This philosophical approach to science, popular in both the 19th and 20th centuries, can eliminate certain kinds of biases that might otherwise cloud or even prevent objective scientific investigations. Mistaken religious or cultural ideas (including superstitions) can, theoretically, be kept out of science by using Naturalism as a philosophical foundation.

A major problem with Naturalism is defining words like "spiritual" and "supernatural." To a person living outside Western technology, electricity would be classified as spiritual power; microscopes and telescopes would be supernatural instruments. But what if the definitions involve only beliefs or reported phenomena that Westerners of the early 21st Century consider spiritual or supernatural? What, then, of the mid-21st Century? With those definitions, some presently-classified spiritual phenomena might one day be explained by higher scientific concepts, beyond present scientific understanding. The problem lies in the practice of Naturalism: Concepts or phenomena now seeming to be spiritual and supernatural are either rejected outright as nonexistent or are hastily interpreted according to presently-well-known scientific concepts. Overzealous supporters of Naturalism philosophy, trying to eliminate fallacious religious ideas, introduce a different kind of bias: prejudice against scientific evidence that has any resemblance to anything spiritual.

An example of this overbearing application of Naturalism philosophy relates to the living-pterosaur investigations of the late 20th and early 21st Centuries: Because most of the investigators were creationists, many supporters of Naturalism rejected the research, even though the concept of extant (presently-living) pterosaurs can be explained under Naturalism. In addition, the evidences presented for living pterosaurs were, in many instances, devoid of spiritual overtones.

Read definitions of the three philosophies of Creation, Intelligent Design, and Naturalism.