A thought experiment:
Assume with me 1) Some geneticists learn how to manipulate human DNA to the degree that they actually encode, from scratch, instructions that will allow the human body to create an entirely new, designed from scratch, protein. They are successful at doing so, and introduce this new DNA sequence into a number of patients. It is wildly successful, and in many generations this artificially introduced DNA sequence and its related protein are found in 10% of the human population.
Now assume that 2) A great catastrophe overtook the world, decimating the population and robbing the survivors of so much of their knowledge. The knowledge of these feats of genetics were lost entirely.
Now assume that 3) As the world recovered from this catastrophe, an aspiring young scientist initiated a (second) project to map the human genome. As he does so, and discovers this particular strand of DNA and its associated protein, he proposes for various empirical reasons that this particular sequence of the human DNA seems not the result of natural processes, but seems the result of purposeful, intelligent agency.
Should this scientist be criticized on the grounds that detecting intelligent agency is not a "scientific" pursuit?