基因组信息、密码进化、折叠动力学和熵产生——理论生物学的几个基本问题

 数千个基因组的测序完成，海量资料数据呼唤着生命科学的理性和实证性更完美地结合。基因组信息学是理论生物学的龙头。本文遵循生命信息运行的密码—序列—结构—功能的主线，论述了生命科学的理性化途径，讨论了若干基因组生物学的基本问题。着重总结了理论生物学领域的部分工作，包括：① 基因组序列识别码的形成和构建，一组描述碱基分布和碱基关联的统计量集合可作为基因组的识别码；② 基因组的进化方向和最大信息原理，提出基因组序列的编码信息量在进化中随时间增长的规律，指出DNA序列局部片段遵循最大信息原理；③ 遗传密码的适应性进化，证明普适标准密码表是突变危险性的适应性极小码，论证了遗传密码既具有稳定性，又具有可进化性；④ 基于量子跃迁的蛋白质折叠动力学，用量子跃迁的观点和理论研究如何处理从序列到结构，导出蛋白质折叠速率公式，解释了现有各种速率实验；⑤ 细胞开关相变和熵产生，研究了最简单生命噬菌体的溶原态/裂解态转变动力学，得到了此类细胞开关中熵产生的特异性规律。

Genome Information,Code Evolution,Folding Dynamics and Entropy Production:Several Fundamental Problems in Theoretical Biology

The rationalization of biology is discussed in an information-centered context. The studies in the field of theoretical biology are reviewed which include the following topics. (1) The formation and construction of the genome recognition code. A set of statistical quantities describing base composition and base correlation can serve as the genome recognition code. (2) The genome evolution direction and the maximum information principle. It is proposed that the quanlity of the function-coding information of a genome grows with time in the course of evolution. It is proposed also that the Shannon information quantity of the local DNA segments obeys the maximum information principle. (3) The adaptive evolution of the genetic code. It is proved that the prevalent standard amino acid code is a mutational deterioration-minimal code of an adaptive evolution and it is demonstrated that the genetic code satisfies both the principles of robust stability and evolvability. (4) The protein folding dynamics based on quantum transition. The protein folding rate formula is deduced based on quantum transition between torsion states by using conformation dynamics. All theoretical results (including the rate and its dependence on chain length, inertia moment and temperature, etc.) are consistent with the updated experimental data. (5) The cell switch and entropy production. The dynamics of lysogenic/lytic transition of lambda phage - the simplest form of the life - is studied from a set of differential equations. The entropy production rate of the typical cell switch is calculated. It is proved that the dynamics of this particular system obeys some topological theorem and thus the obtained results are of general nature.