The whole Origins discussion centers around two opposing epistemologies: Naturalism versus SuperNaturalism. Originally Naturalism itself dealt with intrinsic make up of what was being studied or examined as the following early definitions of “Natural/Naturalism” indicates:
"Natural / Naturalism: That which is produced or affected by nature, or by the laws of growth formation for motion and impressed upon bodies or beings by unseen power — as natural growth of animals according to the stated course of things — according to the constitution or character of a thing; something derived from nature as opposed to that which is an outgrowth or habit." — Webster’s Universal Dictionary, 1936
Then even earlier:
“Natural / Naturalism: The doctrine of those who deny a supernatural agency in the miracles and revelations recorded in the Bible, and in spiritual influences; also, any system of philosophy which refers the phenomena of nature to a blind force or forces acting necessarily or according to fixed laws, excluding origination or direction by one intelligent will." — Webster’s Dictionary 1913
Natural history: in its broad sense the description of whatever is created or, of the whole universe, including the heavens and the earth, and all the productions of the earth; it is generally limited to a description of the earth and its productions, including zoology Botany geology mineralogy, Etc.
From the above definition we can understand a simplified version such as this:
Original meaning of natural, or naturalism was simply, “looking within the “something" to learn about the “something" with no exclusion of the “What" that brought that something into existence.” This is "the intrinsic to the 'something.'” It does not exclude what produced the something.
The original definition of "naturalism" never excluded GOD, nor any outside source. Instead it simply meant to look within the “objects" immediate material context to understand the phenomenal world. It had nothing to do with the origin of things.
Illustration: By studying just a Piper Cub airplane we can learn about how the airframe was built, We can see how the frame parts are made to interlock with each other; we can see how the wings are attached, how the motor is placed, How the controls are put in to function, etc., etc, etc. In doing this, we have studied the "nature" of the Piper Cub, and in doing so, we didn't negate the design engineer of the aircraft. We maintained the idea that what we were looking at was designed even though we did not invoke the idea of a designer, or that it was the result of an intelligence. This was the original meaning of "Natural or Naturalism."
Now the mauled modern definition is ….
Naturalism: a philosophical viewpoint according to which EVERYTHING arises from natural properties and causes, and supernatural or spiritual explanations [this includes an Intelligent Designer-ajd] are EXCLUDED or DISCOUNTED. — Oxford Dictionary, Apple application.
So, by the modern definition, if any intelligence is involved in any experiment to verify a "naturalistic" explanation for the development of a biological process then by definition, what took place was not a real representation of what is natural.