Actually, that is the question, not the answer. I have started with the double assumption that there is a thing called "intelligence" and that the actions driven by "intelligent" agents should be distinguishable from those of undirected processes.
Based on this assumption, archeologist identify "tool marks" when discriminating an arrow head from a uniquely worn stone in order to conclude that humans inhabited a site. In the same fashion, I propose we should be looking for "tool marks" on creation, left by God which indicate that the universe, life and mankind were created by an intelligent God, not by undirected processes.
Now is where things get complicated.
What would God's tool marks look like? Certainly, if He created the natural processes by which the universe functions, it may be incredibly difficult, or even impossible to distinguish a tool mark from a natural process. The first question we must ask is actually whether such a search is even feasible. Many, both Christians and non, may say it's not, because religion is religion and science is science and you can't use one to inform the other. While I whole-heartily disagree with this position, I will leave the details of that argument for another time. I believe we can glorify God through our search into the wonders of His creation, but more importantly, I believe that He has not abandoned us here. "For since the creation of the world God's invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that men are without excuse." It has always been God's way to use the natural world to point the way to Himself, so that men are able (if intellectually honest) to know there is a creator and to seek Him. It is not in God's character to become more difficult to recognize because we have studied His creation through the lens of the telescope or the microscope. Rather, we should find him all the more. What complicates our study are our own philosophies and theories which we bring to the lab, denying God before we have even looked into His wonders.
So, then, for what tool marks should we be searching? What are the ways in which the creation itself testifies that it was created? How can we, scientifically, pursue the origins of the universe and discern between that which occurred from a directed, intelligent process and that which has resulted from undirected, natural laws? This is my quest.
