The first thing to know is that there is a one-to-one correlation between the chakras and different parts of the physical body. This is unknown to most yoga enthusiasts, who focus on the well-established role of the glands in chakra functions. The correlation applies especially to the junctional points between the autonomic and voluntary functions of the body. Just as Ida and Pingala are represented as rivers crossing the Susumna at various points, so do the sympathetic and parasympathetic nervous systems intersect at similar points on the anatomy, and are often controlled simultaneously by the conscious mind. Hence the caduceus is the symbol for medicine and is a good representation of the chakra system.

The first chakra is at the anal sphincter, and is controlled both voluntarily and involuntarily. The second chakra is at the urinary sphincter, and is controlled both voluntarily and involuntarily. You don’t leak at these two places, do you?

The third chakra is parallel to the pyloric valve and the lower esophageal sphincter. These are usually thought of as involuntary, but can be controlled by swallowing and thinking about food.

The fourth chakra governs breathing, which is both voluntary and involuntary. The heart is also controlled by the fourth chakra, and is usually involuntary in its action, but can be controlled indirectly by thinking pleasant or scary thoughts. Just like God controls the universe indirectly through the gunas.

The fifth chakra is located at the vocal cords, and these constrict and open at will, but also they contract involuntarily as a participant in the gag reflex and swallowing reflex.

The sectors of the vagus nerve transmit most of the parasympathetic (vegetative) functions to the thyroid, heart, digestive organs, urinary and anal sphincters. The sympathetic (fight or flight) nervous system runs in two chains parallel to the spine and on either side of it. It too innervates each of these sets of organs.

Yoga postures effect changes in these organs and nerves by placing pressure on glands, which cause them to express their secretions. Nerves are gently stretched and stimulated, causing them to regain their normal tone. Hence the relaxation that many people feel.

Meditation and yoga are well accepted by medical doctors to be effective in controlling back pain, migraines, anxiety and depression. Medical students taught yoga/meditation practices are much less likely to experience emotional difficulties during exam time. Asthmatics show measurable improvement in their function as a result of yoga practice, and seizure patients have fewer seizures. Jailed inmates who learn yoga and meditation are far less likely to return to jail after their release, when compared with their companions who have not engaged in such classes.

The left nostril has been found to correlate with parasympathetic function, and breathing through it brings calm. It can be opened by a reflex connecting the right armpit to that nostril, by pressing the armpit with the fist or the knee.

Constipation is improved by performing utksepa mudra (flexing the legs to the chest several times) followed by drinking room temperature water and walking around with the navel exposed. The mudra massages the intestines, the water rehydrates and softens the intestinal contents after a night of breathing out water and CO2, and the cool air stimulates the chakra directly. Simultaneously, the gastro-colic reflex takes over to create a good bowel movement in the morning.

Three-part yogic breathing, using first the diaphragm, then the ribs, and finally the arms, allows for full expansion and function of the lungs, as well as stimulating lymphatic flow from the extremities to the core by means of the pumping action of the diaphragm causing a relative negative pressure in the chest.

Prostatic secretion and emptying is enhanced by asanas which place pressure on it (Janushirsasana, for example) as well as vasti mudra (Pressing the perineum while stool is passing). This helps prevent prostatitis, enhances urinary flow in people with BPH (benign prostatic hyperplasia), and helps with sexual control by minimizing the pressure and congestion within this organ which stores seminal fluid.

Similarly, ovaries and uterus are pressed and massaged during asanas like yoga mudra, cobra and dirgha pranam.

Positioning the eyes during certain asanas like cobra, bhavasana, virasana and matsyasana (fish) and matsyendrasana (twist) enhances the musculature of the eyes thereby maintaining their youth. Old people often lose their ability to look up, and this accounts for a pessimistic approach based purely on physiology.

Nasal lavage using nasapana or neti pot is well accepted and shown to minimize allergy and sinusitis. Washing out the eyes during half-bath also helps to eliminate accumulated dust and pollen. Holding the breath while splashing water in the face stimulates the diving reflex (man is, after all, an aquatic mammal living on land) and causes relaxation of the body and slowing of the heart rate.

Meditation has been shown to activate different parts of the brain viewed with dynamic MRI. Transcendental Meditation practitioners synchronize the brain waves from one part of the brain to the other, and even between one person and the other.

Mantras are physiologic harmonizers, and people using Om Mane Padme Hum have a similar physiologic slowing to those using Ave Maria.

These are but a few of the correlates between yoga and so-called Modern Medical Science. There are over 1000 relevant abstracts listed in PubMed.