Thread: "irreducible" complexity predicted in 1918

The information that I've been able to find so far on how to construct those graphs says:

"Each gene, each input, and each output is represented by a node in a directed graph in which there is an arrow from one node to another if and only if there is a causal link between the two nodes."

I'm a little confused. I guess we should stick to unicellular organisms. So an input is a state of the environment, an output is the production of a protein and a gene is the genetic material for a protein?

Is that right?

Also, will the graph be cyclic in general? That is, are there positive feedback loops or not?