Design principles of a bacterial signalling network

Nature 438, 504-507 (24 Nov. 2005)
Markus Kollmann, Linda Løvdok, Kilian Bartholomé, Jens Timmer and Victor Sourjik

From the Abstract:

"Cellular biochemical networks have to function in a noisy environment using imperfect components. In particular, networks involved in gene regulation or signal transduction allow only for small output tolerances, and the underlying network structures can be expected to have undergone evolution for inherent robustness against perturbations. Here we combine theoretical and experimental analyses to investigate an optimal design for the signalling network of bacterial chemotaxis, one of the most thoroughly studied signalling networks in biology".

"Moreover, the underlying topological design principles compensating for intercellular variations seem to be universal among all known or predicted bacterial chemosensory systems."

[bipod wrote: "The “evolution of robustness against perturbations” is a worthy research project, don’t ya think".]

In that same link [bipod's] we can read the next comments:

"... a “gene net” [is] a gathering, a grouping of a network of gene actions and their products into discrete units during the course of development. ... The gene nets must become isolated from one another and proceed independently. It is not total independence; they still must keep in touch with one another, for this is the way pattern formation is achieved. But the signals between them are likely to be few and quite specific. ... (An interesting aside: It has been pointed out to me [to Krauze] by my former colleague Jon Seger that a properly structured “modular” computer program is put together in a way that is analogous to the gene nets postulated here.)”

Krauze's Reference:
John Tyler Bonner, The Evolution of Complexity by Means of Natural Selection (Princeton University Press, 1988), pp. 174-5.

AdR commented:

"That sounds much like ‘design-by-contract’.

"So studying the underlying design, one can deduct the gene organization."

"...gene nets show a striking similarity to the design patterns that software architects would use. The best (and scientific) approach would then be that you start modelling the gene nets on software methodologies... That’s more than neodarwinism ever dreamed of."

"The question in this stage is whether it is a coincidence that the gene nets show similarities with design patterns. I’d say it is not, because the design patterns just define ‘best practices’ for the architecture of complex systems."