Tlusty Tsvi
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel.
J Theor Biol. 2007 Nov 21;249(2):331-42. doi: 10.1016/j.jtbi.2007.07.029. Epub 2007 Aug 10.
The genetic code maps the 64 nucleotide triplets (codons) to 20 amino acids. Some argue that the specific form of the code with its 20 amino acids might be a 'frozen accident' because of the overwhelming effects of any further change. Others see it as a consequence of primordial biochemical pathways and their evolution. Here we examine a scenario in which evolution drives the emergence of a genetic code by selecting for an amino acid map that minimizes the impact of errors. We treat the stochastic mapping of codons to amino acids as a noisy information channel with a natural fitness measure. Organisms compete by the fitness of their codes and, as a result, a genetic code emerges at a supercritical transition in the noisy channel, when the mapping of codons to amino acids becomes non-random. At the phase transition, a small expansion is valid and the emergent code is governed by smooth modes of the Laplacian of errors. These modes are in turn governed by the topology of the error-graph, in which codons are connected if they are likely to be confused. This topology sets an upper bound-which is related to the classical map-coloring problem-on the number of possible amino acids. The suggested scenario is generic and may describe a mechanism for the formation of other error-prone biological codes, such as the recognition of DNA sites by proteins in the transcription regulatory network.
遗传密码将64个核苷酸三联体（密码子）映射为20种氨基酸。一些人认为，由于任何进一步变化的压倒性影响，具有20种氨基酸的密码子的特定形式可能是一种“冻结的偶然事件”。另一些人则将其视为原始生化途径及其进化的结果。在这里，我们研究了一种情况，即进化通过选择一种能将错误影响最小化的氨基酸映射来驱动遗传密码的出现。我们将密码子到氨基酸的随机映射视为一个具有自然适应度度量的噪声信息通道。生物体通过其密码的适应度进行竞争，结果，当密码子到氨基酸的映射变得非随机时，一种遗传密码在噪声通道的超临界转变中出现。在相变时，一个小的扩展是有效的，并且出现的密码由误差拉普拉斯算子的平滑模式控制。这些模式又由误差图的拓扑结构控制，在误差图中，如果密码子可能被混淆，则它们相互连接。这种拓扑结构为可能的氨基酸数量设定了一个上限，这与经典的地图着色问题有关。所提出的情况是通用的，可能描述了其他易出错的生物密码形成的机制，例如转录调控网络中蛋白质对DNA位点的识别。
