The Deception of Scientific Naturalism

Photo by Yuriy Kleymenov on Unsplash


Scientific investigation, which was originally a Christian endeavor, has been turned on its head and has become an exclusively secularized enterprise based in naturalism. This has resulted in an unnatural fact/value dichotomy where seemingly theistic truth claims have been excluded from consideration as genuine knowledge. Thus giving the perception, as Douglas Groothuis states, “[that] Science speaks to facts; religion to values.”This bias has not only resulted in an insufficient methodology for scientific discovery, but also an unethical definition of what is considered to be acceptable knowledge. While the implications of scientific discovery extends and touches every aspect of human life, science has chosen to limit the acceptable parameters of its discovery to natural and empirical criteria. This has resulted in the exclusion of any theistic perspective, Christian or otherwise, from consideration within the realm of scientific discovery. The impact of these phenomena has given birth to a new brand of atheism known as Scientific Naturalism. The thesis is that scientific discovery is not a “value-neutral” endeavor and that it has become largely motivated by presupposed secular worldviews, and that broadening scientific discovery to consider theistic concepts would be in the greater interest of humanity. This paper will focus on the following five areas to support this thesis:

  1. The Christian heritage of scientific discovery,
  2. The deficiency of empirical methodology,
  3. The implications of empirical methods for humanity,
  4. The intersection of fact and faith, and
  5. How theistic perspectives can contribute to scientific discovery.  

The Christian Heritage of Scientific Discovery

To begin, it will be helpful to briefly look at the history of the relationship between theology and science to gain a footing on the foundational basis for which this debate stands today. Science is really a movement spanning the centuries. What the term “movement” intends is that it has no single founder, but has been a development of ideas over the course of the history of the world.Because nearly everyone enjoys and benefits from the advancements of science, methods of scientific inquiry are seldom seriously questioned although the implications are far reaching impacting all of humanity. What is discovered concerning the relationship between Christianity and science is that up until the nineteenth century there was a cooperative relationship between the two. In fact, Frances Bacon in the sixteen century remarked, “Science was religion’s most faithful handmaiden.”In Medieval times, scientific inquiry was spurred by the fundamental Christian belief that God’s creation was “rationally knowable and should be investigated and used for the common good and the glory of God” states Douglas Groothuis.4 C. S. Lewis put it this way, “Men became scientific because they expected Law in Nature, and they expected Law in Nature because they believed in a Lawgiver.”5 This seemingly inherent calling upon studied men to investigate God’s creation led to the establishment of universities to facilitate the further study of the known world. Later, with the advancement of “physics, astronomy, and mathematics” in the seventeenth and eighteenth centuries, the scientific revolution was ignited and well underway.6

Historians largely attribute the scientific revolution of the seventeenth and eighteenth centuries to a philosophical change in the approach to science that paved way to new ideas rather than technological advancements.7 Although it is not clearly understood what spurred the initial change in thought, Cornelius Hunter states, “Most historians agree that religious thought played an important role in the birth of modern science…to some extent it enabled or supported the movement that would become modern science.”8 Although uncertain, it is believed religion was at the foundation of science as it has served as a foundation for every intellectual pursuit in the history of mankind. As philosophical approaches changed in science, two names rise to the top of the scientific movement and exemplify the two philosophical approaches that have developed into opposing worldviews today: Francis Bacon and René Descartes. Although both men were Christians, each had an entirely different philosophical approach to science. Bacon had a practical view of science and sought to establish limits to scientific investigation. He was an empiricist who limited his inquiry to only that which was subject to sensory perception.  On the other hand, Descartes resisted limitations to scientific inquiry and was open to the investigation of speculation and rationalization. At the onset, Bacon and Descartes represent to divergent paths to scientific inquiry: one driven by empiricism, and the other driven by ideology.9 It is this last viewpoint illustrated by Descartes that has been pushed out of the marketplace of scientific inquiry today and is at the center of this study. While this is a very high level overview of their work, it is a fair assessment of their philosophically different approaches to scientific inquiry. 

It should be noted that both men, Bacon and Descartes, held foundational theistic worldviews. For Bacon, the concern was to limit scientific discovery to secondary naturalistic causes so that the sensory evidence could speak for itself without external constraints. According to Hunter, “[Bacon] did not imagine, as lesser thinkers would later assert, that science could be wholly apart from religion and free of its influence.”10 As mentioned earlier, for Bacon, “science was religion’s most faithful handmaiden,”11 as it was there to investigate and explore God’s creation. Descartes obtained his education from Jesuit scholars in Holland. Among his contributions to science are his development of a “deductive system based on mathematical formulas to establish certain proofs for the existence of both the human soul and God.”12 For Descartes, human thought was a result of the existence of the soul of man. Hence, his often quoted, “I think, therefore I exist”—or often quoted as “I am.”13 Descartes resisted the tendency of diminishing the existence of the human soul to matter and preserved its immortality through dualism. A. F. Holmes states, “He introduced a dualistic theory in which the human body and soul are two separate and independent entities; the soul can therefore remain and is immortal.”14  Because of the theistic foundation of these men at the onset of modern science, historians have largely accepted the foundational role of a biblical and theistic worldview in modern science.15  Although Bacon desired to limit science to empiricism, he still assumed God’s role in creation, therefore, science was not, in the seventeenth century, a closed system of cause-and-effect evolutionary processes (which came later with Darwin), and man was still understood to be exceptional as being created in God’s own image.16

Moving into the eighteenth century, however, with the age of enlightenment another shift of thought began to prevail from a Christian to a naturalistic worldview. In simplistic terms, God, after creating the world and placing all of its working components in operation, simply stepped aside and allowed it to work without his hand of interference in its operation. According to L. Russ Bush, while God is still viewed as the originator or the known world, he is no longer viewed as its “provincial upholder.”17 As such, the worldview of Deism was widely held, as naturalistic law had not yet been fully developed. Deism was a “compromise theory” comments Bush. “God was transcendent, but he was not imminent…this deistic view is internally inconsistent and, thus, unstable. It is arbitrary to believe in a Creator and then relegate him to a position of no imminent power.”18 Some, such as Larry Chapp, see the compromise of deism as a turning point in the battle for God. Chapp writes, Deism creates a God who is not so much the metaphysical cause of the cosmos as simply the first efficient cause…but the notion of an efficient agency, the first efficient cause cannot help but appear as a finite part of the cosmos.19

Chapp goes on to state, “insofar as theology had abandoned genuinely theological principles as its guiding methodological criteria, it was now open to the charge that it had nothing specific to offer beyond appeals to gaps in the nexus of naturalistic causes.”20 Thus, Chapp sees in this theological compromise in the understanding of the nature of God and His role in creation as somewhat of a deathblow to the Christian worldview. In the perception of the secular world, theists were no longer driving scientific discovery, but rather simply inserting God in place of that which was unknown at the time. This perception of theism became the precedent for all future advancement. 

The Rise of Uniformitarianism

Another important development impacting the relationship between Christianity and science was the development of uniformitarianism, which originated with the work of Scottish geologist James Hutton in 1785. Hutton believed that supernatural theories were not needed to explain the geological history of the earth, but that it could be explained by studying deep soil samples and erosion patterns that were formed by the weathering of bedrock over thousands of years. Hutton’s theories were later further developed by Cambridge scholar, William Whewell, who penned the title of uniformitarianism to Hutton’s theory for a natural explanation for the origin of the earth. However, neither of these ideas really caught on with the scientific community until the work of Sir Charles Lyell, which in essence confirmed Hutton’s earlier work by “suggesting an extended geological time scale for every geological event” states Bush.21 Although Lyell professed to be a Christian, he confidently maintained that the earth was ancient on the basis that God was ancient. Lyell, in his studies had concluded that the first ice age had occurred around 1,000,000 B.C. Although he later discovered based on his investigation of the erosion at Niagara Falls that his calculations of the age of the earth were incorrect and later reluctantly changed the year of the most recent ice age to 35,000 b.c., however, pushing the date back as far as he could. Bush suggests Lyell was forced to push the date back as far as possible because uniformitarian geology demands enormous amounts of time for the theory to be plausible.22

Evolution’s Challenge to the Image Deo

While earlier scientific methodologies were unwilling to directly challenge the exceptionally unique origin of mankind, by the mid-nineteenth century, evolutionary theory did just that by theorizing the processes by which all life originated. The theory of evolution challenged the very creation of mankind by suggesting that man was product of evolutionary causation rather than a creation formed in the image of God. While most churches initially rejected Darwinism, by the end of the century, however, many had begun to use it as a way of demonstrating the creative abilities of God, which also allowed conformity to popular scientific theory.23 Through the progression of industrialization and urbanization and new technological advancements, science appeared in the public eye as the way to riches and power and the ideal model for the betterment of society. With this progressive growth, came the rise of university expansion. Historian Edward Purcell states, “Between 1868 and 1891 millionaires founded Cornell, Johns Hopkins, Vanderbilt, Clark, Chicago, and Stanford; between the years of 1878 and 1898 private sources donated some $140 million to higher education.”24 Along with these wealthy industrialists, the federal government contributed heavily as well. Enrollment into these secular institutions climbed steadily from 52,000 in 1870 to 355,000 in 1910, states Purcell.25  Many of the organizers and men leading these institutions were professing evolutionists with strong beliefs in natural science, and the instructors recruited by these men were of like minds. Purcell believes, based on the rise of students majoring in biology, chemistry, physics, or mathematics at the time, “the expansion and transformation of American higher education coincided with the rise of the new science, and they reinforced one another.”26 Moreover, evidence of coercion is not unmerited as Purcell notes, “The new academic professions began to rival and then surpass the prestige of the ministry as a career choice, and clergymen were replaced as college presidents by a new generation of professional academic administrators.” Additionally, Purcell goes on to write, “When Andrew Carnegie set up a pension plan for retired college professors in 1905, he specifically excluded denominational institutions from eligibility.”27 Therefore, the nineteenth century witnessed an entire shift in the philosophical paradigm for education. While previous institutions—Harvard, Princeton, and Yale—were established with the intent of Christian education, institutions in the nineteenth century were deliberately formed on a naturalistic basis. 

With the secularization of the university, Christianity and other theistic beliefs were pushed out of the sciences. Although still having some hold on psychology and areas of the mind and human behavioral sciences, it was not long before that was challenged as well. The proposition of Freud in 1927 that religious beliefs were merely “wish fulfillment” rather than based in reality established in many minds that man’s soul was only based on natural phenomena.28 Man was now viewed as a product of impersonal natural forces of causation that had evolved from lower life forms, rather than exceptional created beings made in the image of God. By today’s terms of scientific naturalism, man no longer exists in the biblical sense. Only by the return to a biblical worldview of creationism and a serious challenge to the theories of evolutionary science will human exceptionalism be restored to mankind.  

The Deficiency of Empirical Methodology

It is largely held that given enough information the truth of a matter will be discovered. However, when it comes to scientific discovery this simply is not the case.29 For after data is collected and analyzed it must be correctly interpreted, and this is often where the weakness lies concerning naturalistic methodologies of scientific discovery. Leonard Brand writes, 

Influential people, like Francis Bacon, have promoted the idea that data faithfully lead us to truth. However, Bacon was overly optimistic. Data almost never directly suggests the interpretation, and data does not guarantee that our interpretation will be correct. The scientist must relate the data to theories and “known facts,” working creatively to interpret them.30

Leonard Brand, Faith, Reason, & Earth History

According to Brand, scientific investigation is often inconclusive and scientists often must choose the interpretation that best fits the evidence. According to the accepted laws of natural science and empiricism, for data to be tested it must be observable and repeatable in some way. As such, there are massive amounts of information science has at its disposal but simply has no way of testing it. It is not that this data is false, but rather it cannot be authenticated by the methodology natural science is bound to for scientific inquiry. Therefore, there often are certain pieces of information that could greatly impact the findings of scientific inquiry, but they have been discarded by science because they do not fit their naturalistic paradigm. Specifically, areas of the metaphysical are absolutely out of reach to the natural sciences today. While Bacon assumed that empiricism was not applicable to the metaphysical he did not deny its existence. Yet the sciences today, while admitting its methodology fails to account for the metaphysical, simply chooses to ignore any part it may play in the known world. Recognizing this, what must be questioned is whether science can accurately interpret a matter based on only pieces of information rather than the whole? 

It has been proven on a number of occasions that a lack of data while applying a naturalistic approach to scientific discovery often leads to creative interpretations that can be incorrect. We have already discussed Lyell’s gross exaggeration of the age of the earth based on his miscalculations of the erosion at Niagara Falls but there have been others, such as Mount St. Helens and the “Little Grand Canyon” that was formed when the mountain erupted in 1980. Within the short period of one day, a one hundred feet deep canyon was carved out as a result of the mudflow stemming from the volcano. Until the time of this event, science told us that formations such as these took million of years to develop.31 However, the event of Mount St. Helens proved that their theories were incorrect, and if their interpretation of data was incorrect with regards to the formation of canyons and the layers of the earth’s crust, then it is also possible their estimation of the age of the earth is incorrect as well. The implications of this finding are significant because if the earth is not as old as naturalists suggest, then it is not possible that life developed on the planet through evolutionary processes because of the extended amount of time required for evolution to take effect. 

Darwin’s evolutionary theories are the perfect illustration of the insufficiency of empiricism and the misinterpretation of data. Darwin noted variations within certain species of Finches—that some had long beaks during seasons of drought enabling them to forage for food, while others during the rainy seasons had shorter beaks. As a result of Darwin’s studies, he concluded that mutation allowed for survival of the species during the drought period. He then proceeded to develop his theory and uniformly apply it to other species on a much larger scale. Of course, he only observed what he was able during his own lifetime. He had no idea what had occurred previous in the history and development of the finches, so it was unknown to him the origin of each species or variations of mutation over an extended period of time. However, in the title of his book “Origin of the Species” it is implied that Darwin’s evolutionary theories are applicable to the whole of life as a means to life’s origin. Others coming after Darwin built on his theories and postulated elaborate theories of how life began. As cell theory was only in its infancy and something that would be developed much later subsequent to the technological advance of the microscope, Darwin did not have the technology or education available to him to conduct a thorough scientific analysis of molecular structure.32 While it is arguable as to how such information may have influenced Darwin and his conclusions, the implications of his studies as they stand, and the way others later developed them as evolutionary science have had a broad impact to science and humanity.  

Teleological Arguments

Many today, particularly proponents of Intelligent Design, argue that Darwin’s studies did not go nearly deep enough for them to be used as a foundation for later studies, particularly when considering Darwin’s evolutionary theories have been used as a springboard for such sweeping hypothesis as those concerning the origin of life and the known world. Recognizing that Darwin did not have sufficient data to support his conclusions, other explanations for the origin of life must be discovered. One explanation is that God created life on earth as specified in the book of Genesis. However, this argument for the scientific naturalist or atheist puts the cart before the horse in a way since one must first explain the existence of God before convincing the atheist of God’s hand in creation. According to Bush, there are three major sources of evidence supporting the existence of God:  

1) The nature of the universe that exists is wholly contingent and in no sense necessary, in either form or substance. 

2) Mind, rationality, and a spiritual nature exist in humans (since mind does not exist in nature itself, nor is mind reducible solely to chemistry or to natural processes), and

3) The unique spiritual experiences that form the historical basis for Christian faith are real, documented, and testable through historical analysis and through personal spiritual conformational experiences.33

L. Russ Bush, The Advancement, 99.

This study will explore each of the preceding sources given by Bush and examine how these evidences serve to explain the origin of life on earth. 

Cosmological and Teleological Arguments for the Existence of God

There is sufficient reason to believe that the known world depends on something outside itself.  Groothuis quoting Charles Taliaferro writes, “For everything that exists, there is a reason for its existence, either due to the causal efficacy of other beings or due to the necessity of its own nature.”34 Natural science uses only those things that are evident within the known world to explain the world around us. However, Groothuis makes the observation, “If everything in the universe can be explained in terms of other things in the universe, this leaves the universe as a whole unexplained.”35 In other words, there must be something supremely greater outside the closed system that served as a cause for the known world. As Groothuis notes, “God explains the existence of the entire universe. God himself, however, requires no explanation outside of himself, since he is an eternal and self-existent being.”36 This idea relates to Bush’s first evidence for the existence of God, “the universe that exists is wholly contingent.”37 In other words, the known universe does not simply exist by it’s own merit and could not have caused itself, but rather something from outside initiated the known cosmos. 

Many naturalists accept this argument recognizing that there is an unknown source that sustains the universe. This also is due to the understanding that the universe does not, in fact, sustain itself and, therefore, is not self-sustaining and independent. As such, the universe is contingent on something else to sustain it. As James E. Taylor writes, “Anything that comes into existence depends for its initial existence on something else, since nothing can bring itself into existence…”38 Therefore, the known universe is a dependent thing that is contingent on something outside itself to sustain its existence. This argument is in direct opposition to the evolutionary theories of scientific naturalism, which postulates the causation for life as the progressive combustion of chemical compounds subject to a series of accidental fortuitous circumstances and evolutionary processes over the period of an enormous amount of time that have led to the development of life. However, the naturalistic explanation for the origin of life cannot be sustained as it begs the question of the source of the chemical compounds, the nature of the circumstances that caused development, and a series of other questions. Even if, like Richard Dawkins suggests, extraterrestrial visitors originally seeded life on earth, it must be asked what was the origin of life for the alien visitors?39 This type of fallacious reasoning is why Dr. Norman Geisler concludes, “Only an incurable commitment to naturalism (i.e., anti–supernaturalism) can account for this arbitrary mis–definition of a scientific approach to origins.”40

The Mind, Rationality and the Spiritual Nature of Humans

The Bible declares that man was created in the Image of God (Gen 1:26-27; 9:6; 1 Cor 11:7). The implications of Scripture’s declarations are significant toward understanding the composition of human beings. With creation, God endowed man with a spirit and/or a spiritual nature, which includes man’s ability to have a relationship with God (Gen 2:7; John 20:22). Man was given the authority to have dominion over the planet, which would have certainly entailed the ability for rational thought and intellect.41 Additionally, from the beginning, man was gifted with a transcendent reality into the supernatural realm. With this in mind, Plato shared an interest with Christian theology in connecting the constitution of physical human existence with the metaphysical.42 Carl Henry states, “Man’s rational experience is made possible only by a divine mind…for Plato, the priority of the rational element can be understood only through an antecedent spiritual Idea-world.”43 Plato’s construction of man’s constitution evoked a theory of “preexistence and recollection,” which served as a foundation for the rational mind possessed by human beings. In Plato, this concept goes beyond man’s sensory perception into the “inner realm of changeless ideas,” states Henry.44 Therefore, historically speaking and reflecting on man’s philosophical roots, it was understood that the composition of human beings included a spiritual nature, which set humans apart from all other living organisms. 

According to the definitions given by Demarest and Matthews, Christian theologians generally interpret God’s creation of man in His own image to include: “a set of psychological and spiritual qualities including a rational mind and free will.”45Metaphysically, this definition entails that “humans are living, active, personal, and immaterial souls/spirits in a material body;” that humans have the “capacity to choose noble goals and are capable of strategies necessary to achieve them,” and morally, humans have “the ability to discern right from wrong with an accompanying sense of moral obligation.”46Additionally, humans are endowed with a conscience that “verifies compliance or noncompliance with the moral law of God.”47

Scientific naturalism chooses to deny the biblical understanding of the composition of man even though many scientific naturalists admit that their naturalistic worldview fails to fit their naturalistic paradigm. Nancy Pearcey writing about these phenomena states, “Adherents of scientific naturalism freely acknowledge that in ordinary life they have to switch to a different paradigm. That ought to tell them something. After all, the purpose of a worldview is to explain the world—and if it fails to explain some part of the world, then there’s something wrong with that worldview.”48 The experiences of some scientific naturalists have led them to the conclusion that there is such a thing as a rational mind or soul that inhabits each individual. Yet others assert there is no “self” at all—no ghost in the machine, so to speak, that controls the will of the person, and that the operating system of the human being is simply a mechanistic network of computers running the operations of the person. According to Nancy Pearcey, “One school of thought, called eliminative materialism, goes so far as to dis-miss consciousness itself as an illusion altogether.”49 However, confidence in the rational mind and human mental capabilities are an absolute necessity for any scientific inquiry. To even raise the question of the reliability of man’s mental capabilities is to assume its reliability to begin with, so it becomes a circular argument to do so. To this end, Bush writes:

How can our observations and analytical ideas and theories be trusted if modern naturalism is true? They are not independent of the process of cause and effect. Observations and theoretical interpretations are subject to false assumptions, poor logic, prejudice, misunderstanding, misperception, and carelessness, but the most serious concern, by far, is the problem of the mind’s lacking independence from the chemical and physical processes it is supposedly studying.50

L. Russ Bush, The Advancement, 48.

Man’s interdependence on the system of which he is a part presents a serious dilemma for naturalists when it comes to scientific inquiry and other areas of human existence. One of which is moral accountability. How can an individual who is driven by a network of mini computers—a mechanistic machinery if you will—be held accountable for making morally ethical decisions with regards to their own life and the lives of others? Globally speaking, the fundamental essence of the justice system is based on the understanding that one is held responsible for their actions. Scientific naturalism rules out the existence of a conscious will within human beings and explains behavior on preconditioning. However, if reconditioning or reprogramming were all that is needed one would think that an individual such as Charles Manson, for example, would have been reprogrammed by now after spending the last forty-six years in prison? Man must, at some point, transcend the natural processes in order to justify any rational study of the cosmos. With God as the creator of man, there is transcendence. With this in mind, Bush writes, “If man is wholly a product of the natural process, at what point does he transcend the process? If he does not transcend it, and if he has no transcendent source of information, then his knowledge can never be objectively justified.”51 Therefore, evidence appears to show that the human mind is much more than chemical processes and machinery. As such, theism provides a more consistent and rational explanation for the existence of man and the known world. 

The Complexity of the Genetic Code

Naturalists suggest that the presence of DNA in each species is evidence to support the theory of common descent, and they use this argument to sustain their argument of an ancestral relationship between man and primates.52 Naturalists have taken this theory to far reaching extremes. Richard Dawkins, for example, suggests that the fact that there is a “genetic code and other biochemical fundamentals,” in bacteria suggests that humans are related to bacteria as well.53 Dr. Norman Geisler, for one, questions this assumption and counters the argument by suggesting that this may just as well be evidence for common ancestry from a common creator.54  Geisler points to other common elements to explain the genetic code common to all life forms on earth. Along with the suggestion that all life descends from a common life source, God, Geisler suggests, “perhaps we all have a common genetic code because a common creator has designed us to live in the same biosphere. After all, if every living creature were distinct biochemically, a food chain probably could not exist.”55To this end, variations in genetic structure may not be possible on earth.

The complexities of the DNA molecule point to evidence of design. It has been noted by molecular biologist Frederick Sanger from his studies in the DNA of viruses that the DNA “actually layers message upon message [within the genetic code],”56 and with every subsequent line there is an entirely different book of information. Sanger compares it to reading Shakespearian plays, “It’s as though you picked up a Shakespeare play and started at the beginning to read Romeo and Juliet—and then started a single letter down to read A Midsummer Night’s Dream.”57 With this, meaning upon meaning is contained within each strand of the DNA molecule. Because of this, many suggest it is simply mathematically impossible for such complexity to develop through evolutionary processes. 

The evolutionary processes of scientific naturalism are largely dependent on significant amounts of time. For the scientific naturalist, practically anything is possible given enough time, and time and chance are two commodities naturalists rely heavily upon. Conversely, Edgar Andrews takes exception to these theories and declares them to be false assumptions. Edgar claims, “What may be mathematically possible may be physically impossible.”58 Andrews goes on to state:

The naturalists claim, “That 100 monkeys banging the keys of 100 typewriters (with no lunch breaks) will eventually produce the works of Shakespeare cannot be altered or revised. This is a completely unrealistic scenario for real-world processes like chemical reactions or genetic mutations, where the whole system undergoing change remains available for further amendment.59

Edgar Andrews, Who Made God, 20.

Andrews explains that the theory of chemical rate processes is well established and that it has been proven that these chemical processes can actually reverse themselves going backward and forward. Each forward step requires a payback of energy. If there is no payback then the step is cancelled out. Andrews further explains,

Applying this to the monkeys (this time without allowing the output generated to be quarantined) we see that progress towards a Shakespeare folio would actually go backwards, not forwards. This follows because the likelihood of the next keystroke being an error is much greater than the likelihood of it being correct (there being twenty-six letters in the alphabet, one would be correct but twenty-five would be mistakes). So if you started the monkeys with a typescript lacking just a single sonnet but otherwise complete and correct, it wouldn’t be long before The Merchant of Venice was in total disarray—let alone Much ado about nothing.60

Edgar Andrews, Who Made God, 22.

Therefore, Andrews who is an established molecular scientist, does not find that the evolutionist’s monkey illustration can sustain the hypothesis of the theory of time and chance mutations which are necessary for macro evolutionary processes to occur. Similarly, Dr Norman Geisler also points out that if macroevolution were true, we would find protein sequences supporting transitions from fish to amphibian to reptile, etc., rather than the isolated molecular structure that have been discovered.61 Therefore, even though all life forms share a common genetic code, there are varying degrees of separation in the protein sequences so that “the basic types are in molecular isolation from one another.” As such, evolutionary theories fail to explain these molecular gaps and cannot be sustained as a working hypothesis for common ancestry and the basis for the origin of life.62

The Observable Evidence of Design

As stated earlier, it is the contention of this paper that Darwin knew nothing about fundamental building blocks of life and the nature of the cell. Biochemist Michael Behe agrees with this assertion on the basis of what he calls “irreducible complexity,” which entails all of the chemical mechanisms being simultaneously in order to facilitate the evolutionary processes.63 In order to provide physical observable evidence supporting Behe’s argument he points to the bacteria flagellum to illustrate his point. Although there are numerous biological mechanisms to which science has no explanation, the flagellum is one that is understood in its complexity, can be observed in action and is testable as a documented scientific discovery.64 Howard Berg, Molecular biologist at Harvard explains the workings of the flagellum as, “’the most efficient machine in the universe.’ The flagellum is a nano-engineered bidirectional motor-driven propeller on the backs of certain bacteria. It spins at tens of thousands of revolutions per minute, can change direction in a quarter turn and propels a bacterium through its watery environment.”65  According to William Dembski, naturalist’s explanation for the development of the flagellum is that the “flagellum is composed of parts that previously were targeted for different uses and that natural selection then co-opted to form a flagellum.”66 In other words, bacteria, through the course of evolutionary processes, borrowed already existing materials to form the flagellum, which is a necessary component to the survival of the organism. While some naturalists who already accept evolution as a presupposition to their studies have accepted this explanation, others do not accept this due to the irreducible complexities of the organism. For example, Dembski points out that the idea of natural selection working on this level is simply implausible, for natural selection only works with preexisting functions—not in the formation of new mechanisms that do not already exist. For instance, Darwin’s longer beaked finches survived due to having a longer beak and therefore perpetuated the existence of that particular variety of finch. However, as Dembski suggests, with regards to the flagellum, we are not talking about an enhancement to a preexisting mechanism, but the co-optation of a new structure. Dembski states,

For co-optation to result in a structure like the bacterial flagellum, we are not talking about enhancing the function of an existing structure or reassigning an existing structure to a different function. Rather, we are talking about reassigning multiple structures previously targeted for different functions to a novel structure exhibiting a novel function. Even the simplest bacterial flagellum requires around forty proteins for its assembly and structure. All these proteins are necessary in the sense that lacking any of them, a working flagellum does not result. The only way for natural selection to form such a structure by co-optation, then, is for natural selection gradually to enfold existing protein parts into evolving structures whose functions co-evolve with the structures.67

William Dembski, The Design Revolution, 277.

To further illustrate the irreducible complexity of the flagellum and how all of the necessary components (the 40 proteins) must be in place in order for the mechanism to function, Behe and others have held up the operation of a mouse trap as an illustration. In order for a mousetrap to function properly the spring, hammer, holding bar and catch must all be the correct size and shape and be in place in precisely the correct order for the mousetrap to function. Basically, each component must be specifically designed and neatly fitted for even the simple mousetrap to function and fulfill its purpose. If any piece of the mousetrap is improperly fitted or missing, the mousetrap is completely inoperable. Therefore, all must be precisely in order for the mousetrap to function. While the inner workings of the bacteria flagellum are far more intricately complex, in theory the concept applies as an illustration of the concept of irreducible complexity. Behe notes, “Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integral unity, in one fell swoop, for natural selection to have anything to act on.”68

With the above in mind, it should also be emphasized again that the bacteria flagellum is documented science that is observable; however, naturalistic explanations cannot explain its origin. As alluded to earlier, there are a number of other chemical components and mechanism in science that have not been explained. Bush argues, “While some may argue that theism is not self-evident…the existence of the genetic code implies a necessary source of information that is not found in the chemistry alone.”69  Bush suggests that life actually “rides on organized chemicals but is not produced merely by chemical complexity.”70 For example, “When an animal or a person dies, all of the chemistry remains, and the organization of that chemistry remains, though it begins to deteriorate after death. Maintaining chemical complexity is not the same as preserving life. Simply to arrange chemicals in organized patterns is not to create life.”71 With this in mind, Edgar Andrews quoting Francis Collins, U.S. government human genome project chief engineer, states, “humans are also unique in ways that defy evolutionary explanation and this points to our spiritual nature.”72 Therefore, the question of life’s origin and composition must be reexamined. The focus must now be redirected to the philosophical components of human existence and their implications. 

The Intersection of Fact and Faith

It has been the contention of this paper that Scientific Naturalism has an epistemology, or theory of knowledge, a view about the workings of universe and world around us and has set certain limitations to the way that knowledge may be obtained and is defined. However, somewhat similar to the Christian worldview, scientific naturalism has a Creation story that seeks to explain how the known world began. This naturalistic narrative begins with a cosmic explosion and involves an evolutionary process that supposedly happened over the course of time. Critical to this evolutionary process are the processes of macro-evolution, which involves change or transmutation from one species to another, and events initiated by earlier events which were governed by the laws of nature whether they were known to exist at the time or not. As discussed earlier, there is not only insufficient evidence to support the theory of macro evolutionary processes, but there is plenty of evidence to prove otherwise; that macroevolution is a biological impossibility. Largely accounting for the error of natural science is its methodologically earthbound approach and unwillingness to explore theistic possibilities to account for the origin of life and the known world. Alvin Plantinga, for one, finds deficiencies in scientific naturalism that cannot be overcome without a significant shift in the established paradigm. However, on the other hand, a Christian worldview provides for the metaphysical epistemology necessary to explore the unexplained areas of science today.73 To this end, to continue to hold onto a worldview that fails to explain the known world, is pointless, and requires far more faith to continue along this path than to change direction and explore a theistic approach with God as the originator and sustainer of all known life. This is exactly what so many scientific naturalists are concluding today. According to Dan Story, “an increasing number of evolutionists are recognizing that evolution is no longer a viable theory of origins. They recognize that time and chance, operating via mutation and natural selection, do not produce new species, let alone account for the origin of life.”74 Unfortunately, until theists take back the educational institutions of the world, scientific naturalism will continue to prevail as the prevailing worldview for life.

The Implications of Empirical Methods for Humanity

As mentioned earlier is our discussion, it is easy to see that following naturalistic methodologies for research can easily lead scientific discovery down the incorrect path. Moreover, however, the cumulative impact stemming from the implications of scientific naturalism have proven to be destructive to humanity. Larry Chapp, reflecting on the implications of the evolutionary basis of naturalism concludes that C. S. Lewis had it right, as he concludes that the cumulative effect of scientific naturalism will lead to the abolition of man. Chapp writes, 

With the loss of a Transcendent reference point, there is no longer any reason to view humanity as in any way privileged in the sense of having an inviolable dignity unlike that of any other life form. Humanity becomes just one more piece of the overall material puzzle to be deciphered through experimental science like all the other data of existence. But more importantly, since one of the primary goals of modern technocratic science is the ability to manipulate and control…But this raises the further question of just who will be in charge of this process of manipulation and control?75

Larry S. Chapp, God of Covenant & Creation, 260-261

Chapp questions what dignity will man have if he is no different than any other organism on the planet. In other words, in what way is he exceptional? As pointed out earlier, if there is no way that man transcends the world around him, vis-a-visGod, then he becomes another member of the food chain. Although as Chapp points out, who decides who is the hunter and who will be the hunted? 

Naturalists point to nature as the sole source of information, however, the natural world does not teach humans anything about transcendence other than to leave gaps that are unexplainable by natural causes. From nature, naturalists conclude that man is the product of evolutionary forces and that only the strong rise to the top and survive. Without any source or constraints of morality, man can justify brute force as the mechanism by which nature selects who is at the top of the food chain. Under the guise of religious philosophy, and with no moral constraint, such epigones as Nietzsche, Freud, Marx and Hitler have led men to destructive paths with scientific naturalism as a basis for their actions. Therefore, it is easily seen from the annals of history the implications of a worldview based on scientific naturalism. 

However, what evidence is there today suggesting that scientific naturalism is destructive to humanity? One excellent example of the destructive implications of scientific naturalism is found in the debate over the federal funding of embryonic stem cell research in the United States. Indicative of the absence of a moral base, the President’s comments regarding the federal funding of this enterprise makes the point clear. When asked the question about federal funding, President Obama replied: “the answer to that question is above my pay grade.”76 In other words, the funding of embryonic stem cell research is a moral question that is metaphysical in nature and something that reaches beyond the post of the President. However, if the President of the United States cannot answer the question, who is to decide? Larry Chapp suggests that since natural science has become the arbiter of such matters and the prevailing worldview influencing and reaching as far as the U.S. Supreme Court, it no doubt will ultimately decide the matter. Chapp cautions, “Technology is no neutral tool to be used within the context of antecedent moral notions of the good. Rather, technology creates and imposes a radically new mindset…Thus technology creates social structures and expectations that become completely and indelibly etched into the cultural metaphysical landscape.”77

How Theistic Perspectives Can Contribute to Scientific Discovery

As mentioned earlier, theistic perspectives can contribute greatly to scientific discovery by providing a fuller paradigm that allows for the exploration of areas not covered and left unexplained by science today. Moreover, a Christian worldview would provide, as it has in the past, the fundamental moral foundation needed to restore human dignity and exceptionalism to mankind; thereby, preventing the decline of human worth and the destructive (sinful) abuses of man toward his own destruction. Without man’s awareness of God, technological advance only leads to further decline. This fact is historically evident by man’s social and cultural decline. For instance, the twentieth century has seen greater technological advancement than any other time in history, yet at the same time man has not progressed within himself, but rather has become more destructive in his tendencies toward himself and humanity. This fact is beyond contestation as it is evident by the rise in murder, suicide, drug abuse, alcoholism, sexual promiscuity, abortion, war and crime. Chapp states, “Without an awareness and affirmation of God, there can be no human project that does not, in the end, destroy itself with its own technological prowess…the simple fact of the matter is that what is needed is an affirmation of God as the bearer of a definitive revelation that is carried forward in human history through the agency of a discernible religious tradition.”78 As Chapp states, a return to God is what is needed to restore humanity, but how to achieve such notion is the next question. To this end, humanity must return to its historical roots in education. 

The Role of Education

As discussed earlier, America’s educational institutions played a significant role in the decline of theistic worldviews while at the same time promoting scientific naturalism as they continue to do today. According to a recent PewResearch study completed in September of 2014, those American households professing to be Christian fell sharply from “78.4% to 70.6%.”79 Although this indicates a sharp decline in the number of families associating themselves as Christian; nevertheless, Pew Research is careful to point out that this number still shows that seven out of every ten American households “continue to identify with some branch of the Christian faith.”80 Yet while an overwhelming percentage of American students come from families that identify with Christianity, these same students are subjected to a curriculum based in a secular theology that is diametrically opposed to their family’s fundamental Christian principles. While this disproportionate representation of Christian values in the classroom is no secret and has been widely debated by Americans and their political representatives, scientific naturalism and other secular philosophies have only gained momentum in the classroom. While the reason for this momentum is speculative, it is clear that the battle for the future minds of America and the world for that matter is in the classroom. It should be noted that this is nothing new. Early twentieth century humanist Charles Frances Potter spoke out long ago about this matter when he stated: “Education is thus a most powerful ally of humanism, and every American school is a school of humanism. What can a theistic Sunday school’s meeting for an hour once a week and teaching only a fraction of the children do to stem the tide of the five-day program of humanistic teaching?”81 Potter did his best to ensure that evolution was taught in the classroom by acting as advisor to Clarence Darrow in his defense of John Thomas Scopes, the schoolteacher charged with teaching evolution in the classroom in 1925. However, Potter’s comments should come to Christians as a wake up call directing their attention to the importance of Children’s ministry and biblical education as a means of providing the fundamental basis for the development of a Christian worldview in their students. The Great Reformer Martin Luther predicted the current state of education as early as the fifteenth century. Luther writes,

I am afraid that the schools will prove the very gates of hell, unless they diligently labor in explaining the Holy Scriptures and engraving them in the heart of the youth. I advise no one to place his child where the Scriptures do not reign paramount. Every institution in which men are not unceasingly occupied with the Word of God must become corrupt.82

Martin Luther

Just as Potter’s comments, Luther’s comments are a call to Christians to be intentional and take serious their call to raise up future generations of Christians through education in the church, classroom, and at home. 


This study has shown how the Christian endeavor of scientific inquiry has become secular through a steady progression of events, which have lead to the rise of scientific naturalism and atheistic worldviews. These same atheistic worldviews have served as a presupposition influencing the outcome of scientific discovery, education, and trends in society. What we have seen is that scientific naturalists would have us believe that science comes first in their discovery, and then the worldview follows. However, from this study we conclude that it is in fact the opposite—that the presupposition of naturalistic philosophy actually shapes or preconditions the scientific discovery, and then actually skews the conclusions of the inquiry. More importantly as we have seen in our study, the damaging implications subsequent to the worldview that follows scientific naturalism leads to disastrous consequences for humanity. This is self-evident and is all around us, technological advancement does not lead to the betterment of human beings. The disproportionate influence of scientific naturalism has gained in momentum and is quickly growing to overtake all theistic worldviews. As such, the role of Christians today, although no different from when Christ gave his disciples the great commission (Matt 28:19-20), is to preach the Gospel of Christ by pointing to Jesus and the Christian worldview as the best paradigm to understand the known world. Christians must make the classroom their focus to reverse the momentum of scientific naturalism and save future generations.


  1. Douglas R. Groothuis, “Intelligent Design and the State University: Accepting the Challenge,” Perspectives on Science and Christian Faith Vol. 60 (2008), 234.
  2. Cornelius Hunter, Science’s Blind Spot: The Unseen Religion of Scientific Naturalism (Baker Publishing Group, 2007), 7. 
  3. Ibid.
  4. Douglas R. Groothuis, Christian Apologetics, 99.
  5. C. S. Lewis, Miracles: a preliminary study (London: Collins, 1947), 110. in John C. Lennox, Gunning for God(Lion Hudson, 2011), 28. Kindle.
  6. Douglas R. Groothuis, Christian Apologetics, 100. 
  7. Cornelius Hunter, Science’s Blind Spot, 13.
  8. Ibid, 13.
  9. Ibid, 13-14.
  10. Ibid., 17.
  11. Ibid., 16.
  12. A.F. Holmes, “Descartes, René,” ed. J.D. Douglas and Philip W. Comfort, Who’s Who in Christian History(Wheaton, IL: Tyndale House, 1992), 202.
  13. Ibid.
  14. Ibid.
  15. John C. Lennox, Gunning for God (Lion Hudson, 2011), 28. Kindle.
  16. L. Russ Bush, The Advancement: Keeping the Faith in an Evolutionary Age (Nashville, TN: Broadman & Holman Publishers, 2003), 19.
  17. Ibid., 20.
  18. L. Russ Bush, The Advancement, 20. 
  19. Larry S. Chapp, God of Covenant and Creation: Scientific Naturalism and its Challenge to the Christian Faith (Continuum UK: T & T Clark Theology, 2011), 2. Kindle.
  20. Ibid.
  21. L. Russ Bush, The Advancement, 27.
  22. Ibid.
  23. Edward A. Purcell Jr., The Crisis of Democratic Theory: Scientific Naturalism and the Problem of Value (University Press of Kentucky, 2013), Kindle Loc. 178. Kindle.
  24. Ibid., 179.
  25. Ibid.
  26. Ibid.
  27. Ibid, 180.
  28. L. Russ Bush, The Advancement, 34. 
  29. Leonard Brand, Faith, Reason, & Earth History: A Paradigm of Earth and Biological Origins by Intelligent Design, 2nd Edition. (Berrien Springs, MI: Andrews University Press, 2009), 15.
  30. Ibid.
  31. Ken Ham, “Mount St. Helens – Evidence for Genesis!” Answers in Genesis (May 17, 2000), accessed June 29, 2015:
  32. Schleiden and Schwall working together detailed the first two principles of cell theory in 1839. Victor Virchow published his work “Biogenic Law” in 1855, which first proposed, “every cell stems from another cell,” and “all disease involves changes to the function or structure of normal cells.” The Complete Microscope Guide. Microscope Master: Research, Reviews and Comparisons. Accessed June 27, 2015:
  33. L. Russ Bush, The Advancement, 99.
  34. Charles Taliaferro, Contemporary Philosophy of Religion (Malden, Mass.: Blackwell, 1998), p. 355 in Douglas Groothuis, Christian Apologetics: A Comprehensive Case for Biblical Faith (Downers Grove, IL; Nottingham, England: IVP Academic; Apollos, 2011), 210. 
  35. Douglas Groothuis, Christian Apologetics, 210–211.
  36. Ibid.
  37. L. Russ Bush, The Advancement, 99.
  38. James E. Taylor, Introducing Apologetics: Cultivating Christian Commitment (Grand Rapids, MI: Baker Academic, 2006), 121.
  39. “Richard Dawkins Talks Aliens and Gods” (June 5, 2013) accessed on July 1, 2015,   
  40. Norman L. Geisler, “Should Creation be Taught as Science in Public Schools,” Christian Apologetics Journal 6, no. 2 (2007): 3.
  41. L. Russ Bush, The Advancement, 37.
  42. Carl F. H. Henry, God, Revelation, and Authority, vol. 1 (Wheaton, IL: Crossway Books, 1999), 286.
  43. Ibid.
  44. Ibid., 284.
  45. Bruce Demarest, “Image of God,” ed. Bruce Demarest and Keith J. Matthews, Dictionary of Everyday Theology and Culture, The Navigators Reference Library (Colorado Springs, CO: NavPress, 2010), 229.
  46. Ibid., 230.
  47. Ibid.
  48. Nancy Pearcey and Phillip E. Johnson, Total Truth: Liberating Christianity from Its Cultural Captivity (Wheaton, IL: Crossway, 2005), Ebook.
  49. Ibid.
  50. L. Russ Bush, The Advancement, 48.
  51. Ibid., 59.
  52. Norman L. Geisler and Frank Turek, I Don’t Have Enough Faith to Be an Atheist, 148–149.
  53. Ibid.
  54. Ibid.
  55. Ibid.
  56. F. Sanger, G. M. Air, B. G. Barrell, et al., “Nucleotide Sequence of Bacteriophage Phi-X-174,” Nature 265 (1977), 687 in Nancy Pearcey and Charles B. Thaxton, The Soul of Science: Christian Faith and Natural Philosophy, Turning Point Christian Worldview Series (Wheaton, IL: Crossway Books, 1994), 226.
  57. Ibid.
  58. Edgar Andrews, Who Made God?: Searching for a Theory of Everything (Darlington, England: EP Books, 2009), 20.
  59. Ibid., 21.
  60. Ibid., 22.
  61. Norman L. Geisler and Frank Turek, I Don’t Have Enough Faith to Be an Atheist, 150–151.
  62. Ibid., 151.
  63. Michael J. Behe, “Evidence for Design at the Foundation of Life,” in Science and Evidence for Design in the Universe, vol. 9, The Proceedings of the Wethersfield Institute (San Francisco: Ignatius Press, 2000), 123.
  64. William A. Dembski, The Design Revolution: Answering the Toughest Questions about Intelligent Design(Downers Grove, IL: InterVarsity Press, 2004), 276–277.
  65. Dr. Howard Berg quoted by William A. Dembski, The Design Revolution: Answering the Toughest Questions about Intelligent Design (Downers Grove, IL: InterVarsity Press, 2004), 276.
  66. William A. Dembski, The Design Revolution, 276.
  67. Ibid., 277.
  68. Michael Behe, Darwin’s Black Box (New York: Free Press, 1996), 39 quoted by Douglas Groothuis, Christian Apologetics: A Comprehensive Case for Biblical Faith (Downers Grove, IL; Nottingham, England: IVP Academic; Apollos, 2011), 305. 
  69. L. Russ Bush, The Advancement, 81.
  70. Ibid.
  71. Ibid.
  72. Edgar Andrews, Who Made God? 85.
  73. Alvin Plantinga, Warranted Christian Belief (Oxford University Press, 2000). 
  74. Dan Story, Defending Your Faith (Grand Rapids, MI: Kregel Publications, 1997), 150.
  75. Larry S. Chapp, God of Covenant and Creation: Scientific Naturalism and its Challenge to the Christian Faith(Continuum UK: T & T Clark, 2011), 266. Kindle.
  76. President Barak Obama quoted by Larry S. Chapp, Larry S. God of Covenant and Creation: Scientific Naturalism and its Challenge to the Christian Faith (Continuum UK: T & T Clark, 2011), 260-261. Kindle.
  77. Ibid., 261.
  78. Ibid., 267.
  79. “American’s Changing Religious Landscape,” PewResearchCenter: Religion & Public Life (May 12, 2015), accessed July 3, 2015:
  80. Ibid.
  81. George Frater, Our Humanist Heritage (Nashville: Thomas Nelson, 1978), 94. 
  82. Martin Luther, “Es muss verderben, alles was nicht Gottes Wort ohn Unterlass treibt. L. Opp. (L.) xvii. 486,” The Covenant of Grace. Accessed June 27, 2015: