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=== Relational biology ===

=== Relational biology ===

Rosen's work proposed a methodology which needs to be developed in addition to the current reductionistic approaches to science by [[molecular biology|molecular biologists]]. He called this methodology ''Relational Biology''. ''Relational'' is a term he correctly attributes to his mentor [[Nicolas Rashevsky]], who published several papers on the importance of set-theoretical relations<ref>{{Cite web |url=http://planetphysics.org/encyclopedia/RelationTheory.html |title=Jon Awbrey ''Relation theory'' (the logical approach to relation theory) |access-date=January 31, 2010 |archive-url=https://web.archive.org/web/20100527004040/http://planetphysics.org/encyclopedia/RelationTheory.html |archive-date=May 27, 2010 |url-status=dead  }}</ref> in biology prior to Rosen's first reports on this subject. Rosen's relational approach to Biology is an extension and amplification of Nicolas Rashevsky's treatment of ''n''-ary relations in, and among, organismic sets that he developed over two decades as a representation of both biological and social "organisms".

Rosen's work proposed a methodology which needs to be developed in addition to the current reductionistic approaches to science by [[molecular biology|molecular biologists]]. He called this methodology ''Relational Biology''. ''Relational'' is a term he correctly attributes to his mentor [[Nicolas Rashevsky]], who published several papers on the importance of set-theoretical relations<ref>{{Cite web |url=http://planetphysics.org/encyclopedia/RelationTheory.html |title=Jon Awbrey ''Relation theory'' (the logical approach to relation theory) |access-date=January 31, 2010 |archive-url=https://web.archive.org/web/20100527004040/http://planetphysics.org/encyclopedia/RelationTheory.html |archive-date=May 27, 2010 |url-status=dead  }}</ref> in biology prior to Rosen's first reports on this subject. Rosen's relational approach to Biology is an extension and amplification of Nicolas Rashevsky's treatment of ''n''-ary relations in, and among, organismic sets that he developed over two decades as a representation of both biological and social "organisms".

Rosen's work proposed a methodology which needs to be developed in addition to the current reductionistic approaches to science by molecular biologists. He called this methodology Relational Biology. Relational is a term he correctly attributes to his mentor Nicolas Rashevsky, who published several papers on the importance of set-theoretical relations in biology prior to Rosen's first reports on this subject. Rosen's relational approach to Biology is an extension and amplification of Nicolas Rashevsky's treatment of n-ary relations in, and among, organismic sets that he developed over two decades as a representation of both biological and social "organisms".

Rosen's work proposed a methodology which needs to be developed in addition to the current reductionistic approaches to science by molecular biologists. He called this methodology Relational Biology. Relational is a term he correctly attributes to his mentor Nicolas Rashevsky, who published several papers on the importance of set-theoretical relations in biology prior to Rosen's first reports on this subject. Rosen's relational approach to Biology is an extension and amplification of Nicolas Rashevsky's treatment of n-ary relations in, and among, organismic sets that he developed over two decades as a representation of both biological and social "organisms".

罗森的工作提出了一种方法论，目前分子生物学家除了对科学的还原论方法的运用之外，还需要发展这种方法论。他称这种方法为关系生物学。他确切地将关系这个术语归功于他的导师尼古拉斯 · 拉舍夫斯基，在罗森第一次就这个专题发表报告之前，拉舍夫斯基就集合理论关系在生物学中的重要性发表了几篇论文。罗森对生物学的关系方法是尼古拉斯 · 拉舍夫斯基对 n 元关系处理方法的延伸和扩展。拉舍夫斯基在过去20年中发展了一些有机体集合，作为生物和社会“有机体”的代表。

罗森的工作提出了一种方法论，目前分子生物学家除了对科学的还原论方法的运用之外，还需要发展这种方法论。他称这种方法为关系生物学。他确切地将关系这个术语归功于他的导师尼古拉斯 · 拉舍夫斯基，在罗森第一次就这个专题发表报告之前，拉舍夫斯基就集合理论关系在生物学中的重要性发表了几篇论文。罗森对生物学的关系方法是尼古拉斯 · 拉舍夫斯基对 n 元关系处理方法的延伸和扩展。拉舍夫斯基在过去20年中发展了一些有机体集合，作为生物和社会“有机体”的代表。

Rosen's relational biology maintains that organisms, and indeed all systems, have a distinct quality called organization which is not part of the language of reductionism, as for example in molecular biology, although it is increasingly employed in systems biology. It has to do with more than purely structural or material aspects. For example, organization includes all relations between material parts, relations between the effects of interactions of the material parts, and relations with time and environment, to name a few. Many people sum up this aspect of complex systems by saying that the whole is more than the sum of the parts. Relations between parts and between the effects of interactions must be considered as additional 'relational' parts, in some sense.

Rosen's relational biology maintains that organisms, and indeed all systems, have a distinct quality called organization which is not part of the language of reductionism, as for example in molecular biology, although it is increasingly employed in systems biology. It has to do with more than purely structural or material aspects. For example, organization includes all relations between material parts, relations between the effects of interactions of the material parts, and relations with time and environment, to name a few. Many people sum up this aspect of complex systems by saying that the whole is more than the sum of the parts. Relations between parts and between the effects of interactions must be considered as additional 'relational' parts, in some sense.

Rosen said that [[organization]] must be independent from the material particles which seemingly constitute a [[living system]]. As he put it:

Rosen said that [[organization]] must be independent from the material particles which seemingly constitute a [[living system]]. As he put it:

罗森说，组织必须独立于看似构成一个生命系统的物质粒子。正如他所说:

 

罗森说，组织必须独立于看似构成一个生命系统的物质粒子。正如他所说的:

Rosen's abstract relational biology approach focuses on a definition of living organisms, and all [[complex system]]s, in terms of their internal ''organization'' as [[Open system (systems theory)|open system]]s that cannot be reduced to their interacting components because of the multiple relations between metabolic, replication and repair components that govern the organism's complex biodynamics.

Rosen's abstract relational biology approach focuses on a definition of living organisms, and all [[complex system]]s, in terms of their internal ''organization'' as [[Open system (systems theory)|open system]]s that cannot be reduced to their interacting components because of the multiple relations between metabolic, replication and repair components that govern the organism's complex biodynamics.

Rosen's abstract relational biology approach focuses on a definition of living organisms, and all complex systems, in terms of their internal organization as open systems that cannot be reduced to their interacting components because of the multiple relations between metabolic, replication and repair components that govern the organism's complex biodynamics.

Rosen's abstract relational biology approach focuses on a definition of living organisms, and all complex systems, in terms of their internal organization as open systems that cannot be reduced to their interacting components because of the multiple relations between metabolic, replication and repair components that govern the organism's complex biodynamics.

He deliberately chose the `simplest' [[Graph (discrete mathematics)|graph]]s and categories for his representations of Metabolism-Repair Systems in small categories of sets endowed only with the discrete "efficient" topology of sets, envisaging this choice as the most general and less restrictive. It turns out however that the efficient entailments of <math>(M{,}R)</math>systems <!--{{clarify|date=September 2013}}--> are "closed to efficient cause",<ref>[http://www.people.vcu.edu/~mikuleck/PPRISS3.html Donald C. Mikulecky Robert Rosen: The well posed question and its answer - Why are organisms different from machines?]</ref> or in simple terms the catalysts ("efficient causes" of metabolism, usually identified as enzymes) are themselves products of metabolism, and thus may not be considered, in a strict mathematical sense, as subcategories of the [[category (mathematics)|category]] of sequential machines or [[automata]]: in direct contradiction of the French philosopher [[Descartes]]' supposition that all animals are only elaborate machines or ''mechanisms''. Rosen stated: "''I argue that the only resolution to such problems'' [of the subject-object boundary and what constitutes objectivity] ''is in the recognition that closed loops of causation are 'objective'; i.e. legitimate objects of scientific scrutiny. These are explicitly forbidden in any machine or mechanism.''"<ref>{{Cite journal|last=Rosen|first=Robert|date=June 1, 1993|title=Drawing the boundary between subject and object: Comments on the mind-brain problem|journal=Theoretical Medicine|language=en|volume=14|issue=2|pages=89–100|doi=10.1007/BF00997269|pmid=8236065|s2cid=24953932|issn=1573-1200}}</ref> Rosen's demonstration of "efficient closure" was to present this clear paradox in mechanistic science, that on the one hand organisms are defined by such causal closures and on the other hand mechanism forbids them; thus we need to revise our understanding of nature. The mechanistic view prevails even today in most of general biology, and most of science, although some claim no longer in [[sociology]] and [[psychology]] where reductionist approaches have failed and fallen out of favour since the early 1970s. However those fields have yet to reach consensus on what the new view should be, as is also the case in most other disciplines, which struggle to retain various aspects of "the machine metaphor" for living and complex systems.

He deliberately chose the `simplest' [[Graph (discrete mathematics)|graph]]s and categories for his representations of Metabolism-Repair Systems in small categories of sets endowed only with the discrete "efficient" topology of sets, envisaging this choice as the most general and less restrictive. It turns out however that the efficient entailments of <math>(M{,}R)</math>systems <!--{{clarify|date=September 2013}}--> are "closed to efficient cause",<ref>[http://www.people.vcu.edu/~mikuleck/PPRISS3.html Donald C. Mikulecky Robert Rosen: The well posed question and its answer - Why are organisms different from machines?]</ref> or in simple terms the catalysts ("efficient causes" of metabolism, usually identified as enzymes) are themselves products of metabolism, and thus may not be considered, in a strict mathematical sense, as subcategories of the [[category (mathematics)|category]] of sequential machines or [[automata]]: in direct contradiction of the French philosopher [[Descartes]]' supposition that all animals are only elaborate machines or ''mechanisms''. Rosen stated: "''I argue that the only resolution to such problems'' [of the subject-object boundary and what constitutes objectivity] ''is in the recognition that closed loops of causation are 'objective'; i.e. legitimate objects of scientific scrutiny. These are explicitly forbidden in any machine or mechanism.''"<ref>{{Cite journal|last=Rosen|first=Robert|date=June 1, 1993|title=Drawing the boundary between subject and object: Comments on the mind-brain problem|journal=Theoretical Medicine|language=en|volume=14|issue=2|pages=89–100|doi=10.1007/BF00997269|pmid=8236065|s2cid=24953932|issn=1573-1200}}</ref> Rosen's demonstration of "efficient closure" was to present this clear paradox in mechanistic science, that on the one hand organisms are defined by such causal closures and on the other hand mechanism forbids them; thus we need to revise our understanding of nature. The mechanistic view prevails even today in most of general biology, and most of science, although some claim no longer in [[sociology]] and [[psychology]] where reductionist approaches have failed and fallen out of favour since the early 1970s. However those fields have yet to reach consensus on what the new view should be, as is also the case in most other disciplines, which struggle to retain various aspects of "the machine metaphor" for living and complex systems.

He deliberately chose the `simplest' graphs and categories for his representations of Metabolism-Repair Systems in small categories of sets endowed only with the discrete "efficient" topology of sets, envisaging this choice as the most general and less restrictive. It turns out however that the efficient entailments of (M{,}R)systems  are "closed to efficient cause",Donald C. Mikulecky Robert Rosen: The well posed question and its answer - Why are organisms different from machines? or in simple terms the catalysts ("efficient causes" of metabolism, usually identified as enzymes) are themselves products of metabolism, and thus may not be considered, in a strict mathematical sense, as subcategories of the category of sequential machines or automata: in direct contradiction of the French philosopher Descartes' supposition that all animals are only elaborate machines or mechanisms. Rosen stated: "I argue that the only resolution to such problems [of the subject-object boundary and what constitutes objectivity] is in the recognition that closed loops of causation are 'objective'; i.e. legitimate objects of scientific scrutiny. These are explicitly forbidden in any machine or mechanism." Rosen's demonstration of "efficient closure" was to present this clear paradox in mechanistic science, that on the one hand organisms are defined by such causal closures and on the other hand mechanism forbids them; thus we need to revise our understanding of nature. The mechanistic view prevails even today in most of general biology, and most of science, although some claim no longer in sociology and psychology where reductionist approaches have failed and fallen out of favour since the early 1970s. However those fields have yet to reach consensus on what the new view should be, as is also the case in most other disciplines, which struggle to retain various aspects of "the machine metaphor" for living and complex systems.

He deliberately chose the `simplest' graphs and categories for his representations of Metabolism-Repair Systems in small categories of sets endowed only with the discrete "efficient" topology of sets, envisaging this choice as the most general and less restrictive. It turns out however that the efficient entailments of (M{,}R)systems  are "closed to efficient cause",Donald C. Mikulecky Robert Rosen: The well posed question and its answer - Why are organisms different from machines? or in simple terms the catalysts ("efficient causes" of metabolism, usually identified as enzymes) are themselves products of metabolism, and thus may not be considered, in a strict mathematical sense, as subcategories of the category of sequential machines or automata: in direct contradiction of the French philosopher Descartes' supposition that all animals are only elaborate machines or mechanisms. Rosen stated: "I argue that the only resolution to such problems [of the subject-object boundary and what constitutes objectivity] is in the recognition that closed loops of causation are 'objective'; i.e. legitimate objects of scientific scrutiny. These are explicitly forbidden in any machine or mechanism." Rosen's demonstration of "efficient closure" was to present this clear paradox in mechanistic science, that on the one hand organisms are defined by such causal closures and on the other hand mechanism forbids them; thus we need to revise our understanding of nature. The mechanistic view prevails even today in most of general biology, and most of science, although some claim no longer in sociology and psychology where reductionist approaches have failed and fallen out of favour since the early 1970s. However those fields have yet to reach consensus on what the new view should be, as is also the case in most other disciplines, which struggle to retain various aspects of "the machine metaphor" for living and complex systems.

他有意地选择“最简单的”图和类别来表示只赋予离散的集合的“有效”拓扑的小类别集合中的代谢-修复系统，设想这种选择是最一般和限制较少的。然而，事实证明(m { ，} r)系统的有效衍生是“对有效原因闭合的”，Donald c. Mikulecky Robert Rosen: 这个问题及其答案——为什么有机体与机器不同？或者用简单的术语来说，新陈代谢的催化剂(新陈代谢的“有效原因”，通常被认为是酶)本身就是新陈代谢的产物，因此，从严格的数学意义上来说，可能不会被认为是连续机器或自动机范畴的子范畴: 这与法国哲学家笛卡尔的假设直接矛盾，即所有的动物都只是复杂的机器或机制。罗森说: “我认为，这些问题[主客体边界和客观性的构成]的唯一解决办法是承认因果关系的封闭循环是‘客观的’;。合法的科学研究对象。任何机器或机械都明确禁止这些操作。”罗森关于“有效闭合”的论证，是为了在机械论科学中提出这样一个明确的悖论: 一方面，生物体是由这种因果闭合定义的，另一方面，机制又禁止它们; 因此，我们需要修正我们对自然的理解。这种机械论的观点甚至在今天的大多数普通生物学和大多数科学中依然盛行，尽管有些人声称社会学和心理学中的还原论方法已经失败，并且自20世纪70年代初以来已经失宠。然而，这些领域尚未就新观点应该是什么达成共识，大多数其他学科也是如此，这些学科努力保留生活和复杂系统的”机器隐喻”的各个方面。

他有意地选择“最简单的”图和类别来表示只赋予离散集合的“有效”拓扑小类别集合中的代谢-修复系统，并且设想这种选择是最一般和限制较少的。然而，事实证明 (M{,}R)系统的有效衍生是“有效因果闭合的”。唐纳德·c·米库勒基·罗伯特·罗森: 这是一个恰当的问题及其答案——为什么有机体不同于机器？或者用简单的术语来说，新陈代谢的催化剂(新陈代谢的“有效原因”，通常被认为是酶)本身就是新陈代谢的产物，因此，从严格的数学意义上来说，可能不会被认为是连续机器或自动机范畴的子范畴: 这与法国哲学家笛卡尔的假设直接矛盾，即所有的动物都只是复杂的机器或机制。罗森说:“我认为，解决这些问题(主体-客体边界和什么构成客观性)的唯一办法是承认因果关系的闭环是‘客观的’;即科学审查的合法对象。任何机器论或机械论都明确禁止这些操作。”罗森关于“有效闭合”的论证，是为了在机械论科学中提出这样一个明确的悖论: 一方面，生物体是由这种因果闭合定义的，另一方面，机制又禁止它们; 因此，我们需要修正我们对自然的理解。这种机械论的观点甚至在今天的大多数普通生物学和大多数科学中依然盛行，尽管有些人声称社会学和心理学中的还原论方法已经失败，并且自20世纪70年代初以来已经失宠。然而，这些领域尚未就新观点应该是什么达成共识，大多数其他学科也是如此，这些学科努力保留生命和复杂系统的”机器隐喻”的各个方面。

=== Complexity and complex scientific models: (''M,R'') systems ===

=== Complexity and complex scientific models: (''M,R'') systems ===

=== Complexity and complex scientific models: (M,R) systems ===

=== Complexity and complex scientific models: (M,R) systems ===

= = = 复杂性和复杂的科学模型: (m，r)系统 = =  

= 复杂性和复杂科学模型:(M,R)系统 =  

The clarification of the distinction between simple and [[complex system|complex scientific models]] became in later years a major goal of Rosen's published reports. Rosen maintained that modeling is at the very essence of science and thought. His book [[Anticipatory Systems; Philosophical, Mathematical, and Methodological Foundations|''Anticipatory Systems'']]<ref>''Anticipatory Systems: Philosophical, Mathematical, and  Methodological Foundations'', Robert Rosen, 2nd edition, with contributions by Judith Rosen, John J. Klineman and Mihai Nadin, 2012, lx + 472 pp., Springer, New York {{ISBN|978-1-4614-1268-7}}</ref> describes, in detail, what he termed the ''modeling relation''. He showed the deep differences between a true modeling relation and a [[simulation]], the latter not based on such a modeling relation.

The clarification of the distinction between simple and [[complex system|complex scientific models]] became in later years a major goal of Rosen's published reports. Rosen maintained that modeling is at the very essence of science and thought. His book [[Anticipatory Systems; Philosophical, Mathematical, and Methodological Foundations|''Anticipatory Systems'']]<ref>''Anticipatory Systems: Philosophical, Mathematical, and  Methodological Foundations'', Robert Rosen, 2nd edition, with contributions by Judith Rosen, John J. Klineman and Mihai Nadin, 2012, lx + 472 pp., Springer, New York {{ISBN|978-1-4614-1268-7}}</ref> describes, in detail, what he termed the ''modeling relation''. He showed the deep differences between a true modeling relation and a [[simulation]], the latter not based on such a modeling relation.

The clarification of the distinction between simple and complex scientific models became in later years a major goal of Rosen's published reports. Rosen maintained that modeling is at the very essence of science and thought. His book Anticipatory SystemsAnticipatory Systems: Philosophical, Mathematical, and  Methodological Foundations, Robert Rosen, 2nd edition, with contributions by Judith Rosen, John J. Klineman and Mihai Nadin, 2012, lx + 472 pp., Springer, New York  describes, in detail, what he termed the modeling relation. He showed the deep differences between a true modeling relation and a simulation, the latter not based on such a modeling relation.

The clarification of the distinction between simple and complex scientific models became in later years a major goal of Rosen's published reports. Rosen maintained that modeling is at the very essence of science and thought. His book Anticipatory SystemsAnticipatory Systems: Philosophical, Mathematical, and  Methodological Foundations, Robert Rosen, 2nd edition, with contributions by Judith Rosen, John J. Klineman and Mihai Nadin, 2012, lx + 472 pp., Springer, New York  describes, in detail, what he termed the modeling relation. He showed the deep differences between a true modeling relation and a simulation, the latter not based on such a modeling relation.

在后来的几年里，罗森发表的报告的主要目标就是澄清简单模型和复杂模型之间的区别。罗森坚持认为，建模是科学和思想的本质。2012，lx + 472 pp. ，Springer，New York. 详细描述了他称之为建模关系的东西。他展示了真实建模关系和模拟之间的深刻差异，后者并不基于这样的建模关系。

在后来的几年里，罗森发表的报告的主要目标就是澄清简单模型和复杂模型之间的区别。罗森坚持认为，建模是科学和思想的本质。他的著作《预期系统健康预防系统:哲学、数学和方法论基础》，罗伯特罗森，第二版，由朱迪丝·罗森，约翰·j·克莱恩曼和米哈伊·纳丁 贡献，2012,lx + 472页，施普林格，纽约详细描述了他所说的建模关系。他展示了真实建模关系和模拟之间的深刻差异，后者并不基于这样的建模关系。

In [[mathematical biology]] he is known as the originator of a class of relational models of living [[organism]]s, called <math>(M{,}R)</math>systems that he devised to capture the minimal capabilities that a material [[system]] would need in order to be one of the simplest ''functional organisms'' that are commonly said to be "alive". In this kind of system, <math>M</math> stands for the metabolic and <math>R</math> stands for the 'repair' subsystems of a simple organism, for example active 'repair' RNA molecules. Thus, his mode for determining or "defining" life in any given system is a functional, not material, mode; although he did consider in his 1970s published reports specific ''dynamic realizations'' of the simplest <math>(M{,}R)</math>systems in terms of enzymes (<math>M</math>), [[RNA]] (<math>R</math>), and functional, duplicating [[DNA]] (his <math>\beta</math>-mapping).

In [[mathematical biology]] he is known as the originator of a class of relational models of living [[organism]]s, called <math>(M{,}R)</math>systems that he devised to capture the minimal capabilities that a material [[system]] would need in order to be one of the simplest ''functional organisms'' that are commonly said to be "alive". In this kind of system, <math>M</math> stands for the metabolic and <math>R</math> stands for the 'repair' subsystems of a simple organism, for example active 'repair' RNA molecules. Thus, his mode for determining or "defining" life in any given system is a functional, not material, mode; although he did consider in his 1970s published reports specific ''dynamic realizations'' of the simplest <math>(M{,}R)</math>systems in terms of enzymes (<math>M</math>), [[RNA]] (<math>R</math>), and functional, duplicating [[DNA]] (his <math>\beta</math>-mapping).

In mathematical biology he is known as the originator of a class of relational models of living organisms, called (M{,}R)systems that he devised to capture the minimal capabilities that a material system would need in order to be one of the simplest functional organisms that are commonly said to be "alive". In this kind of system, M stands for the metabolic and R stands for the 'repair' subsystems of a simple organism, for example active 'repair' RNA molecules. Thus, his mode for determining or "defining" life in any given system is a functional, not material, mode; although he did consider in his 1970s published reports specific dynamic realizations of the simplest (M{,}R)systems in terms of enzymes (M), RNA (R), and functional, duplicating DNA (his \beta-mapping).

In mathematical biology he is known as the originator of a class of relational models of living organisms, called (M{,}R)systems that he devised to capture the minimal capabilities that a material system would need in order to be one of the simplest functional organisms that are commonly said to be "alive". In this kind of system, M stands for the metabolic and R stands for the 'repair' subsystems of a simple organism, for example active 'repair' RNA molecules. Thus, his mode for determining or "defining" life in any given system is a functional, not material, mode; although he did consider in his 1970s published reports specific dynamic realizations of the simplest (M{,}R)systems in terms of enzymes (M), RNA (R), and functional, duplicating DNA (his \beta-mapping).

在数学生物学中，他被认为是一类生物有机体关系模型的创始人，这类关系模型被称为(m { ，} r)系统，他设计这类系统是为了捕捉物质系统成为通常被称为“活的”的最简单的功能有机体所需要的最低能力。在这种系统中，m 代表新陈代谢，r 代表简单有机体的修复子系统，例如活跃的修复 RNA 分子。因此，他在任何给定系统中确定或“定义”生命的模式是功能性的，而不是物质性的; 尽管他在20世纪70年代发表的报告中考虑了最简单(m { ，} r)系统在酶(m)、 RNA (r)和功能性复制 DNA (他的 beta-mapping)方面的具体动态实现。

在数学生物学中，他被认为是一类生物有机体关系模型的创始人，这类关系模型被称为 (M{,}R)系统，他设计这类系统是为了捕捉物质系统成为通常被称为“活的”的最简单的功能有机体所需要的最低能力。在这种系统中，m 代表新陈代谢，r 代表简单有机体的修复子系统，例如活跃的修复 RNA 分子。因此，他在任何给定系统中确定或“定义”生命的模式是功能性的，而不是物质性的; 尽管他在20世纪70年代发表的报告中考虑了最简单 (M{,}R)系统在酶(m)、 RNA (r)和功能性复制 DNA (他的β模型)方面的具体动态实现。

He went, however, even further in this direction by claiming that when studying a [[complex system]], one ''"can throw away the matter and study the organization"'' to learn those things that are essential to defining in general an entire class of systems. This has been, however, taken too literally by a few of his former students who have not completely assimilated Robert Rosen's injunction of the need for a theory of ''dynamic realizations'' of such abstract components in specific molecular form in order to close the modeling loop {{clarify|date=September 2013}} for the simplest functional organisms (such as, for example, single-cell algae or [[microorganisms]]).<ref>Robert Rosen. 1970. ''Dynamical Systems Theory in Biology'', New York: Wiley Interscience.</ref> He supported this claim (that he actually attributed to [[Nicolas Rashevsky]]) based on the fact that living organisms are a class of systems with an extremely wide range of material "ingredients", different structures, different habitats, different modes of living and [[reproduction]], and yet we are somehow able to recognize them all as ''living'', or functional organisms, without being however ''[[vitalism|vitalist]]s''.

He went, however, even further in this direction by claiming that when studying a [[complex system]], one ''"can throw away the matter and study the organization"'' to learn those things that are essential to defining in general an entire class of systems. This has been, however, taken too literally by a few of his former students who have not completely assimilated Robert Rosen's injunction of the need for a theory of ''dynamic realizations'' of such abstract components in specific molecular form in order to close the modeling loop {{clarify|date=September 2013}} for the simplest functional organisms (such as, for example, single-cell algae or [[microorganisms]]).<ref>Robert Rosen. 1970. ''Dynamical Systems Theory in Biology'', New York: Wiley Interscience.</ref> He supported this claim (that he actually attributed to [[Nicolas Rashevsky]]) based on the fact that living organisms are a class of systems with an extremely wide range of material "ingredients", different structures, different habitats, different modes of living and [[reproduction]], and yet we are somehow able to recognize them all as ''living'', or functional organisms, without being however ''[[vitalism|vitalist]]s''.

He went, however, even further in this direction by claiming that when studying a complex system, one "can throw away the matter and study the organization" to learn those things that are essential to defining in general an entire class of systems. This has been, however, taken too literally by a few of his former students who have not completely assimilated Robert Rosen's injunction of the need for a theory of dynamic realizations of such abstract components in specific molecular form in order to close the modeling loop  for the simplest functional organisms (such as, for example, single-cell algae or microorganisms).Robert Rosen. 1970. Dynamical Systems Theory in Biology, New York: Wiley Interscience. He supported this claim (that he actually attributed to Nicolas Rashevsky) based on the fact that living organisms are a class of systems with an extremely wide range of material "ingredients", different structures, different habitats, different modes of living and reproduction, and yet we are somehow able to recognize them all as living, or functional organisms, without being however vitalists.

He went, however, even further in this direction by claiming that when studying a complex system, one "can throw away the matter and study the organization" to learn those things that are essential to defining in general an entire class of systems. This has been, however, taken too literally by a few of his former students who have not completely assimilated Robert Rosen's injunction of the need for a theory of dynamic realizations of such abstract components in specific molecular form in order to close the modeling loop  for the simplest functional organisms (such as, for example, single-cell algae or microorganisms).Robert Rosen. 1970. Dynamical Systems Theory in Biology, New York: Wiley Interscience. He supported this claim (that he actually attributed to Nicolas Rashevsky) based on the fact that living organisms are a class of systems with an extremely wide range of material "ingredients", different structures, different habitats, different modes of living and reproduction, and yet we are somehow able to recognize them all as living, or functional organisms, without being however vitalists.

然而，他在这个方向上走得更远，声称在研究一个复杂系统时，人们“可以抛开这个问题，研究组织”，去学习那些对于一般地定义一整类系统至关重要的东西。然而，罗伯特 · 罗森以前的一些学生对此过于字面化，他们没有完全吸收罗伯特 · 罗森的观点，即需要一种动态实现特定分子形式的抽象组分的理论，以便为最简单的功能有机体(例如单细胞藻类或微生物)闭合建模循环。罗伯特 · 罗森。1970.生物学动态系统理论，纽约: Wiley Interscience。他支持这种说法(他实际上将其归因于尼古拉斯 · 拉舍夫斯基) ，因为生命有机体是一类系统，具有极其广泛的物质“成分”、不同的结构、不同的栖息地、不同的生存和繁殖方式，然而我们却能够以某种方式将它们全部识别为活的或功能性的有机体，而不管它们多么有生命力。

然而，他在这个方向上走得更远，声称在研究一个复杂系统时，人们“可以抛开物质并且只研究组织”，去学习那些对于一般地定义一整类系统至关重要的东西。然而，罗伯特 · 罗森以前的一些学生对此过于字面化，他们没有完全吸收罗伯特 · 罗森的观点，即需要一种动态实现特定分子形式的抽象组分的理论，以便为最简单的功能有机体(例如单细胞藻类或微生物)闭合建模循环。罗伯特·罗森.1970.生物学的动力系统理论，纽约:威利交叉科学。他支持这种说法(他实际上将其归因于尼古拉斯 · 拉舍夫斯基) ，因为生命有机体是一类系统，具有极其广泛的物质“成分”、不同的结构、不同的栖息地、不同的生存和繁殖方式，然而我们却能够以某种方式将它们全部识别为活的或功能性的有机体，而不管它们多么有生命力。

His approach, just like Rashevsky's latest theories of organismic sets,<ref>{{cite journal | last1 = Rashevsky | first1 = N | year = 1965 | title = The Representation of Organisms in Terms of (logical) Predicates | journal = Bulletin of Mathematical Biophysics | volume = 27 | issue = 4| pages = 477–491 | doi=10.1007/bf02476851| pmid = 4160663 }}</ref><ref>{{cite journal | last1 = Rashevsky | first1 = N | year = 1969 | title = Outline of a Unified Approach to Physics, Biology and Sociology | journal = Bulletin of Mathematical Biophysics | volume = 31 | issue = 1| pages = 159–198 | doi=10.1007/bf02478215| pmid = 5779774 }}</ref> emphasizes [[biological organization]] over [[molecular structure]] in an attempt to bypass the ''structure-functionality relationships'' that are important to all experimental biologists, including [[physiology|physiologists]]. In contrast, a study of the specific material details of any given organism, or even of a type of organisms, will only tell us about how that type of organism "does it". Such a study doesn't approach what is common to all functional organisms, i.e. "life". Relational approaches to theoretical biology would therefore allow us to study organisms in ways that preserve those essential qualities that we are trying to learn about, and that are common only to ''functional'' organisms.

His approach, just like Rashevsky's latest theories of organismic sets,<ref>{{cite journal | last1 = Rashevsky | first1 = N | year = 1965 | title = The Representation of Organisms in Terms of (logical) Predicates | journal = Bulletin of Mathematical Biophysics | volume = 27 | issue = 4| pages = 477–491 | doi=10.1007/bf02476851| pmid = 4160663 }}</ref><ref>{{cite journal | last1 = Rashevsky | first1 = N | year = 1969 | title = Outline of a Unified Approach to Physics, Biology and Sociology | journal = Bulletin of Mathematical Biophysics | volume = 31 | issue = 1| pages = 159–198 | doi=10.1007/bf02478215| pmid = 5779774 }}</ref> emphasizes [[biological organization]] over [[molecular structure]] in an attempt to bypass the ''structure-functionality relationships'' that are important to all experimental biologists, including [[physiology|physiologists]]. In contrast, a study of the specific material details of any given organism, or even of a type of organisms, will only tell us about how that type of organism "does it". Such a study doesn't approach what is common to all functional organisms, i.e. "life". Relational approaches to theoretical biology would therefore allow us to study organisms in ways that preserve those essential qualities that we are trying to learn about, and that are common only to ''functional'' organisms.

His approach, just like Rashevsky's latest theories of organismic sets, emphasizes biological organization over molecular structure in an attempt to bypass the structure-functionality relationships that are important to all experimental biologists, including physiologists. In contrast, a study of the specific material details of any given organism, or even of a type of organisms, will only tell us about how that type of organism "does it". Such a study doesn't approach what is common to all functional organisms, i.e. "life". Relational approaches to theoretical biology would therefore allow us to study organisms in ways that preserve those essential qualities that we are trying to learn about, and that are common only to functional organisms.

His approach, just like Rashevsky's latest theories of organismic sets, emphasizes biological organization over molecular structure in an attempt to bypass the structure-functionality relationships that are important to all experimental biologists, including physiologists. In contrast, a study of the specific material details of any given organism, or even of a type of organisms, will only tell us about how that type of organism "does it". Such a study doesn't approach what is common to all functional organisms, i.e. "life". Relational approaches to theoretical biology would therefore allow us to study organisms in ways that preserve those essential qualities that we are trying to learn about, and that are common only to functional organisms.

他的方法，就像拉舍夫斯基最新的有机组合理论一样，强调生物组织多于分子结构，试图绕过对包括生理学家在内的所有实验生物学家都很重要的结构-功能关系。相比之下，对任何特定有机体，甚至是某种有机体的特定物质细节的研究，只会告诉我们这种有机体是如何“做到这一点的”。这样的研究并没有探讨所有功能性生物体的共同之处。“生活”。因此，理论生物学的相关方法将允许我们以保留那些我们试图学习的基本特性的方式来研究生物体，而这些特性只有功能性生物体才具有。

他的方法，就像拉舍夫斯基最新的有机组合理论一样，强调生物组织多于分子结构，试图绕过对包括生理学家在内的所有实验生物学家都很重要的结构-功能关系。相比之下，对任何特定有机体，甚至是某种有机体的特定物质细节的研究，只会告诉我们这种有机体是如何“做到这一点的”。这样的一项研究并没有涉及到所有功能性生物体的共同特征，即“生命”。因此，与理论生物学相关的方法将使我们能够以这种方式来研究生物，这种方式能够保持我们试图了解的、只有功能性生物才具有的那些基本特性。

Robert Rosen's approach belongs conceptually to what is now known as [[Functional genomics|Functional Biology]], as well as [[Systems biology|Complex Systems Biology]], ''albeit'' in a highly abstract, mathematical form.

Robert Rosen's approach belongs conceptually to what is now known as [[Functional genomics|Functional Biology]], as well as [[Systems biology|Complex Systems Biology]], ''albeit'' in a highly abstract, mathematical form.

=== Quantum Biochemistry and Quantum Genetics ===

=== Quantum Biochemistry and Quantum Genetics ===

=== Quantum Biochemistry and Quantum Genetics ===

=== 量子生物化学与量子遗传学 ===

 

=== Quantum Biochemistry and Quantum Genetics ===

Rosen also questioned what he believed to be many aspects of mainstream interpretations of [[biochemistry]] and [[genetics]]. He objects to the idea that functional aspects in biological systems can be investigated via a material focus. One example: Rosen disputes that the functional capability of a biologically active [[protein]] can be investigated purely using the genetically encoded sequence of [[amino acid]]s. This is because, he said, a protein must undergo a process of folding to attain its characteristic three-dimensional shape before it can become functionally active in the system. Yet, only the [[amino acid sequence]] is genetically coded. The mechanisms by which proteins fold are not completely known. He concluded, based on examples such as this, that [[phenotype]] cannot always be directly attributed to [[genotype]] and that the chemically active aspect of a biologically active protein relies on more than the sequence of amino acids, from which it was constructed: there must be some other important factors at work, that he did not however attempt to specify or pin down.

Rosen also questioned what he believed to be many aspects of mainstream interpretations of [[biochemistry]] and [[genetics]]. He objects to the idea that functional aspects in biological systems can be investigated via a material focus. One example: Rosen disputes that the functional capability of a biologically active [[protein]] can be investigated purely using the genetically encoded sequence of [[amino acid]]s. This is because, he said, a protein must undergo a process of folding to attain its characteristic three-dimensional shape before it can become functionally active in the system. Yet, only the [[amino acid sequence]] is genetically coded. The mechanisms by which proteins fold are not completely known. He concluded, based on examples such as this, that [[phenotype]] cannot always be directly attributed to [[genotype]] and that the chemically active aspect of a biologically active protein relies on more than the sequence of amino acids, from which it was constructed: there must be some other important factors at work, that he did not however attempt to specify or pin down.

==Comparison with other theories of life==

==Comparison with other theories of life==

==与其他生命理论的比较 ==

 

= = 与其他生命理论的比较 = =  

 

(''M,R'') systems 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>

(''M,R'') systems 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> [[Autopoiesis|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]], and the [[Autocatalytic set|autocatalytic sets]]<ref>{{cite journal | doi= 10.1016/0022-5193(69)90015-0|last1 = Kauffman|first1= S. A. |title = Metabolic stability and epigenesis in randomly constructed genetic nets| journal = J. Theor. Biol. |volume =22|issue=3|date=1969|pages=437–467}}</ref> of [[Stuart Kauffman]], similar to an earlier proposal by [[Freeman Dyson]].<ref>{{cite journal | doi= 10.1007/bf01733901 | title =A model for the origin of life| last = Dyson| first = F. J.|journal = J. Mol. Evol.| volume = 18| issue = 5| pages=344–350| date =1982}}</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> [[Autopoiesis|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]], and the [[Autocatalytic set|autocatalytic sets]]<ref>{{cite journal | doi= 10.1016/0022-5193(69)90015-0|last1 = Kauffman|first1= S. A. |title = Metabolic stability and epigenesis in randomly constructed genetic nets| journal = J. Theor. Biol. |volume =22|issue=3|date=1969|pages=437–467}}</ref> of [[Stuart Kauffman]], similar to an earlier proposal by [[Freeman Dyson]].<ref>{{cite journal | doi= 10.1007/bf01733901 | title =A model for the origin of life| last = Dyson| first = F. J.|journal = J. Mol. Evol.| volume = 18| issue = 5| pages=344–350| date =1982}}</ref>  

==Last Universal Common Ancestor (LUCA)==

==Last Universal Common Ancestor (LUCA)==

==Last Universal Common Ancestor (LUCA)==

==最后的共同祖先(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 | doi= 10.3390/life11090872 | 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 | doi= 10.3390/life11090872 | 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>

}}</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>