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The similarities between bacterial genomes and computer code

  • 02 April 2013
  • Written by 
  • Published in Biology

Modelling of Linux package dependencies shows a striking similarity with the evolutionary characteristics of bacterial genomes.

Computational biologist Sergei Maslov of Brookhaven National Laboratory worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components "survive" in two complex systems: bacterial genomes and operating systems on Linux computers.  Darwin's "survival of the fittest" seems aptly to describe both systems.

Combining the data of the DOE's Systems Biology Knowledgebase and the results of the Linux package popularity contest (popcon), Maslov and Pang attempted to determine not only why it is that some genes (or computer packages) are very common, while others are not; but also how many components in a system are critical to its survival.

"If a bacteria genome doesn't have a particular gene, it will be dead on arrival," Maslov said. "How many of those genes are there? The same goes for large software systems. They have multiple components that work together and the systems require just the right components working together to thrive."

 

Sergei Maslov. Credit: Brookhaven National Laboratory

The overall finding has a certain universality to it.  "It is almost expected that the frequency of usage of any component is correlated with how many other components depend on it," said Maslov. "But we found that we can determine the number of crucial components - those without which other components couldn't function - by a simple calculation that holds true both in biological systems and computer systems."

Simply put, taking the square root of the number of interdependent components will give the number of key components that are so fundamentally important that nothing can exist without them.

Both bacteria and the Linux environment are examples open access systems with independently installed components.  "Bacteria are the ultimate BitTorrents of biology," said Maslov.  "They have this enormous common pool of genes that they are freely sharing with each other. Bacterial systems can easily add or remove genes from their genomes through what's called horizontal gene transfer, a kind of file sharing between bacteria," he added.

Of course this theory cannot hold true for a Windows operating system, for it is composed only of proprietary components.

The abstract of Maslov and Pang's paper is here (the full paper is behind a paywall).  Additional supporting information is here.

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