“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.
I don't have a comment on the substance of Gerstein's interesting argument here. And I will leave as an exercise for my Rhetoric students a proper examination of the role of the urban metaphors that Gerstein seems to prefer -- pyramids, street-traffic -- to the imagery of the computer he would seem to want to discard as inapt (if he does, I agree with him, although I think the mischief he is calling our attention to scarcely scratches the surface).
But I do have a more general observation to make.
Needless to say, the point of calling attention to the aptness of metaphors in scientific formulations is not to discard the figurations without which few truly novel scientific insights can emerge into legibility at all, let alone well-warranted scientific complexities be communicated to non-scientists who must grasp them well enough or recognize those who do well enough to deliberate about their political implications in sensible ways.
Nor do I simply want endlessly to re-iterate the abstruse point that all literality traffics endlessly together with figurality, that they interminably stabilize and de-stabilize one another, that the vitalities of both the literal and the figurative registers of language depend on one another, however much this traffic is disavowed by those who seek certainties rather than confidence from warranted consensus science -- that sort of point is true enough, and important enough, but, honestly, there are other points to make, and that one once learned gets boring even if you are a complete theoryhead (like me).
The point, as I see it, is to insist that rigorous analysis of argumentative claims must always do justice not only to logical entailments and empirical warrants, but also to tropological associations in concrete detail, else one's beliefs will be far less considered and hence far less reasonable than they could and ought to be.
It seems to me that this third, indispensable, dimension of critical thinking and argumentation still tends to be neglected even by those who claim to value reasonableness otherwise.