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

Abstract

Background: The 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.

Methods: Presented 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.

Results: Both 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.

Conclusions: The 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 discrepancies in the descriptive framework, particularly with respect to positing the role of epigenetic processes in an information-processing context. Further expansions arising from this comparison include the view of cells as parallel computing machines and a new approach towards characterizing cellular control systems.

Figure 1

Computer Hard Drive. Computer Hard drive showing multiple disks and read/write head. Picture from "How things Work" by Marshall Brain.

Figure 2

Magnetic Boundary Condition. In general, allowing a magnetic region to represent a logical "1" if magnetized N-S and a logical "0" if magnetized S-N results in a non orthogonal detection of flux transitions by the read head. Figure A shows that the intended pattern of bits "0 1 1 1 0" is not detected by the read head. Figure B shows the equivalent magnetic region layout which yields the detected bit pattern of "0 1 0."

Figure 3

DNA organization. (redrawn from Kosak and Groudine, 2004). Architecture of DNA organization within the nucleus. Current view of how active genes are positioned in the nucleus and silenced genes are compartmentalized.

Figure 4

Organized cluster mapping of DNA to Nucleus. Mapping of DNA strand into DNA Hard Drive: A) shows the DNA strand decomposed into its information structure. The top layer (gray) contain the strategic placement of insulators, the middle layer contains the regulatory control regions (red) that controls the copy process of the genes and the bottom layer contains the genes organized into a form that allows co-expression. B) Shows the mapping of the insulators to the nuclear lamin substrate to form insulator clusters. These cluster are placed such that they structurally partition the genes into organized clusters. The regulatory control regions (red) now become specific to the rosette pattern formed from the insulator clusters. This results in a rosette pattern of genes and their control regions. C) Shows the placement of the rosette patterns to the nuclear lamin substrate within the nucleus thus creating the DNA hard drive. The red lines indicate the lamin. Pictures B and C from Maya, Corces, Capelson and Victor, "Biology of the cell" with permission. Available online 09 September 2004.

Figure 5

Flow chart comparison of high level formatting of DNA and CHD. Formatting models of both the DNA Hard Drive and the Computer Hard Drive. Figure A shows the path for high level formatting of the DNA molecule. Starting with the physical organization of the chromosomes into specific territories which then results in high level formatting layered on the DNA molecule itself and finally implemented onto the sub-nuclear lamin in the form of rosette patterns of gene clusters. Figure B consists of the computer hard drive illustrating high level formatting processes. Notice the similarities between the two models which show a degree of functional equivalence.

Figure 6

System diagram representing information request/process. The cell produces a system level call for a protein product. The request is processed by the operating system (BioOS) and is translated by Bio-BIOS (transduction circuitry firmware) into the DHD language (which may be a function of BFAT). Translated signal from Bio-BIOS is sent to the nucleus. Once in the nucleus, RNA/protein circuitry defined as the DHD controller assembles the transcription process. Transcription of the DNA produces the pre mRNA which becomes a temporary buffer. Final editing is accomplished through the spliceosome as implicitly defined by BFAT for the proper RNA copy of the requested gene including its derivatives via alternative splicing. Finally, a 5' cap and 3' poly (A) tail is added to the edited mRNA enabling it as a serial bus structure. Additional control effort are leveraged against the post mRNA regulating the protein production process.

Figure 7

Shared Memory. Processors P1 through P9 all share the same memory as they each wait their turn in the queue.

Figure 8

NUMA. Three memory banks, or nodes are designated for each group of three processors. This allows nearly equal access times for any processor within the node. This assumes that the processors within each node are relatively the same distance from the node.