A Secularized Counter-Reformation, “Hidden in Plain View”:
How Naturalistic Assumptions Oppose Scripture’s Authoritative Relevancy

James J. S. Johnson, JD, ThD, CNHG


The Protestant Reformation’s priority of the Holy Bible, as the ultimate authority for truth and morality, was opposed by at least two major sociopolitical forces, one quite easily recognized, and a parallel version “hidden in plain view”.
The more conspicuous opposition, obviously, was the “Counter-Reformation” reaction of Roman Catholicism. However, what is less often recognized, by Reformation history scholars (especially those who have never studied the scholarly history analysis of Francis Schaeffer ), is that the other major antagonistic force, that strove (and strives) against the Reformation’s recovery of Scriptural authority, was and is Deism’s “child”, secular humanism.
In short, the theistic-yet-Bible-rejecting epistemology of Deism (which ultimately bowed to human reason as its source and authority) morphed into secular humanism.
Consequently, it is a routinely ignored (hidden-in-plain-view) fact that the Protestant Reformation’s Scripture-affirming epistemology has been – and now is – embattled by secularized (human reason-based) epistemologies.
In particular, the origins-related information in Scripture is embattled by humanistic epistemologies that are rationalized as “plausible” using the blended assumptions of Hutton-Lyell uniformitarianism and Darwinian “natural selection” theories, so those “science falsely so-called” theories oppose Reformation epistemology.
By refusing to recognize the authority and relevance of Holy Scripture, secularized epistemologies (and secular etiology theories that disagree with Genesis) function as a secularized arm of the Counter-Reformation movement.
From its beginning, the Counter-Reformation movement was (and is) a religious and political backlash to the Reformation’s theology and its effects.
Accordingly, historic deeds and dynamics of Roman Catholicism’s Counter-Reformation, from the Spanish Inquisition to the Gunpowder Plot, have been repeatedly documented and analyzed (and, ironically, ignored) by many, for half a millennium.
With the religious Counter-Reformation (of Roman Catholicism), the Bible’s ultimate authoritativeness was (and is) magisterially replaced by Rome’s ruling clergy (and their ecclesiastical powers), who profess rights to collectively sit in judgment of (and thus sit “above”) the Holy Bible’s providentially preserved text.
However, in “secular” deistic ideologies, what magisterially replaces the authoritative role of the Bible? Human reason.
In particular, deistic thinking idolizes human reasoning that chooses to avoid Biblical revelation, as the epistemological authority for determining what is true, what is right, what is good, and what is relevant when investigating the past.
Deistic humanism (a/k/a secular humanism), like religious humanism, is a mankind-worshipping religion.
However – unlike religious humanism – secular humanism, in order to appear “secular” (i.e., rationalistic, “natural”, etc.), is a religion-by-another-name, that recruits secularized vocabulary (and employs secularized politics), in order to oppose the Holy Bible as the ultimate authority for truth and morality.
One example of a secularized (i.e., closed-Bible) approach to investigating about origins is the so-called “Intelligent Design Movement” (championed by the Discovery Institute), which is predominantly a modern revival/recycling of the “Enlightenment Era” deism.
How the Intelligent Design Movement Treats the Bible as Irrelevant
Is it possible to profess confidence in God’s Word, yet act like the Bible is not authoritatively relevant? Yes, according to the Lord Jesus Christ, who was confronted with that very situation when He called into question the public professions and practices of the Pharisees. He called their behavior “hypocrisy.” . . . .
Pre-Darwinian Deists and Secular Theories of Earth History
During the 1700s and early 1800s, following the secular influence of the Enlightenment philosophers, a closed-Bible approach to studying earth history became popular in certain professedly Christian academic circles. While insisting that the world of nature be studied apart from biblical revelation about nature, these Christian academics displayed obvious hypocrisy toward God’s Word—“It is God’s Word, but look here at what we discovered in nature.” This disregard for biblical truth opened the gates of “Christian” academia to interlopers influenced essentially by deism, whose errors thrived in closed-Bible environments.
Typically, these scholars did not publicly blast the Bible as being “wrong” or “irrelevant” regarding earth history, so their failure to treat biblical geologic information as authoritatively relevant was not a frontal assault. However, their educational practices followed and promoted secular theories about earth history that without question contradicted biblical data (e.g., old-earth scenarios that discarded the Genesis account of the global Flood)—elevating these theories as more reliable and more important, and thus more relevant, than what the Bible itself taught about nature.
In other words, they conformed to the secular culture of their society, rather than treating the Scriptures as the authoritatively relevant Word of God.
Modern Deists Nullify God’s Truth
In our time, founders of the Intelligent Design Movement (IDM) employed the “wedge” strategy, an approach to design-focused science that intentionally uses a closed-Bible approach to investigating earth history and origins, with a goal to remove “religion” from academic discussions in order to prove that science “naturally” exhibits design.
However, this practice effectively nullifies the Genesis record, functionally denying that the first book of the Bible is authoritatively relevant for explaining origins.
Accordingly, IDM’s closed-Bible approach is just as flawed and disappointing as the approaches used by the geoscientists of the early 1800s—those same old-earth geoscientists who provided a uniformitarian platform for Charles Darwin’s natural selection theory.
The Wedge strategy of IDM, as a form of apologetics, disappoints [to put it mildly!] on several serious grounds.
First, the epistemological price for “marketing” IDM is just too high. As a strategy, IDM abandons public acknowledgment of the Lord Jesus Christ as earth’s Designer and Creator in order to gain a hearing on the topic of biological design. As a consequence, avoiding talk about the identity of the Designer allows the apologetic of IDM to accommodate theistic evolution, or any other unbiblical kind of “designer,” as the imagined producer of complicated life forms.
Second, IDM’s failure to treat Scripture as authoritatively relevant opens the door to evolutionary anthropological theories, such as one proposed by [theistic evolutionist] William Dembski, who imagines that hominid animals were morphed into Adam and Eve and then specially blessed by a miraculous amnesia of their evolutionary ancestry.
In effect, Dembski’s advocacy for “design” has, in fact, placed a “wedge” of false [epistemological] doctrine in the Church. Special revelation (truth provided in Scripture, e.g., Romans 5:12) is effectively separated from general revelation (truth observed in nature, e.g., Psalm 19:1).
Third, the commitment to a closed-Bible approach by IDM for explaining earth’s origins unsurprisingly forfeits any standards for preventing “unequally yoked” alliances between believers and unbelievers, and even uses the word “apologetics” while practicing wholesale ecumenicalism. Does the earth’s Creator, the Lord Jesus Christ, really need a mixed-bag of such religiously diverse experts from Presbyterians to Baptists to Catholic evolutionists to Moonies? Contrast IDM’s team [illustrated by the Discovery Institute] of “strange bedfellows” with Nehemiah’s policy of rejecting heterodox ecumenical teamwork!
Fourth, what ultimate message is conveyed by a closed-Bible approach to discussing origins? It is a mask worn to appeal to the world, like an actor on a theatrical stage. This approach to analyzing earth history, and our own origins, effectively denies that the Holy Bible is authoritatively relevant in what it says.
Admittedly, movements like Intelligent Design [Movement], which essentially take the characteristics of religious deism, do occasionally post “gains” for God’s natural revelation (e.g., showing biology’s “irreducible complexity”). But the price paid for these gains is a net loss, because it gives the appearance that God’s Word is not needed and, thus, not authoritatively relevant to origins science—and nothing is more false than that.
Accordingly, using a deistic pushback to the Protestant Reformation’s “get-back-to-the-Bible” revival, secularists have advocated deistic/atheistic (i.e., rejecting-the-Bible-as-authoritatively-true-or-relevant) assumptions — relying upon an empiricism-enshrined “reason” as a (supposedly adequate) methodology for acquiring reliable truth about creation’s present and past.
In particular, deistic assumptions, applied to natural science categories, historically led to inventing and endorsing anti-creationist theories of “evolution”, as a rationalistic “high-brow” (i.e., pseudo-intellectual) attempt to escape Genesis’s record of our origins — with the peer-pressured endorsement of such “evolutionary” theories being lobbied prior and apart from any evidentiary prove-up of those grandiose speculations.
Why the rush to accepting deistic cosmogonies?
And why are evolutionary theories so desperately and vociferously defended by secular humanists (whether they wear the name “deist” or “atheist” or something else)?
Since one of the strongest proofs of God’s Creatorship is the physical creation that we live in (which includes our own physical bodies and the food we eat ), the non-theistic humanist is immediately confronted with the witness of creation, as an inescapable exhibit of God’s Creatorship. Trying to evade that reality, the non-theistic humanist lunges into an ephemeral illusion of uniformitarian ages and “natural selection”-invented phylogenetic “evolution” as substitutes for the Creator-God, Whose deeds are reported in Genesis. This is fallen human reason trying to find a replacement for God the Creator, groping in quixotic optimism that the ideas of Hutton, Lyell, and Darwin will “save” humanity from accountability to the God of Genesis.
How deistic humanism idolizes (despite mankind’s undeniable fallenness) human reason, and human ability, including an idolatrous epistemology that strives to replace the history reported in Genesis – by providing a theoretical tale of uniformitarian origins that relies on material accidents (and miraculous levels of luck), but it must be so materialistic that even an atheist can endorse it!
Successfully denying reality is, of course, ultimately impossible. And, for mere mortals, doing the impossible is, to say the least (!), not easily accomplished, — so secular humanists cannot be too choosy about what materialistic myths to accept as etiological replacements for the Creator-God of the Bible.
Consequently, the most popular effort aimed at that Creator-replacement target, since the AD1700s, has been the Hutton-Lyell uniformitarian assumption, which illogically reverses evidentiary norms of forensic science by assuming that the past is “key” to the present, which requires rejecting Genesis’s historical data.
Furthermore, the extended version that relies, for its imagined etiology, upon Charles Darwin’s magic-producing mantra, “natural selection” — a deceptive phrase that attempts to replace the etiological need for a true Creator Who can and does make selections, in order to make and order the huge biodiversity (of humans and animals, especially) that inhabit planet Earth.
By sleight-of-hand semantics, appearing to equate the bait-and-switch oxymoron-phrase “natural selection” with the tautological bromide “survival of the fittest”, Darwin’s imaginings must paint a plausible picture of origins (including credible cosmogonical and biogenetic etiologies) that luckily produce a creation (like the one we live in), yet which allegedly do so without a Creator-God (like the One described in the book of Genesis). And, for starters, the deists proudly promote their materialistic Creator-replacement enterprise — swaggeringly strutting as they hawk their snake-oil medicine, with an academic institution haughtiness that competes with the bluff-and-bluster pomp and pageantry of Hans Christian Anderson’s classic satire, The Emperor’s New Clothes.
But the scientific vocabulary that accompanies evolutionary myths (e.g., “natural” joined to “selection”; the biochemical “language” of DNA, RNA, and protein synthesis. The DNA “code”, which is supposed (by naturalistic evolutionists) to be all a matter of materialistic luck, is just the first of many embarrassments for materialistic cosmogonists. As a matter of forensic science, it gets much worse.
Among many other insoluble problems with this replacement cosmogony, however, was the problem of “missing links” – because if (and the “if” is unimaginable huge) humans supposedly “evolved” from ape-like ancestors, who themselves supposedly “evolved” from (if the imagined “transitional forms”) four-legged mammals, who supposedly somehow were biogenetic descendants fish, etc., etc., — where are the physical remains of those many “intermediate” (a/k/a “transitional”) animals, in that imagined long, long, long, long lineage of goo-through-the-zoo-to-you?
The basic idea of biological evolution is that random [i.e., accidental, unintended, unchosen] genetic mutations, over immense periods of time, have led to the appearance of physical or other traits that have provided organisms with a survival advantage. Consequently, because the surviving organisms, whether plant or animal, have had more reproductive success, new species have developed and, gradually, this process has brought about more and more varied types of living things [tracing back to common ancestors].
A study of [Charles] Darwin’s writings will reveal the immutable rule that those newly developed traits must have conferred a survival advantage in order to become more prevalent in the population.
A sticking point is the issue of “transitional forms” [a/k/a “missing links”], viz., those organisms which had not yet completely “evolved” certain traits [i.e., postulated “transitional” organisms that somehow acquired new and partially “complete” features, such as a partially developed wing, not yet capable of successful flight, or a partially developed lung, not yet capable of successfully breathing air].
Darwin found that the fossil record is sorely lacking in [such imagined] transitional forms, and he pondered why they were not “embedded in countless numbers in the crust of the [imagined-to-be-eons-old] earth.” [Quoting Charles Darwin, On the Origin of Species by Means of Natural Selection, 3rd ed. (London: John Murray, 1861), page 190.]
Thus, a major counterpoint to Darwin’s theory [of so-called “natural selection”] is that any biological structure (e.g., the eye) must work properly [i.e., advantageously so as to promote competitively “better” survival consequences] from the start, or the poor creature possessing only a partly “evolved” body would not be the most fit for survival.
Quoting Jonathan C. O’Quinn, “Gearing Up for Survival”, CREATION MATTERS, 20(5):12 (September-October 2015). This provides two glaring proof problems for evolutionists:
(1) what “transitional form” phenotypes are actually “advantageous”, for competitive survival and competitive reproduction purposes?
(2) Even if such “transitional forms” (of animals-evolving-into-other-kinds-of-animals ever existed), why is it that their physical remains are never found, in the fossil record (or elsewhere)?
In short, if evolutionary tales were true, when judges by forensic science proof standards — or, if evolutionary tales were even potentially plausible, by combining simple logic with imagined etiology scenarios, — the whole world should be cluttered with the physical remains of “missing links” (i.e., what evolutionists euphemistically call hypothetical “transitional forms” or “intermediates”) — if evolutionists were correct about the past we should be flooded with millions (if not billions) of “intermediate” hybrid-kind animal bones. But we are not avalanched in “missing link” skeletons – not even a snowdrift!
For this forensic absence of what evolutionary theory (when subjected to simple logic) requires, there is no plausible excuse. In other words, there is no excusing evidence or explanation that allows “common-ancestor-of-all-life” evolutionary etiologies to be “plausible”, that adequately explains away how or why the “missing links” are still “missing.
Evolutionists often speak of missing links. They say that the bridge between man and the apes is the “missing link,” the hypothetical ape-like ancestor of both. But there are supposed missing links all over the evolutionary tree. For instance, dogs and bears are thought to be evolutionary cousins, related to each other through a missing link. The same could be said for every other stop on the tree. All of the animal types are thought to have arisen by the transformation of some other animal type, and at each branching node is a missing link, and between the node and the modern form are many more. If you still don’t know what a missing link is, don’t worry. No one knows what a missing link is, because they are missing! We’ve never seen one.
Moreover, evolutionary theory’s gradual-lucky-changes-over-many-generations assumption is shown as implausible, because half-evolved phenotypical traits could have provided an “survival advantage” to satisfy the Darwinist assumption that competitive survivability is populationally enhanced, accidently, by newly (and materialistically) acquired phenotypical traits (like new wings or new lungs).
Of course, more evidences and analysis could be given, to show the illogic and irrationality of secularized origin theories (and their assumptions, e.g., uniformitarianism, eons of “deep time”, “natural selection” as a phylogenetic “process”, etc.), — but the problems above suffice to show that secularized origin theories are not scientifically sound. Rather, they exist and are quixotically fought for as a desperately “needed” substitute for the history reported in Genesis.
In sum, naturalistic assumptions oppose Scripture’s authoritative relevancy, for no sound epistemological reasons. Rather, secularized etiology myths constitute a secularized attack – a secularized Counter-Reformation – against the authority (and especially the authoritative relevancy) of God’s Word.


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