Western philosophers and scientists have recognised that there are vital centres inside the brain like Pineal and Pituitary glands and other glandular bodies like thalamus and hypothalamus which perform important functions in human activity. The great philosopher Descartes held the view that pineal gland is the seat of the soul and before him St. Paul obviously referring to this brain centre said, it is the temple of God where the spirit of God dwelleth. The Bible dictionary gives the meaning of pineal as the face of god. The function of the pineal gland which is situated almost at the centre of the brain is not yet fully ascertained. It is believed that it has something to do with procreation and that may be the reason why it is called pineal which lends itself to an interpretation as the penis which is EL. The penis here is the neural penis. 'EL' means God or creative power. This agrees with the notion of the Hindus that Shiva linga is situated in the lotus heart inside the brain on a level with the middle of the brow.

The biologist Oscar Bagnell thinks that the pineal gland is associated with ultra violet reception in thought transmission or telepathy and Arthur Lammers and Edgar Cace, two psychic investigators, agreed with Descartes that the pineal gland is the seat of subconscious or soul mind while the pituitary gland is the seat of conscious mind.

The pituitary gland is situated below the pineal gland in close proximity with thalamas and hypothalamus bodies and the region of the medulla oblongata on a level with the mid point of the eye brows. It contains two lobes, the anterior and posterior. The anterior lobe is formed from the extoderm of the roof of the mouth and the posterior lobe is the downward growth from the brain. Though no larger than a pea, this gland produces a whole battery of powerful hormones which act on the tissues of the body and other glands. If the anterior portion is sub-normal, it retards growth. If it is abnormal, it increases growth resulting in gigantism. The posterior portion of the gland, produces pitutrine which tones up and controls kidneys, intestines and capillaries. For the above reasons, pituitary gland is considered as the master gland of the body.

Regarding thalamas and hypothalamus, Demitry Chebotaryov Director of the Institute of Gerentology, Soviet Union, says that this tiny section of the brain covered by these bodies have revealed many surprising details regarding the advent of old age and that this tiny area is the border of the two worlds, viz., the outer world in which we live and the inner world of our body in which we think. Through the nervous system, the hypothalamus is said to obtain information from outside and passes it on to the endocrine system either along nerve channels or with the aid of hormones.

It may be noted that the pineal, the pituitary and thalamus bodies are situated in the core of the brain situated above the medulla oblongata which as identified is the Muladharam of which Ganesha is said to be the presiding deity, and some knowledge about these powerful brain centres vis-a-vis the various mystical terms bearing on certain psychic centres in the brain may be useful in this critical study of Ganesha.