Creation Questions

Author: Wesley Coleman

  • The Irreducibility of Life

    The Irreducibility of Life

    In his paper “Life Transcending Physics and Chemistry,” Michael Polanyi examines biological machines in a way that illuminates the explanatory failures of materialism. The prevailing materialist paradigm that life can be fully explained by the laws of inanimate nature fails to account for higher ordered realities which have operations and structures that involve non-material judgements and interpretations. He specifically addresses the views of scientists such as Francis Crick, who, along with James Watson, argued for a total reductionist and nominalist view based on their discovery of DNA. For Polanyi, there is a life-transcending nature that all biological organisms have which is akin to machines and their transcendent properties. His central argument is based on the concept of “boundary control,” which argues the notion that there are laws that govern physical reactions (as Crick would accept) yet there are particular laws of form and function which are unique and separate from those lower-level laws.

    There is a real clash between Polanyi’s position and the reductionist/nominalist position which is commonly held by molecular biologists. To start to broach this divergence he explains how the contemporaneous discovery of the genetic function of DNA was interpreted as the final blow to vitalist thought within sciences. He writes:

    “The discovery by Watson and Crick of the genetic function of DNA (deoxyribonucleic acid), combined with the evidence these scientists provided for the self-duplication of DNA, is widely held to prove that living beings can be interpreted, at least in principles, by the laws of physics and chemistry.”

     Polanyi explicitly rejects Crick’s interpretation; that position is of the mainstream and popular level academia. Crick states that his principle “has so far been accepted by few biologists and has been sharply rejected by Francis Crick, who is convinced that all life can be ultimately accounted for by the laws of inanimate nature.” This same sentiment can indeed be found in Crick’s book “Molecules and Man.” Crick writes the following:

    “Thus eventually one may hope to have the whole of biology “explained” in terms of the level below it, and so on right down to the atomic level.”

    To dismantle the materialist argument, Polanyi utilizes the analogy of a machine. A machine cannot be defined or understood solely through the physical and chemical properties of its materials. Take a watch and put it into a machine that can read a detailed atomic map of the device: can even the best chemist give any coherent reason as to whether the watch is functioning or not? Worse—can one even tell you what a watch is, if all that exists is matter in motion for no particular reason? Polanyi writes it best:

    “A complete physical-chemical topography of my watch—even though the topography included the changes caused by the movements in the watch—would not tell us what this object is. On the other hand, if we know watches, we would recognize an object as a watch by a description of it which says that it tells the time of the day… We know watches and can describe one only in terms like ‘telling the time,’ ‘hands,’ ‘face,’ ‘marked,’ which are all incapable of being expressed by the variables of physics, length, mass, and time.”

    Once you see this distinction, you are invariably led (as Polanyi was) to two unique substratum of explanation; what he calls the concept of dual control. Obviously, there are physical laws which dictate constraints and operations of all material and all material things can be explained by these very laws. However, those laws are only meaningfully called constraints when there is some notion of intention or design to be constrained. The shape of any machine, man-made or biological, is not determined by natural laws. Not only is it not determined by them, it cannot be determined by them in any way. Polanyi elaborates on this relationship:

    “The machine is a machine by having been built and being then controlled according to principles of engineering. The laws of physics and chemistry are indifferent to these principles; they would go on working in the fragments of the machine if it were smashed. But they serve the machine while it lasts; machines rely for their operations always on the laws of physics and chemistry.”

    As I hinted at before, Polanyi also applies this logic to biological systems, arguing that morphology is a boundary condition in the same way that a design of a machine is a boundary condition. Biology cannot be reduced to physics because the structure that defines a living being is not the result of physical-chemical equilibration. Physical laws do not intend to create nor do they care that anything functions. Instead, “biological principles are seen then to control the boundary conditions within which the forces of physics and chemistry carry on the business of life.”

    Where Polanyi and Crick truly have the disagreement, then, is in their interpretation of the explanatory power of nature and how DNA is implicated within these frameworks. While Crick views DNA as a chemical agent that proves reducibility, Polanyi argues that the very nature of DNA as an information carrier proves the opposite. For a molecule to function as a code, its sequence cannot be determined by chemical necessity. If chemical laws dictated the arrangement of the DNA molecule, it would be a rigid crystal incapable of conveying complex, variable information. Polanyi writes:

    “Thus in an ideal code, all alternative sequences being equally probable, its sequence is unaffected by chemical laws, and is an arithmetical or geometrical design, not explicable in chemical terms.”

    By treating DNA as a transmitter of information, Polanyi aligns it with other non-physical forms of communication, such as a book. The physical chemistry of the ink and paper does not explain the content of the text. Similarly, the chemical properties of DNA do not explain the genetic information it carries. Polanyi contends that Crick’s own theory inadvertently supports this non-materialist conclusion:

    “The theory of Crick and Watson, that four alternative substituents lining a DNA chain convey an amount of information approximating that of the total number of such possible configurations, amounts to saying that the particular alignment present in a DNA molecule is not determined by chemical forces.”

    Therefore, the pattern of the organism, derived from the information in DNA, represents a constraint that physics cannot explain. It is a boundary condition that harnesses matter. Polanyi concludes that the organization of life is a specific, highly improbable configuration that transcends the laws governing its atomic constituents:

    “When this structure reappears in an organism, it is a configuration of particles that typifies a living being and serves its functions; at the same time, this configuration is a member of a large group of equally probable (and mostly meaningless) configurations. Such a highly improbable arrangement of particles is not shaped by the forces of physics or chemistry. It constitutes a boundary condition, which as such transcends the laws of physics and chemistry.”

    In this way, Polanyi refutes the nominalist materialist perspective by demonstrating that the governing principles of life—its form, function, and information content—are logically distinct from, and irreducible to, the physical laws that govern inanimate matter. Physical laws are, then, merely a piece of the puzzle of the explanation. What’s more, they are insufficient to account for the existence of particular organizations of matter which physical laws and chemistry are not determinative of.

  • Human Eyes – Optimized Design

    Human Eyes – Optimized Design

    Is the human eye poorly designed? Or is it optimal?

    If you ask most proponents of modern evolutionary theory, you will often hear that the eye is a pinnacle of unfortunate evolutionary history and dysteleology.

    There are three major arguments that are used in defending this view:

    The human eye:

    1. is inverted (retina) and wired backwards
    2. has a blind spot due to nerve exit
    3. Is fragile due to retinal detachment

    #1 THE HUMAN EYE IS INVERTED

    The single most famous critique is, of course, the backward wiring of the retina. An optimal sensor should use its entire surface area for data collection, right? The vertebrate eye requires obstruction of the eye-path by axons and capillaries before it hits the photoreceptors.

    Take the cephalopod eye: it has an everted retina, the photo receptors face the light and the nerves are behind them meaning there is no need for a blind spot. The human reversed wiring represents a mere local (rather than global) maximum where the eye could only optimize so far due to its evolutionary history.

    Yet, this argument misses non-negotiable constraints. There is a metabolic necessity for the human eye which doesn’t exist in the squid or octopus.

    Photoreceptors (the rods and cones) have the highest metabolic rate of any cell in the body. They generate extreme heat and oxygen levels and undergo constant repair from constant reaction from photons. The energy demand is massive. This is an issue of thermoregulation, not just optics.

    The reason this is important is because the vertebrate eye is structured with an inverted retina precisely for the survival and longevity of these high-energy photoreceptors. These cells require massive, continuous nutrient and oxygen delivery, and rapid waste removal.

    The current inverted orientation is the only geometric configuration that allows the photoreceptors to be placed in direct contact with the Retinal Pigment Epithelium (RPE) and the choroid. The choroid, a vascular layer, serves as the cooling system and high-volume nutrient source, similar to a cooling unit directly attached to a high-performance processor.

    If the retina were wired forward, the neural cabling would form a barrier, blocking the connection between the photoreceptors and the choroid. This would inevitably lead to nutrient starvation and thermal damage. Not only that, but human photoreceptors constantly shed toxic outer segments due to damage, which must be removed via phagocytosis by the RPE. The eye needs the tips of the photoreceptors to be physically embedded in the RPE. 

    If the nerve fibers were placed in front they would form a barrier, preventing waste removal. This specific geometry is a geometric imperative for long-term molecular recycling and allows for eyes that last for 80+ years on the regular.

    Critics often insist however that even given the neural and capillary layers being necessary for metabolism, it is still a poor design because they block or scatter incoming light. 

    Yet, research has demonstrated that Müller glial cells span the thickness of the retina and act as essentially living fiber-optic cables. These cells possess a higher refractive index than the surrounding tissue, which gives them the capability to channel light directly to the cones with minimal scattering.

    So this criticism actually goes from being a poor design choice into an awesome low-pass filter which improves the signal-to-noise ratio and visual acuity of the human eye.

    But wait, there’s more! The neural layers contain yellow pigments (lutein and zeaxanthin) which absorb excess blue and ultraviolet light that is highly phototoxic! This layer is basically a forcefield against harmful rays (photo-oxidative damage) which extends the lifespan of these super delicate sensors.

    #2 THE HUMAN EYE HAS A BLIND SPOT

    However, the skeptics will still push back (which leads to point number 2): But surely a good design would not include a blind spot where the optic nerve runs through! And indeed this point is a fairly powerful one at a glance. But on further inspection, we see that this exit point, where literally millions of nerve fibers bundle together to pass the photoreceptors, is an example of optimized routing and not a critical flaw of any kind.

    This is true for many reasons. For one, by having the nerves bundle into this reinforced exit point, in this way, maximized the structural robustness of the remaining retina. Basically, if it were not this way, and the nerve fibers exited individually or even in small clusters across the retina, it would radically lower the integrity of the whole design. It would make the retina prone to tearing during rapid eye movements (saccades). In other words, we wouldn’t be getting much REM sleep! That, but also, we’d be missing out on most looking around of any kind.

    I’d say, even if that was the only advantage, the loss of a tiny fraction of our visual field is worth the trade-off.

    Second, and this is important, the blind spot is functionally irrelevant. What do I mean by that? I mean that humans were designed with two eyes for the purpose of seeing depth-of-field, i.e., understanding where things are in space. You can’t do that with one eye, so that’s not an option. With two eyes, the functional retina of the left eye covers the blind spot of the right eye, and vice versa. There is no problem in this design if both the vision is covered and depth-of-field are covered 100% accurately: which they are.

    Third, the optic disc is also used for integrated signal processing, containing melanopsin-driven cells that calibrate brightness perception for the entire eye, using the exit cable as a sensor probe. That means that the nerves also detect brightness and run the logistics in a localized region which is incredibly efficient.

    #3 THE HUMAN EYE IS VULNERABLE

    That is, the vulnerability specifically refers to retinal detachment. That is when the neural retina separates from the RPE. Why does this happen? It is a consequence of the retina being held loosely against the choroid, largely by hydrostatic pressure. Critics call this a failure point. Wouldn’t a good design be one where the RPE is solidly in place, especially if it needs to be connected to the retina? Well… no, not remotely.

    The RPE must actively transport massive amounts of fluid (approximately 10 liters per day) out of the subretinal space to the choroid to prevent edema (swelling) and maintain clear vision. A mechanically fused retina would impede this rapid fluid transport and waste exchange. Basically, the critics offer a solution which is really a non-solution. There is no possible way the eye could function at all by the means they suggest as the alternative “superior” version.

    So, what have we learned?

    The human eye is not a collection of accidents, but a masterpiece of constrained optimization. When the entire system (eye and brain) is evaluated, the result is astonishing performance. The eye achieves resolution at the diffraction limit (the theoretical physical limit imposed by the wave nature of light!) at the fovea, meaning it is hitting the maximum acuity possible for an aperture of its size.

    The arguments that the eye is “sub-optimal” often rely on comparing it to the structurally simpler cephalopod eye. Yet, cephalopod eyes lack trichromatic vision (they don’t see color like we do), have lower acuity (on the scale of hundreds of times worse clarity), and only function for a lifespan of 1–2 years (whereas the human eye must self-repair and maintain high performance for eight decades). The eye’s complexity—the Müller cells, the foveal pit, and the inverted architecture—are the necessary subsystems required to achieve this maximal performance within the constraints of vertebrate biology and physics.

    That’s not even getting to things like mitochondrial microlens in our cells which are essential for processing light. Recent research suggests that mitochondria in cone photoreceptors may actually function as micro-lenses to concentrate light, adding another layer of optical optimization. Optimization which would need to be there, perhaps a lot earlier than even the reversed lens structure.

    The fact that the eye is so optimal still remains, despite the critics best attempts at thwarting it. Therefore, the question remains, how could something so optimized evolve by random chance mutation, as well as so early and often in the history of biota?

  • Mutation is not Creation

    Mutation is not Creation

    Evolution is certainly a tricky word.

    For a creationist, it’s clear as day why. There are two equivocal definitions being used which blur the lines and convolute any attempt at productive dialogue.

    “Change in allele frequencies in a population over time.”

    The breakdown: Alleles represent versions of genes in which a part of the gene is different, which often makes the overall functional outcome in some way different.

    The frequencies in a population are the ratio of members with or without an allele.

    Finally, the premise of this definition is that the number of organisms in a population with a certain trait can grow or diminish over time.

    This seems to me a very uncontroversial thing to hold to. Insofar as evolution could be a fact, this is certainly hard to deny.

    All that is needed for this first definition is mechanisms for sorting and redistribution of existing variation.

    However, what is commonly inferred from the term is an altogether separate conception:

    “All living things are descended from a common ancestor.”

    This is clearly different. An evolutionist may agree, but argue that these are merely differences in degree (or scale). But is that the case?

    The only way to know whether the one definition flows seamlessly into the next or whether this is a true equivocation is to understand the underlying mechanism. For instance, let’s talk about movement.

    South America and Asia are roughly four times further apart than Australia and Antarctica. Yet, I could say, rightly, that I could walk from South America to Asia, but I could not say the same about Australia and Antarctica. Why is this? If I can walk four times the distance in one instance, why should I be thus restricted?

    The obvious reason is this: Australia and Antarctica are separated by the entire width of the deep, open Southern Ocean and the Tasman Sea. I should not expect that I can traverse, by walking, two places with no land betwixt them.

    The takeaway is this: My extrapolation is only good so long as my mechanism is sufficient. Walking is only possible with land bridges. Without land bridges, it doesn’t matter the distance; you’re not going to make it.

    This second definition requires mechanisms for sorting and redistribution of existing variation as well as creation of new biological information and structures.

    With that consideration, let us now take this lesson and apply it to the mechanisms of change which evolutionists espouse.

    There are many, but we will quickly narrow our search.

    Natural Selection: This is any process that acts as a culling from the environment (which can be ecology, climate, niche, etc).

    Gene Flow: This is the reproductive isolation of populations.

    Genetic Drift/Draft: This is any process that causes fluctuations in alleles due to a lack of selection pressures.

    Sexual Selection/Non-Random Mating: This is the process by which organisms preferentially choose phenotypes.

    The point of this exercise is to observe that these are all mechanisms of sorting and redistribution of existing variation, but they are not the mechanisms that create that variation in the first place. Any mechanism that lacks creative power is insufficient to account for our second definition.

    The mechanism that is left is, you might have guessed, mutation.

    Here’s the problem: mutation is its own conflation. We need to unravel the many ways in which DNA can change. There are many kinds of mutations, and what’s true for one may not be true for another. For example, it is often said that mutations are:

    1. Copying errors
    2. Creative
    3. Random with respect to fitness

    However, this is hardly the case for many various types of phenomena that are classified as mutations.

    For instance, take recombination.

    Recombination is not a copy error. It is a very particular and facilitated meiotic process that requires deliberate attention and agency.

    Recombination is not creative. Although it can technically cause a change in allele frequencies (as a new genotype is being created), so can every other non-creative process. It can no more create new genetic material than a card shuffler can create new cards.

    Recombination is not random with respect to fitness. Even with recombination, like a card shuffler, being random in one sense, there is a telos about particular random processes that make them constitute something not altogether random. If we take a card shuffler, it is not random with respect to the “fitness” of the card game. In fact, it is specifically designed to make a fairer and balanced game night. Likewise, recombination, particularly homologous recombination (HR), is fundamentally a high-fidelity DNA repair pathway. It is designed to prevent the uninterrupted spread of broken or worse genes within a single genotype. Like the card shuffler, the mechanism of recombination has no foresight, but it has an explicit function nonetheless.

    Besides recombination, there are many discrete ways in which mutations can happen. On the small scale, we see things like Single Nucleotide Polymorphisms (SNPs) and Insertions and Deletions (Indels). Zooming out, we also find mutations such as duplications & deletions of genes or multiple genes (e.g., CNVs), exon shuffling, and transposable elements. On the grand scale, we see events such as whole genome duplications and epigenetic modifications as well.

    On the small scale, Single Nucleotide Polymorphisms (SNPs) and Insertions and Deletions (Indels) are the equivalent of typos or missing characters within an existing blueprint. While a typo can certainly change the meaning of a sentence, it cannot generate a completely new architectural plan. It modifies the existing instruction set; it does not introduce a novel concept or function absent in the original text. These are powerful modifiers, but their action is always upon pre-existing information.

    It is also the case that these mutations can never rightly be called evolution. They are not creative; they are only destructive mechanisms. Copy errors create noise, not clarity, in information systems.

    Further, these small-scale mutations happen within the context of the preexisting structure and integrity of the genome. So that, even those which are said to be beneficial are preordained to be so by some higher design principles. For instance, much work has been done to show that nucleosomes protect DNA from damage and structural variants stabilize regions where they emerge:

    “Structural variants (SVs) tend to stabilize regions in which they emerge, with the effect most pronounced for pathogenic SVs. In contrast, the effects of chromothripsis are seen across regions less prone to breakages. We find that viral integration may bring genome fragility, particularly for cancer-associated viruses.” (Pflughaupt et al.)

    “Eukaryotic DNA is organized in nucleosomes, which package DNA and regulate its accessibility to transcription, replication, recombination, and repair… living cells nucleosomes protect DNA from high-energy radiation and reactive oxygen species.” (Brambilla et al.)

    Moving to the medium scale, consider duplications and deletions (CNVs) and exon shuffling. Gene duplication, often cited as a source of novelty, is simply copying an entire, functional module—a paragraph or even a full chapter. This provides redundancy. It is often supposed that this allows one copy to drift while the original performs its necessary task. But gene duplications are not simply ignored by the genome or selective processes. They are often immediately discarded if they don’t infer a use, or otherwise, they are incorporated in a certain way.

    “Gene family members may have common non-random patterns of origin that recur independently in different evolutionary lineages (such as monocots and dicots, studied here), and that such patterns may result from specific biological functions and evolutionary needs.” (Wang et al.)

    Here we see that there is often a causal link between the needs of the organism and the duplication event itself. Further, we observe a highly selective process of monitoring post-duplication:

    “Recently, a nonrandom process of gene loss after these different polyploidy events has been postulated [12,31,38]. Maere et al. [12] have shown that gene decay rates following duplication differ considerably between different functional classes of genes, indicating that the fate of a duplicated gene largely depends on its function.” (Casneuf et al.)

    Even if the function conferred was redundancy, redundancy is not creation; it is merely an insurance policy for existing information. Where, precisely, is the mechanism that takes that redundant copy and molds it into a fundamentally new structure or process—say, turning a light-sensing pigment gene into a clotting factor? What is the search space that will have to be traversed? Indels and SNPs are not sufficient to modify a duplication into something entirely novel. Novel genes require novel sequences for coding specific proteins and novel sequences for regulation. Duplication at best provides a scratch pad, which is highly sensitive to being tampered with.

    Exon shuffling, similarly, is a process of reorganization, splicing together pre-existing functional protein domains. This is the biological equivalent of an editor cutting and pasting sentences from one section into another. The result can be a new combination, but every word and grammatical rule was already present. It is the sorting and redistribution of parts.

    Further, exon shuffling is a highly regulated process that has been shown to be constrained by splice frame rules and mediated by TEs in introns.

    “Exon shuffling follows certain splice frame rules. Introns can interrupt the reading frame of a gene by inserting a sequence between two consecutive codons (phase 0 introns), between the first and second nucleotide of a codon (phase 1 introns), or between the second and third nucleotide of a codon (phase 2 introns).” (Wikipedia Contributors)

    This Wikipedia article gives you a taste for the precision and intense regulation, prerequisite and premeditated, in order to perform what are essentially surgical operations to create specialized proteins for cellular operation. One of the reasons it is such a delicate process is portrayed in this journal article:

    “Successful shuffling requires that the domain in question is bordered by introns that are of the same phase, that is, that the domain is symmetrical in accordance with the phase-compatibility rules of exon shuffling (Patthy 1999b), because shuffling of asymmetrical exons/domains will result in a shift of the reading frame in the downstream exons of recipient genes.” (Kaessmann)

    In the same way, transposable elements are constrained by the epigenetic and structural goings-on of the genome. Research shows that transposase recognizes DNA structure at insertion sites, and there are physical constraints caused by chromatin:

    “We show that all four of these measures of DNA structure deviate significantly from random at P element insertion sites. Our results argue that the donor DNA and transposase complex performing P element integration may recognize a structural feature of the target DNA.” (Liao Gc et al.)

    Finally, we look at the grand scale. Whole Genome Duplication (WGD) is the ultimate copy-paste—duplicating the entire instructional library. Again, this provides massive redundancy but offers zero novel genetic information. This is not creative in any meaningful sense, even at the largest scale.

    As for epigenetic modifications, these are critical regulatory mechanisms that determine when and how existing genes are expressed. They are the rheostats and switches of the cell, changing the output and timing without ever altering the source code (the DNA sequence). They are regulatory, not informational creators.

    The central issue remains: The second definition of evolution requires the creation of new organizational blueprints and entirely novel biological functions.

    The mechanism of change relied upon—mutation—is, across all its various types, fundamentally a system of copying, modification, deletion, shuffling, or regulation of existing, functional genetic information. None of these phenomena, regardless of their scale, demonstrates the capacity to generate the required novel information (the “land bridge”) necessary to traverse the vast gap between one kind of organism and another. Again, they are really great mechanisms for change over time, but they are pitiable creative mechanisms.

    Therefore, the argument that the two definitions of evolution are merely differences of scale falls apart. The extrapolation from observing a shift in coat color frequency (Definition 1) to positing a common ancestor for all life (Definition 2) is logically insufficient. It requires a creative mechanism that is qualitatively different from the mechanisms of sorting and modification we observe. Lacking that demonstrated, information-generating mechanism, we are left with two equivocal terms, where one is an undeniable fact of variation and the other is an unsupported inference of mechanism—a proposal to walk across the deep, open ocean with only the capacity to walk on land.

    Works Cited

    Brambilla, Francesca, et al. “Nucleosomes Effectively Shield DNA from Radiation Damage in Living Cells.” Nucleic Acids Research, vol. 48, no. 16, 10 July 2020, pp. 8993–9006, pmc.ncbi.nlm.nih.gov/articles/PMC7498322/, https://doi.org/10.1093/nar/gkaa613. Accessed 30 Oct. 2025.

    Casneuf, Tineke, et al. “Nonrandom Divergence of Gene Expression Following Gene and Genome Duplications in the Flowering Plant Arabidopsis Thaliana.” Genome Biology, vol. 7, no. 2, 2006, p. R13, https://doi.org/10.1186/gb-2006-7-2-r13. Accessed 7 Sept. 2021.

    Kaessmann, H. “Signatures of Domain Shuffling in the Human Genome.” Genome Research, vol. 12, no. 11, 1 Nov. 2002, pp. 1642–1650, https://doi.org/10.1101/gr.520702. Accessed 16 Jan. 2020.

    Liao Gc, et al. “Insertion Site Preferences of the P Transposable Element in Drosophila Melanogaster.” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 7, 14 Mar. 2000, pp. 3347–3351, https://doi.org/10.1073/pnas.97.7.3347. Accessed 1 Dec. 2023.

    Pflughaupt, Patrick, et al. “Towards the Genomic Sequence Code of DNA Fragility for Machine Learning.” Nucleic Acids Research, vol. 52, no. 21, 23 Oct. 2024, pp. 12798–12816, https://doi.org/10.1093/nar/gkae914. Accessed 8 Nov. 2025.

    Wang, Yupeng, et al. “Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms.” PLoS ONE, vol. 6, no. 12, 2 Dec. 2011, p. e28150, https://doi.org/10.1371/journal.pone.0028150. Accessed 20 Dec. 2021.

    Wikipedia Contributors. “Exon Shuffling.” Wikipedia, Wikimedia Foundation, 31 Oct. 2025, en.wikipedia.org/wiki/Exon_shuffling.

  • Jesus Is The Logos

    Jesus Is The Logos

    Based on a cross-sectional analysis of Revelation, John, Hebrews, Colossians, and 1 Timothy, the conclusion that the Logos is a pre-existent, divine person, Jesus Christ, is not merely suggested, but is textually inescapable.

    Let me explain:

    The argument begins with the most direct statement of identity and nature:

    “In the beginning was the WORD, and the Word was with God, and the Word was God.” — John 1:1

    This verse establishes two critical facts: The Word is eternal and the Word is distinct in personhood but shares divinity.

    This divine person is definitively named at the climactic moment of Christ’s return:

    “He was clothed with a robe dipped in blood, and His name is called The Word of God.” — Revelation 19:13

    Jesus is explicitly named the “Word of God.” Jesus is linked to the Word across multiple apostolic authors. John introduces the concept immediately:

    “All things were made through Him, and without Him nothing was made that was made.” — John 1:3

    The Apostle Paul and the author of Hebrews use the identical theological framework to describe Jesus:

    Colossians 1:16: “For by Him all things were created that are in heaven and that are on earth… All things were created through Him and for Him.”

    1 Corinthians 8:6: “…one Lord Jesus Christ, through whom are all things, and through whom we live.”

    Hebrews 1:2: “…spoken to us by His Son, through whom also He made the worlds.”

    Jesus is the sole, ultimate agent “through whom all things consist and were created.” Jesus of Nazareth must, therefore, be the Logos of John 1:1-3. This divine Creator is also the perfect revelation of the Father, known through the Incarnation.

    “The WORD became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father…” — John 1:14

    The mystery of godliness, that God appeared in the flesh (1 Timothy 3:16), is explained by the Logos taking on humanity. Furthermore, He is defined by His relationship to the invisible God:

    “He is the image of the invisible God…” — Colossians 1:15

    “[He is] the brightness of His glory and the express image of His person, and upholding all things by the word of His power…” — Hebrews 1:3

    The Greek word for “express image” in Hebrews 1:3 is charaktēr, meaning an exact replica or the imprint left by a stamp or engraving tool. This confirms that the person of Jesus (the Word) is the precise, perfect, and essential representation of the invisible Father.

    The evidence forms an irrefutable loop: The one who is called the Word of God (Revelation) is the one who is God (John 1:1). This same figure is the one through whom all things were created (John 1:3, Colossians 1:16, 1 Corinthians 8:6). Finally, this divine Creator became flesh (John 1:14) to reveal the exact image of God (Hebrews 1:3). The biblical testimony is unified, establishing the inescapable truth that Jesus Christ is the eternal, divine WORD (Logos).

  • Specious Extrapolations in Origin of Species

    Specious Extrapolations in Origin of Species

    In The Origin of Species, Darwin outlines evidence against the contemporary notion of species fixity, i.e., the idea that species represent immovable boundaries. He first uses the concepts of variations alongside his introduced mechanism of natural selection to create a plausible case for not merely variations, breeds, or races of organisms, but indeed species as commonly descended. Then, in chapter 4, after introducing a taxonomic tree as a picture of biota diversification, he writes, 

    “I see no reason to limit the process of modification, as now explained, to the formation of genera alone.”

    This sentence encapsulates the theoretical move that introduced the concept of universal common ancestry as a permissible and presently accepted scientific model. There is much to discuss regarding the arguments and warrants of the modern debate; however, let us take Darwin on his own terms. In those premier paragraphs of his seminal work, was Darwin’s extrapolation merited? Do the mechanisms and the evidence put forth for them bring us to this inevitable conclusion, or perhaps is the argument yet inconclusive? In this essay, we will argue that, while Darwin’s analogical reasoning was ingenious, his reliance on uniformitarianism and nominalism may render his extrapolation less secure than it first appears.

    In order to explain this, one must first understand the logical progression Darwin must follow. There are apparently three major assumptions—or premises. These are (1) analogism–artificial selection is analogous to natural selection, (2) uniformitarianism–variation is a mostly consistent and uniform process through biological time, and (3) nominalism–all variations and, therefore, all forms, vary by degree only and not kind. Here, we use ‘nominalism’ in the sense that species categories reflect human classification rather than intrinsic natural divisions, a position Darwin implicitly adopts.

    Of his three assumptions, one shows itself to be particularly strong—that of analogism. He spends most of the first four chapters defending this premise from multiple angles. He goes into detail on the powers of artificial selection in chapter one. His detail helps us identify which particular aspect of artificial selection leads to the observed robustness and fitness within its newly delineated populations. For this, he highlights mild selection over a long time. While one can see a drastic change in quick selection, this type of selection is less sustainable. It offers a narrower range of variable options (as variations take time to emerge).

    However, even with this carefully developed premise, let us not overlook its flaws. Notice that the evidence for the power of long-term selection is said to show that it brings about more robust or larger changes within some organisms in at least some environments. However, what evidence does Darwin present to demonstrate this case?

    Darwin does not provide a formal, quantifiable, long-term experiment to demonstrate the superiority of mild, long-term selection. Instead, he relies on descriptive, historical examples from breeders’ practices and then uses a logical argument based on the nature of variation. Thus, Darwin’s appeal demonstrates plausibility, not proof. This is an important distinction if one is to treat natural selection as a mechanism of universal transformation rather than limited adaptation.

    Even still, the extrapolation of differential selection and the environment’s role in that is not egregiously contentious or strange. Moreover, perhaps surprisingly, the assumption of analogism seems to be the most mutable extrapolation. The processes which stand in more doubt are Uniformitarianism and Nominalism (which will be the issue of the rest of this essay). The assumptions of uniformitarianism and nominalism undergird Darwin’s broader inference. When formalized, they resemble the following abductive arguments:

    Argument from Persistent Variation and Selection:

    Premise 1: If the mechanisms of variation and natural selection are persistent through time, then we can infer universal common descent.

    Premise 2: The mechanisms of variation and natural selection are persistent through time.

    Conclusion: Therefore, we can infer universal common descent.

    Argument from Difference in Degree:

    Premise 1: If all life differs only by degree and not kind, then we can infer that variation is a sufficient process to create all modern forms of life.

    Premise 2: All life differs only by degree and not kind,

    Conclusion: Therefore, we infer that variation is a sufficient process to create all modern forms of life.

    From these inferential conclusions, we see the importance of the two final assumptions as a fountainhead of the stream of Darwinian theory. 

    Before moving on, a few disclaimers are in order. It is worth noting that both arguments are contingent on the assumption that biology has existed throughout long geological time scales, but that is to be put aside for now. Notice we are now implicitly granting the assumption of analogism, and this imported doctrine is, likewise, essential to any common descent arguments. Finally, it is also worth clarifying that Darwin’s repeated insistence that ‘no line of demarcation can be drawn’ between varieties and species exemplifies the nominalist premise on which this argument from degree depends.

    To test these assumptions and determine whether they are as plausible as Darwin takes them to be, we first need to examine their constituent evidence and whether they provide empirical or logical support for Darwin’s thesis.

    The uniformitarian view can be presented in several ways. For Darwin, the view was the lens through which he saw biology, based on the Principles of Geology as articulated by Charles Lyell. Overall, it is not a poor inferential standard by any means. There are, however, certain caveats that limit its relevance in any science. Essentially, the mechanism in question must be precisely known, in that what X can do is never extrapolated into what X cannot do as part of its explanatory power. 

    How Darwin frames the matter is to say, “I observe X happening at small scales, therefore X can accumulate indefinitely.” This is not inherently incorrect or poor science in and of itself. However, one might ask: if one does not know the specific mechanisms involved in this variation process, is it really plausible to extrapolate these unknown variables far into the past or the future? Without knowing how variation actually works (no Mendelian genetics, no understanding of heredity’s material basis), Darwin is in a conundrum. He cannot justify the assumption that variation is unlimited if he cannot explain what it would even mean for that proposition to be true across deep time. It is like measuring the Mississippi’s sediment deposition rate, as was done for over 170 years, and extrapolating it back in time, when the river spanned the Gulf of Mexico. Alternatively, it is like measuring the processes of water erosion along the White Cliffs of Dover and extrapolating back in time until it reaches the European continent. In the first case, there is an apparent flaw in assuming constant deposition rates. In the second case, it is evident that water alone could not have caused the original break between England and France.

    It is the latter issue that is of deep concern here. There are too many unknowns in this equation to make it remotely scientific. It is not true that observing a phenomenon consistently requires understanding its mechanisms to extrapolate. However, Darwin’s theory is historical in a way that gravity, disease, or early mechanistic explanations were not. It cannot be immediately tested. Darwin, at best, leaves us to do the bulk of the grunt work after indulging in what can only be called guesswork.

    Darwin’s second line of reasoning to reach the universal common ancestry thesis relies heavily on a philosophical view of reality: nominalism. For nominalism to be correct, all traits and features would need to be quantitatively different (longer/shorter, harder/softer, heavier/lighter, rougher/smoother) without any that are qualitatively different (light/dark, solid/liquid/gas, color/sound, circle/square). In order to determine whether biology contains quality distinctions, we must understand how and in what way kinds become differentiable.

    The best polemical examples of discrete things, which differ more than just in degree, are colors. Colors could be hard to pin down on occasion. Darwin would have an easy time, as he did with species and variation taxonomical discourse, pointing out the divisive groups of thought in the classification of colors. Intuitively, there is a straightforward flow of some red to some blue. Even if they are mostly distinguishable, is not that cloud or wash of in-betweens enough to question the whole enterprise of genuine or authentic categories?

    However, moving from blue to yellow is not just an increase or decrease in something; it is a change to an entirely new color identity. It is a new form. The perceptual experience of blue is qualitatively different from the perceptual experience of yellow. Meaning they affect the viewer in particular and different ways. Hues, specifically, are indeed highly differentiated and are clear species within the genus of color. An artist mixing blue and yellow to create green does not thereby prove that blue and yellow are not real, distinct colors—only that intermediates are possible. Likewise, it is no business of the taxonomer, which calls some species and others variations, to negate the realness of any of these separate groups and count them as arbitrary and nominal. If colors—which exist on a continuous spectrum of wavelengths—still exhibit qualitative differences, then Darwin’s assumption that ALL biological features exist only on quantitative gradients becomes questionable.

    However, Darwin has done this very thing, representing different kinds of structures with different developmental origins and functional architectures as a mere spectrum with no distinct affections or purposes. Darwin needs variation to be infinitely plastic, but what does he say to real biological constraints? Is it ever hard to tell the difference between a plant and an animal? A beak from fangs? A feather from fur? A nail from a claw? A leaf from a pine needle? What if body plans have inherent organizational logic that resists certain transformations? He is treating organisms like clay that can be molded into any form, but what if they are more like architectural structures with load-bearing walls? Darwin is missing good answers to these concerns. All of which need answers in order to call the Argument from Difference in Degree sound or convincing. 

    This critique does not diminish Darwin’s achievement in proposing a naturalistic mechanism for adaptation. Instead, it highlights the philosophical assumptions embedded in his leap from observable variation to universal common descent. Assumptions that, in 1859, lacked the mechanistic grounding that would make such extrapolation scientifically secure.

  • The Five Major Challenges To Hume’s Skepticism

    The Five Major Challenges To Hume’s Skepticism

    In David Hume’s book A Treatise of Human Nature, he constructs what he calls the science of man. One cannot rightly understand any other species of science before this foundational science. The most radical and paradigm-shifting realization, for Hume, is that if all that exists are impressions and ideas, there are no grounds to truly justify putting any two impressions together causally, no matter how we might be inclined or disposed to do so, either by vulgar habit or through any rational means. This profound insight — that impressions are singular moments of a particular feeling with no relation except that of imagination — forced philosophers (including critics such as Reid) to deeply re-evaluate theories of knowledge acquisition and general epistemic concerns.

    Reid says this in his dedication for An Inquiry into the Human Mind, “His reasoning appeared to me to be just: there was therefore a necessity to call in question the principles upon which it was founded, or to admit the conclusions.” However, there are more reasons than the mere founding principles to reject Hume’s rationale. Drawing on a recent and rigorous debate, here are the five major critiques that make me skeptical of Hume’s skeptical conclusions.

    1. Circular Reasoning (The Problem of Induction)

    Hume uses causal reasoning (observing past regularities and inferring principles about human nature) to undermine the rational basis of causal reasoning. Suppose Hume justifies the separation of cause and correlation from experience, and he uses the distinction to describe and also argue against cause-and-effect as existing outside the mind (outside a relation/idea). In that case, he is making a circular argument. The implications of this circular reasoning are profound, as it challenges the very basis of our understanding of cause and effect. If belief in necessary connection is understood apart from reason, then there is equally no reason to undermine causal reasoning. The basis for an essential connection is reason and logical deduction. Thus, we can infer it from particular impressions, or it is not, and thus we can infer it based on specific impressions. Nothing falls on his skeptical rebuttal. You cannot easily conceive of a cause without an effect, any more than a premise without a conclusion.

    2. The Self-Refutation of Assertion and Communication

    The fact that Hume is making an argument refutes his point entirely. On what grounds can Hume either 1. make a distinction between kinds of necessity or 2. place either relations or matters of fact squarely into one category? Unthinkable things are equivalent to non-existent things, according to Hume. Therefore, you cannot make claims about external reality with reference to non-existent concepts. Even concepts of the imagination must exist by virtue of real impressions that have newly associated connections. Where are the impressions for a law such as non-contradiction?

    Hume believes we cannot know a table exists, so this is not simply descriptive. His outward attempts to convince others, and the fact that he has followers who support his theory, testify against him. Psychological interpretations of reality are false simply because meaning exists apart from the mechanical goings-on of the mind, and that meaning is communicable. The very fact that Hume is articulating his theory indicates such. Even a phenomenological view is better than psychologism.

    3. The Ad Hoc Assumption of External Existence

    Hume asks for the impression that gives rise to the idea of continuation and external existence separate from our perception, but where does he get the idea of continuation and external existence in the first place? If everything is sense impressions, how is he arguing against anything contrary to sense impressions? This is all very ad hoc. Calling concepts fabrications of the imagination and such. Does he not realize that by doing so, he’s condemning his very principles, which allowed him to condemn continuation and external existence?

    4. The Active Nature of Impressions, Not Raw Data

    There is also another popular critique of Hume. That is the notion of the tree falling in the woods. The tree falls without making a sound. A sound is something that can only be heard. The point being, Hume’s impressions already imply cause-and-effect before they are even interpreted or registered. Here is another thing. If two people hear a recording of an orchestra, but one of them has finely tuned ears for orchestration while the other does not, then, on first glance, the one with finely tuned ears will hear the counter-melody played on the violin. The one that does not is not surprising. However, Hume would have to acknowledge this as an impression reflected, interpreted by relation (all of which in a near-instant), yet that implies a higher acuity has been granted to the one in the realm of a particular sense. If sense is raw data, and therefore something that you receive and not create, it stands to reason that you should not be able to improve in the tacit reception of raw data. This analogy highlights the inherent contradictions in Hume’s argument, suggesting that our senses are not passive receptors of information but active interpreters that can improve over time.

    5. The Flawed Equivalence of Conceivability and Possibility

    A rigorous philosophical objection to Hume’s conclusion on necessity centers on his premise that what is conceivable is logically possible. Hume argues that because we can conceive of a cause without its usual effect (e.g., imagining the sun not rising) without contradiction, the necessary connection is not a truth of reason, but of habit. However, this conflates a psychological possibility (what we can imagine) with a metaphysical possibility (what could actually happen in reality). Contemporary critics argue that our inability to conceive of a contradiction in a causal break may reflect our epistemic limitations —our ignorance of deep, non-obvious natural laws —rather than a statement about the world itself. Therefore, the supposed “freedom” of the imagination that underpins his skepticism is merely a function of our ignorance of actual natural necessity, and his argument fails to prove that the necessity is truly absent from the objects themselves.

  • The Agnostic Nature of Phylogenetic Trees and Nested Hierarchies

    The Agnostic Nature of Phylogenetic Trees and Nested Hierarchies

    The evidence typically presented as definitive proof for the theory of common descent, the nested hierarchy of life and genetic/trait similarities, is fundamentally agnostic. This is because evolutionary theory, in its broad explanatory power, can be adapted to account for virtually any observed biological pattern post-hoc, thereby undermining the claim that these patterns represent unique or strong predictions of common descent over alternative models, such as common design.

    I. The Problematic Nature of “Prediction” in Evolutionary Biology

    1. Strict Definition of Scientific Prediction: A true scientific prediction involves foretelling a specific, unobserved phenomenon before its discovery. It is not merely explaining an existing observation or broadly expecting a general outcome.
    2. Absence of Specific Molecular Predictions:
      • Prior to the molecular biology revolution (pre-1950s/1960s), no scientist explicitly predicted the specific molecular similarity of DNA sequences across diverse organisms, the precise double-helix structure, or the near-universal genetic code. These were empirical discoveries, not pre-existing predictions.
      • Evolutionary explanations for these molecular phenomena (e.g., the “frozen accident” hypothesis for the universal genetic code) were formulated after the observations were made, rendering them post-hoc explanations rather than predictive triumphs.
      • Interpreting broad conceptual statements from earlier evolutionary thinkers (like Darwin’s “one primordial form”) as specific molecular predictions is an act of “eisegesis”—reading meaning into the text—rather than drawing direct, testable predictions from it. A primordial form does not necessitate universal code, universal protein sequences, universal logic, or universal similarity.

    II. The Agnosticism of the Nested Hierarchy

    1. The Nested Hierarchy as an Abstract Pattern: The observation that life can be organized into a nested hierarchy (groups within groups, e.g., species within genera, genera within families) is an abstract pattern of classification. This pattern existed and was recognized (e.g., by Linnaeus) long before Darwin’s theory of common descent.
    2. Compatibility with Common Design: A designer could, for various good reasons (e.g., efficiency, aesthetic coherence, reusability of components, comprehensibility), choose to create life forms that naturally fall into a nested hierarchical arrangement. Therefore, the mere existence of this abstract pattern does not uniquely or preferentially support common descent over a common design model.
    3. Irrelevance of Molecular “Details” for this Specific Point: While specific molecular “details” (such as shared pseudogenes, endogenous retroviruses, or chromosomal fusions) are often cited as evidence for common descent, these are arguments about the mechanisms or specific content of the nested hierarchy. These are not agnostic and can be debated fruitfully. However, they do not negate the fundamental point that the abstract pattern of nestedness itself remains agnostic, as it could be produced by either common descent or common design.

    III. Evolutionary Theory’s Excessive Explanatory Flexibility (Post-Hoc Rationalization)

    1. Fallacy of Affirming the Consequent: The logical structure “If evolutionary theory (Y) is true, then observation (X) is expected” does not logically imply “If observation (X) is true, then evolutionary theory (Y) must be true,” especially if the theory is so flexible that it can explain almost any X.
    2. Capacity to Account for Contradictory or Diverse Outcomes:
      • Genetic Similarity: Evolutionary theory could equally well account for a model with no significant genetic similarity between organisms (e.g., if different biochemical pathways or environmental solutions were randomly achieved, or if genetic signals blurred too quickly over time). For example, a world with extreme porportions of horizontal gene transfer (as seen in prokaryotic and rare eukaryotic cells)
      • Phylogenetic Branching: The theory is flexible enough to account for virtually any observed phylogenetic branching pattern. If, for instance, humans were found to be more genetically aligned with pigs than with chimpanzees, evolutionary theory would simply construct a different tree and provide a new narrative of common ancestry. This flexability puts a wedge in any measure of predictability claimed by the theory.
      • “Noise” in Data: If genetic data were truly “noise” (random and unpatterned), evolutionary theory could still rationalize this by asserting that “no creator would design that way, and randomness fully accounts for it,” thus always providing an explanation regardless of the pattern. In fact, a noise pattern is perhaps one of the few patterns better explained by random physical processes. Why would a designer, who has intentionality, create in such a slapdash way?
      • Convergence vs. Divergence: The theory’s ability to explain both convergent evolution (morphological similarity without close genetic relatedness) and divergent evolution (genetic differences leading to distinct forms) should imediately signal red-flags, as this is a telltale sign of a post-hoc fitting of observations rather than a result of specific prediction.
        • To illustrate this point, Let’s imagine we have seven distinct traits (A, B, C, D, E, F, G) and five hypothetical populations of creatures (P1-P5), each possessing a unique combination of these traits. For example, P1 has {A, B, C}, P2 has {A, D, E}, P3 has {A, F, G}, P4 has {B, D, F}, and P5 has {E, G}. When examining this distribution, we can construct a plausible “evolutionary story.” Trait ‘A’, present in P1, P2, and P3, could be identified as a broadly ancestral trait. P1 might be an early branch retaining traits B and C, while P2 and P3 diversified by gaining D/E and F/G respectively.
        • However, the pattern becomes more complex with populations like P4 and P5. P4’s mix of traits {B, D, F} suggests it shares B with P1, D with P2, and F with P3. An evolutionary narrative would then employ concepts like trait loss (e.g., B being lost in P2/P3/P5’s lineage), convergent evolution (e.g., F evolving independently in P4 and P3), or complex branching patterns. Similarly, P5’s {E, G} would be explained by inheriting E from P2 and G from P3, while also undergoing significant trait loss (A, B, C, D, F).
        • And this is the crux of the argument, given any observed distribution of traits, evolutionary theory’s flexible set of explanatory mechanisms—including common ancestry, trait gain, trait loss, and convergence—can always construct a coherent historical narrative. This ability to fit diverse patterns post-hoc renders the mere existence of a nested hierarchy, disconnected from specific underlying molecular details, as agnostic evidence for common descent over other models like common design.

    IV. Challenges to Specific Evolutionary Explanations and Assumptions

    1. Conservation of the Genetic Code:
      • The claim that the genetic code must remain highly conserved post-LUCA due to “catastrophic fitness consequences” of change is an unsubstantiated assumption. Granted, it could be true, but one can imagine plausible scenarios which could demonstrate exceptions.
      • Further, evolutionary theory already postulates radical changes, including the very emergence of complex systems “from scratch” during abiogenesis. If such fundamental transformations are possible, then the notion that a “new style of codon” is impossible over billions of years, even via incremental “patches and updates,” appears inconsistent.
      • Laboratory experiments that successfully engineer organisms to incorporate unnatural amino acids demonstrate the inherent malleability of the genetic code. Yet no experiment has demonstrate abiogenesis, a much more implausible event with less evolutionary time to play with. Why limit the permissible improbable things arbitrarily?
      • There is no inherent evolutionary reason to expect a single, highly conserved “language” for the genetic code; if information can be created through evolutionary processes, then multiple distinct solutions should be the rule.
    2. Functionality of “Junk” DNA and Shared Imperfections:
      • The assertion that elements like pseudogenes and endogenous retroviruses (ERVs) are “non-functional” or “mistakes” is often an “argument from ignorance” or an “anti-God/atheism-of-the-gaps” fallacy. Much of the genome’s function is still unknown, and many supposedly “non-functional” elements are increasingly found to have regulatory or other biological roles. For instance, see my last article on the DDX11L2 “pseudo” gene which operates as a regulatory element including as a secondary promoter.
      • If these elements are functional, their homologous locations are easily explained by a common design model, where a designer reuses functional components across different creations.
      • The “functionality” of ERVs, for instance, is often downplayed in arguments for common descent, despite their known roles in embryonic development, antiviral defense, and regulation, thereby subtly shifting the goalposts of the argument.
    3. Probabilities of Gene Duplication and Fusion:
      • The probability assigned to beneficial gene duplications and fusions (which are crucial for creating new genetic information and structures) seems inconsistently high when compared to the low probability assigned to the evolution of new codon styles. If random copying errors can create functional whole genes or fusions, then the “impossibility” of a new codon style seems a little arbitrary.

    Conclusion:

    The overarching argument is that while common descent can certainly explain the observed patterns in biology, its explanatory power often relies on post-hoc rationalization and a flexibility that allows it to account for almost any outcome. This diminishes the distinctiveness and predictive strength of the evidence, leaving it ultimately agnostic when compared to alternative models that can also account for the same observations through different underlying mechanisms.

  • Evidence for an Active Alternative Promoter in the Human DDX11L2 Gene

    Evidence for an Active Alternative Promoter in the Human DDX11L2 Gene

    Abstract

    The human genome contains numerous regulatory elements that control gene expression, including canonical and alternative promoters. While DDX11L2 is annotated as a pseudogene, its functional relevance in gene regulation has been a subject of interest. This study leverages publicly available genomic data from the UCSC Genome Browser, integrating information from the ENCODE project and ReMap database, to investigate the transcriptional activity within a specific intronic region of the DDX11L2 gene (chr2:113599028-113603778, hg38 assembly). Our analysis reveals the co-localization of key epigenetic marks, candidate cis-regulatory elements (cCREs), and RNA Polymerase II binding, providing robust evidence for an active alternative promoter within this region. These findings underscore the complex regulatory landscape of the human genome, even within annotated pseudogenes.

    1. Introduction

    Gene expression is a tightly regulated process essential for cellular function, development, and disease. A critical step in gene expression is transcription initiation, primarily mediated by RNA Polymerase II (Pol II) in eukaryotes. Transcription initiation typically occurs at promoter regions, which are DNA sequences located upstream of a gene’s coding sequence. However, a growing body of evidence indicates the widespread use of alternative promoters, which can initiate transcription from different genomic locations within or outside of a gene’s canonical promoter, leading to diverse transcript isoforms and complex regulatory patterns [1].

    The DDX11L2 gene, located on human chromosome 2, is annotated as a DEAD/H-box helicase 11 like 2 pseudogene. Pseudogenes are generally considered non-functional copies of protein-coding genes that have accumulated mutations preventing their translation into functional proteins. Despite this annotation, some pseudogenes have been found to play active regulatory roles, for instance, by producing non-coding RNAs or acting as cis-regulatory elements [2]. Previous research has suggested the presence of an active promoter within an intronic region of DDX11L2, often discussed in the context of human chromosome evolution [3].

    This study aims to independently verify the transcriptional activity of this specific intronic region of DDX11L2 by analyzing comprehensive genomic and epigenomic datasets available through the UCSC Genome Browser. We specifically investigate the presence of key epigenetic hallmarks of active promoters, the classification of cis-regulatory elements, and direct evidence of RNA Polymerase II binding.

    2. Materials and Methods

    2.1 Data Sources

    Genomic and epigenomic data were accessed and visualized using the UCSC Genome Browser (genome.ucsc.edu), utilizing the Human Genome assembly hg38. The analysis focused on the genomic coordinates chr2:113599028-113603778, encompassing the DDX11L2 gene locus.

    The following data tracks were enabled and examined in detail:

    ENCODE Candidate cis-Regulatory Elements (cCREs): This track integrates data from multiple ENCODE assays to classify genomic regions based on their regulatory potential. The “full” display mode was selected to visualize the color-coded classifications (red for promoter-like, yellow for enhancer-like, blue for CTCF-bound) [4].

    Layered H3K27ac: This track displays ChIP-seq signal for Histone H3 Lysine 27 acetylation, a histone modification associated with active promoters and enhancers. The “full” display mode was used to visualize peak enrichment [5].

    ReMap Atlas of Regulatory Regions (RNA Polymerase II ChIP-seq): This track provides a meta-analysis of transcription factor binding sites from numerous ChIP-seq experiments. The “full” display mode was selected, and the sub-track specifically for “Pol2” (RNA Polymerase II) was enabled to visualize its binding profiles [6].

    DNase I Hypersensitivity Clusters: This track indicates regions of open chromatin, which are accessible to regulatory proteins. The “full” display mode was used to observe DNase I hypersensitive sites [4].

    GENCODE Genes and RefSeq Genes: These tracks were used to visualize the annotated gene structure of DDX11L2, including exons and introns.

    2.2 Data Analysis

    The analysis involved visual inspection of the co-localization of signals across the enabled tracks within the DDX11L2 gene region. Specific attention was paid to the first major intron, where previous studies have suggested an alternative promoter. The presence and overlap of red “Promoter-like” cCREs, H3K27ac peaks, and Pol2 binding peaks were assessed as indicators of active transcriptional initiation. The names associated with the cCREs (e.g., GSE# for GEO accession, transcription factor, and cell line) were noted to understand the experimental context of their classification.

    3. Results

    Analysis of the DDX11L2 gene locus on chr2 (hg38) revealed consistent evidence supporting the presence of an active alternative promoter within its first intron.

    3.1 Identification of Promoter-like cis-Regulatory Elements:

    The ENCODE cCREs track displayed multiple distinct red bars within the first major intron of DDX11L2, specifically localized around chr2:113,601,200 – 113,601,500. These red cCREs are computationally classified as “Promoter-like,” indicating a high likelihood of promoter activity based on integrated epigenomic data. Individual cCREs were associated with specific experimental identifiers, such as “GSE46237.TERF2.WI-38VA13,” “GSE102884.SMC3.HeLa-Kyoto_WAPL_PDS-depleted,” and “GSE102884.SMC3.HeLa-Kyoto_PDS5-depleted.” These labels indicate that the “promoter-like” classification for these regions was supported by ChIP-seq experiments targeting transcription factors like TERF2 and SMC3 in various cell lines (WI-38VA13, HeLa-Kyoto, and HeLa-Kyoto under specific depletion conditions).

    3.2 Enrichment of Active Promoter Histone Marks:

    A prominent peak of H3K27ac enrichment was observed in the Layered H3K27ac track. This peak directly overlapped with the cluster of red “Promoter-like” cCREs, spanning approximately chr2:113,601,200 – 113,601,700. This strong H3K27ac signal is a hallmark of active regulatory elements, including promoters.

    3.3 Direct RNA Polymerase II Binding:

    Crucially, the ReMap Atlas of Regulatory Regions track, specifically the sub-track for RNA Polymerase II (Pol2) ChIP-seq, exhibited a distinct peak that spatially coincided with both the H3K27ac enrichment and the “Promoter-like” cCREs in the DDX11L2 first intron. This direct binding of Pol2 is a definitive indicator of transcriptional machinery engagement at this site.

    3.4 Open Chromatin State:

    The presence of active histone marks and Pol2 binding strongly implies an open chromatin configuration. Examination of the DNase I Hypersensitivity Clusters track reveals a corresponding peak, further supporting the accessibility of this region for transcription factor binding and initiation.

    4. Discussion

    The integrated genomic data from the UCSC Genome Browser provides compelling evidence for an active alternative promoter within the first intron of the human DDX11L2 gene. The co-localization of “Promoter-like” cCREs, robust H3K27ac signals, and direct RNA Polymerase II binding collectively demonstrates that this region is actively engaged in transcriptional initiation.

    The classification of cCREs as “promoter-like” (red bars) is based on a sophisticated integration of multiple ENCODE assays, reflecting a comprehensive biochemical signature of active promoters. The specific experimental identifiers associated with these cCREs (e.g., ERG, TERF2, SMC3 ChIP-seq data) highlight the diverse array of transcription factors that can bind to and contribute to the regulatory activity of a promoter. While ERG, TERF2, and SMC3 are not RNA Pol II itself, their presence at this locus, in conjunction with Pol II binding and active histone marks, indicates a complex regulatory network orchestrating transcription from this alternative promoter.

    The strong H3K27ac peak serves as a critical epigenetic signature, reinforcing the active state of this promoter. H3K27ac marks regions of open chromatin that are poised for, or actively undergoing, transcription. Its direct overlap with Pol II binding further strengthens the assertion of active transcription initiation.

    The direct observation of RNA Polymerase II binding is the most definitive evidence for transcriptional initiation. Pol II is the core enzyme responsible for synthesizing messenger RNA (mRNA) and many non-coding RNAs. Its presence at a specific genomic location signifies that the cellular machinery for transcription is assembled and active at that site.

    The findings are particularly interesting given that DDX11L2 is annotated as a pseudogene. This study adds to the growing body of literature demonstrating that pseudogenes, traditionally considered genomic “fossils,” can acquire or retain functional regulatory roles, including acting as active promoters for non-coding RNAs or influencing the expression of neighboring genes [2]. The presence of an active alternative promoter within DDX11L2 suggests a more intricate regulatory landscape than implied by its pseudogene annotation alone.

    5. Conclusion

    Through the integrated analysis of ENCODE and ReMap data on the UCSC Genome Browser, this study provides strong evidence that an intronic region within the human DDX11L2 gene functions as an active alternative promoter. The co-localization of “Promoter-like” cCREs, high H3K27ac enrichment, and direct RNA Polymerase II binding collectively confirms active transcriptional initiation at this locus. These findings contribute to our understanding of the complex regulatory architecture of the human genome and highlight the functional potential of regions, such as pseudogenes, that may have been previously overlooked.

    References

    [1] Carninci P. and Tagami H. (2014). The FANTOM5 project and its implications for mammalian biology. F1000Prime Reports, 6: 104.

    [2] Poliseno L. (2015). Pseudogenes: Architects of complexity in gene regulation. Current Opinion in Genetics & Development, 31: 79-84.

    [3] Tomkins J.P. (2013). Alleged Human Chromosome 2 “Fusion Site” Encodes an Active DNA Binding Domain Inside a Complex and Highly Expressed Gene—Negating Fusion. Answers Research Journal, 6: 367–375. (Note: While this paper was a starting point, the current analysis uses independent data for verification).

    [4] ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414): 57–74.

    [5] Rada-Iglesias A., et al. (2011). A unique chromatin signature identifies active enhancers and genes in human embryonic stem cells. Nature Cell Biology, 13(9): 1003–1013.

    [6] Chèneby J., et al. (2018). ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Nucleic Acids Research, 46(D1): D267–D275.

  • J. Budziszewski’s Natural Theology of Sex: A Pathway to Biblical Understanding

    J. Budziszewski’s Natural Theology of Sex: A Pathway to Biblical Understanding

    J. Budziszewski, in his insightful work On the Meaning of Sex, presents a compelling natural theological framework that grounds sexual ethics in the inherent design and purpose of human beings. This approach, by meticulously analyzing the given structure of human nature, offers a robust pathway that can successfully lead to a Biblical understanding of sexuality and gender. Budziszewski argues that meaning is not arbitrarily assigned but is discovered through the inherent design of creation, and it is this foundational concept that shapes his comprehensive view of sexual morality.

    A) The Foundational Idea: Inherent Design and Purpose

    The bedrock of Budziszewski’s philosophy, especially concerning the questions of sexuality and gender, is the conviction that meaning is intrinsic to reality, particularly to human nature itself. He firmly asserts, “Meaning isn’t arbitrary. Yes, we can associate sex in our minds with anything we choose—with pain, pleasure, tedium, amusement, alienation, reconciliation, fertility, sterility, misery, joy, life, death, or what have you. This is true of all things, not just sex. We can associate anything with anything” (7). However, he immediately clarifies that subjective association does not alter objective meaning. For Budziszewski, human nature is not an external master but “the deep structure of what we really are” (8). True freedom, then, is not the ability to transcend this nature, but rather the ability to align our wills with it, to allow “the meanings and purposes that lie fallow in sexuality [to] unfold” (8). He explains that the human will is not separate from nature but an integral part of it, asserting that the will’s nobility lies in its capacity to discern and direct itself according to the inherent wisdom embedded in our being.

    Budziszewski confronts common objections to this idea, particularly the notion that one cannot derive an “ought” from an “is.” He dismantles this dogma by using simple, yet powerful, examples. When discussing the lungs, he posits, “When we say that their purpose is to oxygenate the blood, are we just making that up? Of course not. The purpose of oxygenation isn’t in the eye of the beholder; it’s in the design of the lungs themselves” (22). This emphasis on “the design of the lungs” is crucial; it implies that purpose is empirically discoverable. Furthermore, he contends that to violate this inherent design, such as by “sniffing glue,” does not change the lung’s purpose but only “violates it” (22). Similarly, regarding eyes, he argues, “If the purpose of eyes is to see, then eyes that see well are good eyes, and eyes that see poorly are poor ones. Given their purpose, this is what it means for eyes to be good. Moreover, good is to be pursued; the appropriateness of pursuing it is what it means for anything to be good. Therefore, the appropriate thing to do with poor eyes is try to turn them into good ones” (22). This demonstrates that understanding a thing’s inherent purpose necessarily implies an “ought”—an imperative to act in accordance with that purpose. He further distinguishes “purpose” from mere “function,” stating that purpose signifies something “ordered or directed to an end,” whereas function merely “signifies the mode in which purpose is present in things rather than in minds” (23). This foundational idea underpins his entire argument: that human beings, as integrated wholes of “mind and flesh united,” must respect the inherent design of their bodies, including their sexuality (23). While he acknowledges that some might dismiss his work as “religious” due to references to “God,” he insists that divine grace, if real, is “inescapably relevant to human life” and can be understood even through natural reasoning (11).

    B) Application to Gender and Sexuality

    Applying this foundational idea, Budziszewski posits that human sexuality possesses “embedded principles and the inbuilt meaning of the human sexual design” (21). He laments that “errors about sex cause such terrible suffering, in our day more than most” (12), and attributes this suffering to the flouting of these inherent meanings. He identifies two fundamental “natural meanings” of sex that are “so tightly stitched that we can start with either one and follow the threads to the other” (24): procreation and union.

    First, regarding procreation, Budziszewski asserts that it is the “bring about and nurture of new life, the formation of families in which children have moms and dads” (24). He outlines two conditions for establishing something’s purpose: it must actually bring about the effect, and the causal connection must explain its existence. Sexuality undeniably meets both: “the sexual powers do bring about procreation,” and “apart from the link between the sexual powers and new life, any explanation of why we have sexual powers at all would be woefully incomplete” (25). This procreative meaning, in turn, necessitates the concept of union. He argues, “For us, procreation requires an enduring partnership between two beings, the man and the woman, who are different, but in ways that enable them to complete and balance each other. Union, then, characterizes the distinctly human mode of procreation” (25). This enduring partnership between a man and a woman is essential not only for conception but also for the raising of children, as “the male is better suited to protection, the female to nurture” (26). Children also need models of both sexes and the relationship between them to thrive and eventually form their own families. He even cites sociologists Sara S. McLanahan and Gary Sandefur, who suggest that “If we were asked to design a system for making sure that children’s basic needs were met, we would probably come up with something quite similar to the two-parent ideal” (26).

    Conversely, Budziszewski demonstrates how starting with the unitive meaning also leads back to procreation. He states, “We join ourselves by doing what? By an act which is intrinsically open to the possibility of new life. In other words, whenever I give myself sexually, I am doing something that cannot help but mean that happy chance” (27). This implies that a true, total self-giving in union de facto means a bodily giving, which inherently carries the possibility of new life. He powerfully illustrates this with the concept of the body’s objective “speech”: “What you intend subjectively can’t change what your act means objectively…When the speech of the mouth contradicts the speech of the body, the body’s speech repeals the mouth’s. To crush your windpipe with my thumbs is to say to you, ‘Now die,’ even if I tell you with my mouth, ‘Be alive’” (27). Sexual union, therefore, objectively “speaks” of total, self-giving, life-affirming communion, regardless of subjective intent. By the end of this analysis, Budziszewski concludes that these are “the natural laws of sex” (33).

    C) Evaluation and Connection to Biblical Understanding

    Budziszewski’s position is remarkably helpful and coherent in discussing gender and sexuality, particularly as it provides a clear pathway to understanding these concepts from a Biblical perspective. His natural law approach, by grounding sexual ethics in discernible human design and purpose, offers a rational basis for moral norms that is not solely reliant on religious dogma, even as it ultimately aligns with it. He addresses the widespread confusion of our age, where “everything is topsy-turvy and confused,” by reminding us that “It is harder to write about what is obvious but unrecognized than about what is really obscure” (15). His method makes the “obvious” — the inherent meaning of sex — recognizable again.

    The direct alignment between Budziszewski’s “natural laws of sex” and Biblical principles is striking. The procreative meaning he identifies, “the bring about and nurture of new life, the formation of families in which children have moms and dads,” finds a direct echo in the Genesis mandate, “Be fruitful and multiply” (Genesis 1:28). This divine command is not an arbitrary rule but an affirmation of the inherent design for flourishing that God embedded within creation, particularly in human sexual powers. The natural purpose of bringing forth new life and fostering it within the structure of a family led by a mother and a father is, for Budziszewski, a self-evident truth discoverable through observation, much like the purpose of lungs or eyes.

    Similarly, his unitive meaning of sex—the “mutual and total self-giving and accepting of two polar, complementary selves in their entirety, soul and body”—is perfectly mirrored in the Biblical concept of “one flesh” (Genesis 2:24; Matthew 19:5-6). This Biblical phrase signifies not merely physical intimacy but a profound, holistic union of two distinct yet complementary individuals (male and female) into a new relational entity. Budziszewski’s argument that sexual union is “intrinsically open to the possibility of new life” and that subjective intent cannot override the objective “speech” of the body powerfully reinforces the sanctity and seriousness of the one-flesh union as depicted in scripture. The Bible’s understanding of marriage as the exclusive context for sexual intimacy, and the procreative blessing associated with it, finds a rational foundation in Budziszewski’s natural law deductions. His framework thus serves as a potent apologetic, demonstrating that the Biblical understanding of sexuality is not a set of arbitrary prohibitions but rather a reflection of the deepest truths embedded in human nature by its Creator.

    In conclusion, J. Budziszewski’s approach to natural theology in On the Meaning of Sex provides an exceptionally valuable framework for understanding sexuality and gender. By firmly grounding his arguments in the inherent design and purpose of human nature, he navigates complex ethical terrain with clarity and precision. His articulation of sex’s natural meanings—procreation and union—is not only philosophically robust but also demonstrably converges with the ethical insights found in Biblical teachings. In a world often characterized by confusion and suffering regarding sexual identity and behavior, Budziszewski’s work offers a compelling and coherent pathway to rediscovering meaning, leading ultimately to a fuller appreciation of sexuality and gender as they are divinely designed and revealed.

    Works Cited

    Budziszewski, J. On the Meaning of Sex. InterVarsity Press, 2012.The New American Standard Bible, 1995.

  • The Pagan Can Be Saved?

    The Pagan Can Be Saved?

    Wesley Coleman

    In Søren Kierkegaard’s Concluding Unscientific Postscript to Philosophical Fragments, Johannes Climacus breaks down notions, based on objective and speculative interpretations, of Christianity, arguing instead that authentic religious truth is fundamentally subjective. As exemplified in his assertion on page 201 regarding truth in prayer, Climacus posits that the manner of an individual’s infinite, passionate relation to the eternal—even in the face of objective uncertainty or perceived untruth—is paramount, superseding intellectual assent to dogma or historical fact and revealing the inherent limitations of any detached, disinterested approach to faith. This stance foregrounds the lived reality of faith as a personal, strenuous endeavor, fundamentally separate from and perhaps at odds with objective inquiry.

    Kierkegaard, through Climacus, opens the Postscript by challenging what he identifies as problematic approaches to understanding Christianity: the historical, the speculative, and the superficial religiousness prevalent in his time. From the very start, Kierkegaard has separated the objective issue of the truth of Christianity from the subjective issue of the subjective individual’s relation to the truth of Christianity (Kierkegaard 22). Climacus contends that the objective point of view, whether focusing on historical or philosophical truth, is inherently flawed when applied to Christianity. An objective inquiry is characterized as “disinterested,” seeking to establish truth through critical consideration of reports or the relation of doctrine to eternal truth. However, for an individual concerned with their eternal happiness, historical certainty, being merely an “approximation,” is profoundly insufficient. This is because “an approximation is too little to build his happiness on and is so unlike an eternal happiness that no result can ensue” (Kierkegaard 22). The scholarly pursuit, while commendable in its erudition, ultimately “distracts” from the issue of an individual’s faith (Kierkegaard 14) and “suppresses” the vital dialectical clarity required for true understanding (Kierkegaard 11).

    The fundamental problem with objectivity, as Climacus elaborates, is its inherent detachment from the individual’s existence. The “objective subject” is too “modest” and “immodest” to include himself in the inquiry; he is interested but “not infinitely, personally, impassionedly interested in his relation to this truth concerning his own eternal happiness” (Kierkegaard 22). This detachment leads to a comical self-deception: “Precisely this is the basis of the scholar’s elevated calm and the parroter’s comical thoughtlessness” (Kierkegaard 22). Christianity, Climacus asserts, is spirit; spirit is inwardness; inwardness is subjectivity; subjectivity is essentially passion, and at its maximum an infinite, personally interested passion for one’s eternal happiness. Therefore, as soon as subjectivity is taken away, and passion from subjectivity, and infinite interest from passion, there is no decision whatsoever. The objective approach, by sacrificing this infinite, personal, impassioned interestedness, paradoxically makes one too objective to have eternal happiness. The speculative point of view fares no better, attempting to permeate Christianity with thought and and make it eternal thought. Yet, if Christianity is truly subjectivity, a matter of inward deepening, then objective indifference cannot come to know anything whatsoever. Like is understood only by like; thus, the knower must be in the requisite state of infinite, passionate interest. Speculative thought, in its objectivity, is “totally indifferent to his and my and your eternal happiness” (Kierkegaard 55), making its “happiness” an illusion as it attempts to be “exclusively eternal within time” (Kierkegaard 56).

    This critique of objective and speculative approaches, which Climacus gradually unfolds finally builds to a climax on page 201 with the passage at hand to be dealt with. The chapter titled “Subjective Truth, Inwardness; Truth Is Subjectivity” in Part Two directly introduces the core concept that “truth becomes appropriation, inwardness, subjectivity, and the point is to immerse oneself, existing, in subjectivity” (Kierkegaard 192). Climacus establishes that for an existing person, “the question about truth persists” not as an abstract definition, but as something to “exist in” (Kierkegaard 191). He dismisses mediation and the abstract “subject-object” as reverting to abstraction (Kierkegaard 192), emphasizing that “an existing person cannot be in two places at the same time, cannot be subject-object” (Kierkegaard 199). The “I-I” is explicitly called a “mathematical point that does not exist at all” (Kierkegaard 197), making it clear, for Climacus, that it is an impossibility for an existing human being to transcend their individual, passionate existence and achieve this abstract oneness. For Climacus, “only ethical and ethical-religious knowing is essential knowing” (Kierkegaard 198), and such knowing is always essentially related to the knower’s own existence.

    The critical distinction, immediately preceding the paragraph in question, is articulated as: “When the question about truth is asked objectively, truth is reflected upon objectively as an object to which the knower relates himself…When the question about truth is asked subjectively, the individual’s relation is reflected upon subjectively. If only the how of this relation is in truth, the individual is in truth, even if he in this way were to relate himself to untruth” (Kierkegaard 199). This prioritizes the mode of relation over the object of relation in its abstracted form separate from engagement.

    Then, the force of Climacus’s argument is finally catalyzed. He starts with an aggressive remark, “now, if the problem is to calculate where there is more truth…then there can be no doubt about the answer for anyone who is not totally botched by scholarship and science” (Kierkegaard 201). The harsh remark is true, it is intuitive for all those not steeped in abstraction. Those who are incapable of grasping the truth are those which have been immersed in a harmful way of thinking, and Climacus’s words are meant to provoke that truth. The phrase “botched by scholarship and science” in particular is reminiscent of the “infinite, personal, impassioned interestedness” which exists in the person practicing the objective issue (Kierkegaard 27).

    Climacus then explicitly rules out any notion of a neutral, balanced approach: “(and, as stated, simultaneously to be on both sides equally is not granted to an existing person but is only a beatifying delusion for a deluded I-I)” (Kierkegaard 201). This re-emphasizes that an existing human being cannot inhabit the abstract “subject-object” or “I-I,” which is a phantom of pure thought (Kierkegaard 192). To attempt such a mediation between objective and subjective approaches is a “delusion,” a fantastical escape from the concrete reality of existing. An existing person is always in a process of becoming (Kierkegaard 192), and this inherent motion precludes the static, all-encompassing view of the “I-I” (Kierkegaard 199).

    The core of the paragraph is the deep dichotomy presented: “whether on the side of the person who only objectively seeks the true God and the approximating truth of the God-idea or on the side of the person who is infinitely concerned that he in truth relate himself to God with the infinite passion of need” (Kierkegaard 201). The dichotomy is on one hand, “the true God” and “approximating truth of the God-idea” and on the other, “infinite passion of need.” The objective seeker remains stuck in approximate knowledge, which, as established earlier, is insufficient for eternal happiness. In contrast, the “infinite passion of need” signifies the highest subjectivity, where the individual’s “eternal happiness” is at stake. This passion brings true existential importance to the individual which is impossible through speculation.

    The paragraph then presents a provocative thought experiment: “If someone who lives in the midst of Christianity enters, with knowledge of the true idea of God, the house of God, the house of the true God, and prays, but prays in untruth, and if someone lives in an idolatrous land but prays with all the passion of infinity, although his eyes are resting upon the image of an idol—where, then, is there more truth?” (Kierkegaard 201). This scenario is incredibly hard for many who view Christianity as something true that one believes about God. This analogy turns that presumption on its head drawing a distinction between the “what” and the “how” of faith (Kierkegaard 199). The person who is a Christian by birth or culture or even intellectually “knows the true idea of God” and prays in the “house of the true God” (Kierkegaard 201) represents the objective approach that assumes faith is an afterthought and something that can be taken for granted. Such an individual may possess all the outward forms and correct doctrines, but their prayer is “in untruth” if it lacks the “infinite passion of inwardness” (Kierkegaard 201). This coincides with Climacus’s earlier assertion that objective Christianity is pagan (Kierkegaard 43), and to know a creed by rote is paganism, because Christianity is inwardness. Their knowledge, being disinterested, is merely a vanishing, unrecognizable atom of objective understanding, not transformative truth.

    Conversely, the individual in an “idolatrous land” who prays “with all the passion of infinity” to an idol, despite the objective untruth of the object, possesses “more truth” (Kierkegaard 201). The passion itself, the subjective “how” of their relation, is the determining factor. This is because the passion of the infinite is the very truth. Their worship, even of an objectively false god, carries the weight of authentic, boundless engagement.

    The conclusion of the paragraph drives the point home: “The one prays in truth to God although he is worshiping an idol; the other prays in untruth to the true God and is therefore in truth worshiping an idol” (Kierkegaard 201). This is not a relativistic dismissal of God’s objective existence, but a radical redefinition of what constitutes truth in the context of an individual’s religious life. The person who prays passionately to an idol is, in their inwardness, genuinely seeking the divine, and this “infinite passion of need” (Kierkegaard 201) creates a true “God-relation” (Kierkegaard 199). Their relation, despite the objective error, is in truth. This is, perhaps, a shocking revelation to the one who calls the heretic ‘unsaved’. Conversely, the person who prays to the true God without this infinite passion effectively turns the true God into an “idol”—an object of detached, intellectual assent rather than a living, transforming presence. This intellectual understanding without passionate inwardness is merely an illusion. It reduces the divine to an object for intellectual scrutiny, precisely what objective thought does to Christianity (Kierkegaard 52).

    Other possible interpretations of this passage, primarily objective or speculative, fail to grasp its radical thrust. An objective interpretation would likely focus on the factual untruth of idol worship, concluding that the idolater is in untruth regardless of their passion. This perspective, however, completely misses Climacus’s central argument that objective knowledge is “indifferent” to the knower’s existence and thus cannot engage with the truth of the infinite (Kierkegaard 193). For an objective approach, the truth is merely “an object to which the knower relates himself” (Kierkegaard 199), failing to recognize that “the individual’s relation is reflected upon subjectively” and the “how” is truth (Kierkegaard 199). This kind of detached, “disinterested” knowledge simply “distracts” from the issue of faith (Kierkegaard 28).

    A speculative interpretation might attempt to mediate between the two positions, arguing that the true understanding lies in a higher synthesis where both the object and the subjective relation are reconciled. However, Climacus explicitly rejects such mediation for an existing person, stating that to be in mediation is to be finished; to exist is to become. Speculative thought, in its quest for a “system” (Kierkegaard 14), “promises everything and keeps nothing at all” for the existing individual. It assumes a “presuppositionless” beginning and ultimately “dissolves into a make-believe” of understanding faith (Kierkegaard 14). By attempting to “explain and annul” the paradox, speculative thought implicitly “corrects” Christianity instead of explaining it. The absolute paradox, which is the eternal truth coming into existence in time, cannot be understood but only believed “against the understanding” (Kierkegaard 217). Any attempt to rationally encompass or explain it is “volatilization” and a return to paganism (Kierkegaard 217). The speculative thinker, in trying to become “objective” and “disappear from himself” (Kierkegaard 56), cannot grasp the existential truth of faith, which is grounded in passion and the “utmost exertion” of the existing self (Kierkegaard 55).

    Furthermore, the interpretation that reduces Christianity to a set of doctrines or a historical phenomenon, implicitly adopted by the “Christian in the midst of Christianity” who prays “in untruth” (Kierkegaard 201), is also rejected. Christianity is not a doctrine but a relational act. The relation to a doctrine is merely intellectual, whereas the relation to Christianity is one of faith, an infinite interestedness. To be a Christian by name only is a serious danger due to the fact that it removes the necessary “infinite passion” (Kierkegaard 16). Such individuals, by “praying in untruth” (Kierkegaard 201), effectively transform the true God into an “idol” (Kierkegaard 201), stripped of the demanding, transformative power that calls for infinite inwardness.

    In conclusion, the paragraph on page 201 profoundly encapsulates Climacus’s core thesis: Christianity’s truth is existentially actualized not through objective knowledge or speculative comprehension, but through the subjective individual’s absolute, infinite passion. This passion, born of an “infinite need” and held fast against “objective uncertainty” (Kierkegaard 203), is the very essence of faith, a “contradiction between the infinite passion of inwardness and the objective uncertainty” (Kierkegaard 204). The example of the passionate idolater versus the dispassionate Christian reveals that the intensity and truthfulness of the subjective relation far outweighs the objective accuracy of the object of worship when it comes to genuine religiousness. This radical emphasis on the “how” of faith over the “what” forces the reader to confront the demanding, terrifying, and deeply personal nature of becoming and being a Christian, a path that rejects the easy and fragmentary reassurances of objective certainty and speculative systems in favor of a lived, passionate existence with a holistic commitment. The radical conclusion that one can have objective error and be in real relationship with God. The radical conclusion that the pagan can be saved. Not because their idol is the true God, but because they have true faith.

    Climacus, Johannes. Concluding Unscientific Postscript to Philosophical Fragments. Edited and translated by Howard V. Hong and Edna H. Hong, Princeton UP, 1992.