Interesting that you mention programming languages in the discussion of gene regulation. You sound like an anti-evolutionist insisting that the genome is a program and was thus intelligently designed. Surely you do not wish to assert that programs are written and modified at random do you?(gore3000, vigorously waving his hand): OOH! OOH! He said "program"!
Not just the writer of the article, but you yourself say it. The comparison is inevitable. In fact from your discussion with tribune7 you are speaking in programming terms. Have you ever heard of a new system inserted in the midst of a program at random? Have you ever heard of a new decision making branch created at random? Of course not.
You see, you describe in post 38 pretty well what has to happen , however you do not see that such could not happen randomly or without specific direction. You cannot just insert what is essentially new code in the middle of a program at random.