Harvard College, 86 Brattle Street Cambridge, MA, 02138, USA.
Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
Biosystems. 2021 Oct;208:104476. doi: 10.1016/j.biosystems.2021.104476. Epub 2021 Jul 5.
The mechanism of biological information flow is of vital importance. However, traditional research surrounding the genetic code that follows the central dogma to a phenotype faces challengers, including missing heritability and two-phased evolution. Here, we propose the karyotype code, which by organizing genes along chromosomes at once preserves species genome information and provides a platform for other genetic and nongenetic information to develop and accumulate. This specific genome-level code, which exists in all living systems, is compared to the genetic code and other organic codes in the context of information management, leading to the concept of hierarchical biological codes and an 'extended' definition of adaptor where the adaptors of a code can be not only molecular structures but also, more commonly, biological processes. Notably, different levels of a biosystem have their own mechanisms of information management, and gene-coded parts inheritance preserves "parts information" while karyotype-coded system inheritance preserves the "system information" which organizes parts information. The karyotype code prompts many questions regarding the flow of biological information, including the distinction between information creation, maintenance, modification, and usage, along with differences between living and non-living systems. How do biological systems exist, reproduce, and self-evolve for increased complexity and diversity? Inheritance is mediated by organic codes which function as informational tools to organize chemical reactions, create new information, and preserve frozen accidents, transforming historical miracles into biological routines.
生物信息流的机制至关重要。然而，传统的研究遵循中心法则到表型的遗传密码面临挑战，包括遗传缺失和两阶段进化。在这里，我们提出了核型密码，它通过一次沿着染色体组织基因，既保留了物种基因组信息，又为其他遗传和非遗传信息的发展和积累提供了平台。这种存在于所有生命系统中的特定基因组水平的密码，在信息管理的背景下与遗传密码和其他有机密码进行了比较，导致了分层生物密码和“扩展”的适应子的概念，其中适应子不仅可以是分子结构，还可以是更常见的生物过程。值得注意的是，生物系统的不同层次都有自己的信息管理机制，基因编码部分的遗传保留了“部分信息”，而核型编码系统的遗传保留了组织部分信息的“系统信息”。核型密码提出了许多关于生物信息流的问题，包括信息的创造、维护、修改和使用之间的区别，以及生命系统和非生命系统之间的区别。生物系统如何存在、繁殖和自我进化以增加复杂性和多样性？遗传是由有机密码介导的，有机密码作为信息工具，组织化学反应，创造新信息，并保存冻结的事故，将历史奇迹转化为生物常规。
