Causes, Effects and Networks in the Genome

Carl Zimmer at the Loom has a great piece on
gene expression networks in E. coli. It turns out that a particular pattern of connections, called a feed-forward loop, is common in the E. coli genome. Since feed-forward loops act as noise filters, the scientists who originally found them in bacterial genes thought they evolved for that reason. That, however, may not be the case:

"A few days ago Dutch scientists launched another attack on the feed-forward loop, called simply 'Feed Forward Loop Circuits as a Side Effect of Genome Evolution'....

The Dutch scientists wondered whether an abundance of feed-forward loops could emerge spontaneously, even if natural selection was not favoring them... They built a network of genes, each of which had sites at which proteins could bind to them and cause them to be expressed. They then allowed the network to evolve according to rules based on what scientists know about how actual genes evolve. The genes could lose their binding sites or they could acquire an extra copy of a binding site. The entire genome could be accidentally duplicated. Genes sometimes disappeared, and sometimes proteins that switched on one gene began to switch on another.

Initially the model produced a random network, which came as no surprise... But over time, something odd occurred. Some genes began to get more and more connected to other genes. And after about 100 generations, a large number of feed-forward loops appeared in the network, in what the scientists liken to an avalanche... The scientists did not have to build in any advantage to feed-forward loops that could make them the object of natural selection. They emerged spontaneously from mutating networks. 'Selection on individual circuits,' the scientists conclude, 'is not needed to explain their abundance.'"

What interests me is not so much the origin of the feed-forward loops as their function. Even if the loops originated as byproducts of other evolutionary processes, are they useful to the organism that has them? Do they still work as noise filters?

These kinds of functional questions are important in the study of food webs, which almost certainly don't evolve by natural selection but do link the species in an ecosystem to each other. How does network structure affect ecosystem dynamics?