The human body is a biological machine. Shrii Shrii Anandamurti

The mind controls this body-machine through its direct connection and interaction with the glands via the hormones and nerves. This relationship is part of the science of Biopsychology.

The human body is composed of the same five fundamental factors as the rest of the universe (the physical body is a part of Saincara, whereas the mind is a part of Pratisaincara). Every factor is distributed throughout the body, but is controlled by a controlling nucleus, or cakra. The cakras are like substations of the mind – each controlling their own assigned area. And just as the mind functions directly through the brain, the cakras function through their own physical counterparts – the endocrine glands.

The propensities of mind (vrttis) associated with each cakra affect the glands and the hormones secreted from those glands (hence the emotions, physical behaviour and functioning of the various body systems). But the glands and the hormones they secrete may also affect the mind

Some examples:

The Muladhara Cakra – at the tip of the spine – controls the solid factor of the body. It forms the base of the body, giving stability to the whole structure. The vrttis associated with it are the fundamental propensities of human psychology: they are kama (physical longing), artha (psychic longing), dharma (psycho-spiritual longing) and moksa (spiritual emancipation). This lowest cakra is also the home of the "sleeping divinity," the psycho-spiritual force called the kundalinii which rises up the spinal column in conjunction with progressive stages of spiritual elevation.

The Svadhisthana Cakra – at the level of the genitals – controls the liquid factor of the body. It is associated with the reproductive glands which, once active, give a sense of dutifulness to the mind, as well as some rationality and intelligence.

The Manipura Cakra – at the level of the navel – controls the luminous factor. It is the centre of the body's heat and energy. The hormones secreted from the glands and sub-glands associated with it manifest the propensities of shyness (shamefulness), melancholia (due to over-secretion) and fearfulness (due to under-secretion).

The Anahata Cakra – at the center of the chest – controls the aerial factor. It is the base of love and all higher human wonts. If there is a high secretion of hormones from this area then love for children is expanded into universal love. This cakra is fully active after the reproductive glands start functioning.

The Vishuddha Cakra – at the throat – controls the ethereal factor. The Thyroid Gland associated with it regulates the body's metabolism, and gives the quality of self-reliance to the mind. Quarrelsomeness and irrationality result from under-secretion. The Parathyroid glands (on either side of the Thyroid) contribute to metabolic regulation, as well as intellectuality and rationality. Under-secretion from these glands causes vanity.

The Ajina Cakra – between the eyebrows – is directly associated with the Pituitary Gland. This gland controls all lower glands through its numerous hormones and nerve connections. It is the seat of the mind. It balances the spiritual and mundane tendencies and causes extroversion of mind during the daytime.

The Sahasrara Cakra is at the crown of the head. Its associated gland – the Pineal – is the master gland, the overall controller of both body and mind. It is the biological clock of the body, and is responsible for introversion of mind at night. Its secretion counters stress and gives the feeling of bliss.