In my book The Cell’s Design, I illustrate how optimization indicates intelligent design. That is, when humans create objects and/or systems, they optimize their creations to handle trade-offs.
Likewise, optimization is a characteristic feature of natural biochemical systems. A few days ago I wrote about the optimization of protein structure and lifetimes; but this optimization is not limited to proteins. Along with DNA structure and a variety of metabolic processes, the genetic code also displays optimization. Check out the articles listed below for details on the optimization of the genetic code.
Today's New Reason to Believe 
Is there anything to say that this optimization didn’t come about by natural selection? Natural selection certainly tends to minimize costs and maximize efficiency. Which isn’t to say it’s perfect; there are certainly some peculiar flaws in our cells. But I don’t see optimization as indicating design.
As a writer in the field, I’m guessing you’ve read Francis Collins’ “The Language of God.” If by some chance you haven’t, it is fantastically informative. He looks specifically at some evidence formerly used to support Intelligent Design that have since been shown to be possible through natural selection.
One much-neglected area that I see as being possible fertile ground for an Intelligent Design debate, though, is in the laws of physics. I’m sure you’ve heard of the fine-tuning argument, and I’ve recently been pondering myself the justification behind the “infinite multiverse” theory put forth by physicists to explain some of the oddities in physics that could otherwise point toward God or Intelligent Design. There are quite a few such oddities among the recent discoveries in physics.