University of Sydney, Faculty of Engineering, Centre for Complex Systems, Faculty of Medicine and Health, Westmead Clinical School.
University of Sydney, Faculty of Engineering, Centre for Complex Systems, Sydney Institute for Infectious Diseases.
Artif Life. 2023 May 1;29(2):261-288. doi: 10.1162/artl_a_00370.
In this ansatz we consider theoretical constructions of RNA polymers into automata, a form of computational structure. The bases for transitions in our automata are plausible RNA enzymes that may perform ligation or cleavage. Limited to these operations, we construct RNA automata of increasing complexity; from the Finite Automaton (RNA-FA) to the Turing machine equivalent 2-stack PDA (RNA-2PDA) and the universal RNA-UPDA. For each automaton we show how the enzymatic reactions match the logical operations of the RNA automaton. A critical theme of the ansatz is the self-reference in RNA automata configurations that exploits the program-data duality but results in computational undecidability. We describe how computational undecidability is exemplified in the self-referential Liar paradox that places a boundary on a logical system, and by construction, any RNA automata. We argue that an expansion of the evolutionary space for RNA-2PDA automata can be interpreted as a hierarchical resolution of computational undecidability by a meta-system (akin to Turing's oracle), in a continual process analogous to Turing's ordinal logics and Post's extensible recursively generated logics. On this basis, we put forward the hypothesis that the resolution of undecidable configurations in RNA automata represent a novelty generation mechanism and propose avenues for future investigation of biological automata.
在这个方案中，我们考虑将 RNA 聚合物理论构建为自动机，这是一种计算结构形式。我们的自动机中跃迁的基础是合理的 RNA 酶，它可能执行连接或切割。限于这些操作，我们构建了越来越复杂的 RNA 自动机；从有限自动机（RNA-FA）到与图灵机等价的 2 栈 PDA（RNA-2PDA）和通用 RNA-UPDA。对于每个自动机，我们展示了酶反应如何与 RNA 自动机的逻辑操作匹配。该方案的一个关键主题是 RNA 自动机配置中的自我引用，它利用了程序-数据对偶性，但导致计算不可判定性。我们描述了计算不可判定性如何在自我参照的说谎者悖论中得到体现，该悖论对逻辑系统设置了边界，并且根据构造，任何 RNA 自动机都存在边界。我们认为，RNA-2PDA 自动机的进化空间的扩展可以被解释为元系统（类似于图灵的预言机）对计算不可判定性的分层解析，这是一个类似于图灵的阶逻辑和波斯特的可扩展递归生成逻辑的连续过程。在此基础上，我们提出了这样的假设，即 RNA 自动机中不可判定配置的解析代表了一种新颖性生成机制，并为未来生物自动机的研究提出了途径。
