个(M, R)对是一个反应系统(RS)。
设R是可发生的反应的集合。一个(M, R)对是一个反应系统(RS)。
设C为一组分子反应对的集合来指定哪些分子可以催化哪些反应:
设C为一组分子反应对的集合来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}
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Cl<sub>R'</sub>(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， Cl<sub>R'</sub>(F)是M的最小子集，使得Cl<sub>R'</sub>(F)以及每个反应r'(A, B) ⊆ R':
A ⊆ Cl<sub>R'</sub>(F) ⇒ B ⊆ Cl<sub>R'</sub>(F)
A ⊆ Cl<sub>R'</sub>(F) ⇒ B ⊆ Cl<sub>R'</sub>(F)
反应系统(Cl<sub>R'</sub>(F), R'))是自催化的，当且仅当对于每个反应r'(A, B) ⊆ R':
# 存在一个分子c ⊆ Cl<sub>R'</sub>(F)使得(c, r') ⊆ C，
# A ⊆ Cl<sub>R'</sub>(F).。
== 实例 ==
设M = {a, b, c, d, f, g}和F = {a, b}。设集合R包含以下反应:
设M = {a, b, c, d, f, g}和F = {a, b}。设集合R包含以下反应:
a + b → c + d，由g催化
a + b → c + d，由g催化
c + b → g + a，由d或f催化
c + b → g + a，由d或f催化
由F = {a, b}，我们可以产生{c, d}，然后从{c, d}中，我们可以产生{g, a}，所以闭包等于:
由F = {a, b}，我们可以产生{c, d}，然后从{c, d}中，我们可以产生{g, a}，所以闭包等于:
Cl<sub>R'</sub>(F) = {a, b, c, d, g}
Cl<sub>R'</sub>(F) = {a, b, c, d, g}
根据定义，最大自催化子集R'包含两个反应:
根据定义，最大自催化子集R'包含两个反应:
a + b → c + d，由g催化
a + b → c + d，由g催化
c + b → g + a，由d催化
c + b → g + a，由d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。
(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。
== 一个随机集合是自催化的概率 ==
对上述模型的研究表明，在某些假设条件下，随机集合RS有很高的概率是自催化的。<ref>{{cite journal | author = Mossel E, Steel M. | title = Random biochemical networks and the probability of self-sustaining autocatalysis | journal = Journal of Theoretical Biology | volume = 233 | issue = 3 | pages = 327–336 | year = 2005 | pmid = 15652142| doi = 10.1016/j.jtbi.2004.10.011| bibcode = 2005JThBi.233..327M | citeseerx = 10.1.1.133.9352 }}</ref>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，从而随机产生出足够多的反应和催化作用，使得RS的一部分实现自供给。出于同样的原因，一个自催化集合会随着分子数的增加而迅速扩展。这些理论结果吸引了人们用自催化集合来科学地解释生命起源问题。
== 形式限制 ==
从形式上讲，很难将分子视为非结构化实体之外的任何东西，因为可能的反应（和分子）集合会变得无限大。因此，还不可能根据所需来衍生出任意长度的聚合物以模拟DNA、RNA或蛋白质。对RNA世界的研究也面临了同样的问题。
从形式上讲，很难将分子视为非结构化实体之外的任何东西，因为可能的反应（和分子）集合会变得无限大。因此，还不可能根据所需来衍生出任意长度的聚合物以模拟DNA、RNA或蛋白质。对RNA世界的研究也面临了同样的问题。
== 语言学方面 ==
与上述适用于人工化学领域的定义相反，目前自催化集合的概念还没有达成一致。
与上述适用于人工化学领域的定义相反，目前自催化集合的概念还没有达成一致。
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。
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。
从结构和自然历史的观点来看，人们可以将形式化定义的ACS（autocatalytic set）视为更初始的概念，而在第二个定义中，系统本身的反映已经被明确地呈现出来，因为催化剂诱导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。
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:
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:
c : Desc(X) -> Desc(X)
c : Desc(X) -> Desc(X)
其中，函数'u'是“通用”构造函数，它根据适当的描述构造定义域中的所有内容，而'c'被用于任意描述的复制函数。实际上，'u'和'c'可以分解为许多的子功能或催化剂。
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。
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。
== 非自治的自催化集合 ==
几乎所有关于自催化集合的文献都没有明确规定这些集合是不是自治的。通常，集合的自治性是默认的。
几乎所有关于自催化集合的文献都没有明确规定这些集合是不是自治的。通常，集合的自治性是默认的。
或许，上述内容强调了自治的自复制和早期生命起源。但是自催化集合的概念实际上更为普遍，在各种技术领域都有实际应用，例如，掌握自我维持的工具链。显然，这样的集合是不自治的，是人类行为的对象。
或许，上述内容强调了自治的自复制和早期生命起源。但是自催化集合的概念实际上更为普遍，在各种技术领域都有实际应用，例如，掌握自我维持的工具链。显然，这样的集合是不自治的，是人类行为的对象。
展现非自治自催化集合的实际重要性的例子可以在编译器构造领域和操作系统中被找到，其中明确讨论了各自构造的自参考性质，通常称为'''自举 Bootstrapping'''。
==Comparison with other theories of life==
== 与其他生命理论的比较 ==
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<ref name="gantibook">{{cite book| isbn= 9780198507260| title = The Principles of Life | last = Gánti | first = Tibor |publisher = Oxford University Press | date = 2003|editor1 = Eörs Száthmary | editor2 = James Griesemer}}</ref>、 曼弗雷德·艾根 Manfred Eigen和彼得·舒斯特 Peter Schuster的超循环<ref>{{cite journal | doi= 10.11007/bf00450633|last1 = Eigen |first1 = M| last2 = Schuster |first2 =P | title = The hypercycle: a principle of natural self-organization. A: emergence of the hypercycle| journal= Naturwissenschaften|volume = 64|issue = 11|pages = 541–565}}</ref><ref>{{cite journal | doi= 10.1007/bf00420631|last1 = Eigen |first1 = M| last2 = Schuster |first2 =P | title = The hypercycle: a principle of natural self-organization. B: the abstract hypercycle| journal= Naturwissenschaften|volume = 65|issue = 1 |pages = 7–41}}</ref>
<ref>{{cite journal | doi= 10.1007/bf00420631|last1 = Eigen |first1 = M| last2 = Schuster |first2 =P | title = The hypercycle: a principle of natural self-organization. C: the realistic hypercycle| journal= Naturwissenschaften|volume = 65|issue = 7 |pages = 41–369}}</ref>、罗伯特·罗森 Robert Rosen的[[Robert Rosen (theoretical biologist)#Complexity and complex scientific models: (M,R) systems |(''M,R'')系统]]<ref>{{cite journal | doi= 10.1007/BF02477890 |last1 = Rosen | first1 = R.| date = 1958 |journal = Bull. Math. Biophys.| volume = 20|issue= 4|pages = 317–341|title = The representation of biological systems from the standpoint of the theory of categories}}</ref><ref>{{cite book| last1 = Rosen | first1 = R.| date = 1991| title = Life Itself: a comprehensive inquiry into the nature, origin, and fabrication of life| publisher = Columbia University Press| place= New York}}</ref>以及Humberto Maturana和Francisco Varela的[[自创生理论]]<ref>{{cite book| last1=Maturana |first1 = H. R.|last2 =Varela|first2 = F. |title = Autopoiesis and cognition: the realisation of the living|date=1980|publisher= D. Reidel Publishing Company| place = Dordrecht}}</ref>。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《What is Life?》。<ref>{{cite book| last1 = Schrödinger| first1 = Erwin|title = What is Life? |publisher = Cambridge University Press|date = 1944}}</ref>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Gánti和Rosen之间的相似之处。<ref>{{cite journal | doi= 10.1016/j.jtbi.2015.05.015|title = Tibor Gánti and Robert Rosen: contrasting approaches to the same problem|last1 =Cornish-Bowden | first1 =A.|journal= J. Theor. Biol. |volume = 381|pages = 6–10|date=2015}}</ref>直到最近，<ref>{{cite journal | doi= 10.1016/j.jtbi.2011.06.033 |title= From ''L’Homme Machine'' to metabolic closure: steps towards understanding life|last1 = Letelier|first1 = J C|last2=Cárdenas |first2 =M L|last3=Cornish-Bowden|first3 =A |journal=J. Theor. Biol. | date = 2011 | volume= 286|issue= 1 | pages= 100–113}}</ref><ref>{{cite journal | doi= 10.1016/j.biosystems.2014.03.002| title=Time rescaling and pattern formation in biological evolution| journal =BioSystems|volume=123 |pages= 19–26|date= 2014|last=Igamberdiev|first=A.U.}}</ref><ref>{{cite journal | doi= 10.1016/j.biosystems.2019.104063
|last2=Cárdenas |first2 =M L|last1=Cornish-Bowden|first1 =A|title =Contrasting theories of life: historical context, current theories. In search of an ideal theory|journal=BioSystems|volume =188|pages=104063|date=2020}}</ref>几乎没有人试图比较不同的理论并一起讨论它们。
= = 与其他生命理论的比较 = =
== 最后普遍的共同祖先(LUCA) ==
一些作者将生命起源的模型与LUCA（the '''L'''ast '''U'''niversal '''C'''ommon '''A'''ncestor）等价。<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
}}</ref>这是一个严重的错误，因为没有认识大量的进化发生在LUCA出现之前，LUCA只是指最后的共同祖先，而不是更古老的第一个祖先。<ref>{{cite journal | doi= 10.1016/j.jtbi.2017.05.023 | title = Life before LUCA |last2=Cárdenas |first2 =M L|last1=Cornish-Bowden|first1 =A| journal = J. Theor. Biol. | volume = 434 | pages=68–74}}</ref>
Gill 和 Forterre 表达了以下基本观点：<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|
issue= 1 |pages=7-15| date = 2016}}</ref>
<blockquote> ''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”。''
</blockquote>
==Last Universal Common Ancestor (LUCA)==
==参考文献==
{{Reflist}}
==编辑推荐==
===集智课程===
====[https://campus.swarma.org/course/2182 复杂性的度量及其对生命起源的启示|专场1]====
该课程介绍了复杂性的度量及其对生命起源的启示。
====[https://campus.swarma.org/course/2153 生命起源的最重要的问题——主体性与层级跃迁]====
生命作为最典型的复杂系统，从细胞到个体再到群体，在不同层次上都展现出各种复杂性，引发不同学科研究者的兴趣。为了促进生命复杂系统的跨学科交流，我们策划“生命复杂性”系列读书会，组织精读和讨论相关研究。生命起源是最迷人的科学问题之一，也是生物、化学、地质等多个学科的汇合地。而从复杂性科学的视角看，生命起源和发展是一个多次涌现、逐层跃迁的过程。
该课程中介绍了关于生命起源的四大经典理论和最新工作，并讨论生命分阶段起源的定量研究设想。
==References==
====[https://campus.swarma.org/course/2261 生命起源与自我复制]====
该课程介绍了生命起源与自我复制的概念以及其它们之间的关系。
====[https://swarma.org/?p=3723 冯·诺依曼的遗产：寻找人工生命的理论根源]====
人工生命是可以回答人工智能无法思考的问题的。尽管自从九十年代之后，人工生命才逐渐发展起来，成为独立于人工智能的科学领域，但它的理论根源却可以追溯到二十世纪五十年代。那个时候，一个伟大的数学家兼发明家冯·诺依曼正在思考如何制造可以复制自身的机器。这个自复制机器的核心目的并不在于生命自复制这个问题本身，而是希望寻找出一条途径，能够让机器一劳永逸地“抵抗熵增”，不断朝越来越复杂的方向进化，而这一方法极有可能就是制造强人工智能机器，甚至是具有自我意识的智能机器的正确途径。
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