The recipes…the sequential steps…in the classic Betty Crocker Cookbook are entirely neutral as to the theistic or atheistic worldview of the chef in the kitchen.
The mother or grandmother working all day in the kitchen preparing homemade Italian spaghetti sauce for a large family dinner gathering later that day, has absolutely zero connection to the quality of the spaghetti sauce based upon whether this mother or grandmother is a devoted Christian theist or a hard-core skeptical atheist.
The misrepresentation here is to lump all religions together on one side of the ledger as being subjective nonsense, and place the atheist all alone on the other side as being the clear-thinking, independent, superstition-free arbiter of empirical reality.
The truth is that theism and atheism are both philosophically intellectual constructions…are belief systems exercising faith in their particular viewpoints…and belong on the same side as equal competitors in the open marketplace of ideas.
Theism and atheism have nothing to do with the sequential steps of scientific investigations that generate empirical, factual evidence.
Introducing theism or atheism into the scientific conversation occurs in the upper-level realm of theorizing and conceptualization, which admits spinning of the narrative because this is the variable, non-empirical nature of storytelling.
The modern Scientific Revolution is justifiably credited with dispelling “old-wives” tales, superstition, witchcraft, soothsaying, and black magic as bogus explanations for the phenomena we see in the natural world.
But it is the sequential steps of the scientific research program that is responsible for producing empirical evidence, and not any particular worldview that by definition must be limited to the category of being skeletal explanatory frameworks that fall outside of hard, bench-top research methodology.
The distinction between the sequential steps of scientific research programs and the skeletal explanatory frameworks that attempt to describe temporarily provisional conclusions, emphatically requires that the atheism of scientific materialism be placed alongside Christian theism as both being unrelated issues in the sequential steps of the making of Italian spaghetti sauce or exploring the cosmos.
But it is important here to see that the qualitative character of the concept communicated through the word “agency” exists on a much higher and elevated plane than the derisive concepts of “old-wives” tales, superstition, and black magic.
It would be absurd to assert that the Scientific Revolution could or would remove the concept of agency from the contemplation of human observation and everyday experience.
The real truth here is that the philosophical worldview of scientific materialism can be jettisoned along with “old-wives” tales and superstitions today, without threatening at all the empirical quality of the sequential steps of scientific research or the raw data this generates.
Philosophical worldviews do not overlap with the specified steps in scientific research any more than the specified steps in following a cookbook recipe requires either a theistic or an atheistic viewpoint in order to be successful.
The modern, nonsensical culture-war issue of whether the conclusions drawn from scientific research must exclude the existence of God is illustrated in the now classic 2005 court case Kitzmiller et al. v. Dover Area School District.
In this court case, as an expert witness testifying against Intelligent Design, the philosopher Dr. Robert Pennock of Michigan State University argued: “science operates by empirical principles of observational testing; hypotheses must be confirmed or disconfirmed by reference to…accessible empirical data.”
This statement says that hypotheses can be confirmed or disconfirmed by reference to accessible empirical data.
Scientific materialists assume upfront that hypotheses (conclusions) confirmed or disconfirmed by reference to accessible empirical data must be done solely within the skeletal explanatory framework of naturalistic materialism to be valid.
What is subtly being represented here is that the definition of what is science and what is non-science, is determined by the modern scientific method that can only generate accessible empirical data.
The fallacy in this reasoning is profoundly mistaken.
Some things we understand in nature, and some things we don’t.
There is zero understanding contained within the exclusively empirical realm of fact-based evidence.
The statement: “The only way to truth is through science,” is a proffer of conceptualization and theorizing that has zero empirical fact-based evidence in support, in terms of some atomic material composition that can be measured, weighed, or heated in a test-tube.
This identifies a two-part dichotomy between the raw data of facts contrasted with the abstract understanding of what some particular ensemble of facts means.
The meaning of the facts that comes through understanding is an independent, stand-alone, fundament reality having a spatial reach as broad as the universe itself, and a duration as long as the eternity of time…being much broader than the raw database of empirical facts alone.
More than one reasonable conclusion can sometimes be drawn from the empirical facts.
If a reasonable conclusion involves intelligent designing agency, then the limitations placed by naturalistic materialism upon the acceptable set of solutions becomes artificial and invalid.
I can look at the organized complexity in living cells, which involves DNA, amino acids that fold into proteins, developmental gene regulatory networks, and epigenetic factors, and reasonably conclude that this requires design, without ever touching or altering the empirical, factual data in the slightest.
The confusion occurs when the scientific materialist illogically intermixes the conclusion-neutral, factual data up into the conceptually abstract zone of non-material conceptualization and theorizing opinion where it does not belong, and at the same time lowers the concept of intelligent design down into the worldview-free, empirical zone of factual evidence where it does not belong.
Conceptualization and theorizing are not empirical, and databases of empirical facts are not conceptual and theoretical.
These two realities work together in tandem, but they do not crossover into each other’s territory, and they do not intermix.
This wizardly manipulation of reality excludes intelligent designing agency from the theorizing and conceptualization phase of the scientific enterprise.
It unjustifiably disallows drawing overall conclusions based upon the facts, conclusions that by definition necessarily can fall just above and outside of the domain of empirical, hard bench-top research.
This is a setting-up of the rules, a prior “rigging of the system” in favor of the atheism of scientific materialism which is incredibly misleading and untrue.
Scientific materialists are not allowed to set-up the rules that define what is science and what is non-science as argued in the conceptual zone of drawing conclusions.
Scientific materialists are not allowed to say that fact-based evidences must limit the conclusions drawn, to the domain of naturalistic materialism alone.
Mankind as a whole can and does make that determination, in the same way that the inference to design is commonly made every time we see the organized complexity in an automobile driving down the road, in a best-selling spy novel, or in the coded arrangement of information in DNA.
There is no logical argument that connects the conceptually philosophical atheism of naturalistic materialism to the neutral, sequential steps of empirical, scientific research programs.
Atheism and research programs belong in two entirely different categories.
This is an excerpt from my book Pondering Our World: Christian Essays on Science and Faith.
 Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design (New York: HarperCollins, 2009), 426.