The application of a formal method to investigate the workings in the natural world is correctly recognized and credited as the start of the modern Scientific Revolution.
This begins with the discovery and use of the scientific method of research, universally applied from that time going forward to today.
Borrowing from a classic illustrative example, if someone in the late 1500’s wanted to investigate the behavior of various objects having different weights, sizes, and shapes free-falling through space, the scientific method might have that someone dropping these various objects off the top of the Leaning Tower of Pisa in Italy, being an excellent research platform.
This would be accompanied by another researcher positioned as an observer on the ground using a mechanical timing device that could determine elapsed time, preferably divided into fractions of a second (a sand hour-glass would not work).
The new scientific method of doing formal research would record the physical description of the objects being dropped, the number of times each object was dropped, the measured distance from the top of the tower to the ground, and the elapsed time duration for each free-fall through space. Secondary information might be the air temperature, time of day, wind speed, and wind direction.
These “findings” could then be recorded in a written field journal that could be copied and read by other people in the growing body of natural scientists around the world, who could then repeat similar follow-up experiments at their local regions using different conditions from the Leaning Tower of Pisa, to generally confirm or disconfirm these findings and to improve upon the accuracy of the research methodology.
The precise recipe of the sequential steps the first pair of researchers followed at the Leaning Tower of Pisa can be repeated and improved-upon by each successive group of researchers investigating this particular phenomenon of free-falling objects in space.
Both the sequential steps of the research protocol and the data produced in this example are entirely naturalistic, as long as we are talking about generating measurable, quantifiable, fact-based evidence alone.
This is the feature of the Scientific Revolution that enabled mankind to replace “old-wives” tales, magic, witchcraft, mythology, superstition, first-glance appearances, and wild speculation with true explanations for the causations of the phenomena in the natural world.
Combined with the two modern Industrial Revolutions that introduced the new advancements of technological inventions, this produced over the past four to five centuries the modern world we inhabit and enjoy today.
Some real-world examples might be helpful here.
When Edwin Hubble, working in the Mount Wilson Observatory in Pasadena, California in 1929 peered through the massive new telescope into the vastness of outer space, he used the scientific method to observe and record the red-shift of the light generated from what he correctly identified as rapidly receding galaxies.
This new scientific discovery was made possible by the improved technology of a larger and better telescope, placed atop a mountain that at that time provided a clear view into deep outer space without the light-pollution that would come later with the population growth of the cities of Pasadena and Los Angeles below.
The scientific method that Hubble followed, the equipment that he used, and the data he discovered, were all naturalistically empirical and fact-based.
As Edwin Hubble viewed outer space through this telescope, he was in real-time observing the orderliness and intelligibility of the vast cosmos that was then translated into empirical, fact-based evidence.
In 1953, the new technology and the scientific method enabled Francis Crick and James Watson to identify the double-helix structure of DNA and its information bearing capacity.
In 1964, Arno Penzias and Robert Wilson discovered quite by accident the background radiation coming from the Big Bang creation of the universe, while working with communication satellites as scientists at Bell Laboratories.
The recent, ten-year long Human Genome Project to map the DNA of human beings that was completed around the year 2000, combined the scientific method, computers, and data sharing from scientists working from all over the world, that revolutionized how science could operate in a collaborative way to solve a particular question, that seemed for many to be out of reach when this project first started.
Semantics Word-Games and Category Errors
The god-of-the-gaps argument used to attack Christian theists over the past few centuries of the Scientific Revolution was never magic-of-the-gaps or “old-wives” tales-of-the-gaps.
It was always referred to as the god-of-the-gaps because the criticism centered around appealing to a divine god as a temporary placeholder for ignorance regarding some particular aspect of the natural world, which could more conveniently be written-off by some people as divine causation, rather than doing the hard work of field or laboratory research using the scientific method.
Using word substitution, the concept of the god-of-the-gaps explanation for the holes in our understanding of phenomena in the natural world could be renamed today as more accurately being design-of-the-gaps or intelligent design-of-the-gaps.
When I see anything man-made like an automobile driving down the street, or the laptop computer I am using to compose this book, or a painting in an art museum, I can immediately recognize design.
The more sophisticated way of saying this is that whenever I see something that exhibits specified complexity, that the immediate inference is upward-pointing towards design.
How about when this observation is of something living, such as a dog chasing a tennis ball thrown by its owner, or a beautiful, well-dressed woman walking down the street in all of her glory?
Does the fact of this physical object of a running dog or a walking woman, being a living thing, change the immediate perception of observing design?
My body can be analyzed through the scientific method to determine my height, weight, the volume displaced while being submerged in a tank of water, my body temperature, and the roughly 215 different cell-types of my body and about 100 nerve cells in my brain.
But my ability to immediately recognize the sophistication of my internal design tells me that I am not the product of a mindless and undirected process.
The contour of my body shape, the symmetry of my arms and my legs to enable bilateral upright movement, the asymmetrical positioning of my various internal organs in my chest and stomach region irrespective of function, and the coordination of all of my varied body-parts is self-evident that I am not the product of an accidental, trial-and-error process no matter how long a period of time we want to give chance to accomplish this.
This is a valid inference to the best explanation that every human being is not only entitled to make, but amazingly has the intellectual and moral tools to make.
We can spend an eternity trying to figure-out how the physics and chemistry of ink bonding to paper can explain the information content conveyed in the letters of the English language in the daily headlines of the New York Times newspaper…and never get there.
The fundamental point here is that my recognition that the automobile I see driving down the street leads to an immediate inference to design, is an empirical fact-based conclusion that is not measurable or quantifiable through the scientific method.
The explosive absurdity of the historical god-of-the-gaps attack against theism is that it unjustifiably assumes a material universe.
In a natural world in which design is obvious all around us, the idea that a divine God would be a plausible explanatory causation in the interim until the scientific method of research can discover the complimentary naturalistic explanation, is not a rationally derogatory or demeaning reality at all.
As Dr. John Lennox so clearly points-out in his interviews and debates online on the Internet, Henry Ford and the combustion engine are both complimentary explanations for the motor car, and are not competing explanations.
When we look at the Big Bang moment of creation of the universe, the origin of life on earth, the enormous quantity of coded information in DNA, the coordination of the nanotechnology of molecular machines in the living cell, the abrupt discontinuities in the introduction of new features in living and non-living forms in the fossil record, the requirement of prior fitness in the environment independent of the gradual incline of increasing complexity in architectural body-plans over the expanse of the geological record, and the immergence of human intellectual and moral reasoning…the immediate inference is upward to intelligent design.
But these inferences to design are not measurable and quantifiable through the scientific method, any more than my recognition of the design component in an automobile can be explained in terms of the measurements and quantities the scientific method is capable of producing.
Of course, the scientific method yields raw, naturalistic data.
It is an indisputable argument to make the case that the scientific method produces only natural data derived from naturalistic experiments, resulting in naturalistic explanatory causations.
Please forgive me here for offering too many following examples in making my case to close-out this essay, but this issue of the empiricism of the scientific method is central to the God and science debate.
In the making of Italian spaghetti sauce there are at least three main realities.
The first is the cookbook recipe of sequential steps.
The second is the taste-test reaction of the spaghetti eaters.
The third is the breaking-down of the various ingredients into their individual chemical components using the scientific method in a laboratory by trained scientists.
Similarly, artistic oil painting, water-color painting, and ink drawing can be divided into at minimum three main realities.
The first is the sequential steps of mechanically producing a work of art.
The second is the opinionated viewing by the public of this artwork in a museum.
The third again is the breaking-down of the painting ingredients into their chemical components via the scientific method in the controlled environment of a laboratory by scientific researchers.
Another easily understood example might be the construction of a new house, which again can be divided into at least three main realities.
The first is the sequential steps of the assembly of the house from the ground up, following a well-established pattern common to all new housing construction.
The second might be the “curb-appeal” of the front elevation of the house as viewed from the street, or the utility of the floor plan for optimal living.
But the third reality once again can go into the highly technical aspects of what is called materials science, which studies the structural strengths of materials, resistance to fire, waterproofing qualities, insulating between heat and cold, and sound insulation.
In these examples, it would be the height of arrogant hubris or more charitably narrow-minded myopia to insist that the scientifically empirical perspective was the only one that mattered.
In each of the third realities given in the three examples above, it was the Scientific Revolution that added this new approach of discovering empirical, fact-based evidence at this level of detail.
But the scientific method is the new kid on the block.
Long before Newton’s equations describing gravity, people could throw a small rock four feet above themselves and observe the repetitive laws of physics that the rock always comes down to the ground, without being able to describe this reality mathematically.
Long before the scientific field of modern chemistry, a mother would explain the sequential steps of dressing the meat from an elk killed by the hunter/gatherer husband, to her daughter in preparation for cooking, before these steps were ever recorded in a cookbook or analyzed chemically in a laboratory for its nutritional value in terms of sodium, sugar, calories, and fat content.
The sequential steps for doing all manner of things, and the theorizing and conceptualization of the good or bad, right or wrong, and best practices compared to poor practices, were a part of the human experience long before the scientific method of research was invented.
Scientific materialists cannot be allowed to be the “skunk at the garden party” by insisting that we have been entirely wrong all this time by placing faith and value in the first two realities in each of the three simple examples given above, and in countless other examples commonly observed and perceived in ordinary life.
When I listen to the debate over whether the methodological materialism inherent in the scientific method excludes agency, I sense however that people are simply talking past one another, not recognizing that the scientific method is only one-third of reality.
Most people can detect the intelligence of design in good Italian spaghetti, world-class paintings in a museum, and pleasing architecture in buildings.
This recognition of intelligence underlying design occurs in the middle, second reality of the examples given above.
It is not up to scientific materialists to tell us that methodological materialism defines the entirely of reality.
It is not the job of scientists to tell us about the limits of reality.
We are capable of making that determination ourselves.
It seems to me that the arguments made by scientific materialists that only natural causations and explanations are allowed in science, makes reasonable sense only until we reach the near end-point of the investigation of a particular area of research…when most or enough of the data is in.
Once we confidently reach the nearly complete, end-points of research projects that generate sufficient data to begin drawing final conclusions, then broader interpretations and the consequences of the evidence must be allowed that fall outside of the domain of materialistic explanations.
This is like eating fully cooked spaghetti, viewing completed artwork hanging in a museum, or walking through a recently constructed new house.
This is what happened in the example of the discovery by Edwin Hubble of an expanding universe that led to the theory of the Big Bang, which has definite theistic implications.
When and if the brilliant scientific method of research discovers in the future a complete matter-and-energy explanation of precisely how the creation of the universe occurred in terms of purely naturalistic causations, the complexity, specificity, and coherently integrated systems of this information would be so magnificent in its scope and breadth as to be fantastically beyond any atheistic explanation.
This is the dilemma for modern science today, in that the atheism of scientific materialism is incapable of recognizing the fundamental dichotomy of perception in the scientific method that when most of the factual data is in, this leads to valid inferences to the best explanations that go beyond the limited domain of materialism.
The more we learn about the information required to produce function and fit within living and non-living systems, the more difficult it is to make a plausible argument that the empirical, fact-based evidence derived through the scientific method can exclude agency from the theorizing and conceptualization drawn from this evidence.
From Pondering Our Creation: Christian Essays on Science and Faith.
 The research methodology in science limited to only naturalistic processes and conclusions.