" ... it is a bit like hardware and software. They do influence the development and evolution of each other."
Not really, John. Software can run on any substrate. The software adapts to the hardware, sure; however, software also evolves independent of the hardware. Gregory Chaitin is doing deep research in this area.
"Genes and gene expression, networks and nodes are similar relationships."
If you mean self similar, I agree.
"You are the one who keeps impressing on me that there is no objective reality, only models(and theories), yet you seem to assume the practice of science is purely objective."
You misunderstand. It is *only* our theories and models that are objective. Because we define the terms. The theory's correspondence to physical phenomena -- experimental results -- makes it both objective and true.
"What is its foundation, other than the human mind and its relation to its environment? Is that an objective foundational basis?"
No, it is not. The terms we agree on inter-subjectively, constitute the objective foundational basis.
Best,
Tom