Supporters of the notion of chakras explain the lack of confirmation of their existence in Western medical science by noting that current technology is not capable of measuring life energy or chakras. Some point out that arguments offered so far against the possibility of the existence of chakras are arguments from ignorance. Skeptics rejoin that if chakras exist then there ought to be evidence of their existence that would be acceptable to the scientific community, i.e., they argue that they find no reason to accept claims about them since there is no empirical evidence to support their existence, which is exactly what the supporters of the notion of chakras have also affirmed.
There is, however, a marked similarity between the positions and roles described for chakras, and the positions and roles of the glands in the endocrine system, opening the possibility that two vastly different systems of conceptualization have been brought to bear to systemize insights about the same phenomenon. By some, chakras are thought of as having their physical manifestation in the body as these glands, and their subjective manifestation as the associated psychological and spiritual experiences. Different systems of conceptualization, Indian and Western scientific, make only a partial convergence in this case since Western science deals only with phenomena that are judged intersubjective….
Parallels have often been drawn… between the positions and functions of the chakras, and of the various organs of the endocrine system.
The highest crown chakra is said to be the chakra of consciousness, the master chakra that controls all the others. Its role would be very similar to that of the pituitary gland, which secretes hormones to control the rest of the endocrine system, and also connects to the central nervous system via the hypothalamus. The thalamus is thought to have a key role in the physical basis of consciousness.
The Ajna Chakra, or third eye, is linked to the pineal gland. Ajna is the chakra of time and awareness and of light. The pineal gland is a light sensitive gland, that produces the hormone melatonin, which regulates the instincts of going to sleep and awakening. It also produces trace amounts of the psychedelic chemical dimethyltryptamine.
(Note: some argue that the pineal and pituitary glands should be exchanged in their relationship to the Crown and Brow chakras, based on the description in Arthur Avalon‘s book on kundalini called Serpent Power.)
The throat chakra, Vishuddha, is said to be related to communication and growth, growth being a form of expression. This chakra is paralleled to the thyroid, a gland that is also in the throat, and which produces thyroid hormone, responsible for growth and maturation.
The heart chakra, Anahata, is related to love, equilibrium, and well-being. It is related to the thymus, located in the chest. This organ is part of the immune system, as well as being part of the endocrine system. It produces T cells responsible for fighting off disease, and is adversely affected by stress.
The solar plexus chakra, Manipura, is related to energy, assimilation and digestion, and is said to correspond to the roles played by the pancreas and the outer adrenal glands, the adrenal cortex. These play a valuable role in digestion, the conversion of food matter into energy for the body.
The sacral chakra, Swadhisthanna, is located in the groin, and is related to sexuality and emotion. This chakra is said to correspond to the testes or the ovaries, that produce the various sex hormones involved in the reproductive cycle, which can cause dramatic mood swings.
The base chakra, Muludhara, is related to survival, excretion, and also to basic human potentiality. It is said the kundalini lies coiled here, ready to uncoil and bring man to his highest spiritual potential in the crown chakra. This centre is located in the region between the genitals and the anus. Although no endocrine organ is placed here, it is said to relate to the inner adrenal glands, the adrenal medulla, responsible for the fight and flight response when survival is under threat. In this region is located a muscle that controls ejaculation in the sexual act. A parallel is drawn between the sperm cell and the ovum, where the genetic code lies coiled, and the legendary kundalini, ready to express itself as a fully developed human being.