A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

Abstract

BackgroundThe robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures.MethodsPresented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves.ResultsBoth the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological systems do not have an external source for a map of their stored information or for an operational instruction set; rather, they must contain an organizational template conserved within their intra-nuclear architecture that "manipulates" the laws of chemistry and physics into a highly robust instruction set. We propose that the epigenetic structure of the intra-nuclear environment and the non-coding RNA may play the roles of a Biological File Allocation Table (BFAT) and biological operating system (Bio-OS) in eukaryotic cells.ConclusionsThe comparison of functional and structural characteristics of the DNA complex and the computer hard drive leads to a new descriptive paradigm that identifies the DNA as a dynamic storage system of biological information. This system is embodied in an autonomous operating system that inductively follows organizational structures, data hierarchy and executable operations that are well understood in the computer science industry. Characterizing the "DNA hard drive" in this fashion can lead to insights arising from discrepancie...

Survey of Engineering Models for Systems Biology

“…However, the complexity of the cell and its corresponding analogies to contemporary computing systems run deeper than simply DNA. The cell as a whole has also been viewed as a computational machine similar to a multiprocessing cluster, with a combination of a centralized instruction set and distributed computing elements [26,27].…”

Is Life Unique?

“…David D’Onofrio [ 129 ], Donald Johnson [ 108 ], M.Conrad [ 130 ], Wang [ 131 ], Ramakrishnan and Bhalla [ 132 ], Yaakov Benenson [ 133 , 134 ] and many others have compared artificial cybernetic systems with life’s cybernetics. Say Ramakrishnan and Bhalla:…”

The Role of Cell Membrane Information Reception, Processing, and Communication in the Structure and Function of Multicellular Tissue

“…This somewhat embarrassing over-estimation of our species genome size was based on the widely accepted assumption that, as the sole repository of cellular information, the genome acts as a central processor [8,9] that exclusively receives, analyzes, and responds to all intracellular and extracellular signals. This concept of the nucleus as the cellular “control center” [10] is implicit in the expectation that the number of genes necessary for each organism must be some increasing function of the size and complexity of that organism.…”