Between Neurons and the Soul — Reflections on Life, Death, and the Continuum of Existence

(Part II of the Reflections Series)

Introduction — The Last Threshold

Life and death are not opposites, but two directions of the same command. What begins as divine order entering matter ends as that order’s release. Between these thresholds, consciousness emerges, learns, and returns.

Modern science describes these transitions in physical terms—conception, metabolism, decay—while revelation speaks of them in timeless ones: creation, soul, resurrection. Both, however, point toward one pattern: the movement of order and consciousness through entropy, under divine will.

Every living system carries a direction—an arrow that points from order toward dissolution. Biology calls this entropy; theology calls it mortality. For centuries, science has examined how the body dies, while revelation has spoken of what lies beyond. Both describe transition, but from different sides of the veil.

This reflection explores that frontier where measurable brain activity ends, yet existence may not. When does life truly cease—when electrical impulses fall silent, or when the rūḥ, the soul, departs? And what happens in those delicate states when awareness loosens from the senses, as if rehearsing that ultimate release?

1. Biological Death: The Science of Ending

At the cellular level, death unfolds as an ordered sequence. Mitochondria cease producing ATP; membranes leak; enzymes digest the very cell that housed them. This programmed self-destruction—apoptosis—maintains tissue balance during life, yet in finality it overtakes the body entirely.

Systemically, the halted heartbeat ends oxygen delivery. Within minutes neurons lose electrochemical gradients; electrical activity ceases; the body enters the irreversible march of entropy. Molecules scatter energy as heat; order dissolves into randomness.

Yet even here the process is gradual. Some cells persist for minutes or hours; DNA endures for days; certain genes briefly reactivate. Death in biology is therefore a gradient, not a point—a reminder that life’s boundary is less a wall than a fading edge.

2. Brain Death: The Modern Boundary

Medicine defines death by the irreversible cessation of all brain function, including brain-stem reflexes that sustain breathing. Machines can maintain circulation, but without the brain’s integrated control, the organism loses unity.

Brain-death testing measures electrical silence; yet the absence of signal does not equal the absence of being. Consciousness remains scientifically elusive: its emergence from neurons is describable, but its essence is not. Modern tools record patterns of neural entropy—fluctuations between order and randomness—but cannot capture awareness itself.

Thus, brain death represents the limit of instrumentation, not necessarily the limit of existence.

3. The Soul’s Departure: Beyond Entropy

Revelation describes death not merely as biological failure but as an act of command:

The rūḥ belongs to the realm of amr—Divine command—not to the material processes it animates (Q 17:85). While the body obeys thermodynamic decay, the soul follows another law entirely.

A useful analogy is that of signal and receiver: the brain is the receiver; the soul, the signal. When the receiver fails, the broadcast ceases locally but the transmission itself continues beyond that circuit. Death marks the moment when Divine command withdraws the signal from the material domain.

4. Death as Transition: The Entropic Veil

Entropy makes decay irreversible; what once held form disperses. Yet the Qur’an presents this dissolution not as annihilation but as passage. The physical world obeys the Second Law of Thermodynamics; the next realm transcends it.

In dying, the human being crosses from a world ruled by entropy into one where order and time no longer dictate existence. Decay applies to flesh; persistence belongs to the soul. Death is therefore less destruction than transfer—a change of the governing constants.

Interlude — The Cooling of the Body

When the heart stops, metabolism ends; no new heat is produced. Body warmth disperses until equilibrium with the surroundings is reached—an expression of entropy’s final balance. Occasional warmth after death stems from residual chemical reactions or muscle stiffening, soon overcome by cooling. Even here, the body obeys the law of return: energy disperses, equilibrium restores silence.

5. States of Conscious Detachment: Between Sleep and Departure

Not all separations of awareness require death. During sleep, anesthesia, or deep meditation, consciousness withdraws from sensory input while vital functions persist. Neuroscience shows that metabolism slows and neural rhythms synchronize—a decrease in neural entropy.

Physiologically, the brain enters ordered rhythm; spiritually, the self experiences reduced attachment to the sensory world. Such detachment resembles a reversible rehearsal of death—a controlled step outside the arrow of time.

In these states, perception may access symbols and truths unfiltered by physical senses—what the Prophet ﷺ called ru’yā ṣāliḥah, “true dreams,” one part of forty-six parts of Prophethood. The veil (ḥijāb) may thin, allowing glimpses of realities beyond entropy. When consciousness returns, the soul re-enters its worldly frame, and the arrow of time resumes.

Just as sleep shows a reversible detachment, death completes the same pattern irreversibly—the full withdrawal of command from the material frame.

6. The Moment of Separation: What We Observe and What We Miss

Outwardly, death appears as stillness: heartbeat gone, eyes unresponsive. Yet the Qur’an speaks of angels drawing out souls gently or forcefully (Q 79:1-2). What we see as cessation is described scripturally as movement—departure through unseen agency.

Near-death experiences, though not proof, often describe light, panoramic recall, and timeless awareness. Consciousness freed from the body may perceive reality non-linearly, outside physical time. To science these are anomalies; to revelation, signs that the frontier between life and death opens only by Divine permission.

7. The Sign of Return: Death and Resurrection in the Same Pattern

Every decay hints at renewal. Cells die for tissues to form; seeds disintegrate for plants to emerge. Death carries the architecture of resurrection.

Matter does not vanish; it transforms. If energy and information are conserved, resurrection is not the violation of natural law but its highest expression—life re-summoned by the One who first set the laws in motion.

8. The Beginning Within the End: From Womb to World

If death marks the release of the soul from matter, conception represents its entry. Between these thresholds unfolds the entire drama of entropy, order, and consciousness.

At fertilization, two microscopic cells merge; within fractions of a second, a single zygote activates an entire human genome. This orchestration of molecular order defies ordinary time—billions of years of evolutionary information become readable in an instant. It echoes the Qur’anic command:

Entropy is then temporarily managed. The embryo maintains improbable order by drawing energy and materials from the mother—a local reversal of entropy sustained by mercy. The maternal body becomes a sanctuary where matter and command cooperate.

My own research on the hormone human chorionic gonadotropin (hCG) and its immunoregulatory breakdown peptides (Immunoregulatory Properties of Break Down Products of Human Choriogonadotropin, 2010), offers a living example of this harmony between biology and mercy.

During early pregnancy, the maternal immune system faces a paradox: the embryo is genetically half foreign, yet it must be protected, not rejected. hCG and its derivative peptides signal the maternal immune network to shift from rejection to acceptance.

In physical terms, this represents the suspension of an entropic drive toward conflict—the immune system’s normal reaction to “foreign” matter—in favor of ordered coexistence. In metaphysical terms, it mirrors divine compassion (raḥmah), allowing a new soul-bearing organism to take form within another.

At some point in this hidden development, the rūḥ is breathed into the body—traditionally near the fourth month. Before this, the embryo exists as pure order without perception; with ensoulment, a new dimension appears: potential for consciousness. The nine months that follow translate timeless command into biological time. Angels act at the speed of command; embryogenesis is that command slowed into visible sequence.

9. Birth, Consciousness, and the Descent into Entropy

With birth, the soul’s connection to matter becomes exposed. The infant leaves the womb’s equilibrium and enters thermodynamic openness—subject to gradients, microbes, and sensory influx. This is the beginning of conscious experience and of disorder.

Each breath and neural impulse consumes energy and increases entropy. The pure awareness that entered the womb now gathers impressions and desires—the nafs, the self shaped by experience. The rūḥ remains pure, but its expression becomes entangled with material process.

Life thus becomes the soul’s education through entropy. The Prophet ﷺ described the newborn as upon the fiṭrah, the pure state; what follows is the struggle to maintain or recover that order amid disorder.

Death is not the opposite of birth but its completion. The same force that drew matter into order now releases it; the soul detaches from decaying systems, separating from the nafs accumulated through experience, and returns to a non-entropic state, its purity restored by Divine mercy.

10. The Full Arc of Existence

Creation is not a line from nothing to nothing; it is a cycle from command to command, from Kun to Kun, bound within divine order yet unfolding in time.

11. Integration into the Entropic Narrative

In the first moments of life, energy and information converge to form structure; in the last, structure dissolves into energy and information. Both transitions occur under one sovereignty. The womb and the grave are not opposites—they are thresholds of concealment. The womb hides becoming; the grave hides returning.

This unified view aligns biology with revelation. Entropy governs matter; command governs existence. The universe, the embryo, and the departing soul all follow the same principle: what is formed by order will dissolve into order again, through the will of Allāh جل جلاله.

12. Beyond Entropy: The Human Witness

All creation obeys entropy, yet the human being uniquely contemplates it. We measure decay, grieve endings, and still perceive meaning. This capacity to witness gives mortality purpose—to awaken humility before the unseen continuity of life.

Science describes the mechanism; revelation reveals the meaning. Between them stands the observer—the human soul—bound to time yet capable of envisioning eternity. To understand death is therefore to study both physics and faith, each reflecting part of the same truth: existence never ceases; it transforms under the will of Allāh ﷻ.

Summary

• Angels: Timeless servants beyond entropy, perfectly obedient to Divine command.

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

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

• 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.

• Brain death: Defines the medical boundary but not the metaphysical end.

• The soul’s departure: Belongs to the realm of Divine command, beyond physical law.

• Sleep and detachment: Mirror temporary withdrawal from entropy.

• Death and resurrection: Form a single cycle—dissolution and renewal under Allāh’sﷻ will.

• All point toward Ākhirah, the eternal, real world beyond entropy and time.

Final Reflection — The Circle of Command

From the unseen spark in the womb to the silence after the last breath, the story of existence is one command unfolding in two directions: Be and Return.

Entropy governs matter, but command governs being. What appears as birth and death are transitions between degrees of order—from divine decree into material sequence, and from material decay back into timeless reality.

In every stage—embryo, consciousness, decay—we witness signs of the same pattern: order emerging from chaos, chaos yielding to order, all within the mercy of the One Who sustains both.

Our science traces the mechanisms; revelation unveils the purpose. The Qur’an speaks not in equations but in truth: “Indeed, to Him we belong, and to Him we return.” (Q 2:156)

From the first molecular whisper of hCG in the womb to the final silence of cellular entropy, the same pattern repeats: divine command sustains, then releases. My scientific journey through these signals has only deepened the awareness that existence itself is a conversation between matter and mercy. As a scientist, I can map the pathways of energy and life, but I cannot grasp the full meaning of existence. The ultimate knowledge of life, death, and return lies with Allāh ﷻ alone—the Source of command, the Restorer of order, the Eternal beyond time.

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

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