Examining the architecture of cellular computing through a comparative study with a computer
Examining the architecture of cellular computing through a comparative study with a computer
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DOI：
10.1098/rsif.2005.0038
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发表时间：
2005-06-22
影响因子：
3.9
通讯作者：
Gribskov, M
中科院分区：
文献类型：
--
作者：
Wang, DG;Gribskov, M
计算机和细胞都分别使用嵌入在简单编码中的信息，二进制软件代码和四倍基因组代码来支持系统运行。对它们的系统架构以及它们的信息存储和利用方案进行了比较研究。在代码之上，两个系统都显示了一个模块化的、多层的体系结构，在计算机的情况下，它是通过硬件实现和软件抽象的结合而产生的人类工程努力。使用计算机作为参考系统，两者之间的架构组件的简单映射很容易检测到。这种比较还揭示了细胞通过对生化网络成分的基因组编码消除了软件-硬件障碍，细胞的“硬件”相当于计算机中央处理器（CPU）。信息加载（基因表达）过程是编码成分丰度的主要决定因素，而这反过来又决定了生化途径的“带宽”。细胞过程以平行的方式在生化途径中实现。另一方面，在计算机中，软件只向CPU提供指令和数据。进程仅表示CPU按顺序进行的操作，并且只能通过CPU分时实现虚拟并行。计算机中的进程管理可能仅仅意味着作业调度，而通过基因表达机制协调通路带宽则代表了细胞中的主要进程管理方案。总之，一个单元可以看作是一台超级并行计算机，它通过受控的硬件组成进行计算。虽然我们对细胞操作的理解最多是非常零散的，但我们在整个工程过程中对计算机有一个全面的了解。讨论了这些知识对系统生物学的潜在利用。
The computer and the cell both use information embedded in simple coding, the binary software code and the quadruple genomic code, respectively, to support system operations. A comparative examination of their system architecture as well as their information storage and utilization schemes is performed. On top of the code, both systems display a modular, multi-layered architecture, which, in the case of a computer, arises from human engineering efforts through a combination of hardware implementation and software abstraction. Using the computer as a reference system, a simplistic mapping of the architectural components between the two is easily detected. This comparison also reveals that a cell abolishes the software-hardware barrier through genomic encoding for the constituents of the biochemical network, a cell's 'hardware' equivalent to the computer central processing unit (CPU). The information loading (gene expression) process acts as a major determinant of the encoded constituent's abundance, which, in turn, often determines the 'bandwidth' of a biochemical pathway. Cellular processes are implemented in biochemical pathways in parallel manners. In a computer, on the other hand, the software provides only instructions and data for the CPU. A process represents just sequentially ordered actions by the CPU and only virtual parallelism can be implemented through CPU time-sharing. Whereas process management in a computer may simply mean job scheduling, coordinating pathway bandwidth through the gene expression machinery represents a major process management scheme in a cell. In summary, a cell can be viewed as a super-parallel computer, which computes through controlled hardware composition. While we have, at best, a very fragmented understanding of cellular operation, we have a thorough understanding of the computer throughout the engineering process. The potential utilization of this knowledge to the benefit of systems biology is discussed.