利用组装理论（Assembly Theory）描绘生物化学中分子的演化图谱
Mapping Evolution of Molecules Across Biochemistry with Assembly Theory
AI总结：
本研究提出用 Assembly Theory 分析天然产物的分子组装空间，比较更广泛分子数据库以量化分子层面的选择与演化偶然性，并为药物发现提供新视角。
摘要：
演化通常被理解为通过基因突变驱动生物体适应度的变化，但这种理解有可能扩展到遗传密码之外。我们提出，天然产物——地球生物化学中处于核心地位的复杂分子——可用于揭示基因之外的演化机制。通过应用 Assembly Theory（AT，组装理论），该理论将选择视为一种不限于生物系统的过程，我们能够描绘并测量这些分子中的演化作用力。AT 使探索天然产物的组装空间成为可能，展示了“自私的基因”原理如何适用于这些复杂化学结构：从庞大的可能性空间中选择极不可能且复杂的分子。通过将天然产物与更广泛的分子数据库进行比较，我们可以评估演化偶然性的程度，从而洞察分子新颖性如何产生并持续存在。该方法不仅在分子层面量化了演化选择，还通过探索天然产物的分子组装空间，为药物发现提供了新途径。我们的方法为测量那些既塑造选择的分子印记、又由其读出的演化过程提供了全新视角。
英文摘要：
Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetic code. We propose that natural products - complex molecules central to Earth's biochemistry can be used to uncover evolutionary mechanisms beyond genes. By applying Assembly Theory (AT), which views selection as a process not limited to biological systems, we can map and measure evolutionary forces in these molecules. AT enables the exploration of the assembly space of natural products, demonstrating how the principles of the selfish gene apply to these complex chemical structures, selecting vastly improbable and complex molecules from a vast space of possibilities. By comparing natural products with a broader molecular database, we can assess the degree of evolutionary contingency, providing insight into how molecular novelty emerges and persists. This approach not only quantifies evolutionary selection at the molecular level but also offers a new avenue for drug discovery by exploring the molecular assembly spaces of natural products. Our method provides a fresh perspective on measuring the evolutionary processes both, shaping and being read out, by the molecular imprint of selection.
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