The hierarchical organization of the transcriptional regulatory network of bacterium E. Coli, left, shows a pyramidal structure compared to the Linux call graph, which has many more routines controlling few generic functions at the bottom.

(PhysOrg.com) -- Nature and software engineers face similar design challenges in creating control systems. The different solutions they employ help explain why living organisms tend to malfunction less than computers, a Yale study has found.

The Yale team compared the evolution of organisms and computer operating systems by analyzing the control networks in both a bacterium Escherichia coli and the Linux operating system. They report their findings online in the May 3 edition of the Proceedings of the National Academy of Sciences.

“It is a commonplace metaphor that the genome is the operating system of a living organism. We wanted to see if the analogy actually holds up,” said Mark Gerstein, the Albert L. Williams Professor of Biomedical Informatics; professor of molecular biophysics and biochemistry, and computer science; and senior author of the paper.

Both E coli and the Linux networks are arranged in hierarchies, but with some notable differences in how they achieve operational efficiencies. The molecular networks in the bacteria are arranged in a pyramid, with a limited number of master regulatory genes at the top that control a broad base of specialized functions, which act independently.

In contrast, the Linux operating system is organized more like an inverted pyramid, with many different top-level routines controlling few generic functions at the bottom of the network. Gerstein said that this organization arises because software engineers tend to save money and time by building upon existing routines rather than starting systems from scratch.

“But it also means the operating system is more vulnerable to breakdowns because even simple updates to a generic routine can be very disruptive,” Gerstein said. To compensate, these generic components have to be continually fine-tuned by designers.

Operating systems are like urban streets - engineers tend to focus on areas that get a lot of traffic,” said Gerstein. “We can do this because we are designing these changes intelligently.”

However, he noted, if the analogy is extended to an organism like E coli, the situation is different: Without fine-tuning, a disruption of such major molecular roadways by random mutations would be fatal. That’s why E. coli cannot afford generic components and has preserved an organization with highly specialized modules, said Gerstein, adding that over billions of years of evolution, such an organization has proven robust, protecting the organism from random damaging mutations.



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