An RNA-based theory of natural universal computation
An RNA-based theory of natural universal computation
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DOI：
10.1016/j.jtbi.2021.110984
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发表时间：
2022-01-21
影响因子：
2
通讯作者：
Akhlaghpour, Hessameddin
中科院分区：
文献类型：
--
作者：
Akhlaghpour, Hessameddin
生命在包括动物行为、单细胞行为和胚胎发育在内的各个领域都面临着计算问题。然而，我们目前还不知道有一个自然存在的生物系统能够进行通用计算，即，范围上的图灵等价。通用有限维动力系统（包括神经网络、细胞内信号级联和基因调控网络的大多数模型）不具备通用计算能力，但被认为能够解释认知和发育。我提出了一类模型，桥梁两个概念，从遥远的领域：组合逻辑（或等价地，lambda演算）和RNA分子生物学。一组基本的RNA编辑规则可以使计算任何可计算函数成为可能，其算法复杂度与图灵机相同。这些模型并没有假设非常复杂的分子机制或任何与我们已知的细胞中发生的过程完全不同的过程。不同的独立酶可以调节每个规则，RNA分子通过其二级结构解决括号匹配的问题。在这些模型中最合理的模型中，所有的编辑规则都可以仅通过相对于预定义基序的固定位置处的切割和连接操作来实现。这表明通用计算完全在分子生物学的范围内。因此，有理由假设生命已经进化--或者可能是从一台尚未被发现的通用计算机开始的。许多尺度上看似无关的计算问题可以使用相同的基于RNA的计算系统来解决。这一理论的实验验证可能会极大地影响我们对记忆，认知，发展，疾病，进化和生命早期阶段的理解。(c)2021爱思唯尔有限公司保留所有权利。
Life is confronted with computation problems in a variety of domains including animal behavior, single -cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biolog-ical system that is capable of universal computation, i.e., Turing-equivalent in scope. Generic finite-dimensional dynamical systems (which encompass most models of neural networks, intracellular signal -ing cascades, and gene regulatory networks) fall short of universal computation, but are assumed to be capable of explaining cognition and development. I present a class of models that bridge two concepts from distant fields: combinatory logic (or, equivalently, lambda calculus) and RNA molecular biology. A set of basic RNA editing rules can make it possible to compute any computable function with identical algorithmic complexity to that of Turing machines. The models do not assume extraordinarily complex molecular machinery or any processes that radically differ from what we already know to occur in cells. Distinct independent enzymes can mediate each of the rules and RNA molecules solve the problem of parenthesis matching through their secondary structure. In the most plausible of these models all of the editing rules can be implemented with merely cleavage and ligation operations at fixed positions rel-ative to predefined motifs. This demonstrates that universal computation is well within the reach of molecular biology. It is therefore reasonable to assume that life has evolved - or possibly began with - a universal computer that yet remains to be discovered. The variety of seemingly unrelated computa-tional problems across many scales can potentially be solved using the same RNA-based computation system. Experimental validation of this theory may immensely impact our understanding of memory, cognition, development, disease, evolution, and the early stages of life.(c) 2021 Elsevier Ltd. All rights reserved.