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本文引用的文献

1
Noise-induced symmetry breaking far from equilibrium and the emergence of biological homochirality.远离平衡的噪声诱导对称破缺与生物手性的出现。
Phys Rev E. 2017 Mar;95(3-1):032407. doi: 10.1103/PhysRevE.95.032407. Epub 2017 Mar 10.
2
Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination.没有专用终止密码子的遗传密码:上下文依赖的翻译终止
Cell. 2016 Jul 28;166(3):691-702. doi: 10.1016/j.cell.2016.06.020. Epub 2016 Jul 14.
3
Toward the Darwinian transition: Switching between distributed and speciated states in a simple model of early life.迈向达尔文式转变:在早期生命的一个简单模型中,分布式状态与物种形成状态之间的转换
Phys Rev E Stat Nonlin Soft Matter Phys. 2015;92(5):052909. doi: 10.1103/PhysRevE.92.052909. Epub 2015 Nov 13.
4
Noise-Induced Mechanism for Biological Homochirality of Early Life Self-Replicators.噪声诱导的早期生命自我复制生物手性机制。
Phys Rev Lett. 2015 Oct 9;115(15):158101. doi: 10.1103/PhysRevLett.115.158101. Epub 2015 Oct 8.
5
Pathways of Genetic Code Evolution in Ancient and Modern Organisms.古代和现代生物体中遗传密码的进化途径
J Mol Evol. 2015 Jun;80(5-6):229-43. doi: 10.1007/s00239-015-9686-8. Epub 2015 Jun 9.
6
Toward major evolutionary transitions theory 2.0.迈向重大进化转变理论2.0
Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10104-11. doi: 10.1073/pnas.1421398112. Epub 2015 Apr 2.
7
Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life.系统发育与超越:生命第一棵树的科学、历史和概念意义。
Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1011-8. doi: 10.1073/pnas.1109716109. Epub 2012 Jan 17.
8
The advantages and disadvantages of horizontal gene transfer and the emergence of the first species.水平基因转移的优缺点与首个物种的出现。
Biol Direct. 2011 Jan 3;6:1. doi: 10.1186/1745-6150-6-1.
9
Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement.基于氨基酸极性需求的分子动力学计算得出的极端遗传密码最优性
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jun;79(6 Pt 1):060901. doi: 10.1103/PhysRevE.79.060901. Epub 2009 Jun 17.
10
Origin and evolution of the genetic code: the universal enigma.遗传密码的起源与演化:这一普遍存在的谜题。
IUBMB Life. 2009 Feb;61(2):99-111. doi: 10.1002/iub.146.

普遍生物学与早期生命的统计力学

Universal biology and the statistical mechanics of early life.

机构信息

Department of Physics and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Loomis Laboratory of Physics, 1110 West Green Street, Urbana, IL 61801-3080, USA

Department of Physics and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Loomis Laboratory of Physics, 1110 West Green Street, Urbana, IL 61801-3080, USA.

出版信息

Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109). doi: 10.1098/rsta.2016.0341.

DOI:10.1098/rsta.2016.0341
PMID:29133441
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5686399/
Abstract

All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. These examples illustrate concrete examples of universal biology: the quest for a fundamental understanding of the basic properties of living systems, independent of precise instantiation in chemistry or other media.This article is part of the themed issue 'Reconceptualizing the origins of life'.

摘要

地球上所有已知的生命至少表现出两个非平凡的共同特征

规范遗传密码和生物手性,这两者都出现在最后普遍共同祖先状态之前。本文描述了使用统计力学工具来描述这一时期的最新努力。在化学进化过程中远离平衡的自我复制生命出现时,自动催化的最小模型表明,手性必然会与早期生命自我复制者的效率共同进化。遗传密码进化的动力系统模型必须解释其普遍性及其高度精细的误差最小化特性。在一个生命起源于集体、网络化阶段的情景中,这些都得到了说明,在这个阶段,没有物种的概念,甚至可能没有个体本身。我们展示了这个阶段是如何在一个有时被称为达尔文过渡的事件中最终结束的,从而导致了目前生物体谱系垂直下降的树状阶段。这些例子说明了普遍生物学的具体例子:对生命系统基本属性的基本理解的探索,而不依赖于化学或其他介质的确切实例。本文是重新思考生命起源主题特刊的一部分。