When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to ‘evolve’ from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven ‘molecular Darwinism’. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales.

中文翻译：

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遗传密码和基因组域的能量映射：对密码进化和分子达尔文主义的影响

当标志性的 DNA 遗传密码以能量差异的形式表达时，人们观察到嵌入在化学序列中的信息，包括一些生物学结果，与独特的自由能分布相关。具体来说，我们发现了密码子使用和密码子自由能之间的相关性，暗示了密码子使用的热力学选择。我们还发现被认为是古代氨基酸和高密码子自由能值之间的相关性。这种相关性可能反映了基于序列的遗传密码从根本上映射为能量密码。从这样的角度来看，人们可以将遗传密码设想为由互锁的热力学循环组成，这些循环允许密码子通过一系列连续的转换和颠换相互“进化”，受热力学和动力学因素调节的能量景观的影响。因此，遗传密码的早期进化可能部分是由差异能量学驱动的，而不是完全由任何基因产物的功能驱动。在这种情况下，除了受表型适应性优势（自然选择）驱动的经典观点外，进化压力部分来自生物物理特性的优化（例如相对稳定性和相对速率）。这种遗传密码的差异能量映射，以及更大的基因组域，可能反映了一种能量解析和进化的基因组景观，与一种差异的、能量驱动的“分子达尔文主义”一致。