The Command, the Cosmos, and the Quantum Soul

(Part III of the Reflections Series)

A Scientific Reflection on Divine Order, Entropy, and Consciousness

Introduction — The Command Behind All Things

In every age, human understanding advances through questions that return, again and again, to one mystery: how does existence sustain itself? From the smallest particle to the most distant galaxy, every phenomenon—motion, decay, renewal—appears guided by an invisible law. Science expresses these laws in equations; revelation expresses them in meaning. Yet both point toward one truth: an underlying command that gives rise to order, energy, and consciousness.

Modern physics has brought this question to its frontier. What classical science once saw as solid matter is now known to be fields of vibrating energy, probabilities, and entanglements—realities that obey mathematical precision but defy human intuition. The Qur’an, more than fourteen centuries earlier, spoke of creation through a single act of will:

Between Kun and Fayakūn lies everything—the entire story of space, time, and the soul.

Quantum physics, though famously difficult to visualize, is not mere theory. Its principles are verified daily in technologies that shape modern life: the lasers in medical instruments, the semiconductors in computers, and now the quantum processors that manipulate information through superposition and entanglement. Quantum theory is not speculation—it is the most accurate description of reality that science possesses. Yet its implications are deeply metaphysical. It tells us that matter itself is not fixed, that reality is layered, and that observation and awareness may play a role in shaping what becomes “real.”

In this essay, I explore how these discoveries, when seen alongside Qur’anic insight, reveal a unified narrative of creation. From the decay of stars to the birth of a child, from the motion of electrons to the awareness within the human soul, every layer of existence follows one universal principle: divine command unfolding through the laws of order and entropy, coherence and dissolution, life and return.

The Entropic World: Time, Decay, and Divine Law

All physical existence is bound by a single direction: the flow of time. In thermodynamics, this direction is defined by entropy—the gradual transformation of energy from order to disorder, from concentrated potential to diffuse randomness. This is the Second Law of Thermodynamics: every closed system tends toward equilibrium, every star will cool, every body will decay.

To the human mind, this principle is visible everywhere. The young age; the constructed building crumbles; the vibrant cell ages and divides until its machinery falters. Time’s arrow points always toward decay. Yet the Qur’an transforms this cold law of physics into a profound moral and spiritual truth:

Entropy, in this light, is not a curse—it is the condition that makes choice, renewal, and meaning possible. Without decay, there could be no growth; without mortality, no moral horizon.

Modern cosmology echoes this view. The universe itself is expanding and cooling, its usable energy gradually dispersing. The Qur’an had already hinted at this cosmic expansion:

Here, expansion and entropy are two faces of the same unfolding command. Matter disperses, yet the total order—written into the laws of physics—remains conserved. Nothing escapes the balance (mīzān) established by the Creator.

Time itself, then, is a manifestation of entropy. It flows in one direction because the universe moves from low entropy (high order) to high entropy (disorder). The “arrow of time” is the arrow of decay—but also of transformation. What dissolves in one form re-emerges in another. Every atom in the human body was once forged in the heart of a dying star. Thus, decay is also continuity: the recycling of divine order through successive states.

This world (dunyā) is therefore an entropic realm—one where energy, information, and form are constantly shifting under divine law. Beyond it lie realms where time does not bind and entropy does not rule.

Life, Death, and the Womb of Command

If death represents the dissolution of order, then birth represents its most astonishing emergence. Between these two thresholds—Kun and Return—the entire drama of human existence unfolds.

At fertilization, two microscopic cells—the sperm and the egg—fuse into a single zygote. In less than a second, billions of years of evolutionary information encoded in DNA are activated. The genome, previously dormant, becomes fully accessible: the so-called “junk DNA,” now known to hold regulatory and developmental codes, awakens in orchestrated precision. Within moments, the genetic blueprint for a human being is established—a process that, if viewed across evolutionary time, seems to compress millennia into an instant.

This is creation at the speed of command. It echoes the Qur’anic verse:

In my own research on pregnancy and immune regulation, I observed how early pregnancy depends on a delicate suspension of biological “conflict.” The mother’s immune system, programmed to reject foreign tissue, must suddenly accept and protect an embryo that is genetically half foreign. Molecules such as human chorionic gonadotropin (hCG) and its peptide fragments act as messengers, guiding the immune network to tolerance. Physically, this represents a reversal of entropy—a momentary triumph of order over chaos. Spiritually, it mirrors divine mercy (raḥmah), where two beings coexist in perfect harmony so that new life may begin.

The Qur’an describes this sequence in remarkable precision:

At a later stage—tradition places it near 120 days—the rūḥ (soul) is breathed into the body. What enters is not biological consciousness but divine order. Before ensoulment, the embryo exists as structured matter without independent awareness; afterward, it carries potential for consciousness—an interface between command and creation.

The nine months of development can thus be seen as the translation of Kun fayakūn into biological time: what the angels execute instantaneously, the embryo unfolds gradually. Birth is the emergence of that hidden order into the open system of the world—a descent from protected equilibrium into thermodynamic struggle.

Just as biology reveals divine order in life and death, quantum science reveals that order even within apparent chaos. Where the cell shows harmony at the molecular scale, the quantum world shows harmony at the subatomic — suggesting that the same command underlies both.

The Quantum Soul — Science of the Unseen Order

Quantum physics may appear abstract, even mystical, yet it is not speculation. A single electron can pass through two slits at once; two photons can remain correlated across continents; and a particle’s position exists only as a range of amplitudes—mathematical waves of possibility—until measured. At this level, matter ceases to behave as “stuff” and begins to behave as information, rippling through fields that span the entire universe.

If the universe’s smallest components already defy common sense, it invites a deeper question: Might these same principles—superposition, entanglement, coherence—reflect something greater about existence itself? Could the strange behavior of particles echo the unseen truths that revelation speaks of—the unity of creation, the reality of the soul, the nearness of Divine command?

This reflection continues the journey that began with From Entropy to Eternity and Between Neurons and the Soul. The first traced how the arrow of time and entropy govern the material universe; the second explored how life and death mirror that same order in the body and the soul. This "The Command, the Cosmos, and the Quantum Soul" third step descends to the quantum foundation—where certainty dissolves, observation matters, and unity reappears in its most mysterious form.

Modern physics has reached a boundary similar to that between body and soul—the quantum domain, where matter dissolves into probability. At this scale, the universe is not a collection of solid objects but of waves of possibility. The electron is not simply here or there; it exists in many potential states simultaneously until it is observed. This is the principle of superposition.

Quantum theory replaces certainty with amplitude — a measure of how strongly each potential state exists. Unlike everyday probability, which deals with chance, quantum amplitude reflects coexistence: all states exist simultaneously, but one becomes manifest when measured. Reality is not random—it is layered, contextual, and always complete in Divine knowledge.

Yet all other possibilities remain encoded in the field, unmanifested but real.

To a reflective mind, this recalls the Qur’anic idea of the Preserved Tablet (Lawḥ al-Maḥfūẓ)—the realm where all outcomes already exist in Divine knowledge, waiting to unfold by command. The wavefunction of the universe, then, might be seen as a scientific whisper of qadar: all possibilities written, each observed life a single visible line drawn from infinite amplitude.

Observation does not create the world; it selects from what the command already contains. Likewise, human will does not create destiny—it manifests one of its written threads. The relation between observer and reality is thus participatory, not independent: creation requires consciousness to perceive, and consciousness requires creation to express.

The Qur’an repeatedly emphasizes that all phenomena occur bi-amrillāh—by divine command. From a scientific standpoint, measurement collapses the wave into a definite state; from a theological one, manifestation occurs when permitted by command. The correspondence is striking: creation is not static but event-based, unfolding as decree interacts with perception.

Table 1. Quantum vs. Classical Reality

The most astonishing feature of this realm is entanglement—when two particles, once linked, remain correlated no matter how far apart they move. A change in one is instantly mirrored in the other, defying the speed of light. Einstein called this “spooky action at a distance,” but it has been repeatedly confirmed in experiment.

Entanglement reveals that separation in space does not mean separation in reality. The Qur’an’s language resonates with this:

This unity of origin, extending through all creation, is not merely poetic—it is physical. Every atom of the human body is entangled, in origin, with the rest of the universe.

All creation, the Qur’an reminds us, issues from one command and remains bound by it. Entanglement thus becomes a physical emblem of tawḥīd—the oneness underlying multiplicity.

At the human scale, we sense this hidden unity through empathy, love, and prayer. When a parent feels a child’s distress far away, or two friends think of each other simultaneously, the phenomenon may not yet be quantifiable, but it hints that consciousness, like entangled particles, might operate within a shared field beyond distance.

Quantum Coherence and Decoherence: Order, Entropy, and Perception

Quantum coherence refers to a system maintaining all its possibilities at once—the unified wave before collapse. When a particle interacts with its environment, this delicate unity breaks apart: it decoheres, producing the classical world of separate things. Decoherence is the microscopic root of entropy—the drift from perfect order into apparent disorder.

Life itself can be read through this lens. Cells, ecosystems, even galaxies sustain fleeting coherence—order maintained against entropic collapse. The Qur’an often describes creation as “balanced” and “in due measure". In every living process, order resists dissolution for a time before yielding; the same pattern echoes from atom to soul.

Spiritually, coherence might symbolize obedience—everything harmonized with Divine will—while decoherence mirrors forgetfulness and separation. The disciplined heart mirrors a coherent quantum system—stable, responsive, and in resonance with divine command. The distracted heart, overwhelmed by worldly interactions, loses that resonance and collapses into randomness.

From quantum coherence to cosmic mercy, from the smallest particle to the largest galaxy, exists between two commands — Be and Return. Entropy governs how matter disperses; quantum coherence shows how information remains whole beneath that dispersion.

Perhaps this is why the Qur’an begins with “In the name of Allah, the Most Merciful, the Most Compassionate” — mercy itself being the sustaining principle that holds creation coherent despite decay. In every cell, molecule, and breath, the balance between disintegration and restoration continues — a reflection of that encompassing mercy.

In the quantum world, even when particles decohere, their information is never truly lost; it is stored in the field. Likewise, the deeds, prayers, and intentions of a human life remain preserved within the unseen architecture of divine knowledge. Nothing escapes the record.

Quantum physics thus provides a language to describe what revelation has long expressed: that existence is relational, layered, and sustained by attention—human and divine.

Table 2. Quantum–Spiritual Parallels

The Observer and the Trust

In quantum experiments, observation collapses the wavefunction; without observation, the system remains in superposition. The observer is therefore intrinsic to reality’s unfolding.

Human consciousness occupies a similar position in creation. We are not passive witnesses; our awareness participates in existence itself. The Qur’an declares:

This amānah—the capacity to know, choose, and be morally responsible—may be the cosmic privilege of consciousness: to observe creation and, through observation, to reveal meaning within it. Just as measurement gives definition to the quantum field, conscious intent gives moral definition to human life.

At this boundary, science meets faith: the “observer effect” becomes a mirror of the spiritual truth that awareness itself is part of the command Be.

The Soul and the Field of Awareness

Neuroscience measures neural firing and chemical flux, but the felt awareness that observes those signals remains outside the equations. Some physicists propose that consciousness itself may arise from quantum coherence within the brain’s micro-architecture—microtubules acting as tiny resonant cavities that sustain superposition before collapsing into conscious moments. Even if this hypothesis proves incomplete, it gestures toward a truth already implied by revelation: that awareness is not merely an electrical by-product but a field linked to something greater.

When the Qur’an speaks of rūḥ as belonging to the realm of amr—the Divine command—it distinguishes the soul from matter’s entropic decay. The brain might be the receiver; the soul the signal transmitted through that universal field. Sleep, meditation, or deep devotion may allow brief re-alignment with that higher coherence: consciousness partially freed from sensory noise, much like a quantum system temporarily isolated from decohering interactions.

Quantum Tunneling — Passing Through the Veil

Among the most extraordinary insights of quantum mechanics is the phenomenon of tunneling. In classical physics, a particle cannot cross a barrier higher than its energy. In the quantum world, however, particles behave as waves of probability. Their existence is not confined to one side of the wall; their wavefunction extends into and beyond it. With a finite probability, the particle can appear on the other side—having passed through what was once considered impenetrable.

This process underlies the fusion of the sun’s hydrogen nuclei, the reactions of enzymes in living cells, and even the operation of modern electronics. Without tunneling, the stars would not shine, nor would life’s chemistry proceed as swiftly as it does. In every instance, what seemed an impossible barrier becomes a passage when viewed from the deeper structure of reality.

The Qurʾān speaks of boundaries in creation—barriers that define realms yet yield when Divine command decrees:

and again:

Yet when the appointed moment arrives, those limits dissolve:

Here, the language of revelation and the mathematics of physics converge. Both affirm that barriers are conditional, upheld until command lifts them. The particle tunnels; the soul crosses. Both transitions occur not by random chance, but through the same principle of Divine permission — bi-amrillāh.

Imām al-Ghazālī, in Mishkāt al-Anwār (“The Niche of Lights”), described physical existence as a veil (ḥijāb) over the pure light of the Real (nūr al-ḥaqīqah). The material world, he wrote, is “a shadow of the unseen world,” sustained only by the radiance that passes through it. Knowledge, remembrance, and sincerity do not break this veil; they render it transparent. The modern physicist would say: the wavefunction is never truly confined—it extends through what appears opaque. Both expressions point to one truth: being is continuous, and what we call separation is only the limit of perception.

Death, sleep, inspiration, and revelation are all forms of tunneling across veils. The rūḥ moves through barriers that the senses cannot penetrate, because its domain is not energetic but commanded. The Qurʾān thus reminds:

Seen this way, tunneling is not only a quantum process—it is a symbol of mercy. It shows that the apparent walls between worlds are not absolute. Every layer of existence, from atoms to souls, remains connected through an unseen continuity of command.

This understanding of quantum tunneling prepares us to reconsider consciousness itself. If matter can traverse barriers without physical passage, perhaps awareness too is not confined within neural boundaries. Just as the wavefunction persists across regions, consciousness may extend beyond the limits of sensory input. In both, presence is defined not by location but by coherence.

Consciousness, Nonlocality, and the Human Mirror

If quantum entanglement reveals connection beyond space, consciousness may be its living mirror. Modern neuroscience can describe patterns of brain activity—electric potentials, oscillations, neurotransmitter fluxes—but not awareness itself. Consciousness is not reducible to molecules; it is the capacity to witness molecules.

This has led some physicists and philosophers to propose that consciousness may be fundamental—a field as intrinsic to the universe as space, time, or energy. In such models, the brain does not generate awareness but filters it, much like a radio tunes an ever-present signal. The rūḥ would then be the divine signal; the brain, its receiver. When the receiver is active, perception localizes; when it fails, the signal continues beyond the instrument.

The verse situates the soul outside material categories—amr is the same word used for divine command. Thus, awareness belongs to a non-entropic domain, one not bound by decay or locality.

Phenomena such as bilocation—the simultaneous awareness or presence of saints (awliyāʾ) in more than one place—are sometimes mentioned in Sufi literature. From a scientific lens, this could be compared, metaphorically, to quantum superposition or nonlocal coherence: awareness not confined to a single coordinate. Whether literal or allegorical, the point remains that human consciousness may not be entirely local—it may resonate across what quantum theory calls the field of probabilities.

In spiritual terms, the bonds among human hearts reflect this same nonlocal unity. The Prophet ﷺ described believers as one body—when one part suffers, the rest responds.

This is a moral truth, but it may also describe an ontological one: that love, empathy, and prayer may represent forms of informational entanglement—states where consciousnesses resonate beyond physical proximity.

Empirical science, of course, cannot measure divine connection, but it can observe parallels. Studies in quantum biology, for instance, show that coherence underlies processes like photosynthesis and bird navigation—life itself may exploit quantum resonance to maintain order within noise. The human soul may be the highest expression of that coherence: aware of itself, capable of tuning toward or away from the Source.

During deep sleep or meditation, neural entropy decreases—the brain enters a more ordered state, even as external awareness fades. The Qur’an presents sleep as a temporary withdrawal of the soul:

In waking life, consciousness is bound to thermodynamic activity—entropy in motion. In sleep, it partly detaches, entering a state less tied to decay. This may explain why true dreams (ru’yā ṣāliḥah) are described as one part of Prophethood (Ṣaḥīḥ al-Bukhārī): the veil thins, coherence is restored, and the soul perceives symbols beyond ordinary causality.

Late-night solitude—particularly in the last third of the night—is emphasized in the Sunnah for devotion. Scientifically, these hours correspond to minimal environmental noise and electromagnetic activity. Spiritually, they coincide with moments of stillness when the heart is most coherent. This physiological quiet may explain why the Prophet ﷺ was known to pray in the stillness of late night: a moment when both the universe and the heart are at their lowest noise. One might say that both physical and spiritual interference were minimized, allowing the soul to resonate most purely with the Divine command.

In this view, tahajjud is not only an act of worship but a state of coherence—an alignment of consciousness with the silent order of creation.

Table 3 — Levels of Coherence in Human States

The Circle of Command — From Kun to Return

When viewed through the unity of knowledge, all scales of existence—quantum, biological, cosmic—reflect one pattern: order arising from command, sustained through coherence, dissolving through entropy, and restored through return.

Every atom follows this cycle. Quantum fields fluctuate into particles and annihilate back into the vacuum. Stars ignite, shine, and collapse, seeding new worlds. The human being is born, learns, decays, and is resurrected. All obey the same law: transformation under divine decree.

The Second Law of Thermodynamics governs matter; the Law of Command governs being. Entropy describes how creation unfolds within time; revelation describes how command sustains it beyond time.

Thus, physics and faith are not opposing disciplines—they study different domains of the same reality. Physics measures the behavior of creation under fixed laws; revelation unveils the origin of those laws and their purpose.

At the deepest level, quantum mechanics reminds us that reality is not static but relational. Observation matters. In human terms, this means that how we perceive the world—gratefully or heedlessly—changes the quality of our existence. The believer’s awareness is a form of constructive observation, aligning inner and outer order.

Table 4. Hierarchy of Realities — From Entropy to Timelessness

Creation, then, is a spectrum of coherence—from full entropy in matter to perfect order in divine command. The human soul occupies a unique midpoint: bound to decay through the body, yet capable of transcendence through awareness. Our task is to sustain coherence—to remember, obey, and reflect the order we come from.

This coherence is not static but moral. Every act of remembrance (dhikr) restores internal order; every act of heedlessness disrupts it. The Qur’an, then, can be read not only as revelation but as the operator of coherence—aligning human consciousness with cosmic order.

In the end, both science and revelation converge on humility. The equations of physics describe how energy transforms; the verses of Qur’an reveal why it transforms. The more we study, the clearer it becomes that existence is not random but relational—woven together by a continuous word:

The same word that summoned particles from the vacuum summons the soul from the womb and will summon humanity again from the grave.

Synthesis — The Unified View of Command and Creation

Summary

• Angels: Timeless servants beyond entropy, perfectly obedient to Divine command — pure coherence without decay.

• Jinn: Hidden beings bridging the material and immaterial realms, mortal yet subtler than matter.

• Humans: Bound by entropy yet carrying the soul — the meeting point of clay and command, matter and consciousness.

• Life’s arc: From the divine spark at conception to the soul’s release at death, all stages follow one law — formation, decay, and return under Kun fayakūn.

• Biological death: Marks the irreversible increase of entropy in living systems; decay as a passage, not annihilation.

• Brain death: Defines the medical boundary but not the metaphysical end — awareness may persist beyond measurable signals.

• The soul’s departure: Belongs to the realm of amr Allāhﷻ (Divine command), beyond physical law and entropy.

• Sleep and conscious detachment: Mirror temporary withdrawal from entropy — partial exits from the arrow of time.

• Sleep, intuition, and empathy: Suggest nonlocal coherence of the human soul.

• Quantum coherence and entanglement: Reflect unity and connectedness — particles and souls remain linked beyond distance, resonating with “He created you from a single soul” (Q 39:6).

• Wave collapse: Echoes Kun fayakūn — manifestation by command.

• Quantum tunneling: In both physics and revelation, apparent barriers yield under Divine command — the particle crosses the wall; the soul passes through veils of perception. What seems impossible in one frame becomes effortless by amr Allāhﷻ.

• Death and resurrection: Form a single cycle — dissolution and renewal under Divine will, as energy, information, and soul return to their Source.

• All point toward Ākhirah — the eternal, real world beyond entropy, time, and decay, where the circle of command finds completion.

Table 5. Trilogy of Reflection — Macro, Micro, and Subatomic Mirrors of Divine Creation

Table 6. The Quantum — Human Continuum

Table 7. Integration with Earlier Articles

Final Reflection

From the smallest quantum fluctuation to the consciousness that observes it, from the embryo’s hidden order to the galaxies’ expansion, everything follows the same circle of command.

Matter obeys entropy; being obeys amr. Time measures decay; eternity measures return.

Modern science, with all its precision, can describe the mechanism but not the meaning. Revelation discloses the meaning but not always the mechanism. Together they reveal a unity: that every vibration of existence is sustained by one act of will.

What we call probability, the Qur’an calls decree (qadar). What we call coherence, revelation calls remembrance (dhikr). What we call observation, it calls witness (shahādah). These are not metaphors but different languages for the same underlying truth—the interface between matter and command.

To study the universe is therefore to study a form of scripture written in energy and law. To study the Qur’an is to read the universe translated into meaning. Both, when understood rightly, lead to awe.

Every atom, every cell, every conscious act is one of those signs.

Quantum tunneling reminds us that nothing in creation is absolutely closed. Every boundary—between atom and atom, life and death, the seen and unseen—is upheld only by command and may open by the same command. Imām al-Ghazālī’s metaphor of veils illuminated by light is echoed here in the physics of probability waves: the light of the Real penetrates all things; the wave of being never ends. Barriers exist only so that the moment of passage may reveal His power.

As a scientist and believer, I reflect on these parallels not to claim certainty, but to recognize order. The ultimate nature of existence—how Kun becomes form and how form returns—is known only to Allāhﷻ, the Source of coherence, the First and the Last, beyond time and decay.

Author: Nisar Khan, PhD (Immunology), Biomedical Scientist, Systems Biology Researcher & Drug Developer. 

These reflections represent personal thoughts as a scientist and believer. They do not claim to describe ultimate truth—only Allāhﷻ knows the full reality of His creation.