The Ionian School, Early Evolution of Life Department, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena, L'Aquila, Italy.
Biosystems. 2022 Nov;221:104750. doi: 10.1016/j.biosystems.2022.104750. Epub 2022 Aug 12.
I support the hypothesis that stereochemical theory is unnatural because it is based on artificial and not simple mechanisms as required for a good theory. Indeed, for stereochemical theory the origin of the genetic code requires, in the first place, a primary interaction, for example, between a codon and an amino acid on a proto-tRNA. But this interaction is a necessary but not sufficient condition, because the evolution of the mRNA molecule, which would really define the genetic code, is still necessary for the complete origin of the genetic code. In other words, the need for two molecules, tRNA and mRNA, to define the genetic code, with their at least partial independence would testify to an artificial mechanism typical of stereochemical theory because it would not guarantee that amino acid-codon (or -anticodon) assignments realized in the first phase of the origin of the genetic code, would necessarily be maintained also in the second phase of its completion. Furthermore, the genetic code encodes for amino acids but amino acids are not the truly functional aspect, they are only intermediaries, of their final products, proteins, which are the only true entities actually coded by genes. Therefore, it would not be immediately clear from the point of view of stereochemical theory, to say why it is the amino acids and not the proteins that are involved in the primary stereochemical interactions that would have led to the origin of the genetic code. Hence, at least some of the stereochemical theory models would be not very credible, not being able to say much about the coding of proteins by genes. Finally, I inspected the genetic code table following the logic that more closely similar amino acids should - according to stereochemical theory - be coded by highly similar codons, finding that only a few pairs of amino acids actually satisfy this logic, further discretizing the stereochemical theory.
我支持立体化学理论不自然的假设，因为它基于人为而非简单的机制，而这是好理论所必需的。事实上，对于立体化学理论，遗传密码的起源首先需要一种原始的相互作用，例如，密码子与原 tRNA 上的氨基酸之间的相互作用。但这种相互作用只是必要而非充分的条件，因为 mRNA 分子的进化，才真正定义了遗传密码，对于遗传密码的完全起源仍然是必需的。换句话说，定义遗传密码需要 tRNA 和 mRNA 这两种分子，它们至少部分独立，这将证明立体化学理论的人为机制，因为它不能保证遗传密码在起源的第一阶段实现的氨基酸-密码子（或-反密码子）分配，在其完成的第二阶段也必然得到维持。此外，遗传密码编码氨基酸，但氨基酸不是真正的功能方面，它们只是其最终产物蛋白质的中间体，而蛋白质才是真正由基因编码的实体。因此，从立体化学理论的角度来看，很难说为什么是氨基酸而不是蛋白质参与了导致遗传密码起源的原始立体化学相互作用。因此，至少一些立体化学理论模型不太可信，无法说明基因如何对蛋白质进行编码。最后，我按照更相似的氨基酸应该根据立体化学理论被高度相似的密码子编码的逻辑，检查了遗传密码表，发现只有少数几对氨基酸实际上满足这个逻辑，这进一步使立体化学理论离散化。
