Have you ever sensed that science and spirituality might be describing the same truth in different languages?

I’ve often reflected on how the vagus nerve, the chakra system, and Interpersonal Neurobiology (IPNB) all seem to meet at the same intersection — where energy, emotion, and connection flow together.

A Meeting Point Between Science and Spirituality

While the connection between chakras and the vagus nerve isn’t formally recognised within mainstream neuroscience, an increasing number of integrative and trauma-informed practitioners are exploring these parallels.

The two systems appear to describe the same process through different languages — one energetic, the other physiological. Ancient traditions spoke of energy flow and alignment, while modern science now studies vagal tone, regulation, and neuroception.

Both ultimately point to the same truth: when the body feels safe and connected, energy and awareness flow freely.

Root to Crown: The Gut–Brain Pathway

The root chakra represents grounding, safety, and belonging — the foundation of our being. The third eye chakra represents clarity, intuition, and insight — our ability to perceive truth and meaning.

In scientific language, the vagus nerve physically connects these realms. It runs from the brainstem through the face, heart, and gut, creating a direct gut–brain communication line.

When the vagus nerve is balanced, we feel safe, grounded, and connected — our body and intuition communicate freely. When it’s dysregulated, we feel unsafe, disconnected, or numb.

In this way, the vagus nerve can be seen as the biological bridge between the root and the third eye — translating instinct into insight, and safety into presence.

Blocked Energy or Trapped Trauma?

Ancient wisdom tells us that energy becomes “blocked” when emotion or life force cannot move freely through the chakras.

Modern trauma science says something strikingly similar: when survival energy (fight, flight, freeze, or fawn) isn’t released, it becomes trapped in the nervous system.

Both perspectives describe a disruption of flow — whether we call it prana or vagal tone. Healing in both systems involves restoring movement, breath, sound, and connection so the energy of life can circulate again.

How the Chakras Relate to the Vagus Nerve

The vagus nerve and chakra system seem to describe the same energy flow through two different lenses: one biological, one energetic.

Chakra Location Theme Related Vagus Function
Root (Muladhara) Base of spine Safety, stability, survival Regulates digestion and elimination; grounding the body in a sense of safety.
Sacral (Svadhisthana) Below the navel Emotion, creativity, relationships Influences reproductive and gut organs; supports emotional flow and connection.
Solar Plexus (Manipura) Upper abdomen Confidence, personal power Controls diaphragm and gut; where we sense our inner strength and gut feeling.
Heart (Anahata) Centre of chest Love, compassion, connection Directly affects heart rate and breathing rhythm; the centre of relational safety.
Throat (Vishuddha) Throat Communication, truth, expression Upper branch controls voice tone, swallowing, and facial expression — the social engagement system in Polyvagal Theory.
Third Eye (Ajna) Forehead Intuition, perception, insight When vagal tone is balanced, brain and body communicate freely, enhancing intuition.
Crown (Sahasrara) Top of head Spiritual connection, unity Reflects integration and coherence; the sense of being connected to something greater.

 

Each chakra aligns with areas influenced by the vagus nerve, creating a shared pathway for safety, regulation, and awareness.

When the vagus nerve functions well, energy naturally rises through the chakras, supporting safety, connection, and consciousness.

When it’s disrupted, the flow of energy — or prana — becomes constricted, and we experience symptoms of imbalance, anxiety, or shutdown.

Trauma and the Flow Between Root and Third Eye

Dr. Wayne Dyer once suggested that trauma disrupts the energetic flow between the root chakra and the third eye, and this insight aligns closely with both ancient and modern understanding.

The root chakra represents our sense of safety and belonging — our foundation.

The third eye represents awareness, clarity, and intuition — our ability to perceive beyond the surface.

When trauma occurs, especially in early life, it destabilises the root, leaving the body in a constant search for safety.

In this state, energy can’t rise freely toward the higher centres, particularly the third eye, where intuitive and spiritual awareness reside. The result is a kind of inner fragmentation — the body and mind no longer move together in harmony.

From a scientific perspective, the vagus nerve mirrors this same disruption. Trauma interrupts the communication between the gut (root) and the brain (third eye) — the very flow that allows instinct and intuition to cooperate. The lower vagal circuits enter survival mode, and the upper pathways that support calm awareness and insight go offline.

This explains why, after trauma, many people feel either hypervigilant and disconnected from their intuition, or numb and dissociated from their body. They can’t “feel” their truth because safety and perception have become disconnected.

Healing, therefore, involves restoring the flow between the root and the third eye — through grounding, breath, sound, movement, and safe relational connection. As safety returns to the body, awareness naturally expands.

The Ahhh sound meditation that Dr. Dyer often taught vibrates through the throat, heart, and head, gently bridging these energetic and neural circuits, helping the nervous system re-establish coherence between body and spirit.

When the root feels safe, the third eye opens — and insight is grounded in embodied awareness.

Interpersonal Neurobiology: The Relational Bridge

Interpersonal Neurobiology (IPNB), a framework developed by Dr. Dan Siegel, shows that integration — linking separate parts into a functional whole — is the foundation of well-being.

It views the mind as an embodied and relational process that regulates energy and information flow.

That’s exactly what both the chakra system and Polyvagal Theory describe:

  • The vagus nerve regulates our internal state and sense of safety.
  • The chakras reflect the energetic expression of that state.
  • IPNB shows how safe, attuned relationships support this integration, restoring harmony across body, mind, and spirit.

Where trauma fragments, integration unites.

Through connection, compassion, and self-awareness, energy begins to flow again — physiologically, emotionally, and spiritually.

In Essence

Science and spirituality are not opposites; they are two mirrors reflecting the same truth:

  • When the nervous system feels safe, energy flows.
  • When energy flows, intuition awakens.
  • When presence meets connection, healing happens.

The vagus nerve, the chakra system, and IPNB each describe what it means to be human — wired for safety, connection, and flow.