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The regulatory genome and the computer.

Sorin Istrail1, Smadar Ben-Tabou De-Leon, Eric H Davidson

  • 1Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA.

Developmental Biology
|September 8, 2007
PubMed
Summary
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Genomic regulatory modules function as "genomic computers," processing genetic information using logic gates. These evolved biological systems differ fundamentally from electronic computers in communication, speed, and design.

Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Animal genomes contain thousands of cis-regulatory modules controlling gene expression.
  • These modules process information via transcription factor binding, analogous to logic gates.

Purpose of the Study:

  • To compare the operating principles of the evolved "genomic computer" with electronic computers.
  • To highlight fundamental differences in their design and function.

Main Methods:

  • Conceptual comparison of biological gene regulatory networks with electronic computing architectures.
  • Analysis of information processing logic (AND, OR, NOT) within cis-regulatory modules.

Main Results:

  • Genomic computers utilize transcription factor diffusion for communication, unlike electronic computers' electron transit.

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  • Significant differences exist in time, speed, processing, memory, robustness, and hardware/software.

    • Conclusions:

    • The genomic computer, a product of evolution, controls spatial gene expression essential for animal development.
    • Its emergence was a foundational requirement for the evolution of animal life.