A Complete Guide to the Chakras and Their Effects on the Mind, Body and Spirit: The Sexual and Root Centers (Part 3)

HJ: The Chakras play an essential role in our daily experience, whether or not we are of them.  This series is intended to help those interested in cultivating a deeper awareness of their chakras gain the understanding necessary to do so.  Often times the information one comes across on the chakras is at a surface level, with no real depth or substance.  This guide is intended to bridge the surface level awareness with a core understanding of how the chakras function on the various levels of the mind-spirit-triad.  If you ever wondered exactly how the chakras work, this is the guide for you.

– Truth

On a Possible Psychophysiology of the Yogic Chakra System (Part 3)

By Dr S.M. Roney-Dougal | Yoga Mag

This is part 3 of a 3 part series.  Part 1 can be read here and part 2 can be read here.

The root of the spinal cord: swadhisthana chakra

Swami Satyananda has stated that swadhisthana is connected with all ‘the phases of the unconscious’, the subliminal mind. “Swadhisthana is made up of all the rubbish which you never wanted, which you never needed, which you never desired but which got in.” (Satyananda, 1972a). Traditionally it has also been linked with sexuality, sensory pleasure, liquid, taste, procreation, self-indulgence, the kidneys and the prostate gland.

I think that swadhisthana is connected with the generative aspect of sexuality embodied by the womb in women, with follicle stimulating hormone and luteinising hormone, oestrogen and androsterones as the hormones of this chakra. These hormones are central to the development of the secondary sexual characteristics – that which makes a man a man and a woman a woman – they define our gender, our selves as sexual people, the pitch of our voice, the shape and strength of our body, whether or not we have a beard, and the differing emotional characteristics related to oestrogen and testosterone – that which is the essence of man or woman.

There is a strong link between the pineal gland and the generative aspect of sexuality. Melatonin levels in the mother are exceptionally high during pregnancy, reaching a peak at birth. The diurnal rise in plasma melatonin appears enhanced as pregnancy progresses, supporting the idea of a role for the maternal pineal in entraining foetal body rhythms.

In animals, there is a biological clock oscillating in the SCN during foetal life before circadian rhythms are overtly expressed and before the retino-hypothalamic pathway has innervated the SCN. (i.e. a unique form of maternal communication coordinates the phase of a developing circadian clock until the developing mammal can respond to light directly through its own eyes.) The foetal SCN shows circadian variation in metabolic activity that is in time with the rhythm in the mother and with the external lighting cycle. Research by Reppert et al (1988) has found that this foetal circadian rhythm can be detected in rats as early as the 19th day of gestation. Pineal NAT is the first measurable circadian rhythm evident, accurately reflecting circadian output from the SCN. Pups which have been reared in an environment with no light cues express a NAT rhythm that is in phase with the circadian time of the mother.

In humans circadian rhythms are not obvious until well into the postnatal period. Human SCN neurons are formed by the 28th week. A significant fraction of incident light is transmitted into the uterus of a pregnant woman. It is possible that direct photic entrainment augments or even replaces maternal-foetal coordination of the circadian phase since the foetus can synthesize and store melatonin. Also after birth social cues are very important in entrainment of the sleep-wake cycle. (Reppert, 1988)

Vasopressin messenger ribonucleic acid (mRNA) can also be used as an intrinsic marker of the oscillatory activity of the SCN during foetal life since circadian rhythm of vasopressin levels in cerebrospinal fluid originates in the SCN. Vasopressin mRNA levels exhibit a prominent day-night variation in adult rats, which begins in the foetal SCN on day 21 of gestation in phase with the mother’s rhythm. In mothers whose SCN has been destroyed on day 7 of gestation, the entraining signal for the foetus no longer works, and the foetal SCN metabolic activity has no day-night rhythm. Also the pineal N activity for 10 day old pups born to SCN-lesioned mothers and reared in constant darkness is completely disrupted and they have no daily rhythm. But, if the mother’s SCN is lesioned after foetal neurogenesis of SCN then foetal synchronization is not disrupted. Destruction of the maternal SCN also eliminates a circadian rhythm to birthing. Possibly also the developing circadian clock is involved in initiating parturition, as different species have different times of day when birth is more likely to happen.

When pups are fostered with a mother whose circadian rhythm is opposite to that of their natural mother, their rhythms change to become synchronous to that of the foster mother. In these cases entrainment of rhythm is possibly linked with feeding activity which occurs on a rhythmic basis. One needs to have the pup entrained so that its feeding cycle is in tune with the mother and the other pups. This ensures that its activity cycle is such that it emerges from the burrow at a safe time of day. When litters with many pups are born they need to all be synchronized in their activity.


Thus the strong connection between the pineal gland and the gonadal system is very apparent in connection with pregnancy and birth. The glandular connection of swadhisthana is with the gonads and related systems so that to some extent it overlaps with mooladhara chakra, and so I look to other aspects of our sexuality – puberty and the menstrual cycle – in the discussion of mooladhara.

The coccygeal plexus: mooladhara chakra

According to Satyananda, mooladhara chakra is the root chakra, intimately connected in the male with the testes, and in the female with the cervix, and with the perineum and anus in both sexes. This chakra is connected with the sense of smell, the nose and the earth element, with passion, the animal instincts, anger, greed, excretory functions, secretory and sexual aspects, attachment, material security, survival and materialism. Working on this chakra releases suppressed emotions and unconscious memories, and causes extreme swings in mood. It is the seat of kundalini, and has obvious and direct connections with sexual energy in its most earthly aspect.

Some systems link the root chakra with the adrenal glands even though the adrenals are located above the kidneys back of the navel. The only information I have come across which justifies this idea is that in embryology the gonads and suprarenals all start in the same place, and the adrenal cortex makes small amounts of androsterones. However, I consider that the yogic description of mooladhara chakra and particularly its connection with kundalini suggests sexuality as its primary physical manifestation and therefore I link this chakra with the gonads, with testosterone in men which is primarily made by the testes (Wilson & Foster, 1992), and with oestrogen and progesterone in women.

As we have already seen, the pineal and the gonadal system interact extensively. Satyananda considers that there is a special connection between ajna chakra and mooladhara, and there are certainly extensive connections between the pineal gland and the gonads. The pineal synthesizes antigonadotropic peptides. In their turn the gonadal hormones inhibit the biosynthesis of the pineal hormone melatonin, although gonadectomy has little influence on magnitude of melatonin increase or on phasing of the rhythm, and prolactin secretion is inhibited by ovarian steroids, suggesting that there is a physical as well as spiritual, mental and emotional links between mind, heart and sex.

Melatonin inhibits gonadal development in children and regulates the onset of sexuality at puberty for humans. There is a fall in plasma melatonin associated with male human pubertal development. The pineal normally becomes calcified at puberty (Ng & Wong, 1986; Vaughan & Reiter, 1986), and there is a sharp decrease in melatonin production at this time.

The pineal night-time melatonin concentration decreases progressively during the menstrual cycle, with an increase at ovulation and peak values during menstruation. Melatonin seems to be ‘taken up’ by the ovaries, testes and uterus. Thus women show a 28 day melatonin rhythm, though many women have a menstrual cycle that is more closely correlated with the 29.5 day lunar cycle and menstruate every full moon. Those using the contraceptive pill have less melatonin since there is a positive relationship between melatonin and progesterone. Melatonin secretion is significantly higher during the late luteal phase than during the preovulatory phase and melatonin levels fall before ovulation: this could be the determinant of the menstrual cycle. The onset of the LH surge is in the early morning when melatonin levels are falling (Brzezinski & Wurtman, 1988). Continuous light, which causes a decrease in melatonin production, also causes a decrease in ovarian melatonin concentration, whilst injections of melatonin result in smaller testes.

I consider that these studies linking the pineal gland with the gonadal endocrines aid understanding of the lore surrounding sexuality and psychic functioning. Children and celibates were almost universally those chosen as temple seers and prophets, the oracle at Delphi being an excellent example of this. Some research suggests that children are more psychic when they are younger, and much of the research into poltergeists suggests that adolescents are often the focus for this wild uncontrolled psychokinetic storm.


Our knowledge of the endocrine system, the chemistry of our body-mind and emotional system, is still meagre. The neurochemists have only just isolated pinoline from the pineal and are still learning about melatonin and serotonin. However, partial as our knowledge may be, it does fit together with what the yogis, ‘scientists of the subtle mind’, tell us about the yogic chakra system. Our disciplines, apparently so different in language and method, appear to corroborate each other.

In conclusion, pinoline can be seen as the physical aspect of ajna chakra as the psychic chakra, and melatonin as the neurohormone of ajna chakra as the command chakra in that it has an inhibitory role for the endocrine organs, many of which are found physically at the traditional places where the chakras are located. Thus vishuddhi at the throat links with the thyroid which is the metabolic regulator, anahata at the heart with the breasts, manipura at the navel with the adrenal glands involved with our reactions to stress, and swadhisthana and mooladhara at the root of the spinal cord with different aspects of the genital system. There are a bewildering number of versions of the yogic chakra system: attempts to correlate the chakras with Western physiological models may not only help us to understand physiology, but also help us find the version of the chakra system that makes the most sense physiologically. Perhaps by linking this spiritual system with Western psychoneuroendocrinology we can create a deeper understanding of the links between mind, body and spirit for the benefit of all of us.

This is part 3 of a 3 part series.  Part 1 can be read here and part 2 can be read here.

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