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A biochemically-realisable relational model of the self-manufacturing cell
Biosystems ( IF 1.6 ) Pub Date : 2021-06-21 , DOI: 10.1016/j.biosystems.2021.104463
Jan-Hendrik S Hofmeyr 1
Affiliation  

As shown by Hofmeyr, the processes in the living cell can be divided into three classes of efficient causes that produce each other, so making the cell closed to efficient causation, the hallmark of an organism. They are the enzyme catalysts of covalent metabolic chemistry, the intracellular milieu that drives the supramolecular processes of chaperone-assisted folding and self-assembly of polypeptides and nucleic acids into functional catalysts and transporters, and the membrane transporters that maintain the intracellular milieu, in particular its electrolyte composition. Each class of efficient cause can be modelled as a relational diagram in the form of a mapping in graph-theoretic form, and a minimal model of a self-manufacturing system that is closed to efficient causation can be constructed from these three mappings using the formalism of relational biology. This fabrication-assembly or (F,A)-system serves as an alternative to Robert Rosen’s replicative metabolism-repair or (M,R)-system, which has been notoriously problematic to realise in terms of real biochemical processes. A key feature of the model is the explicit incorporation of formal cause, which arrests the infinite regress that plagues all relational models of the cell. The (F,A)-system is extended into a detailed relational model of the self-manufacturing cell that has a clear biochemical realisation. This (F,A) cell model allows the interpretation and visualisation of concepts such as the metabolism and repair components of Rosen’s (M,R)-system, John von Neumann’s universal constructor, Howard Pattee’s symbol-function split via the symbol-folding transformation, Marcello Barbieri’s genotype–ribotype–phenotype ontology, and Tibor Gánti’s chemoton.



中文翻译:

自我制造细胞的生化可实现关系模型

正如霍夫迈尔 (Hofmeyr) 所展示的,活细胞中的过程可以分为三类相互产生的有效原因,因此使细胞接近有效因果关系,这是生物体的标志。它们是共价代谢化学的酶催化剂,驱动分子伴侣辅助折叠和多肽和核酸自组装成功能催化剂和转运蛋白的超分子过程的细胞内环境,以及膜转运蛋白维持细胞内环境,特别是其电解质组成。每一类有效原因都可以用图论形式的映射形式建模为关系图,并且可以使用形式主义从这三个映射构建一个接近有效因果关系的自我制造系统的最小模型关系生物学。这种制造-组装或 ( F,A )-系统可替代罗伯特·罗森 (Robert Rosen) 的复制代谢-修复或 ( M,R )-系统,后者在真正的生化过程中难以实现。该模型的一个关键特征是形式原因的明确结合,它阻止了困扰所有细胞关系模型的无限回归。( F,A)-系统扩展为具有明确生化实现的自制造细胞的详细关系模型。此 ( F,A ) 细胞模型允许解释和可视化概念,例如 Rosen ( M, R ) 系统的新陈代谢和修复成分、约翰·冯·诺依曼 (John von Neumann) 的通用构造函数、霍华德·帕蒂 (Howard Pattee) 通过符号折叠转换拆分的符号函数, Marcello Barbieri 的基因型-核糖型-表型本体论,和 Tibor Gánti 的化学。

更新日期:2021-06-23
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