The Science of the Chakras & Benefits of Meditation

Stephanie Miller

January 18, 2018

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Benefits Of Meditation

Have you ever noticed that when you get stressed out your body has a physiological response to the emotions that you are going through? Whether you have good or bad stress you are dealing with your body responds to all of the thoughts being processed by the mind. This can be overwhelming at times and often our thoughts can become shrouded with negativity, which can then cause us to have low energy or become irritable. The good news is we can help control this by using meditation techniques which have been scientifically proven to help clear the mind, boost mood, and even help with depression!

Today, I’d like to take a moment to discuss some of the amazing benefits of meditation and what us yogis refer to as the chakras. If you’ve ever taken a yoga class before and felt like some poses were a little confrontational, and some rather unpleasant emotions come up, you are not alone. You see, in each of us, our body holds onto every memory, emotion, and experience that we’ve been through. Your body is an emotional storage center full of information. The practice of yoga and meditation is to designed to draw awareness to the holding patterns and unhealthy coping mechanisms and to then reprogram our mind and muscles so that we become more aligned in our truth and connected to both the mind and body.

Many people when new to the practice of yoga often hear lots of unfamiliar words and phrases thrown at them. I’m sure many of us have been there before. Perhaps you’ve been in a yoga class where the instructor starts spouting off on energy centers in the body and you had a ‘WTF’ moment. All joking aside, let’s take the opportunity to demystify the concept of the chakra system and how it relates to the practice of yoga. Both yoga and meditation have proven scientific evidence in their benefits. But what about the chakra system?

What Are Chakras?

Chakras are an essential part of Ayurveda. Ayurveda is a 5,000 year old system of healthcare. It originated in ancient India and many still practice it as an alternative to traditional medicine today. Ayurvedic tradition recognizes seven main chakras which can be seen as emotional energetic junctions in the body which connects our consciousness (mind) to body (matter). Each chakra represents a different aspect of our humanity: physical, emotional, spiritual, mental, energetic & even social. When we recognize these aspects of ourselves we can listen to our bodies and make a conscious decision to change what may be out of balance and move towards greater health and wellness.

The chakras make up a system of energy in what’s called the subtle energy body. Many people have a hard time relating to what that concept actually means. Think of it like this, and try to imagine if the following scenario is relatable. Have you ever been heartbroken, or lost someone close to you? What did that mean to you? We know factually, that your heart didn’t break- but instead you had an emotional experience and felt a loss from that relationship or situation. That empty, hurt feeling in the chest is actually the subtle energy of the heart chakra. Let’s try another example. Have you ever felt that you had a lot to say, and when it came time to voice your feelings on something important, you literally felt choked up and couldn’t find the words needed to express your concerns? This would represent a blockage in the subtle energy of the throat chakra. In simple terms, the chakra system is an ancient explanation as to how emotions can be felt in the body. Starting to get it?

Benefits of Meditation

Benefits of Meditation

The chakras are aligned through the center of our being. They run through an energetic channel along the spine, beginning from the tailbone up to the crown of the head. This channel is called ‘sushumna nadi’, and the energy that flows through this channel to each of the chakras is referred to as kundalini. In the practice of kundalini yoga, it is said that Shakti (primal energy) is located at the base of the spine, coiled up like a snake. It is through various methods (combination of yoga & meditation) that kundalini is awakened so that the energy flows freely through each of the chakras from the ‘root’ of the spine up to the crown of the head. This kundalini energy ascends & descends connecting our physical and emotional energy with that of the universe. Kundalini energy is not to be confused with prana.

What Is Prana?

In Hindu philosophy and ayervedic practices prana is also known as “life force” or “vital energy”. In Chinese medicine, they call it qi or chi. Fun fact: this “vital energy” is exactly what George Lucas was talking about in Star Wars. This became known as “the force” in his movies. Prana is our life force. It is believed to enter the body through each breath we take. In yoga practice, pranayama is a technique used to control the breath. It is one of eight limbs described by yoga guru Patanjali in the eight limb path of yoga. This yogic philosophy is designed to help one live a meaningful and purposeful life of ethical conduct and self discipline.

The Nervous System

Albert Einstein once said, “Science without religion is lame, and religion without science is blind”. With those words in mind, let’s take a moment to explore some of the science behind the chakra system. Please remember that this is a concept devised by an ancient primal civilization, long before they had knowledge about modern anatomy & physiology. But, there are many experts that believe that the vagus nerve in the body correlates with the chakra system! There have been many modern yogis that have referenced the vagus nerve as having similar qualities as the ‘kundalini snake’. Many scientists have nicknamed it the ‘wandering nerve’ because it connects to every single one of the bodily organs and even some of the skeletal muscles. It is widely known for it’s parasympathic nervous response, also known as the “rest & digest” function of the nervous system.

We know that the impulses of our nervous system runs on energy in the form of electrical impulses that pass from synapse to synapse. It’s not only electricity that travels through our nerves, but messages & instructions are carried throughout the entire body. Perhaps it’s just a coincidence that the vagus nerve has major plexuses in the body that align with the seven major chakras?

What is very interesting to note is there have been many studies conducted on vagus nerve stimulation that have shown to reduce inflammation in the body, reduce anxiety disorders, improve memory, help with depression as well as reduce alcohol dependence & substance abuse.

Meditation & Yoga For Health

Now, let’s take a moment to think about what triggers vagus nerve stimulation? If you guessed yoga & meditation you are correct!

According to the National Center for Complementary and Integrative Health, “Meditation may physically change the brain and body and could potentially help to improve many health problems and promote healthy behaviors”. “Results from a 2012 NCCIH-funded study suggest that meditation can affect activity in the amygdala (a part of the brain involved in processing emotions), and that different types of meditation can affect the amygdala differently even when the person is not meditating”.

For more information on the scientific basis for integrative medicine, please check out the research the US National Library of Medicine National Institutes of Health has published.

Their research examines psychoneuroimmunology and documents the mind-body connection trough interactions of the endocrine, immune, nervous and emotional stress systems within the body. Very interesting stuff indeed! Many have known about this mind-body connection for a long time. By studying energy medicine and taking concepts from both eastern and western theories, I believe we are on the verge changing healthcare as we know it!

Many yogis believe that through our most painful experiences we are given an opportunity to make decisions which enable the spirit to grow & evolve into our higher (ideal) selves. So, everything we experience throughout our lives holds some sort of purpose so that we can hopefully take a valuable lesson away from it all. These experiences we have affect us emotionally, spiritually and also on the physical level. All of our thoughts and feelings from our experiences create a psychological imprint in the mind/body, whether we notice it right away or not.


These subtle impressions are something in yoga & Hindu philosophy known as ‘samskaras’. It begins with a thought, emotion or sensation that draws conscious awareness. Then, there is a reaction that we create with thoughts or emotions that gets stored in the subconscious where it creates a subtle sensory impression. These impressions are stored in neural pathways in our brain.

For example, most of us can relate to being in a stressful or intense situation and recall exactly how that made us feel in that moment. Sometimes this can be a reoccurring issue that we are not addressing and correcting. We might go about with dealing with our stress in ways that don’t allow us to really deal with the issue at hand; or we ignore the underlying causes all together. We say to ourselves, “I’m so stressed!!” And when we choose to ignore our emotions and feelings that arise and the mental/emotional stress can sometimes manifest in our body almost instantly, perhaps in the form of a headache, tight shoulders, or back pain.

The Chakras

So, let’s break it down a little, shall we? Each of us has seven ‘main’ energy centers within our bodies, they run parallel with the spine and each one has certain qualities and associations. It’s important to understand each chakra and its characteristics so that we can become more connected with our higher selves.

It’s also really important though that we don’t let any chakras become ‘out of balance’ or over power any of the rest. It’s all about maintaining a proper balance. I’m going to briefly explain a little about each chakra, so that we are introduced to these concepts.


Muladhara, is the first chakra, many people know this as the ‘root chakra’. It lays down the ‘support’ for the rest of the chakras and it located at the base of the spine. It reminds us that we are alive, and is associated with survival. When this chakra becomes out of balance some of its manifestations is obesity, or on the opposite of the spectrum- anorexia. If we feel some of our most basic needs are being unmet, we might go about dealing with that stress by eating too much, or not eating at all. Our biggest challenge is to accept our bodies, to feel comfortable in them and love them. That’s why eating is associated with the first chakra. When we eat, we are nourished and we feel grounded. We become grounded, and allows us to begin to find peace and stillness. Mentioned earlier, each chakra affects a part of the endocrine system and the hormones, this chakra affects the adrenals. When survival is threatened, the root chakra becomes out of balance & the stress hormones cortisol and adrenalin are released.


The second chakra is known as Svadhisthana, it is also referred to as the ‘sacral/splenic chakra’ center. When it becomes out of balance there can be problems with the bladder, kidneys, low back pain, or PMS. This chakra is located right below the navel and is associated with the womb and/or urogenital area. Estrogens and testosterone are affected by this chakra. Some of the functions associated with this area are our emotions, sexuality, desire, pleasure, creativity and procreation. Socialization best describes this chakra, noting the need to connect with other human beings. This is where our desire for nurturing, warmth and touch comes from. Being denied these simple things can lead imbalances in our lives; whereas over indulgence here will also cause some serious imbalances.


The third chakra is called Manipura. It functions primarily as our will power and is associated with the ego. It is located around the solar plexus area. The endocrine organ associated with this chakra is the pancreas. Health problems associated with this can affect the digestive system. Some issues would include diabetes, constipation, ulcers, and irritable bowels. The solar plexus chakra has a lot to do with confidence and belonging. When it’s open we feel accepted and we know our place within the universe. This chakra is where we begin to really become more emotional. This 3rd chakra is where we develop a sense of self, and we gain the confidence to live the life that we want to live. When it becomes closed, we feel emotionally blocked, or even numb. People blocked here may not understand deep emotions or experience any kind of empathy for others. It’s also important to note that when this chakra becomes too open & out of balance one could display over confidence, narcissism and the need to control others to gain power.

You may have begun to notice the chakra system starts out rather primal, and as we advance through the chakra system it becomes more emotionally complex. Each one builds up to the next as we move from primitive survival to living with conscious awareness.


The fourth chakra is the ‘heart chakra’, also known as Anahata. This chakra obviously represents love; both our ability to give and receive. Body parts affected by this chakra are the lungs, heart & most of the upper torso. So, naturally when this chakra becomes blocked the body has malfunctions such as asthma, COPD, heart disease, bronchitis, etc. Its endocrine counterpart is the thymus gland. The thymus gland has an important role in immune response. Is it coincidental that sometimes after periods of deep heartache we also can become physically sick due to a compromised immune system? Many of us have heard stories of spouses becoming sick & dying shortly after the passing of their loved one. This gives another meaning to the phrase ‘died of a broken heart’. This chakra allows us to experience a deep, fulfilling joy in life. The love that we feel is expressed towards everything we encounter. It becomes a way of being; we are able to express our love to others and in return be loved back. When it becomes blocked we feel needy and jealous; or we are unable to truly love perhaps because we have not fully healed from past heartbreaks or loss.


The fifth chakra is the ‘throat chakra’, called Visuddha. We can feel this energetic center when we engage jalandara bandha (yogic chin lock). This chakra represents our ability to express ourselves through communication, finding our voice and also being able to speak our truth. The gland affected by this chakra is the thyroid. The body parts associated this chakra are the neck, shoulders, ears, nose, throat and tongue. It’s also associated with hearing. So this means that in order to be fully open we are able to express our own truth; as well as receive and listen to others. When this chakra is blocked we may show symptoms of a sore throat, stiff neck, thyroid issues or hearing problems. Non physical signs of a blockage would be social anxiety and fear of speaking. When the throat chakra is out of balance & too open we may be expressing harsh words that hurt others and perhaps even gossiping or lying.


The sixth chakra is widely known as the ‘third eye’, or Ajna chakra. This is where we begin to develop our intuition and be able to ‘see’ and trust those intuitive feelings. It is located right between the eyes, and affects the pineal gland. When this chakra becomes out of balance, we may experience blurred vision, headaches, dry eyes and sinus pressure. This chakra is actually located within the frontal lobe of the brain, so it really does affect us mentally. When it becomes blocked, we may experience lots of self doubt, over think everything or not trust our own decision making skills. When it’s open, we have a vision and we are able to trust that we are on the right path. The beauty of this chakra is that when it’s open it allows us to see past all the illusions and open to seeing things from another’s perspective and without judgment. It is within this place we develop a deep sense wisdom and acceptance. When this chakra becomes dysfunctional we may believe that we already know it all and fail to see things from another person’s perspective.


The ‘crown chakra’ is the seventh and last chakra in the system. It is called Sahasrara and is represented by a lotus with a thousand flower petals. It’s located at the top of the head and represents our thoughts. Its function is to understand, and has an ability to manifest information. When it’s fully open we are able to experience complete bliss. The endocrine function it affects is the pituitary gland aka the ‘master gland’ which essentially impacts several of the other hormone glands within the body. It also affects our entire central nervous system. It has a major role in regulating vital body functions and our general wellbeing. When our crown chakra becomes blocked we feel boredom, confusion, and even mental disorders like OCD or depression. When it is open, we are able to understand, to know and to trust in the universe. We are able to transcend and become part of a greater and higher consciousness. It is in this mindset that we are completely able to let go of all attachments. It is here that we know that our physical bodies are impermanent; and that we are so much more than that- our consciousness and spirit are what connects us all to the entire universe and the energy of our soul is eternal.

How To Balance Your Chakras?

Whew! That was a lot of deep information. And that just scratches the surface!

Now, you might be asking yourself what you can do to help balance your energy. As mentioned earlier, taking a few minutes out of your day to just be present and meditate on any areas you may feel are out of balance. Taking a couple yoga classes each week, or booking a massage every month or so are also great ways to practice self care & keep your physical/emotional energy in check!

So, with all of that said, hopefully the take away here is that it’s important to be aware of both our thoughts and actions to better keep our lives in balance.

This is because our mental state can affect our body – and vice versa. Becoming more aware of our thoughts, and correcting our behaviors (or reactions) are just some of the things we can do to keep our chakras in balance. Because in the big picture, that’s what it’s all about!

Wishing you all health & happiness!