“复杂系统生物学”的版本间的差异

2020年11月2日 (一) 23:19的版本

复杂系统生物学 Complex system biology （CSB）是数学和理论生物学的一个分支或子领域，研究生物有机体结构和功能的复杂性，以及生物和物种的出现与进化，重点研究生物网络及其内部的复杂相互作用，以及生命所必须的基本关系与关系模式。因此，CBS是一个旨在发现和建模生命所必需的关系模式理论科学领域，它只与复杂系统理论和被称为系统生物学的生物学的系统方法有部分重叠;这是因为后者主要局限于生物组织和有机体的简化模型，以及对与生物学复杂性相关的哲学或语义问题的一般性考虑。此外，人们把广泛的抽象理论复杂系统作为应用数学的一个领域进行研究，无论其是否与生物学、化学或物理相关。

Network Representation of a Complex Adaptive System

一个复杂自适应系统的网络表示

生物体和生物圈的复杂性

研究人员一直困扰于如何完整定义单个生物体、物种、生态系统、生物进化和生物圈的复杂性，而且这仍然是一个悬而未决的问题。

大多数复杂系统模型通常是根据统计物理学、信息论和非线性动力学的概念来制定的；这些方法并不关注或者说不包括与组织、拓扑属性或代数拓扑有关的复杂性的概念部分，如基因组、交互体和生物有机体的网络连通性这些重要概念。近年来，人们把以信息论、网络拓扑/抽象图论概念为基础的两种互补方法在神经科学和人类认知等领域结合起来。人们普遍认为，组织的复杂程度存在一种应与本体论的现实层次相区别层次结构，现代等级分类的分类方法也承认生物圈的例如:生物领域和生物圈、生物的界、门、纲、目、科、属和种等复杂层次结构。由于生物体具有动态性和组成的可变性、内在的“模糊性”、自生属性、自我繁殖的能力等等，生物体不符合一般系统的“标准”的定义，因此它们在功能和结构上都是“超级复杂”的；因此，在CSB中，生物体只能被定义为一种简单动态系统，“元系统”。这样一个有机体、物种、“生态系统”等等的元系统定义，并不等同于自生系统理论中对系统中的系统的定义。它也不同于K·D·帕尔默在元系统工程中提出的定义，即生物体不同于具有固定输入输出转换函数的机器和自动机，或不同于具有固定相空间的连续动力系统，这与笛卡尔哲学思想相反；因此，尽管“非确定性自动机”和“模糊自动机”也被定义了，但生物体不能仅仅用五组a（状态、启动状态、输入和输出集/字母、转换函数）来定义。然而，棋盘自动机 tessellation automata或元胞自动机 cellular automata 提供了一种直观的、可视化的/计算的视角来洞察较低层次的复杂性，因此已经成为一种越来越流行的离散模型，研究领域包括可计算理论、应用数学、物理、计算机科学、理论生物学/系统生物学、癌症模拟和微观结构建模。利用遗传算法实现元胞自动机是一个桥接棋盘自动机和CSB中的高层次复杂性方法之间差距的新兴领域。

of taxonomic ranks, such as: biological domain and biosphere, biological kingdom, Phylum, biological class, order, family, genus and species. Because of their dynamic and composition variability, intrinsic "fuzziness", autopoietic attributes, ability to self-reproduce, and so on, organisms do not fit into the 'standard' definition of general systems, and they are therefore 'super-complex' in both their function and structure; organisms can be thus be defined in CSB only as 'meta-systems' of simpler dynamic systems^[1]^[2] Such a meta-system definition of organisms, species, 'ecosystems', and so on, is not equivalent to the definition of a system of systems as in Autopoietic Systems Theory,;^[3] it also differs from the definition proposed for example by K.D. Palmer in meta-system engineering,^[4] organisms being quite different from machines and automata with fixed input-output transition functions, or a continuous dynamical system with fixed phase space,引用错误：没有找到与</ref>对应的<ref>标签 contrary to the Cartesian philosophical thinking; thus, organisms cannot be defined merely in terms of a quintuple A of (states, startup state, input and output sets/alphabet, transition function),^[5] although 'non-deterministic automata', as well as 'fuzzy automata' have also been defined. Tessellation or cellular automata provide however an intuitive, visual/computational insight into the lower levels of complexity, and have therefore become an increasingly popular, discrete model studied in computability theory, applied mathematics, physics, computer science, theoretical biology/systems biology, cancer simulations and microstructure modeling. Evolving cellular automata using genetic algorithms^[6]^[7] contrary to the Cartesian philosophical thinking; thus, organisms cannot be defined merely in terms of a quintuple A of (states, startup state, input and output sets/alphabet, transition function), although 'non-deterministic automata', as well as 'fuzzy automata' have also been defined. Tessellation or cellular automata provide however an intuitive, visual/computational insight into the lower levels of complexity, and have therefore become an increasingly popular, discrete model studied in computability theory, applied mathematics, physics, computer science, theoretical biology/systems biology, cancer simulations and microstructure modeling. Evolving cellular automata using genetic algorithms^[8]^[9] is also an emerging field attempting to bridge the gap between the tessellation automata and the higher level complexity approaches in CSB.

Evolving Cellular Automata with Genetic Algorithms: A Review of Recent Work, Melanie Mitchell, James P. Crutchfeld, Rajarshi Das (In Proceedings of the First International Conference on Evolutionary Computation and Its Applications (EvCA'96). Moscow, Russia: Russian Academy of Sciences, 1996.)</ref> is also an emerging field attempting to bridge the gap between the tessellation automata and the higher level complexity approaches in CSB.

复杂系统生物学的主题

Animated Molecular Model of a DNA double helix

一个DNA双螺旋的动画分子模型

Telomerase structure and function

端粒酶的结构与功能

A Complex Signal Transduction Pathway

一个复杂的信号转导途径

以下只是复杂系统生物学所涵盖的部分主题列表:

生物与物种的关系与进化 Organisms and species relations and evolution
物种间的相互作用 Interactions among Species
进化论和种群遗传学 Evolution theories and population genetics
- 群体遗传学模型 Population genetics models
- 表观遗传学 Epigenetics
- 分子进化理论 Molecular evolution theories
量子生物计算学Quantum biocomputation

Quantum genetics^[10]

量子遗传

Relational biology^[11]^[12]^[13]^[14]

关系生物学

Self-reproduction^[15] (also called self-replication in a more general context)

自我繁殖(在更一般的情况下也称为自我复制)

计算基因模型 Computational gene models
- DNA拓扑学 DNA topology
- DNA测序理论 DNA sequencing theory
进化发育生物学 Evolutionary developmental biology
自我生产 Autopoiesis
蛋白质折叠 Protein folding
端粒酶在体内的构象和功能 Telomerase conformations and functions in vivo
表观遗传学 Epigenetics
交互组学 Interactomics^[16]^[17]^[17] < ref name ="hayete2007">

{{cite journal

{引用期刊

|author1=Hayete, B |author2=Gardner, TS |author3=Collins, JJ | year = 2007

1 = Hayete，b | author2 = Gardner，TS | author3 = Collins，JJ | year = 2007

| title = Size matters: network inference tackles the genome scale

| title = 规模问题: 网络推理解决了基因组规模

| journal = Molecular Systems Biology

分子系统生物学

| volume = 3 |issue = 1| pages = 77

3 | issue = 1 | pages = 77

| doi = 10.1038/msb4100118

| pmid = 17299414

17299414

| pmc = 1828748

1828748

}}</ref>

} </ref >

Cell signaling

细胞信号传导

Signal transduction networks

信号转导网络

Complex neural nets

复杂神经网络

Genetic networks

基因网络

Morphogenesis

形态发生

Digital morphogenesis

数字形态发生

Complex adaptive systems

复杂自适应系统

Topological models of morphogenesis

形态形成的拓扑模型

Population dynamics of fisheries

渔业种群动态

Epidemiology

流行病学

Theoretical ecology

理论生态学

Immune system

免疫系统

Biographies

传记模板:Colbegin

Charles Darwin

D'Arcy Thompson

William Ross Ashby

Ludwig von Bertalanffy

Ronald Brown

Joseph Fourier

Brian Goodwin

George Karreman

Charles S. Peskin

Nicolas Rashevsky

Robert Rosen

Anatol Rapoport

Rosalind Franklin

Francis Crick

René Thom

Vito Volterra

Norbert Wiener

Notes

笔记

↑ 引用错误：无效<ref>标签；未给name属性为springerlink的引用提供文字
↑ Metasystem Transition Theory, Valentin Turchin, Cliff Joslyn, 1993-1997
↑ Reflexive Autopoietic Systems Theory
↑ Meta-system Engineering, Kent D. Palmer, 1996

↑ John E. Hopcroft, Rajeev Motwani, Jeffrey D. Ullman.2000. Introduction to Automata Theory, Languages, and Computation (2nd Edition)Pearson Education.

↑ The Evolutionary Design of Collective Computation in Cellular Automata, James P. Crutchfeld, Melanie Mitchell, Rajarshi Das (In J. P. Crutchfield and P. K. Schuster (editors), Evolutionary Dynamics|Exploring the Interplay of Selection, Neutrality, Accident, and Function. New York: Oxford University Press, 2002.)
↑ Framework for Systems with Dynamic Topology. International Journal of Computing Anticipatory System's 14:259–270
↑ Evolving Cellular Automata with Genetic Algorithms: A Review of Recent Work, Melanie Mitchell, James P. Crutchfeld, Rajarshi Das (In Proceedings of the First International Conference on Evolutionary Computation and Its Applications (EvCA'96). Moscow, Russia: Russian Academy of Sciences, 1996.)
↑ Peak, West; Messinger, Mott; Messinger, SM; Mott, KA (2004). "Evidence for complex, collective dynamics and emergent, distributed computation in plants". Proceedings of the National Academy of Sciences of the USA. 101 (4): 918–922. Bibcode:2004PNAS..101..918P. doi:10.1073/pnas.0307811100. PMC 327117. PMID 14732685.
↑ Rosen, R. 1960. (1960). "A quantum-theoretic approach to genetic problems". Bulletin of Mathematical Biophysics. 22 (3): 227–255. doi:10.1007/BF02478347.
↑ 引用错误：无效<ref>标签；未给name属性为ReferenceA的引用提供文字
↑ Baianu, I. C.: 2006 (2006). "Robert Rosen's Work and Complex Systems Biology". Axiomathes. 16 (1–2): 25–34. doi:10.1007/s10516-005-4204-z.
↑ Rosen, R.: 1958b (1958). "The Representation of Biological Systems from the Standpoint of the Theory of Categories". Bulletin of Mathematical Biophysics. 20 (4): 317–341. doi:10.1007/BF02477890.
↑ PlanetMath
↑ "PlanetMath". PlanetMath. Retrieved 2010-03-17.
↑ ^16.0 ^16.1 {{cite journal {{cite journal {引用期刊 | author = Faith, JJ | author = Faith, JJ 作者 = Faith，JJ | year = 2007 | year = 2007 2007年 | title = Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles | title = Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles | title = 大比例绘制和验证表达式概要中的大肠桿菌转录调控 | journal = PLOS Biology | journal = PLOS Biology | journal = PLOS Biology | volume = 5 | issue = 1 | pages = 54–66 | volume = 5 | issue = 1 | pages = 54–66 5 | issue = 1 | pages = 54-66 | doi = 10.1371/journal.pbio.0050008 | doi = 10.1371/journal.pbio.0050008 10.1371/journal.pbio. 0050008 | pmid = 17214507 | pmid = 17214507 17214507 | pmc = 1764438 | pmc = 1764438 1764438 | display-authors = 1 | display-authors = 1 | display-authors = 1 | last2 = Hayete | last2 = Hayete 2 = Hayete | first2 = Boris | first2 = Boris 2 = Boris | last3 = Thaden | last3 = Thaden 3 = Thaden | first3 = Joshua T. | first3 = Joshua T. 3 = Joshua t. | last4 = Mogno | last4 = Mogno 4 = Mogno | first4 = Ilaria | first4 = Ilaria 4 = Ilaria | last5 = Wierzbowski | last5 = Wierzbowski 5 = Wierzbowski | first5 = Jamey | first5 = Jamey 5 = Jamey | last6 = Cottarel | last6 = Cottarel 6 = Cottarel | first6 = Guillaume | first6 = Guillaume 6 = Guillaume | last7 = Kasif | last7 = Kasif 7 = Kasif | first7 = Simon | first7 = Simon 7 = Simon | last8 = Collins | last8 = Collins 8 = Collins | first8 = James J. | first8 = James J. 8 = James j. | last9 = Gardner | last9 = Gardner 9 = Gardner | first9 = Timothy S. | first9 = Timothy S. 9 = Timothy s. }}
↑ ^17.0 ^17.1 ^17.2 }} 引用错误：无效<ref>标签；name属性“Hayete2007”使用不同内容定义了多次

References cited

参考文献引用

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Baianu, I. C., Computer Models and Automata Theory in Biology and Medicine., Monograph, Ch.11 in M. Witten (Editor), Mathematical Models in Medicine, vol. 7., Vol. 7: 1513-1577 (1987),Pergamon Press:New York, (updated by Hsiao Chen Lin in 2004

Bonner, J. T. 1988. The Evolution of Complexity by Means of Natural Selection. Princeton: Princeton University Press.

Donald Snooks, Graeme, "A general theory of complex living systems: Exploring the demand side of dynamics", Complexity, vol. 13, no. 6, July/August 2008.

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; Mathematical Biology: II. Spatial Models and Biomedical Applications, 2003

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@@ 第45行： / 第45行： @@
 以下只是复杂系统生物学所涵盖的部分主题列表:
-* [[Organism]]s and [[species]] relations and evolution
+* 生物与物种的关系与进化 [[Organism]]s and [[species]] relations and evolution
-生物与物种的关系与进化
+* 物种间的相互作用 [[Intertidal ecology|Interactions among Species]]
-* [[Intertidal ecology|Interactions among Species]]
+* 进化论和种群遗传学 [[Evolution]] theories and [[population genetics]]
-物种间的相互作用
+** 群体遗传学模型 [[Population genetics]] models
-* [[Evolution]] theories and [[population genetics]]
+** 表观遗传学 [[Epigenetics]]
-进化论和种群遗传学
+** 分子进化理论 [[Molecular evolution]] theories
-** [[Population genetics]] models
+* 量子生物计算学[[Quantum computer|Quantum biocomputation]]
-群体遗传学模型
-** [[Epigenetics]]
-表观遗传学
-** [[Molecular evolution]] theories
-分子进化理论
-* [[Quantum computer|Quantum biocomputation]]
-量子生物计算学
 * [[DNA computing|Quantum genetics]]<ref>{{Cite journal | doi = 10.1007/BF02478347 | author = Rosen, R. 1960. | year =  1960| title = A quantum-theoretic approach to genetic problems | url = | journal = Bulletin of Mathematical Biophysics | volume = 22 | issue = 3| pages = 227–255 }}</ref>
 量子遗传
@@ 第65行： / 第59行： @@
 * [[DNA|Self-reproduction]]<ref>{{cite web|url=http://planetmath.org/?method=l2h&from=objects&name=NaturalTransformationsOfOrganismicStructures&op=getobj|title=PlanetMath |publisher=PlanetMath |date= |accessdate=2010-03-17}}</ref> (also called [[self-replication]] in a more general context)
 自我繁殖(在更一般的情况下也称为自我复制)
-* [[Computational gene|Computational gene models]]
+* 计算基因模型 [[Computational gene|Computational gene models]]
-计算基因模型
+** DNA拓扑学 [[DNA topology]]
-** [[DNA topology]]
+** DNA测序理论 [[DNA sequencing theory]]
-DNA拓扑学
+*进化发育生物学 [[Evolutionary developmental biology]]
-** [[DNA sequencing theory]]
+* 自我生产 [[Autopoiesis]]
-DNA测序理论
+* 蛋白质折叠 [[Protein folding]]
-*[[Evolutionary developmental biology]]
+* 端粒酶在体内的构象和功能 [[Telomerase]] conformations and functions ''in vivo''
-进化发育生物学
+* 表观遗传学 [[Epigenetics]]
-* [[Autopoiesis]]
+* 交互组学 [[Interactomics]]<ref name="Faith2007">
-自我生产
-* [[Protein folding]]
-蛋白质折叠
-* [[Telomerase]] conformations and functions ''in vivo''
-端粒酶在体内的构象和功能
-* [[Epigenetics]]
-表观遗传学
-* [[Interactomics]]<ref name="Faith2007">
-交互组学
 {{cite journal