How do you make a goldfish? You break things, just like Michael Behe said.
Can you think of an un-designed process that employs external machinery to maintain the state of another machine?
The way an embryo develops shows a method of patterning that makes use of physical processes as if they conform to a predetermined plan.
A dependency graph is not any old ad hoc hypothesis. It was posited because it is something that we observe in software engineering.
Scientists are delving into the remarkable way a zygote grows through its embryonic stages to an adult.